Gene organization and primary structure of a ribosomal RNA operon from Escherichia coli

Relationship of diversity and the secondary structure in 16S-23S rDNA internal transcribed spacer: a case in Vibrio parahaemolyticus

The 16S-23S rDNA internal transcribed spacer (ITS) sequence, located in the rrn operon, has been analyzed and evaluated for use in phylogenetic analysis and the detection target of bacteria. The ITS region displays a high level of diversity, being present in multiple copies and displaying variability in both length and sequence, and it carries more phylogenetic information than 16S rDNA. However, appropriately identifying ITS regions to use in analyses is challenging. To solve this problem, we analyzed the ITS regions in Vibrio parahaemolyticus and predicted the secondary structure of each analogous rrn transcript. The genomic DNA of V. parahaemolyticus contains approximately 8-14 rrns, making it more complex than the sequences of most other bacterial species. We analyzed 216 ITSs, of which 206 ITSs come from 18 complete genomes, and 10 ITSs were identified in the present study. The subunits of each ITS were distinguished by their predicted secondary structures. We propose a refined backbone model of the V. parahaemolyticus ITS that can be applied to the sequences of other bacteria. The backbone includes C, V, tDNA and linker blocks. These blocks, which may represent true functional units, may be used as potential targets for phylogenetic analysis or molecular detection.

Isolation and screening of aflatoxin-detoxifying yeast and bacteria from ruminal fluids to reduce aflatoxin B1 contamination in dairy cattle feed

AIMS

To obtain yeast and bacteria from ruminal fluids that possess aflatoxin B1 (AFB1 ) detoxifying ability for use in animal feed.

METHODS AND RESULTS

Sources of isolation were ruminal fluids of three nonfistulated dairy cows, fed diets containing cassava pulp, rice straw or distillery yeast sludge. The isolation was carried out to screen for the isolates that were active in both anaerobic and aerobic conditions. Three yeast and three bacteria isolates were selected. Up to 85% of AFB1 was detoxified by yeast isolates and up to 60% AFB1 reduction was evident by bacteria isolates. Two yeast isolates were identified as Kluyveromyces marxianus and one isolate as Pichia kudriavzevii. The three bacteria isolates were identified as Enterococcus faecium, Corynebacterium phoceense and C. vitaeruminis. All strains showed high biomass production when cultivated in medium with 80 g l-1 glucose.

CONCLUSIONS

The isolated yeast and bacteria with AFB1 detoxifying ability showed a good potential to be applied as an aflatoxin-detoxifying agent to ingredients used to feed dairy cattle.

SIGNIFICANCE AND IMPACT OF THE STUDY

The abilities of isolates to survive and be active in anaerobic and aerobic conditions rendered them to be active in cattle's rumen. Their biomass could be produced in bulk and used as feed supplement for aflatoxin detoxification in dairy cattle.

Amplification of bacterial genomic DNA from all ascitic fluids with a highly sensitive polymerase chain reaction

Due to varying positive rates of polymerase chain reaction (PCR) amplification, interpretation of conventional PCR results for non‑infectious ascites remains problematic. The present study developed a highly sensitive PCR protocol and investigated the positive rate of PCR for the 16S ribosomal (r)RNA gene in non‑infectious ascites. Following the design of a new PCR primer pair for the 16S rRNA gene (800F and 1400R), the sequences of PCR products were analyzed and the lower limit for bacterial DNA detection evaluated. The positive rate of PCR for 16S rRNA gene in non‑infectious ascites was also evaluated. PCR with the primer pair amplified the genomic DNA of 16S rRNA genes of major disease‑causing bacterial strains. Additionally, PCR with this primer pair provided highly sensitive detection of bacterial genomic DNA (lower limit, 0.1 pg of template DNA). When DNA samples isolated from ascites were used, the 16S rRNA gene was amplified independently of the presence of bacterial infection. PCR products contained the genomic DNA fragments of multiple bacterial species. Bacterial genomic DNA can be amplified from all ascitic fluids using a highly sensitive PCR protocol. Careful attention is required to interpret the results based on simple amplification of 16S rRNA gene with conventional PCR.

Specific enrichment of hyperthermophilic electroactive Archaea from deep-sea hydrothermal vent on electrically conductive support

While more and more investigations are done to study hyperthermophilic exoelectrogenic communities from environments, none have been performed yet on deep-sea hydrothermal vent. Samples of black smoker chimney from Rainbow site on the Atlantic mid-oceanic ridge have been harvested for enriching exoelectrogens in microbial electrolysis cells under hyperthermophilic (80 °C) condition. Two enrichments were performed in a BioElectrochemical System specially designed: one from direct inoculation of crushed chimney and the other one from inoculation of a pre-cultivation on iron (III) oxide. In both experiments, a current production was observed from 2.4 A/m² to 5.8 A/m² with a set anode potential of -0.110 V vs Ag/AgCl. Taxonomic affiliation of the exoelectrogen communities obtained on the electrode exhibited a specific enrichment of Archaea belonging to Thermococcales and Archeoglobales orders, even when both inocula were dominated by Bacteria.

Molecular study of wound healing after using biosynthesized BNC/Fe3O4 nanocomposites assisted with a bioinformatics approach

Background

Molecular investigation of wound healing has allowed better understanding about interaction of genes and pathways involved in healing progression.

Objectives

The aim of this study was to prepare magnetic/bacterial nanocellulose (Fe₃O₄/BNC) nanocomposite films as ecofriendly wound dressing in order to evaluate their physical, cytotoxicity and antimicrobial properties. The molecular study was carried out to evaluate expression of genes involved in healing of wounds after treatment with BNC/Fe₃O₄ films.

