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Chen M, Yang J, Xue C, Tu T, Su Z, Feng H, Shi M, Zeng G, Zhang D, Qian X. Community composition of phytopathogenic fungi significantly influences ectomycorrhizal fungal communities during subtropical forest succession. Appl Microbiol Biotechnol 2024; 108:99. [PMID: 38204135 PMCID: PMC10781812 DOI: 10.1007/s00253-023-12992-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 11/21/2023] [Accepted: 12/28/2023] [Indexed: 01/12/2024]
Abstract
Ectomycorrhizal fungi (EMF) can form symbiotic relationships with plants, aiding in plant growth by providing access to nutrients and defense against phytopathogenic fungi. In this context, factors such as plant assemblages and soil properties can impact the interaction between EMF and phytopathogenic fungi in forest soil. However, there is little understanding of how these fungal interactions evolve as forests move through succession stages. In this study, we used high-throughput sequencing to investigate fungal communities in young, intermediate, and old subtropical forests. At the genus level, EMF communities were dominated by Sebacina, Russula, and Lactarius, while Mycena was the most abundant genus in pathogenic fungal communities. The relative abundances of EMF and phytopathogenic fungi in different stages showed no significant difference with the regulation of different factors. We discovered that interactions between phytopathogenic fungi and EMF maintained a dynamic balance under the influence of the differences in soil quality attributed to each forest successional stage. The community composition of phytopathogenic fungi is one of the strong drivers in shaping EMF communities over successions. In addition, the EMF diversity was significantly related to plant diversity, and these relationships varied among successional stages. Despite the regulation of various factors, the positive relationship between the diversity of phytopathogenic fungi and EMF remained unchanged. However, there is no significant difference in the ratio of the abundance of EMF and phytopathogenic fungi over the course of successions. These results will advance our understanding of the biodiversity-ecosystem functioning during forest succession. KEY POINTS: •Community composition of both EMF and phytopathogenic fungi changed significantly over forest succession. •Phytopathogenic fungi is a key driver in shaping EMF community. •The effect of plant Shannon's diversity on EMF communities changed during the forest aging process.
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Affiliation(s)
- Meirong Chen
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jiazhi Yang
- Guangdong Forestry Survey and Planning Institute, Guangzhou, China
| | - Chunquan Xue
- Guangdong Forestry Survey and Planning Institute, Guangzhou, China.
| | - Tieyao Tu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Zhiyao Su
- South China Agriculture University, Guangzhou, China
| | - Hanhua Feng
- Guangdong Forestry Survey and Planning Institute, Guangzhou, China
| | - Miaomiao Shi
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Gui Zeng
- College of Life Sciences, China West Normal University, Nanchong, China
| | - Dianxiang Zhang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.
| | - Xin Qian
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China.
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Chen J, Lin L, Tu Q, Peng Q, Wang X, Liang C, Zhou J, Yu X. Metagenomic-based discovery and comparison of the lignin degrading potential of microbiomes in aquatic and terrestrial ecosystems via the LCdb database. Mol Ecol Resour 2024; 24:e13950. [PMID: 38567644 DOI: 10.1111/1755-0998.13950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 02/05/2024] [Accepted: 03/08/2024] [Indexed: 04/04/2024]
Abstract
Lignin, as an abundant organic carbon, plays a vital role in the global carbon cycle. However, our understanding of the global lignin-degrading microbiome remains elusive. The greatest barrier has been absence of a comprehensive and accurate functional gene database. Here, we first developed a curated functional gene database (LCdb) for metagenomic profiling of lignin degrading microbial consortia. Via the LCdb, we draw a clear picture describing the global biogeography of communities with lignin-degrading potential. They exhibit clear niche differentiation at the levels of taxonomy and functional traits. The terrestrial microbiomes showed the highest diversity, yet the lowest correlations. In particular, there were few correlations between genes involved in aerobic and anaerobic degradation pathways, showing a clear functional redundancy property. In contrast, enhanced correlations, especially closer inter-connections between anaerobic and aerobic groups, were observed in aquatic consortia in response to the lower diversity. Specifically, dypB and dypA, are widespread on Earth, indicating their essential roles in lignin depolymerization. Estuarine and marine consortia featured the laccase and mnsod genes, respectively. Notably, the roles of archaea in lignin degradation were revealed in marine ecosystems. Environmental factors strongly influenced functional traits, but weakly shaped taxonomic groups. Null mode analysis further verified that composition of functional traits was deterministic, while taxonomic composition was highly stochastic, demonstrating that the environment selects functional genes rather than taxonomic groups. Our study not only develops a useful tool to study lignin degrading microbial communities via metagenome sequencing but also advances our understanding of ecological traits of these global microbiomes.
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Affiliation(s)
- Jiyu Chen
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Lu Lin
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Qichao Tu
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Qiannan Peng
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Xiaopeng Wang
- Key Laboratory of Applied Marine Biotechnology, Ministry of Education, Ningbo University, Ningbo, China
| | - Congying Liang
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Jiayin Zhou
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Xiaoli Yu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-Sen University, Guangzhou, China
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Sun S, Guo C, Wang J, Ren L, Qu J, Guan Q, Dou N, Zhang J, Chen Q, Wang Q, Wang J, Li J, Gao Z, Zhou B. Effect of initial moisture content, resulting from different ratios of vegetable waste to maize straw, on compost was mediated by composting temperatures and microbial communities at low temperatures. CHEMOSPHERE 2024; 357:141808. [PMID: 38548086 DOI: 10.1016/j.chemosphere.2024.141808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 01/25/2024] [Accepted: 03/24/2024] [Indexed: 05/12/2024]
Abstract
Owing to the huge amounts and perishable character of vegetable wastes, composting is one of the best options for recycling vegetable wastes post-harvest. The initial moisture content (MC) is critical for optimizing composting process, but the effect of high MC in undehydrated vegetable wastes on composting was rarely reported. For this, the plant-scale windrows were prepared by mixing cauliflower waste and maize straw at different ratios to control initial MC of 70 % (T1-70) and 80 % (T2-80), respectively, and composted in winter. As composting progressed, substantial organic matter degradation, progressive humification, decreases in electrical conductivity and increases of pH and germination index (GI) were observed in both treatments. Nonetheless, T1-70 accelerated heating rate early during composting, prolonged high temperature period (>50 °C) by 30 d, thus increased the harmless level of composting, and significantly improved the humification of end-products compared to T2-80. Results also revealed that T1-70 activated more indigenous microbes and enhanced microbial interactions early during composting, with the fungi enriched in T1-70 playing an important role in accelerating the composting process. Remarkably, the difference in composting temperatures, humification degree, and microbial communities between the two treatments was most significant during the maturation phase. In this phase, MWH_CFBk5, Planktosalinus, Pseudopedobacter, and Luteimonas enriched in T1-70 were positively correlated with humification indices. It is suggested that the effect of initial MC, resulting from different ratios of vegetable waste to maize straw, on their composting was mediated by the composting temperature and microbial communities at low temperatures.
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Affiliation(s)
- Shanshan Sun
- Department of Microbiology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Cheng Guo
- Department of Microbiology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Jianyu Wang
- Department of Microbiology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Li Ren
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
| | - Jianping Qu
- Department of Microbiology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Qi Guan
- Department of Microbiology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Nongxiao Dou
- Department of Microbiology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Jiahui Zhang
- Department of Microbiology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Qiuhua Chen
- Department of Microbiology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Qi Wang
- Department of Microbiology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | | | - Jieming Li
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China.
| | - Zheng Gao
- Department of Microbiology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China; State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China.
| | - Bo Zhou
- Department of Microbiology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China; National Engineering Research Center for Efficient Utilization of Soil and Fertilizer, Tai'an, 271018, China.
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4
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Wang B, Hu K, Li C, Zhang Y, Hu C, Liu Z, Ding J, Chen L, Zhang W, Fang J, Zhang H. Geographic distribution of bacterial communities of inland waters in China. ENVIRONMENTAL RESEARCH 2024; 249:118337. [PMID: 38325783 DOI: 10.1016/j.envres.2024.118337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 01/08/2024] [Accepted: 01/27/2024] [Indexed: 02/09/2024]
Abstract
Microorganisms are integral to freshwater ecological functions and, reciprocally, their activity and diversity are shaped by the ecosystem state. Yet, the diversity of bacterial community and its driving factors at a large scale remain elusive. To bridge this knowledge gap, we delved into an analysis of 16S RNA gene sequences extracted from 929 water samples across China. Our analyses revealed that inland water bacterial communities showed a weak latitudinal diversity gradient. We found 530 bacterial genera with high relative abundance of hgcI clade. Among them, 29 core bacterial genera were identified, that is strongly linked to mean annual temperature and nutrient loadings. We also detected a non-linear response of bacterial network complexity to the increasing of human pressure. Mantel analysis suggested that MAT, HPI and P loading were the major factors driving bacterial communities in inland waters. The map of taxa abundance showed that the abundant CL500-29 marine group in eastern and southern China indicated high eutrophication risk. Our findings enhance our understanding of the diversity and large-scale biogeographic pattern of bacterial communities of inland waters and have important implications for microbial ecology.
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Affiliation(s)
- Binhao Wang
- School of Engineering, Hangzhou Normal University, Hangzhou, 310018, China
| | - Kaiming Hu
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China
| | - Chuqiao Li
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China
| | - Yinan Zhang
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China
| | - Chao Hu
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China
| | - Zhiquan Liu
- School of Engineering, Hangzhou Normal University, Hangzhou, 310018, China
| | - Jiafeng Ding
- School of Engineering, Hangzhou Normal University, Hangzhou, 310018, China
| | - Lin Chen
- Hangzhou Xixi National Wetland Park Ecology & Culture Research Center, Hangzhou, 310030, China; Zhejiang Xixi Wetland Ecosystem National Observation and Research Station, Hangzhou, 310030, China
| | - Wei Zhang
- Hangzhou Xixi National Wetland Park Ecology & Culture Research Center, Hangzhou, 310030, China; Zhejiang Xixi Wetland Ecosystem National Observation and Research Station, Hangzhou, 310030, China
| | - Jing Fang
- Hangzhou Xixi National Wetland Park Ecology & Culture Research Center, Hangzhou, 310030, China; Zhejiang Xixi Wetland Ecosystem National Observation and Research Station, Hangzhou, 310030, China
| | - Hangjun Zhang
- School of Engineering, Hangzhou Normal University, Hangzhou, 310018, China; Hangzhou International Urbanology Research Center and Center for Zhejiang Urban Governance Studies, Hangzhou, 311121, China.
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Tang L, Yan J, Zhou X, Wang J, Gao Y, Mosa A, Czech B, Oleszczuk P, Ling W. Dissolved organic matter influences the indigenous bacterial community and polycyclic aromatic hydrocarbons biodegradation in soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 924:171662. [PMID: 38485009 DOI: 10.1016/j.scitotenv.2024.171662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 03/08/2024] [Accepted: 03/09/2024] [Indexed: 03/21/2024]
Abstract
In polycyclic aromatic hydrocarbon (PAH) contaminated soils, bioremediation is superior to other strategies owing to its low cost and environmental friendliness. However, dissolved organic matter (DOM) and indigenous bacterial communities can affect the efficiency of PAH-degrading bacteria (PDB). This study found that exogenous PDB (C1) including the genera Acinetobacter, Stenotrophomonas, and Comamonas, decreased the bacterial diversity of Alfisol, Ultisol, Inceptisol, and Mollisol, and DOM enhanced the diffusion of PDB and the bioavailability of PAH. In addition, bacteria preferred to ingest low molecular weight DOM fractions, and the abundances of lipid-like and protein-like substances decreased by 0.12-3.03 % and 1.73-4.60 %. The DOM fractions had a more marked influence on the indigenous bacteria than the exogenous PDB, and PDB dominated the PAH biodegradation process in the soils. More COO functional groups promoted the utilization of higher molecular weight-related homologue fractions by bacteria, and lower molecular weight fractions carrying more CH2 functional groups declined during biodegradation. This study investigated the variations in bacterial communities during biodegradation and revealed the effects of DOM fractions on biodegradation in PAH-contaminated soils at the molecular level. These results will promote the development of bioremediation strategies for organics-contaminated soil and provide guidance for prediction models of soil biodegradation kinetics.
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Affiliation(s)
- Lei Tang
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Jiayi Yan
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Xian Zhou
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Jian Wang
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Yanzheng Gao
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Ahmed Mosa
- Soils Department, Faculty of Agriculture, Mansoura University, 35516 Mansoura, Egypt
| | - Bozena Czech
- Department of Radiochemistry and Environmental Chemistry, Maria Curie-Skłodowska University, 20-031 Lublin, Poland
| | - Patryk Oleszczuk
- Department of Radiochemistry and Environmental Chemistry, Maria Curie-Skłodowska University, 20-031 Lublin, Poland
| | - Wanting Ling
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China.
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Fernández-Guisuraga JM, Ansola G, Pinto R, Marcos E, Calvo L, Sáenz de Miera LE. Resistance of soil bacterial communities from montane heathland ecosystems in the Cantabrian mountains (NW Spain) to a gradient of experimental nitrogen deposition. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 920:171079. [PMID: 38373460 DOI: 10.1016/j.scitotenv.2024.171079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 02/14/2024] [Accepted: 02/16/2024] [Indexed: 02/21/2024]
Abstract
Elevated atmospheric nitrogen (N) deposition on terrestrial ecosystems has become one of the most important drivers of microbial diversity loss on a global scale, and has been reported to alter the soil function of nutrient-poor, montane Calluna vulgaris heathlands in the context of global change. In this work we analyze for the first time the shifts of bacterial communities in response to experimental addition of N in Calluna heathlands as a simulation of atmospheric deposition. Specifically, we evaluated the effects of five N addition treatments (0, 10, 20, and 50 kg N ha-1 yr-1 for 3-years; and 56 kg N ha-1 yr-1 for 10-years) on the resistance of soil bacterial communities as determined by changes in their composition and alpha and beta diversities. The study was conducted in montane Calluna heathlands at different development stages (young and mature phases) in the southern side of the Cantabrian Mountains (NW Spain). Our results evidenced a substantial increase of long-term (10-years) N inputs on soil extractable N-NH4+, particularly in young Calluna stands. The alpha diversity of soil bacterial communities in mature Calluna stands did not show a significant response to experimental N addition, whereas it was significantly higher under long-term chronic N addition (56 kg N ha-1 yr-1 for 10-years) in young Calluna stands. These bacterial community shifts are mainly attributable to a decrease in the dominance of Acidobacteria phylum, the most representative in montane Calluna ecosystems, in favor of copiotrophic taxa such as Actinobacteria or Proteobacteria phyla, favored under increased N availability. Future research should investigate what specific ecosystem functions performed by soil bacterial communities may be sensitive to increased nitrogen depositions, which may have substantial implications for the understanding of montane Calluna ecosystems' stability.
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Affiliation(s)
- José Manuel Fernández-Guisuraga
- Departamento de Biodiversidad y Gestión Ambiental, Facultad de Ciencias Biológicas y Ambientales, Universidad de León, 24071 León, Spain; Centro de Investigação e de Tecnologias Agroambientais e Biológicas, Universidade de Trás-os-Montes e Alto Douro, 5000-801 Vila Real, Portugal.
| | - Gemma Ansola
- Departamento de Biodiversidad y Gestión Ambiental, Facultad de Ciencias Biológicas y Ambientales, Universidad de León, 24071 León, Spain
| | - Rayo Pinto
- Departamento de Biodiversidad y Gestión Ambiental, Facultad de Ciencias Biológicas y Ambientales, Universidad de León, 24071 León, Spain
| | - Elena Marcos
- Departamento de Biodiversidad y Gestión Ambiental, Facultad de Ciencias Biológicas y Ambientales, Universidad de León, 24071 León, Spain
| | - Leonor Calvo
- Departamento de Biodiversidad y Gestión Ambiental, Facultad de Ciencias Biológicas y Ambientales, Universidad de León, 24071 León, Spain
| | - Luis E Sáenz de Miera
- Departamento de Biología Molecular, Facultad de Ciencias Biológicas y Ambientales, Universidad de León, 24071 León, Spain
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Gao X, Wang S, Kong W, Li G, Zhang L, Yin X. Floristic changes and environmental drivers of soil fungi and archaea in different salt-tolerant plant communities in the intertidal habitat of coastal wetlands. ENVIRONMENTAL GEOCHEMISTRY AND HEALTH 2024; 46:167. [PMID: 38592380 DOI: 10.1007/s10653-024-01951-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 03/08/2024] [Indexed: 04/10/2024]
Abstract
Microorganisms are crucial elements of terrestrial ecosystems, which play significant roles in improving soil physicochemical properties, providing plant growth nutrients, degrading toxic and harmful chemicals, and biogeochemical cycling. Variations in the types and quantities of root exudates among different plants greatly alter soil physicochemical properties and result in variations in the diversity, structure, and function of soil microorganisms. Not much is understood about the differences of soil fungi and archaea communities for different plant communities in coastal wetlands, and their response mechanisms to environmental changes. In this study, fungal and archaea communities in soils of Suaeda salsa, Phragmites australis, and Spartina alterniflora in the intertidal habitat of coastal wetlands were selected for research. Soil fungi and archaea were analyzed for diversity, community structure, and function using high throughput ITS and 16S rRNA gene sequencing. The study revealed significant differences in fungi and archaea's diversity and community structure in the rhizosphere soil of three plant communities. At the same time, there is no significant difference in the functional groups. SOM, TP, AP, MC, EC and SOM, TN, TP, AP, MC, EC are the primary environmental determinants affecting changes in soil fungal and archaeal communities, respectively. Variations in the diversity, community structure, and ecological functions of fungi and archaea can be used as indicators characterizing the impact of external disturbances on the soil environment, providing a theoretical foundation for the effective utilization of soil microbial resources, thereby achieving the goal of environmental protection and health promotion.
