101
|
Westoby M, Gillings MR, Madin JS, Nielsen DA, Paulsen IT, Tetu SG. Trait dimensions in bacteria and archaea compared to vascular plants. Ecol Lett 2021; 24:1487-1504. [PMID: 33896087 DOI: 10.1111/ele.13742] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 02/25/2021] [Accepted: 03/04/2021] [Indexed: 01/04/2023]
Abstract
Bacteria and archaea have very different ecology compared to plants. One similarity, though, is that much discussion of their ecological strategies has invoked concepts such as oligotrophy or stress tolerance. For plants, so-called 'trait ecology'-strategy description reframed along measurable trait dimensions-has made global syntheses possible. Among widely measured trait dimensions for bacteria and archaea three main axes are evident. Maximum growth rate in association with rRNA operon copy number expresses a rate-yield trade-off that is analogous to the acquisitive-conservative spectrum in plants, though underpinned by different trade-offs. Genome size in association with signal transduction expresses versatility. Cell size has influence on diffusive uptake and on relative wall costs. These trait dimensions, and potentially others, offer promise for interpreting ecology. At the same time, there are very substantial differences from plant trait ecology. Traits and their underpinning trade-offs are different. Also, bacteria and archaea use a variety of different substrates. Bacterial strategies can be viewed both through the facet of substrate-use pathways, and also through the facet of quantitative traits such as maximum growth rate. Preliminary evidence shows the quantitative traits vary widely within substrate-use pathways. This indicates they convey information complementary to substrate use.
Collapse
Affiliation(s)
- Mark Westoby
- Department of Biological Sciences, Macquarie University, Sydney, NSW, Australia
| | - Michael R Gillings
- Department of Biological Sciences, Macquarie University, Sydney, NSW, Australia
| | - Joshua S Madin
- Hawaii Institute of Marine Biology, University of Hawaii, Kaneohe, HI, USA
| | - Daniel A Nielsen
- Department of Biological Sciences, Macquarie University, Sydney, NSW, Australia
| | - Ian T Paulsen
- Dept of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Sasha G Tetu
- Dept of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
| |
Collapse
|
102
|
Xenophontos C, Taubert M, Harpole WS, Küsel K. Phylogenetic and metabolic diversity have contrasting effects on the ecological functioning of bacterial communities. FEMS Microbiol Ecol 2021; 97:6136281. [PMID: 33587113 DOI: 10.1093/femsec/fiab017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 02/12/2021] [Indexed: 12/14/2022] Open
Abstract
Quantifying the relative contributions of microbial species to ecosystem functioning is challenging, because of the distinct mechanisms associated with microbial phylogenetic and metabolic diversity. We constructed bacterial communities with different diversity traits and employed exoenzyme activities (EEAs) and carbon acquisition potential (CAP) from substrates as proxies of bacterial functioning to test the independent effects of these two aspects of biodiversity. We expected that metabolic diversity, but not phylogenetic diversity would be associated with greater ecological function. Phylogenetically relatedness should intensify species interactions and coexistence, therefore amplifying the influence of metabolic diversity. We examined the effects of each diversity treatment using linear models, while controlling for the other, and found that phylogenetic diversity strongly influenced community functioning, positively and negatively. Metabolic diversity, however, exhibited negative or non-significant relationships with community functioning. When controlling for different substrates, EEAs increased along with phylogenetic diversity but decreased with metabolic diversity. The strength of diversity effects was related to substrate chemistry and the molecular mechanisms associated with each substrate's degradation. EEAs of phylogenetically similar groups were strongly affected by within-genus interactions. These results highlight the unique flexibility of microbial metabolic functions that must be considered in further ecological theory development.
Collapse
Affiliation(s)
- Constantinos Xenophontos
- Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger Str. 159, 07743 Jena, Germany, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103 Leipzig, Germany
| | - Martin Taubert
- Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger Str. 159, 07743 Jena, Germany, Germany
| | - W Stanley Harpole
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103 Leipzig, Germany.,Department of Physiological Diversity, Helmholtz-Center for Environmental Research (UFZ), Permoserstraße 15, 04318 Leipzig, Germany.,Institute of Biology, Martin Luther University of Halle-Wittenberg, Weinbergweg 10, 06120 Halle (Saale), Germany
| | - Kirsten Küsel
- Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger Str. 159, 07743 Jena, Germany, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103 Leipzig, Germany
| |
Collapse
|
103
|
Garrison CE, Field EK. Introducing a "core steel microbiome" and community functional analysis associated with microbially influenced corrosion. FEMS Microbiol Ecol 2021; 97:5998222. [PMID: 33220682 DOI: 10.1093/femsec/fiaa237] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 11/19/2020] [Indexed: 12/20/2022] Open
Abstract
Microorganisms attached to aquatic steel structures play key roles in nutrient cycling and structural degradation processes. Corrosion-causing microbes are often the focus of studies involving microbially influenced corrosion, yet the roles of remaining community members remain unclear. This study characterizes the composition and functional potential of a 'core steel microbiome' across stainless steel types (304 and 316) and historic shipwreck steel along salinity gradients in North Carolina estuaries. We found higher phylogenetic evenness and diversity on steel surfaces compared to sediment, and at lower salinities. The core steel microbiome was composed of heterotrophic generalist taxa, and community composition was most strongly influenced by salinity. Substrate type was a secondary factor becoming more influential at higher salinities. The core steel microbiome included members of Sphingobacteriia, Cytophagia, Anaerolineaceae, Verrucomicrobiaceae, Chitinophagaceae, and Rheinheimera. While salinity differences led to phylogenetic separations across microbial community assemblages, functional genes were conserved across salinity and steel type. Generalist taxa on steel surfaces likely provide functional stability and biofilm protection for the community with limited functional trade-offs compared to surrounding environments. Further, characterization of a core steel microbiome increases the understanding of these complex steel surface microbial communities and their similarities to core microbiomes in other environments.
Collapse
Affiliation(s)
- Cody E Garrison
- Department of Biology, East Carolina University, 1000 E 5th St, Greenville, NC 27858, USA
| | - Erin K Field
- Department of Biology, East Carolina University, 1000 E 5th St, Greenville, NC 27858, USA
| |
Collapse
|
104
|
Wang C, Morrissey EM, Mau RL, Hayer M, Piñeiro J, Mack MC, Marks JC, Bell SL, Miller SN, Schwartz E, Dijkstra P, Koch BJ, Stone BW, Purcell AM, Blazewicz SJ, Hofmockel KS, Pett-Ridge J, Hungate BA. The temperature sensitivity of soil: microbial biodiversity, growth, and carbon mineralization. ISME JOURNAL 2021; 15:2738-2747. [PMID: 33782569 DOI: 10.1038/s41396-021-00959-1] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 02/19/2021] [Accepted: 03/04/2021] [Indexed: 11/09/2022]
Abstract
Microorganisms drive soil carbon mineralization and changes in their activity with increased temperature could feedback to climate change. Variation in microbial biodiversity and the temperature sensitivities (Q10) of individual taxa may explain differences in the Q10 of soil respiration, a possibility not previously examined due to methodological limitations. Here, we show phylogenetic and taxonomic variation in the Q10 of growth (5-35 °C) among soil bacteria from four sites, one from each of Arctic, boreal, temperate, and tropical biomes. Differences in the temperature sensitivities of taxa and the taxonomic composition of communities determined community-assembled bacterial growth Q10, which was strongly predictive of soil respiration Q10 within and across biomes. Our results suggest community-assembled traits of microbial taxa may enable enhanced prediction of carbon cycling feedbacks to climate change in ecosystems across the globe.
Collapse
Affiliation(s)
- Chao Wang
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV, USA.,CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, Liaoning, China
| | - Ember M Morrissey
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV, USA.
| | - Rebecca L Mau
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA.,Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Michaela Hayer
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
| | - Juan Piñeiro
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV, USA
| | - Michelle C Mack
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
| | - Jane C Marks
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA.,Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Sheryl L Bell
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Samantha N Miller
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA.,Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Egbert Schwartz
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA.,Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Paul Dijkstra
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA.,Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Benjamin J Koch
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA.,Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Bram W Stone
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
| | - Alicia M Purcell
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
| | - Steven J Blazewicz
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Kirsten S Hofmockel
- Physical and Life Sciences Directorate, Lawrence Livermore National Lab, Livermore, CA, USA.,Ecology, Evolution and Organismal Biology Department, Iowa State University, Ames, IA, USA
| | - Jennifer Pett-Ridge
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Bruce A Hungate
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA.,Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| |
Collapse
|
105
|
Wilhelm RC, DeRito CM, Shapleigh JP, Madsen EL, Buckley DH. Phenolic acid-degrading Paraburkholderia prime decomposition in forest soil. ISME COMMUNICATIONS 2021; 1:4. [PMID: 36717596 PMCID: PMC9723775 DOI: 10.1038/s43705-021-00009-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 02/21/2021] [Accepted: 03/01/2021] [Indexed: 02/03/2023]
Abstract
Plant-derived phenolic acids are catabolized by soil microorganisms whose activity may enhance the decomposition of soil organic carbon (SOC). We characterized whether phenolic acid-degrading bacteria enhance SOC mineralization in forest soils when primed with 13C-labeled p-hydroxybenzoic acid (pHB). We further tested whether pHB-induced priming could explain differences in SOC content among mono-specific tree plantations in a 70-year-old common garden experiment. pHB addition primed significant losses of SOC (3-13 µmols C g-1 dry wt soil over 7 days) compared to glucose, which reduced mineralization (-3 to -8 µmols C g-1 dry wt soil over 7 days). The principal degraders of pHB were Paraburkholderia and Caballeronia in all plantations regardless of tree species or soil type, with one predominant phylotype (RP11ASV) enriched 23-fold following peak pHB respiration. We isolated and confirmed the phenolic degrading activity of a strain matching this phylotype (RP11T), which encoded numerous oxidative enzymes, including secretion signal-bearing laccase, Dyp-type peroxidase and aryl-alcohol oxidase. Increased relative abundance of RP11ASV corresponded with higher pHB respiration and expression of pHB monooxygenase (pobA), which was inversely proportional to SOC content among plantations. pobA expression proved a responsive measure of priming activity. We found that stimulating phenolic-acid degrading bacteria can prime decomposition and that this activity, corresponding with differences in tree species, is a potential mechanism in SOC cycling in forests. Overall, this study highlights the ecology and function of Paraburkholderia whose associations with plant roots and capacity to degrade phenolics suggest a role for specialized bacteria in the priming effect.
Collapse
Affiliation(s)
- Roland C Wilhelm
- School of Integrative Plant Science, Bradfield Hall, Cornell University, Ithaca, NY, USA.
| | | | - James P Shapleigh
- Department of Microbiology, Wing Hall, Cornell University, Ithaca, NY, USA
| | - Eugene L Madsen
- Department of Microbiology, Wing Hall, Cornell University, Ithaca, NY, USA
| | - Daniel H Buckley
- School of Integrative Plant Science, Bradfield Hall, Cornell University, Ithaca, NY, USA
| |
Collapse
|
106
|
Sun ZZ, Ji BW, Zheng N, Wang M, Cao Y, Wan L, Li YS, Rong JC, He HL, Chen XL, Zhang YZ, Xie BB. Phylogenetic Distribution of Polysaccharide-Degrading Enzymes in Marine Bacteria. Front Microbiol 2021; 12:658620. [PMID: 33815349 PMCID: PMC8012555 DOI: 10.3389/fmicb.2021.658620] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 02/25/2021] [Indexed: 11/13/2022] Open
Abstract
Deconstruction is an essential step of conversion of polysaccharides, and polysaccharide-degrading enzymes play a key role in this process. Although there is recent progress in the identification of these enzymes, the diversity and phylogenetic distribution of these enzymes in marine microorganisms remain largely unknown, hindering our understanding of the ecological roles of marine microorganisms in the ocean carbon cycle. Here, we studied the phylogenetic distribution of nine types of polysaccharide-degrading enzymes in marine bacterial genomes. First, we manually compiled a reference sequence database containing 961 experimentally verified enzymes. With this reference database, we annotated 9,335 enzyme sequences from 2,182 high-quality marine bacterial genomes, revealing extended distribution for six enzymes at the phylum level and for all nine enzymes at lower taxonomic levels. Next, phylogenetic analyses revealed intra-clade diversity in the encoding potentials and phylogenetic conservation of a few enzymes at the genus level. Lastly, our analyses revealed correlations between enzymes, with alginate lyases demonstrating the most extensive correlations with others. Intriguingly, chitinases showed negative correlations with cellulases, alginate lyases, and agarases in a few genera. This result suggested that intra-genus lifestyle differentiation occurred many times in marine bacteria and that the utilization of polysaccharides may act as an important driver in the recent ecological differentiation of a few lineages. This study expanded our knowledge of the phylogenetic distribution of polysaccharide enzymes and provided insights into the ecological differentiation of marine bacteria.
