Trinickia violacea sp. nov. and Trinickia terrae sp. nov., isolated from forest soil.

Two Gram-stain negative, aerobic and rod-shaped bacterial strains, DHOD12T and 7GSK02T, were isolated from forest soil of Dinghushan Biosphere Reserve, Guangdong Province, PR China. Strain DHOD12T grew at 4-42 °C (optimum, 28-33 °C), pH 4.0-8.5 (optimum, pH 5.5-6.5) and in the presence of 0-1.5 % (w/v; optimum, 0-0.5 %)NaCl; while strain 7GSK02T grew at 12-42 °C (optimum, 28-33 °C), pH 4.0-8.5 (optimum, pH 5.0-6.0) and in the presence of 0-0.5 % (w/v; optimum, 0 %) NaCl. Strains DHOD12T and 7GSK02T had the highest 16S rRNA sequence similarities of 98.0 and 98.3 % with the same species Trinickia mobilis DHG64T, respectively, and 98.4 % between themselves. In the 16S rRNA phylogeny, they formed a clade that was sister to a major cluster consisting of all described Trinickia species. Phylogenomic analyses with the UBCG and PhyloPhlAn methods consistently showed that strains DHOD12T and 7GSK02T formed a clade with T. mobilis DHG64T that was a sister of a cluster containing the remainder of the Trinickia species. The DNA G+C contents of strains DHOD12T and 7GSK02T were 63.1 and 64.6 mol%, respectively. Digital DNA-DNA hybridization and average nucleotide identity values of strains DHOD12T, 7GSK02T and their closely related strains were in the ranges of 21.6-31.4 % and 77.1-86.9 %, respectively. These two strains had the same major respiratory quinone, ubiquinone-8, and both had C16 : 0, C17 : 0 cyclo and summed feature 8 (C18 : 1 ω7c/C18 : 1 ω6c) as their major fatty acids. Their major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. Genomic analysis indicated that the two strains could have the potential to degrade aromatic compounds like other Trinickia species. On the basis of phenotypic and phylogenetic results, strains DHOD12T and 7GSK02T represent two novel species of the genus Trinickia, for which the names Trinickia violacea sp. nov. (type strain DHOD12T=LMG 30258T=CGMCC 1.15436T) and Trinickia terrae sp. nov. (type strain 7GSK02T=CGMCC 1.15432T=KCTC 62468T) are proposed.

Global chromosome rearrangement induced by CRISPR-Cas9 reshapes the genome and transcriptome of human cells.

Chromosome rearrangement plays important roles in development, carcinogenesis and evolution. However, its mechanism and subsequent effects are not fully understood. Large-scale chromosome rearrangement has been performed in the simple eukaryote, wine yeast, but the relative research in mammalian cells remains at the level of individual chromosome rearrangement due to technical limitations. In this study, we used CRISPR-Cas9 to target the highly repetitive human endogenous retrotransposons, LINE-1 and Alu, resulting in a large number of DNA double-strand breaks in the chromosomes. While this operation killed the majority of the cells, we eventually obtained live cell groups. Karyotype analysis and genome re-sequencing proved that we have achieved global chromosome rearrangement (GCR) in human cells. The copy number variations of the GCR genomes showed typical patterns observed in tumor genomes. The ATAC-seq and RNA-seq further revealed that the epigenetic and transcriptomic landscapes were deeply reshaped by GCR. Gene expressions related to p53 pathway, DNA repair, cell cycle and apoptosis were greatly altered to facilitate the cell survival. Our study provided a new application of CRISPR-Cas9 and a practical approach for GCR in complex mammalian genomes.

The Integration Preference of Sleeping Beauty at Non-TA Site Is Related to the Transposon End Sequences.

Recently, we proved that Sleeping Beauty (SB) transposon integrates into non-TA sites at a lower frequency. Here, we performed a further study on the non-TA integration of SB and showed that (1) SB can integrate into non-TA sites in HEK293T cells as well as in mouse cell lines; (2) Both the hyperactive transposase SB100X and the traditional SB11 catalyze integrations at non-TA sites; (3) The consensus sequence of the non-TA target sites only occurs at the opposite side of the sequenced junction between the transposon end and the genomic sequences, indicating that the integrations at non-TA sites are mainly aberrant integrations; and (4) The consensus sequence of the non-TA target sites is corresponding to the transposon end sequence. The consensus sequences changed following the changes of the transposon ends. This result indicated that the interaction between the SB transposon end and genomic DNA (gDNA) may be involved in the target site selection of the SB integrations at non-TA sites.

