Burkholderia insulsa sp. nov., a facultatively chemolithotrophic bacterium isolated from an arsenic-rich shallow marine hydrothermal system

Comparative analysis of esophageal gland microbes between two body sizes of Gigantopelta aegis, a hydrothermal snail from the Southwest Indian Ridge

Microbial communities within animals provide nutritional foundation and energy supply for the hydrothermal ecosystem. The peltospirid snail Gigantopelta aegis forms large aggregation in the Longqi vent field on the Southwest Indian Ridge. This endemic species is characterized by a changeable diet and morphology, especially reflected in internal organs such as remarkably enlarged esophageal glands. Here, 16S full-length rRNA gene analysis was performed to compare the variations in esophageal gland microbiota between two body size groups (small and large) of G. aegis. Phyla Proteobacteria and Bacteroidetes were the dominant featured bacteria contributing to the microbial community. No significant differences between the small and large groups were revealed by the diversity index and principal component analysis (PCA) clustering. The differences were in the relative abundance of bacteria. Compared with small-sized snails, the larger ones housed more Thiogranum (9.94% to 34.86%) and fewer Sediminibacterium (29.38% to 4.54%). Functional prediction for all of the microbiota showed that the pathways related to metabolism appeared highly abundant in smaller G. aegis. However, for the larger ones, the most distinctive pathways were those of environmental information processing. Facultative symbiotic Sulfurovum was marked as a core node in the co-occurrence network and suggested an influence on habitat selection of G. aegis in hydrothermal fields. In summary, variations in bacteria composition and potential functions possibly reflected changes in the anatomical structure and dietary habits of G. aegis. These dominant bacteria shared capabilities in nutritional supplementation and ecological niche expansion in the host, potentially a key adaptation for hydrothermal survival.IMPORTANCEDominant in the Longqi hydrothermal vent Southwest Indian Ridge, Gigantopelta aegis was observed to undergo unique and significant morphological changes and diet shifts known as cryptometamorphosis. During this process, G. aegis developed a specialized bacteria-housing organ, the esophageal gland, in the later life stages. Our research discovered variations in esophageal gland microbes between different body size groups of snails. These bacteria were closely related to the development and health of G. aegis. Full-length 16S rRNA gene analysis revealed more Thiogranum and fewer Sediminibacterium, suggesting a potential association with environmental adaptation. In the small-sized group, the potential functions were enriched in metabolism, while in larger G. aegis individuals, predictions indicated adaptive functions such as environmental information processing. Also, symbiotic Sulfurovum could be one of the factors influencing the habitat selection of G. aegis. Understanding the complex relationship between benthic macrofauna and microbes helps us describe the mechanisms of survival in extreme environments.

Antimony resistant bacteria isolated from Budúcnosť adit (Pezinok-Kolársky vrch deposit) in western Slovakia

Potentially toxic elements (PTE), such as antimony (Sb), are dangerous putative contaminants for ground and surface waters around abandoned mines and ore deposits in Slovakia. Nearby mines antimony is commonly coprecipitated in ochre sediments precipitated from Fe-rich drainage waters and, therefore, these sites function as natural scavengers of this metalloid. Bacteria are well known to contribute to the process of redox state maintenance, biosorption and bioaccumulation of antimony and, consequently, to antimony precipitation or release from iron oxides complexes. Here we isolated 48 bacterial strains from circumneutral hydrous ferric oxides (HFO) rich iron ochres accumulated in the waters running from tailing pounds nearby Budúcnosť mine, Pezinok, Slovakia and polluted with high, but fluctuating, concentrations of antimony (130 μg/l Sb in water and 2317 mg/kg Sb in iron ochre in average). The isolated strains were V1-V9 16S rRNA sequenced and the resulting taxonomic affiliations of isolated strains were compared with taxonomy assignments obtained by V4 16S rRNA next generation sequencing approach, including two independent NGS analysis pipelines and different taxonomy classifiers ((IDTAXA (RDP, GTDB, SILVA, CONTAX), MEGAN (NCBI), RDP a SILVAngs). A Sb resistant subgroup of isolated strains (Pseudomonas A60B, Pseudomonas A59, Pseudomonas A28, Aeromonas A21, Aeromonas A13, Aeromonas A60A, Acinetobacter A14, Buttiauxella A58, Shewanella A20A a Yersinia A68), well growing at high Sb concentration (300 mg/l Sb), was tested for an ability of the strains to retain Sb from cultivation media. Based on ICP-MS measurements of the dried biomasses we concluded that all the strains can retain antimony from growth media to some extent, with strains Shewanella A20A, Buttiauxella A58, Yersinia A68 and Aeromonas A60A being the most effective.

