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Ye X, Yu Y, Liu J, Zhu Y, Yu Z, Liu P, Wang Y, Wang K. Seasonal environmental factors drive microbial community succession and flavor quality during acetic acid fermentation of Zhenjiang aromatic vinegar. Front Microbiol 2024; 15:1442604. [PMID: 39171262 PMCID: PMC11335490 DOI: 10.3389/fmicb.2024.1442604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2024] [Accepted: 07/24/2024] [Indexed: 08/23/2024] Open
Abstract
This study investigated the impact of seasonal environmental factors on microorganisms and flavor compounds during acetic acid fermentation (AAF) of Zhenjiang aromatic vinegar (ZAV). Environmental factors were monitored throughout the fermentation process, which spanned multiple seasons. Methods such as headspace solid phase microextraction gas chromatography-mass spectrometry (HS-SPME-GC-MS), high performance liquid chromatography (HPLC), and high-throughput sequencing were employed to examine how these environmental factors influenced the flavor profile and microbial community of ZAV. The findings suggested that ZAV brewed in autumn had the strongest flavor and sweetness. The key microorganisms responsible for the flavor of ZAV included Lactobacillus acetotolerans, Lactobacillus plantarum, Lactobacillus reuteri, Lactobacillus fermentum, Acetobacter pasteurianus. Moreover, correlation analysis showed that room temperature had a significant impact on the composition of the microbial community, along with other key seasonal environmental factors like total acid, pH, reducing sugar, and humidity. These results provide a theoretical foundation for regulating core microorganisms and environmental factors during fermentation, enhancing ZAV quality.
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Affiliation(s)
- Xiaoting Ye
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Yongjian Yu
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang, China
- Jiangsu Provincial Engineering Research Center of Grain Bioprocessing, Zhenjiang, China
| | - Jiaxin Liu
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang, China
- Jiangsu Provincial Engineering Research Center of Grain Bioprocessing, Zhenjiang, China
| | - Yuanyuan Zhu
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang, China
- Jiangsu Provincial Engineering Research Center of Grain Bioprocessing, Zhenjiang, China
| | - Zhen Yu
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang, China
- Jiangsu Provincial Engineering Research Center of Grain Bioprocessing, Zhenjiang, China
| | - Peng Liu
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang, China
- Jiangsu Provincial Engineering Research Center of Grain Bioprocessing, Zhenjiang, China
| | - Yuqin Wang
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang, China
- Jiangsu Provincial Engineering Research Center of Grain Bioprocessing, Zhenjiang, China
| | - Ke Wang
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang, China
- Jiangsu Provincial Engineering Research Center of Grain Bioprocessing, Zhenjiang, China
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2
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Liu Y, Chen Y, Chen J, Zhang J, Teng HH. Combined toxicity of Cd and aniline to soil bacteria varying with exposure sequence. ENVIRONMENT INTERNATIONAL 2024; 190:108916. [PMID: 39094404 DOI: 10.1016/j.envint.2024.108916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 07/16/2024] [Accepted: 07/25/2024] [Indexed: 08/04/2024]
Abstract
Joint toxicity of organic-metal co-contamination can vary depending on organisms, toxicants, and even the sequence of exposure. This study examines how the combined toxicity of aniline (An) and cadmium (Cd) to soil bacteria in microcosms changes when the order of contaminant introduction is altered. Through analyzing biodiversity, molecular ecological network, functional redundancy, functional genes and pathways, we find the treatment of Cd followed by An brings about the strongest adverse impact to the bacterial consortium, followed by the reverse-ordered exposure and the simple mixture of the two chemicals. On the level of individual organisms, exposure sequence also affects the bacteria that are otherwise resistant to the standalone toxicity of both An and Cd. The dynamic behavior of aniline-cadmium composite is interpreted by considering the tolerance of organisms to individual chemicals, the interactions of the two toxicants, the recovery time, as well as the priority effect. The overall effect of the composite contamination is conceptualized by treating the chemicals as environmental filters screening the growth of the community.
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Affiliation(s)
- Yanjiao Liu
- School of Earth System Science, Institute of Surface-Earth System Science, Tianjin University, Tianjin 300072, China
| | - Yuxuan Chen
- School of Earth System Science, Institute of Surface-Earth System Science, Tianjin University, Tianjin 300072, China
| | - Jiubin Chen
- School of Earth System Science, Institute of Surface-Earth System Science, Tianjin University, Tianjin 300072, China
| | - Jianchao Zhang
- School of Earth System Science, Institute of Surface-Earth System Science, Tianjin University, Tianjin 300072, China.
| | - H Henry Teng
- School of Earth System Science, Institute of Surface-Earth System Science, Tianjin University, Tianjin 300072, China.
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3
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Gontijo JB, Paula FS, Bieluczyk W, França AG, Navroski D, Mandro JA, Venturini AM, Asselta FO, Mendes LW, Moura JMS, Moreira MZ, Nüsslein K, Bohannan BJM, Bodelier PLE, Rodrigues JLM, Tsai SM. Methane-cycling microbial communities from Amazon floodplains and upland forests respond differently to simulated climate change scenarios. ENVIRONMENTAL MICROBIOME 2024; 19:48. [PMID: 39020395 PMCID: PMC11256501 DOI: 10.1186/s40793-024-00596-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 07/10/2024] [Indexed: 07/19/2024]
Abstract
Seasonal floodplains in the Amazon basin are important sources of methane (CH4), while upland forests are known for their sink capacity. Climate change effects, including shifts in rainfall patterns and rising temperatures, may alter the functionality of soil microbial communities, leading to uncertain changes in CH4 cycling dynamics. To investigate the microbial feedback under climate change scenarios, we performed a microcosm experiment using soils from two floodplains (i.e., Amazonas and Tapajós rivers) and one upland forest. We employed a two-factorial experimental design comprising flooding (with non-flooded control) and temperature (at 27 °C and 30 °C, representing a 3 °C increase) as variables. We assessed prokaryotic community dynamics over 30 days using 16S rRNA gene sequencing and qPCR. These data were integrated with chemical properties, CH4 fluxes, and isotopic values and signatures. In the floodplains, temperature changes did not significantly affect the overall microbial composition and CH4 fluxes. CH4 emissions and uptake in response to flooding and non-flooding conditions, respectively, were observed in the floodplain soils. By contrast, in the upland forest, the higher temperature caused a sink-to-source shift under flooding conditions and reduced CH4 sink capability under dry conditions. The upland soil microbial communities also changed in response to increased temperature, with a higher percentage of specialist microbes observed. Floodplains showed higher total and relative abundances of methanogenic and methanotrophic microbes compared to forest soils. Isotopic data from some flooded samples from the Amazonas river floodplain indicated CH4 oxidation metabolism. This floodplain also showed a high relative abundance of aerobic and anaerobic CH4 oxidizing Bacteria and Archaea. Taken together, our data indicate that CH4 cycle dynamics and microbial communities in Amazonian floodplain and upland forest soils may respond differently to climate change effects. We also highlight the potential role of CH4 oxidation pathways in mitigating CH4 emissions in Amazonian floodplains.
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Affiliation(s)
- Júlia B Gontijo
- Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, SP, Brazil.
- Department of Land, Air and Water Resources, University of California, Davis, CA, USA.
| | - Fabiana S Paula
- Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, SP, Brazil
| | - Wanderlei Bieluczyk
- Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, SP, Brazil
| | - Aline G França
- Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, SP, Brazil
| | - Deisi Navroski
- Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, SP, Brazil
| | - Jéssica A Mandro
- Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, SP, Brazil
| | | | - Fernanda O Asselta
- Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, SP, Brazil
| | - Lucas W Mendes
- Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, SP, Brazil
| | - José M S Moura
- Instituto de Formação Interdisciplinar e Intercultural, Universidade Federal do Oeste do Pará, Santarém, PA, Brazil
| | - Marcelo Z Moreira
- Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, SP, Brazil
| | - Klaus Nüsslein
- Department of Microbiology, University of Massachusetts, Amherst, MA, USA
| | - Brendan J M Bohannan
- Department of Biology, Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
| | - Paul L E Bodelier
- Netherlands Institute of Ecology, NIOO-KNAW, Wageningen, GE, The Netherlands
| | - Jorge L Mazza Rodrigues
- Department of Land, Air and Water Resources, University of California, Davis, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Siu M Tsai
- Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, SP, Brazil
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Sachdeva S, Sarethy IP. Diving into freshwater microbial metabolites: Pioneering research and future prospects. INTERNATIONAL JOURNAL OF ENVIRONMENTAL HEALTH RESEARCH 2024:1-19. [PMID: 38887995 DOI: 10.1080/09603123.2024.2351153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 04/30/2024] [Indexed: 06/20/2024]
Abstract
In practically every facet of life, especially nutrition, agriculture, and healthcare, microorganisms offer a prospective origin for abundant natural substances and products. Among these microorganisms, bacteria also possess the capability to rapidly acclimate to diverse environments, utilize varied resources, and effectively respond to environmental fluctuations, including those influenced by human activities like pollution and climate change. The ever-changing environment of freshwater bodies influences bacterial communities, offering opportunities for improving health and environmental conservation that remain unexplored. Herein, the study discusses the bacterial taxa along with specialised metabolites with antioxidant, antibacterial, and anticancer activity that have been identified from freshwater environments, thus achieving Sustainable Development Goals addressing health and wellbeing (SDG-3), economic growth (SDG-8) along with industrial development (SDG-9). The present review is intended as a compendium for research teams working in the fields of medicinal chemistry, organic chemistry, clinical research, and natural product chemistry.
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Affiliation(s)
- Saloni Sachdeva
- Department of Biotechnology, Jaypee Institute of Information Technology, Noida, India
| | - Indira P Sarethy
- Department of Biotechnology, Jaypee Institute of Information Technology, Noida, India
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5
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Weng ZH, Kopittke PM, Schweizer S, Jin J, Armstrong R, Rose M, Zheng Y, Franks A, Tang C. Shining a Light on How Soil Organic Carbon Behaves at Fine Scales under Long-Term Elevated CO 2: An 8 Year Free-Air Carbon Dioxide Enrichment Study. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:8724-8735. [PMID: 38717952 DOI: 10.1021/acs.est.3c10680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Building and protecting soil organic carbon (SOC) are critical to agricultural productivity, soil health, and climate change mitigation. We aim to understand how mechanisms at the organo-mineral interfaces influence SOC persistence in three contrasting soils (Luvisol, Vertisol, and Calcisol) under long-term free air CO2 enrichment conditions. A continuous wheat-field pea-canola rotation was maintained. For the first time, we provided evidence to a novel notion that persistent SOC is molecularly simple even under elevated CO2 conditions. We found that the elevated CO2 condition did not change the total SOC content or C forms compared with the soils under ambient CO2 as identified by synchrotron-based soft X-ray analyses. Furthermore, synchrotron-based infrared microspectroscopy confirmed a two-dimensional microscale distribution of similar and less diverse C forms in intact microaggregates under long-term elevated CO2 conditions. Strong correlations between the distribution of C forms and O-H groups of clays can explain the steady state of the total SOC content. However, the correlations between C forms and clay minerals were weakened in the coarse-textured Calcisol under long-term elevated CO2. Our findings suggested that we should emphasize identifying management practices that increase the physical protection of SOC instead of increasing complexity of C. Such information is valuable in developing more accurate C prediction models under elevated CO2 conditions and shift our thinking in developing management practices for maintaining and building SOC for better soil fertility and future environmental sustainability.
