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Qiu Z, He X, Yu H, Zhu C, Shen W. Differential responses of soil bacterial communities to elevated CO 2 between strongly CO 2-responsive and weakly CO 2-responsive rice cultivars. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 869:161843. [PMID: 36709908 DOI: 10.1016/j.scitotenv.2023.161843] [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: 12/03/2022] [Revised: 01/22/2023] [Accepted: 01/22/2023] [Indexed: 06/18/2023]
Abstract
Effects of elevated CO2 (eCO2) on paddy soil microbial communities remain unclear, particularly when different rice cultivars exposed to eCO2. We thus compared responses of soil bacterial communities to ambient CO2 (aCO2) and eCO2 (aCO2 + 200 μmol CO2 mol-1) between two weakly CO2-responsive (Wuyunjing27, W27; Huaidao5, H5) and two strongly CO2-responsive rice cultivars (Yongyou1540, Y1540; LongIIyou1988, L1988) throughout six growth stages (early tillering, late tillering, jointing, heading, grain filling and ripening) in a paddy field in Jiangdu, China in 2018. No significant changes in soil bacterial diversities were observed between eCO2 and aCO2 or between cultivars for any single growth stage at the OTU level, but α diversity significantly changed at the phylum level except for the ripening stage. For a single cultivar, particularly two strongly CO2-responsive cultivars, over their whole growth stage, eCO2 enhanced differences in bacterial β diversity at both OTU and phylum levels under H5, Y1540 and L1988. Soil bacterial community complexity at the phylum level under eCO2 was weakened under W27, H5 and Y1540, but enhanced under L1988. eCO2-induced changes in soil DOC under these four cultivars had significantly positive impact on bacterial abundances. However, structural equation modeling illustrated that changes in soil DOC induced by eCO2 significantly decreased soil bacterial community richness. eCO2 did not significantly affect relationships between soil bacterial community diversities and rice yields, but displayed significantly negative correlations between strongly CO2-responsive rice cultivars' yields and relative abundances of Proteobacteria at the ripening stage. Dynamics that how soil microbial communities can differentiate their eCO2 responses between strongly- and weakly-responsive rice cultivars will provide a new insight into promoting rice productivity and soil health.
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Affiliation(s)
- Zijian Qiu
- Jiangsu Key Laboratory of Atmospheric Environment Monitoring and Pollution Control, Collaborative Innovation Center of Atmospheric Environment and Equipment Technology, School of Environmental Science and Engineering, Nanjing University of Information Science and Technology, Nanjing 210044, China
| | - Xinhua He
- Centre of Excellence for Soil Biology, College of Resources and Environment, Southwest University, Chongqing 400715, China; School of Biological Sciences, University of Western Australia, Perth 6009, WA, Australia; Department of Land, Air and Water Resources, University of California at Davis, Davis, CA 95616, USA
| | - Haiyang Yu
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315800, China; State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Chunwu Zhu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Weishou Shen
- Jiangsu Key Laboratory of Atmospheric Environment Monitoring and Pollution Control, Collaborative Innovation Center of Atmospheric Environment and Equipment Technology, School of Environmental Science and Engineering, Nanjing University of Information Science and Technology, Nanjing 210044, China.
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2
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Liu N, Hu H, Ma W, Deng Y, Dimitrov D, Wang Q, Shrestha N, Su X, Feng K, Liu Y, Hao B, Zhang X, Feng X, Wang Z. Relationships Between Soil Microbial Diversities Across an Aridity Gradient in Temperate Grasslands : Soil Microbial Diversity Relationships. MICROBIAL ECOLOGY 2023; 85:1013-1027. [PMID: 35364696 DOI: 10.1007/s00248-022-01997-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 03/11/2022] [Indexed: 05/04/2023]
Abstract
Soil microbes assemble in highly complex and diverse microbial communities, and microbial diversity patterns and their drivers have been studied extensively. However, diversity correlations and co-occurrence patterns between bacterial, fungal, and archaeal domains and between microbial functional groups in arid regions remain poorly understood. Here we assessed the relationships between the diversity and abundance of bacteria, fungi, and archaea and explored how environmental factors influence these relationships. We sampled soil along a 1500-km-long aridity gradient in temperate grasslands of Inner Mongolia (China) and sequenced the 16S rRNA gene of bacteria and archaea and the ITS2 gene of fungi. The diversity correlations and co-occurrence patterns between bacterial, fungal, and archaeal domains and between different microbial functional groups were evaluated using α-diversity and co-occurrence networks based on microbial abundance. Our results indicate insignificant correlations among the diversity patterns of bacterial, fungal, and archaeal domains using α-diversity but mostly positive correlations among diversity patterns of microbial functional groups based on α-diversity and co-occurrence networks along the aridity gradient. These results suggest that studying microbial diversity patterns from the perspective of functional groups and co-occurrence networks can provide additional insights on patterns that cannot be accessed using only overall microbial α-diversity. Increase in aridity weakens the diversity correlations between bacteria and fungi and between bacterial and archaeal functional groups, but strengthens the positive diversity correlations between bacterial functional groups and between fungal functional groups and the negative diversity correlations between bacterial and fungal functional groups. These variations of the diversity correlations are associated with the different responses of microbes to environmental factors, especially aridity. Our findings demonstrate the complex responses of microbial community structure to environmental conditions (especially aridity) and suggest that understanding diversity correlations and co-occurrence patterns between soil microbial groups is essential for predicting changes in microbial communities under future climate change in arid regions.