Collapse
Affiliation(s)
- Zhong-Zhi Sun
- Microbial Technology Institute and State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Bo-Wen Ji
- Microbial Technology Institute and State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Ning Zheng
- Microbial Technology Institute and State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Meng Wang
- Microbial Technology Institute and State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Ye Cao
- Microbial Technology Institute and State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Lu Wan
- Microbial Technology Institute and State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Yi-Song Li
- Microbial Technology Institute and State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Jin-Cheng Rong
- Microbial Technology Institute and State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Hai-Lun He
- School of Life Sciences, Central South University, Changsha, China
| | - Xiu-Lan Chen
- Microbial Technology Institute and State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Yu-Zhong Zhang
- College of Marine Life Sciences and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China.,Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Bin-Bin Xie
- Microbial Technology Institute and State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| |
Collapse
|
107
|
Wan W, Grossart HP, He D, Yuan W, Yang Y. Stronger environmental adaptation of rare rather than abundant bacterioplankton in response to dredging in eutrophic Lake Nanhu (Wuhan, China). WATER RESEARCH 2021; 190:116751. [PMID: 33348071 DOI: 10.1016/j.watres.2020.116751] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 12/08/2020] [Accepted: 12/13/2020] [Indexed: 06/12/2023]
Abstract
Deciphering responses of rare versus abundant bacterioplankton to environmental change, crucial for understanding and mitigating of cyanobacterial blooms, is an important but poorly investigated subject. Using MiSeq sequencing, we investigated the taxonomic and phylogenetic diversity of rare and abundant bacterioplankton in eutrophic Lake Nanhu before and after dredging. We estimated environmental breadths and phylogenetic signals of ecological preferences of rare and abundant bacterioplankton, and investigated community function and bacterioplankton assembly processes. Both taxonomic and phylogenic distances of rare and abundant bacterioplankton communities were significantly positively correlated with the dissimilarity of environmental factors. Threshold indicator taxa analysis and Blomberg's K statistic indicated that rare taxa held broader environmental thresholds and stronger phylogenetic signals for ecological traits than abundant taxa. Environmental adaptations of both rare and abundant taxa exhibited distinct changes after dredging. Higher functional redundancy occurred in the abundant compared to the rare bacterioplankton, with functions of rare bacterioplankton decreasing and for the abundant ones increasing after dredging. The null model revealed that dispersal limitation belonging to stochastic processes determined the abundant bacterioplankton community assembly, whereas variable selection belonging to deterministic processes drove the rare one. Rare bacterioplankton was more environmentally constrained than the abundant one. Dissolved oxygen was the decisive factor in determining the balance between stochasticity and determinism in both rare and abundant bacterioplankton. Our study extends our knowledge of environmental adaptation of rare versus abundant bacterioplankton to massive disturbing measures, i.e. dredging, and allows to estimate dredging performance for mitigating cyanobacterial blooms from a molecular ecology viewpoint.
Collapse
Affiliation(s)
- Wenjie Wan
- Key Laboratory of Aquatic Botany and Watershed Ecology Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, PR China; Center of the Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, PR China
| | - Hans-Peter Grossart
- Leibniz-Institude of Freshwater Ecology and Inland Fisheries (IGB), 16775, Neuglobsow, Germany; University of Potsdam, Institute of Biochemistry and Biology, Maulbeerallee 2, 14469, Potsdam, Germany
| | - Donglan He
- College of Life Science, South-Central University for Nationalities, Wuhan 430070, PR China
| | - Wenke Yuan
- Key Laboratory of Aquatic Botany and Watershed Ecology Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, PR China; Center of the Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, PR China
| | - Yuyi Yang
- Key Laboratory of Aquatic Botany and Watershed Ecology Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, PR China; Center of the Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, PR China.
| |
Collapse
|
108
|
Álvarez-Pérez S, Dhami MK, Pozo MI, Crauwels S, Verstrepen KJ, Herrera CM, Lievens B, Jacquemyn H. Genetic admixture increases phenotypic diversity in the nectar yeast Metschnikowia reukaufii. FUNGAL ECOL 2021. [DOI: 10.1016/j.funeco.2020.101016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
109
|
Competitive Exclusion and Metabolic Dependency among Microorganisms Structure the Cellulose Economy of an Agricultural Soil. mBio 2021; 12:mBio.03099-20. [PMID: 33402535 PMCID: PMC8545098 DOI: 10.1128/mbio.03099-20] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Microorganisms that degrade cellulose utilize extracellular reactions that yield free by-products which can promote interactions with noncellulolytic organisms. We hypothesized that these interactions determine the ecological and physiological traits governing the fate of cellulosic carbon (C) in soil. We performed comparative genomics with genome bins from a shotgun metagenomic-stable isotope probing experiment to characterize the attributes of cellulolytic and noncellulolytic taxa accessing 13C from cellulose. We hypothesized that cellulolytic taxa would exhibit competitive traits that limit access, while noncellulolytic taxa would display greater metabolic dependency, such as signatures of adaptive gene loss. We tested our hypotheses by evaluating genomic traits indicative of competitive exclusion or metabolic dependency, such as antibiotic production, growth rate, surface attachment, biomass degrading potential, and auxotrophy. The most 13C-enriched taxa were cellulolytic Cellvibrio (Gammaproteobacteria) and Chaetomium (Ascomycota), which exhibited a strategy of self-sufficiency (prototrophy), rapid growth, and competitive exclusion via antibiotic production. Auxotrophy was more prevalent in cellulolytic Actinobacteria than in cellulolytic Proteobacteria, demonstrating differences in dependency among cellulose degraders. Noncellulolytic taxa that accessed 13C from cellulose (Planctomycetales, Verrucomicrobia, and Vampirovibrionales) were also more dependent, as indicated by patterns of auxotrophy and 13C labeling (i.e., partial labeling or labeling at later stages). Major 13C-labeled cellulolytic microbes (e.g., Sorangium, Actinomycetales, Rhizobiales, and Caulobacteraceae) possessed adaptations for surface colonization (e.g., gliding motility, hyphae, attachment structures) signifying the importance of surface ecology in decomposing particulate organic matter. Our results demonstrated that access to cellulosic C was accompanied by ecological trade-offs characterized by differing degrees of metabolic dependency and competitive exclusion.
Collapse
|
110
|
Stothart MR, Greuel RJ, Gavriliuc S, Henry A, Wilson AJ, McLoughlin PD, Poissant J. Bacterial dispersal and drift drive microbiome diversity patterns within a population of feral hindgut fermenters. Mol Ecol 2020; 30:555-571. [PMID: 33231332 DOI: 10.1111/mec.15747] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 11/16/2020] [Accepted: 11/17/2020] [Indexed: 12/15/2022]
Abstract
Studies of microbiome variation in wildlife often emphasize host physiology and diet as proximate selective pressures acting on host-associated microbiota. In contrast, microbial dispersal and ecological drift are more rarely considered. Using amplicon sequencing, we characterized the bacterial microbiome of adult female (n = 86) Sable Island horses (Nova Scotia, Canada) as part of a detailed individual-based study of this feral population. Using data on sampling date, horse location, age, parental status, and local habitat variables, we contrasted the ability of spatiotemporal, life history, and environmental factors to explain microbiome diversity among Sable Island horses. We extended inferences made from these analyses with both phylogeny-informed and phylogeny-independent null modelling approaches to identify deviations from stochastic expectations. Phylogeny-informed diversity measures were correlated with spatial and local habitat variables, but null modelling results suggested that heterogeneity in ecological drift, rather than differential selective pressures acting on the microbiome, was responsible for these correlations. Conversely, phylogeny-independent diversity measures were best explained by host spatial and social structure, suggesting that taxonomic composition of the microbiome was shaped most strongly by bacterial dispersal. Parental status was important but correlated with measures of β-dispersion rather than β-diversity (mares without foals had lower alpha diversity and more variable microbiomes than mares with foals). Our results suggest that between host microbiome variation within the Sable Island horse population is driven more strongly by bacterial dispersal and ecological drift than by differential selective pressures. These results emphasize the need to consider alternative ecological processes in the study of microbiomes.
Collapse
Affiliation(s)
- Mason R Stothart
- Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Ruth J Greuel
- Department of Biology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Stefan Gavriliuc
- Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Astrid Henry
- Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Alastair J Wilson
- Centre for Ecology and Conservation, University of Exeter, Penryn, UK
| | | | - Jocelyn Poissant
- Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| |
Collapse
|
111
|
Using metacommunity ecology to understand environmental metabolomes. Nat Commun 2020; 11:6369. [PMID: 33311510 PMCID: PMC7732844 DOI: 10.1038/s41467-020-19989-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 10/29/2020] [Indexed: 12/26/2022] Open
Abstract
Environmental metabolomes are fundamentally coupled to microbially-linked biogeochemical processes within ecosystems. However, significant gaps exist in our understanding of their spatiotemporal organization, limiting our ability to uncover transferrable principles and predict ecosystem function. We propose that a theoretical paradigm, which integrates concepts from metacommunity ecology, is necessary to reveal underlying mechanisms governing metabolomes. We call this synthesis between ecology and metabolomics ‘meta-metabolome ecology’ and demonstrate its utility using a mass spectrometry dataset. We developed three relational metabolite dendrograms using molecular properties and putative biochemical transformations and performed ecological null modeling. Based upon null modeling results, we show that stochastic processes drove molecular properties while biochemical transformations were structured deterministically. We further suggest that potentially biochemically active metabolites were more deterministically assembled than less active metabolites. Understanding variation in the influences of stochasticity and determinism provides a way to focus attention on which meta-metabolomes and which parts of meta-metabolomes are most likely to be important to consider in mechanistic models. We propose that this paradigm will allow researchers to study the connections between ecological systems and their molecular processes in previously inaccessible detail. Despite growing interest in environmental metabolomics, we lack conceptual frameworks for considering how metabolites vary across space and time in ecological systems. Here, the authors apply (species) community assembly concepts to metabolomics data, offering a way forward in understanding the assembly of metabolite assemblages.
Collapse
|
112
|
Doherty SJ, Barbato RA, Grandy AS, Thomas WK, Monteux S, Dorrepaal E, Johansson M, Ernakovich JG. The Transition From Stochastic to Deterministic Bacterial Community Assembly During Permafrost Thaw Succession. Front Microbiol 2020; 11:596589. [PMID: 33281795 PMCID: PMC7691490 DOI: 10.3389/fmicb.2020.596589] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 10/27/2020] [Indexed: 01/04/2023] Open
Abstract
The Northern high latitudes are warming twice as fast as the global average, and permafrost has become vulnerable to thaw. Changes to the environment during thaw leads to shifts in microbial communities and their associated functions, such as greenhouse gas emissions. Understanding the ecological processes that structure the identity and abundance (i.e., assembly) of pre- and post-thaw communities may improve predictions of the functional outcomes of permafrost thaw. We characterized microbial community assembly during permafrost thaw using in situ observations and a laboratory incubation of soils from the Storflaket Mire in Abisko, Sweden, where permafrost thaw has occurred over the past decade. In situ observations indicated that bacterial community assembly was driven by randomness (i.e., stochastic processes) immediately after thaw with drift and dispersal limitation being the dominant processes. As post-thaw succession progressed, environmentally driven (i.e., deterministic) processes became increasingly important in structuring microbial communities where homogenizing selection was the only process structuring upper active layer soils. Furthermore, laboratory-induced thaw reflected assembly dynamics immediately after thaw indicated by an increase in drift, but did not capture the long-term effects of permafrost thaw on microbial community dynamics. Our results did not reflect a link between assembly dynamics and carbon emissions, likely because respiration is the product of many processes in microbial communities. Identification of dominant microbial community assembly processes has the potential to improve our understanding of the ecological impact of permafrost thaw and the permafrost-climate feedback.
