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Shinfuku MS, Domeignoz-Horta LA, Choudoir MJ, Frey SD, Mitchell MF, Ranjan R, DeAngelis KM. Seasonal effects of long-term warming on ecosystem function and bacterial diversity. PLoS One 2024; 19:e0311364. [PMID: 39446706 PMCID: PMC11500971 DOI: 10.1371/journal.pone.0311364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Accepted: 09/09/2024] [Indexed: 10/26/2024] Open
Abstract
Across biomes, soil biodiversity promotes ecosystem functions. However, whether this relationship will be maintained within ecosystems under climate change is uncertain. Here, using two long-term soil warming experiments, we investigated how warming affects the relationship between ecosystem functions and bacterial diversity across seasons, soil horizons, and warming duration. Soils were sampled from these warming experiments located at the Harvard Forest Long-Term Ecological Research (LTER) site, where soils had been heated +5°C above ambient for 13 or 28 years at the time of sampling. We assessed seven measurements representative of different ecosystem functions and nutrient pools. We also surveyed bacterial community diversity. We found that ecosystem function was significantly affected by season, with autumn samples having a higher intercept than summer samples in our model, suggesting a higher overall baseline of ecosystem function in the fall. The effect of warming on bacterial diversity was similarly affected by season, where warming in the summer was associated with decreased bacterial evenness in the organic horizon. Despite the decreased bacterial evenness in the warmed plots, we found that the relationship between ecosystem function and bacterial diversity was unaffected by warming or warming duration. Our findings highlight that season is a consistent driver of ecosystem function as well as a modulator of climate change effects on bacterial community evenness.
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Affiliation(s)
- Melissa S. Shinfuku
- Microbiology Department, University of Massachusetts, Amherst, MA, United States of America
| | - Luiz A. Domeignoz-Horta
- Microbiology Department, University of Massachusetts, Amherst, MA, United States of America
- INRAE, AgroParisTech, UMR EcoSys, Université Paris-Saclay, Palaiseau, France
| | - Mallory J. Choudoir
- Microbiology Department, University of Massachusetts, Amherst, MA, United States of America
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States of America
| | - Serita D. Frey
- Center for Soil Biogeochemistry and Microbial Ecology, Department of Natural Resources and the Environment, University of New Hampshire, Durham, NH, United States of America
| | - Megan F. Mitchell
- Graduate Program in Organismic and Evolutionary Biology, University of Massachusetts, Amherst, MA, United States of America
| | - Ravi Ranjan
- Genomics Resource Laboratory, Institute for Applied Life Sciences, University of Massachusetts, Amherst, MA, United States of America
| | - Kristen M. DeAngelis
- Microbiology Department, University of Massachusetts, Amherst, MA, United States of America
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2
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Lin L, Xiong J, Yue T, Xu W, Liu L, Wang F, Yang S, Cao W. Phosphorus starvation response genes and function coupling: A mechanism to regulate phosphorus availability in a subtropical estuary. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 928:172575. [PMID: 38641105 DOI: 10.1016/j.scitotenv.2024.172575] [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: 02/03/2024] [Revised: 04/01/2024] [Accepted: 04/16/2024] [Indexed: 04/21/2024]
Abstract
Phosphorus (P) plays an important role in regulating primary production in estuarine environments. However, knowledge of the P-functional gene composition of microbial communities and the mechanisms of microbial adaptation to changes in available P in estuaries remain limited. This study coupling 16 s rDNA and metagenomics sequencing was conducted to reveal the relationship between P cycling functional genes, microbial interactions, and P availability in the Jiulong River Estuary. The results showed that the relative abundance of P cycling functions genes was highest in winter, and lowest in summer. Spatially, the total relative abundance of P cycling functions genes was higher in the riverward than that in the seaward. P cycling functional microbial interactions and P cycling gene coupling were strongest in summer and in the seaward. Changes in both temperature and salinity had significant direct and indirect effects on P cycling function, and the influence of salinity on P cycling function was greater than that on the microbial community in the estuary. Salinity had significant direct negative effects on inorganic P-solubilization (IP), organic P-mineralization (OP), and P uptake and transport functions (PT). Whereas, salinity had a significant positive effect on P-starvation response regulation (PR) function. Thus, salinity and microbial communities regulate the soluble reactive phosphate concentrations in estuarine environments by strengthening internal coupling among P cycling functions, promoting PR function, and facilitating PT gene expression. PR is the most important predictors, PR, PT, and PR-PT together explained 38.56 % of the overall soluble reactive phosphorus (SRP) variation. Over 66 % of the explained SRP variations can be predicted by the PR, PT, and PR-PT functional genes. This finding improves the knowledge base of the microbial processes for P cycling and provides a foundation for eutrophication management strategies in the estuary.
