Assessing the Diversity and Metabolic Potential of Psychrotolerant Arsenic-Metabolizing Microorganisms From a Subarctic Peatland Used for Treatment of Mining-Affected Waters by Culture-Dependent and -Independent Techniques

Abstract

Arsenic contamination in water by natural causes or industrial activities is a major environmental concern, and treatment of contaminated waters is needed to protect water resources and minimize the risk for human health. In mining environments, treatment peatlands are used in the polishing phase of water treatment to remove arsenic (among other contaminants), and peat microorganisms play a crucial role in arsenic removal. The present study assessed culture-independent diversity obtained through metagenomic and metatranscriptomic sequencing and culture-dependent diversity obtained by isolating psychrotolerant arsenic-tolerant, arsenite-oxidizing, and arsenate-respiring microorganisms from a peatland treating mine effluent waters of a gold mine in Finnish Lapland using a dilution-to-extinction technique. Low diversity enrichments obtained after several transfers were dominated by the genera Pseudomonas, Polaromonas, Aeromonas, Brevundimonas, Ancylobacter, and Rhodoferax. Even though maximal growth and physiological activity (i.e., arsenite oxidation or arsenate reduction) were observed at temperatures between 20 and 28°C, most enrichments also showed substantial growth/activity at 2–5°C, indicating the successful enrichments of psychrotolerant microorganisms. After additional purification, eight arsenic-tolerant, five arsenite-oxidizing, and three arsenate-respiring strains were obtained in pure culture and identified as Pseudomonas, Rhodococcus, Microbacterium, and Cadophora. Some of the enriched and isolated genera are not known to metabolize arsenic, and valuable insights on arsenic turnover pathways may be gained by their further characterization. Comparison with phylogenetic and functional data from the metagenome indicated that the enriched and isolated strains did not belong to the most abundant genera, indicating that culture-dependent and -independent methods capture different fractions of the microbial community involved in arsenic turnover. Rare biosphere microorganisms that are present in low abundance often play an important role in ecosystem functioning, and the enriched/isolated strains might thus contribute substantially to arsenic turnover in the treatment peatland. Psychrotolerant pure cultures of arsenic-metabolizing microorganisms from peatlands are needed to close the knowledge gaps pertaining to microbial arsenic turnover in peatlands located in cold climate regions, and the isolates and enrichments obtained in this study are a good starting point to establish model systems. Improved understanding of their metabolism could moreover lead to their use in biotechnological applications intended for bioremediation of arsenic-contaminated waters.

Assessment of microbial communities from cold mine environments and subsequent enrichment, isolation and characterization of putative antimony- or copper-metabolizing microorganisms

“…These results were expected Pseudomonas is a fast-growing, metabolically versatile genus (Jones et al, 2021). In fact, Pseudomonas has been reported in previous studies (Ponce-Soto et al, 2015) for increasing its abundance during enrichment experiments, including in experiments from cold-metal contaminated sites (Ziegelhöfer and Kujala, 2021). Some genera like Corynebacterium or Kocuria, which were relatively high in the environmental samples from sites A and B, had reduced relative abundances in the enrichments.…”

“…In particular, one of the isolates was related to Pseudomonas veronii, a metal tolerant species of this genus, which has been studied for bioremediation (Malla et al, 2018) and whose genome has been found to have the heavy metal resistance gene arsBDR (Morales et al, 2016). Furthermore, As-tolerant Pseudomonas strains have been previously isolated from same location as site C (Ziegelhöfer and Kujala, 2021). However, unlike the strains presented in this study, the previously reported Pseudomonas showed an optimum growth at 20-28°C, implying this might be a different isolated strain as the optimum temperatures for the Pseudomonas presented here was 10°C.…”

Metabolically versatile psychrotolerant Antarctic bacterium Pseudomonas sp. ANT_H12B is an efficient producer of siderophores and accompanying metabolites (SAM) useful for agricultural purposes

“…ANT_H12B exhibited the highest siderophores production when glycolytic substrate (glucose) was used. This finding suggests that the metabolic profiles of psychrotolerant bacteria can differ significantly, even in microorganisms from the similar taxon [ 60 , 61 ]. Pseudomonas strains generally prefer organic acids due to the regulation of catabolic repression and absence of phosphofructokinase, an important enzyme in the glycolytic pathway [ 25 ].…”

Unraveling microbial processes involved in carbon and nitrogen cycling and greenhouse gas emissions in rewetted peatlands by molecular biology

“…No metatranscriptomic studies assessing changes in active functions after rewetting and compare to pristine peatlands were found in our literature search, but some have been carried out in natural peatlands (Lin et al 2014 ; Hausmann et al 2019 ). Additionally, other metatranscriptomic analyses have focused so far on Sphagnum associated microbiomes (Ivanova et al 2018 ; Stough et al 2018 ; Dedysh and Ivanova 2019 ; Carrell et al 2022a , b ; Kolton et al 2022 ), arctic peatlands (Tveit et al 2013 , 2014 , 2015 ; Belova et al 2018 ; Dedysh and Ivanova 2019 ; Ziegelhofer and Kujala 2021 ; Bender et al 2021 ) and specific microbial groups such as protists (Geisen et al 2015 ) and Planctomycetes (Ravin et al 2018 ; Ivanova et al 2018 ; Dedysh and Ivanova 2019 ). Additionally, in cases where peat chemical composition cannot be measured, metatranscriptomics could prove helpful as the function of active genes can provide information to some extent regarding what substrate is being used (with the caveat that information in databases used to functionally annotate genes are limited).…”