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Affiliation(s)
- Xin Gao
- Institute of Water Ecology and Environment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Shuping Wang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Weijing Kong
- Institute of Water Ecology and Environment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China.
| | - Guowen Li
- Institute of Water Ecology and Environment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Lieyu Zhang
- Institute of Water Ecology and Environment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Xuwang Yin
- Liaoning Provincial Key Laboratory for Hydrobiology, College of Fisheries and Life Science, Dalian Ocean University, Dalian, 116023, China
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Zhang N, Chen K, Wu C, Jiang H, Du Y, Chen Z, Wang X, Qi D, Yang Z. Vertical differentiation drives the changes in the main microflora and metabolites of carbon and nitrogen cycling in the early freeze-thaw period in the Qinghai Lake Basin. Front Microbiol 2024; 15:1329647. [PMID: 38650884 PMCID: PMC11033449 DOI: 10.3389/fmicb.2024.1329647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Accepted: 03/28/2024] [Indexed: 04/25/2024] Open
Abstract
Global climate change has altered the frequency of soil freeze-thaw cycles, but the response of soil microorganisms to different elevation gradients during the early freeze-thaw period remains unclear. So far, the influence of the altitudinal gradient on the microbial community and metabolic characteristics in the early freeze-thaw period of the Qinghai Lake Basin remains unclear. To this end, we collected soil at different elevations in the early freeze-thaw period of the Qinghai Lake Basin and investigated the influence of the elevation gradient on soil microbial community characteristics and soil metabolic processes as well as the corresponding environmental driving mechanism by high-throughput sequencing and LC-MS (Liquid Chromatograph-Mass Spectrometer) nontargeted metabolite determination. The results showed that Proteobacteria were the dominant microflora in the Qinghai Lake Basin. The dominant phyla associated with carbon and nitrogen are Proteobacteria and Firmicutes, both of which are significantly affected by elevation. The soil physicochemical factors jointly affected the soil microbial communities and metabolism. Total phosphorus nitrate nitrogen and pH were the main driving factors of the microbial community, and metabolites were sensitive to changes in chemical factors. In short, the microbial community structure and function, soil physicochemical factors and soil metabolic processes were significantly affected by the altitudinal gradient in the early freeze-thaw period, while the microbial community diversity showed no significant response to the altitudinal gradient. Additionally, a high potassium content in the soil may promote the growth and reproduction of bacteria associated with carbon and nitrogen cycling, as well as the production of metabolites.
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Affiliation(s)
- Ni Zhang
- Qinghai Province Key Laboratory of Physical Geography and Environmental Process, College of Geographical Science, Qinghai Normal University, Xining, China
- Key Laboratory of Tibetan Plateau Land Surface Processes and Ecological Conservation (Ministry of Education), Qinghai Normal University, Xining, China
- National Positioning Observation and Research Station of Qinghai Lake Wetland Ecosystem in Qinghai, National Forestry and Grassland Administration, Haibei, China
| | - Kelong Chen
- Qinghai Province Key Laboratory of Physical Geography and Environmental Process, College of Geographical Science, Qinghai Normal University, Xining, China
- Key Laboratory of Tibetan Plateau Land Surface Processes and Ecological Conservation (Ministry of Education), Qinghai Normal University, Xining, China
- National Positioning Observation and Research Station of Qinghai Lake Wetland Ecosystem in Qinghai, National Forestry and Grassland Administration, Haibei, China
| | - Chenxi Wu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Hongchen Jiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
- Qinghai Provincial Key Laboratory of Geology and Environment of Salt Lakes, Qinghai Institute of Salt Lakes, Chinese Academy of Sciences, Xining, China
| | - Yangong Du
- Qinghai Provincial Key Laboratory of Restoration Ecology for Cold Region, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Zhirong Chen
- College of Resources, Environment and Life Sciences, Ningxia Normal University, Guyuan, China
| | - Xinye Wang
- Qinghai Province Key Laboratory of Physical Geography and Environmental Process, College of Geographical Science, Qinghai Normal University, Xining, China
- Key Laboratory of Tibetan Plateau Land Surface Processes and Ecological Conservation (Ministry of Education), Qinghai Normal University, Xining, China
- National Positioning Observation and Research Station of Qinghai Lake Wetland Ecosystem in Qinghai, National Forestry and Grassland Administration, Haibei, China
| | - Desheng Qi
- Qinghai Province Key Laboratory of Physical Geography and Environmental Process, College of Geographical Science, Qinghai Normal University, Xining, China
- Key Laboratory of Tibetan Plateau Land Surface Processes and Ecological Conservation (Ministry of Education), Qinghai Normal University, Xining, China
- National Positioning Observation and Research Station of Qinghai Lake Wetland Ecosystem in Qinghai, National Forestry and Grassland Administration, Haibei, China
| | - Ziwei Yang
- Qinghai Province Key Laboratory of Physical Geography and Environmental Process, College of Geographical Science, Qinghai Normal University, Xining, China
- Key Laboratory of Tibetan Plateau Land Surface Processes and Ecological Conservation (Ministry of Education), Qinghai Normal University, Xining, China
- National Positioning Observation and Research Station of Qinghai Lake Wetland Ecosystem in Qinghai, National Forestry and Grassland Administration, Haibei, China
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Luo F, Mi W, Liu W, Ma X, Liu K, Ju Z, Li W. Soil microbial community are more sensitive to ecological regions than cropping systems in alpine annual grassland of the Qinghai-Tibet Plateau. Front Microbiol 2024; 15:1345235. [PMID: 38559358 PMCID: PMC10978683 DOI: 10.3389/fmicb.2024.1345235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Accepted: 03/01/2024] [Indexed: 04/04/2024] Open
Abstract
Introduction Modern agriculture emphasizes the design of cropping systems using ecological function and production services to achieve sustainability. The functional characteristics of plants (grasses vs. legumes) affect changes in soil microbial communities that drive agroecosystem services. Information on the relationship between legume-grass mixtures and soil microorganisms in different ecological zones guides decision-making toward eco-friendly and sustainable forage production. However, it is still poorly understood how cropping patterns affect soil microbial diversity in alpine grasslands and whether this effect varies with altitude. Methods To fill this gap in knowledge, we conducted a field study to investigate the effects of growing oats (Avena sativa L.), forage peas (Pisum sativum L.), common cornflower (Vicia sativa L.), and fava beans (Vicia faba L.) in monocultures and mixtures on the soil microbial communities in three ecological zones of the high alpine zone. Results We found that the fungal and bacterial community structure differed among the cropping patterns, particularly the community structure of the legume mixed cropping pattern was very different from that of monocropped oats. In all ecological zones, mixed cropping significantly (p < 0.05) increased the α-diversity of the soil bacteria and fungi compared to oat monoculture. The α-diversity of the soil bacteria tended to increase with increasing elevation (MY [2,513 m] < HZ [2,661 m] < GN [3,203 m]), while the opposite was true for fungi (except for the Chao1 index in HZ, which was the lowest). Mixed cropping increased the abundance of soil fungi and bacteria across ecological zones, particularly the relative abundances of Nitrospira, Nitrososphaera, Phytophthora, and Acari. Factors affecting the bacterial community structure included the cropping pattern, the ecological zone, water content, nitrate-nitrogen, nitrate reductase, and soil capacity, whereas factors affecting fungal community structure included the cropping pattern, the ecological zone, water content, pH, microbial biomass nitrogen, and catalase. Discussion Our study highlights the variation in soil microbial communities among different in alpine ecological regions and their resilience to cropping systems. Our results also underscore that mixed legume planting is a sustainable and effective forage management practice for the Tibetan Plateau.
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Affiliation(s)
- Feng Luo
- Key Laboratory of Superior Forage Germplasm in the Qinghai-Tibetan Plateau, Qinghai Academy of Animal Husbandry and Veterinary Sciences, Qinghai University, Xining, China
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Qinghai University, Xining, China
| | - Wenbo Mi
- Key Laboratory of Superior Forage Germplasm in the Qinghai-Tibetan Plateau, Qinghai Academy of Animal Husbandry and Veterinary Sciences, Qinghai University, Xining, China
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Qinghai University, Xining, China
| | - Wenhui Liu
- Key Laboratory of Superior Forage Germplasm in the Qinghai-Tibetan Plateau, Qinghai Academy of Animal Husbandry and Veterinary Sciences, Qinghai University, Xining, China
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Qinghai University, Xining, China
| | - Xiang Ma
- Key Laboratory of Superior Forage Germplasm in the Qinghai-Tibetan Plateau, Qinghai Academy of Animal Husbandry and Veterinary Sciences, Qinghai University, Xining, China
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Qinghai University, Xining, China
| | - KaiQiang Liu
- Key Laboratory of Superior Forage Germplasm in the Qinghai-Tibetan Plateau, Qinghai Academy of Animal Husbandry and Veterinary Sciences, Qinghai University, Xining, China
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Qinghai University, Xining, China
| | - Zeliang Ju
- Key Laboratory of Superior Forage Germplasm in the Qinghai-Tibetan Plateau, Qinghai Academy of Animal Husbandry and Veterinary Sciences, Qinghai University, Xining, China
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Qinghai University, Xining, China
| | - Wen Li
- Key Laboratory of Superior Forage Germplasm in the Qinghai-Tibetan Plateau, Qinghai Academy of Animal Husbandry and Veterinary Sciences, Qinghai University, Xining, China
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Qinghai University, Xining, China
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Zhang X, Wang Y, Wang J, Yu M, Zhang R, Mi Y, Xu J, Jiang R, Gao J. Elevation Influences Belowground Biomass Proportion in Forests by Affecting Climatic Factors, Soil Nutrients and Key Leaf Traits. PLANTS (BASEL, SWITZERLAND) 2024; 13:674. [PMID: 38475521 DOI: 10.3390/plants13050674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Revised: 02/27/2024] [Accepted: 02/27/2024] [Indexed: 03/14/2024]
Abstract
Forest biomass allocation is a direct manifestation of biological adaptation to environmental changes. Studying the distribution patterns of forest biomass along elevational gradients is ecologically significant for understanding the specific impacts of global change on plant resource allocation strategies. While aboveground biomass has been extensively studied, research on belowground biomass remains relatively limited. Furthermore, the patterns and driving factors of the belowground biomass proportion (BGBP) along elevational gradients are still unclear. In this study, we investigated the specific influences of climatic factors, soil nutrients, and key leaf traits on the elevational pattern of BGBP using data from 926 forests at 94 sites across China. In this study, BGBP data were calculated from the root biomass to the depth of 50 cm. Our findings indicate considerable variability in forest BGBP at a macro scale, showing a significant increasing trend along elevational gradients (p < 0.01). BGBP significantly decreases with increasing temperature and precipitation and increases with annual mean evapotranspiration (MAE) (p < 0.01). It decreases significantly with increasing soil phosphorus content and increases with soil pH (p < 0.01). Key leaf traits (leaf nitrogen (LN) and leaf phosphorus (LP)) are positively correlated with BGBP. Climatic factors (R2 = 0.46) have the strongest explanatory power for the variation in BGBP along elevations, while soil factors (R2 = 0.10) and key leaf traits (R2 = 0.08) also play significant roles. Elevation impacts BGBP directly and also indirectly through influencing such as climate conditions, soil nutrient availability, and key leaf traits, with direct effects being more pronounced than indirect effects. This study reveals the patterns and controlling factors of forests' BGBP along elevational gradients, providing vital ecological insights into the impact of global change on plant resource allocation strategies and offering scientific guidance for ecosystem management and conservation.
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Affiliation(s)
- Xing Zhang
- Key Laboratory for the Conservation and Regulation Biology of Species in Special Environments, College of Life Science, Xinjiang Normal University, Urumqi 830054, China
| | - Yun Wang
- Key Laboratory for the Conservation and Regulation Biology of Species in Special Environments, College of Life Science, Xinjiang Normal University, Urumqi 830054, China
| | - Jiangfeng Wang
- Key Laboratory for the Conservation and Regulation Biology of Species in Special Environments, College of Life Science, Xinjiang Normal University, Urumqi 830054, China
| | - Mengyao Yu
- Key Laboratory for the Conservation and Regulation Biology of Species in Special Environments, College of Life Science, Xinjiang Normal University, Urumqi 830054, China
| | - Ruizhi Zhang
- Key Laboratory for the Conservation and Regulation Biology of Species in Special Environments, College of Life Science, Xinjiang Normal University, Urumqi 830054, China
| | - Yila Mi
- Key Laboratory for the Conservation and Regulation Biology of Species in Special Environments, College of Life Science, Xinjiang Normal University, Urumqi 830054, China
| | - Jiali Xu
- Key Laboratory for the Conservation and Regulation Biology of Species in Special Environments, College of Life Science, Xinjiang Normal University, Urumqi 830054, China
| | - Ruifang Jiang
- Xinjiang Uyghur Autonomous Region Forestry Planning Institute, Urumqi 830046, China
| | - Jie Gao
- Key Laboratory for the Conservation and Regulation Biology of Species in Special Environments, College of Life Science, Xinjiang Normal University, Urumqi 830054, China
- Key Laboratory of Earth Surface Processes of Ministry of Education, College of Urban and Environmental Sciences, Peking University, Beijing 100863, China
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Wu P, Hu D, Guo J, Li J, Zhong Q, Cheng D. Unraveling the spatial-temporal distribution patterns of soil abundant and rare bacterial communities in China's subtropical mountain forest. Front Microbiol 2024; 15:1323887. [PMID: 38410396 PMCID: PMC10895375 DOI: 10.3389/fmicb.2024.1323887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 01/24/2024] [Indexed: 02/28/2024] Open
Abstract
Introduction The pivotal roles of both abundant and rare bacteria in ecosystem function are widely acknowledged. Despite this, the diversity elevational patterns of these two bacterial taxa in different seasons and influencing factors remains underexplored, especially in the case of rare bacteria. Methods Here, a metabarcoding approach was employed to investigate elevational patterns of these two bacterial communities in different seasons and tested the roles of soil physico-chemical properties in structuring these abundant and rare bacterial community. Results and discussion Our findings revealed that variation in elevation and season exerted notably effects on the rare bacterial diversity. Despite the reactions of abundant and rare communities to the elevational gradient exhibited similarities during both summer and winter, distinct elevational patterns were observed in their respective diversity. Specifically, abundant bacterial diversity exhibited a roughly U-shaped pattern along the elevation gradient, while rare bacterial diversity increased with the elevational gradient. Soil moisture and N:P were the dominant factor leading to the pronounced divergence in elevational distributions in summer. Soil temperature and pH were the key factors in winter. The network analysis revealed the bacteria are better able to adapt to environmental fluctuations during the summer season. Additionally, compared to abundant bacteria, the taxonomy of rare bacteria displayed a higher degree of complexity. Our discovery contributes to advancing our comprehension of intricate dynamic diversity patterns in abundant and rare bacteria in the context of environmental gradients and seasonal fluctuations.
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Affiliation(s)
- Panpan Wu
- Institute of Geography, Fujian Normal University, Fuzhou, Fujian, China
- Fujian Provincial Key Laboratory of Plant Ecophysiology, Fujian Normal University, Fuzhou, China
| | - Dandan Hu
- Institute of Geography, Fujian Normal University, Fuzhou, Fujian, China
- Fujian Provincial Key Laboratory of Plant Ecophysiology, Fujian Normal University, Fuzhou, China
| | - Jiaheng Guo
- Institute of Geography, Fujian Normal University, Fuzhou, Fujian, China
- Fujian Provincial Key Laboratory of Plant Ecophysiology, Fujian Normal University, Fuzhou, China
| | - Jinlong Li
- Institute of Geography, Fujian Normal University, Fuzhou, Fujian, China
- Fujian Provincial Key Laboratory of Plant Ecophysiology, Fujian Normal University, Fuzhou, China
| | - Quanlin Zhong
- Institute of Geography, Fujian Normal University, Fuzhou, Fujian, China
- Fujian Provincial Key Laboratory of Plant Ecophysiology, Fujian Normal University, Fuzhou, China
| | - Dongliang Cheng
- Institute of Geography, Fujian Normal University, Fuzhou, Fujian, China
- Fujian Provincial Key Laboratory of Plant Ecophysiology, Fujian Normal University, Fuzhou, China
- Key Laboratory of Humid Subtropical Eco-geographical Process, Ministry of Education, Fuzhou, China
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Liu X, Chu H, Godoy O, Fan K, Gao GF, Yang T, Ma Y, Delgado-Baquerizo M. Positive associations fuel soil biodiversity and ecological networks worldwide. Proc Natl Acad Sci U S A 2024; 121:e2308769121. [PMID: 38285947 PMCID: PMC10861899 DOI: 10.1073/pnas.2308769121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 12/27/2023] [Indexed: 01/31/2024] Open
Abstract
Microbial interactions are key to maintaining soil biodiversity. However, whether negative or positive associations govern the soil microbial system at a global scale remains virtually unknown, limiting our understanding of how microbes interact to support soil biodiversity and functions. Here, we explored ecological networks among multitrophic soil organisms involving bacteria, protists, fungi, and invertebrates in a global soil survey across 20 regions of the planet and found that positive associations among both pairs and triads of soil taxa governed global soil microbial networks. We further revealed that soil networks with greater levels of positive associations supported larger soil biodiversity and resulted in lower network fragility to withstand potential perturbations of species losses. Our study provides unique evidence of the widespread positive associations between soil organisms and their crucial role in maintaining the multitrophic structure of soil biodiversity worldwide.
