Phytoextraction efficiency of Pteris vittata grown on a naturally As-rich soil and characterization of As-resistant rhizosphere bacteria.

This study evaluated the phytoextraction capacity of the fern Pteris vittata grown on a natural arsenic-rich soil of volcanic-origin from the Viterbo area in central Italy. This calcareous soil is characterized by an average arsenic concentration of 750 mg kg-1, of which 28% is bioavailable. By means of micro-energy dispersive X-ray fluorescence spectrometry (µ-XRF) we detected As in P. vittata fronds after just 10 days of growth, while a high As concentrations in fronds (5,000 mg kg-1), determined by Inductively coupled plasma-optical emission spectrometry (ICP-OES), was reached after 5.5 months. Sixteen arsenate-tolerant bacterial strains were isolated from the P. vittata rhizosphere, a majority of which belong to the Bacillus genus, and of this majority only two have been previously associated with As. Six bacterial isolates were highly As-resistant (> 100 mM) two of which, homologous to Paenarthrobacter ureafaciens and Beijerinckia fluminensis, produced a high amount of IAA and siderophores and have never been isolated from P. vittata roots. Furthermore, five isolates contained the arsenate reductase gene (arsC). We conclude that P. vittata can efficiently phytoextract As when grown on this natural As-rich soil and a consortium of bacteria, largely different from that usually found in As-polluted soils, has been found in P. vittata rhizosphere.

Novel facultative Methylocella strains are active methane consumers at terrestrial natural gas seeps.

BACKGROUND: Natural gas seeps contribute to global climate change by releasing substantial amounts of the potent greenhouse gas methane and other climate-active gases including ethane and propane to the atmosphere. However, methanotrophs, bacteria capable of utilising methane as the sole source of carbon and energy, play a significant role in reducing the emissions of methane from many environments. Methylocella-like facultative methanotrophs are a unique group of bacteria that grow on other components of natural gas (i.e. ethane and propane) in addition to methane but a little is known about the distribution and activity of Methylocella in the environment. The purposes of this study were to identify bacteria involved in cycling methane emitted from natural gas seeps and, most importantly, to investigate if Methylocella-like facultative methanotrophs were active utilisers of natural gas at seep sites. RESULTS: The community structure of active methane-consuming bacteria in samples from natural gas seeps from Andreiasu Everlasting Fire (Romania) and Pipe Creek (NY, USA) was investigated by DNA stable isotope probing (DNA-SIP) using 13C-labelled methane. The 16S rRNA gene sequences retrieved from DNA-SIP experiments revealed that of various active methanotrophs, Methylocella was the only active methanotrophic genus common to both natural gas seep environments. We also isolated novel facultative methanotrophs, Methylocella sp. PC1 and PC4 from Pipe Creek, able to utilise methane, ethane, propane and various non-gaseous multicarbon compounds. Functional and comparative genomics of these new isolates revealed genomic and physiological divergence from already known methanotrophs, in particular, the absence of mxa genes encoding calcium-containing methanol dehydrogenase. Methylocella sp. PC1 and PC4 had only the soluble methane monooxygenase (sMMO) and lanthanide-dependent methanol dehydrogenase (XoxF). These are the first Alphaproteobacteria methanotrophs discovered with this reduced functional redundancy for C-1 metabolism (i.e. sMMO only and XoxF only). CONCLUSIONS: Here, we provide evidence, using culture-dependent and culture-independent methods, that Methylocella are abundant and active at terrestrial natural gas seeps, suggesting that they play a significant role in the biogeochemical cycling of these gaseous alkanes. This might also be significant for the design of biotechnological strategies for controlling natural gas emissions, which are increasing globally due to unconventional exploitation of oil and gas.

Lanthanide-Dependent Methylotrophs of the Family Beijerinckiaceae: Physiological and Genomic Insights.

