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Longhi TV, Robaina RR, Leite RP, Balbi-Peña MI. Survival of Xanthomonas vasicola pv. vasculorum in Soil and in Corn Crop Residues under the Humid Subtropical Climate of Southern Brazil. Life (Basel) 2024; 14:825. [PMID: 39063579 PMCID: PMC11278283 DOI: 10.3390/life14070825] [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: 05/03/2024] [Revised: 05/27/2024] [Accepted: 05/29/2024] [Indexed: 07/28/2024] Open
Abstract
Bacterial leaf streak caused by Xanthomonas vasicola pv. vasculorum (Xvv) is an emerging disease in several corn-producing regions around the world. In Brazil, there is a lack of information on the survival of this bacterium in soil and crop residues. Thus, the objective of this study was to determine the survival of Xvv in soil and also in infected corn crop residues under the humid subtropical climate of southern Brazil. The survival of Xvv in soil was initially investigated in sandy and clayey soils maintained at 20, 25 and 30 °C under controlled conditions. The survival of the bacterium under field conditions was studied in artificially infested clayey soil. The survival of Xvv in corn crop residues was investigated in infected residues maintained on the soil surface or buried in the soil at 20 cm deep. Under controlled conditions, regardless of the type of soil, the bacterium survived longer at 20 °C than at higher temperatures. The bacterium survived for 40 days in clayey soil kept at 20 °C and four days in sandy soil maintained at 30 °C. Under field conditions, the survival of Xvv in the soil was only for 48 h and in infected corn crop residues for up to 15 days in the samples maintained on the soil surface. In samples of infected corn residues buried in the soil, the bacterium was only detected at the time the experiment was set up. In general, the results obtained in this study revealed that Xvv survives for a short period of time in soil and in infected corn crop residues under humid subtropical conditions. Therefore, soil and corn residues may not be highly important sources of primary inoculum for the development of bacterial leaf streak on corn crops under these conditions.
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Affiliation(s)
- Talita Vigo Longhi
- Instituto de Desenvolvimento Rural do Paraná—IAPAR/Emater (IDR-Paraná), km 375 Celso Garcia Cid Road, Londrina 86047-902, Brazil; (T.V.L.); (R.R.R.); (R.P.L.J.)
- Departamento de Agronomia, Universidade Estadual de Londrina (UEL), km 380 Celso Garcia Cid Road, Londrina 86057-970, Brazil
| | - Renata Rodrigues Robaina
- Instituto de Desenvolvimento Rural do Paraná—IAPAR/Emater (IDR-Paraná), km 375 Celso Garcia Cid Road, Londrina 86047-902, Brazil; (T.V.L.); (R.R.R.); (R.P.L.J.)
| | - Rui Pereira Leite
- Instituto de Desenvolvimento Rural do Paraná—IAPAR/Emater (IDR-Paraná), km 375 Celso Garcia Cid Road, Londrina 86047-902, Brazil; (T.V.L.); (R.R.R.); (R.P.L.J.)
| | - Maria Isabel Balbi-Peña
- Departamento de Agronomia, Universidade Estadual de Londrina (UEL), km 380 Celso Garcia Cid Road, Londrina 86057-970, Brazil
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Xu M, Yang X, Shao J, Huang J, Fan W, Yang A, Ci H, Wang Y, Gan J, Han Y, Zeng J. Biogeographic effects shape soil bacterial communities across intertidal zones on island beaches through regulating soil properties. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 930:172785. [PMID: 38677414 DOI: 10.1016/j.scitotenv.2024.172785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 04/06/2024] [Accepted: 04/24/2024] [Indexed: 04/29/2024]
Abstract
Island coastal zones are often mistakenly perceived as "ecological desert". Actually, they harbour unique communities of organisms. The biodiversity on islands is primarily influenced by the effects of area and isolation (distance from the mainland), which mainly focused on plants and animals, encompassing studies of entire islands. However, the application of area and isolation effects to soil microorganisms on island beaches across the intertidal zones remains largely unexplored. We hypothesized that island area and isolation shape soil bacterial communities by regulating soil properties on island beaches, due to the fact that local soil properties might be strongly influenced by land-use, which may vary among islands of different sizes and isolations. To test this hypothesis, we conducted a study on 108 plots spanning 4 intertidal zones on 9 representative island beaches within Zhoushan Archipelago, eastern China. We employed one-way ANOVA and Tukey's honestly significant difference (HSD) test to assess the differences in diversity, composition of soil bacterial communities and soil properties among intertidal zones. Redundancy analysis and structural equation modelling (SEM) were used to examine the direct and indirect impacts of beach area and isolation on soil bacterial communities. Our findings revealed that the area and isolation did not significantly influence soil bacterial diversity and the relative abundance of dominant soil bacterial phyla. However, soil nitrogen (soil N), phosphorus (soil P), organic carbon (SOC), available potassium content (soil AK), and electrical conductivity (soil EC) showed significant increases with the area and isolation. As the tidal gradient increased on beaches, soil bacterial OTU richness, Chao 1, and relative abundance of Planctomycetota and Crenarchaeota decreased, while relative abundance of other soil bacterial phyla increased. We found that influences of island area and isolation shape soil bacterial communities on beaches by regulating soil properties, particularly soil moisture, salinity, and nutrients, all of which are also influenced by area and isolation. Island with larger areas and in lower intertidal zones, characterized by higher soil water content (SWC), soil EC, and soil AK, exhibited greater soil bacterial diversity and fewer dominant soil bacterial phyla. Conversely, in the higher intertidal zones with vegetation containing higher soil N and SOC, lower soil bacterial diversity and more dominant soil bacterial phyla were observed. These findings have the potential to enhance our new understanding of how island biogeography in interpreting island biome patterns.
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Affiliation(s)
- Mingshan Xu
- Zhejiang Institute of Hydraulics & Estuary (Zhejiang Institute of Marine Planning and Design), Hangzhou 310020, Zhejiang, China
| | - Xiaodong Yang
- Institute of East China Sea, Ningbo University, Ningbo 315211, Zhejiang, China; Department of Geography and Spatial Information Techniques, Ningbo University, Ningbo 315211, Zhejiang, China.
| | - Jie Shao
- Zhejiang Institute of Hydraulics & Estuary (Zhejiang Institute of Marine Planning and Design), Hangzhou 310020, Zhejiang, China
| | - Junbao Huang
- Zhejiang Institute of Hydraulics & Estuary (Zhejiang Institute of Marine Planning and Design), Hangzhou 310020, Zhejiang, China
| | - Wenzhou Fan
- Zhejiang Institute of Hydraulics & Estuary (Zhejiang Institute of Marine Planning and Design), Hangzhou 310020, Zhejiang, China
| | - Anna Yang
- Zhejiang Zhoushan Archipelago Observation and Research Station, Tiantong National Forest Ecosystem Observation and Research Station, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, China
| | - Hang Ci
- Zhejiang Zhoushan Archipelago Observation and Research Station, Tiantong National Forest Ecosystem Observation and Research Station, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, China
| | - Yongju Wang
- Zhejiang Institute of Hydraulics & Estuary (Zhejiang Institute of Marine Planning and Design), Hangzhou 310020, Zhejiang, China
| | - Jianjun Gan
- Zhejiang Institute of Hydraulics & Estuary (Zhejiang Institute of Marine Planning and Design), Hangzhou 310020, Zhejiang, China
| | - Yu Han
- Zhejiang Institute of Hydraulics & Estuary (Zhejiang Institute of Marine Planning and Design), Hangzhou 310020, Zhejiang, China
| | - Jian Zeng
- Zhejiang Institute of Hydraulics & Estuary (Zhejiang Institute of Marine Planning and Design), Hangzhou 310020, Zhejiang, China.
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Li Y, Xu G, Yu Y. Freeze-thaw aged polyethylene and polypropylene microplastics alter enzyme activity and microbial community composition in soil. JOURNAL OF HAZARDOUS MATERIALS 2024; 470:134249. [PMID: 38603909 DOI: 10.1016/j.jhazmat.2024.134249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 03/26/2024] [Accepted: 04/08/2024] [Indexed: 04/13/2024]
Abstract
In cold regions, microplastics (MPs) in the soil undergo freeze-thaw (FT) aging process. Little is known about how FT aged MPs influence soil physico-chemical properties and microbial communities. Here, two environmentally relevant concentrations (50 and 500 mg/kg) of 50 and 500 µm polyethylene (PE) and polypropylene (PP) MPs treated soils were subjected to 45-day FT cycles (FTCs). Results showed that MPs experienced surface morphology, hydrophobicity and crystallinity alterations after FTCs. After 45-day FTCs, the soil urease (SUE) activity in control (MPs-free group that underwent FTCs) was 33.49 U/g. SUE activity in 50 µm PE group was reduced by 19.66 %, while increased by 21.16 % and 37.73 % in 500 µm PE and PP groups compared to control. The highest Shannon index was found in 50 µm PP-MPs group at 50 mg/kg, 2.26 % higher than control (7.09). Compared to control (average weighted degree=8.024), all aged MPs increased the complexity of network (0.19-1.43 %). Bacterial biomarkers of aged PP-MPs were associated with pollutant degradation. Aged PP-MPs affected genetic information, cellular processes, and disrupted the biosynthesis of metabolites. This study provides new insights into the potential hazards of MPs after FTCs on soil ecosystem in cold regions.
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Affiliation(s)
- Yanjun Li
- Key Laboratory of Wetland Ecology and Environment, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guanghui Xu
- Key Laboratory of Wetland Ecology and Environment, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Yong Yu
- Key Laboratory of Wetland Ecology and Environment, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China.
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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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5
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Camenzind T, Aguilar-Trigueros CA, Hempel S, Lehmann A, Bielcik M, Andrade-Linares DR, Bergmann J, Dela Cruz J, Gawronski J, Golubeva P, Haslwimmer H, Lartey L, Leifheit E, Maaß S, Marhan S, Pinek L, Powell JR, Roy J, Veresoglou SD, Wang D, Wulf A, Zheng W, Rillig MC. Towards establishing a fungal economics spectrum in soil saprobic fungi. Nat Commun 2024; 15:3321. [PMID: 38637578 PMCID: PMC11026409 DOI: 10.1038/s41467-024-47705-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 04/10/2024] [Indexed: 04/20/2024] Open
Abstract
Trait-based frameworks are promising tools to understand the functional consequences of community shifts in response to environmental change. The applicability of these tools to soil microbes is limited by a lack of functional trait data and a focus on categorical traits. To address this gap for an important group of soil microorganisms, we identify trade-offs underlying a fungal economics spectrum based on a large trait collection in 28 saprobic fungal isolates, derived from a common grassland soil and grown in culture plates. In this dataset, ecologically relevant trait variation is best captured by a three-dimensional fungal economics space. The primary explanatory axis represents a dense-fast continuum, resembling dominant life-history trade-offs in other taxa. A second significant axis reflects mycelial flexibility, and a third one carbon acquisition traits. All three axes correlate with traits involved in soil carbon cycling. Since stress tolerance and fundamental niche gradients are primarily related to the dense-fast continuum, traits of the 2nd (carbon-use efficiency) and especially the 3rd (decomposition) orthogonal axes are independent of tested environmental stressors. These findings suggest a fungal economics space which can now be tested at broader scales.
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Affiliation(s)
- Tessa Camenzind
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, 14195, Berlin, Germany.
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany.
| | - Carlos A Aguilar-Trigueros
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, 2751, Australia
- Department of Biological and Environmental Science, University of Jyväskylä, P.O. Box 35, 40014, Jyväskylä, Finland
| | - Stefan Hempel
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, 14195, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - Anika Lehmann
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, 14195, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - Milos Bielcik
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, 14195, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - Diana R Andrade-Linares
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Ingolstaedter Landstraße 1, 85764, Neuherberg, Germany
| | - Joana Bergmann
- Leibniz Centre for Agricultural Landscape Research (ZALF), 15374, Müncheberg, Germany
| | - Jeane Dela Cruz
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, 14195, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - Jessie Gawronski
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, 14195, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - Polina Golubeva
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, 14195, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - Heike Haslwimmer
- Institute of Soil Science and Land Evaluation, Soil Biology department, University of Hohenheim, Emil-Wolff-Str. 27, 70599, Stuttgart, Germany
| | - Linda Lartey
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, 14195, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - Eva Leifheit
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, 14195, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - Stefanie Maaß
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, 14195, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - Sven Marhan
- Institute of Soil Science and Land Evaluation, Soil Biology department, University of Hohenheim, Emil-Wolff-Str. 27, 70599, Stuttgart, Germany
| | - Liliana Pinek
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, 14195, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - Jeff R Powell
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, 2751, Australia
| | - Julien Roy
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, 14195, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - Stavros D Veresoglou
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, 518107, China
| | - Dongwei Wang
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, 14195, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - Anja Wulf
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, 14195, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - Weishuang Zheng
- Marine Institute for Bioresources and Environment, Peking University Shenzhen Institute, Shenzhen, 518057, China
| | - Matthias C Rillig
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, 14195, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
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Guo Z, Liu CA, Hua K, Wang D, Wu P, Wan S, He C, Zhan L, Wu J. Changing soil available substrate primarily caused by fertilization management contributed more to soil respiration temperature sensitivity than microbial community thermal adaptation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:169059. [PMID: 38061650 DOI: 10.1016/j.scitotenv.2023.169059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 11/28/2023] [Accepted: 11/30/2023] [Indexed: 01/18/2024]
Abstract
Substrate depletion and microbial community thermal adaptation are major mechanisms that regulate the temperature sensitivity (Q10) of soil microbial respiration. Traditionally, the Q10 of soil microbial respiration is measured using laboratory incubation, which has limits in the continuous input of available substrates and the time scale for microbial community thermal adaptation. How the available substrate and the soil microbial community regulate the Q10 of soil microbial respiration under natural warming conditions remains unclear. To fill this gap in knowledge, a long-term field experiment was conducted consisting of two years of soil respiration observations combined with a soil available substrate and microbial community thermal adaptation analysis under seasonal warming conditions. The Q10 of soil respiration was calculated using the square root method, and it was more affected by the available substrate than by microbial community thermal adaptation. Fertilization management has a stronger effect on soil available substrate than temperature. As the temperature increased, NH4-N proved itself to be important for the bacterial community in the process of Q10 regulation, while dissolved organic carbon and nitrogen were key factors for the fungal community. Based on the niche breadth of microbial community composition, the changing Q10 of the soil respiration was not only closely associated with the specialist community, but also the generalist and neutralist communities. Furthermore, bacterial community thermal adaptation primarily occurred through shifts in the abundances of specialists and neutralists, while changes in species richness and species replacement occurred for the fungal generalists and neutralists. This work indicates that changing available nitrogen and DOC primarily caused by fertilization management contributed more in regulating the Q10 of soil microbial respiration than microbial community thermal adaptation, and there are different mechanisms for bacterial and fungal community thermal adaptation under warming.