Collapse
Affiliation(s)
- Stacey Jarvis Doherty
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, United States
- Cold Regions Research and Engineering Laboratory, Engineer Research Development Center, United States Army Corps of Engineers, Hanover, NH, United States
| | - Robyn A. Barbato
- Cold Regions Research and Engineering Laboratory, Engineer Research Development Center, United States Army Corps of Engineers, Hanover, NH, United States
| | - A. Stuart Grandy
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, NH, United States
| | - W. Kelley Thomas
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, United States
| | - Sylvain Monteux
- Department of Soil and Environment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Ellen Dorrepaal
- Climate Impacts Research Centre, Department of Ecology and Environmental Sciences, Umeå University, Abisko, Sweden
| | - Margareta Johansson
- Department of Physical Geography and Ecosystem Science, Lund University, Lund, Sweden
| | - Jessica G. Ernakovich
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, United States
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, NH, United States
| |
Collapse
|
113
|
Ning D, Yuan M, Wu L, Zhang Y, Guo X, Zhou X, Yang Y, Arkin AP, Firestone MK, Zhou J. A quantitative framework reveals ecological drivers of grassland microbial community assembly in response to warming. Nat Commun 2020; 11:4717. [PMID: 32948774 PMCID: PMC7501310 DOI: 10.1038/s41467-020-18560-z] [Citation(s) in RCA: 378] [Impact Index Per Article: 94.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 08/26/2020] [Indexed: 12/28/2022] Open
Abstract
Unraveling the drivers controlling community assembly is a central issue in ecology. Although it is generally accepted that selection, dispersal, diversification and drift are major community assembly processes, defining their relative importance is very challenging. Here, we present a framework to quantitatively infer community assembly mechanisms by phylogenetic bin-based null model analysis (iCAMP). iCAMP shows high accuracy (0.93-0.99), precision (0.80-0.94), sensitivity (0.82-0.94), and specificity (0.95-0.98) on simulated communities, which are 10-160% higher than those from the entire community-based approach. Application of iCAMP to grassland microbial communities in response to experimental warming reveals dominant roles of homogeneous selection (38%) and 'drift' (59%). Interestingly, warming decreases 'drift' over time, and enhances homogeneous selection which is primarily imposed on Bacillales. In addition, homogeneous selection has higher correlations with drought and plant productivity under warming than control. iCAMP provides an effective and robust tool to quantify microbial assembly processes, and should also be useful for plant and animal ecology.
Collapse
Affiliation(s)
- Daliang Ning
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, 100084, Beijing, China
| | - Mengting Yuan
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
- Department of Environmental Science Policy and Management, University of California, Berkeley, CA, 94720, USA
| | - Linwei Wu
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
| | - Ya Zhang
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
| | - Xue Guo
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, 100084, Beijing, China
| | - Xishu Zhou
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
- School of Minerals Processing and Bioengineering, Central South University, 410083, Changsha, Hunan, China
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, 100084, Beijing, China
| | - Adam P Arkin
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, 94710, USA
- Department of Bioengineering, University of California, Berkeley, CA, 94720, USA
| | - Mary K Firestone
- Department of Environmental Science Policy and Management, University of California, Berkeley, CA, 94720, USA
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, 94704, USA
| | - Jizhong Zhou
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA.
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, 100084, Beijing, China.
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, 94704, USA.
- School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, 73019, USA.
| |
Collapse
|
114
|
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.
Collapse
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:
| |
Collapse
|
115
|
Gavriilidou A, Gutleben J, Versluis D, Forgiarini F, van Passel MWJ, Ingham CJ, Smidt H, Sipkema D. Comparative genomic analysis of Flavobacteriaceae: insights into carbohydrate metabolism, gliding motility and secondary metabolite biosynthesis. BMC Genomics 2020; 21:569. [PMID: 32819293 PMCID: PMC7440613 DOI: 10.1186/s12864-020-06971-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 08/05/2020] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Members of the bacterial family Flavobacteriaceae are widely distributed in the marine environment and often found associated with algae, fish, detritus or marine invertebrates. Yet, little is known about the characteristics that drive their ubiquity in diverse ecological niches. Here, we provide an overview of functional traits common to taxonomically diverse members of the family Flavobacteriaceae from different environmental sources, with a focus on the Marine clade. We include seven newly sequenced marine sponge-derived strains that were also tested for gliding motility and antimicrobial activity. RESULTS Comparative genomics revealed that genome similarities appeared to be correlated to 16S rRNA gene- and genome-based phylogeny, while differences were mostly associated with nutrient acquisition, such as carbohydrate metabolism and gliding motility. The high frequency and diversity of genes encoding polymer-degrading enzymes, often arranged in polysaccharide utilization loci (PULs), support the capacity of marine Flavobacteriaceae to utilize diverse carbon sources. Homologs of gliding proteins were widespread among all studied Flavobacteriaceae in contrast to members of other phyla, highlighting the particular presence of this feature within the Bacteroidetes. Notably, not all bacteria predicted to glide formed spreading colonies. Genome mining uncovered a diverse secondary metabolite biosynthesis arsenal of Flavobacteriaceae with high prevalence of gene clusters encoding pathways for the production of antimicrobial, antioxidant and cytotoxic compounds. Antimicrobial activity tests showed, however, that the phenotype differed from the genome-derived predictions for the seven tested strains. CONCLUSIONS Our study elucidates the functional repertoire of marine Flavobacteriaceae and highlights the need to combine genomic and experimental data while using the appropriate stimuli to unlock their uncharted metabolic potential.
Collapse
Affiliation(s)
- Asimenia Gavriilidou
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Johanna Gutleben
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Dennis Versluis
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Francesca Forgiarini
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Mark W. J. van Passel
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
- Present address: Ministry of Health, Welfare and Sport, Parnassusplein 5, 2511 VX, The Hague, The Netherlands
| | | | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Detmer Sipkema
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| |
Collapse
|
116
|
Silva MOD, Pernthaler J. Biomass addition alters community assembly in ultrafiltration membrane biofilms. Sci Rep 2020; 10:11552. [PMID: 32665605 PMCID: PMC7360762 DOI: 10.1038/s41598-020-68460-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 06/15/2020] [Indexed: 11/25/2022] Open
Abstract
Freshwater biofilms assemble from a pool of rare water column genotypes. Random density fluctuations and temporal species turnover of functionally equivalent potential colonizers result in compositional variability of newly formed biofilm communities. We hypothesized that stronger environmental filtering as induced by enhanced substrate levels might reduce the impact of a locally variable pool of colonizers and instead select for more universal habitat specialists. Our model were heterotrophic biofilms that form on membranes during gravity-driven ultrafiltration of lake water. In four separate experiments, biomass of the cyanobacterium Microcystis was added to the feed water of one set of treatments (BM) and the resulting biofilm communities were compared to unamended controls (CTRL). Biomass addition led to a significant shift of community assembly processes: Replicate BM biofilms were more similar to each other than by chance in 3 of 4 experiments, whereas the opposite was the case for CTRL communities. Moreover, BM communities were more stochastically assembled across experiments from a common 'regional' pool of biofilm colonizers, whereas the composition of CTRL communities was mainly determined by experiment-specific 'local' genotypes. Interestingly, community assembly processes were also related to both, physiology (aerobic vs. anaerobic lifestyle) and the phylogenetic affiliation of biofilm bacteria.
Collapse
Affiliation(s)
- Marisa O D Silva
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Seestrasse 187, 8802, Kilchberg, Switzerland
| | - Jakob Pernthaler
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Seestrasse 187, 8802, Kilchberg, Switzerland.
| |
Collapse
|
117
|
Xu W, Xiang P, Liu X, Ma LQ. Closely-related species of hyperaccumulating plants and their ability in accumulation of As, Cd, Cu, Mn, Ni, Pb and Zn. CHEMOSPHERE 2020; 251:126334. [PMID: 32169705 DOI: 10.1016/j.chemosphere.2020.126334] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 02/20/2020] [Accepted: 02/24/2020] [Indexed: 06/10/2023]
Abstract
Soil contamination by heavy metals is widespread. Heavy metals of concern include As, Cd, Cu, Cr, Mn, Ni, Pb, and Zn. Hyperaccumulating plants are efficient in accumulating metals, which have potential to remediate metal-contaminated soils. Species of closely-related hyperaccumulating plants have been used to screen their ability in metal accumulation. However, there is limited evidence to show that closely-related plant species have similar ability in metal accumulation. Using a global database of 664 hyperaccumulating plants, we constructed a phylogeny of hyperaccumulating plants of As, Cd, Cu, Cr, Mn, Ni, Pb, and Zn. We evaluated the phylogenetic randomness of plants hyperaccumulating different metals by comparing the minimum number of trait-state changes across the phylogenetic tree to a null model. Based on the D value, we evaluated whether closely-related plants tend to accumulate similar metals. Based on the Blomberg's K and Pagel's λ, we tested whether closely-related plants have similar ability in metal accumulation. Excluding Cd and Pb, closely-related plant species tend to accumulate similar metal, however, its ability cannot be predicted based on phylogenetic relations except Ni. Therefore, we concluded that focusing on species of closely-related hyperaccumulating plants can help to screen new hyperaccumulators although their ability could be different.
Collapse
Affiliation(s)
- Wumei Xu
- Institute of Environmental Remediation and Human Health, Southwest Forestry University, Kunming, 650224, China; School of Energy and Environment Science, Yunnan Normal University, Kunming, 650500, China
| | - Ping Xiang
- Institute of Environmental Remediation and Human Health, Southwest Forestry University, Kunming, 650224, China
| | - Xue Liu
- Institute of Environmental Remediation and Human Health, Southwest Forestry University, Kunming, 650224, China.
| | - Lena Q Ma
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China; Institute of Environmental Remediation and Human Health, Southwest Forestry University, Kunming, 650224, China.
| |
Collapse
|
118
|
Muscarella ME, Howey XM, Lennon JT. Trait-based approach to bacterial growth efficiency. Environ Microbiol 2020; 22:3494-3504. [PMID: 32510726 DOI: 10.1111/1462-2920.15120] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 05/29/2020] [Accepted: 06/02/2020] [Indexed: 12/30/2022]
Abstract
Bacterial growth efficiency (BGE) is the proportion of assimilated carbon that is converted into biomass and reflects the balance between growth and energetic demands. Often measured as an aggregate property of the community, BGE is highly variable within and across ecosystems. To understand this variation, we first identified how species identity and resource type affect BGE using 20 bacterial isolates belonging to the phylum Proteobacteria that were enriched from north temperate lakes. Using a trait-based approach that incorporated genomic and phenotypic information, we characterized the metabolism of each isolate and tested for predicted trade-offs between growth rate and efficiency. A substantial amount of variation in BGE could be explained at broad (i.e., order, 20%) and fine (i.e., strain, 58%) taxonomic levels. While resource type was a relatively weak predictor across species, it explained >60% of the variation in BGE within a given species. A metabolic trade-off (between maximum growth rate and efficiency) and genomic features revealed that BGE may be a species-specific metabolic property. Our study suggests that genomic and phylogenetic information may help predict aggregate microbial community functions like BGE and the fate of carbon in ecosystems.
