Roseomonas deserti sp. nov., isolated from crude oil contaminated desert sand

Sabulicella glaciei sp. nov., Isolated from Glacier, and Reclassification of Roseomonas rubea, Roseomonas ponticola and Roseomonas oleicola as Neoroseomonas rubea comb. nov., Falsiroseomonas ponticola comb. nov. and Falsiroseomonas oleicola comb. nov

A Gram-stain-negative, short rod-shaped strain, MDT2-1-1T, was isolated from cryoconite samples collected from the Midui glacier in Tibet, China. It grew aerobically from 7 to 40 °C, within a pH range of 6.0-10.0, and in NaCl concentration of 0 to 1.0% (w/v). The pairwise 16S rRNA gene sequence similarity, average nucleotide identity and digital DNA-DNA hybridization values between strains MDT2-1-1T and Sabulicella rubraurantiaca SYSU D01096T were 99.4%, 89.7% and 38.9%, respectively. Considering the results from phylogeny, phenotypic and genotypic data, strain MDT2-1-1T (=CGMCC 1.11170T = NBRC 110485T) was suggested to represent a novel species of the genus Sabulicella, for which the name Sabulicella glaciei sp. nov. is proposed. Furthermore, based on the phylogenomic analysis, it is recommended that Roseomonas rubea, Roseomonas ponticola and Roseomonas oleicola be reclassified as Neoroseomonas rubea comb. nov., Falsiroseomonas ponticola comb. nov. and Falsiroseomonas oleicola comb. nov., respectively. Considering the illegitimate status of the genera names Pararoseomonas and Pseudoroseomonas, the species within the genera Pararoseomonas and Pseudoroseomonas should be transferred to Muricoccus and Teichococcus, respectively. Therefore, we proposed the following new combinations: Muricoccus aeriglobus comb. nov., Muricoccus aerilatus comb. nov., Muricoccus harenae comb. nov., Muricoccus nepalensis comb. nov., Muricoccus pecuniae comb. nov., Muricoccus radiodurans comb. nov., Muricoccus vinaceus comb. nov., Teichococcus aerofrigidensis comb. nov., Teichococcus aerophilus comb. nov., Teichococcus aestuarii comb. nov., Teichococcus cervicalis comb. nov., Teichococcus coralli comb. nov., Teichococcus deserti comb. nov., Teichococcus globiformis comb. nov., Teichococcus hibiscisoli comb. nov., Teichococcus musae comb. nov., Teichococcus oryzae comb. nov., Teichococcus rhizosphaerae comb. nov., Teichococcus ruber comb. nov., Teichococcus suffuscus comb. nov., Teichococcus vastitatis comb. nov., and Teichococcus wenyumeiae comb. nov.

Paixão S, S. Fernandes A, C. Roseiro J, Alves L. New Insights on Carotenoid Production by Gordonia alkanivorans Strain 1B

Gordonia alkanivorans strain 1B is a desulfurizing bacterium and a hyper-pigment producer. Most carotenoid optimization studies have been performed with light, but little is still known on how carbon/sulfur-source concentrations influence carotenoid production under darkness. In this work, a surface response methodology based on a two-factor Doehlert distribution (% glucose in a glucose/fructose 10 g/L mixture; sulfate concentration) was used to study carotenoid and biomass production without light. These responses were then compared to those previously obtained under light. Moreover, carbon consumption was also monitored, and different metabolic parameters were further calculated. The results indicate that both light and glucose promote slower growth rates, but stimulate carotenoid production and carbon conversion to carotenoids and biomass. Fructose induces higher growth rates, and greater biomass production at 72 h; however, its presence seems to inhibit carotenoid production. Moreover, although at a much lower yield than under light, results demonstrate that under darkness the highest carotenoid production can be achieved with 100% glucose (10 g/L), ≥27 mg/L sulfate, and high growth time (>216 h). These results give a novel insight into the metabolism of strain 1B, highlighting the importance of culture conditions optimization to increase the process efficiency for carotenoid and/or biomass production.

Phylotaxogenomics for the Reappraisal of the Genus Roseomonas With the Creation of Six New Genera

The genus Roseomonas is a significant group of bacteria which is invariably of great clinical and ecological importance. Previous studies have shown that the genus Roseomonas is polyphyletic in nature. Our present study focused on generating a lucid understanding of the phylogenetic framework for the re-evaluation and reclassification of the genus Roseomonas. Phylogenetic studies based on the 16S rRNA gene and 92 concatenated genes suggested that the genus is heterogeneous, forming seven major groups. Existing Roseomonas species were subjected to an array of genomic, phenotypic, and chemotaxonomic analyses in order to resolve the heterogeneity. Genomic similarity indices (dDDH and ANI) indicated that the members were well-defined at the species level. The Percentage of Conserved Proteins (POCP) and the average Amino Acid Identity (AAI) values between the groups of the genus Roseomonas and other interspersing members of the family Acetobacteraceae were below 65 and 70%, respectively. The pan-genome evaluation depicted that the pan-genome was an open type and the members shared 958 core genes. This claim of reclassification was equally supported by the phenotypic and chemotaxonomic differences between the groups. Thus, in this study, we propose to re-evaluate and reclassify the genus Roseomonas and propose six novel genera as Pararoseomonas gen. nov., Falsiroseomonas gen. nov., Paeniroseomonas gen. nov., Plastoroseomonas gen. nov., Neoroseomonas gen. nov., and Pseudoroseomonas gen. nov.

