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Du J, Gao Q, Sun F, Liu B, Jiao Y, Liu Q. Agricultural soil microbiomes at the climate frontier: Nutrient-mediated adaptation strategies for sustainable farming. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2025; 295:118161. [PMID: 40203703 DOI: 10.1016/j.ecoenv.2025.118161] [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: 12/30/2024] [Revised: 03/27/2025] [Accepted: 04/06/2025] [Indexed: 04/11/2025]
Abstract
The equilibrium transformation of soil microbial community dynamics and succession across various temporal and spatial dimensions plays a critical role in maintaining plant adaptability. Intensive agricultural practices accelerate the succession of plant microbial communities, rendering their restoration function more vulnerable. Climate change, with its variable impacts, affects the resilience of plant microbial communities through regulatory and mediating effects. Investigating the spatiotemporal dynamics of soil microbial communities in the context of climate change offers valuable insights into developing robust and resilient microbial ecosystems. This review examines the regulatory role of soil resources in plant microbial communities, the interactive effects of climate change on soil resource regulation, and the prediction of microbial community structures through resource allocation. Additionally, it explores the mechanisms that sustain ecological resilience in plant microbial community systems, emphasizing the application of the profit-averaging law.
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Affiliation(s)
- Jianfeng Du
- School of Resources and Environment, Henan Institute of Science and Technology, Xinxiang, Henan 453003, PR China
| | - Qixiong Gao
- School of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Fuxin Sun
- School of Resources and Environment, Henan Institute of Science and Technology, Xinxiang, Henan 453003, PR China
| | - Baoyou Liu
- Plant Protection Institute, Yantai Academy of Agricultural Sciences, Yantai, Shandong 265500, PR China
| | - Yang Jiao
- School of Resources and Environment, Henan Institute of Science and Technology, Xinxiang, Henan 453003, PR China.
| | - Qili Liu
- School of Resources and Environment, Henan Institute of Science and Technology, Xinxiang, Henan 453003, PR China.
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Francis Justine M, Kaiwen P, Tadesse Z, Hongyan Z, Lin Z. Cooling has stimulated soil carbon storage in forest ecosystems. ENVIRONMENTAL RESEARCH 2024; 245:118012. [PMID: 38154564 DOI: 10.1016/j.envres.2023.118012] [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: 09/18/2023] [Revised: 11/14/2023] [Accepted: 12/21/2023] [Indexed: 12/30/2023]
Abstract
The interactive effect of soil cooling and nitrogen (N) addition can accurately simulate climatic and anthropogenic effects on terrestrial and other land-based ecosystems, but direct empirical measurements on the effects of cooling and N addition on soil carbon (C) and N are lacking. Hence, transplanting soils into colder regions was used to evaluate the effects of cooling and N addition on soil C and N. We used PVCs of 30 cm in height and 8 cm in diameter to extract soil samples. Soil C and N were significantly (P < 0.05) increased by transplanting soils into colder regions. In contrast, cooling has insignificantly (P > 0.05) increased the soil dissolved organic C (DOC) and dissolved organic (DON), but the effect was negatively significant on soil pH compared to the C/N ratio. Similarly, N addition significantly increased the measured soil N stock. However, the effect was negatively significant on soil pH (P < 0.05) compared to the C/N ratio (P > 0.05). Nevertheless, the interaction of cooling and N addition did not affect the soil C and N storage. A similar effect was observed on the soil DOC and DON. The results presented here illustrate that transplanting soils into colder regions and N deposition has perfectly simulated the effects of climate-forcing factors on soil C and N storage in terrestrial and other land-based ecosystems. Accordingly, this study suggests that low temperatures have stimulated the accumulation of the measured soil organic and dissolved properties, but the effect is less consequential when low temperature interacts with N addition in high-elevation areas where ecosystem structures and functions are limited by temperature and may serve as a baseline for future research on land feedbacks to the climate system.
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Affiliation(s)
- Meta Francis Justine
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization and Ecological Restoration of Biodiversity Conservation, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China; International College, University of Chinese Academy of Sciences, Beijing, 100049, China; Ministry of Environment and Forestry, Juba, South Sudan
| | - Pan Kaiwen
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization and Ecological Restoration of Biodiversity Conservation, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Zebene Tadesse
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization and Ecological Restoration of Biodiversity Conservation, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China; International College, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhou Hongyan
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization and Ecological Restoration of Biodiversity Conservation, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China; International College, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhang Lin
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization and Ecological Restoration of Biodiversity Conservation, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.
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Li S, Zhong L, Zhang B, Fan C, Gao Y, Wang M, Xiao H, Tang X. Microplastics induced the differential responses of microbial-driven soil carbon and nitrogen cycles under warming. JOURNAL OF HAZARDOUS MATERIALS 2024; 465:133141. [PMID: 38056262 DOI: 10.1016/j.jhazmat.2023.133141] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 11/27/2023] [Accepted: 11/28/2023] [Indexed: 12/08/2023]
Abstract
The input of microplastics (MPs) and warming interfere with soil carbon (C) or nitrogen (N) cycles. Although the effects of warming and/or MPs on the cycles have been well studied, the biological coupling of microbial-driven cycles was neglected. Here, the synergistic changes of the cycles were investigated using batch incubation experiments. As results, the influences of MPs were not significant at 15, 20, and 25 °C, and yet, high temperature (i.e., 30 °C) reduced the respiration of high-concentration MPs-amended soil by 9.80%, and increased dissolved organic carbon (DOC) by 14.74%. In contrast, high temperature did not change the effect of MPs on N. The decrease of microbial biomass carbon (MBC) and the constant of microbial biomass nitrogen (MBN) indicated that microbial N utilization was enhanced, which might be attributed to the enrichments of adapted populations, such as Conexibacter, Acidothermus, and Acidibacter. These observations revealed that high temperature and MPs drove the differential response of soil C and N cycles. Additionally, the transcriptomic provided genomic evidence of the response. In summary, the high temperature was a prerequisite for the MPs-driven response, which underscored new ecological risks of MPs under global warming and emphasized the need for carbon emission reduction and better plastic product regulation.
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Affiliation(s)
- Shuang Li
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Linrui Zhong
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Baowei Zhang
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Changzheng Fan
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China.
| | - Yuying Gao
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Mier Wang
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Huannian Xiao
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Xiang Tang
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China; Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, PR China.
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Zhang X, Feng Q, Cao J, Liu W, Qin Y, Zhu M, Han T. Grazing practices affect soil microbial networks but not diversity and composition in alpine meadows of northeastern Qinghai-Tibetan plateau. ENVIRONMENTAL RESEARCH 2023; 235:116656. [PMID: 37451580 DOI: 10.1016/j.envres.2023.116656] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 07/04/2023] [Accepted: 07/11/2023] [Indexed: 07/18/2023]
Abstract
Livestock grazing is the primary practice in alpine meadows and can alter soil microbiomes, which is critical for ecosystem functions and services. Seasonal grazing (SG) and continuous grazing (CG) are two kinds of different grazing practices that dominate alpine meadows on the Qinghai-Tibetan Plateau (QTP), and how they affect soil microbial communities remains in-depth exploration. The present study was conducted to investigate the effects of different grazing practices (i.e., SG and CG) on the diversity, composition, and co-occurrence networks of soil bacteria and fungi in QTP alpine meadows. Soil microbial α- and β-diversity showed no obvious difference between SG and CG grasslands. Grazing practices had little impact on soil microbial composition, except that the relative abundance of Proteobacteria and Ascomycota showed significant difference between SG and CG grasslands. Soil microbial networks were more complex and less stable in SG grasslands than that in CG grasslands, and the bacterial networks were more complex than fungal networks. Soil fungal diversity was more strongly correlated with environmental factors than bacteria, whereas both fungal and bacterial structures were mainly influenced by soil pH, total nitrogen, and ammonium nitrogen. These findings indicate that microbial associations are more sensitive to grazing practices than microbial diversity and composition, and that SG may be a better grazing practice for ecological benefits in alpine meadows.
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Affiliation(s)
- Xiaofang Zhang
- Key Laboratory of Ecohydrology of Inland River Basin, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Qi Feng
- Key Laboratory of Ecohydrology of Inland River Basin, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China.
| | - Jianjun Cao
- College of Geography and Environmental Science, Northwest Normal University, Lanzhou, 730070, China.
| | - Wei Liu
- Key Laboratory of Ecohydrology of Inland River Basin, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China; Qilian Mountains Eco-Environment Research Center in Gansu Province, Lanzhou, 730000, China
| | - Yanyan Qin
- Qilian Mountains Eco-Environment Research Center in Gansu Province, Lanzhou, 730000, China; Key Laboratory of Land Surface Process and Climate Change in Cold and Arid Regions, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
| | - Meng Zhu
- Key Laboratory of Ecohydrology of Inland River Basin, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
| | - Tuo Han
- Key Laboratory of Ecohydrology of Inland River Basin, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
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Fu F, Li J, Li Y, Chen W, Ding H, Xiao S. Simulating the effect of climate change on soil microbial community in an Abies georgei var. smithii forest. Front Microbiol 2023; 14:1189859. [PMID: 37333631 PMCID: PMC10272780 DOI: 10.3389/fmicb.2023.1189859] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 05/11/2023] [Indexed: 06/20/2023] Open
Abstract
Qinghai-Tibet Plateau is considered a region vulnerable to the effects of climate change. Studying the effects of climate change on the structure and function of soil microbial communities will provide insight into the carbon cycle under climate change. However, to date, changes in the successional dynamics and stability of microbial communities under the combined effects of climate change (warming or cooling) remain unknown, which limits our ability to predict the consequences of future climate change. In this study, in situ soil columns of an Abies georgei var. smithii forest at 4,300 and 3,500 m elevation in the Sygera Mountains were incubated in pairs for 1 year using the PVC tube method to simulate climate warming and cooling, corresponding to a temperature change of ±4.7°C. Illumina HiSeq sequencing was applied to study alterations in soil bacterial and fungal communities of different soil layers. Results showed that warming did not significantly affect the fungal and bacterial diversity of the 0-10 cm soil layer, but the fungal and bacterial diversity of the 20-30 cm soil layer increased significantly after warming. Warming changed the structure of fungal and bacterial communities in all soil layers (0-10 cm, 10-20 cm, and 20-30 cm), and the effect increased with the increase of soil layers. Cooling had almost no significant effect on fungal and bacterial diversity in all soil layers. Cooling changed the structure of fungal communities in all soil layers, but it showed no significant effect on the structure of bacterial communities in all soil layers because fungi are more adapted than bacteria to environments with high soil water content (SWC) and low temperatures. Redundancy analysis (RDA) and hierarchical analysis showed that changes in soil bacterial community structure were primarily related to soil physical and chemical properties, whereas changes in soil fungal community structure primarily affected SWC and soil temperature (Soil Temp). The specialization ratio of fungi and bacteria increased with soil depth, and fungi were significantly higher than bacteria, indicating that climate change has a greater impact on microorganisms in deeper soil layers, and fungi are more sensitive to climate change. Furthermore, a warmer climate could create more ecological niches for microbial species to coexist and increase the strength of microbial interactions, whereas a cooler climate could have the opposite effect. However, we found differences in the intensity of microbial interactions in response to climate change in different soil layers. This study provides new insights to understand and predict future effects of climate change on soil microbes in alpine forest ecosystems.
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Affiliation(s)
- Fangwei Fu
- Research Institute of Tibet Plateau Ecology, Tibet Agriculture and Animal Husbandry University, Nyingchi, Tibet, China
- Key Laboratory of Forest Ecology in Tibet Plateau, Ministry of Education, Nyingchi, Tibet, China
- National Key Station of Field Scientific Observation and Experiment, Nyingchi, Tibet, China
- Key Laboratory of Alpine Vegetation Ecological Security in Tibet, Nyingchi, Tibet, China
| | - Jiangrong Li
- Research Institute of Tibet Plateau Ecology, Tibet Agriculture and Animal Husbandry University, Nyingchi, Tibet, China
- Key Laboratory of Forest Ecology in Tibet Plateau, Ministry of Education, Nyingchi, Tibet, China
- National Key Station of Field Scientific Observation and Experiment, Nyingchi, Tibet, China
- Key Laboratory of Alpine Vegetation Ecological Security in Tibet, Nyingchi, Tibet, China
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China
| | - Yueyao Li
- Research Institute of Tibet Plateau Ecology, Tibet Agriculture and Animal Husbandry University, Nyingchi, Tibet, China
- Key Laboratory of Forest Ecology in Tibet Plateau, Ministry of Education, Nyingchi, Tibet, China
- National Key Station of Field Scientific Observation and Experiment, Nyingchi, Tibet, China
- Key Laboratory of Alpine Vegetation Ecological Security in Tibet, Nyingchi, Tibet, China
| | - Wensheng Chen
- Research Institute of Tibet Plateau Ecology, Tibet Agriculture and Animal Husbandry University, Nyingchi, Tibet, China
- Key Laboratory of Forest Ecology in Tibet Plateau, Ministry of Education, Nyingchi, Tibet, China
- National Key Station of Field Scientific Observation and Experiment, Nyingchi, Tibet, China
- Key Laboratory of Alpine Vegetation Ecological Security in Tibet, Nyingchi, Tibet, China
| | - Huihui Ding
- Research Institute of Tibet Plateau Ecology, Tibet Agriculture and Animal Husbandry University, Nyingchi, Tibet, China
- Key Laboratory of Forest Ecology in Tibet Plateau, Ministry of Education, Nyingchi, Tibet, China
- National Key Station of Field Scientific Observation and Experiment, Nyingchi, Tibet, China
- Key Laboratory of Alpine Vegetation Ecological Security in Tibet, Nyingchi, Tibet, China
| | - Siying Xiao
- Research Institute of Tibet Plateau Ecology, Tibet Agriculture and Animal Husbandry University, Nyingchi, Tibet, China
- Key Laboratory of Forest Ecology in Tibet Plateau, Ministry of Education, Nyingchi, Tibet, China
- National Key Station of Field Scientific Observation and Experiment, Nyingchi, Tibet, China
- Key Laboratory of Alpine Vegetation Ecological Security in Tibet, Nyingchi, Tibet, China
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Medriano CA, Chan A, De Sotto R, Bae S. Different types of land use influence soil physiochemical properties, the abundance of nitrifying bacteria, and microbial interactions in tropical urban soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 869:161722. [PMID: 36690092 DOI: 10.1016/j.scitotenv.2023.161722] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 01/13/2023] [Accepted: 01/16/2023] [Indexed: 06/17/2023]
Abstract
Anthropogenic activities have led to unexpected changes in microbial community composition and structure, resulting in an interruption of soil ecological roles in urban environments. We questioned the impact of the different land use (e.g., agricultural, industrial, recreational, coastal, and residential areas) on the distribution of nitrifying bacteria and microbial interaction in tropical soil. The dominant nitrifying bacteria were ammonia-oxidizing archaea (AOA) in tropical soils up to 107 copies/g of soil, while the abundance of ammonia-oxidizing bacteria (AOB) was significantly higher in agricultural soil only. Comammox (CMX) was ubiquitous up to 105 copies/g of tropical soil, indicating that CMX might share ecological niches with AOA and considerably contribute to nitrification in urban areas. The most abundant phylum is Actinobacteria, accounting for 27-34 % relative abundance among most land-use types, but Proteobacteria was observed as the most prevalent phylum in agricultural soil. The physicochemical properties (e.g., soil pH and nutrient contents) of different types of land use influenced microbial richness and diversities associated with nitrogen cycling. Multivariate analysis disclosed that agricultural soils were distinct from other land uses because of the concentrations of nutrients and heavy metals and the abundance of microorganisms associated with nitrogen cycles. Also, the microbial co-occurrence network revealed that agricultural soils were a highly interconnected network of the microbial community. In this study, C: N ratio might have a significant impact on ecological networks and the abundance of nitrogen-related taxa, which could influence microbial interactions and complexity in tropical soils. Thus, the impact of anthropogenic land use induced changes in microbial composition and diversity, co-occurrence network, and nitrifying bacteria, leading to potential transformation in ecological services of tropical soils and nitrogen cycling in urban environments.