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Affiliation(s)
- Zhe H Weng
- Department of Animal, Plant & Soil Sciences, Centre for AgriBioscience, La Trobe University, Melbourne, Victoria 3086, Australia
- School of Agriculture and Food Sciences, The University of Queensland, St. Lucia, Queensland 4072, Australia
- School of Agriculture, Food, and Wine, The University of Adelaide, Urrbrae, South Australia 5064, Australia
| | - Peter M Kopittke
- School of Agriculture and Food Sciences, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Steffen Schweizer
- School of Life Sciences, Technical University of Munich, Freising 85354, Germany
| | - Jian Jin
- Department of Animal, Plant & Soil Sciences, Centre for AgriBioscience, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Roger Armstrong
- Agriculture Victoria Research, Department of Energy, Environment and Climate Action, Horsham, Victoria 3401, Australia
| | - Michael Rose
- NSW Department of Primary Industries, Wollongbar Primary Industries Institute, Wollongbar, New South Wales 2477, Australia
| | - Yunyun Zheng
- Department of Animal, Plant & Soil Sciences, Centre for AgriBioscience, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Ashley Franks
- Department of Microbiology, Anatomy, Physiology and Pharmacology, La Trobe University, Melbourne, Victoria 3086, Australia
- Centre for Future Landscapes, La Trobe University, Melbourne, Victoria 3086, Australia
- La Trobe Institute for Sustainable Agriculture and Food, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Caixian Tang
- Department of Animal, Plant & Soil Sciences, Centre for AgriBioscience, La Trobe University, Melbourne, Victoria 3086, Australia
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Lennon JT, Abramoff RZ, Allison SD, Burckhardt RM, DeAngelis KM, Dunne JP, Frey SD, Friedlingstein P, Hawkes CV, Hungate BA, Khurana S, Kivlin SN, Levine NM, Manzoni S, Martiny AC, Martiny JBH, Nguyen NK, Rawat M, Talmy D, Todd-Brown K, Vogt M, Wieder WR, Zakem EJ. Priorities, opportunities, and challenges for integrating microorganisms into Earth system models for climate change prediction. mBio 2024; 15:e0045524. [PMID: 38526088 PMCID: PMC11078004 DOI: 10.1128/mbio.00455-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2024] Open
Abstract
Climate change jeopardizes human health, global biodiversity, and sustainability of the biosphere. To make reliable predictions about climate change, scientists use Earth system models (ESMs) that integrate physical, chemical, and biological processes occurring on land, the oceans, and the atmosphere. Although critical for catalyzing coupled biogeochemical processes, microorganisms have traditionally been left out of ESMs. Here, we generate a "top 10" list of priorities, opportunities, and challenges for the explicit integration of microorganisms into ESMs. We discuss the need for coarse-graining microbial information into functionally relevant categories, as well as the capacity for microorganisms to rapidly evolve in response to climate-change drivers. Microbiologists are uniquely positioned to collect novel and valuable information necessary for next-generation ESMs, but this requires data harmonization and transdisciplinary collaboration to effectively guide adaptation strategies and mitigation policy.
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Affiliation(s)
- J. T. Lennon
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - R. Z. Abramoff
- Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Ronin Institute, Montclair, New Jersey, USA
| | - S. D. Allison
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, California, USA
- Department of Earth System Science, University of California Irvine, Irvine, California, USA
| | | | - K. M. DeAngelis
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, USA
| | - J. P. Dunne
- NOAA/OAR Geophysical Fluid Dynamics Laboratory, Princeton, New Jersey, USA
| | - S. D. Frey
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, New Hampshire, USA
| | - P. Friedlingstein
- College of Engineering, Mathematics, and Physical Sciences, University of Exeter, Exeter, United Kingdom
| | - C. V. Hawkes
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, USA
| | - B. A. Hungate
- Department of Biological Sciences, Center for Ecosystem Science, Northern Arizona University, Flagstaff, Arizona, USA
| | - S. Khurana
- Department of Physical Geography, Bolin Centre for Climate Research, Stockholm University, Stockholm, Sweden
| | - S. N. Kivlin
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, Tennessee, USA
| | - N. M. Levine
- Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
| | - S. Manzoni
- Department of Physical Geography, Bolin Centre for Climate Research, Stockholm University, Stockholm, Sweden
| | - A. C. Martiny
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, California, USA
| | - J. B. H. Martiny
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, California, USA
| | - N. K. Nguyen
- American Society for Microbiology, Washington, DC, USA
| | - M. Rawat
- National Science Foundation, Washington, DC, USA
| | - D. Talmy
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
| | - K. Todd-Brown
- Department of Environmental Engineering Sciences, University of Florida, Gainesville, Florida, USA
| | - M. Vogt
- Institute for Biogeochemistry and Pollutant Dynamics, ETH Zürich, Zürich, Switzerland
| | - W. R. Wieder
- National Center for Atmospheric Research, Boulder, Colorado, USA
- Institute of Arctic and Alpine Research, University of Colorado, Boulder, Colorado, USA
| | - E. J. Zakem
- Department of Global Ecology, Carnegie Institution for Science, Stanford, California, USA
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7
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Zhang G, Bai J, Zhai Y, Jia J, Zhao Q, Wang W, Hu X. Microbial diversity and functions in saline soils: A review from a biogeochemical perspective. J Adv Res 2024; 59:129-140. [PMID: 37392974 PMCID: PMC11081963 DOI: 10.1016/j.jare.2023.06.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Revised: 06/24/2023] [Accepted: 06/27/2023] [Indexed: 07/03/2023] Open
Abstract
BACKGROUND Soil salinization threatens food security and ecosystem health, and is one of the important drivers to the degradation of many ecosystems around the world. Soil microorganisms have extremely high diversity and participate in a variety of key ecological processes. They are important guarantees for soil health and sustainable ecosystem development. However, our understanding of the diversity and function of soil microorganisms under the change of increased soil salinization is fragmented. AIM OF REVIEW Here, we summarize the changes in soil microbial diversity and function under the influence of soil salinization in diverse natural ecosystems. We particularly focus on the diversity of soil bacteria and fungi under salt stress and the changes in their emerging functions (such as their mediated biogeochemical processes). This study also discusses how to use the soil microbiome in saline soils to deal with soil salinization for supporting sustainable ecosystems, and puts forward the knowledge gaps and the research directions that need to be strengthened in the future. KEY SCIENTIFIC CONCEPTS OF REVIEW Due to the rapid development of molecular-based biotechnology (especially high-throughput sequencing technology), the diversity and community composition and functional genes of soil microorganisms have been extensively characterized in different habitats. Clarifying the responding pattern of microbial-mediated nutrient cycling under salt stress and developing and utilizing microorganisms to weaken the adverse effects of salt stress on plants and soil, which are of guiding significance for agricultural production and ecosystem management in saline lands.
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Affiliation(s)
- Guangliang Zhang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, PR China; Advanced Institute of Natural Sciences, Beijing Normal University, Zhuhai 519087, PR China
| | - Junhong Bai
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, PR China.
| | - Yujia Zhai
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, PR China
| | - Jia Jia
- Henan Key Laboratory of Ecological Environment Protection and Restoration of Yellow River Basin, Yellow River Institute of Hydraulic Research, Zhengzhou 45003, PR China
| | - Qingqing Zhao
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Ji'nan 250103, PR China
| | - Wei Wang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, PR China
| | - Xingyun Hu
- Fujian Provincial Key Laboratory for Subtropical Resources and Environment, Fujian Normal University, Fuzhou 350007, PR China
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8
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Wu Y, Zhou S, Li Y, Niu L, Wang L. Climate and local environment co-mediate the taxonomic and functional diversity of bacteria and archaea in the Qinghai-Tibet Plateau rivers. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:168968. [PMID: 38042190 DOI: 10.1016/j.scitotenv.2023.168968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 11/18/2023] [Accepted: 11/26/2023] [Indexed: 12/04/2023]
Abstract
Understanding the environmental response patterns of riverine microbiota is essential for predicting the potential impact of future environmental change on river ecosystems. Vulnerable plateau ecosystems are particularly sensitive to climate and local environmental changes, however, the environmental response patterns of the taxonomic and functional diversity of riverine microbiota remain unclear. Here, we conducted a systematic investigation of the taxonomic and functional diversity of bacteria and archaea from riparian soils, sediments, and water across the elevation of 1800- 4800 m in the Qinghai-Tibet Plateau rivers. We found that within the elevation range of 1800 to 3800 m, riparian soils and sediments exhibited similarities and stabilities in microbial taxonomic and functional diversity, and water microbiomes were more sensitive with great fluctuations in microbial diversity. Beyond the elevation of 3800 m, microbial diversity declined across all riverine matrixes. Local environmental conditions can influence the sensitivity of microbiomes to climate change. The combination of critical climate and local environmental factors, including total nitrogen, total organic carbon, as well as climate variables associated with temperature and precipitation, provided better explanations for microbial diversity than single-factor analyses. Under the extremely adverse scenario of high greenhouse gas emission concentrations (SSP585), we anticipate that by the end of this century, the bacterial, archaeal, and microbial functional diversity across the river network of the Yangtze and Yellow source basin would potentially change by -16.9- 5.2 %, -16.1- 5.7 %, and -9.3- 6.4 %, respectively. Overall, climate and local environments jointly shaped the microbial diversity in plateau river ecosystems, and water microbiomes would provide early signs of environmental changes. Our study provides effective theoretical foundations for the conservation of river biodiversity and functional stability under environmental changes.
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Affiliation(s)
- Yunyu Wu
- College of Hydrology and Water Resources, Hohai University, Nanjing 210024, PR China
| | - Shubu Zhou
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210024, PR China
| | - Yi Li
- College of Hydrology and Water Resources, Hohai University, Nanjing 210024, PR China.
| | - Lihua Niu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210024, PR China.
| | - Linqiong Wang
- College of Oceanography, Hohai University, Nanjing 210024, PR China
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9
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Schmidt RL, Azarbad H, Bainard L, Tremblay J, Yergeau E. Intermittent water stress favors microbial traits that better help wheat under drought. ISME COMMUNICATIONS 2024; 4:ycae074. [PMID: 38863723 PMCID: PMC11165427 DOI: 10.1093/ismeco/ycae074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 05/01/2024] [Accepted: 05/16/2024] [Indexed: 06/13/2024]
Abstract
Microorganisms can improve plant resistance to drought through various mechanisms, such as the production of plant hormones, osmolytes, antioxidants, and exopolysaccharides. It is, however, unclear how previous exposure to water stress affects the functional capacity of the soil microbial community to help plants resist drought. We compared two soils that had either a continuous or intermittent water stress history (WSH) for almost 40 years. We grew wheat in these soils and subjected it to water stress, after which we collected the rhizosphere soil and shotgun sequenced its metagenome. Wheat growing in soil with an intermittent WSH maintained a higher biomass when subjected to water stress. Genes related to indole-acetic acid and osmolyte production were more abundant in the metagenome of the soil with an intermittent WSH as compared to the soil with a continuous WSH. We suggest that an intermittent WSH selects traits beneficial for life under water stress.
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Affiliation(s)
- Ruth Lydia Schmidt
- Centre Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique, Laval, QC, H7V 1B7, Canada
| | - Hamed Azarbad
- Department of Biology, Evolutionary Ecology of Plants, Philipps-University Marburg, Karl-von-Frisch-Strasse 8, 35043 Marburg, Germany
| | - Luke Bainard
- Agassiz Research and Development Centre, Agriculture and Agri-Food Canada, 6947 #7 Highway, Agassiz, BC, V0M 1A2, Canada
| | - Julien Tremblay
- Centre Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique, Laval, QC, H7V 1B7, Canada
| | - Etienne Yergeau
- Centre Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique, Laval, QC, H7V 1B7, Canada
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10
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Zhang Y, Cheng X, van Groenigen KJ, García-Palacios P, Cao J, Zheng X, Luo Y, Hungate BA, Terrer C, Butterbach-Bahl K, Olesen JE, Chen J. Shifts in soil ammonia-oxidizing community maintain the nitrogen stimulation of nitrification across climatic conditions. GLOBAL CHANGE BIOLOGY 2024; 30:e16989. [PMID: 37888833 DOI: 10.1111/gcb.16989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 10/01/2023] [Accepted: 10/04/2023] [Indexed: 10/28/2023]
Abstract
Anthropogenic nitrogen (N) loading alters soil ammonia-oxidizing archaea (AOA) and bacteria (AOB) abundances, likely leading to substantial changes in soil nitrification. However, the factors and mechanisms determining the responses of soil AOA:AOB and nitrification to N loading are still unclear, making it difficult to predict future changes in soil nitrification. Herein, we synthesize 68 field studies around the world to evaluate the impacts of N loading on soil ammonia oxidizers and nitrification. Across a wide range of biotic and abiotic factors, climate is the most important driver of the responses of AOA:AOB to N loading. Climate does not directly affect the N-stimulation of nitrification, but does so via climate-related shifts in AOA:AOB. Specifically, climate modulates the responses of AOA:AOB to N loading by affecting soil pH, N-availability and moisture. AOB play a dominant role in affecting nitrification in dry climates, while the impacts from AOA can exceed AOB in humid climates. Together, these results suggest that climate-related shifts in soil ammonia-oxidizing community maintain the N-stimulation of nitrification, highlighting the importance of microbial community composition in mediating the responses of the soil N cycle to N loading.