Genome-based taxonomy of Burkholderia sensu lato: Distinguishing closely related species

The taxonomy of Burkholderia sensu lato (s.l.) has been revisited using genome-based tools, which have helped differentiate closely related species. Many species from this group are indistinguishable through phenotypic traits and 16S rRNA gene sequence analysis. Furthermore, they also exhibit whole-genome Average Nucleotide Identity (ANI) values in the twilight zone for species circumscription (95-96%), which may impair their correct classification. In this work, we provided an updated Burkholderia s.l. taxonomy focusing on closely related species and give other recommendations for those developing genome-based taxonomy studies. We showed that a combination of ANI and digital DNA-DNA hybridization (dDDH) applying the universal cutoff values of 95% and 70%, respectively, successfully discriminates Burkholderia s.l. species. Using genome metrics with this pragmatic criterion, we demonstrated that i) Paraburkholderia insulsa should be considered a later heterotypic synonym of Paraburkholderia fungorum; ii) Paraburkholderia steynii differs from P. terrae by harboring symbiotic genes; iii) some Paraburkholderia are indeed different species based on dDDH values, albeit sharing ANI values close to 95%; iv) some Burkholderia s.l. indeed represent new species from the genomic viewpoint; iv) some genome sequences should be evaluated with care due to quality concerns.

Genome-based Reclassification of Paraburkholderia insulsa as a Later Heterotypic Synonym of Paraburkholderia fungorum and Proposal of Paraburkholderia terrae subsp. terrae subsp. nov. and Paraburkholderia terrae subsp. steynii subsp. nov

Based on the 16S rRNA gene sequences similarity of > 99.8%, the phylogeny of 88 Paraburkholderia strains was reconstructed. Further, they were subjected to overall genome-related indices (OGRI), which resulted in the identification of distinct pairs of species that were closely related. A pair consist of the type strains of Paraburkholderia insulsa and Paraburkholderia fungorum possessed a dDDH value of 87.9%, correspondingly, and the average nucleotide identity (ANI) value was 98.5%. Based on the phylogenetic analysis, OGRI and phenotypical evidence, P. insulsa was proposed as a later heterotypic synonym of P. fungorum. Furthermore, a pair comprising type strains of Paraburkholderia terrae and Paraburkholderia steynii possessed dDDH and ANI values of 71.2% and 96.6%, respectively, and difference in phenotypic traits, which supports a subspecies proposal within these taxa. Thus, the recently described Paraburkholderia steynii was proposed into two subspecies namely Paraburkholderia terrae subsp terrae subsp. nov and as Paraburkholderia terrae subsp. steynii subsp. nov.