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Affiliation(s)
- Zhibin Guo
- Soil and Fertilizer Research Institute, Anhui Academy of Agricultural Sciences, Hefei, Anhui 230031, China; Key Laboratory of Nutrient Cycling and Resources Environment of AnHui Province, Hefei, Anhui 230031, China
| | - Chang-An Liu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun town, Mengla County, Yunnan Province 666303, China.
| | - Keke Hua
- Soil and Fertilizer Research Institute, Anhui Academy of Agricultural Sciences, Hefei, Anhui 230031, China; Key Laboratory of Nutrient Cycling and Resources Environment of AnHui Province, Hefei, Anhui 230031, China
| | - Daozhong Wang
- Soil and Fertilizer Research Institute, Anhui Academy of Agricultural Sciences, Hefei, Anhui 230031, China; Key Laboratory of Nutrient Cycling and Resources Environment of AnHui Province, Hefei, Anhui 230031, China.
| | - Pingping Wu
- Soil and Fertilizer Research Institute, Anhui Academy of Agricultural Sciences, Hefei, Anhui 230031, China; Key Laboratory of Nutrient Cycling and Resources Environment of AnHui Province, Hefei, Anhui 230031, China
| | - Shuixia Wan
- Soil and Fertilizer Research Institute, Anhui Academy of Agricultural Sciences, Hefei, Anhui 230031, China; Key Laboratory of Nutrient Cycling and Resources Environment of AnHui Province, Hefei, Anhui 230031, China
| | - Chuanlong He
- Soil and Fertilizer Research Institute, Anhui Academy of Agricultural Sciences, Hefei, Anhui 230031, China; Key Laboratory of Nutrient Cycling and Resources Environment of AnHui Province, Hefei, Anhui 230031, China
| | - Linchuan Zhan
- Soil and Fertilizer Research Institute, Anhui Academy of Agricultural Sciences, Hefei, Anhui 230031, China; Key Laboratory of Nutrient Cycling and Resources Environment of AnHui Province, Hefei, Anhui 230031, China
| | - Ji Wu
- Soil and Fertilizer Research Institute, Anhui Academy of Agricultural Sciences, Hefei, Anhui 230031, China; Key Laboratory of Nutrient Cycling and Resources Environment of AnHui Province, Hefei, Anhui 230031, China.
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7
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Jaeger ACH, Hartmann M, Conz RF, Six J, Solly EF. Prolonged water limitation shifts the soil microbiome from copiotrophic to oligotrophic lifestyles in Scots pine mesocosms. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13211. [PMID: 37991154 PMCID: PMC10866073 DOI: 10.1111/1758-2229.13211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 10/23/2023] [Indexed: 11/23/2023]
Abstract
Reductions in soil moisture due to prolonged episodes of drought can potentially affect whole forest ecosystems, including soil microorganisms and their functions. We investigated how the composition of soil microbial communities is affected by prolonged episodes of water limitation. In a mesocosm experiment with Scots pine saplings and natural forest soil maintained at different levels of soil water content over 2 years, we assessed shifts in prokaryotic and fungal communities and related these to changes in plant development and soil properties. Prolonged water limitation induced progressive changes in soil microbial community composition. The dissimilarity between prokaryotic communities at different levels of water limitation increased over time regardless of the recurrent seasons, while fungal communities were less affected by prolonged water limitation. Under low soil water contents, desiccation-tolerant groups outcompeted less adapted, and the lifestyle of prokaryotic taxa shifted from copiotrophic to oligotrophic. While the abundance of saprotrophic and ligninolytic groups increased alongside an accumulation of dead plant material, the abundance of symbiotic and nutrient-cycling taxa decreased, likely impairing the development of the trees. Overall, prolonged episodes of drought appeared to continuously alter the structure of microbial communities, pointing to a potential loss of critical functions provided by the soil microbiome.
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Affiliation(s)
- Astrid C. H. Jaeger
- Sustainable Agroecosystems Group, Department of Environmental Systems ScienceETH ZurichZurichSwitzerland
| | - Martin Hartmann
- Sustainable Agroecosystems Group, Department of Environmental Systems ScienceETH ZurichZurichSwitzerland
| | - Rafaela Feola Conz
- Sustainable Agroecosystems Group, Department of Environmental Systems ScienceETH ZurichZurichSwitzerland
| | - Johan Six
- Sustainable Agroecosystems Group, Department of Environmental Systems ScienceETH ZurichZurichSwitzerland
| | - Emily F. Solly
- Sustainable Agroecosystems Group, Department of Environmental Systems ScienceETH ZurichZurichSwitzerland
- Helmholtz Centre for Environmental Research—UFZLeipzigGermany
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8
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Ramoneda J, Fan K, Lucas JM, Chu H, Bissett A, Strickland MS, Fierer N. Ecological relevance of flagellar motility in soil bacterial communities. THE ISME JOURNAL 2024; 18:wrae067. [PMID: 38648266 PMCID: PMC11095265 DOI: 10.1093/ismejo/wrae067] [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: 01/30/2024] [Revised: 03/27/2024] [Accepted: 04/18/2024] [Indexed: 04/25/2024]
Abstract
Flagellar motility is a key bacterial trait as it allows bacteria to navigate their immediate surroundings. Not all bacteria are capable of flagellar motility, and the distribution of this trait, its ecological associations, and the life history strategies of flagellated taxa remain poorly characterized. We developed and validated a genome-based approach to infer the potential for flagellar motility across 12 bacterial phyla (26 192 unique genomes). The capacity for flagellar motility was associated with a higher prevalence of genes for carbohydrate metabolism and higher maximum potential growth rates, suggesting that flagellar motility is more prevalent in environments with higher carbon availability. To test this hypothesis, we applied a method to infer the prevalence of flagellar motility in whole bacterial communities from metagenomic data and quantified the prevalence of flagellar motility across four independent field studies that each captured putative gradients in soil carbon availability (148 metagenomes). We observed a positive relationship between the prevalence of bacterial flagellar motility and soil carbon availability in all datasets. Since soil carbon availability is often correlated with other factors that could influence the prevalence of flagellar motility, we validated these observations using metagenomic data from a soil incubation experiment where carbon availability was directly manipulated with glucose amendments. This confirmed that the prevalence of bacterial flagellar motility is consistently associated with soil carbon availability over other potential confounding factors. This work highlights the value of combining predictive genomic and metagenomic approaches to expand our understanding of microbial phenotypic traits and reveal their general environmental associations.
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Affiliation(s)
- Josep Ramoneda
- Cooperative Institute for Research in Environmental Sciences (CIRES), University of Colorado, 80309 Boulder, CO, United States
- Spanish Research Council (CSIC), Center for Advanced Studies of Blanes (CEAB), 17300 Blanes, Spain
| | - Kunkun Fan
- Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 210008 Nanjing, China
| | - Jane M Lucas
- Cary Institute of Ecosystem Studies, 12545 Millbrook, NY, United States
| | - Haiyan Chu
- Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 210008 Nanjing, China
- University of Chinese Academy of Sciences, 101408 Beijing, China
| | | | - Michael S Strickland
- Department of Soil and Water Systems, University of Idaho, 83843 Moscow, ID, United States
| | - Noah Fierer
- Cooperative Institute for Research in Environmental Sciences (CIRES), University of Colorado, 80309 Boulder, CO, United States
- Department of Ecology and Evolutionary Biology, University of Colorado, 80309 Boulder, CO, United States
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9
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Wang W, Lei J, Li M, Zhang X, Xiang X, Wang H, Lu X, Ma L, Liu X, Tuovinen OH. Archaea are better adapted to antimony stress than their bacterial counterparts in Xikuangshan groundwater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 905:166999. [PMID: 37714340 DOI: 10.1016/j.scitotenv.2023.166999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 09/08/2023] [Accepted: 09/09/2023] [Indexed: 09/17/2023]
Abstract
Archaea are important ecological components of microbial communities in various environments, but are currently poorly investigated in antimony (Sb) contaminated groundwater particularly on their ecological differences in comparison with bacteria. To address this issue, groundwater samples were collected from Xikuangshan aquifer along an Sb gradient and subjected to 16S rRNA gene amplicon sequencing and bioinformatic analysis. The results demonstrated that bacterial communities were more susceptibly affected by elevated Sb concentration than their archaeal counterparts, and the positive stimulation of Sb concentration on bacterial diversity coincided with the intermediate disturbance hypothesis. Overall, the balance of environmental variables (Sb, pH, and EC), competitive interactions, and stochastic events jointly regulated bacterial and archaeal communities. Linear fitting analysis revealed that Sb significantly drove the deterministic process (heterogeneous selection) of bacterial communities, whereas stochastic process (dispersal limitation) contributed more to archaeal community assembly. In contract, the assembly of Sb-resistant bacteria and archaea was dominated by the stochastic process (undominated), which implied the important role of diversification and drift instead of selection. Compared with Sb-resistant microorganisms, bacterial and archaeal communities showed lower niche width, which may result from the constraints of Sb concentration and competitive interaction. Moreover, Sb-resistant archaea had a higher niche than that of Sb-resistant bacteria via investing on flexible metabolic pathways such as organic metabolism, ammonia oxidation; and carbon fixation to enhance their competitiveness. Our results offered new insights into the ecological adaptation mechanisms of bacteria and archaea in Sb-contaminated groundwater.
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Affiliation(s)
- Weiqi Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China; School of Environmental Studies, China University of Geosciences, Wuhan 430074, China
| | - Jingwen Lei
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China; School of Environmental Studies, China University of Geosciences, Wuhan 430074, China
| | - Min Li
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China; School of Environmental Studies, China University of Geosciences, Wuhan 430074, China
| | - Xinyue Zhang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China; School of Environmental Studies, China University of Geosciences, Wuhan 430074, China
| | - Xing Xiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China; College of Life Science, Shangrao Normal University, Shangrao 334000, China
| | - Hongmei Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China; School of Environmental Studies, China University of Geosciences, Wuhan 430074, China.
| | - Xiaolu Lu
- School of Environmental Studies, China University of Geosciences, Wuhan 430074, China
| | - Liyuan Ma
- School of Environmental Studies, China University of Geosciences, Wuhan 430074, China
| | - Xiaoyan Liu
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China; School of Environmental Studies, China University of Geosciences, Wuhan 430074, China
| | - Olli H Tuovinen
- Department of Microbiology, Ohio State University, Columbus 43210, USA
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10
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Scales NC, Huynh KT, Weihe C, Martiny JBH. Desiccation induces varied responses within a soil bacterial genus. Environ Microbiol 2023; 25:3075-3086. [PMID: 37664956 DOI: 10.1111/1462-2920.16494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 08/02/2023] [Indexed: 09/05/2023]
Abstract
Desiccation impacts a suite of physiological processes in microbes by elevating levels of damaging reactive oxygen species and inducing DNA strand breaks. In response to desiccation-induced stress, microbes have evolved specialized mechanisms to help them survive. Here, we performed a 128-day lab desiccation experiment on nine strains from three clades of an abundant soil bacterium, Curtobacterium. We sequenced RNA from each strain at three time points to investigate their response. Curtobacterium was highly resistant to desiccation, outlasting both Escherichia coli and a famously DNA damage-resistant bacterium, Deinococcus radiodurans. However, within the genus, there were also 10-fold differences in survival rates among strains. Transcriptomic profiling revealed responses shared within the genus including up-regulation of genes involved in DNA damage repair, osmolyte production, and efflux pumps, but also up-regulation of pathways and genes unique to the three clades. For example, trehalose synthesis gene otsB, the chaperone groEL, and the oxygen scavenger katA were all found in either one or two clades but not the third. Here, we provide evidence of considerable variation in closely related strains, and further elucidation of the phylogenetic conservation of desiccation tolerance remains an important goal for microbial ecologists.
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Affiliation(s)
- N C Scales
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California, USA
| | - K T Huynh
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California, USA
| | - C Weihe
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California, USA
| | - J B H Martiny
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California, USA
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11
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Cordero I, Leizeaga A, Hicks LC, Rousk J, Bardgett RD. High intensity perturbations induce an abrupt shift in soil microbial state. THE ISME JOURNAL 2023; 17:2190-2199. [PMID: 37814127 PMCID: PMC10690886 DOI: 10.1038/s41396-023-01512-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 08/29/2023] [Accepted: 09/04/2023] [Indexed: 10/11/2023]
Abstract
Soil microbial communities play a pivotal role in regulating ecosystem functioning. But they are increasingly being shaped by human-induced environmental change, including intense "pulse" perturbations, such as droughts, which are predicted to increase in frequency and intensity with climate change. While it is known that soil microbial communities are sensitive to such perturbations and that effects can be long-lasting, it remains untested whether there is a threshold in the intensity and frequency of perturbations that can trigger abrupt and persistent transitions in the taxonomic and functional characteristics of soil microbial communities. Here we demonstrate experimentally that intense pulses of drought equivalent to a 30-year drought event (<15% WHC) induce a major shift in the soil microbial community characterised by significantly altered bacterial and fungal community structures of reduced complexity and functionality. Moreover, the characteristics of this transformed microbial community persisted after returning soil to its previous moisture status. As a result, we found that drought had a strong legacy effect on bacterial community function, inducing an enhanced growth rate following subsequent drought. Abrupt transitions are widely documented in aquatic and terrestrial plant communities in response to human-induced perturbations. Our findings demonstrate that such transitions also occur in soil microbial communities in response to high intensity pulse perturbations, with potentially deleterious consequences for soil health.