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Affiliation(s)
- Carl Angelo Medriano
- Civil and Environmental Engineering Department, National University of Singapore, 1 Engineering Drive 3, Singapore 117580, Singapore
| | - Amabel Chan
- Civil and Environmental Engineering Department, National University of Singapore, 1 Engineering Drive 3, Singapore 117580, Singapore
| | - Ryan De Sotto
- Civil and Environmental Engineering Department, National University of Singapore, 1 Engineering Drive 3, Singapore 117580, Singapore
| | - Sungwoo Bae
- Civil and Environmental Engineering Department, National University of Singapore, 1 Engineering Drive 3, Singapore 117580, Singapore.
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Insights into Bacterial Communities and Diversity of Mangrove Forest Soils along the Upper Gulf of Thailand in Response to Environmental Factors. BIOLOGY 2022; 11:biology11121787. [PMID: 36552296 PMCID: PMC9775068 DOI: 10.3390/biology11121787] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 11/29/2022] [Accepted: 11/30/2022] [Indexed: 12/13/2022]
Abstract
The comprehensive data for the dynamic adaptation of bacterial community structure in response to environmental factors is important for the maintenance of the mangrove ecosystem. This aspect was investigated with soils and surface water from six mangrove forests in six provinces along the Upper Gulf of Thailand shoreline. Mangrove soils were variable with respect to pH (acidic to slightly alkaline) and had low amounts of organic matter (OM). Illumina next-generation sequencing attested that the number of observed species as well as the bacterial diversity and richness among all sites were not significantly different. The gamma-, alpha-Proteobacteria, Desulfobacteria, Bacteroidia, Anaerolineae, Bathyarchaeia, Acidobacteriae, Nitrososphaeria, Clostridia, and Thermoplasmata were more abundant bacterial classes present in all sites. Soil OM was the major factor that mostly modulated the bacterial community structure, while salinity influenced the number of observed species and bacterial richness. These results provide informative data on the bacterial community, in response to both environmental factors and heavy metal pollutants, that is prominent for sustainable development and management of mangrove forests.
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Niu T, Xie J, Li J, Zhang J, Zhang X, Ma H, Wang C. Response of rhizosphere microbial community of Chinese chives under different fertilization treatments. Front Microbiol 2022; 13:1031624. [PMID: 36478855 PMCID: PMC9719922 DOI: 10.3389/fmicb.2022.1031624] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 11/02/2022] [Indexed: 09/29/2023] Open
Abstract
Soil microorganisms play an irreplaceable role in agricultural production, however, an understanding of response of soil microorganisms to slow-release and common fertilizer applications is limited. In this study, different amounts of slow- release fertilizer were used to overwintering Chinese chives growing area in a plastic greenhouse to investigate the effects of on rhizosphere soil physicochemical properties and soil microbial communities (bacteria and fungi) of Chinese chives. The result displayed that application of slow-release fertilizer significantly improved soil nutrients, soil enzyme activity, and soil microbial community structure and diversity compared to conventional fertilizer application. Compared with T1 treatment, the content of total nitrogen (TN) and available phosphorus (AP), and the SU-E activity in the soil of T2 (NPK: 62.8 kg · 667 m-2) increased by 42.58%, 16.67%, and 9.70%, respectively, showing the best effects. In addition, soil bacterial diversity index and soil microbial community structure were improved as indicated by increased relative abundance of each species, such as Byssovorax, Sandaracinus, and Cellvibrio. Oppositely, the both soil fungal diversity and the number of species decreased after fertilizationthe relative abundance of Ascomycota increased in each fertilization treatment detected by ITS sequencing. Further, the relative abundance of pathogenic fungi such as Pezizomycetes, Cantharellales, and Pleosporales decreased in the T2 treatment. Principal Coordinates Analysis (PCoA) showed that both the amount of fertilizer applied and the type of fertilizer applied affected the soil microbial community structure. RDA evidenced that soil bacteria, Proteobacteria and Gemmatimonadetes, were closely correlated with soil AN, SOM, and AK. Acidobacteria were closely correlated with soil pH, TN, and AP. Ascomycota was closely correlated with soil pH and TN. In conclusion, the application of slow-release fertilizers and reduced fertilizer applicationcould improve soil physical and chemical properties as well as soil microbial community structure and diversity, contributing to sustainable soil development. The recommended fertilization rate for overwintering Chinese chives is NPK: 62.8 kg · 667 m-2.
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Affiliation(s)
- Tianhang Niu
- College of Horticulture, Gansu Agricultural University, Lanzhou, China
| | - Jianming Xie
- College of Horticulture, Gansu Agricultural University, Lanzhou, China
| | - Jing Li
- College of Horticulture, Gansu Agricultural University, Lanzhou, China
| | - Jing Zhang
- College of Horticulture, Gansu Agricultural University, Lanzhou, China
| | - Xiaodan Zhang
- College of Horticulture, Gansu Agricultural University, Lanzhou, China
| | - Hongyan Ma
- Lanzhou New Area Agricultural Science and Technology Development Co., Ltd., Lanzhou, China
| | - Cheng Wang
- College of Horticulture, Gansu Agricultural University, Lanzhou, China
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Yu H, Le Roux JJ, Zhao M, Li W. Mikania sesquiterpene lactones enhance soil bacterial diversity and fungal and bacterial activities. Biol Invasions 2022. [DOI: 10.1007/s10530-022-02907-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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10
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Ma X, Wang T, Shi Z, Chiariello NR, Docherty K, Field CB, Gutknecht J, Gao Q, Gu Y, Guo X, Hungate BA, Lei J, Niboyet A, Le Roux X, Yuan M, Yuan T, Zhou J, Yang Y. Long-term nitrogen deposition enhances microbial capacities in soil carbon stabilization but reduces network complexity. MICROBIOME 2022; 10:112. [PMID: 35902889 PMCID: PMC9330674 DOI: 10.1186/s40168-022-01309-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 06/20/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Anthropogenic activities have increased the inputs of atmospheric reactive nitrogen (N) into terrestrial ecosystems, affecting soil carbon stability and microbial communities. Previous studies have primarily examined the effects of nitrogen deposition on microbial taxonomy, enzymatic activities, and functional processes. Here, we examined various functional traits of soil microbial communities and how these traits are interrelated in a Mediterranean-type grassland administrated with 14 years of 7 g m-2 year-1 of N amendment, based on estimated atmospheric N deposition in areas within California, USA, by the end of the twenty-first century. RESULTS Soil microbial communities were significantly altered by N deposition. Consistent with higher aboveground plant biomass and litter, fast-growing bacteria, assessed by abundance-weighted average rRNA operon copy number, were favored in N deposited soils. The relative abundances of genes associated with labile carbon (C) degradation (e.g., amyA and cda) were also increased. In contrast, the relative abundances of functional genes associated with the degradation of more recalcitrant C (e.g., mannanase and chitinase) were either unchanged or decreased. Compared with the ambient control, N deposition significantly reduced network complexity, such as average degree and connectedness. The network for N deposited samples contained only genes associated with C degradation, suggesting that C degradation genes became more intensely connected under N deposition. CONCLUSIONS We propose a conceptual model to summarize the mechanisms of how changes in above- and belowground ecosystems by long-term N deposition collectively lead to more soil C accumulation. Video Abstract.
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Affiliation(s)
- Xingyu Ma
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
- China Urban Construction Design & Research Institute Co., Ltd, Beijing, 100120, China
| | - Tengxu Wang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
- North China Municipal Engineering Design & Research Institute Co., Ltd., the Beijing Branch, Beijing, 100081, China
| | - Zhou Shi
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
| | - Nona R Chiariello
- Department of Global Ecology, Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - Kathryn Docherty
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI, 49008, USA
| | - Christopher B Field
- Department of Global Ecology, Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - Jessica Gutknecht
- Department of Soil Ecology, Helmholtz Centre for Environmental Research - UFZ, 06120, Halle, Germany
- Present address: Department of Soil, Water, and Climate, University of Minnesota, Twin Cities, Saint Paul, MN, 55104, USA
| | - Qun Gao
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Yunfu Gu
- Department of Microbiology, College of Resource, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xue Guo
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Bruce A Hungate
- Center for Ecosystem Science and Society, and Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Jiesi Lei
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Audrey Niboyet
- Sorbonne Université, Université Paris Cité, UPEC, CNRS, INRAE, IRD, Institut d'Ecologie et des Sciences de l'Environnement de Paris, iEES-Paris, Paris, France
- AgroParisTech, Paris, France
| | - Xavier Le Roux
- Microbial Ecology Centre LEM, INRAE, CNRS, University of Lyon, University Lyon 1, VetAgroSup, UMR INRAE 1418, 43 boulevard du 11 novembre 1918, 69622, Villeurbanne, France
| | - Mengting Yuan
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
- Department of Environmental Science, Policy and Management, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Tong Yuan
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
| | - Jizhong Zhou
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA.
- Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China.
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11
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Soil Slope Exposure Affects Physico-Chemical and Microbiological Properties in Soil Aggregate Size Fractions. LAND 2022. [DOI: 10.3390/land11050750] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Slope exposure is known to affect soil biogeochemical processes in mountainous forest ecosystems, but little attention has yet been paid to its influence at a soil aggregate scale. Therefore, we evaluated the effects of slope exposure (north- vs south-facing slope) on the physico-chemical and microbiological properties of bulk soil and dry-sieved and water-stable aggregate size fractions in both organic (OF) and mineral (AE) horizons in an Italian alpine forest. The changes in organic carbon (OC) and nitrogen (ON) fractions were assessed together with a battery of thirteen enzyme activities involved in the main nutrient cycles. In addition, soil biological properties including microbial biomass (estimated as double-stranded DNA content), and microbial activity (assessed as the ratio between the extra-(exDNA) and intracellular (iDNA) fractions of the total soil DNA pool) were determined. The OF horizon at the north-facing slope was enriched in recalcitrant and insoluble OC and ON fractions and characterized by a lower microbial activity, as indicated by the higher exDNA/iDNA ratio with respect to the south-facing slope. On the contrary, exDNA and iDNA contents, microbial biomass, as well as most of the enzyme activities, reached higher levels at the southern exposure in the AE horizon. These exposure-effects were bulk soil- and aggregate size fraction-specific. Overall, lower values of the chemical and microbiological parameters were found in the water-stable fraction. Our findings indicate that slope exposure (and thus topography), soil horizon, and aggregate size distinctly influence soil OC dynamics in mountain ecosystems.
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12
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Abstract
Soil microbes are considered the second genome of plants. Understanding the distribution and network of aluminum (Al)-tolerant microorganisms is helpful to alleviate Al toxicity to plants in acidic soils. Here, we examined soluble Al3+ and bacterial communities carrying Al resistance genes in paddy soils with a soil pH range of 3.6 to 8.7. In the acidic soil with pH <5.1, the content of Al3+ increased significantly. There were abundant and diverse Al-tolerant microorganisms in acidic soils, including Clostridium, Bacillus, Paenibacillus, Desulfitobacterium, and Desulfosporosinus, etc. Moreover, compared with neutral and alkaline soils, the network structure of Al-tolerant microorganisms was more complex. The potential roles of major Al-tolerant microbial taxa on each other in the ecological network were identified by a directed network along 0.01 pH steps. The influential taxa in the network had a broader niche and contained more antioxidant functional genes to resist Al stress, indicating their survival advantage over the sensitive taxa. Our study is the first to explore the distribution of Al-tolerant microorganisms in continental paddies and reveal their potential associations mediated by pH, which provides a basis for further utilization of microbial resources in acidic agricultural soils. IMPORTANCE Aluminum (Al) toxicity is the primary limiting factor of crop production in acidic soils with pH <5.0. Numerous studies have focused on the mechanism of Al toxicity and tolerance in plants; however, the effects of Al toxicity on soil microorganisms and their tolerance remain less studied. This study investigated the distribution and association patterns of Al-tolerant microorganisms across continental paddy fields with a soil pH range of 3.6 to 8.7. The results showed that soil pH filters exchangeable Al3+ content, diversity, and potential associations of Al-tolerant microbial community. The influential taxa in community network play an important role in Al tolerance and have potential applications in mitigating Al toxicity and promoting crop growth in acidic soils.