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Affiliation(s)
- Nana Liu
- Institute of Ecology and Key Laboratory for Earth Surface Processes of the Ministry of Education, College of Urban and Environmental Sciences, Peking University, Beijing, 100871, China
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Huifeng Hu
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Wenhong Ma
- College of Ecology and Environment, Inner Mongolia University, Hohhot, 010021, China
| | - Ye Deng
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Dimitar Dimitrov
- Department of Natural History, University Museum of Bergen, University of Bergen, Bergen, Norway
| | - Qinggang Wang
- Department of Ecology and Ecological Engineering, College of Resources and Environmental Sciences, and Key Laboratory of Biodiversity and Organic Farming of Beijing City, China Agricultural University, Beijing, 100193, China
| | - Nawal Shrestha
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Xiangyan Su
- Institute of Ecology and Key Laboratory for Earth Surface Processes of the Ministry of Education, College of Urban and Environmental Sciences, Peking University, Beijing, 100871, China
| | - Kai Feng
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Yuqing Liu
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Baihui Hao
- College of Ecology and Environment, Inner Mongolia University, Hohhot, 010021, China
| | - Xinying Zhang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Xiaojuan Feng
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
| | - Zhiheng Wang
- Institute of Ecology and Key Laboratory for Earth Surface Processes of the Ministry of Education, College of Urban and Environmental Sciences, Peking University, Beijing, 100871, China.
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3
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Rosado-Porto D, Ratering S, Moser G, Deppe M, Müller C, Schnell S. Soil metatranscriptome demonstrates a shift in C, N, and S metabolisms of a grassland ecosystem in response to elevated atmospheric CO 2. Front Microbiol 2022; 13:937021. [PMID: 36081791 PMCID: PMC9445814 DOI: 10.3389/fmicb.2022.937021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 08/01/2022] [Indexed: 11/16/2022] Open
Abstract
Soil organisms play an important role in the equilibrium and cycling of nutrients. Because elevated CO2 (eCO2) affects plant metabolism, including rhizodeposition, it directly impacts the soil microbiome and microbial processes. Therefore, eCO2 directly influences the cycling of different elements in terrestrial ecosystems. Hence, possible changes in the cycles of carbon (C), nitrogen (N), and sulfur (S) were analyzed, alongside the assessment of changes in the composition and structure of the soil microbiome through a functional metatranscriptomics approach (cDNA from mRNA) from soil samples taken at the Giessen free-air CO2 enrichment (Gi-FACE) experiment. Results showed changes in the expression of C cycle genes under eCO2 with an increase in the transcript abundance for carbohydrate and amino acid uptake, and degradation, alongside an increase in the transcript abundance for cellulose, chitin, and lignin degradation and prokaryotic carbon fixation. In addition, N cycle changes included a decrease in the transcript abundance of N2O reductase, involved in the last step of the denitrification process, which explains the increase of N2O emissions in the Gi-FACE. Also, a shift in nitrate (NO 3 - ) metabolism occurred, with an increase in transcript abundance for the dissimilatoryNO 3 - reduction to ammonium (NH 4 + ) (DNRA) pathway. S metabolism showed increased transcripts for sulfate (SO 4 2 - ) assimilation under eCO2 conditions. Furthermore, soil bacteriome, mycobiome, and virome significantly differed between ambient and elevated CO2 conditions. The results exhibited the effects of eCO2 on the transcript abundance of C, N, and S cycles, and the soil microbiome. This finding showed a direct connection between eCO2 and the increased greenhouse gas emission, as well as the importance of soil nutrient availability to maintain the balance of soil ecosystems.