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Affiliation(s)
- Xu Liu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing210008, China
- University of Chinese Academy of Sciences, Beijing100049, China
| | - Haiyan Chu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing210008, China
- University of Chinese Academy of Sciences, Beijing100049, China
| | - Oscar Godoy
- Departamento de Biología, Instituto Universitario de Ciencias del Mar, Universidad de Cádiz, Puerto RealE-11510, Spain
| | - Kunkun Fan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing210008, China
- University of Chinese Academy of Sciences, Beijing100049, China
| | - Gui-Feng Gao
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing210008, China
- University of Chinese Academy of Sciences, Beijing100049, China
| | - Teng Yang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing210008, China
- University of Chinese Academy of Sciences, Beijing100049, China
| | - Yuying Ma
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing210008, China
- University of Chinese Academy of Sciences, Beijing100049, China
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico. Instituto de Recursos Naturales y Agrobiología de Sevilla, Consejo Superior de Investigaciones Científicas, SevillaE-41012, Spain
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Lei S, Wang X, Wang J, Zhang L, Liao L, Liu G, Wang G, Song Z, Zhang C. Effect of aridity on the β-diversity of alpine soil potential diazotrophs: insights into community assembly and co-occurrence patterns. mSystems 2024; 9:e0104223. [PMID: 38059620 PMCID: PMC10804954 DOI: 10.1128/msystems.01042-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 10/23/2023] [Indexed: 12/08/2023] Open
Abstract
Microbial diversity plays a vital role in the maintenance of ecosystem functions. However, the current understanding of mechanisms that shape microbial diversity along environmental gradients at broad spatial scales is relatively limited, especially for specific functional groups, such as potential diazotrophs. Here, we conducted an aridity-gradient transect survey from 60 sites across the Tibetan Plateau, the largest alpine ecosystem of the planet, to investigate the ecological processes (e.g., local species pools, community assembly processes, and co-occurrence patterns) that underlie the β-diversity of alpine soil potential diazotrophic communities. We found that aridity strongly and negatively affected the abundance, richness, and β-diversity of soil diazotrophs. Diazotrophs displayed a distance-decay pattern along the aridity gradient, with organisms living in lower aridity habitats having a stronger distance-decay pattern. Arid habitats had lower co-occurrence complexity, including the number of edges and vertices, the average degree, and the number of keystone taxa, as compared with humid habitats. Local species pools explained limited variations in potential diazotrophic β-diversity. In contrast, co-occurrence patterns and stochastic processes (e.g., dispersal limitation and ecological drift) played a significant role in regulating potential diazotrophic β-diversity. The relative importance of stochastic processes and co-occurrence patterns changed with increasing aridity, with stochastic processes weakening whereas that of co-occurrence patterns enhancing. The genera Geobacter and Paenibacillus were identified as keystone taxa of co-occurrence patterns that are associated with β-diversity. In summary, aridity affects the co-occurrence patterns and community assembly by regulating soil and vegetation characteristics and ultimately shapes the β-diversity of potential diazotrophs. These findings highlight the importance of co-occurrence patterns in structuring microbial diversity and advance the current understanding of mechanisms that drive belowground communities.IMPORTANCERecent studies have shown that community assembly processes and species pools are the main drivers of β-diversity in grassland microbial communities. However, co-occurrence patterns can also drive β-diversity formation by influencing the dispersal and migration of species, the importance of which has not been reported in previous studies. Assessing the impact of co-occurrence patterns on β-diversity is important for understanding the mechanisms of diversity formation. Our study highlights the influence of microbial co-occurrence patterns on β-diversity and combines the drivers of community β-diversity with drought variation, revealing that drought indirectly affects β-diversity by influencing diazotrophic co-occurrence patterns and community assembly.
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Affiliation(s)
- Shilong Lei
- The Research Center of Soil and Water Conservation and Ecological Environment, Chinese Academy of Sciences and Ministry of Education, Yangling, Shaanxi, China
- Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry of Water Resources, Yangling, Shaanxi, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiangtao Wang
- College of Animal Science, Tibet Agriculture and Animal Husbandry University, Nyingchi, China
| | - Jie Wang
- College of Forestry, Guizhou University, Guiyang, China
| | - Lu Zhang
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, Shaanxi, China
| | - Lirong Liao
- The Research Center of Soil and Water Conservation and Ecological Environment, Chinese Academy of Sciences and Ministry of Education, Yangling, Shaanxi, China
- Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry of Water Resources, Yangling, Shaanxi, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Guobin Liu
- The Research Center of Soil and Water Conservation and Ecological Environment, Chinese Academy of Sciences and Ministry of Education, Yangling, Shaanxi, China
- Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry of Water Resources, Yangling, Shaanxi, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Guoliang Wang
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, Shaanxi, China
- Institute of Soil and Water Conservation, Chinese Academy of Science, Yangling, Shaanxi, China
| | - Zilin Song
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, China
| | - Chao Zhang
- The Research Center of Soil and Water Conservation and Ecological Environment, Chinese Academy of Sciences and Ministry of Education, Yangling, Shaanxi, China
- Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry of Water Resources, Yangling, Shaanxi, China
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, Shaanxi, China
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Niu S, Xie J, Wang G, Li Z, Zhang K, Li H, Xia Y, Tian J, Yu E, Xie W, Gong W. Community assembly patterns and processes of bacteria in a field-scale aquaculture wastewater treatment system. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 907:167913. [PMID: 37858824 DOI: 10.1016/j.scitotenv.2023.167913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 10/15/2023] [Accepted: 10/16/2023] [Indexed: 10/21/2023]
Abstract
Microbial communities are responsible for the biological treatment of wastewater, however, our comprehension of their diversity, assembly patterns, and functions remains limited. In this study, we analyzed bacterial communities in both water and sediment samples. These samples were gathered from a novel field-scale aquaculture wastewater treatment system (FAWTS), which employs a multi-stage purification process to eliminate nutrients from pond culture wastewater. Significant variations were observed in bacterial diversity and composition across various ponds within the system and at different stages of the culture. Notably, the bacterial community in the FAWTS displayed a distinct species abundance distribution. The influence of dispersal-driven processes on shaping FAWTS communities was found to be relatively weak. The utilization of neutral and null models unveiled that the assembly of microbial communities was primarily governed by stochastic processes. Moreover, environmental factors variables such as total nitrogen (TN), dissolved oxygen (DO), and temperature were found to be associated with both the composition and assembly of bacterial communities, influencing the relative significance of stochastic processes. Furthermore, we discovered a close relationship between that bacterial community composition and system functionality. These findings hold significant implications for microbial ecologists and environmental engineers, as they can collaboratively refine operational strategies while preserving biodiversity. This, in turn, promotes the stability and efficiency of the FAWTS. In summary, our study contributes to an enhanced mechanistic understanding of microbial community diversity, assembly patterns, and functionality within the FAWTS, offering valuable insights into both microbial ecology and wastewater treatment processes.
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Affiliation(s)
- Shuhui Niu
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong 510380, China; Guangdong Ecological Remediation of Aquaculture Pollution Research Center, Guangzhou, Guangdong 510380, China
| | - Jun Xie
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong 510380, China; Guangdong Ecological Remediation of Aquaculture Pollution Research Center, Guangzhou, Guangdong 510380, China; Hainan Fisheries Innovation Research Institute, Chinese Academy of Fishery Sciences, Sanya, Hainan 572000, China
| | - Guangjun Wang
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong 510380, China; Guangdong Ecological Remediation of Aquaculture Pollution Research Center, Guangzhou, Guangdong 510380, China; Hainan Fisheries Innovation Research Institute, Chinese Academy of Fishery Sciences, Sanya, Hainan 572000, China
| | - Zhifei Li
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong 510380, China; Guangdong Ecological Remediation of Aquaculture Pollution Research Center, Guangzhou, Guangdong 510380, China; Hainan Fisheries Innovation Research Institute, Chinese Academy of Fishery Sciences, Sanya, Hainan 572000, China
| | - Kai Zhang
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong 510380, China; Guangdong Ecological Remediation of Aquaculture Pollution Research Center, Guangzhou, Guangdong 510380, China; Hainan Fisheries Innovation Research Institute, Chinese Academy of Fishery Sciences, Sanya, Hainan 572000, China
| | - Hongyan Li
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong 510380, China; Guangdong Ecological Remediation of Aquaculture Pollution Research Center, Guangzhou, Guangdong 510380, China; Hainan Fisheries Innovation Research Institute, Chinese Academy of Fishery Sciences, Sanya, Hainan 572000, China
| | - Yun Xia
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong 510380, China; Guangdong Ecological Remediation of Aquaculture Pollution Research Center, Guangzhou, Guangdong 510380, China; Hainan Fisheries Innovation Research Institute, Chinese Academy of Fishery Sciences, Sanya, Hainan 572000, China
| | - Jingjing Tian
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong 510380, China; Guangdong Ecological Remediation of Aquaculture Pollution Research Center, Guangzhou, Guangdong 510380, China; Hainan Fisheries Innovation Research Institute, Chinese Academy of Fishery Sciences, Sanya, Hainan 572000, China
| | - Ermeng Yu
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong 510380, China; Guangdong Ecological Remediation of Aquaculture Pollution Research Center, Guangzhou, Guangdong 510380, China; Hainan Fisheries Innovation Research Institute, Chinese Academy of Fishery Sciences, Sanya, Hainan 572000, China
| | - Wenping Xie
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong 510380, China; Guangdong Ecological Remediation of Aquaculture Pollution Research Center, Guangzhou, Guangdong 510380, China; Hainan Fisheries Innovation Research Institute, Chinese Academy of Fishery Sciences, Sanya, Hainan 572000, China
| | - Wangbao Gong
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong 510380, China; Guangdong Ecological Remediation of Aquaculture Pollution Research Center, Guangzhou, Guangdong 510380, China; Hainan Fisheries Innovation Research Institute, Chinese Academy of Fishery Sciences, Sanya, Hainan 572000, China.
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Caballol M, Redondo MÁ, Catalán N, Corcobado T, Jung T, Marçais B, Milenković I, Nemesio-Gorriz M, Stenlid J, Oliva J. Climate acts as an environmental filter to plant pathogens. THE ISME JOURNAL 2024; 18:wrae010. [PMID: 38366172 PMCID: PMC10926774 DOI: 10.1093/ismejo/wrae010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 01/17/2024] [Accepted: 01/18/2024] [Indexed: 02/18/2024]
Abstract
Climate shapes the distribution of plant-associated microbes such as mycorrhizal and endophytic fungi. However, the role of climate in plant pathogen community assembly is less understood. Here, we explored the role of climate in the assembly of Phytophthora communities at >250 sites along a latitudinal gradient from Spain to northern Sweden and an altitudinal gradient from the Spanish Pyrenees to lowland areas. Communities were detected by ITS sequencing of river filtrates. Mediation analysis supported the role of climate in the biogeography of Phytophthora and ruled out other environmental factors such as geography or tree diversity. Comparisons of functional and species diversity showed that environmental filtering dominated over competitive exclusion in Europe. Temperature and precipitation acted as environmental filters at different extremes of the gradients. In northern regions, winter temperatures acted as an environmental filter on Phytophthora community assembly, selecting species adapted to survive low minimum temperatures. In southern latitudes, a hot dry climate was the main environmental filter, resulting in communities dominated by drought-tolerant Phytophthora species with thick oospore walls, a high optimum temperature for growth, and a high maximum temperature limit for growth. By taking a community ecology approach, we show that the establishment of Phytophthora plant pathogens in Europe is mainly restricted by cold temperatures.
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Affiliation(s)
- Maria Caballol
- Department of Agricultural and Forest Sciences and Engineering, University of Lleida, Lleida 25198, Spain
- Joint Research Unit CTFC – AGROTECNIO-CERCA, Lleida 25198, Spain
| | - Miguel Ángel Redondo
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, PO Box 7026, Uppsala 750 07, Sweden
| | - Núria Catalán
- Institute of Environmental Assessment and Water Research, IDAEA-CSIC, Barcelona 08034, Spain
| | - Tamara Corcobado
- Mendel University in Brno, Faculty of Forestry and Wood Technology, Department of Forest Protection and Wildlife Management, Phytophthora Research Centre, Brno 613 00, Czech Republic
- Austrian Research Centre for Forests (BFW), Seckendorff-Gudent-Weg 8, Vienna 1131, Austria
| | - Thomas Jung
- Mendel University in Brno, Faculty of Forestry and Wood Technology, Department of Forest Protection and Wildlife Management, Phytophthora Research Centre, Brno 613 00, Czech Republic
| | - Benoît Marçais
- Université de Lorraine - INRAE, UMR Interactions Arbres/Microorganismes, Nancy 54000, France
| | - Ivan Milenković
- Mendel University in Brno, Faculty of Forestry and Wood Technology, Department of Forest Protection and Wildlife Management, Phytophthora Research Centre, Brno 613 00, Czech Republic
- University of Belgrade-Faculty of Forestry, Belgrade 11030, Serbia
| | | | - Jan Stenlid
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, PO Box 7026, Uppsala 750 07, Sweden
| | - Jonàs Oliva
- Department of Agricultural and Forest Sciences and Engineering, University of Lleida, Lleida 25198, Spain
- Joint Research Unit CTFC – AGROTECNIO-CERCA, Lleida 25198, Spain
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Zhou Y, Meng F, Ochieng B, Xu J, Zhang L, Kimirei IA, Feng M, Zhu L, Wang J. Climate and Environmental Variables Drive Stream Biofilm Bacterial and Fungal Diversity on Tropical Mountainsides. MICROBIAL ECOLOGY 2024; 87:28. [PMID: 38182675 DOI: 10.1007/s00248-023-02335-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Accepted: 12/22/2023] [Indexed: 01/07/2024]
Abstract
High mountain freshwater systems are particularly sensitive to the impacts of global warming and relevant environmental changes. Microorganisms contribute substantially to biogeochemical processes, yet their distribution patterns and driving mechanism in alpine streams remain understudied. Here, we examined the bacterial and fungal community compositions in stream biofilm along the elevational gradient of 745-1874 m on Mt. Kilimanjaro and explored their alpha and beta diversity patterns and the underlying environmental drivers. We found that the species richness and evenness monotonically increased towards higher elevations for bacteria, while were non-significant for fungi. However, both bacterial and fungal communities showed consistent elevational distance-decay relationships, i.e., the dissimilarity of assemblage composition increased with greater elevational differences. Bacterial alpha diversity patterns were mainly affected by chemical variables such as total nitrogen and phosphorus, while fungi were affected by physical variables such as riparian shading and stream width. Notably, climatic variables such as mean annual temperature strongly affected the elevational succession of bacterial and fungal community compositions. Our study is the first exploration of microbial biodiversity and their underlying driving mechanisms for stream ecosystems in tropical alpine regions. Our findings provide insights on the response patterns of tropical aquatic microbial community composition and diversity under climate change.
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Affiliation(s)
- Yanan Zhou
- College of Life Sciences, Nanjing Normal University, Nanjing, 210046, China
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Fanfan Meng
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Beryl Ochieng
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jianing Xu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
- School of Civil Engineering, Southeast University, Nanjing, 210096, China
| | - Lu Zhang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | | | - Muhua Feng
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Lifeng Zhu
- College of Life Sciences, Nanjing Normal University, Nanjing, 210046, China.
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, China.
| | - Jianjun Wang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China.
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Luo F, Zhao Y, Xu JY, Wang HT, Zhu D. Network complexity of bacterial community driving antibiotic resistome in the microbiome of earthworm guts under different land use patterns. JOURNAL OF HAZARDOUS MATERIALS 2024; 461:132732. [PMID: 37813029 DOI: 10.1016/j.jhazmat.2023.132732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 10/05/2023] [Indexed: 10/11/2023]
Abstract
Recently, the study of antibiotic resistance in the soil animal microbiome has attracted extensive attention; however, the patterns of antibiotic resistance genes (ARGs) in soil and soil animals related to different land use types remain poorly studied. In the present study, soil and earthworms were collected from four different land-use types (farmland, hospital, park land, and mountain park), and 162 ARGs in the microbiomes of the soil and earthworms were quantified using high-throughput quantitative PCR. Our study showed that the abundance and number of ARGs were higher in soil samples than in earthworm guts, but earthworms as the living organisms created relatively isolated ambient surroundings, which allowed for a more heterogeneous ARGs profile. Meanwhile, land use significantly influenced the abundance, number and co-occurrence pattern of ARGs in the soil and earthworm samples. Furthermore, abiotic and biotic factors had significant effects on the ARGs profile, among which pH had a negative effect on the ARGs profiles of both soil and earthworm microbiomes, and bacterial network complexity had a positive effect on the earthworm ARGs profile. Our study provides new insights into the distribution and dispersal of ARGs in the soil animal gut microbiome under different land use patterns.
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Affiliation(s)
- Fang Luo
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China; State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory for Pesticide Residue Detection of Ministry of Agriculture and Rural Affairs, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Yang Zhao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory for Pesticide Residue Detection of Ministry of Agriculture and Rural Affairs, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Jia-Yang Xu
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hong-Tao Wang
- College of Geography and Environmental Science, Henan University, Kaifeng 475004, China
| | - Dong Zhu
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China.