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13
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Hu Y, Jiang H, Chen Y, Wang Z, Yan Y, Sun P, Lu X. Nitrogen addition altered the microbial functional potentials of carbon and nitrogen transformation in alpine steppe soils on the Tibetan Plateau. Glob Ecol Conserv 2021. [DOI: 10.1016/j.gecco.2021.e01937] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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14
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Liu Y, Patko D, Engelhardt I, George TS, Stanley-Wall NR, Ladmiral V, Ameduri B, Daniell TJ, Holden N, MacDonald MP, Dupuy LX. Plant-environment microscopy tracks interactions of Bacillus subtilis with plant roots across the entire rhizosphere. Proc Natl Acad Sci U S A 2021; 118:e2109176118. [PMID: 34819371 PMCID: PMC8640753 DOI: 10.1073/pnas.2109176118] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/05/2021] [Indexed: 11/18/2022] Open
Abstract
Our understanding of plant-microbe interactions in soil is limited by the difficulty of observing processes at the microscopic scale throughout plants' large volume of influence. Here, we present the development of three-dimensional live microscopy for resolving plant-microbe interactions across the environment of an entire seedling growing in a transparent soil in tailor-made mesocosms, maintaining physical conditions for the culture of both plants and microorganisms. A tailor-made, dual-illumination light sheet system acquired photons scattered from the plant while fluorescence emissions were simultaneously captured from transparent soil particles and labeled microorganisms, allowing the generation of quantitative data on samples ∼3,600 mm3 in size, with as good as 5 µm resolution at a rate of up to one scan every 30 min. The system tracked the movement of Bacillus subtilis populations in the rhizosphere of lettuce plants in real time, revealing previously unseen patterns of activity. Motile bacteria favored small pore spaces over the surface of soil particles, colonizing the root in a pulsatile manner. Migrations appeared to be directed toward the root cap, the point of "first contact," before the subsequent colonization of mature epidermis cells. Our findings show that microscopes dedicated to live environmental studies present an invaluable tool to understand plant-microbe interactions.
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Affiliation(s)
- Yangminghao Liu
- School of Science and Engineering, University of Dundee, Dundee DD1 4HN, United Kingdom
| | - Daniel Patko
- Ecological Sciences, The James Hutton Institute, Dundee DD2 5DA, United Kingdom
- Department of Conservation of Natural Resources, Neiker, Derio 48160, Spain
| | - Ilonka Engelhardt
- Ecological Sciences, The James Hutton Institute, Dundee DD2 5DA, United Kingdom
- Department of Conservation of Natural Resources, Neiker, Derio 48160, Spain
| | - Timothy S George
- Ecological Sciences, The James Hutton Institute, Dundee DD2 5DA, United Kingdom
| | | | - Vincent Ladmiral
- Institut Charles Gerhardt de Montpellier, Université de Montpellier, CNRS, ENSCM, Montpellier 34090, France
| | - Bruno Ameduri
- Institut Charles Gerhardt de Montpellier, Université de Montpellier, CNRS, ENSCM, Montpellier 34090, France
| | - Tim J Daniell
- Plants, Photosynthesis and Soil, School of Biosciences, The University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Nicola Holden
- Northern Faculty, Scotland's Rural College, Aberdeen AB21 9YA, United Kingdom
| | - Michael P MacDonald
- School of Science and Engineering, University of Dundee, Dundee DD1 4HN, United Kingdom;
| | - Lionel X Dupuy
- Ecological Sciences, The James Hutton Institute, Dundee DD2 5DA, United Kingdom;
- Department of Conservation of Natural Resources, Neiker, Derio 48160, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao 48009, Spain
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15
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Zhang C, Jiao S, Shu D, Wei G. Inter-phylum negative interactions affect soil bacterial community dynamics and functions during soybean development under long-term nitrogen fertilization. STRESS BIOLOGY 2021; 1:15. [PMID: 37676329 PMCID: PMC10441860 DOI: 10.1007/s44154-021-00015-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/14/2021] [Indexed: 09/08/2023]
Abstract
Understanding interspecies interactions is essential to predict the response of microbial communities to exogenous perturbation. Herein, rhizospheric and bulk soils were collected from five developmental stages of soybean, which grew in soils receiving 16-year nitrogen inputs. Bacterial communities and functional profiles were examined using high-throughput sequencing and quantitative PCR, respectively. The objective of this study was to identify the key bacterial interactions that influenced community dynamics and functions. We found that the stages of soybean development outcompeted nitrogen fertilization management in shaping bacterial community structure, while fertilization treatments significantly shaped the abundance distribution of nitrogen functional genes. Temporal variations in bacterial abundances increased in bulk soils, especially at the stage of soybean branching, which helps to infer underlying negative interspecies interactions. Members of Cyanobacteria and Actinobacteria actively engaged in inter-phylum negative interactions in bulk soils and soybean rhizosphere, respectively. Furthermore, the negative interactions between nitrogen-fixing functional groups and the reduction of nifH gene abundance were coupled during soybean development, which may help to explain the linkages between population dynamics and functions. Overall, these findings highlight the importance of inter-phylum negative interactions in shaping the correlation patterns of bacterial communities and in determining soil functional potential.
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Affiliation(s)
- Chunfang Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Shuo Jiao
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Duntao Shu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, China.
| | - Gehong Wei
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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16
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Yang Y. Emerging Patterns of Microbial Functional Traits. Trends Microbiol 2021; 29:874-882. [PMID: 34030967 DOI: 10.1016/j.tim.2021.04.004] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 04/21/2021] [Accepted: 04/22/2021] [Indexed: 01/03/2023]
Abstract
Functional traits are measurable characteristics that affect an organism's fitness under certain environmental conditions. The use of functional traits in microbial ecology holds great promise for improving our ability to develop biogeochemical models and predict ecosystem responses to global changes. Notably, functional traits could be decoupled from taxonomic relatedness, owing to horizontal gene transfer among microorganisms and adaptive evolution. In recent years, our knowledge about microbial functional traits has been substantially enhanced, thereby revealing the multitude of ecological processes in driving community assembly and dynamics. Here, I summarize the emerging patterns of how microbial functional traits respond to changing environments, which considerably differ from better-studied microbial taxonomy. I use niche and neutral theories to explain microbial functional traits. Finally, I highlight future challenges to analyze, elucidate, and utilize functional traits in microbial ecology.
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Affiliation(s)
- Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China.
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17
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Li Y, Ge Y, Wang J, Shen C, Wang J, Liu YJ. Functional redundancy and specific taxa modulate the contribution of prokaryotic diversity and composition to multifunctionality. Mol Ecol 2021; 30:2915-2930. [PMID: 33905157 DOI: 10.1111/mec.15935] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 04/20/2021] [Accepted: 04/21/2021] [Indexed: 12/29/2022]
Abstract
Observational and experimental evidence has revealed the functional importance of microbial diversity. However, the effects of microbial diversity loss on ecosystem functions are not consistent across studies, which are probably tempered by microbial functional redundancy, specific taxa and functions evaluated. Here we conducted diversity manipulation experiments in two independent soils with distinct prokaryotic communities, and investigated how the initial community traits (e.g., distinct functional redundancy and taxonomic composition) modulate the contribution of prokaryotic diversity loss and composition shift to eight ecosystem functions related to soil nutrient cycling. We found that diversity loss impaired three functions (potential nitrification rate, N2 -fixation activity and phosphatase) and multifunctionality only in the communities with low functional redundancy, but all examined functions were unaffected in the communities with high functional redundancy. All significantly affected functions belonged to specialized functions, while the broad function (soil basal respiration) was unaffected. Moreover, prokaryotic composition explained more functional variation than diversity, which was ascribed to the crucial role of specific taxa that influence particular functions. Taken together, this study provides empirical evidence for identifying the mechanism underlying the ecosystem response to changes in microbial community, with implications for improving the prediction of ecosystem process models and managing microbial communities to promote ecosystem services.
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Affiliation(s)
- Yan Li
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yuan Ge
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jichen Wang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Congcong Shen
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jianlei Wang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Yong-Jun Liu
- Key Laboratory of Pollinating Insect Biology, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
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18
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Microbial metabolism and necromass mediated fertilization effect on soil organic carbon after long-term community incubation in different climates. ISME JOURNAL 2021; 15:2561-2573. [PMID: 33712697 DOI: 10.1038/s41396-021-00950-w] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 02/23/2021] [Indexed: 11/08/2022]
Abstract
Understanding the effects of changing climate and long-term human activities on soil organic carbon (SOC) and the mediating roles of microorganisms is critical to maintain soil C stability in agricultural ecosystem. Here, we took samples from a long-term soil transplantation experiment, in which large transects of Mollisol soil in a cold temperate region were translocated to warm temperate and mid-subtropical regions to simulate different climate conditions, with a fertilization treatment on top. This study aimed to understand fertilization effect on SOC and the role of soil microorganisms featured after long-term community incubation in warm climates. After 12 years of soil transplantation, fertilization led to less reduction of SOC, in which aromatic C increased and the consumption of O-alkyl C and carbonyl C decreased. Soil live microbes were analyzed using propidium monoazide to remove DNAs from dead cells, and their network modulization explained 60.4% of variations in soil labile C. Single-cell Raman spectroscopy combined with D2O isotope labeling indicated a higher metabolic activity of live microbes to use easily degradable C after soil transplantation. Compared with non-fertilization, there was a significant decrease in soil α- and β-glucosidase and delay on microbial growth with fertilization in warmer climate. Moreover, fertilization significantly increased microbial necromass as indicated by amino sugar content, and its contribution to soil resistant C reached 22.3%. This study evidentially highlights the substantial contribution of soil microbial metabolism and necromass to refractory C of SOC with addition of nutrients in the long-term.
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19
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Gao Y, Ding J, Yuan M, Chiariello N, Docherty K, Field C, Gao Q, Gu B, Gutknecht J, Hungate BA, Le Roux X, Niboyet A, Qi Q, Shi Z, Zhou J, Yang Y. Long-term warming in a Mediterranean-type grassland affects soil bacterial functional potential but not bacterial taxonomic composition. NPJ Biofilms Microbiomes 2021; 7:17. [PMID: 33558544 PMCID: PMC7870951 DOI: 10.1038/s41522-021-00187-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 01/07/2021] [Indexed: 12/12/2022] Open
Abstract
Climate warming is known to impact ecosystem composition and functioning. However, it remains largely unclear how soil microbial communities respond to long-term, moderate warming. In this study, we used Illumina sequencing and microarrays (GeoChip 5.0) to analyze taxonomic and functional gene compositions of the soil microbial community after 14 years of warming (at 0.8–1.0 °C for 10 years and then 1.5–2.0 °C for 4 years) in a Californian grassland. Long-term warming had no detectable effect on the taxonomic composition of soil bacterial community, nor on any plant or abiotic soil variables. In contrast, functional gene compositions differed between warming and control for bacterial, archaeal, and fungal communities. Functional genes associated with labile carbon (C) degradation increased in relative abundance in the warming treatment, whereas those associated with recalcitrant C degradation decreased. A number of functional genes associated with nitrogen (N) cycling (e.g., denitrifying genes encoding nitrate-, nitrite-, and nitrous oxidereductases) decreased, whereas nifH gene encoding nitrogenase increased in the warming treatment. These results suggest that microbial functional potentials are more sensitive to long-term moderate warming than the taxonomic composition of microbial community.
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Affiliation(s)
- Ying Gao
- Institute of Desertification Studies, Chinese Academy of Forestry, Beijing, China.,State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Junjun Ding
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China.,Key Laboratory of Dryland Agriculture, Ministry of Agriculture of the People's Republic of China, Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Mengting Yuan
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Nona Chiariello
- Department of Global Ecology, Carnegie Institution for Science, Stanford, CA, USA
| | - Kathryn Docherty
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI, USA
| | - Chris Field
- Department of Global Ecology, Carnegie Institution for Science, Stanford, CA, USA
| | - Qun Gao
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Baohua Gu
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Jessica Gutknecht
- Department of Soil Ecology, Helmholtz Centre for Environmental Research - UFZ, Halle, Germany.,Department of Soil, Water, and Climate, University of Minnesota, Twin Cities, Saint Paul, MN, USA
| | - Bruce A Hungate
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA.,Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Xavier Le Roux
- Mirobial Ecology Centre LEM, INRA, CNRS, University of Lyon, University Lyon 1, UMR INRA 1418, Villeurbanne, France
| | - Audrey Niboyet
- Institut d'Ecologie et des Sciences de l'Environnement de Paris (Sorbonne Université, CNRS, INRA, IRD, Université Paris Diderot, UPEC), Paris, France.,AgroParisTech, Paris, France
| | - Qi Qi
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Zhou Shi
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Jizhong Zhou
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China.,Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA.,Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China.
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20
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Li X, Song Y, Bian Y, Gu C, Yang X, Wang F, Jiang X. Insights into the mechanisms underlying efficient Rhizodegradation of PAHs in biochar-amended soil: From microbial communities to soil metabolomics. ENVIRONMENT INTERNATIONAL 2020; 144:105995. [PMID: 32758715 DOI: 10.1016/j.envint.2020.105995] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 06/08/2020] [Accepted: 07/16/2020] [Indexed: 05/15/2023]
Abstract
The combined effects of biochar amendment and the rhizosphere on the soil metabolic microbiome during the remediation of polycyclic aromatic hydrocarbon (PAH)-contaminated soil remain unknown. In this study, we attempted to characterize a PAH degradation network by coupling the direct PAH degradation with soil carbon cycling. From microbial community structure and functions to metabolic pathways, we revealed the modulation strategies by which biochar and the rhizosphere benefited PAH degradation in soil. Firstly, some PAH degraders were enriched by biochar and the rhizosphere, and their combination promoted the cooperation among these PAH degraders. Simultaneously, under the combined effects of biochar and the rhizosphere, the functional genes participating in upstream PAH degradation were greatly upregulated. Secondly, there were strong co-occurrences between soil microbial community members and metabolites, in particular, some PAH degraders and the metabolites, such as PAH degradation products or common carbon resources, were highlighted in the networks. It shows that the overall downstream carbon metabolism of PAH degradation was also greatly upregulated by the combined effects of biochar and plant roots, showing good survival of the soil microbiome and contributing to PAH biodegradation. Taken together, both soil carbon metabolism and direct contaminant biodegradation are likely to be modulated by the combined effects of biochar and plant roots, jointly benefitting to PAH degradation by soil microbiome. Our study is the first to link PAH degradation with native carbon metabolism by coupling sequencing and soil metabolomics technology, providing new insights into a systematic understanding of PAH degradation by indigenous soil microbiome and their networks.
