Water microbiology articles within Nature Communications

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  • Article
    | Open Access

    Aerobic methanotrophic bacteria are considered strict aerobes but are often highly abundant in hypoxic or anoxic environments. Here, the authors show that acidophilic methanotrophs can respire nitrous oxide and grow anaerobically on diverse non-methane substrates, including methanol, C-C substrates, and hydrogen.

    • Samuel Imisi Awala
    • , Joo-Han Gwak
    •  & Sung-Keun Rhee

  • Article
    | Open Access

    Phytoplankton blooms provoke bacterioplankton blooms, from which bacterial biomass (necromass) is released via zooplankton grazing and viral lysis. Here, Beidler et al. show that the bacterial biomass, including alpha-glucan polysaccharides generated from the consumption of algal organic matter, is reused by microbes in vitro and during a diatom-dominated bloom.

    • Irena Beidler
    • , Nicola Steinke
    •  & Thomas Schweder

  • Article
    | Open Access

    Carbohydrate binding modules (CBMs) are non-catalytic domains found within multi-modular carbohydrate-active enzymes like glycoside hydrolases. Here, the authors show the crystal structures of two CBM family 92 members, which use three different surface binding sites to bind to β-glucans.

    • Meng-Shu Hao
    • , Scott Mazurkewich
    •  & Lauren S. McKee

  • Article
    | Open Access

    Little is known about viral communities in deep-sea seamounts. In this study, the authors performed metagenomic and virome analysis from sediments in the western Pacific Ocean and characterize the diversity, distribution and potential ecological roles of viruses in deep-sea seamount sediments.

    • Meishun Yu
    • , Menghui Zhang
    •  & Min Jin

  • Article
    | Open Access

    This study shows that a multitrophic community model jointly recapitulates diel rhythms in abundances of Prochlorococcus picocyanobacteria, as well as viral infection, viral abundances and grazer abundances. Model-data integration implies that grazing predominantly controls Prochlorococcus abundances in surface waters of the North Pacific Subtropical Gyre, despite high viral densities.

    • Stephen J. Beckett
    • , David Demory
    •  & Joshua S. Weitz

  • Article
    | Open Access

    Herbicides used in terrestrial environments pollute coastal ecosystems. Here, the authors analyse the presence of 32 herbicides at 661 bays and gulfs worldwide from 1990 to 2022, showing how under current herbicide stress, phytoplankton primary productivity was inhibited by more than 5% at 25%.

    • Liqiang Yang
    • , Xiaotong He
    •  & Yongyu Zhang

  • Article
    | Open Access

    The Tibetan Plateau is the largest plateau in the world and hosts a variety of aquatic ecosystems. Here, the authors present a gene and genome catalogue of Tibetan Plateau aquatic microbiomes, greatly expanding known taxonomic and functional diversity for the region and giving insights into its microbial biogeography.

    • Mingyue Cheng
    • , Shuai Luo
    •  & Kang Ning

  • Article
    | Open Access

    It is unclear whether microbes can efficiently degrade biodegradable plastics in the extreme environmental conditions of the seafloor. Here, Omura et al. show that biodegradable plastics can be degraded by the action of microorganisms on the deep-sea floor, although with much less efficiency than in coastal settings.

    • Taku Omura
    • , Noriyuki Isobe
    •  & Tadahisa Iwata

  • Article
    | Open Access

    Phage satellites are bacterial genetic elements that co-opt phage machinery for their own dissemination. Here, Barcia-Cruz et al. identify a family of satellites, named PICMIs, that are characterized by reduced gene content and are broadly distributed in marine bacteria of the family Vibrionaceae.

    • Rubén Barcia-Cruz
    • , David Goudenège
    •  & Frédérique Le Roux

  • Article
    | Open Access

    This study investigates the dynamic associations among microbes in the world’s tropical and subtropical oceans. It reveals that potential interactions vary with ocean depth and location, with most surface associations not persisting in deeper waters. The results contribute to understanding the ocean microbiome in the context of global change.

