A Semisynthesis Platform for the Efficient Production and Exploration of Didemnin-Based Drugs

Plitidepsin (or dehydrodidemnin B), an approved anticancer drug, belongs to the didemnin family of cyclic depsipeptides, which are found in limited quantities in marine tunicate extracts. Herein, we introduce a new approach that integrates microbial and chemical synthesis to generate plitidepsin and its analogues. We screened a Tistrella strain library to identify a potent didemnin B producer, and then introduced a second copy of the didemnin biosynthetic gene cluster into its genome, resulting in a didemnin B titer of approximately 75 mg/L. Next, we developed two straightforward chemical strategies to convert didemnin B into plitidepsin, one of which involved a one-step synthetic route giving over 90 % overall yield. Furthermore, we synthesized 13 new didemnin derivatives and three didemnin probes, enabling research into structure-activity relationships and interactions between didemnin and proteins. Our study highlights the synergistic potential of biosynthesis and chemical synthesis in overcoming the challenge of producing complex natural products sustainably and at scale.

Shumkonia mesophila gen. nov., sp. nov., a novel representative of Shumkoniaceae fam. nov. and its potentials for extracellular polymeric substances formation and sulfur metabolism revealed by genomic analysis

A microaerophilic, mesophilic, chemoorganoheterotrophic bacterium, designated Y-P2T, was isolated from oil sludge enrichment in China. Cells of the strain were Gram-stain-negative, non-motile, non-spore-forming, rod-shaped or slightly curved with 0.8-3.0 µm in length and 0.4-0.6 µm in diameter. The strain Y-P2T grew optimally at 25 °C (range from 15 to 30 °C) and pH 7.0 (range from pH 6.0 to 7.5) without NaCl. The major cellular fatty acids were C16:0, summed feature 3 (C16:1 ω7c and/or C16:1 ω6c), summed feature 8 (C18:1 ω7c and/or C18:1 ω6c). The main polar liquids of strain Y-P2T comprised phosphatidylethanolamine (PE) and phosphatidylglycerol (PG). The respiratory quinone was Q-10. Acetate and H2 were the fermentation products of glucose. The DNA G + C content was 66.0%. Strain Y-P2T shared the highest 16S rRNA gene sequence similarity (90.3-90.6%) with species within Oceanibaculum of family Thalassobaculaceae in Rhodospirillales. Phylogenetic analyses based on 16S rRNA gene sequences and genomes showed that strain Y-P2T formed a distinct evolutionary lineage within the order Rhodospirillales. On the basis of phenotypic, phylogenetic and phylogenomic data, we propose that strain Y-P2T represents a novel species in a novel genus, for which Shumkonia mesophila gen. nov., sp. nov., within a new family Shumkoniaceae fam. nov. The type strain is Y-P2T (= CCAM 826 T = JCM 34766 T).

Ectoines production from biogas in pilot bubble column bioreactors and their subsequent extraction via bio-milking

Despite the potential of biogas from waste/wastewater treatment as a renewable energy source, the presence of pollutants and the rapid decrease in the levelized cost of solar and wind power constrain the use of biogas for energy generation. Biogas conversion into ectoine, one of the most valuable bioproducts (1000 €/kg), constitutes a new strategy to promote a competitive biogas market. The potential for a stand-alone 20 L bubble column bioreactor operating at 6% NaCl and two 10 L interconnected bioreactors (at 0 and 6% NaCl, respectively) for ectoine production from biogas was comparatively assessed. The stand-alone reactor supported the best process performance due to its highest robustness and efficiency for ectoine accumulation (20-52 mgectoine/gVSS) and CH4 degradation (up to 84%). The increase in N availability and internal gas recirculation did not enhance ectoine synthesis. However, a 2-fold increase in the internal gas recirculation resulted in an approximately 1.3-fold increase in CH4 removal efficiency. Finally, the recovery of ectoine through bacterial bio-milking resulted in efficiencies of >70% without any negative impact of methanotrophic cell recycling to the bioreactors on CH4 biodegradation or ectoine synthesis.

Effects of reducing, stabilizing, and antibiotic agents on "Candidatus Kuenenia stuttgartiensis"

Anaerobic ammon ium oxidizing (anammox) bacteria oxidize ammonium and reduce nitrite, producing N₂, and could play a major role in energy-optimized wastewater treatment. However, sensitivity to various environmental conditions and slow growth currently hinder their wide application. Here, we attempted to determine online the effect of environmental stresses on anammox bacteria by using an overnight batch activity test with whole cells, in which anammox activity was calculated by quantifying N₂ production via headspace-pressure monitoring. A planktonic mixed culture dominated by "Candidatus Kuenenia stuttgartiensis" strain CSTR1 was cultivated in a 30-L semi-continuous stirring tank reactor. In overnight resting-cell anammox activity tests, oxygen caused strong inhibition of anammox activity, which was reversed by sodium sulfite (30 µM). The tested antibiotics sulfamethoxazole, kanamycin, and ciprofloxacin elicited their effect on a dose-dependent manner; however, strain CSTR1 was highly resistant to sulfamethoxazole. Anammox activity was improved by activated carbon and Fe₂O₃. Protein expression analysis from resting cells after anammox activity stimulation revealed that NapC/NirT family cytochrome c (KsCSTR_12840), hydrazine synthase, hydrazine dehydrogenase, hydroxylamine oxidase, and nitrate:nitrite oxidoreductase were upregulated, while a putative hydroxylamine oxidoreductase HAO (KsCSTR_49490) was downregulated. These findings contribute to the growing knowledge on anammox bacteria physiology, eventually leading to the control of anammox bacteria growth and activity in real-world application. KEY POINTS: • Sulfite additions can reverse oxygen inhibition of the anammox process • Anammox activity was improved by activated carbon and ferric oxide • Sulfamethoxazole marginally affected anammox activity.

Magnetospirillum sulfuroxidans sp. nov., capable of sulfur-dependent lithoautotrophy and a taxonomic reevaluation of the order Rhodospirillales

A spiral-shaped, highly motile bacterium was isolated from freshwater sulfidic sediment. Strain J10^T is a facultative autotroph utilizing sulfide, thiosulfate, and sulfur as the electron donors in microoxic conditions. Despite high 16S rRNA gene sequence sequence identity to Magnetospirillum gryphiswaldense MSR-1 ^T (99.6 %), digital DNA-DNA hybridisation homology and average nucleotide identity between the two strains was of the different species level (25 % and 83 %, respectively). Strain J10^T is not magnetotactic. The DNA G + C content of strain J10^T is 61.9 %. The predominant phospholipid ester-linked fatty acids are C18:1ω7, C16:1ω7, and C16:0. Strain J10^T (=DSM 23205 ^T = VKM B-3486 ^T) is the first strain of the genus Magnetospirillum showing lithoautotrophic growth and is proposed here as a novel species, Magnetospirillum sulfuroxidans sp. nov. In addition, we propose to establish a framework for distinguishing genera and families within the order Rhodospirillales based on phylogenomic analysis using the threshold values for average amino acid identity at ̴ 72 % for genera and ̴ 60 % for families. According to this, we propose to divide the existing genus Magnetospirillum into three genera: Magnetospirillum, Paramagnetospirillum, and Phaeospirillum, constituting a separate family Magnetospirillaceae fam. nov. in the order Rhodospirillales. Furthermore, phylogenomic data suggest that this order should accomodate six more new family level groups including Magnetospiraceae fam. nov., Magnetovibrionaceae fam. nov., Dongiaceae fam. nov., Niveispirillaceae fam. nov., Fodinicurvataceae fam. nov., and Oceanibaculaceae fam. nov.

