Genome Sequence of an Alkane-Degrading Bacterium,Alcanivorax pacificus Type Strain W11-5, Isolated from Deep Sea Sediment

Alcanivorax pacificus W11-5^T was isolated from a pyrene-degrading consortium, enriched from the deep sea sediment of the Pacific Ocean. Strain W11-5^T can degrade various n-alkanes. Here we report the draft genome of W11-5^T and genes associated with alkane degradation.     

Identification of different alkane hydroxylase systems in Rhodococcus ruber strain SP2B,an hexane‐degrading actinomycete

Aims: To investigate the alkane‐hydroxylating system of isolate SP2B, closely related to Rhodococcus ruber DSM 43338^T and uncharacterized so far for its alkane degradation genes. Methods and Results: Although isolate SP2B and reference strain can grow on by‐products from hexane degradation, the type strain R. ruber was unable, unlike SP2B isolate, to use short‐chain alkanes, as assessed by gas chromatography. Using PCR with specific or degenerated primers, inverse PCR and Southern blot, two alkane hydroxylase encoding genes (alkB) were detected in both bacteria, which is in agreement with their alkane range. The first AlkB was related to Rhodococcus AlkB7 enzymes and contains a nonbulky residue at a specific position, suggesting it might be involved in medium‐ and long‐chain alkane oxidation. The second partial alkB gene potentially belongs to alkB5‐type, which was found in bacteria unable to use hexane. Moreover, a partial P450 cytochrome alkane hydroxylase, thought to be responsible for the hexane degradation, was detected only in the isolated strain. Conclusions: Rhodococcus ruber SP2B should prove to be a promising candidate for bioremediation studies of contaminated sites because of its large degradation range of alkanes. Significance and Impact of the Study: This is the first thorough study on R.ruber alkane degradation systems.     

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.     

Bacillus daqingensis sp. nov. isolated from near poultry farm soil

A novel bacterial strain, designated PFS-5^T, was isolated from the soil environment with feces of a live poultry farm located in Cheonan, Republic of Korea. Strain PFS-5^T was Gram-staining-positive, motile, strictly aerobic bacterium, rod-shaped, and endospore-forming. The strain contained meso-diaminopimelic acid in their peptidoglycan and MK-7 menaquinone. The major fatty acids were anteiso-C_15:0 (44.2%), C_16:0 (22.2%), and iso-C_15:0 (16.7%). The DNA G+C content was 40.1 mol%. Comparative 16S rRNA gene sequence analysis identified strain PFS-5^T in the genus Bacillus, exhibiting the highest level of sequence similarity with type strain of B. herbersteinensis D-1,5a^T (96.9%), B. humi LMG 22167^T (96.7%), B. alkalitelluris BA288^T (96.1%), B. litoralis SW-211^T (96.0%), and B. luteolus YIM93174^T (95.5%). The major polar lipids of PFS-5^T were diphosphatidylglycerol and phosphatidylglycerol. On the basis of result from poly-phasic data, strain PFS-5^T represents a novel species, for which the name Bacillus cheonanensis sp. nov. is proposed (Type strai PFS-5^T = KACC 17469^T = JCM19333^T).     

Cloning and expression of three ladA-type alkane monooxygenase genes from an extremely thermophilic alkane-degrading bacterium Geobacillus thermoleovorans B23

An extremely thermophilic bacterium, Geobacillus thermoleovorans B23, is capable of degrading a broad range of alkanes (with carbon chain lengths ranging between C11 and C32) at 70 °C. Whole-genome sequence analysis revealed that unlike most alkane-degrading bacteria, strain B23 does not possess an alkB-type alkane monooxygenase gene. Instead, it possesses a cluster of three ladA-type genes, ladAα_B23, ladAβ_B23, and ladB _B23, on its chromosome, whose protein products share significant amino acid sequence identities, 49.8, 34.4, and 22.7 %, respectively, with that of ladA alkane monooxygenase gene found on a plasmid of Geobacillus thermodetrificans NG 80-2. Each of the three genes, ladAα_B23, ladAβ_B23, and ladB _B23, was heterologously expressed individually in an alkB1 deletion mutant strain, Pseudomonas fluorescens KOB2Δ1. It was found that all three genes were functional in P. fluorescens KOB2Δ1, and partially restored alkane degradation activity. In this study, we suggest that G. thermoleovorans B23 utilizes multiple LadA-type alkane monooxygenases for the degradation of a broad range of alkanes.     

