Dyella solisilvae sp. nov., isolated from mixed pine and broad-leaved forest soil

Prevalence of differential microbiome in healthy, diseased and nipped colonies of corals, Porites lutea in the Gulf of Kachchh, north-west coast of India

Coral reefs are constantly subjected to multiple stresses like diseases and fish predation, which can profoundly influence the coral microbiome. This study investigated the differences in bacterial community structure of healthy, white syndrome affected and blenny nipped coral colonies of Porites lutea, collected from the coral reefs of Gulf of Kachchh, north-west coast of India. Present study observed that the stressed coral colonies harbored more OTUs and contained higher diversity values compared to healthy corals colonies. Similarly, beta diversity analysis indicated the dissimilarities among the three coral samples analyzed. Though the taxonomy analysis indicated bacterial phyla like Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria among the entire coral samples studied, there was a variation in their relative abundances. Huge variations were observed in the relative dominance at the bacterial genera level. About 13phyla and 11 genera was identified in healthy coral. The PBN sample was found to contain Proteobacteria, Cyanobacteria, Verrucomicrobia, and Lentisphaerae as dominant phyla and Endozoicomonas, Dyella, Woeseia, and Winogradskyella as dominant genera. The PWS sample contained Proteobacteria, Lentisphaerae, Spirochaetes, and Tenericutes as dominant phyla and Endozoicomonas, Arcobacter, Sunxiuqinia, and Carboxylicivirgia as dominant genera. Among the healthy samples, sequences belonging to Uncultured Rhodospirillaceae were dominant, while Woeseia and sequences belonging to Uncultured Rhodovibrionaceae were dominant among the blenny nipped white syndrome infected corals. Although any previously established pathogen was not identified, present study revealed the presence of a potentially pathogenic bacterium, Arcobacter, among the diseased corals. It also demonstrated a dynamic microbiome among the Porites lutea colonies on subjecting to various stresses.

Dyella telluris sp. nov. and Dyella acidiphila sp. nov., isolated from forest soil of Dinghushan Biosphere Reserve, China

Cells of bacterial strains G9^T and 7MK23^T, isolated from forest soil samples collected from the Dinghushan Biosphere Reserve, Guangdong Province, PR China, were Gram-stain-negative, aerobic and rod-shaped. Strain G9^T was motile with single polar flagellum and grew at 12-37 °C (optimum, 28 °C), pH 4.5-8.0 (optimum, pH 6.0-7.5) and in the presence of 0-3.5 % NaCl (optimum, 1.5%, w/v); while strain 7MK23^T was non-motile and grew at 12-42 °C (optimum, 28-33 °C), pH 2.5-8.5 (optimum, pH 4.5-6.5) and NaCl levels of 0-1.0 % (optimum, 0-0.5 %, w/v). Phylogenetic analysis based on 16S rRNA gene sequences revealed that both isolates fell within the cluster of the genus Dyella. The closely related species (with a 16S rRNA gene sequence similarity >98.65%) of strain G9^T were Dyella terrae JS14-6^T (99.0 %), D. kyungheensis THG-B117^T (98.8 %) and D. amyloliquefaciens DHC06^T (98.7 %) while that of strain 7MK23^T were D. mobilis DHON07^T (99.2 %) and D. flava DHOC52^T (99.1 %), but the average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strains G9^T, 7MK23^T and the closely related Dyella species listed above were in the ranges of 77.5-83.8 % and 22.0-27.0 %, much lower than the species demarcation lines of 95.5 and 70 %, respectively. Phylogenomic analyses using UBCG and Phylophlan also supported that these two strains represent two novel species of Dyella. The major fatty acids of strain G9^T were iso-C_15 : 0, iso-C_17 : 1  ω9c and iso-C_17 : 0 while that of strain 7MK23^T were iso-C_15 : 0 and anteiso-C_15 : 0. Ubiquinone-8 was the only respiratory quinone detected in both strains. The polar lipids of strain G9^T consisted of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, and several unknown phospholipids, aminophospholipids, aminolipids and lipid while strain 7MK23^T contained phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine and several unknown phospholipids and aminophospholipids. The DNA G+C contents of strains G9^T and 7MK23^T were 64.7 and 63.4 mol%, respectively. On the basis of 16S rRNA gene sequence phylogenetic and phylogenomic analyses as well as phenotypic data obtained, we propose that strains G9^T and 7MK23^T represent two novel species of the genus Dyella, for which the names Dyella telluris sp. nov. (type strain G9^T=KACC 21725^T=GDMCC 1.2132^T) and Dyella acidiphila sp. nov. (type strain 7MK23^T=KCTC 62739^T=GDMCC 1.1446^T) are proposed.