Collapse
Affiliation(s)
- Mario E Muscarella
- Department of Biology, Indiana University, Bloomington, IN, USA.,Département des Sciences Biologiques, Université du Québec à Montréal, Montréal, QC, Canada
| | - Xia Meng Howey
- Department of Biology, Indiana University, Bloomington, IN, USA
| | - Jay T Lennon
- Department of Biology, Indiana University, Bloomington, IN, USA
| |
Collapse
|
119
|
Goelen T, Sobhy IS, Vanderaa C, Wäckers F, Rediers H, Wenseleers T, Jacquemyn H, Lievens B. Bacterial phylogeny predicts volatile organic compound composition and olfactory response of an aphid parasitoid. OIKOS 2020. [DOI: 10.1111/oik.07301] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Tim Goelen
- Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), Dept of Microbial and Molecular Systems, KU Leuven BE‐3001 Leuven Belgium
| | - Islam S. Sobhy
- Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), Dept of Microbial and Molecular Systems, KU Leuven BE‐3001 Leuven Belgium
- Dept of Plant Protection, Faculty of Agriculture, Suez Canal Univ. Ismailia Egypt
| | - Christophe Vanderaa
- Laboratory of Socio‐Ecology & Social Evolution, Biology Dept, KU Leuven Leuven Belgium
| | - Felix Wäckers
- Biobest, Westerlo, Belgium, and: Lancaster Environment Centre, Lancaster Univ. Lancaster UK
| | - Hans Rediers
- Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), Dept of Microbial and Molecular Systems, KU Leuven BE‐3001 Leuven Belgium
| | - Tom Wenseleers
- Laboratory of Socio‐Ecology & Social Evolution, Biology Dept, KU Leuven Leuven Belgium
| | - Hans Jacquemyn
- Laboratory of Plant Conservation and Population Biology, Biology Dept, KU Leuven Leuven Belgium
| | - Bart Lievens
- Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), Dept of Microbial and Molecular Systems, KU Leuven BE‐3001 Leuven Belgium
| |
Collapse
|
120
|
Jaffe AL, Castelle CJ, Matheus Carnevali PB, Gribaldo S, Banfield JF. The rise of diversity in metabolic platforms across the Candidate Phyla Radiation. BMC Biol 2020; 18:69. [PMID: 32560683 PMCID: PMC7304191 DOI: 10.1186/s12915-020-00804-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 06/01/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND A unifying feature of the bacterial Candidate Phyla Radiation (CPR) is a limited and highly variable repertoire of biosynthetic capabilities. However, the distribution of metabolic traits across the CPR and the evolutionary processes underlying them are incompletely resolved. RESULTS Here, we selected ~ 1000 genomes of CPR bacteria from diverse environments to construct a robust internal phylogeny that was consistent across two unlinked marker sets. Mapping of glycolysis, the pentose phosphate pathway, and pyruvate metabolism onto the tree showed that some components of these pathways are sparsely distributed and that similarity between metabolic platforms is only partially predicted by phylogenetic relationships. To evaluate the extent to which gene loss and lateral gene transfer have shaped trait distribution, we analyzed the patchiness of gene presence in a phylogenetic context, examined the phylogenetic depth of clades with shared traits, and compared the reference tree topology with those of specific metabolic proteins. While the central glycolytic pathway in CPR is widely conserved and has likely been shaped primarily by vertical transmission, there is evidence for both gene loss and transfer especially in steps that convert glucose into fructose 1,6-bisphosphate and glycerate 3P into pyruvate. Additionally, the distribution of Group 3 and Group 4-related NiFe hydrogenases is patchy and suggests multiple events of ancient gene transfer. CONCLUSIONS We infer that patterns of gene gain and loss in CPR, including acquisition of accessory traits in independent transfer events, could have been driven by shifts in host-derived resources and led to sparse but varied genetic inventories.
Collapse
Affiliation(s)
- Alexander L Jaffe
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Cindy J Castelle
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | | | - Simonetta Gribaldo
- Department of Microbiology, Unit Evolutionary Biology of the Microbial Cell, Institut Pasteur, Paris, France
| | - Jillian F Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA, USA.
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.
| |
Collapse
|
121
|
Zou Y, Yan J, Hou S, Yi Y, Cui B. Intensive land uses modify assembly process and potential metabolic function of edaphic bacterial communities in the Yellow River Delta, China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 720:137713. [PMID: 32325607 DOI: 10.1016/j.scitotenv.2020.137713] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 02/26/2020] [Accepted: 03/02/2020] [Indexed: 06/11/2023]
Abstract
Coastal reclamation is a global threat to natural ecosystems, disturbing biological community structure, diversity and ecological function through habitat conversion. We have limited insights into the changes brought about by coastal reclamation for different land-use types. We used the Yellow River Delta (YRD) as a model because it is a region with intensive land reclamation, and we investigated the structural and functional variations of bacterial communities and their relations to edaphic properties under different land-use types. Our results showed that the high soil organic carbon (SOC), nitrate concentrations and salinity were found in oil field, aquaculture pond and salt pan, respectively, and low values in natural wetland. Land use was found to have significant influence on bacterial community diversity. To investigate the phylogenetic conservation of specific traits, we analyzed the relationship between soil bacterial assembly processes and edaphic properties. Bacterial traits phylogenetically conserved, and differs in depth. Our findings suggest that SOC served as a deep trait due to it negative correlation with deeper branches of phylogenetic clustering, while nitrate functioned as a shallow trait due to its positive correlation with phylogenetic clustering at finer branches. Soil salinity acted as a complex trait effected on both finer and deeper branches. Further potential functional gene co-occurrence network analysis revealed that land reclamation induced shifts of metabolic function by altering the functional gene connectivity. We found that the photosynthesis pathway was enriched in hub modules related to oil field (OF), while methane metabolism was enriched in hub modules linked to sea cucumber pond (CP1). In addition, two-component systems (TCS) were enriched with nitrate, ammonia, SOC and salinity-related modules. Therefore, our study highlights the importance of integrating multi-function and multi-process identification and prediction of coastal diverse reclamation impacts on coastal ecosystems.
Collapse
Affiliation(s)
- Yuxuan Zou
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, School of Environment, Beijing Normal University, 100875 Beijing, China
| | - Jiaguo Yan
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, School of Environment, Beijing Normal University, 100875 Beijing, China
| | - Shengwei Hou
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Yujun Yi
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, School of Environment, Beijing Normal University, 100875 Beijing, China
| | - Baoshan Cui
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, School of Environment, Beijing Normal University, 100875 Beijing, China.
| |
Collapse
|
122
|
Meyer KM, Hopple AM, Klein AM, Morris AH, Bridgham SD, Bohannan BJM. Community structure - Ecosystem function relationships in the Congo Basin methane cycle depend on the physiological scale of function. Mol Ecol 2020; 29:1806-1819. [PMID: 32285532 DOI: 10.1111/mec.15442] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 02/28/2020] [Accepted: 04/02/2020] [Indexed: 11/30/2022]
Abstract
Belowground ecosystem processes can be highly variable and difficult to predict using microbial community data. Here, we argue that this stems from at least three issues: (a) complex covariance structure of samples (with environmental conditions or spatial proximity) can make distinguishing biotic drivers a challenge; (b) communities can control ecosystem processes through multiple mechanisms, making the identification of these controls a challenge; and (c) ecosystem function assessments can be broad in physiological scale, encapsulating multiple processes with unique microbially mediated controls. We test these assertions using methane (CH4 )-cycling processes in soil samples collected along a wetland-to-upland habitat gradient in the Congo Basin. We perform our measurements of function under controlled laboratory conditions and statistically control for environmental covariates to aid in identifying biotic drivers. We divide measurements of microbial communities into four attributes (abundance, activity, composition, and diversity) that represent different forms of community control. Lastly, our process measurements differ in physiological scale, including broader processes (gross methanogenesis and methanotrophy) that involve more mediating groups, to finer processes (hydrogenotrophic methanogenesis and high-affinity CH4 oxidation) with fewer mediating groups. We observed that finer scale processes can be more readily predicted from microbial community structure than broader scale processes. In addition, the nature of those relationships differed, with broad processes limited by abundance while fine-scale processes were associated with diversity and composition. These findings demonstrate the importance of carefully defining the physiological scale of ecosystem function and performing community measurements that represent the range of possible controls on ecosystem processes.
Collapse
Affiliation(s)
- Kyle M Meyer
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
| | - Anya M Hopple
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
| | - Ann M Klein
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
| | - Andrew H Morris
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
| | - Scott D Bridgham
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
| | | |
Collapse
|
123
|
de Vries FT, Griffiths RI, Knight CG, Nicolitch O, Williams A. Harnessing rhizosphere microbiomes for drought-resilient crop production. Science 2020; 368:270-274. [PMID: 32299947 DOI: 10.1126/science.aaz5192] [Citation(s) in RCA: 286] [Impact Index Per Article: 71.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Root-associated microbes can improve plant growth, and they offer the potential to increase crop resilience to future drought. Although our understanding of the complex feedbacks between plant and microbial responses to drought is advancing, most of our knowledge comes from non-crop plants in controlled experiments. We propose that future research efforts should attempt to quantify relationships between plant and microbial traits, explicitly focus on food crops, and include longer-term experiments under field conditions. Overall, we highlight the need for improved mechanistic understanding of the complex feedbacks between plants and microbes during, and particularly after, drought. This requires integrating ecology with plant, microbiome, and molecular approaches and is central to making crop production more resilient to our future climate.
Collapse
Affiliation(s)
- Franciska T de Vries
- Department of Earth and Environmental Sciences, University of Manchester, Manchester M13 9PT, UK. .,Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1090 GE Amsterdam, Netherlands
| | | | - Christopher G Knight
- Department of Earth and Environmental Sciences, University of Manchester, Manchester M13 9PT, UK
| | - Oceane Nicolitch
- Department of Earth and Environmental Sciences, University of Manchester, Manchester M13 9PT, UK
| | - Alex Williams
- Department of Earth and Environmental Sciences, University of Manchester, Manchester M13 9PT, UK
| |
Collapse
|
124
|
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'.
Collapse
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
| |
Collapse
|
125
|
Gionchetta G, Oliva F, Romaní AM, Bañeras L. Hydrological variations shape diversity and functional responses of streambed microbes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 714:136838. [PMID: 32018979 DOI: 10.1016/j.scitotenv.2020.136838] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 01/08/2020] [Accepted: 01/19/2020] [Indexed: 06/10/2023]
Abstract
Microbiota inhabiting the intermittent streambeds mediates several in-stream processes that are essential for ecosystem function. Reduced stream discharge caused by the strengthened intermittency and increased duration of the dry phase is a spreading global response to changes in climate. Here, the impacts of a 5-month desiccation, one-week rewetting and punctual storms, which interrupted the dry period, were examined. The genomic composition of total (DNA) and active (RNA) diversity, and the community level physiological profiles (CLPP) were considered as proxies for functional diversity to describe both prokaryotes and eukaryotes inhabiting the surface and hyporheic streambeds. Comparisons between the genomic and potential functional responses helped to understand how and whether the microbial diversity was sensitive to the environmental conditions and resource acquisition, such as water stress and extracellular enzyme activities, respectively. RNA expression showed the strongest relationship with the environmental conditions and resource acquisition, being more responsive to changing conditions compared to DNA diversity, especially in the case of prokaryotes. The DNA results presumably reflected the legacy of the treatments because inactive, dormant, or dead cells were included, suggesting a slow microbial biomass turnover or responses of the microbial communities to changes mainly through physiological acclimation. On the other hand, microbial functional diversity was largely explained by resources acquisition, such as metrics of extracellular enzymes, and appeared vulnerable to the hydrological changes and duration of desiccation. The data highlight the need to improve the functional assessment of stream ecosystems with the application of complementary metrics to better describe the streambed microbial dynamics under dry-rewet stress.
