Clone Library Sequencing Research Articles

Insights into the abundance, expression and diversity of key denitrification genes in an ecologically managed greenhouse agricultural soil

Understanding the bacteria associated with nitrification and denitrification is crucial for comprehending the processes that lead to nitrous oxide emissions in agricultural greenhouse soils. Therefore, it is important to determine their abundance and expression to gain insight into these processes.The aim of this study was to explore the bacterial communities associated with denitrification in a greenhouse agricultural soil amended with crop residues and manure for six years. For this purpose, we proceeded to detect and quantify the genes nirK and nirS and the gene nosZ through clone library construction, sequencing, phylogenetic analysis, and quantitative polymerase chain reaction (qPCR). Sequence analysis based on the clone library revealed that many of the nirS or nirK genes detected were not closely related to known denitrifier bacteria, but some of the nosZ sequences were related to the genera such as Pseudomonas, Halomonas, and Marinobacter. Furthermore, the qPCR revealed a high abundance of DNA copies in nirK, 6.08 × 109 ± 1.16 × 109, while nirS and nosZ showed lower values, 9.05 × 106 ± 1.65 × 106 and 8.71 × 106 ± 1.44 × 106, respectively. However, the highest expression rate was observed for nirS (mRNA/DNA ratio = 3.10 × 10− 3), while nirK and nosZ showed 10-fold lower expression rates (4.4 × 10− 4 and 3.5 × 10− 4, respectively). The results of this work provide a preliminary overview of the diversity, abundance and expression of key genes associated with the denitrification process in this type of soil and are a starting point for further studies to understand how this type of soil management can influence the denitrification process.

AcetoBase Version 2: a database update and re-analysis of formyltetrahydrofolate synthetase amplicon sequencing data from anaerobic digesters.

AcetoBase is a public repository and database of formyltetrahydrofolate synthetase (FTHFS) sequences. It is the first systematic collection of bacterial FTHFS nucleotide and protein sequences from genomes and metagenome-assembled genomes and of sequences generated by clone library sequencing. At its publication in 2019, AcetoBase (Version 1) was also the first database to establish connections between the FTHFS gene, the Wood–Ljungdahl pathway and 16S ribosomal RNA genes. Since the publication of AcetoBase, there have been significant improvements in the taxonomy of many bacterial lineages and accessibility/availability of public genomics and metagenomics data. The update to the AcetoBase reference database described here (Version 2) provides new sequence data and taxonomy, along with improvements in web functionality and user interface. The evaluation of this latest update by re-analysis of publicly accessible FTHFS amplicon sequencing data previously analysed with AcetoBase Version 1 revealed significant improvements in the taxonomic assignment of FTHFS sequences. Database URL: https://acetobase.molbio.slu.se

Methanotrophs Contribute to Nitrogen Fixation in Emergent Macrophytes.

Root-associated aerobic methanotroph plays an important role in reducing methane emissions from wetlands. In this study, we examined the activity of methane-dependent nitrogen fixation and active nitrogen-fixing bacterial communities on the roots of Typha angustifolia and Scirpus triqueter using a 15N-N2 feeding experiment and a cDNA-based clone library sequence of the nifH gene, respectively. A 15N-N2 feeding experiment showed that the N2 fixation rate of S. triqueter (1.74 μmol h–1 g–1 dry weight) was significantly higther than that of T. angustifolia (0.48 μmol h–1 g–1 dry weight). The presence of CH4 significantly increased the incorporation of 15N-labeled N2 into the roots of both plants, and the rate of CH4-dependent N2 fixation of S. triqueter (5.6 μmol h–1 g–1 dry weight) was fivefold higher than that of T. angustifolia (0.94 μmol h–1 g–1 dry weight). The active root-associated diazotrophic communities differed between the plant species. Diazotrophic Methylosinus of the Methylocystaceae was dominant in S. triqueter, while Rhizobium of the Rhizobiaceae was dominant in T. angustifolia. However, there were no significant differences in the copy numbers of nifH between plant species. These results suggest that N2 fixation was enhanced by the oxidation of CH4 in the roots of macrophytes grown in natural wetlands and that root-associated Methylocystacea, including Methylosinus, contribute to CH4 oxidation-dependent N2 fixation.