The wide distribution and horizontal transfers of beta satellite DNA in eukaryotes.

Beta satellite DNA (satDNA), also known as Sau3A sequences, are repetitive DNA sequences reported in human and primate genomes. It is previously thought that beta satDNAs originated in old world monkeys and bursted in great apes. In this study, we searched 7821 genome assemblies of 3767 eukaryotic species and found that beta satDNAs are widely distributed across eukaryotes. The four major branches of eukaryotes, animals, fungi, plants and Harosa/SAR, all have multiple clades containing beta satDNAs. These results were also confirmed by searching whole genome sequencing data (SRA) and PCR assay. Beta satDNA sequences were found in all the primate clades, as well as in Dermoptera and Scandentia, indicating that the beta satDNAs in primates might originate in the common ancestor of Primatomorpha or Euarchonta. In contrast, the widely patchy distribution of beta satDNAs across eukaryotes presents a typical scenario of multiple horizontal transfers.

Pararobbsia silviterrae gen. nov., sp. nov., isolated from forest soil and reclassification of Burkholderia alpina as Pararobbsia alpina comb. nov.

A novel Gram-stain-negative, aerobic, non-spore-forming, non-motile and rod-shaped bacterial strain, DHC34T, was isolated from forest soil of Dinghushan Biosphere Reserve, Guangdong Province, China (112° 31' E 23° 10' N). It grew optimally on R2A medium at 28 °C, at pH 6.0-7.0 and in the presence of 0-1 % (w/v) NaCl. Strain DHC34T was closely related to Burkholderia alpina LMG 28138T (98.5 % 16S rRNA gene sequence similarity). 16S rRNA gene sequence analysis showed that strain DHC34T formed a clade with B. alpina LMG 28138T, which is next to but branched deeply with Robbsia andropogonis ICMP 2807T. The phylogenetic relationships among these three strains were also supported with the phylogram based on concatenated partial gyrB, recA and trpB gene sequences. The phylogenomic tree generated with the UBCG tool showed that strains DHC34T and R. andropogonis ICMP 2807T were in a different clade. The DNA-DNA relatedness values between strain DHC34T and B. alpina LMG 28138T and R. andropogonis ICMP 2807T were much lower than 70 %. Strain DHC34T contained ubiquinone 8 as the major respiratory quinone. Its major fatty acids were C16 : 0, C17 : 0 cyclo and C19 : 0 cyclo ω8c. The DNA G+C content of strain DHC34T was 64.2 mol%. The major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, three unidentified aminophospholipids, four unidentified phospholipids, one unidentified aminolipid and a polar lipid. The phenotypic, phylogenetic, genotypic and chemotaxonomic data showed that strain DHC34T represents a novel species of a new genus in the family Burkholderiaceae, for which the name Pararobbsia silviterrae gen. nov., sp. nov. is proposed. The type strain of Pararobbsia silviterrae is DHC34T (=KCTC 42628T=LMG 28845T). On the basis of the current data, Burkholderia alpina is renamed as Pararobbsia alpina comb. nov.

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 DHC06T, 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 DHC06T formed a clade with Dyella solisilvae DHG54T and Dyella terrae KACC 12748T within the genus of Dyella. Strain DHC06T had 16S rRNA gene sequence similarities of 98.6, 98.3, 98.3 and 98.2 % to Dyella japonica DSM 16301T, Dyella terrae JS14-6T, Dyella soli KACC 12747T and Dyella solisilvae DHG54T, respectively. The distinctiveness of strain DHC06Tfrom all described Dyellaspecies was also supported by the results of phylogenomic analysis based on 92 single-copy gene sequences. The DDH values among strain DHC06T and closely related Dyella species were all lower than 70 %. Strain DHC06T contained Q-8 as the only respiratory quinone. Its main fatty acids were iso-C15 : 0, iso-C17 : 1 ω9c and summed feature 3 (C16 : 1 ω6c/C16 : 1 ω7c). The DNA G+C content of strain DHC06T 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 DHC06T represents a novel species of the genus Dyella, for which the name Dyella amyloliquefaciens sp. nov. (type strain DHC06T=GDMCC 1.1186T=LMG 30090T) is proposed.

