Taxonomically-linked growth phenotypes during arsenic stress among arsenic resistant bacteria isolated from soils overlying the Centralia coal seam fire

Microbial arsenic methylation in soil-water systems and its environmental significance

In this review, we have summarized the current knowledge about the environmental importance, relevance, and consequences of microbial arsenic (As) methylation in various ecosystems. In this regard, we have presented As biomethylation in terrestrial and aquatic ecosystems particularly in rice paddy soils and wetlands. The functions of As biomethylation by microbial consortia in anaerobic and aerobic conditions are extensively discussed. In addition, we have tried to explain the interconnections between As transformation and carbon (C), such as microbial degradation of organic compounds and methane (CH4) emission. These processes can cause As release because of the reduction of arsenate (As(V)) to the more mobile arsenite (As(III)) as well as As methylation and the formation of toxic trivalent methylated As species in anaerobic conditions. Furthermore, the sulfur (S) transformation can form highly toxic thiolated As species owing to its interference with As biomethylation. Besides, we have focused on many other mutual interlinks that remain elusive between As and C, including As biomethylation, thiolation, and CH4 emission, in the soil-water systems. Recent developments have clarified the significant and complex interactions between the coupled microbial process in anoxic and submerged soils. These processes, performed by little-known/unknown microbial taxa or well-known members of microbial communities with unrecognized metabolic pathways, conducted several concurrent reactions that contributed to global warming on our planet and have unfavorable impacts on water quality and human food resources. Finally, some environmental implications in rice production and arsenic removal from soil-water systems are discussed. Generally, our understanding of the ecological and metabolic evidence for the coupling and synchronous processes of As, C, and S are involved in environmental contamination-caused toxicity in human food, including high As content in rice grain, water resources, and global warming through methanogenesis elucidate combating global rice safety, drinking water, and climate changes.

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

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.

Reconstructing Draft Genomes Using Genome Resolved Metagenomics Reveal Arsenic Metabolizing Genes and Secondary Metabolites in Fresh Water Lake in Eastern India

Rabindra Sarovar lake is an artificial freshwater lake in the arsenic infested eastern region of India. In this study, using the genome resolved metagenomics approach; we have deciphered the taxonomic diversity as well as the functional insights of the gene pools specific to this region. Initially, a total of 113 Metagenome Assembled Genomes (MAGs) were recovered from the two predominant seasons, that is, rainy (n = 50) and winter (n = 63). After bin refinement and de-replication, 27 MAGs (18 from Winter season and 9 from Rainy season) were reconstructed. These MAGs were either of high-quality (n = 10) or of medium quality (n = 17) that was determined based on genome completeness and contamination. These 27 MAGs spanning across 6 bacterial phyla and the most predominant ones were Proteobacteria, Bacteroidetes, and Cyanobacteria regardless of the season. Functional annotation across the MAGs suggested the existence of all known types of arsenic resistance and metabolism genes. Besides, important secondary metabolites such as zoocin_A, prochlorosin, and microcin were also abundantly present in these genomes. The metagenomic study of this lake provides the first insights into the microbiome composition and functional classification of the gene pools in two predominant seasons. The presence of arsenic metabolism and resistance genes in the recovered genomes is a sign of adaptation of the microbes to the arsenic contamination in this region. The presence of secondary metabolite genes in the lake microbiome has several implications including the potential use of these for the pharmaceutical industry.

Microbes involved in arsenic mobilization and respiration: a review on isolation, identification, isolates and implications

Microorganisms play an important role in arsenic (As) cycling in the environment. Microbes mobilize As directly or indirectly, and natural/geochemical processes such as sulphate and iron reduction, oxidative sulphide mineral dissolution, arsenite (AsO₃^3-) oxidation and arsenate (AsO₄^3-) respiration further aid in As cycle in the environment. Arsenate serves as an electron donor for the microbes during anaerobic conditions in the sediment. The present work reviews the recent development in As contamination, various As-metabolizing microbes and their phylogenetic diversity, to understand the role of microbial communities in As respiration and mobilization. It also summarizes the contemporary understanding of the intricate biochemistry and molecular biology of natural As metabolisms. Some successful examples of engineered microbes by harnessing these natural mechanisms for effective remediation are also discussed. The study indicates that there is an exigent need to have a clear understanding of environmental aspects of As mobilization and subsequent oxidation-reduction by a suitable microbial consortium.