Responses of potential ammonia oxidation and ammonia oxidizers community to arsenic stress in seven types of soil

Soil arsenic contamination is of great concern because of its toxicity to human, crops, and soil microorganisms. However, the impacts of arsenic on soil ammonia oxidizers communities remain unclear. Seven types of soil spiked with 0 or 100 mg arsenic per kg soil were incubated for 180 days and sampled at days 1, 15, 30, 90 and 180. The changes in the community composition and abundance of ammonia oxidizing bacteria (AOB) and ammonia oxidizing archaea (AOA) were analyzed by terminal restriction fragment length polymorphism (T-RFLP) analysis, clone library sequencing, and quantitative PCR (qPCR) targeting amoA gene. Results revealed considerable variations in the potential ammonia oxidation (PAO) rates in different soils, but soil PAO was not consistently significantly inhibited by arsenic, probably due to the low bioavailable arsenic contents or the existence of functional redundancy between AOB and AOA. The variations in AOB and AOA communities were closely associated with the changes in arsenic fractionations. The amoA gene abundances of AOA increased after arsenic addition, whereas AOB decreased, which corroborated the notion that AOA and AOB might occupy different niches in arsenic-contaminated soils. Phylogenetic analysis of amoA gene-encoded proteins revealed that all AOB clone sequences belonged to the genus Nitrosospira, among which those belonging to Nitrosospira cluster 3a were dominant. The main AOA sequence detected belonged to Thaumarchaeal Group 1.1b, which was considered to have a high ability to adapt to environmental changes. Our results provide new insights into the impacts of arsenic on the soil nitrogen cycling.

Dynamics and Distribution of Marine Synechococcus Abundance and Genotypes during Seasonal Hypoxia in a Coastal Marine Ranch

Marine Synechococcus are an ecologically important picocyanobacterial group widely distributed in various oceanic environments. Little is known about the dynamics and distribution of Synechococcus abundance and genotypes during seasonal hypoxia in coastal zones. In this study, an investigation was conducted in a coastal marine ranch along two transects in Muping, Yantai, where hypoxic events (defined here as the dissolved oxygen concentration <3 mg L−1) occurred in the summer of 2015. The hypoxia occurred in the bottom waters from late July and persisted until late August. It was confined at nearshore stations of the two transects, one running across a coastal ranch and the other one outside. During this survey, cell abundance of Synechococcus was determined with flow cytometry, showing great variations ranging from 1 × 104 to 3.0 × 105 cells mL−1, and a bloom of Synechococcus occurred when stratification disappeared and hypoxia faded out outside the ranch. Regression analysis indicated that dissolved oxygen, pH, and inorganic nutrients were the most important abiotic factors in explaining the variation in Synechococcus cell abundance. Diverse genotypes (mostly belonged to the sub-clusters 5.1 and 5.2) were detected using clone library sequencing and terminal restriction fragment length polymorphism analysis of the 16S–23S rRNA internal transcribed spacer region. The richness of genotypes was significantly related to salinity, temperature, silicate, and pH, but not dissolved oxygen. Two environmental factors, temperature and salinity, collectively explained 17% of the variation in Synechococcus genotype assemblage. With the changes in population composition in diverse genotypes, the Synechococcus assemblages survived in the coastal hypoxia event and thrived when hypoxia faded out.

Seagrass (Zostera marina) promotes nitrification potential and selects specific ammonia oxidizers in coastal sediments