Methylotrophic bacteria use methanol and related C1 compounds as carbon and energy sources. Methanol dehydrogenases are essential for methanol oxidation, while lanthanides are important cofactors of many pyrroloquinoline quinone-dependent methanol dehydrogenases and related alcohol dehydrogenases. We describe here the physiological and genomic characterization of newly isolated Beijerinckiaceae bacteria that rely on lanthanides for methanol oxidation. A broad physiological diversity was indicated by the ability to metabolize a wide range of multicarbon substrates, including various sugars, and organic acids, as well as diverse C1 substrates such as methylated amines and methylated sulfur compounds. Methanol oxidation was possible only in the presence of low-mass lanthanides (La, Ce, and Nd) at submicromolar concentrations (>100 nM). In a comparison with other Beijerinckiaceae, genomic and transcriptomic analyses revealed the usage of a glutathione- and tetrahydrofolate-dependent pathway for formaldehyde oxidation and channeling methyl groups into the serine cycle for carbon assimilation. Besides a single xoxF gene, we identified two additional genes for lanthanide-dependent alcohol dehydrogenases, including one coding for an ExaF-type alcohol dehydrogenase, which was so far not known in Beijerinckiaceae Homologs for most of the gene products of the recently postulated gene cluster linked to lanthanide utilization and transport could be detected, but for now it remains unanswered how lanthanides are sensed and taken up by our strains. Studying physiological responses to lanthanides under nonmethylotrophic conditions in these isolates as well as other organisms is necessary to gain a more complete understanding of lanthanide-dependent metabolism as a whole.IMPORTANCE We supplemented knowledge of the broad metabolic diversity of the Beijerinckiaceae by characterizing new members of this family that rely on lanthanides for methanol oxidation and that possess additional lanthanide-dependent enzymes. Considering that lanthanides are critical resources for many modern applications and that recovering them is expensive and puts a heavy burden on the environment, lanthanide-dependent metabolism in microorganisms is an exploding field of research. Further research into how isolated Beijerinckiaceae and other microbes utilize lanthanides is needed to increase our understanding of lanthanide-dependent metabolism. The diversity and widespread occurrence of lanthanide-dependent enzymes make it likely that lanthanide utilization varies in different taxonomic groups and is dependent on the habitat of the microbes.

Facultative methanotrophs are abundant at terrestrial natural gas seeps.

BACKGROUND: Natural gas contains methane and the gaseous alkanes ethane, propane and butane, which collectively influence atmospheric chemistry and cause global warming. Methane-oxidising bacteria, methanotrophs, are crucial in mitigating emissions of methane as they oxidise most of the methane produced in soils and the subsurface before it reaches the atmosphere. Methanotrophs are usually obligate, i.e. grow only on methane and not on longer chain alkanes. Bacteria that grow on the other gaseous alkanes in natural gas such as propane have also been characterised, but they do not grow on methane. Recently, it was shown that the facultative methanotroph Methylocella silvestris grew on ethane and propane, other components of natural gas, in addition to methane. Therefore, we hypothesised that Methylocella may be prevalent at natural gas seeps and might play a major role in consuming all components of this potent greenhouse gas mixture before it is released to the atmosphere. RESULTS: Environments known to be exposed to biogenic methane emissions or thermogenic natural gas seeps were surveyed for methanotrophs. 16S rRNA gene amplicon sequencing revealed that Methylocella were the most abundant methanotrophs in natural gas seep environments. New Methylocella-specific molecular tools targeting mmoX (encoding the soluble methane monooxygenase) by PCR and Illumina amplicon sequencing were designed and used to investigate various sites. Functional gene-based assays confirmed that Methylocella were present in all of the natural gas seep sites tested here. This might be due to its ability to use methane and other short chain alkane components of natural gas. We also observed the abundance of Methylocella in other environments exposed to biogenic methane, suggesting that Methylocella has been overlooked in the past as previous ecological studies of methanotrophs often used pmoA (encoding the alpha subunit of particulate methane monooxygenase) as a marker gene. CONCLUSION: New biomolecular tools designed in this study have expanded our ability to detect, and our knowledge of the environmental distribution of Methylocella, a unique facultative methanotroph. This study has revealed that Methylocella are particularly abundant at natural gas seeps and may play a significant role in biogeochemical cycling of gaseous hydrocarbons.

Chelatococcus composti sp. nov., isolated from penicillin fermentation fungi residue with pig manure co-compost.

