A comparison of taxon co-occurrence patterns for macro- and microorganisms

We examine co-occurrence patterns of microorganisms to evaluate community assembly “rules.” We use methods previously applied to macroorganisms, both to evaluate their applicability to microorganisms and to allow comparison of co-occurrence patterns observed in microorganisms to those found in macroorganisms. We use a null model analysis of 124 incidence matrices from microbial communities, including bacteria, archaea, fungi, and algae, and we compare these results to previously published findings from a meta-analysis of almost 100 macroorganism data sets. We show that assemblages of microorganisms demonstrate nonrandom patterns of co-occurrence that are broadly similar to those found in assemblages of macroorganisms. These results suggest that some taxon co-occurrence patterns may be general characteristics of communities of organisms from all domains of life. We also find that co-occurrence in microbial communities does not vary among taxonomic groups or habitat types. However, we find that the degree of co-occurrence does vary among studies that use different methods to survey microbial communities. Finally, we discuss the potential effects of the undersampling of microbial communities on our results, as well as processes that may contribute to nonrandom patterns of co-occurrence in both macrobial and microbial communities such as competition, habitat filtering, historical effects, and neutral processes

Effects of Pre-Natal Vitamin D Supplementation with Partial Correction of Vitamin D Deficiency on Early Life Healthcare Utilisation: A Randomised Controlled Trial

Funded by Asthma UK grant number 09/ 36

Genome-wide imputation study identifies novel HLA locus for pulmonary fibrosis and potential role for auto-immunity in fibrotic idiopathic interstitial pneumonia.

To access publisher's full text version of this article, please click on the hyperlink in Additional Links field or click on the hyperlink at the top of the page marked Files. This article is open access.Fibrotic idiopathic interstitial pneumonias (fIIP) are a group of fatal lung diseases with largely unknown etiology and without definitive treatment other than lung transplant to prolong life. There is strong evidence for the importance of both rare and common genetic risk alleles in familial and sporadic disease. We have previously used genome-wide single nucleotide polymorphism data to identify 10 risk loci for fIIP. Here we extend that work to imputed genome-wide genotypes and conduct new RNA sequencing studies of lung tissue to identify and characterize new fIIP risk loci.We performed genome-wide genotype imputation association analyses in 1616 non-Hispanic white (NHW) cases and 4683 NHW controls followed by validation and replication (878 cases, 2017 controls) genotyping and targeted gene expression in lung tissue. Following meta-analysis of the discovery and replication populations, we identified a novel fIIP locus in the HLA region of chromosome 6 (rs7887 P meta  = 3.7 × 10(-09)). Imputation of classic HLA alleles identified two in high linkage disequilibrium that are associated with fIIP (DRB1*15:01 P = 1.3 × 10(-7) and DQB1*06:02 P = 6.1 × 10(-8)). Targeted RNA-sequencing of the HLA locus identified 21 genes differentially expressed between fibrotic and control lung tissue (Q < 0.001), many of which are involved in immune and inflammatory response regulation. In addition, the putative risk alleles, DRB1*15:01 and DQB1*06:02, are associated with expression of the DQB1 gene among fIIP cases (Q < 1 × 10(-16)).We have identified a genome-wide significant association between the HLA region and fIIP. Two HLA alleles are associated with fIIP and affect expression of HLA genes in lung tissue, indicating that the potential genetic risk due to HLA alleles may involve gene regulation in addition to altered protein structure. These studies reveal the importance of the HLA region for risk of fIIP and a basis for the potential etiologic role of auto-immunity in fIIP.National Heart, Lung and Blood Institute R01-HL095393 R01-HL097163 P01-HL092870 RC2-HL101715 U01-HL089897 U01-HL089856 U01-HL108642 P50-HL089493

Identification of Key Organisms, Genes and Pathways in Benzene-degrading Methanogenic Cultures

Benzene is a carcinogenic hydrocarbon and a widespread groundwater contaminant. Microbial mineralization of benzene is possible, but the process is slow and not well understood under the anaerobic conditions that are often prevalent at contaminated sites. The goals of this study were to gain a better understanding of key organisms, genes and metabolic pathways associated with benzene degradation in methanogenic enrichment cultures. Conditions required for the successful growth of the cultures were also explored. Potential key organisms were identified via 16S rRNA gene cloning studies, performed using several cultures that had been enriched in parallel from the same hydrocarbon-contaminated site. In all cultures, closely related members of the Syntrophobacterales were found to have survived and thrived over nearly a decade of enrichment. These organisms, referred to as ORM2-like organisms, were phylogenetically most similar to those present in cultures enriched from other benzene-contaminated sites. To link organisms with their potential roles in anaerobic benzene biodegradation, we sequenced, assembled and analyzed the metagenome of one of the benzene-degrading methanogenic cultures. Several assemblies were created from Illumina sequencing data and a combination of these proved to be optimal. An unsupervised binning method was developed to achieve near-complete genomes of the three most abundant phylotypes, including a group of three closely-related ORM2-like species, a hydrogen-utilizing Methanoregula sp., and a previously unidentified organism in the culture, classified as a member of the Candidate Division OD1. The ORM2-like organisms were found to harbor a suite of genes linked to the degradation of the central metabolite benzoyl-CoA. Proteomic data confirmed that these genes were expressed under benzene-degrading conditions, providing strong evidence for the role of ORM2-like organisms as benzene fermenters. Activity of hydrogenotrophic and acetoclastic methanogens was confirmed; other organisms may play peripheral roles that increase the culture robustness. The absence of an easily identified putative anaerobic benzene carboxylase in the ORM2-like genomes suggests a novel mechanism for benzene activation by these organisms. The work presented here provides a valuable blueprint that could be used in identifying biomarkers of anaerobic benzene biodegradation, or in exploring the genomes of organisms from novel genera, orders and even phyla.Ph