The Genome of the Moderate Halophile Amycolicicoccus subflavus DQS3-9A1T Reveals Four Alkane Hydroxylation Systems and Provides Some Clues on the Genetic Basis for Its Adaptation to a Petroleum Environment

The moderate halophile Amycolicicoccus subflavus DQS3-9A1^T is the type strain of a novel species in the recently described novel genus Amycolicicoccus, which was isolated from oil mud precipitated from oil produced water. The complete genome of A. subflavus DQS3-9A1^T has been sequenced and is characteristic of harboring the genes for adaption to the harsh petroleum environment with salinity, high osmotic pressure, and poor nutrient levels. Firstly, it characteristically contains four types of alkane hydroxylases, including the integral-membrane non-heme iron monooxygenase (AlkB) and cytochrome P450 CYP153, a long-chain alkane monooxygenase (LadA) and propane monooxygenase. It also accommodates complete pathways for the response to osmotic pressure. Physiological tests proved that the strain could grow on n-alkanes ranging from C10 to C36 and propane as the sole carbon sources, with the differential induction of four kinds of alkane hydroxylase coding genes. In addition, the strain could grow in 1–12% NaCl with the putative genes responsible for osmotic stresses induced as expected. These results reveal the effective adaptation of the strain DQS3-9A1^T to harsh oil environment and provide a genome platform to investigate the global regulation of different alkane metabolisms in bacteria that are crucially important for petroleum degradation. To our knowledge, this is the first report to describe the co-existence of such four types of alkane hydroxylases in a bacterial strain.     

Bacillus sediminis sp. nov., isolated from an electroactive biofilm

A Gram-stain positive, facultative anaerobic, motile, spore-forming rod-shaped bacterium with peritrichous flagella, designated DX-5^T, was isolated from an electroactive biofilm. Growth was observed to occur at 35–60 °C, at pH 7.0–10.0 and with 0.5–10 % (w/v) NaCl (optimum growth: 50 °C, pH 8.0 and 0.5–3 % NaCl). Cells were determined to be catalase- and oxidase-positive. The predominant respiratory quinone was identified as MK-7; the major polar lipids were determined to be diphosphatidylglycerol, phosphatidylglycerol, glycolipid, aminoglycolipid and an unidentified phospholipid; the DNA G+C content was determined to be 46.6 mol%; and the major fatty acids (>5 %) were identified as anteiso-C_15:0 (33.6 %), iso-C_15:0 (24.1 %) and anteiso-C_17:0 (13.4 %). The phylogenetic analysis based on 16S rRNA gene sequence comparisons indicated that strain DX-5^T should be assigned to the genus Bacillus, and was related most closely to the type strains of B. fortis DSM 16012^T (96.3 %), B. composti KACC 16872^T (96.3 %) and B. fordii DSM 16014^T (95.8 %). Results of phenotypic, chemotaxonomic and genotypic analysis indicated that strain DX-5^T represents a novel species, for which the name B. sediminis sp. nov. is proposed. The type strain is DX-5^T (=CGMCC 1.12412^T = KCTC 33102^T).     

Diaminobutyricibacter tongyongensis gen. nov., sp. nov. and Homoserinibacter gongjuensis gen. nov., sp. nov. Belong to the Family Microbacteriaceae