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18
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Li H, Zhang H, Li H, Duan L, Zhang X, Gao Y, Hall IR, Hemming SR, LeVay LJ. Sedimentary DNA reveals the link between microbial community dynamics and climate during the late last glaciation in the offshore region of the Zambezi River, Southwest Indian Ocean. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 906:167787. [PMID: 37844644 DOI: 10.1016/j.scitotenv.2023.167787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 10/04/2023] [Accepted: 10/10/2023] [Indexed: 10/18/2023]
Abstract
Reconstructing the relationship between microbial communities and past abrupt climate change is of great importance for understanding current biodiversity patterns and predicting changes under future climate scenarios. However, little is currently known about how microbial communities respond to changes in key environmental stages due to a lack of research in this area. Here, we examine the variability in the communities of bacteria, archaea, and fungi from sediments deposited offshore region of the Zambezi River between 21.7 and 9.6 thousand years ago (ka) (covering the last glacial maximum, or LGM, and the early Holocene) using DNA metabarcoding approach via high-throughput sequencing. The results showed that (1) microbial assemblages differed across three key time intervals, with the last deglaciation having the most homogeneous prokaryotic assemblages, while for fungal communities in the LGM, and the early Holocene and LGM differing the most; (2) the warm early Holocene showed the highest diversity, whereas the lowest diversity was found in the LGM; and (3) the selected indicator species better reflected the climatic characteristics of different environmental stages. These results highlight the power of ancient sedimentary DNA to refine our understanding of microbial dynamics in marine sedimentary systems near large rivers, thus providing a basis for better modeling ecological processes in further research.
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Affiliation(s)
- Haoyu Li
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, 650500 Kunming, China
| | - Hucai Zhang
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, 650500 Kunming, China.
| | - Huayong Li
- School of Resource Environment and Tourism, Anyang Normal University, Anyang 455000, China
| | - Lizeng Duan
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, 650500 Kunming, China
| | - Xiaonan Zhang
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, 650500 Kunming, China
| | - Youhong Gao
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, 650500 Kunming, China
| | - Ian R Hall
- Department of Earth Sciences, Cardiff University, Main College, Park Place, PO Box 914, Cardiff, Wales CF10 3AT, United Kingdom
| | - Sidney R Hemming
- Lamont-Doherty Earth Observatory, Columbia University, 61 Route 9W, Palisades, NY, 10964, USA
| | - Leah J LeVay
- International Ocean Discovery Program, Texas A&M University, College Station, TX 77845, USA
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Bonthond G, Beermann J, Gutow L, Neumann A, Barboza FR, Desiderato A, Fofonova V, Helber SB, Khodami S, Kraan C, Neumann H, Rohde S, Schupp PJ. Benthic microbial biogeographic trends in the North Sea are shaped by an interplay of environmental drivers and bottom trawling effort. ISME COMMUNICATIONS 2023; 3:132. [PMID: 38102238 PMCID: PMC10724143 DOI: 10.1038/s43705-023-00336-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 11/09/2023] [Accepted: 11/16/2023] [Indexed: 12/17/2023]
Abstract
Microbial composition and diversity in marine sediments are shaped by environmental, biological, and anthropogenic processes operating at different scales. However, our understanding of benthic microbial biogeography remains limited. Here, we used 16S rDNA amplicon sequencing to characterize benthic microbiota in the North Sea from the top centimeter of 339 sediment samples. We utilized spatially explicit statistical models, to disentangle the effects of the different predictors, including bottom trawling intensity, a prevalent industrial fishing practice which heavily impacts benthic ecosystems. Fitted models demonstrate how the geographic interplay of different environmental and anthropogenic drivers shapes the diversity, structure and potential metabolism of benthic microbial communities. Sediment properties were the primary determinants, with diversity increasing with sediment permeability but also with mud content, highlighting different underlying processes. Additionally, diversity and structure varied with total organic matter content, temperature, bottom shear stress and bottom trawling. Changes in diversity associated with bottom trawling intensity were accompanied by shifts in predicted energy metabolism. Specifically, with increasing trawling intensity, we observed a transition toward more aerobic heterotrophic and less denitrifying predicted metabolism. Our findings provide first insights into benthic microbial biogeographic patterns on a large spatial scale and illustrate how anthropogenic activity such as bottom trawling may influence the distribution and abundances of microbes and potential metabolism at macroecological scales.
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Affiliation(s)
- Guido Bonthond
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Schleusenstrasse 1, 26382, Wilhelmshaven, Germany.
| | - Jan Beermann
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570, Bremerhaven, Germany
| | - Lars Gutow
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570, Bremerhaven, Germany
| | | | | | - Andrea Desiderato
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570, Bremerhaven, Germany
- Department of Invertebrate Zoology and Hydrobiology, University of Lodz, 90-136, Lodz, Poland
| | - Vera Fofonova
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570, Bremerhaven, Germany
| | - Stephanie B Helber
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Schleusenstrasse 1, 26382, Wilhelmshaven, Germany
| | - Sahar Khodami
- Senckenberg am Meer Wilhelmshaven, German Centre for Marine Biodiversity Research, Südstrand 44, 26382, Wilhelmshaven, Germany
| | - Casper Kraan
- Thünen Institute of Sea Fisheries, Herwigstraße 31, 27572, Bremerhaven, Germany
| | - Hermann Neumann
- Thünen Institute of Sea Fisheries, Herwigstraße 31, 27572, Bremerhaven, Germany
| | - Sven Rohde
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Schleusenstrasse 1, 26382, Wilhelmshaven, Germany
| | - Peter J Schupp
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Schleusenstrasse 1, 26382, Wilhelmshaven, Germany
- Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB), Ammerländer Heerstrasse 231, D-26129, Oldenburg, Germany
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20
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Wang X, Wang P, Wang C, Chen J, Hu B, Yuan Q, Du C, Xing X. Cascade damming impacts on microbial mediated nitrogen cycling in rivers. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 903:166533. [PMID: 37625716 DOI: 10.1016/j.scitotenv.2023.166533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 08/19/2023] [Accepted: 08/22/2023] [Indexed: 08/27/2023]
Abstract
Rivers display essential role in nitrogen (N) cycling in terrestrial and aquatic ecosystems, but now they are suffering from damming worldwide, especially from cascade damming. Despite of the importance of microorganisms in biogeochemical nutrient cycling, little attention has been paid to microbial functional biogeography under damming disturbances. Here, the Geochip microarray was applied to investigate the microbial mediated N cycling across the single-dammed Yarlung Tsangpo-Brahmaputra River and the cascade-dammed Lancang-Mekong River in southwest China. Our results showed that the N cycling processes (nitrogen fixation, ammonification, denitrification, nitrification and anammox) were stimulated in reservoirs in both rivers and the enhancement was inversely coupled with hydraulic retention time, but the recovery of N-cycling gene abundance in downstream of dam was intervened by cascade damming. Moreover, N-cycling gene composition was significantly altered in the single-dammed river, while no remarkable change was found in the cascade-dammed reaches. However, different from the unvaried gene composition, cascade damming intervened the recovery of N-cycling gene flow connectivity and resulted in the continuous decrease of connectivity in cascade damming reaches. In addition, in the single-dammed river, nutrients were the important drivers for variation in gene abundance, while they did not influence gene composition. Meanwhile, the abundance and composition of N-cycling genes in the cascade-dammed river were both significantly correlated to geographical parameters and water physical characteristics. Therefore, our study has vital implications for anticipating microbial functional response and biogeochemical feedback to ongoing cascade damming, contributing to the protection of river ecosystems under river regulation.
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Affiliation(s)
- Xun Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
| | - Peifang Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China.
| | - Chao Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
| | - Juan Chen
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
| | - Bin Hu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
| | - Qiusheng Yuan
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
| | - Chenggong Du
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnology around Hongze Lake, Huaiyin Normal University, Huai'an, Jiangsu 223300, China
| | - Xiaolei Xing
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
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21
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Shen Z, Yu B, Shao K, Gao G, Tang X. Warming reduces microeukaryotic diversity, network complexity and stability. ENVIRONMENTAL RESEARCH 2023; 238:117235. [PMID: 37775010 DOI: 10.1016/j.envres.2023.117235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 09/22/2023] [Accepted: 09/25/2023] [Indexed: 10/01/2023]
Abstract
Unraveling how climate warming affects microorganisms and the underlying mechanisms has been a hot topic in climate change and microbial ecology. To date, many studies have reported microbial responses to climate warming, especially in soil ecosystems, however, knowledge of how warming influences microeukaryotic diversity, network complexity and stability in lake ecosystems, in particular the possible underlying mechanisms, is largely unknown. To address this gap, we conducted 20 mesocosms spanning five temperature scenarios (26 °C, 27.5 °C, 29 °C, 30.5 °C, and 32 °C) in Lake Bosten, a hotspot for studying climate change, and investigated microeukaryotic communities using 18S rRNA gene sequencing. Our results demonstrated that warming, time, and their interactions significantly reduced microeukaryotic α-diversity (two-way ANOVA: P<0.01). Although warming did not significantly affect microeukaryotic community structure (ANOSIM: P>0.05), it enhanced species turnover. Microeukaryotic networks exhibited distinct co-occurrence patterns and topological properties across temperature scenarios. Warming reduced network complexity and stability, as well as altered species interactions. Collectively, these findings are likely to have implications for ecological management of lake ecosystems, in particular semi-arid and arid regions, and for predicting ecological consequences of climate change.
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Affiliation(s)
- Zhen Shen
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Bobing Yu
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Keqiang Shao
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Guang Gao
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiangming Tang
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China.
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22
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Pino V, Fajardo M, McBratney A, Minasny B, Wilson N, Baldock C. Australian soil microbiome: A first sightseeing regional prediction driven by cycles of soil temperature and pedogenic variations. Mol Ecol 2023; 32:6243-6259. [PMID: 36862079 DOI: 10.1111/mec.16911] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Revised: 02/05/2023] [Accepted: 02/27/2023] [Indexed: 03/03/2023]
Abstract
Declines in soil multifunctionality (e.gsoil capacity to provide food and energy) are closely related to changes in the soil microbiome (e.g., diversity) Determining ecological drivers promoting such microbiome changes is critical knowledge for protecting soil functions. However, soil-microbe interactions are highly variable within environmental gradients and may not be consistent across studies. Here we propose that analysis of community dissimilarity (β-diversity) is a valuable tool for overviewing soil microbiome spatiotemporal changes. Indeed, β-diversity studies at larger scales (modelling and mapping) simplify complex multivariate interactions and refine our understanding of ecological drivers by also giving the possibility of expanding the environmental scenarios. This study represents the first spatial investigation of β-diversity in the soil microbiome of New South Wales (800,642 km2 ), Australia. We used metabarcoding soil data (16S rRNA and ITS genes) as exact sequence variants (ASVs) and UMAP (Uniform Manifold Approximation and Projection) as the distance metric. β-Diversity maps (1000-m resolution)-concordance correlations of 0.91-0.96 and 0.91-0.95 for bacteria and fungi, respectively-showed soil biome dissimilarities driven primarily by soil chemistry-pH and effective cation exchange capacity (ECEC)-and cycles of soil temperature-land surface temperature (LST-phase and LST-amplitude). Regionally, the spatial patterns of microbes parallel the distribution of soil classes (e.g., Vertosols) beyond spatial distances and rainfall, for example. Soil classes can be valuable discriminants for monitoring approaches, for example pedogenons and pedophenons. Ultimately, cultivated soils exhibited lower richness due to declines in rare microbes which might compromise soil functions over time.
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Affiliation(s)
- Vanessa Pino
- School of Life and Environmental Sciences & Sydney Institute of Agriculture, Faculty of Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Mario Fajardo
- School of Life and Environmental Sciences & Sydney Institute of Agriculture, Faculty of Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Alex McBratney
- School of Life and Environmental Sciences & Sydney Institute of Agriculture, Faculty of Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Budiman Minasny
- School of Life and Environmental Sciences & Sydney Institute of Agriculture, Faculty of Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Neil Wilson
- Metagenomic Laboratory, Metagen Pty, Ltd., Gatton, Queensland, Australia
| | - Chris Baldock
- Metagenomic Laboratory, Metagen Pty, Ltd., Gatton, Queensland, Australia
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Yang S, Wu J, Wang H, Yang Q, Zhang H, Yang L, Li D, Deng Y, Zhong Y, Peng P. New dechlorination products and mechanisms of tris(2-chloroethyl) phosphate by an anaerobic enrichment culture from a vehicle dismantling site. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 338:122704. [PMID: 37806429 DOI: 10.1016/j.envpol.2023.122704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 09/15/2023] [Accepted: 10/04/2023] [Indexed: 10/10/2023]
Abstract
End-of-life vehicles (ELVs) dismantling sites are the notorious hotspots of chlorinated organophosphate esters (Cl-OPEs). However, the microbial-mediated dechlorination of Cl-OPEs at such sites has not yet been explored. Herein, the dechlorination products, pathways and mechanisms of tris(2-chloroethyl) phosphate (TCEP, a representative Cl-OPE) by an anaerobic enrichment culture (ZNE) from an ELVs dismantling plant were investigated. Our results showed that dechlorination of TCEP can be triggered by reductive transformation to form bis(2-chloroethyl) phosphate (BCEP), mono-chloroethyl phosphate (MCEP) and by hydrolytic dechlorination to form bis(2-chloroethyl) 2-hydroxyethyl phosphate (TCEP-OH), 2-chloroethyl bis(2-hydroxyethyl) phosphate (TCEP-2OH), 2-chloroethyl (2-hydroxyethyl) hydrogen phosphate (BCEP-OH). The combination of 16S rRNA gene amplicon sequencing, quantitative real-time PCR (qPCR) and metagenomics revealed that the Dehalococcoides played an important role in the reductive transformation of TCEP to BCEP and MCEP. A high-quality metagenome-assembled genome (completeness >99% and contamination <1%) of Dehalococcoides was obtained. The sulfate-reducing bacteria harboring haloacid dehalogenase genes (had) may be responsible for the hydrolytic dechlorination of TCEP. These findings provide insights into microbial-mediated anaerobic transformation products and mechanisms of TCEP at ELVs dismantling sites, having implications for the environmental fate and risk assessment of Cl-OPEs at those sites.
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Affiliation(s)
- Sen Yang
- State Key Laboratory of Organic Geochemistry and Guangdong-Hong Kong-Maco Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China; Guangdong Provincial Key Laboratory of Environmental Protection and Resources Utilization, Guangzhou, 510640, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Junhong Wu
- State Key Laboratory of Organic Geochemistry and Guangdong-Hong Kong-Maco Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China; Guangdong Provincial Key Laboratory of Environmental Protection and Resources Utilization, Guangzhou, 510640, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Heli Wang
- State Key Laboratory of Organic Geochemistry and Guangdong-Hong Kong-Maco Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China; Guangdong Provincial Key Laboratory of Environmental Protection and Resources Utilization, Guangzhou, 510640, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qian Yang
- State Key Laboratory of Organic Geochemistry and Guangdong-Hong Kong-Maco Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China; Guangdong Provincial Key Laboratory of Environmental Protection and Resources Utilization, Guangzhou, 510640, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Huanheng Zhang
- Guangzhou Environmental Protection Investment Group Co., Ltd., Guangzhou, 510016, China
| | - Lihua Yang
- South China Sea Resource Exploitation and Protection Collaborative Innovation Center, Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Dan Li
- School of Environment and Civil Engineering, Dongguan University of Technology, Dongguan, 523808, China
| | - Yirong Deng
- Guangdong Key Laboratory of Contaminated Sites Environmental Management and Remediation, Guangdong Provincial Academy of Environmental Science, Guangzhou, 510045, China
| | - Yin Zhong
- State Key Laboratory of Organic Geochemistry and Guangdong-Hong Kong-Maco Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China; Guangdong Provincial Key Laboratory of Environmental Protection and Resources Utilization, Guangzhou, 510640, China.
| | - Ping'an Peng
- State Key Laboratory of Organic Geochemistry and Guangdong-Hong Kong-Maco Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China; Guangdong Provincial Key Laboratory of Environmental Protection and Resources Utilization, Guangzhou, 510640, China
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24
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Pang J, Tu F, Han Y, Zhang E, Zhang Y, Zhang T. Age-related change in muscle strength, muscle mass, and fat mass between the dominant and non-dominant upper limbs. Front Public Health 2023; 11:1284959. [PMID: 38074765 PMCID: PMC10701377 DOI: 10.3389/fpubh.2023.1284959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 11/13/2023] [Indexed: 12/18/2023] Open
Abstract
Background Any form of physical activity is recommended for the older adults to maintain their physical function; however, the effect of daily activities on muscle function still needs to be investigated. Humans always use one dominant hand to perform tasks, providing a natural situation for research on the effect of daily activities on muscle function. Methods Five hundred and twenty-six healthy adults were recruited from the community in Beijing. Muscle strength was assessed using a handgrip dynamometer, lean mass, fat mass, bone area and bone mineral content of upper limbs were assessed using dual-energy X ray-absorptiometry. The results were compared between the dominant and non-dominant upper limbs. Results The dominant upper limb had better muscle strength, lean mass, bone area and bone mineral content than the non-dominant side. The difference in muscle strength and lean mass between the two upper limbs decreased with the advanced age. In older age, fat mass of upper limbs increased in men, but not in women. Conclusion Daily activities can maintain better muscle function in the dominant upper limb than in the non-dominant side; however, the delaying effect on age-related decline in muscle function was limited.
