Mucibacter soli gen. nov., sp. nov., a new member of the family Chitinophagaceae producing mucin

Saline soil improvement promotes the transformation of microbial salt tolerance mechanisms and microbial-plant-animal ecological interactions

The improvement of coastal saline land would alleviate the problem of insufficient arable land and provide new solutions for guaranteeing food security and ecological environment modification. In this study, five typical soil samples were collected from Tongzhou Bay, China. The changes in bacterial, animal and plant community composition before and after improvement were comprehensively investigated by a combination of high-throughput sequencing and macro-barcode sequencing analysis of eDNA. The study aimed (1) to characterize the species composition and diversity of the bacterial communities in saline soils, (2) to elucidate the mechanisms of salt tolerance of the bacterial communities, and (3) to investigate the impacts of the microbial salt tolerance mechanisms on the regional bacteria and fauna. The results showed that over 15 years of improvement, the composition of the bacteria in the saline-alkaline plots evolved significantly, changing from Desulfovibrio (10.60%) and Campylobacter (11.20%), to Acidobacter (12.91%). After the improvement, salt stress on the bacterial phyla gradually decreased. The functional differentiation of the bacterial phyla became more pronounced. As ion concentrations decreased, the main mechanism of salt tolerance of the bacterial bacteria changed from mainly mechanism of inorganic ion accumulation (55.56%), supplemented by flexible halophilic enzymes (31.77%), to mainly mechanism of compatible solute (44.80%). The mechanism of microbial salt tolerance directly affected micro-diversity and indirectly influenced the diversity of environmental species (R = 0.54). The results of this study provide a scientific basis for coastal saline land as a microbiodiversity marker and for the exploration of microbial improvement of saline land.

Cast from the Past? Microbial Diversity of a Neolithic Stone Circle

We studied the microbial diversity colonizing limestone rock pools at a Neolithic Monument (Arbor Low, Derbyshire, England). Five pools were analyzed: four located at the megaliths of the stone circle and one pool placed at the megalith at the Gib Hill burial mound 300 m distant. Samples were taken from rock pool walls and sediments, and investigated through molecular metabarcoding. The microbiome consisted of 23 phyla of bacteria (831 OTUs), 4 phyla of archaea (19 OTUs), and 27 phyla of microbial eukarya (596 OTUs). For bacteria, there were statistically significant differences in wall versus sediment populations, but not between pools. For archaea and eukarya, significant differences were found only between pools. The most abundant bacterial phylum in walls was Cyanobacteriota, and Pseudomonadota in sediments. For archaea and microbial eukarya, the dominant phyla were Euryarcheota and Chlorophyta, respectively, in both wall and sediments. The distant pool (P5) showed a markedly different community structure in phyla and species, habitat discrimination, and CHN content. Species sorting and dispersal limitation are discussed as mechanisms structuring the microbiome assemblages and their spatial connectivity. The Arbor Low microbiome is composed of terrestrial representatives common in extreme environments. The high presence of Cyanobacteriota and Chlorophyta in the Arbor Low stones is troubling, as these microorganisms can induce mechanical disruption by penetrating the limestone matrix through endolithic/chasmoendolithic growth. Future research should focus on the metabolic traits of strains to ascertain their implication in bioweathering and/or biomineralization.

Simplicispira sedimenti sp. nov., isolated from a sediment of drainage ditch in winery

A Gram-stain-negative, motile (by single polar flagellum) and rod-shaped bacterium, designated W1-6T, was isolated from a sediment of drainage ditch in winery in Guiyang, south-western China. Strain W1-6T showed the highest 16S rRNA gene sequence similarities with the type strain of Acidovorax wautersii (98.1%) and Simplicispira lacusdiani (97.9%). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain W1-6T was placed adjacent to the members of the genus Simplicispira and formed a separat subclade. Cells showed oxidase and catalase negative reactions. The only respiratory quinone detected was ubiquinone-8 (Q-8). Summed feature 3 (C16:1 ω7c and/or C16:1 ω6c), C16:0 and summed feature 8 (C18:1 ω7c and/or C18:1 ω6c) were predominant cellular fatty acids (> 10%) of strain W1-6T. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and five unidentified phospholipids were found in the polar lipid extraction. The genomic DNA G + C content was 65.6%. Strain W1-6T shared the highest digital DNA-DNA hybridization [dDDH, (27.6%)] and average nucleotide identity [ANI (84.3%)] values with the type strain of S. lacusdiani. The dDDH and ANI values were below the cutoff level (dDDH 70%; ANI 95-96%) for species delineation. The polyphasic characteristics indicated that the strain W1-6T represents a novel species of the genus Simplicispira, for which the name Simplicispira sedimenti sp. nov. is proposed. The type strain is W1-6T (= CGMCC 1.16274T = NBRC 115624T).