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Affiliation(s)
- David Rosado-Porto
- Institute of Applied Microbiology, Justus Liebig University, Giessen, Germany
- Faculty of Basic and Biomedical Sciences, Simón Bolívar University, Barranquilla, Colombia
| | - Stefan Ratering
- Institute of Applied Microbiology, Justus Liebig University, Giessen, Germany
| | - Gerald Moser
- Institute of Plant Ecology, Justus Liebig University, Giessen, Germany
| | - Marianna Deppe
- Institute of Plant Ecology, Justus Liebig University, Giessen, Germany
| | - Christoph Müller
- Institute of Plant Ecology, Justus Liebig University, Giessen, Germany
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Dublin, Ireland
| | - Sylvia Schnell
- Institute of Applied Microbiology, Justus Liebig University, Giessen, Germany
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Actinobacteria in the Algerian Sahara: Diversity, adaptation mechanism and special unexploited biotopes for the isolation of novel rare taxa. Biologia (Bratisl) 2021. [DOI: 10.1007/s11756-021-00928-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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5
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Plant-archaea relationships: a potential means to improve crop production in arid and semi-arid regions. World J Microbiol Biotechnol 2020; 36:133. [PMID: 32772189 DOI: 10.1007/s11274-020-02910-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 08/04/2020] [Indexed: 12/14/2022]
Abstract
Crop production in arid and semi-arid regions of the world is limited by several abiotic factors, including water stress, temperature extremes, low soil fertility, high soil pH, low soil water-holding capacity, and low soil organic matter. Moreover, arid and semi-arid areas experience low levels of rainfall with high spatial and temporal variability. Also, the indiscriminate use of chemicals, a practice that characterizes current agricultural practice, promotes crop and soil pollution potentially resulting in serious human health and environmental hazards. A reliable and sustainable alternative to current farming practice is, therefore, a necessity. One such option includes the use of plant growth-promoting microbes that can help to ameliorate some of the adverse effects of these multiple stresses. In this regard, archaea, functional components of the plant microbiome that are found both in the rhizosphere and the endosphere may contribute to the promotion of plant growth. Archaea can survive in extreme habitats such as areas with high temperatures and hypersaline water. No cases of archaea pathogenicity towards plants have been reported. Archaea appear to have the potential to promote plant growth, improve nutrient supply and protect plants against various abiotic stresses. A better understanding of recent developments in archaea functional diversity, plant colonizing ability, and modes of action could facilitate their eventual usage as reliable components of sustainable agricultural systems. The research discussed herein, therefore, addresses the potential role of archaea to improve sustainable crop production in arid and semi-arid areas.
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6
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Liu Y, Tong T, Li B, Xie S. Dynamics of bacterial communities in a river water treatment wetland. ANN MICROBIOL 2019. [DOI: 10.1007/s13213-019-01454-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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7
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Li Y, Wu Z, Dong X, Jia Z, Sun Q. Variance in bacterial communities, potential bacterial carbon sequestration and nitrogen fixation between light and dark conditions under elevated CO 2 in mine tailings. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 652:234-242. [PMID: 30366324 DOI: 10.1016/j.scitotenv.2018.10.253] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 10/19/2018] [Accepted: 10/19/2018] [Indexed: 05/20/2023]
Abstract
This study is the first to show the response of bacterial communities with primary carbon and nitrogen fixers to elevated CO2 (eCO2) in light and dark conditions based on 6 months of culture growth. Carbon sequestration and nitrogen fixation were analyzed by 13C and 15N isotope labeling using 13C-labeled CO2 and 15N-labeled N2, followed by pyrosequencing and DNA-based stable isotope probing (SIP) to identify carbon fixers and nitrogen fixers. The results indicated that eCO2 decreased the Chao 1 richness, and the eCO2-light treatment exhibited the highest Shannon diversity. In addition, eCO2 (in either light or dark conditions) greatly increased the relative abundances of bacteria belonging to the classes Betaproteobacteria and Alphaproteobacteria. The 13C atom % in the mine tailings increased from 1.108 to 1.84 ± 0.11 under light conditions and 1.52 ± 0.17 under dark conditions after 6 months of culture growth. Ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) form I-coding gene (cbbL) copy numbers were 164.30-fold and 40.36-fold higher than RubisCO form II-coding gene (cbbM) copy numbers in the heavy fractions with a buoyant density of 1.7388 g·mL-1 relative to the buoyant density gradients of DNA fractions obtained under eCO2-light and eCO2-dark treatment, respectively. The Proteobacteria-like cbbL genes were dominant in the carbon fixers. In addition, the 15N atom % in the mine tailings increased from 0.366 to 0.454 ± 0.021 in light conditions and 0.437 ± 0.018 in dark conditions. Furthermore, uncultured nitrogen-fixing bacteria were the dominant nitrogen fixers in light conditions, and bacteria harboring the Bradyrhizobium-like nifH and Leptospirillum-like nifH genes were the dominant nitrogen fixers in dark conditions. These first data for a mine tailing ecosystem are inconsistent with those obtained for a range of other ecosystems, in which the effects of CO2 were limited to several nonphotoautotrophic communities and different nitrogen fixers.
