Microbial ecology articles within Nature Communications

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  • Article
    | Open Access

    Pacific oyster mortality syndrome is a poorly understood cause of mortality in commercially important oyster species. Here, the authors use multiple infection experiments to show that the syndrome is caused by sequential infection by herpesvirus and opportunistic bacteria.

    • Julien de Lorgeril
    • , Aude Lucasson
    •  & Guillaume Mitta

  • Article
    | Open Access

    Peatlands recovering from acidification release dissolved organic carbon (DOC), but no biological role has yet been identified in this process. Here, the authors show that pH increases enhance phenol oxidase activity, pore-water DOC concentrations and lead to greater abundances in Actinobacteria and fungi.

    • Hojeong Kang
    • , Min Jung Kwon
    •  & Chris Freeman

  • Article
    | Open Access

    Land use intensification could modify microbial activity and thus ecosystem function. Here, Malik et al. sample microbes and carbon-related functions across a land use gradient, demonstrating that microbial biomass and carbon use efficiency are reduced in human-impacted near-neutral pH soils.

    • Ashish A. Malik
    • , Jeremy Puissant
    •  & Robert I. Griffiths

  • Article
    | Open Access

    Permafrost thaw allows biological activity in previously frozen ground, leading to a potential release of climate-relevant gases. Here the authors show that thawing permafrost emits volatile organic compounds but that their release to the atmosphere is limited by microbial consumption in the overlaying soil.

    • Magnus Kramshøj
    • , Christian N. Albers
    •  & Riikka Rinnan

  • Article
    | Open Access

    Higher-order interactions occur when one species mediates the interaction between two others. Here, the authors model microbial growth and competition to show that higher-order interactions can arise from tradeoffs in growth traits, leading to neutral coexistence and other complex dynamics.

    • Michael Manhart
    •  & Eugene I. Shakhnovich

  • Article
    | Open Access

    The means by which planktonic cyanobacteria were able to persist through the Archean despite high fluxes of UV radiation are unclear. Here, the authors show that Fe(III)-Si rich precipitates in the Archean photic zone could have provided early planktonic cyanobacteria an effective shield against UV-C radiation.

    • Aleksandra M. Mloszewska
    • , Devon B. Cole
    •  & Kurt. O Konhauser

  • Article
    | Open Access

    Drought conditions can alter the composition of soil microbial communities, but the effects of drought on network properties have not been tested. Here, de Vries and colleagues show that co-occurrence networks are destabilised under drought for bacteria but not fungi.

    • Franciska T. de Vries
    • , Rob I. Griffiths
    •  & Richard D. Bardgett

  • Article
    | Open Access

    Network stability is a central topic in theoretical ecology, with most work focusing on mutualistic or food web networks. Here, the authors explore the stability of microbial networks based on the consumption and exchange of resources, showing that asymmetry in crossfeeding relationships can destabilize networks.

    • Stacey Butler
    •  & James P. O’Dwyer

  • Article
    | Open Access

    Power et al. catalogue the microbial biodiversity and physicochemistry of around 1000 hotsprings across New Zealand, providing insights into the ecological conditions that drive community assembly in these ecosystems.

    • Jean F. Power
    • , Carlo R. Carere
    •  & Matthew B. Stott

  • Article
    | Open Access

    Microbiota composition fluctuates in response to changes in environmental and lifestyle factors. Here, Hicks et al. show that the faecal microbiota of wild gorillas and chimpanzees is temporally dynamic, with shifts that correlate with seasonal rainfall patterns and periods of high and low frugivory.

    • Allison L. Hicks
    • , Kerry Jo Lee
    •  & Brent L. Williams

  • Article
    | Open Access

    Ammonia-oxidising archaea (AOA) were only discovered a little over a decade ago and remain poorly characterized despite their ubiquity and importance for nitrogen cycling. Here, the authors define a taxonomy of AOA based on a resolved amoA phylogeny and describe emergent global patterns in AOA diversity.

    • Ricardo J. Eloy Alves
    • , Bui Quang Minh
    •  & Christa Schleper

  • Article
    | Open Access

    Nitrite tends to peak at the base of the sunlit zone in the ocean, but the ecological drivers of the local and global distributions of nitrite are not known. Here, Zakem et al. use a marine ecosystem model to show how the interactions of nitrifying microbes mediate nitrite accumulation.

    • Emily J. Zakem
    • , Alia Al-Haj
    •  & Michael J. Follows

  • Article
    | Open Access

    It is unclear how cell adhesion and elongation coordinate during formation of bacterial microcolonies. Here, Duvernoy et al. monitor microcolony formation in rod-shaped bacteria, and show that patterns of surface colonization derive from the spatial distribution of adhesive factors on the cell envelope.

    • Marie-Cécilia Duvernoy
    • , Thierry Mora
    •  & Nicolas Desprat

  • Article
    | Open Access

    Polysaccharides are the primary structural cell wall and energy storage molecules of seaweed. Here, the authors show how the geographically restricted dietary polysaccharide agarose is selectively utilized by the human intestinal bacterium Bacteroides uniformis, providing insight into how carbohydrate metabolism evolves within the human microbiome.

