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Wilhelm RC, Amsili JP, Kurtz KSM, van Es HM, Buckley DH. Ecological insights into soil health according to the genomic traits and environment-wide associations of bacteria in agricultural soils. ISME COMMUNICATIONS 2023; 3:1. [PMID: 37081121 PMCID: PMC9829723 DOI: 10.1038/s43705-022-00209-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 12/12/2022] [Accepted: 12/20/2022] [Indexed: 04/22/2023]
Abstract
Soil microbiomes are sensitive to current and previous soil conditions, and bacterial 'bioindicators' of biological, physical, and chemical soil properties have considerable potential for soil health assessment. However, the lack of ecological or physiological information for most soil microorganisms limits our ability to interpret the associations of bioindicators and, thus, their utility for guiding management. We identified bioindicators of tillage intensity and twelve soil properties used to rate soil health using a 16S rRNA gene-based survey of farmland across North America. We then inferred the genomic traits of bioindicators and evaluated their environment-wide associations (EWAS) with respect to agricultural management practice, disturbance, and plant associations with 89 studies from agroecosystems. Most bioindicators were either positively correlated with biological properties (e.g., organic matter) or negatively correlated with physical and chemical properties. Higher soil health ratings corresponded with smaller genome size and higher coding density, while lower ratings corresponded with larger genomes and higher rrn copy number. Community-weighted genome size explained most variation in health ratings. EWAS linked prominent bioindicators with the impacts of environmental disturbances. Our findings provide ecological insights into bioindicators of soil properties relevant to soil health management, illustrating the tight coupling of microbiome and soil function.
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Affiliation(s)
- Roland C Wilhelm
- School of Integrative Plant Sciences, Bradfield Hall, Cornell University, Ithaca, NY, 14853, USA.
| | - Joseph P Amsili
- School of Integrative Plant Sciences, Bradfield Hall, Cornell University, Ithaca, NY, 14853, USA
| | - Kirsten S M Kurtz
- School of Integrative Plant Sciences, Bradfield Hall, Cornell University, Ithaca, NY, 14853, USA
| | - Harold M van Es
- School of Integrative Plant Sciences, Bradfield Hall, Cornell University, Ithaca, NY, 14853, USA
| | - Daniel H Buckley
- School of Integrative Plant Sciences, Bradfield Hall, Cornell University, Ithaca, NY, 14853, USA
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2
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Li W, Xie L, Zhao C, Hu X, Yin C. Nitrogen Fertilization Increases Soil Microbial Biomass and Alters Microbial Composition Especially Under Low Soil Water Availability. MICROBIAL ECOLOGY 2022:10.1007/s00248-022-02103-8. [PMID: 36044056 DOI: 10.1007/s00248-022-02103-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 08/23/2022] [Indexed: 06/15/2023]
Abstract
Soil microbial biomass and composition are affected by resource supply and water availability. However, the response of soil microbial communities to nitrogen fertilization under different water availability conditions is unclear. Therefore, this study conducted a 6-year pot experiment comprising five watering regimes (40%, 50%, 60%, 80%, and 100% of field capacity (FC)) and three nitrogen fertilization levels (NH4NO3 solution; 0 [N0], 20 [N1], and 40 [N2] g N m-2 year-1) to investigate soil microbial biomass, composition, and properties. The results indicated that soil microbial biomass and composition were more strongly affected by nitrogen fertilization compared with water regime. Nitrogen fertilization increased soil microbial biomass and altered soil microbial community composition, especially under low soil water availability. Soil microbial biomass was positively linearly associated with soil water regimes under N0, whereas it responded polynomially to soil water regimes under N1 and N2. The maximal soil microbial biomass was observed at FC80 for N1 and FC60 for N2. Furthermore, the biomass of soil microbial groups with high nitrogen and carbon acquisition ability as well as the enzyme activities of carbon and nitrogen cycling (β-1,4-glucosidase and β-1,4-N-acetyl-glucosaminidase, respectively) were stimulated by nitrogen fertilization. Soil microbial biomass was affected directly by nitrogen fertilization and indirectly by nitrogen and water regimes, via altering soil pH, dissolved inorganic nitrogen (NH4+-N and NO3--N) concentration, and soil organic carbon concentration. This study provides new insights into the effect of interaction between soil nitrogen and water availabilities on soil microbial biomass, composition, and its underlying mechanism.
