Phylogenomic analyses and comparative genomic studies of Thermus strains isolated from Tengchong and Tibet Hot Springs, China.

Genus Thermus is the main focus of researcher among the thermophiles. Members of this genus are the inhabitants of both natural and artificial thermal environments. We performed phylogenomic analyses and comparative genomic studies to unravel the genomic diversity among the strains belonging to the genus Thermus in geographically different thermal springs.

Heterozygous CAPZA2 mutations cause global developmental delay, hypotonia with epilepsy: a case report and the literature review.

CAPZA2 encodes the α2 subunit of CAPZA, which is vital for actin polymerization and depolymerization in humans. However, understanding of diseases associated with CAPZA2 remains limited. To date, only three cases have been documented with neurodevelopmental abnormalities such as delayed motor development, speech delay, intellectual disability, hypotonia, and a history of seizures.

The evolution of morphological development is congruent with the species phylogeny in the genus .

As the canonical model organism to dissect bacterial morphological development, species has attracted much attention from the microbiological society. However, the evolution of development-related genes in remains elusive. Here, we evaluated the distribution of development-related genes, thus indicating that the majority of these genes were ubiquitous in genomes.

Thermophilic Dehalococcoidia with unusual traits shed light on an unexpected past.

Although the phylum Chloroflexota is ubiquitous, its biology and evolution are poorly understood due to limited cultivability. Here, we isolated two motile, thermophilic bacteria from hot spring sediments belonging to the genus Tepidiforma and class Dehalococcoidia within the phylum Chloroflexota. A combination of cryo-electron tomography, exometabolomics, and cultivation experiments using stable isotopes of carbon revealed three unusual traits: flagellar motility, a peptidoglycan-containing cell envelope, and heterotrophic activity on aromatics and plant-associated compounds.

Comparative genomic analysis and proposal of Clostridium yunnanense sp. nov., Clostridium rhizosphaerae sp. nov., and Clostridium paridis sp. nov., three novel Clostridium sensu stricto endophytes with diverse capabilities of acetic acid and ethanol production.

Objectives: Genus Clostridium sensu stricto is generally regarded as the true Clostridium genus, which includes important human and animal pathogens and industrially relevant microorganisms. Besides, it is also a prominent member of plant-associated endophytes. However, our knowledge of endophytic Clostridium is limited.

Azospirillum Endophyticum sp. nov., an Endophyte of Paris Polyphylla Smith var. Yunnanensis.

A Gram-negative, facultative anaerobic bacterial strain, designated YIM B02556, was isolated from the root of Paris polyphylla Smith var. yunnanensis collected from Yunnan Province, southwest China. By using a polyphasic approach, its taxonomic position was investigated.

Genome-based analyses reveal heterotypic synonyms of Streptomyces species and associated subspecies.

In the genus Streptomyces, several validly described species have been reduced to synonyms of earlier described species though additional synonyms remain to be detected given the previous dependence on traditional phenotypic methods. In this study, genome-based procedures, including DNA-DNA hybridization analyses, overall genome-related indices, such as ANI, dDDH and AAI, revealed that certain strains recorded genomic indices above the threshold values used to define species boundaries. The results of phylogenetic and phylogenomic trees based on concatenated and phylogenomic analyses showed that 33 out of 364 tested species could be assigned to 15 species groups and that 18 Streptomyces species names be reclassified as later heterotypic synonyms of earlier validly published species.

Potassium accumulation characteristics and expression of related genes involved in potassium metabolism in a high-potassium variety: tobacco () as a model.

We investigated potassium (K) accumulation characteristics and expression of K metabolism related genes in one high-K variety (ND202) and a common variety (NC89) of tobacco (Nicotiana tabacum L.). Results showed that K accumulation and leaf K content in ND202 were higher than those in NC89.

Tobacco Root Microbial Community Composition Significantly Associated With Root-Knot Nematode Infections: Dynamic Changes in Microbiota and Growth Stage.

The root-knot nematode (RKN) is an important pathogen that affects the growth of many crops. Exploring the interaction of biocontrol bacteria-pathogens-host root microbes is the theoretical basis for improving colonization and controlling the effect of biocontrol bacteria in the rhizosphere. Therefore, 16S and 18S rRNA sequencing technology was used to explore the microbial composition and diversity of tobacco roots (rhizosphere and endophytic) at different growth stages in typical tobacco RKN-infected areas for 2 consecutive years.

Neobacillus paridis sp. nov., an endophyte of Paris polyphylla Smith var. yunnanensis.

A novel endophytic strain, designated YIM B02564, was isolated from the root of Paris polyphylla Smith var. yunnanensis obtained from Yunnan Province, southwest China. By using a polyphasic approach, cells of the strain were characterized as facultative anaerobic, Gram-positive and rod-shaped.

Janibacter endophyticus sp. nov., an Endophytic Actinobacterium Isolated from the Root of Paris polyphylla Smith var. Yunnanensis.

A novel endophytic actinobacterium, designated as strain YIM B02568, was isolated from the root of Paris polyphylla Smith var. Yunnanensis obtained from Yunnan Province, southwest China. Strain YIM B02568 was characterized using a polyphasic approach.

Chryseobacterium paridis sp. nov., an endophytic bacterial species isolated from the root of Paris polyphylla Smith var. yunnanensis.