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Affiliation(s)
- Yong Zhang
- Key Laboratory of Soil Ecology and Health in Universities of Yunnan Province, School of Ecology and Environmental Science, Yunnan University, Kunming, China
- State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an, China
| | - Xiaoli Cheng
- Key Laboratory of Soil Ecology and Health in Universities of Yunnan Province, School of Ecology and Environmental Science, Yunnan University, Kunming, China
| | - Kees Jan van Groenigen
- Department of Geography, Faculty of Environment, Science and Economy, University of Exeter, Exeter, UK
| | - Pablo García-Palacios
- Instituto de Ciencias Agrarias, Consejo Superior de Investigaciones Científicas, Madrid, Spain
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Junji Cao
- Institute of Atmospheric Physics, Chinese Academy of Sciences, Beijing, China
| | - Xunhua Zheng
- Institute of Atmospheric Physics, Chinese Academy of Sciences, Beijing, China
| | - Yiqi Luo
- School of Integrative Plant Science, Cornell University, New York, Ithaca, USA
| | - Bruce A Hungate
- Department of Biological Sciences, Northern Arizona University, Arizona, Flagstaff, USA
| | - Cesar Terrer
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Massachusetts, Cambridge, USA
| | - Klaus Butterbach-Bahl
- Institute for Meteorology and Climate Research, Atmospheric Environmental Research, Karlsruhe Institute of Technology, Garmisch-Partenkirchen, Germany
- Center for Landscape Research in Sustainable Agricultural Futures, Land-CRAFT, Department of Agroecology, Aarhus University, Aarhus, Denmark
| | - Jørgen Eivind Olesen
- Department of Agroecology, Aarhus University, Tjele, Denmark
- Aarhus University Centre for Circular Bioeconomy, Aarhus University, Tjele, Denmark
- iCLIMATE Interdisciplinary Centre for Climate Change, Aarhus University, Roskilde, Denmark
| | - Ji Chen
- State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an, China
- Department of Agroecology, Aarhus University, Tjele, Denmark
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11
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Gronniger JL, Gray PC, Niebergall AK, Johnson ZI, Hunt DE. A Gulf Stream frontal eddy harbors a distinct microbiome compared to adjacent waters. PLoS One 2023; 18:e0293334. [PMID: 37943816 PMCID: PMC10635494 DOI: 10.1371/journal.pone.0293334] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 10/10/2023] [Indexed: 11/12/2023] Open
Abstract
Mesoscale oceanographic features, including eddies, have the potential to alter productivity and other biogeochemical rates in the ocean. Here, we examine the microbiome of a cyclonic, Gulf Stream frontal eddy, with a distinct origin and environmental parameters compared to surrounding waters, in order to better understand the processes dominating microbial community assembly in the dynamic coastal ocean. Our microbiome-based approach identified the eddy as distinct from the surround Gulf Stream waters. The eddy-associated microbial community occupied a larger area than identified by temperature and salinity alone, increasing the predicted extent of eddy-associated biogeochemical processes. While the eddy formed on the continental shelf, after two weeks both environmental parameters and microbiome composition of the eddy were most similar to the Gulf Stream, suggesting the effect of environmental filtering on community assembly or physical mixing with adjacent Gulf Stream waters. In spite of the potential for eddy-driven upwelling to introduce nutrients and stimulate primary production, eddy surface waters exhibit lower chlorophyll a along with a distinct and less even microbial community, compared to the Gulf Stream. At the population level, the eddy microbiome exhibited differences among the cyanobacteria (e.g. lower Trichodesmium and higher Prochlorococcus) and in the heterotrophic alpha Proteobacteria (e.g. lower relative abundances of specific SAR11 phylotypes) versus the Gulf Stream. However, better delineation of the relative roles of processes driving eddy community assembly will likely require following the eddy and surrounding waters since inception. Additionally, sampling throughout the water column could better clarify the contribution of these mesoscale features to primary production and carbon export in the oceans.
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Affiliation(s)
| | - Patrick C. Gray
- Marine Laboratory, Duke University, Beaufort, NC, United States of America
| | | | - Zackary I. Johnson
- Marine Laboratory, Duke University, Beaufort, NC, United States of America
- Biology and Civil & Environmental Engineering, Duke University, Durham, NC, United States of America
| | - Dana E. Hunt
- Marine Laboratory, Duke University, Beaufort, NC, United States of America
- Biology and Civil & Environmental Engineering, Duke University, Durham, NC, United States of America
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12
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Li Y, Wang F, Yang H, Li H, Hu C. Balanced biogeographic and local environmental effects determine the patterns of microbial diversity in biocrusts at multi-scales. Front Microbiol 2023; 14:1284864. [PMID: 38029206 PMCID: PMC10666793 DOI: 10.3389/fmicb.2023.1284864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction Biodiversity maintenance and its underlying mechanisms are central issues of ecology. However, predicting the composition turnovers of microbial communities at multiple spatial scales remains greatly challenging because they are obscured by the inconsistent impacts of climatic and local edaphic conditions on the assembly process. Methods Based on the Illumina MeSeq 16S/18S rRNA sequencing technology, we investigated soil bacterial and eukaryotic communities in biocrusts with different successional levels at a subcontinental scale of Northern China. Results Results showed that irrespective of spatial scale, bacterial α diversity increased but eukaryotic diversity decreased with the primary succession, whereas both β diversities decreased at the subcontinental scale compared with smaller scales, indicating that the biogeographic pattern of soil microorganisms was balanced by successional convergence and distance decay effect. We found that the convergence of bacterial and eukaryotic communities was attributed to the turnovers of generalist and specialist species, respectively. In this process, edaphic and climatic factors showed unique roles in the changes of diversity at local/subcontinental scales. Moreover, the taxonomic diversity tended to be more susceptible to climatic and edaphic conditions, while biotic factors (photosynthesis and pigments) were more important to phylogenetic diversity. Conclusion Taken together, our study provided comprehensive insights into understanding the pattern of microbial diversity at multiple spatial scales of drylands.
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Affiliation(s)
- Yuanlong Li
- Hunan Provincial Key Laboratory of Carbon Neutrality and Intelligent Energy, School of Resource and Environment, Hunan University of Technology and Business, Changsha, China
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Fengdi Wang
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Haijian Yang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Hua Li
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Chunxiang Hu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
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13
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Martiny JBH, Martiny AC, Brodie E, Chase AB, Rodríguez-Verdugo A, Treseder KK, Allison SD. Investigating the eco-evolutionary response of microbiomes to environmental change. Ecol Lett 2023; 26 Suppl 1:S81-S90. [PMID: 36965002 DOI: 10.1111/ele.14209] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 02/13/2023] [Accepted: 03/06/2023] [Indexed: 03/27/2023]
Abstract
Microorganisms are the primary engines of biogeochemical processes and foundational to the provisioning of ecosystem services to human society. Free-living microbial communities (microbiomes) and their functioning are now known to be highly sensitive to environmental change. Given microorganisms' capacity for rapid evolution, evolutionary processes could play a role in this response. Currently, however, few models of biogeochemical processes explicitly consider how microbial evolution will affect biogeochemical responses to environmental change. Here, we propose a conceptual framework for explicitly integrating evolution into microbiome-functioning relationships. We consider how microbiomes respond simultaneously to environmental change via four interrelated processes that affect overall microbiome functioning (physiological acclimation, demography, dispersal and evolution). Recent evidence in both the laboratory and the field suggests that ecological and evolutionary dynamics occur simultaneously within microbiomes; however, the implications for biogeochemistry under environmental change will depend on the timescales over which these processes contribute to a microbiome's response. Over the long term, evolution may play an increasingly important role for microbially driven biogeochemical responses to environmental change, particularly to conditions without recent historical precedent.
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Affiliation(s)
- Jennifer B H Martiny
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California, USA
| | - Adam C Martiny
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California, USA
- Department of Earth System Science, University of California, Irvine, California, USA
| | - Eoin Brodie
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, California, USA
| | - Alexander B Chase
- Department of Earth Sciences, Southern Methodist University, Dallas, Texas, USA
| | | | - Kathleen K Treseder
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California, USA
| | - Steven D Allison
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California, USA
- Department of Earth System Science, University of California, Irvine, California, USA
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14
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Bissett A, Mamet SD, Lamb EG, Siciliano SD. Linking niche size and phylogenetic signals to predict future soil microbial relative abundances. Front Microbiol 2023; 14:1097909. [PMID: 37645222 PMCID: PMC10461061 DOI: 10.3389/fmicb.2023.1097909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 07/10/2023] [Indexed: 08/31/2023] Open
Abstract
Bacteria provide ecosystem services (e.g., biogeochemical cycling) that regulate climate, purify water, and produce food and other commodities, yet their distribution and likely responses to change or intervention are difficult to predict. Using bacterial 16S rRNA gene surveys of 1,381 soil samples from the Biomes of Australian Soil Environment (BASE) dataset, we were able to model relative abundances of soil bacterial taxonomic groups and describe bacterial niche space and optima. Hold out sample validated hypothetical causal networks (structural equation models; SEM) were able to predict the relative abundances of bacterial taxa from environmental data and elucidate soil bacterial niche space. By using explanatory SEM properties as indicators of microbial traits, we successfully predicted soil bacterial response, and in turn potential ecosystem service response, to near-term expected changes in the Australian climate. The methods developed enable prediction of continental-scale changes in bacterial relative abundances, and demonstrate their utility in predicting changes in bacterial function and thereby ecosystem services. These capabilities will be strengthened in the future with growing genome-level data.
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Affiliation(s)
| | | | - Eric G. Lamb
- University of Saskatchewan, Saskatoon, SK, Canada
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15
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Lian T, Cheng L, Liu Q, Yu T, Cai Z, Nian H, Hartmann M. Potential relevance between soybean nitrogen uptake and rhizosphere prokaryotic communities under waterlogging stress. ISME COMMUNICATIONS 2023; 3:71. [PMID: 37433864 PMCID: PMC10336055 DOI: 10.1038/s43705-023-00282-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 06/28/2023] [Accepted: 07/03/2023] [Indexed: 07/13/2023]
Abstract
Waterlogging in soil can limit the availability of nitrogen to plants by promoting denitrification and reducing nitrogen fixation and nitrification. The root-associated microorganisms that determine nitrogen availability at the root-soil interface can be influenced by plant genotype and soil type, which potentially alters the nitrogen uptake capacity of plants in waterlogged soils. In a greenhouse experiment, two soybean genotypes with contrasting capacities to resist waterlogging stress were grown in Udic Argosol and Haplic Alisol soils with and without waterlogging, respectively. Using isotope labeling, high-throughput amplicon sequencing and qPCR, we show that waterlogging negatively affects soybean yield and nitrogen absorption from fertilizer, atmosphere, and soil. These effects were soil-dependent and more pronounced in the waterlogging-sensitive than tolerant genotype. The tolerant genotype harbored more ammonia oxidizers and less nitrous oxide reducers. Anaerobic, nitrogen-fixing, denitrifying and iron-reducing bacteria such as Geobacter/Geomonas, Sphingomonas, Candidatus Koribacter, and Desulfosporosinus were proportionally enriched in association with the tolerant genotype under waterlogging. These changes in the rhizosphere microbiome might ultimately help the plant to improve nitrogen uptake under waterlogged, anoxic conditions. This research contributes to a better understanding of the adaptability of soybean genotypes under waterlogging stress and might help to formulate fertilization strategies that improve nitrogen use efficiency of soybean. Schematic representation of the effects of waterlogging on nitrogen uptake and rhizosphere microbiota in dependence of soil type and soybean genotype.
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Affiliation(s)
- Tengxiang Lian
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, Guangdong, China.
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China.
- Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland.
| | - Lang Cheng
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, Guangdong, China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China
| | - Qi Liu
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, Guangdong, China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China
| | - Taobing Yu
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, Guangdong, China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China
| | - Zhandong Cai
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, Guangdong, China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China
| | - Hai Nian
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, Guangdong, China.
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China.
| | - Martin Hartmann
- Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland.
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16
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Cowan DA, Cary SC, DiRuggiero J, Eckardt F, Ferrari B, Hopkins DW, Lebre PH, Maggs-Kölling G, Pointing SB, Ramond JB, Tribbia D, Warren-Rhodes K. 'Follow the Water': Microbial Water Acquisition in Desert Soils. Microorganisms 2023; 11:1670. [PMID: 37512843 PMCID: PMC10386458 DOI: 10.3390/microorganisms11071670] [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: 05/03/2023] [Revised: 06/12/2023] [Accepted: 06/16/2023] [Indexed: 07/30/2023] Open
Abstract
Water availability is the dominant driver of microbial community structure and function in desert soils. However, these habitats typically only receive very infrequent large-scale water inputs (e.g., from precipitation and/or run-off). In light of recent studies, the paradigm that desert soil microorganisms are largely dormant under xeric conditions is questionable. Gene expression profiling of microbial communities in desert soils suggests that many microbial taxa retain some metabolic functionality, even under severely xeric conditions. It, therefore, follows that other, less obvious sources of water may sustain the microbial cellular and community functionality in desert soil niches. Such sources include a range of precipitation and condensation processes, including rainfall, snow, dew, fog, and nocturnal distillation, all of which may vary quantitatively depending on the location and geomorphological characteristics of the desert ecosystem. Other more obscure sources of bioavailable water may include groundwater-derived water vapour, hydrated minerals, and metabolic hydro-genesis. Here, we explore the possible sources of bioavailable water in the context of microbial survival and function in xeric desert soils. With global climate change projected to have profound effects on both hot and cold deserts, we also explore the potential impacts of climate-induced changes in water availability on soil microbiomes in these extreme environments.
