Metagenomic characterization of oyster shell dump reveals predominance of Firmicutes bacteria

Metagenomic analyses were conducted to evaluate the biodiversity of oyster shell bacteria, under storage conditions, on the basis of 16s rDNA sequences. Temperature was recorded during a one year storage period, and the highest temperature (about 60 degrees C) was observed after five months ofstorage. Bacterial diversity was greatest in the initial stage sample, with 33 different phylotypes classified under seven phyla (Proteobacteria, Bacteroidetes, Firmicutes, Actinobacteria, Planctomycetes, Verrucomicrobia and unclassified bacteria), with 42.22% ofphylotypes belonging to Proteobacteria. The lowest diversity was found in the high temperature (fermentation) stage sample, with 10 different phylotypes belonging to Firmicutes (78.57%) and Bacteroidetes. In the final stage sample, bacteria were found belonging to Proteobacteria, Bacteroidetes, and Firmicutes, and some were unclassified bacteria. Of the bacteria constituting the final stage metagenome, 69.70% belonged to Firmicutes. Our results show that bacteria belonging to phylum Firmicutes were predominant during fermentation, and during the final stages of oyster shell storage, which suggests that these bacteria supposed to be the key players for oyster shell biodegradation.     

Molecular characterization of bacterial population in the forest soil of Kashmir,India

The bacterial diversity in the forest soil of Kashmir, India was investigated by 16S rDNA-dependent molecular phylogeny. Small subunit rRNA (16S rDNA) from forest soil metagenome were amplified by polymerase chain reaction (PCR) using primers specific to the domain bacteria. 30 unique phylotypes were obtained by PCR based RFLP of 16S rRNA genes using endonucleases Hae 111 and Msp 1, which were most suitable to score the genetic diversity. The use of 16S rRNA analysis allowed identification of several bacterial populations in the soil belonging to the following phyla: Firmicutes (33.3%), Bacteroidetes (13.3%), Proteobacterium (6.6%), Planctomycete (3.3%), and Deferribacteraceae (3.3%) in addition to the others that were not classified, beyond Archaea domain, However, 36.6% of the retrieved bacterial sequences could not be grouped with any phylum/lineage. The large amount of unclassified clone sequence could imply that novel groups of bacteria were present in the forest soil.     

Bacterial Diversity and Structural Changes of Oyster Shell during 1-Year Storage

We examined the biodiversity of bacteria associated with oyster-shell waste during a 1-year storage period using 16S ribosomal DNA analysis. Temperature variation and structural changes of oyster shell were observed during storage. Initial and final temperatures were at 16-17 degrees C, but a high temperature of about 60 degrees C was recorded after approximately 6 months of storage. The crystal structure and nanograin of the oyster shell surface were sharp and large in size initially and became gradually blunter and smaller over time. Phylogenetic analysis revealed that Firmicutes were dominant in the oyster-shell waste initially, during the high-temperature stage, and after 1 year of storage (making up >65% of the biodiversity at all three sampling times). Bacillus licheniformis was presumed as the predominate Firmicutes present. These bacteria are likely to have important roles in the biodegradation of oyster shell.     

Phylogenetic and functional prokaryotic diversity in the Hoito-Gol mesothermal mineral spring (Eastern Sayan Mountains,Buryat Republic)

High-throughput sequencing was used for comparative analysis of microbial communities of the water and mat from the Hoito-Gol mesothermal mineral sulfide spring (Eastern Sayan Mountains, Buryat Republic). Activity of microbial communities was determined. While both spring biotopes were dominated by members of three bacterial phyla—Proteobacteria, Bacteroidetes, and Firmicutes—they differed drastically in the composition of predominant phylotypes (at the genus level). In the water, the organisms widespread in aquatic environments were predominant, mostly aerobic chemoorganotrophs of the genera Acinetobacter, Pedobacter, and Flavobacterium. In the microbial mat, the organisms actively involved in the sulfur cycle predominated, including sulfur-reducing bacteria Sulfurospirillum, sulfate-reducing deltaproteobacteria, sulfuroxidizing chemoautotrophic bacteria, anoxygenic phototrophic bacteria of the phyla Chloroflexi and Chlorobi, as well as purple bacteria belonging to the α-, ß-, and γ-Proteobacteria. Microbial mats of the spring exhibited higher phylogenetic diversity compared to high-temperature mats containing photosynthetic microorganisms.     