Understanding Microbial Arsenic-Mobilization in Multiple Aquifers: Insight from DNA and RNA Analyses

Biogeochemical processes critically control the groundwater arsenic (As) enrichment; however, the key active As-mobilizing biogeochemical processes and associated microbes in high dissolved As and sulfate aquifers are poorly understood. To address this issue, the groundwater-sediment geochemistry, total and active microbial communities, and their potential functions in the groundwater-sediment microbiota from the western Hetao basin were determined using 16S rRNA gene (rDNA) and associated 16S rRNA (rRNA) sequencing. The relative abundances of either sediment or groundwater total and active microbial communities were positively correlated. Interestingly, groundwater active microbial communities were mainly associated with ammonium and sulfide, while sediment active communities were highly related to water-extractable nitrate. Both sediment-sourced and groundwater-sourced active microorganisms (rRNA/rDNA ratios > 1) noted Fe(III)-reducers (induced by ammonium oxidation) and As(V)-reducers, emphasizing the As mobilization via Fe(III) and/or As(V) reduction. Moreover, active cryptic sulfur cycling between groundwater and sediments was implicated in affecting As mobilization. Sediment-sourced active microorganisms were potentially involved in anaerobic pyrite oxidation (driven by denitrification), while groundwater-sourced organisms were associated with sulfur disproportionation and sulfate reduction. This study provides an extended whole-picture concept model of active As-N-S-Fe biogeochemical processes affecting As mobilization in high dissolved As and sulfate aquifers.

The Hidden Genomic Diversity, Specialized Metabolite Capacity, and Revised Taxonomy of Burkholderia Sensu Lato

Burkholderia sensu lato is a collection of closely related genera within the family Burkholderiaceae that includes species of environmental, industrial, biotechnological, and clinical importance. Multiple species within the complex are the source of diverse specialized metabolites, many of which have been identified through genome mining of their biosynthetic gene clusters (BGCs). However, the full, true genomic diversity of these species and genera, and their biosynthetic capacity have not been investigated. This study sought to cluster and classify over 4000 Burkholderia sensu lato genome assemblies into distinct genomic taxa representing named and uncharacterized species. We delineated 235 species groups by average nucleotide identity analyses that formed seven distinct phylogenomic clades, representing the genera of Burkholderia sensu lato: Burkholderia, Paraburkholderia, Trinickia, Caballeronia, Mycetohabitans, Robbsia, and Pararobbisa. A total of 137 genomic taxa aligned with named species possessing a sequenced type strain, while 93 uncharacterized species groups were demarcated. The 95% ANI threshold proved capable of delineating most genomic species and was only increased to resolve several closely related species. These analyses enabled the assessment of species classifications of over 4000 genomes, and the correction of over 400 genome taxonomic assignments in public databases into existing and uncharacterized genomic species groups. These species groups were genome mined for BGCs, their specialized metabolite capacity calculated per species and genus, and the number of distinct BGCs per species estimated through kmer-based de-replication. Mycetohabitans species dedicated a larger proportion of their relatively small genomes to specialized metabolite biosynthesis, while Burkholderia species harbored more BGCs on average per genome and possessed the most distinct BGCs per species compared to the remaining genera. Exploring the hidden genomic diversity of this important multi-genus complex contributes to our understanding of their taxonomy and evolutionary relationships, and supports future efforts toward natural product discovery.

Paraburkholderia dioscoreae sp. nov., a novel plant associated growth promotor

A novel bacterium, designated strain Msb3T, was recently isolated from leaves of the yam family plant Dioscorea bulbifera (Dioscoreaceae). Phylogenetic analysis based on the 16S rRNA gene sequence indicated that this strain belonged to the genus Paraburkholderia with Paraburkholderia xenovorans as nearest validly named neighbour taxon (99.3 % sequence similarity towards the P. xenovorans type strain). Earlier genome sequence analysis revealed a genome of 8.35 Mb in size with a G+C content of 62.5 mol%, which was distributed over two chromosomes and three plasmids. Here, we confirm that strain Msb3T represents a novel Paraburkholderia species. In silico DNA-DNA hybridization and average nucleotide identity (OrthoANIu) analyses towards P. xenovorans LB400T yielded 58.4 % dDDH and 94.5 % orthoANIu. Phenotypic and metabolic characterization revealed growth at 15 °C on tryptic soy agar, growth in the presence of 1 % NaCl and the lack of assimilation of phenylacetic acid as distinctive features. Together, these data demonstrate that strain Msb3T represents a novel species of the genus Paraburkholderia, for which we propose the name Paraburkholderia dioscoreae sp. nov. The type strain is Msb3T (=LMG 31881T, DSM 111632T, CECT 30342T).

