ABSTRACT
A gram-stain-negative, aerobic, non-spore-forming, rod-shaped, non-motile bacterium strain R4HLG17T was isolated from Tamarix ramosissima roots growing in Kumtag desert. The strain grew at salinities of 0-16% (w/v) NaCl (optimum 5-6%), pH 5-9 (optimum 7) and at 16-45 °C. Based on 16S rRNA gene sequence similarity, strain R4HLG17T belonged to the family Halomonadaceae and was most closely related to Halomonas lutea DSM 23508T(95.1%), followed by Halotalea alkalilenta AW-7T(94.8%), Salinicola acroporae S4-41T(94.8%), Salinicola halophilus CG4.1T(94.6%), and Larsenimonas salina M1-18T(94.4%). Multilocus sequence analysis (MLSA) based on the partial sequences of 16S rRNA, atpA, gyrB, rpoD, and secA genes indicated that the strain R4HLG17T formed an independent and monophyletic branch related to other genera of Halomonadaceae, supporting its placement as a new genus in this family. The draft genome of strain R4HLG17T was 3.6 Mb with a total G + C content of 55.1%. The average nucleotide identity to Halomonas lutea DSM 23508T was 83.5%. Q-9 was detected as the major respiratory quinone and summed feature 8 (C18:1ω7c/C18:1ω6c), summed feature 3 (C16:1ω7c/C16:1ω6c), and C16:0 as predominant cellular fatty acids. On the basis of chemotaxonomic, phylogenetic, and phenotypic evidence, strain R4HLG17T is concluded to represent a novel species of a new genus within Halomonadaceae, for which the name Phytohalomonas tamaricis gen. nov., sp. nov., is proposed. The type strain is R4HLG17T (=ACCC 19929T=KCTC 52415T).
Subject(s)
Halomonadaceae/classification , Plant Roots/microbiology , Tamaricaceae/microbiology , Bacterial Typing Techniques , Base Composition , DNA, Bacterial/genetics , Desert Climate , Fatty Acids/analysis , Halomonadaceae/chemistry , Halomonadaceae/genetics , Multilocus Sequence Typing , Nucleic Acid Hybridization , Phylogeny , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , Species SpecificityABSTRACT
A Gram-negative rod, designated strain 1N-3T, was isolated from a rhizome of Phragmites australis grown in Kumtag Desert, China. Phylogenetic analysis showed that the strain is closely related to Phyllobacterium salinisoli LMG 30173T with 99.0% sequence similarity in the 16S rRNA gene and 92.9% in the atpD gene. Growth was observed at salinities of 0-4% (w/v), over a pH range of 5.0-10.0 (optimum 8.0) and at temperatures of 15-40 °C (optimum 30 °C). The predominant cellular fatty acids were identified as summed feature 8 (C18:1ω7c/C18:1ω6c). The G+C content of strain 1N-3T was determined to be 60.1%. Based on phenotypic, chemotaxonomic, phylogenetic properties and genomic comparison, it is concluded that strain 1N-3T represents a novel species of the genus Phyllobacterium, for which the name Phyllobacterium phragmitis sp. nov. is proposed. The type strain is 1N-3T (=KCTC 62183T =ACCC 60071T).
Subject(s)
Endophytes/isolation & purification , Phyllobacteriaceae/genetics , Poaceae/microbiology , Rhizome/microbiology , Bacterial Typing Techniques , Base Composition , China , DNA, Bacterial/genetics , Desert Climate , Endophytes/classification , Endophytes/genetics , Endophytes/metabolism , Fatty Acids/chemistry , Fatty Acids/metabolism , Phyllobacteriaceae/classification , Phyllobacteriaceae/isolation & purification , Phyllobacteriaceae/metabolism , Phylogeny , RNA, Ribosomal, 16S/geneticsABSTRACT
Strain 6GN-30T, a Gram-stain-negative, aerobic, non-spore-forming, rod-shaped, motile bacterium was isolated from Ephedra sinica roots in the Kumtag Desert. On the basis of the 16S rRNA gene sequence, the isolate represented a member of the genus Mesorhizobium of the family Phyllobacteriaceae. The results of a phylogenetic analysis indicated that 6GN-30T was phylogenetically related to Mesorhizobium soliNHI-8T. Strain 6GN-30T grew at a salinity of 0-1.0â% (w/v) NaCl (with optimum growth in the absence of NaCl), pH 6.0-9.0 (optimum 7.0-8.0) and 15-45 °C. The major cellular fatty acids were summed feature 8 (C18â:â1ω7c/C18â:â1ω6c), C19â:â0cyclo ω8c, iso-C17â:â0, C18â:â0, and C16â:â0. The draft genome of 6GN-30T was 6.11 Mb long, with a DNA G+C content of 66.4 mol%. The average nucleotide identity to M. soliNHI-8T was 84.32â%. The strain contained diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine,aminophospholipids and phospholipids. The chemotaxonomic, phylogenetic and phenotypic data indicate that 6GN-30T represents a novel species of the genus Mesorhizobiumfor which the name Mesorhizobiumephedrae sp. nov. is proposed. The type strain is 6GN-30T (=ACCC 60073T=KCTC 62410T).
