Marine metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1136951 | ENA |
REPOSITORIES: ENA
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Project description:Lignin is the most abundant renewable source of aromatic carbon and its microbial depolymerization and metabolism under aerobic conditions is well studied. However, lignin breakdown in the absence of oxygen remains poorly understood. Here, we established long-term bacterial enrichment cultures supplied with diverse lignins as the sole carbon source under denitrifying conditions. Denitrification dynamics were followed by monitoring nitrogenous gases. Metagenomics analysis recovered 62 metagenome-assembled genomes (MAGs), several of which encoded enzymes for both denitrification and anaerobic metabolism of aromatic compounds. Quantitative metaproteomics confirmed expression of such enzymes and additionally showed that several MAGs expressed redox-active auxiliary-activity enzymes and other uncharacterised proteins that are potential candidates for involvement in lignin depolymerisation. The detection of several oxygen-dependent oxidoreductases despite anaerobic conditions prompt intriguing discussion of potential mechanistic explanations. This systems-level study expands our understanding of lignin turnover in anaerobic environments by bacteria and suggest enzymatic targets for further exploration of their role in lignin depolymerization under oxygen-limited conditions.
2026-03-25 | PXD070955 | Pride
Project description:LEAP 2016 Metagenome Assembled Genomes (MAGs)
| PRJNA767111 | ENA
Project description:The deep marine subsurface is one of the largest unexplored biospheres on Earth, where members of the phylum Chloroflexi are abundant and globally distributed. However, the deep-sea Chloroflexi have remained elusive to cultivation, hampering a more thorough understanding of their metabolisms. In this work, we have successfully isolated a representative of the phylum Chloroflexi, designated strain ZRK33, from deep-sea cold seep sediments. Phylogenetic analyses based on 16S rRNA genes, genomes, RpoB and EF-tu proteins indicated that strain ZRK33 represents a novel class within the phylum Chloroflexi, designated Sulfochloroflexia. We present a detailed description of the phenotypic traits, complete genome sequence and central metabolisms of the novel strain ZRK33. Notably, sulfate and thiosulfate could significantly promote the growth of the new isolate, possibly through accelerating the hydrolysis and uptake of saccharides. Thus, this result reveals that strain ZRK33 may play a crucial part in sulfur cycling in the deep-sea environments. Moreover, the putative genes associated with assimilatory and dissimilatory sulfate reduction are broadly distributed in the genomes of 27 metagenome-assembled genomes (MAGs) from deep-sea cold seep and hydrothermal vents sediments. Together, we propose that the deep marine subsurface Chloroflexi play key roles in sulfur cycling for the first time. This may concomitantly suggest an unsuspected availability of sulfur-containing compounds to allow for the high abundance of Chloroflexi in the deep sea.
2024-05-22 | PXD023380 | Pride
Project description:Metagenome-assembled genomes (MAGs) of octocoral symbionts
| PRJEB50578 | ENA
Project description:several metagenomic assembled genomes (MAGs) from sediments
| PRJNA957236 | ENA
Project description:marine oxygen minimum zones single-cell and community genomes Raw sequence reads
| PRJNA393056 | ENA
Project description:Anthropogenic activities such as urbanization and agriculture can potentially pose a threat to neighboring freshwaters through nitrate and phosphorous contamination, which over time may lead to lake eutrophication. In such nitrogen-polluted environments, oxygen is depleted, and plants die and decompose. This enhances denitrifying microbes that respire under hypoxic/anoxic conditions by reducing nitrate instead of molecular oxygen and using plant remnants (lignocellulose) as carbon source. Microbial lignocellulose degradation has been well-studied for both aerobic- and anaerobic conditions; however, its degradation during denitrification remains largely unknown. Here we have applied a combination of gas kinetics and meta-omics techniques to enrich and analyze microbial communities from 10 eutrophic lakes to identify a set of core microbial metagenome-assembled genomes (MAGs) present in all the eutrophic lakes. We have further investigated their strategies and enzyme profiles for degrading lignocellulose under denitrifying conditions. We identified Pseudomonadota, Bacteroidota, Verrucomicrobiota, and Actinomycetota as the most abundant phyla and they were present in enrichments from all eutrophic lakes having a key role in denitrification and fermentation. Lignocellulose degradation was, however, dominated by species outside the core microbiome, i.e., there were differing key degraders between lakes, suggesting some level of lake-specialization. Among these we observed potential respiratory DNRA pathways, and they expressed a broad range of CAZymes targeting the various lignocellulose subfractions. Interestingly, many of the detected MAGs contained NO dismutases, enzymes postulated to convert NO to molecular oxygen and dinitrogen gas.
2026-04-30 | PXD069160 | Pride