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Mu Us Sandy Land in China is a very fragile ecological environment due to serious desertification. While attempting to gain insights into the biodiversity of biological soil crusts of Mu Us Sandy Land, a novel bacterial strain, SLN-3T, was isolated. It was phylogenetically placed into the genus Arthrobacter within the family Micrococcaceae based on its 16S rRNA gene sequence. The most closely related species were Arthrobacter ruber MDB1-42T (98.6%) and Arthrobacter agilis DSM 20550T (98.3%). Cells of the novel species were Gram-stain-positive, aerobic, and non-endospore-forming. The values of average nucleotide identity and the digital DNA-DNA hybridization between SLN-3T and MDB1-42T were 84.9% and 21.3%, respectively. The draft genome size of strain SLN-3T was 3.67 Mb, and its genomic G+C content was 68.1%. The predominant cellular fatty acids were anteiso-C15:0 and C17:0 anteiso. Glucose, galactose, and ribose were the whole-cell sugars. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, glycolipid, and phospholipid. The peptidoglycan contained lysine, glutamic acid, and alanine. The predominant menaquinone was MK-9(H2). Based on the data from the chemotaxonomic, phylogenetic, and phenotypic evidence, a novel species named Arthrobacter crusticola sp. nov is proposed, whose type strain is SLN-3T (= ACCC 61595T = JCM 33723T).

A novel gram-negative, aerobic, non-spore-forming, rod-shaped, and non-nitrogen-fixing bacterium, named SPY-1T, was isolated from biological soil crusts collected at Mu Us Sandy Land, China. Based on 16S rRNA sequence similarity, strain SPY-1T was most closely related to Neorhizobium alkalisoli CCTCC AB 2014138T (98.7%), Neorhizobium huautlense CGMCC 1.2538T (98.6%), Neorhizobium galegae DSM 11542T (98.4%), Rhizobium wenxiniae 166T (97.9%), and Rhizobium smilacinae CCTCC AB 2013016T (97.5%). Phylogenetic analysis based on 16S rRNA sequencing and multilocus sequence analysis of partial sequences of atpD-glnII-glnA-recA-ropD-thrC housekeeping genes both indicated that strain SPY-1T was a member of the genus Rhizobium. The draft genome of strain SPY-1T was 4.75 Mb in size, and the G + C content was 60.0%. The average nucleotide identity (ANI) values to N. alkalisoli CCTCC AB 2014138T and R. smilacinae CCTCC AB 2013016T were both 84.0%. The digital DNA–DNA hybridization (dDDH) values to N. alkalisoli CCTCC AB 2014138T and R. smilacinae CCTCC AB 2013016T were 20.9% and 20.2%, respectively. The major cellular fatty acids were summed feature 8 (C18:1ω7c and/or C18:1ω6c) and C16:0. Based on the data from chemotaxonomic, phylogenetic, and phenotypic evidence, strain SPY-1T represents a novel species in the genus Rhizobium, for which the name Rhizobium deserti sp. nov. is proposed. The type strain is SPY-1T (= ACCC 61627T = JCM 33732T).

A Gram-stain-negative, rod-shaped bacterium, designated as strain GL-C-18T, was isolated from soil sample collected at Mu Us Sandy Land, China, and its taxonomic position was investigated using a polyphasic approach. Growth was observed in the presence of 0–1 % (w/v) NaCl (optimum, 0 %), pH 6.0–9.0 (optimum, pH 7.0–8.0) and 20–37 °C. On the basis of 16S rRNA gene sequence similarity, strain GL-C-18T belonged to the family Sphingomonadaceae and was most closely related to Sphingosinicella vermicomposti YC7378T (95.7 %), Sphingomonas oligophenolica S213T (95.0 %) and Sphingobium boeckii 301T (94.8 %). The draft genome of strain GL-C-18T was 6.09 Mb, and the G+C content was 66.0 %. The average nucleotide identity value to Sphingosinicella vermicomposti YC7378T was 83.7 %. The predominant respiratory quinone was Q-10. The major fatty acids were C18 : 1ω7c, summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), C16:0 and C14 : 0 2OH. The main polar lipids were sphingoglycolipid, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phosphatidylcholine. On the basis of chemotaxonomic, phylogenetic and phenotypic evidence, strain GL-C-18T represents a novel species of the genus Sphingomonas , for which the name Sphingomonas deserti sp. nov. is proposed. The type strain is GL-C-18T (=ACCC 60076T=KCTC 62411T).

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 0–6 % (w/v; optimum 0–2 %), 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 90.5 %. The respiratory quinone was MK-7, and the major polar lipids were phosphatidylethanolamine and phosphoglycolipid. The predominant cellular fatty acids were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), iso-C15 : 0 and iso-C17 : 0 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 Sphingobacterium haloxyli sp. nov. is proposed. The type strain is 5JN-11T (=ACCC 60072T=KCTC 62457T).

