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Zhao J, Xie X, Jiang Y, Li J, Fu Q, Qiu Y, Fu X, Yao Z, Dai Z, Qiu Y, Chen H. Effects of simulated warming on soil microbial community diversity and composition across diverse ecosystems. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 911:168793. [PMID: 37996030 DOI: 10.1016/j.scitotenv.2023.168793] [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: 09/27/2023] [Revised: 11/20/2023] [Accepted: 11/20/2023] [Indexed: 11/25/2023]
Abstract
Soil warming can directly affect the microbial community, or indirectly affect the microbial community by affecting soil moisture, nutrient availability, vegetation growth, etc. However, the response of microorganisms to soil warming is complex, and there is no uniform conclusion on the impact and mechanism of warming on microbial diversity. As the global climate gradually warms, a comprehensive assessment of warming on soil microbial community changes is essential to understand and predict the response of microbial geochemical processes to soil warming. Here, we perform a meta-analysis of studies to investigate changes in soil microbial communities along soil warming gradients and the response of soil microbes to elevated temperature in different ecosystems. We found that the α diversity index of soil microorganisms decreased significantly with the increase in temperature, and the β diversity altered with the increase in soil temperature and the shifts in ecosystem. Most bacteria only alter when the temperature rises higher. Compared to the non-warming condition, the relative abundance of Acidobacteria, Proteobacteria, Bacteroidetes, Planctomycetes and Verrucomicrobia decreased by 19 %, 11 %, 19 %, 8 % and 6 %, respectively, and the relative abundance of Firmicutes increased by 34 %. Compared to farmland, forest, grassland and tundra ecosystems, soil microorganisms in wetland ecosystems were more sensitive to temperature increase, and the changes in bacteria were consistent with the overall alterations. This meta-analysis revealed significant changes in the composition of microbial communities on soil warming. With the decrease in biodiversity under increasing temperature conditions, these dominant microbiomes, which can grow well under high-temperature conditions, will play a stronger role in regulating nutrient and energy flow. Our analysis adds a global perspective to the temperature response of soil microbes, which is critical to improving our understanding of the mechanisms of how soil microbes change in response to climate warming.
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Affiliation(s)
- Jiayi Zhao
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Xuan Xie
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Yuying Jiang
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Jiaxin Li
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Qi Fu
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Yingbo Qiu
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Xianheng Fu
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Zhiyuan Yao
- School of Civil and Environmental Engineering, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Zhongmin Dai
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Yunpeng Qiu
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Huaihai Chen
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong 518107, China.
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2
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Radujković D, Vicca S, van Rooyen M, Wilfahrt P, Brown L, Jentsch A, Reinhart KO, Brown C, De Gruyter J, Jurasinski G, Askarizadeh D, Bartha S, Beck R, Blenkinsopp T, Cahill J, Campetella G, Canullo R, Chelli S, Enrico L, Fraser L, Hao X, Henry HAL, Hohn M, Jouri MH, Koch M, Lawrence Lodge R, Li FY, Lord JM, Milligan P, Minggagud H, Palmer T, Schröder B, Szabó G, Zhang T, Zimmermann Z, Verbruggen E. Consistent predictors of microbial community composition across spatial scales in grasslands reveal low context-dependency. Mol Ecol 2023; 32:6924-6938. [PMID: 37873915 DOI: 10.1111/mec.17178] [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: 07/01/2022] [Revised: 08/26/2023] [Accepted: 10/12/2023] [Indexed: 10/25/2023]
Abstract
Environmental circumstances shaping soil microbial communities have been studied extensively. However, due to disparate study designs, it has been difficult to resolve whether a globally consistent set of predictors exists, or context-dependency prevails. Here, we used a network of 18 grassland sites (11 of those containing regional plant productivity gradients) to examine (i) if similar abiotic or biotic factors predict both large-scale (across sites) and regional-scale (within sites) patterns in bacterial and fungal community composition, and (ii) if microbial community composition differs consistently at two levels of regional plant productivity (low vs. high). Our results revealed that bacteria were associated with particular soil properties (such as base saturation) and both bacteria and fungi were associated with plant community composition across sites and within the majority of sites. Moreover, a discernible microbial community signal emerged, clearly distinguishing high and low-productivity soils across different grasslands independent of their location in the world. Hence, regional productivity differences may be typified by characteristic soil microbial communities across the grassland biome. These results could encourage future research aiming to predict the general effects of global changes on soil microbial community composition in grasslands and to discriminate fertile from infertile systems using generally applicable microbial indicators.