Genomic Aromatic Compound Degradation Potential of Novel Paraburkholderia Species: Paraburkholderia domus sp. nov., Paraburkholderia haematera sp. nov. and Paraburkholderia nemoris sp. nov

We performed a taxonomic and comparative genomics analysis of 67 novel Paraburkholderia isolates from forest soil. Phylogenetic analysis of the recA gene revealed that these isolates formed a coherent lineage within the genus Paraburkholderia that also included Paraburkholderiaaspalathi, Paraburkholderiamadseniana, Paraburkholderiasediminicola, Paraburkholderiacaffeinilytica, Paraburkholderiasolitsugae and Paraburkholderiaelongata and four unidentified soil isolates from earlier studies. A phylogenomic analysis, along with orthoANIu and digital DNA–DNA hybridization calculations revealed that they represented four different species including three novel species and P. aspalathi. Functional genome annotation of the strains revealed several pathways for aromatic compound degradation and the presence of mono- and dioxygenases involved in the degradation of the lignin-derived compounds ferulic acid and p-coumaric acid. This co-occurrence of multiple Paraburkholderia strains and species with the capacity to degrade aromatic compounds in pristine forest soil is likely caused by the abundant presence of aromatic compounds in decomposing plant litter and may highlight a diversity in micro-habitats or be indicative of synergistic relationships. We propose to classify the isolates representing novel species as Paraburkholderia domus with LMG 31832^T (=CECT 30334) as the type strain, Paraburkholderia nemoris with LMG 31836^T (=CECT 30335) as the type strain and Paraburkholderia haematera with LMG 31837^T (=CECT 30336) as the type strain and provide an emended description of Paraburkholderia sediminicola Lim et al. 2008.

Multiple effects of nitrate amendment on the transport, transformation and bioavailability of antimony in a paddy soil-rice plant system

Nitrate (NO₃^-) is known to be actively involved in the processes of mineralization and heavy metal transformation; however, it is unclear whether and how it affects the bioavailability of antimony (Sb) in paddy soils and subsequent Sb accumulation in rice. Here, the effects of NO₃^- on Sb transformation in soil-rice system were investigated with pot experiments over the entire growth period. Results demonstrated that NO₃^- reduced Sb accumulation in brown rice by 15.6% compared to that in the control. After amendment with NO₃^-, the Sb content in rice plants increased initially and then gradually decreased (in roots by 46.1%). During the first 15 days, the soil pH increased, the oxidation of Sb(III) and sulfides was promoted, but the reduction of iron oxide minerals was inhibited, resulting in the release of adsorbed and organic-bound Sb from soil. The microbial arsenite-oxidizing marker gene aoxB played an important role in Sb(III) oxidation. From days 15 to 45, after NO₃^- was partially consumed, the soil pH decreased, and the reductive dissolution of Fe(III)-bearing minerals was enhanced; consequently, iron oxide-bound Sb was transformed into adsorbed and dissolved Sb species. After day 45, NO₃^- was completely reduced, Sb(V) was evidently reduced to Sb(III), and green rust was generated gradually. Thus, the available Sb decreased due to its enhanced affinity for iron oxides. Moreover, NO₃^- inhibited the reductive dissolution of iron minerals, which ultimately caused low Sb availability. Therefore, NO₃^- can chemically and biologically reduce the Sb availability in paddy soils and alleviate Sb accumulation in rice. This study provides a potential strategy for decreasing Sb accumulation in rice in the Sb-contaminated sites.

