Metagenomic and Metatranscriptomic Study of Microbial Metal Resistance in an Acidic Pit Lake

Abstract

Cueva de la Mora (CM) is an acidic, meromictic pit lake in the Iberian Pyrite Belt characterized by extremely high metal(loid) concentrations and strong gradients in oxygen, metal, and nutrient concentrations. We hypothesized that geochemical variations with depth would result in differences in community composition and in metal resistance strategies among active microbial populations. We also hypothesized that metal resistance gene (MRG) expression would correlate with toxicity levels for dissolved metal species in the lake. Water samples were collected in the upper oxic layer, chemocline, and deep anoxic layer of the lake for shotgun metagenomic and metatranscriptomic sequencing. Metagenomic analyses revealed dramatic differences in the composition of the microbial communities with depth, consistent with changing geochemistry. Based on relative abundance of taxa identified in each metagenome, Eukaryotes (predominantly Coccomyxa) dominated the upper layer, while Archaea (predominantly Thermoplasmatales) dominated the deep layer, and a combination of Bacteria and Eukaryotes were abundant at the chemocline. We compared metal resistance across communities using a curated list of protein-coding MRGs with KEGG Orthology identifiers (KOs) and found that there were broad differences in the metal resistance strategies (e.g., intracellular metal accumulation) expressed by Eukaryotes, Bacteria, and Archaea. Although normalized abundances of MRG and MRG expression were generally higher in the deep layer, expression of metal-specific genes was not strongly related to variations in specific metal concentrations, especially for Cu and As. We also compared MRG potential and expression in metagenome assembled genomes (MAGs) from the deep layer, where metal concentrations are highest. Consistent with previous work showing differences in metal resistance mechanisms even at the strain level, MRG expression patterns varied strongly among MAG populations from the same depth. Some MAG populations expressed very few MRG known to date, suggesting that novel metal resistance strategies remain to be discovered in uncultivated acidophiles.

Prokaryotic communities in the historic silver mine Reiche Zeche

“…However, in four of the five AMD-pool habitats sequences affiliated with the Candidate Sva0485 clade (class Deltaproteobacteria) were found to occur up to a relative abundance of 9.5% as in sample S3. Clade Sva0485 is known to be present in different AMD ecosystems and to contain potential sulfate-reducing bacteria (Ayala-Muñoz et al 2020;Vuillemin et al 2018). The ecological role of this taxon remains still unknown due Obscuribacterales to the lack of physiological and genomic insights (Tan et al 2019).…”

Extremofiles 2.0

“…This, for several reasons, some, fundamental and related with the search for the limits of life [ 2 ], and others, more pragmatic and focused on the biotechnological potential of extremophiles, has sparked a marked growth of interest in the ecology of extreme environments [ 3 ]. The 2019–2020 version of Extremofiles 2.0, a Special Issue of Microorganisms devoted to extremophiles, has gathered eleven papers dealing with different aspects of microorganisms that thrive in extreme environments: five on halophiles [ 4 , 5 , 6 , 7 , 8 ], three on acidophiles [ 9 , 10 , 11 ], one on thermophiles [ 12 ], one on psycrophiles [ 13 ] and one on metal resistant microorganisms [ 14 ].…”

“…Ayala-Muñoz et al analyzed the diversity of an acidic, meromictic pit lake in the Iberian Pyrite Belt, Cueva de la Mora, in which Eukaryotes, predominantly Coccomyxa , dominated the upper layer, while Archaea, predominantly Thermoplasmatales, dominated the deep layer, and a combination of bacteria and eukaryotes were abundant in the chemocline [ 11 ].…”

Sulfidogenesis at low pH and its application for treatment of metalliferous wastewaters

“…Independent of cultivation, metagenomics can provide a more detailed picture of the genetic potential in a microbial community, which can be partly verified by combining it with metatranscriptomics in order to identify actively transcribed genes. For example, metagenomics assembled genomes (MAGs) obtained from an AMD site in the USA indicated the importance of previously unrecognized taxa in the cycling of iron (Grettenberger and Hamilton, 2021), and combined metagenomics and metatranscriptomics studies were used to investigate active metal resistance strategies employed by microorganisms in the water column of the APL Cueva de la Mora (IPB) (Ayala-Muñoz et al, 2020).…”

“…In FC we observed a high relative abundance of reads assigned to Desulfomonile in the water column at pH 4. acidophiles, the Desulfomonile taxa detected in FC are not necessarily more acidophilic than the SRB isolated to date. However, its high abundance (18 % of total reads) in the chemocline of the APL Cueva de la Mora at pH 3.95 Ayala-Muñoz et al, 2020), suggests it could tolerate increasing acidity. In addition, it was detected in high abundance (12.3 %) in the monimolimnion of Brunita pit lake, one of the most extreme pit lakes in terms of salinity and dissolved metal concentrations (Fe 2+ , Zn 2+ , Mn 2+ ).…”