Study design, materials, and methods

Magnetic nanoparticles were biosynthesized by using Aloe vera extract in new isolated bacterial nanocellulose (BNC) RM1. The nanocomposites were characterized using X-ray diffraction, Fourier transform infrared, and field emission scanning electron microscopy. Moreover, swelling property and metal ions release profile of the nanocomposites were investigated. The ability of nanocomposites to promote wound healing of human dermal fibroblast cells in vitro was examined. Bioinformatics databases were used to identify genes with important healing effect. Key genes which interfered with healing were studied by quantitative real time PCR.

Results

Spherical magnetic nanoparticles (15–30 nm) were formed and immobilized within the structure of BNC. The BNC/Fe₃O₄ was nontoxic (IC₅₀>500 μg/mL) with excellent wound healing efficiency after 48 hours. The nanocomposites showed good antibacterial activity ranging from 6±0.2 to 13.40±0.10 mm against Staphylococcus aureus, Staphylococcus epidermidis and Pseudomonas aeruginosa. The effective genes for the wound healing process were TGF-B1, MMP2, MMP9, Wnt4, CTNNB1, hsa-miR-29b, and hsa-miR-29c with time dependent manner. BNC/Fe₃O₄ has an effect on microRNA by reducing its expression and therefore causing an increase in the gene expression of other genes, which consequently resulted in wound healing.

Conclusion

This eco-friendly nanocomposite with excellent healing properties can be used as an effective wound dressing for treatment of cutaneous wounds.

Functional metagenomic approach to identify overlooked antibiotic resistance mutations in bacterial rRNA

Our knowledge as to how bacteria acquire antibiotic resistance is still fragmented, especially for the ribosome-targeting drugs. In this study, with the aim of finding novel mechanisms that render bacteria resistant to the ribosome-targeting antibiotics, we developed a general method to systematically screen for antibiotic resistant 16 S ribosomal RNAs (rRNAs), which are the major target for multiple antibiotics (e.g. spectinomycin, tetracycline, and aminoglycosides), and identify point mutations therein. We used Escherichia coli ∆7, a null mutant of the rrn (ribosomal RNA) operons, as a surrogate host organism to construct a metagenomic library of 16 S rRNA genes from the natural (non-clinical) environment. The library was screened for spectinomycin resistance to obtain four resistant 16 S rRNA genes from non-E. coli bacterial species. Bioinformatic analysis and site-directed mutagenesis identified three novel mutations - U1183C (the first mutation discovered in a region other than helix 34), and C1063U and U1189C in helix 34 - as well as three well-described mutations (C1066U, C1192G, and G1193A). These results strongly suggest that uncharacterized antibiotic resistance mutations still exist, even for traditional antibiotics.

Novosphingobium lubricantis sp. nov., isolated from a coolant lubricant emulsion

A yellow-pigmented, Gram-stain-negative, rod-shaped, non-spore-forming bacterium (strain KSS165-70^T) was isolated from a coolant lubricant emulsion. The 16S rRNA gene sequence analysis of strain KSS165-70^T showed high sequence similarity to the type strains of Novosphingobium subterraneum (98.1 %), Novosphingobium lentum (97.9 %) and Novosphingobium taihuense (97.8 %). Sequence similarities to type strains of all other Novosphingobium species were below 97.5 %. Ubiquinone Q-10 was detected as the major respiratory quinone. The predominant fatty acid C18 : 1ω7c and the typical 2-hydroxy fatty acid C14 : 0 2-OH were detected. The polar lipid profile contained the major lipids diphosphatidylglycerol, phosphatedylethanolamine, sphingoglycolipid, phosphatidylcholine and two unidentified phospholipids. The polyamine pattern contained the major compound spermidine. Characterization by 16S rRNA gene sequence analysis, physiological parameters, pigment analysis, and ubiquinone, polar lipid and fatty acid composition revealed that strain KSS165-70^T represents a new species of the genus Novosphingobium. For this reason, we propose the name Novosphingobium lubricantis sp. nov. with the type strain KSS165-70^T (=CIP 111490^T=CCM 8814^T).

Characterization and Rheological Behavior of Dextran from Weissella confusa R003

Dextran from Weissella confusa R003 isolated from sugar cane juice was purified and characterized. Dextran synthesis was performed by fermenting W. confusa R003 in MRS medium containing 10% (w/v) sucrose with continuous shaking at 125 rpm and at 30°C. For 24 hours, the 50% efficiency yield was obtained. Dextran in the culture medium was purified by ethanol precipitation. Structural analysis of dextran using 1H NMR, 13C NMR, and 2D NMR techniques showed the existence of glucoses with 97.4%  α (1→6) linkage in the main chains and 2.6%  α (1→3) in branches. The estimation of molecular weight by dynamic light scattering exhibited average molecular weight of 1.0 × 104 kDa. At low concentration (2.5% w/v), dextran behaved like liquid structure, while, increasing the concentration (5.0 and 10.0% w/v), it was revealed as viscoelastic behavior. The highest gelling phenomenon was found in the concentration of 10% w/v and at 37°C. Due to its production and properties, it may be suitable for commercial production and application in the field of foods as well as hydrogel.