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Affiliation(s)
- Ling Lin
- Key Laboratory of the Ministry of Education for Coastal Wetland Ecosystems, Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, College of the Environment and Ecology, Xiamen University, Xiang'an South Road, Xiamen 361102, China
| | - Jiangzhiqian Xiong
- Key Laboratory of the Ministry of Education for Coastal Wetland Ecosystems, Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, College of the Environment and Ecology, Xiamen University, Xiang'an South Road, Xiamen 361102, China
| | - Tianchen Yue
- China ASEAN College of Marine Sciences, Xiamen University Malaysia, Jalan Sunsuria Bandar Sunsuria, Sepang 43900, Malaysia
| | - Wenfeng Xu
- Fujian Xiamen Environmental Monitoring Central Station, Xing'lin South Road, Xiamen 361022, China
| | - Lihua Liu
- Fujian Xiamen Environmental Monitoring Central Station, Xing'lin South Road, Xiamen 361022, China
| | - Feifei Wang
- Key Laboratory of the Ministry of Education for Coastal Wetland Ecosystems, Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, College of the Environment and Ecology, Xiamen University, Xiang'an South Road, Xiamen 361102, China
| | - Shengchang Yang
- Key Laboratory of the Ministry of Education for Coastal Wetland Ecosystems, Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, College of the Environment and Ecology, Xiamen University, Xiang'an South Road, Xiamen 361102, China
| | - Wenzhi Cao
- Key Laboratory of the Ministry of Education for Coastal Wetland Ecosystems, Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, College of the Environment and Ecology, Xiamen University, Xiang'an South Road, Xiamen 361102, China.
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3
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Liang Q, Mod HK, Luo S, Ma B, Yang K, Chen B, Qi W, Zhao Z, Du G, Guisan A, Ma X, Le Roux X. Taxonomic and functional biogeographies of soil bacterial communities across the Tibet plateau are better explained by abiotic conditions than distance and plant community composition. Mol Ecol 2023. [PMID: 37060060 DOI: 10.1111/mec.16952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 03/26/2023] [Accepted: 03/29/2023] [Indexed: 04/16/2023]
Abstract
The processes governing soil bacteria biogeography are still not fully understood. It remains unknown how the importance of environmental filtering and dispersal differs between bacterial taxonomic and functional biogeography, and whether their importance is scale-dependent. We sampled soils across the Tibet plateau, with distances among plots ranging from 20 m to 1550 km. Taxonomic composition of bacterial community was characterized by 16S amplicon sequencing and functional community composition by qPCR targeting 9 functional groups involved in N dynamics. Factors representing climate, soil and plant community were measured to assess different facets of environmental dissimilarity. Both bacterial taxonomic and functional dissimilarities were more related to abiotic dissimilarity than biotic (vegetation) dissimilarity or distance. Taxonomic dissimilarity was mostly explained by differences in soil pH and mean annual temperature (MAT), while functional dissimilarity was linked to differences in soil N and P availabilities and N:P ratio. Soil pH and MAT remained the main determinants of taxonomic dissimilarity across spatial scales. In contrast, the explanatory variables of N-related functional dissimilarity varied across the scales, with soil moisture and organic matter having the highest role across short distances (<~330 km), and available P, N:P ratio and distance being important over long distances (>~660 km). Our results demonstrate how biodiversity dimension (taxonomic versus functional aspects) and spatial scale influence the factors driving soil bacterial biogeography.