A novel Gram-stain-negative bacterium, designated strain PC-2T, was isolated from penicillin fermentation fungi residue with pig manure co-compost in China. Phylogenetic analysis, based on 16S rRNA gene sequence comparisons, revealed that strain PC-2T should be assigned to the genus Chelatococcus and that it had 98.9 % similarity with Chelatococcus daeguensis, 98.8 % with Chelatococcus sambhunathii, 98.4 %, with Chelatococcus caeni and 96.0 % with Chelatococcus asaccharovorans. The G+C content of genomic DNA was 70.9 mol%. On the basis of the phylogenetic analysis, DNA-DNA relatedness values, phenotypic characteristics and chemotaxonomic data, strain PC-2 T represents a novel species of the genus Chelatococcus, for which the name Chelatococcus composti sp. nov. is proposed. The type strain is PC-2T (=DSM 101465T=CGMCC 1.15283T).

Chelatococcus reniformis sp. nov., isolated from a glacier.

A Gram-stain-negative, non-motile, reniform bacterial strain, B2974T, was isolated from an ice core of the Muztagh Glacier, on the Tibetan Plateau, China. Strain B2974T grew optimally at pH 7.0-7.5 and 25-30 °C in the presence of 0-2.0 % (w/v) NaCl. 16S rRNA gene sequence similarity analysis indicated that strain B2974T was closely related to Chelatococcus asaccharovorans LMG 25503T at a level of 97.1 %. The major quinone of strain B2974T was ubiquinone Q10. The predominant fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C19 : 0 cyclo ω8c. sym-Homospermidine was the major polyamine. The genomic DNA G+C content of the strain was 64 mol%. In DNA-DNA hybridization tests, strain B2974T shared 49.32 % DNA-DNA relatedness with the type strain of Chelatococcus asaccharovorans LMG 25503T. Based on the results of phenotypic and chemotaxonomic characteristics, strain B2974T was considered as a novel species of the genus Chelatococcus, for which the name Chelatococcus reniformis sp. nov. is proposed. The type strain is B2974T (=JCM 30308T=CGMCC 1.12919T).

Proteomics and Metabolomics Analyses to Elucidate the Desulfurization Pathway of Chelatococcus sp.

Desulfurization of dibenzothiophene (DBT) and alkylated DBT derivatives present in transport fuel through specific cleavage of carbon-sulfur (C-S) bonds by a newly isolated bacterium Chelatococcus sp. is reported for the first time. Gas chromatography-mass spectrometry (GC-MS) analysis of the products of DBT degradation by Chelatococcus sp. showed the transient formation of 2-hydroxybiphenyl (2-HBP) which was subsequently converted to 2-methoxybiphenyl (2-MBP) by methylation at the hydroxyl group of 2-HBP. The relative ratio of 2-HBP and 2-MBP formed after 96 h of bacterial growth was determined at 4:1 suggesting partial conversion of 2-HBP or rapid degradation of 2-MBP. Nevertheless, the enzyme involved in this conversion process remains to be identified. This production of 2-MBP rather than 2-HBP from DBT desulfurization has a significant metabolic advantage for enhancing the growth and sulfur utilization from DBT by Chelatococcus sp. and it also reduces the environmental pollution by 2-HBP. Furthermore, desulfurization of DBT derivatives such as 4-M-DBT and 4, 6-DM-DBT by Chelatococcus sp. resulted in formation of 2-hydroxy-3-methyl-biphenyl and 2-hydroxy -3, 3/- dimethyl-biphenyl, respectively as end product. The GC and X-ray fluorescence studies revealed that Chelatococcus sp. after 24 h of treatment at 37°C reduced the total sulfur content of diesel fuel by 12% by per gram resting cells, without compromising the quality of fuel. The LC-MS/MS analysis of tryptic digested intracellular proteins of Chelatococcus sp. when grown in DBT demonstrated the biosynthesis of 4S pathway desulfurizing enzymes viz. monoxygenases (DszC, DszA), desulfinase (DszB), and an NADH-dependent flavin reductase (DszD). Besides, several other intracellular proteins of Chelatococcus sp. having diverse biological functions were also identified by LC-MS/MS analysis. Many of these enzymes are directly involved with desulfurization process whereas the other enzymes/proteins support growth of bacteria at an expense of DBT. These combined results suggest that Chelatococcus sp. prefers sulfur-specific extended 4S pathway for deep-desulphurization which may have an advantage for its intended future application as a promising biodesulfurizing agent.

