This work isolated strain D14T from deep-sea water, and proposes to classify it as a novel species, Metabolovarius oceani sp.
Abstract
The rare biosphere harbors immense microbial diversity, yet most low-abundance taxa remain uncultured and functionally enigmatic. Here, we isolated strain D14T from deep-sea water, and propose to classify it as a novel species, Metabolovarius oceani sp. nov., within the novel family Metabolovariaceae fam. nov. M. oceani represents the first cultivated member of the candidate family NORP267, a globally distributed but elusive alphaproteobacterial lineage known only from metagenome-assembled genomes. It possesses broad metabolic capabilities, including CO2 fixation, polyhydroxyalkanoate biosynthesis, complete denitrification and thiosulfate oxidation, and is capable of aerobic growth under both heterotrophic and autotrophic conditions and of anaerobic autotrophic denitrification via thiosulfate oxidation. Despite its versatile metabolic repertoire and global distribution, Metabolovariaceae remains consistently low in abundance across diverse habitats. The isolation of M. oceani permits direct experimental insights into the evolutionary adaptations, physiological resilience, and potential ecosystem roles of rare but metabolically versatile microorganisms within the microbial dark matter.
Soda lakes represent some of the most extreme aquatic ecosystems on Earth, yet their microbial diversity and functional potential remain poorly characterized, particularly in East Africa. This study presents the first shotgun metagenomic analysis of bacterial communities inhabiting both water and sediment of Small Momela Lake, a soda lake in northern Tanzania. Samples were sequenced using Illumina NovaSeq and analyzed with MetaPhlAn4 and HUMAnN3 to resolve taxonomic composition, diversity patterns and predicted metabolic functions. Results showed 27 distinct species within Pseudomonadota, Bacteroidota, Firmicutes, Cyanobacteria and Verrucomicrobia dominated by sulfur-cycling Thioalkalivibrio denitrificans and uncultured Candidatus lineages. Notably, based on currently available literature multiple taxa were detected for the first time in soda lake environments globally, within Africa and East Africa, expanding the known biogeography of extremophiles. Functional profiling revealed a strong enrichment of nucleotide and amino acid biosynthesis pathways, alongside marker genes linked to pH homeostasis, osmotic stress tolerance, sulfur metabolism and carbon fixation. These features suggest pronounced metabolic flexibility supporting microbial persistence under extreme alkaline and saline conditions. These findings underscore Small Momela Lake as a critical reservoir of novel, functional bacterial resources with promising applications in biotechnology and bioprospecting.
A. A. Siima, Sadikiel E. Kaale, F. Mpenda et al.· Discover Life· 0 citations
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.
Weijia Zhang, Aoran Hu, Ziheng Wu et al.· Cell Host and Microbe· 0 citations
Myxococcota are globally distributed bacteria renowned for their remarkable ecological and biotechnological significance due to their complex lifestyles, social behaviour, and secondary metabolite production. Despite their ubiquity in diverse environments, including soil, marine, and extreme habitats, their diversity and ecological roles remain underexplored. Here, we utilized the Microflora Danica dataset, encompassing >10,000 metagenomes and >400 rRNA gene datasets from various environments in Denmark, to investigate the distribution, diversity, and metabolic potential of Myxococcota. We show that Myxococcota are ubiquitous but strongly structured by environment, with soil-associated lineages enriched in predatory and multicellular development traits, whereas aquatic-associated taxa exhibit alternative lifestyles, including anaerobic metabolism and phototrophy. Comparative genomic analysis reveals widespread potential for secondary metabolite production, hydrocarbon degradation, and organohalide transformation, alongside diverse contribution to carbon and nutrient cycling. Together, these findings redefine Myxococcota as a functionally diverse and ecologically differentiated phylum, extending beyond canonical predation and multicellularity, and underscore their promise as large reservoir of unexplored functional potential for biotechnological applications in drug discovery and environmental remediation.
F. Petriglieri, Yu Yang, Z. Kondrotaite et al.· bioRxiv· 0 citations
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