Seagrasses accelerate sedimentation, release oxygen and organic matter through their roots, and compete with ammonia oxidizers for ammonia/ammonium in surface sediments and overlying water, all of which can influence benthic aerobic nitrification. To understand the effects of seagrass vegetation on benthic nitrification, the heterogeneity of nitrification activities and functional microbial communities between seagrass-vegetated and adjacent bare sediments was investigated. Surface (0–5 cm) sediments were sampled from a Zostera marina-colonized coastal lagoon in northern China. The potential nitrification rates (PNR) and relative contributions of ammonia-oxidizing bacteria (PNRaob) and ammonia-oxidizing archaea (PNRaoa) were determined based on the sediment slurry incubation with kanamycin inhibition method. The abundances and community compositions of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) were determined using qPCR, clone library, and high-throughput sequencing. The total PNR (PNRtotal) in the seagrass-colonized sediments were significant higher than those in the bare sediments (P < 0.05), to which PNRaob contributed 59.7% and 55.8% in vegetated and unvegetated sediments, respectively. The concentrations of chlorophyll a and dissolved inorganic nitrogen were key factors determining benthic PNR. AOB outnumbered AOA by one order of magnitude by targeting amoA gene abundance, and no significant difference (P > 0.05) in amoA gene abundance and diversity was observed between the two habitats. Most AOB genotypes were affiliated to Nitrosomonas, of which NL7 was selectively enriched in the vegetated region, while N. cryotolerans prevailed in the bare. Two distinct AOA groups Crenarchaeota 1.1b and Crenarchaeota 1.1a dominated in vegetated and unvegetated sediments, respectively. Dissolved oxygen of overlying water and TOC:TN of sediment significantly influenced AOB community, while AOA community was strongly driven by nitrate and metal iron in sediments. Seagrass vegetation substantially enhances nitrification potential and selects specific ammonia oxidizers in coastal sediments.

Abundance and diversity of diazotrophs in the surface sediments of Kongsfjorden, an Arctic fjord

Diazotrophy in the Arctic environment is poorly understood compared to tropical and subtropical regions. Hence in this study, we report the abundance and diversity of diazotrophs in Arctic fjord sediments and elucidate the role of environmental factors on the distribution of diazotrophs. The study was conducted during the boreal summer in the Kongsfjorden, an Arctic fjord situated in the western coast of Spitsbergen. The abundance of nifH gene was measured through quantitative real-time PCR and the diversity of diazotrophs was assessed by nifH targeted clone library and next generation sequence analysis. Results revealed that the abundance of nifH gene in the surface sediments ranged from 2.3 × 106 to 3.7 × 107 copies g- 1. The δ-proteobacterial diazotrophs (71% of total sequence) were the dominant class observed in this study. Major genera retrieved from the sequence analysis were Desulfovibrionaceae (25% of total sequence), Desulfuromonadaceae (18% of total sequence) and Desulfobacteriaceae (10% of total sequence); these are important diazotrophic iron and sulfur-reducing bacterial clade in the Kongsfjorden sediments. The abundance of nifH gene showed a significant positive correlation TOC/TN ratio (r2 = 0.96, p ≤ 0.05) and total organic carbon (p ≤ 0.05) content in the fjord sediments. The higher TOC/TN ratio (4.24-14.5) indicated low nitrogen content organic matter in the fjord sediments through glacier runoff, which enhances the abundance and diversity of nitrogen fixing microorganisms.

Impaired host response and the presence of Acinetobacter baumannii in the serum microbiome of type-II diabetic patients.

SummaryType II diabetes (T2D) affects over 10% of the US population and is a growing disease worldwide that manifests with numerous comorbidities and defects in inflammation. This dysbiotic host response allows for infection of the host by numerous microorganisms. In the course of T2D disease, individuals can develop chronic infections including foot ulcers and periodontitis, which lead to further complications and opportunistic infections in multiple body sites. In this study, we investigated the serum of healthy subjects and patients with T2D with (T2DP) or without periodontitis for both microbiome signatures in addition to cytokine profiles. Surprisingly, we detected the presence of Acinetobacter baumanii in the serum of 23% individuals with T2D/T2DP tested. In T2DP, IL-1β, TNF-α, MCP-1, IL-6, IL-8, and IFN-γ were significantly elevated in ABC-positive subjects. As an emerging pathogen, A. baumanii infection represents a risk for impaired inflammation and the development of comorbidities in subjects with T2D.