Paraburkholderia pallida sp. nov. and Paraburkholderia silviterrae sp. nov., isolated from forest soil.

Two Gram-stain-negative, aerobic, motile, white-pigmented and rod-shaped bacterial strains, 7MH5T and 4 M-K11T, were isolated from forest soil of Dinghushan Biosphere Reserve, Guangdong Province, PR China. Strain 7MH5T grew at 4-37 °C (optimum, 28-33 °C), pH 3.5-9.0 (pH 4.0-5.5) and in the presence of 0-3 % (w/v) NaCl (0-1.5 w/v); while strain 4 M-K11T grew at 4-42 °C (20-33 °C), pH 3.5-8.5 (pH 4.5-6.0) and in the presence of 0-2.5 % (w/v) NaCl (0-1.5 w/v). Strains 7MH5T and 4 M-K11T have the highest 16S rRNA gene sequence similarities of 98.6 and 98.7 % to Paraburkholderia peleae PP52-1T, and 98.4 % between themselves. In the 16S rRNA gene sequence phylogram, strains 4 M-K11T and Paraburkholderia ferrariae NBRC 106233T formed a clade while 7MH5T were relatively distinct from other Paraburkholderia species. Based on the UBCG phylogenomic analysis, strains 7MH5T and 4 M-K11T formed a clade with Paraburkholderia oxyphila NBRC 105797T and Paraburkholderia sacchari LMG 19450T in the genus of Paraburkholderia. The DNA G+C contents of strains 7MH5T and 4 M-K11T were 64.2 and 64.3 %, respectively. Digital DNA-DNA hybridization and the average nucleotide identity values of strains 7MH5T, 4 M-K11T and closely related strains were in the ranges of 25.2-63.6 % and 81.0-95.5 %, respectively. The two strains had the same major respiratory quinone: ubiquinone-8. Strain 7MH5T had C16 : 0, C17 : 0cyclo, C19 : 0cyclo ω8c and summed feature 8 (C18 : 1 ω7c/C18 : 1 ω6c) as its major fatty acids, while strain 4 M-K11T had major fatty acids of C16 : 0, C17 : 0cyclo and summed feature 2 (iso-C16 : 1 I/C14 : 0-3OH). The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. On the basis of phenotypic and phylogenetic analyses based on both 16S rRNA gene and whole genome sequences, as well as chemotaxonomic data, strains 7MH5T and 4 M-K11T represent two novel species of the genus Paraburkholderia, for which the names Paraburkholderia pallida sp. nov. (type strain 7MH5T=GDMCC 1.1450T=KACC 19962T) and Paraburkholderia silviterrae sp. nov. (type strain 4 M-K11T=GDMCC 1.1284T=CGMCC 1.15450T=KACC 19961T=LMG 29217T) are 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 DHOA06T and 4 M-K27T, were isolated from soil samples collected from the forest of Dinghushan Biosphere Reserve, Guangdong Province, PR China (112° 31' E 23° 10' N). Strains DHOA06T and 4 M-K27T 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 DHOA06T and 4 M-K27T formed two isolated clades with members of the genus Dyella, but they each occupied a distinctive position within the genus. Strains DHOA06T and 4 M-K27T showed the highest 16S rRNA gene sequence similarities to Dyellacaseinilytica DHOB09T (98.7 %) and Dyellaacidisoli 4M-Z03T (98.8 %), respectively. DNA-DNA hybridization values of strains DHOA06T/DHOB09T and 4 M-K27T/4M-Z03T 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 DHOA06T 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 DHOA06T had phosphatidylmethylethanolamine and one unidentified lipid in addition. The DNA G+C contents of strains DHOA06T and 4 M-K27T were 59.1 and 61.7 mol%, respectively. Based on the above results, we propose that strains DHOA06T and 4 M-K27T represent two novel species of the genus Dyella, namely Dyelladinghuensis sp. nov. (type strain DHOA06T = KCTC 52129T=NBRC 111978T) and Dyellachoica sp. nov. (type strain 4 M-K27T=GDMCC 1.1189T=LMG 30267T).

