The Characterization of Microbiome and Interactions on Weathered Rocks in a Subsurface Karst Cave, Central China

Karst caves are a natural oligotrophic subsurface biosphere widely distributed in southern China. Despite the progress in bacterial and fungal diversity, the knowledge about interactions between bacteria, fungi, and minerals is still limited in caves. Hence, for the first time, we investigated the interaction between bacteria and fungi living on weathered rocks in the Heshang Cave via high-throughput sequencing of 16S rRNA and ITS1 genes, and co-occurrence analysis. The mineral compositions of weathered rocks were analyzed by X-ray diffraction. Bacterial communities were dominated by Actinobacteria (33.68%), followed by Alphaproteobacteria (8.78%), and Planctomycetia (8.73%). In contrast, fungal communities were dominated by Sordariomycetes (21.08%) and Dothideomycetes (14.06%). Mineral substrata, particularly phosphorus-bearing minerals, significantly impacted bacterial (hydroxyapatite) and fungal (fluorapatite) communities as indicated by the redundancy analysis. In comparison with fungi, the development of bacterial communities was more controlled by the environmental selection indicated by the overwhelming contribution of deterministic processes. Co-occurrence network analysis showed that all nodes were positively linked, indicating ubiquitous cooperation within bacterial groups and fungal groups, as well as between bacteria and fungi under oligotrophic conditions in the subsurface biosphere. In total, 19 bacterial ASVs and 34 fungal OTUs were identified as keystone taxa, suggesting the fundamental role of fungi in maintaining the microbial ecosystem on weathered rocks. Ascomycota was most dominant in keystone taxa, accounting for 26.42%, followed by Actinobacteria in bacteria (24.53%). Collectively, our results confirmed the highly diverse bacterial and fungal communities on weathered rocks, and their close cooperation to sustain the subsurface ecosystem. Phosphorus-bearing minerals were of significance in shaping epipetreous bacterial and fungal communities. These observations provide new knowledge about microbial interactions between bacteria, fungi, and minerals in the subterranean biosphere.

Analysis of 1,000 Type-Strain Genomes Improves Taxonomic Classification of Bacteroidetes

Although considerable progress has been made in recent years regarding the classification of bacteria assigned to the phylum Bacteroidetes, there remains a need to further clarify taxonomic relationships within a diverse assemblage that includes organisms of clinical, piscicultural, and ecological importance. Bacteroidetes classification has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees and a limited number of phenotypic features. Here, draft genome sequences of a greatly enlarged collection of genomes of more than 1,000 Bacteroidetes and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa proposed long ago such as Bacteroides, Cytophaga, and Flavobacterium but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which can be considered valuable taxonomic markers. We detected many incongruities when comparing the results of the present study with existing classifications, which appear to be caused by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. The few significant incongruities found between 16S rRNA gene and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences and the impediment in using ordinary bootstrapping in phylogenomic studies, particularly when combined with too narrow gene selections. While a significant degree of phylogenetic conservation was detected in all phenotypic characters investigated, the overall fit to the tree varied considerably, which is one of the probable causes of misclassifications in the past, much like the use of plesiomorphic character states as diagnostic features.

Flavisolibacter nicotianae sp. nov., isolated from rhizosphere soil of Nicotiana tabacum L

A Gram-stain-negative, aerobic, non-motile and rod-shaped bacterium, designated strain X7XT, was isolated from a rhizosphere soil sample of Nicotiana tabacum L. collected from a tobacco factory located in Kunming, south-western China. The cells showed oxidase-positive and catalase-positive reactions. Growth occurred at 20-40 °C and pH 6.0-8.0, with optimal growth at 30 °C and pH 7.0. The predominant respiratory quinone was MK-7. The major fatty acids were identified as iso-C15 : 0, iso-C17 : 0 3OH and summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c). The cellular polar lipids contained phosphatidylethanolamine, an unidentified aminophospholipid, two unidentified glycolipids, four unidentified aminolipids and four unidentified lipids. The genomic DNA G+C content was 49.7 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain X7XT should be affiliated to the genus Flavisolibacter. Results from further analysis showed that strain X7XT had highest 16S rRNA gene sequence similarity to Flavisolibacter metallilatus TX0661T (96.4 %) and 'Flavisolibacter swuensis' SR2-4-2T (96.4 %), followed by other species of the genus Flavisolibacter. The polyphasic taxonomic characteristics indicated that strain X7XT represents a novel species of the genus Flavisolibacter, for which the name Flavisolibacternicotianae sp. nov. (type strain X7XT=KCTC 62326T=CGMCC 16451T) is proposed.

Flavisolibacter galbus sp. nov., isolated from soil in Jeju Island

A Gram-stain negative, non-motile, and yellow-coloured bacterium, designated 17J28-26^T, was isolated from soil in Jeju Island, Korea. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain 17J28-26^T formed a distinct lineage within the family Chitinophagaceae (order Chitinophagales, class Chitinophagia), and is closely related to Flavisolibacter ginsenosidimutans (96.8% 16S rRNA gene sequence similarity), and Flavisolibacter ginsengisoli (96.6%). Growth was observed at 18-37 °C (optimum 30 °C) in R2A medium at pH 7.0. The major cellular fatty acids of strain 17J28-26^T were summed feature 3 (C_16:1 ω6c and/or C_16:1 ω7c), and iso-C_15:0. The predominant respiratory quinone was MK-7. The major polar lipid was identified as phosphatidylethanolamine. Based on biochemical, chemotaxonomic and phylogenetic characteristics, strain 17J28-26^T represents a novel bacterial species within the family Chitinophagaceae, for which the name Flavisolibacter galbus sp. nov. is proposed. The type strain of Flavisolibacter galbus is 17J28-26^T (= KCTC 62222^T = JCM 33203^T).