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Affiliation(s)
- Jing Pang
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital, National Center of Gerontology of National Health Commission, Beijing, China
| | - Fuyi Tu
- School of Science, Chongqing University of Posts and Telecommunications, Chongqing, China
| | - Yiwen Han
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital, National Center of Gerontology of National Health Commission, Beijing, China
| | - Enyi Zhang
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital, National Center of Gerontology of National Health Commission, Beijing, China
| | - Yan Zhang
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital, National Center of Gerontology of National Health Commission, Beijing, China
| | - Tiemei Zhang
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital, National Center of Gerontology of National Health Commission, Beijing, China
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Wang H, Xu Y, Kumar A, Knorr KH, Zhao X, Perez JPH, Sun G, Yu ZG. Temperature and organic carbon quality control the anaerobic carbon mineralization in peat profiles via modulating microbes: A case study of Changbai Mountain. ENVIRONMENTAL RESEARCH 2023; 237:116904. [PMID: 37595828 DOI: 10.1016/j.envres.2023.116904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 08/01/2023] [Accepted: 08/15/2023] [Indexed: 08/20/2023]
Abstract
Peatlands account for a significant fraction of the global carbon stock. However, the complex interplay of abiotic and biotic factors governing anaerobic carbon mineralization in response to warming remains unclear. In this study, peat sediments were collected from a typical northern peatland-Changbai Mountain to investigate the behavior and mechanism of anaerobic carbon mineralization in response to depth (0-200 cm) and temperature (5 °C, 15 °C and 20 °C), by integrating geochemical and microbial analysis. Several indices including humification indexes (HI), aromaticity, and water extractable organic carbon (WEOC) components were applied to evaluate carbon quality, while 16S rRNA sequencing was used to measure microbial composition. Regardless of temperature, degradations of carbon quality and associated reduction in microbial abundance as well as diversity resulted in a decrease in anaerobic carbon mineralization (both CO2 and CH4) towards greater depth. Warming either from 5 °C to 15 °C or 20 °C significantly increased anaerobic carbon mineralization in all depth profiles by improving carbon availability. Enhanced carbon availabilities were mediated by the change in microbial composition (p < 0.01) and an increase in metabolic activities, which was particularly evident in the enhanced β-glucosidase activity and microbial collaborations. A remarkable increase of over 10-fold in the relative abundance of the Geothrix genus was observed under warming. Overall, warming resulted in an enhanced contribution of CH4 emission and a higher ratio of hydrogenotrophic methanogenesis, as evidenced by carbon isotope fractionation factors. In addition, deep peat soils (>100 cm) with recalcitrant carbon demonstrated greater temperature sensitivity (Q10: ∼2.0) than shallow peat soils (Q10:∼1.2) when temperature increased from 15 °C to 20 °C. The findings of this study have significantly deepened our understanding for mechanisms of carbon quality and microbe-driven anaerobic carbon mineralization in peatlands under global warming.
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Affiliation(s)
- Hongyan Wang
- School of Hydrology and Water Resources, Nanjing University of Information Science and Technology, Nanjing, 210044, China; Key Laboratory of Watershed Earth Surface Processes and Ecological Security, Zhejiang Normal University, Jinhua, 321004, China; State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Yijie Xu
- School of Hydrology and Water Resources, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Amit Kumar
- School of Hydrology and Water Resources, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Klaus-Holger Knorr
- University of Münster, Institute for Landscape Ecology, Ecohydrology and Biogeochemistry Group, Heisenbergstr. 2, Münster, 48149, Germany
| | - Xiaoning Zhao
- School of Geographical Sciences, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Jeffrey Paulo H Perez
- Sec. 3.2 Organic Geochemistry, GFZ German Research Centre for Geosciences, Telegrafenberg, 14473, Potsdam, Germany
| | - Guoxin Sun
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Zhi-Guo Yu
- School of Hydrology and Water Resources, Nanjing University of Information Science and Technology, Nanjing, 210044, China.
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Niu B, Chen Q, Jiao H, Yang X, Shao M, Wang J, Si G, Lei T, Yang Y, Zhang G, Guggenberger G. Networks of mineral-associated organic matter fractions in forest ecosystems. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 898:165555. [PMID: 37454842 DOI: 10.1016/j.scitotenv.2023.165555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 06/23/2023] [Accepted: 07/13/2023] [Indexed: 07/18/2023]
Abstract
Mineral-associated organic matter (MAOM), the largest soil carbon pool, is formed through a series of organo-mineral interaction mechanisms. However, different organo-mineral fractions relevant to specific stabilization mechanisms and their response to environmental variables are poorly understood, which hinders accurate prediction of MAOM preservation under climate change. We applied sequential chemical extraction to separate MAOM into different organo-mineral fractions. To assess of response of different organo-mineral fractions to climate change, alpine forest soils with high environmental sensitivity along a controlled environmental gradient were selected. Residual OM and weakly adsorbed OM were the primary organo-mineral fractions, accounting for approximately 45.1-67.7 % and 16.4-30.6 %, respectively, of the total organic carbon (TOC). Climate exerted considerable indirect effects on the preservation of organo-mineral fractions through weathering and edaphic and biotic variables. Moreover, organo-mineral fractions were closely associated with metal cations (mainly Fe3+/Al3+) and secondary minerals, forming complex networks. Water-soluble OM (WSOM), weakly adsorbed OM and Fe/Al oxyhydroxides-stabilized OM were tightly linked, occupying the central position of the networks, and were closely related to soil pH, moisture and prokaryotic composition, indicating that edaphic and biotic factors might play important roles in maintaining the network structure and topology. In addition, Fe/Al-OM complexes, oxyhydroxides-stabilized OM and residual OM in the network were greatly impacted by climate and weathering factors, including precipitation, temperature and the plagioclase index of alteration (PIA). The complex network among organo-mineral fractions sheds light on MAOM dynamic stabilization for better predicting MAOM preservation under climate change.
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Affiliation(s)
- Bin Niu
- State Key Laboratory of Tibetan Plateau Earth System, Environment and Resources (TPESER), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100101, China
| | - Qiuyu Chen
- State Key Laboratory of Tibetan Plateau Earth System, Environment and Resources (TPESER), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China; University of Manchester, Manchester M139PL, UK
| | - Hongzhe Jiao
- State Key Laboratory of Tibetan Plateau Earth System, Environment and Resources (TPESER), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaoqin Yang
- State Key Laboratory of Tibetan Plateau Earth System, Environment and Resources (TPESER), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100101, China
| | - Ming Shao
- State Key Laboratory of Tibetan Plateau Earth System, Environment and Resources (TPESER), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China; Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Jian Wang
- Land and Resource College, China West Normal University, Nanchong 637009, China
| | - Guicai Si
- Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Tianzhu Lei
- Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Yibo Yang
- State Key Laboratory of Tibetan Plateau Earth System, Environment and Resources (TPESER), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Gengxin Zhang
- State Key Laboratory of Tibetan Plateau Earth System, Environment and Resources (TPESER), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China.
| | - Georg Guggenberger
- Institute of Soil Science, Leibniz Universität Hannover, Hanover 30419, Germany
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Tang X, Zhang M, Fang Z, Yang Q, Zhang W, Zhou J, Zhao B, Fan T, Wang C, Zhang C, Xia Y, Zheng Y. Changing microbiome community structure and functional potential during permafrost thawing on the Tibetan Plateau. FEMS Microbiol Ecol 2023; 99:fiad117. [PMID: 37766397 DOI: 10.1093/femsec/fiad117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 09/13/2023] [Accepted: 09/27/2023] [Indexed: 09/29/2023] Open
Abstract
Large amounts of carbon sequestered in permafrost on the Tibetan Plateau (TP) are becoming vulnerable to microbial decomposition in a warming world. However, knowledge about how the responsible microbial community responds to warming-induced permafrost thaw on the TP is still limited. This study aimed to conduct a comprehensive comparison of the microbial communities and their functional potential in the active layer of thawing permafrost on the TP. We found that the microbial communities were diverse and varied across soil profiles. The microbial diversity declined and the relative abundance of Chloroflexi, Bacteroidetes, Euryarchaeota, and Bathyarchaeota significantly increased with permafrost thawing. Moreover, warming reduced the similarity and stability of active layer microbial communities. The high-throughput qPCR results showed that the abundance of functional genes involved in liable carbon degradation and methanogenesis increased with permafrost thawing. Notably, the significantly increased mcrA gene abundance and the higher methanogens to methanotrophs ratio implied enhanced methanogenic activities during permafrost thawing. Overall, the composition and functional potentials of the active layer microbial community in the Tibetan permafrost region are susceptible to warming. These changes in the responsible microbial community may accelerate carbon degradation, particularly in the methane releases from alpine permafrost ecosystems on the TP.
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Affiliation(s)
- Xiaotong Tang
- State Key Laboratory of Continental Dynamics, Department of Geology, Northwest University, Xi'an, Shaanxi 710069, China
| | - Miao Zhang
- School of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Zhengkun Fang
- State Key Laboratory of Continental Dynamics, Department of Geology, Northwest University, Xi'an, Shaanxi 710069, China
| | - Qing Yang
- School of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Wan Zhang
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Jiaxing Zhou
- State Key Laboratory of Continental Dynamics, Department of Geology, Northwest University, Xi'an, Shaanxi 710069, China
| | - Bixi Zhao
- School of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Tongyu Fan
- State Key Laboratory of Continental Dynamics, Department of Geology, Northwest University, Xi'an, Shaanxi 710069, China
| | - Congzhen Wang
- State Key Laboratory of Continental Dynamics, Department of Geology, Northwest University, Xi'an, Shaanxi 710069, China
| | - Chuanlun Zhang
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Yu Xia
- School of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Yanhong Zheng
- State Key Laboratory of Continental Dynamics, Department of Geology, Northwest University, Xi'an, Shaanxi 710069, China
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28
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Yu C, Zhu Z, Meng K, Zhang H, Xu M. Unveiling the impact and mechanisms of Cd-driven ecological assembly and coexistence of bacterial communities in coastal sediments of Yellow Sea. JOURNAL OF HAZARDOUS MATERIALS 2023; 460:132309. [PMID: 37639798 DOI: 10.1016/j.jhazmat.2023.132309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 07/30/2023] [Accepted: 08/13/2023] [Indexed: 08/31/2023]
Abstract
The microbial community assembly processes and underlying mechanisms in response to heavy metal accumulation in coastal sediments remain underexplored. In this study, the heavy metal concentration in samples were found below the marine sediment quality standards. Through partial Mantel tests and linear regression analysis, Cd was identified as the major influencing factor, displaying strongest correlation with the bacterial community in the sediments. The class Desulfuromonadia was identified as a biomarker which showed enrichment in the sediments with high Cd content. Additionally, the results of null model and the neutral community model demonstrated the prominent role of stochastic processes in the assembly of bacterial community. However, with the increase in Cd concentration, the influence of selection processes intensified, resulting in a decline in species migration rate and subsequent reduction in ecological niche width. Furthermore, the intensified competition and an increase in keystone species among bacterial populations further enhanced the stability of the microbial co-occurrence network in response to high Cd concentration. This study offers an insight into the effects of heavy metal on microbial assembly and coexistence, which are conducive to marine ecosystem management and conservation.
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Affiliation(s)
- Chengfeng Yu
- College of Marine Science and Engineering, Nanjing Normal University, Nanjing 210023, China; Coastal Zone Resources and Environment Engineering Research Center of Jiangsu Province, Nanjing 210023, China
| | - Zhiyong Zhu
- College of Marine Science and Engineering, Nanjing Normal University, Nanjing 210023, China; Coastal Zone Resources and Environment Engineering Research Center of Jiangsu Province, Nanjing 210023, China
| | - Kun Meng
- Jiangsu Yunfan Testing Technology Co., Ltd., Nanjing 210033, China
| | - Huan Zhang
- College of Marine Science and Engineering, Nanjing Normal University, Nanjing 210023, China; Coastal Zone Resources and Environment Engineering Research Center of Jiangsu Province, Nanjing 210023, China.
| | - Min Xu
- College of Marine Science and Engineering, Nanjing Normal University, Nanjing 210023, China; Coastal Zone Resources and Environment Engineering Research Center of Jiangsu Province, Nanjing 210023, China.
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29
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Zhu N, Yu Q, Song L, Sheng H. The Inhibiting Effects of High-Dose Biochar Application on Soil Microbial Metagenomics and Rice ( Oryza sativa L.) Production. Int J Mol Sci 2023; 24:15043. [PMID: 37894726 PMCID: PMC10606461 DOI: 10.3390/ijms242015043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 10/07/2023] [Accepted: 10/09/2023] [Indexed: 10/29/2023] Open
Abstract
Biochar is usually considered as an organic improver which can improve soil and increase crop yields. However, the unrestricted application of biochar to normal-fertility farmland will cause chemical stress on crops and affect agricultural production. At present, the effects and mechanisms of high-dose applications of biochar on rice (Oryza sativa L.) production and soil biological characteristics have not been fully studied. In this greenhouse pot experiment, combined with soil microbial metagenomics, three treatments in triplicates were conducted to explore the responses of rice production, soil chemical properties, and soil biological properties to high-dose applications of biochar (5%, w/w) prepared using peanut waste (peanut hulls and straw). The results show that peanut hulls, with a loose texture and pore structure, are a raw material with stronger effects for preparing biochar than peanut straw in terms of its physical structure. In a rice monoculture system, high-dose applications of biochar (5%, w/w) can slightly increase the grains per spike, while significantly inhibiting the spike number per pot and the percentage of setting. High-dose applications of biochar also have significant negative effects on the diversity and stability of soil bacterial and archaeal communities. Moreover, the microbial metabolism and nutrient cycling processes are also significantly affected by changing the soil carbon/nitrogen ratio. This study discusses the response mechanisms of rice production and soil biology to high-dose biochar applications, and complements the understanding of irrational biochar application on agricultural production and land sustainability.
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Affiliation(s)
- Nanyan Zhu
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225000, China;
| | - Qiaoqiao Yu
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou 225000, China;
| | - Lingqi Song
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou 225000, China;
| | - Haijun Sheng
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou 225000, China;
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30
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Huang Z, Su Y, Lin S, Wu G, Cheng H, Huang G. Elevational patterns of microbial species richness and evenness across climatic zones and taxonomic scales. Ecol Evol 2023; 13:e10594. [PMID: 37818244 PMCID: PMC10560872 DOI: 10.1002/ece3.10594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 09/01/2023] [Accepted: 09/25/2023] [Indexed: 10/12/2023] Open
Abstract
Understanding the elevational patterns of soil microbial diversity is crucial for microbial biogeography, yet the elevational patterns of diversity across different climatic zones, trophic levels, and taxonomic levels remain unclear. In this study, we investigated the elevational patterns of species richness, species evenness and the relationship between species richness and evenness (RRE) in the forest soil bacterial and fungal communities and individual phyla across three climatic zones (tropical, subtropical, and cold temperate). Our results revealed that soil bacterial richness (alpha diversity) decreased with elevation, while fungal richness exhibited a hump-shaped pattern in the tropical and cold-temperate forests. Elevational patterns of evenness in bacterial and fungal communities showed the hump-shaped pattern across climatic zones, except for bacterial evenness in the tropical forest. Both bacterial and fungal richness and evenness were positively correlated in the subtropical and cold-temperate forests, while negatively correlated for bacteria in the tropical forest. The richness and evenness of soil microorganisms across different regions were controlled by climatic and edaphic factors. Soil pH was the most important factor associated with the variations in bacterial richness and evenness, while mean annual temperature explained the major variations in fungal richness. Our results addressed that the varieties of elevational patterns of microbial diversity in climatic zones and taxonomic levels, further indicating that richness and evenness may respond differently to environmental gradients.
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Affiliation(s)
- Zhengyi Huang
- School of Geographical Sciences, School of Carbon Neutrality Future TechnologyFujian Normal UniversityFuzhouChina
| | - Yangui Su
- School of Geographical Sciences, School of Carbon Neutrality Future TechnologyFujian Normal UniversityFuzhouChina
| | - Sinuo Lin
- School of Geographical Sciences, School of Carbon Neutrality Future TechnologyFujian Normal UniversityFuzhouChina
| | - Guopeng Wu
- School of Geographical Sciences, School of Carbon Neutrality Future TechnologyFujian Normal UniversityFuzhouChina
| | - Hao Cheng
- School of Geographical Sciences, School of Carbon Neutrality Future TechnologyFujian Normal UniversityFuzhouChina
| | - Gang Huang
- School of Geographical Sciences, School of Carbon Neutrality Future TechnologyFujian Normal UniversityFuzhouChina
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31
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Rui J, Zhao Y, Cong N, Wang F, Li C, Liu X, Hu J, Ling N, Jing X. Elevational distribution and seasonal dynamics of alpine soil prokaryotic communities. Front Microbiol 2023; 14:1280011. [PMID: 37808282 PMCID: PMC10557256 DOI: 10.3389/fmicb.2023.1280011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Accepted: 09/06/2023] [Indexed: 10/10/2023] Open
Abstract
The alpine grassland ecosystem is a biodiversity hotspot of plants on the Qinghai-Tibetan Plateau, where rapid climate change is altering the patterns of plant biodiversity along elevational and seasonal gradients of environments. However, how belowground microbial biodiversity changes along elevational gradient during the growing season is not well understood yet. Here, we investigated the elevational distribution of soil prokaryotic communities by using 16S rRNA amplicon sequencing along an elevational gradient between 3,200 and 4,200 m, and a seasonal gradient between June and September in the Qinghai-Tibetan alpine grasslands. First, we found soil prokaryotic diversity and community composition significantly shifted along the elevational gradient, mainly driven by soil temperature and moisture. Species richness did not show consistent elevational trends, while those of evenness declined with elevation. Copiotrophs and symbiotic diazotrophs declined with elevation, while oligotrophs and AOB increased, affected by temperature. Anaerobic or facultatively anaerobic bacteria and AOA were hump-shaped, mainly influenced by moisture. Second, seasonal patterns of community composition were mainly driven by aboveground biomass, precipitation, and soil temperature. The seasonal dynamics of community composition indicated that soil prokaryotic community, particularly Actinobacteria, was sensitive to short-term climate change, such as the monthly precipitation variation. At last, dispersal limitation consistently dominated the assembly process of soil prokaryotic communities along both elevational and seasonal gradients, especially for those of rare species, while the deterministic process of abundant species was relatively higher at drier sites and in drier July. The balance between deterministic and stochastic processes in abundant subcommunities might be strongly influenced by water conditions (precipitation/moisture). Our findings suggest that both elevation and season can alter the patterns of soil prokaryotic biodiversity in alpine grassland ecosystem of Qinghai-Tibetan Plateau, which is a biodiversity hotspot and is experiencing rapid climate change. This work provides new insights into the response of soil prokaryotic communities to changes in elevation and season, and helps us understand the temporal and spatial variations in such climate change-sensitive regions.