Paraburkholderia dinghuensis sp. nov., isolated from soil.

A novel Gram-stain-negative, aerobic, non-spore-forming, non-motile and rod-shaped bacterial strain, designated DHOA04T, was isolated from a forest soil sample collected at Dinghushan Biosphere Reserve, Guangdong Province, PR China (112° 31' E 23° 10' N). It grew optimally at 28-33 °C and pH 6.5-7.0. Strain DHOA04T contained Q-8 as the major respiratory quinone. Its main fatty acids were C16 : 0, C17 : 0cyclo, summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c) and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). The DNA G+C content of DHOA04T was 63.0 mol%, which is in the range of the genus Paraburkholderia. The average nucleotide identity and digital DNA-DNA hybridization values for the complete genomes were 81.6-83.0 and 25.5-27.0 % between strain DHOA04T and five closely related type strains. The major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol and two unidentified aminophospholipids. On the basis of 16S rRNA gene sequence analysis, the strain was found to be closely related to members of the genus Paraburkholderia, but clearly separated from the established species. Phylogenetic analysis based on the 16S rRNA gene sequences using the maximum-likelihood algorithm indicated that strain DHOA04T was most closely related to Paraburkholderia ferrariae NBRC 106233T. The phenotypic, chemotaxonomic and phylogenetic data, and genome analysis showed that strain DHOA04T represents a novel species of the genus Paraburkholderia, for which the name Paraburkholderia dinghuensis sp. nov. is proposed. The type strain is DHOA04T (=KCTC 42627T=LMG 28839T).

Trinickia dinghuensis sp. nov. and Trinickia fusca sp. nov., isolated from forest soil.

Two Gram-stain-negative, aerobic, non-spore forming and rod-shaped bacterial strains, designated DHOM06T and 7MK8-2T, were isolated from forest soil sampled at Dinghushan Biosphere Reserve, Guangdong Province, PR China. Strain DHOM06T grew at 12-37 °C (optimum, 28-33 °C), pH 4.5-7.5 (pH 5.5) and in the presence of 0-0.5 % NaCl (w/v); while strain 7MK8-2T grew at 12-42 °C (28-33 °C), pH 4.0-8.5 (pH 4.5-5.5) and in the presence of 0-1.0 % NaCl (w/v). Strains DHOM06T and 7MK8-2T each has a 16S rRNA gene sequence similarity of 97.1-98.9 % as well as 97.4-97.9 % to Trinickia strains, respectively. In the 16S rRNA gene sequence phylogram, both strains and all five currently described Trinickia species formed a clade but they were all distinct from each other. The average nucleotide identity and digital DNA-DNA hybridization values for strains DHOM06T and 7MK8-2T and all Trinickia species were in the range of 77.4-82.6 % and 21.7-26.2 %, respectively. The DNA G+C content of DHOM06T and 7MK8-2T was 63.2 and 63.5 mol%, respectively, based on total genome calculations. These two strains contained ubiquinone 8 as the major respiratory quinone and C16 : 0, C17 : 0cyclo, C19 : 0cyclo ω8c, summed feature 3 (C16 : 1ω7c/C16 : 1ω6c) and summed feature 8 (C18 : 1ω7c/C18 : 1ω6c) as the major cellular fatty acids. The major polar lipids of DHOM06T and 7MK8-2T were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. On the basis of phenotypic, chemotaxonomic, phylogenetic and genomic analysis data, strains DHOM06T and 7MK8-2T represent two novel species of the genus Trinickia, for which the names Trinickia dinghuensis sp. nov. (type strain DHOM06T=GDMCC 1.1280T=LMG 30259T) and Trinickia fusca sp. nov. (type strain 7MK8-2T=GDMCC 1.1449T=KCTC 62469T) are proposed.

Paraburkholderia telluris sp. nov., isolated from subtropical forest soil.