    • Benjamin Pluvinage
    • , Julie M. Grondin
    •  & D. Wade Abbott

  • Article
    | Open Access

    The role of ecosystem structure in microbial activity related to greenhouse gas production is poorly understood. Here, Taş and colleagues show that microbial communities and ecosystem function vary across fine-scale topography in a polygonal tundra.

    • Neslihan Taş
    • , Emmanuel Prestat
    •  & Janet K. Jansson

  • Article
    | Open Access

    Spatial organisation of bacteria could contribute to the persistence of anoxic hotspots in soils, however such processes are difficult to observe directly. Here, the authors develop an experimental platform mimicking resource gradients postulated in soil aggregates to assess bacterial spatial organisation.

    • Benedict Borer
    • , Robin Tecon
    •  & Dani Or

  • Article
    | Open Access

    Oral microbial communities are excellent sites for examining the mechanisms of structural variation in the microbiota. Here, the authors use spatial and ecological analysis to examine over 9000 dental and mucosal microbiota samples. They find that saliva plays a key role in structuring bacterial communities in the mouth.

    • Diana M. Proctor
    • , Julia A. Fukuyama
    •  & David A. Relman

  • Article
    | Open Access

    Marine microbial eukaryotes and zooplankton display enormous diversity and largely unexplored physiologies. Here, the authors use metatranscriptomics to analyze four organismal size fractions from open-ocean stations, providing the largest reference collection of eukaryotic transcripts from any single biome.

    • Quentin Carradec
    • , Eric Pelletier
    •  & Patrick Wincker

  • Article
    | Open Access

    Whether marine microbes form strongly differentiated communities over time remains unknown. Here, Martin-Platero and colleagues develop a time series analysis to characterize marine bacteria and Eukarya communities at a fine temporal grain, revealing cohesive but rapidly changing communities.

    • Antonio M. Martin-Platero
    • , Brian Cleary
    •  & Martin F. Polz

  • Article
    | Open Access

    Body size is hypothesised to be a major determinant of β-diversity in passively-dispersing marine organisms. Here, Villarino et al. show that plankton body size determines rates of dispersal along marine currents, with shorter dispersal and higher species spatial turnover in larger organisms.

    • Ernesto Villarino
    • , James R. Watson
    •  & Guillem Chust

  • Article
    | Open Access

    Bacillus subtilis withstands starvation by forming dormant spores that revive when nutrients become available. Here, Mutlu et al. show that sporulation timing controls spore revival through a phenotypic ‘memory’ that arises from the carry-over of a metabolic enzyme from the vegetative cell into the spore.

    • Alper Mutlu
    • , Stephanie Trauth
    •  & Ilka B. Bischofs

  • Article
    | Open Access

    Metagenomic sequencing provides a window into microbial community structure and metabolic potential. Here, Swenson et al. integrate metabolomics and shotgun sequencing to functionally link microbial community structure with environmental chemistry in biological soil crust (biocrust).

    • Tami L. Swenson
    • , Ulas Karaoz
    •  & Trent R. Northen

  • Article
    | Open Access

    Interactions between bacteria and fungi are common and contribute to ecosystem processes. Here, Jung et al. show that the interaction between two plant pathogens (a seed-borne bacterium and an air-borne fungus) promotes their own survival and dispersal, as well as disease progression on rice plants.

    • Boknam Jung
    • , Jungwook Park
    •  & Jungkwan Lee

  • Article
    | Open Access

    Predatory or competitive interactions between microbes are poorly understood but likely influence global nutrient cycles. Here, the authors show that Pseudomonas bacteria could immobilize algal cells, potential prey, by releasing secondary metabolites that induce a Ca2+ signal and algal deflagellation.

    • Prasad Aiyar
    • , Daniel Schaeme
    •  & Maria Mittag

  • Article
    | Open Access

    Convenient methods for assessing microbial community structure in terms of biomass are lacking. Here, the authors present a metaproteomics-based approach for assessing microbial community structure using protein abundance as a measure for biomass contributions of individual populations.

    • Manuel Kleiner
    • , Erin Thorson
    •  & Marc Strous

  • Article
    | Open Access

    Methane production is traditionally not found in oxygenated soils, a paradigm incorporated in global greenhouse gas modelling efforts. Here the authors show geochemical and biological evidence of active methanogenesis in bulk-oxic wetland soils, attributing up to 80% of the total methane budget for the site.

    • Jordan C. Angle
    • , Timothy H. Morin
    •  & Kelly C. Wrighton

  • Article
    | Open Access

    Little is known about Marinimicrobia, a group of bacteria that are prevalent in the oceans. Here, the authors study global populations of Marinimicrobia using single-cell genomics, metagenomics and metatranscriptomics, showing potential co-metabolic interactions and participation in the sulfur and nitrogen cycles.