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Affiliation(s)
- Qingqing Liang
- School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Heidi K Mod
- Department of Geosciences and Geography, University of Helsinki, Helsinki, Finland
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Shuaiwei Luo
- College of Ecology, Lanzhou University, Lanzhou, China
| | - Beibei Ma
- School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Kena Yang
- School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Beibei Chen
- School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Wei Qi
- College of Ecology, Lanzhou University, Lanzhou, China
| | - Zhigang Zhao
- College of Ecology, Lanzhou University, Lanzhou, China
| | - Guozhen Du
- College of Ecology, Lanzhou University, Lanzhou, China
| | - Antoine Guisan
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Institute of Earth Surface Dynamics, University of Lausanne, Lausanne, Switzerland
| | - Xiaojun Ma
- School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Xavier Le Roux
- INRAE, Université de Lyon, Université Lyon 1, CNRS, vetAgroSup, UMR 1418 INRAE, UMR 5557 CNRS, Ecologie Microbienne LEM, Villeurbanne, France
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4
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Zhu R, Liu C, Xu YD, He W, Liu J, Chen J, An Y, Shi S. Ratio of carbon and nitrogen in fertilizer treatment drives distinct rhizosphere microbial community composition and co-occurrence networks. Front Microbiol 2022; 13:968551. [PMID: 36160210 PMCID: PMC9493311 DOI: 10.3389/fmicb.2022.968551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 08/15/2022] [Indexed: 11/25/2022] Open
Abstract
Fertilization is the main strategy to accelerate vegetation restoration and improve the rhizosphere microbial community in the northeast China. However, the responses of rhizosphere microbial community structure, specific microbial community and symbiotic pattern to manure fertilization in grassland (alfalfa only) are not well clear. In this study, the variation of bacterial community structures in R_Manure (extracted liquid of fermented cow manure), E_Manure (extracted residue of fermented cow manure), F_Manure (full fermented cow manure), and Control (without fermented cow manure) collected from the rhizosphere microbial community of alfalfa were analyzed by the application of an Illumina HiSeq high-throughput sequencing technique. A total of 62,862 microbial operational taxonomic units (OTUs) were detected and derived from 21 phyla of known bacteria. The dominant bacteria in the rhizosphere include Proteobacteria (70.20%), Acidobacteria (1.24%), Actinobacteria (2.11%), Bacteroidetes (6.15%), Firmicutes (4.21%), and Chlorofexi (2.13%) accounting for 86% of the dominant phyla in all treatments. At the genus level, the dominant genus include NB1-j, Lysobacter, Alphaproteobacteria, Subgroup_6, Actinomarinales, Saccharimonadales, Aneurinibacillus, MO-CFX2, SBR1031, Caldilineaceae, and so on with the average relative abundance (RA) of 1.76%, 1.52%, 1.30%, 1.24%, 1.61%, 2.39%, 1.36%, 1.42%, 1.27%, and 1.03%, respectively. Bacterial diversities and community structures were significantly differentiated by different treatments of fertilization. The results of community structure composition showed that R_Manure treatment significantly increased the population abundance of Firmicutes, Chlorofexi, and Patescibacteria by 34.32%, 6.85%, and 2.70%, and decreased the population abundance of Proteobacteria and Actinobacteria by 16.83% and 1.04%, respectively. In addition, it showed that all treatments significantly resulted in an increase or decrease at the genus level. R_Manure had the higher richness and diversity of the bacterial community, with the greatest topology attributes of the co-occurrence networks. Through the analysis of the molecular ecological network (MENA), the co-occurrence networks had a shorter average path distance and diameter in R_Manure than in others, implying more stability to environmental changes. Redundancy analysis (RDA) showed that the ratio of carbon and nitrogen (C/N) was the main factor affecting rhizosphere microbial community composition while driving distinct rhizosphere bacterial community and its co-occurrence networks. The R_Manure associated with more C/N had relatively complex microbial co-occurrence network with a large number of nodes and edges, while the microbial network of others associated with less C/N had fewer taxa with loose mutual interactions. These results suggested that organic fertilizer with high C/N can regulate the rhizosphere microorganism, while high C/N can determine bacterial community structures, specific bacterial taxa, and their relationships with the nodule size of alfalfa. These significant changes can be used to evaluate soil fertility and fertilizer management in the artificial grassland system, while the potential biological indicators of the rhizosphere microbial community will play an important role in future eco-agriculture.
