Comprehensive insights into arsenic- and iron-redox genes, their taxonomy and associated environmental drivers deciphered by a meta-analysis.

In nature, arsenic (As) and iron (Fe) biotransformation are interconnected, influencing local As mobility and toxicity. While As- or Fe-metabolizing microorganisms are widely documented, knowledge concerning their cycling genes, associated with geophysicochemical data and taxonomic distribution, remains scarce. We performed a meta-analysis to explore the distribution and environmental importance of As- and Fe-redox genes (AsRGs and FeRGs) and predict their significant correlations and hosts. The most abundant and ubiquitous AsRGs and FeRGs were arsC and ccoN, respectively. The ccoN gene had the highest frequency at pH ≥ 9.1, in which dissolved Fe(II) is scarce, possibly contributing to enhanced host survival. Fe(III) oxidation genes iro and ccoN appear to be associated with As(V) detoxification in mesophilic environments. No correlation was observed between Fe(III) reduction gene omcB and arsenate reductase genes. Cytochromes with putative roles in Fe-redox reactions were identified (including yceJ and fbcH) and were significantly correlated with As(V) reduction genes under diverse geophysicochemical conditions. The taxonomies of AsRGs and FeRGs-carrying contigs revealed great diversity, among which various, such as Chlamydea (arsC) and Firmicutes (omcB), were previously undescribed. Nearly all (98.9%) of the AsRGs and FeRGs were not carried by any plasmid sequences. This meta-analysis expands our understanding of the global environmental, taxonomic and functional microbiome involved in As- and Fe-redox transformations. Moreover, these findings should help guide studies on putative in vivo functional roles of cytochromes in Fe-redox pathways.

Characterizing a riverine microbiome impacted by extreme disturbance caused by a mining sludge tsunami.

Studies on disturbance events in riverine systems caused by environmental disasters and their effects on microbial diversity are scarce. Here, we evaluated the impact of the collapse of an iron ore dam holding approximately 50 million cubic meters of waste on both water and sediment microbiomes by deeply sequencing the 16S rRNA gene. Samples were taken from two impacted rivers and one reference river 7, 30 and 150 days postdisturbance. The impacted community structure changed greatly over spatiotemporal scales, being less diverse and more uneven, particularly on day 7 for the do Carmo River (the closest to the dam). However, the reference community structure remained similar between sampling events. Moreover, the impacted sediments were positively correlated with metals. The taxa abundance varied greatly over spatiotemporal scales, allowing for the identification of several potential bioindicators, e.g., Comamonadaceae, Novosphingobium, Sediminibacterium and Bacteriovorax. Our results showed that the impacted communities consisted mostly of Fe(II) oxidizers and Fe(III) reducers, aromatic compound degraders and predator bacteria. Network analysis showed a highly interconnected microbiome whose interactions switched from positive to negative or vice versa between the impacted and reference communities. This work revealed potential molecular signatures associated with the rivers heavily impacted by metals that might be useful sentinels for predicting riverine health.

Leprous lesion presents enrichment of opportunistic pathogenic bacteria.

Leprosy is a chronic infectious disease that remains a major challenge to public health in endemic countries. Increasing evidence has highlighted the importance of microbiota for human general health and, as such, the study of skin microbiota is of interest. But while studies are continuously revealing the complexity of human skin microbiota, the microbiota of leprous cutaneous lesions has not yet been characterized. Here we used Sanger and massively parallel small sub-unit rRNA (SSU) rRNA gene sequencing to characterize the microbiota of leprous lesions, and studied how it differs from the bacterial skin composition of healthy individuals previously described in the literature. Taxonomic analysis of leprous lesions revealed main four phyla: Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria, with Proteobacteria presenting the highest diversity. There were considerable differences in the distribution of Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria, with the first two phyla enriched and the other markedly diminished in the leprous lesions, when compared with healthy skin. Propionibacterium, Corynebacterium and Staphylococcus, resident and abundant in healthy skin, were underrepresented in skin from leprous lesions. Most of the taxa found in skin from leprous lesions are not typical in human skin and potentially pathogenic, with the Burkholderia, Pseudomonas and Bacillus genera being overrepresented. Our data suggest significant shifts of the microbiota with emergence and competitive advantage of potentially pathogenic bacteria over skin resident taxa.

Bacteria and genes involved in arsenic speciation in sediment impacted by long-term gold mining.

The bacterial community and genes involved in geobiocycling of arsenic (As) from sediment impacted by long-term gold mining were characterized through culture-based analysis of As-transforming bacteria and metagenomic studies of the arsC, arrA, and aioA genes. Sediment was collected from the historically gold mining impacted Mina stream, located in one of the world's largest mining regions known as the "Iron Quadrangle". A total of 123 As-resistant bacteria were recovered from the enrichment cultures, which were phenotypically and genotypically characterized for As-transformation. A diverse As-resistant bacteria community was found through phylogenetic analyses of the 16S rRNA gene. Bacterial isolates were affiliated with Proteobacteria, Firmicutes, and Actinobacteria and were represented by 20 genera. Most were AsV-reducing (72%), whereas AsIII-oxidizing accounted for 20%. Bacteria harboring the arsC gene predominated (85%), followed by aioA (20%) and arrA (7%). Additionally, we identified two novel As-transforming genera, Thermomonas and Pannonibacter. Metagenomic analysis of arsC, aioA, and arrA sequences confirmed the presence of these genes, with arrA sequences being more closely related to uncultured organisms. Evolutionary analyses revealed high genetic similarity between some arsC and aioA sequences obtained from isolates and clone libraries, suggesting that those isolates may represent environmentally important bacteria acting in As speciation. In addition, our findings show that the diversity of arrA genes is wider than earlier described, once none arrA-OTUs were affiliated with known reference strains. Therefore, the molecular diversity of arrA genes is far from being fully explored deserving further attention.