Unique ecological functions of viral communities potentially influence microbial adaptability in deep-sea ferromanganese nodule deposits.

Ferromanganese nodule deposits represent unique deep-sea habitats characterized by metal-rich environments. However, the composition and ecological functions of viral communities inhabiting the regions remain poorly understood. Here, we investigated the composition, distribution patterns, and potential ecological roles of viral community in both sediments and nodules from ferromanganese nodule deposits. Our results indicated that viral community distribution was influenced by sediment depth, habitat type, and microbial community. Furthermore, viruses may enhance the environmental adaptability of microbial hosts by encoding auxiliary metabolic genes, thereby indirectly influencing the biogeochemical cycles of carbon, phosphorus, and sulfur. Notably, viral genomes in ferromanganese nodule deposits contained a high frequency of metal resistance genes (MRGs). At the viral operational taxonomic unit (vOTU) level, the proportion of MRG- encoding vOTUs was 2.46-67.50 times higher in deep-sea habitats than in other marine environments, suggesting potential horizontal gene transfer of MRGs between hosts in sediments and ferromanganese nodules. Laboratory experiments confirmed that some virus-encoded MRGs could significantly enhance microbial metal resistance. Overall, this study provides a comprehensive characterization of viral communities in ferromanganese nodule deposits, highlighting their role in microbial adaptation and providing valuable insights for environmental impact assessments of deep-sea mining.

• Publication year

  2026

• Venue

  Journal of Hazardous Materials

• Publication date

  2026-01-07

• Fields of study

  Biology, Medicine, Environmental Science

• Identifiers
  DOI 10.1016/j.jhazmat.2026.141083PMID 41518806
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Thorium-234 as a tracer for deep-sea mining sediment plume deposition

  2025cited by this paper
• CoverM: read alignment statistics for metagenomics

  2025cited by this paper
• Viromes vs. mixed community metagenomes: choice of method dictates interpretation of viral community ecology

  2024cited by this paper
• Biodiversity of mudflat intertidal viromes along the Chinese coasts

  2024cited by this paper
• Viral diversity within marine biofilms and interactions with corrosive microbes.

  2024cited by this paper
• Global marine microbial diversity and its potential in bioprospecting

  2024cited by this paper
• Endemism shapes viral ecology and evolution in globally distributed hydrothermal vent ecosystems

  2024cited by this paper
• Diversity and potential host-interactions of viruses inhabiting deep-sea seamount sediments

  2024cited by this paper
• Genomic characteristics of nine Nitrospirota metagenome-assembled genomes in deep-sea sediments from East Pacific polymetallic nodules zone.

  2024cited by this paper
• Profiles of phage in global hospital wastewater: Association with microbial hosts, antibiotic resistance genes, metal resistance genes, and mobile genetic elements.

  2024cited by this paper
• Viral Communities Contribute More to the Lysis of Antibiotic-Resistant Bacteria than the Transduction of Antibiotic Resistance Genes in Anaerobic Digestion Revealed by Metagenomics

  2024cited by this paper
• Viral potential to modulate microbial methane metabolism varies by habitat

  2024cited by this paper
• A glimpse of microbial potential in metal metabolism in the Clarion-Clipperton Fracture Zone in the eastern Pacific Ocean based on metagenomic analysis.

  2024cited by this paper
• Metagenomic analysis unveils the underexplored roles of prokaryotic viruses in a full-scale landfill leachate treatment plant.

  2023cited by this paper
• ICEberg 3.0: functional categorization and analysis of the integrative and conjugative elements in bacteria

  2023cited by this paper
• A systematic analysis of marine lysogens and proviruses

  2023cited by this paper
• Identification of mobile genetic elements with geNomad

  2023cited by this paper
• Distinct adaptive strategies and microbial interactions of soil viruses under different metal(loid) contaminations.