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Affiliation(s)
- Irene Cordero
- Department of Earth and Environmental Sciences, The University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK.
- Department of Community Ecology, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Zuercherstrasse 111, 8903, Birmensdorf, Switzerland.
| | - Ainara Leizeaga
- Department of Earth and Environmental Sciences, The University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
- Department of Biology, Lund University, Lund, Sweden
| | | | | | - Richard D Bardgett
- Department of Earth and Environmental Sciences, The University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
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12
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Riisgaard-Jensen M, Dottorini G, Nierychlo M, Nielsen PH. Primary settling changes the microbial community of influent wastewater to wastewater treatment plants. WATER RESEARCH 2023; 244:120495. [PMID: 37651867 DOI: 10.1016/j.watres.2023.120495] [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: 05/31/2023] [Revised: 08/14/2023] [Accepted: 08/16/2023] [Indexed: 09/02/2023]
Abstract
The continuous immigration of bacteria in influent wastewater strongly impacts the microbial community of activated sludge (AS) in wastewater treatment plants (WWTP), both in terms of species composition and their abundance. Therefore, it is of interest to elucidate the route of immigrating bacteria into the biological tanks, including the effect of primary settlers. These are commonly used pretreatment units that can possibly selectively increase or reduce the relative abundance of certain bacteria. Species-level identification of the microbial composition of influent wastewater before and after primary settling was carried out in four full-scale municipal WWTPs biweekly over one year by 16S rRNA gene amplicon sequencing. Overall, 37-49% of incoming COD was removed in the primary settlers. Most genera and species were present in the wastewater to all four plants and the trend of these were investigated across the primary settlers. Approximately 50% of the genera had the same trend across at least three WWTPs. Few genera significantly increased in relative read abundance (3.7%) after settling, while 22.3% showed a significant reduction in relative abundance. We investigated process-critical species in AS, such as known nitrifiers, polyphosphate-accumulating organisms, and filamentous bacteria. Most taxa were affected similarly in all WWTPs including multiple genera involved in bulking in AS. However, some genera, e.g., important polyphosphate-accumulating bacteria, had inconsistent trends across WWTPs, suggesting that the characteristics of the wastewater are important for the trend of some bacteria through primary settling. In all cases, primary settling changed the microbial community of the influent wastewater, posing an obvious candidate for upstream control to optimize the assembly of the microbial communities in activated sludge.
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Affiliation(s)
- Marie Riisgaard-Jensen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark.
| | - Giulia Dottorini
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Marta Nierychlo
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Per Halkjær Nielsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark.
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13
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Ndinga-Muniania C, Wornson N, Fulcher MR, Borer ET, Seabloom EW, Kinkel L, May G. Cryptic functional diversity within a grass mycobiome. PLoS One 2023; 18:e0287990. [PMID: 37471328 PMCID: PMC10358963 DOI: 10.1371/journal.pone.0287990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 06/17/2023] [Indexed: 07/22/2023] Open
Abstract
Eukaryotic hosts harbor tremendously diverse microbiomes that affect host fitness and response to environmental challenges. Fungal endophytes are prominent members of plant microbiomes, but we lack information on the diversity in functional traits affecting their interactions with their host and environment. We used two culturing approaches to isolate fungal endophytes associated with the widespread, dominant prairie grass Andropogon gerardii and characterized their taxonomic diversity using rDNA barcode sequencing. A randomly chosen subset of fungi representing the diversity of each leaf was then evaluated for their use of different carbon compound resources and growth on those resources. Applying community phylogenetic analyses, we discovered that these fungal endophyte communities are comprised of phylogenetically distinct assemblages of slow- and fast-growing fungi that differ in their use and growth on differing carbon substrates. Our results demonstrate previously undescribed and cryptic functional diversity in carbon resource use and growth in fungal endophyte communities of A. gerardii.
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Affiliation(s)
- Cedric Ndinga-Muniania
- Plant and Microbial Biology Graduate Program, University of Minnesota, St. Paul, Minnesota, United States of America
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Nicholas Wornson
- School of Statistics, University of Minnesota, Minneapolis, Minnesota, United States of America
- Department of Plant Pathology, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Michael R Fulcher
- Foreign Disease-Weed Science Research Unit, United States Department of Agriculture, Frederick, Maryland, United States of America
| | - Elizabeth T Borer
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Eric W Seabloom
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Linda Kinkel
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota, United States of America
- Department of Plant Pathology, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Georgiana May
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota, United States of America
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14
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Ricks KD, Yannarell AC. Soil moisture incidentally selects for microbes that facilitate locally adaptive plant response. Proc Biol Sci 2023; 290:20230469. [PMID: 37357863 PMCID: PMC10291722 DOI: 10.1098/rspb.2023.0469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 06/01/2023] [Indexed: 06/27/2023] Open
Abstract
While a plant's microbiome can facilitate adaptive phenotypes, the plant's role in selecting for these microbes is unclear. Do plants actively recruit microbes beneficial to their current environment, or are beneficial microbes only an incidental by-product of microbial adaptation? We addressed these questions through a multigeneration greenhouse experiment, selecting for either dry- or wet-adapted soil microbial communities, either with or without plants. After three plant generations, we conducted a full reciprocal transplant of each soil community onto wet- and dry-treated plants. We found that plants generally benefited from soil microbes, and this benefit was greater whenever their current watering conditions matched the microbes' historical watering conditions. Principally, the plant's presence was not necessary in the historical treatments for this environmental matching benefit to emerge. Moreover, we found microbes from droughted soils could better tolerate drought stress. Taken together, these results suggest that the moisture environment selects for microbes that benefit plants under those specific moisture conditions, and that these beneficial properties arise as a by-product of microbial adaptation to the watering environment and not as a co-adapting plant-microbe system. This work highlights that understanding the selective agents on these plant-associated microbes will lead to a better understanding of plant adaptation.
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Affiliation(s)
- Kevin D. Ricks
- Program in Ecology, Evolution, and Conservation Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Anthony C. Yannarell
- Program in Ecology, Evolution, and Conservation Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Natural Resources and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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15
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Kim A, Sevanto S, Moore ER, Lubbers N. Latent Dirichlet Allocation modeling of environmental microbiomes. PLoS Comput Biol 2023; 19:e1011075. [PMID: 37289841 PMCID: PMC10249879 DOI: 10.1371/journal.pcbi.1011075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 04/05/2023] [Indexed: 06/10/2023] Open
Abstract
Interactions between stressed organisms and their microbiome environments may provide new routes for understanding and controlling biological systems. However, microbiomes are a form of high-dimensional data, with thousands of taxa present in any given sample, which makes untangling the interaction between an organism and its microbial environment a challenge. Here we apply Latent Dirichlet Allocation (LDA), a technique for language modeling, which decomposes the microbial communities into a set of topics (non-mutually-exclusive sub-communities) that compactly represent the distribution of full communities. LDA provides a lens into the microbiome at broad and fine-grained taxonomic levels, which we show on two datasets. In the first dataset, from the literature, we show how LDA topics succinctly recapitulate many results from a previous study on diseased coral species. We then apply LDA to a new dataset of maize soil microbiomes under drought, and find a large number of significant associations between the microbiome topics and plant traits as well as associations between the microbiome and the experimental factors, e.g. watering level. This yields new information on the plant-microbial interactions in maize and shows that LDA technique is useful for studying the coupling between microbiomes and stressed organisms.
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Affiliation(s)
- Anastasiia Kim
- Computer, Computational, and Statistical Sciences Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Sanna Sevanto
- Earth and Environmental Sciences Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Eric R. Moore
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Nicholas Lubbers
- Computer, Computational, and Statistical Sciences Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
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16
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Ramoneda J, Stallard-Olivera E, Hoffert M, Winfrey CC, Stadler M, Niño-García JP, Fierer N. Building a genome-based understanding of bacterial pH preferences. SCIENCE ADVANCES 2023; 9:eadf8998. [PMID: 37115929 PMCID: PMC10146879 DOI: 10.1126/sciadv.adf8998] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The environmental preferences of many microbes remain undetermined. This is the case for bacterial pH preferences, which can be difficult to predict a priori despite the importance of pH as a factor structuring bacterial communities in many systems. We compiled data on bacterial distributions from five datasets spanning pH gradients in soil and freshwater systems (1470 samples), quantified the pH preferences of bacterial taxa across these datasets, and compiled genomic data from representative bacterial taxa. While taxonomic and phylogenetic information were generally poor predictors of bacterial pH preferences, we identified genes consistently associated with pH preference across environments. We then developed and validated a machine learning model to estimate bacterial pH preferences from genomic information alone, a model that could aid in the selection of microbial inoculants, improve species distribution models, or help design effective cultivation strategies. More generally, we demonstrate the value of combining biogeographic and genomic data to infer and predict the environmental preferences of diverse bacterial taxa.
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Affiliation(s)
- Josep Ramoneda
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO, USA
- Corresponding author. (J.R.); (N.F.)
| | - Elias Stallard-Olivera
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO, USA
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Michael Hoffert
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO, USA
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Claire C. Winfrey
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO, USA
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Masumi Stadler
- Département des Sciences Biologiques, Université du Québec à Montréal, Case Postale 8888, Succursale Centre-Ville, Montréal, QC H3C 3P8, Canada
| | - Juan Pablo Niño-García
- Département des Sciences Biologiques, Université du Québec à Montréal, Case Postale 8888, Succursale Centre-Ville, Montréal, QC H3C 3P8, Canada
- Escuela de Microbiología, Universidad de Antioquia, Ciudad Universitaria Calle 67 No 12 53-108, Medellín, Colombia
| | - Noah Fierer
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO, USA
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
- Corresponding author. (J.R.); (N.F.)
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17
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Li G, Wang K, Qin Q, Li Q, Mo F, Nangia V, Liu Y. Integrated Microbiome and Metabolomic Analysis Reveal Responses of Rhizosphere Bacterial Communities and Root exudate Composition to Drought and Genotype in Rice (Oryza sativa L.). RICE (NEW YORK, N.Y.) 2023; 16:19. [PMID: 37039929 PMCID: PMC10090257 DOI: 10.1186/s12284-023-00636-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 04/04/2023] [Indexed: 06/19/2023]
Abstract
BACKGROUND As climate change events become more frequent, drought is an increasing threat to agricultural production and food security. Crop rhizosphere microbiome and root exudates are critical regulators for drought adaptation, yet our understanding on the rhizosphere bacterial communities and root exudate composition as affected by drought stress is far from complete. In this study, we performed 16S rRNA gene amplicon sequencing and widely targeted metabolomic analysis of rhizosphere soil and root exudates from two contrasting rice genotypes (Nipponbare and Luodao 998) exposed to drought stress. RESULTS A reduction in plant phenotypes was observed under drought, and the inhibition was greater for roots than for shoots. Additionally, drought exerted a negligible effect on the alpha diversity of rhizosphere bacterial communities, but obviously altered their composition. In particular, drought led to a significant enrichment of Actinobacteria but a decrease in Firmicutes. We also found that abscisic acid in root exudates was clearly higher under drought, whereas lower jasmonic acid and L-cystine concentrations. As for plant genotypes, variations in plant traits of the drought-tolerant genotype Luodao 998 after drought were smaller than those of Nipponbare. Interestingly, drought triggered an increase in Bacillus, as well as an upregulation of most organic acids and a downregulation of all amino acids in Luodao 998. Notably, both Procrustes analysis and Mantel test demonstrated that rhizosphere microbiome and root exudate metabolomic profiles were highly correlated. A number of differentially abundant genera responded to drought and genotype, including Streptomyces, Bacillus and some members of Actinobacteria, were significantly associated with organic acid and amino acid contents in root exudates. Further soil incubation experiments showed that Streptomyces was regulated by abscisic acid and jasmonic acid under drought. CONCLUSIONS Our results reveal that both drought and genotype drive changes in the compositions of rice rhizosphere bacterial communities and root exudates under the greenhouse condition, and that organic acid exudation and suppression of amino acid exudation to select specific rhizosphere bacterial communities may be an important strategy for rice to cope with drought. These findings have important implications for improving the adaptability of rice to drought from the perspective of plant-microbe interactions.
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Affiliation(s)
- Gege Li
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Kexin Wang
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Qun Qin
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Qi Li
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Fei Mo
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Vinay Nangia
- International Center for Agricultural Research in the Dry Areas, 999055, Rabat, Morocco
| | - Yang Liu
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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18
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Baldrian P, López-Mondéjar R, Kohout P. Forest microbiome and global change. Nat Rev Microbiol 2023:10.1038/s41579-023-00876-4. [PMID: 36941408 DOI: 10.1038/s41579-023-00876-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/23/2023] [Indexed: 03/23/2023]
Abstract
Forests influence climate and mitigate global change through the storage of carbon in soils. In turn, these complex ecosystems face important challenges, including increases in carbon dioxide, warming, drought and fire, pest outbreaks and nitrogen deposition. The response of forests to these changes is largely mediated by microorganisms, especially fungi and bacteria. The effects of global change differ among boreal, temperate and tropical forests. The future of forests depends mostly on the performance and balance of fungal symbiotic guilds, saprotrophic fungi and bacteria, and fungal plant pathogens. Drought severely weakens forest resilience, as it triggers adverse processes such as pathogen outbreaks and fires that impact the microbial and forest performance for carbon storage and nutrient turnover. Nitrogen deposition also substantially affects forest microbial processes, with a pronounced effect in the temperate zone. Considering plant-microorganism interactions would help predict the future of forests and identify management strategies to increase ecosystem stability and alleviate climate change effects. In this Review, we describe the impact of global change on the forest ecosystem and its microbiome across different climatic zones. We propose potential approaches to control the adverse effects of global change on forest stability, and present future research directions to understand the changes ahead.