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Affiliation(s)
- Xiaona Li
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Nanjing 210008, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Yang Song
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Nanjing 210008, China; University of the Chinese Academy of Sciences, Beijing 100049, China.
| | - Yongrong Bian
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Nanjing 210008, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Chenggang Gu
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Nanjing 210008, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Xinglun Yang
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Nanjing 210008, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Fang Wang
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Nanjing 210008, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Xin Jiang
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Nanjing 210008, China; University of the Chinese Academy of Sciences, Beijing 100049, China
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21
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Lohmann P, Benk S, Gleixner G, Potthast K, Michalzik B, Jehmlich N, von Bergen M. Seasonal Patterns of Dominant Microbes Involved in Central Nutrient Cycles in the Subsurface. Microorganisms 2020; 8:E1694. [PMID: 33143231 PMCID: PMC7716230 DOI: 10.3390/microorganisms8111694] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/23/2020] [Accepted: 10/29/2020] [Indexed: 01/08/2023] Open
Abstract
Microbial communities play a key role for central biogeochemical cycles in the subsurface. Little is known about whether short-term seasonal drought and rewetting events influence the dominant microbes involved in C- and N-cycles. Here, we applied metaproteomics at different subsurface sites in winter, summer and autumn from surface litter layer, seepage water at increasing subsoil depths and remote located groundwater from two wells within the Hainich Critical Zone Exploratory, Germany. We observed changes in the dominance of microbial families at subsurface sampling sites with increasing distances, i.e., Microcoleaceae dominated in topsoil seepage, while Candidatus Brocadiaceae dominated at deeper and more distant groundwater wells. Nitrifying bacteria showed a shift in dominance from drought to rewetting events from summer by Nitrosomandaceae to autumn by Candidatus Brocadiaceae. We further observed that the reductive pentose phosphate pathway was a prominent CO2-fixation strategy, dominated by Woeseiaceae in wet early winter, which decreased under drought conditions and changed to a dominance of Sphingobacteriaceae under rewetting conditions. This study shows that increasing subsurface sites and rewetting event after drought alter the dominances of key subsurface microbes. This helps to predict the consequences of annual seasonal dynamics on the nutrient cycling microbes that contribute to ecosystem functioning.
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Affiliation(s)
- Patrick Lohmann
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research GmbH—UFZ, 04318 Leipzig, Germany; (P.L.); (N.J.)
| | - Simon Benk
- Department of Molecular Biogeochemistry, Max-Planck-Institute for Biogeochemistry, 07745 Jena, Germany; (S.B.); (G.G.)
| | - Gerd Gleixner
- Department of Molecular Biogeochemistry, Max-Planck-Institute for Biogeochemistry, 07745 Jena, Germany; (S.B.); (G.G.)
| | - Karin Potthast
- Department of Soil Science, Friedrich Schiller University, 07743 Jena, Germany; (K.P.); (B.M.)
| | - Beate Michalzik
- Department of Soil Science, Friedrich Schiller University, 07743 Jena, Germany; (K.P.); (B.M.)
- German Center for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
| | - Nico Jehmlich
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research GmbH—UFZ, 04318 Leipzig, Germany; (P.L.); (N.J.)
| | - Martin von Bergen
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research GmbH—UFZ, 04318 Leipzig, Germany; (P.L.); (N.J.)
- Institute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, University of Leipzig, 04103 Leipzig, Germany
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22
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Rodriguez R, Durán P. Natural Holobiome Engineering by Using Native Extreme Microbiome to Counteract the Climate Change Effects. Front Bioeng Biotechnol 2020; 8:568. [PMID: 32582678 PMCID: PMC7287022 DOI: 10.3389/fbioe.2020.00568] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 05/11/2020] [Indexed: 12/14/2022] Open
Abstract
In the current scenario of climate change, the future of agriculture is uncertain. Climate change and climate-related disasters have a direct impact on biotic and abiotic factors that govern agroecosystems compromising the global food security. In the last decade, the advances in high throughput sequencing techniques have significantly improved our understanding about the composition, function and dynamics of plant microbiome. However, despite the microbiome have been proposed as a new platform for the next green revolution, our knowledge about the mechanisms that govern microbe-microbe and microbe-plant interactions are incipient. Currently, the adaptation of plants to environmental changes not only suggests that the plants can adapt or migrate, but also can interact with their surrounding microbial communities to alleviate different stresses by natural microbiome selection of specialized strains, phenomenon recently called "Cry for Help". From this way, plants have been co-evolved with their microbiota adapting to local environmental conditions to ensuring the survival of the entire holobiome to improve plant fitness. Thus, the strong selective pressure of native extreme microbiomes could represent a remarkable microbial niche of plant stress-amelioration to counteract the negative effect of climate change in food crops. Currently, the microbiome engineering has recently emerged as an alternative to modify and promote positive interactions between microorganisms and plants to improve plant fitness. In the present review, we discuss the possible use of extreme microbiome to alleviate different stresses in crop plants under the current scenario of climate change.
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Affiliation(s)
- Rodrigo Rodriguez
- Biocontrol Research Laboratory, Universidad de La Frontera, Temuco, Chile
| | - Paola Durán
- Biocontrol Research Laboratory, Universidad de La Frontera, Temuco, Chile
- Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco, Chile
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23
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Soil bacterial diversity correlates with precipitation and soil pH in long-term maize cropping systems. Sci Rep 2020; 10:6012. [PMID: 32265458 PMCID: PMC7138807 DOI: 10.1038/s41598-020-62919-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 03/09/2020] [Indexed: 11/25/2022] Open
Abstract
Unraveling the key drivers of bacterial community assembly in agricultural soils is pivotal for soil nutrient management and crop productivity. Presently, the drivers of microbial community structure remain unexplored in maize cropping systems under complex and variable environmental scenarios across large spatial scales. In this study, we conducted high-throughput 16S rRNA gene sequencing and network analysis to identify the major environmental factors driving bacterial community diversity and co-occurrence patterns in 21 maize field soils across China. The results show that mean annual precipitation and soil pH are the major environmental factors that shape soil bacterial communities in maize soils. The similarities of bacterial communities significantly decreased with increasing geographic distance between different sites. The differences in spatial turnover rates across bacterial phyla indicate the distinct dispersal capabilities of bacterial groups, and some abundant phyla exhibited high dispersal capabilities. Aeromicrobium, Friedmanniella, Saccharothrix, Lamia, Rhodococcus, Skermanella, and Pedobacter were identified as keystone taxa. Based on the node-level and network-level topological features, members of the core microbiome were more frequently found in the center of the ecosystem network compared with other taxa. This study highlights the major environmental factors driving bacterial community assembly in agro-ecosystems and the central ecological role of the core microbiome in maintaining the web of complex bacterial interactions.
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Soil Microbial Community Assembly and Interactions Are Constrained by Nitrogen and Phosphorus in Broadleaf Forests of Southern China. FORESTS 2020. [DOI: 10.3390/f11030285] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Subtropical and tropical broadleaf forests play important roles in conserving biodiversity and regulating global carbon cycle. Nonetheless, knowledge about soil microbial diversity, community composition, turnover and microbial functional structure in sub- and tropical broadleaf forests is scarce. In this study, high-throughput sequencing was used to profile soil microbial community composition, and a micro-array GeoChip 5.0 was used to profile microbial functional gene distribution in four sub- and tropical broadleaf forests (HS, MES, HP and JFL) in southern China. The results showed that soil microbial community compositions differed dramatically among all of four forests. Soil microbial diversities in JFL were the lowest (5.81–5.99) and significantly different from those in the other three forests (6.22–6.39). Furthermore, microbial functional gene interactions were the most complex and closest, likely in reflection to stress associated with the lowest nitrogen and phosphorus contents in JFL. In support of the importance of environmental selection, we found selection (78–96%) dominated microbial community assembly, which was verified by partial Mantel tests showing significant correlations between soil phosphorus and nitrogen content and microbial community composition. Taken together, these results indicate that nitrogen and phosphorus are pivotal in shaping soil microbial communities in sub- and tropical broadleaf forests in southern China. Changes in soil nitrogen and phosphorus, in response to plant growth and decomposition, will therefore have significant changes in both microbial community assembly and interaction.
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25
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Liang Y, Xiao X, Nuccio EE, Yuan M, Zhang N, Xue K, Cohan FM, Zhou J, Sun B. Differentiation strategies of soil rare and abundant microbial taxa in response to changing climatic regimes. Environ Microbiol 2020; 22:1327-1340. [PMID: 32067386 DOI: 10.1111/1462-2920.14945] [Citation(s) in RCA: 122] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 02/10/2020] [Accepted: 02/14/2020] [Indexed: 01/14/2023]
Abstract
Despite the important roles of soil microbes, especially the most diverse rare taxa in maintaining community diversity and multifunctionality, how different climate regimes alter the stability and functions of the rare microbial biosphere remains unknown. We reciprocally transplanted field soils across a latitudinal gradient to simulate climate change and sampled the soils annually after harvesting the maize over the following 6 years (from 2005 to 2011). By sequencing microbial 16S ribosomal RNA gene amplicons, we found that changing climate regimes significantly altered the composition and dynamics of soil microbial communities. A continuous succession of the rare and abundant communities was observed. Rare microbial communities were more stable under changing climatic regimes, with lower variations in temporal dynamics, and higher stability and constancy of diversity. More nitrogen cycling genes were detected in the rare members than in the abundant members, including amoA, napA, nifH, nirK, nirS, norB and nrfA. Random forest analysis and receiver operating characteristics analysis showed that rare taxa may act as potential contributors to maize yield under changing climatics. The study indicates that the taxonomically and functionally diverse rare biosphere has the potential to increase functional redundancy and enhance the ability of soil communities to counteract environmental disturbances. With ongoing global climate change, exploring the succession process and functional changes of rare taxa may be important in elucidating the ecosystem stability and multifunctionality that are mediated by microbial communities.
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Affiliation(s)
- Yuting Liang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Xian Xiao
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Erin E Nuccio
- Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA
| | - Mengting Yuan
- Department of Environmental Science Policy and Management, University of California, Berkeley, CA, 94720, USA
| | - Na Zhang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China.,University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Kai Xue
- University of the Chinese Academy of Sciences, Beijing, 100049, China.,Institute for Environmental Genomics, Department of Microbiology and Plant Biology, and School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, 73019, USA
| | - Frederick M Cohan
- Department of Biology, Wesleyan University, Middletown, CT, 06459-0170, USA
| | - Jizhong Zhou
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, and School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, 73019, USA.,Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, 94270, USA
| | - Bo Sun
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
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26
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Bin Jang H, Bolduc B, Zablocki O, Kuhn JH, Roux S, Adriaenssens EM, Brister JR, Kropinski AM, Krupovic M, Lavigne R, Turner D, Sullivan MB. Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks. Nat Biotechnol 2019; 37:632-639. [PMID: 31061483 DOI: 10.1038/s41587-019-0100-8] [Citation(s) in RCA: 524] [Impact Index Per Article: 87.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 03/11/2019] [Indexed: 01/03/2023]
Abstract
Microbiomes from every environment contain a myriad of uncultivated archaeal and bacterial viruses, but studying these viruses is hampered by the lack of a universal, scalable taxonomic framework. We present vConTACT v.2.0, a network-based application utilizing whole genome gene-sharing profiles for virus taxonomy that integrates distance-based hierarchical clustering and confidence scores for all taxonomic predictions. We report near-identical (96%) replication of existing genus-level viral taxonomy assignments from the International Committee on Taxonomy of Viruses for National Center for Biotechnology Information virus RefSeq. Application of vConTACT v.2.0 to 1,364 previously unclassified viruses deposited in virus RefSeq as reference genomes produced automatic, high-confidence genus assignments for 820 of the 1,364. We applied vConTACT v.2.0 to analyze 15,280 Global Ocean Virome genome fragments and were able to provide taxonomic assignments for 31% of these data, which shows that our algorithm is scalable to very large metagenomic datasets. Our taxonomy tool can be automated and applied to metagenomes from any environment for virus classification.
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Affiliation(s)
- Ho Bin Jang
- Department of Microbiology, Ohio State University, Columbus, OH, USA
| | - Benjamin Bolduc
- Department of Microbiology, Ohio State University, Columbus, OH, USA
| | - Olivier Zablocki
- Department of Microbiology, Ohio State University, Columbus, OH, USA
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD, USA
| | - Simon Roux
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Evelien M Adriaenssens
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK.,Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - J Rodney Brister
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Andrew M Kropinski
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada.,Department of Food Science, University of Guelph, Guelph, Ontario, Canada
| | - Mart Krupovic
- Unité Biologie Moléculaire du Gène chez les Extrêmophiles, Institut Pasteur, Paris, France
| | - Rob Lavigne
- Laboratory of Gene Technology, Department of Biosystems, Faculty of BioScience Engineering, KU Leuven, Leuven, Belgium
| | - Dann Turner
- Centre for Research in Biosciences, Department of Applied Sciences, Faculty of Health and Applied Sciences, University of the West of England, Bristol, UK
| | - Matthew B Sullivan
- Department of Microbiology, Ohio State University, Columbus, OH, USA. .,Department of Civil, Environmental and Geodetic Engineering, Ohio State University, Columbus, OH, USA.