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Affiliation(s)
- Wanting Li
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu, 610041, People's Republic of China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, People's Republic of China
| | - Lulu Xie
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu, 610041, People's Republic of China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, People's Republic of China
| | - Chunzhang Zhao
- State Environmental Protection Key Laboratory of Synergetic Control and Joint Remediation for Soil & Water Pollution, College of Ecology and Environment, Chengdu University of Technology, Chengdu, 610059, People's Republic of China
| | - Xuefeng Hu
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu, 610041, People's Republic of China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, People's Republic of China
| | - Chunying Yin
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu, 610041, People's Republic of China.
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3
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Chuckran PF, Hungate BA, Schwartz E, Dijkstra P. Variation in genomic traits of microbial communities among ecosystems. FEMS MICROBES 2021. [DOI: 10.1093/femsmc/xtab020] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
ABSTRACT
Free-living bacteria in nutrient limited environments often exhibit traits which may reduce the cost of reproduction, such as smaller genome size, low GC content and fewer sigma (σ) factor and 16S rRNA gene copies. Despite the potential utility of these traits to detect relationships between microbial communities and ecosystem-scale properties, few studies have assessed these traits on a community-scale. Here, we analysed these traits from publicly available metagenomes derived from marine, soil, host-associated and thermophilic communities. In marine and thermophilic communities, genome size and GC content declined in parallel, consistent with genomic streamlining, with GC content in thermophilic communities generally higher than in marine systems. In contrast, soil communities averaging smaller genomes featured higher GC content and were often from low-carbon environments, suggesting unique selection pressures in soil bacteria. The abundance of specific σ-factors varied with average genome size and ecosystem type. In oceans, abundance of fliA, a σ-factor controlling flagella biosynthesis, was positively correlated with community average genome size—reflecting known trade-offs between nutrient conservation and chemotaxis. In soils, a high abundance of the stress response σ-factor gene rpoS was associated with smaller average genome size and often located in harsh and/or carbon-limited environments—a result which tracks features observed in culture and indicates an increased capacity for stress response in nutrient-poor soils. This work shows how ecosystem-specific constraints are associated with trade-offs which are embedded in the genomic features of bacteria in microbial communities, and which can be detected at the community level, highlighting the importance of genomic features in microbial community analysis.
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Affiliation(s)
- Peter F Chuckran
- Center for Ecosystem Science and Society (ECOSS) and Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Bruce A Hungate
- Center for Ecosystem Science and Society (ECOSS) and Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Egbert Schwartz
- Center for Ecosystem Science and Society (ECOSS) and Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Paul Dijkstra
- Center for Ecosystem Science and Society (ECOSS) and Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, United States of America
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4
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Werner CM, Tuomi M, Eskelinen A. Trait-based responses to cessation of nutrient enrichment in a tundra plant community. Oecologia 2021; 197:675-684. [PMID: 34716491 PMCID: PMC8585805 DOI: 10.1007/s00442-021-05064-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 10/17/2021] [Indexed: 11/25/2022]
Abstract
Plant communities worldwide show varied responses to nutrient enrichment-including shifts in species identity, decreased diversity, and changes in functional trait composition-but the factors determining community recovery after the cessation of nutrient addition remain uncertain. We manipulated nutrient levels in a tundra community for 6 years of nutrient addition followed by 8 years of recovery. We examined how community recovery was mediated by traits related to plant resource-use strategy and plant ability to modify their environment. Overall, we observed persistent effects of fertilization on plant communities. We found that plants with fast-growing traits, including higher specific leaf area, taller stature and lower foliar C:N, were more likely to show a persistent increase in fertilized plots than control plots, maintaining significantly higher cover in fertilized plots 8 years after cessation of fertilization. Additionally, although graminoids responded most strongly to the initial fertilization treatment, forb species were more vulnerable to fertilization effects in the long-term, showing persistent decline and no recovery in 8 years. Finally, these persistent fertilization effects were accompanied by modified environmental conditions, including persistent increases in litter depth and soil phosphorous and lower soil C:N. Our results demonstrate the potential for lasting effects of nutrient enrichment in nutrient-limited systems and identify species traits related to rapid growth and nutrient-use efficiency as the main predictors of the persistence of nutrient enrichment effects. These findings highlight the usefulness of trait-based approach for understanding the persistent feedbacks of nutrient enrichment, plant dynamics, and niche construction via litter and nutrient build-up.