    • Ina M. Deutschmann
    • , Erwan Delage
    •  & Ramiro Logares

  • Article
    | Open Access

    The ability of marine bacteria to direct their movement in response to chemical gradients influences inter-species interactions, nutrient turnover, and ecosystem productivity. Here, Clerc et al. show that marine bacteria are strongly attracted to algal polysaccharides, and this chemotactic behaviour is enhanced by dimethylsulfoniopropionate (DMSP), a ubiquitous algal metabolite.

    • Estelle E. Clerc
    • , Jean-Baptiste Raina
    •  & Roman Stocker

  • Article
    | Open Access

    Most clinical isolates of the pathogenic yeast Candida orthopsilosis are hybrids of two parental lineages, only one of which has been identified. Here, del Olmo et al. show that C. orthopsilosis strains isolated from warm seawater are hybrids closely related to clinical isolates, and identify the missing parental lineage, thus providing a more complete view of the genomic evolution of this species.

    • Valentina del Olmo
    • , Verónica Mixão
    •  & Toni Gabaldón

  • Article
    | Open Access

    Here, the authors provide evidence that marine viruses spread via aerosolization and rain through the natural water cycle. Hosts from the first centimeters of the marine water column show signs of immunity against rain viruses. Those have DNA adaptations facilitating their stay in the air.

    • Janina Rahlff
    • , Sarah P. Esser
    •  & Alexander J. Probst

  • Article
    | Open Access

    Viruses are ubiquitous in the oceans, exhibiting high abundance and diversity. Here, Yi et al. present a systematic catalogue and analysis of genomic sequences from marine prokaryotes and their proviruses, thus contributing to a better understanding of the ecology of these microorganisms.

    • Yi Yi
    • , Shunzhang Liu
    •  & Huahua Jian

  • Article
    | Open Access

    Common methods for water disinfection involve oxidation or irradiation, and are often associated with a high carbon footprint and formation of toxic byproducts. Here, the authors describe a nano-structured material that is highly effective at killing bacteria in water through a hydrodynamic mechanism driven by mild water flow, in the absence of additional energy supply.

    • Lu Peng
    • , Haojie Zhu
    •  & Hong-Ying Hu

  • Article
    | Open Access

    Bacterial remineralization of algal organic matter promotes algal growth but is rarely quantified. Here, Mayali et al. quantify bacterial incorporation of algal-derived organic carbon and nitrogen, and algal incorporation of remineralized carbon and nitrogen, for 15 bacterial co-cultures growing with the diatom Phaeodactylum tricornutum to identify functional guilds of metabolic interactions.

    • Xavier Mayali
    • , Ty J. Samo
    •  & Peter K. Weber

  • Article
    | Open Access

    Anaerobic digestion of municipal mixed sludge is a microbial-mediated process that produces renewable natural gases such as methane. Here, Kieft et al. present the results of a two-year study of microbial community structure and function at a wastewater treatment plant, shedding light on metabolic interactions between microorganisms in relation with methane production.

    • Brandon Kieft
    • , Niko Finke
    •  & Steven J. Hallam

  • Article
    | Open Access

    Bacteria of the SAR202 clade are ubiquitously distributed in the ocean, but their biology is poorly understood due to the lack of cultivated isolates. Here, Lim et al. report the cultivation of marine SAR202 bacteria and provide insights into the physiology of these enigmatic microorganisms.

    • Yeonjung Lim
    • , Ji-Hui Seo
    •  & Jang-Cheon Cho

  • Article
    | Open Access

    The material-based evolution of organisms has attracted broad interdisciplinary interest, however, the fabrication of material-integrated organelles remains inadequately exploited. Here the authors engineer a bioartificial organism by integrating a semiartificial and specific virus-scavenging organelle to scavenge pathogenic waterborne viruses.

    • Huixin Li
    • , Yanpeng Xu
    •  & Ruikang Tang

  • Article
    | Open Access

    Here, the authors report the isolation and genetic characterization of 25 unique crAss-like phages (termed “crAssBcn”) infecting Bacteroides intestinalis, and show that CrAssBcn phages are commonly found in fecal samples from people around the globe, indicating their wide distribution.

