151
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Greslehner GP. Not by structures alone: Can the immune system recognize microbial functions? STUDIES IN HISTORY AND PHILOSOPHY OF BIOLOGICAL AND BIOMEDICAL SCIENCES 2020; 84:101336. [PMID: 32830048 DOI: 10.1016/j.shpsc.2020.101336] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 07/10/2020] [Accepted: 07/13/2020] [Indexed: 06/11/2023]
Abstract
A central question for immunology is: what does the immune system recognize and according to which principles does this kind of recognition work? Immunology has been dominated by the idea of recognizing molecular structures and triggering an appropriate immune response when facing non-self or danger. Recently, characterizations in terms of function have turned out to be more conserved and explanatory in microbiota research than taxonomic composition for understanding microbiota-host interactions. Starting from a conceptual analysis of the notions of structure and function, I raise the title question whether it is possible for the immune system to recognize microbial functions. I argue that this is indeed the case, making the claim that some function-associated molecular patterns are not indicative of the presence of certain taxa (''who is there'') but of biochemical activities and effects (''what is going on''). In addition, I discuss case studies which show that there are immunological sensors that can directly detect microbial activities, irrespective of their specific structural manifestation. At the same time, the discussed account puts the causal role notions of function on a more realist and objective basis.
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Affiliation(s)
- Gregor P Greslehner
- ImmunoConcept, UMR5164, CNRS & University of Bordeaux, 146 Rue Léo Saignat, 33076, Bordeaux, France.
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152
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Ihua MW, FitzGerald JA, Guihéneuf F, Jackson SA, Claesson MJ, Stengel DB, Dobson ADW. Diversity of bacteria populations associated with different thallus regions of the brown alga Laminaria digitata. PLoS One 2020; 15:e0242675. [PMID: 33237941 PMCID: PMC7688147 DOI: 10.1371/journal.pone.0242675] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 11/08/2020] [Indexed: 12/20/2022] Open
Abstract
Stipitate kelp species such as Laminaria digitata dominate most cold-water subtidal rocky shores and form underwater forests which are among the most productive coastal systems worldwide. Laminaria also sustains rich bacterial communities which offer a variety of biotechnological applications. However, to date, in-depth studies on the diversity and uniqueness of bacterial communities associated with this macroalgal species, their ecological role and their interactions with the alga are under-represented. To address this, the epibacterial populations associated with different thallus regions (holdfast, stipe, meristem, blade) of this brown seaweed were investigated using high-throughput Illumina sequencing of the 16S rRNA genes. The results show that epibacterial communities of the brown seaweed are significantly different and specific to the thallus region, with the shared bacterial population comprising of only 1.1% of the total amplicon sequence variants. The diverse holdfast and blade tissues formed distinct clusters while the meristem and stipe regions are more closely related. The data obtained further supports the hypothesis that macroalgal bacterial communities are shaped by morphological niches and display specificity.
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Affiliation(s)
- Maureen W. Ihua
- School of Microbiology, University College Cork, Cork, Ireland
| | - Jamie A. FitzGerald
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | | | | | - Marcus J. Claesson
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Dagmar B. Stengel
- Botany and Plant Science, School of Natural Sciences, Ryan Institute for Environmental, Marine and Energy Research, National University of Ireland Galway, Galway, Ireland
| | - Alan D. W. Dobson
- School of Microbiology, University College Cork, Cork, Ireland
- Environmental Research Institute, University College Cork, Cork, Ireland
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153
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Estrada-Peña A, Cabezas-Cruz A, Obregón D. Behind Taxonomic Variability: The Functional Redundancy in the Tick Microbiome. Microorganisms 2020; 8:E1829. [PMID: 33233565 PMCID: PMC7699746 DOI: 10.3390/microorganisms8111829] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 11/17/2020] [Accepted: 11/18/2020] [Indexed: 12/30/2022] Open
Abstract
The taxonomic composition and diversity of tick midgut microbiota have been extensively studied in different species of the genera Rhipicephalus, Ixodes, Amblyomma, Haemaphysalis, Hyalomma, Dermacentor, Argas and Ornithodoros, while the functional significance of bacterial diversity has been proportionally less explored. In this study, we used previously published 16S amplicon sequence data sets from three Ixodes scapularis cohorts, two of uninfected nymphs, and one of larvae experimentally infected with Borrelia burgdorferi, to test the functional redundancy of the tick microbiome. We predicted the metabolic profiling of each sample using the state-of-the-art metagenomics tool PICRUSt2. The results showed that the microbiomes of all I. scapularis samples share only 80 taxa (24.6%, total 324), while out of the 342 metabolic pathways predicted, 82.7%, were shared by all the ticks. Borrelia-infected larvae lack 15.4% of pathways found in the microbiome of uninfected nymphs. Taxa contribution analysis showed that the functional microbiome of uninfected ticks was highly redundant, with, in some cases, up to 198 bacterial taxa contributing to a single pathway. However, Borrelia-infected larvae had a smaller redundancy with 6.7% of pathways provided by more than 100 genera, while 15.7-19.2% of pathways were provided by more than 100 genera in the two cohorts of uninfected ticks. In addition, we compared the functional profiles of three microbial communities from each data set, identified through a network-based approach, and we observed functional similarity between them. Based on the functional redundancy and functional similarity of the microbiome of ticks in different developmental stages and infection status, we concluded that the tick gut microbiota is a self-regulating community of very diverse bacteria contributing to a defined set of metabolic pathways and functions with yet unexplored relevance for tick fitness and/or bacterial community stability. We propose a change of focus in which the tick microbiome must be analyzed in all dimensions, highlighting their functional traits, instead of the conventional taxonomic profiling.
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Affiliation(s)
| | - Alejandro Cabezas-Cruz
- UMR BIPAR, INRAE, ANSES, Ecole Nationale Vétérinaire d’Alfort, Université Paris-Est, 94700 Maisons-Alfort, France;
| | - Dasiel Obregón
- Center for Nuclear Energy in Agriculture, University of Sao Paulo, Piracicaba, São Paulo 13400-970, Brazil
- School of Environmental Sciences, University of Guelph, Guelph, ON N1G 2W1, Canada
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154
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Renoud S, Bouffaud ML, Dubost A, Prigent-Combaret C, Legendre L, Moënne-Loccoz Y, Muller D. Co-occurrence of rhizobacteria with nitrogen fixation and/or 1-aminocyclopropane-1-carboxylate deamination abilities in the maize rhizosphere. FEMS Microbiol Ecol 2020; 96:5818760. [PMID: 32275303 DOI: 10.1093/femsec/fiaa062] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 04/01/2020] [Indexed: 12/20/2022] Open
Abstract
The plant microbiota may differ depending on soil type, but these microbiota probably share the same functions necessary for holobiont fitness. Thus, we tested the hypothesis that phytostimulatory microbial functional groups are likely to co-occur in the rhizosphere, using groups corresponding to nitrogen fixation (nifH) and 1-aminocyclopropane-1-carboxylate deamination (acdS), i.e. two key modes of action in plant-beneficial rhizobacteria. The analysis of three maize fields in two consecutive years showed that quantitative PCR numbers of nifH and of acdS alleles differed according to field site, but a positive correlation was found overall when comparing nifH and acdS numbers. Metabarcoding analyses in the second year indicated that the diversity level of acdS but not nifH rhizobacteria in the rhizosphere differed across fields. Furthermore, between-class analysis showed that the three sites differed from one another based on nifH or acdS sequence data (or rrs data), and the bacterial genera contributing most to field differentiation were not the same for the three bacterial groups. However, co-inertia analysis indicated that the genetic structures of both functional groups and of the whole bacterial community were similar across the three fields. Therefore, results point to co-selection of rhizobacteria harboring nitrogen fixation and/or 1-aminocyclopropane-1-carboxylate deamination abilities.
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Affiliation(s)
- Sébastien Renoud
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, 43 bd du 11 novembre 1918, F-69622 Villeurbanne, France
| | - Marie-Lara Bouffaud
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, 43 bd du 11 novembre 1918, F-69622 Villeurbanne, France
| | - Audrey Dubost
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, 43 bd du 11 novembre 1918, F-69622 Villeurbanne, France
| | - Claire Prigent-Combaret
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, 43 bd du 11 novembre 1918, F-69622 Villeurbanne, France
| | - Laurent Legendre
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, 43 bd du 11 novembre 1918, F-69622 Villeurbanne, France.,Univ Lyon, Université de St Etienne, 10, Rue Tréfilerie - F-42023 Saint-Etienne, France
| | - Yvan Moënne-Loccoz
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, 43 bd du 11 novembre 1918, F-69622 Villeurbanne, France
| | - Daniel Muller
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, 43 bd du 11 novembre 1918, F-69622 Villeurbanne, France
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155
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Stencel A. Do seasonal microbiome changes affect infection susceptibility, contributing to seasonal disease outbreaks? Bioessays 2020; 43:e2000148. [PMID: 33165975 DOI: 10.1002/bies.202000148] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 09/24/2020] [Accepted: 09/29/2020] [Indexed: 12/13/2022]
Abstract
The aim of the present paper is to explore whether seasonal outbreaks of infectious diseases may be linked to changes in host microbiomes. This is a very important issue, because one way to have more control over seasonal outbreaks is to understand the factors that underlie them. In this paper, I will evaluate the relevance of the microbiome as one of such factors. The paper is based on two pillars of reasoning. Firstly, on the idea that microbiomes play an important role in their hosts' defence against infectious diseases. Secondly, on the idea that microbiomes are not stable, but change seasonally. These two ideas are combined in order to argue that seasonal changes in a given microbiome may influence the functionality of the host's immune system and consequently make it easier for infectious agents to infect the host at certain times of year. I will argue that, while this is only a theoretical possibility, certain studies may back up such claims. Furthermore, I will show that this does not necessarily contradict other hypotheses aimed at explaining seasonal outbreaks; in fact, it may even enhance them.
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Affiliation(s)
- Adrian Stencel
- Institute of Philosophy, Jagiellonian University, Kraków, Poland
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156
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Louca S, Rubin IN, Madilao LL, Bohlmann J, Doebeli M, Wegener Parfrey L. Effects of forced taxonomic transitions on metabolic composition and function in microbial microcosms. ENVIRONMENTAL MICROBIOLOGY REPORTS 2020; 12:514-524. [PMID: 32618124 DOI: 10.1111/1758-2229.12866] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Accepted: 06/29/2020] [Indexed: 06/11/2023]
Abstract
Surveys of microbial systems indicate that in many situations taxonomy and function may constitute largely independent ('decoupled') axes of variation. However, this decoupling is rarely explicitly tested experimentally, partly because it is hard to directly induce taxonomic variation without affecting functional composition. Here we experimentally evaluate this paradigm using microcosms resembling lake sediments and subjected to two different levels of salinity (0 and 19) and otherwise similar environmental conditions. We used DNA sequencing for taxonomic and functional profiling of bacteria and archaea and physicochemical measurements to monitor metabolic function, over 13 months. We found that the taxonomic composition of the saline systems gradually but strongly diverged from the fresh systems. In contrast, the metabolic composition (in terms of proportions of various genes) remained nearly identical across treatments and over time. Oxygen consumption rates and methane concentrations were substantially lower in the saline treatment, however, their similarity either increased (for oxygen) or did not change significantly (for methane) between the first and last sampling time, indicating that the lower metabolic activity in the saline treatments was directly and immediately caused by salinity rather than the gradual taxonomic divergence. Our experiment demonstrates that strong taxonomic shifts need not directly affect metabolic rates.
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Affiliation(s)
- Stilianos Louca
- Department of Biology, University of Oregon, Eugene, OR, USA
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
| | - Ilan N Rubin
- Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
- Department of Zoology, University of British Columbia, Vancouver, BC, Canada
| | - Lufiani L Madilao
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
- Wine Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Jörg Bohlmann
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
- Wine Research Centre, University of British Columbia, Vancouver, BC, Canada
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - Michael Doebeli
- Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
- Department of Zoology, University of British Columbia, Vancouver, BC, Canada
- Department of Mathematics, University of British Columbia, Vancouver, BC, Canada
| | - Laura Wegener Parfrey
- Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
- Department of Zoology, University of British Columbia, Vancouver, BC, Canada
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
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157
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Grajal-Puche A, Murray CM, Kearley M, Merchant M, Nix C, Warner JK, Walker DM. Microbial Assemblage Dynamics Within the American Alligator Nesting Ecosystem: a Comparative Approach Across Ecological Scales. MICROBIAL ECOLOGY 2020; 80:603-613. [PMID: 32424717 DOI: 10.1007/s00248-020-01522-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 05/05/2020] [Indexed: 06/11/2023]
Abstract
Understanding the ecological processes that shape species assemblage patterns is central to community ecology. The effects of ecological processes on assemblage patterns are scale-dependent. We used metabarcoding and shotgun sequencing to determine bacterial taxonomic and functional assemblage patterns among varying defined focal scales (micro-, meso-, and macroscale) within the American alligator (Alligator mississippiensis) nesting microbiome. We correlate bacterial assemblage patterns among eight nesting compartments within and proximal to alligator nests (micro-), across 18 nests (meso-), and between 4 geographic sampling sites (macro-), to determine which ecological processes may drive bacterial assemblage patterns within the nesting environment. Among all focal scales, bacterial taxonomic and functional richness (α-diversity) did not statistically differ. In contrast, bacterial assemblage structure (β-diversity) was unique across all focal scales, whereas functional pathways were redundant within nests and across geographic sites. Considering these observed scale-based patterns, taxonomic bacterial composition may be governed by unique environmental filters and dispersal limitations relative to microbial functional attributes within the alligator nesting environment. These results advance pattern-process dynamics within the field of microbial community ecology and describe processes influencing the American alligator nest microbiome.
