New polyketides and sesquiterpenoids from the deep-sea sulphide-derived fungus Phoma sp. 3A00413.

Phoma fungi are known to produce a diverse range of natural products which possess various biological activities such as antifungal, antimicrobial, insecticidal, cytotoxic, and immunomodulatory effects. In our present study, we have isolated two novel polyketides (1 and 3), one new sesquiterpenoid (2), and eight known compounds (4-11) from the culture of Phoma sp. 3A00413, a deep-sea sulphide-derived fungus. The structures of compounds 1-3 were elucidated using NMR, MS, NMR calculation, and ECD calculation. In vitro antibacterial activities of all the isolated compounds were evaluated against Escherichia coli, Vibrio parahaemolyticus vp-HL, Vibrio parahaemolyticus, Staphylococcus aureus, Vibrio vulnificus, and Salmonella enteritidis. Compounds 1, 7, and 8 exhibited weak inhibition against Staphylococcus aureus growth, while compounds 3 and 7 showed weak inhibition against Vibrio vulnificus growth. Importantly, compound 3 demonstrated exceptional potency against Vibrio parahaemolyticus, with a minimum inhibitory concentration (MIC) of 3.1 µM.

Cupidesulfovibrio liaohensis gen. nov., sp. nov., a novel sulphate-reducing bacterium isolated from an oil reservoir and reclassification of Desulfovibrio oxamicus and Desulfovibrio termitidis as Cupidesulfovibrio oxamicus comb. nov. and Cupidesulfovibrio termitidis comb. nov.

A novel sulphate-reducing, Gram-stain-negative, anaerobic strain, isolate XJ01T, recovered from production fluid at the LiaoHe oilfield, PR China, was the subject of a polyphasic study. The isolate together with Desulfovibrio oxamicus NCIMB 9442T and Desulfovibrio termitidis DSM 5308T formed a distinct, well-supported clade in the Desulfovibrionaceae 16S rRNA gene tree. The taxonomic status of the clade was underscored by complementary phenotypic data. The three isolates comprising the clade formed distinct phyletic branches and were distinguished using a combination of physiological features and by low average nucleotide identity and digital DNA-DNA hybridization values. Consequently, it is proposed that isolate XJ01T represents a novel genus and species for which the name Cupidesulfovibrio liaohensis gen. nov., sp. nov. is proposed with the type strain XJ01T (=CGMCC 1.5227T=DSM 107637T). It is also proposed that D. oxamicus and D. termitidis be reclassified as Cupidesulfovibrio oxamicus comb. nov. and Cupidesulfovibrio termitidis comb. nov., respectively.

Actinophytocola xanthii sp. nov., an actinomycete isolated from rhizosphere soil of the plant Xanthium sibiricum.

A novel actinomycete strain, 11-183T, was isolated from the rhizosphere soil of Xanthium sibiricum, which was collected in Tangshan, Hebei, China. A phylogenetic analysis based on 16S rRNA gene sequences showed that strain 11-183T formed a clade within the genus Actinophytocola, with a maximum similarity of 98.44 % to Actinophytocola xinjiangensis QAIII60T, followed by 97.76 % similarity to Actinophytocola sediminis YIM M13705T. The average nucleotide identity and digital DNA-DNA hybridization values differed by 79.24 and 23.4 %, respectively, between strain 11-183T and Actinophytocolaxinjiangensis QAIII60T. Strain 11-183T grew well on N-Z-amine agar, and it produced a scant, white aerial mycelium. The isolate formed pale yellow to brown-black colonies and a dense, non-fragmented, branched substrate mycelium, and produced aerial hyphae on which nodular spore chains formed. Growth was observed at salinities ranging from 0 to 2 %, at pH values ranging from pH 6.5 to 8.0 and at temperatures ranging from 15 to 37 °C. The cell-wall amino acids included meso-diaminopimelic acid. Whole cell hydrolysates contained galactose and glucose. The principal fatty acids were iso-C16 : 0, iso-C16 : 1 H and C17 : 1ω6c. Diphosphatidylglycerol, phosphatidylmonomethylethanolamine and phosphatidylethanolamine were the diagnostic phospholipids. The isoprenoid quinones included MK-9(H4) and MK-10(H4). The G+C content of the genomic DNA was 71.7 mol%. Based on the genotypic and phenotypic data, we conclude that strain 11-183T belongs to a novel species of the genus Actinophytocola. The name proposed for the novel species is Actinophytocola xanthii sp. nov., with the type strain 11-183T (=KCTC 39690T= MCCC 1K02062T).