Cometabolism of the Superphylum Patescibacteria with Anammox Bacteria in a Long-Term Freshwater Anammox Column Reactor

Although the anaerobic ammonium oxidation (anammox) process has attracted attention regarding its application in ammonia wastewater treatment based on its efficiency, the physiological characteristics of anammox bacteria remain unclear because of the lack of pure-culture representatives. The coexistence of heterotrophic bacteria has often been observed in anammox reactors, even in those fed with synthetic inorganic nutrient medium. In this study, we recovered 37 draft genome bins from a long-term-operated anammox column reactor and predicted the metabolic pathway of coexisting bacteria, especially Patescibacteria (also known as Candidate phyla radiation). Genes related to the nitrogen cycle were not detected in Patescibacterial bins, whereas nitrite, nitrate, and nitrous oxide-related genes were identified in most of the other bacteria. The pathway predicted for Patescibacteria suggests the lack of nitrogen marker genes and its ability to utilize poly-N-acetylglucosamine produced by dominant anammox bacteria. Coexisting Patescibacteria may play an ecological role in providing lactate and formate to other coexisting bacteria, supporting growth in the anammox reactor. Patescibacteria-centric coexisting bacteria, which produce anammox substrates and scavenge organic compounds produced within the anammox reactor, might be essential for the anammox ecosystem.

Oleiliquidispirillum nitrogeniifigens gen. nov., sp. nov., a new member of the family Rhodospirillaceae isolated from oil reservoir water

A novel Gram-staining-negative, spiral-shaped bacterium, designated strain 64-1^T, was isolated from oil reservoir water collected from Liaohe oilfield, north-eastern China. Growth occurred at 15-55 °C and pH 6.0-10.0. The sole respiratory quinone was Q-10. The predominant cellular fatty acids were summed feature 8 (C_18 : 1  ω7c /C_18 : 1  ω6c), C_16 : 0 and C_19 : 0 cyclo ω8c. The polar lipids consisted of phosphatidylethanolamine (PE), phosphatidylglycerol (PG), phosphatidylcholine (PC), an unidentified aminophospholipid (UAPL), an unidentified aminolipid (UAL) and two unidentified polar lipids (UPL). The genomic DNA G+C content of strain 64-1^T was 64.5 mol%. Strain 64-1^T shared the highest 16S rRNA gene sequence similarities with Phaeospirillum chandramohanii JA145^T (92.0 %) and Telmatospirillum siberiense 26-4b1^T (91.8 %). In the phylogenetic trees, the strain constituted a sub-cluster within the family Rhodospirillaceae. Based on the results of morphological, physiological, biochemical and phylogenetic analysis, strain 64-1^T represents a new species of a novel genus within the family Rhodospirillaceae, for which the name Oleiliquidispirillum nitrogeniifigens gen. nov., sp. nov. is proposed. The type strain is 64-1^T (=CGMCC 1.16798^T=LMG 31399^T).

Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria

The class Alphaproteobacteria is comprised of a diverse assemblage of Gram-negative bacteria that includes organisms of varying morphologies, physiologies and habitat preferences many of which are of clinical and ecological importance. Alphaproteobacteria classification has proved to be difficult, not least when taxonomic decisions rested heavily on a limited number of phenotypic features and interpretation of poorly resolved 16S rRNA gene trees. Despite progress in recent years regarding the classification of bacteria assigned to the class, there remains a need to further clarify taxonomic relationships. Here, draft genome sequences of a collection of genomes of more than 1000 Alphaproteobacteria and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa recognized as problematic long ago but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera and of a variety of genera to other families. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which are confirmed as valuable taxonomic markers. Similarly, analysis of the gene content was shown to provide valuable taxonomic insights in the class. Significant incongruities between 16S rRNA gene and whole genome trees were not found in the class. The incongruities that became obvious when comparing the results of the present study with existing classifications appeared to be caused mainly by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. Another probable cause of misclassifications in the past is the partially low overall fit of phenotypic characters to the sequence-based tree. Even though a significant degree of phylogenetic conservation was detected in all characters investigated, the overall fit to the tree varied considerably.

Hypericibacter terrae gen. nov., sp. nov. and Hypericibacter adhaerens sp. nov., two new members of the family Rhodospirillaceae isolated from the rhizosphere of Hypericum perforatum

Two strains of the family Rhodospirillaceae were isolated from the rhizosphere of the medicinal plant Hypericum perforatum. Cells of both strains were Gram-stain-negative, motile by means of a single polar flagellum, non-spore-forming, non-capsulated, short rods that divided by binary fission. Colonies were small and white. Strains R5913^T and R5959^T were oxidase-positive, mesophilic, neutrophilic and grew optimally without NaCl. Both grew under aerobic and microaerophilic conditions and on a limited range of substrates with best results on yeast extract. Major fatty acids were C_19 : 0 cyclo ω8c and C_16 : 0; in addition, C_18 : 1ω7c was also found as a predominant fatty acid in strain R5913^T. The major respiratory quinone was ubiquinone 10 (Q-10). The DNA G+C contents of strains R5913^T and R5959^T were 66.0 and 67.4 mol%, respectively. 16S rRNA gene sequence comparison revealed that the closest relatives (<92 % similarity) of the strains are Oceanibaculum pacificum MCCC 1A02656^T, Dongia mobilis CGMCC 1.7660^T, Dongia soli D78^T and Dongia rigui 04SU4-P^T. The two novel strains shared 98.6 % sequence similarity and represent different species on the basis of low average nucleotide identity of their genomes (83.8 %). Based on the combined phenotypic, genomic and phylogenetic investigations, the two strains represent two novel species of a new genus in the family Rhodospirillaceae, for which the name Hypericibacter gen. nov. is proposed, comprising the type species Hypericibacter terrae sp. nov. (type strain R5913^T=DSM 109816^T=CECT 9472^T) and Hypericibacter adhaerens sp. nov. (type strain R5959^T=DSM 109817^T=CECT 9620^T).

Synergistic biodegradation of phenanthrene and fluoranthene by mixed bacterial cultures

Polycyclic aromatic hydrocarbons (PAHs) are highly recalcitrant compounds and difficult to degrade. Therefore in this work, using a bioremediation approach, mixed bacterial cultures (ASPF) was developed and enriched from polluted marine sediments capable of degrading 400 mg/L of phenanthrene and fluoranthene in Bushnell Hass medium. ASPF consists of 22 bacterial genera dominated by Azoarcus and Chelativorans. The biostimulation effect of three water soluble fertilizers (NPK, urea, and ammonium sulfate) showed that NPK and ammonium sulfate have enhanced the degradation, whereas urea has decreased their degradation. ASPF was also able to degrade phenanthrene and fluoranthene in the presence of petroleum hydrocarbons. But degradation was found to decrease in the presence of pathway intermediates (phthalic acid and catechol) due to enzymatic feedback inhibition. Optimum degradation of both PAHs was observed under room temperature, suggesting the practical applicability of ASPF.