The WRKY family of transcription factors is one of the most important families of plant transcriptional regulators, and the members regulate multiple biological processes. However, there is limited information on WRKYs in Dendrobium officinale. In this study, 52 WRKY family genes of D. officinale were surveyed for the first time. Conserved domain, phylogenetic, exon-intron construction, and expression analyses were performed for the DoWRKY genes. Two major types of intron splicing (PR and VQR introns) were found, and the intron insertion position was observed to be relatively conserved in the conserved DoWRKY domains. The expression profiles of nine DoWRKYs were analyzed in cold- and methyl jasmonate (MeJA)-treated D. officinale seedlings; the DoWRKYs showed significant expression changes at different levels, which suggested their vital roles in stress tolerance. Moreover, the expression trends of most of the DoWRKYs after the simultaneous cold stress and MeJA treatment were the opposite of those of DoWRKYs after the individual cold stress and MeJA treatments, suggesting that the two stresses might have antagonistic effects and affect the adaptive capacity of the plants to stresses. Twelve DoWRKY genes were differentially expressed between symbiotic and asymbiotic germinated seeds; all were upregulated in the symbiotic germinated seeds except DoWRKY16. These differences in expression of DoWRKYs might be involved in promoting in vitro symbiotic germination of seeds with Tulasnella-like fungi. Our findings will be useful for further studies on the WRKY family genes in orchids.

A novel gram-negative, aerobic, non-spore-forming, rod-shaped and non-nitrogen fixing bacterium named strain 24NRT was isolated from wild Lilium pumilum bulbs in Fuping, Baoding City, Hebei province, PR China. The 16S rRNA gene sequences of strains 24NRT showed the highest similarity to Neorhizobium alkalisoli DSM 21826T (98.5%) and N. galegae HAMBI 540T (98.1%). Phylogenetic analysis based on 16S rRNA genes and multilocus sequence analysis (MLSA) based on the partial sequences of atpD-glnII-glnA-recA-ropD-thrC housekeeping genes both indicated that strain 24NRT is a member of the genus Neorhizobium. The average nucleotide identity between the genome sequence of strain 24NRT and that of the isolate N. alkalisoli DSM 21826T was 83.1%, and the digital DNA–DNA hybridization was 20.1%. The G+C content of strain 24NRT was 60.3 mol %. The major cellular fatty acids were summed feature 8 (C18:1ω7c and/or C18:1ω6c) and C19:0 cyclo ω8c. Based on phenotypic, phylogenetic, and genotypic data, strain 24NRT is considered to represent a novel species of the genus Neorhizobium, for which the name Neorhizobium lilium sp. nov. is proposed. The type strain is 24NRT (= ACCC 61588T = JCM 33731T).

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).

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).

Strain N5SSJ16T, a Gram-negative-staining, non-spore-forming, rod-shaped, non-motile bacterium, was isolated from Haloxylon ammodendron stems. The strain grew in the presence of 0–4 % (w/v) NaCl (optimum growth in the absence of NaCl), at pH 7–9 (optimum: pH 8) and at 12–50 °C. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain N5SSJ16T was related phylogenetically to Parapedobacter composti 4M40T (96.5 %) and Parapedobacter luteus 4M29T (95.9 %). The cellular fatty acids were iso-C15 : 0, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), summed feature 9 (C16 : 0 10-methyl and/or iso-C17 : 1ω9c) and iso-C17 : 0 3-OH. MK-7 was the respiratory quinone. The main polar lipids were phosphatidylethanolamine, unidentified aminophospholipid and two unknown lipids. The G+C content of the DNA was 45.8 mol%. On the basis of chemotaxonomic, phylogenetic and phenotypic evidence, strain N5SSJ16T represents a novel species of the genus Parapedobacter , for which the name Parapedobacter deserti sp. nov. is proposed. The type strain is N5SSJ16T (=ACCC 19928T=KCTC 52416T).

Two Gram-staining-negative, aerobic, non-spore-forming rod-shaped, non-motile bacteria, designated strains R156-2T and T58-2 were isolated from the roots of Cymbidium goeringii. The colonies were yellow-pigmented. On the basis of 16S rRNA gene sequence similarity, strains R156-2T and T58-2 were shown to be members of the genus Chitinophaga . Strains R156-2T and T58-2 showed the greatest level of sequence similarity with Chitinophaga niabensis (96.0–96.3 %). The major menaquinone was MK-7. The main cellular fatty acids were iso-C15 : 0, C16 : 1ω5c and iso-C17 : 0 3-OH. Phenotypic and genotypic analyses indicated that strains R156-2T and T58-2 could not be assigned to any recognized species. Therefore, strains R156-2T and T58-2 represent a novel species of the genus Chitinophaga , for which the name Chitinophaga cymbidii sp. nov. is proposed. The type strain is R156-2T ( = ACCC 05363T = KCTC 23738T). The DNA G+C content of this strain is 51.9 mol%.

