Jul 2026· Cell Host and Microbe· 0 citations· 170 references
Medicine
TL;DR
Analysis of microbiome samples collected from hadal seawaters via in situ filtration during 12 human-occupied vehicle dives identifies 135,073 non-redundant active proteins, with over 95% being hadal-specific.
Abstract
Microorganisms dominate life in the hadal zone, yet extreme sampling difficulty and low biomass have precluded characterization of their in situ activities. Here, we analyze microbiome samples collected from hadal seawaters via in situ filtration during 12 human-occupied vehicle dives. DNA-protein co-extraction and metagenome-guided metaproteomic analysis identify 135,073 non-redundant active proteins, with over 95% being hadal-specific. Metaproteomic quantification distinguishes highly active and less active taxa that differ in biogeographic origins and genomic traits. Hadal microorganisms operate a metabolic regime fundamentally distinct from the upper ocean, preferentially utilizing refractory organic matter (aromatics, halogenated compounds, and D-amino acids) and expanded electron acceptors (thiosulfate and heavy metals), collectively shaping hadal element cycling. Active viruses extend beyond "Piggyback-the-Winner" dynamics, enhancing host adaptation through auxiliary metabolic genes. These findings provide proteome-level evidence of hadal microbial activities and reveal biogeochemical cycling distinct from that of the upper ocean, highlighting the underappreciated significance of hadal microbiomes within global ocean ecosystems.
Hadal trenches form where one tectonic plate descends beneath another, creating the deepest ocean habitats. Despite extreme pressure and limited energy supply, their microbiomes sustain biogeochemical cycling and support trench ecosystems. In this Review, we synthesize culture-based studies, single cell genomics and metagenomic surveys to (1) map the distribution of bacterial and archaeal lineages, (2) examine adaptations involving membranes, proteins, genome maintenance and nutrient use, (3) describe microbial roles across oxic and anoxic sediment zones, (4) assess partnerships between microbes and trench fauna, and (5) evaluate the biotechnological potential of extremozymes and bioactive compounds. Moreover, we compare patterns across studied trenches and identify major uncertainties caused by limited sampling, cultivation and in situ experimentation. By doing so, this Review provides a roadmap for targeted isolation, in situ experimentation and the discovery of uncommon extremozymes and bioactive compounds. Hadal trench microbes thrive under extreme conditions, and actively shape ecosystem functions through nutrient regeneration, energy flow, and interdependent relationships
A. Barcan, R. Barcan, Li-Sheng He et al.· Communications Earth & Envir...· 0 citations
Proteins are abundant biomolecules that serve key functions in marine microbial communities, such as enzymes catalyzing biogeochemical reactions and transporters acquiring scarce nutrients. The measurement of proteins in biologically diverse microbial communities, such as those in ocean environments, is called metaproteomics. In recent years, metaproteomics methodologies have matured into powerful and practical approaches that contribute valuable functional and diagnostic information about microbial physiology, metabolism, and biogeochemistry. In this review, we introduce the conceptual foundations and methodological principles of marine metaproteomics; discuss current applications in marine microbiology, ocean biogeochemistry, and ecosystem diagnosis; and evaluate emerging frontiers, including quantitative stoichiometric inference, biomarker development, and global-scale interoperability. We argue that metaproteomics has reached a pivotal stage: poised not only to complement other meta-omics approaches but also to become an accessible central tool for diagnosing marine ecosystem function and understanding microbial responses to environmental change.
M. Saito, N. Held, Loay J. Jabre· Annual Review of Marine Scie...· 0 citations
It is demonstrated that environmental filtering shapes both the taxonomic and functional organization of Antarctic microbiomes and highlight polar ecosystems as reservoirs of unexplored biosynthetic diversity with potential biotechnological relevance.