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Affiliation(s)
- Chhaya M Werner
- Department of Physiological Diversity, Helmholtz Center for Environmental Research (UFZ), 04318, Leipzig, Germany.
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103, Leipzig, Germany.
- Department of Ecology and Genetics, University of Oulu, 90014, Oulu, Finland.
| | - Maria Tuomi
- Department of Arctic and Marine Biology, UiT, The Arctic University of Norway, 9019, Tromso, Norway
| | - Anu Eskelinen
- Department of Physiological Diversity, Helmholtz Center for Environmental Research (UFZ), 04318, Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103, Leipzig, Germany
- Department of Ecology and Genetics, University of Oulu, 90014, Oulu, Finland
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5
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Wu R, Davison MR, Gao Y, Nicora CD, Mcdermott JE, Burnum-Johnson KE, Hofmockel KS, Jansson JK. Moisture modulates soil reservoirs of active DNA and RNA viruses. Commun Biol 2021; 4:992. [PMID: 34446837 PMCID: PMC8390657 DOI: 10.1038/s42003-021-02514-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 07/18/2021] [Indexed: 02/07/2023] Open
Abstract
Soil is known to harbor viruses, but the majority are uncharacterized and their responses to environmental changes are unknown. Here, we used a multi-omics approach (metagenomics, metatranscriptomics and metaproteomics) to detect active DNA viruses and RNA viruses in a native prairie soil and to determine their responses to extremes in soil moisture. The majority of transcribed DNA viruses were bacteriophage, but some were assigned to eukaryotic hosts, mainly insects. We also demonstrated that higher soil moisture increased transcription of a subset of DNA viruses. Metaproteome data validated that the specific viral transcripts were translated into proteins, including chaperonins known to be essential for virion replication and assembly. The soil viral chaperonins were phylogenetically distinct from previously described marine viral chaperonins. The soil also had a high abundance of RNA viruses, with highest representation of Reoviridae. Leviviridae were the most diverse RNA viruses in the samples, with higher amounts in wet soil. This study demonstrates that extreme shifts in soil moisture have dramatic impacts on the composition, activity and potential functions of both DNA and RNA soil viruses.
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Affiliation(s)
- Ruonan Wu
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Michelle R Davison
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Yuqian Gao
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Carrie D Nicora
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Jason E Mcdermott
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Kristin E Burnum-Johnson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Kirsten S Hofmockel
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
- Department of Agronomy, Iowa State University, Ames, IA, USA
| | - Janet K Jansson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA.
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6
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Igwe AN, Quasem B, Liu N, Vannette RL. Plant phenology influences rhizosphere microbial community and is accelerated by serpentine microorganisms in Plantago erecta. FEMS Microbiol Ecol 2021; 97:6300443. [PMID: 34132353 DOI: 10.1093/femsec/fiab085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 06/14/2021] [Indexed: 11/14/2022] Open
Abstract
Serpentine soils are drought-prone and rich in heavy metals, and plants growing on serpentine soils host distinct microbial communities that may affect plant survival and phenotype. However, whether the rhizosphere communities of plants from different soil chemistries are initially distinct or diverge over time may help us understand drivers of microbial community structure and function in stressful soils. Here, we test the hypothesis that rhizosphere microbial communities will converge over time (plant development), independent of soil chemistry and microbial source. We grew Plantago erecta in serpentine or nonserpentine soil, with serpentine or nonserpentine microbes and tracked plant growth and root phenotypes. We used 16S rRNA gene barcoding to compare bacterial species composition at seedling, vegetative, early- and late-flowering phases. Plant phenotype and rhizosphere bacterial communities were mainly structured by soil type, with minor contributions by plant development, microbe source and their interactions. Serpentine microorganisms promoted early flowering in plants on nonserpentine soils. Despite strong effects of soil chemistry, the convergence in bacterial community composition across development demonstrates the importance of the plant-microbe interactions in shaping microbial assembly processes across soil types.
