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Rodriguez CI, Isobe K, Martiny JBH. Short-term dietary fiber interventions produce consistent gut microbiome responses across studies. mSystems 2024; 9:e0013324. [PMID: 38742890 PMCID: PMC11237734 DOI: 10.1128/msystems.00133-24] [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] [Received: 01/29/2024] [Accepted: 04/15/2024] [Indexed: 05/16/2024] Open
Abstract
The composition of the human gut microbiome varies tremendously among individuals, making the effects of dietary or treatment interventions difficult to detect and characterize. The consumption of fiber is important for gut health, yet the specific effects of increased fiber intake on the gut microbiome vary across studies. The variation in study outcomes might be due to inter-individual (or inter-population) variation or to the details of the interventions including the types of fiber, length of study, size of cohort, and molecular approaches. Thus, to identify generally (on average) consistent fiber-induced responses in the gut microbiome of healthy individuals, we re-analyzed 16S rRNA sequencing data from 21 dietary fiber interventions from 12 human studies, which included 2,564 fecal samples from 538 subjects across all interventions. Short-term increases in dietary fiber consumption resulted in highly consistent gut bacterial community responses across studies. Increased fiber consumption explained an average of 1.5% of compositional variation (vs 82% of variation attributed to the individual), reduced alpha-diversity, and resulted in phylogenetically conserved responses in relative abundances among bacterial taxa. Additionally, we identified bacterial clades, at approximately the genus level, that were highly consistent in their response (on average, increasing or decreasing in their relative abundance) to dietary fiber interventions across the studies. IMPORTANCE Our study is an example of the power of synthesizing and reanalyzing 16S rRNA microbiome data from many intervention studies. Despite high inter-individual variation of the composition of the human gut microbiome, dietary fiber interventions cause a consistent response both in the degree of change and the particular taxa that respond to increased fiber.
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Affiliation(s)
- Cynthia I. Rodriguez
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California, USA
| | - Kazuo Isobe
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China
| | - Jennifer B. H. Martiny
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California, USA
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2
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Ye H, Zhao Y, He S, Wu Z, Yue M, Hong M. Metagenomics reveals the response of desert steppe microbial communities and carbon-nitrogen cycling functional genes to nitrogen deposition. Front Microbiol 2024; 15:1369196. [PMID: 38596372 PMCID: PMC11002186 DOI: 10.3389/fmicb.2024.1369196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 03/11/2024] [Indexed: 04/11/2024] Open
Abstract
Introduction Nitrogen (N) deposition seriously affects the function of carbon (C) and N cycling in terrestrial ecosystems by altering soil microbial communities, especially in desert steppe ecosystems. However, there is a need for a comprehensive understanding of how microorganisms involved in each C and N cycle process respond to N deposition. Methods In this study, shotgun metagenome sequencing was used to investigate variations in soil C and N cycling-related genes in the desert steppe in northern China after 6 years of the following N deposition: N0 (control); N30 (N addition 30 kg ha-1 year-1): N50 (N addition 50 kg ha-1 year-1). Results N deposition significantly increased the relative abundance of Actinobacteria (P < 0.05) while significantly decreased the relative abundances of Proteobacteria and Acidobacteria (P < 0.05). This significantly impacted the microbial community composition in desert steppe soils. The annual addition or deposition of 50 kg ha-1 year-1 for up to 6 years did not affect the C cycle gene abundance but changed the C cycle-related microorganism community structure. The process of the N cycle in the desert steppe was affected by N deposition (50 kg ha-1 year-1), which increased the abundance of the pmoA-amoA gene related to nitrification and the nirB gene associated with assimilation nitrite reductase. There may be a niche overlap between microorganisms involved in the same C and N cycling processes. Discussion This study provides new insights into the effects of N deposition on soil microbial communities and functions in desert steppe and a better understanding of the ecological consequences of anthropogenic N addition.
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Affiliation(s)
- He Ye
- Inner Mongolia Key Laboratory of Soil Quality and Nutrient Resources, College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Agricultural Ecological Security and Green Development at Universities of Inner Mongolia Autonomous Region, Hohhot, China
| | - Yu Zhao
- Inner Mongolia Key Laboratory of Soil Quality and Nutrient Resources, College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Agricultural Ecological Security and Green Development at Universities of Inner Mongolia Autonomous Region, Hohhot, China
| | - Shilong He
- Inner Mongolia Key Laboratory of Soil Quality and Nutrient Resources, College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Agricultural Ecological Security and Green Development at Universities of Inner Mongolia Autonomous Region, Hohhot, China
| | - Zhendan Wu
- Inner Mongolia Key Laboratory of Soil Quality and Nutrient Resources, College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Agricultural Ecological Security and Green Development at Universities of Inner Mongolia Autonomous Region, Hohhot, China
| | - Mei Yue
- Inner Mongolia Key Laboratory of Soil Quality and Nutrient Resources, College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Agricultural Ecological Security and Green Development at Universities of Inner Mongolia Autonomous Region, Hohhot, China
| | - Mei Hong
- Inner Mongolia Key Laboratory of Soil Quality and Nutrient Resources, College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Agricultural Ecological Security and Green Development at Universities of Inner Mongolia Autonomous Region, Hohhot, China
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Sun Y, Guo J, Alejandro Jose Mur L, Xu X, Chen H, Yang Y, Yuan H. Nitrogen starvation modulates the sensitivity of rhizobacterial community to drought stress in Stevia rebaudiana. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 354:120486. [PMID: 38417363 DOI: 10.1016/j.jenvman.2024.120486] [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: 09/28/2023] [Revised: 02/06/2024] [Accepted: 02/20/2024] [Indexed: 03/01/2024]
Abstract
Alterations in water regimes or nitrogen (N) availability lead to shifts in the assemblage of rhizosphere microbial community; however, how the rhizosphere microbiome response to concurrent changes in water and N availability remains largely unclear. Herein, we investigated the taxonomic and functional characteristics of rhizobacteria associated with stevia (Stevia rebaudiana Bertoni) under varying combinations of water and N levels. Community diversity and predicted functions of rhizobacteria were predominantly altered by drought stress, with N-starvation modulating these effects. Moreover, N fertilization simplified the ecological interactions within rhizobacterial communities and heightened the relative role of stochastic processes on community assembly. In terms of rhizobacterial composition, we observed both common and distinctive changes in drought-responsive bacterial taxa under different N conditions. Generally, the relative abundance of Proteobacteria and Bacteroidetes phyla were depleted by drought stress but the Actinobacteria phylum showed increases. The rhizobacterial responses to drought stress were influenced by N availability, where the positive response of δ-proteobacteria and the negative response of α- and γ-proteobacteria, along with Bacteroidetes, were further heightened under N starvation. By contrast, under N fertilization conditions, an amplified negative or positive response to drought were demonstrated in Firmicutes and Actinobacteria phyla, respectively. Further, the drought-responsive rhizobacteria were mostly phylogenetically similar, but this pattern was modulated under N-rich conditions. Overall, our findings indicate an N-dependent specific restructuring of rhizosphere bacteria under drought stress. These changes in the rhizosphere microbiome could contribute to enhancing plant stress tolerance.
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Affiliation(s)
- Yuming Sun
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, 210014, China
| | - Junjie Guo
- State Key Lab of Biocontrol, School of Agriculture, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, Guangdong, 518107, China.
| | - Luis Alejandro Jose Mur
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, SY23 3DA, UK
| | - Xiaoyang Xu
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, 210014, China
| | - Hao Chen
- State Key Lab of Biocontrol, School of Agriculture, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, Guangdong, 518107, China
| | - Yongheng Yang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, 210014, China
| | - Haiyan Yuan
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, 210014, China.
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Ranheim Sveen T, Hannula SE, Bahram M. Microbial regulation of feedbacks to ecosystem change. Trends Microbiol 2024; 32:68-78. [PMID: 37500365 DOI: 10.1016/j.tim.2023.06.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 06/12/2023] [Accepted: 06/14/2023] [Indexed: 07/29/2023]
Abstract
Microbes are key biodiversity components of all ecosystems and control vital ecosystem functions. Although we have just begun to unravel the scales and factors that regulate microbial communities, their role in mediating ecosystem stability in response to disturbances remains underexplored. Here, we review evidence of how, when, and where microbes regulate or drive disturbance feedbacks. Negative feedbacks dampen the impacts of disturbance, which maintain ecosystem stability, whereas positive feedbacks instead erode stability by amplifying the disturbance. Here we describe the processes underlying the responses to disturbance using a hierarchy of functional traits, and we exemplify how these may drive biogeochemical feedbacks. We suggest that the feedback potential of functional traits at different hierarchical levels is contingent on the complexity and heterogeneity of the environment.
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Affiliation(s)
- T Ranheim Sveen
- Department of Ecology, Swedish University of Agricultural Sciences, Ulls Väg 16, 756 51 Uppsala, Sweden.
| | - S E Hannula
- Institute of Environmental Sciences, Leiden University, Leiden 2333, The Netherlands
| | - M Bahram
- Department of Ecology, Swedish University of Agricultural Sciences, Ulls Väg 16, 756 51 Uppsala, Sweden; Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
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Pan X, Raaijmakers JM, Carrión VJ. Importance of Bacteroidetes in host-microbe interactions and ecosystem functioning. Trends Microbiol 2023; 31:959-971. [PMID: 37173204 DOI: 10.1016/j.tim.2023.03.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 03/30/2023] [Accepted: 03/31/2023] [Indexed: 05/15/2023]
Abstract
Bacteroidetes are prevalent in soil ecosystems and are associated with various eukaryotic hosts, including plants, animals, and humans. The ubiquity and diversity of Bacteroidetes exemplify their impressive versatility in niche adaptation and genomic plasticity. Over the past decade, a wealth of knowledge has been obtained on the metabolic functions of clinically relevant Bacteroidetes, but much less attention has been given to Bacteroidetes living in close association with plants. To improve our understanding of the functional roles of Bacteroidetes for plants and other hosts, we review the current knowledge of their taxonomy and ecology, in particular their roles in nutrient cycling and host fitness. We highlight their environmental distribution, stress resilience, genomic diversity, and functional importance in diverse ecosystems, including, but not limited to, plant-associated microbiomes.