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Affiliation(s)
- Junpeng Rui
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
- Center for Grassland Microbiome, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Yuwei Zhao
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
- Center for Grassland Microbiome, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Nan Cong
- Lhasa Plateau Ecosystem Research Station, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China
| | - Fuxin Wang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Chao Li
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Xiang Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Jingjing Hu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Ning Ling
- Center for Grassland Microbiome, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Xin Jing
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
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32
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Fang J, Wei S, Gao Y, Zhang X, Cheng Y, Wang J, Ma J, Shi G, Bai L, Xie R, Zhao X, Ren Y, Lu Z. Character variation of root space microbial community composition in the response of drought-tolerant spring wheat to drought stress. Front Microbiol 2023; 14:1235708. [PMID: 37779714 PMCID: PMC10541208 DOI: 10.3389/fmicb.2023.1235708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 08/31/2023] [Indexed: 10/03/2023] Open
Abstract
Drought is the most prevalent environmental stress in crop production, posing a significant danger to food security. Microorganisms in the crop root zone affect crop growth and development, enhance effective nutrient use, and resist adversity hazards. To analyze the changes and functional differences of root space microbial (endosphere-rhizosphere-bulk soil) communities in spring wheat under drought stress. In this study, the root, rhizosphere, and bulk soil of the drought-tolerant group (DTG, three varieties) and drought-sensitive group (DSG, three varieties) were collected. The control (CK, 25-28%), moderate drought (MD, 15-18%), and severe drought (SD, 9-12%) were analyzed by high-throughput sequencing and bioinformatics. The results showed significant differences in the diversity of Bacteria and Fungi in the root space of spring wheat under drought stress (P < 0.05), with the drought-tolerant group exhibiting higher microbial diversity. The microbial community change in spring wheat root space was mainly determined by the niche differentiation of endosphere, rhizosphere, and bulk soil and declined from endosphere to bulk soil due to drought. The antagonism between microbial and root-space species increased, and the community's complexity and stability deteriorated. Enriching drought-resistant preference groups like Actinobaciota, Variovorax, Streptomyces, and Conocybe altered the structure and function of the microbial community in the root space of spring wheat. Spring wheat's root space Bacteria and Fungi have different strategies to respond to drought.
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Affiliation(s)
- Jing Fang
- School of Life Science, Inner Mongolia University, Hohhot, China
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
- Key Laboratory of Black Soil Protection and Utilization (Hohhot), Ministry of Agriculture and Rural Affairs, Hohhot, China
| | - Shuli Wei
- School of Life Science, Inner Mongolia University, Hohhot, China
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
- Key Laboratory of Black Soil Protection and Utilization (Hohhot), Ministry of Agriculture and Rural Affairs, Hohhot, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Restoration and Pollution Control, Hohhot, China
| | - Yanrong Gao
- School of Life Science, Inner Mongolia University, Hohhot, China
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
- Key Laboratory of Black Soil Protection and Utilization (Hohhot), Ministry of Agriculture and Rural Affairs, Hohhot, China
| | - Xiangqian Zhang
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
- Key Laboratory of Black Soil Protection and Utilization (Hohhot), Ministry of Agriculture and Rural Affairs, Hohhot, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Restoration and Pollution Control, Hohhot, China
- College of Agronomy, Inner Mongolia Agricultural University, Hohhot, China
| | - Yuchen Cheng
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
- Key Laboratory of Black Soil Protection and Utilization (Hohhot), Ministry of Agriculture and Rural Affairs, Hohhot, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Restoration and Pollution Control, Hohhot, China
| | - Jianguo Wang
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
- Key Laboratory of Black Soil Protection and Utilization (Hohhot), Ministry of Agriculture and Rural Affairs, Hohhot, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Restoration and Pollution Control, Hohhot, China
| | - Jie Ma
- School of Life Science, Inner Mongolia University, Hohhot, China
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
- Key Laboratory of Black Soil Protection and Utilization (Hohhot), Ministry of Agriculture and Rural Affairs, Hohhot, China
| | - Gongfu Shi
- School of Life Science, Inner Mongolia University, Hohhot, China
| | - Lanfang Bai
- College of Agronomy, Inner Mongolia Agricultural University, Hohhot, China
| | - Rui Xie
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
- Key Laboratory of Black Soil Protection and Utilization (Hohhot), Ministry of Agriculture and Rural Affairs, Hohhot, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Restoration and Pollution Control, Hohhot, China
| | - Xiaoqing Zhao
- School of Life Science, Inner Mongolia University, Hohhot, China
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
- Key Laboratory of Black Soil Protection and Utilization (Hohhot), Ministry of Agriculture and Rural Affairs, Hohhot, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Restoration and Pollution Control, Hohhot, China
| | - Yongfeng Ren
- School of Life Science, Inner Mongolia University, Hohhot, China
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
- Key Laboratory of Black Soil Protection and Utilization (Hohhot), Ministry of Agriculture and Rural Affairs, Hohhot, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Restoration and Pollution Control, Hohhot, China
| | - Zhanyuan Lu
- School of Life Science, Inner Mongolia University, Hohhot, China
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
- Key Laboratory of Black Soil Protection and Utilization (Hohhot), Ministry of Agriculture and Rural Affairs, Hohhot, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Restoration and Pollution Control, Hohhot, China
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Riit T, Cleary M, Adamson K, Blomquist M, Burokienė D, Marčiulynienė D, Oliva J, Poimala A, Redondo MA, Strømeng GM, Talgø V, Tedersoo L, Thomsen IM, Uimari A, Witzell J, Drenkhan R. Oomycete Soil Diversity Associated with Betula and Alnus in Forests and Urban Settings in the Nordic-Baltic Region. J Fungi (Basel) 2023; 9:926. [PMID: 37755034 PMCID: PMC10532727 DOI: 10.3390/jof9090926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 09/07/2023] [Accepted: 09/09/2023] [Indexed: 09/28/2023] Open
Abstract
This study aimed to determine the differences and drivers of oomycete diversity and community composition in alder- and birch-dominated park and natural forest soils of the Fennoscandian and Baltic countries of Estonia, Finland, Lithuania, Norway, and Sweden. For this, we sequenced libraries of PCR products generated from the DNA of 111 soil samples collected across a climate gradient using oomycete-specific primers on a PacBio high-throughput sequencing platform. We found that oomycete communities are most affected by temperature seasonality, annual mean temperature, and mean temperature of the warmest quarter. Differences in composition were partly explained by the higher diversity of Saprolegniales in Sweden and Norway, as both total oomycete and Saprolegniales richness decreased significantly at higher longitudes, potentially indicating the preference of this group of oomycetes for a more temperate maritime climate. None of the evaluated climatic variables significantly affected the richness of Pythiales or Peronosporales. Interestingly, the relative abundance and richness of Pythiales was higher at urban sites compared to forest sites, whereas the opposite was true for Saprolegniales. Additionally, this is the first report of Phytophthora gallica and P. plurivora in Estonia. Our results indicate that the composition of oomycetes in soils is strongly influenced by climatic factors, and, therefore, changes in climate conditions associated with global warming may have the potential to significantly alter the distribution range of these microbes, which comprise many important pathogens of plants.
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Affiliation(s)
- Taavi Riit
- Institute of Forestry and Engineering, Estonian University of Life Sciences, F. R. Kreutzwaldi 5, 51006 Tartu, Estonia; (T.R.)
| | - Michelle Cleary
- Southern Swedish Forest Research Centre, Swedish University of Agricultural Sciences, Sundsvägen 3, 230 53 Alnarp, Sweden
| | - Kalev Adamson
- Institute of Forestry and Engineering, Estonian University of Life Sciences, F. R. Kreutzwaldi 5, 51006 Tartu, Estonia; (T.R.)
| | - Mimmi Blomquist
- Southern Swedish Forest Research Centre, Swedish University of Agricultural Sciences, Sundsvägen 3, 230 53 Alnarp, Sweden
| | - Daiva Burokienė
- Nature Research Centre, Akademijos Str. 2, LT-08412 Vilnius, Lithuania
| | - Diana Marčiulynienė
- Southern Swedish Forest Research Centre, Swedish University of Agricultural Sciences, Sundsvägen 3, 230 53 Alnarp, Sweden
- Institute of Forestry, Lithuanian Research Centre for Agriculture and Forestry, Liepų Str. 1, LT-53101 Girionys, Lithuania
| | - Jonàs Oliva
- Department of Agricultural and Forest Sciences and Engineering, University of Lleida, 25198 Lleida, Spain
- Joint Research Unit CTFC–Agrotecnio, 25198 Lleida, Spain
| | - Anna Poimala
- Natural Resources Institute Finland (LUKE), Latokartanonkaari 9, 00790 Helsinki, Finland
| | - Miguel Angel Redondo
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, P.O. Box 7026, 750 07 Uppsala, Sweden
| | - Gunn Mari Strømeng
- Norwegian Institute of Bioeconomy Research, NIBIO, Høgskoleveien 7, 1433 Ås, Norway
| | - Venche Talgø
- Norwegian Institute of Bioeconomy Research, NIBIO, Høgskoleveien 7, 1433 Ås, Norway
| | - Leho Tedersoo
- Mycology and Microbiology Center, University of Tartu, J. Liivi 2, 50409 Tartu, Estonia
| | - Iben Margrete Thomsen
- Department of Geosciences and Natural Resource Management, University of Copenhagen, Rolighedsvej 23, 1958 Frederiksberg C, Denmark
| | - Anne Uimari
- Natural Resources Institute Finland (LUKE), Juntintie 154, 77600 Suonenjoki, Finland
| | - Johanna Witzell
- Southern Swedish Forest Research Centre, Swedish University of Agricultural Sciences, Sundsvägen 3, 230 53 Alnarp, Sweden
- Department of Forestry and Wood Technology, Linnaeus University, 351 95 Växjö, Sweden
| | - Rein Drenkhan
- Institute of Forestry and Engineering, Estonian University of Life Sciences, F. R. Kreutzwaldi 5, 51006 Tartu, Estonia; (T.R.)
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Téfit MA, Budiman T, Dupriest A, Yew JY. Environmental microbes promote phenotypic plasticity in reproduction and sleep behaviour. Mol Ecol 2023; 32:5186-5200. [PMID: 37577956 PMCID: PMC10544802 DOI: 10.1111/mec.17095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 06/13/2023] [Accepted: 07/25/2023] [Indexed: 08/15/2023]
Abstract
The microbiome has been hypothesized as a driving force of phenotypic variation in host organisms that is capable of extending metabolic processes, altering development and in some cases, conferring novel functions that are critical for survival. Only a few studies have directly shown a causal role for the environmental microbiome in altering host phenotypic features. To assess the extent to which environmental microbes induce variation in host life-history traits and behaviour, we inoculated axenic Drosophila melanogaster with microbes isolated from drosophilid populations collected from two different field sites and generated two populations with distinct bacterial and fungal profiles. We show that microbes isolated from environmental sites with modest abiotic differences induce large variation in host reproduction, fatty acid levels, stress tolerance and sleep behaviour. Importantly, clearing microbes from each experimental population removed the phenotypic differences. The results support the causal role of environmental microbes as drivers of host phenotypic plasticity and potentially, rapid adaptation and evolution.
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Affiliation(s)
- Mélisandre A Téfit
- School of Ocean and Earth Science and Technology, Pacific Biosciences Research Center, University of Hawai'i at Mānoa, Honolulu, Hawaii, USA
| | - Tifanny Budiman
- School of Ocean and Earth Science and Technology, Pacific Biosciences Research Center, University of Hawai'i at Mānoa, Honolulu, Hawaii, USA
| | - Adrianna Dupriest
- School of Ocean and Earth Science and Technology, Pacific Biosciences Research Center, University of Hawai'i at Mānoa, Honolulu, Hawaii, USA
| | - Joanne Y Yew
- School of Ocean and Earth Science and Technology, Pacific Biosciences Research Center, University of Hawai'i at Mānoa, Honolulu, Hawaii, USA
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35
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Ding B, Feng L, Ba S, Jiang X, Liu G, Liu W. Temperature drives elevational diversity patterns of different types of organisms in Qinghai-Tibetan Plateau wetlands. iScience 2023; 26:107252. [PMID: 37502256 PMCID: PMC10368813 DOI: 10.1016/j.isci.2023.107252] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 04/03/2023] [Accepted: 06/27/2023] [Indexed: 07/29/2023] Open
Abstract
The spatial pattern and driving mechanism of biodiversity along elevational gradients are key topics in ecology. However, it is still unclear whether the multidimensional diversity of different types of organisms shows a similar response to elevation changes. Here, we measured the species and phylogenetic diversity of plants, bacteria, fungi, and microbial functional groups (nitrifiers, denitrifiers, methanogens, and methanotrophs) in 36 wetland sites on the Qinghai-Tibetan Plateau. The results showed that both species and phylogenetic diversity of plants, bacteria, and fungi exhibited a significant elevational gradient, in direct contrast to no significant diversity changes observed for denitrifiers, methanogens, and methanotrophs along the same altitude gradient. Our findings suggest that elevation and temperature were more likely to associate with the diversity of plants, bacteria, and fungi than the diversity of microbial functional groups, with important implications for assessing the effect of ongoing climate warming on biodiversity in Qinghai-Tibetan alpine wetlands.
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Affiliation(s)
- Bangjing Ding
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Lian Feng
- College of Science, Tibet University, Lhasa 850000, China
- Center for Carbon Neutrality in the Earth’s Third Pole, Tibet University, Lhasa 850000, China
| | - Sang Ba
- College of Science, Tibet University, Lhasa 850000, China
- Center for Carbon Neutrality in the Earth’s Third Pole, Tibet University, Lhasa 850000, China
| | - Xiaoliang Jiang
- Ganjiang Innovation Academy, Jiangxi Province Key Laboratory of Cleaner Production of Rare Earths, Chinese Academy of Science, Ganzhou 321119, China
| | - Guihua Liu
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Wenzhi Liu
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
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Gonzalez JM, Aranda B. Microbial Growth under Limiting Conditions-Future Perspectives. Microorganisms 2023; 11:1641. [PMID: 37512814 PMCID: PMC10383181 DOI: 10.3390/microorganisms11071641] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 06/02/2023] [Accepted: 06/20/2023] [Indexed: 07/30/2023] Open
Abstract
Microorganisms rule the functioning of our planet and each one of the individual macroscopic living creature. Nevertheless, microbial activity and growth status have always been challenging tasks to determine both in situ and in vivo. Microbial activity is generally related to growth, and the growth rate is a result of the availability of nutrients under adequate or adverse conditions faced by microbial cells in a changing environment. Most studies on microorganisms have been carried out under optimum or near-optimum growth conditions, but scarce information is available about microorganisms at slow-growing states (i.e., near-zero growth and maintenance metabolism). This study aims to better understand microorganisms under growth-limiting conditions. This is expected to provide new perspectives on the functions and relevance of the microbial world. This is because (i) microorganisms in nature frequently face conditions of severe growth limitation, (ii) microorganisms activate singular pathways (mostly genes remaining to be functionally annotated), resulting in a broad range of secondary metabolites, and (iii) the response of microorganisms to slow-growth conditions remains to be understood, including persistence strategies, gene expression, and cell differentiation both within clonal populations and due to the complexity of the environment.
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Affiliation(s)
- Juan M Gonzalez
- Instituto de Recursos Naturales y Agrobiología de Sevilla, Consejo Superior de Investigaciones Científicas, IRNAS-CSIC, E-41012 Sevilla, Spain
| | - Beatriz Aranda
- Instituto de Recursos Naturales y Agrobiología de Sevilla, Consejo Superior de Investigaciones Científicas, IRNAS-CSIC, E-41012 Sevilla, Spain
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Tang Y, Fan D, Guo W, Kong W. Controls on diversity of core and indicative microbial subcommunities in Tibetan Plateau grassland soils. FEMS Microbiol Ecol 2023; 99:fiad059. [PMID: 37237437 DOI: 10.1093/femsec/fiad059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 05/10/2023] [Accepted: 05/25/2023] [Indexed: 05/28/2023] Open
Abstract
Core subcommunity represents the less diversity but high abundance, while indicative subcommunity is highly diverse but low abundance in soils. The core subcommunity fundamentally maintains ecosystem stability, while the indicative plays important roles in vital ecosystem functions and is more sensitive to environmental change. However, their environmental driving factors and responses to human disturbances remain less defined. Herein, we explored the patterns of core and indicative soil microbes and their responses to animal grazing in dry grasslands across the Tibetan Plateau, using the Illumina sequencing of 16S rRNA gene. The results revealed that the core subcommunity diversity and richness were lower than the indicative in soils. The indicative subcommunity diversity exhibited substantially stronger correlations with nutrient-associated factors than the core diversity, including soil organic carbon, nitrogen, and plant biomass. The core and indicative microbial subcommunities both strongly varied with grassland ecosystems, while the latter was also significantly influenced by grazing. The variation partitioning analysis revealed that indicative microbial subcommunity was explained less by environmental factors than core subcommunity (34.5% vs 73.0%), but more influenced by grazing (2.6% vs 0.1%). Our findings demonstrated that the indicative microbes were particularly sensitive to soil nutrient-associated factors and human disturbances in alpine dry grasslands.