Isolation and identification of biocellulose-producing bacterial strains from Malaysian acidic fruits.

UNLABELLED: Biocellulose (BC) is pure extracellular cellulose produced by several species of micro-organisms that has numerous applications in the food, biomedical and paper industries. However, the existing biocellulose-producing bacterial strain with high yield was limited. The aim of this study was to isolate and identify the potential biocellulose-producing bacterial isolates from Malaysian acidic fruits. One hundred and ninety-three bacterial isolates were obtained from 19 local acidic fruits collected in Malaysia and screened for their ability to produce BC. A total of 15 potential bacterial isolates were then cultured in standard Hestrin-Schramm (HS) medium statically at 30°C for 2 weeks to determine the BC production. The most potent bacterial isolates were identified using 16S rRNA gene sequence analysis, morphological and biochemical characteristics. Three new and potent biocellulose-producing bacterial strains were isolated from soursop fruit and identified as Stenotrophomonas maltophilia WAUPM42, Pantoea vagans WAUPM45 and Beijerinckia fluminensis WAUPM53. Stenotrophomonas maltophilia WAUPM42 was the most potent biocellulose-producing bacterial strain that produced the highest amount of BC 0·58 g l(-1) in standard HS medium. Whereas, the isolates P. vagans WAUPM45 and B. fluminensis WAUPM53 showed 0·50 and 0·52 g l(-1) of BC production, respectively. SIGNIFICANCE AND IMPACT OF THE STUDY: Biocellulose (BC) is pure extracellular cellulose that is formed by many micro-organisms in the presence of carbon source and acidic condition. It can replace plant-based cellulose in multifarious applications due to its unique characteristics. In this study, three potential biocellulose-producing bacterial strains were obtained from Malaysian acidic fruits and identified as Stenotrophomonas maltophilia WAUPM42, Pantoea vagans WAUPM45 and Beijerinckia fluminensis WAUPM53. This study reports for the first time the new biocellulose-producing bacterial strains isolated from Malaysian acidic fruits.

Methylocapsa palsarum sp. nov., a methanotroph isolated from a subArctic discontinuous permafrost ecosystem.

An aerobic methanotrophic bacterium was isolated from a collapsed palsa soil in northern Norway and designated strain NE2T. Cells of this strain were Gram-stain-negative, non-motile, non-pigmented, slightly curved thick rods that multiplied by normal cell division. The cells possessed a particulate methane monooxygenase enzyme (pMMO) and utilized methane and methanol. Strain NE2T grew in a wide pH range of 4.1­8.0 (optimum pH 5.2­6.5) at temperatures between 6 and 32 °C (optimum 18­25 °C), and was capable of atmospheric nitrogen fixation under reduced oxygen tension. The major cellular fatty acids were C18 : 1ω7c, C16 : 0 and C16 : 1ω7c, and the DNA G+C content was 61.7 mol%. The isolate belonged to the family Beijerinckiaceae of the class Alphaproteobacteria and was most closely related to the facultative methanotroph Methylocapsa aurea KYGT (98.3 % 16S rRNA gene sequence similarity and 84 % PmoA sequence identity). However, strain NE2T differed from Methylocapsa aurea KYGT by cell morphology, the absence of pigmentation, inability to grow on acetate, broader pH growth range, and higher tolerance to NaCl. Therefore, strain NE2T represents a novel species of the genus Methylocapsa, for which we propose the name Methylocapsa palsarum sp. nov. The type strain is NE2T ( = LMG 28715T = VKM B-2945T).

Pseudochelatococcus lubricantis gen. nov., sp. nov. and Pseudochelatococcus contaminans sp. nov. from coolant lubricants.