Bacterial composition of nasal discharge in children based on highly accurate 16S rRNA gene sequencing analysis

Nasopharyngeal colonization by bacteria is a prerequisite for progression to respiratory disease and an important source of horizontal spread within communities. We aimed to perform quantitative analysis of the bacterial cells and reveal the microbiota of the nasal discharge in children at the species level based on highly accurate 16S rRNA gene sequencing. This study enrolled 40 pediatric patients with rhinorrhea. The bacterial cells in the nasal discharge were counted by epifluorescence microscopic analysis. The microbiota was analyzed by using the 16S rRNA gene clone library sequencing method. We demonstrated that a high abundance (median 2.2 × 107 cells/mL) of bacteria was contained in the nasal discharge of children. Of the 40 samples, 37 (92.5%) were dominated by OTUs corresponding to Haemophilus aegyptius/influenzae, Moraxella catarrhalis/nonliquefaciens, or Streptococcus pneumoniae. These samples showed higher cell abundance and lower alpha diversity than the remaining three samples in which the other bacteria coexisted. In addition, 12 sequences with low homology to type strains were considered as previously unknown bacterial lineages. In conclusion, the nasal discharge of most young children contains a large amount of respiratory pathogens and several unknown bacteria, which could not only cause endogenous infection but also be a source of transmission to others.

Functional diversity and abundance of nitrogen cycle-related genes in paddy soil

The nitrogen cycle and the associated microbes play an important role in natural ecosystems, including terrestrial habitats; they also have a major effect on climate change. The aim of this study was to explore microbial communities in rice paddy soil by detecting and quantifying some key functional genes involved in the nitrogen cycle using molecular techniques such as conventional polymerase chain reaction (PCR), clone library construction, sequencing, phylogenetic analysis, and real-time PCR. The genes analyzed were as follows: nitrogenase reductase gene (nifH), hydrazine synthase gene (hzsA), nitrous oxide reductase gene (nosZ), copper-containing (nirK) and cytochrome cd1-containing (nirS) nitrite reductase genes, nitrite oxidoreductase gene (nxrB), and ammonium monooxygenase gene (amoA). The sequence assessment using the clone library targeting these genes revealed high diversity and dominance of bacterial communities. Furthermore, real-time PCR using SYBR green dye and some primers specific for each gene revealed the high abundance of nxrB (4.1 × 109 ± 0.4 × 109 copies g−1 soil) and low abundance of hzsA (4.0 × 105 ± 1.1 × 105 copies g−1 soil). The findings of our study will be useful to explore microbial communities in terrestrial habitats, such as agricultural paddy fields.

Geographical Isolation, Buried Depth, and Physicochemical Traits Drive the Variation of Species Diversity and Prokaryotic Community in Three Typical Hypersaline Environments.

The prokaryotic community composition, species diversity and the distribution patterns at various taxonomic levels in a salt lake (Chaka salt lake), solar salterns (Taipei saltworks and Dongfang saltworks), and salt mines (Yuanyongjing salt mine, Xiangyan salt mine, and Dinyuan salt mine) were investigated using clone library or Illumina MiSeq sequencing. The clone library approach revealed that the salt lake harbors low species diversity (H’ = 0.98) as compared to the solar saltern (H’ = 4.36) and salt mine (H’ = 3.57). The dominant group in the salt lake is a species from the genus Haloparvum which constitutes about 85% of the total sequences analyzed. The species diversities in salt salterns and salt mines are richer than in the salt lake, and the dominant group is less significant in terms of total percentage. High-throughput sequencing showed that geographical isolation greatly impacted on the microbial community (phyla level) and species diversity (operational taxonomic units (OTUs) level) of salt mines. Species of the genus Natronomonas are found in all three types of environments investigated. In addition, the microbial community and species diversity of different stratums of the salt mine are very similar. Furthermore, species of the genus Halorubrum flourish in the newest stratum of salt mine and have become the dominant group. This study provides some new knowledge on the species diversity and prokaryotic community composition of three typical hypersaline environments.