Culturable diversity of heterotrophic bacteria in Forlidas Pond (Pensacola Mountains) and Lundström Lake (Shackleton Range), Antarctica

Cultivation techniques were used to study the heterotrophic bacterial diversity in two microbial mat samples originating from the littoral zone of two continental Antarctic lakes (Forlidas Pond and Lundstr?m Lake) in the Dufek Massif (within the Pensacola Mountains group of the Transantarctic Mountains) and Shackleton Range, respectively. Nearly 800 isolates were picked after incubation on several growth media at different temperatures. They were grouped using a whole-genome fingerprinting technique, repetitive element palindromic PCR and partial 16S rRNA gene sequencing. Phylogenetic analysis of the complete 16S rRNA gene sequences of 82 representatives showed that the isolates belonged to four major phylogenetic groups: Actinobacteria, Bacteroidetes, Proteobacteria and Firmicutes. A relatively large difference between the samples was apparent. Forlidas Pond is a completely frozen water body underlain by hypersaline brine, with summer thaw forming a slightly saline littoral moat. This was reflected in the bacterial diversity with a dominance of isolates belonging to Firmicutes, whereas isolates from the freshwater Lundstr?m Lake revealed a dominance of Actinobacteria. A total of 42 different genera were recovered, including first records from Antarctica for Albidiferax, Bosea, Curvibacter, Luteimonas, Ornithinibacillus, Pseudoxanthomonas, Sphingopyxis and Spirosoma. Additionally, a considerable number of potential new species and new genera were recovered distributed over different phylogenetic groups. For several species where previously only the type strain was available in cultivation, we report additional strains. Comparison with public databases showed that overall, 72% of the phylotypes are cosmopolitan whereas 23% are currently only known from Antarctica. However, for the Bacteroidetes, the majority of the phylotypes recovered are at present known only from Antarctica and many of these represent previously unknown species.     

普洱地区茶叶内生细菌与根际土壤细菌群落结构分析

[目的]茶叶内生细菌、根际土壤细菌在普洱茶的发酵中起着重要的作用,还可以促进茶树生长,诱导茶树抗病性.研究其群落结构组成及相互关系可为微生物资源开发利用提供理论依据.[方法]本研究以普洱地区茶树叶片和根际土壤为材料,采用高通量测序技术,对茶叶及根际土壤细菌的16S核糖体RNA基因(16S rRNA)进行测序,比较分析茶...     

Bacteria abundance and diversity of different life stages of Plutella xylostella (Lepidoptera: Plutellidae), revealed by bacteria culture‐dependent and PCR‐DGGE methods

Microbial abundance and diversity of different life stages (fourth instar larvae, pupae and adults) of the diamondback moth, Plutella xylostella L., collected from field and reared in laboratory, were investigated using bacteria culture‐dependent method and PCR‐DGGE analysis based on the sequence of bacteria 16S rRNA V3 region gene. A large quantity of bacteria was found in all life stages of P. xylostella. Field population had higher quantity of bacteria than laboratory population, and larval gut had higher quantity than pupae and adults. Culturable bacteria differed in different life stages of P. xylostella. Twenty‐five different bacterial strains were identified in total, among them 20 strains were presented in larval gut, only 8 strains in pupae and 14 strains in adults were detected. Firmicutes bacteria, Bacillus sp., were the most dominant species in every life stage. 15 distinct bands were obtained from DGGE electrophoresis gel. The sequences blasted in GenBank database showed these bacteria belonged to six different genera. Phylogenetic analysis showed the sequences of the bacteria belonged to the Actinobacteri, Proteobacteria and Firmicutes. Serratia sp. in Proteobacteria was the most abundant species in larval gut. In pupae, unculturable bacteria were the most dominant species, and unculturable bacteria and Serratia sp. were the most dominant species in adults. Our study suggested that a combination of molecular and traditional culturing methods can be effectively used to analyze and to determine the diversity of gut microflora. These known bacteria may play important roles in development of P. xylostella.     