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Affiliation(s)
- Yazhou Tang
- Inner Mongolia Key Laboratory of Environmental Pollution Control and Waste Resource Recycle, Ministry of Education Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Dandan Fan
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences (CAS), Beijing 100101, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100039, China
| | - Wei Guo
- Inner Mongolia Key Laboratory of Environmental Pollution Control and Waste Resource Recycle, Ministry of Education Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China
| | - Weidong Kong
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences (CAS), Beijing 100101, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100039, China
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38
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Islam SU, Mangral ZA, Hussain K, Tariq L, Bhat BA, Khuroo AA, Hassan Dar TU. Unravelling diversity, drivers, and indicators of soil microbiome of Trillium govanianum, an endangered plant species of the Himalaya. ENVIRONMENTAL RESEARCH 2023; 227:115819. [PMID: 37011799 DOI: 10.1016/j.envres.2023.115819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 03/19/2023] [Accepted: 03/30/2023] [Indexed: 05/08/2023]
Abstract
In an era of global environmental change, conservation of threatened biodiversity and ecosystem restoration are formidable ecological challenges. The forest understory strata and the belowground soil environment including rhizospheric microbial communities, which are crucial for ecosystem functioning and overall forest biodiversity maintenance, have remained understudied. Here, we investigate the soil microbiome of Trillium govanianum - an endangered Himalayan Forest herb, to unravel the underground diversity, drivers, and potential indicators of the microbial community. We collected rhizospheric and bulk soil samples for microbiome and physicochemical analysis at three sites along an elevation gradient (2500-3300 m) in Kashmir Himalaya. Amplicon sequencing of 16 S rRNA and ITS was used to identify the bacterial and fungal soil microorganisms. We found significant differences in the structure and diversity of microbial community (bacterial and fungal) between the rhizosphere and bulk soil along the altitudinal gradient, and noticeable shifts in the nutrient level in dominant microbial phyla associated with T. govanianum. A significant difference between soil physicochemical parameters and increasing altitude suggests that microbial community structure is determined by altitude and soil type. Similarly, the microbial communities showed a significant (P < 0.05) correlation with soil physicochemical variables along the altitudinal gradient. The moisture content in bacterial and total organic carbon in fungal communities showed the most substantial impact on the physiochemical drivers. We also identify potential bacterial and fungal plant growth promoter indicator species in the soil microbiome of T. govanianum. Overall, our findings provide novel research insights that can be pivotal in designing integrated species recovery programs and long-term restoration plans for T. govanianum, with learnings for biodiversity conservation elsewhere.
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Affiliation(s)
- Shahid Ul Islam
- Department of Biotechnology, School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Rajouri, Jammu and Kashmir, India
| | - Zahid Ahmed Mangral
- Department of Biotechnology, School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Rajouri, Jammu and Kashmir, India
| | - Khalid Hussain
- Centre for Biodiversity and Taxonomy, Department of Botany, University of Kashmir, Srinagar, Jammu and Kashmir, India
| | - Lubna Tariq
- Department of Biotechnology, School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Rajouri, Jammu and Kashmir, India
| | - Basharat Ahmad Bhat
- Department of Bio-Resources, School of Biological Sciences, University of Kashmir, Srinagar, Jammu and Kashmir, India
| | - Anzar Ahmad Khuroo
- Centre for Biodiversity and Taxonomy, Department of Botany, University of Kashmir, Srinagar, Jammu and Kashmir, India
| | - Tanvir Ul Hassan Dar
- Department of Biotechnology, School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Rajouri, Jammu and Kashmir, India.
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He Q, Wang S, Feng K, Michaletz ST, Hou W, Zhang W, Li F, Zhang Y, Wang D, Peng X, Yang X, Deng Y. High speciation rate of niche specialists in hot springs. THE ISME JOURNAL 2023:10.1038/s41396-023-01447-4. [PMID: 37286739 DOI: 10.1038/s41396-023-01447-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 05/24/2023] [Accepted: 05/26/2023] [Indexed: 06/09/2023]
Abstract
Ecological and evolutionary processes simultaneously regulate microbial diversity, but the evolutionary processes and their driving forces remain largely unexplored. Here we investigated the ecological and evolutionary characteristics of microbiota in hot springs spanning a broad temperature range (54.8-80 °C) by sequencing the 16S rRNA genes. Our results demonstrated that niche specialists and niche generalists are embedded in a complex interaction of ecological and evolutionary dynamics. On the thermal tolerance niche axis, thermal (T) sensitive (at a specific temperature) versus T-resistant (at least in five temperatures) species were characterized by different niche breadth, community abundance and dispersal potential, consequently differing in potential evolutionary trajectory. The niche-specialized T-sensitive species experienced strong temperature barriers, leading to completely species shift and high fitness but low abundant communities at each temperature ("home niche"), and such trade-offs thus reinforced peak performance, as evidenced by high speciation across temperatures and increasing diversification potential with temperature. In contrast, T-resistant species are advantageous of niche expansion but with poor local performance, as shown by wide niche breadth with high extinction, indicating these niche generalists are "jack-of-all-trades, master-of-none". Despite of such differences, the T-sensitive and T-resistant species are evolutionarily interacted. Specifically, the continuous transition from T-sensitive to T-resistant species insured the exclusion probability of T-resistant species at a relatively constant level across temperatures. The co-evolution and co-adaptation of T-sensitive and T-resistant species were in line with the red queen theory. Collectively, our findings demonstrate that high speciation of niche specialists could alleviate the environmental-filtering-induced negative effect on diversity.
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Affiliation(s)
- Qing He
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100190, China
| | - Shang Wang
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China.
| | - Kai Feng
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China
| | - Sean T Michaletz
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Weiguo Hou
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, 100083, China
| | - Wenhui Zhang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, 100083, China
| | - Fangru Li
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, 100083, China
| | - Yidi Zhang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, 100083, China
| | - Danrui Wang
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100190, China
| | - Xi Peng
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100190, China
| | - Xingsheng Yang
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100190, China
| | - Ye Deng
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China.
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100190, China.
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40
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Kang Y, Wu H, Zhang Y, Wu Q, Guan Q, Lu K, Lin Y. Differential distribution patterns and assembly processes of soil microbial communities under contrasting vegetation types at distinctive altitudes in the Changbai Mountain. Front Microbiol 2023; 14:1152818. [PMID: 37333641 PMCID: PMC10272400 DOI: 10.3389/fmicb.2023.1152818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 03/29/2023] [Indexed: 06/20/2023] Open
Abstract
Diversity patterns and community assembly of soil microorganisms are essential for understanding soil biodiversity and ecosystem processes. Investigating the impacts of environmental factors on microbial community assembly is crucial for comprehending the functions of microbial biodiversity and ecosystem processes. However, these issues remain insufficiently investigated in related studies despite their fundamental significance. The present study aimed to assess the diversity and assembly of soil bacterial and fungal communities to altitude and soil depth variations in mountain ecosystems by using 16S and ITS rRNA gene sequence analyses. In addition, the major roles of environmental factors in determining soil microbial communities and assembly processes were further investigated. The results showed a U-shaped pattern of the soil bacterial diversity at 0-10 cm soil depth along altitudes, reaching a minimum value at 1800 m, while the fungal diversity exhibited a monotonically decreasing trend with increasing altitude. At 10-20 cm soil depth, the soil bacterial diversity showed no apparent changes along altitudinal gradients, while the fungal Chao1 and phylogenetic diversity (PD) indices exhibited hump-shaped patterns with increasing altitude, reaching a maximum value at 1200 m. Soil bacterial and fungal communities were distinctively distributed with altitude at the same depth of soil, and the spatial turnover rates in fungi was greater than in bacteria. Mantel tests suggested soil physiochemical and climate variables significantly correlated with the β diversity of microbial community at two soil depths, suggesting both soil and climate heterogeneity contributed to the variation of bacterial and fungal community. Correspondingly, a novel phylogenetic null model analysis demonstrated that the community assembly of soil bacterial and fungal communities were dominated by deterministic and stochastic processes, respectively. The assembly processes of bacterial community were significantly related to the soil DOC and C:N ratio, while the fungal community assembly processes were significantly related to the soil C:N ratio. Our results provide a new perspective to assess the responses of soil microbial communities to variations with altitude and soil depth.
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Affiliation(s)
- Yujuan Kang
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Haitao Wu
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Yifan Zhang
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
- College of Tourism and Geography Sciences, Jilin Normal University, Siping, China
| | - Qiong Wu
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
- College of Tourism and Geography Sciences, Jilin Normal University, Siping, China
| | - Qiang Guan
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Kangle Lu
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Yiling Lin
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
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41
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Cruz-Paredes C, Tájmel D, Rousk J. Variation in Temperature Dependences across Europe Reveals the Climate Sensitivity of Soil Microbial Decomposers. Appl Environ Microbiol 2023; 89:e0209022. [PMID: 37162342 DOI: 10.1128/aem.02090-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023] Open
Abstract
Temperature is a major determinant of biological process rates, and microorganisms are key regulators of ecosystem carbon (C) dynamics. Temperature controls microbial rates of decomposition, and thus warming can stimulate C loss, creating positive feedback to climate change. If trait distributions that define temperature relationships of microbial communities can adapt to altered temperatures, they could modulate the strength of this feedback, but if this occurs remains unclear. In this study, we sampled soils from a latitudinal climate gradient across Europe. We established the temperature relationships of microbial growth and respiration rates and used these to investigate if and with what strength the community trait distributions for temperature were adapted to their local environment. Additionally, we sequenced bacterial and fungal amplicons to link the variance in community composition to changes in temperature traits. We found that microbial temperature trait distributions varied systematically with climate, suggesting that an increase in mean annual temperature (MAT) of 1°C will result in warm-shifted microbial temperature trait distributions equivalent to an increase in temperature minimum (Tmin) of 0.20°C for bacterial growth, 0.07°C for fungal growth, and 0.10°C for respiration. The temperature traits for bacterial growth were thus more responsive to warming than those for respiration and fungal growth. The microbial community composition also varied with temperature, enabling the interlinkage of taxonomic information with microbial temperature traits. Our work shows that the adaptation of microbial temperature trait distributions to a warming climate will affect the C-climate feedback, emphasizing the need to represent this to capture the microbial feedback to climate change. IMPORTANCE One of the largest uncertainties of global warming is if the microbial decomposer feedback will strengthen or weaken soil C-climate feedback. Despite decades of research effort, the strength of this feedback to warming remains unknown. We here present evidence that microbial temperature relationships vary systematically with environmental temperatures along a climate gradient and use this information to forecast how microbial temperature traits will create feedback between the soil C cycle and climate warming. We show that the current use of a universal temperature sensitivity is insufficient to represent the microbial feedback to climate change and provide new estimates to replace this flawed assumption in Earth system models. We also demonstrate that temperature relationships for rates of microbial growth and respiration are differentially affected by warming, with stronger responses to warming for microbial growth (soil C formation) than for respiration (C loss from soil to atmosphere), which will affect the atmosphere-land C balance.
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Affiliation(s)
| | - Dániel Tájmel
- Microbial Ecology, Department of Biology, Lund University, Lund, Sweden
| | - Johannes Rousk
- Microbial Ecology, Department of Biology, Lund University, Lund, Sweden
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42
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Hu Y, Fair H, Liu Q, Wang Z, Duan B, Lu X. Diversity and co-occurrence networks of bacterial and fungal communities on two typical debris-covered glaciers, southeastern Tibetan Plateau. Microbiol Res 2023; 273:127409. [PMID: 37186995 DOI: 10.1016/j.micres.2023.127409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 04/19/2023] [Accepted: 05/09/2023] [Indexed: 05/17/2023]
Abstract
Debris-covered glaciers (DCGs) are globally distributed and thought to contain greater microbial diversity than clean surface continental glaciers, but the ecological characteristics of microbial communities on the surface of DCGs have remained underexplored. Here, we investigated bacterial and fungal diversity and co-occurrence networks on the supraglacial debris habitat of two DCGs (Hailuogou and Dagongba Glaciers) in the southeastern Tibetan Plateau. We found that the supraglacial debris harbored abundant microbes with Proteobacteria occupying more than half (51.5%) of the total bacteria operational taxonomic units. The composition, diversity, and co-occurrence networks of both bacterial and fungal communities in the debris were significantly different between Hailuogou Glacier and Dagongba Glacier even though the glaciers are geographically adjacent within the same mountain range. Bacteria were more diverse in the debris of the Dagongba Glacier, where a lower surface velocity and thicker debris layer allowed the supraglacial debris to continuously weather and accumulate nutrients. Fungi were more diverse in the debris of the Hailuogou Glacier, which experiences a wetter monsoonal climate, is richer in calcium, has greater debris instability, and greater ice velocity than the Dagongba Glacier. These factors may provide ideal conditions for the dispersal and propagation of fungi spores on the Hailuogou Glacier. In addition, we found an obvious gradient of bacterial diversity along the supraglacial debris transect on the Hailuogou Glacier. Bacterial diversity was lower where debris cover was thin and scattered and became more diverse near the glacial terminus in thick, slow-moving debris. No such increasing bacterial pattern was detected on the Dagongba Glacier, which implies a positive relationship of debris age, thickness, and weathering on bacterial diversity. Additionally, a highly connected bacterial co-occurrence network with low modularity was found in the debris of the Hailuogou Glacier. In contrast, debris from the Dagongba Glacier exhibited less connected but more modularized co-occurrence networks of both bacterial and fungal communities. These findings indicate that less disturbed supraglacial debris conditions are crucial for microbes to form stable communities on DCGs.
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Affiliation(s)
- Yang Hu
- Key Laboratory of Mountain Surface Processes and Ecological Regulation, Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu, Sichuan 610299, China; University of Chinese Academy of Sciences, Beijing 100101, China
| | - Heather Fair
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, Minnesota 55108, USA
| | - Qiao Liu
- Key Laboratory of Mountain Surface Processes and Ecological Regulation, Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu, Sichuan 610299, China
| | - Ziwei Wang
- Key Laboratory of Mountain Surface Processes and Ecological Regulation, Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu, Sichuan 610299, China; University of Chinese Academy of Sciences, Beijing 100101, China
| | - Baoli Duan
- Key Laboratory of Mountain Surface Processes and Ecological Regulation, Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu, Sichuan 610299, China.
| | - Xuyang Lu
- Key Laboratory of Mountain Surface Processes and Ecological Regulation, Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu, Sichuan 610299, China.
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Dai W, Liu Y, Yao D, Wang N, Ye X, Cui Z, Wang H. Phylogenetic diversity of stochasticity-dominated predatory myxobacterial community drives multi-nutrient cycling in typical farmland soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 871:161680. [PMID: 36682558 DOI: 10.1016/j.scitotenv.2023.161680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 01/03/2023] [Accepted: 01/14/2023] [Indexed: 06/17/2023]
Abstract
Predatory myxobacteria are keystone taxa in the soil microbial food web that potentially regulate soil microbial community structure and ecosystem functions. However, little is known about the community assembly processes of myxobacteria in typical farmland soils over large geographic scales, in addition to their relationship with soil multi-nutrient cycling. Here, we used high-throughput sequencing techniques and phylogenetic null modeling analysis to investigate the distribution patterns and assembly processes of myxobacteria communities, in addition to interactions between myxobacteria communities and soil multi-nutrient cycling. Anaeromyxobacter (28.5 %) and Haliangium (19.6 %) were the dominant myxobacteria genera in all samples, and myxobacteria community similarities exhibited distinct distance-decay relationships. Stochastic processes (~77.8 %) were the dominant ecological processes driving the assembly of predatory myxobacteria communities over large geographical scales and under three fertilization regimes. Myxobacteria community structure was influenced by geographic factors (location and climate), soil factors (soil pH, soil organic carbon, total nitrogen, and total potassium), and fertilization, with myxobacteria community assembly being more sensitive to geographic factors. Organic-inorganic combined fertilization (NPKM) increased the proportions of deterministic processes in myxobacteria community assembly. Moreover, myxobacteria community assembly and diversity were closely associated with soil multi-nutrient cycling. Hence, myxobacteria phylogenetic α-diversity represented by NTI index is a potential bioindicators for soil multi-nutrient cycling. Overall, our findings comprehensively reveal the mechanisms of assembly of myxobacteria communities in soils over large geographic scales, and provide a theoretical basis for further research on the role of predatory bacteria on soil nutrient cycling in agro-ecosystems.
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Affiliation(s)
- Wei Dai
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100000, China
| | - Yang Liu
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100000, China
| | - Dandan Yao
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100000, China
| | - Ning Wang
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100000, China
| | - Xianfeng Ye
- Key Laboratory of Agricultural Environmental Microbiology of Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhongli Cui
- Key Laboratory of Agricultural Environmental Microbiology of Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Hui Wang
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100000, China.