  2023cited by this paper
• Microbe-driven elemental cycling enables microbial adaptation to deep-sea ferromanganese nodule sediment fields

  2023cited by this paper
• Dissecting the metal resistance genes contributed by virome from mining-affected metal contaminated soils

  2023cited by this paper
• Tree Visualization By One Table (tvBOT): a web application for visualizing, modifying and annotating phylogenetic trees

  2023cited by this paper
• Viruses interact with hosts that span distantly related microbial domains in dense hydrothermal mats

  2023cited by this paper
• Research advances, challenges and perspectives for recovering valuable metals from deep-sea ferromanganese minerals: A comprehensive review

  2023cited by this paper
• Viruses in deep-sea cold seep sediments harbor diverse survival mechanisms and remain genetically conserved within species

  2023cited by this paper
• Virus diversity and interactions with hosts in deep-sea hydrothermal vents

  2022cited by this paper
• Viral community-wide auxiliary metabolic genes differ by lifestyles, habitats, and hosts

  2022cited by this paper
• ColabFold: making protein folding accessible to all

  2022cited by this paper
• Bioleaching Test of Polymetallic Nodule Samples from the IOM Exploration Area

  2022cited by this paper
• The role of bacterial ATP-binding cassette (ABC) transporters in pathogenesis and virulence: Therapeutic and vaccine potential.

  2022cited by this paper
• Global patterns of diversity and metabolism of microbial communities in deep-sea hydrothermal vent deposits

  2022cited by this paper
• Community structure of deep-sea benthic metazoan meiofauna in the polymetallic nodule fields in the eastern Clarion-Clipperton Fracture Zone, Pacific Ocean

  2022cited by this paper
• Patterns and ecological drivers of viral communities in acid mine drainage sediments across Southern China

  2022cited by this paper
• Microbiomes in the Challenger Deep slope and bottom-axis sediments

  2022cited by this paper
• Assessment of scientific gaps related to the effective environmental management of deep-seabed mining

  2022cited by this paper
• Revealing taxon-specific heavy metal-resistance mechanisms in denitrifying phosphorus removal sludge using genome-centric metaproteomics

  2021cited by this paper
• METABOLIC: high-throughput profiling of microbial genomes for functional traits, metabolism, biogeochemistry, and community-scale functional networks

  2021cited by this paper
• Heterotrophic bacterial diazotrophs are more abundant than their cyanobacterial counterparts in metagenomes covering most of the sunlit ocean

  2021cited by this paper
• VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses

  2021cited by this paper
• Highly accurate protein structure prediction with AlphaFold

  2021cited by this paper
• Expanding standards in viromics: in silico evaluation of dsDNA viral genome identification, classification, and auxiliary metabolic gene curation

  2021cited by this paper
• eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale

  2021cited by this paper
• Diversity and distribution of viruses inhabiting the deepest ocean on Earth

  2021cited by this paper
• Novel Chloroflexi genomes from the deepest ocean reveal metabolic strategies for the adaptation to deep-sea habitats

  2021cited by this paper
• Lifestyle of sponge symbiont phages by host prediction and correlative microscopy

  2021cited by this paper
• Deep sea sediments associated with cold seeps are a subsurface reservoir of viral diversity

  2020cited by this paper
• czcD gene from Bacillus megaterium and Microbacterium liquefaciens as a potential nickel–vanadium soil pollution biomarker

  2020cited by this paper
• The effect of phage genetic diversity on bacterial resistance evolution

  2020cited by this paper
• Identifying viruses from metagenomic data using deep learning

  2020cited by this paper
• Phage diversity, genomics and phylogeny

  2020cited by this paper
• Deep-ocean polymetallic nodules as a resource for critical materials

  2020cited by this paper
• Dataset for: "BACPHLIP: Predicting bacteriophage lifestyle from conserved protein domains"

  2020cited by this paper
• VIBRANT: automated recovery, annotation and curation of microbial viruses, and evaluation of viral community function from genomic sequences

  2020cited by this paper
• TBtools - an integrative toolkit developed for interactive analyses of big biological data.

  2020cited by this paper
• DRAM for distilling microbial metabolism to automate the curation of microbiome function

  2020cited by this paper
• The contribution of microbial communities in polymetallic nodules to the diversity of the deep-sea microbiome of the Peru Basin (4130–4198 m depth)

  2020cited by this paper
• CheckV assesses the quality and completeness of metagenome-assembled viral genomes

  2020cited by this paper
• ViralRecall—A Flexible Command-Line Tool for the Detection of Giant Virus Signatures in ‘Omic Data

  2020cited by this paper
• Heavy-Metal-Resistant Microorganisms in Deep-Sea Sediments Disturbed by Mining Activity: An Application Toward the Development of Experimental in vitro Systems

  2019cited by this paper
• Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

  2019cited by this paper
• Pavian: interactive analysis of metagenomics data for microbiome studies and pathogen identification

  2019cited by this paper
• Bacterial ABC transporters of iron containing compounds.