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Affiliation(s)
| | - Christopher M Murray
- Department of Biological Sciences, Southeastern Louisiana University, Hammond, LA, 70402, USA
- Biology Department, Tennessee Technological University, Cookeville, TN, 38505, USA
| | - Matthew Kearley
- Department of Biological Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Mark Merchant
- Department of Chemistry, McNeese State University, Lake Charles, LA, 70609, USA
| | - Christopher Nix
- Alabama Wildlife and Freshwater Fisheries Division, Montgomery, AL, 36130, USA
| | | | - Donald M Walker
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN, 37132, USA.
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158
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Lam TJ, Stamboulian M, Han W, Ye Y. Model-based and phylogenetically adjusted quantification of metabolic interaction between microbial species. PLoS Comput Biol 2020; 16:e1007951. [PMID: 33125363 PMCID: PMC7657538 DOI: 10.1371/journal.pcbi.1007951] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 11/11/2020] [Accepted: 09/10/2020] [Indexed: 11/18/2022] Open
Abstract
Microbial community members exhibit various forms of interactions. Taking advantage of the increasing availability of microbiome data, many computational approaches have been developed to infer bacterial interactions from the co-occurrence of microbes across diverse microbial communities. Additionally, the introduction of genome-scale metabolic models have also enabled the inference of cooperative and competitive metabolic interactions between bacterial species. By nature, phylogenetically similar microbial species are more likely to share common functional profiles or biological pathways due to their genomic similarity. Without properly factoring out the phylogenetic relationship, any estimation of the competition and cooperation between species based on functional/pathway profiles may bias downstream applications. To address these challenges, we developed a novel approach for estimating the competition and complementarity indices for a pair of microbial species, adjusted by their phylogenetic distance. An automated pipeline, PhyloMint, was implemented to construct competition and complementarity indices from genome scale metabolic models derived from microbial genomes. Application of our pipeline to 2,815 human-gut associated bacteria showed high correlation between phylogenetic distance and metabolic competition/cooperation indices among bacteria. Using a discretization approach, we were able to detect pairs of bacterial species with cooperation scores significantly higher than the average pairs of bacterial species with similar phylogenetic distances. A network community analysis of high metabolic cooperation but low competition reveals distinct modules of bacterial interactions. Our results suggest that niche differentiation plays a dominant role in microbial interactions, while habitat filtering also plays a role among certain clades of bacterial species.
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Affiliation(s)
- Tony J. Lam
- Luddy School of Informatics, Computing and Engineering Indiana University, Bloomington, IN, USA
| | - Moses Stamboulian
- Luddy School of Informatics, Computing and Engineering Indiana University, Bloomington, IN, USA
| | - Wontack Han
- Luddy School of Informatics, Computing and Engineering Indiana University, Bloomington, IN, USA
| | - Yuzhen Ye
- Luddy School of Informatics, Computing and Engineering Indiana University, Bloomington, IN, USA
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159
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Methe BA, Hiltbrand D, Roach J, Xu W, Gordon SG, Goodner BW, Stapleton AE. Functional gene categories differentiate maize leaf drought-related microbial epiphytic communities. PLoS One 2020; 15:e0237493. [PMID: 32946440 PMCID: PMC7500591 DOI: 10.1371/journal.pone.0237493] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 07/11/2020] [Indexed: 11/18/2022] Open
Abstract
The phyllosphere epiphytic microbiome is composed of microorganisms that colonize the external aerial portions of plants. Relationships of plant responses to specific microorganisms–both pathogenic and beneficial–have been examined, but the phyllosphere microbiome functional and metabolic profile responses are not well described. Changing crop growth conditions, such as increased drought, can have profound impacts on crop productivity. Also, epiphytic microbial communities provide a new target for crop yield optimization. We compared Zea mays leaf microbiomes collected under drought and well-watered conditions by examining functional gene annotation patterns across three physically disparate locations each with and without drought treatment, through the application of short read metagenomic sequencing. Drought samples exhibited different functional sequence compositions at each of the three field sites. Maize phyllosphere functional profiles revealed a wide variety of metabolic and regulatory processes that differed in drought and normal water conditions and provide key baseline information for future selective breeding.
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Affiliation(s)
- Barbara A. Methe
- J Craig Venter Institute, Medical Center Drive, Rockville, MD, United States of America
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, United States of America
| | - David Hiltbrand
- Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, NC, United States of America
| | - Jeffrey Roach
- Research Computing, University of North Carolina Chapel Hill, Chapel Hill, NC, United States of America
| | - Wenwei Xu
- Agricultural and Extension Center, Texas A and M AgriLife Research, Lubbock, TX, United States of America
| | - Stuart G. Gordon
- Biology Department, Presbyterian College, Clinton, SC, United States of America
| | - Brad W. Goodner
- Department, Hiram College, Hiram, OH, United States of America
| | - Ann E. Stapleton
- Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, NC, United States of America
- * E-mail:
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160
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Santillan E, Constancias F, Wuertz S. Press Disturbance Alters Community Structure and Assembly Mechanisms of Bacterial Taxa and Functional Genes in Mesocosm-Scale Bioreactors. mSystems 2020; 5:e00471-20. [PMID: 32843539 PMCID: PMC7449608 DOI: 10.1128/msystems.00471-20] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 08/03/2020] [Indexed: 12/20/2022] Open
Abstract
Press disturbances are of interest in microbial ecology, as they can drive microbial communities to alternative stable states. However, the effect of press disturbances in community assembly mechanisms, particularly with regard to taxa and functional genes at different levels of abundance (i.e., common and rare), remains largely unknown. Here, we tested the effect of a continuous alteration in substrate feeding scheme on the structure, function, and assembly of bacterial communities. Two sets of replicate 5-liter sequencing batch reactors were operated at two different organic carbon loads for a period of 74 days, following 53 days of acclimation after inoculation with sludge from a full-scale treatment plant. Temporal dynamics of community taxonomic and functional gene structure were derived from metagenomics and 16S rRNA gene metabarcoding data. Disturbed reactors exhibited different community function, structure, and assembly compared to undisturbed reactors. Bacterial taxa and functional genes showed dissimilar α-diversity and community assembly patterns. Deterministic assembly mechanisms were generally stronger in disturbed reactors and in common fractions compared to rare ones. Function quickly recovered after the disturbance was removed, but community structure did not. Our results highlight that functional gene data from metagenomics can indicate patterns of community assembly that differ from those obtained from taxon data. This study reveals how a joint evaluation of assembly mechanisms and community structure of bacterial taxa and functional genes as well as ecosystem function can unravel the response of complex microbial systems to a press disturbance.IMPORTANCE Ecosystem management must be viewed in the context of increasing frequencies and magnitudes of various disturbances that occur at different scales. This work provides a glimpse of the changes in assembly mechanisms found in microbial communities exposed to sustained changes in their environment. These mechanisms, deterministic or stochastic, can cause communities to reach a similar or variable composition and function. For a comprehensive view, we use a joint evaluation of temporal dynamics in assembly mechanisms and community structure for both bacterial taxa and their functional genes at different abundance levels, in both disturbed and undisturbed states. We further reverted the disturbance state to contrast recovery of function with community structure. Our findings are relevant, as very few studies have employed such an approach, while there is a need to assess the relative importance of assembly mechanisms for microbial communities across different spatial and temporal scales, environmental gradients, and types of disturbance.
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Affiliation(s)
- Ezequiel Santillan
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
- Department of Civil and Environmental Engineering, University of California, Davis, California, USA
| | - Florentin Constancias
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
| | - Stefan Wuertz
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
- Department of Civil and Environmental Engineering, University of California, Davis, California, USA
- School of Civil and Environmental Engineering, Nanyang Technological University, Singapore
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161
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Grisnik M, Bowers O, Moore AJ, Jones BF, Campbell JR, Walker DM. The cutaneous microbiota of bats has in vitro antifungal activity against the white nose pathogen. FEMS Microbiol Ecol 2020; 96:5710932. [PMID: 31960913 DOI: 10.1093/femsec/fiz193] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 01/20/2020] [Indexed: 01/31/2023] Open
Abstract
Since its introduction into the USA, Pseudogymnoascus destructans (Pd), the fungal pathogen of white-nose syndrome, has killed millions of bats. Recently, bacteria capable of inhibiting the growth of Pd have been identified within bat microbial assemblages, leading to increased interest in elucidating bacterial assemblage-pathogen interactions. Our objectives were to determine if bat cutaneous bacteria have antifungal activity against Pd, and correlate differences in the bat cutaneous microbiota with the presence/absence of Pd. We hypothesized that the cutaneous microbiota of bats is enriched with antifungal bacteria, and that the skin assemblage will correlate with Pd status. To test this, we sampled bat microbiota, adjacent roost surfaces and soil from Pd positive caves to infer possible overlap of antifungal taxa, we tested these bacteria for bioactivity in vitro, and lastly compared bacterial assemblages using both amplicon and shotgun high-throughput DNA sequencing. Results suggest that the presence of Pd has an inconsistent influence on the bat cutaneous microbial assemblage across sites. Operational taxonomic units (OTUs) that corresponded with cultured antifungal bacteria were present within all sample types but were significantly more abundant on bat skin relative to the environment. Additionally, the microbial assemblage of Pd negative bats was found to have more OTUs that corresponded to antifungal taxa than positive bats, suggesting an interaction between the fungal pathogen and cutaneous microbial assemblage.
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Affiliation(s)
- Matthew Grisnik
- Middle Tennessee State University, Toxicology and Disease Group, Biology Department, 1672 Greenland Drive, Murfreesboro, Tennessee 37132, USA
| | - Olivia Bowers
- Middle Tennessee State University, Toxicology and Disease Group, Biology Department, 1672 Greenland Drive, Murfreesboro, Tennessee 37132, USA
| | - Andrew J Moore
- Tennessee Technological University, Department of Biological Sciences, 1100 N. Dixie Ave, Cookeville, Tennessee 38505, USA
| | - Benjamin F Jones
- Tennessee Technological University, Department of Biological Sciences, 1100 N. Dixie Ave, Cookeville, Tennessee 38505, USA
| | - Joshua R Campbell
- Tennessee Wildlife Resources Agency, 5105 Edmondson Pike, Nashville, Tennessee 37211, USA
| | - Donald M Walker
- Middle Tennessee State University, Toxicology and Disease Group, Biology Department, 1672 Greenland Drive, Murfreesboro, Tennessee 37132, USA
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162
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Metagenomic profiling of the community structure, diversity, and nutrient pathways of bacterial endophytes in maize plant. Antonie van Leeuwenhoek 2020; 113:1559-1571. [PMID: 32803452 DOI: 10.1007/s10482-020-01463-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 07/11/2020] [Indexed: 01/06/2023]
Abstract
This study investigated the diversity, structure and nutrient pathways of the root-associated bacterial endophytes of maize plant cultivated using different fertilizers to verify the claim that inorganic fertilizers have some toxic effects on plant microbiome and not are ecofriendly. Whole DNA was extracted from the roots of maize plants cultivated with organic fertilizer, inorganic fertilizer and maize planted without any fertilizer at different planting sites in an experimental field and sequenced using shotgun metagenomics. Our results using the Subsystem database revealed a total of 28 phyla and different nutrient pathways in all the samples. The major phyla observed were Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria, Acidobacteria, Chloroflexi, Verrucomicrobia, Tenericutes, Planctomycetes, Cyanobacteria, and Chlorobi. Bacteroidetes dominated maize from organic fertilizer sites, Firmicutes dominated the no fertilizers site while Proteobacteria dominated Inorganic fertilizer. The diversity analysis showed that the abundance of endophytic bacteria in all the sites is in the order organic fertilizer (FK) > no fertilizer (CK) > inorganic fertilizer (NK). Furthermore, the major nutrient cycling pathways identified are linked with nitrogen and phosphorus metabolism which were higher in FK samples. Going by the results obtained, this study suggests that organic fertilizer could be a boost to sustainable agricultural practices and should be encouraged. Also, a lot of novel endophytic bacteria groups were identified in maize. Mapping out strategies to isolate and purify this novel endophytic bacteria could help in promoting sustainable agriculture alongside biotechnological applications in future.
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163
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Baltrus DA. Bacterial dispersal and biogeography as underappreciated influences on phytobiomes. CURRENT OPINION IN PLANT BIOLOGY 2020; 56:37-46. [PMID: 32278259 DOI: 10.1016/j.pbi.2020.02.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 02/14/2020] [Accepted: 02/25/2020] [Indexed: 06/11/2023]
Abstract
Bacterial strains are not distributed evenly throughout the environment. Here I explore how differential distribution and dispersal patterns of bacteria could affect interactions and coevolutionary dynamics with plants, and highlight ways that variation could be taken advantage of to develop robust and effective microbial consortia to inoculate crops. Questions about biogeographical patterns in viruses, fungi, and other eukaryotes are equally as prevalent and important for agriculture, and are in some cases more thoroughly explored. For simplicity as well as to bring attention to bacterial biogeography and dispersal in the context of plant interactions, I focus solely on bacterial patterns and questions for this article. The next few years will no doubt bring great advances in our understanding of dispersal capabilities and population dynamics for many plant-associated bacteria, and one of the next looming challenges will be learning to harvest this diversity in ways that can benefit agriculture.
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Affiliation(s)
- David A Baltrus
- School of Plant Sciences, University of Arizona, Tucson AZ, USA; School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson AZ, USA.