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Affiliation(s)
- Xinya Pan
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708, PB, Wageningen, The Netherlands; Institute of Biology, Leiden University, Sylviusweg 72, 2333, BE, Leiden, The Netherlands
| | - Jos M Raaijmakers
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708, PB, Wageningen, The Netherlands; Institute of Biology, Leiden University, Sylviusweg 72, 2333, BE, Leiden, The Netherlands
| | - Víctor J Carrión
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708, PB, Wageningen, The Netherlands; Institute of Biology, Leiden University, Sylviusweg 72, 2333, BE, Leiden, The Netherlands; Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain; Department of Microbiology and Plant Protection, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", IHSM-UMA-CSIC, Málaga, Spain.
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Mukherjee A, Tikariha H, Bandla A, Pavagadhi S, Swarup S. Global analyses of biosynthetic gene clusters in phytobiomes reveal strong phylogenetic conservation of terpenes and aryl polyenes. mSystems 2023; 8:e0038723. [PMID: 37409823 PMCID: PMC10469690 DOI: 10.1128/msystems.00387-23] [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: 04/21/2023] [Accepted: 05/30/2023] [Indexed: 07/07/2023] Open
Abstract
There are gaps in our understandings on how did the evolutionary relationships among members of the phytobiomes shape their ability to produce tremendously complex specialized metabolites under the influence of plant host. To determine these relationships, we investigated the phylogenetic conservation of biosynthetic gene clusters (BGCs) on a global collection of 4,519 high-quality and nonredundant (out of 12,181) bacterial isolates and metagenome-assembled genomes from 47 different plant hosts and soil, by adopting three independent phylogenomic approaches (D-test, Pagel's λ, and consenTRAIT). We report that the BGCs are phylogenetically conserved to varying strengths and depths in their different classes. We show that the ability to produce specialized metabolites qualifies as a complex trait, and the depth of conservation is equivalent to ecologically relevant complex microbial traits. Interestingly, terpene and aryl polyene BGCs had the strongest phylogenetic conservation in the phytobiomes, but not in the soil microbiomes. Furthermore, we showed that terpenes are largely uncharacterized in phytobiomes and pinpointed specific clades that harbor potentially novel terpenes. Taken together, this study sheds light on the evolution of specialized metabolites' biosynthesis potential in phytobiomes under the influence of plant hosts and presents strategies to rationally guide the discovery of potentially novel classes of metabolites. IMPORTANCE This study expands our understandings of the biosynthetic potential of phytobiomes by using such worldwide and extensive collection of microbiomes from plants and soil. Apart from providing such vital resource for the plant microbiome researchers, this study provides fundamental insights into the evolution of biosynthetic gene clusters (BGCs) in phytobiomes under the influence of plant host. Specifically, we report that the strength of phylogenetic conservation in microbiomes varies for different classes of BGCs and is influenced as a result of plant host association. Furthermore, our results indicate that biosynthetic potential of specialized metabolites is deeply conserved equivalent to other complex and ecologically relevant microbial traits. Finally, for the most conserved class of specialized metabolites (terpenes), we identified clades harboring potentially novel class of molecules. Future studies could focus on plant-microbe coevolution and interactions through specialized metabolites building upon these findings.
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Affiliation(s)
- Arijit Mukherjee
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore, Singapore
| | - Hitesh Tikariha
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore, Singapore
| | - Aditya Bandla
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore, Singapore
- NUS Environmental Research Institute, National University of Singapore, Singapore, Singapore
| | - Shruti Pavagadhi
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore, Singapore
- NUS Environmental Research Institute, National University of Singapore, Singapore, Singapore
| | - Sanjay Swarup
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore, Singapore
- NUS Environmental Research Institute, National University of Singapore, Singapore, Singapore
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7
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Rodriguez CI, Isobe K, Martiny JBH. Short-term dietary fiber interventions produce consistent gut microbiome responses across studies. RESEARCH SQUARE 2023:rs.3.rs-3283675. [PMID: 37674721 PMCID: PMC10479438 DOI: 10.21203/rs.3.rs-3283675/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/08/2023]
Abstract
Background The composition of the human gut microbiome varies tremendously among individuals, making the effects of dietary or treatment interventions difficult to detect and characterize. The consumption of fiber is important for gut health, yet the specific effects of increased fiber intake on the gut microbiome vary across studies. The variation in study outcomes might be due to inter-individual (or inter-population) variation or to the details of the interventions including the types of fiber, length of study, size of cohort, and molecular approaches. Thus, to identify consistent fiber-induced responses in the gut microbiome of healthy individuals, we re-analyzed 16S rRNA sequencing data from 21 dietary fiber interventions from 12 human studies, which included 2564 fecal samples from 538 subjects across all interventions. Results Short-term increases in dietary fiber consumption resulted in highly consistent gut microbiome responses across studies. Increased fiber consumption explained an average of 1.5% of compositional variation (versus 82% of variation attributed to the individual), reduced alpha diversity, and resulted in phylogenetically conserved responses in relative abundances among bacterial taxa. Additionally, we identified bacterial clades, at approximately the genus level, that were highly consistent in their response (increasing or decreasing in their relative abundance) to dietary fiber interventions across the studies. Conclusions Our study is an example of the power of synthesizing and reanalyzing microbiome data from many intervention studies. Despite high inter-individual variation of the composition of the human gut microbiome, dietary fiber interventions cause a consistent response both in the degree of change as well as the particular taxa that respond to increased fiber.
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8
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Sun P, Wang M, Zheng W, Li S, Zhu X, Chai X, Zhao S. Unbalanced diets enhance the complexity of gut microbial network but destabilize its stability and resistance. STRESS BIOLOGY 2023; 3:20. [PMID: 37676325 PMCID: PMC10441997 DOI: 10.1007/s44154-023-00098-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 06/05/2023] [Indexed: 09/08/2023]
Abstract
Stability is a fundamental ecological property of the gut microbiota and is associated with host health. Numerous studies have shown that unbalanced dietary components disturb the gut microbial composition and thereby contribute to the onset and progression of disease. However, the impact of unbalanced diets on the stability of the gut microbiota is poorly understood. In the present study, four-week-old mice were fed a plant-based diet high in refined carbohydrates or a high-fat diet for four weeks to simulate a persistent unbalanced diet. We found that persistent unbalanced diets significantly reduced the gut bacterial richness and increased the complexity of bacterial co-occurrence networks. Furthermore, the gut bacterial response to unbalanced diets was phylogenetically conserved, which reduced network modularity and enhanced the proportion of positive associations between community taxon, thereby amplifying the co-oscillation of perturbations among community species to destabilize gut microbial communities. The disturbance test revealed that the gut microbiota of mice fed with unbalanced diets was less resistant to antibiotic perturbation and pathogenic bacteria invasion. This study may fill a gap in the mechanistic understanding of the gut microbiota stability in response to diet and provide new insights into the gut microbial ecology.
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Affiliation(s)
- Penghao Sun
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Mengli Wang
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Wei Zheng
- College of Resources and Environment Sciences, Northwest A&F University, Yangling, China
| | - Shuzhen Li
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
| | - Xiaoyan Zhu
- College of Veterinary Medicine, Northwest A&F University, Yangling, China.
| | - Xuejun Chai
- College of Basic Medicine, Xi'an Medical University, Xi'an, China.
| | - Shanting Zhao
- College of Veterinary Medicine, Northwest A&F University, Yangling, China.
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Cui W, Li R, Fan Z, Wu L, Zhao X, Wei G, Shu D. Weak environmental adaptation of rare phylotypes sustaining soil multi-element cycles in response to decades-long fertilization. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 871:162063. [PMID: 36746286 DOI: 10.1016/j.scitotenv.2023.162063] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 01/29/2023] [Accepted: 02/02/2023] [Indexed: 06/18/2023]
Abstract
Deciphering the ecological role of soil communities in the maintenance of multiple ecosystem functions is pivotal for the conservation and sustainability of soil biodiversity. However, few studies have investigated niche differentiation of abundant and rare microbiota, as well as their contributions to multiple soil elemental cycles, particularly in agroecosystems that have received decades of intense fertilization. Here, we characterized the environmental thresholds and phylogenetic signals for the environmental adaptation of both abundant and rare microbial subcommunities via amplicon sequencing and metagenomic sequencing and explored their importance in sustaining soil multiple nutrient cycling in agricultural fields that were fertilized for two decades. The results showed that rare taxa exhibited narrower niche breadths and weaker phylogenetic signals than abundant species. The assembly of abundant subcommunity was shaped predominantly by dispersal limitation (explained 71.1 % of the variation in bacteria) and undominated processes (explained 75 % of the variation in fungi), whereas the assembly of rare subcommunity was dominated by homogeneous selection process (explained 100 % of the variation in bacteria and 60 % of the variation in fungi). Soil ammonia nitrogen was the leading factor mediating the balance between stochastic and deterministic processes in both abundant (R2 = 0.15, P < 0.001) and rare (R2 = 0.08, P < 0.001) bacterial communities. Notably, the rare biosphere largely contributed to key soil processes such as carbon (R2bacteria = 0.03, P < 0.05; R2fungi = 0.05, P < 0.05) and nitrogen (R2bacteria = 0.03, P < 0.05; R2fungi = 0.17, P < 0.001) cycling. Collectively, these findings facilitate our understanding of the maintenance of rhizosphere bacterial and fungal diversity in response to agricultural fertilization and highlight the key role of rare taxa in sustaining agricultural ecosystem functions.