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27
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Zhao M, Sun B, Wu L, Wang F, Wen C, Wang M, Liang Y, Hale L, Zhou J, Yang Y. Dissimilar responses of fungal and bacterial communities to soil transplantation simulating abrupt climate changes. Mol Ecol 2019; 28:1842-1856. [DOI: 10.1111/mec.15053] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 02/02/2019] [Accepted: 02/11/2019] [Indexed: 12/12/2022]
Affiliation(s)
- Mengxin Zhao
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection Chinese Academy of Agricultural Sciences Beijing China
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment Tsinghua University Beijing China
| | - Bo Sun
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science Chinese Academy of Sciences Nanjing China
| | - Linwei Wu
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment Tsinghua University Beijing China
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, and School of Civil Engineering and Environmental Sciences University of Oklahoma Norman Oklahoma
| | - Feng Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science Chinese Academy of Sciences Nanjing China
- Ningbo Academy of Agricultural Sciences Ningbo China
| | - Chongqing Wen
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, and School of Civil Engineering and Environmental Sciences University of Oklahoma Norman Oklahoma
- Fisheries College Guangdong Ocean University Zhanjiang China
| | - Mengmeng Wang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment Tsinghua University Beijing China
| | - Yuting Liang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science Chinese Academy of Sciences Nanjing China
| | - Lauren Hale
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, and School of Civil Engineering and Environmental Sciences University of Oklahoma Norman Oklahoma
| | - Jizhong Zhou
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment Tsinghua University Beijing China
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, and School of Civil Engineering and Environmental Sciences University of Oklahoma Norman Oklahoma
- Earth and Environmental Sciences Lawrence Berkeley National Laboratory Berkeley California
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment Tsinghua University Beijing China
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28
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Wang PH, Correia K, Ho HC, Venayak N, Nemr K, Flick R, Mahadevan R, Edwards EA. An interspecies malate-pyruvate shuttle reconciles redox imbalance in an anaerobic microbial community. ISME JOURNAL 2019; 13:1042-1055. [PMID: 30607026 DOI: 10.1038/s41396-018-0333-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 11/26/2018] [Accepted: 11/29/2018] [Indexed: 11/09/2022]
Abstract
Microbes in ecosystems often develop coordinated metabolic interactions. Therefore, understanding metabolic interdependencies between microbes is critical to deciphering ecosystem function. In this study, we sought to deconstruct metabolic interdependencies in organohalide-respiring consortium ACT-3 containing Dehalobacter restrictus using a combination of metabolic modeling and experimental validation. D. restrictus possesses a complete set of genes for amino acid biosynthesis yet when grown in isolation requires amino acid supplementation. We reconciled this discrepancy using flux balance analysis considering cofactor availability, enzyme promiscuity, and shared protein expression patterns for several D. restrictus strains. Experimentally, 13C incorporation assays, growth assays, and metabolite analysis of D. restrictus strain PER-K23 cultures were performed to validate the model predictions. The model resolved that the amino acid dependency of D. restrictus resulted from restricted NADPH regeneration and predicted that malate supplementation would replenish intracellular NADPH. Interestingly, we observed unexpected export of pyruvate and glutamate in parallel to malate consumption in strain PER-K23 cultures. Further experimental analysis using the ACT-3 transfer cultures suggested the occurrence of an interspecies malate-pyruvate shuttle reconciling a redox imbalance, reminiscent of the mitochondrial malate shunt pathway in eukaryotic cells. Altogether, this study suggests that redox imbalance and metabolic complementarity are important driving forces for metabolite exchange in anaerobic microbial communities.
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Affiliation(s)
- Po-Hsiang Wang
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, M5S 3E5, Canada
| | - Kevin Correia
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, M5S 3E5, Canada
| | - Han-Chen Ho
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, M5S 3E5, Canada
| | - Naveen Venayak
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, M5S 3E5, Canada
| | - Kayla Nemr
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, M5S 3E5, Canada
| | - Robert Flick
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, M5S 3E5, Canada
| | - Radhakrishnan Mahadevan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, M5S 3E5, Canada.
| | - Elizabeth A Edwards
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, M5S 3E5, Canada.
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29
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Xu H, Lin C, Chen W, Shen Z, Liu Z, Chen T, Wang Y, Li Y, Lu C, Luo J. Effects of pipe material on nitrogen transformation, microbial communities and functional genes in raw water transportation. WATER RESEARCH 2018; 143:188-197. [PMID: 29957407 DOI: 10.1016/j.watres.2018.06.040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 06/15/2018] [Accepted: 06/17/2018] [Indexed: 06/08/2023]
Abstract
Raw water transportation pipelines are vital in an urban water supply system for transporting raw water to drinking water treatment plants. This study investigated the effects of pipe material on nitrogen transformation, microbial communities and characteristics of related function genes in paint-lined steel pipe (PLSP) and cement-lined steel pipe (CLSP) raw water model systems. We established quantitative relationships between specific functional genes and change rates of nitrogen pollutants, which were verified by field investigation on nitrogen pollutant transformations in real raw water transportation systems. The results showed that the CLSP produced higher ammonia nitrogen (NH4+-N) transformation rates and higher effluent concentrations of nitrate nitrogen (NO3--N) and dissolved organic nitrogen (DON) than the PLSP. Both pipes achieved high and stable nitrite nitrogen (NO2--N) and low total nitrogen (TN) removal efficiency. Nitrification was found to be the dominant process in both model systems, especially in the CLSP. Characteristics of microbial communities and nitrogen functional genes, which were analysed by high-throughput pyrosequencing and quantitative polymerase chain reaction (qPCR), respectively, varied between the two pipe systems. Nitrogen transformation pathways, identified by path analysis, were also different between the PLSP and CLSP due to different microbial community characteristics and synergistic effects of nitrogen functional genes. In the CLSP, (NH4+-N→NO2--N) with part denitrification, was the primary transformation pathway of ammonia nitrogen (NH4+-N), while only ammonia oxidization contributed to NH4+-N transformation in the PLSP. (NO2--N→NO3--N) was the main pathway involved in NO2--N transformation and NO3--N accumulation. The TN removal showed complex relationships with nitrification, denitrification and nitrogen fixation processes. These findings provided molecular-level insights into nitrogen pollutant transformations during the transportation of raw water through different types of pipes and technical support for the selection of raw water pipe materials. In our study area, the Taihu basin, China, PLSP was better than CLSP for distributing raw water in a short transportation distance, due to the lower effluent concentrations of DON and NO3--N and less abundance of microorganisms.
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Affiliation(s)
- Hang Xu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, No.1 Xikang Road, Nanjing, 210098, China.
| | - Chenshuo Lin
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, No.1 Xikang Road, Nanjing, 210098, China
| | - Wei Chen
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, No.1 Xikang Road, Nanjing, 210098, China
| | - Zhen Shen
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, No.1 Xikang Road, Nanjing, 210098, China
| | - Zhigang Liu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, No.1 Xikang Road, Nanjing, 210098, China; Ningbo Water Supply Co., Ltd, No.348 Xinhe Road, Ningbo, 315041, China
| | - Taoyuan Chen
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, No.1 Xikang Road, Nanjing, 210098, China
| | - Yueting Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, No.1 Xikang Road, Nanjing, 210098, China
| | - Yang Li
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, No.1 Xikang Road, Nanjing, 210098, China
| | - Chunhui Lu
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, China
| | - Jian Luo
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA 30332-0355, USA
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30
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Albright MBN, Johansen R, Lopez D, Gallegos-Graves LV, Steven B, Kuske CR, Dunbar J. Short-Term Transcriptional Response of Microbial Communities to Nitrogen Fertilization in a Pine Forest Soil. Appl Environ Microbiol 2018; 84:e00598-18. [PMID: 29802185 PMCID: PMC6052259 DOI: 10.1128/aem.00598-18] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 05/15/2018] [Indexed: 01/05/2023] Open
Abstract
Numerous studies have examined the long-term effect of experimental nitrogen (N) deposition in terrestrial ecosystems; however, N-specific mechanistic markers are difficult to disentangle from responses to other environmental changes. The strongest picture of N-responsive mechanistic markers is likely to arise from measurements over a short (hours to days) time scale immediately after inorganic N deposition. Therefore, we assessed the short-term (3-day) transcriptional response of microbial communities in two soil strata from a pine forest to a high dose of N fertilization (ca. 1 mg/g of soil material) in laboratory microcosms. We hypothesized that N fertilization would repress the expression of fungal and bacterial genes linked to N mining from plant litter. However, despite N suppression of microbial respiration, the most pronounced differences in functional gene expression were between strata rather than in response to the N addition. Overall, ∼4% of metabolic genes changed in expression with N addition, while three times as many (∼12%) were significantly different across the different soil strata in the microcosms. In particular, we found little evidence of N changing expression levels of metabolic genes associated with complex carbohydrate degradation (CAZymes) or inorganic N utilization. This suggests that direct N repression of microbial functional gene expression is not the principle mechanism for reduced soil respiration immediately after N deposition. Instead, changes in expression with N addition occurred primarily in general cell maintenance areas, for example, in ribosome-related transcripts. Transcriptional changes in functional gene abundance in response to N addition observed in longer-term field studies likely result from changes in microbial composition.IMPORTANCE Ecosystems are receiving increased nitrogen (N) from anthropogenic sources, including fertilizers and emissions from factories and automobiles. High levels of N change ecosystem functioning. For example, high inorganic N decreases the microbial decomposition of plant litter, potentially reducing nutrient recycling for plant growth. Understanding how N regulates microbial decomposition can improve the prediction of ecosystem functioning over extended time scales. We found little support for the conventional view that high N supply represses the expression of genes involved in decomposition or alters the expression of bacterial genes for inorganic N cycling. Instead, our study of pine forest soil 3 days after N addition showed changes in microbial gene expression related to cell maintenance and stress response. This highlights the challenge of establishing predictive links between microbial gene expression levels and measures of ecosystem function.
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Affiliation(s)
| | - Renee Johansen
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - Deanna Lopez
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | | | - Blaire Steven
- Department of Environmental Sciences, Connecticut Agricultural Experiment Station, New Haven, Connecticut, USA
| | - Cheryl R Kuske
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - John Dunbar
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
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31
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Wang M, Ding J, Sun B, Zhang J, Wyckoff KN, Yue H, Zhao M, Liang Y, Wang X, Wen C, Zhou J, Yang Y. Microbial responses to inorganic nutrient amendment overridden by warming: Consequences on soil carbon stability. Environ Microbiol 2018; 20:2509-2522. [PMID: 30051561 DOI: 10.1111/1462-2920.14239] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2017] [Revised: 04/03/2018] [Accepted: 04/06/2018] [Indexed: 11/26/2022]
Abstract
Eutrophication and climate warming, induced by anthropogenic activities, are simultaneously occurring worldwide and jointly affecting soil carbon stability. Therefore, it is of great interest to examine whether and how they interactively affect soil microbial community, a major soil carbon driver. Here, we showed that climate warming, simulated by southward transferring Mollisol soil in agricultural ecosystems from the cold temperate climate zone (N) to warm temperate climate (C) and subtropical climate zone (S), decreased soil organic matter (SOM) by 6%-12%. In contrast, amendment with nitrogen, phosphorus and potassium enhanced plant biomass by 97% and SOM by 6% at the N site, thus stimulating copiotrophic taxa but reducing oligotrophic taxa in relative abundance. However, microbial responses to nutrient amendment were overridden by soil transfer in that nutrient amendment had little effect at the C site but increased recalcitrant carbon-degrading fungal Agaricomycetes and Microbotryomycetes taxa derived from Basidiomycota by 4-17 folds and recalcitrant carbon-degrading genes by 23%-40% at the S site, implying a possible priming effect. Consequently, SOM at the S site was not increased by nutrient amendment despite increased plant biomass by 108%. Collectively, we demonstrate that soil transfer to warmer regions overrides microbial responses to nutrient amendment and weakens soil carbon sequestration.
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Affiliation(s)
- Mengmeng Wang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Junjun Ding
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China.,Key Laboratory of Dryland Agriculture, Ministry of Agriculture, Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Bo Sun
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Junyu Zhang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Kristen N Wyckoff
- Department of Civil and Environmental Engineering, The University of Tennessee, Knoxville, TN, 37996, USA
| | - Haowei Yue
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China.,Bureau of Environmental Protection and Water Resources, 1 Hongyi Road, Futian District, Shenzhen, 518000, China
| | - Mengxin Zhao
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Yuting Liang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Xiaoyue Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Chongqing Wen
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA.,Fisheries College, Guangdong Ocean University, Zhanjiang, 524025, China
| | - Jizhong Zhou
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China.,Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA.,Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
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32
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Zou W, Wang Z, Song Q, Tang S, Peng Y. Recruitment-promoting of dormant Microcystis aeruginosa by three benthic bacterial species. HARMFUL ALGAE 2018; 77:18-28. [PMID: 30005799 DOI: 10.1016/j.hal.2018.05.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 04/27/2018] [Accepted: 05/24/2018] [Indexed: 06/08/2023]
Abstract
The frequent occurrence of Microcystis aeruginosa blooms benefit from the dormant Microcystis cells, which will be recruited from sediment into overlying water to form a dominant population and algal blooms when external environmental conditions are suitable. Previous studies have unveiled factors involved in M. aeruginosa recruitment and bloom initiation, including nutrition, illumination, temperature, and hydrodynamic force. In this study, three dominant benthic bacterial species isolated from Lake Chongtian with frequent blooms-forming were identified through next generation sequencing (NGS) techniques, and laboratory experiments were conducted on the recruitment of dormant M. aeruginosa cells via co-culture with these bacteria at 10 °C, 15 °C, 20 °C and 25 °C. The results showed that the bacterial strains in sediment proliferated quickly before recruitment of dormant M. aeruginosa cells, subsequently significantly promoted the recruitment of dormant M. aeruginosa via allelochemical (metabolite) production, lower N:P values and lower dissolved oxygen concentrations in the sediment-water interface, and enhanced photosynthesis of M. aeruginosa cells. Furthermore, dormant M. aeruginosa was recruited from sediment at 10 °C when bacterial activity was present, but not recruited when bacterial activity was absent. At 15 °C,20 °Cand 25 °C, there were no remarkable differences in the recruitment rate of dormant M. aeruginosa cells among all bacterial groups, although their recruitment rate were significantly higher than that at 10 °C.These findings suggested that, under laboratory conditions, three benthic bacteria not only had a great influence on promoting the recruitment of dormant M. aeruginosa cells under desirable temperatures, but also can spur recruitment of dormant M. aeruginosacells from sediment at lower temperature (10 °C).
