Insights into chemoautotrophic traits of a prevalent bacterial phylum CSP1-3, herein .

Candidate bacterial phylum CSP1-3 has not been cultivated and is poorly understood. Here, we analyzed 112 CSP1-3 metagenome-assembled genomes and showed they are likely facultative anaerobes, with 3 of 5 families encoding autotrophy through the reductive glycine pathway (RGP), Wood-Ljungdahl pathway (WLP) or Calvin-Benson-Bassham (CBB), with hydrogen or sulfide as electron donors. Chemoautotrophic enrichments from hot spring sediments and fluorescence hybridization revealed enrichment of six CSP1-3 genera, and both transcribed genes and DNA-stable isotope probing were consistent with proposed chemoautotrophic metabolisms.

Advancements in prokaryotic systematics and the role of Bergey's International Society for Microbial Systematicsin addressing challenges in the meta-data era.

Prokaryotes are ubiquitous in the biosphere, important for human health and drive diverse biological and environmental processes. Systematics of prokaryotes, whose origins can be traced to the discovery of microorganisms in the 17th century, has transitioned from a phenotype-based classification to a more comprehensive polyphasic taxonomy and eventually to the current genome-based taxonomic approach. This transition aligns with a foundational shift from studies focused on phenotypic traits that have limited comparative value to those using genome sequences.

Cultivation of novel Atribacterota from oil well provides new insight into their diversity, ecology, and evolution in anoxic, carbon-rich environments.

Background: The Atribacterota are widely distributed in the subsurface biosphere. Recently, the first Atribacterota isolate was described and the number of Atribacterota genome sequences retrieved from environmental samples has increased significantly; however, their diversity, physiology, ecology, and evolution remain poorly understood.

Results: We report the isolation of the second member of Atribacterota, Thermatribacter velox gen.

Sphingosinicella terrae sp. nov. Isolated from a Desert Soil and Reclassification of Sphingomonas deserti as Sphingosinicella deserti comb. nov.

A motile, rod-shaped and yellow-coloured bacterium, designated strain SYSU D60001, was isolated from a desert soil sample. Cells were Gram-stain-negative, catalase-negative and oxidase-positive. The major cellular fatty acids were summed feature 8 (C ω7c and/or C ω6c) and C.

Comparative genomic analysis of provides insights into the evolutionary history of an incomplete denitrification pathway.

Biological denitrification is a crucial process in the nitrogen biogeochemical cycle, and has been reported to be a significant heterotrophic denitrifier in terrestrial geothermal environments. However, neither the denitrification potential nor the evolutionary history of denitrification genes in the genus or phylum is well understood. Here, we performed a comparative analysis of 23 genomes and identified denitrification genes in 15  strains.

Haloterrigena gelatinilytica sp. nov., a new extremely halophilic archaeon isolated from salt-lake.

Two extremely halophilic strains, designated SYSU A558-1 and SYSU A121-1, were isolated from a saline sediment sample collected from Aiding salt-lake, China. Cells of strains SYSU A558-1 and SYSU A121-1 were Gram-stain-negative, coccoid, and non-motile. The strains were aerobic and grew at NaCl concentration of 10-30% (optimum, 20-22%), at 20-55 °C (optimum, 37-42 °C) and at pH 6.

Diversity and Distribution of Anaerobic Ammonium Oxidation Bacteria in Hot Springs of Conghua, China.

Anaerobic ammonium oxidation (anammox) is an important process of the nitrogen cycle, and the anammox bacteria have been studied in a wide variety of environments. However, the distribution, diversity, and abundance of anammox bacteria in hot springs remain enigmatic. In this study, the anammox process was firstly investigated in hot springs of Conghua, China.

Halegenticoccus tardaugens sp. nov., an extremely halophilic archaeon isolated from a saline soil.

Two extremely halophilic archaea, isolates SYSU A00711 and SYSU A00630, were isolated from a sediment soil sample collected from the Aiding lake, China. Cells of these isolates were cocci, non-motile and stained Gram-negative. They grew optimally at 37 °C, with 20-22% NaCl (w/v) and at pH 7.

Nesterenkonia haasae sp. nov., an alkaliphilic actinobacterium isolated from a degraded pasture in Songnen Plain.

An alkaliphilic actinobacterial strain, designated Hz 6-5, was isolated from saline-alkaline soil from Songnen Plain in north-eastern China. The isolate formed light yellow-colored colonies and its cells were Gram-staining positive, non-motile, and non-spore-forming short rods. The strain was aerobic with optimal growth at 33 °C, pH 9.

gen. nov., sp. nov., a novel cellulose- and xylan-degrading member of the family isolated from a hot spring.

Two anaerobic bacteria, designated strains SYSU GA16112 and SYSU GA16107, were isolated from a hot spring in Tengchong County, Yunnan Province, south-west PR China. Phylogenetic analyses based on 16S rRNA gene sequences showed that strains SYSU GA16112 and SYSU GA16107 belong to the family . Cells of strains SYSU GA16112 and SYSU GA16107 were Gram-stain-negative, rod-shaped and non-motile.

From ecophysiology to cultivation methodology: filling the knowledge gap between uncultured and cultured microbes.