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Affiliation(s)
- Alexandria N Igwe
- University of Miami, Department of Biology, 1301 Memorial Drive, Coral Gables, FL 33146, USA
| | - Bibi Quasem
- University of California, Davis, Department of Entomology and Nematology, One Shields Avenue, Davis, CA 95616, USA
| | - Naomi Liu
- University of California, Davis, Department of Entomology and Nematology, One Shields Avenue, Davis, CA 95616, USA
| | - Rachel L Vannette
- University of California, Davis, Department of Entomology and Nematology, One Shields Avenue, Davis, CA 95616, USA
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7
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Willing CE, Pierroz G, Coleman-Derr D, Dawson TE. The generalizability of water-deficit on bacterial community composition; Site-specific water-availability predicts the bacterial community associated with coast redwood roots. Mol Ecol 2020; 29:4721-4734. [PMID: 33000868 DOI: 10.1111/mec.15666] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 09/18/2020] [Accepted: 09/21/2020] [Indexed: 12/01/2022]
Abstract
Experimental drought has been shown to delay the development of the root microbiome and increase the relative abundance of Actinobacteria, however, the generalizability of these findings to natural systems or other diverse plant hosts remains unknown. Bacterial cell wall thickness and growth morphology (e.g., filamentous or unicellular) have been proposed as traits that may mediate bacterial responses to environmental drivers. Leveraging a natural gradient of water-availability across the coast redwood (Sequoia sempervirens) range, we tested three hypotheses: (a) that site-specific water-availability is an important predictor of bacterial community composition for redwood roots and rhizosphere soils; (b) that there is relative enrichment of Actinobacteria and other monoderm bacterial groups within the redwood microbiome in response to drier conditions; and (c) that bacterial growth morphology is an important predictor of bacteria response to water-availability, where filamentous taxa will become more dominant at drier sites compared to unicellular bacteria. We find that both α- and β-diversity of redwood bacterial communities is partially explained by water-availability and that Actinobacterial enrichment is a conserved response of land plants to water-deficit. Further, we highlight how the trend of Actinobacterial enrichment in the redwood system is largely driven by the Actinomycetales. We propose bacterial growth morphology (filamentous vs. unicellular) as an additional mechanism behind the increase in Actinomycetales with increasing aridity. A trait-based approach including cell-wall thickness and growth morphology may explain the distribution of bacterial taxa across environmental gradients and help to predict patterns of bacterial community composition for a wide range of host plants.
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Affiliation(s)
- Claire E Willing
- Department of Environmental Science, Policy and Management, UC Berkeley, Berkeley, CA, USA
| | - Grady Pierroz
- Department of Plant and Microbial Biology, UC Berkeley, Berkeley, CA, USA.,Plant Gene Expression Center, USDA-ARS, Albany, CA, USA
| | - Devin Coleman-Derr
- Department of Plant and Microbial Biology, UC Berkeley, Berkeley, CA, USA.,Plant Gene Expression Center, USDA-ARS, Albany, CA, USA
| | - Todd E Dawson
- Department of Environmental Science, Policy and Management, UC Berkeley, Berkeley, CA, USA.,Department of Integrative Biology, UC Berkeley, Berkeley, CA, USA
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8
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Eskelinen A, Gravuer K, Harpole WS, Harrison S, Virtanen R, Hautier Y. Resource-enhancing global changes drive a whole-ecosystem shift to faster cycling but decrease diversity. Ecology 2020; 101:e03178. [PMID: 32870523 DOI: 10.1002/ecy.3178] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 05/19/2020] [Accepted: 07/14/2020] [Indexed: 11/11/2022]
Abstract
Many global changes take the form of resource enhancements that have potential to transform multiple aspects of ecosystems from slower to faster cycling, including a suite of both above- and belowground variables. We developed a novel analytic approach to measure integrated ecosystem responses to resource-enhancing global changes, and how such whole ecosystem slow-to-fast transitions are linked to diversity and exotic invasions in real-world ecosystems. We asked how 5-yr experimental rainfall and nutrient enhancements in a natural grassland system affected 16 ecosystem functions, pools, and stoichiometry variables considered to indicate slow vs. fast cycling. We combined these metrics into a novel index we termed "slow-fast multifunctionality" and assessed its relationship to plant community diversity and exotic plant dominance. Nutrient and rainfall addition interacted to affect average slow-fast multifunctionality. Nutrient addition alone pushed the system toward faster cycling, but this effect weakened with the joint addition of rainfall and nutrients. Variables associated with soil nutrient pools and cycling most strongly contributed to this antagonistic interaction. Nutrient and water addition together, respectively, had additive or synergistic effects on plant trait composition and productivity, demonstrating divergence of above- and belowground ecosystem responses. Our novel metric of faster cycling was strongly associated with decreased plant species richness and increased exotic species dominance. These results demonstrate the breadth of interacting community and ecosystem changes that ensue when resource limitation is relaxed.