Interactive effect of trivalent iron on activated sludge digestion and biofilm structure in attached growth reactor of waste tire rubber

Waste tire rubber (WTR) has been introduced as an alternative, novel media for biofilm development in several experimental systems including attached growth bioreactors. In this context, four laboratory-scale static batch bioreactors containing WTR as a support material for biofilm development were run under anoxic condition for 90 days using waste activated sludge as an inoculum under the influence of different concentrations (2.5, 6.5, 8.5 mg/l) of trivalent ferric iron (Fe³⁺). The data revealed that activated sludge with a Fe³⁺ concentration of 8.5 mg/l supported the maximum bacterial biomass [4.73E + 10 CFU/ml cm²]; besides, it removed 38% more Chemical oxygen demand compared to Fe³⁺ free condition from the reactor. Biochemical testing and 16S rDNA phylogenetic analysis of WTR-derived biofilm communities further suggested the role of varying concentrations of Fe³⁺ on the density and diversity of members of Enterobacteria(ceae), ammonium (AOB) and nitrite oxidizing bacteria. Furthermore, Fluorescent in situ hybridization with phylogenetic oligonucleotide probes and confocal laser scanning microscopy of WTR biofilms indicated a significant increase in density of eubacteria (3.00E + 01 to.05E + 02 cells/cm²) and beta proteobacteria (8.10E + 01 to 1.42E + 02 cells/cm²), respectively, with an increase in Fe³⁺ concentration in the reactors, whereas, the cell density of gamma proteobacteria in biofilms decreased.

Parendozoicomonas haliclonae gen. nov. sp. nov. isolated from a marine sponge of the genus Haliclona and description of the family Endozoicomonadaceae fam. nov. comprising the genera Endozoicomonas, Parendozoicomonas, and Kistimonas

Two Gram-stain-negative, facultative anaerobic, motile, rod-shaped strains, S-B4-1U^T and JOB-63a, forming small whitish transparent colonies on marine agar, were isolated from a sponge of the genus Haliclona. The strains shared 99.7% 16S rRNA gene sequence identity and a DNA-DNA hybridization value of 100%, but were differentiated by genomic fingerprinting using rep-PCRs. 16S rRNA gene sequence phylogeny placed the strains as a sister branch to the monophyletic genus Endozoicomonas (Oceanospirillales; Gammaproteobacteria) with 92.3-94.3% 16S rRNA gene sequence similarity to Endozoicomonas spp., 91.9 and 92.1% to Candidatus Endonucleobacter bathymodiolin, and 91.9 to 92.1% to the type strains of Kistimonas spp. Core genome based phylogeny of strain S-B4-1U^T confirmed the phylogenetic placement. Major fatty acids were summed feature 3 (C_16:1 ω7c/C_16:1 ω6c) and 8 (C_18:1 ω7c/C_18:1 ω6c) followed by C_10:0 3-OH, C_16:0, and C_18:0. The G+C content was 50.1-51.4mol%. The peptidoglycan diamino acid of strain S-B4-1U^T was meso-diaminopimelic acid, the predominant polyamine spermidine, the major respiratory quinone ubiquinone Q-9; phosphatidylethanolamine, phosphatidylglycerol and phosphatidylserine were major polar lipids. Based on the clear phylogenetic distinction, the genus Parendozoicomonas gen. nov. is proposed, with Parendozoicomonas haliclonae sp. nov. as type species and strain S-B4-1U^T (=CCM 8713^T=DSM 103671^T=LMG 29769^T) as type strain and JOB-63a as a second strain of the species. Based on the 16S rRNA gene sequence phylogeny of the Oceanospirillales within the Gammaproteobacteria, the Endozoicomonaceae fam. nov. is proposed including the genera Endozoicomonas, Parendozoicomonas, and Kistimonas as well as the Candidatus genus Endonucleobacter.

Valorization of pyrolysis water: a biorefinery side stream, for 1,2-propanediol production with engineered Corynebacterium glutamicum

BACKGROUND

A future bioeconomy relies on the efficient use of renewable resources for energy and material product supply. In this context, biorefineries have been developed and play a key role in converting lignocellulosic residues. Although a holistic use of the biomass feed is desired, side streams evoke in current biorefinery approaches. To ensure profitability, efficiency, and sustainability of the overall conversion process, a meaningful valorization of these materials is needed. Here, a so far unexploited side stream derived from fast pyrolysis of wheat straw-pyrolysis water-was used for production of 1,2-propanediol in microbial fermentation with engineered Corynebacterium glutamicum.

RESULTS

A protocol for pretreatment of pyrolysis water was established and enabled growth on its major constituents, acetate and acetol, with rates up to 0.36 ± 0.04 h^-1. To convert acetol to 1,2-propanediol, the plasmid pJULgldA expressing the glycerol dehydrogenase from Escherichia coli was introduced into C. glutamicum. 1,2-propanediol was formed in a growth-coupled biotransformation and production was further increased by construction of C. glutamicum Δpqo ΔaceE ΔldhA Δmdh pJULgldA. In a two-phase aerobic/microaerobic fed-batch process with pyrolysis water as substrate, this strain produced 18.3 ± 1.2 mM 1,2-propanediol with a yield of 0.96 ± 0.05 mol 1,2-propanediol per mol acetol and showed an overall volumetric productivity of 1.4 ± 0.1 mmol 1,2-propanediol L^-1 h^-1.

CONCLUSIONS

This study implements microbial fermentation into a biorefinery based on pyrolytic liquefaction of lignocellulosic biomass and accesses a novel value chain by valorizing the side stream pyrolysis water for 1,2-PDO production with engineered C. glutamicum. The established bioprocess operated at maximal product yield and accomplished the so far highest overall volumetric productivity for microbial 1,2-PDO production with an engineered producer strain. Besides, the results highlight the potential of microbial conversion of this biorefinery side stream to other valuable products.

