A putative terpene cyclase gene (CcPtc1) is required for fungal development and virulence in Cytospora chrysosperma

Cytospora chrysosperma is a destructive plant pathogenic fungus, which causes canker disease on numerous woody plants. However, knowledge concerning the interaction between C. chrysosperma and its host remains limited. Secondary metabolites produced by phytopathogens often play important roles in their virulence. Terpene cyclases (TC), polyketide synthases (PKS) and non-ribosomal peptide synthetases (NRPS) are the key components for the synthesis of secondary metabolites. Here, we characterized the functions of a putative terpene type secondary metabolite biosynthetic core gene CcPtc1 in C. chrysosperma, which was significantly up-regulated in the early stages of infection. Importantly, deletion of CcPtc1 greatly reduced fungal virulence to the poplar twigs and they also showed significantly reduced fungal growth and conidiation compared with the wild-type (WT) strain. Furthermore, toxicity test of the crude extraction from each strain showed that the toxicity of crude extraction secreted by ΔCcPtc1 were strongly compromised in comparison with the WT strain. Subsequently, the untargeted metabolomics analyses between ΔCcPtc1 mutant and WT strain were conducted, which revealed 193 significantly different abundant metabolites (DAMs) inΔCcPtc1 mutant compared to the WT strain, including 90 significantly downregulated metabolites and 103 significantly up-regulated metabolites, respectively. Among them, four key metabolic pathways that reported to be important for fungal virulence were enriched, including pantothenate and coenzyme A (CoA) biosynthesis. Moreover, we also detected significant alterations in a series of terpenoids, among which (+)-ar-turmerone, pulegone, ethyl chrysanthemumate, and genipin were significantly down-regulated, while cuminaldehyde and (±)-abscisic acid were significantly up-regulated. In conclusion, our results demonstrated that CcPtc1 acts as a virulence-related secondary metabolism factor and provides new insights into the pathogenesis of C. chrysosperma.

Taxogenomics Resolves Conflict in the Genus Rhodobacter: A Two and Half Decades Pending Thought to Reclassify the Genus Rhodobacter

The genus Rhodobacter is taxonomically well studied, and some members are model organisms. However, this genus is comprised of a heterogeneous group of members. 16S rRNA gene-based phylogeny of the genus Rhodobacter indicates a motley assemblage of anoxygenic phototrophic bacteria (genus Rhodobacter) with interspersing members of other genera (chemotrophs) making the genus polyphyletic. Taxogenomics was performed to resolve the taxonomic conflicts of the genus Rhodobacter using twelve type strains. The phylogenomic analysis showed that Rhodobacter spp. can be grouped into four monophyletic clusters with interspersing chemotrophs. Genomic indices (ANI and dDDH) confirmed that all the current species are well defined, except Rhodobacter megalophilus. The average amino acid identity values between the monophyletic clusters of Rhodobacter members, as well as with the chemotrophic genera, are less than 80% whereas the percentage of conserved proteins values were below 70%, which has been observed among several genera related to Rhodobacter. The pan-genome analysis has shown that there are only 1239 core genes shared between the 12 species of the genus Rhodobacter. The polyphasic taxonomic analysis supports the phylogenomic and genomic studies in distinguishing the four Rhodobacter clusters. Each cluster is comprised of one to seven species according to the current Rhodobacter taxonomy. Therefore, to address this taxonomic discrepancy we propose to reclassify the members of the genus Rhodobacter into three new genera, Luteovulum gen. nov., Phaeovulum gen. nov. and Fuscovulum gen. nov., and provide an emended description of the genus Rhodobacter sensu stricto. Also, we propose reclassification of Rhodobacter megalophilus as a sub-species of Rhodobacter sphaeroides.

Propionate metabolism and diversity of relevant functional genes by in silico analysis and detection in subsurface petroleum reservoirs

Propionate is a common metabolic intermediate occurring in environmental samples including petroleum reservoirs. Available microbial genomes were obtained from the NCBI database and analyzed in silico by hmmscan to check three metabolic pathways of propionate production in petroleum reservoir systems. The succinate pathway was the dominant one while the other two (lactate and 1,2-propanediol pathways) contributed less to the formation of propionate according to the Hidden Markov Model calculation. The mmdA gene encoding methylmalonyl-CoA decarboxylase was used as a biomarker gene to detect the diversity of microbes involved in the propionate formation in Jiangsu oil reservoirs. The mmdA gene clone library showed that microbes affiliated within the genus of Archaeoglobus, Thermococcus, Anaerobaculum, as well as more than ten other genera were the potential microorganisms involved in the production of propionate. Meanwhile, as the biomarker genes involved in the other two propionate-producing pathways, the functional genes of lcdA and pduP were tested with PCR amplification, but no positive results were observed in Jiangsu oil reservoirs.

Halovulum dunhuangense gen. nov., sp. nov., isolated from a saline terrestrial spring