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Affiliation(s)
- Dajana Radujković
- Department of Biology, Plants and Ecosystems (PLECO), Universiteitsplein 1, University of Antwerp, Wilrijk, Belgium
| | - Sara Vicca
- Department of Biology, Plants and Ecosystems (PLECO), Universiteitsplein 1, University of Antwerp, Wilrijk, Belgium
| | - Margaretha van Rooyen
- Department of Plant and Soil Science, University of Pretoria, Pretoria, South Africa
| | - Peter Wilfahrt
- Department of Disturbance Ecology, University of Bayreuth, Bayreuth, Germany
- Department of Ecology, Evolution, and Behavior, University Minnesota, Saint Paul, Minnesota, USA
| | - Leslie Brown
- Applied Behavioural Ecology & Ecosystem Research Unit, Dept. Environmental Sciences, University of South Africa, Florida, South Africa
| | - Anke Jentsch
- Department of Disturbance Ecology, University of Bayreuth, Bayreuth, Germany
| | - Kurt O Reinhart
- United States Department of Agriculture-Agricultural Research Service (or USDA-ARS), Fort Keogh Livestock& Range Research Laboratory, Miles City, Montana, USA
| | - Charlotte Brown
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
- Desert Laboratory on Tumamoc Hill, University of Arizona, Tucson, Arizona, USA
| | - Johan De Gruyter
- Department of Biology, Plants and Ecosystems (PLECO), Universiteitsplein 1, University of Antwerp, Wilrijk, Belgium
| | - Gerald Jurasinski
- Landscape Ecology, University of Rostock, Rostock, Germany
- Institute of Botany and Landscape Ecology, University of Greifswald, Greifswald, Germany
| | - Diana Askarizadeh
- Department of Rehabilitation of Arid and Mountainous Regions, Faculty of Natural Resources, University of Tehran, Tehran, Iran
| | - Sandor Bartha
- Centre for Ecological Research, Institute of Ecology and Botany, Vácrátót, Hungary
| | - Ryan Beck
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, Alberta, Canada
| | - Theodore Blenkinsopp
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - James Cahill
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Giandiego Campetella
- Unit of Plant Diversity and Ecosystems Management, School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
| | - Roberto Canullo
- Unit of Plant Diversity and Ecosystems Management, School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
| | - Stefano Chelli
- Unit of Plant Diversity and Ecosystems Management, School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
| | - Lucas Enrico
- Instituto Multidisciplinario de Biología Vegetal (CONICET-UNC) and FCEFyN, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Lauchlan Fraser
- Department of Natural Resource Science, Thompson Rivers University, Kamloops, British Columbia, Canada
| | - Xiying Hao
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, Alberta, Canada
| | - Hugh A L Henry
- Department of Biology, University of Western Ontario, London, Ontario, Canada
| | - Maria Hohn
- Department of Botany, Hungarian University of Agriculture and Life Sciences, Budapest, Hungary
| | | | - Marian Koch
- Soil Physics, University of Rostock, Rostock, Germany
| | | | - Frank Yonghong Li
- School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Janice M Lord
- Department of Botany - Te Tari Huaota, University of Otago, Dunedin, New Zealand
| | - Patrick Milligan
- Department of Biology, University of Florida, Gainesville, Florida, USA
| | - Hugjiltu Minggagud
- School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Todd Palmer
- Department of Biology, University of Florida, Gainesville, Florida, USA
| | | | - Gábor Szabó
- Environmental Sciences Doctoral School, Hungarian University of Agriculture and Life Sciences, Gödöllő, Hungary
| | - Tongrui Zhang
- School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Zita Zimmermann
- Centre for Ecological Research, Institute of Ecology and Botany, Vácrátót, Hungary
| | - Erik Verbruggen
- Department of Biology, Plants and Ecosystems (PLECO), Universiteitsplein 1, University of Antwerp, Wilrijk, Belgium
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Liu D, Lin L, Zhang T, Xu Q, Wang M, Gao M, Bhople P, Pritchard HW, Yang X, Yu F. Wild Panax plants adapt to their thermal environment by harboring abundant beneficial seed endophytic bacteria. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.967692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The seed microbiome of crop wild relatives is a potential reservoir of beneficial traits that potentially improve their host plant resilience to fluctuating environments and pathogenic threats. Herein, we studied the seed microbiome of three species of the medicinal genus Panax (P. vietnamensis, P. japonicas, and P. stipuleanatus) collected from seven locations in Southwest China. We used qPCR and metabarcoding high-throughput sequencing to target both endophytic bacteria and fungi. Seed bacterial absolute abundance (1.1 × 109∼1.0 × 107 gene copy numbers per gram seed) was substantially higher than that of fungi (7.6 × 105∼3.7 × 102). Host plant genotype was the main driver of seed microbiome composition for both bacteria and fungi. Panax growing hypothermal environments significantly shaped their seed endophytic bacterial but not fungal microbiota. The three Panax species’ seeds harbored unique microbes [averaged ∼150 amplicon sequence variants (ASVs)], sharing only 12 bacterial ASVs (half affiliated to Halomonas) and four fungal ASVs. Network analysis showed that the Panax seed endophytic bacteria tend to form inter-weaved functional modules that are majorly connected by core members from the genus Halomonas, Pseudomonas, and Pantoea. These genera have been associated with nutrient cycling, plant, disease suppression, and tolerance to environmental fluctuation. Together, these novel insights may shade light on the ecological strategies of wild Panax plants adaptation to their thermal environment by possessing abundant beneficial seed endophytic bacteria.
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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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Truffle Microbiome Is Driven by Fruit Body Compartmentalization Rather than Soils Conditioned by Different Host Trees. mSphere 2021; 6:e0003921. [PMID: 34378984 PMCID: PMC8386477 DOI: 10.1128/msphere.00039-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Truffles are among the most expensive edible mushrooms; their value is worth billions of U.S. dollars annually in international markets. They establish ectomycorrhizal symbiotic relationships with diverse host tree roots and produce hypogeous ascomata. Their whole life cycle is closely related to their associated microbiome. However, whether truffle-associated compartments or host tree rhizospheres are the vital driver for truffle ascomata microbiome is unclear. To identify and compare fungal and bacterial communities in four truffle-associated compartments (Tuber indicum: bulk soil, adhering soil to peridium, peridium, and gleba) from three host trees, we sequenced their ITS (fungal) and 16S (bacterial) ribosomal DNA using the Illumina MiSeq high-throughput platform. We further applied the amplicon data to analyze the core microbiome and microbial ecological networks. Tuber indicum microbiome composition was strongly driven by its associated compartments rather than by their symbiotic host trees. Truffle microbiome was bacteria dominated, and its bacterial community formed a substantially more complex interacting network compared to that of the fungal community. The core fungal community changed from Basidiomycota dominated (bulk soil) to Rozellomycota dominated (interphase soil); the core bacterial community shifted from Bacteroidetes to Proteobacteria dominance from truffle peridium to gleba tissue. Especially, at the truffle and soil interphase, the niche-based selection of truffle microbiome was verified by (i) a clear exclusion of four bacterial phyla (Rokubacteria, Nitrospirae, Chloroflexi, and Planctomycetes) in gleba; (ii) a significant decrease in alpha-diversity (as revealed by Chao 1, Shannon, and Simpson indices); and (iii) the complexity of the network substantially decreased from bulk soil to soil-truffle interphase and further to the peridium and gleba. The network analysis of microbiome showed that the microbial positive interactions were higher in truffle tissues than in both bulk soil and peridium-adhering soil and that Cupriavidus, Bradyrhizobium, Aminobacter, and Mesorhizobium spp. were the keystone network hubs in the truffle gleba. This study provides insights into the factors that drive the truffle microbiome dynamics and the recruitment and function of the microbiome components. IMPORTANCE Currently, the factors that drive the microbiome associated with truffles, the most highly prized fungi in the world, are largely unknown. We demonstrate for the first time here that truffle microbiome composition is strongly driven by associated compartments rather than by symbiotic host trees. The truffle microbiome was bacteria dominated, and its bacterial community formed a substantially more complex (with the higher numbers of nodes, links, and modules) interacting network compared to that of the fungal community. Network analysis showed a higher number of positive microbial interactions with each other in truffle tissues than in both bulk soil and peridium-adhering soil. For the first time, the fungal community structure associated with truffles using high-throughput sequencing, microbial networks, and keystone species analyses is presented. This study provides novel insights into the factors that drive the truffle microbiome dynamics and the recruitment and function of the microbiome components, showing that they are more complex than previously thought.