Paraburkholderia madseniana sp. nov., a phenolic acid-degrading bacterium isolated from acidic forest soil

RP11^T was isolated from forest soil following enrichment with 4-hydroxybenzoic acid. Cells of RP11^T are aerobic, non-sporulating, exhibit swimming motility, and are rods (0.8 µm by 1.4 µm) that often occur as diplobacillus or in short chains (3-4 cells). Optimal growth on minimal media containing 4-hydroxybenzoic acid (µ=0.216 hr^-1) occurred at 30 °C, pH 6.5 or 7.0 and 0% salinity. Comparative chemotaxonomic, genomic and phylogenetic analyses revealed the isolate was distinct from its closest relative type strains identified as Paraburkholderia aspalathi LMG 27731^T, Paraburkholderia fungorum LMG 16225^T and Paraburkholderia caffeinilytica CF1^T. Strain RP11^T is genetically distinct from P. aspalathi, its closest relative, in terms of 16S rRNA gene sequence similarity (98.7%), genomic average nucleotide identity (94%) and in silico DNA-DNA hybridization (56.7 %±2.8). The composition of fatty acids and substrate utilization pattern differentiated strain RP11^T from its closest relatives, including growth on phthalic acid. Strain RP11^T encoded the greatest number of aromatic degradation genes of all eleven closely related type strains and uniquely encoded a phthalic acid dioxygenase and paralog of the 3-hydroxybenzoate 4-monooxygenase. The only ubiquinone detected in strain RP11^T was Q-8, and the major cellular fatty acids were C_16 : 0, 3OH-C_16 : 0, C_17 : 0 cyclo, C_19 : 0 cyclo ω8c, and summed feature 8 (C_18 : 1 ω7c/ω6c). On the basis of this polyphasic approach, it was determined that strain RP11^T represents a novel species from the genus Paraburkholderia for which the name Paraburkholderia madseniana sp. nov. is proposed. The type strain is RP11^T (=DSM 110123^T=LMG 31517^T).

Paraburkholderia telluris sp. nov., isolated from subtropical forest soil

Strain DHOC27^T is a Gram-stain-negative, aerobic, non-motile, light yellow-pigmented and rod-shaped bacterium isolated from the forest soil of Dinghushan Biosphere Reserve, Guangdong Province, PR China. It grew at 4-37 °C (optimal 28-33 °C), pH 4.0-8.5 (optimal 4.5-6.0) and 0-1.5 (optimal 0-0.5) % (w/v) NaCl. The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain formed a clade with Paraburkholderia phenazinium LMG 2247^T, Paraburkholderia. sartisoli LMG 24000^T and Paraburkholderia. pallidirosea DHOK13^T, with a sequence similarity of 98.5, 97.5 and 98.1 % to the above strains, respectively. The DNA G+C content of DHOC27^T was 62.3 mol%. The digital DNA-DNA relatedness values and the average nucleotide identities between strain DHOC27^T and P. phenazinium LMG 2247^T and P. sartisoli LMG 24000^T were 26.9 and 24.3 % and 82.3 and 79.9 %, respectively. C16 : 0, C17 : 0 cyclo and C19 : 0 cyclo ω8c were the major fatty acids, and ubiquinone-8 was the major respiratory quinone detected, all of which supported the affiliation of DHOC27^T to the genus Paraburkholderia. On the basis of the data presented above, strain DHOC27^T represents a novel species of the genus Paraburkholderia and the name Paraburkholderia telluris sp. nov. is proposed. The type strain is DHOC27^T (=LMG 30263^T=GDMCC 1.1281^T).

Two new 2-alkylquinolones, inhibitory to the fish skin ulcer pathogen Tenacibaculum maritimum, produced by a rhizobacterium of the genus Burkholderia sp

Exploration of rhizobacteria of the genus Burkholderia as an under-tapped resource of bioactive molecules resulted in the isolation of two new antimicrobial 2-alkyl-4-quinolones. (E)-2-(Hept-2-en-1-yl)quinolin-4(1H)-one (1) and (E)-2-(non-2-en-1-yl)quinolin-4(1H)-one (3) were isolated from the culture broth of strain MBAF1239 together with four known alkylquinolones (2 and 4-6), pyrrolnitrin (7), and BN-227 (8). The structures of 1 and 3 were unambiguously characterized using NMR spectroscopy and mass spectrometry. Compounds 1-8 inhibited the growth of the marine bacterium Tenacibaculum maritimum, an etiological agent of skin ulcers in marine fish, offering new opportunities to develop antibacterial drugs for fish farming.