Paracnuella aquatica gen. nov., sp. nov., a member of the family Chitinophagaceae isolated from a hot spring

A Gram-stain-negative, rod-shaped bacterium (designated strain N24^T) with gliding motility was isolated from thermal spring water sampled at Xi'an, PR China. Cells were 0.4-0.8 µm wide and 1.8-7.8 µm long. Optimal growth occurred at 33 °C and pH 7.0 on Reasoner's 2A (R2A) agar. Strain N24^T could produce exopolysaccharide on R2A agar at 33 °C. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain N24^T formed a distinct phyletic lineage within the family Chitinophagaceae and was most closely related to members of the genera Flavisolibacter, Cnuella, Niveitalea, Flavitalea, Flaviaesturariibacter and Niastella with 91.7-93.9 % 16S rRNA gene sequence similarities. The major fatty acids of strain N24^T were iso-C15 : 0 (31.8 %), iso-C17 : 0 3-OH (16.1 %) and iso-C15 : 1 G (12.9 %). The polar lipid profile consisted of phosphatidylethanolamine, two aminolipids and six unknown lipids; the quinone system consisted of menaquinone-7 (MK-7). The genomic G+C content was 49.3 mol%. On the basis of the evidence presented in this study, strain N24^T represents a novel species of a new genus in the family Chitinophagaceae, for which the name Paracnuella aquatica gen. nov., sp. nov. is proposed. The type species is N24^T (=KCTC 62083^T=MCCC 1H00301^T).

Flavisolibacter metallilatus sp. nov., isolated from an automotive air conditioning system and emended description of the genus Flavisolibacter

A Gram-stain-negative, aerobic, non-motile, rod-shaped and pale yellow-pigmented bacterium, designated strain TX0661^T, was isolated from an automotive air conditioning system collected in the Republic of Korea. 16S rRNA gene sequence analysis showed that the strain TX0661^T was grouped with members of the genus Flavisolibacter and the strain had 98.2-95.3 % 16S rRNA gene sequence similarities to the species of the genus Flavisolibacter. DNA-DNA relatedness between TX0661^T and Flavisolibacter ginsenosidimutans KCTC 22818^T and Flavisolibacter ginsengisoli KCTC 12657^T was less than 30 %. The low levels of DNA-DNA relatedness identified strain TX0661^T as a novel species in the genus Flavisolibacter. The strain grew at 28-37 °C (optimum, 37 °C), at pH 6.0-7.0 (optimum, pH 6.5) and in the presence of 0-0.5 % (w/v, optimum, 0.5 %) NaCl. It contained summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), iso-C15 : 0 and iso-C17 : 0 3-OH as major fatty acids and MK-7 as the predominant menaquinone. The polar lipid profile revealed that the presence of phosphatidylethanolamine, aminoglycophospholipid, two unidentified aminolipids and two unidentified lipids. The DNA G+C content of the strain was 49.1 mol%. Based on phenotypic, genotypic and chemotaxonomic data, strain TX0661^T represents a novel species in the genus Flavisolibacter, for which the name Flavisolibactermetallilatus sp. nov. (=KACC 19145^T=KCTC 52779^T=NBRC 111784^T) is proposed.

Interactions of plant growth-promoting rhizobacteria and soil factors in two leguminous plants

Although the rhizomicrobiome has been extensively studied, little is known about the interactions between soil properties and the assemblage of plant growth-promoting microbes in the rhizosphere. Herein, we analysed the composition and structure of rhizomicrobiomes associated with soybean and alfalfa plants growing in different soil types using deep Illumina 16S rRNA sequencing. Soil pH, P and K significantly affected the composition of the soybean rhizomicrobiome, whereas soil pH and N had a significant effect on the alfalfa rhizomicrobiome. Plant biomass was influenced by plant species, the composition of the rhizomicrobiome, soil pH, N, P and plant growth stage. The beta diversity of the rhizomicrobiome was the second most influential factor on plant growth (biomass). Rhizomicrobes associated with plant biomass were identified and divided into four groups: (1) positively associated with soybean biomass; (2) negatively associated with soybean biomass; (3) positively associated with alfalfa biomass; and (4) negatively associated with alfalfa biomass. Genera assemblages among the four groups differentially responded to soil properties; Group 1 and Group 2 were significantly correlated with soil pH and P, whereas Group 3 and Group 4 were significantly correlated with soil N, K and C. The influence of soil properties on the relative abundance of plant biomass-associated rhizomicrobes differed between soybean and alfalfa. The results suggest the rhizomicrobiome has a pronounced influence on plant growth, and the rhizomicrobiome assemblage and plant growth-associated microbes are differentially structured by soil properties and leguminous plant species.