Algihabitans albus gen. nov., sp. nov., isolated from a culture of the green alga Ulva prolifera

A bacterial strain, designated HHTR 118^T, was isolated from a culture of the green alga Ulvaprolifera obtained from offshore seawater of Qingdao, Shandong Province, China. Cells of strain HHTR 118^T were rod-shaped and motile with a single flagellum, and approximately 0.3-0.4 µm wide and 0.8-1.4 µm long. The strain was Gram-stain-negative, strictly aerobic, catalase-negative and oxidase-positive. Optimal growth was observed at 30 °C, at pH 8.0 and with 1 % (w/v) NaCl. Nitrate was not reduced. Sucrose, sodium citrate and l-leucine stimulated growth, but not lactose, fructose, xylose, d-mannose, glucose, raffinose, rhamnose, ornithine or lysine. The DNA G+C content of strain HHTR 118^T calculated on the basis of the genome sequence was 64.9 mol% and the genome size is 4.6 Mbp. The major quinone was ubiquinone 10 and the predominant cellular fatty acids (>10 % of total fatty acids) were summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c). The predominant polar lipids were phosphatidylglycerol, one unidentified phospholipid, two unidentified aminolipids and three unidentified polar lipids. Phylogenetic analysis, based on 16S rRNA gene sequences, demonstrated that strain HHTR 118^T was affiliated with the family Rhodospirillaceae. On the basis of the 16S rRNA gene sequence data as well as physiological and biochemical characteristics, we concluded that strain HHTR 118^T represents a novel species of a novel genus. We propose the name of Algihabitans albus gen. nov., sp. nov. for this novel species. The type strain of the novel species is strain HHTR 118^T (=KCTC 62395^T=MCCC 1K03486^T).

Identification of microbial species present in a pesticide dissipation process in biobed systems using typical substrates from southeastern Mexico as a biomixture at a laboratory scale

Biobed systems are an important option to control point pollution in agricultural areas. Substrates used and microbial diversity present in a biomixture perform an essential function in pesticide dissipation. In this study, the effects of soil (50% of volume/volume [V/V] proportion for all biomixtures) and four soil-based biomixtures (miniaturized biobeds; addition of novel substrates from southeastern Mexico) on dissipation of high concentrations of 2,4-dichlorophenoxyacetic acid (2,4-D), atrazine, carbofuran, diazinon, and glyphosate and on microbial diversity in biomixtures were evaluated. Small residual amounts of all pesticides at 20 (<2%) and 41 (<1%) days were observed; however, the lowest efficiency rates were observed in soil. Glyphosate was the only pesticide that completely dissipated in soil and biomixtures. Archaea, bacteria, and fungi were identified in biobeds, with bacteria being the most diverse microorganisms according to the identified species. The presence of white-rot fungi (normally related to pesticide degradation in biomixtures) was observed. Effects of the pesticide type and of biomixtures on pesticide dissipation were significant (P<0.05); however, only the effect of biomixtures on microbial diversity was significant (P<0.05); microbial diversity and richness had a significant effect on the residual amount of pesticides (P<0.05). Microbial diversity in terms of phyla was directly related to physicochemical parameters such as organic matter, lignin, water-holding capacity, and pH of soil and biomixtures.

Oceanibaculum nanhaiense sp. nov., isolated from surface seawater

A taxonomic study was carried out on strain L54-1-50^T, which was isolated from surface seawater of the South China Sea. Cells of strain L54-1-50^T were Gram-stain-negative, rod-shaped, oxidase-positive and catalase-positive. Growth was observed at salinities from 0 to 9 % (optimum 2 %, w/v), at pH 6.0-10.0 (optimum 8.0-9.0) and at temperatures from 10 to 45 °C (optimum 25-37 °C), but not at 4 or 50 °C. The 16S rRNA gene sequence analysis indicated that strain L54-1-50^T was a member of the genus Oceanibaculum, related to Oceanibaculum indicum P24^T (98.8 %) and Oceanibaculum pacificum MC2UP-L3^T (97.7 %). The digital DNA-DNA hybridization values between strain L54-1-50^T and the two type strains O. indicum P24^T and O. pacificum MC2UP-L3^T were 35.4±2.5 and 23.7±2.5 %, respectively. The average nucleotide identity values between strain L54-1-50^T and two type strains were 79.7 and 88.3 %, respectively. The major cellular fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), C16 : 0 and C18 : 1 2-OH. The respiratory quinone was Q-10. The polar lipids comprised diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylglycerol, two unidentified phospholipids and three unidentified lipids. The G+C content of the chromosomal DNA was 65.1 mol%. The combined genotypic and phenotypic data showed that strain L54-1-50^T represents a novel species of the genus Oceanibaculum, for which the name Oceanibaculumnanhaiense sp. nov. is proposed, with the type strain L54-1-50^T (=KCTC 52312^T=MCCC 1A05150^T).

Integrated analysis of bacterial and microeukaryotic communities from differentially active mud volcanoes in the Gulf of Cadiz

The present study assesses the diversity and composition of sediment bacterial and microeukaryotic communities from deep-sea mud volcanoes (MVs) associated with strike-slip faults in the South-West Iberian Margin (SWIM). We used a 16S/18S rRNA gene based pyrosequencing approach to characterize and correlate the sediment bacterial and microeukaryotic communities from MVs with differing gas seep regimes and from an additional site with no apparent seeping activity. In general, our results showed significant compositional changes of bacterial and microeukaryotic communities in sampling sites with different seepage regimes. Sediment bacterial communities were enriched with Methylococcales (putative methanotrophs) but had lower abundances of Rhodospirillales, Nitrospirales and SAR202 in the more active MVs. Within microeukaryotic communities, members of the Lobosa (lobose amoebae) were enriched in more active MVs. We also showed a strong correlation between Methylococcales populations and lobose amoeba in active MVs. This study provides baseline information on the diversity and composition of bacterial and microeukaryotic communities in deep-sea MVs associated with strike-slip faults.

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).

