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Persistent activity of aerobic methane-oxidizing bacteria in anoxic lake waters due to metabolic versatility
The occurrence of aerobic methane-oxidizing bacteria in anoxic environments is puzzling, as oxygen is thought to be required for methane oxidation. Here, Schorn et al. show that the methane assimilation activity of these bacteria is similar under hypoxic and anoxic conditions in a stratified lake, and the bacteria use fermentation-based methanotrophy as well as denitrification under anoxic conditions.
- Sina Schorn
- , Jon S. Graf
- & Jana Milucka
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A non-methanogenic archaeon within the order Methanocellales
Several groups of archaea, such as the order Methanocellales, are characterised by their ability to produce methane. Here, Suzuki et al. identify a Methanocellales archaeon that lacks essential methanogenesis genes and seems to be instead a CO2-reducing, electron-fueled acetogen.
- Shino Suzuki
- , Shun’ichi Ishii
- & Kenneth H. Nealson
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Growth of electroautotrophic microorganisms using hydrovoltaic energy through natural water evaporation
Devices based on microbial biofilms can be used to generate hydrovoltaic energy from water evaporation. Here, Ren et al. show that, in addition, electroautotrophic bacteria can use evaporation-induced hydrovoltaic electrons for growth in biofilms.
- Guoping Ren
- , Jie Ye
- & Shungui Zhou
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Global biogeography of microbes driving ocean ecological status under climate change
Zhang et al. propose the ecological status of the ocean by considering microbial diversity, structure, and biogeochemical potential. Ecological status of 32.44% surface ocean will change due to climate change in 2100, assuming no policy intervention.
- Zhenyan Zhang
- , Qi Zhang
- & Haifeng Qian
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Phosphorus deficiency alleviates iron limitation in Synechocystis cyanobacteria through direct PhoB-mediated gene regulation
Iron and phosphorus exist at low concentrations in surface waters and may be co-limiting resources for phytoplankton growth. Here, the authors show that phosphorus deficiency increases the growth of iron-limited cyanobacteria through a PhoB-mediated regulatory network.
- Guo-Wei Qiu
- , Wen-Can Zheng
- & Bao-Sheng Qiu
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Nitrous oxide respiration in acidophilic methanotrophs
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
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Alpha-glucans from bacterial necromass indicate an intra-population loop within the marine carbon cycle
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
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Freshwater genome-reduced bacteria exhibit pervasive episodes of adaptive stasis
Here, by applying evolutionary genomics approaches to metagenomics data of lake microbiomes, the authors reveal that freshwater species with small genomes face extended periods with their niche adaptation capabilities frozen.
- Lucas Serra Moncadas
- , Cyrill Hofer
- & Adrian-Stefan Andrei
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Structural and biochemical analysis of family 92 carbohydrate-binding modules uncovers multivalent binding to β-glucans
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
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Diversity and potential host-interactions of viruses inhabiting deep-sea seamount sediments
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
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Disentangling top-down drivers of mortality underlying diel population dynamics of Prochlorococcus in the North Pacific Subtropical Gyre
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
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Herbicide leakage into seawater impacts primary productivity and zooplankton globally
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
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A genome and gene catalog of the aquatic microbiomes of the Tibetan Plateau
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
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Microbial decomposition of biodegradable plastics on the deep-sea floor
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
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Phage-inducible chromosomal minimalist islands (PICMIs), a novel family of small marine satellites of virulent phages
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
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Disentangling microbial networks across pelagic zones in the tropical and subtropical global ocean
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
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Strong chemotaxis by marine bacteria towards polysaccharides is enhanced by the abundant organosulfur compound DMSP
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
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Origin of fungal hybrids with pathogenic potential from warm seawater environments
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
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Marine viruses disperse bidirectionally along the natural water cycle
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
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Multi-heme cytochrome-mediated extracellular electron transfer by the anaerobic methanotroph ‘Candidatus Methanoperedens nitroreducens’
Anaerobic methanotrophic archaea play crucial roles in the methane cycle. Here, Zhang et al. provide experimental evidence supporting that multi-heme cytochromes mediate extracellular electron transfer for the reduction of metals and electrodes in these microorganisms.
- Xueqin Zhang
- , Georgina H. Joyce
- & Shihu Hu
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A systematic analysis of marine lysogens and proviruses
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
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Hydrodynamic tearing of bacteria on nanotips for sustainable water disinfection
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
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Single-cell isotope tracing reveals functional guilds of bacteria associated with the diatom Phaeodactylum tricornutum
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
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Genome-resolved correlation mapping links microbial community structure to metabolic interactions driving methane production from wastewater
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
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Cultivation of marine bacteria of the SAR202 clade
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
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Material-engineered bioartificial microorganisms enabling efficient scavenging of waterborne viruses
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
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Characterization of crAss-like phage isolates highlights Crassvirales genetic heterogeneity and worldwide distribution
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
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Important role of endogenous microbial symbionts of fish gills in the challenging but highly biodiverse Amazonian blackwaters
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
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A joint proteomic and genomic investigation provides insights into the mechanism of calcification in coccolithophores
Coccolithophorid algae are globally important for marine biogeochemical cycles, but the molecular basis of their biology is poorly understood. Using proteomics and a new genome, Skeffington et al. identify candidate proteins involved in calcification in Emiliania huxleyi.