Two bacterial strains, KIS66-7^T and 5GH26-15^T, were isolated from soil samples collected in the South Korean cities of Tongyong and Gongju, respectively. Both strains were aerobic, Gram-stain-positive, mesophilic, flagellated, and rodshaped. A phylogenetic analysis revealed that both strains belonged to the family Microbacteriaceae of the phylum Actinobacteria. The 16S rRNA gene sequence of strain KIS66-7^T had the highest similarities with those of Labedella gwakjiensis KSW2-17^T (97.3%), Cryobacterium psychrophilum DSM 4854T (97.2%), Leifsonia lichenia 2Sb^T (97.2%), Leifsonia naganoensis JCM 10592^T (97.0%), and Cryobacterium mesophilum MSL-15^T (97.0%). Strain 5GH26-15^T showed the highest sequence similarities with Leifsonia psychrotolerans LI1T (97.4%) and Schumannella luteola KHIAT (97.1%). The 16S rRNA gene sequence from KIS66-7^T exhibited 96.4% similarity with that from 5GH26-15^T. Strain KIS66-7^T contained a B2γ type peptidoglycan structure with D-DAB as the diamino acid; MK-13, MK-12, and MK-14 as the respiratory quinones; ai-C_15:0, ai-C_17:0, and i-C_16:0 as the major cellular fatty acids; and diphosphatidylglycerol, phatidylglycerol, and glycolipids as the predominant polar lipids. Strain 5GH26-15T had a B2β type peptidoglycan structure with D-DAB as the diamino acid; MK-14 and MK-13 as the respiratory quinones; ai-C_15:0, i-C_16:0, and ai-C{vn17:0} as the major cellular fatty acids; and diphosphatidylglycerol, phatidylglycerol, and glycolipids as the predominant polar lipids. Both strains had low DNA-DNA hybridization values (<40%) with closely related taxa. Based on our polyphasic taxonomic characterization, we propose that strains KIS66-7^T and 5GH26-15^T represent novel genera and species, for which we propose the names Diaminobutyricibacter tongyongensis gen. nov., sp. nov. (type strain KIS66-7^T=KACC 15515^T=NBRC 108724^T) and Homoserinibacter gongjuensis gen. nov., sp. nov. (type strain 5GH26-15^T=KACC 15524^T=NBRC 108755^T) within the family Microbacteriaceae.     

Differential protein expression during growth on linear versus branched alkanes in the obligate marine hydrocarbon-degrading bacterium Alcanivorax borkumensis SK2T

Alcanivorax borkumensis SK2^T is an important obligate hydrocarbonoclastic bacterium (OHCB) that can dominate microbial communities following marine oil spills. It possesses the ability to degrade branched alkanes which provides it a competitive advantage over many other marine alkane degraders that can only degrade linear alkanes. We used LC–MS/MS shotgun proteomics to identify proteins involved in aerobic alkane degradation during growth on linear (n-C₁₄) or branched (pristane) alkanes. During growth on n-C₁₄, A. borkumensis expressed a complete pathway for the terminal oxidation of n-alkanes to their corresponding acyl-CoA derivatives including AlkB and AlmA, two CYP153 cytochrome P450s, an alcohol dehydrogenase and an aldehyde dehydrogenase. In contrast, during growth on pristane, an alternative alkane degradation pathway was expressed including a different cytochrome P450, an alcohol oxidase and an alcohol dehydrogenase. A. borkumensis also expressed a different set of enzymes for β-oxidation of the resultant fatty acids depending on the growth substrate utilized. This study significantly enhances our understanding of the fundamental physiology of A. borkumensis SK2^T by identifying the key enzymes expressed and involved in terminal oxidation of both linear and branched alkanes. It has also highlights the differential expression of sets of β-oxidation proteins to overcome steric hinderance from branched substrates.     

Alkane‐degrading properties of Dietzia sp. H0B,a key player in the Prestige oil spill biodegradation (NW Spain)

Aims: Investigation of the alkane‐degrading properties of Dietzia sp. H0B, one of the isolated Corynebacterineae strains that became dominant after the Prestige oil spill. Methods and Results: Using molecular and chemical analyses, the alkane‐degrading properties of strain Dietzia sp. H0B were analysed. This Grampositive isolate was able to grow on n‐alkanes ranging from C₁₂ to C₃₈ and branched alkanes (pristane and phytane). 8‐Hexadecene was detected as an intermediate of hexadecane degradation by Dietzia H0B, suggesting a novel alkane‐degrading pathway in this strain. Three putative alkane hydroxylase genes (one alkB homologue and two CYP153 gene homologues of cytochrome P450 family) were PCR‐amplified from Dietzia H0B and differed from previously known hydroxylase genes, which might be related to the novel degrading activity observed on Dietzia H0B. The alkane degradation activity and the alkB and CYP153 gene expression were observed constitutively regardless of the presence of the substrate, suggesting additional, novel pathways for alkane degradation. Conclusions: The results from this study suggest novel alkane‐degrading pathways in Dietzia H0B and a genetic background coding for two different putative oil‐degrading enzymes, which is mostly unexplored and worth to be subject of further functional analysis. Significance and Impact of the Study: This study increases the scarce information available about the genetic background of alkane degradation in genus Dietzia and suggests new pathways and novel expression mechanisms of alkane degradation.     