Limibacillus halophilus gen. nov., sp. nov., a moderately halophilic bacterium in the family Rhodospirillaceae isolated from reclaimed land

A Gram-stain-negative, aerobic, non-motile, non-spore-forming and short rod-shaped bacterial strain, designated CAU 1121T, was isolated from reclaimed land in the Republic of Korea and its taxonomic position was investigated using a polyphasic approach. The bacterium grew optimally at 37 °C, at pH 6.5 and in the presence of 2 % (w/v) NaCl. Based on 16S rRNA gene sequence similarity, the novel isolate belonged to the family Rhodospirillaceae within the class Alphaproteobacteria and formed an independent lineage within the evolutionary radiation encompassed by the phylum Proteobacteria. Strain CAU 1121T exhibited very low levels of 16S rRNA gene sequence similarity with its phylogenetic neighbours Pelagibius litoralis (similarity, 92.5 %), Fodinicurvata fenggangensis (similarity, 91.4 %), Fodinicurvata sediminis (similarity, 90.7 %) and Tistlia consotensis (similarity, 91.0 %). Strain CAU 1121T contained ubiquinone-10 as the only respiratory quinone and C18 : 1ω7c as the major cellular fatty acid. The DNA G+C content of the strain was 65 mol%. On the basis of phylogenetic inference, and physiological and chemotaxonomic data, it is proposed that strain CAU 1121T represents a novel genus and novel species in the family Rhodospirillaceae, for which the name Limibacillus halophilus gen. nov., sp. nov. is suggested. The type strain is CAU 1121T ( = KCTC 42420T = CECT 8803T = NBRC 110928T).

Polycyclic aromatic hydrocarbons in deep sea sediments: Microbe-pollutant interactions in a remote environment

Recalcitrant polycyclic aromatic hydrocarbons (PAHs) released into seawater end up in the deep sea sediments (DSSs). However, their fate here is often oversimplified by theoretical models. Biodegradation of PAHs in DSSs, is assumed to be similar to biodegradation in surface habitats, despite high hydrostatic pressures and low temperatures that should significantly limit PAH biodegradation. Bacteria residing in the DSSs (related mainly to α- and γ-Proteobacteria) have been shown to or predicted to possess distinct genes, enzymes and metabolic pathways, indicating an adaptation of these bacterial communities to the psychro-peizophilic conditions of the DSSs. This work summarizes some of the most recent research on DSS hydrocarbonoclastic populations and mechanisms of PAH degradation and discusses the challenges posed by future high CO2 and UV climate scenarios on biodegradation of PAHs in DSSs.

The diversity of PAH-degrading bacteria in a deep-sea water column above the Southwest Indian Ridge

The bacteria involved in organic pollutant degradation in pelagic deep-sea environments are largely unknown. In this report, the diversity of polycyclic aromatic hydrocarbon (PAH)-degrading bacteria was analyzed in deep-sea water on the Southwest Indian Ridge (SWIR). After enrichment with a PAH mixture (phenanthrene, anthracene, fluoranthene, and pyrene), nine bacterial consortia were obtained from depths of 3946–4746 m. While the consortia degraded all four PAHs when supplied in a mixture, when PAHs were tested individually, only phenanthrene supported growth. Thus, degradation of the PAH mixture reflected a cometabolism of anthracene, fluoranthene, and pyrene with phenanthrene. Further, both culture-dependent and independent methods revealed many new bacteria involved in PAH degradation. Specifically, the alpha and gamma subclasses of Proteobacteria were confirmed as the major groups within the communities. Additionally, Actinobacteria, the CFB group and Firmicutes were detected. Denaturing Gradient Gel Electrophoresis (DGGE) analysis showed that bacteria closely affiliated with Alcanivorax, Novosphingobium, and Rhodovulum occurred most frequently in different PAH-degrading consortia. By using general heterotrophic media, 51 bacteria were isolated from the consortia and of these 34 grew with the PAH mixture as a sole carbon source. Of these, isolates most closely related to Alterierythrobacter, Citricella, Erythrobacter, Idiomarina, Lutibacterium, Maricaulis, Marinobacter, Martelella, Pseudidiomarina, Rhodobacter, Roseovarius, Salipiger, Sphingopyxis, and Stappia were found to be PAH degraders. To the best of our knowledge, this is the first time these bacteria have been identified in this context. In summary, this report revealed significant diversity among the PAH-degrading bacteria in the deep-sea water column. These bacteria may play a role in PAH removal in deep-sea environments.

Tamlana nanhaiensis sp. nov., isolated from surface seawater collected from the South China Sea

A polyphasic taxonomic study was performed on a strain, designated FHC16(T), which was isolated from surface seawater collected from the South China Sea. Cells of strain FHC16(T) are Gram stain-negative, oxidase- and catalase-positive and non-motile rods. Growth was observed at 15-37 °C (optimum, 25-30 °C), at pH 6.0-9.0 (optimum, pH 7.0) and in the presence of 0-5 % (w/v) NaCl (optimum, 3%). 16S rRNA gene sequence analysis showed that strain FHC16(T) is most closely related to Tamlana sedimentorum JCM 19808(T) (98.2% sequence similarity). The ANI value between strain FHC16(T) and T. sedimentorum JCM 19808(T) was found to be 81.82-81.81%. The DNA-DNA hybridization estimated value between strain FHC16(T) and T. sedimentorum JCM 19808(T) was determined to be 25.8 ± 2.41%. The principal fatty acids (>5% of the total) were found to be iso-C(15:0), iso G-C(15:1), iso-C(17:0) 3-OH, iso-C(15:0) 3-OH and summed feature 3 (comprising C(16:1)ω7c/C(16:1)ω6c). The strain was found to have MK-6 as the major respiratory menaquinone, which is consistent with the other three recognized Tamlana species, T. sedimentorum, Tamlana crocina and Tamlana agarivorans. The polar lipids were found to comprise phosphatidylethanolamine, one unidentified aminophospholipid, two unidentified aminolipids and seven unidentified lipids. The G+C content of the chromosomal DNA was determined to be 34.2 mol%. On the basis of phenotypic, chemotaxonomic and molecular data, strain FHC16(T) is considered to represent a novel species of the genus Tamlana, for which the name Tamlana nanhaiensis sp. nov. is proposed. The type strain is FHC16(T) (.LMG 27420(T) = CGMCC 1.12469(T) = MCCC 1A06648(T)).

Emcibacter nanhaiensis gen. nov. sp. nov., isolated from sediment of the South China Sea

A new aerobic, Gram stain-negative, oxidase- and catalase- positive, ovoid or rod-shaped bacterial strain, designated HTCJW17(T), was isolated from a sediment collected from the South China Sea and subjected to a polyphasic taxonomic characterization. The isolate forms small, creamy-white, opaque and circular colonies on agar plates. Growth occurs between 15 and 45 °C, 1-7 % (w/v) NaCl and pH 6-9. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain HTCJW17(T) belongs to the family Kordiimonadaceae of the order Kordiimonadales, with highest sequence similarity to Kordiimonas gwangyangensis GW14-5(T) (91.1 %). The major fatty acids were identified to be summed feature 8 (C18:1 ω7c/ω6c; 56.6 %), C14:0 (8.5 %), C14:0 2-OH (8.4 %), summed feature 3 (C16:1 ω7c/C16:1 ω6c; 6.2 %), and C16:0 (5.2 %). The polar lipids were determined to be phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, six unidentified glycolipids and two unidentified phospholipids. The respiratory quinone was identified as ubiquinone Q-10. The genomic DNA G+C content was determined to be 56.3 mol%. On the basis of genotypic, chemotaxonomic and phenotypic distinctness, we propose a novel genus, Emcibacter gen. nov., with Emcibacter nanhaiensis sp. nov. as the type species. The type strain is HTCJW17(T) (=CGMCC 1.12471(T) = LMG 27419(T) = MCCC 1A06723(T)).