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Affiliation(s)
- Ruifen Zhu
- Pratacultural College, Gansu Agricultural University, Lanzhou, China
- Pratacultural Institute, Chongqing Academy of Animal Sciences, Rongchang, China
- Pratacultural Institute Science, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Chang Liu
- Pratacultural Institute, Chongqing Academy of Animal Sciences, Rongchang, China
| | - Yuan Dong Xu
- Pratacultural Institute, Chongqing Academy of Animal Sciences, Rongchang, China
| | - Wei He
- Pratacultural Institute, Chongqing Academy of Animal Sciences, Rongchang, China
| | - Jielin Liu
- Pratacultural Institute Science, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Jishan Chen
- Pratacultural Institute, Chongqing Academy of Animal Sciences, Rongchang, China
| | - Yajun An
- Gansu Yasheng Agricultural Research Institute Co., Ltd., Lanzhou, China
| | - Shangli Shi
- Pratacultural College, Gansu Agricultural University, Lanzhou, China
- *Correspondence: Shangli Shi
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5
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Chen H, Ma K, Lu C, Fu Q, Qiu Y, Zhao J, Huang Y, Yang Y, Schadt CW, Chen H. Functional Redundancy in Soil Microbial Community Based on Metagenomics Across the Globe. Front Microbiol 2022; 13:878978. [PMID: 35586865 PMCID: PMC9108720 DOI: 10.3389/fmicb.2022.878978] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 04/13/2022] [Indexed: 12/30/2022] Open
Abstract
Understanding the contribution of soil microbial communities to ecosystem processes is critical for predicting terrestrial ecosystem feedbacks under changing climate. Our current understanding lacks a consistent strategy to formulate the linkage between microbial systems and ecosystem processes due to the presumption of functional redundancy in soil microbes. Here we present a global soil microbial metagenomic analysis to generalize patterns of microbial taxonomic compositions and functional potentials across climate and geochemical gradient. Our analyses show that soil microbial taxonomic composition varies widely in response to climate and soil physicochemical gradients, while microbial functional attributes based on metagenomic gene abundances are redundant. Among 17 climate zones, microbial taxonomic compositions were more distinct than functional potentials, as climate and edaphic properties showed more significant influence on microbial taxonomic compositions than on functional potentials. Microbial taxonomies formed a larger and more complex co-occurrence network with more module structures than functional potentials. Functional network was strongly inter-connected among different categories, whereas taxonomic network was more positively interactive in the same taxonomic groups. This study provides strong evidence to support the hypothesis of functional redundancy in soil microbes, as microbial taxonomic compositions vary to a larger extent than functional potentials based on metagenomic gene abundances in terrestrial ecosystems across the globe.
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Affiliation(s)
- Huaihai Chen
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, China
| | - Kayan Ma
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, China
| | - Caiyan Lu
- Key Laboratory of Pollution Ecology and Environment Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
- Key Lab of Conservation Tillage and Ecological Agriculture, Shenyang, China
| | - Qi Fu
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, China
| | - Yingbo Qiu
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, China
| | - Jiayi Zhao
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, China
| | - Yu Huang
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, China
| | - Yuchun Yang
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, China
| | | | - Hao Chen
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, China
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6
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Chen Y, Liu F, Kang L, Zhang D, Kou D, Mao C, Qin S, Zhang Q, Yang Y. Large-scale evidence for microbial response and associated carbon release after permafrost thaw. GLOBAL CHANGE BIOLOGY 2021; 27:3218-3229. [PMID: 33336478 DOI: 10.1111/gcb.15487] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 12/04/2020] [Indexed: 06/12/2023]
Abstract
Permafrost thaw could trigger the release of greenhouse gases through microbial decomposition of the large quantities of carbon (C) stored within frozen soils. However, accurate evaluation of soil C emissions from thawing permafrost is still a big challenge, partly due to our inadequate understanding about the response of microbial communities and their linkage with soil C release upon permafrost thaw. Based on a large-scale permafrost sampling across 24 sites on the Tibetan Plateau, we employed meta-genomic technologies (GeoChip and Illumina MiSeq sequencing) to explore the impacts of permafrost thaw (permafrost samples were incubated for 11 days at 5°C) on microbial taxonomic and functional communities, and then conducted a laboratory incubation to investigate the linkage of microbial taxonomic and functional diversity with soil C release after permafrost thaw. We found that bacterial and fungal α diversity decreased, but functional gene diversity and the normalized relative abundance of C degradation genes increased after permafrost thaw, reflecting the rapid microbial response to permafrost thaw. Moreover, both the microbial taxonomic and functional community structures differed between the thawed permafrost and formerly frozen soils. Furthermore, soil C release rate over five month incubation was associated with microbial functional diversity and C degradation gene abundances. By contrast, neither microbial taxonomic diversity nor community structure exhibited any significant effects on soil C release over the incubation period. These findings demonstrate that permafrost thaw could accelerate C emissions by altering the function potentials of microbial communities rather than taxonomic diversity, highlighting the crucial role of microbial functional genes in mediating the responses of permafrost C cycle to climate warming.