Genome sequence of Gallaecimonas xiamenensis type strain 3-C-1.

Gallaecimonas xiamenensis 3-C-1(T) was isolated from a crude-oil-degrading consortium enriched from the surface seawater around Xiamen Island. Here, we present the draft genome of strain 3-C-1(T), which contains 4,062,282 bp with a G+C content of 60.58% and contains 3,798 protein-coding genes and 65 tRNAs.

Genome sequence of Idiomarina xiamenensis type strain 10-D-4.

Idiomarina xiamenensis strain 10-D-4(T) was isolated from an oil-degrading consortium enriched from surface seawater around the Xiamen island. Here, we present the draft genome of strain 10-D-4(T), which contains 2,899,282 bp with a G+C content of 49.48% and contains 2,673 protein-coding genes and 43 tRNA genes.

Genome sequence of Thalassospira xiamenensis type strain M-5.

Thalassospira xiamenensis M-5(T) was isolated from the surface water of a waste oil pool at the oil storage dock in the city of Xiamen, Fujian Province, China. Here, we present the draft genome of strain M-5(T), which contains 4,705,237 bp with a G+C content of 54.65% and contains 4,343 protein-coding genes and 46 tRNA genes.

Genome sequence of the alkane-degrading bacterium Alcanivorax hongdengensis type strain A-11-3.

Alcanivorax hongdengensis A-11-3(T) was isolated from an oil-enriched consortium enriched from the surface seawater of Hong-Deng dock in the Straits of Malacca and Singapore. Strain A-11-3(T) can degrade n-alkane and produce a lipopeptide biosurfactant. Here we report the genome of A-11-3(T) and the genes associated with alkane degradation.

Genome sequence of Nitratireductor indicus type strain C115.

Nitratireductor indicus strain C115(T) was isolated from a crude-oil-degrading consortium enriched from deep seawater of the Indian Ocean. Here, we present the draft genome of strain C115(T), which contains 4,992,479 bp with a G+C content of 60.8% and contains 4,825 protein-coding genes and 45 tRNA genes.

Gene diversity of CYP153A and AlkB alkane hydroxylases in oil-degrading bacteria isolated from the Atlantic Ocean.

Alkane hydroxylases, including the integral-membrane non-haem iron monooxygenase (AlkB) and cytochrome P450 CYP153 family, are key enzymes in bacterial alkane oxidation. Although both genes have been detected in a number of bacteria and environments, knowledge about the diversity of these genes in marine alkane-degrading bacteria is still limited, especially in pelagic areas. In this report, 177 bacterial isolates, comprising 43 genera, were obtained from 18 oil-degrading consortia enriched from surface seawater samples collected from the Atlantic Ocean. Many isolates were confirmed to be the first oil-degraders in their affiliated genera including Brachybacterium, Idiomarina, Leifsonia, Martelella, Kordiimonas, Parvibaculum and Tistrella. Using degenerate PCR primers, alkB and CYP153A P450 genes were surveyed in these bacteria. In total, 82 P450 and 52 alkB gene fragments were obtained from 80 of the isolates. These isolates mainly belonged to Alcanivorax, Bacillus, Erythrobacter, Martelella, Parvibaculum and Salinisphaera, some of which were reported, for the first time, to encode alkane hydroxylases. Phylogenetic analysis showed that both genes were quite diverse and formed several clusters, most of which were generated from various Alcanivorax bacteria. Noticeably, some sequences, such as those from the Salinisphaera genus, were grouped into a distantly related novel cluster. Inspection of the linkage between gene and host revealed that alkB and P450 tend to coexist in Alcanivorax and Salinisphaera, while in all isolates of Parvibaculum, only P450 genes were found, but of multiple homologues. Multiple homologues of alkB mostly cooccurred in Alcanivorax isolates. Conversely, distantly related isolates contained similar or even identical sequences. In summary, various oil-degrading bacteria, which harboured diverse P450 and alkB genes, were found in the surface water of Atlantic Ocean. Our results help to show the diversity of P450 and alkB genes in prokaryotes, and to portray the geographic distribution of oil-degrading bacteria in marine environments.