Genome streamlining in CPR bacteria transitioning from soil to groundwater
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PROVIDER: PRJEB65930 | ENA |
REPOSITORIES: ENA
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Project description:BackgroundTo better understand the influence of habitat on the genetic content of bacteria, with a focus on members of Candidate Phyla Radiation (CPR) bacteria, we studied the effects of transitioning from soil via seepage waters to groundwater on genomic composition of ultra-small Parcubacteria, the dominating CPR class in seepage waters, using genome resolved metagenomics.ResultsBacterial metagenome-assembled genomes (MAGs), (318 total, 32 of Parcubacteria) were generated from seepage waters and compared directly to groundwater counterparts. The estimated average genome sizes of members of major phyla Proteobacteria, Bacteroidota and Cand. Patescibacteria (Candidate Phyla Radiation - CPR bacteria) were significantly higher in soil-seepage water as compared to their groundwater counterparts. Seepage water Parcubacteria (Paceibacteria) exhibited 1.18-fold greater mean genome size and 2-fold lower mean proportion of pseudogenes than those in groundwater. Bacteroidota and Proteobacteria also showed a similar trend of reduced genomes in groundwater compared to seepage. While exploring gene loss and adaptive gains in closely related CPR lineages in groundwater, we identified a membrane protein, and a lipoglycopeptide resistance gene unique to a seepage Parcubacterium genome. A nitrite reductase gene was also identified and was unique to the groundwater Parcubacteria genomes, likely acquired from other planktonic microbes via horizontal gene transfer.ConclusionsOverall, our data suggest that bacteria in seepage waters, including ultra-small Parcubacteria, have significantly larger genomes and higher metabolic enrichment than their groundwater counterparts, highlighting possible genome streamlining of the latter in response to habitat selection in an oligotrophic environment.
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Project description:Here, we applied a microarray-based metagenomics technology termed GeoChip 5.0 to examined functional gene structure of microbes in three biomes, including boreal, temperate and tropical area.
2024-05-10 | GSE172195 | GEO
Project description:characterization of soil communities with metagenomics and metaproteomics
2018-11-21 | PXD011738 | Pride
Project description:integrating metagenomics and metaproteomics to study microbial communities that have undergone long-term P addition experiment
2018-01-08 | PXD005910 | Pride
Project description:Evaluation of different strategies to interpret metaproteomics data acquired on soil samples from a floodplain along the Seine River (France) incorporating sample-specific metagenomics data, soil genome catalogue database, and generic sequence database.
2022-02-17 | PXD026798 | Pride
Project description:This study assessed the perception of urban residents of A'Seeb city, Oman, about the impact of their activities on environment. A sociological survey using questionnaire was used to know the residents' perceptions about urban gardening, municipal-waste disposal, and soil and water contamination. Viable pathogenic bacteria, water soluble metals, basic cations, salinity, and texture were quantified and identified in soil and groundwater in proximity of urban gardens and municipal-waste disposal sites. The majority of surveyed residents are not paying attention to the negative consequences of their activities on soil and environment. Although the measured heavy metals concentrations in some of the contaminated sites were significant but still below the international standards. Fecal contaminants reported in in some samples from gardens, garbage-disposal sites and groundwater. Human pathogens belonging to risk group-2 including Klebsiella pneumonia, Shigella spp and E. Coil were identified. More socio-environmental studies required to correlate the behavior of urban residents and pollution and to delineate the sources of the detected pathogenic bacteria. Our results set a foundation for future studies on urban soils and associated residence behaviors and practices in Oman and the neighboring Gulf countries.