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Affiliation(s)
- Weili Cui
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Yangling, Shaanxi 712100, China; State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Ruochen Li
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Yangling, Shaanxi 712100, China; State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhen Fan
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Yangling, Shaanxi 712100, China; State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Likun Wu
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Yangling, Shaanxi 712100, China; State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xining Zhao
- Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry of Water Resources, 712100 Yangling, Shaanxi, China; Institute of Soil and Water Conservation, Northwest A&F University, 712100 Yangling, Shaanxi, China
| | - Gehong Wei
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Yangling, Shaanxi 712100, China; State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Duntao Shu
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Yangling, Shaanxi 712100, China; State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China.
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Distinct Growth Responses of Tundra Soil Bacteria to Short-Term and Long-Term Warming. Appl Environ Microbiol 2023; 89:e0154322. [PMID: 36847530 PMCID: PMC10056963 DOI: 10.1128/aem.01543-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023] Open
Abstract
Increases in Arctic temperatures have thawed permafrost and accelerated tundra soil microbial activity, releasing greenhouse gases that amplify climate warming. Warming over time has also accelerated shrub encroachment in the tundra, altering plant input abundance and quality, and causing further changes to soil microbial processes. To better understand the effects of increased temperature and the accumulated effects of climate change on soil bacterial activity, we quantified the growth responses of individual bacterial taxa to short-term warming (3 months) and long-term warming (29 years) in moist acidic tussock tundra. Intact soil was assayed in the field for 30 days using 18O-labeled water, from which taxon-specific rates of 18O incorporation into DNA were estimated as a proxy for growth. Experimental treatments warmed the soil by approximately 1.5°C. Short-term warming increased average relative growth rates across the assemblage by 36%, and this increase was attributable to emergent growing taxa not detected in other treatments that doubled the diversity of growing bacteria. However, long-term warming increased average relative growth rates by 151%, and this was largely attributable to taxa that co-occurred in the ambient temperature controls. There was also coherence in relative growth rates within broad taxonomic levels with orders tending to have similar growth rates in all treatments. Growth responses tended to be neutral in short-term warming and positive in long-term warming for most taxa and phylogenetic groups co-occurring across treatments regardless of phylogeny. Taken together, growing bacteria responded distinctly to short-term and long-term warming, and taxa growing in each treatment exhibited deep phylogenetic organization. IMPORTANCE Soil carbon stocks in the tundra and underlying permafrost have become increasingly vulnerable to microbial decomposition due to climate change. The microbial responses to Arctic warming must be understood in order to predict the effects of future microbial activity on carbon balance in a warming Arctic. In response to our warming treatments, tundra soil bacteria grew faster, consistent with increased rates of decomposition and carbon flux to the atmosphere. Our findings suggest that bacterial growth rates may continue to increase in the coming decades as faster growth is driven by the accumulated effects of long-term warming. Observed phylogenetic organization of bacterial growth rates may also permit taxonomy-based predictions of bacterial responses to climate change and inclusion into ecosystem models.
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Phylogenetic Conservation of Soil Microbial Responses to Elevated Tropospheric Ozone and Nitrogen Fertilization. mSystems 2023; 8:e0072122. [PMID: 36625584 PMCID: PMC9948724 DOI: 10.1128/msystems.00721-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Plant primary productivity and crop yields have been reduced due to the doubled level of global tropospheric ozone. Little is known about how elevated ozone affects soil microbial communities in the cropland ecosystem and whether such effects are sensitive to the nitrogen (N) supply. Here, we examined the responses of bacterial and fungal communities in maize soils to elevated ozone (+60 ppb ozone) across different levels of N fertilization (+60, +120, and +240 kg N ha-1yr-1). The fungal alpha diversity was decreased (P < 0.05), whereas the bacterial alpha diversity displayed no significant change under elevated ozone. Significant (P < 0.05) effects of N fertilization and elevated ozone on both the bacterial and fungal communities were observed. However, no interactive effects between N fertilization and elevated ozone were observed for bacterial and fungal communities (P > 0.1). The bacterial responses to N fertilization as well as the bacterial and fungal responses to elevated ozone were all phylogenetically conserved, showing universal homogeneous selection (homogeneous environmental conditions leading to more similar community structures). In detail, bacterial Alphaproteobacteria, Actinobacteria, and Chloroflexi, as well as fungal Ascomycota, were increased by elevated ozone, whereas bacterial Gammaproteobacteria, Bacteroidetes, and Elusimicrobia, as well as fungal Glomeromycota, were decreased by elevated ozone (P < 0.05). These ozone-responsive phyla were generally correlated (P < 0.05) with plant biomass, plant carbon (C) uptake, and soil dissolved organic C, demonstrating that elevated ozone affects plant-microbe interactions. Our study highlighted that microbial responses to elevated ozone display a phylogenetic clustering pattern, suggesting that response strategies to elevated ozone stress may be phylogenetically conserved ecological traits. IMPORTANCE The interactions of plant and soil microbial communities support plant growth and health. The increasing tropospheric ozone decreases crop biomass and also alters soil microbial communities, but the ways in which crops and their associated soil microbial communities respond to elevated tropospheric ozone are not clear, and it is also obscure whether the interactions between ozone and the commonly applied N fertilization exist. We showed that the microbial responses to both elevated ozone and N fertilization were phylogenetically conserved. However, the microbial communities that responded to N fertilization and elevated ozone were different, and this was further verified by the lack of an interactive effect between N fertilization and elevated ozone. Given that the global tropospheric ozone concentration will continue to increase in the coming decades, the decrease of specific microbial populations caused by elevated ozone would result in the extinction of certain microbial taxa. This ozone-induced effect will further harm crop production, and awareness is urgently needed.
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Distinct Responses of Abundant and Rare Soil Bacteria to Nitrogen Addition in Tropical Forest Soils. Microbiol Spectr 2023; 11:e0300322. [PMID: 36622236 PMCID: PMC9927163 DOI: 10.1128/spectrum.03003-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Soil microbial responses to anthropogenic nitrogen (N) enrichment at the overall community level has been extensively studied. However, the responses of community dynamics and assembly processes of the abundant versus rare bacterial taxa to N enrichment have rarely been assessed. Here, we present a study in which the effects of short- (2 years) and long-term (13 years) N additions to two nearby tropical forest sites on abundant and rare soil bacterial community composition and assembly were documented. The N addition, particularly in the long-term experiment, significantly decreased the bacterial α-diversity and shifted the community composition toward copiotrophic and N-sensitive species. The α-diversity and community composition of the rare taxa were more affected, and they were more closely clustered phylogenetically under N addition compared to the abundant taxa, suggesting the community assembly of the rare taxa was more governed by deterministic processes (e.g., environmental filtering). In contrast, the abundant taxa exhibited higher community abundance, broader environmental thresholds, and stronger phylogenetic signals under environmental changes than the rare taxa. Overall, these findings illustrate that the abundant and rare bacterial taxa respond distinctly to N addition in tropical forests, with higher sensitivity of the rare taxa, but potentially broader environmental acclimation of the abundant taxa. IMPORTANCE Atmospheric nitrogen (N) deposition is a worldwide environmental problem and threatens biodiversity and ecosystem functioning. Understanding the responses of community dynamics and assembly processes of abundant and rare soil bacterial taxa to anthropogenic N enrichment is vital for the management of N-polluted forest soils. Our sequence-based data revealed distinct responses in bacterial diversity, community composition, environmental acclimation, and assembly processes between abundant and rare taxa under N-addition soils in tropical forests. These findings provide new insight into the formation and maintenance of bacterial diversity and offer a way to better predict bacterial responses to the ongoing atmospheric N deposition in tropical forests.
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Sun M, Li M, Zhou Y, Liu J, Shi W, Wu X, Xie B, Deng Y, Gao Z. Nitrogen deposition enhances the deterministic process of the prokaryotic community and increases the complexity of the microbial co-network in coastal wetlands. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 856:158939. [PMID: 36170917 DOI: 10.1016/j.scitotenv.2022.158939] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 08/15/2022] [Accepted: 09/18/2022] [Indexed: 06/16/2023]
Abstract
Global nitrogen deposition has increased significantly in recent years. At present, research on the effects of different amounts and types of nitrogen deposition on soil microorganisms in coastal wetlands is scarce. In this study, based on 7 years of simulated nitrogen deposition at multiple levels (low, medium, high) and of multiple types (NH4NO3, NH4Cl, KNO3), the effects of different nitrogen deposition conditions on the diversity, community assembly processes, co-networks, and community function of soil prokaryotes in coastal wetlands were examined. The results showed that, compared with that in control, the microbial α diversity increased significantly under nitrogen deposition (P < 0.05). However, it decreased significantly in the high-NH4NO3 and high-NH4Cl treatments (P < 0.05). The deterministic process of community assembly was strengthened under the different types of nitrogen deposition. Compared with that under NH4+-N deposition, the microbial co-network under NO3--N deposition was more complex. Network stability significantly decreased under different NH4+-N deposition levels. In addition, the results of FAPROTAX functional prediction showed that microbial community functional groups associated with carbon and nitrogen cycling changed significantly (P < 0.05). In conclusion, our results emphasize that nitrogen deposition environments cause changes in soil microbial community structure and interactions, and may also affect soil carbon and nitrogen cycling, but the effects of different forms and levels of nitrogen deposition are not consistent. This study provides new insights for evaluating the changes in soil microbial communities in coastal wetlands caused by different types of long-term nitrogen deposition, and has scientific significance for assessing the ecological effects of long-term nitrogen deposition.