Characterization of bacterial community in the stomach of yellow catfish (<Emphasis Type="Italic">Pelteobagrus fulvidraco</Emphasis>)

In this study, the traditional culture-based technique and the 16S rDNA sequencing method were used to investigate the characterization of bacterial community in the stomach contents and mucus of yellow catfish (Pelteobagrus fulvidraco). The culture-based technique disclosed that the average bacterial numbers in the gastric contents and mucus were 5.79 × 10⁷ cfu/g (cfu: colony forming unit) and 1.89 × 10⁵ cfu/g, respectively. Several different bacteria were obtained from gastric contents, including species from genera Bradyrhizobium, Phyllobacterium, Plesiomonas, Hafnia, Edwardsiella, Pseudomonas, and Bacillus. However, only two species were isolated from the gastric mucus, including species from genera Plesiomonas and Aeromonas. Forty-five phylotypes were observed from the 65 positive clones from the stomach contents (library SC); nineteen phylotypes were detected from the 45 clones from the stomach mucus (library SM). Further analyses revealed that the fish stomach harbored characteristic microbiota, where Firmicutes was dominant, followed by Proteobacteria and Bacteroidetes and Fusobacteria. This characterization of bacterial community is markedly different from that of the fish intestine, where Proteobacteria is predominant, followed by Fusobacteria and Firmicutes. Chloroflexi (1.5%) was only found in the library SC, while Actinobacteria (4.4%) was only found in the library SM, suggesting that microbiota of GI contents was quite different from that of GI mucus. In addition, several species of bacteria found in the stomach may be potentially opportunistic pathogens, indicating that fish digestive tract is a reservoir for many nosocomial pathogens.     

Microbial diversity in Tunisian geothermal springs as detected by molecular and culture-based approaches

Prokaryotic diversities of 12 geothermal hot springs located in Northern, Central and Southern Tunisia were investigated by culture-based and molecular approaches. Enrichment cultures for both aerobic and anaerobic microorganisms were successfully obtained at temperatures ranging from 50 to 75°C. Fourteen strains including four novel species were cultivated and assigned to the phyla Firmicutes (9), Thermotogae (2), Betaproteobacteria (1), Synergistetes (1) and Bacteroidetes (1). Archaeal or universal oligonucleotide primer sets were used to generate 16S rRNA gene libraries. Representative groups included Proteobacteria, Firmicutes, Deinococcus-Thermus, Thermotogae, Synergistetes, Bacteroidetes, Aquificae, Chloroflexi, candidate division OP9 in addition to other yet unclassified strains. The archaeal library showed a low diversity of clone sequences belonging to the phyla Euryarchaeota and Crenarchaeota. Furthermore, we confirmed the occurrence of sulfate reducers and methanogens by amplification and sequencing of dissimilatory sulfite reductase (dsrAB) and methyl coenzyme M reductase α-subunit (mcrA) genes. Altogether, we discuss the diverse prokaryotic communities arising from the 12 geothermal hot springs studied and relate these findings to the physico-chemical features of the hot springs.     

Diversity of cultivable bacteria from deep-sea sediments of the Colombian Caribbean and their potential in bioremediation

The diversity of deep-sea cultivable bacteria was studied in seven sediment samples of the Colombian Caribbean. Three hundred and fifty two marine bacteria were isolated according to its distinct morphological character on the solid media, then DNA sequences of the 16S rRNA were amplified to identify the isolated strains. The identified bacterial were arranged in three phylogenetic groups, Firmicutes, Proteobacteria, and Actinobacteria, with 34 different OTUs defined at ≥?97% of similarity and 70 OTUs at ≥?98.65%, being the 51% Firmicutes, 34% Proteobacteria and 15% Actinobacteria. Bacillus and Fictibacillus were the dominant genera in Firmicutes, Halomonas and Pseudomonas in Proteobacteria and Streptomyces and Micromonospora in Actinobacteria. In addition, the strains were tested for biosurfactants and lipolytic enzymes production, with 120 biosurfactant producing strains (mainly Firmicutes) and, 56 lipolytic enzymes producing strains (Proteobacteria). This report contributes to the understanding of the diversity of the marine deep-sea cultivable bacteria from the Colombian Caribbean, and their potential application as bioremediation agents.