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Sharma K, Palatinszky M, Nikolov G, Berry D, Shank EA. Transparent soil microcosms for live-cell imaging and non-destructive stable isotope probing of soil microorganisms. eLife 2020; 9:e56275. [PMID: 33140722 PMCID: PMC7609051 DOI: 10.7554/elife.56275] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Accepted: 10/16/2020] [Indexed: 01/02/2023] Open
Abstract
Microscale processes are critically important to soil ecology and biogeochemistry yet are difficult to study due to soil's opacity and complexity. To advance the study of soil processes, we constructed transparent soil microcosms that enable the visualization of microbes via fluorescence microscopy and the non-destructive measurement of microbial activity and carbon uptake in situ via Raman microspectroscopy. We assessed the polymer Nafion and the crystal cryolite as optically transparent soil substrates. We demonstrated that both substrates enable the growth, maintenance, and visualization of microbial cells in three dimensions over time, and are compatible with stable isotope probing using Raman. We applied this system to ascertain that after a dry-down/rewetting cycle, bacteria on and near dead fungal hyphae were more metabolically active than those far from hyphae. These data underscore the impact fungi have facilitating bacterial survival in fluctuating conditions and how these microcosms can yield insights into microscale microbial activities.
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Affiliation(s)
- Kriti Sharma
- Department of Biology, University of North CarolinaChapel HillUnited States
| | - Márton Palatinszky
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of ViennaViennaAustria
| | - Georgi Nikolov
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of ViennaViennaAustria
| | - David Berry
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of ViennaViennaAustria
| | - Elizabeth A Shank
- Department of Biology, University of North CarolinaChapel HillUnited States
- Department of Microbiology and Immunology, University of North CarolinaChapel HillUnited States
- Program in Systems Biology, University of Massachusetts Medical SchoolWorcesterUnited States
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Voříšková J, Elberling B, Priemé A. Fast response of fungal and prokaryotic communities to climate change manipulation in two contrasting tundra soils. ENVIRONMENTAL MICROBIOME 2019; 14:6. [PMID: 33902718 PMCID: PMC7989089 DOI: 10.1186/s40793-019-0344-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 08/24/2019] [Indexed: 05/31/2023]
Abstract
BACKGROUND Climate models predict substantial changes in temperature and precipitation patterns across Arctic regions, including increased winter precipitation as snow in the near future. Soil microorganisms are considered key players in organic matter decomposition and regulation of biogeochemical cycles. However, current knowledge regarding their response to future climate changes is limited. Here, we explore the short-term effect of increased snow cover on soil fungal, bacterial and archaeal communities in two tundra sites with contrasting water regimes in Greenland. In order to assess seasonal variation of microbial communities, we collected soil samples four times during the plant-growing season. RESULTS The analysis revealed that soil microbial communities from two tundra sites differed from each other due to contrasting soil chemical properties. Fungal communities showed higher richness at the dry site whereas richness of prokaryotes was higher at the wet tundra site. We demonstrated that fungal and bacterial communities at both sites were significantly affected by short-term increased snow cover manipulation. Our results showed that fungal community composition was more affected by deeper snow cover compared to prokaryotes. The fungal communities showed changes in both taxonomic and ecological groups in response to climate manipulation. However, the changes were not pronounced at all sampling times which points to the need of multiple sampling in ecosystems where environmental factors show seasonal variation. Further, we showed that effects of increased snow cover were manifested after snow had melted. CONCLUSIONS We demonstrated rapid response of soil fungal and bacterial communities to short-term climate manipulation simulating increased winter precipitation at two tundra sites. In particular, we provide evidence that fungal community composition was more affected by increased snow cover compared to prokaryotes indicating fast adaptability to changing environmental conditions. Since fungi are considered the main decomposers of complex organic matter in terrestrial ecosystems, the stronger response of fungal communities may have implications for organic matter turnover in tundra soils under future climate.