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Affiliation(s)
- Yang Li
- School of Resources and Environmental Engineering, Anhui University, Hefei, Anhui Province, China; State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, Jiangsu Province, China
| | - Zhaojun Wu
- School of Resources and Environmental Engineering, Anhui University, Hefei, Anhui Province, China
| | - Xingchen Dong
- College of Resources and Environmental Sciences, Gansu Agricultural University, Lanzhou, Gansu Province, China
| | - Zhongjun Jia
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, Jiangsu Province, China
| | - Qingye Sun
- School of Resources and Environmental Engineering, Anhui University, Hefei, Anhui Province, China.
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8
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Dong Y, Wang Z, Sun H, Yang W, Xu H. The Response Patterns of Arbuscular Mycorrhizal and Ectomycorrhizal Symbionts Under Elevated CO 2: A Meta-Analysis. Front Microbiol 2018; 9:1248. [PMID: 29942293 PMCID: PMC6004511 DOI: 10.3389/fmicb.2018.01248] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 05/23/2018] [Indexed: 12/20/2022] Open
Abstract
Elevated carbon dioxide (eCO2), a much-discussed topic in global warming, influences development and functions of mycorrhizal fungi and plants. However, due to the inconsistent results reported in various publications, the response patterns of symbionts associated with the arbuscular mycorrhizal (AM) or with ectomycorrhizal (ECM) fungi to eCO2 remains still unclear. Therefore, we performed a meta-analysis to identify how eCO2 affected mycorrhizal fungi and if there is a significant different response between AM and ECM symbionts. Our results demonstrated that eCO2 increased mycorrhizal plants biomass (+26.20%), nutrient contents [+2.45% in nitrogen (N), and +10.66% in phosphorus (P)] and mycorrhizal fungal growth (+22.87% in extraradical hyphal length and +21.77% in mycorrhizal fungal biomass), whereas plant nutrient concentrations decreased (-11.86% in N and -12.01% in P) because the increase in plant biomass was greater than that in nutrient content. The AM plants exhibited larger increases in their biomass (+33.90%) and in their N (+21.99%) and P contents (+19.48%) than did the ECM plants (+20.57% in biomass, -4.28% in N content and -13.35% in P content). However, ECM fungi demonstrated increased responses of mycorrhizal fungal biomass (+29.98%) under eCO2 compared with AM fungi (+6.61%). These data indicate different patterns in the growth of AM and ECM symbionts under eCO2: AM symbionts contributed more to plant growth, while ECM symbionts were more favorable to mycorrhizal fungal growth. In addition, the responses of plant biomass to eCO2 showed no significant difference between short-term and long-term groups, whereas a significant difference in the responses of mycorrhizal fungal growth was found between the two groups. The addition of N increased plant growth but decreased mycorrhizal fungal abundance, and P addition increased total plant biomass and extraradical hyphal length, but shoot biomass largely increased in low P conditions. Mixtures of mycorrhizal fungi affected the total plant and root biomasses more than a single mycorrhizal fungus. Clarifying the different patterns in AM and ECM symbionts under eCO2 would contribute to a better understanding of the interactions between mycorrhizal fungi and plant symbionts under the conditions of global climate change as well as of the coevolution of flora with Earth's environment.
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Affiliation(s)
- Yuling Dong
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhenyu Wang
- School of Biological and Chemical Engineering, Liaoning Institute of Science and Technology, Benxi, China
| | - Hao Sun
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Weichao Yang
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Hui Xu
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
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9
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Reese AT, Lulow K, David LA, Wright JP. Plant community and soil conditions individually affect soil microbial community assembly in experimental mesocosms. Ecol Evol 2017; 8:1196-1205. [PMID: 29375790 PMCID: PMC5773302 DOI: 10.1002/ece3.3734] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Revised: 11/15/2017] [Accepted: 11/26/2017] [Indexed: 01/23/2023] Open
Abstract
Soils harbor large, diverse microbial communities critical for local and global ecosystem functioning that are controlled by multiple and poorly understood processes. In particular, while there is observational evidence of relationships between both biotic and abiotic conditions and microbial composition and diversity, there have been few experimental tests to determine the relative importance of these two sets of factors at local scales. Here, we report the results of a fully factorial experiment manipulating soil conditions and plant cover on old‐field mesocosms across a latitudinal gradient. The largest contributor to beta diversity was site‐to‐site variation, but, having corrected for that, we observed significant effects of both plant and soil treatments on microbial composition. Separate phyla were associated with each treatment type, and no interactions between soil and plant treatment were observed. Individual soil characteristics and biotic parameters were also associated with overall beta‐diversity patterns and phyla abundance. In contrast, soil microbial diversity was only associated with site and not experimental treatment. Overall, plant community treatment explained more variation than soil treatment, a result not previously appreciated because it is difficult to dissociate plant community composition and soil conditions in observational studies across gradients. This work highlights the need for more nuanced, multifactorial experiments in microbial ecology and in particular indicates a greater focus on relationships between plant composition and microbial composition during community assembly.