Subject(s)
Desert Climate , Ephedra/microbiology , Mesorhizobium/classification , Phylogeny , Plant Roots/microbiology , Bacterial Typing Techniques , Base Composition , China , DNA, Bacterial/genetics , Fatty Acids/chemistry , Mesorhizobium/genetics , Mesorhizobium/isolation & purification , Nucleic Acid Hybridization , Phospholipids/chemistry , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNAABSTRACT
A Gram-negative, aerobic, non-spore-forming, rod-shaped, motile bacterium, named strain 59N8T, was isolated from Phragmites communis roots in the Kumtag Desert. Phylogenetic analysis based on the 16S rRNA gene sequence showed that the isolate belongs to the genus Zobellella within the family Aeromonadaceae. The analysis showed that strain 59N8T was most closely related to Zobellella taiwanensis ZT1T. The average nucleotide identity value with Zobellella taiwanensis ZT1T was 88.2â%, and the digital DNA-DNA hybridization value was 29.7±2.4â%, which was calculated using the Genome-to-Genome Distance Calculator. The G+C content of strain 59N8T was 62.8 mol%. Strain 59N8T grew at 0-5â% (w/v) NaCl (optimum, 0-4â%), pH 6.0-9.0 (optimum, 7.0-8.0) and at 10-45 °C. The major cellular fatty acids were summed feature 8 (C18â:â1ω7c/C18â:â1ω6c), summed feature 3 (C16â:â1ω7c/C16â:â1ω6c) and C16â:â0. The major polar lipids in strain 59N8T were phosphatidylethanolamine and phosphatidylglycerol. Based on the chemotaxonomic, phylogenetic and phenotypic data, strain 59N8T represents a novel species in the genus Zobellella, for which the name Zobellellaendophytica sp. nov. is proposed. The type strain is 59N8T (=ACCC 60074T=KCTC 62456T).
Subject(s)
Aeromonadaceae/classification , Phylogeny , Plant Roots/microbiology , Poaceae/microbiology , Aeromonadaceae/genetics , Aeromonadaceae/isolation & purification , Bacterial Typing Techniques , Base Composition , China , DNA, Bacterial/genetics , Desert Climate , Fatty Acids/chemistry , Nucleic Acid Hybridization , Phospholipids/chemistry , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNAABSTRACT
A Gram-stain-negative, non-motile, aerobic, non-spore-forming, rod-shaped, bacterial strain, designated 5JN-11T, was isolated from Haloxylonammodendron stems in Kumtag desert, Xinjiang province, China. Strain 5JN-11T grew at salinities of 0-6â% (w/v; optimum 0-2â%), a pH of 7.0-9.0 (pH 7.0-8.0) and temperatures of 20-42 °C (28-30 °C). Based on 16S rRNA gene sequences, the strain was designated a member of the genus Sphingobacterium and the phylogenetic analysis showed that strain 5JN-11T shared the highest similarity to Sphingobacterium gobiense H7T, followed by Sphingobacterium chuzhouense DH-5T and Sphingobacterium arenae H-12T. The unfinished draft genome of strain 5JN-11T was 4.69 Mb. The G+C content of strain 5JN-11T was 42.8 mol%. The average nucleotide identity to S. gobiense H7T was 90.5â%. The respiratory quinone was MK-7, and the major polar lipids were phosphatidylethanolamine and phosphoglycolipid. The predominant cellular fatty acids were summed feature 3 (C16â:â1ω7c and/or C16â:â1ω6c), iso-C15â:â0 and iso-C17â:â0 3-OH. On the basis of phenotypic, genotypic and phylogenetic evidence, strain 5JN-11T represents a novel species in the genus Sphingobacterium, for which the name Sphingobacteriumhaloxyli sp. nov. is proposed. The type strain is 5JN-11T (=ACCC 60072T=KCTC 62457T).
Subject(s)
Chenopodiaceae/microbiology , Phylogeny , Plant Stems/microbiology , Sphingobacterium/classification , Bacterial Typing Techniques , Base Composition , China , DNA, Bacterial/genetics , Desert Climate , Fatty Acids/chemistry , Nucleic Acid Hybridization , Phospholipids/chemistry , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , Sphingobacterium/genetics , Sphingobacterium/isolation & purification , Vitamin K 2/analogs & derivatives , Vitamin K 2/chemistryABSTRACT
DNA methylation is an important mechanism of epigenetic modification. Methylation changes during stress responses and developmental processes have been well studied; however, their role in plant adaptation to the day/night cycle is poorly understood. In this study, we detected global methylation patterns in leaves of the black poplar Populus nigra 'N46' at 8:00 and 24:00 by methylated DNA immunoprecipitation sequencing (MeDIP-seq). We found 10,027 and 10,242 genes to be methylated in the 8:00 and 24:00 samples, respectively. The methylated genes appeared to be involved in multiple biological processes, molecular functions, and cellular components, suggesting important roles for DNA methylation in poplar cells. Comparing the 8:00 and 24:00 samples, only 440 differentially methylated regions (DMRs) overlapped with genic regions, including 193 hyper- and 247 hypo-methylated DMRs, and may influence the expression of 137 downstream genes. Most hyper-methylated genes were associated with transferase activity, kinase activity, and phosphotransferase activity, whereas most hypo-methylated genes were associated with protein binding, ATP binding, and adenyl ribonucleotide binding, suggesting that different biological processes were activated during the day and night. Our results indicated that methylated genes were prevalent in the poplar genome, but that only a few of these participated in diurnal gene expression regulation.