Strain DHOC27T is a Gram-stain-negative, aerobic, non-motile, light yellow-pigmented and rod-shaped bacterium isolated from the forest soil of Dinghushan Biosphere Reserve, Guangdong Province, PR China. It grew at 4-37 °C (optimal 28-33 °C), pH 4.0-8.5 (optimal 4.5-6.0) and 0-1.5 (optimal 0-0.5) % (w/v) NaCl. The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain formed a clade with Paraburkholderia phenazinium LMG 2247T, Paraburkholderia. sartisoli LMG 24000T and Paraburkholderia. pallidirosea DHOK13T, with a sequence similarity of 98.5, 97.5 and 98.1 % to the above strains, respectively. The DNA G+C content of DHOC27T was 62.3 mol%. The digital DNA-DNA relatedness values and the average nucleotide identities between strain DHOC27T and P. phenazinium LMG 2247T and P. sartisoli LMG 24000T were 26.9 and 24.3 % and 82.3 and 79.9 %, respectively. C16 : 0, C17 : 0 cyclo and C19 : 0 cyclo ω8c were the major fatty acids, and ubiquinone-8 was the major respiratory quinone detected, all of which supported the affiliation of DHOC27T to the genus Paraburkholderia. On the basis of the data presented above, strain DHOC27T represents a novel species of the genus Paraburkholderia and the name Paraburkholderia telluris sp. nov. is proposed. The type strain is DHOC27T (=LMG 30263T=GDMCC 1.1281T).

Dyella monticola sp. nov. and Dyella psychrodurans sp. nov., isolated from monsoon evergreen broad-leaved forest soil of Dinghu Mountain, China.

Cells of bacterial strains 4 G-K06T and 4MSK11T, isolated from soil samples collected from monsoon evergreen broad-leaved forest of the Dinghushan Mountain (112° 31' E 23° 10' N), Guangdong Province, PR China, were Gram-stain-negative, aerobic, non-spore-forming, non-motile and rod-shaped. Strain 4 G-K06T grew at 10-37 °C, pH 3.5-7.5 and 0-3.5 % (w/v) NaCl; while 4MSK11T grew at 4-42 °C, pH 3.5-7.5 and 0-2.5 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed strain 4 G-K06T formed a clade with Dyellaflagellata 4 M-K16T, Dyella acidisoli 4M-Z03T, Dyellahumi DHG40T and Dyellanitratireducens DHG59T, while strain 4MSK11T formed a clade with Dyellacaseinilytica DHOB09T and Dyellamobilis DHON07T, both within the genus Dyella. The result of the partial atpD, gyrB and lepA gene sequence analysis supported the conclusion based on 16S rRNA gene sequence analysis, which showed that these two strains represent two novel species of Dyella. The average nucleotide identity and digital DNA-DNA hybridization value for the whole genomes were 75.0-79.0 and 20.3-22.6 % between strains 4 G-K06T, 4MSK11T and those described Dyella species with genome sequences; while the DNA-DNA hybridization rates between strains 4 G-K06T, 4MSK11T and closely related Dyella species (without genome sequence) were 29.5-41.8 %. The major cellular fatty acids of these two strains were iso-C15 : 0, iso-C16 : 0 and iso-C17 : 1ω9c, while the major polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and several unidentified phospholipids and aminophospholipids. The only ubiquinone of these two strains was ubiquinone-8. The DNA G+C contents of 4 G-K06T and 4MSK11T were 60.4 and 61.3 mol%, respectively. On the basis of the evidence presented here, strains 4 G-K06T and 4MSK11T represent two novel species of the genus Dyella, for which the names Dyella monticola sp. nov. (type strain 4 G-K06T=LMG 30268T=GDMCC 1.1188T) and Dyella psychrodurans sp. nov. (type strain 4MSK11T=KCTC 62280T=GDMCC 1.1185T) are proposed.

