Arsenic metabolism in high altitude modern stromatolites revealed by metagenomic analysis

Abstract

Modern stromatolites thrive only in selected locations in the world. Socompa Lake, located in the Andean plateau at 3570 masl, is one of the numerous extreme Andean microbial ecosystems described over recent years. Extreme environmental conditions include hypersalinity, high UV incidence, and high arsenic content, among others. After Socompa’s stromatolite microbial communities were analysed by metagenomic DNA sequencing, taxonomic classification showed dominance of Proteobacteria, Bacteroidetes and Firmicutes, and a remarkably high number of unclassified sequences. A functional analysis indicated that carbon fixation might occur not only by the Calvin-Benson cycle, but also through alternative pathways such as the reverse TCA cycle, and the reductive acetyl-CoA pathway. Deltaproteobacteria were involved both in sulfate reduction and nitrogen fixation. Significant differences were found when comparing the Socompa stromatolite metagenome to the Shark Bay (Australia) smooth mat metagenome: namely, those involving stress related processes, particularly, arsenic resistance. An in-depth analysis revealed a surprisingly diverse metabolism comprising all known types of As resistance and energy generating pathways. While the ars operon was the main mechanism, an important abundance of arsM genes was observed in selected phyla. The data resulting from this work will prove a cornerstone for further studies on this rare microbial community.

Disentangling the drivers of functional complexity at the metagenomic level in Shark Bay microbial mat microbiomes

“…Any build-up of ammonium produced by DNRA microorganisms is hypothesized to be assimilated by other members of the mat community, as a high number of glutamine synthase (glnA, glnE) and glutamate synthase genes (glnB, glnD) were identified throughout the mat. A similar scenario has been observed in Socompa Lake stromatolites [68] and hypersaline mats from Hot Lake [103], where it was found that ammonium is likely assimilated by microbial community members instead of being oxidized.…”

“…Of the 87 MAGs, 75 have arsenate resistance genes (arc3, arsC, arsA, arsB, and arsH) and one Planctomycetes MAG (SM_039) contains genes that encode for energetic arsenic respiration genes (AoxAB). In the Shark Bay metagenomes aoxAB genes were affiliated to Alphaproteobacteria, and these genes are responsible for respiratory arsenite oxidation and related to energetic metabolism in other mats [68].…”

Predominance of deterministic microbial community dynamics in salterns exposed to different light intensities

“…These findings suggested that such high‐irradiation communities are well adapted to extreme salinity and irradiation, a fact that is supported by our observed relative high abundance of genes related to DNA protection and repair. These findings were also consistent with those reported for high altitude hypersaline lake with strong light incidence (Kurth et al ., ). Results from communities thriving under very low‐irradiation conditions exhibited slight differences.…”

“…the archaeal Halobacteria and the bacterial halophilic family of Salinibacteraceae, order Rhodothermia (Gomariz et al, 2014;Mora-Ruiz et al, 2018), but with relatively high species and genus diversity within each lineage. To cope with these extreme conditions of salt concentrations close to or above NaCl saturation (~36%) and direct sun irradiation, halophilic microorganisms have evolved osmotic survival strategies, such as osmoprotectants and compatible solutes, and also distinct DNA repair systems and photolyases to cope with UV radiation stresses (Kurth et al, 2017). Besides salinity, irradiation is probably the second most relevant environmental driver in such systems.…”

Uncovering Photolyase/Cryptochrome Genes Diversity in Aquatic Microbiomes Exposed to Diverse UV-B Regimes

“…The metagenomes selected from NCBI using biosample information were the following, each one with its respective SRA entry: Lake Diamante (ERR1824222) (Rascovan et al ., 2016), Socompa stromatolite (SRR3341855) (Kurth et al ., 2017), Tibetan Plateau sediment (SRR3322106) (Chen et al ., 2016), Amazon River (SRR1790676) (Satinsky et al ., 2015), Lake Rauer (SRR6129205) (Tschitschko et al ., 2018), Dewar Creek hot spring (SRR5580900), Greenland cryoconite (SRR5275901) (Hauptmann et al ., 2017), Lake Montjoie (SRR5818193) (Tran et al ., 2018), Olkiluoto Island groundwater (SRR6976411) and human gut (SRR6517782) (Ye et al ., 2018). The metagenome of the human gut is assumed as UVB free environment, acting as a negative control.…”