A bacterial strain, YYQ-30T, isolated from a mixed water–sand–sediment sample collected from a terrestrial spring located in Dunhuang, China, was characterized with respect to its morphology, physiology and taxonomy. Cells of the strain were Gram-stain-negative, aerobic, oxidase- and catalase-positive, non-flagellated, oval to rod-shaped (0.5–1.0 μm wide and 1.1–6.6 μm long) and divided by binary fission. Growth was observed in the presence of 0–10.0 % (w/v) NaCl with optimal growth at 0–3.0 %, at pH 6.0–9.0 (optimum pH 7.0–8.5) and at 10–45 °C (optimum 30–37 °C). The isolate could reduce nitrate to nitrite and hydrolyse aesculin and gelatin (weakly), but was unable to degrade Tween 80 or starch. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain YYQ-30T belongs to the family Rhodobacteraceae and forms a distinct lineage with the type strain of Albimonas donghaensis and forms a branch within a cluster constituted by the type strains of species of the genera Albimonas, Rhodovulum, Albidovulum, Haematobacter and Tropicimonas; levels of 16S rRNA gene sequence similarity between strain YYQ-30T and members of related genera ranged from 94.1 to 89.7  %. Strain YYQ-30T contained Q-10 as the predominant ubiquinone and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c; 70.0  %), C18 : 0 (9.5  %), summed feature 2 (one or more of C14  :  0 3-OH, iso-C16  :  1 I and C12  :  0 aldehyde; 6.9  %) and 11-methyl C18  :  1ω7c (6.0  %) as the principal fatty acids. The polar lipids comprised diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, three unidentified phospholipids, two unidentified aminolipids and five unknown lipids. The pufLM gene was detected. The G+C content of the genomic DNA was 71.7 mol%. Based on the phylogenetic, chemotaxonomic and phenotypic data obtained in this study, strain YYQ-30T is considered to represent a novel species in a new genus within the family Rhodobacteraceae, for which the name Halovulum dunhuangense gen. nov., sp. nov. is proposed. The type strain of Halovulum dunhuangense is YYQ-30T ( = LMG 27418T = MCCC 1A06483T).

Reclassification of Gemmobacter changlensis to a new genus as Cereibacter changlensis gen. nov., comb. nov

We propose a new genus to accommodate the phototrophic bacterium Gemmobacter changlensis [Chen W. M., Cho, N. T., Huang, W. C., Young, C. C. & Sheu, S. Y. (2013) Int J Syst Evol Microbiol 63, 470–478] based on multiple strain analysis. Differences in the major diagnostic properties such as ability to grow phototrophically, the presence of internal photosynthetic membranes, the light harvesting complexes, fatty acids, carotenoids, bacterial chlorophylls, polar lipid composition and some other phenotypic properties warrant the creation of a new genus, designated Cereibacter gen. nov., to accommodate the phototrophic members of the genus Gemmobacter , as represented by the type species Cereibacter changlensis comb. nov.

Rhodovulum mangrovi sp. nov., a phototrophic alphaproteobacterium isolated from a mangrove forest sediment sample

A novel Gram-staining-negative, purple non-sulfur bacterium, strain AK41T, was isolated from a sediment sample collected from Coringa mangrove forest, Andhra Pradesh, India. A red–brownish-coloured culture was obtained on modified Pfennig medium after enrichment with 2 % NaCl and 0.3 % pyruvate under 2000 lx illumination. Individual cells were ovoid–rod-shaped and non-motile. Bacteriochlorophyll a and carotenoids of the spheroidene series were present as photosynthetic pigments. Strain AK41T was halophilic and grew photoheterotrophically with a number of organic compounds as carbon sources and electron donors. It was unable to grow photoautotrophically. It did not utilize sulfide or thiosulfate as electron donors. The fatty acids were found to be dominated by C16 : 0 and C18 : 1ω7c. Strain AK41T contained phosphatidylglycerol, phosphatidylethanolamine, an unknown aminolipid and four unknown lipids as polar lipids. Q-10 was the predominant respiratory quinone. The DNA G+C content of strain AK41T was 68.9 mol%. 16S rRNA gene sequence analysis indicated that strain AK41T was a member of the genus Rhodovulum and was closely related to Rhodovulum sulfidophilum , with 96.0 % similarity to the type strain; the 16S rRNA gene sequence similarity to the type strains of other species of the genus Rhodovulum was 93.9–95.8 %. Phylogenetic analyses indicated that strain AK41T clustered with the type strains of Rhodovulum marinum , Rdv. kholense , Rdv. sulfidophilum and Rdv. visakhapatnamense with sequence similarity of 95.9–96.2 %. Based on data from the current study, strain AK41T is proposed to represent a novel species of the genus Rhodovulum , for which the name Rhodovulum mangrovi sp. nov. is proposed. The type strain of Rhodovulum mangrovi is AK41T ( = MTCC 11825T = JCM 19220T).

Falsirhodobacter halotolerans gen. nov., sp. nov., isolated from dry soils of a solar saltern

Two bacterial strains (JA744T and JA745) were isolated from dry soil samples collected from solar salterns at Humma, Odisha, India. Both strains were Gram-stain-negative, catalase- and oxidase-positive, motile rods. Major fatty acids in both strains included C18 : 1ω7c, C18 : 0 and C16 : 0, while minor amounts of C10 : 0 3-OH, C12 : 0, C12 : 0 3-OH, C14 : 0 and C16 : 0 were also present. Diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol, an unidentified glycolipid, five unidentified lipids, an unidentified aminolipid and an unidentified phospholipid made up the polar lipids of both strains. Both strains had bacteriohopane derivatives (BHD1,2) and diploptene as major hopanoids. Mean genomic DNA G+C content was 75±1 mol% and the two strains were closely related (mean DNA–DNA hybridization >90 %). Phylogenetic analysis based on the 16S rRNA gene sequence showed that the two strains clustered with species of the genus Rhodobacter belonging to the family Rhodobacteraceae of the class Alphaproteobacteria . The highest sequence similarity was observed with Rhodobacter sphaeroides ATH2.4.1T (96 %) and other members of the genera Rhodobacter and Pseudorhodobacter (<96 %). However, the two strains were positioned distinctly outside the group formed by the other genera of the family Rhodobacteraceae . Distinct morphological, physiological and genotypic differences from previously described taxa support the classification of these isolates as representatives of a novel species in a new genus, for which the name Falsirhodobacter halotolerans gen. nov., sp. nov. is proposed. The type strain of Falsirhodobacter halotolerans is JA744T ( = KCTC 32158T  = NBRC 108897T).