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

A Gram-stain-negative, aerobic, motile, yellow-pigmented, rod-shaped with a single polar flagellum bacterial strain, designated strain DHG54T, was isolated from a forest soil sample of Dinghushan Biosphere Reserve, Guangdong Province, China. Strain DHG54T grew at 12-37 °C (optimum, 28 °C), pH 4.5-8.0 (optimum, pH 6.0-7.0) and in the presence of 0-3.0 % (w/v) NaCl (optimum, 0-1.5 %, w/v). Based on 16S rRNA gene sequence analysis, strain DHG54T formed a clade with the members of the genus Dyella and showed highest sequence similarities of 98.2 % to Dyella japonica DSM 16301T and Dyella terrae KACC 12748T. This was also supported by phylogenetic analysis based on the concatenated partial gyrB, lepA and recA housekeeping gene sequences. DNA-DNA hybridization results between strain DHG54T and closely related Dyella species were all lower than 70 %. Ubiquinone-8 was the only respiratory quinone, and iso-C15 : 0, iso-C17 : 0 and iso-C17 : 1 ω9c were major fatty acids. The DNA G+C content of strain DHG54T was 65.4 mol%. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. On the basis of the polyphasic characterization results presented here, strain DHG54T represents a novel species of the genus Dyella, for which the name Dyellasolisilvae sp. nov. (type strain DHG54T=GDMCC 1.1187T = LMG 30091T) is proposed.

Paraburkholderia acidiphila sp. nov., Paraburkholderia acidisoli sp. nov. and Burkholderia guangdongensis sp. nov., isolated from forest soil, and reclassification of Burkholderia ultramafica as Paraburkholderia ultramafica comb. nov.

Three Gram-stain-negative, aerobic, motile and rod-shaped bacterial strains, 7Q-K02T, DHF22T and DHOM02T, were isolated from forest soil sampled at Dinghushan Biosphere Reserve, Guangdong Province, China. Strains 7Q-K02T, DHF22T and DHOM02T grew at 4-37, 4-42 and 12-37 °C, pH 3.0-8.5, 3.5-8.5 and 5.0-8.0, and in the presence of 0-3.0, 0-3.5 and 0-2.5 % (w/v) NaCl; with optima at 28-33, 28 and 28-33 °C, pH 3.5-6.5, 4.0-5.5 and 6.5-7.0, and 0-1.5, 0-1.5 and 0.5-1.5 % (w/v) NaCl, respectively. Strains 7Q-K02T and DHF22T have the highest 16S rRNA gene sequence similarities of 99.0 and 98.0 % to Paraburkholderia sacchari LMG 19450T and 97.7 % between themselves, while strain DHOM02T shares the highest similarity of 98.4 % to 'Burkholderia rinojensis' A396T followed by 98.3 % to Burkholderia plantarii ATCC 43733T. In the 16S rRNA gene sequence phylogram, strain 7Q-K02T formed a sister branch with Paraburkholderia sacchari, Paraburkholderia oxyphila and Paraburkholderia paradisi, and strain DHF22T was separated from all other species within the genus Paraburkholderia, while strain DHOM02T formed a separated clade with members of the genus Burkholderia. The DNA G+C contents of strains 7Q-K02T, DHF22T and DHOM02T wwe 64.3, 65.4 and 66.6 %, respectively. Digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values of strains 7Q-K02T, DHF22T and closely related Paraburkholderia strains were in the ranges of 25.5-43.7 % and 81.5-91.3 %, respectively. While dDDH and ANI values between strain DHOM02T and Burkholderia strains with genome sequence data were in the ranges of 22.4-31.0 % and 78.2-86.1 %, respectively. These three strains have the same major respiratory quinone: ubiquinone-8. Strains 7Q-K02T, DHF22T and DHOM02T have C16 : 0, C17 : 0 cyclo, C19 : 0 cyclo ω8c and summed feature 8 (C18 : 1 ω7c/C18 : 1 ω6c) as their major fatty acid compositions. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. On the basis of phenotypic, phylogenetic, genomic analyses and chemotaxonomic data, strains 7Q-K02T and DHF22T represent two novel species of the genus Paraburkholderia, for which the names Paraburkholderia acidiphila sp. nov. (type strain 7Q-K02T=CGMCC 1.15433T=KCTC 62472T=LMG 29209T) and Paraburkholderia acidisoli sp. nov. (type strain DHF22T=GDMCC 1.1448T=LMG 30262T) are proposed, while strain DHOM02T represents a novel species in the genus Burkholderia, for which the name Burkholderia guangdongensis sp. nov. (type strain DHOM02T=KCTC 42625T=LMG 28843T) is proposed. We also propose to transfer Burkholderia ultramafica to the genus Paraburkholderia as Paraburkholderia ultramafica comb. nov. based mainly on the results of phylogenomic analysis.