Paraburkholderia aromaticivorans sp. nov., an aromatic hydrocarbon-degrading bacterium, isolated from gasoline-contaminated soil

A Gram-stain-negative, facultatively aerobic, aromatic hydrocarbon-degrading bacterium, designated strain BN5^T, was isolated from gasoline-contaminated soil. Cells were motile and slightly curved rods with a single flagellum showing catalase and oxidase activities. Growth was observed at 20-37 °C (optimum, 25-30 °C), pH 3-7 (optimum, pH 5-6) and 0-2 % NaCl (optimum, 0 %). Ubiquinone-8 was the predominant respiratory quinone. The major fatty acids were C16 : 0, cyclo-C19 : 0ω8c and summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c). Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unidentified phosphoamino lipid, three unidentified amino lipids and eight unidentified lipids were the identified polar lipids. The DNA G+C content was 62.93 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain BN5^T formed a phylogenic lineage with members of the genus Paraburkholderia and showed the highest 16S rRNA gene sequence similarities to Paraburkholderia phytofirmans PsJN^T (99.4 %), Paraburkholderia dipogonis DL7^T (98.8 %) and Paraburkholderia insulsa PNG-April^T (98.8 %). The average nucleotide identity and in silico DNA-DNA hybridization (DDH) values between strain BN5^T and P. phytofirmans PsJN^T were 88.5 and 36.5 %, respectively. The DDH values for strain BN5^T with P. dipogonis LMG 28415^T and P. insulsa DSM 28142^T were 41.0±4.9 % (reciprocal, 33.0±4.3 %) and 47.1±6.6 % (reciprocal, 51.7±5.4 %), respectively. Based on its physiological, chemotaxonomic and phylogenetic features, we conclude that strain BN5^T is a novel species of the genus Paraburkholderia, for which the name Paraburkholderia aromaticivorans sp. nov. is proposed. The type strain is BN5^T (=KACC 19419^T=JCM 32303^T).

Dominant bacterial phyla in caves and their predicted functional roles in C and N cycle

BACKGROUND

Bacteria present in cave often survive by modifying their metabolic pathway or other mechanism. Understanding these adopted bacteria and their survival strategy inside the cave is an important aspect of microbial ecology. Present study focuses on the bacterial community and geochemistry in five caves of Mizoram, Northeast India. The objective of this study was to explore the taxonomic composition and presumed functional diversity of cave sediment metagenomes using paired end Illumina sequencing using V3 region of 16S rRNA gene and bioinformatics pipeline.

RESULTS

Actinobacteria, Proteobacteria, Verrucomicrobia and Acidobacteria were the major phyla in all the five cave sediment samples. Among the five caves the highest diversity is found in Lamsialpuk with a Shannon index 12.5 and the lowest in Bukpuk (Shannon index 8.22). In addition, imputed metagenomic approach was used to predict the functional role of microbial community in biogeochemical cycling in the cave environments. Functional module showed high representation of genes involved in Amino Acid Metabolism in (20.9%) and Carbohydrate Metabolism (20.4%) in the KEGG pathways. Genes responsible for carbon degradation, carbon fixation, methane metabolism, nitrification, nitrate reduction and ammonia assimilation were also predicted in the present study.