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Affiliation(s)
- Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic.
| | - Rubén López-Mondéjar
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
- Department of Soil and Water Conservation and Waste Management, CEBAS-CSIC, Campus Universitario de Espinardo, Murcia, Spain
| | - Petr Kohout
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
- Faculty of Science, Charles University, Prague, Czech Republic
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19
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Zhao Y, Wang H, Guo T, Li Z, Mi W, Cao Z. Response of soil C-, N-, and P- acquisition enzymes to moisture pulses in desert grassland to shrubland state transition. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 861:160569. [PMID: 36455741 DOI: 10.1016/j.scitotenv.2022.160569] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 11/24/2022] [Accepted: 11/25/2022] [Indexed: 06/17/2023]
Abstract
Grassland-shrubland state transition causes profound effects on soil nutrients and microorganisms, yet little is known about how these soil characteristics are influenced by rainfall and litter changes during transition. Here, we examined water (high or low moisture pulse) and litter (grass or shrub) effects on these soil characteristics in grassland-shrubland mosaics consisting of desert grassland (DG), grassland edge (GE), shrubland edge (SE), and shrubland (SL) sites. The results showed that the transition of DG-GE-SE-SL significantly reduced soil moisture, total carbon (C), total nitrogen (N), total phosphorus (P), microbial biomass carbon, and microbial biomass nitrogen, revealing evident soil degradation during this transition. After applying water and litter, soil microbial respiration (SMR) and the activities of all enzymes were promoted to varying degrees among the sites. Specifically, SMR was promoted under a low moisture pulse but suppressed under a high moisture pulse along the transition from DG to SL. Two C-acquisition enzymes, cellobiohydrolase and β-1,4-glucosidase, became increasingly active from DG to SL. Another C-acquisition enzyme of β-1,4-xylosidase and an N-acquisition enzyme of leucine aminopeptidase showed the strongest preferences for low moisture pulses in SL. These results indicated that shrub encroachment retained certain microbes with an advanced ability to acquire to C and N from dry and infertile soil in SL. Although a P-acquisition enzyme of alkaline phosphatase showed a decreasing trend along the transition from DG to SL, similar like those C- and N- acquisition enzymes, it was not sensitive to varying moisture levels, suggesting that alkaline phosphatase was affected by other soil physicochemical properties rather than soil moisture. The joint analysis of soil extracellular enzymes and nutrients indicated that microbial biomass carbon played a more important role than other soil characteristics in determining soil extracellular enzyme activities along the transition from DG to SL. Future research on dissecting soil microbial communities is warranted to better understand the microbiological mechanisms behind these phenomena in the shrub encroachment process.
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Affiliation(s)
- Yanan Zhao
- School of Agriculture, Ningxia University, Yinchuan, China; Key Laboratory for Restoration and Reconstruction of Degraded Ecosystems in Northwestern China of Ministry of Education, Ningxia University, Yinchuan, China
| | - Hongmei Wang
- School of Agriculture, Ningxia University, Yinchuan, China; Key Laboratory for Restoration and Reconstruction of Degraded Ecosystems in Northwestern China of Ministry of Education, Ningxia University, Yinchuan, China.
| | - Tiandou Guo
- School of Agriculture, Ningxia University, Yinchuan, China; Key Laboratory for Restoration and Reconstruction of Degraded Ecosystems in Northwestern China of Ministry of Education, Ningxia University, Yinchuan, China
| | - Zhili Li
- School of Agriculture, Ningxia University, Yinchuan, China; Key Laboratory for Restoration and Reconstruction of Degraded Ecosystems in Northwestern China of Ministry of Education, Ningxia University, Yinchuan, China
| | - Wenbao Mi
- School of Geography and Planning, Ningxia University, Yinchuan, China
| | - Zhe Cao
- School of Agriculture, Ningxia University, Yinchuan, China.
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20
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Bolin LG, Lennon JT, Lau JA. Traits of soil bacteria predict plant responses to soil moisture. Ecology 2023; 104:e3893. [PMID: 36208193 DOI: 10.1002/ecy.3893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 09/02/2022] [Accepted: 09/09/2022] [Indexed: 02/03/2023]
Abstract
Microorganisms can help plants and animals contend with abiotic stressors, but why they provide such benefits remains unclear. Here we investigated byproduct benefits, which occur when traits that increase the fitness of one species provide incidental benefits to another species with no direct cost to the provider. In a greenhouse experiment, microbial traits predicted plant responses to soil moisture such that bacteria with self-beneficial traits in drought increased plant early growth, size at reproduction, and chlorophyll concentration under drought, while bacteria with self-beneficial traits in well-watered environments increased these same plant traits in well-watered soils. Thus, microbial traits that promote microbial success in different moisture environments also promote plant success in these same environments. Our results demonstrate that byproduct benefits, a concept developed to explain the evolution of cooperation in pairwise mutualisms, can also extend to interactions between plants and nonsymbiotic soil microbes.
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Affiliation(s)
- Lana G Bolin
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - Jay T Lennon
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - Jennifer A Lau
- Department of Biology, Indiana University, Bloomington, Indiana, USA.,Environmental Resilience Institute, Indiana University, Bloomington, Indiana, USA
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21
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Vineis JH, Bulseco AN, Bowen JL. Microbial chemolithoautotrophs are abundant in salt marsh sediment following long-term experimental nitrate enrichment. FEMS Microbiol Lett 2023; 370:fnad082. [PMID: 37541957 DOI: 10.1093/femsle/fnad082] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 07/13/2023] [Accepted: 07/25/2023] [Indexed: 08/06/2023] Open
Abstract
Long-term anthropogenic nitrate (NO3-) enrichment is a serious threat to many coastal systems. Nitrate reduction coupled with the oxidation of reduced forms of sulfur is conducted by chemolithoautotrophic microbial populations in a process that decreases nitrogen (N) pollution. However, little is known about the diversity and distribution of microbes capable of carbon fixation within salt marsh sediment and how they respond to long-term NO3- loading. We used genome-resolved metagenomics to characterize the distribution, phylogenetic relationships, and adaptations important to microbial communities within NO3--enriched sediment. We found NO3- reducing sulfur oxidizers became dominant members of the microbial community throughout the top 25 cm of the sediment following long-term NO3- enrichment. We also found that most of the chemolithoautotrophic genomes recovered contained striking metabolic versatility, including the potential for complete denitrification and evidence of mixotrophy. Phylogenetic reconstruction indicated that similar carbon fixation strategies and metabolic versatility can be found in several phylogenetic groups, but the genomes recovered here represent novel organisms. Our results suggest that the role of chemolithoautotrophy within NO3--enriched salt marsh sediments may be quantitatively more important for retaining carbon and filtering NO3- than previously indicated and further inquiry is needed to explicitly measure their contribution to carbon turnover and removal of N pollution.
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Affiliation(s)
- Joseph H Vineis
- Department of Marine and Environmental Sciences, Marine Science Center, Northeastern University, 30 Nahant Road, Nahant, MA 01908, United States
| | - Ashley N Bulseco
- Department of Marine and Environmental Sciences, Marine Science Center, Northeastern University, 30 Nahant Road, Nahant, MA 01908, United States
| | - Jennifer L Bowen
- Department of Marine and Environmental Sciences, Marine Science Center, Northeastern University, 30 Nahant Road, Nahant, MA 01908, United States
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22
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The Impacts of Phosphorus-Containing Compounds on Soil Microorganisms of Rice Rhizosphere Contaminated by Lead. DIVERSITY 2023. [DOI: 10.3390/d15010069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The cost effectiveness of using exogenous phosphorus to remediate heavy metals in soil, which would alter the structure of the soil microbial community, had been widely acknowledged. In the present study, phospholipid fatty acid (PLFA) technology was taken as the breakthrough point, and rhizosphere soil microorganisms in different growth stages (jointing stage and maturity stage) of Minghui 86 (MH) and Yangdao No.6 (YD) rice were taken as the research objects. As revealed by the results, the rhizosphere soil microorganisms of MH and YD had distinct sensitivities to exogenous phosphorus and had a certain inhibitory effect on MH and YD enhancement. The sensitivity of rice root soil microorganisms to exogenous phosphorus also varied in different growth stages of rice. Bacteria were the dominant microorganism in the soil microbial community of rice roots, and the gain of exogenous phosphorus had a certain impact on the structure of the two soil microbial communities. Through analysis of the microbial community characteristics of MH rice and YD soil after adding exogenous phosphorus, further understanding was attained with respect to the effect of exogenous phosphorus on the microbial community characteristics of rice rhizosphere soil and the impact thereof on ecological functions.
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23
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Schrad N, Pensky J, Gorski G, Beganskas S, Fisher AT, Saltikov C. Soil characteristics and redox properties of infiltrating water are determinants of microbial communities at managed aquifer recharge sites. FEMS Microbiol Ecol 2022; 98:6795929. [PMID: 36331034 DOI: 10.1093/femsec/fiac130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 10/10/2022] [Accepted: 11/02/2022] [Indexed: 11/06/2022] Open
Abstract
In this study, we conducted a meta-analysis of soil microbial communities at three, pilot-scale field sites simulating shallow infiltration for managed aquifer recharge (MAR). We evaluated shifts in microbial communities after infiltration across site location, through different soils, with and without carbon-rich amendments added to test plots. Our meta-analysis aims to enable more effective MAR basin design by identifying potentially important interactions between soil physical-geochemical parameters and microbial communities across several geographically separate MAR basins. We hypothesized infiltration and carbon amendments would lead to common changes in subsurface microbial communities at multiple field sites but instead found distinct differences. Sites with coarser (mainly sandy) soil had large changes in diversity and taxa abundance, while sites with finer soils had fewer significant changes in genera, despite having the greatest increase in nitrogen cycling. Below test plots amended with a carbon-rich permeable reactive barrier, we observed more nitrate removal and a decrease in genera capable of nitrification. Multivariate statistics determined that the soil texture (a proxy for numerous soil characteristics) was the main determinant of whether the microbial community composition changed because of infiltration. These results suggest that microbial communities in sandy soil with carbon-rich amendments are most impacted by infiltration. Soil composition is a critical parameter that links between microbial communities and nutrient cycling during infiltration and could influence the citing and operation of MAR to benefit water quality and supply.
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Affiliation(s)
- Nicole Schrad
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, United States
| | - Jennifer Pensky
- Department of Earth and Planetary Sciences, University of California, Santa Cruz, Santa Cruz, CA 95064, United States
| | - Galen Gorski
- Department of Earth and Planetary Sciences, University of California, Santa Cruz, Santa Cruz, CA 95064, United States.,Present Address: U.S. Geological Survey, Reston VA, 20192, United States
| | - Sarah Beganskas
- Water Resource Management, Delaware River Basin Commission, 25 Cosey Road, West Trenton, NJ, 08628, United States
| | - Andrew T Fisher
- Department of Earth and Planetary Sciences, University of California, Santa Cruz, Santa Cruz, CA 95064, United States
| | - Chad Saltikov
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, United States
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24
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Yang X, Li Y, Niu B, Chen Q, Hu Y, Yang Y, Song L, Wang J, Zhang G. Temperature and Precipitation Drive Elevational Patterns of Microbial Beta Diversity in Alpine Grasslands. MICROBIAL ECOLOGY 2022; 84:1141-1153. [PMID: 34694450 DOI: 10.1007/s00248-021-01901-w] [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: 06/26/2021] [Accepted: 10/11/2021] [Indexed: 06/13/2023]
Abstract
Understanding the mechanisms underlying biodiversity patterns is a central issue in ecology, while how temperature and precipitation jointly control the elevational patterns of microbes is understudied. Here, we studied the effects of temperature, precipitation and their interactions on the alpha and beta diversity of soil archaea and bacteria in alpine grasslands along an elevational gradient of 4300-5200 m on the Tibetan Plateau. Alpha diversity was examined on the basis of species richness and evenness, and beta diversity was quantified with the recently developed metric of local contributions to beta diversity (LCBD). Typical alpine steppe and meadow ecosystems were distributed below and above 4850 m, respectively, which was consistent with the two main constraints of mean annual temperature (MAT) and mean annual precipitation (MAP). Species richness and evenness showed decreasing elevational patterns in archaea and nonsignificant or U-shaped patterns in bacteria. The LCBD of both groups exhibited significant U-shaped elevational patterns, with the lowest values occurring at 4800 m. For the three diversity metrics, soil pH was the primary explanatory variable in archaea, explaining over 20.1% of the observed variation, whereas vegetation richness, total nitrogen and the K/Al ratio presented the strongest effects on bacteria, with relative importance values of 16.1%, 12.5% and 11.6%, respectively. For the microbial community composition of both archaea and bacteria, the moisture index showed the dominant effect, explaining 17.6% of the observed variation, followed by MAT and MAP. Taken together, temperature and precipitation exerted considerable indirect effects on microbial richness and evenness through local environmental and energy supply-related variables, such as vegetation richness, whereas temperature exerted a larger direct influence on LCBD and the community composition. Our findings highlighted the profound influence of temperature and precipitation interactions on microbial beta diversity in alpine grasslands on the Tibetan Plateau.
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Affiliation(s)
- Xiaoqin Yang
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yue Li
- China University of Geosciences, Beijing, 100083, China
| | - Bin Niu
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qiuyu Chen
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, 100101, China
- Key Laboratory of Alpine Ecology, CAS Center for Excellence in Tibetan Plateau Earth Sciences and Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yilun Hu
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, 100101, China
- Key Laboratory of Alpine Ecology, CAS Center for Excellence in Tibetan Plateau Earth Sciences and Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yibo Yang
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, 100101, China
| | - Lili Song
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jianjun Wang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China.
| | - Gengxin Zhang
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, 100101, China.
- Key Laboratory of Alpine Ecology, CAS Center for Excellence in Tibetan Plateau Earth Sciences and Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, 100101, China.