Dyella amyloliquefaciens sp. nov., isolated from forest soil

A Gram-stain-negative, aerobic, yellow-pigmented, rod-shaped and motile with single polar flagellum bacterial strain, designated DHC06^T, was isolated from forest soil sampled at Dinghushan Biosphere Reserve, Guangdong Province, PR China. The strain grew at 4-37 °C (optimum, 28 °C), pH 4.5-8.0 (pH 6.0-7.5) and in the presence of 0-4.0 % (2.0 %, w/v) NaCl. In the 16S rRNA gene sequence phylogram, strain DHC06^T formed a clade with Dyella solisilvae DHG54^T and Dyella terrae KACC 12748^T within the genus of Dyella. Strain DHC06^T had 16S rRNA gene sequence similarities of 98.6, 98.3, 98.3 and 98.2 % to Dyella japonica DSM 16301^T, Dyella terrae JS14-6^T, Dyella soli KACC 12747^T and Dyella solisilvae DHG54^T, respectively. The distinctiveness of strain DHC06^Tfrom all described Dyellaspecies was also supported by the results of phylogenomic analysis based on 92 single-copy gene sequences. The DDH values among strain DHC06^T and closely related Dyella species were all lower than 70 %. Strain DHC06^T contained Q-8 as the only respiratory quinone. Its main fatty acids were iso-C_15 : 0, iso-C_17 : 1 ω9c and summed feature 3 (C_16 : 1 ω6c/C_16 : 1 ω7c). The DNA G+C content of strain DHC06^T was 64.6 mol%. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. On the basis of phenotypic, 16S rRNA gene sequence and genomic analyses and chemotaxonomic data, strain DHC06^T represents a novel species of the genus Dyella, for which the name Dyella amyloliquefaciens sp. nov. (type strain DHC06^T=GDMCC 1.1186^T=LMG 30090^T) is proposed.

Dyella dinghuensis sp. nov. and Dyella choica sp. nov., isolated from forest soil

Two aerobic, Gram-stain-negative, non-motile, rod-shaped bacterial strains, designated as DHOA06^T and 4 M-K27^T, were isolated from soil samples collected from the forest of Dinghushan Biosphere Reserve, Guangdong Province, PR China (112° 31' E 23° 10' N). Strains DHOA06^T and 4 M-K27^T grew at pH 4.5-7.0 (optimum, pH 5.0-6.0) and pH 4.5-6.5 (pH 6.0), respectively. Both strains grew at 12-37 °C (optimum, 28 °C) and NaCl levels up to 1.0 % (optimum 0 %, w/v). Phylogenetic analysis based on both 16S rRNA gene sequences and the concatenated partial atpD, gyrB andlepA gene sequences showed that strains DHOA06^T and 4 M-K27^T formed two isolated clades with members of the genus Dyella, but they each occupied a distinctive position within the genus. Strains DHOA06^T and 4 M-K27^T showed the highest 16S rRNA gene sequence similarities to Dyellacaseinilytica DHOB09^T (98.7 %) and Dyellaacidisoli 4M-Z03^T (98.8 %), respectively. DNA-DNA hybridization values of strains DHOA06^T/DHOB09^T and 4 M-K27^T/4M-Z03^T were 27.4±2.4 % and 38.8±1.0 %, respectively. Ubiquinone-8 was the only respiratory quinone detected in both strains. Their major fatty acids consisted of iso-C15 : 0, iso-C16 : 0 and iso-C17 : 1ω9c, and strain DHOA06^T had iso-C17 : 0 in addition. Their polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, one unidentified aminophospholipid, one unidentified phospholipid and two unidentified aminolipids, and strain DHOA06^T had phosphatidylmethylethanolamine and one unidentified lipid in addition. The DNA G+C contents of strains DHOA06^T and 4 M-K27^T were 59.1 and 61.7 mol%, respectively. Based on the above results, we propose that strains DHOA06^T and 4 M-K27^T represent two novel species of the genus Dyella, namely Dyelladinghuensis sp. nov. (type strain DHOA06^T = KCTC 52129^T=NBRC 111978^T) and Dyellachoica sp. nov. (type strain 4 M-K27^T=GDMCC 1.1189^T=LMG 30267^T).