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Affiliation(s)
- Wansheng Zou
- College of Bioscience and Biotechnology, Hunan Agriculture University, 1# NongdaRoad, Changsha, 410128, Hunan, China; Collaborative Innovation Center for Efficient and Health Production of Fisheries in Hunan Province, Hunan University of Arts and Science, Changde, 415000, Hunan, China.
| | - Zhi Wang
- College of Bioscience and Biotechnology, Hunan Agriculture University, 1# NongdaRoad, Changsha, 410128, Hunan, China; School of Life Science, Hunan Normal University, Changsha, 410000, Hunan, China.
| | - Qisheng Song
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA.
| | - Shaoxian Tang
- College of Bioscience and Biotechnology, Hunan Agriculture University, 1# NongdaRoad, Changsha, 410128, Hunan, China.
| | - Yuande Peng
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, Hunan, China.
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Zeng J, Shen JP, Wang JT, Hu HW, Zhang CJ, Bai R, Zhang LM, He JZ. Impacts of Projected Climate Warming and Wetting on Soil Microbial Communities in Alpine Grassland Ecosystems of the Tibetan Plateau. MICROBIAL ECOLOGY 2018; 75:1009-1023. [PMID: 29124311 DOI: 10.1007/s00248-017-1098-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 10/24/2017] [Indexed: 06/07/2023]
Abstract
Climate change is projected to have impacts on precipitation and temperature regimes in drylands of high elevation regions, with especially large effects in the Qinghai-Tibetan Plateau. However, there was limited information about how the projected climate change will impact on the soil microbial community and their activity in the region. Here, we present results from a study conducted across 72 soil samples from 24 different sites along a temperature and precipitation gradient (substituted by aridity index ranging from 0.079 to 0.89) of the Plateau, to assess how changes in aridity affect the abundance, community composition, and diversity of bacteria, ammonia-oxidizers, and denitrifers (nirK/S and nosZ genes-containing communities) as well as nitrogen (N) turnover enzyme activities. We found V-shaped or inverted V-shaped relationships between the aridity index (AI) and soil microbial parameters (gene abundance, community structures, microbial diversity, and N turnover enzyme activities) with a threshold at AI = 0.27. The increasing or decreasing rates of the microbial parameters were higher in areas with AI < 0.27 (alpine steppes) than in mesic areas with 0.27 < AI < 0.89 (alpine meadow and swamp meadow). The results indicated that the projected warming and wetting have a strong impact on soil microbial communities in the alpine steppes.
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Affiliation(s)
- Jun Zeng
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- College of Resources and Environment, University of the Chinese Academy of Sciences, Beijing, 100049, China
- Institute of Applied Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, China
| | - Ju-Pei Shen
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
- College of Resources and Environment, University of the Chinese Academy of Sciences, Beijing, 100049, China.
| | - Jun-Tao Wang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Hang-Wei Hu
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Cui-Jing Zhang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Ren Bai
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Li-Mei Zhang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- College of Resources and Environment, University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Ji-Zheng He
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
- College of Resources and Environment, University of the Chinese Academy of Sciences, Beijing, 100049, China.
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, 3010, Australia.
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Yang Z, Yang S, Van Nostrand JD, Zhou J, Fang W, Qi Q, Liu Y, Wullschleger SD, Liang L, Graham DE, Yang Y, Gu B. Microbial Community and Functional Gene Changes in Arctic Tundra Soils in a Microcosm Warming Experiment. Front Microbiol 2017; 8:1741. [PMID: 28974946 PMCID: PMC5610689 DOI: 10.3389/fmicb.2017.01741] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 08/25/2017] [Indexed: 11/24/2022] Open
Abstract
Microbial decomposition of soil organic carbon (SOC) in thawing Arctic permafrost is important in determining greenhouse gas feedbacks of tundra ecosystems to climate. However, the changes in microbial community structure during SOC decomposition are poorly known. Here we examine these changes using frozen soils from Barrow, Alaska, USA, in anoxic microcosm incubation at −2 and 8°C for 122 days. The functional gene array GeoChip was used to determine microbial community structure and the functional genes associated with SOC degradation, methanogenesis, and Fe(III) reduction. Results show that soil incubation after 122 days at 8°C significantly decreased functional gene abundance (P < 0.05) associated with SOC degradation, fermentation, methanogenesis, and iron cycling, particularly in organic-rich soil. These observations correspond well with decreases in labile SOC content (e.g., reducing sugar and ethanol), methane and CO2 production, and Fe(III) reduction. In contrast, the community functional structure was largely unchanged in the −2°C incubation. Soil type (i.e., organic vs. mineral) and the availability of labile SOC were among the most significant factors impacting microbial community structure. These results demonstrate the important roles of microbial community in SOC degradation and support previous findings that SOC in organic-rich Arctic tundra is highly vulnerable to microbial degradation under warming.
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Affiliation(s)
- Ziming Yang
- Environmental Sciences Division, Oak Ridge National LaboratoryOak Ridge, TN, United States.,Department of Chemistry, Oakland UniversityRochester, MI, United States
| | - Sihang Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua UniversityBeijing, China
| | - Joy D Van Nostrand
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of OklahomaNorman, OK, United States
| | - Jizhong Zhou
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua UniversityBeijing, China.,Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of OklahomaNorman, OK, United States.,Earth and Environmental Sciences, Lawrence Berkeley National LaboratoryBerkeley, CA, United States
| | - Wei Fang
- Environmental Sciences Division, Oak Ridge National LaboratoryOak Ridge, TN, United States
| | - Qi Qi
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua UniversityBeijing, China
| | - Yurong Liu
- Research Center for Eco-Environmental Sciences, Chinese Academy of SciencesBeijing, China
| | - Stan D Wullschleger
- Environmental Sciences Division, Oak Ridge National LaboratoryOak Ridge, TN, United States.,Oak Ridge National Laboratory, Climate Change Science InstituteOak Ridge, TN, United States
| | - Liyuan Liang
- Environmental Sciences Division, Oak Ridge National LaboratoryOak Ridge, TN, United States.,Environmental Molecular Sciences Laboratory, Pacific Northwest National LaboratoryRichland, WA, United States
| | - David E Graham
- Biosciences Division, Oak Ridge National LaboratoryOak Ridge, TN, United States
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua UniversityBeijing, China
| | - Baohua Gu
- Environmental Sciences Division, Oak Ridge National LaboratoryOak Ridge, TN, United States
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Escalas A, Troussellier M, Yuan T, Bouvier T, Bouvier C, Mouchet MA, Flores Hernandez D, Ramos Miranda J, Zhou J, Mouillot D. Functional diversity and redundancy across fish gut, sediment and water bacterial communities. Environ Microbiol 2017; 19:3268-3282. [PMID: 28618142 DOI: 10.1111/1462-2920.13822] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 06/07/2017] [Indexed: 11/26/2022]
Abstract
This article explores the functional diversity and redundancy in a bacterial metacommunity constituted of three habitats (sediment, water column and fish gut) in a coastal lagoon under anthropogenic pressure. Comprehensive functional gene arrays covering a wide range of ecological processes and stress resistance genes to estimate the functional potential of bacterial communities were used. Then, diversity partitioning was used to characterize functional diversity and redundancy within (α), between (β) and across (γ) habitats. It was showed that all local communities exhibit a highly diversified potential for the realization of key ecological processes and resistance to various environmental conditions, supporting the growing evidence that macro-organisms microbiomes harbour a high functional potential and are integral components of functional gene dynamics in aquatic bacterial metacommunities. Several levels of functional redundancy at different scales of the bacterial metacommunity were observed (within local communities, within habitats and at the metacommunity level). The results suggested a high potential for the realization of spatial ecological insurance within this ecosystem, that is, the functional compensation among microorganisms for the realization and maintenance of key ecological processes, within and across habitats. Finally, the role of macro-organisms as dispersal vectors of microbes and their potential influence on marine metacommunity dynamics were discussed.
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Affiliation(s)
- Arthur Escalas
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
| | - Marc Troussellier
- UMR 9190 MARBEC, IRD-CNRS-UM-IFREMER, Université Montpellier, 34095 Montpellier Cedex, France
| | - Tong Yuan
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
| | - Thierry Bouvier
- UMR 9190 MARBEC, IRD-CNRS-UM-IFREMER, Université Montpellier, 34095 Montpellier Cedex, France
| | - Corinne Bouvier
- UMR 9190 MARBEC, IRD-CNRS-UM-IFREMER, Université Montpellier, 34095 Montpellier Cedex, France
| | - Maud A Mouchet
- UMR 7204 CESCO, Muséum d'Histoire Naturelle, 55 rue Buffon, Paris, 75005, France
| | - Domingo Flores Hernandez
- Centro de Ecología, Pesquerias y Oceanographia de Golfo de México, Universidad Autonoma de Campeche, Campeche, Mexico
| | - Julia Ramos Miranda
- Centro de Ecología, Pesquerias y Oceanographia de Golfo de México, Universidad Autonoma de Campeche, Campeche, Mexico
| | - Jizhong Zhou
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA.,Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - David Mouillot
- UMR 9190 MARBEC, IRD-CNRS-UM-IFREMER, Université Montpellier, 34095 Montpellier Cedex, France.,Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, 4811, Australia
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Ma X, Zhao C, Gao Y, Liu B, Wang T, Yuan T, Hale L, Nostrand JDV, Wan S, Zhou J, Yang Y. Divergent taxonomic and functional responses of microbial communities to field simulation of aeolian soil erosion and deposition. Mol Ecol 2017; 26:4186-4196. [PMID: 28570016 DOI: 10.1111/mec.14194] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2016] [Revised: 04/10/2017] [Accepted: 05/15/2017] [Indexed: 01/09/2023]
Abstract
Aeolian soil erosion and deposition have worldwide impacts on agriculture, air quality and public health. However, ecosystem responses to soil erosion and deposition remain largely unclear in regard to microorganisms, which are the crucial drivers of biogeochemical cycles. Using integrated metagenomics technologies, we analysed microbial communities subjected to simulated soil erosion and deposition in a semiarid grassland of Inner Mongolia, China. As expected, soil total organic carbon and plant coverage were decreased by soil erosion, and soil dissolved organic carbon (DOC) was increased by soil deposition, demonstrating that field simulation was reliable. Soil microbial communities were altered (p < .039) by both soil erosion and deposition, with dramatic increase in Cyanobacteria related to increased stability in soil aggregates. amyA genes encoding α-amylases were specifically increased (p = .01) by soil deposition and positively correlated (p = .02) to DOC, which likely explained changes in DOC. Surprisingly, most of microbial functional genes associated with carbon, nitrogen, phosphorus and potassium cycling were decreased or unaltered by both erosion and deposition, probably arising from acceleration of organic matter mineralization. These divergent responses support the necessity to include microbial components in evaluating ecological consequences. Furthermore, Mantel tests showed strong, significant correlations between soil nutrients and functional structure but not taxonomic structure, demonstrating close relevance of microbial function traits to nutrient cycling.
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Affiliation(s)
- Xingyu Ma
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Cancan Zhao
- State Key Laboratory of Cotton Biology, Key Laboratory of Plant Stress Biology, College of Life Sciences, Henan University, Kaifeng, China
| | - Ying Gao
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Bin Liu
- State Key Laboratory of Cotton Biology, Key Laboratory of Plant Stress Biology, College of Life Sciences, Henan University, Kaifeng, China
| | - Tengxu Wang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Tong Yuan
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Lauren Hale
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Joy D Van Nostrand
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Shiqiang Wan
- State Key Laboratory of Cotton Biology, Key Laboratory of Plant Stress Biology, College of Life Sciences, Henan University, Kaifeng, China
| | - Jizhong Zhou
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China.,Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA.,Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
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37
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Qi Q, Zhao M, Wang S, Ma X, Wang Y, Gao Y, Lin Q, Li X, Gu B, Li G, Zhou J, Yang Y. The Biogeographic Pattern of Microbial Functional Genes along an Altitudinal Gradient of the Tibetan Pasture. Front Microbiol 2017; 8:976. [PMID: 28659870 PMCID: PMC5468456 DOI: 10.3389/fmicb.2017.00976] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 05/15/2017] [Indexed: 01/30/2023] Open
Abstract
As the highest place of the world, the Tibetan plateau is a fragile ecosystem. Given the importance of microbial communities in driving soil nutrient cycling, it is of interest to document the microbial biogeographic pattern here. We adopted a microarray-based tool named GeoChip 4.0 to investigate grassland microbial functional genes along an elevation gradient from 3200 to 3800 m above sea level open to free grazing by local herdsmen and wild animals. Interestingly, microbial functional diversities increase with elevation, so does the relative abundances of genes associated with carbon degradation, nitrogen cycling, methane production, cold shock and oxygen limitation. The range of Shannon diversities (10.27–10.58) showed considerably smaller variation than what was previously observed at ungrazed sites nearby (9.95–10.65), suggesting the important role of livestock grazing on microbial diversities. Closer examination showed that the dissimilarity of microbial community at our study sites increased with elevations, revealing an elevation-decay relationship of microbial functional genes. Both microbial functional diversity and the number of unique genes increased with elevations. Furthermore, we detected a tight linkage of greenhouse gas (CO2) and relative abundances of carbon cycling genes. Our biogeographic study provides insights on microbial functional diversity and soil biogeochemical cycling in Tibetan pastures.