    • María Dolores Ramos-Barbero
    • , Clara Gómez-Gómez
    •  & Maite Muniesa

  • Article
    | Open Access

    Amazonian blackwaters are acidic and physiologically-challenging, but are one of Earth’s most diversified ecosystems. This study revealed that fish survival in these hostile habitats depends on the colonization of their gills by endogenous blackwater Betaproteobacteria, with the potential to regulate host ionoregulatory processes.

    • Sylvain François-Étienne
    • , Leroux Nicolas
    •  & Derome Nicolas

  • Article
    | Open Access

    Cable bacteria are centimeter-long filamentous microbes that conduct electrons via internal wires, thus coupling sulfide oxidation between sediment layers. Here, Bjerg et al. show that the anoxic part of oxygen-respiring cable bacteria attracts swarms of other bacteria, which appear to transfer electrons to cable bacteria via soluble metabolites.

    • Jesper J. Bjerg
    • , Jamie J. M. Lustermans
    •  & Andreas Schramm

  • Article
    | Open Access

    Temperature shapes the adaptation and composition of microbiomes, but whether their enzymes drive the thermal response remains unknown. Using an analysis of seven enzyme classes from worldwide marine microbiome data, this study shows that enzyme thermal properties explain microbial thermal plasticity and they are both finely tuned by the thermal variability of the environment.

    • Ramona Marasco
    • , Marco Fusi
    •  & Daniele Daffonchio

  • Article
    | Open Access

    Genome mining for biosynthetic gene clusters (BGCs) can be used for the discovery of new compounds of biotechnological interest. Here, the authors use metagenomics and metatranscriptomics to identify diverse BGCs in free-living and particle-associated microbial communities through the stratified water column of the Cariaco Basin, Venezuela.

    • David Geller-McGrath
    • , Paraskevi Mara
    •  & Maria Pachiadaki

  • Article
    | Open Access

    The mechanisms underlying methane production in oxygenated waters of oceans and lakes are unclear. Here, Perez-Coronel and Beman show that aerobic methane production in freshwater incubation experiments is associated with (bacterio)chlorophyll metabolism and photosynthesis, and with Proteobacterial degradation of methylphosphonate.

    • Elisabet Perez-Coronel
    •  & J. Michael Beman

  • Article
    | Open Access

    Ultra-high resolution mass spectrometry revealed that plastic bags leach labile compounds. Bioassays performed in Scandinavian lakes indicated that these compounds are incorporated into biomass faster and more efficiently than natural organic matter.

    • Eleanor A. Sheridan
    • , Jérémy A. Fonvielle
    •  & Andrew J. Tanentzap

  • Article
    | Open Access

    Using CRISPR-Cas9 mediated-knockout and overexpression analyses, this study shows that a trypsin in the diatom Phaeodactylum tricornutum promotes phosphorus uptake and inhibits nitrogen uptake but its expression is downregulated under nitrogen stress and upregulated under phosphorus stress. Together, the findings suggest this trypsin is a coordinate regulator of nutrient homeostasis.

    • Yanchun You
    • , Xueqiong Sun
    •  & Senjie Lin

  • Article
    | Open Access

    The effects of fertiliser from intensive agriculture are well recognised, but not so well for fine-sediment. Here we show how widespread ingress of agriculturally derived fine-sediment since the 1940s markedly amplifies methane emissions from streams.

    • Yizhu Zhu
    • , J. Iwan Jones
    •  & Mark Trimmer

  • Article
    | Open Access

    In glacier-fed streams, ecological windows of opportunity allow complex microbial biofilms to develop and transiently form the basis of the food web. Using metagenomics, this study reveals the metabolic strategies and key genomic underpinnings of adaptive traits that enable these biofilms to exploit environmental opportunities.