     

基于高通量测序分析盐角草根部内生细菌多样性及动态规律

【目的】探讨盐角草根部内生细菌群落多样性特征,揭示内生细菌群落结构在宿主关键发育期动态变化规律。【方法】通过罗氏454高通量测序获得内生细菌16S r RNA片段,然后进行生物信息分析。【结果】共获得20363条16S r RNA基因序列。各样品中可操作分类单元(operational taxonomic units,OTUs)在552–941之间。根部内生细菌群落主要包括4个门,其中Proteobacteri门占主导地位,其余依次是Firmicutes,Actinobacteria,Bacteroidetes。在Proteobacteria门中,Gammaproteobacteria是第一大纲,其后是Betaproteobacteria纲。宿主5个发育时期共同拥有7个细菌属,包括Azomonas,Serratia,Pantoea,Serpens,Pseudomonas,Halomonas,Kushneria。整体上看,Gammaproteobacteria纲在宿主5个发育时期呈现增长趋势。优势菌属在5个发育期存在差异,分别为Delftia,Kushneria,Serratia,Pantoea,Erwinia。所有文库总共含2108个特异OTUs,共同拥有5个相同OTUs。花期OTUs数量最多,结种期内生细菌多样性降低。在宿主的5个发育时期中,土壤p H、月均温和土壤盐含量这3个环境因子组成的集合对其内生细菌群落变化具有显著影响。【结论】盐角草内生细菌群落多样性丰富,宿主发育期决定了内生细菌群落结构。     

The fate of lignin and lignin‐derived compounds in anaerobic environments

During ODP Leg 201 microbial communities in Eastern Equatorial Pacific Ocean and Peru Margin sediments were investigated. The sediment layers sampled extended down to 420 m below the sea floor, with estimated ages of up to 40 million years. Contamination-free anoxic slurries were inoculated into media containing different substrate combinations, all at micromolar concentration. These culture media were designed for a broad spectrum of physiological groups. A total of 162 pure cultures were isolated that could be grouped into 19 different phylotypes based on 16S rRNA gene analysis. The isolates belonged to the Alpha-, Gamma- and Deltaproteobacteria, the Firmicutes, Actinobacteria, and Bacteroidetes. The genera most frequently isolated were Bacillus (68 isolates) and Rhizobium (40 isolates). Comparison of strains with the same phylotypes by enterobacterial repetitive intergenic consensus (ERIC-PCR) analysis revealed the presence of several subgroups that did not correlate with medium, sediment depth or sampling site. The majority of the isolates, although obtained from anoxic environments and isolated under strictly anoxic conditions, turned out to be facultativly aerobic. Physiologically, the isolates were characterized as generalists, able to utilize a broad variety of electron donors with either oxygen, nitrate and in some cases manganese oxides as electron acceptors. The diversity inferred from physiological tests was even higher than that on the phylogenetic or genomic level. The outcome of the contamination tests, the isolation of close relatives of already known subsurface bacteria, the repeated finding of the same phylotype from different sites and the level of diversity present in the culture collection strongly suggest that indigenous deep-biosphere bacteria had been isolated.     

Biodiversity and physiological characteristics of Antarctic and Arctic lichens-associated bacteria

The diversity and physiological characteristics of culturable bacteria associated with lichens from different habitats of the Arctic and Antarctica were investigated. The 68 retrieved isolates could be grouped on the basis of their 16S rRNA gene sequences into 26 phylotypes affiliated with the phyla Actinobacteria, Bacteroidetes, Deinococcus-Thermus, and Firmicutes and with the classes Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria. Isolates belonging to the Alphaproteobacteria were the most abundant, followed by those belonging to Actinobacteria, Betaproteobacteria, Gammaproteobacteria, Bacteroidetes, Firmicutes, and Deinococcus-Thermus. Phylogenetic analysis showed that approximately 21 % of the total isolates represented a potentially novel species or genus (≤97 % sequence similarity). Strains belonging to the genera Sphingomonas, Frondihabitans, Hymenobacter, and Burkholderia were recovered from lichen samples from both geographic locations, implying common and important bacterial functions within lichens. Extracellular protease activities were detected in six isolates, affiliated with Burkholderia, Frondihabitans, Hymenobacter, Pseudomonas, and Rhodanobacter. Extracellular lipase activities were detected in 37 isolates of the genera Burkholderia, Deinococcus, Frondihabitans, Pseudomonas, Rhodanobacter, Sphingomonas, and Subtercola. This is the first report on the culturable bacterial diversity present within lichens from Arctic and Antarctica and the isolates described herein are valuable resources to decode the functional and ecological roles of bacteria within lichens. In addition, the low similarity (≤97 %) of the recovered isolates to known species and their production of cold-active enzymes together suggest that lichens are noteworthy sources of novel bacterial strains for use in biotechnological applications.     