Collapse
Affiliation(s)
- G Gionchetta
- GRECO, Institute of Aquatic Ecology, University of Girona, 17003 Girona, Spain.
| | - F Oliva
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain
| | - A M Romaní
- GRECO, Institute of Aquatic Ecology, University of Girona, 17003 Girona, Spain
| | - L Bañeras
- Molecular Microbial Ecology Group, Institute of Aquatic Ecology, University of Girona, 17003 Girona, Spain
| |
Collapse
|
126
|
Huang L, Bai J, Wen X, Zhang G, Zhang C, Cui B, Liu X. Microbial resistance and resilience in response to environmental changes under the higher intensity of human activities than global average level. GLOBAL CHANGE BIOLOGY 2020; 26:2377-2389. [PMID: 31943531 DOI: 10.1111/gcb.14995] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 11/20/2019] [Accepted: 12/17/2019] [Indexed: 06/10/2023]
Abstract
With the increasing intensity of global human activities, the ecosystem function, which is supported by the microbial community, will be dramatically changed and impaired. To investigate microbial resistance and resilience of microbial communities to human activities, we chose two typical types of human disturbances, urbanization, and reclamation under the higher intensity of human activities than the global average level. We examined microbial traits, including the abundance, diversity, phylogeny, and co-occurrence interactions in soil microbial communities, together with the nitrification activities observed in the subtropical coastal ecosystem of the Pearl River Estuary and in soil microcosm experiments. Microbial communities were less resistant to the environmental changes caused by urbanization than to those caused by reclamation, which was significantly reflected in the nitrogen and/or carbon-related patterns. However, most of the microbial traits could be recovered almost to the original level without significant differences in the microcosm after 40 days of incubation. The co-occurrence interactions between nitrifiers and other microbial communities were dramatically changed and could not be completely recovered, but this change did not affect their nitrification activities for balancing the ammonium in the soil to the original level during the recovery stage, suggesting that the interactions between microbial communities might have fewer effects on their activities than previously thought. This study quantitatively demonstrated that microbial communities as a whole can recover to a status similar to the original state in a short time after the removal of stress at a large ecosystem scale even under the higher intensity of human activities than global average level in coastal ecosystems, which implied a strong recovery capacity of soil microbial community even after intense human disturbance.
Collapse
Affiliation(s)
- Laibin Huang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, China
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Junhong Bai
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, China
| | - Xiaojun Wen
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, China
| | - Guangliang Zhang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, China
| | - Chengdong Zhang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, China
| | - Baoshan Cui
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, China
| | - Xinhui Liu
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, China
| |
Collapse
|
127
|
Alneberg J, Bennke C, Beier S, Bunse C, Quince C, Ininbergs K, Riemann L, Ekman M, Jürgens K, Labrenz M, Pinhassi J, Andersson AF. Ecosystem-wide metagenomic binning enables prediction of ecological niches from genomes. Commun Biol 2020; 3:119. [PMID: 32170201 PMCID: PMC7070063 DOI: 10.1038/s42003-020-0856-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 02/25/2020] [Indexed: 11/16/2022] Open
Abstract
The genome encodes the metabolic and functional capabilities of an organism and should be a major determinant of its ecological niche. Yet, it is unknown if the niche can be predicted directly from the genome. Here, we conduct metagenomic binning on 123 water samples spanning major environmental gradients of the Baltic Sea. The resulting 1961 metagenome-assembled genomes represent 352 species-level clusters that correspond to 1/3 of the metagenome sequences of the prokaryotic size-fraction. By using machine-learning, the placement of a genome cluster along various niche gradients (salinity level, depth, size-fraction) could be predicted based solely on its functional genes. The same approach predicted the genomes’ placement in a virtual niche-space that captures the highest variation in distribution patterns. The predictions generally outperformed those inferred from phylogenetic information. Our study demonstrates a strong link between genome and ecological niche and provides a conceptual framework for predictive ecology based on genomic data. Alneberg et al. conduct metagenomics binning of water samples collected over major environmental gradients in the Baltic Sea. They use machine-learning to predict the placement of genome clusters along niche gradients based on the content of functional genes.
Collapse
Affiliation(s)
- Johannes Alneberg
- Department of Gene Technology, Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Christin Bennke
- Leibniz Institute for Baltic Sea Research, Warnemünde, Germany
| | - Sara Beier
- Leibniz Institute for Baltic Sea Research, Warnemünde, Germany.,CNRS, Laboratoire d'Océanographie Microbienne, LOMIC, Sorbonne Université, Banyuls/mer, France
| | - Carina Bunse
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus, University, Kalmar, Sweden.,Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB), Oldenburg, Germany.,Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Bremerhaven, Germany
| | | | - Karolina Ininbergs
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden.,Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden
| | - Lasse Riemann
- Department of Biology, Marine Biological Section, University of Copenhagen, Helsingør, Denmark
| | - Martin Ekman
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Klaus Jürgens
- Leibniz Institute for Baltic Sea Research, Warnemünde, Germany
| | | | - Jarone Pinhassi
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus, University, Kalmar, Sweden
| | - Anders F Andersson
- Department of Gene Technology, Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden.
| |
Collapse
|
128
|
Jain A, Krishnan KP, Begum N, Singh A, Thomas FA, Gopinath A. Response of bacterial communities from Kongsfjorden (Svalbard, Arctic Ocean) to macroalgal polysaccharide amendments. MARINE ENVIRONMENTAL RESEARCH 2020; 155:104874. [PMID: 31975691 DOI: 10.1016/j.marenvres.2020.104874] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 01/06/2020] [Accepted: 01/07/2020] [Indexed: 06/10/2023]
Abstract
Macroalgae are abundant in coastal Arctic habitats and contain a large amount of polysaccharides. Increased macroalgal productivity due to warmer temperatures and reduced sea-ice cover contribute a significant amount of polysaccharide-rich detritus in the region. To study bacterial degradation of macroalgal polysaccharides and their potential impact on biogeochemical processes we studied the response of bacterial communities from Kongsfjorden, Svalbard (Arctic Ocean) to alginate (AL) and agarose (AG) amendments, using an ex-situ microcosm experiment. Our results show that bacterial communities responded to the increased availability of macroalgal polysaccharides and community shift was congruent with a significant decline in nutrient concentrations. Initially-rare bacterial taxa affiliated with Gammaproteobacteria and Bacteroidia responded to the polysaccharide addition. Each polysaccharide addition incited the growth of certain distinct bacteria taxa. Compared to the un-amended control microcosms (CM), Polaribacter, Colwellia, Pseudoalteromonas, and unclassified Gammaproteobacteria responded to AL addition, whereas Paraglaciecola, Lentimonas, Colwellia, unclassified Gammaproteobacteria, unclassified Alteromonadales, and unclassified Alteromonadaceae responded to the AG addition. These results suggest that polysaccharides shift bacterial community composition towards copiotrophic bacterial taxa, with implications for carbon and nutrient cycling in coastal Svalbard.
Collapse
Affiliation(s)
- Anand Jain
- Cryobiology Laboratory, National Centre for Polar and Ocean Research, Vasco da Gama, Goa, India.
| | | | - Nazira Begum
- Cryobiology Laboratory, National Centre for Polar and Ocean Research, Vasco da Gama, Goa, India
| | - Archana Singh
- Cryobiology Laboratory, National Centre for Polar and Ocean Research, Vasco da Gama, Goa, India
| | - Femi Anna Thomas
- Cryobiology Laboratory, National Centre for Polar and Ocean Research, Vasco da Gama, Goa, India
| | - Anu Gopinath
- Department of Aquatic Environment Management, Kerala University of Fisheries and Ocean Studies, Kochi, Kerala, India
| |
Collapse
|
129
|
Pold G, Domeignoz-Horta LA, Morrison EW, Frey SD, Sistla SA, DeAngelis KM. Carbon Use Efficiency and Its Temperature Sensitivity Covary in Soil Bacteria. mBio 2020; 11:e02293-19. [PMID: 31964725 PMCID: PMC6974560 DOI: 10.1128/mbio.02293-19] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 12/02/2019] [Indexed: 01/11/2023] Open
Abstract
The strategy that microbial decomposers take with respect to using substrate for growth versus maintenance is one essential biological determinant of the propensity of carbon to remain in soil. To quantify the environmental sensitivity of this key physiological trade-off, we characterized the carbon use efficiency (CUE) of 23 soil bacterial isolates across seven phyla at three temperatures and with up to four substrates. Temperature altered CUE in both an isolate-specific manner and a substrate-specific manner. We searched for genes correlated with the temperature sensitivity of CUE on glucose and deemed those functional genes which were similarly correlated with CUE on other substrates to be validated as markers of CUE. Ultimately, we did not identify any such robust functional gene markers of CUE or its temperature sensitivity. However, we found a positive correlation between rRNA operon copy number and CUE, opposite what was expected. We also found that inefficient taxa increased their CUE with temperature, while those with high CUE showed a decrease in CUE with temperature. Together, our results indicate that CUE is a flexible parameter within bacterial taxa and that the temperature sensitivity of CUE is better explained by observed physiology than by genomic composition across diverse taxa. We conclude that the bacterial CUE response to temperature and substrate is more variable than previously thought.IMPORTANCE Soil microbes respond to environmental change by altering how they allocate carbon to growth versus respiration-or carbon use efficiency (CUE). Ecosystem and Earth System models, used to project how global soil C stocks will continue to respond to the climate crisis, often assume that microbes respond homogeneously to changes in the environment. In this study, we quantified how CUE varies with changes in temperature and substrate quality in soil bacteria and evaluated why CUE characteristics may differ between bacterial isolates and in response to altered growth conditions. We found that bacterial taxa capable of rapid growth were more efficient than those limited to slow growth and that taxa with high CUE were more likely to become less efficient at higher temperatures than those that were less efficient to begin with. Together, our results support the idea that the CUE temperature response is constrained by both growth rate and CUE and that this partly explains how bacteria acclimate to a warming world.
Collapse
Affiliation(s)
- Grace Pold
- Graduate Program in Organismic and Evolutionary Biology, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Luiz A Domeignoz-Horta
- Department of Microbiology, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Eric W Morrison
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, New Hampshire, USA
| | - Serita D Frey
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, New Hampshire, USA
| | - Seeta A Sistla
- Natural Resources Management and Environmental Sciences, California Polytechnic State University, San Luis Obispo, California, USA
| | - Kristen M DeAngelis
- Department of Microbiology, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| |
Collapse
|
130
|
Rodriguez CI, Martiny JBH. Evolutionary relationships among bifidobacteria and their hosts and environments. BMC Genomics 2020; 21:26. [PMID: 31914919 PMCID: PMC6950798 DOI: 10.1186/s12864-019-6435-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 12/26/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The assembly of animal microbiomes is influenced by multiple environmental factors and host genetics, although the relative importance of these factors remains unclear. Bifidobacteria (genus Bifidobacterium, phylum Actinobacteria) are common first colonizers of gut microbiomes in humans and inhabit other mammals, social insects, food, and sewages. In humans, the presence of bifidobacteria in the gut has been correlated with health-promoting benefits. Here, we compared the genome sequences of a subset of the over 400 Bifidobacterium strains publicly available to investigate the adaptation of bifidobacteria diversity. We tested 1) whether bifidobacteria show a phylogenetic signal with their isolation sources (hosts and environments) and 2) whether key traits encoded by the bifidobacteria genomes depend on the host or environment from which they were isolated. We analyzed Bifidobacterium genomes available in the PATRIC and NCBI repositories and identified the hosts and/or environment from which they were isolated. A multilocus phylogenetic analysis was conducted to compare the genetic relatedness the strains harbored by different hosts and environments. Furthermore, we examined differences in genomic traits and genes related to amino acid biosynthesis and degradation of carbohydrates. RESULTS We found that bifidobacteria diversity appears to have evolved with their hosts as strains isolated from the same host were non-randomly associated with their phylogenetic relatedness. Moreover, bifidobacteria isolated from different sources displayed differences in genomic traits such as genome size and accessory gene composition and on particular traits related to amino acid production and degradation of carbohydrates. In contrast, when analyzing diversity within human-derived bifidobacteria, we observed no phylogenetic signal or differences on specific traits (amino acid biosynthesis genes and CAZymes). CONCLUSIONS Overall, our study shows that bifidobacteria diversity is strongly adapted to specific hosts and environments and that several genomic traits were associated with their isolation sources. However, this signal is not observed in human-derived strains alone. Looking into the genomic signatures of bifidobacteria strains in different environments can give insights into how this bacterial group adapts to their environment and what types of traits are important for these adaptations.