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164
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Fungus-growing insects host a distinctive microbiota apparently adapted to the fungiculture environment. Sci Rep 2020; 10:12384. [PMID: 32709946 PMCID: PMC7381635 DOI: 10.1038/s41598-020-68448-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 06/24/2020] [Indexed: 01/09/2023] Open
Abstract
Some lineages of ants, termites, and beetles independently evolved a symbiotic association with lignocellulolytic fungi cultivated for food, in a lifestyle known as fungiculture. Fungus-growing insects' symbiosis also hosts a bacterial community thought to integrate their physiology. Similarities in taxonomic composition support the microbiota of fungus-growing insects as convergent, despite differences in fungus-rearing by these insects. Here, by comparing fungus-growing insects to several hosts ranging diverse dietary patterns, we investigate whether the microbiota taxonomic and functional profiles are characteristic of the fungiculture environment. Compared to other hosts, the microbiota associated with fungus-growing insects presents a distinctive taxonomic profile, dominated by Gammaproteobacteria at class level and by Pseudomonas at genera level. Even with a functional profile presenting similarities with the gut microbiota of herbivorous and omnivorous hosts, some differentially abundant features codified by the microbiota of fungus-growing insects suggest these communities occupying microhabitats that are characteristic of fungiculture. These features include metabolic pathways involved in lignocellulose breakdown, detoxification of plant secondary metabolites, metabolism of simple sugars, fungal cell wall deconstruction, biofilm formation, antimicrobials biosynthesis, and metabolism of diverse nutrients. Our results suggest that the microbiota could be functionally adapted to the fungiculture environment, codifying metabolic pathways potentially relevant to the fungus-growing insects' ecosystems functioning.
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165
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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.
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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.
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166
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Abstract
The taxonomic and functional diversity inherent to the soil microbiome complicate assessments of the metabolic potential carried out by the community members. An alternative approach is to break down the soil microbiome into reduced-complexity subsets based on metabolic capacities (functional modules) prior to sequencing and analysis. Here, we demonstrate that this approach successfully identified specific phylogenetic and biochemical traits of the soil microbiome that otherwise remained hidden from a more top-down analysis. The soil microbiome represents one of the most complex microbial communities on the planet, encompassing thousands of taxa and metabolic pathways, rendering holistic analyses computationally intensive and difficult. Here, we developed an alternative approach in which the complex soil microbiome was broken into components (“functional modules”), based on metabolic capacities, for individual characterization. We hypothesized that reproducible, low-complexity communities that represent functional modules could be obtained through targeted enrichments and that, in combination, they would encompass a large extent of the soil microbiome diversity. Enrichments were performed on a starting soil inoculum with defined media based on specific carbon substrates, antibiotics, alternative electron acceptors under anaerobic conditions, or alternative growing conditions reflective of common field stresses. The resultant communities were evaluated through 16S rRNA amplicon sequencing. Less permissive modules (anaerobic conditions, complex polysaccharides, and certain stresses) resulted in more distinct community profiles with higher richness and more variability between replicates, whereas modules with simple substrates were dominated by fewer species and were more reproducible. Collectively, approximately 27% of unique taxa present in the liquid soil extract control were found across functional modules. Taxa that were underrepresented or undetected in the source soil were also enriched across the modules. Metatranscriptomic analyses were carried out on a subset of the modules to investigate differences in functional gene expression. These results demonstrate that by dissecting the soil microbiome into discrete components it is possible to obtain a more comprehensive view of the soil microbiome and its biochemical potential than would be possible using more holistic analyses.
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167
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Vogel MA, Mason OU, Miller TE. Host and environmental determinants of microbial community structure in the marine phyllosphere. PLoS One 2020; 15:e0235441. [PMID: 32614866 PMCID: PMC7332025 DOI: 10.1371/journal.pone.0235441] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Accepted: 06/15/2020] [Indexed: 11/21/2022] Open
Abstract
Although seagrasses are economically and ecologically critical species, little is known about their blade surface microbial communities and how these communities relate to the plant host. To determine microbial community composition and diversity on seagrass blade surfaces and in the surrounding seawater,16S rRNA gene sequencing (iTag) was used for samples collected at five sites along a gradient of freshwater input in the northern Gulf of Mexico on three separate sampling dates. Additionally, seagrass surveys were performed and environmental parameters were measured to characterize host characteristics and the abiotic conditions at each site. Results showed that Thalassia testudinum (turtle grass) blades hosted unique microbial communities that were distinct in composition and diversity from the water column. Environmental conditions, including water depth, salinity, and temperature, influenced community structure as blade surface microbial communities varied among sites and sampling dates in correlation with changes in environmental parameters. Microbial community composition also correlated with seagrass host characteristics, including growth rates and blade nutrient composition. There is some evidence for a core community for T. testudinum as 21 microorganisms from five phyla (Cyanobacteria, Proteobacteria, Planctomycetes, Chloroflexi, and Bacteroidetes) were present in all blade surface samples. This study provides new insights and understanding of the processes that influence the structure of marine phyllosphere communities, how these microbial communities relate to their host, and their role as a part of the seagrass holobiont, which is an important contribution given the current decline of seagrass coverage worldwide.
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Affiliation(s)
- Margaret A. Vogel
- Department of Biological Science, Florida State University, Tallahassee, Florida, United States of America
- * E-mail:
| | - Olivia U. Mason
- Department of Earth, Ocean, and Atmospheric Science, Florida State University, Tallahassee, Florida, United States of America
| | - Thomas E. Miller
- Department of Biological Science, Florida State University, Tallahassee, Florida, United States of America
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168
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Sea Cucumber Intestinal Regeneration Reveals Deterministic Assembly of the Gut Microbiome. Appl Environ Microbiol 2020; 86:AEM.00489-20. [PMID: 32358014 DOI: 10.1128/aem.00489-20] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 04/28/2020] [Indexed: 01/08/2023] Open
Abstract
The gut microbiome has far-reaching effects on host organism health, so understanding the processes that underlie microbial community assembly in the developing gut is a current research priority. Here, a holothurian (also known as sea cucumber; phylum Echinodermata) host is explored as a promising model system for studying the assembly of the gut microbiome. Holothurians have a unique capacity for evisceration (expulsion of the internal organs), followed by rapid regeneration of the gut, decoupling host ontogeny from gut tissue development and permitting experimental manipulation of the gut microbiome in mature host individuals. Here, evisceration was induced in the sea cucumber Sclerodactyla briareus, and regenerating stomach and intestine microbiomes were characterized before and on days 0, 13, 17, and 20 after evisceration using Illumina sequencing of 16S rRNA genes. Regenerating stomach and intestine tissues had microbial communities significantly different from those of mature tissues, with much higher alpha diversity and evenness of taxa in regenerating tissues. Despite immersion in a diverse pool of sediment and seawater microbes in flowthrough seawater aquaria, regenerating gut microbiomes differed at each stage of regeneration and displayed a highly similar community structure among replicates, providing evidence for deterministic host selection of a specific microbial consortium. Moreover, regenerating gut tissues acquired a microbiome that likely conferred energetic and immune advantages to the sea cucumber host, including microbes that can fix carbon and degrade invading pathogens.IMPORTANCE The gut microbiome is pertinent to many aspects of animal health, and there is a great need for natural but tractable experimental systems to examine the processes shaping gut microbiome assembly. Here, the holothurian (sea cucumber) Sclerodactyla briareus was explored as an experimental system to study microbial colonization in the gut, as S. briareus individuals have the ability to completely eviscerate and rapidly regenerate their digestive organs. After induced evisceration, microbial community assembly was characterized over 20 days in regenerating animals. This study demonstrated that colonization of the sea cucumber gut was deterministic; despite immersion in a diverse consortium of environmental microbes, a specific subset of microbes proliferated in the gut, including taxa that likely conferred energetic and immune advantages to the host. Sea cucumbers have the potential to revolutionize our understanding of gut microbiome assembly, as rapid and repeatable gut tissue regeneration provides a promising and tractable experimental system.
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169
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Carey CJ, Glassman SI, Bruns TD, Aronson EL, Hart SC. Soil microbial communities associated with giant sequoia: How does the world's largest tree affect some of the world's smallest organisms? Ecol Evol 2020; 10:6593-6609. [PMID: 32724535 PMCID: PMC7381575 DOI: 10.1002/ece3.6392] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 03/29/2020] [Accepted: 04/22/2020] [Indexed: 02/01/2023] Open
Abstract
Giant sequoia (Sequoiadendron giganteum) is an iconic conifer that lives in relict populations on the western slopes of the California Sierra Nevada. In these settings, it is unusual among the dominant trees in that it associates with arbuscular mycorrhizal fungi rather than ectomycorrhizal fungi. However, it is unclear whether differences in microbial associations extend more broadly to nonmycorrhizal components of the soil microbial community. To address this question, we used next-generation amplicon sequencing to characterize bacterial/archaeal and fungal microbiomes in bulk soil (0-5 cm) beneath giant sequoia and co-occurring sugar pine (Pinus lambertiana) individuals. We did this across two groves with distinct parent material in Yosemite National Park, USA. We found tree-associated differences were apparent despite a strong grove effect. Bacterial/archaeal richness was greater beneath giant sequoia than sugar pine, with a core community double the size. The tree species also harbored compositionally distinct fungal communities. This pattern depended on grove but was associated with a consistently elevated relative abundance of Hygrocybe species beneath giant sequoia. Compositional differences between host trees correlated with soil pH and soil moisture. We conclude that the effects of giant sequoia extend beyond mycorrhizal mutualists to include the broader community and that some but not all host tree differences are grove-dependent.
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Affiliation(s)
| | - Sydney I. Glassman
- Department of Microbiology and Plant PathologyUniversity of CaliforniaRiversideCAUSA
| | - Thomas D. Bruns
- Department of Plant and Microbial BiologyUniversity of CaliforniaBerkeleyCAUSA
| | - Emma L. Aronson
- Department of Microbiology and Plant PathologyUniversity of CaliforniaRiversideCAUSA
| | - Stephen C. Hart
- Department of Life and Environmental Sciences and the Sierra Nevada Research InstituteUniversity of CaliforniaMercedCAUSA
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170
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Stewart JD, Shakya KM, Bilinski T, Wilson JW, Ravi S, Choi CS. Variation of near surface atmosphere microbial communities at an urban and a suburban site in Philadelphia, PA, USA. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 724:138353. [PMID: 32408469 DOI: 10.1016/j.scitotenv.2020.138353] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 03/28/2020] [Accepted: 03/30/2020] [Indexed: 06/11/2023]
Abstract
Microorganisms are abundant in the near surface atmosphere and make up a significant fraction of organic aerosols with implications on both human health and ecosystem services. Despite their importance, studies investigating biogeographical patterns of the atmospheric microbiome between urban and suburban areas are limited. Urban and suburban locations (including their microbial communities) vary considerably depending on climate, topography, industrial activities, demographics and other socio-economic factors. Hence, we need more location-specific data to make informed decision affecting air quality, human health, and the implication of a changing climate and policy decisions. The objective of this study was to describe how the atmospheric microbiome varies in composition and function between urban and suburban sites. We used high-throughput sequencing to analyze microbial communities collected at different times from PM2.5 samples collected by active sampling method (using a pump and an impactor) and dust settling of TSP collected by passive sampling method (no pump and no impactor) from an urban and suburban site. We found diverse communities unique in composition at both sites with equivalent functional potential. Taxonomic composition varied significantly with Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes, and Other phyla in greater relative abundance at the urban site. In contrast, Cyanobacteria, Tenericutes, Fusobacteria, and Deinococcus, were enriched at the suburban site. Community diversity also demonstrated a high degree of temporal variation within site. We identified over one-third of the communities as potentially pathogenic taxa (urban: 47.52% ± 14.40%, suburban: 34.53% ± 14.60%) and determined the majority of organisms come from animal-associated host or are environmental non-specific. Potentially pathogenic taxa and source environments were similar between active- and passive- sampling method results. Our research is novel it adds to the underrepresented set of studies on atmospheric microbial structure and function across land types and is the first to compare suburban and urban atmospheric communities.
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Affiliation(s)
- J D Stewart
- Department of Geography & the Environment, Villanova University, PA, USA
| | - K M Shakya
- Department of Geography & the Environment, Villanova University, PA, USA.
| | - T Bilinski
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - J W Wilson
- Department of Biology, Villanova University, PA, USA
| | - S Ravi
- Department of Earth & Environmental Science, Temple University, PA, USA
| | - Chong Seok Choi
- Department of Earth & Environmental Science, Temple University, PA, USA
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171
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Gubelit YI, Grossart HP. New Methods, New Concepts: What Can Be Applied to Freshwater Periphyton? Front Microbiol 2020; 11:1275. [PMID: 32670226 PMCID: PMC7328189 DOI: 10.3389/fmicb.2020.01275] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 05/19/2020] [Indexed: 12/24/2022] Open
Abstract
Microbial interactions play an essential role in aquatic ecosystems and are of the great interest for both marine and freshwater ecologists. Recent development of new technologies and methods allowed to reveal many functional mechanisms and create new concepts. Yet, many fundamental aspects of microbial interactions have been almost exclusively studied for marine pelagic and benthic ecosystems. These studies resulted in a formulation of the Black Queen Hypothesis, a development of the phycosphere concept for pelagic communities, and a realization of microbial communication as a key mechanism for microbial interactions. In freshwater ecosystems, especially for periphyton communities, studies focus mainly on physiology, biodiversity, biological indication, and assessment, but the many aspects of microbial interactions are neglected to a large extent. Since periphyton plays a great role for aquatic nutrient cycling, provides the basis for water purification, and can be regarded as a hotspot of microbial biodiversity, we highlight that more in-depth studies on microbial interactions in periphyton are needed to improve our understanding on functioning of freshwater ecosystems. In this paper we first present an overview on recent concepts (e.g., the "Black Queen Hypothesis") derived from state-of-the-art OMICS methods including metagenomics, metatranscriptomics, and metabolomics. We then point to the avenues how these methods can be applied for future studies on biodiversity and the ecological role of freshwater periphyton, a yet largely neglected component of many freshwater ecosystems.
