Pseudomonas syringae is a gram-negative plant pathogen that generally infects plants such as tomato and threatens global crop production. In this study, a novel lytic phage (named Pseudomonas phage D6) infecting P. syringae pv. tomato DC3000 was isolated from the karst cave sediments and characterized. The latent period of phage D6 was shown to be 60 min, and the burst size was 16 plaque forming units/cell. Phage D6 was stable at 30 − 40°C and lost infectivity after heated to 70°C. The infectivity of phage D6 was unaffected at pH 6 − 10, but was inactivated at pH ≤ 5 or ≥ 12. The genome of phage D6 is a linear double-stranded DNA of 307,402 bp with a G + C content of 48.43%. It showed low similarity to known phage genomes in the GenBank database and Viral sequence database. Genomic and phylogenetic analyses revealed that phage D6 is a newly discovered phage. A total of 410 open reading frames (ORFs) and 14 tRNAs were predicted in the genome, 92 of which encode for proteins with predicted functions. In conclusion, the lytic phage D6 identified in this study belongs to a novel phage of the class Caudoviricetes, and has potential application in biological control of plant diseases.

A novel, Gram-stain-positive, aerobic, non-endospore-forming, non-motile and rod-shaped bacterium designated PO-11T was isolated from sediment of karst cave collected in Libo county, Guizhou Province, PR China. The isolate grew optimally on R2A agar at 25 °C, pH 8.0 and with 0.5 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that PO-11T belonged to the genus Arthrobacter and was most closely related to Arthrobacter methylotrophus TGAT (98.3 % sequence similarity), Arthrobacter alkaliphilus LC6T (97.7 %) and Arthrobacter ramosus CCM1646T (97.1 %). Genome sequencing revealed a genome size of 4 073 119 bp and the genomic DNA G+C content was 66.16 mol%. Its DNA–DNA relatedness values with A. methylotrophus TGAT, A. alkaliphilus LC6T and A. ramosus CCM1646T were 23.0, 22.9 and 23.2 %, respectively. The main fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. The major respiratory quinone was MK-9(H2). The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, glycolipid, phosphatidylethanolamine, phosphatidylinositol and unidentified lipids. Thus, based on phylogenetic and phenotypic and chemotaxonomic data, strain PO-11T represents a novel species of the genus Arthrobacter , for which the name Arthrobacter cavernae sp. nov. is proposed. The type strain is strain PO-11T (=CCTCC AB 2021070T=LMG 32459T).

Background Vibrio parahaemolyticus is a major foodborne pathogen that contaminates aquatic products and causes great economic losses to aquaculture. Because of the emergence of multidrug-resistant V. parahaemolyticus strains, bacteriophages are considered promising agents for their biocontrol as an alternative or supplement to antibiotics. In this study, a lytic vibriophage, vB_VpaM_R16F (R16F), infecting V. parahaemolyticus 1.1997T was isolated, characterized and evaluated for its biocontrol potential. Methods A vibriophage R16F was isolated from sewage from a seafood market with the double-layer agar method. R16F was studied by transmission electron microscopy, host range, sensitivity of phage particles to chloroform, one-step growth curve and lytic activity. The phage genome was sequenced and in-depth characterized, including phylogenetic and taxonomic analysis. Results R16F belongs to the myovirus morphotype and infects V. parahaemolyticus, but not nine other Vibrio spp. As characterized by determining its host range, one-step growth curve, and lytic activity, phage R16F was found to highly effective in lysing host cells with a short latent period (< 10 min) and a small burst size (13 plaque-forming units). R16F has a linear double-stranded DNA with genome size 139,011 bp and a G + C content of 35.21%. Phylogenetic and intergenomic nucleotide sequence similarity analysis revealed that R16F is distinct from currently known vibriophages and belongs to a novel genus. Several genes (e.g., encoding ultraviolet damage endonuclease and endolysin) that may enhance environmental competitiveness were found in the genome of R16F, while no antibiotic resistance- or virulence factor-related gene was detected. Conclusions In consideration of its biological and genetic properties, this newly discovered phage R16F belongs to a novel genus and may be a potential alternate biocontrol agent.

The gut microbiota is essential for the nutrition, growth, and adaptation of the host. Diestrammena japanica, a scavenger that provides energy to the cave ecosystem, is a keystone species in the karst cave in China. It inhabits every region of the cave, regardless of the amount of light. However, its morphology is dependent on the intensity of light. Whether the gut bacteria reflect its adaptation to the cave environment remains unknown. In this research, D. japanica was collected from the light region, weak light region, and dark region of three karst caves. The gut bacterial features of these individuals, including composition, diversity, potential metabolism function, and the co-occurrence network of their gut microbiota, were investigated based on 16S rRNA gene deep sequencing assay. The residues of amino acids in the ingluvies were also evaluated. In addition, we explored the contribution of gut bacteria to the cave adaptation of D. japanica from three various light zones. Findings showed that gut bacteria were made up of 245 operational taxonomic units (OTUs) from nine phyla, with Firmicutes being the most common phylum. Although the composition and diversity of the gut bacterial community of D. japanica were not significantly different among the three light regions, bacterial groups may serve different functions for D. japanica in differing light strengths. D. japanica has a lower rate of metabolism in cave habitats than in light regions. We infer that the majority of gut bacteria are likely engaged in nutrition and supplied D. japanica with essential amino acids. In addition, gut bacteria may play a role in adapting D. japanica’s body size. Unveiling the features of the gut bacterial community of D. japanica would shed light on exploring the roles of gut bacteria in adapting hosts to karst cave environments.

Vibrio parahaemolyticusis a major foodborne pathogen that contaminates aquatic 11 products and causes great economic losses to aquaculture. Because of the emergence of 12 multidrug-resistantV. parahaemolyticusstrains, bacteriophages are considered promising agents 13 for their biocontrol as an alternative or supplement to antibiotics. Here, a lytic vibriophage, 14 vB_VpaM_R16F (R16F), was isolated from sewage from a seafood market by infectingV. 15 parahaemolyticus1.1997T. R16F was found to infectV. parahaemolyticus, but not nine other Vibrio spp. 16 The phage belongs to the myovirus morphotype and lysed host cells with a short latent period 17 (<10 min) and a small burst size (13 plaque-forming units). R16F has a linear double-stranded 18 DNA with genome size 139,011 bp and a G+C content of 35.21%. Phylogenetic and intergenomic 19 nucleotide sequence similarity analysis revealed that R16F is distinct from currently known 20 vibriophages and belongs to a novel genus. Several genes (e.g., encoding ultraviolet damage 21 endonuclease and endolysin) that may enhance environmental competitiveness were found in the 22 genome of R16F, while no antibiotic resistance- or virulence factor-related gene was detected. In 23 consideration of its biological and genetic properties, R16F is suggested to be a candidate 24 biocontrol agent for use againstV. parahaemolyticus.