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Project description:Recent interest in improving soil health and agricultural sustainability recognizes the value of soil organic carbon (SOC) sequestration and nutrient cycling. The main goal of this study was to evaluate the response of various SOC and nitrogen (N) components in semiarid cropping systems transitioning from limited-irrigation to dryland and a restored grassland in the Southern High Plains of USA. Cropping systems evaluated include dryland winter wheat (Triticum aestivum L.)-sorghum (Sorghum bicolor L.)-fallow with conventional tillage (DLCTF) and no-tillage (DLNTF), limited-irrigation winter wheat-sorghum-fallow with no-tillage and cover cropping (LINTC) and no-tillage fallow (LINTF), and an undisturbed grassland (NG). Soil samples were collected from 0-15 cm and 15-30 cm depths and analyzed for SOC, total N, inorganic N, and soil microbial biomass carbon (SMBC) contents. The CO2 and N2O release during a eight-weeks long laboratory incubation were also analyzed. Results show 14% and 13% reduction in SOC and total N from 0-30 cm depth with the transition from limited-irrigation to dryland cropping systems while 51% more SOC and 41% more total N with the transition to grassland. The SMBC was 42% less in dryland cropping systems and 100% more in NG than the limited-irrigation cropping systems. However, the grassland was N limited, with 93% less inorganic N in NG compared to only 11% less in dryland cropping systems than in limited-irrigation cropping systems. The microbial respiration measured as CO2-C was highest in NG, followed by limited-irrigation and dryland cropping systems. The N2O-N release showed the lowest rate of N loss from dryland cropping systems, followed by NG and limited-irrigation cropping systems. This study demonstrated loss of SOC and N in agroecosystems transitioned to dryland crop-fallow systems, with greater magnitude of change observed in the biologically active fraction of soil organic matter. Grassland restoration could be an important strategy to increase SOC and nutrients in hot, dry, semiarid agroecosystems transitioning to dryland.
| S-EPMC7583628 | biostudies-literature
Project description:Cable bacteria of the family Desulfobulbaceae couple spatially separated sulfur oxidation and oxygen or nitrate reduction by long-distance electron transfer, which can constitute the dominant sulfur oxidation process in shallow sediments. However, it remains unknown how cells in the anoxic part of the centimeter-long filaments conserve energy. We found 16S rRNA gene sequences similar to groundwater cable bacteria in a 1-methylnaphthalene-degrading culture (1MN). Cultivation with elemental sulfur and thiosulfate with ferrihydrite or nitrate as electron acceptors resulted in a first cable bacteria enrichment culture dominated >90% by 16S rRNA sequences belonging to the Desulfobulbaceae. Desulfobulbaceae-specific fluorescence in situ hybridization (FISH) unveiled single cells and filaments of up to several hundred micrometers length to belong to the same species. The Desulfobulbaceae filaments also showed the distinctive cable bacteria morphology with their continuous ridge pattern as revealed by atomic force microscopy. The cable bacteria grew with nitrate as electron acceptor and elemental sulfur and thiosulfate as electron donor, but also by sulfur disproportionation when Fe(Cl)2 or Fe(OH)3 were present as sulfide scavengers. Metabolic reconstruction based on the first nearly complete genome of groundwater cable bacteria revealed the potential for sulfur disproportionation and a chemo-litho-autotrophic metabolism. The presence of different types of hydrogenases in the genome suggests that they can utilize hydrogen as alternative electron donor. Our results imply that cable bacteria not only use sulfide oxidation coupled to oxygen or nitrate reduction by LDET for energy conservation, but sulfur disproportionation might constitute the energy metabolism for cells in large parts of the cable bacterial filaments.
| S-EPMC6976610 | biostudies-literature
Project description:Candidate phyla radiation (CPR) bacteria and DPANN archaea are unisolated, small-celled symbionts that are often detected in groundwater. The effects of groundwater geochemistry on the abundance, distribution, taxonomic diversity and host association of CPR bacteria and DPANN archaea has not been studied. Here, we performed genome-resolved metagenomic analysis of one agricultural and seven pristine groundwater microbial communities and recovered 746 CPR and DPANN genomes in total. The pristine sites, which serve as local sources of drinking water, contained up to 31% CPR bacteria and 4% DPANN archaea. We observed little species-level overlap of metagenome-assembled genomes (MAGs) across the groundwater sites, indicating that CPR and DPANN communities may be differentiated according to physicochemical conditions and host populations. Cryogenic transmission electron microscopy imaging and genomic analyses enabled us to identify CPR and DPANN lineages that reproducibly attach to host cells and showed that the growth of CPR bacteria seems to be stimulated by attachment to host-cell surfaces. Our analysis reveals site-specific diversity of CPR bacteria and DPANN archaea that coexist with diverse hosts in groundwater aquifers. Given that CPR and DPANN organisms have been identified in human microbiomes and their presence is correlated with diseases such as periodontitis, our findings are relevant to considerations of drinking water quality and human health.
| S-EPMC7906910 | biostudies-literature