Earth is dominated by a myriad of microbial communities, but the majority fails to grow under in situ laboratory conditions. The basic cause of unculturability is that bacteria dominantly occur as biofilms in natural environments. Earlier improvements in the culture techniques are mostly done by optimizing media components.

Isolation of Clostridium from Yunnan-Tibet hot springs and description of Clostridium thermarum sp. nov. with lignocellulosic ethanol production.

Lignocellulose is considered a major source of renewable energy that serve as an alternative to the fossil fuels. Members of the genus Clostridium are some of the many microorganisms that have the ability to degrade lignocellulose efficiently to sugar, which can be further converted to biofuel. In this study, we isolated twelve Clostridium strains from hot spring samples of Yunnan and Tibet, of which isolates SYSU GA15002 and SYSU GA17076 showed low 16S rRNA gene sequence identity profiles to any of the validly named Clostridium strains (<94.

Unraveling bacteria-mediated degradation of lignin-derived aromatic compounds in a freshwater environment.

Terrestrial organic carbon-lignin plays a crucial role in the global carbon balance. However, limited studies presented the functional and ecological traits of lignin decomposers population in natural aquatic ecosystem. In this study, we performed a multi-omics analysis by deploying amplicon, metagenomic, and metatranscriptomic approaches to identify the key potential degraders and pathways involved lignin-derived aromatic compounds in the later stage of lignin degradation.

Network-directed efficient isolation of previously uncultivated Chloroflexi and related bacteria in hot spring microbial mats.

The perplexity of the complex multispecies community interactions is one of the many reasons why majority of the microorganisms are still uncultivated. We analyzed the entire co-occurrence networks between the OTUs of Tibet and Yunnan hot spring samples, and found that less abundant OTUs such as genus Tepidimonas (relative abundant <1%) had high-degree centricity (key nodes), while dominant OTUs particularly genus Chloroflexus (relative abundant, 13.9%) formed the peripheral vertexes.

sp. nov., isolated from a high altitude Atacama Desert soil.

The taxonomic status of a strain, designated H13, isolated from a high altitude Atacama Desert soil, was established by using a polyphasic approach. The strain was found to have chemotaxonomic, cultural and morphological characteristics consistent with its classification within the genus and formed a well-supported clade in the phylogenomic tree together with the type strains of , and . Strain H13 was distinguished from its closest relatives by low average nucleotide identity (93.

gen. nov., sp. nov., a novel member of the family isolated from an activated sludge sample.

A coccobacilli-shaped proteobacterium, designated strain SYSU XM001, was isolated from an activated sludge sample collected from JiMei sewage treatment plant, Xiamen, PR China. Cells were Gram-stain-negative, catalase-positive and oxidase-negative. The 16S rRNA gene sequence of strain SYSU XM001 shared less than 92 % sequence identities with members of the class , with highest sequence similarity to TH1-2 (91.

sp. nov., a thermophilic bacterium isolated from a hot spring.

A thermophilic bacterium, designated SYSU G03088, was isolated from Moincer hot spring, Tibet, PR China. Polyphasic taxonomic analyses and whole-genome sequencing were used to determine the taxonomic position and genomic profiles of the strain. Phylogenetic analysis using 16S rRNA gene sequence indicated that SYSU G03088 showed highest sequence similarity to CGMCC 1.

Update on the classification of higher ranks in the phylum .

Genome analysis is one of the main criteria for description of new taxa. Availability of genome sequences for all the actinobacteria with a valid nomenclature will, however, require another decade's works of sequencing. This paper describes the rearrangement of the higher taxonomic ranks of the members of the phylum '', using the phylogeny of 16S rRNA gene sequences and supported by the phylogeny of the available genome sequences.

Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea.

Rapid growth of genome data provides opportunities for updating microbial evolutionary relationships, but this is challenged by the discordant evolution of individual genes. Here we build a reference phylogeny of 10,575 evenly-sampled bacterial and archaeal genomes, based on a comprehensive set of 381 markers, using multiple strategies. Our trees indicate remarkably closer evolutionary proximity between Archaea and Bacteria than previous estimates that were limited to fewer "core" genes, such as the ribosomal proteins.

reveals that Li . 2006 is a later heterotypic synonym of Al-Tai and Ruan 1994.

A genome-based phylogeny of the publicly available genomes of the genus reveals that YIM 90130 is closely related to DSM 44494. Overall genome relatedness indices between the genomes of the two species were above the threshold values necessary for defining a new species (dDDH, 82.9 %; ANIb, 97.

gen. nov., sp. nov. and sp. nov., new members of the family isolated from coastal seawater.

Two -like bacteria, designated strains SYSU SYW-5 and SYSU SYW-6, were isolated from coastal seawater sampled at Huizhou Double-Moon Bay, Guangdong Province, PR China. Cells were found to be Gram-stain-negative, non-motile, non-spore-forming and of pleomorphic shape (coccobacilli or rod). Chemotaxonomic analysis of the plasma membrane revealed ubiquinone-8 as the respiratory quinone, and saturated branched-chain (anteiso-C) and saturated straight-chain (C) fatty acids as major components (>8 % of total fatty acid).