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Affiliation(s)
- Mengyue Sun
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an 271018, China; College of Life Sciences, Shandong Agricultural University, Tai'an 271018, China
| | - Mingcong Li
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an 271018, China; College of Life Sciences, Shandong Agricultural University, Tai'an 271018, China; Shandong Engineering Research Center of Plant-Microbia Restoration for Saline-alkali Land, Tai'an 271018, China
| | - Yuqi Zhou
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China
| | - Jiai Liu
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an 271018, China; College of Life Sciences, Shandong Agricultural University, Tai'an 271018, China
| | - Wenchong Shi
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an 271018, China; College of Life Sciences, Shandong Agricultural University, Tai'an 271018, China
| | | | - Baohua Xie
- Key Laboratory of Coastal Zone Environmental Processes and Ecological Remediation, CAS, Shandong provincial Key Laboratory of Coastal Environmental Processes, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, Shandong, China; Yellow River Delta Field Observation and Research Station of Coastal Wetland Ecosystem, Chinese Academy of Sciences, Dongying 257500, China.
| | - Ye Deng
- CAS Key Laboratory for Environmental Biotechnology, 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.
| | - Zheng Gao
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an 271018, China; College of Life Sciences, Shandong Agricultural University, Tai'an 271018, China; Shandong Engineering Research Center of Plant-Microbia Restoration for Saline-alkali Land, Tai'an 271018, China.
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14
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Sorouri B, Rodriguez CI, Gaut BS, Allison SD. Variation in Sphingomonas traits across habitats and phylogenetic clades. Front Microbiol 2023; 14:1146165. [PMID: 37138640 PMCID: PMC10150699 DOI: 10.3389/fmicb.2023.1146165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 03/29/2023] [Indexed: 05/05/2023] Open
Abstract
Whether microbes show habitat preferences is a fundamental question in microbial ecology. If different microbial lineages have distinct traits, those lineages may occur more frequently in habitats where their traits are advantageous. Sphingomonas is an ideal bacterial clade in which to investigate how habitat preference relates to traits because these bacteria inhabit diverse environments and hosts. Here we downloaded 440 publicly available Sphingomonas genomes, assigned them to habitats based on isolation source, and examined their phylogenetic relationships. We sought to address whether: (1) there is a relationship between Sphingomonas habitat and phylogeny, and (2) whether there is a phylogenetic correlation between key, genome-based traits and habitat preference. We hypothesized that Sphingomonas strains from similar habitats would cluster together in phylogenetic clades, and key traits that improve fitness in specific environments should correlate with habitat. Genome-based traits were categorized into the Y-A-S trait-based framework for high growth yield, resource acquisition, and stress tolerance. We selected 252 high quality genomes and constructed a phylogenetic tree with 12 well-defined clades based on an alignment of 404 core genes. Sphingomonas strains from the same habitat clustered together within the same clades, and strains within clades shared similar clusters of accessory genes. Additionally, key genome-based trait frequencies varied across habitats. We conclude that Sphingomonas gene content reflects habitat preference. This knowledge of how environment and host relate to phylogeny may also help with future functional predictions about Sphingomonas and facilitate applications in bioremediation.
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Affiliation(s)
- Bahareh Sorouri
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, United States
- *Correspondence: Bahareh Sorouri,
| | - Cynthia I. Rodriguez
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, United States
| | - Brandon S. Gaut
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, United States
| | - Steven D. Allison
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, United States
- Department of Earth System Science, University of California Irvine, Irvine, CA, United States
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15
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Yue H, Banerjee S, Liu C, Ren Q, Zhang W, Zhang B, Tian X, Wei G, Shu D. Fertilizing-induced changes in the nitrifying microbiota associated with soil nitrification and crop yield. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 841:156752. [PMID: 35718181 DOI: 10.1016/j.scitotenv.2022.156752] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 06/07/2022] [Accepted: 06/13/2022] [Indexed: 06/15/2023]
Abstract
Ammonia oxidizing archaea (AOA) and bacteria (AOB), nitrite-oxidizing bacteria (NOB), and comammox Nitrospira (CMX) play pivotal roles in global nitrogen-cycling network. Despite its importance, the driving forces for niche specialization of these nitrifiers, as well as their relative contributions to nitrification and crop yield have not been fully understood. Here, we investigated the niche specialization and environmental prevalence of nitrifying communities, and their importance for the nitrification rate and crop yield across a gradient of nitrogen inputs in a two-decade old field experiment. The results of 15N-tracer and quantitative PCR revealed that AOB and NOB jointly determined the gross nitrification rates across mineral fertilizer treatments, whereas AOA and AOB contributed more than other nitrifiers to nitrification under with organic fertilizer amendments. Linear regression model revealed that crop yield could be linked with AOB and NOB under inorganic farming but closely associated with CMX under organic management. Amplicon sequencing of these functional genes further demonstrated that mineral and organic fertilizers have distinct influences on the β-diversity and niche breadth of these nitrifying communities, indicating that fertilization triggered niche specialization of nitrifying guilds in agricultural soils. Notably, organic fertilization enhanced the network complexity of these nitrifiers by harboring keystone taxa. Random forest analysis provide robustly evidence for the hypothesis that abundance of functional genes contributed more than a- and β-diversity of these nitrifiers for driving nitrification rates and crop yields. Collectively, these findings provide the empirical evidence for the environmental adaptation and niche specialization of nitrifying communities, and their contributions in nitrification and crop yield when confronted with long-term nitrogen inputs.
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Affiliation(s)
- Hong Yue
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Samiran Banerjee
- Department of Microbiological Sciences, North Dakota State University, Fargo 58102, ND, USA
| | - Conghui Liu
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Qiyong Ren
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Wu Zhang
- Heihe Branch, Heilongjiang Academy of Agricultural Sciences, Heihe, Heilongjiang 150086, China
| | - Baogang Zhang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
| | - Xiaohong Tian
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Gehong Wei
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China; Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Yangling, Shaanxi 712100, China
| | - Duntao Shu
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China; Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Yangling, Shaanxi 712100, China.
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16
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Seasonal Succession and Temperature Response Pattern of a Microbial Community in the Yellow Sea Cold Water Mass. Appl Environ Microbiol 2022; 88:e0116922. [PMID: 36000863 PMCID: PMC9469719 DOI: 10.1128/aem.01169-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Explaining the temporal dynamics of marine microorganisms is critical for predicting their changing pattern under environmental disturbances. Although the effect of temperature on microbial seasonality has been widely studied, the phylogenetic structure of the temperature response pattern and the extent to which temperature shift leads to disruptive community changes are still unclear. Here, we explored the microbial seasonal dynamics in the Yellow Sea Cold Water Mass (YSCWM) that occurs in summer and disappears in winter and tested the temperature thresholds and phylogenetic coherence in response to temperature change. The existence of YSCWM generates strong temperature gradients in summer and confers little temperature change during seasonal transition, thus representing a unique intermediate state. The microbial community of YSCWM is more similar to that in the previous YSCWM in winter than that outside YSCWM. Temperature alone explains >50% of the community variation, suggesting that a temperature shift can induce a nearly seasonality-level community variance in summer. Persistence of most previous winter YSCWM inhabitants in YSCWM leads to conservation in predicted functional potentials and cooccurrence patterns, indicating a decisive role of temperature in maintaining functionality. Evaluation of the temperature threshold reveals that a small temperature change can lead to significant community turnover, with most taxa negatively responding to an elevation in temperature. The temperature response pattern is phylogenetically structured, and closely related taxa show an incohesive response. Our study provides novel insights into microbial seasonality and into how marine microorganisms respond to temperature fluctuations. IMPORTANCE Microbial seasonality is driven by a set of covarying factors including temperature. There is still a lack of understanding of the details of the phylogenetic structure and susceptibility of microbial communities in response to temperature variation. Through examination of the microbial community in a seasonally occurring summer cold water mass, which experiences little temperature change during seasonal transition, we show here that the cold water mass leads to nearly seasonality-level variations in community composition and predicted functional profile in summer. Moreover, massive community turnover occurs within a small temperature shift, with most taxa decreasing in abundance in response to increased temperature, and contrasting response patterns are observed between phylogenetically closely related taxa. These results suggest temperature as the fundamental factor over other covarying factors in structuring microbial seasonality, providing important insights into the variation mode of the microbial community under temperature disturbances.
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17
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Tran T, French E, Iyer-Pascuzzi AS. In vitro functional characterization predicts the impact of bacterial root endophytes on plant growth. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:5758-5772. [PMID: 35596672 DOI: 10.1093/jxb/erac228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 05/18/2022] [Indexed: 06/15/2023]
Abstract
Utilizing beneficial microbes for crop improvement is one strategy to achieve sustainable agriculture. However, identifying microbial isolates that promote crop growth is challenging, in part because using bacterial taxonomy to predict an isolate's effect on plant growth may not be reliable. The overall aim of this work was to determine whether in vitro functional traits of bacteria were predictive of their in planta impact. We isolated 183 bacterial endophytes from field-grown roots of two tomato species, Solanum lycopersicum and S. pimpinellifolium. Sixty isolates were screened for six in vitro functional traits: auxin production, siderophore production, phosphate solubilization, antagonism to a soilborne pathogen, and the presence of two antimicrobial metabolite synthesis genes. Hierarchical clustering of the isolates based on the in vitro functional traits identified several groups of isolates sharing similar traits. We called these groups 'functional groups'. To understand how in vitro functional traits of bacteria relate to their impact on plants, we inoculated three isolates from each of the functional groups on tomato seedlings. Isolates within the same functional group promoted plant growth at similar levels, regardless of their host origin or taxonomy. Together, our results demonstrate the importance of examining root endophyte functions for improving crop production.