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Affiliation(s)
- Yulia I. Gubelit
- Laboratory of Freshwater Hydrobiology, Zoological Institute, Russian Academy of Science, Saint Petersburg, Russia
| | - Hans-Peter Grossart
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- Department of Experimental Limnology, Leibniz-Institute for Freshwater Ecology and Inland Fisheries, Stechlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
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172
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Doane MP, Morris MM, Papudeshi B, Allen L, Pande D, Haggerty JM, Johri S, Turnlund AC, Peterson M, Kacev D, Nosal A, Ramirez D, Hovel K, Ledbetter J, Alker A, Avalos J, Baker K, Bhide S, Billings E, Byrum S, Clemens M, Demery AJ, Lima LFO, Gomez O, Gutierrez O, Hinton S, Kieu D, Kim A, Loaiza R, Martinez A, McGhee J, Nguyen K, Parlan S, Pham A, Price-Waldman R, Edwards RA, Dinsdale EA. The skin microbiome of elasmobranchs follows phylosymbiosis, but in teleost fishes, the microbiomes converge. MICROBIOME 2020; 8:93. [PMID: 32534596 PMCID: PMC7293782 DOI: 10.1186/s40168-020-00840-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 04/15/2020] [Indexed: 05/16/2023]
Abstract
BACKGROUND The vertebrate clade diverged into Chondrichthyes (sharks, rays, and chimeras) and Osteichthyes fishes (bony fishes) approximately 420 mya, with each group accumulating vast anatomical and physiological differences, including skin properties. The skin of Chondrichthyes fishes is covered in dermal denticles, whereas Osteichthyes fishes are covered in scales and are mucous rich. The divergence time among these two fish groups is hypothesized to result in predictable variation among symbionts. Here, using shotgun metagenomics, we test if patterns of diversity in the skin surface microbiome across the two fish clades match predictions made by phylosymbiosis theory. We hypothesize (1) the skin microbiome will be host and clade-specific, (2) evolutionary difference in elasmobranch and teleost will correspond with a concomitant increase in host-microbiome dissimilarity, and (3) the skin structure of the two groups will affect the taxonomic and functional composition of the microbiomes. RESULTS We show that the taxonomic and functional composition of the microbiomes is host-specific. Teleost fish had lower average microbiome within clade similarity compared to among clade comparison, but their composition is not different among clade in a null based model. Elasmobranch's average similarity within clade was not different than across clade and not different in a null based model of comparison. In the comparison of host distance with microbiome distance, we found that the taxonomic composition of the microbiome was related to host distance for the elasmobranchs, but not the teleost fishes. In comparison, the gene function composition was not related to the host-organism distance for elasmobranchs but was negatively correlated with host distance for teleost fishes. CONCLUSION Our results show the patterns of phylosymbiosis are not consistent across both fish clades, with the elasmobranchs showing phylosymbiosis, while the teleost fish are not. The discrepancy may be linked to alternative processes underpinning microbiome assemblage, including possible historical host-microbiome evolution of the elasmobranchs and convergent evolution in the teleost which filter specific microbial groups. Our comparison of the microbiomes among fishes represents an investigation into the microbial relationships of the oldest divergence of extant vertebrate hosts and reveals that microbial relationships are not consistent across evolutionary timescales. Video abstract.
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Affiliation(s)
- Michael P Doane
- Sydney Institute of Marine Science, Mosman, NSW, Australia
- Biology Department, San Diego State University, San Diego, CA, USA
| | - Megan M Morris
- Biology Department, San Diego State University, San Diego, CA, USA
- Department Biology, Stanford University, Stanford, California, USA
| | - Bhavya Papudeshi
- National Center for Genome Analysis Support, Indiana University, San Diego, Indiana, USA
| | - Lauren Allen
- Biology Department, San Diego State University, San Diego, CA, USA
| | - Dnyanada Pande
- Computer Sciences Department, San Diego State University, San Diego, CA, USA
| | - John M Haggerty
- Biology Department, San Diego State University, San Diego, CA, USA
| | - Shaili Johri
- Biology Department, San Diego State University, San Diego, CA, USA
- Hopkins Marine Station, Stanford University, Pacific Grove, CA, USA
| | - Abigail C Turnlund
- Biology Department, San Diego State University, San Diego, CA, USA
- Australian Centre for Ecogenomics, The University of Queensland, St. Lucia, Queens, USA
| | | | - Dovi Kacev
- Scripps Institute of Oceanography, University of California-San Diego, La Jolla, California, USA
| | - Andy Nosal
- Scripps Institute of Oceanography, University of California-San Diego, La Jolla, California, USA
- Department of Environmental and Ocean Sciences, University of San Diego, San Diego, CA, USA
| | - Deni Ramirez
- Whale Shark Mexico, ConCiencia Mexico AC, La Paz, BC, USA
| | - Kevin Hovel
- Biology Department, San Diego State University, San Diego, CA, USA
| | - Julia Ledbetter
- Biology Department, San Diego State University, San Diego, CA, USA
| | - Amanda Alker
- Biology Department, San Diego State University, San Diego, CA, USA
| | - Jackeline Avalos
- Biology Department, San Diego State University, San Diego, CA, USA
| | - Kristi Baker
- Biology Department, San Diego State University, San Diego, CA, USA
| | - Shruti Bhide
- Biology Department, San Diego State University, San Diego, CA, USA
| | - Emma Billings
- Biology Department, San Diego State University, San Diego, CA, USA
| | - Steven Byrum
- Department of Biology, University of Florida, Gainesville, FL, USA
| | - Molly Clemens
- Biology Department, San Diego State University, San Diego, CA, USA
| | | | | | - Oscar Gomez
- Biology Department, San Diego State University, San Diego, CA, USA
| | - Omar Gutierrez
- Biology Department, San Diego State University, San Diego, CA, USA
| | - Selena Hinton
- Biology Department, San Diego State University, San Diego, CA, USA
| | - Donald Kieu
- Biology Department, San Diego State University, San Diego, CA, USA
| | - Angie Kim
- Biology Department, San Diego State University, San Diego, CA, USA
| | - Rebeca Loaiza
- Biology Department, San Diego State University, San Diego, CA, USA
| | | | - Jordan McGhee
- Biology Department, San Diego State University, San Diego, CA, USA
| | - Kristine Nguyen
- Biology Department, San Diego State University, San Diego, CA, USA
| | - Sabrina Parlan
- Biology Department, San Diego State University, San Diego, CA, USA
| | - Amanda Pham
- Biology Department, San Diego State University, San Diego, CA, USA
| | - Rosalyn Price-Waldman
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Robert A Edwards
- Biology Department, San Diego State University, San Diego, CA, USA
- Viral Information Institute, San Diego State University, San Diego, CA, USA
| | - Elizabeth A Dinsdale
- Biology Department, San Diego State University, San Diego, CA, USA.
- Viral Information Institute, San Diego State University, San Diego, CA, USA.
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173
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Bonthond G, Bayer T, Krueger-Hadfield SA, Barboza FR, Nakaoka M, Valero M, Wang G, Künzel S, Weinberger F. How do microbiota associated with an invasive seaweed vary across scales? Mol Ecol 2020; 29:2094-2108. [PMID: 32408381 DOI: 10.1111/mec.15470] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 04/18/2020] [Accepted: 05/05/2020] [Indexed: 01/13/2023]
Abstract
Communities are shaped by scale dependent processes. To study the diversity and variation of microbial communities across scales, the invasive and widespread seaweed Agarophyton vermiculophyllum presents a unique opportunity. We characterized pro- and eukaryotic communities associated with this holobiont across its known distribution range, which stretches over the northern hemisphere. Our data reveal that community composition and diversity in the holobiont vary at local but also larger geographic scales. While processes acting at the local scale (i.e., within population) are the main structuring drivers of associated microbial communities, changes in community composition also depend on processes acting at larger geographic scales. Interestingly, the largest analysed scale (i.e., native and non-native ranges) explained variation in the prevalence of predicted functional groups, which could suggest a functional shift in microbiota occurred over the course of the invasion process. While high variability in microbiota at the local scale supports A. vermiculophyllum to be a generalist host, we also identified a number of core taxa. These geographically independent holobiont members imply that cointroduction of specific microbiota may have additionally promoted the invasion process.
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Affiliation(s)
- Guido Bonthond
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Till Bayer
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | | | | | - Masahiro Nakaoka
- Akkeshi Marine Station, Field Science Center for Northern Biosphere, Hokkaido University, Akkeshi, Japan
| | - Myriam Valero
- UMI EBEA 3614, CNRS, UCCh, UACH, Station Biologique de Roscoff, Sorbonne Université, Roscoff, France
| | - Gaoge Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China.,Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Sven Künzel
- Max Planck Institute for Evolutionary Biology, Plön, Germany
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174
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Mönnich J, Tebben J, Bergemann J, Case R, Wohlrab S, Harder T. Niche-based assembly of bacterial consortia on the diatom Thalassiosira rotula is stable and reproducible. THE ISME JOURNAL 2020; 14:1614-1625. [PMID: 32203123 PMCID: PMC7242391 DOI: 10.1038/s41396-020-0631-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 03/03/2020] [Accepted: 03/10/2020] [Indexed: 12/22/2022]
Abstract
With each cell division, phytoplankton create new space for primary colonization by marine bacteria. Although this surface microenvironment is available to all planktonic bacterial colonizers, we show the assembly of bacterial consortia on a cosmopolitan marine diatom to be highly specific and reproducible. While phytoplankton-bacteria interactions play fundamental roles in marine ecosystems, namely primary production and the carbon cycle, the ecological paradigm behind epiphytic microbiome assembly remains poorly understood. In a replicated and repeated primary colonization experiment, we exposed the axenic diatom Thalassiosira rotula to several complex and compositionally different bacterial inocula derived from phytoplankton species of varying degrees of relatedness to the axenic Thalassiosira host or natural seawater. This revealed a convergent assembly of diverse and compositionally different bacterial inocula, containing up to 2071 operational taxonomic units (OTUs), towards a stable and reproducible core community. Four of these OTUs already accounted for a cumulative abundance of 60%. This core community was dominated by Rhodobacteraceae (30.5%), Alteromonadaceae (27.7%), and Oceanospirillales (18.5%) which was qualitatively and quantitatively most similar to its conspecific original. These findings reject a lottery assembly model of bacterial colonization and suggest selective microhabitat filtering. This is likely due to diatom host traits such as surface properties and different levels of specialization resulting in reciprocal stable-state associations.
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Affiliation(s)
- Julian Mönnich
- Marine Chemistry, Department of Chemistry and Biology, University of Bremen, 28359, Bremen, Germany
| | - Jan Tebben
- Section Ecological Chemistry, Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, 27570, Bremerhaven, Germany
| | - Jennifer Bergemann
- Marine Chemistry, Department of Chemistry and Biology, University of Bremen, 28359, Bremen, Germany
| | - Rebecca Case
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore, 637551, Singapore
| | - Sylke Wohlrab
- Section Ecological Chemistry, Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, 27570, Bremerhaven, Germany
- Helmholtz Institute for Functional Marine Biodiversity, 23129, Oldenburg, Germany
| | - Tilmann Harder
- Marine Chemistry, Department of Chemistry and Biology, University of Bremen, 28359, Bremen, Germany.
- Section Ecological Chemistry, Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, 27570, Bremerhaven, Germany.
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175
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Jankowiak JG, Gobler CJ. The Composition and Function of Microbiomes Within Microcystis Colonies Are Significantly Different Than Native Bacterial Assemblages in Two North American Lakes. Front Microbiol 2020; 11:1016. [PMID: 32547511 PMCID: PMC7270213 DOI: 10.3389/fmicb.2020.01016] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 04/24/2020] [Indexed: 11/21/2022] Open
Abstract
The toxic cyanobacterium Microcystis is one of the most pervasive harmful algal bloom (HAB) genera and naturally occurs in large colonies known to harbor diverse heterotrophic bacterial assemblages. While colony-associated microbiomes may influence Microcystis blooms, there remains a limited understanding of the structure and functional potential of these communities and how they may be shaped by changing environmental conditions. To address this gap, we compared the dynamics of Microcystis-attached (MCA), free-living (FL), and whole water (W) microbiomes during Microcystis blooms using next-generation amplicon sequencing (16S rRNA), a predictive metagenome software, and other bioinformatic approaches. Microbiomes were monitored through high resolution spatial-temporal surveys across two North American lakes, Lake Erie (LE) and Lake Agawam (LA; Long Island, NY, United States) in 2017, providing the largest dataset of these fractions to date. Sequencing of 126 samples generated 7,922,628 sequences that clustered into 7,447 amplicon sequence variants (ASVs) with 100% sequence identity. Across lakes, the MCA microbiomes were significantly different than the FL and W fractions being significantly enriched in Gemmatimonadetes, Burkholderiaceae, Rhizobiales, and Cytophagales and depleted of Actinobacteria. Further, although MCA communities harbored > 900 unique ASVs, they were significantly less diverse than the other fractions with diversity inversely related to bloom intensity, suggesting increased selection pressure on microbial communities as blooms intensified. Despite taxonomic differences between lakes, predicted metagenomes revealed conserved functional potential among MCA microbiomes. MCA communities were significantly enriched in pathways involved in N and P cycling and microcystin-degradation. Taxa potentially capable of N2-fixation were significantly enriched (p < 0.05) and up to four-fold more abundant within the MCA faction relative to other fractions, potentially aiding in the proliferation of Microcystis blooms during low N conditions. The MCA predicted metagenomes were conserved over 8 months of seasonal changes in temperature and N availability despite strong temporal succession in microbiome composition. Collectively, these findings indicate that Microcystis colonies harbor a statistically distinct microbiome with a conserved functional potential that may help facilitate bloom persistence under environmentally unfavorable conditions.