Collapse
Affiliation(s)
- Cynthia I Rodriguez
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, 92697, USA.
| | - Jennifer B H Martiny
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, 92697, USA
| |
Collapse
|
131
|
Goelen T, Sobhy IS, Vanderaa C, Boer JG, Delvigne F, Francis F, Wäckers F, Rediers H, Verstrepen KJ, Wenseleers T, Jacquemyn H, Lievens B. Volatiles of bacteria associated with parasitoid habitats elicit distinct olfactory responses in an aphid parasitoid and its hyperparasitoid. Funct Ecol 2020. [DOI: 10.1111/1365-2435.13503] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Tim Goelen
- Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM) Department of Microbial and Molecular Systems KU Leuven Leuven Belgium
| | - Islam S. Sobhy
- Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM) Department of Microbial and Molecular Systems KU Leuven Leuven Belgium
- Department of Plant Protection Faculty of Agriculture Suez Canal University Ismailia Egypt
| | - Christophe Vanderaa
- Laboratory of Socio‐Ecology & Social Evolution Biology Department KU Leuven Leuven Belgium
| | - Jetske G. Boer
- Department of Terrestrial Ecology Netherlands Institute of Ecology (NIOO‐KNAW) Wageningen The Netherlands
| | - Frank Delvigne
- Microbial Processes and Interactions (MiPI) TERRA Université de Liège‐Gembloux Agro‐Bio Tech Gembloux Belgium
| | - Frédéric Francis
- Functional & Evolutionary Entomology TERRA Université de Liège‐Gembloux Agro‐Bio Tech Gembloux Belgium
| | - Felix Wäckers
- Biobest Westerlo Belgium
- Lancaster Environment Centre Lancaster University Lancaster UK
| | - Hans Rediers
- Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM) Department of Microbial and Molecular Systems KU Leuven Leuven Belgium
| | - Kevin J. Verstrepen
- Lab for Systems Biology VIB Center for Microbiology & Centre of Microbial and Plant Genetics (CMPG) Lab for Genetics and Genomics Department of Microbial and Molecular Systems KU Leuven Leuven Belgium
| | - Tom Wenseleers
- Laboratory of Socio‐Ecology & Social Evolution Biology Department KU Leuven Leuven Belgium
| | - Hans Jacquemyn
- Laboratory of Plant Conservation and Population Biology Biology Department KU Leuven Leuven Belgium
| | - Bart Lievens
- Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM) Department of Microbial and Molecular Systems KU Leuven Leuven Belgium
| |
Collapse
|
132
|
Isobe K, Ise Y, Kato H, Oda T, Vincenot CE, Koba K, Tateno R, Senoo K, Ohte N. Consequences of microbial diversity in forest nitrogen cycling: diverse ammonifiers and specialized ammonia oxidizers. THE ISME JOURNAL 2020; 14:12-25. [PMID: 31481743 PMCID: PMC6908637 DOI: 10.1038/s41396-019-0500-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 08/06/2019] [Accepted: 08/14/2019] [Indexed: 11/09/2022]
Abstract
We tested the ecosystem functions of microbial diversity with a focus on ammonification (involving diverse microbial taxa) and nitrification (involving only specialized microbial taxa) in forest nitrogen cycling. This study was conducted on a forest slope, in which the soil environment and plant growth gradually changed. We measured the gross and net rates of ammonification and nitrification, the abundance of predicted ammonifiers and nitrifiers, and their community compositions in the soils. The abundance of predicted ammonifiers did not change along the soil environmental gradient, leading to no significant change in the gross ammonification rate. On the other hand, the abundance of nitrifiers and the gross nitrification rate gradually changed. These accordingly determined the spatial distribution of net accumulation of ammonium and nitrate available to plants. The community composition of predicted ammonifiers gradually changed along the slope, implying that diverse ammonifiers were more likely to include taxa that were acclimated to the soil environment and performed ammonification at different slope locations than specialized nitrifiers. Our findings suggest that the abundance of ammonifiers and nitrifiers directly affects the corresponding nitrogen transformation rates, and that their diversity affects the stability of the rates against environmental changes. This study highlights the role of microbial diversity in biogeochemical processes under changing environments and plant growth.
Collapse
Affiliation(s)
- Kazuo Isobe
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan.
| | - Yuta Ise
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Hiroyu Kato
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Tomoki Oda
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | | | - Keisuke Koba
- Center for Ecological Research, Kyoto University, Kyoto, Japan
| | - Ryunosuke Tateno
- Field Science Education and Research Center, Kyoto University, Kyoto, Japan
| | - Keishi Senoo
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan
| | - Nobuhito Ohte
- Graduate School of Informatics, Kyoto University, Kyoto, Japan
| |
Collapse
|
133
|
Ramin KI, Allison SD. Bacterial Tradeoffs in Growth Rate and Extracellular Enzymes. Front Microbiol 2019; 10:2956. [PMID: 31921094 PMCID: PMC6933949 DOI: 10.3389/fmicb.2019.02956] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 12/09/2019] [Indexed: 11/13/2022] Open
Abstract
Like larger organisms, bacteria possess traits, or phenotypic characteristics, that influence growth and impact ecosystem processes. Still, it remains unclear how these traits are organized across bacterial lineages. Using 49 bacterial strains isolated from leaf litter in Southern California, we tested the hypothesis that bacterial growth rates trade off against extracellular enzyme investment. We also tested for phylogenetic conservation of these traits under high and low resource conditions represented, respectively, by Luria broth (LB) and a monomer-dominated medium extracted from plant litter. In support of our hypotheses, we found a negative correlation between the maximum growth rate and the total activity of carbon-, nitrogen-, and phosphorus-degrading extracellular enzymes. However, this tradeoff was only observed under high resource conditions. We also found significant phylogenetic signal in maximum growth rate and extracellular enzyme investment under high and low resource conditions. Driven by our bacterial trait data, we proposed three potential life history strategies. Resource acquisition strategists invest heavily in extracellular enzyme production. Growth strategists invest in high growth rates. Bacteria in a third category showed lower potential for enzyme production and growth, so we tentatively classified them as maintenance strategists that may perform better under conditions we did not measure. These strategies were related to bacterial phylogeny, with most growth strategists belonging to the phylum Proteobacteria and most maintenance and resource acquisition strategists belonging to the phylum Actinobacteria. By accounting for extracellular enzyme investment, our proposed life history strategies complement existing frameworks, such as the copiotroph-oligotroph continuum and Grime’s competitor-stress tolerator-ruderal triangle. Our results have biogeochemical implications because allocation to extracellular enzymes versus growth or stress tolerance can determine the fate and form of organic matter cycling through surface soil.
Collapse
Affiliation(s)
- Kelly I Ramin
- 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
| |
Collapse
|
134
|
Paver SF, Newton RJ, Coleman ML. Microbial communities of the Laurentian Great Lakes reflect connectivity and local biogeochemistry. Environ Microbiol 2019; 22:433-446. [PMID: 31736217 PMCID: PMC6973239 DOI: 10.1111/1462-2920.14862] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 10/29/2019] [Accepted: 11/14/2019] [Indexed: 11/29/2022]
Abstract
The Laurentian Great Lakes are a vast, interconnected freshwater system spanning strong physicochemical gradients, thus constituting a powerful natural laboratory for addressing fundamental questions about microbial ecology and evolution. We present a comparative analysis of pelagic microbial communities across all five Laurentian Great Lakes, focusing on Bacterial and Archaeal picoplankton characterized via 16S rRNA amplicon sequencing. We collected samples throughout the water column from the major basins of each lake in spring and summer over 2 years. Two oligotypes, classified as LD12 (Alphaproteobacteria) and acI‐B1 (Actinobacteria), were among the most abundant in every sample. At the same time, microbial communities showed distinct patterns with depth during summer stratification. Deep hypolimnion samples were frequently dominated by a Chloroflexi oligotype that reached up to 19% relative abundance. Stratified surface communities differed between the colder, less productive upper lakes (Superior, Michigan, Huron) and warmer, more productive lower lakes (Erie, Ontario), in part due to an Actinobacteria oligotype (acI‐C2) that averaged 7.7% of sequences in the lower lakes but <0.2% in the upper lakes. Together, our findings suggest that both hydrologic connectivity and local selective pressures shape microbial communities in the Great Lakes and establish a framework for future investigations.
Collapse
Affiliation(s)
- Sara F Paver
- Department of the Geophysical Sciences, University of Chicago, Chicago, IL, USA
| | - Ryan J Newton
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Maureen L Coleman
- Department of the Geophysical Sciences, University of Chicago, Chicago, IL, USA
| |
Collapse
|
135
|
Shade A, Stopnisek N. Abundance-occupancy distributions to prioritize plant core microbiome membership. Curr Opin Microbiol 2019; 49:50-58. [PMID: 31715441 DOI: 10.1016/j.mib.2019.09.008] [Citation(s) in RCA: 101] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 09/16/2019] [Accepted: 09/21/2019] [Indexed: 10/25/2022]
Abstract
Core microbiome members are consistent features of a dataset that are hypothesized to reflect underlying functional relationships with the host. A review of the recent plant-microbiome literature reveals a variety of study-specific approaches used to define the core, which presents a challenge to building a general plant-microbiome framework. Abundance-occupancy distributions, used in macroecology to describe changes in community diversity over space, offer an ecological approach for prioritizing core membership for both spatial and temporal studies. Additionally, neutral models fit to the abundance-occupancy distributions can provide insights into deterministically selected core members. We provide examples and code to systematically explore a core plant microbiome from abundance-occupancy distributions. Though we focus on examples from and discussions relevant to the plant microbiome, the abundance-occupancy method can be widely and generally applied to prioritize core membership for any microbiome.
Collapse
Affiliation(s)
- Ashley Shade
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing MI 48824, United States; Department of Plant Soil and Microbial Sciences, Michigan State University, East Lansing MI 48824, United States; Plant Resilience Institute, Michigan State University, East Lansing MI 48824, United States; Great Lakes Bioenergy Research Center, Michigan State University, East Lansing MI 48824, United States; Program in Ecology, Evolutionary Biology and Behavior, Michigan State University, East Lansing, United States.
| | - Nejc Stopnisek
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing MI 48824, United States; Plant Resilience Institute, Michigan State University, East Lansing MI 48824, United States; Great Lakes Bioenergy Research Center, Michigan State University, East Lansing MI 48824, United States
| |
Collapse
|
136
|
Lumibao CY, Borer ET, Condon B, Kinkel L, May G, Seabloom EW. Site-specific responses of foliar fungal microbiomes to nutrient addition and herbivory at different spatial scales. Ecol Evol 2019; 9:12231-12244. [PMID: 31832156 PMCID: PMC6854330 DOI: 10.1002/ece3.5711] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 09/04/2019] [Accepted: 09/06/2019] [Indexed: 12/14/2022] Open
Abstract
The plant microbiome can affect host function in many ways and characterizing the ecological factors that shape endophytic (microbes living inside host plant tissues) community diversity is a key step in understanding the impacts of environmental change on these communities. Phylogenetic relatedness among members of a community offers a way of quantifying phylogenetic diversity of a community and can provide insight into the ecological factors that shape endophyte microbiomes. We examined the effects of experimental nutrient addition and herbivory exclusion on the phylogenetic diversity of foliar fungal endophyte communities of the grass species Andropogon gerardii at four sites in the Great Plains of the central USA. Using amplicon sequencing, we characterized the effects of fertilization and herbivory on fungal community phylogenetic diversity at spatial scales that spanned within-host to between sites across the Great Plains. Despite increasing fungal diversity and richness, at larger spatial scales, fungal microbiomes were composed of taxa showing random phylogenetic associations. Phylogenetic diversity did not differ systematically when summed across increasing spatial scales from a few meters within plots to hundreds of kilometers among sites. We observed substantial shifts in composition across sites, demonstrating distinct but similarly diverse fungal communities were maintained within sites across the region. In contrast, at the scale of within leaves, fungal communities tended to be comprised of closely related taxa regardless of the environment, but there were no shifts in phylogenetic composition among communities. We also found that nutrient addition (fertilization) and herbivory have varying effects at different sites. These results suggest that the direction and magnitude of the outcomes of environmental modifications likely depend on the spatial scale considered, and can also be constrained by regional site differences in microbial diversity and composition.