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Affiliation(s)
- Yongliang Chen
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
| | - Futing Liu
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Luyao Kang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Dianye Zhang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Dan Kou
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Chao Mao
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shuqi Qin
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Qiwen Zhang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Yuanhe Yang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
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7
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Zhu R, Liu J, Wang J, Han W, Shen Z, Muraina TO, Chen J, Sun D. Comparison of soil microbial community between reseeding grassland and natural grassland in Songnen Meadow. Sci Rep 2020; 10:16884. [PMID: 33037306 PMCID: PMC7547709 DOI: 10.1038/s41598-020-74023-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 09/18/2020] [Indexed: 11/23/2022] Open
Abstract
Microorganisms have important ecological functions in ecosystems. Reseeding is considered as one of the main strategies for preventing grassland degradation in China. However, the response of soil microbial community and diversity to reseeding grassland (RG) and natural grassland (NG) remains unclear, especially in the Songnen Meadow. In this study, the soil microbial community compositions of two vegetation restoration types (RG vs NG) were analyzed using a high-throughput sequencing technique. A total of 23,142 microbial OTUs were detected, phylogenetically derived from 11 known bacterial phyla. Soil advantage categories included Proteobacteria, Acidobacteria, Actinobacteria, and Bacteroidetes, which together accounted for > 78% of the all phyla in vegetation restoration. The soil microbial diversity was higher in RG than in NG. Two types of vegetation restoration had significantly different characteristics of soil microbial community (P < 0.001). Based on a molecular ecological network analysis, we found that the network in RG had a longer average path distance and modularity than in NG network, making it more resilient to environment changes. Meanwhile, the results of the canonical correspondence analysis and molecular ecological network analysis showed that soil pH (6.34 ± 0.35 in RG and 7.26 ± 0.28 in NG) was the main factor affecting soil microbial community structure, followed by soil moisture (SM) in the Songnen meadow, China. Besides, soil microbial community characteristics can vary significantly in different vegetation restoration. Thus, we suggested that it was necessary and reasonable for this area to popularize reseeding grassland in the future.
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Affiliation(s)
- Ruifen Zhu
- Institute of Pratacultural Science, Heilongjiang Academy of Agricultural Sciences, 368 Xue Fu Road, Nangang District, Harbin, 150086, China
| | - Jielin Liu
- Institute of Pratacultural Science, Heilongjiang Academy of Agricultural Sciences, 368 Xue Fu Road, Nangang District, Harbin, 150086, China
| | - Jianli Wang
- Institute of Pratacultural Science, Heilongjiang Academy of Agricultural Sciences, 368 Xue Fu Road, Nangang District, Harbin, 150086, China
| | - Weibo Han
- Institute of Pratacultural Science, Heilongjiang Academy of Agricultural Sciences, 368 Xue Fu Road, Nangang District, Harbin, 150086, China
| | - Zhongbao Shen
- Institute of Pratacultural Science, Heilongjiang Academy of Agricultural Sciences, 368 Xue Fu Road, Nangang District, Harbin, 150086, China
| | - Taofeek O Muraina
- National Hulunber Grassland Ecosystem Observation and Research Station, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 10008, China
- Department of Animal Health and Production, Oyo State College of Agriculture and Technology, P.M.B. 10, Igbo-Ora, Oyo State, Nigeria
| | - Jishan Chen
- Institute of Pratacultural Science, Heilongjiang Academy of Agricultural Sciences, 368 Xue Fu Road, Nangang District, Harbin, 150086, China.
| | - Dequan Sun
- Institute of Pratacultural Science, Heilongjiang Academy of Agricultural Sciences, 368 Xue Fu Road, Nangang District, Harbin, 150086, China.