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Affiliation(s)
- Jana Voříšková
- Center for Permafrost (CENPERM), Department of Geosciences and Natural Resource Management, University of Copenhagen, Copenhagen, Denmark
- Department of Geochemistry, Geological Survey of Denmark and Greenland (GEUS), Copenhagen, Denmark
- Ecology Department, Climate and Ecosystem Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Bo Elberling
- Center for Permafrost (CENPERM), Department of Geosciences and Natural Resource Management, University of Copenhagen, Copenhagen, Denmark
| | - Anders Priemé
- Center for Permafrost (CENPERM), Department of Geosciences and Natural Resource Management, University of Copenhagen, Copenhagen, Denmark
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
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Whitman T, Neurath R, Perera A, Chu-Jacoby I, Ning D, Zhou J, Nico P, Pett-Ridge J, Firestone M. Microbial community assembly differs across minerals in a rhizosphere microcosm. Environ Microbiol 2018; 20:4444-4460. [PMID: 30047192 DOI: 10.1111/1462-2920.14366] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 07/20/2018] [Accepted: 07/20/2018] [Indexed: 11/30/2022]
Abstract
Mineral-associated microbes drive many critical soil processes, including mineral weathering, soil aggregation and cycling of mineral-sorbed organic matter. To investigate the interactions between soil minerals and microbes in the rhizosphere, we incubated three types of minerals (ferrihydrite, kaolinite and quartz) and a native soil mineral fraction near roots of a common Californian annual grass, Avena barbata, growing in its resident soil. We followed microbial colonization of these minerals for up to 2.5 months - the plant's lifespan. Bacteria and fungi that colonized mineral surfaces during this experiment differed across mineral types and differed from those in the background soil, implying that microbial colonization was the result of processes in addition to passive movement with water to mineral surfaces. Null model analysis revealed that dispersal limitation was a dominant factor structuring mineral-associated microbial communities for all mineral types. Once bacteria arrived at a mineral surface, capacity for rapid growth appeared important, as ribosomal copy number was significantly correlated with relative enrichment on minerals. Glomeromycota (a phylum associated with arbuscular mycorrhizal fungi) appeared to preferentially associate with ferrihydrite surfaces. The mechanisms enabling the colonization of soil minerals may be foundational in shaping the overall soil microbiome composition and development of persistent organic matter in soils.