Collapse
Affiliation(s)
- Candice Y. Lumibao
- Department of Ecology, Evolution and BehaviorUniversity of MinnesotaSt. PaulMinnesota
| | - Elizabeth T. Borer
- Department of Ecology, Evolution and BehaviorUniversity of MinnesotaSt. PaulMinnesota
| | - Bradford Condon
- Department of Ecology, Evolution and BehaviorUniversity of MinnesotaSt. PaulMinnesota
| | - Linda Kinkel
- Department of Plant PathologyUniversity of MinnesotaSt. PaulMinnesota
| | - Georgiana May
- Department of Ecology, Evolution and BehaviorUniversity of MinnesotaSt. PaulMinnesota
| | - Eric W. Seabloom
- Department of Ecology, Evolution and BehaviorUniversity of MinnesotaSt. PaulMinnesota
| |
Collapse
|
137
|
Aguirre de Cárcer D. A conceptual framework for the phylogenetically constrained assembly of microbial communities. MICROBIOME 2019; 7:142. [PMID: 31666129 PMCID: PMC6822436 DOI: 10.1186/s40168-019-0754-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 09/24/2019] [Indexed: 05/17/2023]
Abstract
Microbial communities play essential and preponderant roles in all ecosystems. Understanding the rules that govern microbial community assembly will have a major impact on our ability to manage microbial ecosystems, positively impacting, for instance, human health and agriculture. Here, I present a phylogenetically constrained community assembly principle grounded on the well-supported facts that deterministic processes have a significant impact on microbial community assembly, that microbial communities show significant phylogenetic signal, and that microbial traits and ecological coherence are, to some extent, phylogenetically conserved. From these facts, I derive a few predictions which form the basis of the framework. Chief among them is the existence, within most microbial ecosystems, of phylogenetic core groups (PCGs), defined as discrete portions of the phylogeny of varying depth present in all instances of the given ecosystem, and related to specific niches whose occupancy requires a specific phylogenetically conserved set of traits. The predictions are supported by the recent literature, as well as by dedicated analyses. Integrating the effect of ecosystem patchiness, microbial social interactions, and scale sampling pitfalls takes us to a comprehensive community assembly model that recapitulates the characteristics most commonly observed in microbial communities. PCGs' identification is relatively straightforward using high-throughput 16S amplicon sequencing, and subsequent bioinformatic analysis of their phylogeny, estimated core pan-genome, and intra-group co-occurrence should provide valuable information on their ecophysiology and niche characteristics. Such a priori information for a significant portion of the community could be used to prime complementing analyses, boosting their usefulness. Thus, the use of the proposed framework could represent a leap forward in our understanding of microbial community assembly and function.
Collapse
|
138
|
Cosetta CM, Wolfe BE. Causes and consequences of biotic interactions within microbiomes. Curr Opin Microbiol 2019; 50:35-41. [PMID: 31627129 DOI: 10.1016/j.mib.2019.09.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Revised: 08/20/2019] [Accepted: 09/06/2019] [Indexed: 10/25/2022]
Abstract
An integrative pattern-process-mechanism approach is revealing the roles of biotic interactions in microbiome assembly. Patterns of microbiome diversity observed in metagenomic studies can be partly explained by interaction processes (e.g. competition, facilitation) and underlying molecular or genetic mechanisms (e.g. antibiotic production, nutrient cross-feeding). Exciting opportunities remain to fully understand the significance and generalizability of biotic interactions within microbiomes. Many microbial interactions have been studied by chasing easily quantifiable phenotypes including changes in growth or pigmentation, but it is likely that diverse cryptic interactions occur without obvious growth changes or macroscopic phenotypes. A narrow phylogenetic breadth of well-studied microbes limits our understanding of whether there are conserved genetic or molecular mechanisms of microbial interactions. Biotic interactions can impose strong selective pressures that could shape rates and modes of microbial evolution, but few studies have examined the evolutionary consequences of interactions within microbiomes. Continued exploration of the chemical and genetic mechanisms underlying biotic interactions may provide novel tools to manipulate and manage microbiomes.
Collapse
Affiliation(s)
- Casey M Cosetta
- Tufts University, Department of Biology, Medford, MA 02155, United States
| | - Benjamin E Wolfe
- Tufts University, Department of Biology, Medford, MA 02155, United States.
| |
Collapse
|
139
|
Petersen IAB, Meyer KM, Bohannan BJM. Meta-Analysis Reveals Consistent Bacterial Responses to Land Use Change Across the Tropics. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00391] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|
140
|
Salmaso N. Effects of Habitat Partitioning on the Distribution of Bacterioplankton in Deep Lakes. Front Microbiol 2019; 10:2257. [PMID: 31636614 PMCID: PMC6788347 DOI: 10.3389/fmicb.2019.02257] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 09/17/2019] [Indexed: 12/04/2022] Open
Abstract
In deep lakes, many investigations highlighted the existence of exclusive groups of bacteria adapted to deep oxygenated and hypoxic and anoxic hypolimnia. Nevertheless, the extent of bacterial strain diversity has been much less scrutinized. This aspect is essential for an unbiased estimation of genetic variation, biodiversity, and population structure, which are essential for studying important research questions such as biogeographical patterns, temporal and spatial variability and the environmental factors affecting this variability. This study investigated the bacterioplankton community in the epilimnetic layers and in the oxygenated and hypoxic/anoxic hypolimnia of five large and deep lakes located at the southern border of the Alps using high throughput sequencing (HTS) analyses (16S rDNA) and identification of amplicon sequence variants (ASVs) resolving reads differing by as little as one nucleotide. The study sites, which included two oligomictic (Garda and Como) and three meromictic lakes (Iseo, Lugano, and Idro) with maximum depths spanning from 124 to 410 m, were chosen among large lakes to represent an oxic-hypoxic gradient. The analyses showed the existence of several unique ASVs in the three layers of the five lakes. In the case of cyanobacteria, this confirmed previous analyses made at the level of strains or based on oligotyping methods. As expected, the communities in the hypoxic/anoxic monimolimnia showed a strong differentiation from the oxygenated layer, with the exclusive presence in single lakes of several unique ASVs. In the meromictic lakes, results supported the hypothesis that the formation of isolated monimolimnia sustained the development of highly diversified bacterial communities through ecological selection, leading to the establishment of distinctive biodiversity zones. The genera identified in these layers are well-known to activate a wide range of redox reactions at low O2 conditions. As inferred from 16S rDNA data, the highly diversified and coupled processes sustained by the monimolimnetic microbiota are essential ecosystem services that enhance mineralization of organic matter and formation of reduced compounds, and also abatement of undesirable greenhouse gasses.
Collapse
Affiliation(s)
- Nico Salmaso
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| |
Collapse
|
141
|
Rizo EZ, Xu S, Tang Q, Papa RDS, Dumont HJ, Qian SS, Han BP. A global analysis of cladoceran body size and its variation linking to habitat, distribution and taxonomy. Zool J Linn Soc 2019. [DOI: 10.1093/zoolinnean/zlz053] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
Body size is a functional trait that influences the overall biology and ecology of an organism. Studying the shape of size–frequency distributions and size variability within different scales, approximates the influence of large-scale ecological and evolutionary processes on a species. In this study we examine the patterns of distribution and variability of body size among freshwater Cladocera across different taxonomic levels, geographic distribution and habitat association. Using extensive literature data, we show the global distribution of body size in freshwater Cladocera. Hierarchical models were used to assess the effect of different categorical variables on size variability. Our results show that almost all size–frequency distributions were skewed right in all categories. The hierarchical model showed that taxonomic affiliation contributes the most to size variability in our dataset, suggesting that size might be a conserved trait. Large genera (≥1mm) have larger estimated variability compared to smaller genera. In general, our observations on size–frequency distributions and size variability show a brief insight in the varying advantages of adaptive body size in this group of organisms in both biology (physiology) and ecology (competition and co-existence). Thus, body size is a trait important to the survival and continuing evolution of Cladocera.
Collapse
Affiliation(s)
- Eric Zeus Rizo
- Department of Ecology, Institute of Hydrobiology, College of Life Sciences and Technology, Jinan University, Guangzhou, Guangdong, People’s Republic of China
| | - Shaolin Xu
- Department of Ecology, Institute of Hydrobiology, College of Life Sciences and Technology, Jinan University, Guangzhou, Guangdong, People’s Republic of China
| | - Quehui Tang
- Department of Ecology, Institute of Hydrobiology, College of Life Sciences and Technology, Jinan University, Guangzhou, Guangdong, People’s Republic of China
| | - Rey Donne S Papa
- Department of Biological Sciences, College of Science, The Graduate School and Research Center for the Natural and Applied Sciences, University of Santo Tomas, Manila, Philippines
| | - Henri J Dumont
- Department of Ecology, Institute of Hydrobiology, College of Life Sciences and Technology, Jinan University, Guangzhou, Guangdong, People’s Republic of China
| | - Song S Qian
- Department of Environmental Sciences, The University of Toledo, Toledo, OH, USA
| | - Bo-Ping Han
- Department of Ecology, Institute of Hydrobiology, College of Life Sciences and Technology, Jinan University, Guangzhou, Guangdong, People’s Republic of China
| |
Collapse
|
142
|
Kivlin SN, Kazenel MR, Lynn JS, Lee Taylor D, Rudgers JA. Plant Identity Influences Foliar Fungal Symbionts More Than Elevation in the Colorado Rocky Mountains. MICROBIAL ECOLOGY 2019; 78:688-698. [PMID: 30715579 DOI: 10.1007/s00248-019-01336-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 01/22/2019] [Indexed: 06/09/2023]
Abstract
Despite colonizing nearly every plant on Earth, foliar fungal symbionts have received little attention in studies on the biogeography of host-associated microbes. Evidence from regional scale studies suggests that foliar fungal symbiont distributions are influenced both by plant hosts and environmental variation in climate and soil resources. However, previous surveys have focused on either one plant host across an environmental gradient or one gradient and multiple plant hosts, making it difficult to disentangle the influence of host identity from the influence of the environment on foliar endophyte communities. We used a culture-based approach to survey fungal symbiont composition in the leaves of nine C3 grass species along replicated elevation gradients in grasslands of the Colorado Rocky Mountains. In these ecosystems, the taxonomic richness and composition of foliar fungal symbionts were mostly structured by the taxonomic identity of the plant host rather than by variation in climate. Plant traits related to size (height and leaf length) were the best predictors of foliar fungal symbiont composition and diversity, and composition did not vary predictably with plant evolutionary history. The largest plants had the most diverse and distinctive fungal communities. These results suggest that across the ~ 300 m elevation range that we sampled, foliar fungal symbionts may indirectly experience climate change by tracking the shifting distributions of plant hosts rather than tracking climate directly.
Collapse
Affiliation(s)
- Stephanie N Kivlin
- Department of Biology, University of New Mexico, Albuquerque, NM, 87114, USA.
- Rocky Mountain Biological Laboratory, Crested Butte, CO, 81224, USA.
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN, 37996, USA.
| | - Melanie R Kazenel
- Department of Biology, University of New Mexico, Albuquerque, NM, 87114, USA
- Rocky Mountain Biological Laboratory, Crested Butte, CO, 81224, USA
| | - Joshua S Lynn
- Department of Biology, University of New Mexico, Albuquerque, NM, 87114, USA
- Rocky Mountain Biological Laboratory, Crested Butte, CO, 81224, USA
| | - D Lee Taylor
- Department of Biology, University of New Mexico, Albuquerque, NM, 87114, USA
| | - Jennifer A Rudgers
- Department of Biology, University of New Mexico, Albuquerque, NM, 87114, USA
- Rocky Mountain Biological Laboratory, Crested Butte, CO, 81224, USA
| |
Collapse
|
143
|
Wang JT, Egidi E, Li J, Singh BK. Linking microbial diversity with ecosystem functioning through a trait framework. J Biosci 2019; 44:109. [PMID: 31719218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Trait-based microbial biogeography provides a path for the mechanistic understanding of relationships between microbial diversity and ecosystem functioning. In this mini-review, we identify the scenarios in which to use traits to characterize the microbial community and propose a simple trait-based conceptual framework to link microbial communities with ecosystem functions.