    • Alyse K. Hawley
    • , Masaru K. Nobu
    •  & Steven J. Hallam

  • Article
    | Open Access

    Microbes live in communities and exchange metabolites, but the resulting dynamics are poorly understood. Here, the authors study the interplay between metabolite production strategies and population dynamics, and find that complex and unexpected dynamics emerge even in simple microbial economies.

    • Yoav Kallus
    • , John H. Miller
    •  & Eric Libby

  • Article
    | Open Access

    The impacts of top down (precipitation) and bottom-up (groundwater rise) wetting processes on carbon sequestration are poorly understood. Here, the authors use incubation experiments to show that drought legacy and pore-scale wetting patterns are important factors controlling short-term carbon dynamics.

    • A. Peyton Smith
    • , Ben Bond-Lamberty
    •  & Vanessa L. Bailey

  • Article
    | Open Access

    High latitude soils can store around 40 % of the Earth’s soil carbon. Here, the authors add 13C-labeled cellulose to frozen mesocosms of boreal forest soils and find that cellulose biopolymers are hydrolysed under frozen conditions and therefore contribute to the slow degradation of soil organic matter.

    • Javier H. Segura
    • , Mats B. Nilsson
    •  & Mats G. Öquist

  • Article
    | Open Access

    Microbes adapting to broad and specialized ranges of environments (generalists and specialists) have distinct ecological roles and properties. Via meta-analysis of community sequencing datasets, Sriswasdi et al. show that generalists have higher speciation rates and persistence advantage over specialists.

    • Sira Sriswasdi
    • , Ching-chia Yang
    •  & Wataru Iwasaki

  • Article
    | Open Access

    The impacts of carbon capture and storage (CCS) on subsurface microorganisms are poorly understood. Here, the authors show that deep ecosystems respond quickly to CO2 injections and that the environmental consequences of their metabolic activities need to be properly assessed for sustainable CCS in basalt.

    • Rosalia Trias
    • , Bénédicte Ménez
    •  & Emmanuelle Gérard

  • Article
    | Open Access

    Peptide CSP regulates natural competence in pneumococci and has been proposed as a quorum-sensing signal or a probe for sensing environmental cues. Here, the authors show that CSP levels can indeed act as an indicator of cell density and also incorporate information on environmental factors or cell history.

    • Stefany Moreno-Gámez
    • , Robin A. Sorg
    •  & Jan-Willem Veening

  • Article
    | Open Access

    Virophages are recently-identified small viruses that infect larger viruses, yet their diversity and ecological roles are poorly understood. Here, Roux and colleagues present time series metagenomics data revealing new virophage genera and their putative ecological interactions in two freshwater lakes.

    • Simon Roux
    • , Leong-Keat Chan
    •  & Matthew B. Sullivan

  • Article
    | Open Access

    The role of dissolved organic carbon (DOC) photo-alteration in the microbial respiration of DOC to CO2 is unclear. Here, the authors show that the impact of this mechanism depends on whether photo-alteration of DOC produces or removes molecules used by native microbial communities prior to light exposure.

    • Collin P. Ward
    • , Sarah G. Nalven
    •  & Rose M. Cory

  • Article
    | Open Access

    The structure and dynamics of microbial communities reflect trade-offs in the ability to use different resources. Here, Josephides and Swain incorporate metabolic trade-offs into an eco-evolutionary model to predict networks of mutational paths and the evolutionary outcomes for microbial communities.

    • Christos Josephides
    •  & Peter S. Swain

  • Article
    | Open Access

    The cells of Achromatium bacteria are remarkably large and contain multiple chromosome copies. Here, Ionescu et al. show that chromosome copies within individual cells display high diversity, similar to that of bacterial communities, and contain tens of transposable elements.

    • Danny Ionescu
    • , Mina Bizic-Ionescu
    •  & Hans-Peter Grossart

  • Article
    | Open Access

    Environmental factors often outweigh host heritable factors in structuring host-associated microbiomes. Here, Bowen et al. show that host lineage is crucial for determination of rhizosphere bacterial communities in Phragmites australis, a globally distributed invasive plant.

    • Jennifer L. Bowen
    • , Patrick J. Kearns
    •  & Laura A. Meyerson

  • Article
    | Open Access

    Lab strains of Pseudomonas are model systems for the evolution of cooperation over public goods (iron-scavenging siderophores). Here, Butaitė et al. add ecological and evolutionary insight into this system by showing that cheating and resistance to cheating both shape competition for iron in natural Pseudomonas communities.

    • Elena Butaitė
    • , Michael Baumgartner
    •  & Rolf Kümmerli

  • Article
    | Open Access

    Some bacteria can feed on live fungi through unclear mechanisms. Here, the authors show that a T3SS-secreted protein, which is homologous to phage tail proteins, allows a Burkholderia gladioli strain to kill and feed on various fungal species.

    • Durga Madhab Swain
    • , Sunil Kumar Yadav
    •  & Gopaljee Jha

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