- Alastair Skeffington
- , Axel Fischer
- & André Scheffel
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Hydrogen and dark oxygen drive microbial productivity in diverse groundwater ecosystems
Microbes in ancient groundwaters can be very diverse and productive. Some microbes seem to produce oxygen in the dark, which others use to consume the greenhouse gas methane. Their metabolisms are relevant for groundwater health and global change.
- S. Emil Ruff
- , Pauline Humez
- & Marc Strous
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Trajectories of freshwater microbial genomics and greenhouse gas saturation upon glacial retreat
Diverse microbial trajectories in carbon and nitrogen cycle processes represent a positive feedback loop of deglaciation on climate warming.
- Jing Wei
- , Laurent Fontaine
- & Alexander Eiler
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O2 partitioning of sulfur oxidizing bacteria drives acidity and thiosulfate distributions in mining waters
Microbial genomics is a widely under-utilized tool in mining in understanding water quality drivers. Here the authors show early acid generation and thiosulfate concentrations are driven by O2 dependent microbial sulfur oxidizing bacterial niches in a mine tailings impoundment
- Kelly J. Whaley-Martin
- , Lin-Xing Chen
- & Lesley A. Warren
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Cable bacteria with electric connection to oxygen attract flocks of diverse bacteria
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
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Enzyme adaptation to habitat thermal legacy shapes the thermal plasticity of marine microbiomes
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
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Diverse secondary metabolites are expressed in particle-associated and free-living microorganisms of the permanently anoxic Cariaco Basin
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
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Viral infection switches the balance between bacterial and eukaryotic recyclers of organic matter during coccolithophore blooms
Algal blooms are hotspots of marine primary production that play central roles in microbial ecology and global elemental cycling. Here, the authors show how bloom termination by viral infection can shift the balance between eukaryotic and prokaryotic recyclers of phytoplankton biomass.
- Flora Vincent
- , Matti Gralka
- & Assaf Vardi
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Multiple sources of aerobic methane production in aquatic ecosystems include bacterial photosynthesis
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
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Terrigenous dissolved organic matter persists in the energy-limited deep groundwaters of the Fennoscandian Shield
Dissolved organic matter in the Fennoscandian Shield deep continental bedrock fracture waters of varying characteristics and ages carries a strong terrigenous signature, and only a small proportion of this potential energy source links to the deep biosphere microbial community.
- Helena Osterholz
- , Stephanie Turner
- & Mark Dopson
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Plastic pollution fosters more microbial growth in lakes than natural organic matter
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
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Trypsin is a coordinate regulator of N and P nutrients in marine phytoplankton
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
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Separating natural from human enhanced methane emissions in headwater streams
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
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Genomic and metabolic adaptations of biofilms to ecological windows of opportunity in glacier-fed streams
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
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MiDAS 4: A global catalogue of full-length 16S rRNA gene sequences and taxonomy for studies of bacterial communities in wastewater treatment plants
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
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Tracking cryptic SARS-CoV-2 lineages detected in NYC wastewater
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
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Genetic diversity in terrestrial subsurface ecosystems impacted by geological degassing
Geological degassing can impact subsurface metabolism. Here, the authors describe microbial communities from a cold-water geyser are described and compared with other deep subsurface sites, finding a key role for an uncultivated archaeon.
- Till L. V. Bornemann
- , Panagiotis S. Adam
- & Alexander J. Probst
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Phylogenetically and functionally diverse microorganisms reside under the Ross Ice Shelf
The Ross Ice Shelf is the most extensive ice shelf of Antarctica and isolates the underlying ocean from sunlight. Here the authors use multi-omics to unravel the phylogenetic and functional diversity of microbial life in this ecosystem.
- Clara Martínez-Pérez
- , Chris Greening
- & Federico Baltar
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Multi-species host range of staphylococcal phages isolated from wastewater
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
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Decline in plankton diversity and carbon flux with reduced sea ice extent along the Western Antarctic Peninsula
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
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| Open Access
Connecting structure to function with the recovery of over 1000 high-quality metagenome-assembled genomes from activated sludge using long-read sequencing
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
Selection and horizontal gene transfer underlie microdiversity-level heterogeneity in resistance gene fate during wastewater treatment