Microbial Diversity in Deep-Sea Sediment Ecosystems

Deep-sea sediment ecosystems host one of the largest microbial biomes on Earth, comprising bacteria, archaea and microeukaryotes adapted to high pressure, low temperature and limited nutrient availability. These communities drive carbon, nitrogen, sulphur, iron and manganese cycling, mediating organic matter degradation, metal transformations and energy flux in the benthic environment. Biodiversity patterns reflect gradients in sediment depth, proximity to hydrothermal or cold-seep activity and the presence of polymetallic nodules or ferromanganese crusts. Surface sediments often harbour aerobic organotrophs and ammonia-oxidising archaea, while deeper layers support anaerobic metabolisms such as sulphate reduction, methanogenesis and anaerobic methane oxidation. Hard substrates like nodules and crusts select for specialised taxa involved in metal cycling and biofilm formation. Recent advances in high-throughput sequencing, single-cell genomics and metagenomics have uncovered hidden lineages and metabolic pathways, highlighting the functional potential of deep-sea microbes in biogeochemical cycling and resource formation. This microbial diversity underpins ecosystem resilience, influences global geochemical budgets and offers novel biotechnological prospects from enzyme discovery to bioremediation.

Research from Nature Portfolio

Recent studies have characterised heterotrophic bacterial diversity in polymetallic-nodule-rich sediments of the Central Indian Ocean Basin, revealing abundant Bacillus, Proteobacteria and Actinobacteria. Quantitative cell counts coupled with phylogenetic analyses uncovered phylum-level variation among sediment cores, while extracellular enzyme assays demonstrated high activities of amylase, lipase and phosphatase, indicating active organic matter breakdown and nutrient recycling. Genomic insights identified key genes for nitrogen, sulphur and carbon metabolism, suggesting these bacteria contribute to both nodule formation and benthic biogeochemical cycling. This work emphasises the links between microbial functional capacity and sediment geochemistry in abyssal habitats.

Microbial Diversity in Deep-Sea Sediment Ecosystems publication trend

The graph below shows the total number of articles in microbial diversity in deep-sea sediment ecosystems across all publications each year (not limited to Nature Index journals).

Technical terms

Operational taxonomic unit (OTU): Cluster of microbial sequences grouped by similarity, used as a proxy for species in diversity analyses.

Metagenome-assembled genome (MAG): Genome reconstructed directly from environmental DNA sequencing, representing individual microbial taxa.

Polymetallic nodule: Mineral concretions rich in metals such as manganese, nickel and cobalt, found on abyssal plains and providing hard substrate for microbial colonisation.

Ferromanganese crust: Iron- and manganese-rich coatings on seamounts and rock outcrops, hosting specialised microbial communities involved in metal cycling.

References

1. Diversity and extracellular enzyme activities of heterotrophic bacteria from sediments of the Central Indian Ocean Basin. Scientific Reports (2019).
2. Bacterial Diversity in Deep-Sea Sediment of West Pacific Nodule Province. Water (2024).
3. The contribution of microbial communities in polymetallic nodules to the diversity of the deep-sea microbiome of the Peru Basin (4130–4198 m depth). Biogeosciences (2020).
4. Microbial metabolisms in an abyssal ferromanganese crust from the Takuyo-Daigo Seamount as revealed by metagenomics. PLOS ONE (2019).