Emergent simplicity in microbial community assembly

Science, Journal Year: 2018, Volume and Issue: 361(6401), P. 469 - 474

Published: Aug. 3, 2018

Interchanging species of similar function Under natural conditions, bacteria form mixed, interacting communities. Understanding how such communities assemble and stabilize is important in a range contexts, from biotechnological applications to what happens our guts. Goldford et al. sampled the microbial soil plants containing hundreds thousands sequence variants. The organisms were passaged after culture low concentrations single carbon sources cross-fed with each other's metabolites; then, resulting sequenced using 16S ribosomal RNA, outcomes modeled mathematically. mix that survived under steady conditions converged reproducibly reflect experimentally imposed rather than initially inoculated—although at coarse phylogenetic levels, taxonomic patterns persisted. Science , this issue p. 469

Language: Английский

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Metabolic network analysis reveals microbial community interactions in anammox granules

Nature Communications, Journal Year: 2017, Volume and Issue: 8(1)

Published: May 31, 2017

Abstract Microbial communities mediating anaerobic ammonium oxidation (anammox) represent one of the most energy-efficient environmental biotechnologies for nitrogen removal from wastewater. However, little is known about functional role heterotrophic bacteria play in anammox granules. Here, we use genome-centric metagenomics to recover 17 draft genomes and a laboratory-scale bioreactor. We combine metabolic network reconstruction with metatranscriptomics examine gene expression identify their potential interactions. find that Chlorobi-affiliated may be highly active protein degraders, catabolizing extracellular peptides while recycling nitrate nitrite. Other heterotrophs also contribute scavenging detritus produced by bacteria, potentially alternative electron donors, such as H 2 , acetate formate. Our findings improve understanding activities interactions between offer first transcriptional insights on ecosystem function

Language: Английский

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Environmental Factors Support the Formation of Specific Bacterial Assemblages on Microplastics

Frontiers in Microbiology, Journal Year: 2018, Volume and Issue: 8

Published: Jan. 19, 2018

While the global distribution of microplastics (MP) in marine environment is currently being critically evaluated, potential role MP as a vector for distinct microbial assemblages or even pathogenic bacteria hardly understood. To gain deeper understanding, we investigated how different situ conditions contribute to composition and specificity MP-associated bacterial communities relation on natural particles. Polystyrene (PS), polyethylene (PE), wooden pellets were incubated 2 weeks along an environmental gradient, ranging from (coastal Baltic Sea) freshwater (waste water treatment plant, WWTP) conditions. The associated well applying high-throughput 16S rRNA gene sequencing. Our setup allowed first time determine MP-dependent -independent assemblage factors subject one system. Most importantly, plastic-specific found develop solely under certain conditions, such lower nutrient concentration higher salinity, while genus Erythrobacter, known ability utilize polycyclic aromatic hydrocarbons (PAH), was specifically across broader section gradient. We discovered no enrichment pathogens PE PS; however, abundant colonization WWTP by commonly with antibiotic resistance suggests possible hotspot horizontal transfer. Taken together, our study clarifies that surrounding prevailingly shapes biofilm communities, but MP-specific exist. These findings point ecological significance specific MP-promoted populations aquatic environments particularly plastic accumulation zones.

Language: Английский

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Common principles and best practices for engineering microbiomes

Nature Reviews Microbiology, Journal Year: 2019, Volume and Issue: 17(12), P. 725 - 741

Published: Sept. 23, 2019

Language: Английский

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Marine Plastic Debris: A New Surface for Microbial Colonization

Environmental Science & Technology, Journal Year: 2020, Volume and Issue: 54(19), P. 11657 - 11672

Published: Sept. 4, 2020

Plastics become rapidly colonized by microbes when released into marine environments. This microbial community—the Plastisphere—has recently sparked a multitude of scientific inquiries and generated breadth knowledge, which we bring together in this review. Besides providing better understanding community composition biofilm development ecosystems, critically discuss current research on plastic biodegradation the identification potentially pathogenic "hitchhikers" Plastisphere. The Plastisphere is at interface between its surrounding milieu, thus drives every interaction that synthetic material has with environment, from ecotoxicity new links food webs to fate plastics water column. We conclude so far not shown communities starkly differ other inert surfaces, particularly true for mature assemblages. Furthermore, despite progress been made field, recognize it time take plastic–Plastisphere–environment interactions step further identifying present gaps our knowledge offering perspective key aspects be addressed future studies: (I) physical characterization biofilms, (II) inclusion relevant controls, (III) study different successional stages, (IV) use environmentally concentrations biofouled microplastics, (V) prioritization gaining mechanistic functional communities.

Language: Английский

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Modifying and reacting to the environmental pH can drive bacterial interactions

PLoS Biology, Journal Year: 2018, Volume and Issue: 16(3), P. e2004248 - e2004248

Published: March 14, 2018

Microbes usually exist in communities consisting of myriad different but interacting species. These interactions are typically mediated through environmental modifications; microbes change the environment by taking up resources and excreting metabolites, which affects growth both themselves also other microbes. We show here that way modify their react to it sets within single-species populations between A very common modification is a pH. find experimentally these pH changes create feedback loops can determine fate bacterial populations; they either facilitate or inhibit growth, extreme cases will cause extinction population. Understanding how single species allowed us estimate pairwise interaction outcomes. Those lead set generic motifs—bistability, successive extended suicide, stabilization—that may be independent parameter modified thus reoccur microbial systems.

Language: Английский

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Microplastic bacterial communities in the Bay of Brest: Influence of polymer type and size

Environmental Pollution, Journal Year: 2018, Volume and Issue: 242, P. 614 - 625

Published: July 14, 2018

Language: Английский

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Microbial interactions and community assembly at microscales

Current Opinion in Microbiology, Journal Year: 2016, Volume and Issue: 31, P. 227 - 234

Published: May 25, 2016

In most environments, microbial interactions take place within microscale cell aggregates. At the scale of these aggregates (∼100 μm), are likely to be dominant driver population structure and dynamics. particular, organisms that exploit interspecific increase ecological performance often co-aggregate. Conversely, antagonize each other will tend spatially segregate, creating distinct micro-communities increased diversity at larger length scales. We argue that, in order understand role biological play community function, it is necessary study spatial organization with enough throughput measure statistical associations between taxa possible alternative states. conclude by proposing strategies tackle this challenge.

Language: Английский

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Evidence for selective bacterial community structuring on microplastics

Environmental Microbiology, Journal Year: 2018, Volume and Issue: 20(8), P. 2796 - 2808

Published: April 3, 2018

In aquatic ecosystems, microplastics are a relatively new anthropogenic substrate that can readily be colonized by biofilm-forming organisms. To examine the effects of type on microbial community assembly, we exposed ambient Baltic bacterioplankton to plastic substrates commonly found in marine environments (polyethylene, polypropylene and polystyrene) as well native (cellulose) inert (glass beads) particles for 2 weeks under controlled conditions. The source communities those biofilms were analyzed Illumina sequencing 16S rRNA gene libraries. All biofilm displayed lower diversity evenness compared with community, suggesting substrate-driven selection. Moreover, plastics-associated distinctly different from non-plastic substrates. Whereas plastics hosted greater than twofold higher abundance Burkholderiales, had significantly proportion Actinobacteria Cytophagia. Variation structure, but not cell abundance, across treatments was strongly linked hydrophobicity. Thus, host distinct bacterial communities, at least during early successional stages.

Language: Английский

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The Ecology and Evolution of Pangenomes

Current Biology, Journal Year: 2019, Volume and Issue: 29(20), P. R1094 - R1103

Published: Oct. 1, 2019

Language: Английский

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