Hyphomonas beringensis sp. nov. and Hyphomonas chukchiensis sp. nov., isolated from surface seawater of the Bering Sea and Chukchi Sea

Two Gram-negative, non-spore-forming, oval to pear shaped motile strains, designated 25B14_1^T and BH-BN04-4^T, isolated from surface seawater from the Bering Sea and Chukchi Sea, respectively, were subjected to polyphasic taxonomic study. Phylogenetic analysis based on 16S rRNA gene sequences demonstrated that strains 25B14_1^T and BH-BN04-4^T clustered together with Hyphomonas atlanticus 22II1-22F38^T and Hyphomonas oceanitis DSM 5155^T, respectively, within genus Hyphomonas. Based on whole genome sequence analysis, the calculated DDH and ANIm values between strain 25B14_1^T and BH-BN04-4^T are 18.8 and 83.19 % respectively. The calculated DDH values of strain 25B14_1^T and BH-BN04-4^T with seven type strains ranged from 18.2 to 19.9 % and from 18.4 to 40.4 %, respectively. The ANIm values of strain 25B14_1^T and BH-BN04-4^T with seven type strains ranged from 83.00 to 84.67 % and from 83.14 to 90.58 %, respectively. Both isolates were found to contain Q-11 as the predominant respiratory quinone. The major fatty acids of strain 25B14_1^T were identified as C_16:0, C_17:0, C_18:1 ω7c-methyl and Summed Feature 8 (C_18:1 ω6c/ω7c as defined by MIDI), while in the case of strain BH-BN04-4^T they were identified as C_16:0, C_18:1 ω7c-methyl and Summed Feature 8 (C_18:1 ω6c/ω7c). The G+C contents of 25B14_1^T and BH-BN04-4^T were determined to be 58.4 and 61.0 mol%, respectively. The combined phenotypic and genotypic data show that the two isolates each represent novel species of the genus Hyphomonas, for which the names Hyphomonas beringensis sp. nov. and Hyphomonas chukchiensis sp. nov. are proposed, with the type strain 25B14_1^T (=MCCC 1A07321^T = LMG 27914^T) and BH-BN04-4^T (=MCCC 1A07481^T = LMG 27915^T), respectively.     

Mixotrophic metabolism in Burkholderia kururiensis subsp. thiooxydans subsp. nov., a facultative chemolithoautotrophic thiosulfate oxidizing bacterium isolated from rhizosphere soil and proposal for classification of the type strain of Burkholderia kururiensis as Burkholderia kururiensis subsp. kururiensis subsp. nov.

A thiosulfate-oxidizing facultative chemolithoautotrophic Burkholderia sp. strain ATSB13^T was previously isolated from rhizosphere soil of tobacco plant. Strain ATSB13^T was aerobic, Gram-staining-negative, rod shaped and motile by means of sub-terminal flagellum. Strain ATSB13^T exhibited mixotrophic growth in a medium containing thiosulfate plus acetate. A phylogenetic study based on 16S rRNA gene sequence analysis indicated that strain ATSB13^T was most closely related to Burkholderia kururiensis KP23^T (98.7%), Burkholderia tuberum STM678^T (96.5%) and Burkholderia phymatum STM815^T (96.4%). Chemotaxonomic data [G+C 64.0 mol%, major fatty acids, C_18:1 ω7c (28.22%), C_16:1 ω7c/15 iso 2OH (15.15%), and C_16:0 (14.91%) and Q-8 as predominant respiratory ubiquinone] supported the affiliation of the strain ATSB13^T within the genus Burkholderia. Though the strain ATSB13^T shared high 16S rRNA gene sequence similarity with the type strain of B. kururiensis but considerably distant from the latter in terms of several phenotypic and chemotaxonomic characteristics. DNA–DNA hybridization between strain ATSB13^T and B. kururiensis KP23^T was 100%, and hence, it is inferred that strain ATSB13^T is a member of B. kururiensis. On the basis of data obtained from this study, we propose that B. kururiensis be subdivided into B. kururiensis subsp. kururiensis subsp. nov. (type strain KP23^T = JCM 10599^T = DSM 13646^T) and B. kururiensis subsp. thiooxydans subsp. nov. (type strain ATSB13^T = KACC 12758^T).     

