Metagenomic signatures of a tropical mining-impacted stream reveal complex microbial and metabolic networks

Abstract

Bacteria from aquatic ecosystems significantly contribute to biogeochemical cycles, but details of their community structure in tropical mining-impacted environments remain unexplored. In this study, we analyzed a bacterial community from circumneutral-pH tropical stream sediment by 16S rRNA and shotgun deep sequencing. Carrapatos stream sediment, which has been exposed to metal stress due to gold and iron mining (21 [g Fe]/kg), revealed a diverse community, with predominance of Proteobacteria (39.4%), Bacteroidetes (12.2%), and Parcubacteria (11.4%). Among Proteobacteria, the most abundant reads were assigned to neutrophilic iron-oxidizing taxa, such as Gallionella, Sideroxydans, and Mariprofundus, which are involved in Fe cycling and harbor several metal resistance genes. Functional analysis revealed a large number of genes participating in nitrogen and methane metabolic pathways despite the low concentrations of inorganic nitrogen in the Carrapatos stream. Our findings provide important insights into bacterial community interactions in a mining-impacted environment.

Novel arsenic-transforming bacteria and the diversity of their arsenic-related genes and enzymes arising from arsenic-polluted freshwater sediment

“…Proteobacteria, Firmicutes, Bacteroidetes and Patescibacteria dominated all samples. This result is consistent with the data from As-rich environments from which these phyla have been recovered 15 , 27 . Overall, there was a variation in the dominant OTU abundance across samples; some of them were absent or rare in the other samples, which could be explained as an effect of the anaerobic enrichment process.…”

“…Lastly, the Patescibacteria superphylum, characterized by having reduced metabolic capacities, is also involved in hydrogen production, sulfur cycling and anaerobic methane oxidation 58 , 59 . Our research group has also reported the presence of Patescibacteria in relatively high abundance in freshwater sediment with high As and metal content 27 .…”

Characterization of the Rumen Microbiota and Volatile Fatty Acid Profiles of Weaned Goat Kids under Shrub-Grassland Grazing and Indoor Feeding

“…Notably, the phylum Gracilibacteria in the domain Bacteria was also identified, and was highly abundant via specific 16S rRNA primers for methanogens (data not shown). This finding was supported by high levels of Gracilibacteria in the methane-enriched environmental samples [37,38], and similarities between the genome sequences of Gracilibacteria and those of archaea [39,40]. Our results showed that Methanobrevibacter was the most abundant genus in the rumen archaeal community of ruminants [5], such as goats [20], cattle [41,42], yaks [15] and impala [43].…”

Metagenome-Assembled Genomes from Monte Cristo Cave (Diamantina, Brazil) Reveal Prokaryotic Lineages As Functional Models for Life on Mars

“…Both anaerobic and aerobic methanotrophic metabolism was observed in previous studies from submerged portions of Nullarbor Cave (Australia) (Holmes et al, 2001), Sulzbrunn Cavern (Germany) (Karwautz et al, 2018), Movile Cave (Romania) (Kumaresan et al, 2018) and Heshang Cave (China) (Zhao et al, 2018). Our samples are not associated with submerged aquatic systems and the presence of anaerobic methane-oxidizing microorganisms on the surface of the cave wall might be explained by a potential stratification with anaerobic microniches lowermost the oxic surface strata, as observed in previous studies (Méndez-García et al, 2014;Reis et al, 2016). The DC_MAG_00021 (Ca.…”

“…Further, the detection of both aerobic and anaerobic microorganisms indicates a stratification condition probably due to the stream influence, which might create anoxic microniches a few centimeters below the surface. The presence of oxic and lowermost anoxic conditions within caves influenced by stratified sediments from a stream was reported in previous studies (Méndez-García et al, 2014;Reis et al, 2016).…”