Two Gram-negative, rod-shaped, non-spore-forming bacteria, isolated from metal working fluids were investigated to determine their taxonomic positions. On the basis of 16S rRNA gene sequence phylogeny, both strains (MPA 1113(T) and MPA 1105(T)) formed a distinct cluster with 97.7 % sequence similarity between them, which was in the vicinity of members of the genera Methylobacterium, Camelimonas, Chelatococcus, Bosea, Salinarimonas and Microvirga to which they showed low sequence similarities (below 94 %). The predominant compounds in the polyamine pattern and in the quinone system of the two strains were spermidine and ubiquinone Q-10, respectively. The polar lipid profiles were composed of the major compounds: phosphatidylmonomethylethanolamine, phosphatidylglycerol, phosphatidylcholine, major or moderate amounts of diphosphatidylglycerol, two unidentified glycolipids and three unidentified aminolipids. Several minor lipids were also detected. The major fatty acids were either C19 : 0 cyclo ω8c or C18 : 1ω7c. The results of fatty acid analysis and physiological and biochemical tests allowed both, the genotypic and phenotypic differentiation of the isolates from each other, while the chemotaxonomic traits allowed them to be differentiated from the most closely related genera. In summary, low 16S rRNA gene sequence similarities and marked differences in polar lipid profiles, as well as in polyamine patterns, is suggestive of a novel genus for which the name Pseudochelatococcus gen. nov. is proposed. MPA 1113(T) ( = CCM 8528(T) = LMG 28286(T) = CIP 110802(T)) and MPA 1105(T) ( = CCM 8527(T) = LMG 28285(T)) are proposed to be the type strains representing two novel species within the novel genus, Pseudochelatococcus gen. nov., for which the names Pseudochelatococcus lubricantis sp. nov. and Pseudochelatococcus contaminans sp. nov. are suggested, respectively.

Chelatococcus caeni sp. nov., isolated from a biofilm reactor sludge sample.

A polyphasic taxonomic study was carried out on strain EBR-4-1(T), which was isolated from a biofilm reactor in the Republic of Korea. The cells of the strain were Gram-stain-negative, non-spore-forming, motile and rod-shaped. Comparative 16S rRNA gene sequence studies showed a clear affiliation of this strain to the Alphaproteobacteria, and it was most closely related to Chelatococcus daeguensis CCUG 54519(T), Chelatococcus sambhunathii HT4(T), and Chelatococcus asaccharovorans DSM 6462(T) with 16S rRNA gene sequence similarities to the type strains of these species of 98.8 %, 98.7 %, and 96.3 %, respectively. The G+C content of the genomic DNA of strain EBR-4-1(T) was 68.7 mol%. Phenotypic and chemotaxonomic data [Q-10 as the major ubiquinone; C19 : 0cycloω8c, C18 : 1 2-OH, and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) as the major fatty acids] supported the affiliation of strain EBR-4-1(T) to the genus Chelatococcus. On the basis of the polyphasic evidence, it is proposed that strain EBR-4-1(T) should be assigned to a new species, Chelatococcus caeni sp. nov. The type strain is EBR-4-1(T) ( = KCTC 32487(T) = JCM 30181(T)).

Isolation and characterization of two novel strains capable of using cyclohexane as carbon source.

Two strains capable of degrading cyclohexane were isolated from the soil and sludge of the wastewater treatment plant of the University of Stuttgart and a biotrickling filter system. The strains were classified as gram negative and identified as Acidovorax sp. CHX100 and Chelatococcus sp. CHX1100. Both strains have demonstrated the capability to degrade cycloalkanes (C5-C8), while only strain CHX1100 used as well short linear n-alkanes (C5-C8) as the sole source of carbon and energy. The growth of Acidovorax sp. CHX100 using cyclohexane was much faster compared to Chelatococcus sp. CHX1100. Degenerated primers were optimized from a set sequences of cyclohexanol dehydrogenase genes (chnA) as well as cyclohexanone monooxygenases (chnB) and used to amplify the gene cluster, which encodes the conversion of cyclohexanol to caprolactone. Phylogenetic analysis has indicated that the two gene clusters belong to different groups. The cyclohexane monooxygenase-induced activity which oxidizes also indole to 5-hydroxyindole has indicated the presence of a CYP-type system monooxygenase involved in the transformation of cyclohexane to cyclohexanol.