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Affiliation(s)
- Don A Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0002, South Africa
| | - S Craig Cary
- School of Biological Sciences, University of Waikato, Hamilton 3216, New Zealand
| | - Jocelyne DiRuggiero
- Departments of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
- Departments of Earth and Planetary Sciences, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Frank Eckardt
- Department of Environmental and Geographical Science, University of Cape Town, Cape Town 7701, South Africa
| | - Belinda Ferrari
- School of Biotechnology and Biological Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - David W Hopkins
- Scotland's Rural College, West Mains Road, Edinburgh EH9 3JG, UK
| | - Pedro H Lebre
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0002, South Africa
| | | | - Stephen B Pointing
- Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore
| | - Jean-Baptiste Ramond
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0002, South Africa
- Departamento Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
| | - Dana Tribbia
- School of Biotechnology and Biological Sciences, University of New South Wales, Sydney, NSW 2052, Australia
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17
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Zhou Q, Zhang J, Fang Q, Zhang M, Wang X, Zhang D, Pan X. Microplastic biodegradability dependent responses of plastisphere antibiotic resistance to simulated freshwater-seawater shift in onshore marine aquaculture zones. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 331:121828. [PMID: 37187278 DOI: 10.1016/j.envpol.2023.121828] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 05/09/2023] [Accepted: 05/13/2023] [Indexed: 05/17/2023]
Abstract
MPs carrying ARGs can travel between freshwater and seawater due to intensive land-sea interaction in onshore marine aquaculture zones (OMAZ). However, the response of ARGs in plastisphere with different biodegradability to freshwater-seawater shift is still unknown. In this study, ARG dynamics and associated microbiota on biodegradable poly (butyleneadipate-co-terephthalate) (PBAT) and non-biodegradable polyethylene terephthalate (PET) MPs were investigated through a simulated freshwater-seawater shift. The results exhibited that freshwater-seawater shift significantly influenced ARG abundance in plastisphere. The relative abundance of most studied ARGs decreased rapidly in plastisphere after they entered seawater from freshwater but increased on PBAT after MPs entered freshwater from seawater. Besides, the high relative abundance of multi-drug resistance (MDR) genes occurred in plastisphere, and the co-change between most ARGs and mobile genetic elements indicated the role of horizontal gene transfer on ARG regulation. Proteobacteria was dominant phylum in plastisphere and the dominant genera, such as Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium, Afipia, Gemmobacter and Enhydrobacter, were significantly associated with qnrS, tet and MDR genes in plastisphere. Moreover, after MPs entered new water environment, the ARGs and microbiota genera in plastisphere changed significantly and tended to converge with those in receiving water. These results indicated that MP biodegradability and freshwater-seawater interaction influenced potential hosts and distributions of ARGs, of which biodegradable PBAT posed a high risk in ARG dissemination. This study would be helpful for understanding the impact of biodegradable MP pollution on spread of antibiotic resistance in OMAZ.
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Affiliation(s)
- Qian Zhou
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Jun Zhang
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Qunkai Fang
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Ming Zhang
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Xiaonan Wang
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Daoyong Zhang
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou, 310014, China.
| | - Xiangliang Pan
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou, 310014, China
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18
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Badger Hanson E, Docherty KM. Mini-review: Current and Future Perspectives on Microbially Focused Restoration Strategies in Tallgrass Prairies. MICROBIAL ECOLOGY 2023; 85:1087-1097. [PMID: 36449026 DOI: 10.1007/s00248-022-02150-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 11/14/2022] [Indexed: 05/04/2023]
Abstract
Ecosystem restoration is a critical conservation strategy, especially for increasing resilience and resistance to climate change. Current restoration efforts that convert reclaimed agricultural land to native tallgrass prairies typically focus on aboveground communities, but it can take decades to restore soil microbial biodiversity and function using these strategies, if they recover at all. This incomplete restoration can have detrimental impacts on longer-term restoration goals, such as supporting late-successional plant species and facilitating soil carbon sequestration. Soil microorganisms are key components in determining the fate of organic material that enters the soil. They mediate decomposition rates and contribute to plant-microbe-soil interactions, produce microbial biomass, necromass, and metabolic products, and physically protect soil carbon through aggregation. Interactions with plants and controls over soil carbon vary widely depending on the specific microbial taxa present, their physiology, their functional capabilities, and their responses to environmental stressors. Thus, the ability for new restorations, prairie conservation corridors, and prairies planted in marginal lands to act as carbon sinks and help balance greenhouse gas emissions can depend on the success of microbial restoration. Next-generation sequencing approaches can support novel methods for evaluating existing restoration practices and developing microbially focused management strategies. This review summarizes the growing body of literature describing microbially focused tallgrass prairie restoration and considers when and how integrating next-generation sequencing approaches into management efforts can be beneficial. We provide a roadmap for future restoration efforts where microbial ecologists, restoration ecologists, and land managers can work together to meet their goals to promote climate-ready restored ecosystems.
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Affiliation(s)
- Ellen Badger Hanson
- Department of Biological Sciences, Western Michigan University, 1903 West Michigan Avenue, Kalamazoo, MI, 49008, USA
| | - Kathryn M Docherty
- Department of Biological Sciences, Western Michigan University, 1903 West Michigan Avenue, Kalamazoo, MI, 49008, USA.
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19
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Divergent Controls on Leaf and Root Litter Decay Linking to Soil C, N, and P Pools Under a Subtropical Land-use Change. Ecosystems 2023. [DOI: 10.1007/s10021-023-00827-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
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20
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Barrón-Sandoval A, Martiny JBH, Pérez-Carbajal T, Bullock SH, Leija A, Hernández G, Escalante AE. Functional significance of microbial diversity in arid soils: biological soil crusts and nitrogen fixation as a model system. FEMS Microbiol Ecol 2023; 99:6998555. [PMID: 36690342 PMCID: PMC9923382 DOI: 10.1093/femsec/fiad009] [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: 07/19/2022] [Revised: 01/11/2023] [Accepted: 01/20/2023] [Indexed: 01/25/2023] Open
Abstract
Microbial communities respond to changes in environmental conditions; however, how compositional shifts affect ecosystem processes is still not well-understood and it is often assumed that different microbial communities will function equally under similar environmental conditions. We evaluated this assumption of functional redundancy using biological soil crusts (BSCs) from two arid ecosystems in Mexico with contrasting climate conditions (hot and cold deserts) following an experimental approach both in the field (reciprocal transplants) and in laboratory conditions (common garden), focusing on the community's composition and potential for nitrogen fixation. Potential of nitrogen fixation was assessed through the acetylene reduction assay. Community composition and diversity was determined with T-RFLPs of nifH gene, high throughput sequencing of 16S rRNA gene amplicons and metagenomic libraries. BSCs tended to show higher potential nitrogen fixation rates when experiencing temperatures more similar to their native environment. Moreover, changes in potential nitrogen fixation, taxonomic and functional community composition, and diversity often depended on an interactive effect of origin of the communities and the environment they experienced. We interpret our results as legacy effects that result from ecological specialization of the BSC communities to their native environment. Overall, we present evidence of nonfunctional redundancy of BSCs in terms of nitrogen fixation.
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Affiliation(s)
- Alberto Barrón-Sandoval
- Laboratorio Nacional de Ciencias de la Sostenibilidad (LANCIS), Instituto de Ecología, UNAM. Circuito Exterior s/n, junto al Jardín Botánico, Coyacán, Mexico City, 014510, Mexico,Department of Ecology and Evolutionary Biology, University of California, 321 Steinhaus Hall, Irvine, CA 92627, United States
| | - Jennifer B H Martiny
- Department of Ecology and Evolutionary Biology, University of California, 321 Steinhaus Hall, Irvine, CA 92627, United States
| | - Teresa Pérez-Carbajal
- Laboratorio Nacional de Ciencias de la Sostenibilidad (LANCIS), Instituto de Ecología, UNAM. Circuito Exterior s/n, junto al Jardín Botánico, Coyacán, Mexico City, 014510, Mexico
| | - Stephen H Bullock
- Department of Conservation Biology, Center for Scientific Research and Higher Education of Ensenada (CICESE), Ctra. Ensenada-Tijuana No. 3918, Ensenada, 22860 Baja CA, Mexico
| | - Alfonso Leija
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Av, Universidad 1001, 62210 Cuernavaca, Morelos, Mexico
| | - Georgina Hernández
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Av, Universidad 1001, 62210 Cuernavaca, Morelos, Mexico
| | - Ana E Escalante
- Corresponding author: Laboratorio Nacional de Ciencias de la Sostenibilidad (LANCIS), Instituto de Ecología, UNAM. Circuito Exterior s/n, junto al Jardín Botánico, Coyacán, Mexico City, 04510. Mexico. Tel: +52(55)5623-7714; E-mail:
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21
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Li K, Veen GFC, Ten Hooven FC, Harvey JA, van der Putten WH. Soil legacy effects of plants and drought on aboveground insects in native and range-expanding plant communities. Ecol Lett 2023; 26:37-52. [PMID: 36414536 PMCID: PMC10098829 DOI: 10.1111/ele.14129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 07/20/2022] [Accepted: 09/14/2022] [Indexed: 11/24/2022]
Abstract
Soils contain biotic and abiotic legacies of previous conditions that may influence plant community biomass and associated aboveground biodiversity. However, little is known about the relative strengths and interactions of the various belowground legacies on aboveground plant-insect interactions. We used an outdoor mesocosm experiment to investigate the belowground legacy effects of range-expanding versus native plants, extreme drought and their interactions on plants, aphids and pollinators. We show that plant biomass was influenced more strongly by the previous plant community than by the previous summer drought. Plant communities consisted of four congeneric pairs of natives and range expanders, and their responses were not unanimous. Legacy effects affected the abundance of aphids more strongly than pollinators. We conclude that legacies can be contained as soil 'memories' that influence aboveground plant community interactions in the next growing season. These soil-borne 'memories' can be altered by climate warming-induced plant range shifts and extreme drought.
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Affiliation(s)
- Keli Li
- Department of Terrestrial Ecology (NIOO-KNAW), Netherlands Institute of Ecology, Wageningen, the Netherlands.,Laboratory of Nematology, Department of Plant Sciences, Wageningen University, Wageningen, the Netherlands
| | - G F Ciska Veen
- Department of Terrestrial Ecology (NIOO-KNAW), Netherlands Institute of Ecology, Wageningen, the Netherlands
| | - Freddy C Ten Hooven
- Department of Terrestrial Ecology (NIOO-KNAW), Netherlands Institute of Ecology, Wageningen, the Netherlands
| | - Jeffrey A Harvey
- Department of Terrestrial Ecology (NIOO-KNAW), Netherlands Institute of Ecology, Wageningen, the Netherlands.,Department of Ecological Science, Section Animal Ecology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Wim H van der Putten
- Department of Terrestrial Ecology (NIOO-KNAW), Netherlands Institute of Ecology, Wageningen, the Netherlands.,Laboratory of Nematology, Department of Plant Sciences, Wageningen University, Wageningen, the Netherlands
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22
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Responses of grassland productivity to mowing intensity and precipitation variability in a temperate steppe. Oecologia 2023; 201:259-268. [PMID: 36507970 DOI: 10.1007/s00442-022-05305-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 12/06/2022] [Indexed: 12/14/2022]
Abstract
Mowing for hay is an important land use in grasslands that is affected by precipitation variability, due to the water-limited nature of these ecosystems. Past land use and precipitation conditions can have legacy effects on ecosystem functions, potentially altering responses to both mowing and precipitation. Nonetheless, it is still unclear how natural variation in precipitation will affect plant responses to changes in mowing intensity. We conducted a seven-year field experiment with three mowing intensity treatments compared to the traditional mowing intensity (5 cm stubble height) as a control: increased mowing (2 cm stubble), decreased mowing (8 cm stubble) and ceased mowing. Decreased mowing increased both plant aboveground net primary productivity [ANPP] and forage yield across the whole community, driven by increases in graminoids, mainly owing to the positive response of plants to precipitation. Both mowing disturbance and precipitation variability had legacy effects on plant ANPP; however, these responses differed among the whole community, graminoid, and forb levels. Current-year community-wide ANPP [ANPPn] was positively associated with current-year precipitation [PPTn] in all mowing treatments, driven by positive precipitation responses of the dominant graminoids. For forbs, however, ANPPn was negatively associated with prior-year growing season precipitation [PPTn-1] across mowing treatments, potentially due to lagged competition with the dominant graminoids. Our results suggest that the response of the dominant graminoids is the primary factor determining the response of ANPP to mowing and precipitation variability in these grassland ecosystems, and highlight that decreasing mowing intensity may maximize both herder's income and grassland sustainability.