Carotenoid production from n-alkanes with a broad range of chain lengths by the novel species Gordonia ajoucoccus A2T

A novel diesel-degrading bacterial strain, A2^T, was isolated from soil that was heavily contaminated with oil. Based on phenotypic, phylogenetic, and DNA analyses, strain A2^T was identified as a novel species of the genus Gordonia and named Gordonia ajoucoccus A2^T (KCTC 11900BP and CECT8382). G. ajoucoccus A2^T is able to synthesize carotenoids and produces mainly γ-carotene and keto-γ-carotene. G. ajoucoccus A2^T is also capable of assimilating n-alkanes with a broad range of chain lengths (C6, C8–C25). Batch culture of G. ajoucoccus A2^T in a bioreactor containing 1 % (v/v) hexadecane or 1 % (v/v) commercial diesel yielded 25 mg L^?1 and 2.6 mg L^?1 of carotenoids, respectively. Gas chromatography/mass spectrometry (GC-MS) analysis of hexadecane and hexane degradation metabolites suggested that G. ajoucoccus A2^T may possess a terminal oxidation pathway that allows it to utilize n-alkanes and hexane as carbon and energy sources. G. ajoucoccus A2^T could therefore serve as a good model system for understanding microbial n-alkane degradation pathways. Additionally, the metabolic capabilities of G. ajoucoccus A2^T suggest potential biotechnological applications, such as the bioproduction of carotenoids from industrial discharge or other sources of n-alkanes.     

Bacillus bingmayongensis sp. nov., isolated from the pit soil of Emperor Qin’s Terra-cotta warriors in China

A Bacillus-like isolate, strain FJAT-13831^T, isolated from the No. 1 pit soil of Emperor Qin’s Terra-cotta Warriors in Xi’an City, China, was studied to determine its taxonomic status. Dominant fatty acids of this organism included iso-C_15:0, iso-C_17:0, C_16:0, iso-C_13:0, anteiso-C_15:0, and iso-C_17:1ω5c. Comparative 16S rRNA gene sequence analysis confirmed the affiliation of this isolate to the genus Bacillus and indicated that it was closely related to Bacillus pseudomycoides DSM 12442^T (99.72 % similarity). A phylogenetic analysis of the gyrB gene sequence similarities exhibited independent clustering of the isolate FJAT-13831^T and showed 93.8 % (<95 %) sequence similarity with its closest phylogenetic neighbour B. pseudomycoides DSM 12442^T. Separate standing of the strain FJAT-13831^T was supported by a whole genome-based phylogenetic analysis with an average nucleotide identity value of 91.47 (<95 %) between isolate FJAT-13831^T and B. pseudomycoides DSM 12442^T and was consistent with the results of DNA–DNA hybridization (69.1 % relatedness). These findings support the conclusion that the isolate FJAT-13831^T represents a novel species, for which the name Bacillus bingmayongensis sp. nov. is proposed. The type strain is FJAT-13831^T (= CGMCC 1.12043^T = DSM 25427^T).     