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Affiliation(s)
- Jennifer G. Jankowiak
- School of Marine and Atmospheric Sciences, Stony Brook University, Southampton, NY, United States
| | - Christopher J. Gobler
- School of Marine and Atmospheric Sciences, Stony Brook University, Southampton, NY, United States
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176
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Worden L. Conservation of community functional structure across changes in composition in consumer-resource models. J Theor Biol 2020; 493:110239. [PMID: 32145224 DOI: 10.1016/j.jtbi.2020.110239] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 02/26/2020] [Accepted: 03/04/2020] [Indexed: 02/04/2023]
Abstract
High-throughput sequencing techniques such as metagenomic and metatranscriptomic technologies allow cataloguing of functional characteristics of microbial community members as well as their phylogenetic identity. Such studies have found that a community's makeup in terms of ecologically relevant functional traits or guilds can be conserved more strictly across varying settings than its composition is in terms of taxa. I use a standard ecological resource-consumer model to examine the dynamics of traits relevant to resource consumption, and analyze determinants of functional structure. This model demonstrates that interaction with essential resources can regulate the community-wide abundances of ecologically relevant traits, keeping them at consistent levels despite large changes in the abundances of the species housing those traits in response to changes in the environment, and across variation between communities in species composition. Functional structure is shown to be able to track differences in environmental conditions faithfully across differences in species composition. Mathematical conditions on consumers' vital rates and functional responses necessary and sufficient to produce conservation of functional community structure across differences in species composition in these models are presented. These conditions imply a nongeneric relation between biochemical rates, and avenues for further research are discussed.
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Affiliation(s)
- Lee Worden
- Francis I. Proctor Foundation for Research in Ophthalmology, Box 0412, University of California, San Francisco, California 94143-0412, United States.
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177
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Greslehner GP. Microbiome Structure and Function: A New Framework for Interpreting Data. Bioessays 2020; 42:e1900255. [DOI: 10.1002/bies.201900255] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 03/11/2020] [Indexed: 02/06/2023]
Affiliation(s)
- Gregor P. Greslehner
- University of Bordeaux and CNRS – ImmunoConcept UMR5164, 146 rue Léo Saignat Bordeaux 33076 France
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178
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Risely A. Applying the core microbiome to understand host-microbe systems. J Anim Ecol 2020; 89:1549-1558. [PMID: 32248522 DOI: 10.1111/1365-2656.13229] [Citation(s) in RCA: 143] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 03/13/2020] [Indexed: 12/16/2022]
Abstract
The host-associated core microbiome was originally coined to refer to common groups of microbes or genes that were likely to be particularly important for host biological function. However, the term has evolved to encompass variable definitions across studies, often identifying key microbes with respect to their spatial distribution, temporal stability or ecological influence, as well as their contribution to host function and fitness. A major barrier to reaching a consensus over how to define the core microbiome and its relevance to biological, ecological and evolutionary theory is a lack of precise terminology and associated definitions, as well the persistent association of the core microbiome with host function. Common, temporal and ecological core microbiomes can together generate insights into ecological processes that act independently of host function, while functional and host-adapted cores distinguish between facultative and near-obligate symbionts that differ in their effects on host fitness. This commentary summarizes five broad definitions of the core microbiome that have been applied across the literature, highlighting their strengths and limitations for advancing our understanding of host-microbe systems, noting where they are likely to overlap, and discussing their potential relevance to host function and fitness. No one definition of the core microbiome is likely to capture the range of key microbes across a host population. Applied together, they have the potential to reveal different layers of microbial organization from which we can begin to understand the ecological and evolutionary processes that govern host-microbe interactions.
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Affiliation(s)
- Alice Risely
- Institute for Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany
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179
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Tromas N, Taranu ZE, Castelli M, Pimentel JSM, Pereira DA, Marcoz R, Shapiro BJ, Giani A. The evolution of realized niches within freshwater
Synechococcus. Environ Microbiol 2020; 22:1238-1250. [DOI: 10.1111/1462-2920.14930] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 01/21/2020] [Accepted: 01/24/2020] [Indexed: 12/15/2022]
Affiliation(s)
- Nicolas Tromas
- Département de sciences biologiquesUniversité de Montréal Montréal QC H2V 2S9 Canada
| | - Zofia E. Taranu
- Environnement et Changement Climatique Canada 105 Rue McGill, Montréal QC H2Y 2E7 Canada
| | | | | | - Daniel A. Pereira
- Federal University of Minas Gerais Belo Horizonte Minas Gerais Brazil
| | - Romane Marcoz
- Département de sciences biologiquesUniversité de Montréal Montréal QC H2V 2S9 Canada
| | - B. Jesse Shapiro
- Département de sciences biologiquesUniversité de Montréal Montréal QC H2V 2S9 Canada
| | - Alessandra Giani
- Federal University of Minas Gerais Belo Horizonte Minas Gerais Brazil
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180
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Nuccio EE, Starr E, Karaoz U, Brodie EL, Zhou J, Tringe SG, Malmstrom RR, Woyke T, Banfield JF, Firestone MK, Pett-Ridge J. Niche differentiation is spatially and temporally regulated in the rhizosphere. THE ISME JOURNAL 2020; 14:999-1014. [PMID: 31953507 PMCID: PMC7082339 DOI: 10.1038/s41396-019-0582-x] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Revised: 10/28/2019] [Accepted: 12/18/2019] [Indexed: 01/14/2023]
Abstract
The rhizosphere is a hotspot for microbial carbon transformations, and is the entry point for root polysaccharides and polymeric carbohydrates that are important precursors to soil organic matter (SOM). However, the ecological mechanisms that underpin rhizosphere carbohydrate depolymerization are poorly understood. Using Avena fatua, a common annual grass, we analyzed time-resolved metatranscriptomes to compare microbial functions in rhizosphere, detritusphere, and combined rhizosphere-detritusphere habitats. Transcripts were binned using a unique reference database generated from soil isolate genomes, single-cell amplified genomes, metagenomes, and stable isotope probing metagenomes. While soil habitat significantly affected both community composition and overall gene expression, the succession of microbial functions occurred at a faster time scale than compositional changes. Using hierarchical clustering of upregulated decomposition genes, we identified four distinct microbial guilds populated by taxa whose functional succession patterns suggest specialization for substrates provided by fresh growing roots, decaying root detritus, the combination of live and decaying root biomass, or aging root material. Carbohydrate depolymerization genes were consistently upregulated in the rhizosphere, and both taxonomic and functional diversity were highest in the combined rhizosphere-detritusphere, suggesting coexistence of rhizosphere guilds is facilitated by niche differentiation. Metatranscriptome-defined guilds provide a framework to model rhizosphere succession and its consequences for soil carbon cycling.
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Affiliation(s)
- Erin E Nuccio
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94551, USA.
| | - Evan Starr
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Ulas Karaoz
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Eoin L Brodie
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, 94720, USA
| | - Jizhong Zhou
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, and School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, 73019, USA
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Susannah G Tringe
- Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Rex R Malmstrom
- Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Tanja Woyke
- Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Jillian F Banfield
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, 94720, USA
| | - Mary K Firestone
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, 94720, USA
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94551, USA.
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181
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Context-dependent dynamics lead to the assembly of functionally distinct microbial communities. Nat Commun 2020; 11:1440. [PMID: 32188849 PMCID: PMC7080782 DOI: 10.1038/s41467-020-15169-0] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 02/18/2020] [Indexed: 11/15/2022] Open
Abstract
Niche construction through interspecific interactions can condition future community states on past ones. However, the extent to which such history dependency can steer communities towards functionally different states remains a subject of active debate. Using bacterial communities collected from wild pitchers of the carnivorous pitcher plant, Sarracenia purpurea, we test the effects of history on composition and function across communities assembled in synthetic pitcher plant microcosms. We find that the diversity of assembled communities is determined by the diversity of the system at early, pre-assembly stages. Species composition is also contingent on early community states, not only because of differences in the species pool, but also because the same species have different dynamics in different community contexts. Importantly, compositional differences are proportional to differences in function, as profiles of resource use are strongly correlated with composition, despite convergence in respiration rates. Early differences in community structure can thus propagate to mature communities, conditioning their functional repertoire. Historical contingency can affect community composition and function, but the extent to which this occurs is unclear. Here the authors use pitcher plant microbial communities to demonstrate that community dynamics and key metabolic functions at equilibrium depend on history and initial composition.
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182
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Suárez J, Triviño V. What Is a Hologenomic Adaptation? Emergent Individuality and Inter-Identity in Multispecies Systems. Front Psychol 2020; 11:187. [PMID: 32194470 PMCID: PMC7064717 DOI: 10.3389/fpsyg.2020.00187] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 01/27/2020] [Indexed: 01/09/2023] Open
Abstract
Contemporary biological research has suggested that some host-microbiome multispecies systems (referred to as "holobionts") can in certain circumstances evolve as unique biological individual, thus being a unit of selection in evolution. If this is so, then it is arguably the case that some biological adaptations have evolved at the level of the multispecies system, what we call hologenomic adaptations. However, no research has yet been devoted to investigating their nature, or how these adaptations can be distinguished from adaptations at the species-level (genomic adaptations). In this paper, we cover this gap by investigating the nature of hologenomic adaptations. By drawing on the case of the evolution of sanguivory diet in vampire bats, we argue that a trait constitutes a hologenomic adaptation when its evolution can only be explained if the holobiont is considered the biological individual that manifests this adaptation, while the bacterial taxa that bear the trait are only opportunistic beneficiaries of it. We then use the philosophical notions of emergence and inter-identity to explain the nature of this form of individuality and argue why it is special of holobionts. Overall, our paper illustrates how the use of philosophical concepts can illuminate scientific discussions, in the trend of what has recently been called metaphysics of biology.
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Affiliation(s)
- Javier Suárez
- LOGOS/BIAP, Department of Philosophy, University of Barcelona, Barcelona, Spain
- Egenis, The Centre for the Study of Life Sciences, Department of Sociology, Philosophy and Anthropology, University of Exeter, Exeter, United Kingdom
| | - Vanessa Triviño
- Department of History of Science, Rey Juan Carlos University, Madrid, Spain
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183
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Xiong W, Song Y, Yang K, Gu Y, Wei Z, Kowalchuk GA, Xu Y, Jousset A, Shen Q, Geisen S. Rhizosphere protists are key determinants of plant health. MICROBIOME 2020; 8:27. [PMID: 32127034 PMCID: PMC7055055 DOI: 10.1186/s40168-020-00799-9] [Citation(s) in RCA: 93] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 02/05/2020] [Indexed: 05/18/2023]
Abstract
BACKGROUND Plant health is intimately influenced by the rhizosphere microbiome, a complex assembly of organisms that changes markedly across plant growth. However, most rhizosphere microbiome research has focused on fractions of this microbiome, particularly bacteria and fungi. It remains unknown how other microbial components, especially key microbiome predators-protists-are linked to plant health. Here, we investigated the holistic rhizosphere microbiome including bacteria, microbial eukaryotes (fungi and protists), as well as functional microbial metabolism genes. We investigated these communities and functional genes throughout the growth of tomato plants that either developed disease symptoms or remained healthy under field conditions. RESULTS We found that pathogen dynamics across plant growth is best predicted by protists. More specifically, communities of microbial-feeding phagotrophic protists differed between later healthy and diseased plants at plant establishment. The relative abundance of these phagotrophs negatively correlated with pathogen abundance across plant growth, suggesting that predator-prey interactions influence pathogen performance. Furthermore, phagotrophic protists likely shifted bacterial functioning by enhancing pathogen-suppressing secondary metabolite genes involved in mitigating pathogen success. CONCLUSIONS We illustrate the importance of protists as top-down controllers of microbiome functioning linked to plant health. We propose that a holistic microbiome perspective, including bacteria and protists, provides the optimal next step in predicting plant performance. Video Abstract.
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Affiliation(s)
- Wu Xiong
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Key Lab of Plant Immunity, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
- Ecology and Biodiversity Group, Department of Biology, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands
| | - Yuqi Song
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Key Lab of Plant Immunity, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Keming Yang
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Key Lab of Plant Immunity, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Yian Gu
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Key Lab of Plant Immunity, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Zhong Wei
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Key Lab of Plant Immunity, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China.
| | - George A Kowalchuk
- Ecology and Biodiversity Group, Department of Biology, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands
| | - Yangchun Xu
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Key Lab of Plant Immunity, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Alexandre Jousset
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Key Lab of Plant Immunity, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
- Ecology and Biodiversity Group, Department of Biology, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands
| | - Qirong Shen
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Key Lab of Plant Immunity, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Stefan Geisen
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Key Lab of Plant Immunity, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
- Department of Terrestrial Ecology, Netherlands Institute for Ecology (NIOO-KNAW), 6708, PB, Wageningen, The Netherlands
- Laboratory of Nematology, Wageningen University & Research, 6700, ES, Wageningen, The Netherlands
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184
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Wang Y, Lu L, Hong Y, Wu J, Zhu G, Ye F, Li Z. Divergent responses of taxonomic and predicted functional profiles of bacterioplankton to reservoir impoundment. ENVIRONMENTAL RESEARCH 2020; 182:109083. [PMID: 31901627 DOI: 10.1016/j.envres.2019.109083] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 12/19/2019] [Accepted: 12/23/2019] [Indexed: 06/10/2023]
Abstract
Freshwater ecosystems are undergoing extensive human disturbance of dam construction which form large amounts of reservoirs and lead to dramatic changes in hydraulic conditions. Bacterioplankton are key component of aquatic ecosystems. Investigation on their taxonomic compositions and associated functions responded to reservoir operation is essential to understand the ecological consequence of dam construction. In this study, we use the Three Gorges Reservoir as a model system. High-throughput sequencing is used to investigate the bacterioplankton community composition, and the bioinformatic tool of Tax4Fun is applied to predict the potential metabolic functions responded to reservoir impoundment. Results show that the taxonomic communities of bacterioplankton are significantly impacted by impoundment. The dominant group of Actinobacteria which accounts for 17.0%-58.1% of the retrieved sequences significantly increases after impoundment on phylum level. The influences of impoundment appear to be more apparent on order level that the relative abundances of four groups including Frankiales, Sphingomonadales, Sphingobacteriales and SubsectionI of class Cyanobacteria significantly vary after impoundment. In contrast, the predicted functional communities of bacterioplankton remain relatively stable that most of predicted functional categories including methane and nitrogen metabolisms have no significant variation after impoundment. Besides, significant distance decay patterns appear on the taxonomic communities after impoundment rather than the predicted functional communities. The environmental variables show significant impacts on the taxonomic community rather than predicted functional community, whereas the spatial variables have no effect on both taxonomic and predicted functional communities. In general, the taxonomic and predicted functional communities of bacterioplankton exhibit divergent responses to the impoundment in reservoir.