Tuwongella immobilis gen. nov., sp. nov., a novel non-motile bacterium within the phylum Planctomycetes

A gram-negative, budding, catalase negative, oxidase positive and non-motile bacterium (MBLW1^T) with a complex endomembrane system has been isolated from a freshwater lake in southeast Queensland, Australia. Phylogeny based on 16S rRNA gene sequence analysis places the strain within the family Planctomycetaceae, related to Zavarzinella formosa (93.3 %), Telmatocola sphagniphila (93.3 %) and Gemmata obscuriglobus (91.9 %). Phenotypic and chemotaxonomic analysis demonstrates considerable differences to the type strains of the related genera. MBLW1^T displays modest salt tolerance and grows optimally at pH values of 7.5–8.0 and at temperatures of 32–36 °C. Transmission electron microscopy analysis demonstrates the presence of a complex endomembrane system, however, without the typically condensed nucleoid structure found in related genera. The major fatty acids are 16 : 1 ω5c, 16 : 0 and 18 : 0. Based on discriminatory results from 16S rRNA gene sequence analysis, phenotypic, biochemical and chemotaxonomic analysis, MBLW1^T should be considered as a new genus and species, for which the name Tuwongella immobilis gen. nov., sp. nov. is proposed. The type strain is MBLW1^T (=CCUG 69661^T=DSM 105045^T).

Description of Anaerotignum aminivorans gen. nov., sp. nov., a strictly anaerobic, amino-acid-decomposing bacterium isolated from a methanogenic reactor, and reclassification of Clostridium propionicum, Clostridium neopropionicum and Clostridium lactatifermentans as species of the genus Anaerotignum

A strictly anaerobic bacterial strain (SH021^T) was isolated from a methanogenic reactor. Cells were Gram-stain-positive, motile, straight or slightly curved rods. The optimum temperature for growth was 35 °C, and the optimum pH was 6.1-7.7. The strain was asaccharolytic and utilized amino acids as growth substrates. The strain produced acetate and propionate from l-alanine and l-serine, and propionate and butyrate from l-threonine. Branched-chain amino acids (l-isoleucine, l-leucine and l-valine) were utilized weakly, and isovalerate or isobutyrate was produced. Strain SH021^T utilized pyruvate and lactate, and converted them to acetate and propionate. The genomic DNA G+C content was 38.2 mol%. Compounds related to iso-C15 : 0 were detected as major components in the cellular fatty acids analysis. The diagnostic diamino acid of the cell-wall peptidoglycan was meso-diaminopimelic acid. On the basis of 16S rRNA gene sequences, the most closely related known species were Clostridium propionicum, Clostridium neopropionicum and Clostridium lactatifermentans in cluster XIVb of the class Clostridia. Based on the phylogenetic and phenotypic data, Anaerotignum aminivorans gen. nov., sp. nov. is proposed to accommodate strain SH021^T (=JCM 31556^T=DSM 103575^T). For the three related species of the genus Clostridium, Anaerotignum propionicum comb. nov. (type strain DSM 1682^T=JCM 1430^T=ATCC 25522^T=CCUG 9280^T=NCIMB 10656^T=VPI 5303^T), Anaerotignum neopropionicum comb. nov. (type strain X4^T=DSM 3847^T=KCTC 15564^T) and Anaerotignum lactatifermentans comb. nov. (type strain G17^T=DSM 14214^T=LMG 20954^T) are proposed with emended descriptions of these species.

Stenotrophomonas bentonitica sp. nov., isolated from bentonite formations

A Gram-stain negative, rod-shaped, aerobic bacterial strain, BII-R7^T, was isolated during a study targeting the culture-dependent microbial diversity occurring in bentonite formations from southern Spain. Comparative 16S rRNA gene sequence analysis showed that BII-R7^T represented a member of the genus Stenotrophomonas (class Gammaproteobacteria), and was related most closely to Stenotrophomonas rhizophila e-p10^T (99.2 % sequence similarity), followed by Stenotrophomonas pavanii ICB 89^T (98.5 %), Stenotrophomonas maltophilia IAM 12423^T, Stenotrophomonas chelatiphaga LPM-5^T and Stenotrophomonas tumulicola T5916-2-1b^T (all 98.3 %). Pairwise sequence similarities to all other type strains of species of the genus Stenotrophomonas were below 98 %. Genome-based calculations (orthologous average nucleotide identity, original average nucleotide identity, genome-to-genome distance and DNA G+C percentage) indicated clearly that the isolate represents a novel species within this genus. Different phenotypic analyses, such as the detection of a quinone system composed of the major compound ubiquinone Q-8 and a fatty acid profile with iso-C_15 : 0 and anteiso-C_15 : 0 as major components, supported this finding at the same time as contributing to a comprehensive characterization of BII-R7^T. Based on this polyphasic approach comprising phenotypic and genotypic/molecular characterization, BII-R7^T can be differentiated clearly from its phylogenetic neighbours, establishing a novel species for which the name Stenotrophomonas bentonitica sp. nov. is proposed with BII-R7^T as the type strain (=LMG 29893^T=CECT 9180^T=DSM 103927^T).

Crosstalk between vertical and horizontal gene transfer: plasmid replication control by a conjugative relaxase

Horizontal gene transfer is a key process in the evolution of bacteria and also represents a source of genetic variation in eukaryotes. Among elements participating in gene transfer, thousands of small (<10 kb) mobile bacterial plasmids that replicate by the rolling circle mechanism represent a driving force in the spread of antibiotic resistances. In general, these plasmids are built as genetic modules that encode a replicase, an antibiotic-resistance determinant, and a relaxase that participates in their conjugative mobilization. Further, they control their relatively high copy number (∼30 copies per genome equivalent) by antisense RNAs alone or combined with a repressor protein. We report here that the MobM conjugative relaxase encoded by the promiscuous plasmid pMV158 participates in regulation of the plasmid copy number by transcriptional repression of the antisense RNA, thus increasing the number of plasmid molecules ready to be horizontally transferred (mobilization) and/or vertically inherited (replication). This type of crosstalk between genetic modules involved in vertical and horizontal gene flow has not been reported before.