Enrichment of Clostridia during the operation of an external-powered bio-electrochemical denitrification system

Bacterial community composition was investigated in a biocathode of an external-powered bio-electrochemical denitrifying system (BEDS), by analyzing 16S rRNA gene sequences determined from a high-throughput 454 pyrosequencing technology. The bacterial community of the inoculum sludge was mainly composed of Proteobacteria, Bacteroidetes, and Acidobacteria. Over 45 days of the BEDS, Bacteroidetes and Firmicutes were enriched on the biocathode. Putative denitrifying Clostridia belonging to the Firmicutes were distinctively detected on the biocathode via phylogenetic analysis and appeared to be ubiquitous in various autotrophic, heterotrophic, and BEDSs. Elucidation of the bacterial community composition in the denitrification system deepens our knowledge about the bacteria involved in bio-electrochemical denitrification.     

Toward the construction of a technology platform for chemicals production from methanol: d-lactic acid production from methanol by an engineered yeast Pichia pastoris

In this study, the effects of di-n-butyl phthalate (DBP) on the phyllosphere bacterial community of field mustard (Brassica campestris L.) at the five-leaf stage were investigated. The indigenous alpha-diversity of the phyllosphere bacteria was altered after spraying with different concentrations of DBP. Shannon diversity indices were significantly changed on day 5 after treatment at DBP concentrations >?400 mg L^?1 (P?>?0.05). Nevertheless, the difference between treatment and control was not significant on day 9 after DBP treatment (P?>?0.05). Exposure to DBP resulted in a decrease in Proteobacteria and Firmicutes, and an increase in Actinobacteria at all sampling intervals. These changes included significant increases in the relative abundance of Paracoccus and Rhodococcus, and significant decreases in that of Pseudomonas, Exiguobacterium, an unclassified genus of Pseudomonadaceae, and an unclassified genus of Enterobacteriaceae. This study provides new evidence for the possibility of using phyllosphere microbiota to remediate DBP contamination.

     

Sequence analysis of percent G+C fraction libraries of human faecal bacterial DNA reveals a high number of Actinobacteria

Background  

The human gastrointestinal (GI) tract microbiota is characterised by an abundance of uncultured bacteria most often assigned in phyla Firmicutes and Bacteroidetes. Diversity of this microbiota, even though approached with culture independent techniques in several studies, still requires more elucidation. The main purpose of this work was to study whether the genomic percent guanine and cytosine (%G+C) -based profiling and fractioning prior to 16S rRNA gene sequence analysis reveal higher microbiota diversity, especially with high G+C bacteria suggested to be underrepresented in previous studies.     

Culture independent characterization of bacteria associated with the mucus of the coral <Emphasis Type="Italic">Acropora digitifera</Emphasis> from the Gulf of Mannar

Corals are sessile eukaryotic hosts which provide a unique surface for microbial colonization. Culture independent studies show that the coral mucus and tissue harbour diverse and abundant prokaryotic communities. However, little is known about the diversity of bacteria associated with the corals of Gulf of Mannar. The present study characterised the bacterial diversity associated with the mucus of the coral Acropora digitifera from the Gulf of Mannar by 16S rRNA gene clone library construction. The bacterial communities of the mucus of A. digitifera were diverse, with representatives within the Alphaproteobacteria, Gammaproteobacteria, Actinobacteria, Firmicutes and several unclassified bacteria. The culture independent bacterial population was totally different from our previous culture dependent study of the mucus and tissue of the same coral. 36% of the bacteria in the clone library of A. digitifera were found to be novel after full length sequencing of the 16S rRNA gene wherein several clones were found to be novel at the Genus and species level. The current study further supports the findings that Actinobacteria amount to a certain proportion among bacterial communities associated with corals.     