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Affiliation(s)
- Qi Qi
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua UniversityBeijing, China
| | - Mengxin Zhao
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua UniversityBeijing, China
| | - Shiping Wang
- Key Laboratory of Alpine Ecology and Biodiversity, Institute of Tibetan Plateau Research, Chinese Academy of SciencesBeijing, China.,CAS Center for Excellence in Tibetan Plateau Earth ScienceBeijing, China
| | - Xingyu Ma
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua UniversityBeijing, China
| | - Yuxuan Wang
- Department of Earth System Science, Tsinghua UniversityBeijing, China.,Department of Earth and Atmospheric Sciences, University of Houston, HoustonTX, United States
| | - Ying Gao
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua UniversityBeijing, China
| | - Qiaoyan Lin
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of SciencesXining, China
| | - Xiangzhen Li
- Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of SciencesChengdu, China
| | - Baohua Gu
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak RidgeTN, United States
| | - Guoxue Li
- College of Resources and Environmental Science, China Agricultural UniversityBeijing, China
| | - Jizhong Zhou
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua UniversityBeijing, China.,Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, NormanOK, United States.,Earth Sciences Division, Lawrence Berkeley National Laboratory, BerkeleyCA, United States.,Collaborative Innovation Center for Regional Environmental Quality, School of Environment, Tsinghua UniversityBeijing, China
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua UniversityBeijing, China
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Fang L, Wang M, Cai L, Cang L. Deciphering biodegradable chelant-enhanced phytoremediation through microbes and nitrogen transformation in contaminated soils. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:14627-14636. [PMID: 28452034 DOI: 10.1007/s11356-017-9029-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2017] [Accepted: 04/11/2017] [Indexed: 06/07/2023]
Abstract
Biodegradable chelant-enhanced phytoremediation offers an alternative treatment technique for metal contaminated soils, but most studies to date have addressed on phytoextraction efficiency rather than comprehensive understanding of the interactions among plant, soil microbes, and biodegradable chelants. In the present study, we investigated the impacts of biodegradable chelants, including nitrilotriacetate, S,S-ethylenediaminedisuccinic acid (EDDS), and citric acid on soil microbes, nitrogen transformation, and metal removal from contaminated soils. The EDDS addition to soil showed the strongest ability to promote the nitrogen cycling in soil, ryegrass tissue, and microbial metabolism in comparison with other chelants. Both bacterial community-level physiological profiles and soil mass specific heat rates demonstrated that soil microbial activity was inhibited after the EDDS application (between day 2 and 10), but this effect completely vanished on day 30, indicating the revitalization of microbial activity and community structure in the soil system. The results of quantitative real-time PCR revealed that the EDDS application stimulated denitrification in soil by increasing nitrite reductase genes, especially nirS. These new findings demonstrated that the nitrogen release capacity of biodegradable chelants plays an important role in accelerating nitrogen transformation, enhancing soil microbial structure and activity, and improving phytoextraction efficiency in contaminated soil.
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Affiliation(s)
- Linchuan Fang
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, 712100, China
| | - Mengke Wang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, China
| | - Lin Cai
- Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China
| | - Long Cang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China.
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Bacterial community and arsenic functional genes diversity in arsenic contaminated soils from different geographic locations. PLoS One 2017; 12:e0176696. [PMID: 28475654 PMCID: PMC5419559 DOI: 10.1371/journal.pone.0176696] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 04/14/2017] [Indexed: 11/19/2022] Open
Abstract
To understand how soil microbial communities and arsenic (As) functional genes respond to soil arsenic (As) contamination, five soils contaminated with As at different levels were collected from diverse geographic locations, incubated for 54 days under flooded conditions, and examined by both MiSeq sequencing of 16S rRNA gene amplicons and functional gene microarray (GeoChip 4.0). The results showed that both bacterial community structure and As functional gene structure differed among geographical locations. The diversity of As functional genes correlated positively with the diversity of 16S rRNA genes (P< 0.05). Higher diversities of As functional genes and 16S rRNA genes were observed in the soils with higher available As. Soil pH, phosphate-extractable As, and amorphous Fe content were the most important factors in shaping the bacterial community structure and As transformation functional genes. Geographic location was also important in controlling both the bacterial community and As transformation functional potential. These findings provide insights into the variation of As transformation functional genes in soils contaminated with different levels of As at different geographic locations, and the impact of environmental As contamination on the soil bacterial community.
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The Composition and Spatial Patterns of Bacterial Virulence Factors and Antibiotic Resistance Genes in 19 Wastewater Treatment Plants. PLoS One 2016; 11:e0167422. [PMID: 27907117 PMCID: PMC5132249 DOI: 10.1371/journal.pone.0167422] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 11/14/2016] [Indexed: 11/19/2022] Open
Abstract
Bacterial pathogenicity and antibiotic resistance are of concern for environmental safety and public health. Accumulating evidence suggests that wastewater treatment plants (WWTPs) are as an important sink and source of pathogens and antibiotic resistance genes (ARGs). Virulence genes (encoding virulence factors) are good indicators for bacterial pathogenic potentials. To achieve a comprehensive understanding of bacterial pathogenic potentials and antibiotic resistance in WWTPs, bacterial virulence genes and ARGs in 19 WWTPs covering a majority of latitudinal zones of China were surveyed by using GeoChip 4.2. A total of 1610 genes covering 13 virulence factors and 1903 genes belonging to 11 ARG families were detected respectively. The bacterial virulence genes exhibited significant spatial distribution patterns of a latitudinal biodiversity gradient and a distance-decay relationship across China. Moreover, virulence genes tended to coexist with ARGs as shown by their strongly positive associations. In addition, key environmental factors shaping the overall virulence gene structure were identified. This study profiles the occurrence, composition and distribution of virulence genes and ARGs in current WWTPs in China, and uncovers spatial patterns and important environmental variables shaping their structure, which may provide the basis for further studies of bacterial virulence factors and antibiotic resistance in WWTPs.
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Jie S, Li M, Gan M, Zhu J, Yin H, Liu X. Microbial functional genes enriched in the Xiangjiang River sediments with heavy metal contamination. BMC Microbiol 2016; 16:179. [PMID: 27502206 PMCID: PMC4976514 DOI: 10.1186/s12866-016-0800-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 08/04/2016] [Indexed: 11/10/2022] Open
Abstract
Background Xiangjiang River (Hunan, China) has been contaminated with heavy metal for several decades by surrounding factories. However, little is known about the influence of a gradient of heavy metal contamination on the diversity, structure of microbial functional gene in sediment. To deeply understand the impact of heavy metal contamination on microbial community, a comprehensive functional gene array (GeoChip 5.0) has been used to study the functional genes structure, composition, diversity and metabolic potential of microbial community from three heavy metal polluted sites of Xiangjiang River. Results A total of 25595 functional genes involved in different biogeochemical processes have been detected in three sites, and different diversities and structures of microbial functional genes were observed. The analysis of gene overlapping, unique genes, and various diversity indices indicated a significant correlation between the level of heavy metal contamination and the functional diversity. Plentiful resistant genes related to various metal were detected, such as copper, arsenic, chromium and mercury. The results indicated a significantly higher abundance of genes involved in metal resistance including sulfate reduction genes (dsr) in studied site with most serious heavy metal contamination, such as cueo, mer, metc, merb, tehb and terc gene. With regard to the relationship between the environmental variables and microbial functional structure, S, Cu, Cd, Hg and Cr were the dominating factor shaping the microbial distribution pattern in three sites. Conclusions This study suggests that high level of heavy metal contamination resulted in higher functional diversity and the abundance of metal resistant genes. These variation therefore significantly contribute to the resistance, resilience and stability of the microbial community subjected to the gradient of heavy metals contaminant in Xiangjiang River. Electronic supplementary material The online version of this article (doi:10.1186/s12866-016-0800-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shiqi Jie
- School of Minerals Processing and Bioengineering, Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, 410083, China
| | - Mingming Li
- School of Minerals Processing and Bioengineering, Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, 410083, China
| | - Min Gan
- School of Minerals Processing and Bioengineering, Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, 410083, China
| | - Jianyu Zhu
- School of Minerals Processing and Bioengineering, Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, 410083, China.
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, 410083, China. .,Department of Botany and Microbiology, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, 73019, USA.
| | - Xueduan Liu
- School of Minerals Processing and Bioengineering, Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, 410083, China
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Zonal Soil Type Determines Soil Microbial Responses to Maize Cropping and Fertilization. mSystems 2016; 1:mSystems00075-16. [PMID: 27822546 PMCID: PMC5069962 DOI: 10.1128/msystems.00075-16] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 06/16/2016] [Indexed: 11/20/2022] Open
Abstract
Soil types heavily influence ecological dynamics. It remains controversial to what extent soil types shape microbial responses to land management changes, largely due to lack of in-depth comparison across various soil types. Here, we collected samples from three major zonal soil types spanning from cold temperate to subtropical climate zones. We examined bacterial and fungal community structures, as well as microbial functional genes. Different soil types had distinct microbial biomass levels and community compositions. Five years of maize cropping (growing corn or maize) changed the bacterial community composition of the Ultisol soil type and the fungal composition of the Mollisol soil type but had little effect on the microbial composition of the Inceptisol soil type. Meanwhile, 5 years of fertilization resulted in soil acidification. Microbial compositions of the Mollisol and Ultisol, but not the Inceptisol, were changed and correlated (P < 0.05) with soil pH. These results demonstrated the critical role of soil type in determining microbial responses to land management changes. We also found that soil nitrification potentials correlated with the total abundance of nitrifiers and that soil heterotrophic respiration correlated with the total abundance of carbon degradation genes, suggesting that changes in microbial community structure had altered ecosystem processes. IMPORTANCE Microbial communities are essential drivers of soil functional processes such as nitrification and heterotrophic respiration. Although there is initial evidence revealing the importance of soil type in shaping microbial communities, there has been no in-depth, comprehensive survey to robustly establish it as a major determinant of microbial community composition, functional gene structure, or ecosystem functioning. We examined bacterial and fungal community structures using Illumina sequencing, microbial functional genes using GeoChip, microbial biomass using phospholipid fatty acid analysis, as well as functional processes of soil nitrification potential and CO2 efflux. We demonstrated the critical role of soil type in determining microbial responses to land use changes at the continental level. Our findings underscore the inherent difficulty in generalizing ecosystem responses across landscapes and suggest that assessments of community feedback must take soil types into consideration. Author Video: An author video summary of this article is available.
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Le Roux X, Bouskill NJ, Niboyet A, Barthes L, Dijkstra P, Field CB, Hungate BA, Lerondelle C, Pommier T, Tang J, Terada A, Tourna M, Poly F. Predicting the Responses of Soil Nitrite-Oxidizers to Multi-Factorial Global Change: A Trait-Based Approach. Front Microbiol 2016; 7:628. [PMID: 27242680 PMCID: PMC4868854 DOI: 10.3389/fmicb.2016.00628] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2016] [Accepted: 04/18/2016] [Indexed: 12/21/2022] Open
Abstract
Soil microbial diversity is huge and a few grams of soil contain more bacterial taxa than there are bird species on Earth. This high diversity often makes predicting the responses of soil bacteria to environmental change intractable and restricts our capacity to predict the responses of soil functions to global change. Here, using a long-term field experiment in a California grassland, we studied the main and interactive effects of three global change factors (increased atmospheric CO2 concentration, precipitation and nitrogen addition, and all their factorial combinations, based on global change scenarios for central California) on the potential activity, abundance and dominant taxa of soil nitrite-oxidizing bacteria (NOB). Using a trait-based model, we then tested whether categorizing NOB into a few functional groups unified by physiological traits enables understanding and predicting how soil NOB respond to global environmental change. Contrasted responses to global change treatments were observed between three main NOB functional types. In particular, putatively mixotrophic Nitrobacter, rare under most treatments, became dominant under the ‘High CO2+Nitrogen+Precipitation’ treatment. The mechanistic trait-based model, which simulated ecological niches of NOB types consistent with previous ecophysiological reports, helped predicting the observed effects of global change on NOB and elucidating the underlying biotic and abiotic controls. Our results are a starting point for representing the overwhelming diversity of soil bacteria by a few functional types that can be incorporated into models of terrestrial ecosystems and biogeochemical processes.
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Affiliation(s)
- Xavier Le Roux
- UMR INRA 1418, UMR CNRS 5557, Microbial Ecology Centre, INRA, CNRS, Université Lyon 1, Université de Lyon Villeurbanne, France
| | - Nicholas J Bouskill
- Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley CA, USA
| | - Audrey Niboyet
- UMR 8079, AgroParisTech, Ecology Systematics and Evolution Laboratory, CNRS, Université Paris-Sud 11 Orsay, France
| | - Laure Barthes
- UMR 8079, AgroParisTech, Ecology Systematics and Evolution Laboratory, CNRS, Université Paris-Sud 11 Orsay, France
| | - Paul Dijkstra
- Ecosystem Science and Society Center, Department of Biological Sciences, Northern Arizona University, Flagstaff AZ, USA
| | - Chris B Field
- Department of Global Ecology, Carnegie Institution, Stanford University, Stanford CA, USA
| | - Bruce A Hungate
- Ecosystem Science and Society Center, Department of Biological Sciences, Northern Arizona University, Flagstaff AZ, USA
| | - Catherine Lerondelle
- UMR INRA 1418, UMR CNRS 5557, Microbial Ecology Centre, INRA, CNRS, Université Lyon 1, Université de Lyon Villeurbanne, France
| | - Thomas Pommier
- UMR INRA 1418, UMR CNRS 5557, Microbial Ecology Centre, INRA, CNRS, Université Lyon 1, Université de Lyon Villeurbanne, France
| | - Jinyun Tang
- Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley CA, USA
| | - Akihiko Terada
- Department of Environmental Engineering, Technical University of Denmark Kongens Lyngby, Denmark
| | - Maria Tourna
- UMR INRA 1418, UMR CNRS 5557, Microbial Ecology Centre, INRA, CNRS, Université Lyon 1, Université de Lyon Villeurbanne, France
| | - Franck Poly
- UMR INRA 1418, UMR CNRS 5557, Microbial Ecology Centre, INRA, CNRS, Université Lyon 1, Université de Lyon Villeurbanne, France
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44
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Freedman ZB, Upchurch RA, Zak DR, Cline LC. Anthropogenic N Deposition Slows Decay by Favoring Bacterial Metabolism: Insights from Metagenomic Analyses. Front Microbiol 2016; 7:259. [PMID: 26973633 PMCID: PMC4773658 DOI: 10.3389/fmicb.2016.00259] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Accepted: 02/16/2016] [Indexed: 12/03/2022] Open
Abstract
Litter decomposition is an enzymatically-complex process that is mediated by a diverse assemblage of saprophytic microorganisms. It is a globally important biogeochemical process that can be suppressed by anthropogenic N deposition. In a northern hardwood forest ecosystem located in Michigan, USA, 20 years of experimentally increased atmospheric N deposition has reduced forest floor decay and increased soil C storage. Here, we paired extracellular enzyme assays with shotgun metagenomics to assess if anthropogenic N deposition has altered the functional potential of microbial communities inhabiting decaying forest floor. Experimental N deposition significantly reduced the activity of extracellular enzymes mediating plant cell wall decay, which occurred concurrently with changes in the relative abundance of metagenomic functional gene pathways mediating the metabolism of carbohydrates, aromatic compounds, as well as microbial respiration. Moreover, experimental N deposition increased the relative abundance of 50 of the 60 gene pathways, the majority of which were associated with saprotrophic bacteria. Conversely, the relative abundance and composition of fungal genes mediating the metabolism of plant litter was not affected by experimental N deposition. Future rates of atmospheric N deposition have favored saprotrophic soil bacteria, whereas the metabolic potential of saprotrophic fungi appears resilient to this agent of environmental change. Results presented here provide evidence that changes in the functional capacity of saprotrophic soil microorganisms mediate how anthropogenic N deposition increases C storage in soil.