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Affiliation(s)
- Tri Tran
- Department of Botany and Plant Pathology, Center for Plant Biology, Purdue University, West Lafayette, IN, USA
| | - Elizabeth French
- Department of Botany and Plant Pathology, Center for Plant Biology, Purdue University, West Lafayette, IN, USA
| | - Anjali S Iyer-Pascuzzi
- Department of Botany and Plant Pathology, Center for Plant Biology, Purdue University, West Lafayette, IN, USA
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18
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Yan Q, Liu Y, Hu A, Wan W, Zhang Z, Liu K. Distinct strategies of the habitat generalists and specialists in sediment of Tibetan lakes. Environ Microbiol 2022; 24:4153-4166. [PMID: 35590455 DOI: 10.1111/1462-2920.16044] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 05/05/2022] [Indexed: 12/01/2022]
Abstract
Microbial metacommunities normally comprise generalists and specialists. Uncovering the mechanisms underlying the diversity patterns of these two sub-communities is crucial for aquatic biodiversity maintenance. However, little is known about the ecological assembly processes and co-occurrence patterns of the habitat generalists and specialists across large spatial scales in plateau lake sediments, particularly regarding their environmental adaptations. Here, we investigated assembly processes of the habitat generalists and specialists in sediment of Tibetan lakes and their role in the stability of metacommunity co-occurrence network. Our results showed that the habitat generalists exhibited broader environmental thresholds and closer phylogenetic clustering than specialist counterparts. In contrast, the specialists exhibited stronger phylogenetic signals of ecological preferences compared with the habitat generalists. Stochastic processes dominated the habitat generalist (63.2%) and specialist (81.3%) community assembly. Sediment pH was the major factor mediating the balance between stochastic and deterministic processes in the habitat generalists and specialists. In addition, revealed by network analysis, the habitat specialists played a greater role in maintaining the stability of metacommunity co-occurrence network. The insights gained from this study can be helpful to understand the mechanisms underlying maintenance of sediment microbial diversity in plateau lakes. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Qi Yan
- Center for the Pan-Third Pole Environment, Lanzhou University, Lanzhou, China.,School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Yongqin Liu
- Center for the Pan-Third Pole Environment, Lanzhou University, Lanzhou, China.,Key Laboratory of Tibetan Environment Changes and Land Surface Processes, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China
| | - Anyu Hu
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
| | - Wenjie Wan
- Key Laboratory of Aquatic Botany and Watershed Ecology Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,Center of the Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
| | - Zhihao Zhang
- Key Laboratory of Tibetan Environment Changes and Land Surface Processes, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China
| | - Keshao Liu
- Key Laboratory of Tibetan Environment Changes and Land Surface Processes, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China
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19
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Barge EG, Leopold DR, Rojas A, Vilgalys R, Busby PE. Phylogenetic conservatism of mycoparasitism and its contribution to pathogen antagonism. Mol Ecol 2022; 31:3018-3030. [DOI: 10.1111/mec.16436] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 03/06/2022] [Accepted: 03/16/2022] [Indexed: 11/30/2022]
Affiliation(s)
- Edward G. Barge
- Department of Botany and Plant Pathology Oregon State University Corvallis OR 97331 USA
| | - Devin R. Leopold
- Department of Botany and Plant Pathology Oregon State University Corvallis OR 97331 USA
| | - Alejandro Rojas
- Department of Entomology and Plant Pathology University of Arkansas Fayetteville AR 72701 USA
| | - Rytas Vilgalys
- Department of Biology Duke University Durham NC 27708 USA
| | - Posy E. Busby
- Department of Botany and Plant Pathology Oregon State University Corvallis OR 97331 USA
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20
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Enright DJ, Frangioso KM, Isobe K, Rizzo DM, Glassman SI. Mega‐fire in Redwood Tanoak Forest Reduces Bacterial and Fungal Richness and Selects for Pyrophilous Taxa that are Phylogenetically Conserved. Mol Ecol 2022; 31:2475-2493. [DOI: 10.1111/mec.16399] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 01/19/2022] [Accepted: 02/03/2022] [Indexed: 11/28/2022]
Affiliation(s)
- Dylan J. Enright
- Department of Microbiology and Plant Pathology University of California 3401 Watkins Drive Riverside CA 92521 USA
| | - Kerri M. Frangioso
- Department of Plant Pathology University of California 1 Shields Ave Davis CA 95616 USA
| | - Kazuo Isobe
- Department of Applied Biological Chemistry Graduate School of Agricultural and Life Sciences The University of Tokyo 1‐1‐1 Yayoi, Bunkyo‐ku Tokyo 113‐8657
| | - David M. Rizzo
- Department of Plant Pathology University of California 1 Shields Ave Davis CA 95616 USA
| | - Sydney I. Glassman
- Department of Microbiology and Plant Pathology University of California 3401 Watkins Drive Riverside CA 92521 USA
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21
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Figueiredo G, Gomes M, Covas C, Mendo S, Caetano T. The Unexplored Wealth of Microbial Secondary Metabolites: the Sphingobacteriaceae Case Study. MICROBIAL ECOLOGY 2022; 83:470-481. [PMID: 33987687 DOI: 10.1007/s00248-021-01762-3] [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: 01/24/2021] [Accepted: 04/19/2021] [Indexed: 06/12/2023]
Abstract
Research on secondary metabolites (SMs) has been mostly focused on Gram-positive bacteria, especially Actinobacteria. The association of genomics with robust bioinformatics tools revealed the neglected potential of Gram-negative bacteria as promising sources of new SMs. The family Sphingobacteriaceae belongs to the phylum Bacteroidetes having representatives in practically all environments including humans, rhizosphere, soils, wastewaters, among others. Some genera of this family have demonstrated great potential as plant growth promoters, bioremediators and producers of some value-added compounds such as carotenoids and antimicrobials. However, to date, Sphingobacteriaceae's SMs are still poorly characterized, and likewise, little is known about their chemistry. This study revealed that Sphingobacteriaceae pangenome encodes a total of 446 biosynthetic gene clusters (BGCs), which are distributed across 85 strains, highlighting the great potential of this bacterial family to produce SMs. Pedobacter, Mucilaginibacter and Sphingobacterium were the genera with the highest number of BGCs, especially those encoding the biosynthesis of ribosomally synthesized and post-translationally modified peptides (RiPPs), terpenes, polyketides and nonribosomal peptides (NRPs). In Mucilaginibacter and Sphingobacterium genera, M. lappiensis ATCC BAA-1855, Mucilaginibacter sp. OK098 (both with 11 BGCs) and Sphingobacterium sp. 21 (6 BGCs) are the strains with the highest number of BGCs. Most of the BGCs found in these two genera did not have significant hits with the MIBiG database. These results strongly suggest that the bioactivities and environmental functions of these compounds, especially RiPPs, PKs and NRPs, are still unknown. Among RiPPs, two genera encoded the production of class I and class III lanthipeptides. The last are associated with LanKC proteins bearing uncommon lyase domains, whose dehydration mechanism deserves further investigation. This study translated genomics into functional information that unveils the enormous potential of environmental Gram-negative bacteria to produce metabolites with unknown chemistries, bioactivities and, more importantly, unknown ecological roles.
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Affiliation(s)
- Gonçalo Figueiredo
- CESAM and Department of Biology, University of Aveiro, 3810-193, Aveiro, Portugal
| | - Margarida Gomes
- CESAM and Department of Biology, University of Aveiro, 3810-193, Aveiro, Portugal
| | - Claúdia Covas
- CESAM and Department of Biology, University of Aveiro, 3810-193, Aveiro, Portugal
| | - Sónia Mendo
- CESAM and Department of Biology, University of Aveiro, 3810-193, Aveiro, Portugal
| | - Tânia Caetano
- CESAM and Department of Biology, University of Aveiro, 3810-193, Aveiro, Portugal.
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22
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Alves RJE, Callejas IA, Marschmann GL, Mooshammer M, Singh HW, Whitney B, Torn MS, Brodie EL. Kinetic Properties of Microbial Exoenzymes Vary With Soil Depth but Have Similar Temperature Sensitivities Through the Soil Profile. Front Microbiol 2021; 12:735282. [PMID: 34917043 PMCID: PMC8669745 DOI: 10.3389/fmicb.2021.735282] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 11/03/2021] [Indexed: 11/13/2022] Open
Abstract
Current knowledge of the mechanisms driving soil organic matter (SOM) turnover and responses to warming is mainly limited to surface soils, although over 50% of global soil carbon is contained in subsoils. Deep soils have different physicochemical properties, nutrient inputs, and microbiomes, which may harbor distinct functional traits and lead to different SOM dynamics and temperature responses. We hypothesized that kinetic and thermal properties of soil exoenzymes, which mediate SOM depolymerization, vary with soil depth, reflecting microbial adaptation to distinct substrate and temperature regimes. We determined the Michaelis-Menten (MM) kinetics of three ubiquitous enzymes involved in carbon (C), nitrogen (N) and phosphorus (P) acquisition at six soil depths down to 90 cm at a temperate forest, and their temperature sensitivity based on Arrhenius/Q10 and Macromolecular Rate Theory (MMRT) models over six temperatures between 4–50°C. Maximal enzyme velocity (Vmax) decreased strongly with depth for all enzymes, both on a dry soil mass and a microbial biomass C basis, whereas their affinities increased, indicating adaptation to lower substrate availability. Surprisingly, microbial biomass-specific catalytic efficiencies also decreased with depth, except for the P-acquiring enzyme, indicating distinct nutrient demands at depth relative to microbial abundance. These results suggested that deep soil microbiomes encode enzymes with intrinsically lower turnover and/or produce less enzymes per cell, reflecting distinct life strategies. The relative kinetics between different enzymes also varied with depth, suggesting an increase in relative P demand with depth, or that phosphatases may be involved in C acquisition. Vmax and catalytic efficiency increased consistently with temperature for all enzymes, leading to overall higher SOM-decomposition potential, but enzyme temperature sensitivity was similar at all depths and between enzymes, based on both Arrhenius/Q10 and MMRT models. In a few cases, however, temperature affected differently the kinetic properties of distinct enzymes at discrete depths, suggesting that it may alter the relative depolymerization of different compounds. We show that soil exoenzyme kinetics may reflect intrinsic traits of microbiomes adapted to distinct soil depths, although their temperature sensitivity is remarkably uniform. These results improve our understanding of critical mechanisms underlying SOM dynamics and responses to changing temperatures through the soil profile.