Genome mining, in silico validation and phase selection of a novel aldo-keto reductase from Candida glabrata for biotransformation

Previously, we published cloning, overexpression, characterization and subsequent exploitation of a carbonyl reductase (cr) gene, belonging to general family aldo-keto reductase from Candida glabrata CBS138 to convert keto ester (COBE) to a chiral alcohol (ethyl-4-chloro-3-hydroxybutanoate or CHBE). Exploiting global transcription factor CRP, rDNA and transporter engineering, we have improved batch production of CHBE by trinomial bioengineering. Herein, we present the exploration of cr gene in Candida glabrata CBS138 through genome mining approach, in silico validation of its activity and selection of its biocatalytic phase. For exploration of the gene under investigation, 3 template genes were chosen namely Saccharomyces cerevisae YDR541c, YGL157w and YOL151w. The CR showed significant homology match, overlapping of substrate binding site and NADPH binding site with the template proteins. The binding affinity of COBE toward CR (-4.6 Kcal/ mol) was found higher than that of the template proteins (-3.5 to -4.5 Kcal/ mol). Biphasic biocatalysis with cofactor regeneration improved product titer 4∼5 times better than monophasic biotransformation. Currently we are working on DNA Shuffling as a next level of strain engineering and we demonstrate this approach herein as a future strategy of biochemical engineering.

Paracandidimonas soli gen. nov., sp. nov., isolated from soil

A slightly yellow-pigmented, Gram-stain-negative, rod-shaped bacterium, strain IMT-305T, was isolated from soil in Alabama, USA. Phylogenetic analysis based on the nearly full-length 16S rRNA gene sequence placed the strain in between the genera Pusillimonas, Parapusillimonas and Candidimonas with highest 16S rRNA gene sequence similarity to the type strain of Parapusillimonas granuli (97.5 %) and Candidimonas nitroreducens (97.4 %). The genomic G+C content of strain IMT-305T was 63.9 mol%. The main cellular fatty acids were C18:1ω7c, C17:0 cyclo, C16:0 and C16:1ω7c/iso-C15:0 2-OH (detected as summed feature 3). The polyamine pattern of strain IMT-305T contained the major compound putrescine and the betaproteobacterial diagnostic 2-hydroxyputrescine and the major respiratory quinone was ubiquinone Q-8. Predominant polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylserine, an unidentified aminolipid, an unidentified aminophospholipid and an unidentified lipid lacking any functional group. Based on phylogenetic, chemotaxonomic and phenotypic analyses a novel species within a new genus, Paracandidimonas soli gen. nov., sp. nov., is proposed. The type strain of Paracandidimonas soli is IMT-305T (=DSM 100048T=CIP 110902T=LMG 28740T=CCM 8599T).

Population and function analysis of cultivable bacteria associated with spores of arbuscular mycorrhizal fungus Gigaspora margarita

This study was aimed to investigate the diversity and function of bacterial population associated with Gigaspora margarita spores. The fungus was propagated in sterilized sand/soil pots using alfalfa (Medicago sativa), grain sorghum (Sorghum bicolor), or maize (Zea mays) as host plants, or in sterilized vermiculite pots using alfalfa as host plants, respectively. Bacteria were isolated from the new-formed spores using diluted plate method, and typical bacterial isolates were identified according to 16S rRNA gene phylogenetic analysis. Total 43 bacterial isolates affiliated to three phyla and 23 genera were obtained. The spore-associated bacterial communities were obviously different among the four source spores, suggesting that plant species or substrates could influence the bacterial population. Bacillus and Streptomyces were most frequently associated with the fungal spores. Function analysis of these bacteria by plate tests, it was found that about 30.2% isolates stimulated the spore germination, five out of seven tested isolates improved the hyphal growth, total 57.5% of the tested isolates solubilized phosphorus at different levels, 15% isolates degraded chitin, and a few isolates suppressed the growth of Escherichia coli or Staphylococcus aureus. In pot experiment, three bacterial isolates (belonging to Curtobacterium, Ensifer, or Bacillus, respectively) displayed improvement effect on alfalfa growth and/or the colonization of roots by G. margarita.

Differential Regulation of rRNA and tRNA Transcription from the rRNA-tRNA Composite Operon in Escherichia coli

Escherichia coli contains seven rRNA operons, each consisting of the genes for three rRNAs (16S, 23S and 5S rRNA in this order) and one or two tRNA genes in the spacer between 16S and 23S rRNA genes and one or two tRNA genes in the 3’ proximal region. All of these rRNA and tRNA genes are transcribed from two promoters, P1 and P2, into single large precursors that are afterward processed to individual rRNAs and tRNAs by a set of RNases. In the course of Genomic SELEX screening of promoters recognized by RNA polymerase (RNAP) holoenzyme containing RpoD sigma, a strong binding site was identified within 16S rRNA gene in each of all seven rRNA operons. The binding in vitro of RNAP RpoD holoenzyme to an internal promoter, referred to the promoter of riRNA (an internal RNA of the rRNA operon), within each 16S rRNA gene was confirmed by gel shift assay and AFM observation. Using this riRNA promoter within the rrnD operon as a representative, transcription in vitro was detected with use of the purified RpoD holoenzyme, confirming the presence of a constitutive promoter in this region. LacZ reporter assay indicated that this riRNA promoter is functional in vivo. The location of riRNA promoter in vivo as identified using a set of reporter plasmids agrees well with that identified in vitro. Based on transcription profile in vitro and Northern blot analysis in vivo, the majority of transcript initiated from this riRNA promoter was estimated to terminate near the beginning of 23S rRNA gene, indicating that riRNA leads to produce the spacer-coded tRNA. Under starved conditions, transcription of the rRNA operon is markedly repressed to reduce the intracellular level of ribosomes, but the levels of both riRNA and its processed tRNA^Glu stayed unaffected, implying that riRNA plays a role in the continued steady-state synthesis of tRNAs from the spacers of rRNA operons. We then propose that the tRNA genes organized within the spacers of rRNA-tRNA composite operons are expressed independent of rRNA synthesis under specific conditions where further synthesis of ribosomes is not needed.