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Affiliation(s)
- Aspen T Reese
- Department of Biology Duke University Durham NC USA.,Department of Molecular Genetics and Microbiology Duke University Durham NC USA
| | | | - Lawrence A David
- Department of Molecular Genetics and Microbiology Duke University Durham NC USA
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10
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Brenzinger K, Kujala K, Horn MA, Moser G, Guillet C, Kammann C, Müller C, Braker G. Soil Conditions Rather Than Long-Term Exposure to Elevated CO 2 Affect Soil Microbial Communities Associated with N-Cycling. Front Microbiol 2017; 8:1976. [PMID: 29093701 PMCID: PMC5651278 DOI: 10.3389/fmicb.2017.01976] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2017] [Accepted: 09/25/2017] [Indexed: 11/13/2022] Open
Abstract
Continuously rising atmospheric CO2 concentrations may lead to an increased transfer of organic C from plants to the soil through rhizodeposition and may affect the interaction between the C- and N-cycle. For instance, fumigation of soils with elevated CO2 (eCO2) concentrations (20% higher compared to current atmospheric concentrations) at the Giessen Free-Air Carbon Dioxide Enrichment (GiFACE) sites resulted in a more than 2-fold increase of long-term N2O emissions and an increase in dissimilatory reduction of nitrate compared to ambient CO2 (aCO2). We hypothesized that the observed differences in soil functioning were based on differences in the abundance and composition of microbial communities in general and especially of those which are responsible for N-transformations in soil. We also expected eCO2 effects on soil parameters, such as on nitrate as previously reported. To explore the impact of long-term eCO2 on soil microbial communities, we applied a molecular approach (qPCR, T-RFLP, and 454 pyrosequencing). Microbial groups were analyzed in soil of three sets of two FACE plots (three replicate samples from each plot), which were fumigated with eCO2 and aCO2, respectively. N-fixers, denitrifiers, archaeal and bacterial ammonia oxidizers, and dissimilatory nitrate reducers producing ammonia were targeted by analysis of functional marker genes, and the overall archaeal community by 16S rRNA genes. Remarkably, soil parameters as well as the abundance and composition of microbial communities in the top soil under eCO2 differed only slightly from soil under aCO2. Wherever differences in microbial community abundance and composition were detected, they were not linked to CO2 level but rather determined by differences in soil parameters (e.g., soil moisture content) due to the localization of the GiFACE sets in the experimental field. We concluded that +20% eCO2 had little to no effect on the overall microbial community involved in N-cycling in the soil but that spatial heterogeneity over extended periods had shaped microbial communities at particular sites in the field. Hence, microbial community composition and abundance alone cannot explain the functional differences leading to higher N2O emissions under eCO2 and future studies should aim at exploring the active members of the soil microbial community.
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Affiliation(s)
- Kristof Brenzinger
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.,Department of Plant Ecology, University of Giessen, Giessen, Germany
| | - Katharina Kujala
- Water Resources and Environmental Engineering Research Unit, University of Oulu, Oulu, Finland
| | - Marcus A Horn
- Department of Ecological Microbiology, University of Bayreuth, Bayreuth, Germany.,Institute of Microbiology, Leibniz Universität Hannover, Hannover, Germany
| | - Gerald Moser
- Department of Plant Ecology, University of Giessen, Giessen, Germany
| | - Cécile Guillet
- Department of Plant Ecology, University of Giessen, Giessen, Germany
| | - Claudia Kammann
- Department of Plant Ecology, University of Giessen, Giessen, Germany.,Climate Change Research for Special Crops, Department of Soil Science and Plant Nutrition, Geisenheim University, Geisenheim, Germany
| | - Christoph Müller
- Department of Plant Ecology, University of Giessen, Giessen, Germany.,School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Gesche Braker
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.,University of Kiel, Kiel, Germany
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11
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Moissl-Eichinger C, Pausan M, Taffner J, Berg G, Bang C, Schmitz RA. Archaea Are Interactive Components of Complex Microbiomes. Trends Microbiol 2017; 26:70-85. [PMID: 28826642 DOI: 10.1016/j.tim.2017.07.004] [Citation(s) in RCA: 138] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 07/06/2017] [Accepted: 07/21/2017] [Indexed: 02/06/2023]
Abstract
Recent findings have shaken our picture of the biology of the archaea and revealed novel traits beyond archaeal extremophily and supposed 'primitiveness'. The archaea constitute a considerable fraction of the Earth's ecosystems, and their potential to shape their surroundings by a profound interaction with their biotic and abiotic environment has been recognized. Moreover, archaea have been identified as a substantial component, or even as keystone species, in complex microbiomes - in the environment or accompanying a holobiont. Species of the Euryarchaeota (methanogens, halophiles) and Thaumarchaeota, in particular, have the capacity to coexist in plant, animal, and human microbiomes, where syntrophy allows them to thrive under energy-deficiency stress. Due to methodological limitations, the archaeome remains mysterious, and many questions with respect to potential pathogenicity, function, and structural interactions with their host and other microorganisms remain.