Celeribacter indicus sp. nov., a polycyclic aromatic hydrocarbon-degrading bacterium from deep-sea sediment and reclassification of Huaishuia halophila as Celeribacter halophilus comb. nov

A taxonomic study was carried out on strain P73T, which was isolated from deep-sea sediment of the Indian Ocean by enrichment of polycyclic aromatic hydrocarbons. The strain was able to degrade biphenyl, naphthalene, 2-methylnaphthalene, 2,6-dimethylnaphthalene, acenaphthene, anthracene, phenanthrene, dibenzothiophene, dibenzofuran, fluorene, 4-methyldibenzothiophene and fluoranthene, but not pyrene or chrysene. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain P73T formed a clade with the genera Celeribacter and Huaishuia within the family Rhodobacteraceae , with highest sequence similarity of 96.98 % to Celeribacter neptunius H 14T, followed by Huaishuia halophila ZXM137T (96.42 %). The bacterium was Gram-stain-negative, oxidase- and catalase-positive, rod-shaped and non-motile. Growth was observed at salinities from 0.5 to 12 % and at temperatures from 10 to 41 °C. The principal fatty acids (>10 %) of strain P73T were summed feature 8 (C18 : 1ω7c/ω6c) and C19 : 0ω8c cyclo. The sole respiratory quinone was Q-10. The major lipids were phosphatidylglycerol, one unknown aminolipid, one unknown phospholipid and one unknown lipid; a second unknown phospholipid and one unknown glycolipid were present as minor components. The G+C content of the chromosomal DNA was 66.0 mol%. The combined genotypic and phenotypic data show that strain P73T represents a novel species of the genus Celeribacter , for which the name Celeribacter indicus sp. nov. is proposed. The type strain is P73T ( = MCCC 1A01112T = LMG 27600T = DSM 27257T). Phylogenetic study and existing phenotypic information also show that Huaishuia halophila should be transferred to the genus Celeribacter as Celeribacter halophilus comb. nov. (type strain ZXM137T = MCCC 1A06432T = CGMCC 1.8891T = LMG 24854T).

Thioclava indica sp. nov., isolated from surface seawater of the Indian Ocean

A short-rod shaped, non-motile and Gram-negative strain, designated as DT23-4(T), was isolated from a dotriacontane-degrading bacterial consortium, enriched in the surface seawater of the Indian Ocean. To delineate its taxonomic position, strain DT23-4(T) was subjected to polyphasic characterization. Strain DT23-4(T) can grow at temperatures from 10 to 41 °C, in the range of pH 6-10 and at salinities from 0 to 18 % (w/v). It is positive for denitrification, oxidase and catalase, but negative for gelatin hydrolysis and indole production. Phylogenetic analysis based on the 16S rRNA gene sequences indicated that strain DT23-4(T) affiliates to the genus Thioclava, sharing high sequence similarity to Thioclava dalianensis DLFJ1-1(T) (98.2 %), Thioclava atlantica 13D2W-2(T) (96.8 %), Thioclava pacifica TL 2(T) (95.9 %) and less than 95.7 % with other species of the family Rhodobacteraceae. The digital DNA:DNA hybridization (dDDH) pairwise values between strain DT23-4(T) and T. dalianensis DLFJ1-1(T), T. atlantica 13D2W-2(T) and T. pacifica TL 2(T) were 21.5 ± 2.3, 20.6 ± 2.3 and 20.9 ± 2.3 %, respectively. Similarly, the average nucleotide identity values between strain DT23-4(T) and these three type strains were 78.0, 77.1 and 77.3 %, respectively. The principal fatty acid was identified as Summed Feature 8 (C18:1 ω7c/ω6c) (81.9 %). The quinone of strain DT23-4(T) was identified as Q10 (100 %). The polar lipids of strain DT23-4(T) were found to contain phosphatidylethanolamine, phosphatidylglycerol, two glycolipids and four phospholipids. The genomic DNA G+C content was determined to be 60.3 mol%. On the basis of genotypic, phenotypic and chemotaxonomic analyses, strain DT23-4(T) can be concluded to represent a novel species of the genus Thioclava, for which the name Thioclava indica sp. nov. is proposed, with the type strain DT23-4(T) (= MCCC 1A00513(T) = LMG 27698(T) = KCTC 33533(T)).

Sulfitobacter pseudonitzschiae sp. nov., isolated from the toxic marine diatom Pseudo-nitzschia multiseries

A taxonomic study was carried out on bacterial strain H3(T), which was isolated from the toxic marine diatom Pseudo-nitzschia multiseries. Cells of strain H3(T) were Gram-stain-negative, rod-shaped, non-motile and capable of reducing nitrate to nitrite, but not denitrification. Growth was observed at NaCl concentrations of 1-9%, pH 6-12 and 10-37 °C. It was unable to degrade aesculin or gelatin. The dominant fatty acids (>10 %) were C18:1ω7c/ω6c (summed feature 8) and C16:0. The respiratory ubiquinone was Q10. The major lipids were phosphatidylethanolamine, phosphatidylglycerol, an aminolipid and one unknown lipid, and the minor lipids were two phospholipids and three unknown lipids. The G+C content of the chromosomal DNA was 61.7 mol%. 16S rRNA gene sequence comparison showed that strain H3(T) was related most closely to Sulfitobacter donghicola DSW-25(T) (97.3% similarity) and levels of similarity with other species of the genus Sulfitobacter were 95.1-96.9%. The mean (± sd) DNA-DNA hybridization value between strain H3(T) and Sulfitobacter donghicola DSW-25(T) was 18.0 ± 2.25%. The average nucleotide identity between strain H3(T) and Sulfitobacter donghicola DSW-25(T) was 70.45%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain H3(T) formed a separate clade close to the genus Sulfitobacter and was distinguishable from phylogenetically related species by differences in several phenotypic properties. On the basis of the phenotypic and phylogenetic data, strain H3(T) represents a novel species of the genus Sulfitobacter, for which the name Sulfitobacter pseudonitzschiae is proposed (type strain H3(T) =DSM 26824(T) =MCCC 1A00686(T)).