Community structure of a sulfate-reducing consortium in lead-contaminated wastewater treatment process

This study evaluated the capacity to remove lead by an indigenous consortium of five sulfate-reducing bacteria (SRB): Desulfobacterium autotrophicum, Desulfomicrobium salsugmis, Desulfomicrobium escambiense, Desulfovibrio vulgaris, and Desulfovibrio carbinolicus, using continuous moving bed biofilm reactor systems. Four continuous moving bed biofilm reactors (referred as R1-R4) were run in parallel for 40 days at lead loading rates of 0, 20, 30 and 40 mg l^-1 day^-1, respectively. The impact of lead on community structure of the SRB consortium was investigated by dsrB gene-based denaturing gradient gel electrophoresis (dsrB-based DGGE), fluorescence in situ hybridization (FISH) and chemical analysis. These results indicated that D. escambiense and D. carbinolicus were dominant in all analyzed samples and played a key role in lead removal in R2 (20 mg l^-1 day^-1) and R3 (30 mg l^-1 day^-1). However, in R4 (40 mg l^-1 day^-1), these two strains were barely detected by FISH and dsrB-based DGGE. As a result, SRB activity was severely affected by lead toxicity. High lead removal efficiencies of lead (99-100%) were observed in R2 and R3 throughout the operation, whereas that in R4 was significantly decreased (91%) after 40 days of operation. This data strongly implied that the investigated SRB consortium might have potential application for lead removal. Moreover, to improve the efficiency of the lead treatment process, the lead loading rates below the inhibitory level to SRB activity should be selected.

Williamsia herbipolensis sp. nov., isolated from the phyllosphere of Arabidopsis thaliana

A Gram-stain-positive, non-endospore-forming actinobacterium (ARP1T) was isolated from the phyllosphere of Arabidopsis thaliana. On the basis of 16S rRNA gene sequence phylogeny strain ARP1T was placed into the genus Williamsia and the closest related species were Williamsia phyllosphaerae (98.5 % 16S rRNA gene sequence similarity), Williamsia deligens (98.5 %), Williamsia maris (98.3 %) and Williamsia serinedens (98.2 %). Genome-based comparison indicated a clear distinction to the type strains of those species with pairwise average nucleotide identities (ANI) between 76.4-78.4 %. The quinone system of strain ARP1T consisted predominantly of menaquinones MK-9(H2), MK-7(H2) and MK-8(H2), and the polar lipid profile contained the major compound diphosphatidylglycerol, and moderate amounts of phosphatidylethanolamine, phosphatidylglycerol and numerous unidentified lipids. Mycolic acids were present. These chemotaxonomic traits and the major fatty acids, which were C16 : 1ω7c, C16 : 0, C18 : 0, C18 : 1ω9c and tuberculostearic acid supported the affiliation of strain ARP1T to the genus Williamsia. Genotypic, physiological and biochemical testing revealed clear differences of strain ARP1T to the most closely related species of the genus Williamsia. Therefore strain ARP1T represents a novel species of this genus, for which the name Williamsia herbipolensis sp. nov. is proposed. The type strain is ARP1T (=DSM 46872T=LMG 28679T).

Falcatimonas natans gen. nov., sp. nov., a strictly anaerobic, amino-acid-decomposing bacterium isolated from a methanogenic reactor of cattle waste

A strictly anaerobic bacterial strain (WN011T) was isolated from a methanogenic reactor treating waste from cattle farms. Cells of the strain were Gram-stain-negative curved rods with a polar flagellum. Spores were not produced. The optimum temperature for growth was 35-37 °C and the optimum pH was 6.7. The strain did not utilize carbohydrates as growth substrates. The strain grew in PY medium and produced acetate, butyrate, isovalerate and H2 as well as propionate and isobutyrate as minor products. Amino acids (l-isoleucine, l-leucine, l-lysine, l-serine, l-threonine and l-valine) added to PY medium enhanced growth of the strain and increased the amounts of fermentation products. Oxidase, catalase and nitrate-reducing activities were negative. Hydrogen sulfide was produced. The genomic DNA G+C content was 38.8 mol%. Compounds related to iso-C15 : 0 (fatty acid, dimethylacetal and aldehyde) were detected as predominant components by the cellular fatty acids analysis. The diagnostic diamino acid of the cell-wall peptidoglycan was meso-diaminopimelic acid. On the basis of 16S rRNA gene sequences, three clones from wastewater were very closely related to strain WN011T (up to 99.9 % sequence similarity). The most closely related described species were those in cluster XIVa of the class Clostridia such as Ruminococcus gauvreauii (93.8 % 16S rRNA gene sequence similarity), Clostridium fimetarium (93.5 %) and Clostridium bolteae(93.5 %). Based on the distinct differences in phylogenetic and phenotypic characteristics of strain WN011T from those of related species, it is concluded that strain WN011T represents a novel species of a new genus in the family Lachnospiraceae, for which the name Falcatimonas natans gen. nov., sp. nov. is proposed. The type strain of the type species is WN011T (=JCM 16476T=DSM 22923T).