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23
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Kuang J, Deng D, Han S, Bates CT, Ning D, Shu W, Zhou J. Resistance potential of soil bacterial communities along a biodiversity gradient in forest ecosystems. MLIFE 2022; 1:399-411. [PMID: 38818486 PMCID: PMC10989803 DOI: 10.1002/mlf2.12042] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 08/29/2022] [Accepted: 08/30/2022] [Indexed: 06/01/2024]
Abstract
Higher biodiversity is often assumed to be a more desirable scenario for maintaining the functioning of ecosystems, but whether species-richer communities are also more disturbance-tolerant remains controversial. In this study, we investigated the bacterial communities based on 472 soil samples from 28 forests across China with associated edaphic and climatic properties. We developed two indexes (i.e., community mean tolerance breadth [CMTB] and community mean response asynchrony [CMRA]) to explore the relationship between diversity and community resistance potential. Moreover, we examined this resistance potential along the climatic and latitudinal gradients. We revealed that CMTB was significantly and negatively related to species richness, resulting from the changes in balance between relative abundances of putative specialists and generalists. In comparison, we found a unimodal relationship between CMRA and richness, suggesting that higher biodiversity might not always lead to higher community resistance. Moreover, our results showed differential local patterns along latitude. In particular, local patterns in the northern region mainly followed general relationships rather than those for the southern forests, which may be attributed to the differences in annual means and annual variations of climate conditions. Our findings highlight that the community resistance potential depends on the composition of diverse species with differential environmental tolerance and responses. This study provides a new, testable evaluation by considering tolerance breadth and response asynchrony at the community level, which will be helpful in assessing the influence of disturbance under rapid shifts in biodiversity and species composition as a result of global environmental change.
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Affiliation(s)
- Jialiang Kuang
- The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of EducationSchool of Environment and Energy, South China University of TechnologyGuangzhouChina
- Institute for Environmental Genomics, and Department of Microbiology and Plant BiologyUniversity of OklahomaNormanOklahomaUSA
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources and Conservation of Guangdong Higher Education InstitutesCollege of Ecology and Evolution, Sun Yat‐sen UniversityGuangzhouChina
| | - Dongmei Deng
- Institute for Environmental Genomics, and Department of Microbiology and Plant BiologyUniversity of OklahomaNormanOklahomaUSA
- Guangxi Key Laboratory of Green Processing of Sugar ResourcesCollege of Biological and Chemical Engineering, Guangxi University of Science and TechnologyLiuzhouChina
| | - Shun Han
- Institute for Environmental Genomics, and Department of Microbiology and Plant BiologyUniversity of OklahomaNormanOklahomaUSA
| | - Colin T. Bates
- Institute for Environmental Genomics, and Department of Microbiology and Plant BiologyUniversity of OklahomaNormanOklahomaUSA
| | - Daliang Ning
- Institute for Environmental Genomics, and Department of Microbiology and Plant BiologyUniversity of OklahomaNormanOklahomaUSA
| | - Wensheng Shu
- School of Life SciencesSouth China Normal UniversityGuangzhouChina
| | - Jizhong Zhou
- Institute for Environmental Genomics, and Department of Microbiology and Plant BiologyUniversity of OklahomaNormanOklahomaUSA
- School of Civil Engineering and Environmental SciencesUniversity of OklahomaNormanOklahomaUSA
- School of Computer SciencesUniversity of OklahomaNormanOklahomaUSA
- Earth and Environmental SciencesLawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
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24
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Yang Q, Veen GF(C, Wagenaar R, Manrubia M, ten Hooven FC, van der Putten WH. Temporal dynamics of range expander and congeneric native plant responses during and after extreme drought events. ECOL MONOGR 2022; 92:e1529. [PMID: 36590329 PMCID: PMC9787952 DOI: 10.1002/ecm.1529] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 12/01/2021] [Accepted: 01/14/2022] [Indexed: 01/04/2023]
Abstract
Climate change is causing range shifts of many species to higher latitudes and altitudes and increasing their exposure to extreme weather events. It has been shown that range-shifting plant species may perform differently in new soil than related natives; however, little is known about how extreme weather events affect range-expanding plants compared to related natives. In this study we used outdoor mesocosms to study how range-expanding plant species responded to extreme drought in live soil from a habitat in a new range with and without live soil from a habitat in the original range (Hungary). During summer drought, the shoot biomass of the range-expanding plant community declined. In spite of this, in the mixed community, range expanders produced more shoot biomass than congeneric natives. In mesocosms with a history of range expanders in the previous year, native plants produced less biomass. Plant legacy or soil origin effects did not change the response of natives or range expanders to summer drought. During rewetting, range expanders had less biomass than congeneric natives but higher drought resilience (survival) in soils from the new range where in the previous year native plant species had grown. The biomass patterns of the mixed plant communities were dominated by Centaurea spp.; however, not all plant species within the groups of natives and of range expanders showed the general pattern. Drought reduced the litter decomposition, microbial biomass, and abundances of bacterivorous, fungivorous, and carnivorous nematodes. Their abundances recovered during rewetting. There was less microbial and fungal biomass, and there were fewer fungivorous nematodes in soils from the original range where range expanders had grown in the previous year. We concluded that in mixed plant communities of range expanders and congeneric natives, range expanders performed better, under both ambient and drought conditions, than congeneric natives. However, when considering the responses of individual species, we observed variations among pairs of congenerics, so that under the present mixed-community conditions there was no uniformity in responses to drought of range expanders versus congeneric natives. Range-expanding plant species reduced soil fungal biomass and the numbers of soil fungivorous nematodes, suggesting that the effects of range-expanding plant species can trickle up in the soil food web.
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Affiliation(s)
- Qiang Yang
- Department of Terrestrial EcologyNetherlands Institute of Ecology (NIOO‐KNAW)WageningenThe Netherlands,State Key Laboratory of Grassland Agro‐ecosystems, School of Life SciencesLanzhou UniversityLanzhouChina
| | - G. F. (Ciska) Veen
- Department of Terrestrial EcologyNetherlands Institute of Ecology (NIOO‐KNAW)WageningenThe Netherlands
| | - Roel Wagenaar
- Department of Terrestrial EcologyNetherlands Institute of Ecology (NIOO‐KNAW)WageningenThe Netherlands
| | - Marta Manrubia
- Department of Terrestrial EcologyNetherlands Institute of Ecology (NIOO‐KNAW)WageningenThe Netherlands
| | - Freddy C. ten Hooven
- Department of Terrestrial EcologyNetherlands Institute of Ecology (NIOO‐KNAW)WageningenThe Netherlands
| | - Wim H. van der Putten
- Department of Terrestrial EcologyNetherlands Institute of Ecology (NIOO‐KNAW)WageningenThe Netherlands,Laboratory of Nematology, Department of Plant SciencesWageningen University (WUR)WageningenThe Netherlands
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25
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Zhang Z, Jatana BS, Campbell BJ, Gill J, Suseela V, Tharayil N. Cross-inoculation of rhizobiome from a congeneric ruderal plant imparts drought tolerance in maize (Zea mays) through changes in root morphology and proteome. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:54-71. [PMID: 35426964 PMCID: PMC9542220 DOI: 10.1111/tpj.15775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Accepted: 04/12/2022] [Indexed: 06/14/2023]
Abstract
Rhizobiome confer stress tolerance to ruderal plants, yet their ability to alleviate stress in crops is widely debated, and the associated mechanisms are poorly understood. We monitored the drought tolerance of maize (Zea mays) as influenced by the cross-inoculation of rhizobiota from a congeneric ruderal grass Andropogon virginicus (andropogon-inoculum), and rhizobiota from organic farm maintained under mesic condition (organic-inoculum). Across drought treatments (40% field capacity), maize that received andropogon-inoculum produced two-fold greater biomass. This drought tolerance translated to a similar leaf metabolomic composition as that of the well-watered control (80% field capacity) and reduced oxidative damage, despite a lower activity of antioxidant enzymes. At a morphological-level, drought tolerance was associated with an increase in specific root length and surface area facilitated by the homeostasis of phytohormones promoting root branching. At a proteome-level, the drought tolerance was associated with upregulation of proteins related to glutathione metabolism and endoplasmic reticulum-associated degradation process. Fungal taxa belonging to Ascomycota, Mortierellomycota, Archaeorhizomycetes, Dothideomycetes, and Agaricomycetes in andropogon-inoculum were identified as potential indicators of drought tolerance. Our study provides a mechanistic understanding of the rhizobiome-facilitated drought tolerance and demonstrates a better path to utilize plant-rhizobiome associations to enhance drought tolerance in crops.
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Affiliation(s)
- Ziliang Zhang
- Department of Plant & Environmental SciencesClemson UniversityClemsonSCUSA
| | | | | | - Jasmine Gill
- Department of Plant & Environmental SciencesClemson UniversityClemsonSCUSA
| | - Vidya Suseela
- Department of Plant & Environmental SciencesClemson UniversityClemsonSCUSA
| | - Nishanth Tharayil
- Department of Plant & Environmental SciencesClemson UniversityClemsonSCUSA
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26
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A Drying-Rewetting Cycle Imposes More Important Shifts on Soil Microbial Communities than Does Reduced Precipitation. mSystems 2022; 7:e0024722. [PMID: 35762785 PMCID: PMC9426475 DOI: 10.1128/msystems.00247-22] [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] [Indexed: 11/20/2022] Open
Abstract
Global changes will result in altered precipitation patterns, among which the increasing frequency of drought events has the highest deleterious potential for agriculture. Soil microbes have shown some promise to help crops adapt to drought events, but it is uncertain how crop-associated microorganisms will respond to altered precipitation patterns. To investigate this matter, we conducted a field experiment where we seeded two wheat cultivars (one resistant to water stress and the other sensitive) that were subjected to four precipitation exclusion (PE) regimes (0%, 25%, 50%, and 75% exclusion). These cultivars were sampled seven times (every 2 weeks, from May to August) within one growing season to investigate short-term microbiome responses to altered precipitation regimes and seasonality using 16S rRNA gene and internal transcribed spacer (ITS) region amplicon sequencing. One of the most striking features of the data set was the dramatic shift in microbial community diversity, structure, and composition together with a doubling of the relative abundance of the archaeal ammonia oxidizer genus Nitrososphaera following an important drying-rewetting event. Comparatively small but significant effects of PE and wheat cultivar on microbial community diversity, composition, and structure were observed. Taken together, our results demonstrate an uneven response of microbial taxa to decreasing soil water content, which was dwarfed by drying-rewetting events, to which soil bacteria and archaea were more sensitive than fungi. Importantly, our study showed that an increase in drying-rewetting cycles will cause larger shifts in soil microbial communities than a decrease in total precipitation, suggesting that under climate changes, the distribution of precipitation will be more important than small variations in the total quantity of precipitation. IMPORTANCE Climate change will have a profound effect on the precipitation patterns of global terrestrial ecosystems. Seasonal and interannual uneven distributions of precipitation will lead to increasing frequencies and intensities of extreme drought and rainfall events, which will affect crop productivity and nutrient contents in various agroecosystems. However, we still lack knowledge about the responses of soil microbial communities to reduced precipitation and drying-rewetting events in agroecosystems. Our results demonstrated an uneven response of the soil microbiome and a dramatic shift in microbial community diversity and structure to a significant drying-rewetting event with a large increase in the relative abundance of archaeal ammonia oxidizers. These findings highlight the larger importance of rewetting of dry soils on microbial communities, as compared to decreased precipitation, with potential for changes in the soil nitrogen cycling.
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27
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Liu Z, Yan Q, Jiang C, Li J, Jian H, Fan L, Zhang R, Xiao X, Meng D, Liu X, Wang J, Yin H. Growth rate determines prokaryote-provirus network modulated by temperature and host genetic traits. MICROBIOME 2022; 10:92. [PMID: 35701838 PMCID: PMC9195381 DOI: 10.1186/s40168-022-01288-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 05/12/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Prokaryote-virus interactions play key roles in driving biogeochemical cycles. However, little is known about the drivers shaping their interaction network structures, especially from the host features. Here, we compiled 7656 species-level genomes in 39 prokaryotic phyla across environments globally and explored how their interaction specialization is constrained by host life history traits, such as growth rate. RESULTS We first reported that host growth rate indicated by the reverse of minimal doubling time was negatively related to interaction specialization for host in host-provirus network across various ecosystems and taxonomy groups. Such a negative linear growth rate-specialization relationship (GrSR) was dependent on host optimal growth temperature (OGT), and stronger toward the two gradient ends of OGT. For instance, prokaryotic species with an OGT ≥ 40 °C showed a stronger GrSR (Pearson's r = -0.525, P < 0.001). Significant GrSRs were observed with the presences of host genes in promoting the infection cycle at stages of adsorption, establishment, and viral release, but nonsignificant with the presence of immune systems, such as restriction-modification systems and CRISPR-Cas systems. Moreover, GrSR strength was increased with the presence of temperature-dependent lytic switches, which was also confirmed by mathematical modeling. CONCLUSIONS Together, our results advance our understanding of the interactions between prokaryotes and proviruses and highlight the importance of host growth rate in interaction specialization during lysogenization. Video Abstract.