Lacibacterium aquatile gen. nov., sp. nov., a new member of the family Rhodospirillaceae isolated from a freshwater lake

A bacterial strain designated LTC-2T was isolated from a freshwater lake in Taiwan and characterized using a polyphasic taxonomic approach. Cells of strain LTC-2T were Gram-reaction-negative, facultatively anaerobic, poly-β-hydroxybutyrate-accumulating, motile by means of a monopolar flagellum, non-spore-forming, slightly curved rods surrounded by a thick capsule and formed creamy white colonies. Growth occurred at 10–37 °C (optimum, 20–30 °C), at pH 6.0–9.0 (optimum, pH 7.0–8.0) and with 0–1.0 % NaCl (optimum, 0 %). The predominant fatty acids were C18 : 1ω7c, summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0. The major isoprenoid quinone was Q-10 and the DNA G+C content was 58.5 mol%. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylmonomethylethanolamine, phosphatidyldimethylethanolamine, two uncharacterized phospholipids and two uncharacterized aminophospholipids. The major polyamines were putrescine, homospermidine and spermidine. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain LTC-2T forms a distinct lineage with respect to closely related genera in the family Rhodospirillaceae , most closely related to the genera Elstera and Dongia , and the levels of 16S rRNA gene sequence similarity with respect to the type species of related genera were less than 94 %. On the basis of the genotypic and phenotypic data, strain LTC-2T represents a novel genus and species of the family Rhodospirillaceae , for which the name Lacibacterium aquatile gen. nov., sp. nov. is proposed. The type strain is LTC-2T ( = BCRC 80445T = LMG 26999T = KCTC 32017T).

Taonella mepensis gen. nov., sp. nov., a member of the family Rhodospirillaceae isolated from activated sludge

A novel Gram-negative, non-spore-forming, rod-shaped strain, H1T, was isolated from activated sludge by micromanipulation. No close relatives among cultured bacterial isolates were found; phylogenetic analysis based on 16S rRNA gene sequences revealed that strain H1T forms a deep single branch in the family Rhodospirillaceae . Cells of strain H1T were slightly curved to straight rods (1.2–1.4×1.5–1.7 µm) and motile by a single polar flagellum. Strain H1T was able to grow in the presence of 0–4 % NaCl and grew optimally at 37 °C and pH 6.0–7.0. Chemotaxonomic analysis revealed that strain H1T possessed Q-10 as the predominant ubiquinone and C18 : 1ω7c, C16 : 0 and C19 : 0 cyclo ω8c as the major fatty acids. The DNA G+C content of strain H1T was 65.1 mol%. Comparative analysis of 16S rRNA gene sequences, and phenotypic and chemotaxonomic data, indicate that strain H1T should represent a novel genus and species of the family Rhodospirillaceae . The name Taonella mepensis gen. nov., sp. nov. is proposed. The type strain of Taonella mepensis is H1T ( = CICC 10529T  = CCTCC AB 2012861T  = KACC 16940T).

Parvularcula dongshanensis sp. nov., isolated from soft coral

A taxonomic study was carried out on strain SH25T, which was isolated from soft coral collected from Dongshan Island, China. The isolate was a heterotrophic organism to the soft coral, and was a Gram-reaction-negative, short rod that was motile by a polar flagellum. Growth was observed at salinities from 0 to 12 % and at temperatures from 10 to 41 °C. It was unable to reduce nitrate to nitrite. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain SH25T belonged to the genus Parvularcula , with highest sequence similarity to Parvularcula lutaonensis CC-MMS-1T (96.1 %) and Parvularcula bermudensis HTCC2503T (94.3 %); 16S rRNA gene sequence similarities to other taxa were below 90.0 %. The dominant fatty acids were C16 : 0 and summed feature 8 (C18 : 1ω7c/ω6c,). The G+C content of the chromosomal DNA was 61.8 mol%. The major quinone was Q10. These combined genotypic and phenotypic data show that strain SH25T represents a novel species of the genus Parvularcula , for which the name Parvularcula dongshanensis sp. nov. is proposed. The type strain is SH25T ( = CCTCC AB 2010355T = LMG 26158T = MCCC 1A06534T).

Genome sequence of Oceanibaculum indicum type strain P24

Oceanibaculum indicum type strain P24 was isolated from a polycyclic-aromatic-hydrocarbon-degrading consortium enriched from a deep-seawater sample collected from the Indian Ocean. Here we present the draft genome of strain P24(T), which contains 3,952,792 bp with a G+C content of 65.5% and contains 3,755 protein-coding genes and 45 tRNAs.

Thioclava dalianensis sp. nov., isolated from surface seawater

A taxonomic study was carried out on strain DLFJ1-1(T), which was isolated from an oil-degrading bacterial consortium, enriched by the surface seawater from around the Dalian Peninsula. The isolate was Gram-reaction-negative, oxidase- and catalase-positive, short-rod-shaped and non-motile. Growth was observed at salinities from 0.5 to 15 % and at temperatures from 4 to 37 °C; the strain was unable to degrade gelatin or to reduce nitrate. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain DLFJ1-1(T) belonged to the genus Thioclava, with the highest sequence similarity (96.4 %) to Thioclava pacifica TL 2(T), while the similarities to other species examined were all below 95.0 %. The principal fatty acids were C19 : 0ω8c cyclo and summed feature 8 (C18 : 1ω7c/ω6c). The major quinone of strain DLFJ1-1(T) was Q10. The major polar lipids of strain DLFJ1-1(T) were phosphatidylethanolamine and phosphatidylglycerol. The G+C content of the chromosomal DNA was 62.5 mol%. The combined genotypic and phenotypic data show that strain DLFJ1-1(T) represents a novel species of the genus Thioclava, for which the name Thioclava dalianensis sp. nov. is proposed, with the type strain DLFJ1-1(T) ( = CGMCC 1.12325(T) = LMG 27290(T) = MCCC 1A03957(T)). An emended description of the genus Thioclava is also proposed.

Limimonas halophila gen. nov., sp. nov., an extremely halophilic bacterium in the family Rhodospirillaceae

A novel, Gram-staining-negative, non-pigmented, rod-shaped, strictly aerobic, extremely halophilic bacterium, designated strain IA16(T), was isolated from the mud of the hypersaline Lake Aran-Bidgol, in Iran. Cells of strain IA16(T) were not motile. Growth occurred with 2.5-5.2 M NaCl (optimum 3.4 M), at pH 6.0-8.0 (optimum pH 7.0) and at 30-50 °C (optimum 40 °C). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain IA16(T) belonged in the family Rhodospirillaceae and that its closest relatives were Rhodovibrio sodomensis DSM 9895(T) (91.6 % sequence similarity), Rhodovibrio salinarum NCIMB 2243(T) (91.2 %), Pelagibius litoralis CL-UU02(T) (88.9 %) and Fodinicurvata sediminis YIM D82(T) (88.7 %). The novel strain's major cellular fatty acids were C19 : 0 cyclo ω7c and C18 : 0 and its polar lipid profile comprised phosphatidylglycerol, diphosphatidylglycerol, four unidentified phospholipids, three unidentified aminolipids and two other unidentified lipids. The cells of strain IA16(T) contained the ubiquinone Q-10. The G+C content of the novel strain's genomic DNA was 67.0 mol%. The physiological, biochemical and phylogenetic differences between strain IA16(T) and other previously described taxa indicate that the strain represents a novel species in a new genus within the family Rhodospirillaceae, for which the name Limimonas halophila gen. nov., sp. nov. is proposed. The type strain of Limimonas halophila is IA16(T) ( = IBRC-M 10018(T)  = DSM 25584(T)).

