Peptidomics and genomics analyses were used to study an anti-infection array of peptides of amphibian skin. 372 cDNA sequences of antimicrobial peptides were characterized from a single individual skin of the frog Odorrana grahami that encode 107 novel antimicrobial peptides. This contribution almost triples the number of currently reported amphibian antimicrobial peptides. The peptides could be organized into 30 divergent groups, including 24 novel groups. The diversity in peptide coding cDNA sequences is, to our knowledge, the most extreme yet described for any animal. The patterns of diversification suggest that point mutations as well as insertion, deletion, and "shuffling" of oligonucleotide sequences were responsible for the diversity. The diversity of antimicrobial peptides may have resulted from the diversity of microorganisms. These diverse peptides exhibited both diverse secondary structure and "host defense" properties.

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Four Gram-negative, motile, rod-shaped bacterial strains were isolated from soil samples collected from south-east China. A taxonomic study including phylogenetic analysis based on 16S rRNA gene sequences and phenotypic characteristics was performed. DNA G+C contents of the four strains were 63–66 mol%. Their predominant ubiquinone was Q-8. The fatty acid profiles contained C16 : 1 ω7c (36·9–54·7 %) and C16 : 0 (22·8–25·5 %) as the major components. Based on their phenotypic characteristics, phylogenetic position as determined by 16S rRNA gene sequence analysis and DNA–DNA hybridization results, the four isolates are considered to represent four novel species of the genus Massilia, for which the names Massilia dura sp. nov. (type strain 16T=CCTCC AB 204070T=KCTC 12342T), Massilia albidiflava sp. nov. (type strain 45T=CCTCC AB 204071T=KCTC 12343T), Massilia plicata sp. nov. (type strain 76T=CCTCC AB 204072T=KCTC 12344T) and Massilia lutea sp. nov. (type strain 101T=CCTCC AB 204073T=KCTC 12345T) are proposed.

BackgroundSalt stress is one of the most representative abiotic stresses that severely affect plant growth and development. MicroRNAs (miRNAs) are well known for their significant involvement in plant responses to abiotic stresses. Although miRNAs implicated in salt stress response have been widely reported in numerous plant species, their regulatory roles in the adaptive response to salt stress in radish (Raphanus sativus L.), an important root vegetable crop worldwide, remain largely unknown.ResultsSolexa sequencing of two sRNA libraries from NaCl-free (CK) and NaCl-treated (Na200) radish roots were performed for systematical identification of salt-responsive miRNAs and their expression profiling in radish. Totally, 136 known miRNAs (representing 43 miRNA families) and 68 potential novel miRNAs (belonging to 51 miRNA families) were identified. Of these miRNAs, 49 known and 22 novel miRNAs were differentially expressed under salt stress. Target prediction and annotation indicated that these miRNAs exerted a role by regulating specific stress-responsive genes, such as squamosa promoter binding-like proteins (SPLs), auxin response factors (ARFs), nuclear transcription factor Y (NF-Y) and superoxide dismutase [Cu-Zn] (CSD1). Further functional analysis suggested that these target genes were mainly implicated in signal perception and transduction, regulation of ion homeostasis, basic metabolic processes, secondary stress responses, as well as modulation of attenuated plant growth and development under salt stress. Additionally, the expression patterns of ten miRNAs and five corresponding target genes were validated by reverse-transcription quantitative PCR (RT-qPCR).ConclusionsWith the sRNA sequencing, salt-responsive miRNAs and their target genes in radish were comprehensively identified. The results provide novel insight into complex miRNA-mediated regulatory network of salt stress response in radish, and facilitate further dissection of molecular mechanism underlying plant adaptive response to salt stress in root vegetable crops.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1416-5) contains supplementary material, which is available to authorized users.

A Gram-negative, non-motile, rod-shaped bacterium, designated strain AKS 1 T , was isolated from a desert soil sample collected from Akesu, XinJiang Province, China. A taxonomic study, including phylogenetic analysis based on 16S rRNA gene sequences and phenotypic characteristics, was performed on the novel isolate. The predominant menaquinone of strain AKS 1 T was MK-7. The major fatty acids included i-C 15 : 0 , ai-C 17 : 1 B/i-C 17 : 1 I and i-C 17 : 0 3-OH. The G+C content of the DNA was 51.4 mol%. Based on the results of phenotypic and genotypic characteristics, strain AKS 1 T should be assigned as representing a novel species of the genus Pontibacter, for which the name Pontibacter akesuensis is proposed. The type strain is AKS 1 T (=KCTC 12758 T =CCTCC AB 206086 T ).The genus Pontibacter belongs to the phylum Bacteroidetes and was first described by Nedashkovskaya et al. (2005b) based on a single isolate from an unidentified sea anemone. The main characteristics of members of the phylum Bacteroidetes include the ability to move by gliding (many lack motility), a rod-shaped or ring-shaped morphology, possession of Gram-negative cell walls and pigmentation. The majority of the members of the phylum Bacteroidetes have been isolated from seawater, sediment or algae. Some marine bacteria of the phylum Bacteroidetes possess menaquinone 7 (MK-7) as their main respiratory quinone (Bowman et al., 2003; Brettar et al., 2004a, b; Nedashkovskaya et al., , 2004 Nedashkovskaya et al., , 2005aRaj & Maloy, 1990;Van Trappen et al., 2004;Yi & Chun, 2004;Yoon et al., 2004Yoon et al., , 2005a. The present investigation was designed to establish the taxonomic position of a novel isolate that formed a common clade with the genus Pontibacter within the phylum Bacteroidetes. Although the novel isolate has some properties characteristic of the phylum Bacteroidetes, it also has many special properties that are distinct from other members of the phylum. Genotypic and phenotypic data show that the strain represents a novel species of the genus Pontibacter.Strain AKS 1 T was isolated from a desert soil sample collected from Akesu, XinJiang Province, north-west China, by using the traditional dilution plating method. LB agar (Sambrook & Russell, 2002) was used for selective isolation and cultures were incubated at 30 uC for 1 week. The novel strain was maintained on LB agar slants at 4 u C and as glycerol suspensions (20 %, v/v) at 280 uC. Biomass for molecular systematic and chemotaxonomic studies was obtained after incubation in LB at 30 uC for 2 days in shake flasks (about 150 r.p.m.), with the pH adjusted to pH 7.8 using NaOH.Cell morphology of the novel isolate was observed by light microscopy (BH2; Olympus) and by transmission electron microscopy (H-7650; Hitachi) after 24 h growth on LB medium. Acid production from carbohydrates was tested using the media and methods described by Gordon et al. (1974). Sole carbon and sole carbon/nitrogen source utilization was investigated using the Biolog GN2 Microplate system (Nedashkovsk...