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Affiliation(s)
- Zhenghua Liu
- Key Laboratory of Biometallurgy of Ministry of Education, School of Minerals Processing and Bioengineering, Central South University, Changsha, 410006, China
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Qingyun Yan
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510006, China
| | - Chengying Jiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Juan Li
- College of Agronomy, Hunan Agricultural University, Changsha, 410125, China
| | - Huahua Jian
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Lu Fan
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Rui Zhang
- State Key Laboratory of Marine Environmental Science, The Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, 361102, China
| | - Xiang Xiao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Delong Meng
- Key Laboratory of Biometallurgy of Ministry of Education, School of Minerals Processing and Bioengineering, Central South University, Changsha, 410006, China
| | - Xueduan Liu
- Key Laboratory of Biometallurgy of Ministry of Education, School of Minerals Processing and Bioengineering, Central South University, Changsha, 410006, China
| | - Jianjun Wang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China.
| | - Huaqun Yin
- Key Laboratory of Biometallurgy of Ministry of Education, School of Minerals Processing and Bioengineering, Central South University, Changsha, 410006, China.
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28
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Yu S, Sayer EJ, Li Z, Mo Q, Wang M, Li Y, Li Y, Xu G, Hu Z, Wang F. Delayed wet season increases soil net N mineralization in a seasonally dry tropical forest. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 823:153314. [PMID: 35124037 DOI: 10.1016/j.scitotenv.2022.153314] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 01/02/2022] [Accepted: 01/17/2022] [Indexed: 06/14/2023]
Abstract
Seasonal precipitation regime plays a vital role in regulating nutrient dynamics in seasonally dry tropical forests. Present evidence suggests that not only wet season precipitation is increasing in the tropics of South China, but also that the wet season is occurring later. However, it is unclear how nutrient dynamics will respond to the projected precipitation regime changes. We assessed the impacts of altered seasonal precipitation on soil net N mineralization in a secondary tropical forest. Since 2013, by reducing throughfall and/or irrigating experimental plots, we delayed the wet season by two months from April-September to June-November (DW treatment) or increased annual precipitation by 25% in July and August (WW treatment). We measured soil net N mineralization rates and assessed soil microbial communities in January, April, August and November in 2015 and 2017. We found that a wetter wet season did not significantly affect soil microbes or net N mineralization rates, even in the mid-wet season (August) when soil water content in the WW treatment increased significantly. By contrast, a delayed wet season enhanced soil microbial biomass and altered microbial community structure, resulting in a two-fold increase in net N mineralization rates relative to controls in the early dry season (November). Structural equation modeling showed that the changes in net N mineralization during the early dry season were associated with altered soil microbial communities, dissolved organic N, and litterfall, which were all affected by enhanced soil water content. Our findings suggest that a delayed wet season could have a greater impact on N dynamics than increased precipitation during the wet season. Changes in the seasonal timing of rainfall might therefore influence the functioning of seasonally dry tropical forests.
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Affiliation(s)
- Shiqin Yu
- School of Geography and Remote Sensing, Guangzhou University, Guangzhou 510006, PR China; Xiaoliang Research Station of Tropical Coastal Ecosystems, Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, and the CAS engineering Laboratory for Ecological Restoration of Island and Coastal Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, PR China
| | - Emma J Sayer
- Lancaster Environment Center, Lancaster University, Lancaster LA1 4YQ, UK; Smithsonian Tropical Research Institute, Balboa, Ancon, Panama City, Panama
| | - Zhian Li
- Xiaoliang Research Station of Tropical Coastal Ecosystems, Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, and the CAS engineering Laboratory for Ecological Restoration of Island and Coastal Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, PR China
| | - Qifeng Mo
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, PR China
| | - Mei Wang
- School of Geographic Sciences, South China Normal University, Guangzhou 510631, China
| | - Yingwen Li
- Xiaoliang Research Station of Tropical Coastal Ecosystems, Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, and the CAS engineering Laboratory for Ecological Restoration of Island and Coastal Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, PR China
| | - Yongxing Li
- Xiaoliang Research Station of Tropical Coastal Ecosystems, Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, and the CAS engineering Laboratory for Ecological Restoration of Island and Coastal Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, PR China
| | - Guoliang Xu
- School of Geography and Remote Sensing, Guangzhou University, Guangzhou 510006, PR China
| | - Zhongmin Hu
- College of Ecology and Environment, Hainan University, Haikou 570228, China
| | - Faming Wang
- Xiaoliang Research Station of Tropical Coastal Ecosystems, Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, and the CAS engineering Laboratory for Ecological Restoration of Island and Coastal Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, PR China.
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29
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Fei S, Kivlin SN, Domke GM, Jo I, LaRue EA, Phillips RP. Coupling of plant and mycorrhizal fungal diversity: its occurrence, relevance, and possible implications under global change. THE NEW PHYTOLOGIST 2022; 234:1960-1966. [PMID: 35014033 DOI: 10.1111/nph.17954] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 12/21/2021] [Indexed: 06/14/2023]
Abstract
First principles predict that diversity at one trophic level often begets diversity at other levels, suggesting plant and mycorrhizal fungal diversity should be coupled. Local-scale studies have shown positive coupling between the two, but the association is less consistent when extended to larger spatial and temporal scales. These inconsistencies are likely due to divergent relationships of different mycorrhizal fungal guilds to plant diversity, scale dependency, and a lack of coordinated sampling efforts. Given that mycorrhizal fungi play a central role in plant productivity and nutrient cycling, as well as ecosystem responses to global change, an improved understanding of the coupling between plant and mycorrhizal fungal diversity across scales will reduce uncertainties in predicting the ecosystem consequences of species gains and losses.
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Affiliation(s)
- Songlin Fei
- Department of Forestry and Natural Resources, Purdue University, 715 W. State St., West Lafayette, IN, 47907, USA
| | - Stephanie N Kivlin
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Grant M Domke
- United States Department of Agriculture Forest Service, Northern Research Station, 1992 Folwell Ave., St. Paul, MN, 55108, USA
| | - Insu Jo
- Manaaki Whenua - Landcare Research, 54 Gerald St., Lincoln, 7608, New Zealand
| | - Elizabeth A LaRue
- Department of Forestry and Natural Resources, Purdue University, 715 W. State St., West Lafayette, IN, 47907, USA
- Department of Biological Sciences, The University of Texas at El Paso, 500 W. University Ave., El Paso, TX, 79968, USA
| | - Richard P Phillips
- Department of Biology, Indiana University, 1001 East Third St., Bloomington, IN, 47405, USA
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30
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Babalola BJ, Li J, Willing CE, Zheng Y, Wang YL, Gan HY, Li XC, Wang C, Adams CA, Gao C, Guo LD. Nitrogen fertilisation disrupts the temporal dynamics of arbuscular mycorrhizal fungal hyphae but not spore density and community composition in a wheat field. THE NEW PHYTOLOGIST 2022; 234:2057-2072. [PMID: 35179789 DOI: 10.1111/nph.18043] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 02/07/2022] [Indexed: 06/14/2023]
Abstract
Elucidating the temporal dynamics of arbuscular mycorrhizal (AM) fungi is critical for understanding their functions. Furthermore, research investigating the temporal dynamics of AM fungi in response to agricultural practices remains in its infancy. We investigated the effect of nitrogen fertilisation and watering reduction on the temporal dynamics of AM fungi, across the lifespan of wheat. Nitrogen fertilisation decreased AM fungal spore density (SD), extraradical hyphal density (ERHD), and intraradical colonisation rate (IRCR) in both watering conditions. Nitrogen fertilisation affected AM fungal community composition in soil but not in roots, regardless of watering conditions. The temporal analysis revealed that AM fungal ERHD and IRCR were higher under conventional watering and lower under reduced watering in March than in other growth stages at low (≤ 70 kg N ha-1 yr-1 ) but not at high (≥ 140) nitrogen fertilisation levels. AM fungal SD was lower in June than in other growth stages and community composition varied with plant development at all nitrogen fertilisation levels, regardless of watering conditions. This study demonstrates that high nitrogen fertilisation levels disrupt the temporal dynamics of AM fungal hyphal growth but not sporulation and community composition.
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Affiliation(s)
- Busayo Joshua Babalola
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jing Li
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, 100101, China
| | | | - Yong Zheng
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, Fujian Normal University, Fuzhou, 350007, China
| | - Yong-Long Wang
- Faculty of Biological Science and Technology, Baotou Teacher's College, Baotou, Inner Mongolia, 014030, China
| | - Hui-Yun Gan
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xing-Chun Li
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Cong Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Catharine A Adams
- Department of Plant and Microbial Biology, University of California-Berkeley, Berkeley, CA, 94720-3102, USA
| | - Cheng Gao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Liang-Dong Guo
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
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31
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Distinct Elevational Patterns and Their Linkages of Soil Bacteria and Plant Community in An Alpine Meadow of the Qinghai-Tibetan Plateau. Microorganisms 2022; 10:microorganisms10051049. [PMID: 35630491 PMCID: PMC9143282 DOI: 10.3390/microorganisms10051049] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 05/15/2022] [Accepted: 05/17/2022] [Indexed: 11/30/2022] Open
Abstract
Soil microbes play important roles in determining plant community composition and terrestrial ecosystem functions, as well as the direction and extent of terrestrial ecosystem feedback to environmental changes. Understanding the distribution patterns of plant and soil microbiota along elevation gradients is necessary to shed light on important ecosystem functions. In this study, soil bacteria along an elevation gradient in an alpine meadow ecosystem of the Qinghai−Tibetan Plateau were investigated using Illumina sequencing and GeoChip technologies. The community structure of the soil bacteria and plants presented a continuous trend along the elevation gradient, and their alpha diversity displayed different distribution patterns; however, there were no linkages between them. Beta diversity of the soil bacteria and plants was significantly influenced by elevational distance changes (p < 0.05). Functional gene categories involved in nitrogen and phosphorus cycling had faster changes than those involved in carbon degradation, and functional genes involved in labile carbon degradation also had faster variations than those involved in recalcitrant carbon degradation with elevational changes. According to Pearson’s correlation, partial Mantel test analysis, and canonical correspondence analysis, soil pH and mean annual precipitation were important environmental variables in influencing soil bacterial diversity. Soil bacterial diversity and plant diversity had different distribution patterns along the elevation gradient.
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32
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Shen H, Zhang Q, Bi R, Xu X, Zhang X, Fan C, Xiong Z. Linkages of nitrogen-cycling microbial resistance and resilience to soil nutrient stoichiometry under dry-rewetting cycles with different fertilizations and temperatures in a vegetable field. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 820:153294. [PMID: 35066034 DOI: 10.1016/j.scitotenv.2022.153294] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/10/2022] [Accepted: 01/16/2022] [Indexed: 06/14/2023]
Abstract
Multiple dry-rewetting (DRW) cycles occur in intensively managed vegetable fields due to frequent tillage and irrigation. Soil nitrogen (N) cycling depends on the resistance and resilience of related microbial populations to DRW cycles, which could be closely related to soil nutrient status. However, the linkage of N-cycling microbial resistance and resilience and soil nutrient stoichiometry remains unknown in vegetable field. Here, we established four fertilization treatments in a four-year greenhouse vegetable field: no N fertilization, synthesized N fertilization, substituting 50% of chemical N with organic fertilizer or biofertilizer. Then, we set up an 85-day DRW-cycling incubation at 15, 25 and 35 °C including a 55-day fluctuating moisture for microbial resistance and then a 30-day constant moisture for microbial resilience. The results showed that microbial resistance was high (resistance index = 0.87- 0.99) in response to DRW cycles, but microbial resilience was generally low (resilience index = -0.36- 0.76), especially in 50% organic substitution or 15 °C. N-cycling microbes showed an important trade-off between their resistance and resilience to DRW cycles. Furthermore, most treatments showed microbial carbon limitation and N abundance during DRW cycles and recovered gradually to the undisturbed state. Microbial resistance was significantly related to the soil nutrient stoichiometry of carbon, N and phosphorus, while microbial resilience was mainly correlated with carbon-related indicators. In conclusion, N-cycling microbes presented good stability with oligotrophic strategy to frequent DRW cycles, which was linked to not only the historical legacy effect of DRW cycles but also soil nutrient stoichiometry in the vegetable field.
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Affiliation(s)
- Haojie Shen
- Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China; Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Qianqian Zhang
- Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China; School of Environmental and Resource Sciences, Zhejiang A & F University, Hangzhou 311300, China
| | - Ruiyu Bi
- Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Xintong Xu
- Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Xi Zhang
- Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Changhua Fan
- Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China; Hainan Key Laboratory of Tropical Eco-circular Agriculture, Danzhou National Agricultural Experimental Station for Agricultural Environment, Institute of Environmental and Plant Protection, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Zhengqin Xiong
- Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China.