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Affiliation(s)
- Yu Wang
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, 510006, China
| | - Lunhui Lu
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China
| | - Yiguo Hong
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, 510006, China
| | - Jiapeng Wu
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, 510006, China
| | - Guibing Zhu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Fei Ye
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, 510006, China.
| | - Zhe Li
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China.
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185
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Trevathan-Tackett SM, Jeffries TC, Macreadie PI, Manojlovic B, Ralph P. Long-term decomposition captures key steps in microbial breakdown of seagrass litter. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 705:135806. [PMID: 31838420 DOI: 10.1016/j.scitotenv.2019.135806] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 11/25/2019] [Accepted: 11/26/2019] [Indexed: 06/10/2023]
Abstract
Seagrass biomass represents an important source of organic carbon that can contribute to long-term sediment carbon stocks in coastal ecosystems. There is little empirical data on the long-term microbial decomposition of seagrass detritus, despite this process being one of the key drivers of carbon-cycling in coastal ecosystems, that is, it influences the amount and quality of carbon available for sequestration. Here, our goal was to investigate how litter quality (leaf vs. rhizome/root) and the microbial communities involved in organic matter remineralisation shift over a 2-year field decomposition study north of Sydney, Australia using the temperate seagrass Zostera muelleri. The sites varied in bulk sediment characteristics and the sediment-associated microbial communities, but these variables overall had little influence on long-term seagrass decomposition rates or seagrass-associated microbiomes. The results showed a clear succession of bacterial and archaeal communities for both tissues types from r-strategists such as α- and γ-proteobacteria to K-strategies, including δ-proteobacteria, Bacteroidia and Spirochaetes. We used a new mathematical model to capture how decay rates varied over time and found that two decomposition events occurred for some seagrass leaf samples, possibly due to exudate input from living seagrass roots growing into the litter bag. The new model also indicated that conventional single exponential models overestimate long-term decay rates, and we detected for the first time the refractory, or stable, phase of decomposition for rhizome/root biomass. The stable phase began at approximately 20% mass remaining and after 600 days, and the persistence of rhizome/root biomass was attributed to the anoxic conditions and the preservation of refractory organic matter. While we predict that rhizome/root biomass will contribute more to the long-term sediment carbon stocks, the preservation of leaf carbon may be enhanced at locations were sedimentation is high and burial in anoxic conditions is rapid and constant.
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Affiliation(s)
- Stacey M Trevathan-Tackett
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW 2007, Australia; Deakin University, Geelong, School of Life and Environmental Sciences, Centre for Integrative Ecology, Burwood Campus, VIC 3125, Australia.
| | - Thomas C Jeffries
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW 2007, Australia; School of Science and Health, University of Western Sydney, Penrith, NSW 2751, Australia; Hawkesbury Institute for the Environment, University of Western Sydney, Penrith, NSW 2751, Australia
| | - Peter I Macreadie
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW 2007, Australia; Deakin University, Geelong, School of Life and Environmental Sciences, Centre for Integrative Ecology, Burwood Campus, VIC 3125, Australia
| | - Bojana Manojlovic
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Peter Ralph
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW 2007, Australia
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186
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Capunitan DC, Johnson O, Terrill RS, Hird SM. Evolutionary signal in the gut microbiomes of 74 bird species from Equatorial Guinea. Mol Ecol 2020; 29:829-847. [PMID: 31943484 DOI: 10.1111/mec.15354] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 01/06/2020] [Accepted: 01/08/2020] [Indexed: 12/26/2022]
Abstract
How the microbiome interacts with hosts across evolutionary time is poorly understood. Data sets including many host species are required to conduct comparative analyses. Here, we analyzed 142 intestinal microbiome samples from 92 birds belonging to 74 species from Equatorial Guinea, using the 16S rRNA gene. Using four definitions for microbial taxonomic units (97%OTU, 99%OTU, 99%OTU with singletons removed, ASV), we conducted alpha and beta diversity analyses. We found that raw abundances and diversity varied between the data sets but relative patterns were largely consistent across data sets. Host taxonomy, diet and locality were significantly associated with microbiomes, at generally similar levels using three distance metrics. Phylogenetic comparative methods assessed the evolutionary relationship between the microbiome as a trait of a host species and the underlying bird phylogeny. Using multiple ways of defining "microbiome traits", we found that a neutral Brownian motion model did not explain variation in microbiomes. Instead, we found a White Noise model (indicating little phylogenetic signal), was most likely. There was some support for the Ornstein-Uhlenbeck model (that invokes selection), but the level of support was similar to that of a White Noise simulation, further supporting the White Noise model as the best explanation for the evolution of the microbiome as a trait of avian hosts. Our study demonstrated that both environment and evolution play a role in the gut microbiome and the relationship does not follow a neutral model; these biological results are qualitatively robust to analytical choices.
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Affiliation(s)
- Darien C Capunitan
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Oscar Johnson
- Museum of Natural Science, Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Ryan S Terrill
- Museum of Natural Science, Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA.,Moore Laboratory of Zoology, Occidental College, Los Angeles, CA, USA
| | - Sarah M Hird
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA.,Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
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187
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Mathai PP, Magnone P, Dunn HM, Sadowsky MJ. Water and sediment act as reservoirs for microbial taxa associated with invasive dreissenid mussels. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 703:134915. [PMID: 31767301 DOI: 10.1016/j.scitotenv.2019.134915] [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: 07/22/2019] [Revised: 10/06/2019] [Accepted: 10/08/2019] [Indexed: 06/10/2023]
Abstract
Zebra mussels (Dreissena polymorpha) are invasive, filter-feeding, bivalves that have disrupted the ecology of thousands of freshwater biomes across North America. Due to their efficient filter-feeding activity, zebra mussels (ZMs) and other bivalves are extensively used to detect chemical contamination in waterways. In this study, we evaluated whether water and sediment serve as major sources of ZM tissue-associated microbiota, and whether ZMs serve as a reservoir for potentially pathogenic microbes in aquatic systems. High-throughput DNA sequencing of 16S rRNA gene was done to characterize the microbial community structure in 472 environmental samples, comprising ZMs, sediment, and the water column, collected from 15 lakes during the summer and fall months. Sequence analyses, done using the SourceTracker program, predicted that water and sediment contributed up to 91 and 86%, respectively, to the structure of microbiota within ZMs, and that mussels from the same site showed nearly identical source microbiota profiles. The relatively high local source contribution suggests that the microbiota in ZM tissue has the potential to reflect biological contamination and this phenomenon can be used to monitor microbial water quality. A preferential enrichment of several taxa was also observed in ZM tissues, including potential pathogenic groups such as Aeromonas, Enterobacteriaceae, and Pseudomonas. Taken together, our results contribute to an improved understanding of ZMs as a sentinel species in aquatic habitats and its potential impact to water quality management.
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Affiliation(s)
- Prince P Mathai
- BioTechnology Institute, University of Minnesota, St. Paul, MN, USA
| | - Paolo Magnone
- BioTechnology Institute, University of Minnesota, St. Paul, MN, USA
| | - Hannah M Dunn
- BioTechnology Institute, University of Minnesota, St. Paul, MN, USA
| | - Michael J Sadowsky
- BioTechnology Institute, University of Minnesota, St. Paul, MN, USA; Department of Soil, Water, and Climate, University of Minnesota, St. Paul, MN, USA; Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, USA.
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188
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Barnes EM, Carter EL, Lewis JD. Predicting Microbiome Function Across Space Is Confounded by Strain-Level Differences and Functional Redundancy Across Taxa. Front Microbiol 2020; 11:101. [PMID: 32117131 PMCID: PMC7018939 DOI: 10.3389/fmicb.2020.00101] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 01/17/2020] [Indexed: 12/30/2022] Open
Abstract
Variation in the microbiome among individual organisms may play a critical role in the relative susceptibility of those organisms to infection, disease, and death. However, predicting microbiome function is difficult because of spatial and temporal variation in microbial diversity, and taxonomic diversity is not predictive of microbiome functional diversity. Addressing this issue may be particularly important when addressing pandemic diseases, such as the global amphibian die-off associated with Bd. Some of the most important factors in probiotic development for disease treatment are whether bacteria with desired function can be found on native amphibians in the local environment. To address this issue, we isolated, sequenced, and assayed the cutaneous bacterial communities of Plethodon cinereus along a gradient of land use change. Our results suggest that cutaneous community composition, but not overall diversity, change with changes in land use, but this does not correspond to significant change in Bd-inhibitory function. We found that Bd-inhibition is a functionally redundant trait, but that level of inhibition varies over phylogenetic, spatial, and temporal scales. This research provides further evidence for the importance of continued examination of amphibian microbial communities across environmental gradients, including biotic and abiotic interactions, when considering disease dynamics.
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Affiliation(s)
- Elle M Barnes
- Department of Biological Sciences, Louis Calder Center - Biological Field Station, Fordham University, Armonk, NY, United States.,Department of Biological Sciences and Center for Urban Ecology, Fordham University, Bronx, NY, United States
| | - Erin L Carter
- Department of Biological Sciences and Center for Urban Ecology, Fordham University, Bronx, NY, United States
| | - J D Lewis
- Department of Biological Sciences, Louis Calder Center - Biological Field Station, Fordham University, Armonk, NY, United States.,Department of Biological Sciences and Center for Urban Ecology, Fordham University, Bronx, NY, United States
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189
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Johnke J, Dirksen P, Schulenburg H. Community assembly of the native C. elegans microbiome is influenced by time, substrate and individual bacterial taxa. Environ Microbiol 2020; 22:1265-1279. [PMID: 32003074 DOI: 10.1111/1462-2920.14932] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 01/17/2020] [Accepted: 01/27/2020] [Indexed: 12/18/2022]
Abstract
Microbiome communities are complex assemblages of bacteria. The dissection of their assembly dynamics is challenging because it requires repeated sampling of both host and source communities. We used the nematode Caenorhabditis elegans as a model to study these dynamics. We characterized microbiome variation from natural worm populations and their substrates for two consecutive years using 16S rDNA amplicon sequencing. We found conservation in microbiome composition across time at the genus, but not amplicon sequencing variant (ASV) level. Only three ASVs were consistently present across worm samples (Comamonas ASV10859, Pseudomonas ASV7162 and Cellvibrio ASV9073). ASVs were more diverse in worms from different rather than the same substrates, indicating an influence of the source community on microbiome assembly. Surprisingly, almost 50% of worm-associated ASVs were absent in corresponding substrates, potentially due to environmental filtering. Ecological network analysis revealed strong effects of bacteria-bacteria interactions on community composition: While a dominant Erwinia strain correlated with decreased alpha-diversity, predatory bacteria of the Bdellovibrio and like organisms associated with increased alpha-diversity. High alpha-diversity was further linked to high worm population growth, especially on species-poor substrates. Our results highlight that microbiomes are individually shaped and sensitive to dramatic community shifts in response to particular competitive species.
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Affiliation(s)
- Julia Johnke
- Evolutionary Ecology and Genetics, Zoological Institute, University of Kiel, Kiel, Germany
| | - Philipp Dirksen
- Evolutionary Ecology and Genetics, Zoological Institute, University of Kiel, Kiel, Germany.,Max-Planck Institute for Evolutionary Biology, Plön, Germany
| | - Hinrich Schulenburg
- Evolutionary Ecology and Genetics, Zoological Institute, University of Kiel, Kiel, Germany.,Max-Planck Institute for Evolutionary Biology, Plön, Germany
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190
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Abstract
It is well understood that genetic differences among hosts contribute to variation in pathogen susceptibility and the ability to associate with symbionts. However, it remains unclear just how influential host genes are in shaping the overall microbiome. Studies of both animal and plant microbial communities indicate that host genes impact species richness and the abundances of individual taxa. Analyses of beta diversity (that is, overall similarity), on the other hand, often conclude that hosts play a minor role in shaping microbial communities. In this review, we discuss recent attempts to identify the factors that shape host microbial communities and whether our understanding of these communities is affected by the traits chosen to represent them.