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25
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Geml J, Leal CM, Nagy R, Sulyok J. Abiotic environmental factors drive the diversity, compositional dynamics and habitat preference of ectomycorrhizal fungi in Pannonian forest types. Front Microbiol 2022; 13:1007935. [PMID: 36312934 PMCID: PMC9597314 DOI: 10.3389/fmicb.2022.1007935] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 09/16/2022] [Indexed: 11/26/2022] Open
Abstract
Ectomycorrhizal (ECM) fungi are among the most diverse and dominant fungal groups in temperate forests and are crucial for ecosystem functioning of forests and their resilience toward disturbance. We carried out DNA metabarcoding of ECM fungi from soil samples taken at 62 sites in the Bükk Mountains in northern Hungary. The selected sampling sites represent the characteristic Pannonian forest types distributed along elevation (i.e., temperature), pH and slope aspect gradients. We compared richness and community composition of ECM fungi among forest types and explored relationships among environmental variables and ECM fungal alpha and beta diversity. The DNA sequence data generated in this study indicated strong correlations between fungal community composition and environmental variables, particularly with pH and soil moisture, with many ECM fungi showing preference for specific zonal, topographic or edaphic forest types. Several ECM fungal genera showed significant differences in richness among forest types and exhibited strong compositional differences mostly driven by differences in environmental factors. Despite the relatively high proportions of compositional variance explained by the tested environmental variables, a large proportion of the compositional variance remained unexplained, indicating that both niche (environmental filtering) and neutral (stochastic) processes shape ECM fungal community composition at landscape level. Our work provides unprecedented insights into the diversity, landscape-level distribution, and habitat preferences of ECM fungi in the Pannonian forests of Northern Hungary.
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Affiliation(s)
- József Geml
- ELKH-EKKE Lendület Environmental Microbiome Research Group, Eszterházy Károly Catholic University, Eger, Hungary
- Research and Development Centre, Eszterházy Károly Catholic University, Eger, Hungary
- *Correspondence: József Geml,
| | - Carla Mota Leal
- ELKH-EKKE Lendület Environmental Microbiome Research Group, Eszterházy Károly Catholic University, Eger, Hungary
| | - Richárd Nagy
- Research and Development Centre, Eszterházy Károly Catholic University, Eger, Hungary
| | - József Sulyok
- Biodiversity Protection Group, Bükk National Park Directorate, Eger, Hungary
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26
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Yates C, Trexler RV, Bonet I, King WL, Hockett KL, Bell TH. Rapid niche shifts in bacteria following conditioning in novel soil environments. Funct Ecol 2022. [DOI: 10.1111/1365-2435.14180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Caylon Yates
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University University Park PA USA
- Intercollege Graduate Degree Program in Ecology, The Pennsylvania State University University Park PA USA
| | - Ryan V. Trexler
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University University Park PA USA
- Intercollege Graduate Degree Program in Ecology, The Pennsylvania State University University Park PA USA
| | - Idalys Bonet
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University University Park PA USA
| | - William L. King
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University University Park PA USA
- Present address: School of Integrative Plant Science Cornell University Ithaca NY
| | - Kevin L. Hockett
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University University Park PA USA
- Intercollege Graduate Degree Program in Ecology, The Pennsylvania State University University Park PA USA
| | - Terrence H. Bell
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University University Park PA USA
- Intercollege Graduate Degree Program in Ecology, The Pennsylvania State University University Park PA USA
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27
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Venturini AM, Dias NMS, Gontijo JB, Yoshiura CA, Paula FS, Meyer KM, Nakamura FM, da França AG, Borges CD, Barlow J, Berenguer E, Nüsslein K, Rodrigues JLM, Bohannan BJM, Tsai SM. Increased soil moisture intensifies the impacts of forest-to-pasture conversion on methane emissions and methane-cycling communities in the Eastern Amazon. ENVIRONMENTAL RESEARCH 2022; 212:113139. [PMID: 35337832 DOI: 10.1016/j.envres.2022.113139] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Revised: 02/24/2022] [Accepted: 03/15/2022] [Indexed: 06/14/2023]
Abstract
Climatic changes are altering precipitation patterns in the Amazon and may influence soil methane (CH4) fluxes due to the differential responses of methanogenic and methanotrophic microorganisms. However, it remains unclear if these climate feedbacks can amplify land-use-related impacts on the CH4 cycle. To better predict the responses of soil CH4-cycling microorganisms and emissions under altered moisture levels in the Eastern Brazilian Amazon, we performed a 30-day microcosm experiment manipulating the moisture content (original moisture; 60%, 80%, and 100% of field capacity - FC) of forest and pasture soils. Gas samples were collected periodically for gas chromatography analysis, and methanogenic archaeal and methanotrophic bacterial communities were assessed using quantitative PCR and metagenomics. Positive and negative daily CH4 fluxes were observed for forest and pasture, indicating that these soils can act as both CH4 sources and sinks. Cumulative emissions and the abundance of methanogenesis-related genes and taxonomic groups were affected by land use, moisture, and their interaction. Pasture soils at 100% FC had the highest abundance of methanogens and CH4 emissions, 22 times higher than forest soils under the same treatment. Higher ratios of methanogens to methanotrophs were found in pasture than in forest soils, even at field capacity conditions. Land use and moisture were significant factors influencing the composition of methanogenic and methanotrophic communities. The diversity and evenness of methanogens did not change throughout the experiment. In contrast, methanotrophs exhibited the highest diversity and evenness in pasture soils at 100% FC. Taken together, our results suggest that increased moisture exacerbates soil CH4 emissions and microbial responses driven by land-use change in the Amazon. This is the first report on the microbial CH4 cycle in Amazonian upland soils that combined one-month gas measurements with advanced molecular methods.
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Affiliation(s)
- Andressa M Venturini
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, 13416-000, Brazil; Princeton Institute for International and Regional Studies, Princeton University, Princeton, NJ, 08544, USA.
| | - Naissa M S Dias
- Environmental Biogeochemistry Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, 13416-000, Brazil
| | - Júlia B Gontijo
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, 13416-000, Brazil
| | - Caio A Yoshiura
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, 13416-000, Brazil
| | - Fabiana S Paula
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, 13416-000, Brazil; Department of Biological Oceanography, Oceanographic Institute, University of São Paulo, São Paulo, SP, 05508-120, Brazil
| | - Kyle M Meyer
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, 97403, USA; Department of Integrative Biology, University of California - Berkeley, Berkeley, CA, 94720, USA
| | - Fernanda M Nakamura
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, 13416-000, Brazil
| | - Aline G da França
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, 13416-000, Brazil
| | - Clovis D Borges
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, 13416-000, Brazil
| | - Jos Barlow
- Lancaster Environment Centre, Lancaster University, Lancaster, LA1 4YQ, UK
| | - Erika Berenguer
- Lancaster Environment Centre, Lancaster University, Lancaster, LA1 4YQ, UK; Environmental Change Institute, University of Oxford, Oxford, OX1 3QY, UK
| | - Klaus Nüsslein
- Department of Microbiology, University of Massachusetts, Amherst, MA, 01003, USA
| | - Jorge L M Rodrigues
- Department of Land, Air, and Water Resources, University of California - Davis, Davis, CA, 95616, USA
| | - Brendan J M Bohannan
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, 97403, USA
| | - Siu M Tsai
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, 13416-000, Brazil
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28
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Pan Y, Kang P, Tan M, Hu J, Zhang Y, Zhang J, Song N, Li X. Root exudates and rhizosphere soil bacterial relationships of Nitraria tangutorum are linked to k-strategists bacterial community under salt stress. FRONTIERS IN PLANT SCIENCE 2022; 13:997292. [PMID: 36119572 PMCID: PMC9471988 DOI: 10.3389/fpls.2022.997292] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 08/10/2022] [Indexed: 06/15/2023]
Abstract
When plants are subjected to various biotic and abiotic stresses, the root system responds actively by secreting different types and amounts of bioactive compounds, while affects the structure of rhizosphere soil bacterial community. Therefore, understanding plant-soil-microbial interactions, especially the strength of microbial interactions, mediated by root exudates is essential. A short-term experiment was conducted under drought and salt stress to investigate the interaction between root exudates and Nitraria tangutorum rhizosphere bacterial communities. We found that drought and salt stress increased rhizosphere soil pH (9.32 and 20.6%) and electrical conductivity (1.38 and 11 times), respectively, while decreased organic matter (27.48 and 31.38%), total carbon (34.55 and 29.95%), and total phosphorus (20 and 28.57%) content of N. tangutorum rhizosphere soil. Organic acids, growth hormones, and sugars were the main differential metabolites of N. tangutorum under drought and salt stress. Salt stress further changed the N. tangutorum rhizosphere soil bacterial community structure, markedly decreasing the relative abundance of Bacteroidota as r-strategist while increasing that of Alphaproteobacteria as k-strategists. The co-occurrence network analysis showed that drought and salt stress reduced the connectivity and complexity of the rhizosphere bacterial network. Soil physicochemical properties and root exudates in combination with salt stress affect bacterial strategies and interactions. Our study revealed the mechanism of plant-soil-microbial interactions under the influence of root exudates and provided new insights into the responses of bacterial communities to stressful environments.
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Affiliation(s)
- Yaqing Pan
- Shapotou Desert Research and Experiment Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
| | - Peng Kang
- College of Biological Sciences and Engineering, North Minzu University, Yinchuan, China
| | - Min Tan
- College of Biological Sciences and Engineering, North Minzu University, Yinchuan, China
| | - Jinpeng Hu
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Yinchuan, China
| | - Yaqi Zhang
- College of Biological Sciences and Engineering, North Minzu University, Yinchuan, China
| | - Jinlin Zhang
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Yinchuan, China
| | - Naiping Song
- Breeding Base for Key Laboratory Land Degradation and Ecological Restoration in Northwest China, Ningxia University, Yinchuan, China
| | - Xinrong Li
- Shapotou Desert Research and Experiment Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
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29
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Growth and Photosynthetic Characteristics of Sesame Seedlings with Gibberellin-Producing Rhodobacter sphaeroides SIR03 and Biochar. INTERNATIONAL JOURNAL OF PLANT BIOLOGY 2022. [DOI: 10.3390/ijpb13030022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The use of plant growth-promoting rhizobacteria (PGPR) with biochar is apprised to be a promising bio-fertilizer for improving the soil fertility and plant growth and development. The current study aimed to identify a potential plant growth-promoting rhizobacterium alongside biochar to improve sesame seedling productivity. Our results revealed that among the nine isolates, SIR01, SIR03, and SIR07 significantly improved the growth and biomass of sesame and Waito-C rice seedlings. The increase in growth of Waito-C rice seedlings through isolate SIR01, SIR03, and SIR07, suggests their ability to produce phytohormones such as GA4, GA9, GA24, and GA34. Furthermore, the application of isolate SIR03 and biochar together revealed a synergistic increase in sesame seedling growth and biomass (fresh and dry weight) compared with their individual applications. This may be explained by enhancement of photosynthetic rate, chlorophyll fluorescence, stomatal conductance, and transpiration rate by the combined SIR03 and biochar treatment. This suggests that co-inoculation with SIR03 alongside the application of biochar can be considered an eco-friendly, low-cost bio-fertilizer to potentially improve sesame seedling growth and development.
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30
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Roy J, Mazel F, Dumack K, Bonkowski M, Rillig MC. Hierarchical phylogenetic community assembly of soil protists in a temperate agricultural field. Environ Microbiol 2022; 24:5498-5508. [PMID: 35837871 DOI: 10.1111/1462-2920.16134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 06/27/2022] [Accepted: 07/09/2022] [Indexed: 11/27/2022]
Abstract
Protists are abundant, diverse and perform essential functions in soils. Protistan community structure and its change across time or space are traditionally studied at the species-level but the relative importance of the processes shaping these patterns depends on the taxon phylogenetic resolution. Using 18S rDNA amplicon data of the Cercozoa, a group of dominant soil protists, from an agricultural field in western Germany, we observed a turnover of relatively closely related taxa (from sequence variants to genus-level clades) across soil depth; while across soil habitats (rhizosphere, bulk soil, drilosphere) we observed turnover of relatively distantly related taxa, confirming Paracercomonadidae as a rhizosphere-associated clade. We extended our approach to show that closely related Cercozoa encounter divergent AM fungi across soil depth and that distantly related Cercozoa encounter closely related AM fungi across soil compartments. This study suggests that soil Cercozoa community assembly at the field-scale is driven by niche-based processes shaped by evolutionary legacy of adaptation to conditions primarily related to soil compartment, followed by soil layer, giving a deeper understanding on the selection pressures that shaped their evolution.
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Affiliation(s)
- Julien Roy
- Institut für Biologie, Ökologie der Pflanzen, Freie Universität Berlin, Berlin, Germany.,Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - Florent Mazel
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Kennet Dumack
- Terrestrial Ecology Group, Institute of Zoology, University of Cologne, Cologne, Germany
| | - Michael Bonkowski
- Terrestrial Ecology Group, Institute of Zoology, University of Cologne, Cologne, Germany
| | - Matthias C Rillig
- Institut für Biologie, Ökologie der Pflanzen, Freie Universität Berlin, Berlin, Germany.,Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
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31
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Li Y, Wang T, Camps-Arbestain M, Whitby CP. The regulators of soil organic carbon mineralization upon lime and/or phosphate addition vary with depth. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 828:154378. [PMID: 35276156 DOI: 10.1016/j.scitotenv.2022.154378] [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: 07/20/2021] [Revised: 03/01/2022] [Accepted: 03/03/2022] [Indexed: 06/14/2023]
Abstract
Knowledge of the key factors regulating soil organic carbon (OC) mineralization in response to fertilizers and lime application is essential to understanding the effects of agricultural land management on soil OC preservation. Microbial community composition and OC availability to microorganisms have been proposed as the two most imperative factors controlling soil OC mineralization, although their relative importance is still under debate. Here we performed a laboratory incubation in combination with high-throughput sequencing and structural equation modeling to examine the mechanisms underlying the responses of OC mineralization in the topsoil and the subsoil of a volcanic soil (an Andosol) to the additions of lime and/or phosphate. Results showed that lime and/or phosphate additions induced distinct shifts in the microbial community composition and functional profiles in the topsoil and the subsoil. We found that OC mineralization relied on microbial community composition and functionality in the topsoil but was strongly related to the quality and quantity of the water-extractable OC (indicative of the OC availability) in the subsoil. These data suggest that the key regulator controlling the response of OC mineralization to lime and/or P additions shifts from microbial community composition to OC availability as soil depth increases in the Andosol. Our findings highlight the central role of mechanisms controlling soil OC mineralization in regulating the responses of mineralization to intensive agricultural management practices.