Galbibacter marinus sp. nov., isolated from deep-sea sediment

A taxonomic study was carried out on a novel bacterium, designated strain ck-I2-15(T), which was isolated from deep-sea sediment collected from the South-west Indian Ocean Ridge. Cells of strain ck-I2-15(T) were Gram-reaction-negative, rod-shaped, non-motile, moderately halophilic and capable of denitrification. Growth was observed with 0-9 % (w/v) NaCl and at temperatures of 10-37 °C. The novel strain was unable to degrade gelatin. The dominant cellular fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 9 (iso-C17 : 1ω9c and/or 10-methyl C16 : 0). The major respiratory quinone was MK6 and the polar lipid profile comprised phosphatidylethanolamine, one unidentified phospholipid, two unidentified aminolipids, one unidentified glycolipid and four other unidentified lipids. The G+C content of the genomic DNA was 38 mol%. 16S rRNA gene sequence comparison indicated that strain ck-I2-15(T) was most closely related to Galbibacter mesophilus Mok-17(T) (92.9 % sequence similarity), followed by 'Joostella atrarenae' M1-2 (92.8 %), Joostella marina En5(T) (92.7 %) and Zhouia amylolytica HN-171(T) (91.6 %). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain ck-I2-15(T) formed a clade with the genus Galbibacter, within the family Flavobacteriaceae. Several phenotypic properties allowed strain ck-I2-15(T) to be distinguished from its closest phylogenetic relatives. On the basis of the phenotypic and phylogenetic data, strain ck-I2-15(T) represents a novel species of the genus Galbibacter, for which the name Galbibacter marinus is proposed. The type strain is ck-I2-15(T) ( = CCTCC AB 209062(T) = LMG 25228(T) = MCCC 1A03044(T)).

Skermanella stibiiresistens sp. nov., a highly antimony-resistant bacterium isolated from coal-mining soil, and emended description of the genus Skermanella

A Gram-negative, aerobic, motile, rod-shaped, antimony-resistant bacterium, designated strain SB22T, was isolated from soil of Jixi coal mine, China. The major cellular fatty acids (>5 %) were C18 : 1ω7c (63.5 %), summed feature 2 (C14 : 0 3-OH and/or iso-C16 : 1 I, 10.8 %) and C16 : 0 (9.9 %). The major polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and an unknown aminolipid. The genomic DNA G+C content was 69.6 mol% and Q-10 was the major respiratory quinone. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain SB22T was most closely related to Skermanella aerolata 5416T-32T (97.3 %), Skermanella parooensis ACM 2042T (95.8 %) and Skermanella xinjiangensis 10-1-101T (92.9 %). The DNA–DNA hybridization value between strain SB22T and S. aerolata KACC 11604T ( = 5416T-32T) was 43.3 %. On the basis of phenotypic, chemotaxonomic and phylogenetic characteristics of strain SB22T and related species, it is considered that the isolate represents a novel species of the genus Skermanella , for which the name Skermanella stibiiresistens sp. nov. is proposed. The type strain is SB22T ( = CGMCC 1.10751T = KCTC 23364T). An emended description of the genus Skermanella is provided.

Genus Enhydrobacter Staley et al. 1987 should be recognized as a member of the family Rhodospirillaceae within the class Alphaproteobacteria

The genus Enhydrobacter, first reported as a member of the family Vibrionaceae, has been placed in the family Moraxellaceae, but as a genus incertae sedis in Bergey's Manual of Systematic Bacteriology 2nd edition. During our taxonomic investigation of Enhydrobacter-like organisms, we observed that the 16S rRNA sequences of E. aerosaccus-type strain versions NCIMB 12535(T) , ATCC 27094( T) and CCUG 58314(T) were very different from the accessible data (accession no. AJ550856). Phylogenetic analysis of our 16S rRNA sequence data revealed that these organisms were located within the family Rhodospirillaceae. The genera Inquilinus, Oceanibaculum, Skermanella and Nisaea were closely related (sequence similarities were 88.3~87.0%), but Enhydrobacter could be distinguished from these genera by growth characteristics, fatty acid profiles (C(19:0) cyclo ω8c; 38.4% C(18:1) ω7c; 32.2%, and C(16:0) ; 8.9% were major components), in being non-flagellated, and differing in enzymatic activities, including trypsin and β-glucosidase. From these data, we conclude that the genus Enhydrobacter should be recognized as an independent genus of the family Rhodospirillaceae within the class Alphaproteobacteria.

Draft genome sequence of strain HIMB100, a cultured representative of the SAR116 clade of marine Alphaproteobacteria

Strain HIMB100 is a planktonic marine bacterium in the class Alphaproteobacteria. This strain is of interest because it is one of the first known isolates from a globally ubiquitous clade of marine bacteria known as SAR116 within the family Rhodospirillaceae. Here we describe preliminary features of the organism, together with the draft genome sequence and annotation. This is the second genome sequence of a member of the SAR116 clade. The 2,458,945 bp genome contains 2,334 protein-coding and 42 RNA genes.

Desertibacter roseus gen. nov., sp. nov., a gamma radiation-resistant bacterium in the family Rhodospirillaceae, isolated from desert sand

A Gram-negative, rod-shaped, strictly aerobic bacterium, strain 2622T, was isolated from gamma-irradiated soil sampled from the Taklimakan desert in Xinjiang, China. Phylogenetic analyses showed that strain 2622T formed a distinct lineage in the family Rhodospirillaceae and shared 91.7 and 90.1 % 16S rRNA gene sequence similarity with its closest relatives, the type strains of Skermanella xinjiangensis and Skermanella aerolata, respectively. The DNA G+C content of strain 2622T was 71.4 mol% and the isoprenoid quinone was ubiquinone Q-10. Based on phenotypic and chemotaxonomic data and phylogenetic analysis, strain 2622T is considered to represent a novel species of a new genus in the family Rhodospirillaceae, for which the name Desertibacter roseus gen. nov., sp. nov. is proposed. The type strain of Desertibacter roseus is strain 2622T ( = CCTCC AB 208152T  = KCTC 22436T).

Parvibaculum indicum sp. nov., isolated from deep-sea water

A taxonomic study was carried out on strain P31T, which was isolated from a polycyclic aromatic hydrocarbon (PAH)-degrading consortium enriched with deep-sea water of the Indian Ocean. The isolate was Gram-reaction-negative, rod-shaped, motile by means of a polar flagellum and incapable of reducing nitrate to nitrite. Growth was observed at 0.5–8 % NaCl and at 10–41 °C. Strain P31T was unable to degrade Tween 80 or gelatin. The major respiratory quinone was ubiquinone 11 (Q-11). The dominant fatty acids were C18 : 1 ω7c (39.79 %), 11-methyl C18 : 1 ω7c (17.84 %), C19 : 0 cyclo ω8c (12.05 %) and C18 : 0 (6.09 %). The G+C content of the chromosomal DNA was 62.1 mol%. A phylogenetic tree based on 16S rRNA gene sequence analysis showed that strain P31T and Parvibaculum lavamentivorans DS-1T formed a distinct lineage in the family Phyllobacteriaceae; these two strains showed 95.7 % sequence similarity, while similarities between P31T and other members of the genus Parvibaculum were below 93 %. Based on the genotypic and phenotypic data, strain P31T represents a novel species of the genus Parvibaculum, for which the name Parvibaculum indicum sp. nov. is proposed. The type strain is P31T (=CCTCC AB 208230T =LMG 24712T =MCCC 1A01132T).

