Diversity of the genus Cryobacterium and proposal of 19 novel species isolated from glaciers

Cryobacterium Inferilacus sp. nov., a Pshychrophilic Ureolitic Bacterium From Lake Untersee in Antarctica

The psychrophilic aerobic heterotrophic bacterium, strain 1639T, was isolated from the low-temperature Lake Untersee in Antarctica. The bacterium was Gram-positive, non-motile, yellow-green-pigmented, non-spore-forming, and a pleomorphic rod. Growth was observed at temperatures of 0-25 °C with an optimum at 10 °C. The strain used urea as a nitrogen source. The major fatty acids were i-C16:0 (49.69%), ai-C15:0 (17.59%), and C16:1 branched (12.03%). Identified polar lipids were phosphatidylglycerols and a glycolipid. The respiratory quinone was determined to be MK-10. The genomic DNA G+C content was 68.03 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 1639T was a member of the genus Cryobacterium, with the highest sequence similarity to C. arcticum SK1T (98.4%), C. soli GCJ02T (98.4%), C. lactosi Sr59T (98.3%), C. zongtaii TMN-42T (98.2%), and C. adonitolivorans RHLS22-1T (98.1%). The ANI and the DNA-DNA hybridization estimate values between strain 1639T and all type strains of species of the genus Cryobacterium were in the range of 84.3-87.8% and 20.5-40.3%, respectively. The combined genotypic and phenotypic data indicate that strain 1639T represents a novel species within the genus Cryobacterium, for which the name Cryobacterium inferilacus sp. nov. is proposed with the type strain 1639T (=KCTC 59142T, =VKM Ac-2907T, UQM 41460T).

A comparative analysis of the rhizosphere microbial communities among three species of the Salix genus

Rhizosphere microorganisms exert a significant influence in counteracting diverse external stresses and facilitating plant nutrient uptake. While certain rhizosphere microorganisms associated with Salix species have been investigated, numerous rhizosphere microorganisms from various Salix species remain underexplored. In this study, we employed high-throughput sequencing to examine the rhizosphere bacterial and fungal communities composition and diversity of three Salix species: Salix zangica (SZ), Salix myrtilllacea (SM), and Salix cheilophila (SC). Furthermore, the BugBase and FUNGuild were utilized to predict the functional roles of bacterial and fungal microorganisms. The findings revealed notable variations in the alpha and beta diversities of bacterial and fungal communities among the three Salix species exhibited significant differences (p < 0.05). The relative abundance of Flavobacterium was highest in the SZ samples, while Microvirga exhibited significant enrichment in the SM samples. Microvirga and Vishniacozyma demonstrate the highest number of nodes within their respective bacterial and fungal community network structures. The functions of bacterial microorganisms, including Gram-positive, potentially pathogenic, Gram-negative, and stress-tolerant types, exhibited significant variation among the three Salix species (p < 0.05). Furthermore, for the function of fungal microbe, the ectomycorrhizal guild had the highest abundance of symbiotic modes. This results demonstrated the critical role of ectomycorrhizal fungi in enhancing nutrient absorption and metabolism during the growth of Salix plants. Additionally, this findings also suggested that S. zangica plant was better well-suited for cultivation in stressful environments. These findings guide future questions about plant-microbe interactions, greatly enhancing our understanding of microbial communities for the healthy development of Salix plants.

Description of Flavobacterium fructosi sp. nov., Flavobacterium xylosi sp. nov. and Flavobacterium zhouii sp. nov., three new members of the genus Flavobacterium

Three novel strains, designated LB3P45T, LS2P90T and ZS1P70T, were isolated from glaciers located on the Tibetan Plateau, PR China. These strains were Gram-stain-negative, aerobic, rod-shaped and yellow or orange coloured. Phylogenetic analysis based on the 16S rRNA gene and genomic sequences indicated that they belong to the genus Flavobacterium. The 16S rRNA gene sequence similarity among the three strains ranged from 97.4 to 98.6%. Strain LB3P45T showed 98.9% and 98.7% similarity to Flavobacterium urumqiense CGMCC 1.9230T and Flavobacterium xinjiangense JCM 11314T, respectively. Strain LS2P90T displayed 99.0% and 98.7% similarity to F. xinjiangense JCM 11314T and F. urumqiense CGMCC 1.9230T. Strain ZS1P70T had the highest sequence similarity with F. xinjiangense JCM 11314T (98.0%) and F. urumqiense CGMCC 1.9230T (97.8%). The average nucleotide identity and digital DNA-DNA hybridization values between these strains and their closest relatives were lower than 93.0% and 47.9%, respectively. All three strains contained summed feature 3 (comprising C16:1 ω7c and/or C16:1 ω6c) as the major fatty acids. Based on phenotypic characteristics, phylogenetic analysis and genotypic data, the three novel species are proposed: Flavobacterium fructosi sp. nov. (LB3P45T=CGMCC 1.11439T=NBRC 114819T), Flavobacterium xylosi sp. nov. (LS2P90T=CGMCC 1.11685T=NBRC 114823T) and Flavobacterium zhouii sp. nov. (ZS1P70T=CGMCC 1.24124T=NBRC 114829T).