Corksorb Enhances Alkane Degradation by Hydrocarbonoclastic Bacteria

Biosorbent materials are effective in the removal of spilled oil from water, but their effect on hydrocarbonoclastic bacteria is not known. Here, we show that corksorb, a cork-based biosorbent, enhances growth and alkane degradation by Rhodococcus opacus B4 (Ro) and Alcanivorax borkumensis SK2 (Ab). Ro and Ab degraded 96 ± 1% and 72 ± 2%, respectively, of a mixture of n-alkanes (2 g L-1) in the presence of corksorb. These values represent an increase of 6 and 24%, respectively, relative to the assays without corksorb. The biosorbent also increased the growth of Ab by 51%. However, no significant changes were detected in the expression of genes involved in alkane uptake and degradation in the presence of corksorb relative to the control without the biosorbent. Nevertheless, transcriptomics analysis revealed an increased expression of rRNA and tRNA coding genes, which confirms the higher metabolic activity of Ab in the presence of corksorb. The effect of corksorb is not related to the release of soluble stimulating compounds, but rather to the presence of the biosorbent, which was shown to be essential. Indeed, scanning electron microscopy images and downregulation of pili formation coding genes, which are involved in cell mobility, suggest that cell attachment on corksorb is a determinant for the improved activity. Furthermore, the existence of native alkane-degrading bacteria in corksorb was revealed, which may assist in situ bioremediation. Hence, the use of corksorb in marine oil spills may induce a combined effect of sorption and stimulated biodegradation, with high potential for enhancing in situ bioremediation processes.

High Culturable Bacterial Diversity From a European Desert: The Tabernas Desert

One of the most diverse ecological niches for microbial bioprospecting is soil, including that of drylands. Drylands are one of the most abundant biomes on Earth, but extreme cases, such as deserts, are considered very rare in Europe. The so-called Tabernas Desert is one of the few examples of a desert area in continental Europe, and although some microbial studies have been performed on this region, a comprehensive strategy to maximize the isolation of environmental bacteria has not been conducted to date. We report here a culturomics approach to study the bacterial diversity of this dryland by using a simple strategy consisting of combining different media, using serial dilutions of the nutrients, and using extended incubation times. With this strategy, we were able to set a large (254 strains) collection of bacteria, the majority of which (93%) were identified through 16S ribosomal RNA (rRNA) gene amplification and sequencing. A significant fraction of the collection consisted of Actinobacteria and Proteobacteria, as well as Firmicutes strains. Among the 254 isolates, 37 different genera were represented, and a high number of possible new taxa were identified (31%), of which, three new Kineococcus species. Moreover, 5 out of the 13 genera represented by one isolate were also possible new species. Specifically, the sequences of 80 isolates held a percentage of identity below the 98.7% threshold considered for potentially new species. These strains belonged to 20 genera. Our results reveal a clear link between medium dilution and isolation of new species, highlight the unexploited bacterial biodiversity of the Tabernas Desert, and evidence the potential of simple strategies to yield surprisingly large numbers of diverse, previously unreported, bacterial strains and species.

Roseomonas bella sp. nov., isolated from lake sediment

A Gram-stain-negative, non-motile, coccus-shaped, catalase- and oxidase-positive, facultatively anaerobic and pink-pigmented bacterium, designated strain CQN31^T, was isolated from sediment of Changqiaohai Lake, Yunnan Province, China. Growth occurred at 4-45 °C (optimum, 37 °C), at pH 6.5-9.5 (optimum, pH 8.0) and with 0-1 % (w/v) NaCl (optimum, 0 %). C_18 : 1 ω7c/C_18 : 1 ω6c and C_16 : 0 were the predominant fatty acids. Phosphatidylcholine (PC), phosphatidylethanolamine (PE), phosphatidylglycerol (PG), diphosphatidylglycerol (DPG), phosphatidyldimethylethanolamine (PME) and one unidentified aminolipid (AL) were the major polar lipids. The G+C content of the genomic DNA was 71.5 %. 16S rRNA gene sequence comparisons indicated that strain CQN31^T shared 96.8 % similarity with Roseomonas wooponensis JCM 19527^T and 95.9 % with R. terricola EM0302^T. Digital DNA-DNA hybridization values between strain CQN31^T and Roseomonas stagni DSM 19981^T, R. rosea DSM 14916^T and R. mucosa NCTC 13291^T were 21.0, 19.4 and 19.8 %, respectively. Average amino acid identity and average nucleotide identity values between strain CQN31^T and R. stagni DSM 19981^T, R. rosea DSM 14916^T and R. mucosa NCTC 13291^T were 73.7, 63.4 and 61.9 %, and 79.2, 77.1 and 77.5%, respectively. Distinct morphological, physiological and genotypic differences from previously described taxa support the classification of strain CQN31^T as a representative of a novel species in the genus Roseomonas, for which the name Roseomonas bella sp. nov. is proposed. The type strain is CQN31^T (=KCTC 62447^T=MCCC 1H00309^T).