The NamesforLife Abstracts, Journal Year: 2022, Volume and Issue: unknown
Published: July 6, 2022
Environmental Microbiology, Journal Year: 2022, Volume and Issue: 25(3), P. 606 - 641
Published: Dec. 14, 2022
Abstract Pelagic microbes have adopted distinct strategies to inhabit the pelagial of lakes and oceans can be broadly categorized in two groups: free‐living, specialized oligotrophs patch‐associated generalists or copiotrophs. In this review, we aim identify genomic traits that enable pelagic freshwater thrive their habitat. To do so, discuss main genetic differences marine are both dominated by difference sediment microbes, where copiotrophs more prevalent. We phylogenomically analysed a collection >7700 metagenome‐assembled genomes, classified habitat preferences on different taxonomic levels, compared metabolic freshwater, marine, microbes. Metabolic mainly associated with transport functions, environmental information processing, components electron chain, osmoregulation isoelectric point proteins. Several lineages known transitions (Nitrososphaeria, SAR11, Methylophilaceae, Synechococcales, Flavobacteriaceae, Planctomycetota) underlying mechanisms process discussed review. Additionally, distribution, ecology make‐up most abundant prokaryotes described details separate chapters for Actinobacteriota, Bacteroidota, Burkholderiales, Verrucomicrobiota, Chloroflexota, ‘ Ca . Patescibacteria’.
Language: Английский
Citations
37
The ISME Journal, Journal Year: 2024, Volume and Issue: 18(1)
Published: Jan. 1, 2024
Implications of geographic separation and temporal dynamics on the evolution free-living bacterial species are widely unclear. However, vast amount metagenome sequencing data generated during last decades from various habitats around world provides an unprecedented opportunity for such investigations. Here, we exploited publicly available new freshwater metagenomes in combination with genomes abundant bacteria to reveal population structure. We focused that were detected across broad ranges at high enough sequence coverage meaningful genomic analyses, associated predominant taxa acI, LD12, Polynucleobacter, Candidatus Methylopumilus. Despite ranges, each appeared as a sequence-discrete cluster, contrast marine taxa, which continuous diversity structures reported global scale. Population differentiation increased significantly spatial distance all species, but notable dispersal barriers (e.g. oceanic) not apparent. Yet, different showed contrasting rates divergence strikingly intra-population time series within individual habitats. The change LD12 over 7 years was minor (FST = 0.04) compared between lakes, whereas Polynucleobacter displayed strong changes merely 2 months up 0.54), similar scale populations separated by thousands kilometers. slowly steadily evolving strain diversity, dynamic exhibited alternating clonal expansions mostly two strains only. Based structures, propose distinct models speciation.
Language: Английский
Citations
4
Archives of Microbiology, Journal Year: 2025, Volume and Issue: 207(4)
Published: Feb. 25, 2025
Abstract Within a citizen science project, 112 freshwater habitats in Austria were sampled to get bacterial cultures belonging the genus Aquirufa using strategy for targeted isolation. We focused on these bacteria because they are widespread and represent typical and, furthermore, typic red pigmentation facilitates preselection. Among 113 obtained strains HETE-83D T , KTFRIE-69F OSTEICH-129V PLAD-142S6K originating from small ponds creek. Phylogenetic reconstructions with 16S rRNA gene sequences genome-based analyses amino acid of 501 core genes showed that all four belonged A. antheringensis branch . Calculation whole-genome average nucleotide identity values digital DNA-DNA hybridization revealed each case new species. The genome sizes between 2.5 2.8 Mbp G + C 41.4 41.8%. Like type cells rod-shaped, liquid colonies agar plates red-pigmented, likely due carotenoids. All except gliding motility soft plates. grew aerobically but only could grow weakly under anaerobic conditions. propose here establish names esocilacus sp. nov. strain (= DSM 118087 = JCM 37094 ), originis 117798 37095 avitistagni 118088 37100 ) echingensis 117799 37096 ).
Language: Английский
Citations
0
Frontiers in Microbiology, Journal Year: 2025, Volume and Issue: 16
Published: March 7, 2025
The movement of groundwater through fractured bedrock provides favorable conditions for subsurface microbial life, characterized by constrained flow pathways and distinctive local environmental conditions. In this study, we examined a ecosystem associated with serpentinized rocks recovered from the Coast Range Ophiolite in northern California, USA. distribution diversity communities at various depths within two separate cores reaching up to 45 m below land surface were investigated microbiological geochemical approaches. Core samples contained low total organic carbon content, DNA yields, copy numbers 16S rRNA genes, yet some still yielded amplifiable sequences. community composition rock was distinct groundwater, source tracking sequences indicated that is not significant into basement rocks. contrast, core shared similarities overlying soil samples, which could indicate potential contamination, weathering shallow serpentinites, or combination both. Individual archaea bacteria predicted be endemic identified differential abundance analyses. Core-enriched those soils included OTUs related Serpentinimonas as well putatively anaerobic, deep subsurface-associated taxa such methanogens Bathyarchaeia . Stable isotope analyses inorganic did reveal chemoautotrophic signal instead consistent primarily vegetation basement. This census archaeal bacterial altered ultramafic useful resource further research activity fueled reactions serpentinization.
Language: Английский
Citations
0
Microbiology Resource Announcements, Journal Year: 2023, Volume and Issue: 12(7)
Published: June 21, 2023
Here, we report the complete genome sequence of Polynucleobacter sp. strain TUM22923, isolated from Antarctic lake sediment. This has a 1,860,127 bp, comprising 1,848 protein-coding sequences. These data could contribute to elucidation streamlining and low-temperature adaptation in members Polynucleobacter, cosmopolitan group ultramicrobacteria.
Language: Английский
Citations
1
Microbiology Resource Announcements, Journal Year: 2023, Volume and Issue: 12(3)
Published: Feb. 16, 2023
The genus Polynucleobacter subcluster PnecC consists of bacteria representing the ubiquitous taxon freshwater bacterioplankton. Here, we report complete genome sequences three sp. (PnecC) strains, namely, KF022, KF023, and KF032, which were isolated from surface water a temperate shallow eutrophic lake its inflow river in Japan.
Language: Английский
Citations
0
Microbiology Resource Announcements, Journal Year: 2023, Volume and Issue: 12(4)
Published: March 1, 2023
Members of the genus Polynucleobacter belonging to subcluster PnecA comprise freshwater bacterioplankton with worldwide distribution. Here, we report complete genome sequences two sp. strains (PnecA), SHI2 and SHI8, isolated from surface water an oligotrophic-dystrophic lake in a humid continental climate Japan.
Language: Английский
Citations
0
The NamesforLife Abstracts, Journal Year: 2009, Volume and Issue: unknown
Published: April 28, 2009
Language: Английский
Citations
0
The NamesforLife Abstracts, Journal Year: 2022, Volume and Issue: unknown
Published: July 6, 2022
Citations
0
The NamesforLife Abstracts, Journal Year: 2022, Volume and Issue: unknown
Published: July 6, 2022
Language: Английский
Citations
0