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Affiliation(s)
- Thea Whitman
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA, USA.,Department of Soil Science, University of Wisconsin-Madison, Madison, WI, USA
| | - Rachel Neurath
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA, USA.,Lawrence Livermore National Laboratory, Physical and Life Science Directorate, Livermore, CA, USA
| | - Adele Perera
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA, USA
| | - Ilexis Chu-Jacoby
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA, USA
| | - Daliang Ning
- Consolidated Core Laboratory, University of Oklahoma, Norman, OK, USA.,Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA.,Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Jizhong Zhou
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA.,Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA.,School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, USA.,Lawrence Berkeley National Laboratory, Earth and Environmental Sciences, Berkeley, CA, USA.,State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Peter Nico
- Lawrence Berkeley National Laboratory, Earth and Environmental Sciences, Berkeley, CA, USA
| | - Jennifer Pett-Ridge
- Lawrence Livermore National Laboratory, Physical and Life Science Directorate, Livermore, CA, USA
| | - Mary Firestone
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA, USA.,Lawrence Berkeley National Laboratory, Earth and Environmental Sciences, Berkeley, CA, USA
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9
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Acclimation of Fine Root Systems to Soil Warming: Comparison of an Experimental Setup and a Natural Soil Temperature Gradient. Ecosystems 2018. [DOI: 10.1007/s10021-018-0280-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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10
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Zhang CJ, Delgado-Baquerizo M, Drake JE, Reich PB, Tjoelker MG, Tissue DT, Wang JT, He JZ, Singh BK. Intraspecies variation in a widely distributed tree species regulates the responses of soil microbiome to different temperature regimes. ENVIRONMENTAL MICROBIOLOGY REPORTS 2018; 10:167-178. [PMID: 29327437 DOI: 10.1111/1758-2229.12613] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 01/06/2018] [Indexed: 06/07/2023]
Abstract
Plant characteristics in different provenances within a single species may vary in response to climate change, which might alter soil microbial communities and ecosystem functions. We conducted a glasshouse experiment and grew seedlings of three provenances (temperate, subtropical and tropical origins) of a tree species (i.e., Eucalyptus tereticornis) at different growth temperatures (18, 21.5, 25, 28.5, 32 and 35.5°C) for 54 days. At the end of the experiment, bacterial and fungal community composition, diversity and abundance were characterized. Measured soil functions included surrogates of microbial respiration, enzyme activities and nutrient cycling. Using Permutation multivariate analysis of variance (PerMANOVA) and network analysis, we found that the identity of tree provenances regulated both structure and function of soil microbiomes. In some cases, tree provenances substantially affected the response of microbial communities to the temperature treatments. For example, we found significant interactions of temperature and tree provenance on bacterial community and relative abundances of Chloroflexi and Zygomycota, and inorganic nitrogen. Microbial abundance was altered in response to increasing temperature, but was not affected by tree provenances. Our study provides novel evidence that even a small variation in biotic components (i.e., intraspecies tree variation) can significantly influence the response of soil microbial community composition and specific soil functions to global warming.
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Affiliation(s)
- Cui-Jing Zhang
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, New South Wales 2751, Australia
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Manuel Delgado-Baquerizo
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, New South Wales 2751, Australia
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO 80309, USA
| | - John E Drake
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, New South Wales 2751, Australia
| | - Peter B Reich
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, New South Wales 2751, Australia
- Department of Forest Resources, University of Minnesota, St. Paul, MN 55108, USA
| | - Mark G Tjoelker
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, New South Wales 2751, Australia
| | - David T Tissue
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, New South Wales 2751, Australia
| | - Jun-Tao Wang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Ji-Zheng He
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Brajesh K Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, New South Wales 2751, Australia
- Global Centre for Land Based Innovation, Western Sydney University, Locked Bag 1797, Penrith, New South Wales 2751, Australia
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11
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Radujkovic D, Verbruggen E, Sigurdsson BD, Leblans NIW, Janssens IA, Vicca S, Weedon JT. Prolonged exposure does not increase soil microbial community compositional response to warming along geothermal gradients. FEMS Microbiol Ecol 2018; 94:4712010. [PMID: 29228354 DOI: 10.1101/102459] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 12/01/2017] [Indexed: 05/26/2023] Open
Abstract
Global change is expected to affect soil microbial communities through their responsiveness to temperature. It has been proposed that prolonged exposure to elevated temperatures may lead to progressively larger effects on soil microbial community composition. However, due to the relatively short-term nature of most warming experiments, this idea has been challenging to evaluate. The present study took the advantage of natural geothermal gradients (from +1°C to +19°C above ambient) in two subarctic grasslands to test the hypothesis that long-term exposure (>50 years) intensifies the effect of warming on microbial community composition compared to short-term exposure (5-7 years). Community profiles from amplicon sequencing of bacterial and fungal rRNA genes did not support this hypothesis: significant changes relative to ambient were observed only starting from the warming intensity of +9°C in the long term and +7°C/+3°C in the short term, for bacteria and fungi, respectively. Our results suggest that microbial communities in high-latitude grasslands will not undergo lasting shifts in community composition under the warming predicted for the coming 100 years (+2.2°C to +8.3°C).