Comparative study on the production of poly(3-hydroxybutyrate) by thermophilic Chelatococcus daeguensis TAD1: a good candidate for large-scale production.

In spite of numerous advantages on operating fermentation at elevated temperatures, very few thermophilic bacteria with polyhydroxyalkanoates (PHAs)-accumulating ability have yet been found in contrast to the tremendous mesophiles with the same ability. In this study, a thermophilic poly(3-hydroxybutyrate) (PHB)-accumulating bacteria (Chelatococcus daeguensis TAD1), isolated from the biofilm of a biotrickling filter used for NOx removal, was extensively investigated and compared to other PHB-accumulating bacteria. The results demonstrate that C. daeguensis TAD1 is a growth-associated PHB-accumulating bacterium without obvious nutrient limitation, which was capable of accumulating PHB up to 83.6 % of cell dry weight (CDW, w/w) within just 24 h at 45 °C from glucose. Surprisingly, the PHB production of C. daeguensis TAD1 exhibited strong tolerance to high heat stress as well as nitrogen loads compared to that of other PHB-accumulating bacterium, while the optimal PHB amount (3.44 ± 0.3 g l(-1)) occurred at 50 °C and C/N = 30 (molar) with glucose as the sole carbon source. In addition, C. daeguensis TAD1 could effectively utilize various cheap substrates (starch or glycerol) for PHB production without pre-hydrolyzed, particularly the glycerol, exhibiting the highest product yield (Y P/S, 0.26 g PHB per gram substrate used) as well as PHB content (80.4 % of CDW, w/w) compared to other carbon sources. Consequently, C. daeguensis TAD1 is a viable candidate for large-scale production of PHB via utilizing starch or glycerol as the raw materials.

Removal of nitric oxide in a biotrickling filter under thermophilic condition using Chelatococcus daeguensis.

UNLABELLED: The development of a thermophilic biotrickling filter (BTF) system to inoculate a newly isolated strain of Chelatococcus daeguensis TAD1 for the effective treatment of nitric oxide (NO) is described. A bench-scale BTF was run under high concentrations of NO and 8% O2 in thermophilic aerobic environment. A novel aerobic denitrifier Chelatococcus daeguensis TAD1 was isolated from the biofilm of an on-site biotrickling filter and it showed a denitrifying capability of 96.1% nitrate removal rate in a 24 h period in aerobic environment at 50 degrees C, with no nitrite accumulation. The inlet NO concentration fluctuated between approximately 133.9 and 669.6 mg m-3 and kept on a steady NOx removal rate above 80% in an oxygen stream of 8%. The BTF system was able to consistently remove 80-93.7% NO when the inlet NO was 535.7 mg m-3 in an oxygen stream of 2-20%. The biological removal efficiency of NO at 50 degrees C is higher than that at 25 degrees C, suggesting that the aerobic denitrifier TAD1 display well denitrification performance under thermophilic condition. Starvation for 2, 4 and 8 days resulted in the re-acclimation times of Chelatococcus daeguensis TAD1 ranging between 4 and 16 hours. A longer recovery time than that for weekend shutdown will be required when a longer starvation occurs. The results presented here demonstrate the feasibility of biotrickling filter for the thermophilic removal of NOx from gas streams. IMPLICATIONS: A novel denitrifier Chelatococcus daeguensis TAD1 was isolated from an on-site biotrickling filter in aerobic environment at 50 degrees C. To date, C. daeguensis has not been previously reported to be an aerobic denitrifier. In this study, a thermophilic biotrickling filter system inoculated with Chelatococcus daeguensis TADI for treatment of nitric oxide is developed. In coal-fired power plants, influent flue gas stream for nitrogen oxides (NOx) removal typically exhibit temperatures between 50 and 60 degrees C. Traditionally, cooling gases to below 40 degrees C prior to biological treatment is inevitable, which is costly. Therefore, the application ofthermophilic microorganisms for the removal of nitric oxide (NO) at this temperature range would offer great savings and would greatly extend the applicability ofbiofilters and biotrickling filters. Until now there has not been any study published about thermophilic biological treatment of NO under aerobic condition.