    • Susheel Bhanu Busi
    • , Massimo Bourquin
    •  & Tom J. Battin

  • Article
    | Open Access

    Microbial communities are responsible for biological wastewater treatment. Here, Dueholm et al. generate more than 5 million high-quality, full-length 16S rRNA gene sequences from wastewater treatment plants across the world to construct a database with a comprehensive taxonomy, providing insights into diversity and function of these microbial communities.

    • Morten Kam Dahl Dueholm
    • , Marta Nierychlo
    •  & Per Halkjær Nielsen

  • Article
    | Open Access

    To monitor the presence of novel SARS-CoV-2 variants in New York City, Smyth et al. perform deep-sequencing of the receptor binding domain of S protein in wastewater samples and find novel cryptic lineages containing mutations affecting ACE2-tropism and showing decreased neutralization by antibodies.

    • Davida S. Smyth
    • , Monica Trujillo
    •  & John J. Dennehy

  • Article
    | Open Access

    The host range of bacteriophages defines their impact on bacterial ecology and diversity. Here, Göller et al. isolate 94 staphylococcal phages from wastewater and determine their host range on 117 staphylococci from 29 species, revealing a predominant multi-species host range and thus great potential for horizontal gene transfer.

    • Pauline C. Göller
    • , Tabea Elsener
    •  & Elena Gómez-Sanz

  • Article
    | Open Access

    Over the past century, the Western Antarctic Peninsula has experienced rapid warming and a substantial loss of sea ice with important implications for plankton biodiversity and carbon cycling. Using a 5-year DNA metabarcoding dataset, this study assesses how interannual variability in sea-ice conditions impacts biodiversity and biological carbon fluxes in this region.

    • Yajuan Lin
    • , Carly Moreno
    •  & Nicolas Cassar

  • Article
    | Open Access

    Microbes play key roles in wastewater treatment. Here, Singleton et al. use long-read and short-read sequencing to recover 1083 high-quality metagenome-assembled genomes from 23 wastewater treatment plants, and combine this information with amplicon data, Raman microspectroscopy and FISH to reveal functionally important lineages.

    • Caitlin M. Singleton
    • , Francesca Petriglieri
    •  & Mads Albertsen

  • Article
    | Open Access

    Herold et al. present an integrated meta-omics framework to investigate how mixed microbial communities, such as oleaginous bacterial populations in biological wastewater treatment plants, respond with distinct adaptation strategies to disturbances. They show that community resistance and resilience are a function of phenotypic plasticity and niche complementarity.

    • Malte Herold
    • , Susana Martínez Arbas
    •  & Paul Wilmes

  • Article
    | Open Access

    Dimethylsulfoniopropionate (DMSP) is an osmolyte produced by marine microbes that plays an important role in nutrient cycling and atmospheric chemistry. Here the authors go to the Mariana Trench—the deepest point in the ocean—and find bacteria are key DMSP producers, and that DMSP has a role in protection against high pressure.

    • Yanfen Zheng
    • , Jinyan Wang
    •  & Xiao-Hua Zhang

  • Article
    | Open Access

    Bacteria capable of anaerobic ammonium oxidation (anammox) produce half of the nitrogen gas in the atmosphere, but much of their physiology is still unknown. Here the authors show that anammox bacteria are capable of a novel mechanism of ammonium oxidation using extracellular electron transfer.

    • Dario R. Shaw
    • , Muhammad Ali
    •  & Pascal E. Saikaly

  • Article
    | Open Access

    Anthropogenic CO2 emissions are causing ocean acidification, which can affect the physiology of some organisms. Here, Botté et al. use metagenomics to show differences in metabolic potential between sponge microbiomes sampled at a shallow volcanic CO2 seep and those from nearby control sites.

    • Emmanuelle S. Botté
    • , Shaun Nielsen
    •  & Nicole S. Webster

  • Article
    | Open Access

    Obtaining data on antimicrobial resistance (AMR) from healthy human populations is difficult. Here, Hendriksen et al. use metagenomic analysis to obtain AMR data from untreated sewage from 79 sites in 60 countries, finding correlations with socio-economic, health and environmental factors.

    • Rene S. Hendriksen
    • , Patrick Munk
    •  & Frank M. Aarestrup

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