Paraburkholderia phosphatilytica sp. nov., a phosphate-solubilizing bacterium isolated from forest soil.

A novel Gram-stain-negative, aerobic, non-spore-forming, non-motile and rod-shaped bacterial strain, 7QSK02T, was isolated from forest soil of Dinghushan Biosphere Reserve, Guangdong Province, China. It grew at 12-37 °C, at pH 4.0-7.5 and in the presence of 0-1.0 % (w/v) NaCl on R2A agar medium, with optimum growth at 28 °C, pH 5.5 and 0 % NaCl. Strain 7QSK02T was closely related to members of the genus Paraburkholderia: P. acidipaludis NBRC 101816T (98.1 % 16S rRNA gene sequence similarity), P. piptadeniae STM 7183T (97.6 %), P. kururiensis JCM 10599T (97.3 %), P. caballeronis TNe-841T (97.3 %) and P. diazotrophica JPY461T (97.1 %). 16S rRNA gene sequence analysis showed that strain 7QSK02T and two closely strains, P. kururiensis JCM 10599T and P. caballeronis TNe-841T, formed a clade within the genus Paraburkholderia, but was clearly separated from the established species. The genomic G+C content of strain 7QSK02T was 64.9 mol% based on total genome calculations. The average nucleotide identity and digital DNA-DNA hybridization value for the complete genomes were 79.2-81.5 and 23.2-24.9 % between strain 7QSK02T and its closely related species listed above. Strain 7QSK02T contained ubiquinone 8 as the major respiratory quinone. Major fatty acids were C16 : 0, C17 : 0 cyclo and C19 : 0 cyclo ω8c. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylmethylethanolamine, one unidentified aminophospholipid, aminolipid and polar lipid. The phenotypic, chemotaxonomic and phylogenetic properties, and genome analysis suggest that strain 7QSK02T represents a novel species of the genus Paraburkholderia, for which the name Paraburkholderia phosphatilytica sp. nov. is proposed. The type strain is 7QSK02T (=GDMCC 1.1283T=CGMCC 1.15470T=KCTC 62473T).

Dyella halodurans sp. nov., isolated from lower subtropical forest soil.

A Gram-stain-negative, aerobic, non-endospore-forming, motile by a polar flagellum, rod-shaped bacterium, designated strain DHOG02T, which produced yellow-pigmented colonies, was isolated from a soil sample collected from the lower subtropical forest of the Dinghushan Biosphere Reserve, Guangdong Province, PR China. Strain DHOG02T grew at 12-37 °C, pH 4-9 and 0-4 % (w/v) NaCl, with optima at 28 °C, pH 6-7 and 0.5 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences showed that this strain formed a clade with Dyella lipolytica DHOB07T and Dyella jejuensis JP1T, with sequence similarities of 98.0 and 97.4 %, respectively. The result of the concatenated partial gyrB, lepA and recA gene sequence analysis confirmed that strain DHOG02T belongs to the genus Dyella, but is distinct from all currently known species of the genus. The G+C content of the genomic DNA was 62 mol%. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, an unidentified aminophospholipid and phospholipid. Ubiquinone-8 was the only respiratory quinone detected, and iso-C15 : 0, iso-C17 : 1ω9c and summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c) were the major fatty acids, all of which supported the affiliation of strain DHOG02T to the genus Dyella. On the basis of the evidence presented here, strain DHOG02T represents a novel species of the genus Dyella, for which the name Dyella halodurans sp. nov. is proposed. The type strain is DHOG02T (=NBRC 111474T=CGMCC 1.15435T).

Edaphobacter flagellatus sp. nov. and Edaphobacter bradus sp. nov., two acidobacteria isolated from forest soil.