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8
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Feng K, Wang S, Wei Z, Wang Z, Zhang Z, Wu Y, Zhang Y, Deng Y. Niche width of above- and below-ground organisms varied in predicting biodiversity profiling along a latitudinal gradient. Mol Ecol 2020; 29:1890-1902. [PMID: 32299139 DOI: 10.1111/mec.15441] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 04/01/2020] [Accepted: 04/02/2020] [Indexed: 11/29/2022]
Abstract
Biodiversity is the foundation of all ecosystems across the planet, and having a better understanding of its global distribution mechanism could be important for biodiversity conservation under global change. A niche width model, combined with metabolic theory, has successfully predicted the increase of α-diversity and decrease of β-diversity in the below-ground microbial community along an altitudinal mountain gradient. In this study, we evaluated this niche width model of above-ground plants (mainly trees and shrubs) and below-ground bulk soil microbial communities (i.e., bacteria and archaea) along a latitudinal gradient of forests in China. The niche widths of both plants and microbes increased with increasing temperature and precipitation, and with proximity to circumneutral pH. However, the α- and β-diversities (observed richness and Bray-Curtis dissimilarity, respectively) could not be accurately predicted by a single niche width model alone, either temperature, precipitation or pH. Considering the interactions among different niche width models, all three niche width models were combined to predict biodiversity at the community level using structural equation modelling. The results showed that the niche width model of circumneutral pH was most important in predicting diversity profiling (i.e., α- and β-diversity) for both plants and microbes, while niche width of precipitation and temperature showed both direct and indirect importance for microbe and plant biodiversity, respectively. Because the current niche width model neglects several scenarios related to taxon and environmental attributes, it still needs to be treated with caution in predicting biodiversity trends.
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Affiliation(s)
- Kai Feng
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Shang Wang
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Ziyan Wei
- Institute for Marine Science and Technology, Shandong University, Qingdao, China
| | - Zhujun Wang
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Zhaojing Zhang
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,Institute for Marine Science and Technology, Shandong University, Qingdao, China
| | - Yueni Wu
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Yuguang Zhang
- The Key Laboratory of Forest Ecology and Environment of State Forestry Administration, Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing, China
| | - Ye Deng
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China.,Institute for Marine Science and Technology, Shandong University, Qingdao, China
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9
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Feng K, Zhang Y, He Z, Ning D, Deng Y. Interdomain ecological networks between plants and microbes. Mol Ecol Resour 2019; 19:1565-1577. [PMID: 31479575 DOI: 10.1111/1755-0998.13081] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 07/26/2019] [Accepted: 08/07/2019] [Indexed: 12/11/2022]
Abstract
While macroscopic interkingdom relationships have been intensively investigated in various ecosystems, the above-belowground ecology in natural ecosystems has been poorly understood, especially for the plant-microbe associations at a regional scale. In this study, we proposed a workflow to construct interdomain ecological networks (IDEN) between multiple plants and various microbes (bacteria and archaea in this study). Across 30 latitudinal forests in China, the regional IDEN showed particular topological features, including high connectance, nested structure, asymmetric specialization and modularity. Also, plant species exhibited strong preference to specific microbial groups, and the observed network was significantly different from randomly rewired networks. Network module analysis indicated that a majority of microbes associated with plants within modules rather than across modules, suggesting specialized associations between plants and microorganisms. Consistent plant-microbe associations were captured via IDENs constructed within individual forest locations, which reinforced the validity of IDEN analysis. In addition, the plant-forest link distribution showed the geographical distribution of plants had higher endemicity than that of microorganisms. With cautious experimental design and data processing, this study shows interdomain species associations between plants and microbes in natural forest ecosystems and provides new insights into our understanding of meta-communities across different domain species.