Loss of Circulating CD4 T Cells with B Cell Helper Function during Chronic HIV Infection

The interaction between follicular T helper cells (T_FH) and B cells in the lymph nodes and spleen has a major impact on the development of antigen-specific B cell responses during infection or vaccination. Recent studies described a functional equivalent of these cells among circulating CD4 T cells, referred to as peripheral T_FH cells. Here, we characterize the phenotype and in vitro B cell helper activity of peripheral T_FH populations, as well as the effect of HIV infection on these populations. In co-culture experiments we confirmed CXCR5+ cells from HIV-uninfected donors provide help to B cells and more specifically, we identified a CCR7^highCXCR5^highCCR6^highPD-1^high CD4 T cell population that secretes IL-21 and enhances isotype-switched immunoglobulin production. This population is significantly decreased in treatment-naïve, HIV-infected individuals and can be recovered after anti-retroviral therapy. We found impaired immunoglobulin production in co-cultures from HIV-infected individuals and found no correlation between the frequency of peripheral T_FH cells and memory B cells, or with neutralization activity in untreated HIV infection in our cohort. Furthermore, we found that within the peripheral T_FH population, the expression level of T_FH-associated genes more closely resembles a memory, non-T_FH population, as opposed to a T_FH population. Overall, our data identify a heterogeneous population of circulating CD4 T cells that provides in vitro help to B cells, and challenges the origin of these cells as memory T_FH cells.     

Hymenobacter swuensis sp. nov., a Gamma-Radiation-Resistant Bacteria Isolated from Mountain Soil

Gram stain-negative and non-motile bacteria, designated as DY53^T and DY43, were isolated from mountain soil in South Korea prior exposure with 5 kGy gamma radiation. Phylogenetic analysis based on 16S rRNA gene sequence revealed that the strains belonged to the family Cytophagaceae in the class Cytophagia. 16S rRNA gene sequence similarity of strains DY53^T and DY43 was 100 %. The highest degrees of sequence similarities of strains DY53^T and DY43 were found with Hymenobacter perfusus A1-12^T (98.8 %), Hymenobacter rigui WPCB131^T (98.5 %), H. yonginensis HMD1010^T (97.9 %), H. xinjiangensis X2-1g^T (96.6 %), and H. gelipurpurascens Txg1^T (96.5 %). The DNA G+C content of the novel strains DY53^T and DY43 were 59.5 mol%. Chemotaxonomic data revealed that strains possessed major fatty acids such as C_15:0 iso, C_15:0 anteiso, C_16:1 ω5c, summed feature 3 (16:1 ω7c/ω6c), summed feature 4 (17:1 anteiso B/iso I) and C_17:0 iso, and major polar lipid was phosphatidylethanolamine. The novel strains showed resistance to gamma radiation, with a D10 value (i.e., the dose required to reduce the bacterial population by tenfold) in excess of 5 kGy. Based on these data, strains DY53^T and DY43 should be classified as representing a novel species, for which the name Hymenobacter swuensis sp. nov. is proposed, with the type strain DY53^T (=KCTC 32018^T = JCM 18582^T) and DY43 (=KCTC 32010).     

<Emphasis Type="Italic">Bacillus ferrooxidans</Emphasis> sp. nov., an iron(II)-oxidizing bacterium isolated from paddy soil

An endospore-forming bacterium, designated YT-3^T, was isolated from a paddy soil in Yingtan, Jiangxi, China. Cells of strain YT-3^T were Gram-positive, rod-shaped, facultative anaerobic, catalase, and oxidase positive. The optimum growth temperature and pH were 30°C (ranged from 15 to 50°C) and 6.5–7.0 (ranged from 3 to 11), respectively. Analysis of the 16S rRNA gene sequence showed that strain YT-3^T was affiliated to the genus Bacillus and displayed the highest similarity to that of Bacillus drentensis JCM 21707^T (98.3%), followed by B. ginsengisoli JCM 17335^T (97.8%) and B. fumarioli JCM 21708^T (97.0%). The similarity of rpoB gene sequence between strain YT-3^T and B. drentensis JCM 21707^T, B. ginsengisoli JCM 17335^T and B. fumarioli JCM 21708T was 80.4%, 81.5%, and 82.1%, respectively. The genomic DNA G + C content was 44.9 mol%. The predominant respiratory quinone was Menaquinone-7, and meso-diaminopimelic acid was present in the peptidoglycan layer of cell wall. The major fatty acids were C_15:0 anteiso (36.2%), C_14:0 iso (19.6%), C_15:0 iso (17.4%), and C_16:0 iso (9.8%). The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phospholipids, and ammoniac phospholipids. The DNA-DNA hybridization values between isolate YT-3^T and B. drentensis (JCM 21707^T), B. ginsengisoli (JCM 17335^T), and B. fumarioli (JCM 21708^T) were 36.3%, 30.3%, and 25.3%, respectively. On the basis of physiological, genetic and biochemical data, strain YT-3^T represented a novel species of the genus Bacillus, for which the name Bacillus ferrooxidans sp. nov was proposed. The type strain is YT-3^T (= KCTC 33875T = CCTCC AB 2017049T).     