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Affiliation(s)
- Alexandra Tabrett
- Plant and Microbial Biology, University of Zurich, Zurich, CH-8008, Switzerland
| | - Matthew W Horton
- Plant and Microbial Biology, University of Zurich, Zurich, CH-8008, Switzerland
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191
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Okie JG, Poret-Peterson AT, Lee ZM, Richter A, Alcaraz LD, Eguiarte LE, Siefert JL, Souza V, Dupont CL, Elser JJ. Genomic adaptations in information processing underpin trophic strategy in a whole-ecosystem nutrient enrichment experiment. eLife 2020; 9:49816. [PMID: 31989922 PMCID: PMC7028357 DOI: 10.7554/elife.49816] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 01/27/2020] [Indexed: 01/03/2023] Open
Abstract
Several universal genomic traits affect trade-offs in the capacity, cost, and efficiency of the biochemical information processing that underpins metabolism and reproduction. We analyzed the role of these traits in mediating the responses of a planktonic microbial community to nutrient enrichment in an oligotrophic, phosphorus-deficient pond in Cuatro Ciénegas, Mexico. This is one of the first whole-ecosystem experiments to involve replicated metagenomic assessment. Mean bacterial genome size, GC content, total number of tRNA genes, total number of rRNA genes, and codon usage bias in ribosomal protein sequences were all higher in the fertilized treatment, as predicted on the basis of the assumption that oligotrophy favors lower information-processing costs whereas copiotrophy favors higher processing rates. Contrasting changes in trait variances also suggested differences between traits in mediating assembly under copiotrophic versus oligotrophic conditions. Trade-offs in information-processing traits are apparently sufficiently pronounced to play a role in community assembly because the major components of metabolism-information, energy, and nutrient requirements-are fine-tuned to an organism's growth and trophic strategy.
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Affiliation(s)
- Jordan G Okie
- School of Earth and Space Exploration, Arizona State University, Tempe, United States
| | | | - Zarraz Mp Lee
- School of Life Sciences, Arizona State University, Tempe, United States
| | | | - Luis D Alcaraz
- Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Luis E Eguiarte
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Janet L Siefert
- Department of Statistics, Rice University, Houston, United States
| | - Valeria Souza
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | | | - James J Elser
- School of Life Sciences, Arizona State University, Tempe, United States.,Flathead Lake Biological Station, University of Montana, Polson, United States
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192
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Revealing the Variation and Stability of Bacterial Communities in Tomato Rhizosphere Microbiota. Microorganisms 2020; 8:microorganisms8020170. [PMID: 31991727 PMCID: PMC7074737 DOI: 10.3390/microorganisms8020170] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Revised: 01/18/2020] [Accepted: 01/22/2020] [Indexed: 12/14/2022] Open
Abstract
Microorganisms that colonize the plant rhizosphere can contribute to plant health, growth and productivity. Although the importance of the rhizosphere microbiome is known, we know little about the underlying mechanisms that drive microbiome assembly and composition. In this study, the variation, assembly and composition of rhizobacterial communities in 11 tomato cultivars, combined with one cultivar in seven different sources of soil and growing substrate, were systematically investigated. The tomato rhizosphere microbiota was dominated by bacteria from the phyla Proteobacteria, Bacteroidetes, and Acidobacteria, mainly comprising Rhizobiales, Xanthomonadales, Burkholderiales, Nitrosomonadales, Myxococcales, Sphingobacteriales, Cytophagales and Acidobacteria subgroups. The bacterial community in the rhizosphere microbiota of the samples in the cultivar experiment mostly overlapped with that of tomato cultivar MG, which was grown in five natural field soils, DM, JX, HQ, QS and XC. The results supported the hypothesis that tomato harbors largely conserved communities and compositions of rhizosphere microbiota that remains consistent in different cultivars of tomato and even in tomato cultivar grown in five natural field soils. However, significant differences in OTU richness (p < 0.0001) and bacterial diversity (p = 0.0014 < 0.01) were observed among the 7 different sources of soil and growing substrate. Two artificial commercial nutrient soils, HF and CF, resulted in a distinct tomato rhizosphere microbiota in terms of assembly and core community compared with that observed in natural field soils. PERMANOVA of beta diversity based on the combined data from the cultivar and soil experiments demonstrated that soil (growing substrate) and plant genotype (cultivar) had significant impacts on the rhizosphere microbial communities of tomato plants (soil, F = 22.29, R2 = 0.7399, p < 0.001; cultivar, F = 2.04, R2 = 0.3223, p = 0.008). Of these two factors, soil explained a larger proportion of the compositional variance in the tomato rhizosphere microbiota. The results demonstrated that the assembly process of rhizosphere bacterial communities was collectively influenced by soil, including the available bacterial sources and biochemical properties of the rhizosphere soils, and plant genotype.
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193
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Moreno-Pino M, Cristi A, Gillooly JF, Trefault N. Characterizing the microbiomes of Antarctic sponges: a functional metagenomic approach. Sci Rep 2020; 10:645. [PMID: 31959785 PMCID: PMC6971038 DOI: 10.1038/s41598-020-57464-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 12/11/2019] [Indexed: 01/22/2023] Open
Abstract
Relatively little is known about the role of sponge microbiomes in the Antarctic marine environment, where sponges may dominate the benthic landscape. Specifically, we understand little about how taxonomic and functional diversity contributes to the symbiotic lifestyle and aids in nutrient cycling. Here we use functional metagenomics to investigate the community composition and metabolic potential of microbiomes from two abundant Antarctic sponges, Leucetta antarctica and Myxilla sp. Genomic and taxonomic analyses show that both sponges harbor a distinct microbial community with high fungal abundance, which differs from the surrounding seawater. Functional analyses reveal both sponge-associated microbial communities are enriched in functions related to the symbiotic lifestyle (e.g., CRISPR system, Eukaryotic-like proteins, and transposases), and in functions important for nutrient cycling. Both sponge microbiomes possessed genes necessary to perform processes important to nitrogen cycling (i.e., ammonia oxidation, nitrite oxidation, and denitrification), and carbon fixation. The latter indicates that Antarctic sponge microorganisms prefer light-independent pathways for CO2 fixation mediated by chemoautotrophic microorganisms. Together, these results show how the unique metabolic potential of two Antarctic sponge microbiomes help these sponge holobionts survive in these inhospitable environments, and contribute to major nutrient cycles of these ecosystems.
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Affiliation(s)
- Mario Moreno-Pino
- GEMA Center for Genomics, Ecology & Environment, Facultad de Ciencias, Universidad Mayor, Santiago, 8580745, Chile
| | - Antonia Cristi
- GEMA Center for Genomics, Ecology & Environment, Facultad de Ciencias, Universidad Mayor, Santiago, 8580745, Chile
| | - James F Gillooly
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - Nicole Trefault
- GEMA Center for Genomics, Ecology & Environment, Facultad de Ciencias, Universidad Mayor, Santiago, 8580745, Chile.
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194
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Santos-Garcia D, Mestre-Rincon N, Zchori-Fein E, Morin S. Inside out: microbiota dynamics during host-plant adaptation of whiteflies. ISME JOURNAL 2020; 14:847-856. [PMID: 31896788 PMCID: PMC7031279 DOI: 10.1038/s41396-019-0576-8] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Accepted: 12/17/2019] [Indexed: 12/14/2022]
Abstract
While most insect herbivores are selective feeders, a small proportion of them feed on a wide range of plants. This polyphagous habit requires overcoming a remarkable array of defenses, which often necessitates an adaptation period. Efforts for understanding the mechanisms involved mostly focus on the insect’s phenotypic plasticity. Here, we hypothesized that the adaptation process might partially rely on transient associations with bacteria. To test this, we followed in a field-like experiment, the adaptation process of Bemisia tabaci, a generalist sap feeder, to pepper (a less-suitable host), after switching from watermelon (a suitable host). Amplicon sequencing of 16S rRNA transcripts from hundreds of dissected guts revealed the presence of active “core” and “transient” bacterial communities, dominated by the phyla Proteobacteria, Actinobacteria, and Firmicutes, and increasing differences between populations grown on watermelon and pepper. Insects grown on pepper for over two generations presented a significant increase in specific genera, mainly Mycobacterium, with a predicted enrichment in degradative pathways of xenobiotics and secondary metabolites. This result correlated with a significant increase in the insect’s survival on pepper. Taken together, our findings suggest that gut-associated bacteria can provide an additional flexible metabolic “tool-box” to generalist sap feeders for facilitating a quick host switching process.
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Affiliation(s)
- Diego Santos-Garcia
- Department of Entomology, The Hebrew University of Jerusalem, P.O. Box 12, 76100, Rehovot, Israel.
| | - Natividad Mestre-Rincon
- Department of Entomology, The Hebrew University of Jerusalem, P.O. Box 12, 76100, Rehovot, Israel
| | - Einat Zchori-Fein
- Department of Entomology, Newe-Ya'ar Research Center, ARO, Ramat-Yishai, Israel
| | - Shai Morin
- Department of Entomology, The Hebrew University of Jerusalem, P.O. Box 12, 76100, Rehovot, Israel
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195
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Cook KV, Li C, Cai H, Krumholz LR, Hambright KD, Paerl HW, Steffen MM, Wilson AE, Burford MA, Grossart H, Hamilton DP, Jiang H, Sukenik A, Latour D, Meyer EI, Padisák J, Qin B, Zamor RM, Zhu G. The global Microcystis interactome. LIMNOLOGY AND OCEANOGRAPHY 2020; 65:S194-S207. [PMID: 32051648 PMCID: PMC7003799 DOI: 10.1002/lno.11361] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 07/22/2019] [Accepted: 09/24/2019] [Indexed: 05/06/2023]
Abstract
Bacteria play key roles in the function and diversity of aquatic systems, but aside from study of specific bloom systems, little is known about the diversity or biogeography of bacteria associated with harmful cyanobacterial blooms (cyanoHABs). CyanoHAB species are known to shape bacterial community composition and to rely on functions provided by the associated bacteria, leading to the hypothesized cyanoHAB interactome, a coevolved community of synergistic and interacting bacteria species, each necessary for the success of the others. Here, we surveyed the microbiome associated with Microcystis aeruginosa during blooms in 12 lakes spanning four continents as an initial test of the hypothesized Microcystis interactome. We predicted that microbiome composition and functional potential would be similar across blooms globally. Our results, as revealed by 16S rRNA sequence similarity, indicate that M. aeruginosa is cosmopolitan in lakes across a 280° longitudinal and 90° latitudinal gradient. The microbiome communities were represented by a wide range of operational taxonomic units and relative abundances. Highly abundant taxa were more related and shared across most sites and did not vary with geographic distance, thus, like Microcystis, revealing no evidence for dispersal limitation. High phylogenetic relatedness, both within and across lakes, indicates that microbiome bacteria with similar functional potential were associated with all blooms. While Microcystis and the microbiome bacteria shared many genes, whole-community metagenomic analysis revealed a suite of biochemical pathways that could be considered complementary. Our results demonstrate a high degree of similarity across global Microcystis blooms, thereby providing initial support for the hypothesized Microcystis interactome.
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Affiliation(s)
- Katherine V. Cook
- Plankton Ecology and Limnology Laboratory, Department of BiologyThe University of OklahomaNormanOklahoma
- Program in Ecology and Evolutionary Biology and the Geographical Ecology Group, Department of BiologyThe University of OklahomaNormanOklahoma
| | - Chuang Li
- Department of Microbiology and Plant Biology and Institute for Energy and the EnvironmentThe University of OklahomaNormanOklahoma
| | - Haiyuan Cai
- Plankton Ecology and Limnology Laboratory, Department of BiologyThe University of OklahomaNormanOklahoma
| | - Lee R. Krumholz
- Department of Microbiology and Plant Biology and Institute for Energy and the EnvironmentThe University of OklahomaNormanOklahoma
| | - K. David Hambright
- Plankton Ecology and Limnology Laboratory, Department of BiologyThe University of OklahomaNormanOklahoma
- Program in Ecology and Evolutionary Biology and the Geographical Ecology Group, Department of BiologyThe University of OklahomaNormanOklahoma
| | - Hans W. Paerl
- Institute of Marine Sciences, The University of North Carolina at Chapel HillMorehead CityNorth Carolina
| | | | - Alan E. Wilson
- School of Fisheries, Aquaculture, and Aquatic SciencesAuburn UniversityAuburnAlabama
| | - Michele A. Burford
- Australian Rivers Institute and School of Environment and Science, Griffith UniversityNathanQueenslandAustralia
| | - Hans‐Peter Grossart
- Department of Experimental Limnology, Leibniz Institute for Freshwater Ecology and Inland Fisheries, Stechlin, and Institute for Biochemistry and BiologyPotsdam UniversityPotsdamGermany
| | - David P. Hamilton
- Australian Rivers Institute and School of Environment and Science, Griffith UniversityNathanQueenslandAustralia
- Environmental Research Institute, University of WaikatoWaikatoNew Zealand
| | - Helong Jiang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and LimnologyChinese Academy of SciencesNanjingChina
| | - Assaf Sukenik
- Israel Oceanographic and Limnological ResearchThe Yigal Allon Kinneret Limnological LaboratoryMigdalIsrael
| | | | - Elisabeth I. Meyer
- Institute for Evolution and Biodiversity, University of MünsterMünsterGermany
| | - Judit Padisák
- Department of LimnologyInstitute of Environmental Science, University of PannoniaVeszprémHungary
| | - Boqiang Qin
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and LimnologyChinese Academy of SciencesNanjingChina
| | | | - Guangwei Zhu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and LimnologyChinese Academy of SciencesNanjingChina
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196
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Hettle AG, Hobbs JK, Pluvinage B, Vickers C, Abe KT, Salama-Alber O, McGuire BE, Hehemann JH, Hui JPM, Berrue F, Banskota A, Zhang J, Bottos EM, Van Hamme J, Boraston AB. Insights into the κ/ι-carrageenan metabolism pathway of some marine Pseudoalteromonas species. Commun Biol 2019; 2:474. [PMID: 31886414 PMCID: PMC6923384 DOI: 10.1038/s42003-019-0721-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 12/02/2019] [Indexed: 01/07/2023] Open
Abstract
Pseudoalteromonas is a globally distributed marine-associated genus that can be found in a broad range of aquatic environments, including in association with macroalgal surfaces where they may take advantage of these rich sources of polysaccharides. The metabolic systems that confer the ability to metabolize this abundant form of photosynthetically fixed carbon, however, are not yet fully understood. Through genomics, transcriptomics, microbiology, and specific structure-function studies of pathway components we address the capacity of newly isolated marine pseudoalteromonads to metabolize the red algal galactan carrageenan. The results reveal that the κ/ι-carrageenan specific polysaccharide utilization locus (CarPUL) enables isolates possessing this locus the ability to grow on this substrate. Biochemical and structural analysis of the enzymatic components of the CarPUL promoted the development of a detailed model of the κ/ι-carrageenan metabolic pathway deployed by pseudoalteromonads, thus furthering our understanding of how these microbes have adapted to a unique environmental niche.