Dynamics of microbiota during mechanical ventilation in aspiration pneumonia

BackgroundThe emergence of multi-drug resistant pathogens is an urgent health-related problem, and the appropriate use of antibiotics is imperative. It is often difficult to identify the causative bacteria in patients with aspiration pneumonia because tracheal aspirate contains contaminants of oral bacteria. We investigated the dynamics of microbiota in mechanically ventilated patients with aspiration pneumonia to develop a treatment strategy.MethodsTwenty-two intubated patients with aspiration pneumonia were recruited. Saliva and tracheal aspirate of the subjects were collected at three time points: (A) within 2 h after intubation, (B) just before administration of antibiotics, and (C) 48-72 h after administration of antibiotics. The microbiota in each specimen was analyzed by using the 16S rRNA gene clone library sequencing method. Bacterial floras of the samples were analyzed by principal component analysis.ResultsPrincipal component analysis based on the composition of genus revealed that although the changes of microbiota in the saliva from (A) to (B) were not clear, the composition of anaerobes in the tracheal aspirate (B) was lower than (A). In fact, the reduction of anaerobes, not in the saliva but in the tracheal aspirate from (A) to (B), was confirmed by incident rate ratios estimated by a multilevel Poisson regression model (p < 0.001). The extent of decrease in anaerobes was fully dependent on the time difference between the sampling of tracheal aspirate (A) and (B)—in particular, over 3 h of mechanical ventilation. This indicates that the alterations of microbiota (involving the reduction of anaerobes in the lower respiratory tract) occurred during mechanical ventilation prior to the administration of antibiotics. After the administration of antibiotics, Enterobacter spp., Corynebacterium spp., Pseudomonas aeruginosa, Klebsiella pneumoniae, Staphylococcus aureus, and Granulicatera adiacens were predominantly detected in the tracheal aspirate (C).ConclusionThe microbiota of the lower respiratory tract changes dynamically during mechanical ventilation and during the administration of antibiotics in intubated patients with aspiration pneumonia. Antibiotics should be selected on the premise that dynamic changes in microbiota (involved in the reduction of anaerobes) may occur during the mechanical ventilation in these patients.

Contrasting environmental factors drive bacterial and eukaryotic community successions in freshly deglaciated soils.

Glacier retreats expose deglaciated soils to microbial colonization and succession; however, the differences in drivers of bacterial and eukaryotic succession remain largely elusive. We explored soil bacterial and eukaryotic colonization and yearly community succession along a deglaciation chronosequence (10 years) on the Tibetan Plateau using qPCR, terminal restriction fragment length polymorphism (T-RFLP) and sequencing of clone libraries. The results exhibited that bacteria and eukaryotes rapidly colonized the soils in the first year of deglaciation, thereafter slowly increasing from 107 up to 1010 and 1011 gene copies g-1 soil, respectively. Bacterial and eukaryotic community changes were observed to group into distinct stages, including early (0-2 year old), transition (3-5 year old) and late stages (6-10 year old). Bacterial community succession was dominantly driven by soil factors (47.7%), among which soil moisture played a key role by explaining 26.9% of the variation. In contrast, eukaryotic community succession was dominantly driven by deglaciation age (22.2%). The dominant bacterial lineage was Cyanobacteria, which rapidly decreased from the early to the transition stage. Eukaryotes were dominated by glacier-originated Cercozoa in early stage soils, while green algae Chlorophyta substantially increased in late stage soils. Our findings revealed contrasting environmental factors driving bacterial and eukaryotic community successions.

High microbial diversity of the nitric oxide dismutation reaction revealed by PCR amplification and analysis of the nod gene

Microbial nitric oxide dismutation reaction (NOD), involved in the biogeochemical nitrogen cycle on Earth, has been implemented to N removal in laboratory-scale wastewater treatment systems, but microorganisms from relatively a few lineages have been implicated to be associated with this biochemical process. Detection of abundant putative (or novel) nitric oxide dismutase-encoding gene PCR products could confer the diversity of nitric oxide dismutase in additional microbial groups other than the two known lineages, but the distribution pattern of nod gene is unclear in different environments including oil reservoirs. Here, we surveyed the distribution and diversity of nod genes by clone library sequencing together with the inference of 16S rRNA gene-based taxonomy by amplicon sequencing in diverse samples including wastewater treatment plants (WWTP), wetland, hydrocarbon-contaminated soil, and oil reservoirs. A total of 730 phylogenetically diverse nod-related sequences recovered from these samples were clustered into 42 operational taxonomic units (OTUs) showing a considerably high diversity of nod gene in these different ecosystems. The abundance of nod gene in five environmental samples were ∼1.80 × 107–2.62 × 108 copies g−1 soil (sludge) and ∼9.67 × 106 copies l−1 water. The dominant microorganisms were Bacteroidetes, Firmicutes, Actinobacteria, and Chloroflexi. Our results expanded significantly the diversity of microbial groups potentially involved in nitric oxide dismutation, suggesting the ubiquity of microbial members in the different ecosystems carrying out NO dismutation reaction. Further studies on the functional capacity of this new microbial group will advance a better understanding of the microbially-driven nitrogen cycling and provide thorough information on N-removal processes and potential applications.