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Affiliation(s)
- Dajana Radujkovic
- Plants and Ecosystems, Department of Biology, University of Antwerp, Universiteitsplein 1, Wilrijk 2610, Belgium
| | - Erik Verbruggen
- Plants and Ecosystems, Department of Biology, University of Antwerp, Universiteitsplein 1, Wilrijk 2610, Belgium
| | - Bjarni D Sigurdsson
- Faculty of Environmental Sciences, Agricultural University of Iceland, Hvanneyr IS - 311 Borgarnes, Iceland
| | - Niki I W Leblans
- Plants and Ecosystems, Department of Biology, University of Antwerp, Universiteitsplein 1, Wilrijk 2610, Belgium
- Faculty of Environmental Sciences, Agricultural University of Iceland, Hvanneyr IS - 311 Borgarnes, Iceland
| | - Ivan A Janssens
- Plants and Ecosystems, Department of Biology, University of Antwerp, Universiteitsplein 1, Wilrijk 2610, Belgium
| | - Sara Vicca
- Plants and Ecosystems, Department of Biology, University of Antwerp, Universiteitsplein 1, Wilrijk 2610, Belgium
| | - James T Weedon
- Plants and Ecosystems, Department of Biology, University of Antwerp, Universiteitsplein 1, Wilrijk 2610, Belgium
- Department of Ecological Science, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
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12
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Prolonged exposure does not increase soil microbial community compositional response to warming along geothermal gradients. FEMS Microbiol Ecol 2017; 94:4712010. [DOI: 10.1093/femsec/fix174] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 12/01/2017] [Indexed: 01/03/2023] Open
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13
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Liang Y, Jiang Y, Wang F, Wen C, Deng Y, Xue K, Qin Y, Yang Y, Wu L, Zhou J, Sun B. Long-term soil transplant simulating climate change with latitude significantly alters microbial temporal turnover. THE ISME JOURNAL 2015; 9:2561-72. [PMID: 25989371 PMCID: PMC4817637 DOI: 10.1038/ismej.2015.78] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 03/27/2015] [Accepted: 04/13/2015] [Indexed: 01/27/2023]
Abstract
To understand soil microbial community stability and temporal turnover in response to climate change, a long-term soil transplant experiment was conducted in three agricultural experiment stations over large transects from a warm temperate zone (Fengqiu station in central China) to a subtropical zone (Yingtan station in southern China) and a cold temperate zone (Hailun station in northern China). Annual soil samples were collected from these three stations from 2005 to 2011, and microbial communities were analyzed by sequencing microbial 16S ribosomal RNA gene amplicons using Illumina MiSeq technology. Our results revealed a distinctly differential pattern of microbial communities in both northward and southward transplantations, along with an increase in microbial richness with climate cooling and a corresponding decrease with climate warming. The microbial succession rate was estimated by the slope (w value) of linear regression of a log-transformed microbial community similarity with time (time-decay relationship). Compared with the low turnover rate of microbial communities in situ (w=0.046, P<0.001), the succession rate at the community level was significantly higher in the northward transplant (w=0.058, P<0.001) and highest in the southward transplant (w=0.094, P<0.001). Climate warming lead to a faster succession rate of microbial communities as well as lower species richness and compositional changes compared with in situ and climate cooling, which may be related to the high metabolic rates and intense competition under higher temperature. This study provides new insights into the impacts of climate change on the fundamental temporal scaling of soil microbial communities and microbial phylogenetic biodiversity.