CONCLUSION

The cave sediments of the biodiversity hotspot region possessing a oligotrophic environment harbours high phylogenetic diversity dominated by Actinobacteria and Proteobacteria. Among the geochemical factors, ferric oxide was correlated with increased microbial diversity. In-silico analysis detected genes involved in carbon, nitrogen, methane metabolism and complex metabolic pathways responsible for the survival of the bacterial community in nutrient limited cave environments. Present study with Paired end Illumina sequencing along with bioinformatics analysis revealed the essential ecological role of the cave bacterial communities. These results will be useful in documenting the biospeleology of this region and systematic understanding of bacterial communities in natural sediment environments as well.

Depth-resolved microbial community analyses in two contrasting soil cores contaminated by antimony and arsenic

Investigation of microbial communities of soils contaminated by antimony (Sb) and arsenic (As) is necessary to obtain knowledge for their bioremediation. However, little is known about the depth profiles of microbial community composition and structure in Sb and As contaminated soils. Our previous studies have suggested that historical factors (i.e., soil and sediment) play important roles in governing microbial community structure and composition. Here, we selected two different types of soil (flooded paddy soil versus dry corn field soil) with co-contamination of Sb and As to study interactions between these metalloids, geochemical parameters and the soil microbiota as well as microbial metabolism in response to Sb and As contamination. Comprehensive geochemical analyses and 16S rRNA amplicon sequencing were used to shed light on the interactions of the microbial communities with their environments. A wide diversity of taxonomical groups was present in both soil cores, and many were significantly correlated with geochemical parameters. Canonical correspondence analysis (CCA) and co-occurrence networks further elucidated the impact of geochemical parameters (including Sb and As contamination fractions and sulfate, TOC, Eh, and pH) on vertical distribution of soil microbial communities. Metagenomes predicted from the 16S data using PICRUSt included arsenic metabolism genes such as arsenate reductase (ArsC), arsenite oxidase small subunit (AoxA and AoxB), and arsenite transporter (ArsA and ACR3). In addition, predicted abundances of arsenate reductase (ArsC) and arsenite oxidase (AoxA and AoxB) genes were significantly correlated with Sb contamination fractions, These results suggest potential As biogeochemical cycling in both soil cores and potentially dynamic Sb biogeochemical cycling as well.

Insertion sequences enrichment in extreme Red sea brine pool vent

Mobile genetic elements are major agents of genome diversification and evolution. Limited studies addressed their characteristics, including abundance, and role in extreme habitats. One of the rare natural habitats exposed to multiple-extreme conditions, including high temperature, salinity and concentration of heavy metals, are the Red Sea brine pools. We assessed the abundance and distribution of different mobile genetic elements in four Red Sea brine pools including the world's largest known multiple-extreme deep-sea environment, the Red Sea Atlantis II Deep. We report a gradient in the abundance of mobile genetic elements, dramatically increasing in the harshest environment of the pool. Additionally, we identified a strong association between the abundance of insertion sequences and extreme conditions, being highest in the harshest and deepest layer of the Red Sea Atlantis II Deep. Our comparative analyses of mobile genetic elements in secluded, extreme and relatively non-extreme environments, suggest that insertion sequences predominantly contribute to polyextremophiles genome plasticity.

Paraburkholderiapallidirosea sp. nov., isolated from a monsoon evergreen broad-leaved forest soil

A Gram-stain-negative, rod-shaped, aerobic and motile bacterial strain, DHOK13T, was isolated from the forest soils of Dinghushan Biosphere Reserve, Guangdong Province, PR China (112° 31' E, 23° 10' N). It grew optimally at 28-33 °C and pH 7.0-7.5. The main fatty acids were C16 : 0, C17 : 0 cyclo, C19 : 0 cycloω8c, summed feature 2 (C12 : 0 aldehyde and/or unknown 10.9525) and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). The organism contained ubiquinone Q-8 as the predominant isoprenoid quinone. The total DNA G+C content of strain DHOK13T was 62.0 mol%. Phylogenetic analysis of the 16S rRNA gene, as well as the sequence of the partial housekeeping genes, gyrB and recA, showed consistently that strain DHOK13T formed an independent cluster with Paraburkholderia phenazinium LMG 2247T. DNA-DNA hybridization studies showed relatively low relatedness values (39 %) of strain DHOK13T with P. phenazinium LMG 2247T. The phenotypic, chemotaxonomic and phylogenetic data showed that strain DHOK13T represents a novel species of the genus Paraburkholderia for which the name Paraburkholderia pallidirosea sp. nov. is proposed. The type strain is DHOK13T (=KCTC 42626T=LMG 28846T).