In order to obtain the effective plant growth-promoting bacteria, we studied the diversity of siderophore-producing endophytic bacteria in the roots of Cymbidium goeringii.We screened for siderophore-producing bacteria from 189 root endophytic strains of Cymbidium goeringii by using chrome azurol S (CAS) agar plate assay. The diversity of siderophore-producing endophytic bacteria was investigated by 16S rRNA gene sequence analysis.We obtained 47 siderophore-producing strains (24.9% of the total strains). Sequence analysis revealed that 47 strains were members of 31 species of 17 genera in four phylogenetic groups (Alphaproteobacteria, Betaproteobacteria, Firmicutes, Actinobacteria). The dominant group was Actinobacteria (42.6%), and the dominant genera were Bacillus and Variovorax. The strains of Variovorax produced relatively high levels of siderophore. In addition, there may be two novel taxonomic units.The results show that there are abundant species diversity of siderophore-producing endophytic bacteria in the roots of Cymbidium goeringii.

Background With the availability of rice and sorghum genome sequences and ongoing efforts to sequence genomes of other cereal and energy crops, the grass family (Poaceae) has become a model system for comparative genomics and for better understanding gene and genome evolution that underlies phenotypic and ecological divergence of plants. While the genomic resources have accumulated rapidly for almost all major lineages of grasses, bamboo remains the only large subfamily of Poaceae with little genomic information available in databases, which seriously hampers our ability to take a full advantage of the wealth of grass genomic data for effective comparative studies. Results Here we report the cloning and sequencing of 10,608 putative full length cDNAs (FL-cDNAs) primarily from Moso bamboo, Phyllostachys heterocycla cv. pubescens, a large woody bamboo with the highest ecological and economic values of all bamboos. This represents the third largest FL-cDNA collection to date of all plant species, and provides the first insight into the gene and genome structures of bamboos. We developed a Moso bamboo genomic resource database that so far contained the sequences of 10,608 putative FL-cDNAs and nearly 38,000 expressed sequence tags (ESTs) generated in this study. Conclusion Analysis of FL-cDNA sequences show that bamboo diverged from its close relatives such as rice, wheat, and barley through an adaptive radiation. A comparative analysis of the lignin biosynthesis pathway between bamboo and rice suggested that genes encoding caffeoyl-CoA O-methyltransferase may serve as targets for genetic manipulation of lignin content to reduce pollutants generated from bamboo pulping.

The distribution of culturable bacteria in the rhizosphere, rhizoplane, and interior root tissues of moso bamboo plants was investigated in this study. Of the 182 isolates showing different colony characteristics on Luria-Bertani and King B plates, 56 operational taxonomic units of 22 genera were identified by 16S ribosomal RNA gene sequence analysis. The majority of root endophytic bacteria were Proteobacteria (67.5%), while the majority of rhizospheric and rhizoplane bacteria were Firmicutes (66.3% and 70.4%, respectively). The most common genus in both the rhizosphere and on the rhizoplane was Bacillus (42.4% and 44.4%, respectively), while Burkholderia was the most common genus inside the roots, comprising 35.0% of the isolates from this root domain. The endophytic bacterial community was less diverse than the rhizoplane and rhizospheric bacterial communities. Members of Lysinibacillus, Bacillus, and Burkholderia were found in all three root domains, whereas many isolates were found in only a single domain. Our results show that the population diversity of culturable bacteria is abundant in the root domains of moso bamboo plants and that obvious differences exist among the rhizospheric, rhizoplane, and endophytic bacterial communities.

To obtain the information of the cultivable microbial population diversity at the rhizosphere of Phyllostachys pubescens.We isolated strains from Tianmu Mountain and Jinyun Mountain by diluting plate counting method and analyzed the 16S rDNA sequence of the isolates.We obtained 51 and 31 strains with different morphological character of colonies from Tianmu Mountain and Jinyun Mountain separately. The 16S rDNA sequence analysis showed that they had similar microbial population diversity. There were 40% and 58% firmicutes, 36.7% and 10.52% actinobacteria, 10% and 5.26% alphaproteobacteria, 10% and 26.32% gammaproteobacteria at the rhizosphere of Phyllostachys pubescens from Tianmu Mountain and Jinyun Mountain separately. The dominant bacteria were the genera Bacillus in both two areas.The result showed that the cultivable microbial population diversity was abundant and there were some potential novel strains at the rhizosphere of Phyllostachys pubescens. Our research made it is possible to further investigate the function of the rhizosphere microbes and there interaction with the bamboo plant.