Composition of the Cutaneous Bacterial Community in Japanese Amphibians: Effects of Captivity, Host Species, and Body Region

The cutaneous microbiota plays a significant role in the biology of their vertebrate hosts, and its composition is known to be influenced both by host and environment, with captive conditions often altering alpha diversity. Here, we compare the cutaneous bacterial communities of 61 amphibians (both wild and captive) from Hiroshima, Japan, using high-throughput amplicon sequencing of a segment of the 16S rRNA gene. The majority of these samples came from a captive breeding facility at Hiroshima University where specimens from six species are maintained under highly standardized conditions for several generations. This allowed to identify host effects on the bacterial communities under near identical environmental conditions in captivity. We found the structure of the cutaneous bacterial community significantly differing between wild and captive individuals of newts, Cynops pyrrhogaster, with a higher alpha diversity found in the wild individuals. Community structure also showed distinct patterns when comparing different species of amphibians kept under highly similar conditions, revealing an intrinsic host effect. Bacterial communities of dorsal vs. ventral skin surfaces did not significantly differ in most species, but a trend of higher alpha diversity on the ventral surface was found in Oriental fire-bellied toads, Bombina orientalis. This study confirms the cutaneous microbiota of amphibians as a highly dynamic system influenced by a complex interplay of numerous factors.

Metagenomic discovery of novel enzymes and biosurfactants in a slaughterhouse biofilm microbial community

DNA derived from environmental samples is a rich source of novel bioactive molecules. The choice of the habitat to be sampled predefines the properties of the biomolecules to be discovered due to the physiological adaptation of the microbial community to the prevailing environmental conditions. We have constructed a metagenomic library in Escherichia coli DH10b with environmental DNA (eDNA) isolated from the microbial community of a slaughterhouse drain biofilm consisting mainly of species from the family Flavobacteriaceae. By functional screening of this library we have identified several lipases, proteases and two clones (SA343 and SA354) with biosurfactant and hemolytic activities. Sequence analysis of the respective eDNA fragments and subsequent structure homology modelling identified genes encoding putative N-acyl amino acid synthases with a unique two-domain organisation. The produced biosurfactants were identified by NMR spectroscopy as N-acyltyrosines with N-myristoyltyrosine as the predominant species. Critical micelle concentration and reduction of surface tension were similar to those of chemically synthesised N-myristoyltyrosine. Furthermore, we showed that the newly isolated N-acyltyrosines exhibit antibiotic activity against various bacteria. This is the first report describing the successful application of functional high-throughput screening assays for the identification of biosurfactant producing clones within a metagenomic library.

A taxonomic framework for cable bacteria and proposal of the candidate genera Electrothrix and Electronema

Cable bacteria are long, multicellular filaments that can conduct electric currents over centimeter-scale distances. All cable bacteria identified to date belong to the deltaproteobacterial family Desulfobulbaceae and have not been isolated in pure culture yet. Their taxonomic delineation and exact phylogeny is uncertain, as most studies so far have reported only short partial 16S rRNA sequences or have relied on identification by a combination of filament morphology and 16S rRNA-targeted fluorescence in situ hybridization with a Desulfobulbaceae-specific probe. In this study, nearly full-length 16S rRNA gene sequences of 16 individual cable bacteria filaments from freshwater, salt marsh, and marine sites of four geographic locations are presented. These sequences formed a distinct, monophyletic sister clade to the genus Desulfobulbus and could be divided into six coherent, species-level clusters, arranged as two genus-level groups. The same grouping was retrieved by phylogenetic analysis of full or partial dsrAB genes encoding the dissimilatory sulfite reductase. Based on these results, it is proposed to accommodate cable bacteria within two novel candidate genera: the mostly marine “Candidatus Electrothrix”, with four candidate species, and the mostly freshwater “Candidatus Electronema”, with two candidate species. This taxonomic framework can be used to assign environmental sequences confidently to the cable bacteria clade, even without morphological information. Database searches revealed 185 16S rRNA gene sequences that affiliated within the clade formed by the proposed cable bacteria genera, of which 120 sequences could be assigned to one of the six candidate species, while the remaining 65 sequences indicated the existence of up to five additional species.

Spatiotemporal dynamics of bacterial and archaeal communities in household biogas digesters from tropical and subtropical regions of Yunnan Province, China

A combination of 16S rRNA gene PCR-based techniques and the determination of abiotic factors were used to study community composition, richness, and evenness and the correlation between biotic and abiotic factors in 19 household biogas digesters in tropical and subtropical regions of Yunnan Province, China. The results revealed that both bacterial and archaeal community composition differed between regions and archaeal community composition was more affected by season than bacterial; regardless of sampling location, the dominant bacterial phyla included Chloroflexi, Bacteroidetes, Firmicutes, and Proteobacteria, and the most dominant archaeal phylum was Euryarchaeota; in digesters from both regions, Chloroflexi as the first or second most dominant bacteria accounted for 21.50-26.10 % of bacterial library sequences, and the phylum Crenarchaeota as the second most dominant archaea accounted for 17.65-19.77 % of archaeal library sequences; the species Methanosaeta concilii as the most dominant archaeal species accounted for 67.80-72.80 % of the sequences. This study found that most of the abundant microbial communities in 19 biogas digesters are similar, and this result will provide enlightenment for finding the universal nature in rural biogas digesters at tropical and subtropical regions in China.