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Affiliation(s)
- Zachary B Freedman
- School of Natural Resources and Environment, University of Michigan Ann Arbor, MI, USA
| | - Rima A Upchurch
- School of Natural Resources and Environment, University of Michigan Ann Arbor, MI, USA
| | - Donald R Zak
- School of Natural Resources and Environment, University of MichiganAnn Arbor, MI, USA; Department of Ecology, Evolution, and Behavior, University of MichiganAnn Arbor, MI, USA
| | - Lauren C Cline
- School of Natural Resources and Environment, University of Michigan Ann Arbor, MI, USA
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45
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Zhang M, Xu Z, Teng Y, Christie P, Wang J, Ren W, Luo Y, Li Z. Non-target effects of repeated chlorothalonil application on soil nitrogen cycling: The key functional gene study. THE SCIENCE OF THE TOTAL ENVIRONMENT 2016; 543:636-643. [PMID: 26613517 DOI: 10.1016/j.scitotenv.2015.11.053] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2015] [Revised: 11/10/2015] [Accepted: 11/10/2015] [Indexed: 05/20/2023]
Abstract
The widespread and increasing application of chlorothalonil (CTN) raises concerns about its non-target impacts, but little information is available on the effect of CTN on the key functional genes related to soil nitrogen (N) cycling, especially in the case of repeated applications. In the present study, a microcosm incubation was conducted to determine CTN residues and the impacts on the abundances of key functional genes related to N cycling after repeated CTN applications. The results demonstrated that repeated CTN applications at the recommended application rate and five times the recommended rate led to the accumulation of CTN residue in soil at concentrations of 5.59 and 78.79 mg kg(-1), respectively, by the end of incubation. Real time PCR (RT-PCR) revealed that repeated CTN applications had negative effects on the chiA and aprA gene abundances. There were significantly negative correlations between CTN residues and abundances of AOA and AOB genes. In addition, the abundances of key functional genes involved in soil denitrification were declined by repeated CTN applications with the sole exception of the nosZ gene. This study suggests that repeated CTN applications could lead to the accumulation of CTN residue and generate somewhat inconsistent and erratic effects on the abundances of key functional genes related to soil N cycling.
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Affiliation(s)
- Manyun Zhang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of the Chinese Academy of Sciences, Beijing 100049, China; Environmental Futures Research Institute, School of Natural Sciences, Griffith University, Nathan, Brisbane, Queensland 4111, Australia
| | - Zhihong Xu
- Environmental Futures Research Institute, School of Natural Sciences, Griffith University, Nathan, Brisbane, Queensland 4111, Australia
| | - Ying Teng
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China.
| | - Peter Christie
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Jun Wang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; Chongqing Research Academy of Environmental Sciences, Chongqing 401147, China
| | - Wenjie Ren
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Yongming Luo
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Zhengao Li
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
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46
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Liang Y, Jiang Y, Wang F, Wen C, Deng Y, Xue K, Qin Y, Yang Y, Wu L, Zhou J, Sun B. Long-term soil transplant simulating climate change with latitude significantly alters microbial temporal turnover. THE ISME JOURNAL 2015; 9:2561-72. [PMID: 25989371 PMCID: PMC4817637 DOI: 10.1038/ismej.2015.78] [Citation(s) in RCA: 97] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 03/27/2015] [Accepted: 04/13/2015] [Indexed: 01/27/2023]
Abstract
To understand soil microbial community stability and temporal turnover in response to climate change, a long-term soil transplant experiment was conducted in three agricultural experiment stations over large transects from a warm temperate zone (Fengqiu station in central China) to a subtropical zone (Yingtan station in southern China) and a cold temperate zone (Hailun station in northern China). Annual soil samples were collected from these three stations from 2005 to 2011, and microbial communities were analyzed by sequencing microbial 16S ribosomal RNA gene amplicons using Illumina MiSeq technology. Our results revealed a distinctly differential pattern of microbial communities in both northward and southward transplantations, along with an increase in microbial richness with climate cooling and a corresponding decrease with climate warming. The microbial succession rate was estimated by the slope (w value) of linear regression of a log-transformed microbial community similarity with time (time-decay relationship). Compared with the low turnover rate of microbial communities in situ (w=0.046, P<0.001), the succession rate at the community level was significantly higher in the northward transplant (w=0.058, P<0.001) and highest in the southward transplant (w=0.094, P<0.001). Climate warming lead to a faster succession rate of microbial communities as well as lower species richness and compositional changes compared with in situ and climate cooling, which may be related to the high metabolic rates and intense competition under higher temperature. This study provides new insights into the impacts of climate change on the fundamental temporal scaling of soil microbial communities and microbial phylogenetic biodiversity.
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Affiliation(s)
- Yuting Liang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Yuji Jiang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Feng Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Chongqing Wen
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Ye Deng
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, China
| | - Kai Xue
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Yujia Qin
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Liyou Wu
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Jizhong Zhou
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
- Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Bo Sun
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
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47
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Li J, Zhang J, Liu L, Fan Y, Li L, Yang Y, Lu Z, Zhang X. Annual periodicity in planktonic bacterial and archaeal community composition of eutrophic Lake Taihu. Sci Rep 2015; 5:15488. [PMID: 26503553 PMCID: PMC4621408 DOI: 10.1038/srep15488] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 09/28/2015] [Indexed: 02/06/2023] Open
Abstract
Bacterioplankton plays a key role in nutrient cycling and is closely related to water eutrophication and algal bloom. We used high-throughput 16S rRNA gene sequencing to profile archaeal and bacterial community compositions in the surface water of Lake Taihu. It is one of the largest lakes in China and has suffered from recurring cyanobacterial bloom. A total of 81 water samples were collected from 9 different sites in 9 different months of 2012. We found that temporal variation of the microbial community was significantly greater than spatial variation (adonis, n = 9999, P < 1e−4). The composition of bacterial community in December was similar to that in January, and so was the archaeal community, suggesting potential annual periodicity. Unsupervised K-means clustering was used to identify the synchrony of abundance variations between different taxa. We found that the cluster consisting mostly of ACK-M1, C111 (members of acIV), Pelagibacteraceae (alfV-A) and Synechococcaceae showed relatively higher abundance in autumn. On the contrary, the cluster of Comamonadaceae and Methylophilaceae (members of lineage betI and betIV) had higher abundance in spring. The co-occurrence relationships between taxa were greatly altered during the cyanobacterial bloom according to our further network module analysis.
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Affiliation(s)
- Junfeng Li
- MOE Key Lab of Bioinformatics; Bioinformatics Division/Center for Synthetic and Systems Biology, TNLIST and Department of Automation, Tsinghua University, Beijing, China
| | - Junyi Zhang
- State Key Lab for Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China.,Wuxi Environmental Monitoring Centre, Wuxi, China
| | - Liyang Liu
- MOE Key Lab of Bioinformatics; Bioinformatics Division/Center for Synthetic and Systems Biology, TNLIST and Department of Automation, Tsinghua University, Beijing, China
| | - Yucai Fan
- State Key Lab for Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Lianshuo Li
- MOE Key Lab of Bioinformatics; Bioinformatics Division/Center for Synthetic and Systems Biology, TNLIST and Department of Automation, Tsinghua University, Beijing, China
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Zuhong Lu
- State Key Lab for Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China.,Department of Biomedical Engineering, Peking University, Beijing, China
| | - Xuegong Zhang
- MOE Key Lab of Bioinformatics; Bioinformatics Division/Center for Synthetic and Systems Biology, TNLIST and Department of Automation, Tsinghua University, Beijing, China
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48
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Wang M, Liu S, Wang F, Sun B, Zhou J, Yang Y. Microbial responses to southward and northward Cambisol soil transplant. Microbiologyopen 2015; 4:931-40. [PMID: 26503228 PMCID: PMC4694145 DOI: 10.1002/mbo3.302] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Revised: 08/25/2015] [Accepted: 09/04/2015] [Indexed: 11/27/2022] Open
Abstract
Soil transplant serves as a proxy to simulate climate changes. Recently, we have shown that southward transplant of black soil and northward transplant of red soil altered soil microbial communities and biogeochemical variables. However, fundamental differences in soil types have prevented direct comparison between southward and northward transplants. To tackle it, herein we report an analysis of microbial communities of Cambisol soil in an agriculture field after 4 years of adaptation to southward and northward soil transplants over large transects. Analysis of bare fallow soils revealed concurrent increase in microbial functional diversity and coarse‐scale taxonomic diversity at both transplanted sites, as detected by GeoChip 3.0 and DGGE, respectively. Furthermore, a correlation between microbial functional diversity and taxonomic diversity was detected, which was masked in maize cropped soils. Mean annual temperature, soil moisture, and nitrate (NO3¯‐N) showed strong correlations with microbial communities. In addition, abundances of ammonium‐oxidizing genes (amoA) and denitrification genes were correlated with nitrification capacity and NO3¯‐N contents, suggesting that microbial responses to soil transplant could alter microbe‐mediated biogeochemical cycle at the ecosystem level.
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Affiliation(s)
- Mengmeng Wang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China.,Collaborative Innovation Center for Regional Environmental Quality, Tsinghua University, Beijing, 100084, China
| | - Shanshan Liu
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Feng Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China.,Ningbo Academy of Agricultural Sciences, Ningbo, 315040, China
| | - Bo Sun
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Jizhong Zhou
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China.,Collaborative Innovation Center for Regional Environmental Quality, Tsinghua University, Beijing, 100084, China.,Institute for Environmental Genomics and Department Microbiology and Plant Science, University of Oklahoma, Norman, Oklahoma, 73019.,Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
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49
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GeoChip profiling of microbial community in response to global changes simulated by soil transplant and cropping. GENOMICS DATA 2015; 2:166-9. [PMID: 26484087 PMCID: PMC4535839 DOI: 10.1016/j.gdata.2014.06.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Accepted: 06/03/2014] [Indexed: 11/20/2022]
Abstract
Microbe plays an important role in driving biogeochemical cycles, thus it is of great interest to understand microbial responses and feedbacks to global changes. We have recently analyzed functional potentials of soil microbial community via a high-throughput, microarray-based metagenomic tool named GeoChip 3.0 to illustrate microbial responses to global changes simulated by soil transplant and/or maize cropping. Here we describe detailed experimental design, data collection and pre-processing to support our published studies by Liu et al. [5] and Zhao et al. [14].
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50
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Ding J, Zhang Y, Wang M, Sun X, Cong J, Deng Y, Lu H, Yuan T, Van Nostrand JD, Li D, Zhou J, Yang Y. Soil organic matter quantity and quality shape microbial community compositions of subtropical broadleaved forests. Mol Ecol 2015; 24:5175-85. [PMID: 26363284 DOI: 10.1111/mec.13384] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 09/05/2015] [Accepted: 09/09/2015] [Indexed: 11/27/2022]
Abstract
As two major forest types in the subtropics, broadleaved evergreen and broadleaved deciduous forests have long interested ecologists. However, little is known about their belowground ecosystems despite their ecological importance in driving biogeochemical cycling. Here, we used Illumina MiSeq sequencing targeting 16S rRNA gene and a microarray named GeoChip targeting functional genes to analyse microbial communities in broadleaved evergreen and deciduous forest soils of Shennongjia Mountain of Central China, a region known as 'The Oriental Botanic Garden' for its extraordinarily rich biodiversity. We observed higher plant diversity and relatively richer nutrients in the broadleaved evergreen forest than the deciduous forest. In odds to our expectation that plant communities shaped soil microbial communities, we found that soil organic matter quantity and quality, but not plant community parameters, were the best predictors of microbial communities. Actinobacteria, a copiotrophic phylum, was more abundant in the broadleaved evergreen forest, while Verrucomicrobia, an oligotrophic phylum, was more abundant in the broadleaved deciduous forest. The density of the correlation network of microbial OTUs was higher in the broadleaved deciduous forest but its modularity was smaller, reflecting lower resistance to environment changes. In addition, keystone OTUs of the broadleaved deciduous forest were mainly oligotrophic. Microbial functional genes associated with recalcitrant carbon degradation were also more abundant in the broadleaved deciduous forests, resulting in low accumulation of organic matters. Collectively, these findings revealed the important role of soil organic matter in shaping microbial taxonomic and functional traits.
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Affiliation(s)
- Junjun Ding
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Yuguang Zhang
- Institute of Forestry Ecology, Environment and Protection and the Key Laboratory of Forest Ecology and Environment of State Forestry Administration, the Chinese Academy of Forestry, Beijing, 100091, China
| | - Mengmeng Wang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Xin Sun
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Jing Cong
- Institute of Forestry Ecology, Environment and Protection and the Key Laboratory of Forest Ecology and Environment of State Forestry Administration, the Chinese Academy of Forestry, Beijing, 100091, China
| | - Ye Deng
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.,Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
| | - Hui Lu
- Institute of Forestry Ecology, Environment and Protection and the Key Laboratory of Forest Ecology and Environment of State Forestry Administration, the Chinese Academy of Forestry, Beijing, 100091, China
| | - Tong Yuan
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
| | - Joy D Van Nostrand
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
| | - Diqiang Li
- Institute of Forestry Ecology, Environment and Protection and the Key Laboratory of Forest Ecology and Environment of State Forestry Administration, the Chinese Academy of Forestry, Beijing, 100091, China
| | - Jizhong Zhou
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China.,Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA.,Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
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