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Affiliation(s)
| | - Manuela Pausan
- Medical University Graz, Internal Medicine, Graz, Austria
| | | | | | - Corinna Bang
- Christian-Albrechts-University Kiel, Kiel, Germany
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12
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Xiao L, Liu G, Li P, Xue S. Elevated CO 2 and nitrogen addition have minimal influence on the rhizospheric effects of Bothriochloa ischaemum. Sci Rep 2017; 7:6527. [PMID: 28747784 PMCID: PMC5529374 DOI: 10.1038/s41598-017-06994-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 06/21/2017] [Indexed: 11/15/2022] Open
Abstract
The influence of elevated CO2 and nitrogen (N) addition on soil microbial communities and the rhizospheric effects of Bothriochloa ischaemum were investigated. A pot-cultivation experiment was conducted in climate-controlled chambers under two levels of CO2 (400 and 800 μmol mol−1) and three levels of N addition (0, 2.5, and 5 g N m−2 y−1). Soil samples (rhizospheric and bulk soil) were collected for the assessment of soil organic carbon (SOC), total N (TN), total phosphorus (TP), basal respiration (BR), and phospholipid fatty acids (PLFAs) 106 days after treatments were conducted. Elevated CO2 significantly increased total and fungal PLFAs in the rhizosphere when combined with N addition, and N addition significantly increased BR in the rhizosphere and total, bacterial, fungal, Gram-positive (G+), and Gram-negative (G−) PLFAs in both rhizospheric and bulk soil. BR and total, bacterial, G+, and G+/G− PLFAs were significantly higher in rhizospheric than bulk soil, but neither elevated CO2 nor N addition affected the positive rhizospheric effects on bacterial, G+, or G+/G− PLFAs. N addition had a greater effect on soil microbial communities than elevated CO2, and elevated CO2 and N addition had minor contributions to the changes in the magnitude of the rhizospheric effects in B. ischaemum.
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Affiliation(s)
- Lie Xiao
- State Key Laboratory Base of Eco-hydraulic Engineering in Arid Area, Xi'an University of Technology, Xi'an, 710048, China.,State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Northwest A&F University, Yangling, 712100, China
| | - Guobin Liu
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Northwest A&F University, Yangling, 712100, China
| | - Peng Li
- State Key Laboratory Base of Eco-hydraulic Engineering in Arid Area, Xi'an University of Technology, Xi'an, 710048, China
| | - Sha Xue
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Northwest A&F University, Yangling, 712100, China.