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Affiliation(s)
- Yang Li
- School of Agriculture and Environment, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand
| | - Tao Wang
- CAS Key Laboratory of Mountain Surface Processes and Ecological Regulation, Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu 610041, China.
| | - Marta Camps-Arbestain
- School of Agriculture and Environment, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand
| | - Catherine P Whitby
- School of Fundamental Sciences, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand
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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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Chen Y, Chen R, Liu Z, Ren B, Wu Q, Zhang J, Tang Y, Wu Q. Bioretention system mediated by different dry-wet alterations on nitrogen removal: Performance, fate, and microbial community. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 827:154295. [PMID: 35247404 DOI: 10.1016/j.scitotenv.2022.154295] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 02/07/2022] [Accepted: 02/28/2022] [Indexed: 06/14/2023]
Abstract
In laboratory experiments, the nitrogen migration and transformation in the stormwater bioretention system under different dry-wet alterations were studied. The removal efficiency showed that nitrogen could be removed efficiently in bioretention system under all dry-wet alterations, and the shorter antecedent dry days (ADDs) (1-5 days) were beneficial to the removal of nitrogen before plants decay, compared to the longer ADDs (7-22 days). Using a new method combined with Hydrus-1D model, water transport was simulated and nitrogen migration in bioretention system was quantified, indicating that NH4+-N was mainly removed in the planting layer, and the removal of NO3--N was occurred in the submerged layer. Fate experiment showed the main fate of the nitrogen was microorganisms (1-5 ADDs) and soil immobilization (7-22 ADDs). Microbial analysis showed that shorter ADDs (1-5 days) were suitable for Firmicutes growth, while Proteobacteria and Actinobacteria accounted for greater abundance under longer ADDs (7-22 days). Canonical correlation analysis (CCA) revealed the relationships between microbial community and environmental factors. Soil moisture content, soil organic matter (SOM), TN (water), root length, and NO3--N (water) were significantly correlated with bacterial community. This work may give new insights into nitrogen migration and transformation, and can provide a reference for the further mechanism study and construction of stormwater bioretention systems.
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Affiliation(s)
- Yao Chen
- School of River and Ocean Engineering, Chongqing Jiaotong University, Chongqing 400074, China; Engineering Laboratory of Environmental Hydraulic Engineering of Chongqing Municipal Development and Reform Commission, Chongqing Jiaotong University, Chongqing 400074, China
| | - Renyu Chen
- School of River and Ocean Engineering, Chongqing Jiaotong University, Chongqing 400074, China
| | - Zhen Liu
- School of River and Ocean Engineering, Chongqing Jiaotong University, Chongqing 400074, China; Engineering Laboratory of Environmental Hydraulic Engineering of Chongqing Municipal Development and Reform Commission, Chongqing Jiaotong University, Chongqing 400074, China.
| | - Bangxing Ren
- Environmental Engineering and Science Program, Department of Chemical and Environmental Engineering (ChEE), University of Cincinnati, Cincinnati, OH 45221-0071, USA
| | - Qiong Wu
- School of River and Ocean Engineering, Chongqing Jiaotong University, Chongqing 400074, China
| | - Jian Zhang
- State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing 400044, China
| | - Yinghui Tang
- School of River and Ocean Engineering, Chongqing Jiaotong University, Chongqing 400074, China
| | - Qingyu Wu
- School of River and Ocean Engineering, Chongqing Jiaotong University, Chongqing 400074, China
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Meena M, Yadav G, Sonigra P, Nagda A, Mehta T, Swapnil P, Marwal A, Kumar S. Multifarious Responses of Forest Soil Microbial Community Toward Climate Change. MICROBIAL ECOLOGY 2022:10.1007/s00248-022-02051-3. [PMID: 35657425 DOI: 10.1007/s00248-022-02051-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 05/24/2022] [Indexed: 06/15/2023]
Abstract
Forest soils are a pressing subject of worldwide research owing to the several roles of forests such as carbon sinks. Currently, the living soil ecosystem has become dreadful as a consequence of several anthropogenic activities including climate change. Climate change continues to transform the living soil ecosystem as well as the soil microbiome of planet Earth. The majority of studies have aimed to decipher the role of forest soil bacteria and fungi to understand and predict the impact of climate change on soil microbiome community structure and their ecosystem in the environment. In forest soils, microorganisms live in diverse habitats with specific behavior, comprising bulk soil, rhizosphere, litter, and deadwood habitats, where their communities are influenced by biotic interactions and nutrient accessibility. Soil microbiome also drives multiple crucial steps in the nutrient biogeochemical cycles (carbon, nitrogen, phosphorous, and sulfur cycles). Soil microbes help in the nitrogen cycle through nitrogen fixation during the nitrogen cycle and maintain the concentration of nitrogen in the atmosphere. Soil microorganisms in forest soils respond to various effects of climate change, for instance, global warming, elevated level of CO2, drought, anthropogenic nitrogen deposition, increased precipitation, and flood. As the major burning issue of the globe, researchers are facing the major challenges to study soil microbiome. This review sheds light on the current scenario of knowledge about the effect of climate change on living soil ecosystems in various climate-sensitive soil ecosystems and the consequences for vegetation-soil-climate feedbacks.
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Affiliation(s)
- Mukesh Meena
- Laboratory of Phytopathology and Microbial Biotechnology, Department of Botany, Mohanlal Sukhadia University, Udaipur, 313001, Rajasthan, India.
| | - Garima Yadav
- Laboratory of Phytopathology and Microbial Biotechnology, Department of Botany, Mohanlal Sukhadia University, Udaipur, 313001, Rajasthan, India
| | - Priyankaraj Sonigra
- Laboratory of Phytopathology and Microbial Biotechnology, Department of Botany, Mohanlal Sukhadia University, Udaipur, 313001, Rajasthan, India
| | - Adhishree Nagda
- Laboratory of Phytopathology and Microbial Biotechnology, Department of Botany, Mohanlal Sukhadia University, Udaipur, 313001, Rajasthan, India
| | - Tushar Mehta
- Laboratory of Phytopathology and Microbial Biotechnology, Department of Botany, Mohanlal Sukhadia University, Udaipur, 313001, Rajasthan, India
| | - Prashant Swapnil
- Department of Botany, School of Biological Science, Central University of Punjab, Bhatinda, Punjab, 151401, India
| | - Avinash Marwal
- Department of Biotechnology, Vigyan Bhawan - Block B, New Campus, Mohanlal Sukhadia University, Udaipur, 313001, Rajasthan, India
| | - Sumit Kumar
- Department of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, 221005, India
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Microbiological Analysis and Metagenomic Profiling of the Bacterial Community of an Anthropogenic Soil Modified from Typic Haploxererts. LAND 2022. [DOI: 10.3390/land11050748] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
This work aimed to characterize the microbial communities of an anthropogenic soil originating from application of pedotechniques to Vertisols in a Mediterranean environment. Bare soil profiles were sampled at three depths (0–10 cm, 10–30 cm, and 30–50 cm) and compared with the original soil not transformed at the same depths. The anthropogenic soils were characterized by a higher CaCO3 concentration (360–640 g/kg) than control soil (190–200 g/kg), while an opposite trend was registered for clay, where control soil showed a higher concentration (465 g/kg on average) than anthropogenic soil (355 g/kg on average). Organic carbon content was much higher in the untransformed soil. All samples were microbiologically investigated using a combined culture-dependent and -independent approach. Each pedon displayed a generally decreasing level with soil depth for the several microbial groups investigated; in particular, filamentous fungi were below the detection limit at 30–50 cm. To isolate bacteria actively involved in soil particle aggregation, colonies with mucoid appearance were differentiated at the strain level and genetically identified: the major groups were represented by Bacillus and Pseudomonas. MiSeq Illumina analysis identified Actinobacteria and Firmicutes as the main groups. A high microbial variability was found in all the three anthropogenic pedons and the microorganisms constitute a mature community.
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Cotta SR, Pellegrinetti TA, Andreote APD, Costa JS, Sarmento H, Fiore MF. Disentangling the lifestyle of bacterial communities in tropical soda lakes. Sci Rep 2022; 12:7939. [PMID: 35562544 PMCID: PMC9106740 DOI: 10.1038/s41598-022-12046-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 04/22/2022] [Indexed: 11/09/2022] Open
Abstract
Microbial lifestyles may reveal niche-specific signatures and can contribute to detecting the effects of abiotic fluctuations on biogeochemical cycles. Microorganisms make a tradeoff between optimizing nutrient uptake, improving biomass yield, and overcoming environmental changes according to environmental hostility. Soda lakes are natural environments rich in carbonate and bicarbonate water, resulting in elevated pH and salinities that frequently approach saturation. We hypothesized that during the dry period (elevated pH and salinity), microorganisms try to overcome this harshness by allocating energy to the cellular maintenance process. As these environmental conditions improve during the wet period, microorganisms will begin to invest in nutrient uptake. To test this hypothesis, we evaluated four soda lakes in two different seasons by applying metagenomics combined with flow cytometry (estimate heterotrophic bacterial biomass). The natural occurrence of cyanobacterial blooms in some lakes is the main driver of carbon. These primary producers provide organic carbon that supports heterotrophic bacterial growth and, consequently, a high biomass yield. Under harsh conditions (dry season), cyanobacteria invest in nutrient uptake mechanisms, whereas heterotrophic bacteria allocate energy to survive at the expense of biomass yield. Lakes without cyanobacteria blooms invest in nutrient uptake independent of environmental hostility. This study clarifies the microbial tradeoffs in hostile environments and the impact of this choice on carbon and energy flux in tropical alkaline lakes.
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Affiliation(s)
- Simone R Cotta
- Center of Nuclear Energy in Agriculture (CENA/USP), University of São Paulo, Piracicaba, SP, CEP: 13416-903, Brazil
| | - Thierry A Pellegrinetti
- Center of Nuclear Energy in Agriculture (CENA/USP), University of São Paulo, Piracicaba, SP, CEP: 13416-903, Brazil
| | - Ana Paula D Andreote
- Center of Nuclear Energy in Agriculture (CENA/USP), University of São Paulo, Piracicaba, SP, CEP: 13416-903, Brazil
| | - Juliana S Costa
- Center of Nuclear Energy in Agriculture (CENA/USP), University of São Paulo, Piracicaba, SP, CEP: 13416-903, Brazil
| | - Hugo Sarmento
- Department of Hydrobiology, Federal University of São Carlos, São Carlos, SP, Brazil
| | - Marli F Fiore
- Center of Nuclear Energy in Agriculture (CENA/USP), University of São Paulo, Piracicaba, SP, CEP: 13416-903, Brazil.
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King WL, Kaminsky LM, Richards SC, Bradley BA, Kaye JP, Bell TH. Farm-scale differentiation of active microbial colonizers. ISME COMMUNICATIONS 2022; 2:39. [PMID: 37938671 PMCID: PMC9723676 DOI: 10.1038/s43705-022-00120-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 03/22/2022] [Accepted: 03/22/2022] [Indexed: 06/17/2023]
Abstract
Microbial movement is important for replenishing lost soil microbial biodiversity and driving plant root colonization, particularly in managed agricultural soils, where microbial diversity and composition can be disrupted. Despite abundant survey-type microbiome data in soils, which are obscured by legacy DNA and microbial dormancy, we do not know how active microbial pools are shaped by local soil properties, agricultural management, and at differing spatial scales. To determine how active microbial colonizers are shaped by spatial scale and environmental conditions, we deployed microbial traps (i.e. sterile soil enclosed by small pore membranes) containing two distinct soil types (forest; agricultural), in three neighboring locations, assessing colonization through 16S rRNA gene and fungal ITS amplicon sequencing. Location had a greater impact on fungal colonizers (R2 = 0.31 vs. 0.26), while the soil type within the microbial traps influenced bacterial colonizers more (R2 = 0.09 vs. 0.02). Bacterial colonizers showed greater colonization consistency (within-group similarity) among replicate communities. Relative to bacterial colonizers, fungal colonizers shared a greater compositional overlap to sequences from the surrounding local bulk soil (R2 = 0.08 vs. 0.29), suggesting that these groups respond to distinct environmental constraints and that their in-field management may differ. Understanding how environmental constraints and spatial scales impact microbial recolonization dynamics and community assembly are essential for identifying how soil management can be used to shape agricultural microbiomes.
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Affiliation(s)
- William L King
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Laura M Kaminsky
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Sarah C Richards
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA, 16802, USA
- Intercollege Graduate Degree Program in Ecology, The Pennsylvania State University, University Park, PA, 16802, USA
- Intercollege Graduate Degree Program in International Agriculture and Development, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Brosi A Bradley
- Department of Ecosystem Science and Management, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Jason P Kaye
- Intercollege Graduate Degree Program in Ecology, The Pennsylvania State University, University Park, PA, 16802, USA
- Department of Ecosystem Science and Management, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Terrence H Bell
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA, 16802, USA.
- Intercollege Graduate Degree Program in Ecology, The Pennsylvania State University, University Park, PA, 16802, USA.
- Intercollege Graduate Degree Program in International Agriculture and Development, The Pennsylvania State University, University Park, PA, 16802, USA.
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38
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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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Zhao XF, Shu WS, Hao YQ. Seasonal Climate Variations Promote Bacterial α-Diversity in Soil. MICROBIAL ECOLOGY 2022; 83:513-517. [PMID: 34059936 DOI: 10.1007/s00248-021-01780-1] [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: 01/03/2021] [Accepted: 05/20/2021] [Indexed: 06/12/2023]
Abstract
Ecological theory suggests that temporal environmental fluctuations can contribute greatly to diversity maintenance. Given bacteria's short generation time and rapid responses to environmental change, seasonal climate fluctuations are very likely to play an important role in maintaining the extremely high α-diversity of soil bacterial community, which has been unfortunately neglected in previous studies. Here, with in-depth analyses of two previously published soil bacterial datasets at global scale, we found that soil bacterial α-diversity was positively correlated with both seasonal variations of temperature and precipitation. Furthermore, piecewise structural equation models showed that seasonal variations of temperature or precipitation had weak but significant positive effect on soil bacterial α-diversity in each dataset. However, it is noteworthy that the importance of seasonal climate variations might be underestimated in the above analyses, due to the potential confounding factors (such as vegetation type) and the lack of sampling across seasons. As a supplement, we analyzed a previously published wheat cropland dataset with samples collected in both winter and the following summer across North China Plain. As expected, bacterial α-diversity was positively correlated with seasonal climate variations in the cropland dataset, and climate seasonality explained a larger proportion of variations in bacterial α-diversity. Collectively, these findings implied that fluctuation-dependent mechanisms of diversity maintenance presumably operate in soil bacterial communities. Based on existing evidence, we speculated that the storage effect may be the main mechanism responsible for diversity maintenance in soil bacterial community, but rigorous experimental tests are needed in the future.