Variability of microbiomes in winter rye, wheat, and triticale affected by snow mold: predicting promising microorganisms for the disease control

BACKGROUND

Snow mold caused by different psychrophilic phytopathogenic fungi is a devastating disease of winter cereals. The variability of the snow mold pathocomplex (the quantitative composition of snow mold fungi) has not been evaluated across different crops or different agrocenoses, and no microbial taxa have been predicted at the whole-microbiome level as potential effective snow mold control agents. Our study aimed to assess the variability of the snow mold pathocomplex in different winter cereal crops (rye, wheat, and triticale) in different agrocenoses following the peak disease progression and to arrange a hierarchical list of microbial taxa predicted to be the main candidates to prevent or, conversely, stimulate the development of snow mold pathogens.

RESULTS

The variability of microbiomes between different crops within a particular agrocenosis was largely determined by fungal communities, whereas the variability of microbiomes of a particular crop in different agrocenoses was largely determined by bacterial communities. The snow mold pathocomplex was the most "constant" in rye, with the lowest level of between-replicate variability and between-agrocenoses variability and (similar to the triticale snow mold pathocomplex) strong dominance of Microdochium over other snow mold fungi. The wheat snow mold pathocomplex was represented by different snow mold fungi, including poorly investigated Phoma sclerotioides. To predict snow mold-control microorganisms, a conveyor of statistical methods was formed and applied; this conveyor enables considering not only the correlation between the abundance of target taxa and a phytopathogen but also the stability and fitness of taxa within plant-associated communities and the reproducibility of the predicted effect of taxa under different conditions. This conveyor can be widely used to search for biological agents against various plant infectious diseases.

CONCLUSIONS

The top indicator microbial taxa for winter wheat and rye following the winter period were Ph. sclerotioides and Microdochium, respectively, both of which are causal agents of snow mold disease. Bacteria from the Cellulomonas, Lechevalieria, and Pseudoxanthomonas genera and fungi from the Cladosporium, Entimomentora, Pseudogymnoascus, and Cistella genera are prime candidates for testing their plant-protective properties against Microdochium-induced snow mold disease and for further use in agricultural practice.

Comparative Analysis of Gut Microbiota between Captive and Wild Long-Tailed Gorals for Ex Situ Conservation

The long-tailed goral is close to extinction, and ex situ conservation is essential to prevent this phenomenon. Studies on the gut microbiome of the long-tailed goral are important for understanding the ecology of this species. We amplified DNA from the 16S rRNA regions and compared the microbiomes of wild long-tailed gorals and two types of captive long-tailed gorals. Our findings revealed that the gut microbiome diversity of wild long-tailed gorals is greatly reduced when they are reared in captivity. A comparison of the two types of captive long-tailed gorals confirmed that animals with a more diverse diet exhibit greater gut microbiome diversity. Redundancy analysis confirmed that wild long-tailed gorals are distributed throughout the highlands, midlands, and lowlands. For the first time, it was revealed that the long-tailed goral are divided into three groups depending on the height of their habitat, and that the gut bacterial community changes significantly when long-tailed gorals are raised through ex situ conservation. This provides for the first time a perspective on the diversity of food plants associated with mountain height that will be available to long-tailed goral in the future.

Genomics-based identification of a cold adapted clade in Deinococcus

BACKGROUND

Microbes in the cold polar and alpine environments play a critical role in feedbacks that amplify the effects of climate change. Defining the cold adapted ecotype is one of the prerequisites for understanding the response of polar and alpine microbes to climate change.

RESULTS

Here, we analysed 85 high-quality, de-duplicated genomes of Deinococcus, which can survive in a variety of harsh environments. By leveraging genomic and phenotypic traits with reverse ecology, we defined a cold adapted clade from eight Deinococcus strains isolated from Arctic, Antarctic and high alpine environments. Genome-wide optimization in amino acid composition and regulation and signalling enable the cold adapted clade to produce CO2 from organic matter and boost the bioavailability of mineral nitrogen.

CONCLUSIONS

Based primarily on in silico genomic analysis, we defined a potential cold adapted clade in Deinococcus and provided an updated view of the genomic traits and metabolic potential of Deinococcus. Our study would facilitate the understanding of microbial processes in the cold polar and alpine environments.