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Affiliation(s)
- Yuting Liang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Yuji Jiang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Feng Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Chongqing Wen
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Ye Deng
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, China
| | - Kai Xue
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Yujia Qin
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Liyou Wu
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Jizhong Zhou
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
- Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Bo Sun
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
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14
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Pold G, Melillo JM, DeAngelis KM. Two decades of warming increases diversity of a potentially lignolytic bacterial community. Front Microbiol 2015; 6:480. [PMID: 26042112 PMCID: PMC4438230 DOI: 10.3389/fmicb.2015.00480] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 04/30/2015] [Indexed: 11/13/2022] Open
Abstract
As Earth's climate warms, the massive stores of carbon found in soil are predicted to become depleted, and leave behind a smaller carbon pool that is less accessible to microbes. At a long-term forest soil-warming experiment in central Massachusetts, soil respiration and bacterial diversity have increased, while fungal biomass and microbially-accessible soil carbon have decreased. Here, we evaluate how warming has affected the microbial community's capability to degrade chemically-complex soil carbon using lignin-amended BioSep beads. We profiled the bacterial and fungal communities using PCR-based methods and completed extracellular enzyme assays as a proxy for potential community function. We found that lignin-amended beads selected for a distinct community containing bacterial taxa closely related to known lignin degraders, as well as members of many genera not previously noted as capable of degrading lignin. Warming tended to drive bacterial community structure more strongly in the lignin beads, while the effect on the fungal community was limited to unamended beads. Of those bacterial operational taxonomic units (OTUs) enriched by the warming treatment, many were enriched uniquely on lignin-amended beads. These taxa may be contributing to enhanced soil respiration under warming despite reduced readily available C availability. In aggregate, these results suggest that there is genetic potential for chemically complex soil carbon degradation that may lead to extended elevated soil respiration with long-term warming.
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Affiliation(s)
- Grace Pold
- Microbiology Department, University of Massachusetts Amherst, MA, USA ; Graduate Program in Organismic and Evolutionary Biology, University of Massachusetts Amherst, MA, USA
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15
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DeAngelis KM, Pold G, Topçuoğlu BD, van Diepen LTA, Varney RM, Blanchard JL, Melillo J, Frey SD. Long-term forest soil warming alters microbial communities in temperate forest soils. Front Microbiol 2015; 6:104. [PMID: 25762989 PMCID: PMC4327730 DOI: 10.3389/fmicb.2015.00104] [Citation(s) in RCA: 133] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2014] [Accepted: 01/27/2015] [Indexed: 01/24/2023] Open
Abstract
Soil microbes are major drivers of soil carbon cycling, yet we lack an understanding of how climate warming will affect microbial communities. Three ongoing field studies at the Harvard Forest Long-term Ecological Research (LTER) site (Petersham, MA) have warmed soils 5°C above ambient temperatures for 5, 8, and 20 years. We used this chronosequence to test the hypothesis that soil microbial communities have changed in response to chronic warming. Bacterial community composition was studied using Illumina sequencing of the 16S ribosomal RNA gene, and bacterial and fungal abundance were assessed using quantitative PCR. Only the 20-year warmed site exhibited significant change in bacterial community structure in the organic soil horizon, with no significant changes in the mineral soil. The dominant taxa, abundant at 0.1% or greater, represented 0.3% of the richness but nearly 50% of the observations (sequences). Individual members of the Actinobacteria, Alphaproteobacteria and Acidobacteria showed strong warming responses, with one Actinomycete decreasing from 4.5 to 1% relative abundance with warming. Ribosomal RNA copy number can obfuscate community profiles, but is also correlated with maximum growth rate or trophic strategy among bacteria. Ribosomal RNA copy number correction did not affect community profiles, but rRNA copy number was significantly decreased in warming plots compared to controls. Increased bacterial evenness, shifting beta diversity, decreased fungal abundance and increased abundance of bacteria with low rRNA operon copy number, including Alphaproteobacteria and Acidobacteria, together suggest that more or alternative niche space is being created over the course of long-term warming.
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Affiliation(s)
| | - Grace Pold
- Department of Microbiology, University of Massachusetts Amherst, MA, USA
| | - Begüm D Topçuoğlu
- Department of Microbiology, University of Massachusetts Amherst, MA, USA
| | - Linda T A van Diepen
- Department of Natural Resources and the Environment, University of New Hampshire Durham, NH, USA
| | - Rebecca M Varney
- Department of Microbiology, University of Massachusetts Amherst, MA, USA
| | | | | | - Serita D Frey
- Department of Natural Resources and the Environment, University of New Hampshire Durham, NH, USA
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