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Affiliation(s)
- Anu Eskelinen
- Department of Physiological Diversity, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.,Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Kelly Gravuer
- Graduate Group in Ecology, Department of Plant Sciences, University of California - Davis, Davis, California, 95616, USA
| | - W Stanley Harpole
- Department of Physiological Diversity, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.,Institute of Biology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Susan Harrison
- Department of Environmental Science and Policy, University of California, Davis, California, 95616, USA
| | - Risto Virtanen
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Yann Hautier
- Ecology and Biodiversity Group, Department of Biology, Utrecht University, Utrecht, The Netherlands
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9
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He Y, Lu L, Peng C, Li H, Zhang J, Li R, Zhou C. High-yield grass Pennisetum sinese Roxb plantation and organic manure alter bacterial and fungal communities structure in an ecological agriculture farm. AMB Express 2020; 10:86. [PMID: 32378065 PMCID: PMC7203373 DOI: 10.1186/s13568-020-01018-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 04/25/2020] [Indexed: 11/10/2022] Open
Abstract
Pennisetum sinese Roxb (P. sinese) is an efficient and economic energy crop for its high productivity, and has been well studied in its application in phytoremediation and fodder production. However, little is known about how P. sinese plantation and fermented manures of P. sinese-feed livestock affect the composition of soil bacterial and fungal communities. In this study, 16S rRNA/ITS1 gene-based Illumina Miseq sequencing was employed to compare the bacterial and fungal community structure among soils that had been subjected to uncultivated control (CK), 2-year P. sinese plantation (P), and P. sinese plantation combined with the use of organic manures (P-OM) in a "P. sinese-breeding industry" ecological agriculture farm. The results found microbial communities were altered by P. sinese plantation and fertilization. The P. sinese plantation resulted in increased Actinobacteria and Planctomycetes abundance. Comparatively, significant increased abundance of Chloroflexi, Firmicutes, Nitrospirae, and Euryarchaeota, and genes related with nitrogen and carbon metabolic pathways based on PICRUSt prediction was observed in P-OM soil. Fungal compositions suggested a markedly increased abundance of Ascomycota in P soil. Potential organic matter decomposers Candida, Thermoascus, and Aspergillus were enriched in P soil, indicating the enhanced role of fungi in litter decomposition. Redundancy analysis suggested that soil properties (NH4+-N, total nitrogen, organic matter content, and soil water content) significantly correlated with the changes of microbial compositions (P < 0.05). These results highlight the divergence of microbial communities occurs during P. sinese-based plantation, implying functional diversification of soil ecosystem in P. sinese fields.