A combined approach of 16S rRNA and a functional marker gene, soxB to reveal the diversity of sulphur-oxidising bacteria in thermal springs.

With the advent of new molecular tools, new taxa of sulphur-oxidising bacteria (SOB) in diverse environments are being discovered. However, there is a significant gap of knowledge about the ecology and diversity of SOB in thermal springs. Here, the species diversity and phylogenetic affiliations of SOB were investigated using 16S rRNA and functional gene marker, soxB in thermal springs of Thane district of Maharashtra, India. Most SOB detected by 16S rDNA sequences belong to different operational taxonomic units (OTU's): Firmicutes, α-, β-, γ-Proteobacteria and Actinobacteria with the dominance of first class. However, the soxB gene clone library sequences had shown affiliation with the β-, γ- and α-Proteobacteria. β-Proteobacteria-related sequences were dominant, with 53.3% clones belonging to genus Hydrogenophaga. The thiosulphate oxidation assay carried out for different isolates having distinct identity showed the mean sulphate-sulphur production from 117.86 ± 0.50 to 218.82 ± 2.56mg SO4-Sl-1 after 9days of incubation. Also, sulphur oxidation by the genus Nitratireductor, Caldimonas, Geobacillus, Paenibacillus, Brevibacillus, Tristrella and Chelatococcus has been reported for the first time that reveals ecological widening over which thiotrophs are distributed.

Metagenomic Approach: Transforming In-Silico Research for Improved Biogas Production

The complexity of the microbial communities and metabolic pathways involved in the microbiological process of biogas production is poorly understood and numerous microorganisms in the fermentation sample of the biogas plant are still unclassified or unknown. The structure and function of microbial communities and the effects of the addition of trace elements are needed to be known, to control and channel the energy sources microbes produce and to capture and store the useful by-products or for targeted screening of novel enzymes. In this review, we discussed an emerging idea that Metagenome sequence data from a biogas-producing microbial community residing in a fermenter of a biogas plant provide the basis for a rational approach to improve the biotechnological process of biogas production. The composition and gene content of a biogas-producing consortium can be determined through metagenomic approach which allows the design of the optimal microbial community structure for any biogas plant for the significant progress in the efficacy and economic improvement of biogas production and biofertilizer of either balanced nutrition or rich in specific element for plant growth produced from the sludge of biogas plant. Biogas-producing microbial community from different production-scale biogas plants supplied with different raw materials as substrates can be analyzed by polyphasic approach to find out the best raw material composition for biogas production. The phylogenetic structure of the microbial community residing in a fermentation sample from a biogas plant can be analysed by an integrated approach using clone library sequences and metagenome sequence data obtained by 454-pyrosequencing.&#x0D; Int. J. Appl. Sci. Biotechnol. Vol 7(1): 6-11

Reductive dechlorination of perchloroethene (PCE) and bacterial community changes in a continuous-flow, two-stage anaerobic column

This study is aimed at investigating the performance of the continuous-flow, two-stage anaerobic column for the reductive dechlorination of perchloroethene (PCE) in a trichloroethene (TCE)-contaminated aquifer without bioaugmentation. Results indicated that complete dechlorination of PCE to cis-dichloroethene (DCE) was observed within the first 12 days after the addition of lactate and PCE (620:1 mg mg−1 mass ratio). The PCE conversion to ethene was initially observed in the 2nd column after 70 days (during phase II) upon the increase of lactate to PCE mass ratio to 5000:1 (mg mg−1). However, the degradation of PCE to ethene occurred in the 1st column after 30 days operation of phase IV (217–310 d) under the high PCE feed conditions (33.65 ± 2.86 μM). 16S rDNA clone library sequence analysis confirmed that Dehalobacter sp., Desulfuromonas sp., Desulfovibrio sp. Geobacter sp., Methanosaeta sp., Methanobacterium paludism, and M. spelaei were the dominant species in the original aquifer, and their relative abundance were further changed following lactate addition. Dehalococcoides mccartyi sequences were retrieved after lactate stimulation. Overall, the continuous-flow, two-stage anaerobic column process exhibited the maximum dechlorination (6.23 μmol L−1 hr−1) of PCE without bioaugmentation, indicating its potential up-scaling application in PCE dechlorination.