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Zhang Z, Li J, Li H, Wang L, Zhou Y, Li S, Zhang Z, Feng K, Deng Y. Environmental DNA metabarcoding reveals the influence of human activities on microeukaryotic plankton along the Chinese coastline. WATER RESEARCH 2023; 233:119730. [PMID: 36801577 DOI: 10.1016/j.watres.2023.119730] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 02/04/2023] [Accepted: 02/10/2023] [Indexed: 06/18/2023]
Abstract
Microeukaryotic plankton, with its extremely diverse taxa, is a key component in both the marine food web and biogeochemical cycling. Coastal seas, which are home to the numerous microeukaryotic plankton that underpin the functions of these aquatic ecosystems, are often impacted by human activities. However, understanding the biogeographical patterns of diversity and community structure of microeukaryotic plankton and the role that major shaping factors play at the continent scale is still a challenge in coastal ecology. Here, the biogeographic patterns of biodiversity, community structure, and co-occurrence patterns were investigated by environmental DNA (eDNA) based approaches. Unlike most eDNA studies, we combined several methods (in silico PCR, mock and environmental communities) to systematically evaluate the specificity and coverage of primers to overcome the limitation of marker selection on biodiversity recovery. The 1380F/1510R primer set showed the best performance for the amplification of coastal plankton with the highest coverage, sensitivity, and resolution. We showed a unimodal pattern for planktonic alpha diversity with latitude (P < 0.001), and nutrient-related factors (NO3N, NO2N, and NH4N) were the leading predictors for spatial patterning. Significant regional biogeographic patterns and potential drivers for planktonic communities were found across coastal regions. All communities generally fitted the regional distance-decay relationship (DDR) model with the strongest spatial turnover rate was found in the Yalujiang (YLJ) estuary (P < 0.001). The environmental factors, especially inorganic nitrogen and heavy metals (HMs), had the greatest impact on planktonic community similarity in the Beibu Bay (BB) and East China Sea (ECS). Furthermore, we observed spatial plankton co-occurrence patterns, and the networked topology and structure were strongly driven by potential anthropogenic activity factors (nutrients and HMs). Overall, our study provided a systematic approach for metabarcode primer selection in eDNA-based biodiversity monitoring and revealed that the spatial pattern of the microeukaryotic plankton community was mainly controlled by regional human activity-related factors.
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Affiliation(s)
- Zheng Zhang
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China
| | - Jiang Li
- Marine Bioresource and Environment Research Center, First Institute of Oceanography, Ministry of Natural Resources; Key Laboratory of Ecological Environment Science and Technology, Ministry of Natural Resources, Qingdao, China, 266061.
| | - Hongjun Li
- State Environmental Protection Key Laboratory of Coastal Ecosystem, National Marine Environmental Monitoring Center, Dalian, 116023, China
| | - Linlin Wang
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China
| | - Yuqi Zhou
- Institute of Soil and Water Resources and Environmental Science College of Environmental and Natural Resource Sciences, Zhejiang University, China
| | - Shuzhen Li
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Zhaojing Zhang
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China
| | - Kai Feng
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100190, China
| | - Ye Deng
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100190, China; Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China.
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Liu N, Hu H, Ma W, Deng Y, Dimitrov D, Wang Q, Shrestha N, Su X, Feng K, Liu Y, Hao B, Zhang X, Feng X, Wang Z. Relationships Between Soil Microbial Diversities Across an Aridity Gradient in Temperate Grasslands : Soil Microbial Diversity Relationships. MICROBIAL ECOLOGY 2023; 85:1013-1027. [PMID: 35364696 DOI: 10.1007/s00248-022-01997-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 03/11/2022] [Indexed: 05/04/2023]
Abstract
Soil microbes assemble in highly complex and diverse microbial communities, and microbial diversity patterns and their drivers have been studied extensively. However, diversity correlations and co-occurrence patterns between bacterial, fungal, and archaeal domains and between microbial functional groups in arid regions remain poorly understood. Here we assessed the relationships between the diversity and abundance of bacteria, fungi, and archaea and explored how environmental factors influence these relationships. We sampled soil along a 1500-km-long aridity gradient in temperate grasslands of Inner Mongolia (China) and sequenced the 16S rRNA gene of bacteria and archaea and the ITS2 gene of fungi. The diversity correlations and co-occurrence patterns between bacterial, fungal, and archaeal domains and between different microbial functional groups were evaluated using α-diversity and co-occurrence networks based on microbial abundance. Our results indicate insignificant correlations among the diversity patterns of bacterial, fungal, and archaeal domains using α-diversity but mostly positive correlations among diversity patterns of microbial functional groups based on α-diversity and co-occurrence networks along the aridity gradient. These results suggest that studying microbial diversity patterns from the perspective of functional groups and co-occurrence networks can provide additional insights on patterns that cannot be accessed using only overall microbial α-diversity. Increase in aridity weakens the diversity correlations between bacteria and fungi and between bacterial and archaeal functional groups, but strengthens the positive diversity correlations between bacterial functional groups and between fungal functional groups and the negative diversity correlations between bacterial and fungal functional groups. These variations of the diversity correlations are associated with the different responses of microbes to environmental factors, especially aridity. Our findings demonstrate the complex responses of microbial community structure to environmental conditions (especially aridity) and suggest that understanding diversity correlations and co-occurrence patterns between soil microbial groups is essential for predicting changes in microbial communities under future climate change in arid regions.
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Affiliation(s)
- Nana Liu
- Institute of Ecology and Key Laboratory for Earth Surface Processes of the Ministry of Education, College of Urban and Environmental Sciences, Peking University, Beijing, 100871, China
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Huifeng Hu
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Wenhong Ma
- College of Ecology and Environment, Inner Mongolia University, Hohhot, 010021, China
| | - Ye Deng
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Dimitar Dimitrov
- Department of Natural History, University Museum of Bergen, University of Bergen, Bergen, Norway
| | - Qinggang Wang
- Department of Ecology and Ecological Engineering, College of Resources and Environmental Sciences, and Key Laboratory of Biodiversity and Organic Farming of Beijing City, China Agricultural University, Beijing, 100193, China
| | - Nawal Shrestha
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Xiangyan Su
- Institute of Ecology and Key Laboratory for Earth Surface Processes of the Ministry of Education, College of Urban and Environmental Sciences, Peking University, Beijing, 100871, China
| | - Kai Feng
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Yuqing Liu
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Baihui Hao
- College of Ecology and Environment, Inner Mongolia University, Hohhot, 010021, China
| | - Xinying Zhang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Xiaojuan Feng
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
| | - Zhiheng Wang
- Institute of Ecology and Key Laboratory for Earth Surface Processes of the Ministry of Education, College of Urban and Environmental Sciences, Peking University, Beijing, 100871, China.
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Feng Y, Wang J, Zhang J, Qi X, Long W, Ding Y, Liu L. Soil microbes support Janzen’s mountain passes hypothesis: The role of local-scale climate variability along a tropical montane gradient. Front Microbiol 2023; 14:1135116. [PMID: 36992924 PMCID: PMC10040759 DOI: 10.3389/fmicb.2023.1135116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 02/17/2023] [Indexed: 03/14/2023] Open
Abstract
Tropical montane ecosystems are the centers of biodiversity, and Janzen proposed that mountain climate variability plays a key role in sustaining this biodiversity. We test this hypothesis for soil bacteria and fungi along a 265–1,400 m elevational gradient on Hainan Island of tropical China, representing diverse vegetation types from deciduous monsoon forest to cloud forest. We found that bacterial and fungal diversity declined as elevation increased, and the dissimilarity of both groups increased with increasing separation in elevation, although changes in bacteria were larger than in fungi. Seasonal alterations and the range of soil moisture in the growing season were found to be the dominant drivers of fungal richness and Shannon diversity, whereas soil pH was the major driver of bacterial diversity. Dissimilarities of bacterial and fungal communities were best predicted by climate, particularly seasonal changes in soil temperature, with weaker influences of soil physicochemistry and vegetation. The dominant effect of seasonality in soil temperature was further detected in cloud forests, which harbored a higher proportion of unique bacterial species and dissimilarity of bacterial and fungal communities. Our findings suggest that local-climate variability plays a crucial role in structuring the distribution of soil microbial communities along a tropical montane gradient, which generally supports Janzen’s hypothesis. Such a sensitivity to climatic variability suggests that soil microbial communities along tropical montane gradients may shift in response to future climate scenarios.
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Affiliation(s)
- Yifan Feng
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education, College of Forestry, Hainan University, Haikou, China
| | - Jianbin Wang
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education, College of Forestry, Hainan University, Haikou, China
| | - Jian Zhang
- Center for Global Change and Complex Ecosystems, Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | - Xuming Qi
- Administration Branch of Bawangling, Hainan Tropical Rain Forest National Park Service, Changjiang, China
| | - Wenxing Long
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education, College of Forestry, Hainan University, Haikou, China
- Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Forest Ecology and Environment of the National Forestry and Grassland Administration, Beijing, China
- Wenxing Long,
| | - Yi Ding
- Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Forest Ecology and Environment of the National Forestry and Grassland Administration, Beijing, China
- Hainan Bawangling Forest Ecosystem Research Station, Changjiang, China
- Yi Ding,
| | - Lan Liu
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education, College of Forestry, Hainan University, Haikou, China
- *Correspondence: Lan Liu,
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Zhou SYD, Lie Z, Liu X, Zhu YG, Peñuelas J, Neilson R, Su X, Liu Z, Chu G, Meng Z, Yan J, Liu J. Distinct patterns of soil bacterial and fungal community assemblages in subtropical forest ecosystems under warming. GLOBAL CHANGE BIOLOGY 2023; 29:1501-1513. [PMID: 36448266 DOI: 10.1111/gcb.16541] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 11/18/2022] [Indexed: 05/26/2023]
Abstract
Climate change globally affects soil microbial community assembly across ecosystems. However, little is known about the impact of warming on the structure of soil microbial communities or underlying mechanisms that shape microbial community composition in subtropical forest ecosystems. To address this gap, we utilized natural variation in temperature via an altitudinal gradient to simulate ecosystem warming. After 6 years, microbial co-occurrence network complexity increased with warming, and changes in their taxonomic composition were asynchronous, likely due to contrasting community assembly processes. We found that while stochastic processes were drivers of bacterial community composition, warming led to a shift from stochastic to deterministic drivers in dry season. Structural equation modelling highlighted that soil temperature and water content positively influenced soil microbial communities during dry season and negatively during wet season. These results facilitate our understanding of the response of soil microbial communities to climate warming and may improve predictions of ecosystem function of soil microbes in subtropical forests.
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Affiliation(s)
- Shu-Yi-Dan Zhou
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
| | - Zhiyang Lie
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Xujun Liu
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Yong-Guan Zhu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
| | - Josep Peñuelas
- Global Ecology Unit CREAF-CSIC-UAB, CSIC, Barcelona, Spain
| | - Roy Neilson
- Ecological Sciences, The James Hutton Institute, Dundee, Scotland, UK
| | - Xiaoxuan Su
- Interdisciplinary Research Center for Agriculture Green Development in Yangtze River Basin, College of Resources and Environment, Southwest University, Chongqing, China
| | - Zhanfeng Liu
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Guowei Chu
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Ze Meng
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Junhua Yan
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Juxiu Liu
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
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Abstract
Shopping malls offer various niches for microbial populations, potentially serving as sources and reservoirs for the spread of microorganisms of public health concern. However, knowledge about the microbiome and the distribution of human pathogens in malls is largely unknown. Here, we examine the microbial community dynamics and genotypes of potential pathogens from floor and escalator surfaces in shopping malls and adjacent road dusts and greenbelt soils. The distribution pattern of microbial communities is driven primarily by habitats and seasons. A significant enrichment of human-associated microbiota in the indoor environment indicates that human interactions with surfaces might be another strong driver for mall microbiomes. Neutral community models suggest that the microbial community assembly is strongly driven by stochastic processes. Distinct performances of microbial taxonomic signatures for environmental classifications indicate the consistent differences of microbial communities of different seasons/habitats and the strong anthropogenic effect on homogenizing microbial communities of shopping malls. Indoor environments harbored higher concentrations of human pathogens than outdoor samples, also carrying a high proportion of antimicrobial resistance-associated multidrug efflux genes and virulence genes. These findings enhanced the understanding of the microbiome in the built environment and the interactions between humans and the built environment, providing a basis for tracking biothreats and communicable diseases and developing sophisticated early warning systems. IMPORTANCE Shopping malls are distinct microbial environments which can facilitate a constant transmission of microorganisms of public health concern between humans and the built environment or between human and human. Despite extensive investigation of the natural environmental microbiome, no comprehensive profile of microbial ecology has been reported in malls. Characterizing microbial distribution, potential pathogens, and antimicrobial resistance will enhance our understanding of how these microbial communities are formed, maintained, and transferred and help establish a baseline for biosurveillance of potential public health threats in malls.
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Zhang H, Xu H, Wang S, Qin M, Zhao D, Wu QL, Zeng J. Habitats modulate influencing factors shaping the spatial distribution of bacterial communities along a Tibetan Plateau riverine wetland. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 860:160418. [PMID: 36435238 DOI: 10.1016/j.scitotenv.2022.160418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 11/10/2022] [Accepted: 11/18/2022] [Indexed: 06/16/2023]
Abstract
The Tibetan Plateau riverine wetland is very sensitive to global climate change. Understanding the mechanisms that maintain the spatial patterns of bacterial communities provides insight into the dominant biogeochemical processes within the plateau riverine wetlands. Nonetheless, the spatial distribution of bacterial communities along these wetlands has rarely been explored. We investigated the spatial patterns of bacterial community within rhizosphere soil, bulk soil, and sediment samples collected along the Yarlung Tsangpo riverine wetland (YTRW), the longest plateau riverine wetland in China. Our results indicated that the diversity of bacterial communities in all three habitats increased significantly along the YTRW. The slope of the linear relationship between distance and bacterial community diversity in sediment was steeper than those for bulk and rhizosphere soils. Furthermore, bacterial communities in all three habitats showed significant distance-decay relationships. A combination of historical factors (geographical distance and climatic factors) and contemporary environmental heterogeneity (edaphic properties) controlled spatial distributions of bacterial communities in all three habitats, although climatic factors were predominant. Climatic factors affected rhizosphere bacterial communities more than those in bulk soil and sediment. Co-occurrence network analysis revealed that the potential interactions between bacterial taxa may decrease along the YTRW. This field investigation highlighted that the climatic factors strongly influenced the spatial distribution of bacterial communities along the YTRW; however, habitat differences among rhizosphere soil, bulk soil, and sediment samples affected the relative importance of climatic factors on spatial distributions of the associated bacterial communities. These findings would improve the understanding of biogeochemical processes in these typical habitats and potential alterations provoked by climate change.
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Affiliation(s)
- Hongjie Zhang
- Joint International Research Laboratory of Global Change and Water Cycle, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, China; State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Huimin Xu
- Joint International Research Laboratory of Global Change and Water Cycle, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, China; State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Shuren Wang
- Joint International Research Laboratory of Global Change and Water Cycle, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, China; State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Mengyu Qin
- Joint International Research Laboratory of Global Change and Water Cycle, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, China; State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Dayong Zhao
- Joint International Research Laboratory of Global Change and Water Cycle, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, China
| | - Qinglong L Wu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China; Center for Evolution and Conservation Biology, Southern Marine Sciences and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Jin Zeng
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China.
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50
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Wang M, Wang C, Yu Z, Wang H, Wu C, Masoudi A, Liu J. Fungal diversities and community assembly processes show different biogeographical patterns in forest and grassland soil ecosystems. Front Microbiol 2023; 14:1036905. [PMID: 36819045 PMCID: PMC9928764 DOI: 10.3389/fmicb.2023.1036905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 01/16/2023] [Indexed: 02/04/2023] Open
Abstract
Soil fungal community has been largely explored by comparing their natural diversity. However, there is a relatively small body of literature concerned with fungal community assembly processes and their co-occurrence network correlations carried out across large spatial-temporal scales with complex environmental gradients in natural ecosystems and different habitats in China. Thus, soil fungal community assembly processes were assessed to predict changes in soil function in 98 different forest and grassland sites from the Sichuan, Hubei, and Hebei Provinces of China using high-throughput sequencing of nuclear ribosomal internal transcribed spacer 2 (ITS-2). The 10 most abundant fungal phyla results showed that Ascomycota was the most abundant phylum in forests from Sichuan province (64.42%) and grassland habitats from Hebei province (53.46%). Moreover, core fungal taxa (487 OTUs) represented 0.35% of total fungal OTUs. We observed higher fungal Shannon diversity and richness (the Chao1 index) from diverse mixed forests of the Sichuan and Hubei Provinces than the mono-cultured forest and grassland habitats in Hebei Province. Although fungal alpha and beta diversities exhibited different biogeographical patterns, the fungal assembly pattern was mostly driven by dispersal limitation than selection in different habitats. Fungal co-occurrence analyses showed that the network was more intense at Saihanba National Forest Park (SNFP, Hebei). In contrast, the co-occurrence network was more complex at boundaries between forests and grasslands at SNFP. Additionally, the highest number of positive (co-presence or co-operative) correlations of fungal genera were inferred from grassland habitat, which led fungal communities to form commensalism relationships compared to forest areas with having higher negative correlations (mutual exclusion or competitive). The generalized additive model (GAM) analysis showed that the association of fungal Shannon diversity and richness indices with geographical coordinates did not follow a general pattern; instead, the fluctuation of these indices was restricted to local geographical coordinates at each sampling location. These results indicated the existence of a site effect on the diversity of fungal communities across our sampling sites. Our observation suggested that higher fungal diversity and richness of fungal taxa in a particular habitat are not necessarily associated with more complex networks.
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