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Affiliation(s)
- Ricardo J Eloy Alves
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Ileana A Callejas
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.,Department of Civil and Environmental Engineering, University of California, Los Angeles, Los Angeles, CA, United States
| | - Gianna L Marschmann
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Maria Mooshammer
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA, United States
| | - Hans W Singh
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Bizuayehu Whitney
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.,Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Margaret S Torn
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.,Energy and Resources Group, University of California, Berkeley, Berkeley, CA, United States
| | - Eoin L Brodie
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.,Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA, United States
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23
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Rykachevsky A, Stepakov A, Muzyukina P, Medvedeva S, Dobrovolski M, Burnaev E, Severinov K, Savitskaya E. SCRAMBLER: A Tool for De Novo CRISPR Array Reconstruction and Its Application for Analysis of the Structure of Prokaryotic Populations. CRISPR J 2021; 4:673-685. [PMID: 34661428 DOI: 10.1089/crispr.2021.0012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
CRISPR arrays are prokaryotic genomic loci consisting of repeat sequences alternating with unique spacers acquired from foreign nucleic acids. As one of the fastest-evolving parts of the genome, CRISPR arrays can be used to differentiate closely related prokaryotic lineages and track individual strains in prokaryotic communities. However, the assembly of full-length CRISPR arrays sequences remains a problem. Here, we developed SCRAMBLER, a tool that includes several pipelines for assembling CRISPR arrays from high-throughput short-read sequencing data. We assessed its performance with model data sets (Escherichia coli strains containing different CRISPR arrays and imitating prokaryotic communities of different complexities) and intestinal microbiomes of extant and extinct pachyderms. Evaluation of SCRAMBLER's performance using model data sets demonstrated its ability to assemble CRISPR arrays correctly from reads containing pairs of spacers, yielding a precision rate of >80% and a recall rate of 60-85% when checked against ground-truth data. Likewise, SCRAMBLER successfully assembled CRISPR arrays from the environmental samples, as attested by their matching with database entries. SCRAMBLER, an open-source software (github.com/biolab-tools/SCRAMBLER), can facilitate analysis of the composition and dynamics of CRISPR arrays in complex communities.
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Affiliation(s)
- Anton Rykachevsky
- Center for Computational and Data-Intensive Science and Engineering and Rutgers, State University of New Jersey, Piscataway, USA
| | - Alexander Stepakov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia; Rutgers, State University of New Jersey, Piscataway, USA
| | - Polina Muzyukina
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia; Rutgers, State University of New Jersey, Piscataway, USA
| | - Sofia Medvedeva
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia; Rutgers, State University of New Jersey, Piscataway, USA
| | - Mark Dobrovolski
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia; Rutgers, State University of New Jersey, Piscataway, USA
| | - Evgeny Burnaev
- Center for Computational and Data-Intensive Science and Engineering and Rutgers, State University of New Jersey, Piscataway, USA
| | - Konstantin Severinov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia; Rutgers, State University of New Jersey, Piscataway, USA.,Laboratory of Genetic Regulation of Prokaryotic Mobile Genetic Elements, Institute of Molecular Genetics of National Research Center "Kurchatov Institute," Moscow, Russia; and Rutgers, State University of New Jersey, Piscataway, USA.,Waksman Institute, Rutgers, State University of New Jersey, Piscataway, USA
| | - Ekaterina Savitskaya
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia; Rutgers, State University of New Jersey, Piscataway, USA
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24
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Li J, Jia C, Lu Q, Hungate BA, Dijkstra P, Wang S, Wu C, Chen S, Li D, Shim H. Mechanistic insights into the success of xenobiotic degraders resolved from metagenomes of microbial enrichment cultures. JOURNAL OF HAZARDOUS MATERIALS 2021; 418:126384. [PMID: 34329005 DOI: 10.1016/j.jhazmat.2021.126384] [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: 03/04/2021] [Revised: 05/17/2021] [Accepted: 06/08/2021] [Indexed: 06/13/2023]
Abstract
Even though microbial communities can be more effective at degrading xenobiotics than cultured micro-organisms, yet little is known about the microbial strategies that underpin xenobiotic biodegradation by microbial communities. Here, we employ metagenomic community sequencing to explore the mechanisms that drive the development of 49 xenobiotic-degrading microbial communities, which were enriched from 7 contaminated soils or sediments with a range of xenobiotic compounds. We show that multiple microbial strategies likely drive the development of xenobiotic degrading communities, notably (i) presence of genes encoding catabolic enzymes to degrade xenobiotics; (ii) presence of genes encoding efflux pumps; (iii) auxiliary catabolic genes on plasmids; and (iv) positive interactions dominate microbial communities with efficient degradation. Overall, the integrated analyses of microbial ecological strategies advance our understanding of microbial processes driving the biodegradation of xenobiotics and promote the design of bioremediation systems.
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Affiliation(s)
- Junhui Li
- Vanderbilt Microbiome Initiative, Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA; Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ 86011, USA.
| | - Chongjian Jia
- Guangdong Eco-Engineering Polytechnic, Guangzhou 510520, China
| | - Qihong Lu
- School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou 510006, China
| | - Bruce A Hungate
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ 86011, USA; Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Paul Dijkstra
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ 86011, USA; Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Shanquan Wang
- School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou 510006, China
| | - Cuiyu Wu
- College of Natural Resources and Environmental Science, South China Agricultural University, Guangzhou 510642, China
| | - Shaohua Chen
- Guangdong Laboratory for Lingnan Modern Agriculture, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China
| | - Deqiang Li
- Department of Pharmacy, The Second Hospital of Hebei Medical University, Shijiazhuang 050000, China
| | - Hojae Shim
- Department of Civil and Environmental Engineering, Faculty of Science and Technology, University of Macau, Macau SAR 999078, China.
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25
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He J, Jiao S, Tan X, Wei H, Ma X, Nie Y, Liu J, Lu X, Mo J, Shen W. Adaptation of Soil Fungal Community Structure and Assembly to Long- Versus Short-Term Nitrogen Addition in a Tropical Forest. Front Microbiol 2021; 12:689674. [PMID: 34512567 PMCID: PMC8424203 DOI: 10.3389/fmicb.2021.689674] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 07/30/2021] [Indexed: 01/28/2023] Open
Abstract
Soil fungi play critical roles in ecosystem processes and are sensitive to global changes. Elevated atmospheric nitrogen (N) deposition has been well documented to impact on fungal diversity and community composition, but how the fungal community assembly responds to the duration effects of experimental N addition remains poorly understood. Here, we aimed to investigate the soil fungal community variations and assembly processes under short- (2 years) versus long-term (13 years) exogenous N addition (∼100 kg N ha–1 yr–1) in a N-rich tropical forest of China. We observed that short-term N addition significantly increased fungal taxonomic and phylogenetic α-diversity and shifted fungal community composition with significant increases in the relative abundance of Ascomycota and decreases in that of Basidiomycota. Short-term N addition also significantly increased the relative abundance of saprotrophic fungi and decreased that of ectomycorrhizal fungi. However, unremarkable effects on these indices were found under long-term N addition. The variations of fungal α-diversity, community composition, and the relative abundance of major phyla, genera, and functional guilds were mainly correlated with soil pH and NO3––N concentration, and these correlations were much stronger under short-term than long-term N addition. The results of null, neutral community models and the normalized stochasticity ratio (NST) index consistently revealed that stochastic processes played predominant roles in the assembly of soil fungal community in the tropical forest, and the relative contribution of stochastic processes was significantly increased by short-term N addition. These findings highlighted that the responses of fungal community to N addition were duration-dependent, i.e., fungal community structure and assembly would be sensitive to short-term N addition but become adaptive to long-term N enrichment.