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Affiliation(s)
- Kai Feng
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Yuguang Zhang
- Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Key Laboratory of Forest Ecology and Environment of State Forestry Administration, Beijing, China
| | - Zhili He
- Environmental Microbiomics Research Center, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, China
| | - Daliang Ning
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, USA
| | - Ye Deng
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
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10
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Habtom H, Pasternak Z, Matan O, Azulay C, Gafny R, Jurkevitch E. Applying microbial biogeography in soil forensics. Forensic Sci Int Genet 2018; 38:195-203. [PMID: 30447564 DOI: 10.1016/j.fsigen.2018.11.010] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2017] [Revised: 10/10/2018] [Accepted: 11/07/2018] [Indexed: 11/28/2022]
Abstract
The ubiquity, heterogeneity and transferability of soil makes it useful as evidence in criminal investigations, especially using new methods that survey the microbial DNA it contains. However, to be used effectively and reliably, more needs to be learned about the natural distribution patterns of microbial communities in soil. In this study we examine these patterns in detail, at local to regional scales (2 m-260 km), across an environmental gradient in three different soil types. Geographic location was found to be more important than soil type in determining the microbial community composition: communities from the same site but different soil types, although significantly different from each other, were still much more similar to each other than were communities from the same soil type but from different sites. At a local scale (25-1000 m), distance-decay relationships were observed in all soil types: the farther apart two soil communities were located, even in the same soil type, the more they differed. At regional-scale distances (1-260 km), differences between communities did not increase with increased geographic distance between them, and the dominant factor determining the community profile was the physico-chemical environment, most notably annual precipitation (R2 = 0.69), soil sodium (R2 = 0.49) and soil ammonium (R2 = 0.47) levels. We introduce a likelihood-ratio framework for quantitative evaluation of soil microbial DNA profile evidence in casework. In conclusion, these profiles, along with detailed knowledge of natural soil microbial biogeography, provide valuable forensic information on soil sample comparison and allow the determination of approximate source location on large (hundreds of km) spatial scales. Moreover, at small spatial scales it may enable pinpointing the source location of a sample to within at least 25 m, regardless of soil type and environmental conditions.
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Affiliation(s)
- Habteab Habtom
- Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Zohar Pasternak
- Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel.
| | - Ofra Matan
- Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Chen Azulay
- Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Ron Gafny
- Forensic Biology Laboratory, Division of Identification and Forensic Science, Israel Police, National Headquarters, Haim Bar-Lev Road, Jerusalem, Israel
| | - Edouard Jurkevitch
- Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
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11
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Tian J, He N, Hale L, Niu S, Yu G, Liu Y, Blagodatskaya E, Kuzyakov Y, Gao Q, Zhou J. Soil organic matter availability and climate drive latitudinal patterns in bacterial diversity from tropical to cold temperate forests. Funct Ecol 2017. [DOI: 10.1111/1365-2435.12952] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Jing Tian
- Key Laboratory of Ecosystem Network Observation and ModelingInstitute of Geographic Sciences and Natural Resources ResearchChinese Academy of Sciences (CAS) Beijing China
| | - Nianpeng He
- Key Laboratory of Ecosystem Network Observation and ModelingInstitute of Geographic Sciences and Natural Resources ResearchChinese Academy of Sciences (CAS) Beijing China
| | - Lauren Hale
- Department of Microbiology and Plant Biology and School of Civil Engineering and Environmental SciencesInstitute for Environmental GenomicsUniversity of Oklahoma Norman OK USA
| | - Shuli Niu
- Key Laboratory of Ecosystem Network Observation and ModelingInstitute of Geographic Sciences and Natural Resources ResearchChinese Academy of Sciences (CAS) Beijing China
| | - Guirui Yu
- Key Laboratory of Ecosystem Network Observation and ModelingInstitute of Geographic Sciences and Natural Resources ResearchChinese Academy of Sciences (CAS) Beijing China
| | - Yuan Liu
- Key Laboratory of Ecosystem Network Observation and ModelingInstitute of Geographic Sciences and Natural Resources ResearchChinese Academy of Sciences (CAS) Beijing China
| | - Evgenia Blagodatskaya
- Institute of Physicochemical and Biological Problems in Soil Science Pushchino Russia
- Department of Agricultural Soil ScienceUniversity of Göttingen Göttingen Germany