A Gram-negative, yellow-pigmented, rod-shaped bacterial strain YIM B02567 was isolated from the root of Paris polyphylla Smith var. yunnanensis in China. Strain YIM B02567 grew optimally at 25-30 °C and at pH 7.

Vallicoccus soli gen. nov., sp. nov., a novel actinobacterium isolated from soil, and description of Vallicoccaceae fam. nov., Motilibacterales ord. nov.

A novel Gram-stain-positive, aerobic, cocci-shaped actinobacterium, designated YIM 75000, was isolated from a soil sample collected from a dry-hot river valley in Yunnan Province, P.R. China.

Plasmids Related to the Symbiotic Nitrogen Fixation Are Not Only Cooperated Functionally but Also May Have Evolved over a Time Span in Family Rhizobiaceae.

Rhizobia are soil bacteria capable of forming symbiotic nitrogen-fixing nodules associated with leguminous plants. In fast-growing legume-nodulating rhizobia, such as the species in the family Rhizobiaceae, the symbiotic plasmid is the main genetic basis for nitrogen-fixing symbiosis, and is susceptible to horizontal gene transfer. To further understand the symbioses evolution in Rhizobiaceae, we analyzed the pan-genome of this family based on 92 genomes of type/reference strains and reconstructed its phylogeny using a phylogenomics approach.

Reclassification of , and as nom. nov., comb. nov. and comb. nov., respectively.

According to Rule 37a of the International Code of Nomenclature of Prokaryotes, the name of a taxon must be changed if the nomenclatural type of the taxon is excluded. Recently, in a transfer of actinobacterial species, three species - Tuo . 2016, Hamada .

A recently evolved diflavin-containing monomeric nitrate reductase is responsible for highly efficient bacterial nitrate assimilation.

Nitrate is one of the major inorganic nitrogen sources for microbes. Many bacterial and archaeal lineages have the capacity to express assimilatory nitrate reductase (NAS), which catalyzes the rate-limiting reduction of nitrate to nitrite. Although a nitrate assimilatory pathway in mycobacteria has been proposed and validated physiologically and genetically, the putative NAS enzyme has yet to be identified.

Activation of potassium released from soil by root-secreted organic acids in different varieties of tobacco (Nicotiana tabacum).

Organic acids secreted from the roots of plants play important roles in nutrient acquisition and metal detoxification; however, the precise underlying mechanisms of these processes remain poorly understood. In the present study we examined the content of organic acids exuded from roots and the effects of these organic acids on the activation of slowly available potassium (K) at different K levels, including normal K supply and K-deficient conditions. In addition, the study system also comprised a high-K tobacco variety (ND202) and two common ones (K326 and NC89).

sp. nov., an endophytic bacterial species isolated from the root of Smith var. .

A Gram-reaction-positive, endospore-forming and rod-shaped bacterial strain, designated py1325, was isolated from the root of Smith var. collected from Yunnan Province, PR China, and subjected to a polyphasic taxonomic characterization. It grew optimally with 0-1 % NaCl (w/v), at pH 7 and at 30 °C.

sp. nov., a thermophilic bacterium from hot spring of the class emended description of the genus and proposal of fam. nov.

A Gram-staining-negative, aerobic, curved rod-shaped and thermophilic bacterial strain, designated YIM 72297, was isolated from a sediment sample collected from a hot spring in Tengchong county, Yunnan province, south-west China. Growth was observed at pH 5.0-9.

Genome-based taxonomic classification within the family Thermoactinomycetaceae.

The family Thermoactinomycetaceaecomprises 43 validly published species, which were identified by a polyphasic taxonomic study based on molecular phylogenetics, physiological and biochemical characteristics. However, phylogenetic analysis merely based on 16S rRNA gene sequences cannot infer a robust and reliable phylogeny. For disentangling the phylogenetic relationships among members of this family, we used a large collection of genome data and the approach of phylogenomics, to re-examine their taxonomy.

Bailinhaonella thermotolerans gen. nov., sp. nov., a new member of the order Streptosporangiales.

A Gram-positive, aerobic, non-motile actinobacterium, designated YIM 75507, that was isolated from a soil sample collected from a dry-hot valley, was subjected to a polyphasic taxonomic study. The isolate formed branched hyphae and no fragmentation was found. Clustered spore chains were borne from aerial mycelium.

Rhodobacter thermarum sp. nov., a novel phototrophic bacterium isolated from sediment of a hot spring.

An ovoid to rod-shaped, phototrophic, purple non-sulfur bacterium was isolated from a sediment sample of a hot spring in Tibet, China. Cells of strain YIM 73036 were Gram-stain negative, non-motile and multiplied by binary fission. Strain YIM 73036 grew optimally at pH 7.

Aquabacterium tepidiphilum sp. nov., a moderately thermophilic bacterium isolated from a hot spring.

A Gram-stain-negative, aerobic, non-spore-forming and rod-shaped bacterium, designated YIM 730274, was isolated from a sediment sample collected from a hot spring located in Tibet, PR China, and was characterized by using a polyphasic taxonomy approach. Cells were motile by means of a polar flagellum. The strain was oxidase- and catalase-positive, and contained polyalkanoates and polyphosphate as storage polymers.