Comparison of Virulence Gene Identification, Ribosomal Spacer PCR, and Pulsed-Field Gel Electrophoresis for Typing of Staphylococcus aureus Strains Isolated from Cases of Subclinical Bovine Mastitis in the United States

Staphylococcus aureus is one of the most important pathogens causing contagious mastitis in dairy cattle worldwide. The objectives of this study were to determine if recently described S. aureus genotype B was present among previously characterized isolates from cases of bovine intramammary infection in the United States and to compare pulsed-field gel electrophoresis (PFGE) to the combination of ribosomal spacer PCR (RS-PCR) and virulence gene identification for typing of S. aureus strains. The hypothesis was that isolates that were previously characterized as contagious would be identified as genotype B and that the results of the two strain-typing methods would be comparable. Isolates were selected from a collection of S. aureus isolates from eight dairy farms. Mammary quarter milk somatic cell count (SCC) and N-acetyl-β-d-gluconaminidase (NAGase) activity data were known and used to evaluate strain pathogenicity. RS-PCR was performed with conventional gel electrophoresis, and PCR was used for toxin gene identification. RS-PCR patterns were associated with a specific virulence gene pattern, as previously reported. Five RS-PCR banding patterns were identified. None of the isolates were characterized as genotype B. No association between RS-PCR types and milk SCC was found; however, NAGase activity was significantly higher in milk from mammary glands infected with RS-PCR banding type 1 (RSP type 1) than in milk from those infected with RSP type 2. The discriminatory power values were 1.0 and 0.46 for PFGE and RS-PCR, respectively. These data suggest that genotype B may have a limited geographic distribution and that PFGE is more discriminatory than RS-PCR performed with conventional gel electrophoresis for typing of S. aureus isolates of bovine origin.

Protein-RNA Dynamics in the Central Junction Control 30S Ribosome Assembly

Interactions between ribosomal proteins (rproteins) and ribosomal RNA (rRNA) facilitate the formation of functional ribosomes. S15 is a central domain primary binding protein that has been shown to trigger a cascade of conformational changes in 16S rRNA, forming the functional structure of the central domain. Previous biochemical and structural studies in vitro have revealed that S15 binds a three-way junction of helices 20, 21, and 22, including nucleotides 652-654 and 752-754. All junction nucleotides except 653 are highly conserved among the Bacteria. To identify functionally important motifs within the junction, we subjected nucleotides 652-654 and 752-754 to saturation mutagenesis and selected and analyzed functional mutants. Only 64 mutants with greater than 10% ribosome function in vivo were isolated. S15 overexpression complemented mutations in the junction loop in each of the partially active mutants, although mutations that produced inactive ribosomes were not complemented by overexpression of S15. Single-molecule Förster or fluorescence resonance energy transfer (smFRET) was used to study the Mg(2+)- and S15-induced conformational dynamics of selected junction mutants. Comparison of the structural dynamics of these mutants with the wild type in the presence and absence of S15 revealed specific sequence and structural motifs in the central junction that are important in ribosome function.

Erwinia iniecta sp. nov., isolated from Russian wheat aphid (Diuraphis noxia)

Short, Gram-negative-staining, rod-shaped bacteria were isolated from crushed bodies of Russian wheat aphid [Diuraphis noxia (Kurdjumov)] and artificial diets after Russian wheat aphid feeding. Based on multilocus sequence analysis involving the 16S rRNA, atpD, infB, gyrB and rpoB genes, these bacterial isolates constitute a novel clade in the genus Erwinia, and were most closely related to Erwinia toletana. Representative distinct strains within this clade were used for comparisons with related species of Erwinia. Phenotypic comparisons using four distinct strains and average nucleotide identity (ANI) measurements using two distinct draft genomes revealed that these strains form a novel species within the genus Erwinia. The name Erwinia iniecta sp. nov. is proposed, and strain B120T ( = CFBP 8182T = NCCB 100485T) was designated the type strain. Erwinia iniecta sp. nov. was not pathogenic to plants. However, virulence to the Russian wheat aphid was observed.

Empedobacter stercoris sp. nov., isolated from an input sample of a biogas plant

Two Gram-stain-negative, rod-shaped bacteria, strains 990B6_12ER2AT and 994B6_12ER2A, were isolated during microbiological analysis of a mixed manure sample which was used as input material for a German biogas plant. Phylogenetic identification based on nearly full-length 16S rRNA gene sequences placed the isolates into the family Flavobacteriaceae within the phylum Bacteroidetes. Strains 990B6_12ER2AT and 994B6_12ER2A shared identical 16S rRNA gene sequences and showed highest 16S rRNA gene sequence similarity to the type strains of Empedobacter falsenii (97.3 %) and Empedobacter brevis (96.8 %).The major cellular fatty acids of strains 990B6_12ER2AT and 994B6_12ER2A were iso-C15 : 0, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and iso-C17 : 0 3-OH.The polyamine pattern contained predominantly sym-homospermidine and the quinone system was menaquinone MK-6. Major polar lipids were phosphatidylethanolamine, one unidentified aminolipid and one unidentified polar lipid not containing an amino residue, a phosphate residue or a sugar moiety. In addition, moderate to minor amounts of several unidentified lipids were detected. The DNA G+C content was 31.7 and 29.0 mol%, for strains 990B6_12ER2AT and 994B6_12ER2A, respectively. On the basis of phylogenetic, chemotaxonomic and physiological analysis we propose a novel species of the genus Empedobacter, Empedobacter stercoris sp. nov. (type strain 990B6_12ER2AT = CIP 110833T = LMG 28501T).