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13
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Lin Y, Liu D, Yuan J, Ye G, Ding W. Methanogenic Community Was Stable in Two Contrasting Freshwater Marshes Exposed to Elevated Atmospheric CO 2. Front Microbiol 2017; 8:932. [PMID: 28596763 PMCID: PMC5442310 DOI: 10.3389/fmicb.2017.00932] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 05/08/2017] [Indexed: 02/01/2023] Open
Abstract
The effects of elevated atmospheric CO2 concentration on soil microbial communities have been previously recorded. However, limited information is available regarding the response of methanogenic communities to elevated CO2 in freshwater marshes. Using high-throughput sequencing and real-time quantitative PCR, we compared the abundance and community structure of methanogens in different compartments (bulk soil, rhizosphere soil, and roots) of Calamagrostis angustifolia and Carex lasiocarpa growing marshes under ambient (380 ppm) and elevated CO2 (700 ppm) atmospheres. C. lasiocarpa rhizosphere was a hotspot for potential methane production, based on the 10-fold higher abundance of the mcrA genes per dry weight. The two marshes and their compartments were occupied by different methanogenic communities. In the C. lasiocarpa marsh, archaeal family Methanobacteriaceae, Rice Cluster II, and Methanosaetaceae co-dominated in the bulk soil, while Methanobacteriaceae was the exclusively dominant methanogen in the rhizosphere soil and roots. Families Methanosarcinaceae and Methanocellaceae dominated in the bulk soil of C. angustifolia marsh. Conversely, Methanosarcinaceae and Methanocellaceae together with Methanobacteriaceae dominated in the rhizosphere soil and roots, respectively, in the C. angustifolia marsh. Elevated atmospheric CO2 increased plant photosynthesis and belowground biomass of C. lasiocarpa and C. angustifolia marshes. However, it did not significantly change the abundance (based on mcrA qPCR), diversity, or community structure (based on high-throughput sequencing) of methanogens in any of the compartments, irrespective of plant type. Our findings suggest that the population and species of the dominant methanogens had weak responses to elevated atmospheric CO2. However, minor changes in specific methanogenic taxa occurred under elevated atmospheric CO2. Despite minor changes, methanogenic communities in different compartments of two contrasting freshwater marshes were rather stable under elevated atmospheric CO2.
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Affiliation(s)
- Yongxin Lin
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of SciencesNanjing, China.,University of the Chinese Academy of SciencesBeijing, China
| | - Deyan Liu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of SciencesNanjing, China
| | - Junji Yuan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of SciencesNanjing, China
| | - Guiping Ye
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of SciencesNanjing, China.,University of the Chinese Academy of SciencesBeijing, China
| | - Weixin Ding
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of SciencesNanjing, China
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14
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Vegetation type and layer depth influence nitrite-dependent methane-oxidizing bacteria in constructed wetland. Arch Microbiol 2016; 199:505-511. [DOI: 10.1007/s00203-016-1328-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 12/03/2016] [Accepted: 12/07/2016] [Indexed: 10/20/2022]
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15
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Long Y, Yi H, Chen S, Zhang Z, Cui K, Bing Y, Zhuo Q, Li B, Xie S, Guo Q. Influences of plant type on bacterial and archaeal communities in constructed wetland treating polluted river water. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:19570-9. [PMID: 27392623 DOI: 10.1007/s11356-016-7166-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 06/28/2016] [Indexed: 05/12/2023]
Abstract
Both bacteria and archaeal communities can play important roles in biogeochemical processes in constructed wetland (CW) system. However, the influence of plant type on microbial community in surface water CW remains unclear. The present study investigated bacterial and archaeal communities in five surface water CW systems with different plant species. The abundance, richness, and diversity of both bacterial and archaeal communities considerably differed in these five CW systems. Compared with the other three CW systems, the CW systems planted with Vetiveria zizanioides or Juncus effusus L. showed much higher bacterial abundance but lower archaeal abundance. Bacteria outnumbered archaea in each CW system. Moreover, the CW systems planted with V. zizanioides or J. effusus L. had relatively lower archaeal but higher bacterial richness and diversity. In each CW system, bacterial community displayed much higher richness and diversity than archaeal community. In addition, a remarkable difference of both bacterial and archaeal community structures was observed in the five studied CW systems. Proteobacteria was the most abundant bacterial group (accounting for 33-60 %). Thaumarchaeota organisms (57 %) predominated in archaeal communities in CW systems planted with V. zizanioides or J. effusus L., while Woesearchaeota (23 or 24 %) and Euryarchaeota (23 or 15 %) were the major archaeal groups in CW systems planted with Cyperus papyrus or Canna indica L. Archaeal community in CW planted with Typha orientalis Presl was mainly composed of unclassified archaea. Therefore, plant type exerted a considerable influence on microbial community in surface water CW system.
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Affiliation(s)
- Yan Long
- Key Laboratory of Water/Soil Toxic Pollutants Control and Bioremediation of Guangdong Higher Education Institutes, School of Environment, Jinan University, Guangzhou, 510632, China
| | - Hao Yi
- South China Institute of Environmental Sciences (SCIES), Ministry of Environment Protection (MEP), Guangzhou, 510655, China
| | - Sili Chen
- South China Institute of Environmental Sciences (SCIES), Ministry of Environment Protection (MEP), Guangzhou, 510655, China
| | - Zhengke Zhang
- South China Institute of Environmental Sciences (SCIES), Ministry of Environment Protection (MEP), Guangzhou, 510655, China
| | - Kai Cui
- South China Institute of Environmental Sciences (SCIES), Ministry of Environment Protection (MEP), Guangzhou, 510655, China
| | - Yongxin Bing
- South China Institute of Environmental Sciences (SCIES), Ministry of Environment Protection (MEP), Guangzhou, 510655, China
| | - Qiongfang Zhuo
- South China Institute of Environmental Sciences (SCIES), Ministry of Environment Protection (MEP), Guangzhou, 510655, China
| | - Bingxin Li
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Shuguang Xie
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China.
| | - Qingwei Guo
- South China Institute of Environmental Sciences (SCIES), Ministry of Environment Protection (MEP), Guangzhou, 510655, China.