| | - Yakov Kuzyakov
- Department of Agricultural Soil ScienceUniversity of Göttingen Göttingen Germany
- Agro‐Technology InstituteRUDN University Moscow Russia
| | - Qun Gao
- Department of Microbiology and Plant Biology and School of Civil Engineering and Environmental SciencesInstitute for Environmental GenomicsUniversity of Oklahoma Norman OK USA
- State Key Joint Laboratory of Environment Simulation and Pollution ControlSchool of EnvironmentTsinghua University Beijing China
| | - Jizhong Zhou
- Department of Microbiology and Plant Biology and School of Civil Engineering and Environmental SciencesInstitute for Environmental GenomicsUniversity of Oklahoma Norman OK USA
- State Key Joint Laboratory of Environment Simulation and Pollution ControlSchool of EnvironmentTsinghua University Beijing China
- Earth and Environmental SciencesLawrence Berkeley National Laboratory Berkeley CA USA
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12
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Wang Y, Zhang R, He Z, Van Nostrand JD, Zheng Q, Zhou J, Jiao N. Functional Gene Diversity and Metabolic Potential of the Microbial Community in an Estuary-Shelf Environment. Front Microbiol 2017; 8:1153. [PMID: 28680420 PMCID: PMC5478683 DOI: 10.3389/fmicb.2017.01153] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2017] [Accepted: 06/07/2017] [Indexed: 01/28/2023] Open
Abstract
Microbes play crucial roles in various biogeochemical processes in the ocean, including carbon (C), nitrogen (N), and phosphorus (P) cycling. Functional gene diversity and the structure of the microbial community determines its metabolic potential and therefore its ecological function in the marine ecosystem. However, little is known about the functional gene composition and metabolic potential of bacterioplankton in estuary areas. The East China Sea (ECS) is a dynamic marginal ecosystem in the western Pacific Ocean that is mainly affected by input from the Changjiang River and the Kuroshio Current. Here, using a high-throughput functional gene microarray (GeoChip), we analyzed the functional gene diversity, composition, structure, and metabolic potential of microbial assemblages in different ECS water masses. Four water masses determined by temperature and salinity relationship showed different patterns of functional gene diversity and composition. Generally, functional gene diversity [Shannon–Weaner’s H and reciprocal of Simpson’s 1/(1-D)] in the surface water masses was higher than that in the bottom water masses. The different presence and proportion of functional genes involved in C, N, and P cycling among the bacteria of the different water masses showed different metabolic preferences of the microbial populations in the ECS. Genes involved in starch metabolism (amyA and nplT) showed higher proportion in microbial communities of the surface water masses than of the bottom water masses. In contrast, a higher proportion of genes involved in chitin degradation was observed in microorganisms of the bottom water masses. Moreover, we found a higher proportion of nitrogen fixation (nifH), transformation of hydroxylamine to nitrite (hao) and ammonification (gdh) genes in the microbial communities of the bottom water masses compared with those of the surface water masses. The spatial variation of microbial functional genes was significantly correlated with salinity, temperature, and chlorophyll based on canonical correspondence analysis, suggesting a significant influence of hydrologic conditions on water microbial communities. Our data provide new insights into better understanding of the functional potential of microbial communities in the complex estuarine-coastal environmental gradient of the ECS.
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Affiliation(s)
- Yu Wang
- State Key Laboratory of Marine Environmental Science, Xiamen UniversityXiamen, China.,Institute of Marine Microbes and Ecospheres, Xiamen UniversityXiamen, China
| | - Rui Zhang
- State Key Laboratory of Marine Environmental Science, Xiamen UniversityXiamen, China.,Institute of Marine Microbes and Ecospheres, Xiamen UniversityXiamen, China
| | - Zhili He
- Institute for Environmental Genomics and Institute for Energy and the Environment and Department of Microbiology and Plant Biology, University of Oklahoma, NormanOK, United States
| | - Joy D Van Nostrand
- Institute for Environmental Genomics and Institute for Energy and the Environment and Department of Microbiology and Plant Biology, University of Oklahoma, NormanOK, United States
| | - Qiang Zheng
- State Key Laboratory of Marine Environmental Science, Xiamen UniversityXiamen, China.,Institute of Marine Microbes and Ecospheres, Xiamen UniversityXiamen, China
| | - Jizhong Zhou
- Institute for Environmental Genomics and Institute for Energy and the Environment and Department of Microbiology and Plant Biology, University of Oklahoma, NormanOK, United States.,Earth Sciences Division, Lawrence Berkeley National Laboratory, BerkeleyCA, United States.,School of Environment, Tsinghua UniversityBeijing, China
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, Xiamen UniversityXiamen, China.,Institute of Marine Microbes and Ecospheres, Xiamen UniversityXiamen, China
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