Nocardioides euryhalodurans sp. nov., Nocardioides seonyuensis sp. nov. and Nocardioides eburneiflavus sp. nov., isolated from soil

Three aerobic, rod-shaped actinobacterial strains, designated MMS17-SY117^T, MMS17-SY207-3^T and MMS17-SY213^T, were isolated from soil and their taxonomic positions were analysed using a polyphasic approach. The isolates showed best growth at 30 °C, pH 7 and 0-1 % (w/v) NaCl. On the basis of 16S rRNA gene sequence similarity, the isolates were affiliated to the genus Nocardioides, and the closest species to MMS17-SY117^T, MMS17-SY207-3^T and MMS17-SY213^T were Nocardioides aestuarii JC2056^T (97.76%), Nocardioides currus IB-3^T (97.41%) and Nocardioides exalbidus RC825^T (98.71%), respectively. Each isolate formed a distinct cluster within the Nocardioides clade in the phylogenetic tree. The orthologous average nucleotide identity and digital DNA-DNA hybridization values were in the range of 74.4-85.7 % and 16.6-39.2 %, respectively, with the type strains of related species. The major polar lipids in all three strains were phosphatidylinositol, phosphatidylglycerol and diphosphatidylglycerol. The predominant fatty acids were iso-C_16 : 0 and C_17 : 1 ω8c. MK-8(H₄) was the major isoprenoid quinone and ll-DAP was the major diamino acid. Galactose, glucose and rhamnose were present in the whole-cell hydrolysate, and MMS17-SY213^T also contained mannose and ribose. The DNA G+C contents of MMS17-SY117^T, MMS17-SY207-3^T and MMS17-SY213^T were 72.2, 70.4 and 71.5 mol%, respectively. The phylogenetic, phenotypic and chemotaxonomic data supported the classification of each strain as representing a new species of Nocardioides, for which the names Nocardioides euryhalodurans sp. nov. (MMS17-SY117^T=KCTC 49175^T=JCM 32831^T), Nocardioides seonyuensis sp. nov. (MMS17-SY207-3^T=KCTC 49176^T=JCM 32832^T) and Nocardioides eburneiflavus sp. nov. (MMS17-SY213^T=KCTC 49177^T=JCM 32833^T) are proposed accordingly.

Gordonia insulae sp. nov., isolated from an island soil

A mycolic acid-containing actinobacterium designated strain MMS17-SY073^T was isolated from island soil. The isolate showed best growth at 25 °C, pH 6, and 0 % (w/v) NaCl. The phylogenetic analysis based on 16S rRNA gene sequences indicated that strain MMS17-SY073^T belongs to the genus Gordonia, and is mostly related to the type strains of Gordonia soli (98.5 % sequence similarity), Gordonia polyisoprenivorans (98.1%), and Gordonia hankookensis (97.8%). The genome-based comparisons showed a clear distinction between the strain and the two neighbouring species, G. soli and G. polyisoprenivorans, with the average nucleotide identities (ANI) of 75.8 and 76.3 %, respectively. Notably, the genome of strain MMS17-SY073^T was the largest in total stretch and gene counts among the complete genomes of Gordonia, and contained a number of biosynthetic gene clusters for secondary metabolites, in particular those for non-ribosomal peptide synthetases. The major polar lipids were diphosphatidyl glycerol (DPG), phosphatidyl glycerol (PG), phosphatidyl ethanolamine (PE), phosphatidyl inositol (PI) and phosphatidyl inositol mannoside (PIM). The isoprenoid quinone was MK-9(H₂), and the main fatty acids were C_16 : 0 (30.2%) and 10-methyl-C_18 : 0 (33.7%). The whole cell hydrolysates contained galactose, arabinose, and meso-diaminopimelic acid. The DNA G+C content was 67.4 mol%. Based on phenotypic, chemotaxonomic and genetic analysis, strain MMS17-SY073^T should be classified as a new species of the genus Gordonia, for which the name Gordonia insulae sp. nov. is proposed (type strain=MMS17-SY073^T=KCTC 49257^T=JCM 33277^T).