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Affiliation(s)
- Jinhong He
- Center for Ecological and Environmental Sciences, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Shuo Jiao
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, China
| | - Xiangping Tan
- Center for Ecological and Environmental Sciences, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Hui Wei
- Department of Ecology, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
| | - Xiaomin Ma
- Center for Ecological and Environmental Sciences, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Yanxia Nie
- Center for Ecological and Environmental Sciences, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Juxiu Liu
- Center for Ecological and Environmental Sciences, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Xiankai Lu
- Center for Ecological and Environmental Sciences, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Jiangming Mo
- Center for Ecological and Environmental Sciences, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Weijun Shen
- College of Forestry, Guangxi University, Nanning, China
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26
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Xie J, Wang X, Xu J, Xie H, Cai Y, Liu Y, Ding X. Strategies and Structure Feature of the Aboveground and Belowground Microbial Community Respond to Drought in Wild Rice (Oryza longistaminata). RICE (NEW YORK, N.Y.) 2021; 14:79. [PMID: 34495440 PMCID: PMC8426455 DOI: 10.1186/s12284-021-00522-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 08/31/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Drought is global environmental stress that limits crop yields. Plant-associated microbiomes play a crucial role in determining plant fitness in response to drought, yet the fundamental mechanisms for maintaining microbial community stability under drought disturbances in wild rice are poorly understood. We make explicit comparisons of leaf, stem, root and rhizosphere microbiomes from the drought-tolerant wild rice (Oryza longistaminata) in response to drought stress. RESULTS We find that the response of the wild rice microbiome to drought was divided into aboveground-underground patterns. Drought reduced the leaf and stem microbial community diversity and networks stability, but not that of the roots and rhizospheres. Contrary to the aboveground microbial networks, the drought-negative response taxa exhibited much closer interconnections than the drought-positive response taxa and were the dominant network hubs of belowground co-occurrence networks, which may contribute to the stability of the belowground network. Notably, drought induces enrichment of Actinobacteria in belowground compartments, but not the aboveground compartment. Additionally, the rhizosphere microbiome exhibited a higher proportion of generalists and broader habitat niche breadth than the microbiome at other compartments, and drought enhanced the proportion of specialists in all compartments. Null model analysis revealed that both the aboveground and belowground-community were governed primarily by the stochastic assembly process, moreover, drought decreased 'dispersal limitation', and enhanced 'drift'. CONCLUSIONS Our results provide new insight into the different strategies and assembly mechanisms of the above and belowground microbial community in response to drought, including enrichment of taxonomic groups, and highlight the important role of the stochastic assembly process in shaping microbial community under drought stress.
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Affiliation(s)
- Jian Xie
- School of Life Sciences, Nanchang University, Nanchang, 330031, Jiangxi, China
| | - Xiaoqing Wang
- School of Life Sciences, Nanchang University, Nanchang, 330031, Jiangxi, China
| | - Jiawang Xu
- School of Life Sciences, Nanchang University, Nanchang, 330031, Jiangxi, China
| | - Hongwei Xie
- Jiangxi Super-Rice Research and Development Center, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200, Jiangxi, China
| | - Yaohui Cai
- Jiangxi Super-Rice Research and Development Center, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200, Jiangxi, China
| | - Yizheng Liu
- School of Life Sciences, Nanchang University, Nanchang, 330031, Jiangxi, China
| | - Xia Ding
- School of Life Sciences, Nanchang University, Nanchang, 330031, Jiangxi, China.
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27
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Behnke GD, Kim N, Zabaloy MC, Riggins CW, Rodriguez-Zas S, Villamil MB. Soil Microbial Indicators within Rotations and Tillage Systems. Microorganisms 2021; 9:1244. [PMID: 34201118 PMCID: PMC8228827 DOI: 10.3390/microorganisms9061244] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 06/01/2021] [Accepted: 06/06/2021] [Indexed: 01/04/2023] Open
Abstract
Recent advancements in agricultural metagenomics allow for characterizing microbial indicators of soil health brought on by changes in management decisions, which ultimately affect the soil environment. Field-scale studies investigating the microbial taxa from agricultural experiments are sparse, with none investigating the long-term effect of crop rotation and tillage on microbial indicator species. Therefore, our goal was to determine the effect of rotations (continuous corn, CCC; continuous soybean, SSS; and each phase of a corn-soybean rotation, Cs and Sc) and tillage (no-till, NT; and chisel tillage, T) on the soil microbial community composition following 20 years of management. We found that crop rotation and tillage influence the soil environment by altering key soil properties, such as pH and soil organic matter (SOM). Monoculture corn lowered pH compared to SSS (5.9 vs. 6.9, respectively) but increased SOM (5.4% vs. 4.6%, respectively). Bacterial indicator microbes were categorized into two groups: SOM dependent and acidophile vs. N adverse and neutrophile. Fungi preferred the CCC rotation, characterized by low pH. Archaeal indicators were mainly ammonia oxidizers with species occupying niches at contrasting pHs. Numerous indicator microbes are involved with N cycling due to the fertilizer-rich environment, prone to aquatic or gaseous losses.
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Affiliation(s)
- Gevan D. Behnke
- Department of Crop Sciences, University of Illinois, Urbana, IL 61801, USA; (G.D.B.); (N.K.); (C.W.R.)
| | - Nakian Kim
- Department of Crop Sciences, University of Illinois, Urbana, IL 61801, USA; (G.D.B.); (N.K.); (C.W.R.)
| | - Maria C. Zabaloy
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS, UNS-CONICET), Departamento de Agronomía, Universidad Nacional del Sur, Bahia Blanca B8000, Argentina;
| | - Chance W. Riggins
- Department of Crop Sciences, University of Illinois, Urbana, IL 61801, USA; (G.D.B.); (N.K.); (C.W.R.)
| | | | - Maria B. Villamil
- Department of Crop Sciences, University of Illinois, Urbana, IL 61801, USA; (G.D.B.); (N.K.); (C.W.R.)
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28
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Gu L, Wu JY, Hua ZL. Benthic prokaryotic microbial community assembly and biogeochemical potentials in E. coli - Stressed aquatic ecosystems during plant decomposition. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 275:116643. [PMID: 33581629 DOI: 10.1016/j.envpol.2021.116643] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 01/26/2021] [Accepted: 01/31/2021] [Indexed: 06/12/2023]
Abstract
Benthic microbes play a crucial role in maintaining the biogeochemical balance of aquatic ecosystems especially the material cycling during plant decomposition. However, those systems in agricultural area are always threatened by agricultural run-off containing a mass of typical pathogenic invader- Escherichia coli. It is therefore vital to clarify the turnover, assembly, and geochemical functions of the E. coli invaded benthic prokaryotic microbial community during plant decomposition. During the decaying process, the key filtering factors of benthic community assembly were NH4+-N (P < 0.001), NO2--N (P < 0.01), and Organic-N (P < 0.05). The E. coli colonized significantly in sediments (P < 0.001) and drove the turnover of the bacterial community (P = 0.001), which enhanced archaeal dominance in the benthic microbial network. E. coli also triggered niche structural variations. The biomass (%) of benthic nutrient cycling genera including Dechloromonas, Pseudomonas, Bacteroides, Candidatus_Methanofastidiosum, and Desulfomicrobium (P < 0.05) was altered by E. coli stress. The structural equation model illustrated that E. coli critically affected the benthic microbial geochemical functions in multiple pathways (P < 0.05). Our results provide new insights into benthic prokaryotic microbial community assembly and nutrient cycling and management under pollution stress.
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Affiliation(s)
- Li Gu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China; Yangtze Institute for Conservation and Development, Hohai University, Jiangsu, 210098, China.
| | - Jian-Yi Wu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China; Yangtze Institute for Conservation and Development, Hohai University, Jiangsu, 210098, China.
| | - Zu-Lin Hua
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China; Yangtze Institute for Conservation and Development, Hohai University, Jiangsu, 210098, China.
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29
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Assessment of phylo-functional coherence along the bacterial phylogeny and taxonomy. Sci Rep 2021; 11:8299. [PMID: 33859339 PMCID: PMC8050241 DOI: 10.1038/s41598-021-87909-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 04/06/2021] [Indexed: 11/25/2022] Open
Abstract
In this report we use available curated phylogenies, taxonomy, and genome annotations to assess the phylogenetic and gene content similarity associated with each different taxon and taxonomic rank. Subsequently, we employ the same data to assess the frontiers of functional coherence along the bacterial phylogeny. Our results show that within-group phylogenetic and gene content similarity of taxa in the same rank are not homogenous, and that these values show extensive overlap between ranks. Functional coherence along the 16S rRNA gene-based phylogeny was limited to 44 particular nodes presenting large variations in phylogenetic depth. For instance, the deep subtree affiliated to class Actinobacteria presented functional coherence, while the shallower family Enterobacteriaceae-affiliated subtree did not. On the other hand, functional coherence along the genome-based phylogeny delimited deep subtrees affiliated to phyla Actinobacteriota, Deinococcota, Chloroflexota, Firmicutes, and a subtree containing the rest of the bacterial phyla. The results presented here can be used to guide the exploration of results in many microbial ecology and evolution research scenarios. Moreover, we provide dedicated scripts and files that can be used to continue the exploration of functional coherence along the bacterial phylogeny employing different parameters or input data (https://git.io/Jec5U).
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30
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Wan W, Gadd GM, Yang Y, Yuan W, Gu J, Ye L, Liu W. Environmental adaptation is stronger for abundant rather than rare microorganisms in wetland soils from the Qinghai-Tibet Plateau. Mol Ecol 2021; 30:2390-2403. [PMID: 33714213 DOI: 10.1111/mec.15882] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 03/03/2021] [Accepted: 03/09/2021] [Indexed: 01/03/2023]
Abstract
Disentangling the biogeographic patterns of rare and abundant microbes is essential in order to understand the generation and maintenance of microbial diversity with respect to the functions they provide. However, little is known about ecological assembly processes and environmental adaptation of rare and abundant microbes across large spatial-scale wetlands. Using Illumina sequencing and multiple statistical analyses, we characterized the taxonomic and phylogenetic diversity of rare and abundant bacteria and fungi in Qinghai-Tibet Plateau wetland soils. Abundant microbial taxa exhibited broader environmental thresholds and stronger phylogenetic signals for ecological traits than rare ones. By contrast, rare taxa showed higher sensitivity to environmental changes and closer phylogenetic clustering than abundant ones. The null model analysis revealed that dispersal limitation belonging to stochastic process dominated community assemblies of abundant bacteria, and rare and abundant fungi, while variable selection belonging to deterministic process governed community assembly of rare bacteria. Neutral model analysis and variation partitioning analysis further confirmed that abundant microbes were less environmentally constrained. Soil ammonia nitrogen was the crucial factor in mediating the balance between stochasticity and determinism of both rare and abundant microbes. Abundant microbes may have better environmental adaptation potential and are less dispersed by environmental changes than rare ones. Our findings extend knowledge of the adaptation of rare and abundant microbes to ongoing environmental change and could facilitate prediction of biodiversity loss caused probably by climate change and human activity in the Qinghai-Tibet Plateau wetlands.