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Wang F, Li Z, Fu B, Lü Y, Liu G, Wang D, Wu X. Short-Term Grazing Exclusion Alters Soil Bacterial Co-occurrence Patterns Rather Than Community Diversity or Composition in Temperate Grasslands. Front Microbiol 2022; 13:824192. [PMID: 35422777 PMCID: PMC9005194 DOI: 10.3389/fmicb.2022.824192] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 01/31/2022] [Indexed: 11/30/2022] Open
Abstract
Grazing exclusion is one of the most common practices for degraded grassland restoration worldwide. Soil microorganisms are critical components in soil and play important roles in maintaining grassland ecosystem functions. However, the changes of soil bacterial community characteristics during grazing exclusion for different types of grassland remain unclear. In this study, the soil bacterial community diversity and composition as well as the co-occurrence patterns were investigated and compared between grazing exclusion (4 years) and the paired adjacent grazing sites for three types of temperate grasslands (desert steppe, typical steppe, and meadow steppe) in the Hulunbuir grassland of Inner Mongolia. Our results showed that short-term grazing exclusion decreased the complexity and connectivity of bacterial co-occurrence patterns while increasing the network modules in three types of temperate grasslands. The effects of grazing exclusion on soil bacterial α-diversity and composition were not significant in typical steppe and meadow steppe. However, short-term grazing exclusion significantly altered the community composition in desert steppe, indicating that the soil bacteria communities in desert steppe could respond faster than those in other two types of steppes. In addition, the composition of bacterial community is predominantly affected by soil chemical properties, such as soil total carbon and pH, instead of spatial distance. These results indicated that short-term grazing exclusion altered the soil bacterial co-occurrence patterns rather than community diversity or composition in three types of temperate grasslands. Moreover, our study suggested that soil bacterial co-occurrence patterns were more sensitive to grazing exclusion, and the restoration of soil bacterial community might need a long term (>4 years) in our study area.
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Affiliation(s)
- Fangfang Wang
- State Key Laboratory of Urban and Regional Ecology, 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
| | - Zongming Li
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China.,Key Laboratory of Agro-Ecological Processes in Subtropical Region and Changsha Research Station for Agricultural & Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
| | - Bojie Fu
- State Key Laboratory of Urban and Regional Ecology, 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.,State Key Laboratory of Earth Surface Processes and Resource Ecology, Faculty of Geographical Science, Beijing Normal University, Beijing, China
| | - Yihe Lü
- State Key Laboratory of Urban and Regional Ecology, 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
| | - Guoping Liu
- College of Animal Science, Yangtze University, Jingzhou, China
| | - Dongbo Wang
- Hulunbuir Eco-environmental Monitoring Center of Inner Mongolia, Hulunbuir, China
| | - Xing Wu
- State Key Laboratory of Urban and Regional Ecology, 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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34
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Rawat VS, Kaur J, Bhagwat S, Pandit MA, Rawat CD. Deploying Microbes as Drivers and Indicators in Ecological Restoration. Restor Ecol 2022. [DOI: 10.1111/rec.13688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Jasleen Kaur
- Department of Botany, Dyal Singh College University of Delhi New Delhi 110003 India
| | - Sakshi Bhagwat
- Department of Biosciences Faculty of Natural Sciences, Jamia Millia Islamia New Delhi 110025 India
| | - Manisha Arora Pandit
- Department of Zoology, Kalindi College University of Delhi New Delhi 110008 India
| | - Charu Dogra Rawat
- Molecular Biology and Genomics Research Laboratory, Ramjas College University of Delhi Delhi 110007 India
- Department of Zoology, Ramjas College University of Delhi Delhi 110007 India
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35
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Evans S, Allison S, Hawkes C. Microbes, memory, and moisture: predicting microbial moisture responses and their impact on carbon cycling. Funct Ecol 2022. [DOI: 10.1111/1365-2435.14034] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sarah Evans
- W.K. Kellogg Biological Station, Ecology and Evolutionary Biology Program Department of Integrative Biology Michigan State University Hickory Corners MI 49083 USA
| | - Steve Allison
- Department of Ecology and Evolutionary Biology Department of Earth System Science University of California Irvine California 92697 USA
| | - Christine Hawkes
- Department of Plant and Microbial Biology North Carolina State University Raleigh NC 27607 USA
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36
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Choudoir MJ, DeAngelis KM. A framework for integrating microbial dispersal modes into soil ecosystem ecology. iScience 2022; 25:103887. [PMID: 35243247 PMCID: PMC8866892 DOI: 10.1016/j.isci.2022.103887] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Dispersal is a fundamental community assembly process that maintains soil microbial biodiversity across spatial and temporal scales, yet the impact of dispersal on ecosystem function is largely unpredictable. Dispersal is unique in that it contributes to both ecological and evolutionary processes and is shaped by both deterministic and stochastic forces. The ecosystem-level ramifications of dispersal outcomes are further compounded by microbial dormancy dynamics and environmental selection. Here we review the knowledge gaps and challenges that remain in defining how dispersal, environmental filtering, and microbial dormancy interact to influence the relationship between microbial community structure and function in soils. We propose the classification of microbial dispersal into three categories, through vegetative or active cells, through dormant cells, and through acellular dispersal, each with unique spatiotemporal dynamics and microbial trait associations. This conceptual framework should improve the integration of dispersal in defining soil microbial community structure-function relationships.
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37
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Life and death in the soil microbiome: how ecological processes influence biogeochemistry. Nat Rev Microbiol 2022; 20:415-430. [DOI: 10.1038/s41579-022-00695-z] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/20/2022] [Indexed: 12/18/2022]
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38
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Darriaut R, Lailheugue V, Masneuf-Pomarède I, Marguerit E, Martins G, Compant S, Ballestra P, Upton S, Ollat N, Lauvergeat V. Grapevine rootstock and soil microbiome interactions: Keys for a resilient viticulture. HORTICULTURE RESEARCH 2022; 9:uhac019. [PMID: 35184168 PMCID: PMC8985100 DOI: 10.1093/hr/uhac019] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 12/18/2021] [Accepted: 01/17/2022] [Indexed: 05/10/2023]
Abstract
Soil microbiota has increasingly been shown to play an integral role in viticulture resilience. The emergence of new metagenomic and culturomic technologies has led to significant advances in the study of microbial biodiversity. In the agricultural sector, soil and plant microbiomes have been found to significantly improve resistance to environmental stressors and diseases, as well as influencing crop yields and fruit quality thus improving sustainability under shifting environments. Grapevines are usually cultivated as a scion grafted on rootstocks, which are selected according to pedoclimatic conditions and cultural practices, known as terroir. The rootstock connects the surrounding soil to the vine's aerial part and impacts scion growth and berry quality. Understanding rootstock and soil microbiome dynamics is a relevant and important field of study, which may be critical to improve viticulture sustainability and resilience. This review aims to highlight the relationship between grapevine roots and telluric microbiota diversity and activity. In addition, this review explores the concept of core microbiome regarding potential applications of soil microbiome engineering with the goal of enhancing grapevine adaptation to biotic and abiotic stress.
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Affiliation(s)
- Romain Darriaut
- EGFV, Univ. Bordeaux, Bordeaux Sciences Agro, INRAE, ISVV, F-33882, Villenave d'Ornon, France
| | - Vincent Lailheugue
- EGFV, Univ. Bordeaux, Bordeaux Sciences Agro, INRAE, ISVV, F-33882, Villenave d'Ornon, France
| | - Isabelle Masneuf-Pomarède
- Université de Bordeaux,
UMR Oenologie 1366, INRAE, Bordeaux INP, Bordeaux Sciences Agro, ISVV, Villenave d'Ornon, France
- Bordeaux Sciences Agro, 33170 Gradignan, France
| | - Elisa Marguerit
- EGFV, Univ. Bordeaux, Bordeaux Sciences Agro, INRAE, ISVV, F-33882, Villenave d'Ornon, France
| | - Guilherme Martins
- Université de Bordeaux,
UMR Oenologie 1366, INRAE, Bordeaux INP, Bordeaux Sciences Agro, ISVV, Villenave d'Ornon, France
- Bordeaux Sciences Agro, 33170 Gradignan, France
| | - Stéphane Compant
- AIT Austrian Institute of Technology, Center for Health and Bioresources, Bioresources Unit, Konrad Lorenz Straße 24, Tulln, A-3430, Austria
| | - Patricia Ballestra
- Université de Bordeaux,
UMR Oenologie 1366, INRAE, Bordeaux INP, Bordeaux Sciences Agro, ISVV, Villenave d'Ornon, France
| | | | - Nathalie Ollat
- EGFV, Univ. Bordeaux, Bordeaux Sciences Agro, INRAE, ISVV, F-33882, Villenave d'Ornon, France
| | - Virginie Lauvergeat
- EGFV, Univ. Bordeaux, Bordeaux Sciences Agro, INRAE, ISVV, F-33882, Villenave d'Ornon, France
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39
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Stengel A, Stanke KM, Quattrone AC, Herr JR. Improving Taxonomic Delimitation of Fungal Species in the Age of Genomics and Phenomics. Front Microbiol 2022; 13:847067. [PMID: 35250961 PMCID: PMC8892103 DOI: 10.3389/fmicb.2022.847067] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Accepted: 01/28/2022] [Indexed: 01/04/2023] Open
Abstract
Species concepts have long provided a source of debate among biologists. These lively debates have been important for reaching consensus on how to communicate across scientific disciplines and for advancing innovative strategies to study evolution, population biology, ecology, natural history, and disease epidemiology. Species concepts are also important for evaluating variability and diversity among communities, understanding biogeographical distributions, and identifying causal agents of disease across animal and plant hosts. While there have been many attempts to address the concept of species in the fungi, there are several concepts that have made taxonomic delimitation especially challenging. In this review we discuss these major challenges and describe methodological approaches that show promise for resolving ambiguity in fungal taxonomy by improving discrimination of genetic and functional traits. We highlight the relevance of eco-evolutionary theory used in conjunction with integrative taxonomy approaches to improve the understanding of interactions between environment, ecology, and evolution that give rise to distinct species boundaries. Beyond recent advances in genomic and phenomic methods, bioinformatics tools and modeling approaches enable researchers to test hypothesis and expand our knowledge of fungal biodiversity. Looking to the future, the pairing of integrative taxonomy approaches with multi-locus genomic sequencing and phenomic techniques, such as transcriptomics and proteomics, holds great potential to resolve many unknowns in fungal taxonomic classification.