William B. Medeiros, Kelly Hidalgo-Martinez, D. D. P. S. Penna et al.· World Journal of Microbiolog...· 0 citations
Kermadec Trench is a hadal ecosystem in the South Pacific with the water depth 10,047 m. The trench bottom harbors a highly active and populated microbial community, despite the surface sediment is characterized as extremely pressurized, oligotrophic and with low oxygen concentration. It is intriguing, as well as technically challenging, to investigate the microbial adaptation strategies therein. Here we performed the in situ RNA fixation on sediment samples with the assistant of Fendouzhe manned submersible, to approach natural status of microbial metabolisms on both genomic and transcriptomic levels. We reconstructed 1369 metagenome-assembled genomes (MAGs), revealing dominant heterotrophic lineages encoding carbohydrate-active enzymes targeting complex macromolecules such as peptidoglycan and β−1,4-mannan. These degradation processes were transcriptionally coupled with flexible respiratory pathways utilizing oxygen, nitrate, and nitrite as electron acceptors. Co-expression analyses and microbial co-occurrence networks demonstrated niche partitioning driven by redox stratification, with slope communities favoring oxidative pathways and bottom communities enriched in reductive metabolisms, including denitrification and N₂O reduction. Despite compositional divergence, both habitats exhibited conserved functional strategies centered on macromolecule recycling and redox-coupled respiration. Our findings highlight a coordinated system of organic matter remineralization and electron acceptor versatility that underpins microbial survival in Earth’s deepest seafloor ecosystems.
Yongxin Lv, Peiyu Liu, Yan Liu et al.· Nature Communications· 0 citations
Marine microbes have long been regarded as central to replenishing the ocean's reservoir of recalcitrant dissolved organic matter (RDOM). However, molecular-level evidence for their role remains inconclusive because RDOM persists for years to millennia, far exceeding timescales accessible to laboratory experiments, and because conventional analytical approaches lack the resolution to discern structural isomers of RDOM that confer functionally important differences in persistence. Using polarity-based liquid chromatography coupled to ultrahigh-resolution mass spectrometry capable of discriminating RDOM isomer clusters, we reveal that marine microbial consortia rapidly (≤ 90 d) convert diverse organic substrates into RDOM with extensive structural isomerism that closely mirrors natural seawater RDOM. A subset of these microbially derived RDOM compounds exhibits near-ubiquitous occurrence (> 99%) in a global dataset and accumulates progressively in the ocean's interior. Together, our findings substantiate the direct microbial contribution to the long-lived oceanic carbon reservoir through the rapid diversification of RDOM isomers, a mechanism that contributes to sustaining the complexity and long-term persistence of the planetary-scale carbon reservoir.
Ruan-Hong Cai, O. Lechtenfeld, Andrew J. Tanentzap et al.· Proceedings of the National...· 2 citations
Atmospheric particulate matter harbors diverse microorganisms, yet their functional potential in biogeochemical cycling and the associated risks of resistome remain poorly understood. Here, we performed metagenomic sequencing on PM2.5 samples collected across four months to unravel the microbial genetic repertoire involved in methane, nitrogen, phosphorus, and sulfur cycling, as well as the resistome, and pathogen composition. A broad range of functional genes was detected for each biogeochemical cycle, with more than 65% of gene subtypes shared across all months, indicating conserved functional signatures. In contrast, more than 80% of the resistome showed temporal variation in abundance, with the lowest richness observed in March. Temporal shifts were also observed in resistome composition, with several resistance determinants reaching higher abundances in April and May. Network analysis indicated frequent co-occurrence among several pathogenic and opportunistic taxa. Contig-based profiling identified 51 potential pathogenic taxa, including 32 human- or animal-associated taxa. In addition, both PM10 and PM2.5 concentrations were associated with pathogen abundance and functional gene richness (e.g., antibiotic resistance genes and virulence factors). Together, this metagenomic survey suggests contrasting temporal patterns between conserved biogeochemical functional potential and more variable resistome-related traits in PM2.5 microbial communities. While constrained by limited temporal coverage and sample size, this study provides preliminary insights into the ecological and potential public health relevance of airborne microbial communities in urban environments.
Yu-Tong Zha, Zhe Wang, Wen-Wei Sun et al.· Environmental Research· 0 citations
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