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10
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Dai T, Zhao Y, Ning D, Huang B, Mu Q, Yang Y, Wen D. Dynamics of coastal bacterial community average ribosomal RNA operon copy number reflect its response and sensitivity to ammonium and phosphate. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 260:113971. [PMID: 31972418 DOI: 10.1016/j.envpol.2020.113971] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 12/29/2019] [Accepted: 01/10/2020] [Indexed: 06/10/2023]
Abstract
The nutrient-rich effluent from wastewater treatment plants (WWTPs) constitutes a significant disturbance to coastal microbial communities, which in turn affect ecosystem functioning. However, little is known about how such disturbance could affect the community's stability, an important knowledge gap for predicting community response to future disturbances. Here, we examined dynamics of coastal sediment microbial communities with and without a history of WWTP's disturbances (named H1 and H0 hereafter) after simulated nutrient input loading at the low level (5 mg L-1 NH4+-N and 0.5 mg L-1 PO43--P) or high level (50 mg L-1 NH4+-N and 5.0 mg L-1 PO43--P) for 28 days. H0 community was highly sensitive to both low and high nutrient loading, showing a faster community turnover than H1 community. In contrast, H1 community was more efficient in nutrient removal. To explain it, we found that H1 community constituted more abundant and diversified r-strategists, known to be copiotrophic and fast in growth and reproduction, than H0 community. As nutrient was gradually consumed, both communities showed a succession of decreasing r-strategists. Accordingly, there was a decrease in community average ribosomal RNA operon (rrn) copy number, a recently established functional trait of r-strategists. Remarkably, the average rrn copy number of H0 communities was strongly correlated with NH4+-N (R2 = 0.515, P = 0.009 for low nutrient loading; R2 = 0.749, P = 0.001 for high nutrient loading) and PO43--P (R2 = 0.378, P = 0.034 for low nutrient loading; R2 = 0.772, P = 0.001 for high nutrient loading) concentrations, while that of H1 communities was only correlated with NH4+-N at high nutrient loading (R2 = 0.864, P = 0.001). Our results reveal the potential of using rrn copy number to evaluate the community sensitivity to nutrient disturbances, but community's historical contingency need to be taken in account.
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Affiliation(s)
- Tianjiao Dai
- College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China; State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Yanan Zhao
- College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Daliang Ning
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China; Institute for Environmental Genomics, Department of Microbiology and Plant Biology, And School of Civil Engineering and Environmental Science, University of Oklahoma, Norman, OK, USA; Consolidated Core Laboratory, University of Oklahoma, Norman, OK, USA
| | - Bei Huang
- Zhejiang Provincial Zhoushan Marine Ecological Environmental Monitoring Station, Zhoushan, 316021, China
| | - Qinglin Mu
- Zhejiang Provincial Zhoushan Marine Ecological Environmental Monitoring Station, Zhoushan, 316021, China
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Donghui Wen
- College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China.
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11
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Gravuer K, Eskelinen A, Winbourne JB, Harrison SP. Vulnerability and resistance in the spatial heterogeneity of soil microbial communities under resource additions. Proc Natl Acad Sci U S A 2020; 117:7263-7270. [PMID: 32165545 PMCID: PMC7132273 DOI: 10.1073/pnas.1908117117] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Spatial heterogeneity in composition and function enables ecosystems to supply diverse services. For soil microbes and the ecosystem functions they catalyze, whether such heterogeneity can be maintained in the face of altered resource inputs is uncertain. In a 50-ha northern California grassland with a mosaic of plant communities generated by different soil types, we tested how spatial variability in microbial composition and function changed in response to nutrient and water addition. Fungal composition lost some of its spatial variability in response to nutrient addition, driven by decreases in mutualistic fungi and increases in antagonistic fungi that were strongest on the least fertile soils, where mutualists were initially most frequent and antagonists initially least frequent. Bacterial and archaeal community composition showed little change in their spatial variability with resource addition. Microbial functions related to nitrogen cycling showed increased spatial variability under nutrient, and sometimes water, additions, driven in part by accelerated nitrification on the initially more-fertile soils. Under anthropogenic changes such as eutrophication and altered rainfall, these findings illustrate the potential for significant changes in ecosystem-level spatial heterogeneity of microbial functions and communities.