Dongia mobilis gen. nov., sp. nov., a new member of the family Rhodospirillaceae isolated from a sequencing batch reactor for treatment of malachite green effluent

A Gram-negative, strictly aerobic and heterotrophic, non-spore-forming bacterial strain, designated LM22T, was isolated from activated sludge of a sequencing batch reactor for the treatment of malachite green effluent. Cells of strain LM22T were slightly curved to straight rods (0.3–0.5×0.6–1.0 μm) and motile by a single polar flagellum. Strain LM22T was negative for oxidase and catalase activities and phototrophic growth. An internal membrane system and bacteriochlorophyll a were absent. Growth occurred at 20–40 °C (optimum 30–35 °C) and pH 6.0–10.0 (optimum pH 7.0–7.5). Strain LM22T did not require NaCl for growth and tolerated up to 2.0 % NaCl (optimum 0.5 %). The major ubiquinone was Q-10. The major fatty acids (>10 % of the total) were C18 : 1 ω7c (32.9 %), C19 : 0 cyclo ω8c (18.7 %), C16 : 0 (12.1 %) and C16 : 0 2-OH (10.5 %). Phylogenetic analysis of 16S rRNA gene sequences showed that Inquilinus limosus AU0476T was the closest relative (90.4 % 16S rRNA gene sequence similarity). The DNA G+C content was 65.6 mol%. On basis of phenotypic, chemotaxonomic and phylogenetic data, strain LM22T was considered to represent a novel genus and species of the family Rhodospirillaceae, for which the name Dongia mobilis gen. nov., sp. nov. is proposed. The type strain of Dongia mobilis is LM22T (=CGMCC 1.7660T =JCM 15798T).

Microbial diversity in Tunisian geothermal springs as detected by molecular and culture-based approaches

Prokaryotic diversities of 12 geothermal hot springs located in Northern, Central and Southern Tunisia were investigated by culture-based and molecular approaches. Enrichment cultures for both aerobic and anaerobic microorganisms were successfully obtained at temperatures ranging from 50 to 75°C. Fourteen strains including four novel species were cultivated and assigned to the phyla Firmicutes (9), Thermotogae (2), Betaproteobacteria (1), Synergistetes (1) and Bacteroidetes (1). Archaeal or universal oligonucleotide primer sets were used to generate 16S rRNA gene libraries. Representative groups included Proteobacteria, Firmicutes, Deinococcus-Thermus, Thermotogae, Synergistetes, Bacteroidetes, Aquificae, Chloroflexi, candidate division OP9 in addition to other yet unclassified strains. The archaeal library showed a low diversity of clone sequences belonging to the phyla Euryarchaeota and Crenarchaeota. Furthermore, we confirmed the occurrence of sulfate reducers and methanogens by amplification and sequencing of dissimilatory sulfite reductase (dsrAB) and methyl coenzyme M reductase α-subunit (mcrA) genes. Altogether, we discuss the diverse prokaryotic communities arising from the 12 geothermal hot springs studied and relate these findings to the physico-chemical features of the hot springs.

Ruegeria pelagia is a later heterotypic synonym of Ruegeria mobilis

The 16S rRNA genes of Ruegeria pelagia NBRC 102038T and Ruegeria mobilis NBRC 101030T were resequenced and the results confirmed that they differ by only one base in their almost full-length sequences (1425 nt). The gyrB gene sequence similarity between the two strains was also high (97.7 %). The outcome of API 20NE, API ZYM and antibiotic susceptibility tests showed that the two strains show only one difference, in β-galactosidase activity, in API tests and five differences in susceptibility among 30 tested antibiotics. In addition, similar BOX-PCR fingerprints were obtained and the DNA–DNA relatedness between the two strains was 91±4 %. On the basis of these results, it is concluded that Ruegeria pelagia Lee et al. 2007 is a later heterotypic synonym of Ruegeria mobilis Muramatsu et al. 2007.

Stappia indica sp. nov., isolated from deep seawater of the Indian Ocean

A taxonomic study was carried out on strain B106T, which was isolated from a polycyclic aromatic hydrocarbon-degrading consortium, enriched with deep seawater from the Indian Ocean. The isolate was Gram-negative, oxidase- and catalase-positive, rod-shaped and motile by means of one polar flagellum. Growth was observed at salinities of 0.5–11 % and at temperatures of 4–42 °C, and the strain was capable of nitrate reduction, but was unable to degrade Tween 80 or gelatin. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain B106T belonged to the genus Stappia, with a highest sequence similarity of 97.7 % to Stappia stellulata IAM 12621T; similarity to other strains was below 95.2 %. DNA–DNA hybridization between strain B106T and S. stellulata IAM 12621T was 43 %. The major fatty acids were C16 : 0 (6.10 %), C18 : 1 ω7c (62.58 %), C18 : 0 (5.17 %), C18 : 1 ω7c 11-methyl (14.48 %) and C19 : 0 ω8c cyclo (4.70 %). The G+C content of the chromosomal DNA was 65.9 mol%. The combined genotypic and phenotypic data showed that strain B106T represents a novel species of the genus Stappia, for which the name Stappia indica sp. nov. is proposed, with the type strain B106T (=PR56-8T=CCTCC AB 208228T=LMG 24625T=MCCC 1A01226T).

Oceanibaculum pacificum sp. nov., isolated from hydrothermal field sediment of the south-west Pacific Ocean

A taxonomic study was carried out on strain LMC2up-L3T, which was isolated from a polycyclic aromatic hydrocarbon-degrading consortium enriched with a sediment sample collected from a hydrothermal field of the south-west Pacific Ocean. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain LMC2up-L3T belonged to the genus Oceanibaculum, with the highest sequence similarity of 98.4 % to Oceanibaculum indicum P24T; similarity to other strains was below 93.1 %. DNA–DNA hybridization between strain LMC2up-L3T and O. indicum P24T was 31 %. rep-PCR fingerprints also differentiated strain LMC2up-L3T from O. indicum P24T. The G+C content of the chromosomal DNA was 67.7 mol%. The principal fatty acids were C16 : 1 (17.8 %), C16 : 0 (21.2 %), C18 : 1 ω7c (23.6 %), C18 : 0 (4.1 %), C18 : 1 2-OH (4.5 %) and C19 : 0 cyclo ω8c (17.4 %). The combined genotypic and phenotypic data show that strain LMC2up-L3T represents a novel species of the genus Oceanibaculum, for which the name Oceanibaculum pacificum sp. nov. is proposed, with the type strain LMC2up-L3T (=CCTCC AB 209059T =LMG 24859T =MCCC 1A02656T). An emended description of the genus Oceanibaculum is also provided.