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Affiliation(s)
- Wenjie Wan
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,Center of the Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
| | - Geoffrey Michael Gadd
- Geomicrobiology Group, School of Life Sciences, University of Dundee, Dundee, UK.,State Key Laboratory of Heavy Oil Processing, State Key Laboratory of Petroleum Pollution Control, China University of Petroleum, Beijing, China
| | - Yuyi Yang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,Center of the Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
| | - Wenke Yuan
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,Center of the Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
| | - Jidong Gu
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong, Hong Kong, SAR, China.,Environmental Engineering, Guangdong Technion Israel Institute of Technology, Guangdong, China
| | - Luping Ye
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,Center of the Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
| | - Wenzhi Liu
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,Center of the Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
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31
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Hao X, Zhu J, Rensing C, Liu Y, Gao S, Chen W, Huang Q, Liu YR. Recent advances in exploring the heavy metal(loid) resistant microbiome. Comput Struct Biotechnol J 2020; 19:94-109. [PMID: 33425244 PMCID: PMC7771044 DOI: 10.1016/j.csbj.2020.12.006] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 12/03/2020] [Accepted: 12/05/2020] [Indexed: 12/18/2022] Open
Abstract
Heavy metal(loid)s exert selective pressure on microbial communities and evolution of metal resistance determinants. Despite increasing knowledge concerning the impact of metal pollution on microbial community and ecological function, it is still a challenge to identify a consistent pattern of microbial community composition along gradients of elevated metal(loid)s in natural environments. Further, our current knowledge of the microbial metal resistome at the community level has been lagging behind compared to the state-of-the-art genetic profiling of bacterial metal resistance mechanisms in a pure culture system. This review provides an overview of the core metal resistant microbiome, development of metal resistance strategies, and potential factors driving the diversity and distribution of metal resistance determinants in natural environments. The impacts of biotic factors regulating the bacterial metal resistome are highlighted. We finally discuss the advances in multiple technologies, research challenges, and future directions to better understand the interface of the environmental microbiome with the metal resistome. This review aims to highlight the diversity and wide distribution of heavy metal(loid)s and their corresponding resistance determinants, helping to better understand the resistance strategy at the community level.
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Affiliation(s)
- Xiuli Hao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Key Laboratory of Soil Environment and Pollution Remediation, Huazhong Agricultural University, Wuhan 430070, China
- Corresponding authors at: State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Jiaojiao Zhu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Christopher Rensing
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Ying Liu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Shenghan Gao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Wenli Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Qiaoyun Huang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Key Laboratory of Soil Environment and Pollution Remediation, Huazhong Agricultural University, Wuhan 430070, China
| | - Yu-Rong Liu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Key Laboratory of Soil Environment and Pollution Remediation, Huazhong Agricultural University, Wuhan 430070, China
- Corresponding authors at: State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.
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Larkin AA, Moreno AR, Fagan AJ, Fowlds A, Ruiz A, Martiny AC. Persistent El Niño driven shifts in marine cyanobacteria populations. PLoS One 2020; 15:e0238405. [PMID: 32936809 PMCID: PMC7494125 DOI: 10.1371/journal.pone.0238405] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 08/15/2020] [Indexed: 11/18/2022] Open
Abstract
In the California Current Ecosystem, El Niño acts as a natural phenomenon that is partially representative of climate change impacts on marine bacteria at timescales relevant to microbial communities. Between 2014–2016, the North Pacific warm anomaly (a.k.a., the “blob”) and an El Niño event resulted in prolonged ocean warming in the Southern California Bight (SCB). To determine whether this “marine heatwave” resulted in shifts in microbial populations, we sequenced the rpoC1 gene from the biogeochemically important picocyanobacteria Prochlorococcus and Synechococcus at 434 time points from 2009–2018 in the MICRO time series at Newport Beach, CA. Across the time series, we observed an increase in the abundance of Prochlorococcus relative to Synechococcus as well as elevated frequencies of ecotypes commonly associated with low-nutrient and high-temperature conditions. The relationships between environmental and ecotype trends appeared to operate on differing temporal scales. In contrast to ecotype trends, most microdiverse populations were static and possibly reflect local habitat conditions. The only exceptions were microdiversity from Prochlorococcous HLI and Synechococcus Clade II that shifted in response to the 2015 El Niño event. Overall, Prochlorococcus and Synechococcus populations did not return to their pre-heatwave composition by the end of this study. This research demonstrates that extended warming in the SCB can result in persistent changes in key microbial populations.
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Affiliation(s)
- Alyse A. Larkin
- Department of Earth System Science, University of California at Irvine, Irvine, California, United States of America
| | - Allison R. Moreno
- Department of Ecology and Evolution, University of California at Irvine, Irvine, California, United States of America
| | - Adam J. Fagan
- Department of Earth System Science, University of California at Irvine, Irvine, California, United States of America
| | - Alyssa Fowlds
- Department of Earth System Science, University of California at Irvine, Irvine, California, United States of America
| | - Alani Ruiz
- Department of Earth System Science, University of California at Irvine, Irvine, California, United States of America
| | - Adam C. Martiny
- Department of Earth System Science, University of California at Irvine, Irvine, California, United States of America
- Department of Ecology and Evolution, University of California at Irvine, Irvine, California, United States of America
- * E-mail:
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Jiao S, Lu Y. Abundant fungi adapt to broader environmental gradients than rare fungi in agricultural fields. GLOBAL CHANGE BIOLOGY 2020; 26:4506-4520. [PMID: 32324306 DOI: 10.1111/gcb.15130] [Citation(s) in RCA: 170] [Impact Index Per Article: 42.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 04/15/2020] [Indexed: 06/11/2023]
Abstract
Soil communities are intricately linked to ecosystem functioning, and a predictive understanding of how communities assemble in response to environmental change is of great ecological importance. Little is known about the assembly processes governing abundant and rare fungal communities across agro-ecosystems, particularly with regard to their environmental adaptation. By considering abundant and rare taxa, we tested the environmental thresholds and phylogenetic signals for ecological preferences of fungal communities across complex environmental gradients to reflect their environmental adaptation, and explored the factors influencing their assembly based on the large-scale soil survey in agricultural fields across eastern China. We found that the abundant taxa exhibited remarkably broader response thresholds and stronger phylogenetic signals for the ecological preferences across environmental gradients compared to the rare taxa. Neutral processes played a key role in shaping the abundant subcommunity compared to the rare subcommunity. Null model analysis revealed that the abundant subcommunity was less clustered phylogenetically and governed primarily by dispersal limitation, while homogeneous selection was the major assembly process in the rare subcommunity. Soil available sulfur was the major factor mediating the balance between stochastic and deterministic processes of both the abundant and rare subcommunities, as indicated by an increase in stochasticity with higher available sulfur concentration. Based on macroecological spatial scale datasets, our study revealed the potential broader environmental adaptation of abundant fungal taxa compared to rare fungal taxa, and identified the factors mediating their distinct community assembly processes in agricultural fields. These results contribute to our understanding of the mechanisms underlying the generation and maintenance of fungal diversity in response to global environmental change.
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Affiliation(s)
- Shuo Jiao
- College of Urban and Environmental Sciences, Peking University, Beijing, P. R. China
- College of Life Sciences, Northwest A&F University, Yangling, P. R. China
| | - Yahai Lu
- College of Urban and Environmental Sciences, Peking University, Beijing, P. R. China
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Isobe K, Bouskill NJ, Brodie EL, Sudderth EA, Martiny JBH. Phylogenetic conservation of soil bacterial responses to simulated global changes. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190242. [PMID: 32200749 PMCID: PMC7133522 DOI: 10.1098/rstb.2019.0242] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/22/2020] [Indexed: 01/03/2023] Open
Abstract
Soil bacterial communities are altered by anthropogenic drivers such as climate change-related warming and fertilization. However, we lack a predictive understanding of how bacterial communities respond to such global changes. Here, we tested whether phylogenetic information might be more predictive of the response of bacterial taxa to some forms of global change than others. We analysed the composition of soil bacterial communities from perturbation experiments that simulated warming, drought, elevated CO2 concentration and phosphorus (P) addition. Bacterial responses were phylogenetically conserved to all perturbations. The phylogenetic depth of these responses varied minimally among the types of perturbations and was similar when merging data across locations, implying that the context of particular locations did not affect the phylogenetic pattern of response. We further identified taxonomic groups that responded consistently to each type of perturbation. These patterns revealed that, at the level of family and above, most groups responded consistently to only one or two types of perturbations, suggesting that traits with different patterns of phylogenetic conservation underlie the responses to different perturbations. We conclude that a phylogenetic approach may be useful in predicting how soil bacterial communities respond to a variety of global changes. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.
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Affiliation(s)
- Kazuo Isobe
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Nicholas J. Bouskill
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Eoin L. Brodie
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, USA
| | - Erika A. Sudderth
- Center for Environmental Studies, Brown University, Providence, RI, USA
| | - Jennifer B. H. Martiny
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA
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