Ontology highlight
ABSTRACT:
PROVIDER: PRJNA623159 | ENA |
REPOSITORIES: ENA
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Project description:Dispersal analysis of cable bacteria through the overlying water
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Project description:Lanthanides (Ln) play essential roles in the metabolism of certain bacteria, catalysing key reactions in methane oxidation. This study investigates the diversity and distribution of Ln-dependent proteins, collectively termed the lanthanome, in aerobic methane-oxidizing bacteria (MOB) using genome, plasmid, and metatranscriptome data from methane-rich lake sediments. A custom database of 180 MOB genomes revealed various methanol dehydrogenase (MDH) isoforms, including XoxF variants, distributed across Proteobacteria and Verrucomicrobia phyla. We conducted an experimental study with Methylosinus trichosporium OB3B exposed to CeCl₃ and an ore containing mixed lanthanides, measuring methane oxidation rates and using proteomics to assess shifts in protein expression. Despite differences in adaptation times, methane oxidation rates were consistent across treatments, indicating similar overall metabolic efficiencies after acclimatisation. The genomic analysis uncovered several Ln-binding proteins, including the TonB-dependent receptors LanA and lutH-like, as well as Lanmodulin and LanPepsy, with unique phylogenetic patterns. Metatranscriptomic data showed active lanthanome expression, particularly in Proteobacteria, with the XoxF5 MDH variant prevalent in MOB genomes. The discovery of Ln-binding proteins in plasmids suggests potential horizontal gene transfer, highlighting adaptive mechanisms of MOB to Ln availability and their ecological role in methane cycling. This work expands our understanding of Ln-utilising bacteria, particularly in the context of lanthanide-driven methane oxidation, and offers potential biotechnological applications for Ln-dependent processes.
2025-04-29 | PXD063434 | Pride
Project description:In this study, we investigated Mn3+-cycling microbial populations enriched from Lake Matano, Indonesia using metagenomics and metaproteomics. Lake Matano contains an active Mn cycle that links the oxic-anoxic interface with anoxic deep waters that are enriched in iron and manganese, and depleted in sulfate, phosphate, and oxidized nitrogen (Crowe et al., 2008; Jones et al., 2011). Sediments were incubated with sequential transfers for ~1 year with Mn3+ as the sole electron acceptor and methane as organic carbon until achieving sediment-free conditions. Here we investigate this novel species of Dechloromonas (Betaproteobacteria), “Candidatus Dechloromonas occultata,” which was the dominant population in enrichment cultures with active Mn3+ reduction. “Ca. D. occultata” expressed electron conduits related to those involved in Fe2+ oxidation (Mto-like), as well as a novel cytochrome c-rich gene cluster putatively involved in extracellular electron transfer, and an atypical nitrous oxide reductase. According to ribosomal counts, Dechloromonas outnumber Geobacter. In terms of functional genes, Dechloromonas expresses a wider variety and number of genes. Dechloromonas therefore seems to have a (selective?) advantage over Geobacter. Previous experiments revealed that Dechloromonas express nitrogen regulators, reductases and scavenging genes, as well as many carbon central metabolic pathways, and aromatic carbon degradation pathways. Dechloromonas is a beta proteobacteria, and these are "experts" in nitrogen metabolism. Geobacter, on the other hand, is well known for carbon degradation. Our previous experiments lead to our hypothesis that Dechloromonas is more active because they are more successful at acquiring nitrogen, a limiting nutrient for Geobacter. This would further suggest that carbon is not the limiting nutrient. We will test 2 hypotheses with the next suite of experiments 1) pyrophosphate supports the community, by allowing carbon fixation , 2)Dechloromonas has a (selective?) advantage over Geobacter. To test this hypothesis, bioreactors will be used to grow biotriplicate cultures of (1)- CH4 vs. pyrophosphate and (2)-CH4 vs. Mn(III) pyrophosphate. Here we have analyzed whole cell pellets using gas phase fractionations on the Q Exactive. Are Dechloromonas capable of out-competing Geobacter when grown in media with methane as the only carbon source bioreactors because they are capable of acquiring more nitrogen? Source of inoculum. Lake Matano is a metal-rich, ancient ocean analog (Crowe et al. 2011, Jones et al. 2011). Organic carbon in Lake Matano is mostly mineralized via methanogenesis before reaching the iron-rich sediments, limiting organic matter bioavailability for metal-reducers (Kuntz et al. 2015). A 15-cm sediment core from 200 m water depth in Lake Matano, Sulawesi Island, Indonesia (02°26′27.1′′S, 121°15′12.3′′E; in situ sediment temperature ~27°C) was sampled in November 2014 and sub-sampled at 5 cm increments. Sediments were sealed in gas-tight Mylar bags with no headspace (Hansen et al. 2000) and stored at 4°C until incubations began in December 2015.
2020-06-30 | PXD011642 | Pride
Project description:Dimitry Y. Sorokin et al., (2021, Russian Academy of Sciences, Russia and Delft University of Technology, The Netherlands) describe the isolation and physiological and genomic properties of a fifth functional group of sulfur-respiring haloarchaea enriched from hypersaline lake sediments with CO as the electron donor. Additional shotgun proteomic profiling of the described strains has been performed.
2022-12-25 | PXD028241 | Pride