Collapse
Affiliation(s)
- Jun-Tao Wang
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW 2753, Australia
| | | | | | | |
Collapse
|
144
|
Goberna M, Montesinos‐Navarro A, Valiente‐Banuet A, Colin Y, Gómez‐Fernández A, Donat S, Navarro‐Cano JA, Verdú M. Incorporating phylogenetic metrics to microbial co‐occurrence networks based on amplicon sequences to discern community assembly processes. Mol Ecol Resour 2019; 19:1552-1564. [DOI: 10.1111/1755-0998.13079] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 07/29/2019] [Accepted: 08/07/2019] [Indexed: 12/21/2022]
Affiliation(s)
- Marta Goberna
- Department of Environment and Agronomy Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA) Madrid Spain
- Department of Ecology Centro de Investigaciones sobre Desertificación (CIDE ‐ CSIC) Moncada Spain
| | | | - Alfonso Valiente‐Banuet
- Instituto de Ecología Universidad Nacional Autónoma de México Mexico D.F. Mexico
- Centro de Ciencias de la Complejidad Ciudad Universitaria Universidad Nacional Autónoma de México Mexico D.F. Mexico
| | - Yannick Colin
- Department of Ecology Centro de Investigaciones sobre Desertificación (CIDE ‐ CSIC) Moncada Spain
| | - Alicia Gómez‐Fernández
- Department of Ecology Centro de Investigaciones sobre Desertificación (CIDE ‐ CSIC) Moncada Spain
| | - Santiago Donat
- Department of Ecology Centro de Investigaciones sobre Desertificación (CIDE ‐ CSIC) Moncada Spain
| | - Jose A. Navarro‐Cano
- Department of Ecology Centro de Investigaciones sobre Desertificación (CIDE ‐ CSIC) Moncada Spain
| | - Miguel Verdú
- Department of Ecology Centro de Investigaciones sobre Desertificación (CIDE ‐ CSIC) Moncada Spain
| |
Collapse
|
145
|
|
146
|
Quantitatively Partitioning Microbial Genomic Traits among Taxonomic Ranks across the Microbial Tree of Life. mSphere 2019; 4:4/4/e00446-19. [PMID: 31462411 PMCID: PMC6714891 DOI: 10.1128/msphere.00446-19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Recently, there has been great progress in defining a complete taxonomy of bacteria and archaea, which has been enabled by improvements in DNA sequencing technology and new bioinformatic techniques. A new, algorithmically defined microbial tree of life describes those linkages, relying solely on genetic data, which raises the issue of how microbial traits relate to taxonomy. Here, we adopted cluster of orthologous group functional categories as a scheme to describe the genomic contents of microbes, a method that can be applied to any microbial lineage for which genomes are available. This simple approach allows quantitative comparisons between microbial genomes with different gene compositions from across the microbial tree of life. Our observations demonstrate statistically significant patterns in cluster of orthologous group functional categories at taxonomic levels that span the range from domain to genus. Widely used microbial taxonomies, such as the NCBI taxonomy, are based on a combination of sequence homology among conserved genes and historically accepted taxonomies, which were developed based on observable traits such as morphology and physiology. A recently proposed alternative taxonomy database, the Genome Taxonomy Database (GTDB), incorporates only sequence homology of conserved genes and attempts to partition taxonomic ranks such that each rank implies the same amount of evolutionary distance, regardless of its position on the phylogenetic tree. This provides the first opportunity to completely separate taxonomy from traits and therefore to quantify how taxonomic rank corresponds to traits across the microbial tree of life. We quantified the relative abundances of clusters of orthologous group functional categories (COG-FCs) as a proxy for traits within the lineages of 13,735 cultured and uncultured microbial lineages from a custom-curated genome database. On average, 41.4% of the variation in COG-FC relative abundance is explained by taxonomic rank, with domain, phylum, class, order, family, and genus explaining, on average, 3.2%, 14.6%, 4.1%, 9.2%, 4.8%, and 5.5% of the variance, respectively (P < 0.001 for all). To our knowledge, this is the first work to quantify the variance in metabolic potential contributed by individual taxonomic ranks. A qualitative comparison between the COG-FC relative abundances and genus-level phylogenies, generated from published concatenated protein sequence alignments, further supports the idea that metabolic potential is taxonomically coherent at higher taxonomic ranks. The quantitative analyses presented here characterize the integral relationship between diversification of microbial lineages and the metabolisms which they host. IMPORTANCE Recently, there has been great progress in defining a complete taxonomy of bacteria and archaea, which has been enabled by improvements in DNA sequencing technology and new bioinformatic techniques. A new, algorithmically defined microbial tree of life describes those linkages, relying solely on genetic data, which raises the issue of how microbial traits relate to taxonomy. Here, we adopted cluster of orthologous group functional categories as a scheme to describe the genomic contents of microbes, a method that can be applied to any microbial lineage for which genomes are available. This simple approach allows quantitative comparisons between microbial genomes with different gene compositions from across the microbial tree of life. Our observations demonstrate statistically significant patterns in cluster of orthologous group functional categories at taxonomic levels that span the range from domain to genus.
Collapse
|
147
|
Buzzard V, Michaletz ST, Deng Y, He Z, Ning D, Shen L, Tu Q, Van Nostrand JD, Voordeckers JW, Wang J, Weiser MD, Kaspari M, Waide RB, Zhou J, Enquist BJ. Continental scale structuring of forest and soil diversity via functional traits. Nat Ecol Evol 2019; 3:1298-1308. [DOI: 10.1038/s41559-019-0954-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Accepted: 06/25/2019] [Indexed: 11/09/2022]
|
148
|
Microbial carbon use efficiency predicted from genome-scale metabolic models. Nat Commun 2019; 10:3568. [PMID: 31395870 PMCID: PMC6687798 DOI: 10.1038/s41467-019-11488-z] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 06/28/2019] [Indexed: 12/18/2022] Open
Abstract
Respiration by soil bacteria and fungi is one of the largest fluxes of carbon (C) from the land surface. Although this flux is a direct product of microbial metabolism, controls over metabolism and their responses to global change are a major uncertainty in the global C cycle. Here, we explore an in silico approach to predict bacterial C-use efficiency (CUE) for over 200 species using genome-specific constraint-based metabolic modeling. We find that potential CUE averages 0.62 ± 0.17 with a range of 0.22 to 0.98 across taxa and phylogenetic structuring at the subphylum levels. Potential CUE is negatively correlated with genome size, while taxa with larger genomes are able to access a wider variety of C substrates. Incorporating the range of CUE values reported here into a next-generation model of soil biogeochemistry suggests that these differences in physiology across microbial taxa can feed back on soil-C cycling.
Collapse
|
149
|
Auladell A, Sánchez P, Sánchez O, Gasol JM, Ferrera I. Long-term seasonal and interannual variability of marine aerobic anoxygenic photoheterotrophic bacteria. THE ISME JOURNAL 2019; 13:1975-1987. [PMID: 30914777 PMCID: PMC6776013 DOI: 10.1038/s41396-019-0401-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 02/21/2019] [Accepted: 03/06/2019] [Indexed: 01/22/2023]
Abstract
We studied the long-term temporal dynamics of the aerobic anoxygenic phototrophic (AAP) bacteria, a relevant functional group in the coastal marine microbial food web, using high-throughput sequencing of the pufM gene coupled with multivariate, time series and co-occurrence analyses at the Blanes Bay Microbial Observatory (NW Mediterranean). Additionally, using metagenomics, we tested whether the used primers captured accurately the seasonality of the most relevant AAP groups. Phylogroup K (Gammaproteobacteria) was the greatest contributor to community structure over all seasons, with phylogroups E and G (Alphaproteobacteria) being prevalent in spring. Diversity indices showed a clear seasonal trend, with maximum values in winter, which was inverse to that of AAP abundance. Multivariate analyses revealed sample clustering by season, with a relevant proportion of the variance explained by day length, temperature, salinity, phototrophic nanoflagellate abundance, chlorophyll a, and silicate concentration. Time series analysis showed robust rhythmic patterns of co-occurrence, but distinct seasonal behaviors within the same phylogroup, and even within different amplicon sequence variants (ASVs) conforming the same operational taxonomic unit (OTU). Altogether, our results picture the AAP assemblage as highly seasonal and recurrent but containing ecotypes showing distinctive temporal niche partitioning, rather than being a cohesive functional group.
Collapse
Affiliation(s)
- Adrià Auladell
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM-CSIC), Pg Marítim de la Barceloneta, 37-49, Barcelona, Catalunya, Spain.
| | - Pablo Sánchez
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM-CSIC), Pg Marítim de la Barceloneta, 37-49, Barcelona, Catalunya, Spain
| | - Olga Sánchez
- Department of Genetics and Microbiology, Universitat Autònoma de Barcelona (UAB), Bellaterra, Catalunya, Spain
| | - Josep M Gasol
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM-CSIC), Pg Marítim de la Barceloneta, 37-49, Barcelona, Catalunya, Spain
- Centre for Marine Ecosystems Research, School of Science, Edith Cowan University, Joondalup, WA, Australia
| | - Isabel Ferrera
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM-CSIC), Pg Marítim de la Barceloneta, 37-49, Barcelona, Catalunya, Spain.
- Centro Oceanográfico de Málaga, Instituto Español de Oceanografía, Fuengirola, Málaga, Spain.
| |
Collapse
|
150
|
Zhao XF, Hao YQ, Zhang DY, Zhang QG. Local biotic interactions drive species-specific divergence in soil bacterial communities. ISME JOURNAL 2019; 13:2846-2855. [PMID: 31358911 DOI: 10.1038/s41396-019-0477-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 06/23/2019] [Accepted: 07/05/2019] [Indexed: 11/09/2022]
Abstract
It is well accepted that environmental heterogeneity and dispersal are key factors determining soil bacterial community composition, yet little is known about the role of local biotic interactions. Here we address this issue with an abundance-manipulation experiment that was conducted in a semiarid grassland. We manually increased the abundance of six randomly chosen resident bacterial species in separate, closed, communities and allowed the communities to recover in situ for 1 year. The single episode of increase in the abundance of different species drove species-specific community divergence accompanied by a decline in local diversity. Four of the six added species caused a decrease in the abundance of their closely related species, suggesting an important role of interspecific competition in driving the observed community divergence. Our results also suggested a lack of effective population regulations to force the relative abundance of manipulated species to revert to original level, which would allow persistence of the divergence among soil bacterial communities. We concluded that biotic interactions were important in determining soil bacterial community composition, which could result in substantial variation in soil bacterial community composition in abiotically homogenous environment.
Collapse
Affiliation(s)
- Xin-Feng Zhao
- School of Life Sciences, South China Normal University, Guangzhou, 510631, Guangdong, China.,State Key Laboratory of Earth Surface Processes and Resource Ecology and MOE Key Laboratory for Biodiversity Science and Ecological Engineering, Beijing Normal University, Beijing, 100875, China
| | - Yi-Qi Hao
- School of Life Sciences, South China Normal University, Guangzhou, 510631, Guangdong, China. .,State Key Laboratory of Earth Surface Processes and Resource Ecology and MOE Key Laboratory for Biodiversity Science and Ecological Engineering, Beijing Normal University, Beijing, 100875, China.
| | - Da-Yong Zhang
- State Key Laboratory of Earth Surface Processes and Resource Ecology and MOE Key Laboratory for Biodiversity Science and Ecological Engineering, Beijing Normal University, Beijing, 100875, China
| | - Quan-Guo Zhang
- State Key Laboratory of Earth Surface Processes and Resource Ecology and MOE Key Laboratory for Biodiversity Science and Ecological Engineering, Beijing Normal University, Beijing, 100875, China
| |
Collapse
|