A Sunflower Lectin with Antifungal Properties and Putative Medical Mycology Applications

Using a new culture method for unculturable soil bacteria, we discovered a novel species, NHI-38^T, from the forest soil of Kyonggi University campus, South Korea. It was a Gram-positive, rod-shaped, and endospore-forming bacterial strain. It grew over a wide pH range (6.5–9.5), with an optimum range of pH 7–9, and in a wide range of temperatures (15–60 °C), with an optimum range of 35–45 °C. Growth was possible at 0–2 % NaCl concentration, and the optimal range was between 0.5 and 1.5 % NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that this new species clustered within the genus Bacillus; it was closely related to “Bacillus abyssalis” SCSIO 15042^T (98.86 %), B. methanolicus NCIMB 13113^T (95.97 %), B. vietnamensis 15-1^T (95.8 %), B. seohaeanensis BH724^T (95.5 %), B. timonensis MM10403188^T (95.33 %), and B. subtilis subsp. subtilis NCIB 3610^T (94.87 %). The main fatty acid components of this bacterium were iso-C_15:0 (35.92 %), summed feature 3 (C_16:1ω7c/C_16:1ω6c; 16.92 %), and anteiso-C_15:0 (14.19 %). The predominant quinone in this bacterial strain was MK-7. The polar lipid profile primarily comprised phosphatidylethanolamine, phosphatidylglycerol, and diphosphatidylglycerol. The genomic DNA G+C composition of the isolate was 40.7 mol%. The DNA–DNA hybridization results indicated that this strain was distinct from other Bacillus species, the degree of similarity being 50 % with “B. abyssalis”, 56 % with B. methanolicus, 47 % with B. vietnamensis, 43 % with B. seohaeanensis, 46 % with B. timonensis, and 32 % with B. subtilis. Based on our results, we regard strain NHI-38^T as a novel member of the Bacillus genus, and we propose the name Bacillus thaonhiensis (=KACC 17216^T = KEMB 9005-019^T = JCM 18863^T).     

Comparison of Mechanisms of Alkane Metabolism under Sulfate-Reducing Conditions among Two Bacterial Isolates and a Bacterial Consortium

Recent studies have demonstrated that fumarate addition and carboxylation are two possible mechanisms of anaerobic alkane degradation. In the present study, we surveyed metabolites formed during growth on hexadecane by the sulfate-reducing isolates AK-01 and Hxd3 and by a mixed sulfate-reducing consortium. The cultures were incubated with either protonated or fully deuterated hexadecane; the sulfate-reducing consortium was also incubated with [1,2-¹³C₂]hexadecane. All cultures were extracted, silylated, and analyzed by gas chromatography-mass spectrometry. We detected a suite of metabolites that support a fumarate addition mechanism for hexadecane degradation by AK-01, including methylpentadecylsuccinic acid, 4-methyloctadecanoic acid, 4-methyloctadec-2,3-enoic acid, 2-methylhexadecanoic acid, and tetradecanoic acid. By using d₃₄-hexadecane, mass spectral evidence strongly supporting a carbon skeleton rearrangement of the first intermediate, methylpentadecylsuccinic acid, was demonstrated for AK-01. Evidence indicating hexadecane carboxylation was not found in AK-01 extracts but was observed in Hxd3 extracts. In the mixed sulfate-reducing culture, however, metabolites consistent with both fumarate addition and carboxylation mechanisms of hexadecane degradation were detected, which demonstrates that multiple alkane degradation pathways can occur simultaneously within distinct anaerobic communities. Collectively, these findings underscore that fumarate addition and carboxylation are important alkane degradation mechanisms that may be widespread among phylogenetically and/or physiologically distinct microorganisms.