Paraburkholderia nodosa is the main N2-fixing species trapped by promiscuous common bean (Phaseolus vulgaris L.) in the Brazilian 'Cerradão'

The bacterial genus Burkholderia comprises species occupying several habitats, including a group of symbionts of leguminous plants-also called beta-rhizobia-that has been recently ascribed to the new genus Paraburkholderia We used common bean (Phaseolus vulgaris L.) plants to trap rhizobia from an undisturbed soil of the Brazilian Cerrado under the vegetation type 'Cerradão'. Genetic characterization started with the analyses of 181 isolates by BOX-PCR, where the majority revealed unique profiles, indicating high inter- and intra-species diversity. Restriction fragment length polymorphism-PCR of the 16S rRNA of representative strains of the BOX-PCR groups indicated two main clusters, and gene-sequencing analysis identified the minority (27%) as Rhizobium and the majority (73%) as Paraburkholderia Phylogenetic analyses of the 16S rRNA and housekeeping (recA and gyrB) genes positioned all strains of the second cluster in the species P. nodosa, and the phylogeny of a symbiotic gene-nodC-was in agreement with the conserved genes. All isolates were stable vis-à-vis nodulating common bean, but, in general, with a low capacity for fixing N2, although some effective strains were identified. The predominance of P. nodosa might be associated with the edaphic properties of the Cerrado biome, and might represent an important role in terms of maintenance of the ecosystem, which is characterized by acid soils with high saturation of aluminum and low N2 content.

Transfer of eleven species of the genus Burkholderia to the genus Paraburkholderia and proposal of Caballeronia gen. nov. to accommodate twelve species of the genera Burkholderia and Paraburkholderia

It has been proposed to split the genus Burkholderia into two genera according to phylogenetic clustering: (1) a genus retaining this name and consisting mainly of animal and plant pathogens and (2) the genus Paraburkholderia including so-called environmental bacteria. The latter genus name has been validly published recently. During the period between the effective and valid publications of the genus name Paraburkholderia, 16 novel species of the genus Burkholderiawere described, but only two of them can be classified as members of this genus based on the emended genus description. Analysis of traits and phylogenetic positions of the other 11 species shows that they belong to the genus Paraburkholderia, and we propose to transfer them to this genus. The reclassified species names are proposed as Paraburkholderia dipogonis comb. nov., Paraburkholderia ginsengiterrae comb. nov., Paraburkholderia humisilvae comb. nov., Paraburkholderia insulsa comb. nov., Paraburkholderia kirstenboschensis comb. nov., Paraburkholderia metalliresistens comb. nov., Paraburkholderia monticola comb. nov., Paraburkholderia panaciterrae comb. nov., Paraburkholderia rhizosphaerae comb. nov., Paraburkholderia solisilvae comb. nov. and Paraburkholderia susongensis comb. nov. The remaining three species are transferred to the new genus Caballeronia gen. nov. proposed to accommodate twelve species of the genera Burkholderia and Paraburkholderia forming a distinctive clade in phylogenetic trees. The new genus members are Caballeronia choica comb. nov., Caballeronia cordobensis comb. nov., Caballeronia glathei comb. nov., Caballeronia grimmiae comb. nov., Caballeronia humi comb. nov., Caballeronia megalochromosomata comb. nov., Caballeronia jiangsuensis comb. nov., Caballeronia sordidicola comb. nov., Caballeronia telluris comb. nov., Caballeronia terrestris comb. nov., Caballeronia udeis comb. nov., and Caballeronia zhejiangensis comb. nov.