Camelimonas abortus sp. nov., isolated from placental tissue of cattle.

A gram-negative, rod-shaped, non-spore-forming bacterium, isolated from placental tissue of a cow, was investigated for its taxonomic position. On the basis of 16S rRNA gene sequence similarities, strain UK34/07-5(T) was shown to belong to the class Alphaproteobacteria, closely related to the type strain of Camelimonas lactis (96.0 % sequence similarity). The polyamine pattern showed the major compound spermidine and moderate amounts of putrescine. The major quinone was ubiquinone Q-10. The polar lipid profile was composed of the major compounds phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol and phosphatidylmonomethylethanolamine and moderate amounts of diphosphatidylglycerol, three unidentified aminolipids and an unidentified phospholipid. The profile of major fatty acids, consisting of C(19 : 0) cyclo ω8c and C(18 : 1)ω7c, with C(18 : 0) 3-OH as the hydroxylated fatty acid, was very similar to that of C. lactis M 2040(T). The results of DNA-DNA hybridization and physiological and biochemical tests allowed both genotypic and phenotypic differentiation of the isolate from C. lactis. The relatively low 16S rRNA gene sequence similarity of 96.0 % to C. lactis M 2040(T) and marked differences in the polar lipid profiles as well as the results of physiological tests and the DNA-DNA hybridization data support the creation of a novel species, for which the name Camelimonas abortus sp. nov. is proposed, with the type strain UK34/07-5(T) ( = CIP 110303(T)  = CCUG 61094(T)  = DSM 24741(T)  = CCM 7941(T)).

Methylorosula polaris gen. nov., sp. nov., an aerobic, facultatively methylotrophic psychrotolerant bacterium from tundra wetland soil.

Three strains of Gram-negative, aerobic, motile bacteria with bipolar flagella were isolated from acidic tundra wetland soils near the city of Vorkuta and from the Chukotka and Yugorsky Peninsulas and designated strains V-022(T), Ch-022 and Ju-022. The cells were rod-shaped, 0.5-0.6 µm in width and 1.3-4.5 µm in length and reproduced by irregular fission. These bacteria were facultative methylotrophs that used methanol, methylamines and a wide range of other sources of carbon and energy such as sugars and polysaccharides, ethanol and amino acids. The isolates used the Calvin-Benson pathway for the assimilation of one-carbon compounds and were unable to fix nitrogen. The new strains were moderately acidophilic and psychrotolerant, capable of growth over a pH range of 4.0 to 7.8, with optimum growth at pH 5.5-6.0. Growth occurred between 4 and 30 °C (optimum 20-25 °C). The principal phospholipid fatty acid was C(18:1)ω7c. The DNA G+C content of strain V-022(T) was 65.2 mol%. Analysis of the 16S rRNA gene sequences revealed that all three isolates V-022(T), Ch-022 and Yu-022 exhibited almost identical 16S rRNA gene sequences (99.9% gene sequence similarity) and formed a new lineage within the class Alphaproteobacteria. The name Methylorosula polaris is suggested to accommodate this new genus and novel species with strain V-022(T) (=DSM 22001(T)=VKM V-2485(T)) as the type strain of the type species.

Evaluation of the coal-degrading ability of Rhizobium and Chelatococcus strains isolated from the formation water of an Indian coal bed.

The rise in global energy demand has prompted researches on developing strategies for transforming coal into a cleaner fuel. This requires isolation of microbes with the capability to degrade complex coal into simpler substrates to support methanogenesis in the coal beds. In this study, aerobic bacteria were isolated from an Indian coal bed that can solubilize and utilize coal as the sole source of carbon. The six bacterial isolates capable of growing on coal agar medium were identified on the basis of their 16S rRNA gene sequences, which clustered into two groups; Group I isolates belonged to the genus Rhizobium, whereas Group II isolates were identified as Chelatococcus species. Out of the 4 methods of whole genome fingerprinting (ERIC-PCR, REP-PCR, BOX-PCR, and RAPD), REPPCR showed maximum differentiation among strains within each group. Only Chelatococcus strains showed the ability to solubilize and utilize coal as the sole source of carbon. On the basis of 16S rRNA gene sequence and the ability to utilize different carbon sources, the Chelatococcus strains showed maximum similarity to C. daeguensis. This is the first report showing occurrence of Rhizobium and Chelatococcus strains in an Indian coal bed, and the ability of Chelatococcus isolates to solubilize and utilize coal as a sole source of carbon for their growth.