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16
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Okubo T, Liu D, Tsurumaru H, Ikeda S, Asakawa S, Tokida T, Tago K, Hayatsu M, Aoki N, Ishimaru K, Ujiie K, Usui Y, Nakamura H, Sakai H, Hayashi K, Hasegawa T, Minamisawa K. Elevated atmospheric CO2 levels affect community structure of rice root-associated bacteria. Front Microbiol 2015; 6:136. [PMID: 25750640 PMCID: PMC4335179 DOI: 10.3389/fmicb.2015.00136] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2014] [Accepted: 02/05/2015] [Indexed: 11/13/2022] Open
Abstract
A number of studies have shown that elevated atmospheric CO2 ([CO2]) affects rice yields and grain quality. However, the responses of root-associated bacteria to [CO2] elevation have not been characterized in a large-scale field study. We conducted a free-air CO2 enrichment (FACE) experiment (ambient + 200 μmol.mol(-1)) using three rice cultivars (Akita 63, Takanari, and Koshihikari) and two experimental lines of Koshihikari [chromosome segment substitution and near-isogenic lines (NILs)] to determine the effects of [CO2] elevation on the community structure of rice root-associated bacteria. Microbial DNA was extracted from rice roots at the panicle formation stage and analyzed by pyrosequencing the bacterial 16S rRNA gene to characterize the members of the bacterial community. Principal coordinate analysis of a weighted UniFrac distance matrix revealed that the community structure was clearly affected by elevated [CO2]. The predominant community members at class level were Alpha-, Beta-, and Gamma-proteobacteria in the control (ambient) and FACE plots. The relative abundance of Methylocystaceae, the major methane-oxidizing bacteria in rice roots, tended to decrease with increasing [CO2] levels. Quantitative PCR revealed a decreased copy number of the methane monooxygenase (pmoA) gene and increased methyl coenzyme M reductase (mcrA) in elevated [CO2]. These results suggest elevated [CO2] suppresses methane oxidation and promotes methanogenesis in rice roots; this process affects the carbon cycle in rice paddy fields.
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Affiliation(s)
- Takashi Okubo
- Environmental Biofunction Division, National Institute for Agro-Environmental SciencesTsukuba, Japan
- Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku UniversitySendai, Japan
| | - Dongyan Liu
- Division of Bioresource Functions, Graduate School of Bioagricultural Sciences, Nagoya UniversityNagoya, Japan
| | - Hirohito Tsurumaru
- Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku UniversitySendai, Japan
| | - Seishi Ikeda
- Large-scale Farming Research Division, Hokkaido Agricultural Research Center, National Agriculture and Food Research OrganizationHokkaido, Japan
| | - Susumu Asakawa
- Division of Bioresource Functions, Graduate School of Bioagricultural Sciences, Nagoya UniversityNagoya, Japan
| | - Takeshi Tokida
- Carbon and Nutrient Cycles Division, National Institute for Agro-Environmental SciencesTsukuba, Japan
| | - Kanako Tago
- Environmental Biofunction Division, National Institute for Agro-Environmental SciencesTsukuba, Japan
| | - Masahito Hayatsu
- Environmental Biofunction Division, National Institute for Agro-Environmental SciencesTsukuba, Japan
| | - Naohiro Aoki
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of TokyoTokyo, Japan
| | - Ken Ishimaru
- Division of Plant Sciences, National Institute of Agrobiological SciencesTsukuba, Japan
| | - Kazuhiro Ujiie
- Division of Plant Sciences, National Institute of Agrobiological SciencesTsukuba, Japan
| | - Yasuhiro Usui
- Agro-Meteorology Division, National Institute for Agro-Environmental SciencesTsukuba, Japan
| | | | - Hidemitsu Sakai
- Agro-Meteorology Division, National Institute for Agro-Environmental SciencesTsukuba, Japan
| | - Kentaro Hayashi
- Carbon and Nutrient Cycles Division, National Institute for Agro-Environmental SciencesTsukuba, Japan
| | - Toshihiro Hasegawa
- Agro-Meteorology Division, National Institute for Agro-Environmental SciencesTsukuba, Japan
| | - Kiwamu Minamisawa
- Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku UniversitySendai, Japan
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