Microbial communities associated with phosphogenic sediments and phosphoclast‐associated DNA of the Benguela upwelling system

The processes that lead to the precipitation of authigenic calcium phosphate minerals in certain marine pore waters remain poorly understood. Phosphogenesis occurs in sediments beneath some oceanic upwelling zones that harbor polyphosphate-accumulating bacteria. These bacteria are believed to concentrate phosphate in sediment pore waters, creating supersaturated conditions with respect to apatite precursors. However, the relationship between microbes and phosphorite formation is not fully resolved. To further study this association, we examined microbial community data generated from two sources: sediment cores recovered from the shelf of the Benguela upwelling region where phosphorites are currently forming, and DNA preserved within phosphoclasts recovered from a phosphorite deposit along the Benguela shelf. iTag and clone library sequencing of the 16S rRNA gene showed that many of our sediment-hosted communities shared large numbers of phylotypes with one another, and that the same metabolic guilds were represented at localities across the shelf. Sulfate-reducing bacteria and sulfur-oxidizing bacteria were particularly abundant in our datasets, as were phylotypes that are known to carry out nitrification and the anaerobic oxidation of ammonium. The DNA extracted from phosphoclasts contained the signature of a distinct microbial community from those observed in the modern sediments. While some aspects of the modern and phosphoclast communities were similar, we observed both an enrichment of certain common microbial classes found in the modern phosphogenic sediments and a relative depletion of others. The phosphoclast-associated DNA could represent a relict signature of one or more microbial assemblages that were present when the apatite or its precursors precipitated. While these taxa may or may not have contributed to the precipitation of the apatite that now hosts their genetic remains, several groups represented in the phosphoclast extract dataset have the genetic potential to metabolize polyphosphate, and perhaps modulate phosphate concentrations in pore waters where carbonate fluorapatite (or its precursors) are known to be precipitating.

Bioreduction of Antimonate by Anaerobic Methane Oxidation in a Membrane Biofilm Batch Reactor

Employing a special anaerobic membrane biofilm batch reactor (MBBR), we demonstrated antimonate (Sb(V)) reduction using methane (CH4) as the sole electron donor. Scanning electron microscopy (SEM), energy dispersive X-ray spectroscopy (EDS), X-ray photoelectron spectroscopy (XPS), X-ray diffraction (XRD), and Raman and photoluminescence (PL) spectra identified that Sb2O3 microcrystals were the main reduced products. The Sb(V) reduction rate increased continually over the 111-day experiment, which supports the enrichment of the microorganisms responsible for Sb(V) reduction to Sb(III). Copy numbers of the mcrA gene and archaeal and bacterial 16 S rRNA genes increased in parallel. Clone library and Illumina sequencing of 16S rRNA gene demonstrated that Methanosarcina became the dominant archaea in the biofilm, suggesting that Methanosarcina might play an important role in Sb(V) reduction in the CH4-based MBBR.

Mining the Core Gut Microbiome from a Sample Indian Population.

Human gut microbiome studies are increasing at a rapid pace to understand contributions of the prokaryotic life to the innate workings of their eukaryotic host. Majority of studies focus on the pattern of gut microbial diversity in various diseases, however, understanding the core microbiota of healthy individuals presents a unique opportunity to study the microbial fingerprint in population specific studies. Present study was undertaken to determine the core microbiome of a healthy population and its imputed metabolic role. A total of 8990, clone library sequences (> 900bp) of 16S rRNA gene from fecal samples of 43 individuals were used. The core gut microbiota was computed using QIIME pipeline. Our results show the distinctive predominance of genus Prevotella and the core composition of genera Prevotella, Bacteroides, Roseburia and Megasphaera in the Indian gut. PICRUSt analysis for functional imputation of the microbiome indicates a higher potential of the microbiota for carbohydrate metabolism. The presence of core microbiota may indicate key functions played by these microbes for the human host.