Diversity of bacterial community in freshwater of Woopo wetland

Diversity of bacterial community in water layer of Woopo wetland was investigated. Cultivable bacterial strains were isolated by the standard dilution plating technique and culture-independent 16S rRNA gene clones were obtained directly from DNA extracts of a water sample. Amplified rDNA restriction analysis (ARDRA) was applied onto both of the isolates and 16S rRNA gene clones. Rarefaction curves, coverage rate and diversity indices of ARDRA patterns were calculated. Representative isolates and clones of all the single isolate/clone phylotype were partially sequenced and analyzed phylogenetically. Sixty-four and 125 phylotypes were obtained from 203 bacterial isolates and 235 culture-independent 16S rRNA gene clones, respectively. Bacterial isolates were composed of 4 phyla, of which Firmicutes (49.8%) and Actinobacteria (32.0%) were predominant. Isolates were affiliated with 58 species. Culture-independent 16S rRNA gene clones were composed of 8 phyla, of which Proteobacteria (62.2%), Actinobacteria (15.5%), and Bacteroidetes (13.7%) were predominant. Diversity of 16S rRNA gene clones originated from cultivation-independent DNA extracts was higher than that of isolated bacteria.     

Diversity analyses of microbial communities in petroleum samples from Brazilian oil fields

Recent studies of oil fields have shown that the microbial diversity is represented by bacteria and archaea of wide distribution, and that many of these organisms have potential to metabolize organic and inorganic compounds. Biodegradation processes in oil industry are of great relevance, since it may be related with the loss of petroleum quality and can bring problems during production. The aim of this study was to compare the microbial communities present in biodegraded (GMR75) and non-biodegraded (PTS1) terrestrial oils from the Potiguar Basin (RN, Brazil) by using cultivation (microbial enrichments and isolation) and molecular approaches (16S rRNA gene libraries). The cultivated microorganisms recovered were affiliated with the phyla Actinobacteria, Firmicutes and Proteobacteria. Both bacterial 16S rRNA gene libraries revealed a great diversity, encompassing representatives from 8 different phyla (Actinobacteria, Bacteroidetes, Deferribacteres, Spirochaetes, Firmicutes, Proteobacteria, Thermotogae and Synergistetes) for the GMR75 sample, and from 5 different phyla (Actinobacteria, Chloroflexi, Firmicutes, Proteobacteria and Thermotoga) for the PTS1 sample. The archaeal 16S rRNA gene library was obtained only for GMR75 oil and all phylotypes were affiliated with the family Methanomicrobiaceae. Diversity results suggest that methanogenesis is the dominant terminal process for hydrocarbon degradation in GMR oil field, driven by anaerobic biodegradation.     

Pediatric obesity is associated with an altered gut microbiota and discordant shifts in Firmicutes populations

An altered gut microbiota has been linked to obesity in adulthood, although little is known about childhood obesity. The aim of this study was to characterize the composition of the gut microbiota in obese (n = 42) and normal‐weight (n = 36) children aged 6 to 16. Using 16S rRNA gene‐targeted sequencing, we evaluated taxa with differential abundance according to age‐ and sex‐normalized body mass index (BMI z‐score). Obesity was associated with an altered gut microbiota characterized by elevated levels of Firmicutes and depleted levels of Bacteroidetes. Correlation network analysis revealed that the gut microbiota of obese children also had increased correlation density and clustering of operational taxonomic units (OTUs). Members of the Bacteroidetes were generally better predictors of BMI z‐score and obesity than Firmicutes, which was likely due to discordant responses of Firmicutes OTUs. In accordance with these observations, the main metabolites produced by gut bacteria, short chain fatty acids (SCFAs), were higher in obese children, suggesting elevated substrate utilisation. Multiple taxa were correlated with SCFA levels, reinforcing the tight link between the microbiota, SCFAs and obesity. Our results suggest that gut microbiota dysbiosis and elevated fermentation activity may be involved in the etiology of childhood obesity.