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Affiliation(s)
- Xin-Feng Zhao
- School of Life Sciences, South China Normal University, No.55 Zhongshan Avenue West, Tianhe District, Guangzhou, 510631, China
| | - Wen-Sheng Shu
- School of Life Sciences, South China Normal University, No.55 Zhongshan Avenue West, Tianhe District, Guangzhou, 510631, China
| | - Yi-Qi Hao
- School of Life Sciences, South China Normal University, No.55 Zhongshan Avenue West, Tianhe District, Guangzhou, 510631, China.
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Ogai K, Nana BC, Lloyd YM, Arios JP, Jiyarom B, Awanakam H, Esemu LF, Hori A, Matsuoka A, Nainu F, Megnekou R, Leke RGF, Ekali GL, Okamoto S, Kuraishi T. Skin microbiome profile of healthy Cameroonians and Japanese. Sci Rep 2022; 12:1364. [PMID: 35079063 PMCID: PMC8789912 DOI: 10.1038/s41598-022-05244-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 01/10/2022] [Indexed: 12/20/2022] Open
Abstract
The commensal microbes of the skin have a significant impact on dermal physiology and pathophysiology. Racial and geographical differences in the skin microbiome are suggested and may play a role in the sensitivity to dermatological disorders, including infectious diseases. However, little is known about the skin microbiome profiles of people living in Central Africa, where severe tropical infectious diseases impose a burden on the inhabitants. This study provided the skin profiles of healthy Cameroonians in different body sites and compared them to healthy Japanese participants. The skin microbiome of Cameroonians was distinguishable from that of Japanese in all skin sites examined in this study. For example, Micrococcus was predominantly found in skin samples of Cameroonians but mostly absent in Japanese skin samples. Instead, the relative abundance of Cutibacterium species was significantly higher in healthy Japanese. Principal coordinate analysis of beta diversity showed that the skin microbiome of Cameroonians formed different clusters from Japanese, suggesting a substantial difference in the microbiome profiles between participants of both countries. In addition, the alpha diversity in skin microbes was higher in Cameroonians than Japanese participants. These data may offer insights into the determinant factors responsible for the distinctness of the skin microbiome of people living in Central Africa and Asia.
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Affiliation(s)
- Kazuhiro Ogai
- AI Hospital/Macro Signal Dynamics Research and Development Center (ai@ku), Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Japan
| | - Benderli Christine Nana
- Biotechnology Center, University of Yaoundé I, Yaoundé, Cameroon
- Department of Animal Biology and Physiology of the Faculty of Science, University of Yaoundé I, Yaoundé, Cameroon
| | - Yukie Michelle Lloyd
- Department of Tropical Medicine, Medical Microbiology and Pharmacology, John A. Burns School of Medicine, University of Hawaii at Manoa, Hawaii, USA
| | - John Paul Arios
- Department of Tropical Medicine, Medical Microbiology and Pharmacology, John A. Burns School of Medicine, University of Hawaii at Manoa, Hawaii, USA
| | - Boonyanudh Jiyarom
- Department of Tropical Medicine, Medical Microbiology and Pharmacology, John A. Burns School of Medicine, University of Hawaii at Manoa, Hawaii, USA
| | - Honore Awanakam
- Biotechnology Center, University of Yaoundé I, Yaoundé, Cameroon
| | - Livo Forgu Esemu
- Biotechnology Center, University of Yaoundé I, Yaoundé, Cameroon
- Institute of Medical Research and Medicinal Plant Studies, Ministry of Scientific Research and Innovation, Yaoundé, Cameroon
| | - Aki Hori
- Laboratory of Host Defense and Responses, Faculty of Pharmacy, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa, 920-1192, Japan
| | - Ayaka Matsuoka
- Faculty of Health Sciences, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Japan
| | - Firzan Nainu
- Laboratory of Host Defense and Responses, Faculty of Pharmacy, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa, 920-1192, Japan
- Department of Pharmacy, Faculty of Pharmacy, Hasanuddin University, Makassar, Indonesia
| | - Rosette Megnekou
- Biotechnology Center, University of Yaoundé I, Yaoundé, Cameroon
- Department of Animal Biology and Physiology of the Faculty of Science, University of Yaoundé I, Yaoundé, Cameroon
| | - Rose Gana Fomban Leke
- Biotechnology Center, University of Yaoundé I, Yaoundé, Cameroon
- Institute of Medical Research and Medicinal Plant Studies, Ministry of Scientific Research and Innovation, Yaoundé, Cameroon
| | | | - Shigefumi Okamoto
- Faculty of Health Sciences, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Japan.
- Advanced Health Care Science Research Unit, Institute for Frontier Science Initiative, Kanazawa University, 5-11-80 Kodatsuno, Kanazawa, Ishikawa, 920-0942, Japan.
| | - Takayuki Kuraishi
- Laboratory of Host Defense and Responses, Faculty of Pharmacy, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa, 920-1192, Japan.
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Beck AE, Kleiner M, Garrell AK. Elucidating Plant-Microbe-Environment Interactions Through Omics-Enabled Metabolic Modelling Using Synthetic Communities. FRONTIERS IN PLANT SCIENCE 2022; 13:910377. [PMID: 35795346 PMCID: PMC9251461 DOI: 10.3389/fpls.2022.910377] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 05/16/2022] [Indexed: 05/10/2023]
Abstract
With a growing world population and increasing frequency of climate disturbance events, we are in dire need of methods to improve plant productivity, resilience, and resistance to both abiotic and biotic stressors, both for agriculture and conservation efforts. Microorganisms play an essential role in supporting plant growth, environmental response, and susceptibility to disease. However, understanding the specific mechanisms by which microbes interact with each other and with plants to influence plant phenotypes is a major challenge due to the complexity of natural communities, simultaneous competition and cooperation effects, signalling interactions, and environmental impacts. Synthetic communities are a major asset in reducing the complexity of these systems by simplifying to dominant components and isolating specific variables for controlled experiments, yet there still remains a large gap in our understanding of plant microbiome interactions. This perspectives article presents a brief review discussing ways in which metabolic modelling can be used in combination with synthetic communities to continue progress toward understanding the complexity of plant-microbe-environment interactions. We highlight the utility of metabolic models as applied to a community setting, identify different applications for both flux balance and elementary flux mode simulation approaches, emphasize the importance of ecological theory in guiding data interpretation, and provide ideas for how the integration of metabolic modelling techniques with big data may bridge the gap between simplified synthetic communities and the complexity of natural plant-microbe systems.
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Affiliation(s)
- Ashley E. Beck
- Department of Biological and Environmental Sciences, Carroll College, Helena, MT, United States
- *Correspondence: Ashley E. Beck,
| | - Manuel Kleiner
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
| | - Anna-Katharina Garrell
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
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42
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Trivedi K, Kumar R, Vijay Anand KG, Bhojani G, Kubavat D, Ghosh A. Structural and functional changes in soil bacterial communities by drifting spray application of a commercial red seaweed extract as revealed by metagenomics. Arch Microbiol 2021; 204:72. [PMID: 34951686 DOI: 10.1007/s00203-021-02644-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 10/21/2021] [Accepted: 11/02/2021] [Indexed: 02/01/2023]
Abstract
Kappaphycus alvarezii seaweed extract (KSWE) is known to enhance crop productivity and impart stress tolerance. Close to one quarter of foliar spray applied to maize falls on the soil, either as drift or from leaf as drip. It was hypothesized that the drift spray would profoundly influence soil microbes under stress. An experiment was conducted with five treatments, with or without KSWE application at critical stages of maize grown under soil moisture stress and compared with an irrigated control. An Illumina platform was employed for the analysis of the V3-V4 region of 16S rRNA gene from the soil metagenome. A total of 345,552 operational taxonomic units were generated which were classified into 55 phyla, 152 classes, 240 orders, 305 families and 593 genera. Shannon's index and Shannon's equitability indicated increased soil bacterial diversity after multiple KSWE applications under conditions of abiotic duress. The abundance of the genera Alicyclobacillus, Anaerolinea, Bacillus, Balneimonas, Nitrospira, Rubrobacter and Steroidobacter decreased (49-79%) under drought imposed at the V5,10 and 15 stages of maize over the irrigated control, while it significantly improved when followed by KSWE application under drought. Flavobacterium, Nitrosomonas, Nitrosovibrio, Rubrobacter genera and several other bacterial taxa which are important for plant growth promotion and nutrient cycling were found to be enriched by KSWE application under drought conditions. Treatments having enriched microbial abundance due to KSWE application under stress recorded higher soil enzymatic activities and plant cob yield, suggesting the contribution of altered soil ecology mediated by KSWE as one of the reasons for improvement of yield.
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Affiliation(s)
- Khanjan Trivedi
- Applied Phycology and Biotechnology Division, CSIR-Central Salt and Marine Chemicals Research Institute, GB Marg, Bhavnagar, Gujarat, 364 002, India
| | - Ranjeet Kumar
- ICMR-Rajendra Memorial Research Institute of Medical Sciences, Patna, Bihar, India
| | - K G Vijay Anand
- Applied Phycology and Biotechnology Division, CSIR-Central Salt and Marine Chemicals Research Institute, GB Marg, Bhavnagar, Gujarat, 364 002, India
| | - Gopal Bhojani
- Applied Phycology and Biotechnology Division, CSIR-Central Salt and Marine Chemicals Research Institute, GB Marg, Bhavnagar, Gujarat, 364 002, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Denish Kubavat
- Applied Phycology and Biotechnology Division, CSIR-Central Salt and Marine Chemicals Research Institute, GB Marg, Bhavnagar, Gujarat, 364 002, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Arup Ghosh
- Applied Phycology and Biotechnology Division, CSIR-Central Salt and Marine Chemicals Research Institute, GB Marg, Bhavnagar, Gujarat, 364 002, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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43
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Barnett SE, Youngblut ND, Koechli CN, Buckley DH. Multisubstrate DNA stable isotope probing reveals guild structure of bacteria that mediate soil carbon cycling. Proc Natl Acad Sci U S A 2021; 118:e2115292118. [PMID: 34799453 PMCID: PMC8617410 DOI: 10.1073/pnas.2115292118] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 10/10/2021] [Indexed: 11/18/2022] Open
Abstract
Soil microorganisms determine the fate of soil organic matter (SOM), and their activities compose a major component of the global carbon (C) cycle. We employed a multisubstrate, DNA-stable isotope probing experiment to track bacterial assimilation of C derived from distinct sources that varied in bioavailability. This approach allowed us to measure microbial contributions to SOM processing by measuring the C assimilation dynamics of diverse microorganisms as they interacted within soil. We identified and tracked 1,286 bacterial taxa that assimilated 13C in an agricultural soil over a period of 48 d. Overall 13C-assimilation dynamics of bacterial taxa, defined by the source and timing of the 13C they assimilated, exhibited low phylogenetic conservation. We identified bacterial guilds composed of taxa that had similar 13C assimilation dynamics. We show that C-source bioavailability explained significant variation in both C mineralization dynamics and guild structure, and that the growth dynamics of bacterial guilds differed significantly in response to C addition. We also demonstrate that the guild structure explains significant variation in the biogeographical distribution of bacteria at continental and global scales. These results suggest that an understanding of in situ growth dynamics is essential for understanding microbial contributions to soil C cycling. We interpret these findings in the context of bacterial life history strategies and their relationship to terrestrial C cycling.
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Affiliation(s)
- Samuel E Barnett
- School of Integrative Plant Science, Cornell University, Ithaca, NY 14853
| | - Nicholas D Youngblut
- School of Integrative Plant Science, Cornell University, Ithaca, NY 14853
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Chantal N Koechli
- School of Integrative Plant Science, Cornell University, Ithaca, NY 14853
- Department of Biological Sciences, University of the Sciences, Philadelphia, PA 19104
| | - Daniel H Buckley
- School of Integrative Plant Science, Cornell University, Ithaca, NY 14853;
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Zhang Y, Chen M, Zhao YY, Zhang AY, Peng DH, Lu F, Dai CC. Destruction of the soil microbial ecological environment caused by the over-utilization of the rice-crayfish co-cropping pattern. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 788:147794. [PMID: 34029817 DOI: 10.1016/j.scitotenv.2021.147794] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 05/07/2021] [Accepted: 05/11/2021] [Indexed: 06/12/2023]
Abstract
The rice-crayfish co-cropping pattern is a traditional method for the intensive utilization of rice fields. In recent years, this pattern has been over-developed in many countries and regions, especially in China, because of its simple agronomic technology and high economic benefits. However, little is known about the potential ecological problems regarding soil microorganisms caused by the over-utilization of this pattern. The results show that rice-crayfish co-cropping, when over-utilized for a long time, reduced soil microbial richness and diversity compared with rice monocropping. A decrease in bacterial abundance in the nitrogen cycle and an increase in bacterial abundance in the carbon cycle led to a decrease in the nitrogen cycle function and an increase in the carbon cycle function. In an analysis of bacteria that are sensitive to cropping patterns, it was found that in the rice-crayfish co-cropping, the relative abundances of sensitive OTUs from Firmicutes (Bacillus and Clostridium) and Chloroflexi (Anaerolineaceae) were significantly higher during the entire growth period than those observed in the rice monocropping pattern, while the relative abundances of sensitive OTUs from Nitrospirae (Nitrospira), Gemmatimonadetes (Gemmatimonas), and Actinobacteria (Nocardioides) were significantly lower than those observed in the rice monocropping pattern. A network analysis shows that growth-period-sensitive OTUs drive the co-occurrence network modules, although the OTUs also have positive and negative correlations among modules but a positive synergistic effect on the regulation of soil nutrients. In addition, OTUs that were sensitive at the booting stage and filling stage were the key microbial groups in the rice-crayfish co-cropping and rice monocropping networks, respectively. Understanding the classifications and functions of sensitive microbes present during the rice growth period is the basis for formulating a microbial flora management strategy for the rice-crayfish co-cropping pattern, which is of great significance for adjusting agricultural management measures and controlling current soil microbial ecological problems.