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Affiliation(s)
- Kelly Gravuer
- Graduate Group in Ecology, University of California, Davis, CA 95616;
| | - Anu Eskelinen
- Department of Physiological Diversity, Helmholtz Center for Environmental Research, 04318 Leipzig, Germany
- Department of Physiological Diversity, German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
- Department of Ecology and Genetics, University of Oulu, FI-90014 Oulu, Finland
| | - Joy B Winbourne
- Graduate Group in Ecology, University of California, Davis, CA 95616
- Department of Earth & Environment, Boston University, Boston, MA 02215
| | - Susan P Harrison
- Department of Environmental Science and Policy, University of California, Davis, CA 95616
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Khilyas IV, Sorokina AV, Elistratova AA, Markelova MI, Siniagina MN, Sharipova MR, Shcherbakova TA, D’Errico ME, Cohen MF. Microbial diversity and mineral composition of weathered serpentine rock of the Khalilovsky massif. PLoS One 2019; 14:e0225929. [PMID: 31830070 PMCID: PMC6907791 DOI: 10.1371/journal.pone.0225929] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 11/15/2019] [Indexed: 01/17/2023] Open
Abstract
Endolithic microbial communities survive nutrient and energy deficient conditions while contributing to the weathering of their mineral substrate. This study examined the mineral composition and microbial communities of fully serpentinized weathered rock from 0.1 to 6.5 m depth at a site within the Khalilovsky massif, Orenburg Region, Southern Ural Mountains, Russia. The mineral composition includes a major content of serpentinite family (mostly consisting of lizardite and chrysotile), magnesium hydrocarbonates (hydromagnesite with lesser amounts of hydrotalcite and pyroaurite) concentrated in the upper layers, and clay minerals. We found that the deep-seated weathered serpentinites are chrysotile-type minerals, while the middle and surface serpentinites mostly consist of lizardite and chrysotile types. Microbial community analysis, based on 16S rRNA gene sequencing, showed a similar diversity of phyla throughout the depth profile. The dominant bacterial phyla were the Actinobacteria (of which unclassified genera in the orders Acidimicrobiales and Actinomycetales were most numerous), Chloroflexi (dominated by an uncultured P2-11E order) and the Proteobacteria (predominantly class Betaproteobacteria). Densities of several groups of bacteria were negatively correlated with depth. Occurrence of the orders Actinomycetales, Gaiellales, Solirubrobacterales, Rhizobiales and Burkholderiales were positively correlated with depth. Our findings show that endolithic microbial communities of the Khalilovsky massif have similar diversity to those of serpentine soils and rocks, but are substantially different from those of the aqueous environments of actively serpentinizing systems.
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Affiliation(s)
- Irina V. Khilyas
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, Russian Federation
- * E-mail:
| | - Alyona V. Sorokina
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, Russian Federation
| | - Anna A. Elistratova
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, Russian Federation
| | - Maria I. Markelova
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, Russian Federation
| | - Maria N. Siniagina
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, Russian Federation
| | - Margarita R. Sharipova
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, Russian Federation
| | - Tatyana A. Shcherbakova
- FSUE Central Research Institute of Geology of Non-metallic Mineral Resources, Kazan, Russian Federation
| | - Megan E. D’Errico
- School of Science and Technology, Sonoma State University, Rohnert Park, CA, United States of America
| | - Michael F. Cohen
- Department of Biology, Sonoma State University, Rohnert Park, CA, United States of America
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Climate drives loss of phylogenetic diversity in a grassland community. Proc Natl Acad Sci U S A 2019; 116:19989-19994. [PMID: 31527249 DOI: 10.1073/pnas.1912247116] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
While climate change has already profoundly influenced biodiversity through local extinctions, range shifts, and altered interactions, its effects on the evolutionary history contained within sets of coexisting species-or phylogenetic community diversity-have yet to be documented. Phylogenetic community diversity may be a proxy for the diversity of functional strategies that can help sustain ecological systems in the face of disturbances. Under climatic warming, phylogenetic diversity may be especially vulnerable to decline in plant communities in warm, water-limited regions, as intensified water stress eliminates drought-intolerant species that may be relicts of past wetter climates and may be distantly related to coexisting species. Here, we document a 19-y decline of phylogenetic diversity in a grassland community as moisture became less abundant and predictable at a critical time of the year. This decline was strongest in native forbs, particularly those with high specific leaf area, a trait indicating drought sensitivity. This decline occurred at the small spatial scale where species interact, but the larger regional community has so far been buffered against loss of phylogenetic diversity by its high levels of physical and biotic heterogeneity.