Methyloferula stellata gen. nov., sp. nov., an acidophilic, obligately methanotrophic bacterium that possesses only a soluble methane monooxygenase.

Two strains of aerobic methanotrophic bacteria, AR4(T) and SOP9, were isolated from acidic (pH 3.8-4.0) Sphagnum peat bogs in Russia. Another phenotypically similar isolate, strain LAY, was obtained from an acidic (pH 4.0) forest soil in Germany. Cells of these strains were Gram-negative, non-pigmented, non-motile, thin rods that multiplied by irregular cell division and formed rosettes or amorphous cell conglomerates. Similar to Methylocella species, strains AR4(T), SOP9 and LAY possessed only a soluble form of methane monooxygenase (sMMO) and lacked intracytoplasmic membranes. Growth occurred only on methane and methanol; the latter was the preferred growth substrate. mRNA transcripts of sMMO were detectable in cells when either methane or both methane and methanol were available. Carbon was assimilated via the serine and ribulose-bisphosphate (RuBP) pathways; nitrogen was fixed via an oxygen-sensitive nitrogenase. Strains AR4(T), SOP9 and LAY were moderately acidophilic, mesophilic organisms capable of growth between pH 3.5 and 7.2 (optimum pH 4.8-5.2) and at 4-33 °C (optimum 20-23 °C). The major cellular fatty acid was 18 : 1ω7c and the quinone was Q-10. The DNA G+C content was 55.6-57.5 mol%. The isolates belonged to the family Beijerinckiaceae of the class Alphaproteobacteria and were most closely related to the sMMO-possessing methanotrophs of the genus Methylocella (96.4-97.0 % 16S rRNA gene sequence similarity), particulate MMO (pMMO)-possessing methanotrophs of the genus Methylocapsa (96.1-97.0 %), facultative methylotrophs of the genus Methylovirgula (96.1-96.3 %) and non-methanotrophic organotrophs of the genus Beijerinckia (96.5-97.0 %). Phenotypically, strains AR4(T), SOP9 and LAY were most similar to Methylocella species, but differed from members of this genus by cell morphology, greater tolerance of low pH, detectable activities of RuBP pathway enzymes and inability to grow on multicarbon compounds. Therefore, we propose a novel genus and species, Methyloferula stellata gen. nov., sp. nov., to accommodate strains AR4(T), SOP9 and LAY. Strain AR4(T) ( = DSM 22108(T)  = LMG 25277(T)  = VKM B-2543(T)) is the type strain of Methyloferula stellata.

Environmental distribution and abundance of the facultative methanotroph Methylocella.

Methylocella spp. are facultative methanotrophs, which are able to grow not only on methane but also on multicarbon substrates such as acetate, pyruvate or malate. Methylocella spp. were previously thought to be restricted to acidic soils such as peatlands, in which they may have a key role in methane oxidation. There is little information on the abundance and distribution of Methylocella spp. in the environment. New primers were designed, and a real-time quantitative PCR method was developed and validated targeting Methylocella mmoX (encoding the α-subunit of the soluble methane monooxygenase) that allowed the quantification of Methylocella spp. in environmental samples. We also developed and validated specific PCR assays, which target 16S rRNA genes of known Methylocella spp. These were used to investigate the distribution of Methylocella spp. in a variety of environmental samples. It was revealed that Methylocella species are widely distributed in nature and not restricted to acidic environments.

Complete genome sequence of Beijerinckia indica subsp. indica.

Beijerinckia indica subsp. indica is an aerobic, acidophilic, exopolysaccharide-producing, N(2)-fixing soil bacterium. It is a generalist chemoorganotroph that is phylogenetically closely related to facultative and obligate methanotrophs of the genera Methylocella and Methylocapsa. Here we report the full genome sequence of this bacterium.