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Affiliation(s)
- Yang Zhang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Centre for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Man Chen
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Centre for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Yuan-Yuan Zhao
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Centre for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Ai-Yue Zhang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Centre for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Da-Hong Peng
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Centre for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Fan Lu
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Centre for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Chuan-Chao Dai
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Centre for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China.
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Fungi in Permafrost-Affected Soils of the Canadian Arctic: Horizon- and Site-Specific Keystone Taxa Revealed by Co-Occurrence Network. Microorganisms 2021; 9:microorganisms9091943. [PMID: 34576837 PMCID: PMC8466989 DOI: 10.3390/microorganisms9091943] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 09/03/2021] [Accepted: 09/09/2021] [Indexed: 01/16/2023] Open
Abstract
Permafrost-affected soil stores a significant amount of organic carbon. Identifying the biological constraints of soil organic matter transformation, e.g., the interaction of major soil microbial soil organic matter decomposers, is crucial for predicting carbon vulnerability in permafrost-affected soil. Fungi are important players in the decomposition of soil organic matter and often interact in various mutualistic relationships during this process. We investigated four different soil horizon types (including specific horizons of cryoturbated soil organic matter (cryoOM)) across different types of permafrost-affected soil in the Western Canadian Arctic, determined the composition of fungal communities by sequencing (Illumina MPS) the fungal internal transcribed spacer region, assigned fungal lifestyles, and by determining the co-occurrence of fungal network properties, identified the topological role of keystone fungal taxa. Compositional analysis revealed a significantly higher relative proportion of the litter saprotroph Lachnum and root-associated saprotroph Phialocephala in the topsoil and the ectomycorrhizal close-contact exploring Russula in cryoOM, whereas Sites 1 and 2 had a significantly higher mean proportion of plant pathogens and lichenized trophic modes. Co-occurrence network analysis revealed the lowest modularity and average path length, and highest clustering coefficient in cryoOM, which suggested a lower network resistance to environmental perturbation. Zi-Pi plot analysis suggested that some keystone taxa changed their role from generalist to specialist, depending on the specific horizon concerned, Cladophialophora in topsoil, saprotrophic Mortierella in cryoOM, and Penicillium in subsoil were classified as generalists for the respective horizons but specialists elsewhere. The litter saprotrophic taxon Cadophora finlandica played a role as a generalist in Site 1 and specialist in the rest of the sites. Overall, these results suggested that fungal communities within cryoOM were more susceptible to environmental change and some taxa may shift their role, which may lead to changes in carbon storage in permafrost-affected soil.
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46
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Towards sustainable agriculture: rhizosphere microbiome engineering. Appl Microbiol Biotechnol 2021; 105:7141-7160. [PMID: 34508284 DOI: 10.1007/s00253-021-11555-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 08/22/2021] [Accepted: 08/24/2021] [Indexed: 11/26/2022]
Abstract
Soil microbiomes are extremely complex, with dense networks of interconnected microbial species underpinning vital functions for the ecosystem. In advanced agricultural research, rhizosphere microbiome engineering is gaining much attention, as the microbial community has been acknowledged to be a crucial partner of associated plants for their health fitness and yield. However, single or combined effects of a wide range of soil biotic and abiotic factors impact the success of engineered microbiomes, as these microbial communities exhibit uneven structural and functional networks in diverse soil conditions. Therefore, once a deep understanding of major influential factors and corresponding microbial responses is developed, the microbiome can be more effectively manipulated and optimized for cropping benefits. In this mini-review, we propose the concept of a microbiome-mediated smart agriculture system (MiMSAS). We summarize some of the advanced strategies for engineering the rhizosphere microbiome to withstand the stresses imposed by dominant abiotic and biotic factors. This work will help the scientific community gain more clarity about engineered microbiome technologies for increasing crop productivity and environmental sustainability.Key points• Individual or combined effects of soil biotic and abiotic variables hamper the implementation of engineered microbiome technologies in the field.• As a traditional approach, reduced-tillage practices coinciding with biofertilization can promote a relatively stable functional microbiome.• Increasing the complexity and efficiency of the synthetic microbiome is one way to improve its field-application success rate.• Plant genome editing/engineering is a promising approach for recruiting desired microbiomes for agricultural benefit.
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47
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Mod HK, Buri A, Yashiro E, Guex N, Malard L, Pinto-Figueroa E, Pagni M, Niculita-Hirzel H, van der Meer JR, Guisan A. Predicting spatial patterns of soil bacteria under current and future environmental conditions. THE ISME JOURNAL 2021; 15:2547-2560. [PMID: 33712699 PMCID: PMC8397778 DOI: 10.1038/s41396-021-00947-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 02/16/2021] [Accepted: 02/19/2021] [Indexed: 02/01/2023]
Abstract
Soil bacteria are largely missing from future biodiversity assessments hindering comprehensive forecasts of ecosystem changes. Soil bacterial communities are expected to be more strongly driven by pH and less by other edaphic and climatic factors. Thus, alkalinisation or acidification along with climate change may influence soil bacteria, with subsequent influences for example on nutrient cycling and vegetation. Future forecasts of soil bacteria are therefore needed. We applied species distribution modelling (SDM) to quantify the roles of environmental factors in governing spatial abundance distribution of soil bacterial OTUs and to predict how future changes in these factors may change bacterial communities in a temperate mountain area. Models indicated that factors related to soil (especially pH), climate and/or topography explain and predict part of the abundance distribution of most OTUs. This supports the expectations that microorganisms have specific environmental requirements (i.e., niches/envelopes) and that they should accordingly respond to environmental changes. Our predictions indicate a stronger role of pH over other predictors (e.g. climate) in governing distributions of bacteria, yet the predicted future changes in bacteria communities are smaller than their current variation across space. The extent of bacterial community change predictions varies as a function of elevation, but in general, deviations from neutral soil pH are expected to decrease abundances and diversity of bacteria. Our findings highlight the need to account for edaphic changes, along with climate changes, in future forecasts of soil bacteria.
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Affiliation(s)
- Heidi K Mod
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.
- Department of Geosciences and Geography, University of Helsinki, Helsinki, Finland.
| | - Aline Buri
- Institute of Earth Surface Dynamics, University of Lausanne, Lausanne, Switzerland
| | - Erika Yashiro
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Nicolas Guex
- Bioinformatics Competence Center, University of Lausanne, Lausanne, Switzerland
- Vital-IT, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Lucie Malard
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | | | - Marco Pagni
- Vital-IT, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Hélène Niculita-Hirzel
- Department of Occupational Health and Environment, Center for Primary Care and Public Health (Unisanté), University of Lausanne, Lausanne, Switzerland
| | | | - Antoine Guisan
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Institute of Earth Surface Dynamics, University of Lausanne, Lausanne, Switzerland
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48
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Alster CJ, Allison SD, Johnson NG, Glassman SI, Treseder KK. Phenotypic plasticity of fungal traits in response to moisture and temperature. ISME COMMUNICATIONS 2021; 1:43. [PMID: 36740602 PMCID: PMC9723763 DOI: 10.1038/s43705-021-00045-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 07/13/2021] [Accepted: 07/23/2021] [Indexed: 02/07/2023]
Abstract
Phenotypic plasticity of traits is commonly measured in plants to improve understanding of organismal and ecosystem responses to climate change but is far less studied for microbes. Specifically, decomposer fungi are thought to display high levels of phenotypic plasticity and their functions have important implications for ecosystem dynamics. Assessing the phenotypic plasticity of fungal traits may therefore be important for predicting fungal community response to climate change. Here, we assess the phenotypic plasticity of 15 fungal isolates (12 species) from a Southern California grassland. Fungi were incubated on litter at five moisture levels (ranging from 4-50% water holding capacity) and at five temperatures (ranging from 4-36 °C). After incubation, fungal biomass and activities of four extracellular enzymes (cellobiohydrolase (CBH), β-glucosidase (BG), β-xylosidase (BX), and N-acetyl-β-D-glucosaminidase (NAG)) were measured. We used response surface methodology to determine how fungal phenotypic plasticity differs across the moisture-temperature gradient. We hypothesized that fungal biomass and extracellular enzyme activities would vary with moisture and temperature and that the shape of the response surface would vary between fungal isolates. We further hypothesized that more closely related fungi would show more similar response surfaces across the moisture-temperature gradient. In support of our hypotheses, we found that plasticity differed between fungi along the temperature gradient for fungal biomass and for all the extracellular enzyme activities. Plasticity also differed between fungi along the moisture gradient for BG activity. These differences appear to be caused by variation mainly at the moisture and temperature extremes. We also found that more closely related fungi had more similar extracellular enzymes activities at the highest temperature. Altogether, this evidence suggests that with global warming, fungal biodiversity may become increasingly important as functional traits tend to diverge along phylogenetic lines at higher temperatures.
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Affiliation(s)
- Charlotte J Alster
- Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, USA.
- School of Science, University of Waikato, Hamilton, New Zealand.
| | - Steven D Allison
- Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, USA
- Department of Earth System Science, University of California, Irvine, Irvine, CA, USA
| | - Nels G Johnson
- USDA Forest Service, Pacific Southwest Research Station, Albany, CA, USA
| | - Sydney I Glassman
- Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, USA
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, USA
| | - Kathleen K Treseder
- Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, USA
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49
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Shoemaker WR, Jones SE, Muscarella ME, Behringer MG, Lehmkuhl BK, Lennon JT. Microbial population dynamics and evolutionary outcomes under extreme energy limitation. Proc Natl Acad Sci U S A 2021; 118:e2101691118. [PMID: 34385301 PMCID: PMC8379937 DOI: 10.1073/pnas.2101691118] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Microorganisms commonly inhabit energy-limited ecosystems where cellular maintenance and reproduction is highly constrained. To gain insight into how individuals persist under such conditions, we derived demographic parameters from a collection of 21 heterotrophic bacterial taxa by censusing 100 populations in an effectively closed system for 1,000 d. All but one taxon survived prolonged resource scarcity, yielding estimated times to extinction ranging over four orders of magnitude from 100 to 105 y. Our findings corroborate reports of long-lived bacteria recovered from ancient environmental samples, while providing insight into mechanisms of persistence. As death rates declined over time, lifespan was extended through the scavenging of dead cells. Although reproduction was suppressed in the absence of exogenous resources, populations continued to evolve. Hundreds of mutations were acquired, contributing to genome-wide signatures of purifying selection as well as molecular signals of adaptation. Consistent ecological and evolutionary dynamics indicate that distantly related bacteria respond to energy limitation in a similar and predictable manner, which likely contributes to the stability and robustness of microbial life.
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Affiliation(s)
- William R Shoemaker
- Department of Biology, Indiana University, Bloomington, IN, 47405;
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095
| | - Stuart E Jones
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556
| | | | | | - Brent K Lehmkuhl
- Department of Biology, Indiana University, Bloomington, IN, 47405
| | - Jay T Lennon
- Department of Biology, Indiana University, Bloomington, IN, 47405;
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50
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Lamit LJ, Romanowicz KJ, Potvin LR, Lennon JT, Tringe SG, Chimner RA, Kolka RK, Kane ES, Lilleskov EA. Peatland microbial community responses to plant functional group and drought are depth-dependent. Mol Ecol 2021; 30:5119-5136. [PMID: 34402116 DOI: 10.1111/mec.16125] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 07/14/2021] [Accepted: 07/27/2021] [Indexed: 12/27/2022]
Abstract
Peatlands store one-third of Earth's soil carbon, the stability of which is uncertain due to climate change-driven shifts in hydrology and vegetation, and consequent impacts on microbial communities that mediate decomposition. Peatland carbon cycling varies over steep physicochemical gradients characterizing vertical peat profiles. However, it is unclear how drought-mediated changes in plant functional groups (PFGs) and water table (WT) levels affect microbial communities at different depths. We combined a multiyear mesocosm experiment with community sequencing across a 70-cm depth gradient, to test the hypotheses that vascular PFGs (Ericaceae vs. sedges) and WT (high vs. low) structure peatland microbial communities in depth-dependent ways. Several key results emerged. (i) Both fungal and prokaryote (bacteria and archaea) community structure shifted with WT and PFG manipulation, but fungi were much more sensitive to PFG whereas prokaryotes were much more sensitive to WT. (ii) PFG effects were largely driven by Ericaceae, although sedge effects were evident in specific cases (e.g., methanotrophs). (iii) Treatment effects varied with depth: the influence of PFG was strongest in shallow peat (0-10, 10-20 cm), whereas WT effects were strongest at the surface and middle depths (0-10, 30-40 cm), and all treatment effects waned in the deepest peat (60-70 cm). Our results underline the depth-dependent and taxon-specific ways that plant communities and hydrologic variability shape peatland microbial communities, pointing to the importance of understanding how these factors integrate across soil profiles when examining peatland responses to climate change.
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Affiliation(s)
- Louis J Lamit
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, Michigan, USA
| | - Karl J Romanowicz
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, Michigan, USA
| | - Lynette R Potvin
- USDA Forest Service Northern Research Station, Houghton, Michigan, USA
| | - Jay T Lennon
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - Susannah G Tringe
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Rodney A Chimner
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, Michigan, USA
| | - Randall K Kolka
- USDA Forest Service Northern Research Station, Grand Rapids, Minnesota, USA
| | - Evan S Kane
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, Michigan, USA.,USDA Forest Service Northern Research Station, Houghton, Michigan, USA
| | - Erik A Lilleskov
- USDA Forest Service Northern Research Station, Houghton, Michigan, USA
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