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Honeyman AS, Day ML, Spear JR. Regional fresh snowfall microbiology and chemistry are driven by geography in storm-tracked events, Colorado, USA. PeerJ 2018; 6:e5961. [PMID: 30498637 PMCID: PMC6252068 DOI: 10.7717/peerj.5961] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 10/16/2018] [Indexed: 01/15/2023] Open
Abstract
Snowfall is a global phenomenon highly integrated with hydrology and ecology. Forays into studying bioaerosols and their dependence on aeolian movement are largely constrained to either precipitation-independent analyses or in silico models. Though snowpack and glacial microbiological studies have been conducted, little is known about the biological component of meteoric snow. Through culture-independent phylogenetic and geochemical analyses, we show that the geographical location at which snow precipitates determines snowfall’s geochemical and microbiological composition. Storm-tracking, furthermore, can be used as a valuable environmental indicator to trace down what factors are influencing bioaerosols. We estimate annual aeolian snowfall deposits of up to ∼10 kg of bacterial/archaeal biomass per hectare along our study area of the eastern Front Range in Colorado. The dominant kinds of microbiota captured in an analysis of seven snow events at two different locations, one urban, one rural, across the winter of 2016/2017 included phyla Proteobacteria, Bacteroidetes, Firmicutes, and Acidobacteria, though a multitude of different kinds of organisms were found in both. Taxonomically, Bacteroidetes were more abundant in Golden (urban plain) snow while Proteobacteria were more common in Sunshine (rural mountain) samples. Chemically, Golden snowfall was positively correlated with some metals and anions. The work also hints at better informing the “everything is everywhere” hypotheses of the microbial world and that atmospheric transport of microbiota is not only common, but is capable of disseminating vast amounts of microbiota of different physiologies and genetics that then affect ecosystems globally. Snowfall, we conclude, is a significant repository of microbiological material with strong implications for both ecosystem genetic flux and general bio-aerosol theory.
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Affiliation(s)
| | - Maria L Day
- Civil and Environmental Engineering, Colorado School of Mines, Golden, CO, USA
| | - John R Spear
- Civil and Environmental Engineering, Colorado School of Mines, Golden, CO, USA
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Schmidt R, Gravuer K, Bossange AV, Mitchell J, Scow K. Long-term use of cover crops and no-till shift soil microbial community life strategies in agricultural soil. PLoS One 2018; 13:e0192953. [PMID: 29447262 PMCID: PMC5814021 DOI: 10.1371/journal.pone.0192953] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 02/01/2018] [Indexed: 01/25/2023] Open
Abstract
Reducing tillage and growing cover crops, widely recommended practices for boosting soil health, have major impacts on soil communities. Surprisingly little is known about their impacts on soil microbial functional diversity, and especially so in irrigated Mediterranean ecosystems. In long-term experimental plots at the West Side Research and Extension Center in California's Central Valley, we characterized soil microbial communities in the presence or absence of physical disturbance due to tillage, in the presence or absence of cover crops, and at three depths: 0-5, 5-15 and 15-30 cm. This characterization included qPCR for bacterial and archaeal abundances, DNA sequencing of the 16S rRNA gene, and phylogenetic estimation of two ecologically important microbial traits (rRNA gene copy number and genome size). Total (bacterial + archaeal) diversity was higher in no-till than standard till; diversity increased with depth in no-till but decreased with depth in standard till. Total bacterial numbers were higher in cover cropped plots at all depths, while no-till treatments showed higher numbers in 0-5 cm but lower numbers at lower depths compared to standard tillage. Trait estimates suggested that different farming practices and depths favored distinctly different microbial life strategies. Tillage in the absence of cover crops shifted microbial communities towards fast growing competitors, while no-till shifted them toward slow growing stress tolerators. Across all treatment combinations, increasing depth resulted in a shift towards stress tolerators. Cover crops shifted the communities towards ruderals-organisms with wider metabolic capacities and moderate rates of growth. Overall, our results are consistent with decreasing nutrient availability with soil depth and under no-till treatments, bursts of nutrient availability and niche homogenization under standard tillage, and increases in C supply and variety provided by cover crops. Understanding how agricultural practices shift microbial abundance, diversity and life strategies, such as presented here, can assist with designing farming systems that can support high yields, while enhancing C sequestration and increasing resilience to climate change.
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Affiliation(s)
- Radomir Schmidt
- Department of Land, Air and Water Resources, University of California, Davis, Davis, California, United States of America
| | - Kelly Gravuer
- Department of Plant Sciences, University of California, Davis, Davis, California, United States of America
| | - Anne V. Bossange
- Department of Land, Air and Water Resources, University of California, Davis, Davis, California, United States of America
| | - Jeffrey Mitchell
- Department of Plant Sciences, University of California, Davis, Davis, California, United States of America
| | - Kate Scow
- Department of Land, Air and Water Resources, University of California, Davis, Davis, California, United States of America
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