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Affiliation(s)
- Ashley Stengel
- Complex Biosystems Interdisciplinary Life Sciences, University of Nebraska-Lincoln, Lincoln, NE, United States
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Kimberly M. Stanke
- Complex Biosystems Interdisciplinary Life Sciences, University of Nebraska-Lincoln, Lincoln, NE, United States
- Department of Chemical and Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Amanda C. Quattrone
- Complex Biosystems Interdisciplinary Life Sciences, University of Nebraska-Lincoln, Lincoln, NE, United States
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, United States
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Joshua R. Herr
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE, United States
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, United States
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, United States
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40
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Huang T, Lu ZM, Peng MY, Liu ZF, Chai LJ, Zhang XJ, Shi JS, Li Q, Xu ZH. Combined effects of fermentation starters and environmental factors on the microbial community assembly and flavor formation of Zhenjiang aromatic vinegar. Food Res Int 2022; 152:110900. [DOI: 10.1016/j.foodres.2021.110900] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 12/08/2021] [Accepted: 12/10/2021] [Indexed: 01/06/2023]
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41
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Dacal M, García‐Palacios P, Asensio S, Wang J, Singh BK, Maestre FT. Climate change legacies contrastingly affect the resistance and resilience of soil microbial communities and multifunctionality to extreme drought. Funct Ecol 2022. [DOI: 10.1111/1365-2435.14000] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Marina Dacal
- Instituto Multidisciplinar para el Estudio del Medio ‘Ramon Margalef’ Universidad de Alicante San Vicente del Raspeig Spain
- Departamento de Biología y Geología Física y Química Inorgánica Universidad Rey Juan Carlos Móstoles Spain
| | - Pablo García‐Palacios
- Departamento de Biología y Geología Física y Química Inorgánica Universidad Rey Juan Carlos Móstoles Spain
- Instituto de Ciencias Agrarias Consejo Superior de Investigaciones Científicas Madrid Spain
| | - Sergio Asensio
- Instituto Multidisciplinar para el Estudio del Medio ‘Ramon Margalef’ Universidad de Alicante San Vicente del Raspeig Spain
| | - Juntao Wang
- Hawkesbury Institute for the Environment Western Sydney University Penrith NSW Australia
- Global Centre for Land‐Based Innovation Western Sydney University Penrith South DC NSW Australia
| | - Brajesh K. Singh
- Hawkesbury Institute for the Environment Western Sydney University Penrith NSW Australia
- Global Centre for Land‐Based Innovation Western Sydney University Penrith South DC NSW Australia
| | - Fernando T. Maestre
- Instituto Multidisciplinar para el Estudio del Medio ‘Ramon Margalef’ Universidad de Alicante San Vicente del Raspeig Spain
- Departamento de Ecología Universidad de Alicante San Vicente del Raspeig Spain
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42
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Microbial generalists and specialists differently contribute to the community diversity in farmland soils. J Adv Res 2021; 40:17-27. [PMID: 36100325 PMCID: PMC9481938 DOI: 10.1016/j.jare.2021.12.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 11/27/2021] [Accepted: 12/09/2021] [Indexed: 11/22/2022] Open
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43
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Qin C, Bartelme R, Chung YA, Fairbanks D, Lin Y, Liptzin D, Muscarella C, Naithani K, Peay K, Pellitier P, St. Rose A, Stanish L, Werbin Z, Zhu K. From DNA sequences to microbial ecology: Wrangling NEON soil microbe data with the
neonMicrobe
R package. Ecosphere 2021. [DOI: 10.1002/ecs2.3842] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- Clara Qin
- Department of Environmental Studies University of California Santa Cruz Santa Cruz California USA
| | - Ryan Bartelme
- BIO5 Institute University of Arizona Tucson Arizona USA
- CyVerse.org Tucson Arizona USA
| | - Y. Anny Chung
- Department of Plant Biology and Department of Plant Pathology University of Georgia Athens Georgia USA
| | - Dawson Fairbanks
- Department of Environmental Science University of Arizona Tucson Arizona USA
| | - Yang Lin
- Department of Soil and Water Sciences University of Florida Gainesville Florida USA
| | | | - Chance Muscarella
- Department of Environmental Science University of Arizona Tucson Arizona USA
| | - Kusum Naithani
- Department of Biological Sciences University of Arkansas Fayetteville Fayetteville Arkansas USA
| | - Kabir Peay
- Department of Biology Stanford University Stanford California USA
| | - Peter Pellitier
- Department of Biology Stanford University Stanford California USA
| | - Ayanna St. Rose
- Department of Biological Sciences University of Arkansas Fayetteville Fayetteville Arkansas USA
| | - Lee Stanish
- Institute of Arctic and Alpine Research University of Colorado Boulder USA
| | - Zoey Werbin
- Department of Biology Boston University Boston Massachusetts USA
| | - Kai Zhu
- Department of Environmental Studies University of California Santa Cruz Santa Cruz California USA
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44
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Kuang J, Bates CT, Wan X, Ning D, Deng D, Shu W, Zhou J. High historical variability weakens the effects of current climate differentiation on microbial community dissimilarity and assembly. GLOBAL CHANGE BIOLOGY 2021; 27:5963-5975. [PMID: 34403163 DOI: 10.1111/gcb.15848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Accepted: 08/02/2021] [Indexed: 06/13/2023]
Abstract
Understanding the influences of global climate change on soil microbial communities is essential in evaluating the terrestrial biosphere's feedback to this alarming anthropogenic disturbance. However, little is known about how intra-site historical climate variability can mediate the influences of current climate differences on community dissimilarity and assembly. To fill this gap, we examined and disentangled the interactive effects of historical climate variability and current climate differences on the soil bacterial community dissimilarity and stochasticity of community assembly among 143 sites from 28 forests across eastern China. We hypothesize that the relative importance of stochasticity and community dissimilarity are related to historical climate variability and that an increasing sum of intra-site historical variability enhances stochasticity while reduces dissimilarity between two communities. To test our hypothesis, we statistically controlled for covariates between sites including differences in soil chemistry, plant diversity, spatial distance, and seasonal climate variations at annual timescales. We observed that an increase in inter-site current climate differences led to a reduced impact of stochasticity in community assembly and a pronounced divergence between communities. In stark contrast, when communities were subjected to a high level of intra-site historical climate fluctuation, the observed impact incurred from current climate differences was substantially weakened. Moreover, the influence of increased historical variability was consistent along the gradient of current temperature differences between sites. However, effects induced by historical fluctuation in precipitation were disproportional and only evident when small inter-site differences were observed. Consequently, if the prior climate variability is ignored, especially regarding environmental factors like temperature, we assert that the influence current climate differentiation has on regulating community dissimilarity and assembly stochasticity will be underestimated. Together, our findings highlight the importance and need of explicitly controlling the mean and the historical variability of climate factors for the next "generation" of climate change experiments to come.
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Affiliation(s)
- Jialiang Kuang
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, USA
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources and Conservation of Guangdong Higher Education Institutes, College of Ecology and Evolution, Sun Yat-sen University, Guangzhou, China
| | - Colin T Bates
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, USA
| | - Xiaoling Wan
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, USA
- The Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Daliang Ning
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, USA
| | - Dongmei Deng
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, USA
- Guangxi Key Laboratory of Green Processing of Sugar Resources, College of Biological and Chemical Engineering, Guangxi University of Science and Technology, Liuzhou, China
| | - Wensheng Shu
- School of Life Sciences, South China Normal University, Guangzhou, China
| | - Jizhong Zhou
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, USA
- Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
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45
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Canarini A, Schmidt H, Fuchslueger L, Martin V, Herbold CW, Zezula D, Gündler P, Hasibeder R, Jecmenica M, Bahn M, Richter A. Ecological memory of recurrent drought modifies soil processes via changes in soil microbial community. Nat Commun 2021; 12:5308. [PMID: 34489463 PMCID: PMC8421443 DOI: 10.1038/s41467-021-25675-4] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 08/06/2021] [Indexed: 01/04/2023] Open
Abstract
Climate change is altering the frequency and severity of drought events. Recent evidence indicates that drought may produce legacy effects on soil microbial communities. However, it is unclear whether precedent drought events lead to ecological memory formation, i.e., the capacity of past events to influence current ecosystem response trajectories. Here, we utilize a long-term field experiment in a mountain grassland in central Austria with an experimental layout comparing 10 years of recurrent drought events to a single drought event and ambient conditions. We show that recurrent droughts increase the dissimilarity of microbial communities compared to control and single drought events, and enhance soil multifunctionality during drought (calculated via measurements of potential enzymatic activities, soil nutrients, microbial biomass stoichiometry and belowground net primary productivity). Our results indicate that soil microbial community composition changes in concert with its functioning, with consequences for soil processes. The formation of ecological memory in soil under recurrent drought may enhance the resilience of ecosystem functioning against future drought events. Legacies of past ecological disturbances are expected but challenging to demonstrate. Here the authors report a 10-year field experiment in a mountain grassland that shows ecological memory of soil microbial community and functioning in response to recurrent drought.
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Affiliation(s)
- Alberto Canarini
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.
| | - Hannes Schmidt
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Lucia Fuchslueger
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Victoria Martin
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Craig W Herbold
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - David Zezula
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Philipp Gündler
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Roland Hasibeder
- Department of Ecology, University of Innsbruck, Innsbruck, Austria
| | - Marina Jecmenica
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Michael Bahn
- Department of Ecology, University of Innsbruck, Innsbruck, Austria
| | - Andreas Richter
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.
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Srivastava DS, Coristine L, Angert AL, Bontrager M, Amundrud SL, Williams JL, Yeung ACY, Zwaan DR, Thompson PL, Aitken SN, Sunday JM, O'Connor MI, Whitton J, Brown NEM, MacLeod CD, Parfrey LW, Bernhardt JR, Carrillo J, Harley CDG, Martone PT, Freeman BG, Tseng M, Donner SD. Wildcards in climate change biology. ECOL MONOGR 2021. [DOI: 10.1002/ecm.1471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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47
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Kalenitchenko D, Peru E, Galand PE. Historical contingency impacts on community assembly and ecosystem function in chemosynthetic marine ecosystems. Sci Rep 2021; 11:13994. [PMID: 34234164 PMCID: PMC8263718 DOI: 10.1038/s41598-021-92613-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 06/01/2021] [Indexed: 11/18/2022] Open
Abstract
Predicting ecosystem functioning requires an understanding of the mechanisms that drive microbial community assembly. Many studies have explored microbial diversity extensively and environmental factors are thought to be the principal drivers of community composition. Community assembly is, however, also influenced by past conditions that might affect present-day assemblages. Historical events, called legacy effects or historical contingencies, remain poorly studied in the sea and their impact on the functioning of the communities is not known. We tested the influence, if any, of historical contingencies on contemporary community assembly and functions in a marine ecosystem. To do so, we verified if different inoculum communities colonizing the same substrate led to communities with different compositions. We inoculated wood with sea water microbes from different marine environments that differ in ecological and evolutionary history. Using 16S rRNA and metagenomic sequencing, it was demonstrated that historical contingencies change the composition and potential metabolisms of contemporary communities. The effect of historical events was transient, dominated by environmental selection as, over time, species sorting was a more important driver of community assembly. Our study shows not only that historical contingencies affect marine ecosystems but takes the analysis a step further by characterizing this effect as strong but transient.
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Affiliation(s)
- Dimitri Kalenitchenko
- CAGE - Centre for Arctic Gas Hydrate, Environment and Climate, Department of Geosciences, UiT The Arctic University of Norway, Tromsø, Norway.
| | - Erwan Peru
- Sorbonne Université, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques (LECOB), Observatoire Océanologique de Banyuls, 66500, Banyuls-sur-Mer, France
| | - Pierre E Galand
- Sorbonne Université, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques (LECOB), Observatoire Océanologique de Banyuls, 66500, Banyuls-sur-Mer, France.
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48
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Wang B, Allison SD. Drought legacies mediated by trait trade‐offs in soil microbiomes. Ecosphere 2021. [DOI: 10.1002/ecs2.3562] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Affiliation(s)
- Bin Wang
- Department of Ecology and Evolutionary Biology University of California Irvine California92697USA
| | - Steven D. Allison
- Department of Ecology and Evolutionary Biology University of California Irvine California92697USA
- Department of Earth System Science University of California Irvine California92697USA
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Soil organic carbon cycling in response to simulated soil moisture variation under field conditions. Sci Rep 2021; 11:10841. [PMID: 34035390 PMCID: PMC8149407 DOI: 10.1038/s41598-021-90359-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 05/04/2021] [Indexed: 02/04/2023] Open
Abstract
The combination of extended dry periods and high intensity rainfall, common in the southeastern US, leads to greater variability in soil moisture and consequently increases uncertainty to microbial processes pertinent to soil carbon (C) mineralization. However, field-based findings on soil moisture sensitivity to soil C cycling are very limited. Therefore, a field experiment was conducted in 2018 and 2019 on a soybean (Glycine max L.) cropland in the southeastern US with three soil moisture treatments: drought (simulated using rainout-shelter from June to October in each year), rainfed (natural precipitation), and irrigated (irrigation and precipitation). Soil respiration was measured weekly from May to November in both years. Soil samples were collected multiple times each year from 0-5, 5-15, and 15-30 cm depths to determine microbial biomass C (MBC), extractable organic C (EOC), hydrolytic enzyme activities, and fungal abundance. The cumulative respiration under drought compared to other treatments was lower by 32% to 33% in 2018 and 38% to 45% in 2019. Increased MBC, EOC, and fungal abundance were observed under drought than other treatments. Specific enzyme activity indicated fewer metabolically active microbes under drought treatment compared to rainfed and irrigated treatments. Also, maintenance of enzyme pool was observed under drought condition. These results provide critical insights on microbial metabolism in response to soil moisture variation and how that influences different pools of soil C under field conditions.
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50
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Microbial Community Resilience across Ecosystems and Multiple Disturbances. Microbiol Mol Biol Rev 2021; 85:85/2/e00026-20. [PMID: 33789927 DOI: 10.1128/mmbr.00026-20] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The ability of ecosystems to withstand disturbances and maintain their functions is being increasingly tested as rates of change intensify due to climate change and other human activities. Microorganisms are crucial players underpinning ecosystem functions, and the recovery of microbial communities from disturbances is therefore a key part of the complex processes determining the fate of ecosystem functioning. However, despite global environmental change consisting of numerous pressures, it is unclear and controversial how multiple disturbances affect microbial community stability and what consequences this has for ecosystem functions. This is particularly the case for those multiple or compounded disturbances that occur more frequently than the normal recovery time. The aim of this review is to provide an overview of the mechanisms that can govern the responses of microbes to multiple disturbances across aquatic and terrestrial ecosystems. We first summarize and discuss properties and mechanisms that influence resilience in aquatic and soil biomes to determine whether there are generally applicable principles. Following, we focus on interactions resulting from inherent characteristics of compounded disturbances, such as the nature of the disturbance, timing, and chronology that can lead to complex and nonadditive effects that are modulating the response of microorganisms.
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