The authors used multi-omics and cultivation approaches to show that deep-sea PVC bacteria have the capacity to degrade polysaccharides and demonstrate that laminarin acts as an effective selective substrate for enriching and isolating the deep-sea PVC superphylum bacteria.
Abstract
The deep sea is home to a vast and largely unexplored microbial biosphere, along with large amounts of complex organic matter (COM). However, the functional capacity of the deep-sea microbiome to metabolize organic matter across diverse regions remains poorly understood. Here, we combine 16S rRNA gene amplicon sequencing, metagenomics, and metatranscriptomics to comprehensively characterize prokaryotic communities across different years (2018 and 2022) and habitats (cold seeps, hydrothermal vents, and seamounts). Our results reveal spatio-temporal community heterogeneity driven by geochemical gradients, alongside a widespread genetic potential for organic matter metabolism. Notably, the PVC (Planctomycetota-Verrucomicrobiota-Chlamydiota) superphylum exhibits extensive polysaccharide degradation capabilities, exemplified by the isolation of Planctomycetota strain WC338 and Lentisphaerota strain WC36 via laminarin enrichment. Growth experiments and transcriptomics confirm their strict laminarin dependence and characterize the underlying catabolic machinery—specifically, the deployment of different glycoside hydrolase (GH) families, which are broadly distributed and prevalent across the PVC superphylum. Furthermore, we demonstrate that laminarin acts as an effective selective substrate for enriching and isolating the deep-sea PVC superphylum bacteria. Collectively, these findings reveal that PVC bacteria—an overlooked group in laminarin degradation—possess specialized adaptations for polysaccharide breakdown and actively participate in laminarin turnover in deep-sea environments. In this study, the authors used multi-omics and cultivation approaches to show that deep-sea PVC bacteria have the capacity to degrade polysaccharides. Two PVC strains isolated via laminarin enrichment showcase specialized adaptations, highlighting their role in marine carbon cycling.
Analysis revealed genes for metabolizing diverse carbohydrate sources, a complete ectoine synthesis cluster essential for halophily, and genes conferring tolerance to osmotic stress, low temperatures, and pH, underscoring its polyextremophilic capacity.
Ian Ariel Barbosa Nunes, Adan Rodrigues de Oliveira, Adonney Allan de Oliveira Veras et al.· Brazilian Journal of Microbi...· 0 citations
ABSTRACT The shallow hydrothermal system of the Tagoro submarine volcano (Canary Islands, Spain) has been discharging low‐temperature, nutrient‐rich, acidic fluids high in CO2 and H2S since March 2012. Despite influencing local microbial communities, the effects of these hydrothermal fluids on community structure and diversity across spatial gradients remain poorly understood. Using 16S rRNA gene sequencing, we observed significant differences in prokaryotic community structure from epipelagic waters to benthic habitats affected by hydrothermal activity. Prokaryotic richness and diversity decreased closer to hydrothermal sources, yet novel taxa were prevalent across all hydrothermally influenced habitats. Archaeal diversity was low and dominated by ammonia‐oxidising Nitrosopumilaceae, while bacterial communities were more diverse, including iron‐oxidising Mariprofundaceae, methane‐oxidising Methylomonadaceae and metabolically versatile Rhodobacteraceae. Molecular analyses revealed microbial specialisation within these families, complementing scanning electron microscopy observations of active bacterial biomineralization in chimney fragments linked to Mariprofundaceae members. Together, these findings offer new insights into the ecology and functional potential of microbial assemblages in the Tagoro hydrothermal system, suggesting their involvement in nitrogen, iron, sulphur and methane cycling. This study advances our understanding of microbial distribution patterns in shallow‐sea hydrothermal fields and highlights the high prevalence of novel taxa with potential biotechnological relevance.
Clàudia Pérez-Barrancos, E. Fraile-Nuez, J. A. Lozano-Rodríguez et al.· Environmental Microbiology· 0 citations
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.
Wei-Jia Zhang, Aoran Hu, Ziheng Wu et al.· Cell Host and Microbe· 0 citations
An extensive culturomics study of 549 isolates from the hypersaline soils of the Odiel Saltmarshes Natural Area and compared the results with previously generated shotgun metagenomic datasets demonstrate the complementarity of culturomics and metagenomics and provide an insight into the microbial communities inhabiting the hypersaline soils of the Odiel Saltmarshes.
Background Bryozoans are ancient colonial animals that have existed for over 470 million years and are widely distributed across aquatic environments. Recently, many spherical colloids (average diameter≈1 meter in diameter), containing bryozoans and diverse microorganisms, were found in the Hanjiang river in China. In this study, we investigated these bryozoan-dominated microbial complexes using metagenomic sequencing, metabolomic profiling, and complementary approaches. Results The results revealed that the microbial structure dominated by bryozoans included eukaryotes such as fungi, microalgae, as well as prokaryotes such as bacteria, and acellular entities such as viruses. All members form a highly integrated consortium that collaboratively maintains community function and stability, which displayed the shape and structure of a regular microbial complex and increased in size. Additionally, the results suggested the predominately presence of Proteobacteria were particularly abundant and are known to produce bryozoans in response to bryozoan signals. Interesting, it was implied that a decrease or even a loss in virulence occurs when pathogenic microorganisms become members of the complex. This is the first study focusing on the composition and metabolites of the unusual microorganism complex. The results discovered the close and intriguing connections within the microbial communities dominated by the ancient organism bryozoan through multi-omics technologies. It showed that both eukaryotes and prokaryotes can coordinate, thereby forming a stable composite structure.
Hui Zhu, Xiao-Zhi Lin, Rui-Xuan Wang et al.· bioRxiv· 0 citations
Biosynthetic gene clusters (BGCs) which encode diverse secondary metabolites are ubiquitous across microbiomes and support critical ecological functions. They also serve as attractive targets for new drug discovery. Here we combined genome-resolved metagenomics with long-read Nanopore RNA sequencing, yielding 1016 bacterial and 124 archaeal medium-to-high quality MAGs from previously unchartered microbial communities in Arctic hydrothermal vent biofilms. We identified 2965 BGCs from 870 metagenome-assembled genomes (MAGs) comprising a distinctive and rich diversity of BGCs, with ribosomally synthesized and post-translationally modified peptides (RiPPs) predominating across all samples. RiPPs and non-ribosomal peptide synthetases (NRPs), also known to encode metabolites with antimicrobial potential, are represented among the most expressed transcripts. Terpenes, though less expressed, contribute to microbial signaling and defense. Notably, we identify hydrogen cyanide (HCN) synthesis pathways in archaeal genomes, challenging the view that cyanogenesis is restricted to bacteria and eukaryotes. Our findings demonstrate that microbial adaptation to extreme environments favors RiPP-based biosynthesis and that HCN may play a role in archaeal ecological interactions. Moreover, microbial communities in Arctic hydrothermal vent biofilms provide a rich reservoir of unique bioactive compounds, with implications for drug discovery.
Thuc Trong Nguyen, I. H. Steen, R. Stokke· Nature Communications· 0 citations
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