  2019cited by this paper
• GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database

  2019cited by this paper
• Microorganisms and metals: a love-hate relationship ?

  2019cited by this paper
• IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

  2019cited by this paper
• Proteomic analysis of the reduction and resistance mechanisms of Shewanella oneidensis MR-1 under long-term hexavalent chromium stress.

  2019cited by this paper
• Diversities and potential biogeochemical impacts of mangrove soil viruses

  2019cited by this paper
• Marine DNA Viral Macro- and Microdiversity from Pole to Pole.

  2019cited by this paper
• Coupling carbon and energy fluxes in the North Pacific Subtropical Gyre

  2019cited by this paper
• Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks

  2019cited by this paper
• Episodic organic carbon fluxes from surface ocean to abyssal depths during long-term monitoring in NE Pacific

  2018cited by this paper
• fastp: an ultra-fast all-in-one FASTQ preprocessor

  2018cited by this paper
• Phage puppet masters of the marine microbial realm

  2018cited by this paper
• Impacts of Deep-Sea Mining on Microbial Ecosystem Services

  2018cited by this paper
• Natural spatial variability of depositional conditions, biogeochemical processes and element fluxes in sediments of the eastern Clarion-Clipperton Zone, Pacific Ocean

  2018cited by this paper
• Mind the seafloor

  2018cited by this paper
• Minimum Information about an Uncultivated Virus Genome (MIUViG)

  2018cited by this paper
• MetaWRAP—a flexible pipeline for genome-resolved metagenomic data analysis

  2018cited by this paper
• Metal homeostasis and resistance in bacteria

  2017cited by this paper
• Resilience of benthic deep-sea fauna to mining activities.

  2017cited by this paper
• Composition, Formation, and Occurrence of Polymetallic Nodules

  2017cited by this paper
• dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication

  2017cited by this paper
• Lysogeny in nature: mechanisms, impact and ecology of temperate phages

  2017cited by this paper
• Piggyback-the-Winner in host-associated microbial communities

  2016cited by this paper
• Threatened by mining, polymetallic nodules are required to preserve abyssal epifauna

  2016cited by this paper
• Biofilms: an emergent form of bacterial life

  2016cited by this paper
• News from the seabed – Geological characteristics and resource potential of deep-sea mineral resources

  2016cited by this paper
• Phages rarely encode antibiotic resistance genes: a cautionary tale for virome analyses

  2016cited by this paper
• Defining “serious harm” to the marine environment in the context of deep-seabed mining

  2016cited by this paper
• Prokaryotic Virus Orthologous Groups (pVOGs): a resource for comparative genomics and protein family annotation

  2016cited by this paper
• Mining Critical Metals and Elements from Seawater: Opportunities and Challenges.

  2015cited by this paper
• The Phyre2 web portal for protein modeling, prediction and analysis

  2015cited by this paper
• MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

  2014cited by this paper
• Trimmomatic: a flexible trimmer for Illumina sequence data

  2014cited by this paper
• Diversity in ABC transporters: Type I, II and III importers

  2014cited by this paper
• Bacteria–phage coevolution as a driver of ecological and evolutionary processes in microbial communities

  2014cited by this paper
• R: A language and environment for statistical computing.

  2014cited by this paper
• Microbial communities associated with ferromanganese nodules and the surrounding sediments

  2013cited by this paper
• BacMet: antibacterial biocide and metal resistance genes database

  2013cited by this paper
• Deep-ocean mineral deposits as a source of critical metals for high- and green-technology applications: Comparison with land-based resources

  2013cited by this paper
• A comparison of microbial communities in deep-sea polymetallic nodules and the surrounding sediments in the Pacific Ocean

  2013cited by this paper

• No citing papers are available for this paper.