Two aerobic and obligately acidophilic bacteria, designated HZ411T and 4MSH08T, were isolated from the forest soil of Dinghushan Biosphere Reserve, Guangdong Province, PR China (23° 10' N, 112° 31' E). These two strains were Gram-stain-negative short rods that multiplied by binary division. HZ411T was motile, with a single polar flagellum, but 4MSH08T was non-motile. The results of the 16S rRNA gene sequence analysis indicated that these two strains formed a common clade with members of the genusEdaphobacterin subdivision 1 of the phylum Acidobacteria but they each occupied a unique position in the genus. HZ411T and 4MSH08T had a 16S rRNA gene sequence similarity of 96.2 % between each other and the highest sequence similarity of 97.7 and 96.9 % to Edaphobacter modestusJbg-1T and Edaphobacter aggregansWbg-1T, respectively. The DNA-DNA hybridization rate between HZ411T and E. modestusJbg-1T was 22.7 %. The DNA G+C contents of HZ411T and 4MSH08T were 57.7 and 59.3 %, respectively. HZ411T and 4MSH08T had similar major (>10 %) fatty acids with very high percentages of iso-C15 : 0 and C16 : 1ω7c, and similar major polar lipid profiles (both contained a phosphatidylethanolamine, phosphatidyldimethylethanolamine and glycolipid and several unidentified aminolipids and polar lipids). On the basis of these physiological, phylogenetic and chemotaxonomic data, we suggest that HZ411T and 4MSH08T represent two novel species of the genus Edaphobacter, for which the names Edaphobacter flagellatus HZ411T (=GDMCC 1.1193=LMG 30085) and Edaphobacter bradus 4MSH08T (=GDMCC 1.1317=KCTC 62475) are proposed.

Paraburkholderia caseinilytica sp. nov., isolated from the pine and broad-leaf mixed forest soil.

A novel Gram-stain-negative, aerobic, non-spore-forming, motile and rod-shaped bacterial strain, designated HM451T, was isolated from forest soil sampled at the Dinghushan Biosphere Reserve, Guangdong Province, PR China (112° 31' E 23° 10' N). It grew optimally at 28 °C, pH 5.0-6.0 and in the presence of 0-2.5 % (w/v) NaCl on R2A medium. Strain HM451T was closely related to Paraburkholderia mimosarum NBRC 106338T (98.6 % 16S rRNA gene sequence similarity), Paraburkholderia heleia NBRC 101817T (98.4 %) and Paraburkholderia silvatlantica SRMrh-20T (98.0 %). The 16S rRNA gene sequence analysis showed that strain HM451T and the three closely related strains formed a clade within the genus Paraburkholderia, but was clearly separated from the established species. The DNA-DNA relatedness value between strain HM451T and its phylogenetically closest relative, P. mimosarum NBRC 106338T, was much lower than 70 %. Strain HM451T contained ubiquinone 8 as the major respiratory quinone. Major fatty acids were C16 : 0, C17 : 0cyclo and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). The DNA G+C content of strain HM451T was 65.4 mol%. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, two unidentified aminophospholipids, one unidentified aminolipid and a polar lipid. The phenotypic, chemotaxonomic and phylogenetic data showed that strain HM451T represents a novel species of the genus Paraburkholderia, for which the name Paraburkholderia caseinilytica sp. nov. is proposed. The type strain is HM451T (=GDMCC 1.1190T=LMG 30092T).

Puia dinghuensis gen. nov., sp. nov., isolated from monsoon evergreen broad-leaved forest soil.

A Gram-stain-negative, rod-shaped, aerobic, non-motile bacterial strain, 4GSH07T, was originally isolated from the monsoon evergreen broad-leaved forest soil of Dinghushan Biosphere Reserve, Guangdong Province, PR China (112° 31' E 23° 10' N). It grew optimally at 28-33 °C and pH 4.0. The 16S rRNA gene sequence analysis showed that strain 4GSH07T had the highest sequence similarity of 94.0 % to Parasegetibacter terrae JCM 19942T, and formed an independent lineage separable from other described genera of the family Chitinophagaceae. The main fatty acids (>5 %) were iso-C15 : 0, iso-C17 : 0 3-OH, C16 : 0 3-OH, summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c) and C15 : 0 2-OH. The organism contained MK-7 as the predominant respiratory quinone, and the total DNA G+C content was 50.3 mol%. The phenotypic, chemotaxonomic and phylogenetic data showed consistently that strain 4GSH07T represents a novel species of a novel genus of the family Chitinophagaceae, for which the name Puia dinghuensis gen. nov., sp. nov., is proposed, with 4GSH07T (=CGMCC 1.15448T=LMG 29214T) as the type strain.