Ferric Sulfate Leaching of Pyrrhotite Tailings between 30 to 55 °C

Mine tailings present major environmental issues in the mining industry. However due to the depletion of high-grade sulfide ores for metal recovery, tailings could also be a potential resource for certain valuable metals. The present study investigates the potential to recover nickel from pyrrhotite tailings. Leaching tests were performed in acidic ferric sulfate media with 0.14 wt % solids to keep the ferric concentration essentially constant. The temperature was varied between 30 and 55 °C, and the ferric concentration was in a range 0.02–0.3 M. The results showed that both temperature and ferric sulfate concentration had significant effects on the nickel extraction kinetics. The shrinking core model (SCM) was applied to the nickel extraction data. The rate controlling step was found to be product layer diffusion. The Arrhenius plot yielded an activation energy of Ea = 62.12 kJ/mol based on apparent reaction rates obtained by the SCM. The reaction order with respect to ferric ion was found to be 1 at the high concentration range. SEM images of partially leached tailings confirmed the presence of elemental sulfur around the pyrrhotite particles, which was responsible for the observed non-linear leaching kinetics (diffusion control)

Ferric Sulfate Leaching of Pyrrhotite Tailings between 30 to 55 °C

Mine tailings present major environmental issues in the mining industry. However due to the depletion of high-grade sulfide ores for metal recovery, tailings could also be a potential resource for certain valuable metals. The present study investigates the potential to recover nickel from pyrrhotite tailings. Leaching tests were performed in acidic ferric sulfate media with 0.14 wt % solids to keep the ferric concentration essentially constant. The temperature was varied between 30 and 55 °C, and the ferric concentration was in a range 0.02–0.3 M. The results showed that both temperature and ferric sulfate concentration had significant effects on the nickel extraction kinetics. The shrinking core model (SCM) was applied to the nickel extraction data. The rate controlling step was found to be product layer diffusion. The Arrhenius plot yielded an activation energy of Ea = 62.12 kJ/mol based on apparent reaction rates obtained by the SCM. The reaction order with respect to ferric ion was found to be 1 at the high concentration range. SEM images of partially leached tailings confirmed the presence of elemental sulfur around the pyrrhotite particles, which was responsible for the observed non-linear leaching kinetics (diffusion control)

Bacterial alpha-diversity varies by DO.

<p>A significant relationship exists between DO concentration and bacterial taxa richness. Points are coded by water depth as either deep (filled symbols) or surface (open symbols) and by season as April (square), June (circle), or October (triangle). Dashed line represents the best fit from the linear regression model of bacterial richness as a function of dissolved oxygen (adjusted R² = 0.7379, p < 0.01).</p

Principal components analysis of environmental characteristics of the sixteen samples ordinated based on Euclidean distance calculated from environmental factors.

<p>Points are coded by water depth as either deep (filled symbols) or surface (open symbols) and by season as April (square), June (circle), or October (triangle). Nitrate, phosphate, salinity, and dissolved oxygen best explain the separation of samples along axis one, and ammonium alone explains variation along axis two based on the variable loadings on each principal component.</p

Bacterial community threshold analysis for DO in Hood Canal.

<p>Taxa-Z plot from TITAN showing the cumulative change points of taxa abundances across the DO gradient. The peak in change-point is considered an approximate community threshold for DO concentration. Z- are taxa that have a negative association with DO and Z+ are taxa that have a positive association with DO.</p

Number of sequences obtained in each sample, as well as the observed and Chao estimates of taxa richness and Pielou’s J index of taxa evenness for all Hood Canal samples based on an operational taxonomic unit cutoff of 97% sequence identity.

<p>BA = Bangor; SP = Sister’s Point; HH = Hama Hama; LC = Lynch Cove; APR = April; JUN = June; OCT = October; S = Surface; D = Deep.</p><p>Number of sequences obtained in each sample, as well as the observed and Chao estimates of taxa richness and Pielou’s J index of taxa evenness for all Hood Canal samples based on an operational taxonomic unit cutoff of 97% sequence identity.</p