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Affiliation(s)
- Andrew G. Hettle
- Department of Biochemistry and Microbiology, University of Victoria, PO Box 1700 STN CSC, Victoria, British Columbia V8W 2Y2 Canada
| | - Joanne K. Hobbs
- Department of Biochemistry and Microbiology, University of Victoria, PO Box 1700 STN CSC, Victoria, British Columbia V8W 2Y2 Canada
| | - Benjamin Pluvinage
- Department of Biochemistry and Microbiology, University of Victoria, PO Box 1700 STN CSC, Victoria, British Columbia V8W 2Y2 Canada
| | - Chelsea Vickers
- Department of Biochemistry and Microbiology, University of Victoria, PO Box 1700 STN CSC, Victoria, British Columbia V8W 2Y2 Canada
- Present Address: School of Biological Sciences, Victoria University, PO Box 600, Wellington, 6012 New Zealand
| | - Kento T. Abe
- Department of Biochemistry and Microbiology, University of Victoria, PO Box 1700 STN CSC, Victoria, British Columbia V8W 2Y2 Canada
- Present Address: Lunenfeld-Tanenbaum Research Institute, Sinai Health System, and Department of Molecular Genetics, University of Toronto, 600 University Ave, Rm 992, Toronto, ON M5G1X5 Canada
| | - Orly Salama-Alber
- Department of Biochemistry and Microbiology, University of Victoria, PO Box 1700 STN CSC, Victoria, British Columbia V8W 2Y2 Canada
| | - Bailey E. McGuire
- Department of Biochemistry and Microbiology, University of Victoria, PO Box 1700 STN CSC, Victoria, British Columbia V8W 2Y2 Canada
| | - Jan-Hendrik Hehemann
- Department of Biochemistry and Microbiology, University of Victoria, PO Box 1700 STN CSC, Victoria, British Columbia V8W 2Y2 Canada
- Present Address: Marum and Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359 Bremen, Germany
| | - Joseph P. M. Hui
- Aquatic and Crop Resource Development Research Centre, National Research Council of Canada, 1411 Oxford Street, Halifax, NS B3H 3Z1 Canada
| | - Fabrice Berrue
- Aquatic and Crop Resource Development Research Centre, National Research Council of Canada, 1411 Oxford Street, Halifax, NS B3H 3Z1 Canada
| | - Arjun Banskota
- Aquatic and Crop Resource Development Research Centre, National Research Council of Canada, 1411 Oxford Street, Halifax, NS B3H 3Z1 Canada
| | - Junzeng Zhang
- Aquatic and Crop Resource Development Research Centre, National Research Council of Canada, 1411 Oxford Street, Halifax, NS B3H 3Z1 Canada
| | - Eric M. Bottos
- Department of Biological Sciences, Thompson Rivers University, 805 TRU Way, Kamloops, British Columbia V2C 0C8 Canada
| | - Jonathan Van Hamme
- Department of Biological Sciences, Thompson Rivers University, 805 TRU Way, Kamloops, British Columbia V2C 0C8 Canada
| | - Alisdair B. Boraston
- Department of Biochemistry and Microbiology, University of Victoria, PO Box 1700 STN CSC, Victoria, British Columbia V8W 2Y2 Canada
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197
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Rambo IM, Dombrowski N, Constant L, Erdner D, Baker BJ. Metabolic relationships of uncultured bacteria associated with the microalgae Gambierdiscus. Environ Microbiol 2019; 22:1764-1783. [PMID: 31775181 DOI: 10.1111/1462-2920.14878] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 11/13/2019] [Accepted: 11/25/2019] [Indexed: 12/14/2022]
Abstract
Microbial communities inhabit algae cell surfaces and produce a variety of compounds that can impact the fitness of the host. These interactions have been studied via culturing, single-gene diversity and metagenomic read survey methods that are limited by culturing biases and fragmented genetic characterizations. Higher-resolution frameworks are needed to resolve the physiological interactions within these algal-bacterial communities. Here, we infer the encoded metabolic capabilities of four uncultured bacterial genomes (reconstructed using metagenomic assembly and binning) associated with the marine dinoflagellates Gambierdiscus carolinianus and G. caribaeus. Phylogenetic analyses revealed that two of the genomes belong to the commonly algae-associated families Rhodobacteraceae and Flavobacteriaceae. The other two genomes belong to the Phycisphaeraceae and include the first algae-associated representative within the uncultured SM1A02 group. Analyses of all four genomes suggest these bacteria are facultative aerobes, with some capable of metabolizing phytoplanktonic organosulfur compounds including dimethylsulfoniopropionate and sulfated polysaccharides. These communities may biosynthesize compounds beneficial to both the algal host and other bacteria, including iron chelators, B vitamins, methionine, lycopene, squalene and polyketides. These findings have implications for marine carbon and nutrient cycling and provide a greater depth of understanding regarding the genetic potential for complex physiological interactions between microalgae and their associated bacteria.
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Affiliation(s)
- Ian M Rambo
- Department of Marine Science, University of Texas at Austin, 750 Channel View Drive, Port Aransas, TX, 78373, USA
| | - Nina Dombrowski
- Department of Marine Science, University of Texas at Austin, 750 Channel View Drive, Port Aransas, TX, 78373, USA.,NIOZ, Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, Utrecht University, Den Burg, The Netherlands
| | - Lauren Constant
- Department of Marine Science, University of Texas at Austin, 750 Channel View Drive, Port Aransas, TX, 78373, USA
| | - Deana Erdner
- Department of Marine Science, University of Texas at Austin, 750 Channel View Drive, Port Aransas, TX, 78373, USA
| | - Brett J Baker
- Department of Marine Science, University of Texas at Austin, 750 Channel View Drive, Port Aransas, TX, 78373, USA
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198
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Rossbach S, Cardenas A, Perna G, Duarte CM, Voolstra CR. Tissue-Specific Microbiomes of the Red Sea Giant Clam Tridacna maxima Highlight Differential Abundance of Endozoicomonadaceae. Front Microbiol 2019; 10:2661. [PMID: 31849854 PMCID: PMC6901920 DOI: 10.3389/fmicb.2019.02661] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Accepted: 10/31/2019] [Indexed: 02/01/2023] Open
Abstract
Giant clams (subfamily Tridacninae) are prevalent members of coral reef communities and engage in symbioses with algal photosymbionts of the family Symbiodiniaceae, similar to their scleractinian coral counterparts. However, we know little about their associated bacterial microbiome members. Here, we explored bacterial community diversity of digestive system, gill, and mantle tissues associated with the giant clam Tridacna maxima across a cross-shelf gradient (inshore, midshore, and offshore reef sites) in the central Red Sea using 16S rRNA gene amplicon sequencing. Different tissues harbor spatially stable and distinct microbial communities. Notably, diverse assemblages of bacteria affiliated to the family Endozoicomonadaceae were prevalent in all tissues, but particularly abundant in gills and to a lesser extent in digestive tissues. Besides Endozoicomonadaceae, bacteria in the families Pasteurellaceae, Alteromonadaceae, and Comamonadaceae were common associates, depending on the tissue queried. Taxonomy-based functional inference identified processes related to nitrogen cycling (among others) to be enriched in giant clam tissues and contributed by Endozoicomonadaceae. Our study highlights the tissue-specificity and broad taxonomic range of Endozoicomonadaceae associates, similar to other marine invertebrates, and suggests their contribution to nitrogen-related pathways. The investigation of bivalve-associated microbiome communities provides an important addition to the pathogen-focused studies for commercially important bivalves (e.g., oysters).
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Affiliation(s)
- Susann Rossbach
- Red Sea Research Centre (RSRC) and Computational Bioscience Research Center (CBRC), Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Anny Cardenas
- Red Sea Research Centre (RSRC) and Computational Bioscience Research Center (CBRC), Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Gabriela Perna
- Red Sea Research Centre (RSRC) and Computational Bioscience Research Center (CBRC), Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Carlos M Duarte
- Red Sea Research Centre (RSRC) and Computational Bioscience Research Center (CBRC), Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Christian R Voolstra
- Red Sea Research Centre (RSRC) and Computational Bioscience Research Center (CBRC), Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.,Department of Biology, University of Konstanz, Konstanz, Germany
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199
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Mayneris-Perxachs J, Fernández-Real JM. Exploration of the microbiota and metabolites within body fluids could pinpoint novel disease mechanisms. FEBS J 2019; 287:856-865. [PMID: 31709683 DOI: 10.1111/febs.15130] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 09/24/2019] [Accepted: 11/08/2019] [Indexed: 12/25/2022]
Abstract
Thanks to the emergence and recent advances in high-throughput sequencing technologies, it is becoming more evident every day that changes in the microbiome composition are linked to a myriad of health conditions. Despite this, the mechanisms of host-microbiota signalling remain largely unknown. The microbiome has an extensive metabolic activity that leads to the generation of a large number of compounds that are likely to influence host health. Therefore, the microbiome-host cross-talk is in part mediated by microbial-derived metabolites. Unlike metagenomics, which only provides information about microbial genes and thus the microbiome functional potential, metabolic phenotyping is well suited to capture their actual metabolic activity. Here, we provide an overview of these approaches and propose an integration of metagenomics, as a microbiome compositional readout, with faecal and plasma/urine metabolomics, as a functional readout, to unravel novel mechanisms linking the microbiome to host health and disease.
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Affiliation(s)
- Jordi Mayneris-Perxachs
- Department of Endocrinology, Diabetes and Nutrition, Hospital of Girona 'Dr Josep Trueta', University of Girona, Girona Biomedical Research Institute (IdibGi), Spain.,CIBERobn Pathophysiology of Obesity and Nutrition, Instituto de Salud Carlos III, Madrid, Spain
| | - José-Manuel Fernández-Real
- Department of Endocrinology, Diabetes and Nutrition, Hospital of Girona 'Dr Josep Trueta', University of Girona, Girona Biomedical Research Institute (IdibGi), Spain.,CIBERobn Pathophysiology of Obesity and Nutrition, Instituto de Salud Carlos III, Madrid, Spain
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200
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Liang Y, Zhang Y, Zhou C, Li H, Kang X, Wang L, Song J, Jiao N. Cumulative impact of long-term intensive mariculture on total and active bacterial communities in the core sediments of the Ailian Bay, North China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 691:1212-1224. [PMID: 31466202 DOI: 10.1016/j.scitotenv.2019.07.200] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 07/10/2019] [Accepted: 07/13/2019] [Indexed: 06/10/2023]
Abstract
The exponential growth of off-shore mariculture worldwide over the last 20 years has had significant impact on coastal sediment biogeochemistry. However, there are no long-term records of the cumulative impacts of mariculture on the benthic bacterial community. Here, total (DNA) and active (RNA) bacterial community compositions were characterized using MiSeq sequencing of 16S rRNA gene in four core sediments of the Ailian Bay, one of the typical intensive mariculture areas in China with more than fifty-year history of kelp and scallop cultivation. The γ-Proteobacteria, δ-Proteobacteria, Acidobacteria and Acitinobacteria were more abundant in the total bacterial communities, while β-Proteobacteria, Anaerolineae, Clostridia, Spirochaetes and Cyanobacteria were enriched in the active bacterial communities. Significant differences were observed between total and active benthic bacterial communities. The influences of different mariculture modes on the total bacterial communities were more significant than those on the active bacterial communities. Only limited groups of the total bacterial communities were significant influenced by the cumulative effects of the long-term mariculture. The bacterial genera with the function in the sulfide cycling and organic consumption were enriched in the total bacterial population of the integrated multi-trophic aquaculture (IMTA) areas. The variations of both total and active bacterial communities were significantly influenced by grain sizes, total organic carbon and nutrients. Both total and active bacterial communities exhibited a slightly stronger response to environmental factors than to spatial (distance) factors. The effects of mutualism might dominate the total and active bacterial networks in the Ailian Bay. The present study demonstrated that the cumulative influences of the long-term and intensive IMTA mariculture on total benthic bacterial communities in the sub-surface sediments of the Ailian Bay were stronger than those on the active benthic bacterial communities, which provided some insights into the potential ecological roles of specific taxa in the sediments of the IMTA ecosystems.
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Affiliation(s)
- Yantao Liang
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China; Institute of Marine Microbes and Ecospheres, State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361101, China
| | - Yongyu Zhang
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
| | - Chao Zhou
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Hongmei Li
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Xuming Kang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Key Laboratory of Testing and Evaluation for Aquatic Product Safety and Quality, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
| | - Long Wang
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Jinming Song
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Nianzhi Jiao
- Institute of Marine Microbes and Ecospheres, State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361101, China
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