Isolation and characterization of bacteria from a brazilian gold mining area with a capacity of arsenic bioaccumulation

In Paracatu, a city in Minas Gerais State (Brazil), the gold mineral extraction produces wastes that contribute to environmental contamination by arsenic. This work describes the evaluation of arsenic concentration from soil of a gold mining area in Paracatu and the selection of arsenic resistant bacteria. In the process of culturing enrichment, 38 bacterial strains were isolated and the minimum inhibitory concentration (MIC) was determined in solid medium for each strain. Three bacterial strains named P1C1Ib, P2Ic and P2IIB were resistant to 3000 mg L^-1 of arsenite. Analysis of 16S rDNA gene sequences revealed that these bacteria belong to Bacillus cereus and Lysinibacillus boronitolerans species. After cultivation of the strains P1C1Ib, P2Ic and P2IIIb, 69.38%-71.88% of arsenite and 82.39%-85.72% of arsenate concentrations were reduced from the culture medium, suggesting the potential application of theses strains in bioremediation processes.

A global survey of arsenic-related genes in soil microbiomes

BACKGROUND

Environmental resistomes include transferable microbial genes. One important resistome component is resistance to arsenic, a ubiquitous and toxic metalloid that can have negative and chronic consequences for human and animal health. The distribution of arsenic resistance and metabolism genes in the environment is not well understood. However, microbial communities and their resistomes mediate key transformations of arsenic that are expected to impact both biogeochemistry and local toxicity.

RESULTS

We examined the phylogenetic diversity, genomic location (chromosome or plasmid), and biogeography of arsenic resistance and metabolism genes in 922 soil genomes and 38 metagenomes. To do so, we developed a bioinformatic toolkit that includes BLAST databases, hidden Markov models and resources for gene-targeted assembly of nine arsenic resistance and metabolism genes: acr3, aioA, arsB, arsC (grx), arsC (trx), arsD, arsM, arrA, and arxA. Though arsenic-related genes were common, they were not universally detected, contradicting the common conjecture that all organisms have them. From major clades of arsenic-related genes, we inferred their potential for horizontal and vertical transfer. Different types and proportions of genes were detected across soils, suggesting microbial community composition will, in part, determine local arsenic toxicity and biogeochemistry. While arsenic-related genes were globally distributed, particular sequence variants were highly endemic (e.g., acr3), suggesting dispersal limitation. The gene encoding arsenic methylase arsM was unexpectedly abundant in soil metagenomes (median 48%), suggesting that it plays a prominent role in global arsenic biogeochemistry.

CONCLUSIONS

Our analysis advances understanding of arsenic resistance, metabolism, and biogeochemistry, and our approach provides a roadmap for the ecological investigation of environmental resistomes.

Arsenic-tolerant microbial consortia from sediments of Copahue geothermal system with potential applications in bioremediation

Although arsenic (As) is recognized as a toxic element for living species, some microorganisms have the ability to tolerate and transform it; recent studies have proposed to take advantage of such capacity to develop sustainable bioremediation strategies. In this study, we evaluated the adaptation to increasing concentrations of As(III) and As(V) of three metabolically different microbial cultures (heterotrophic, autotrophic-acidophilic, and anaerobic) obtained from a sample with low-soluble As content from the Copahue geothermal system. At the end of the adaptation process, the heterotrophic culture was able to grow at 20 mM and 450 mM of As(III) and As(V), respectively; the autotrophic-acidophilic culture showed tolerance to 15 mM of As(III) and 150 mM of As(V), whereas the anaerobic culture only developed in As(V) at concentrations up to 50 mM. The most tolerant consortia were characterized by their growth performance, complexity, and the presence of genes related to As metabolism and resistance. Regarding the consortia complexity, the predominant genera identified were: Paenibacillus in both heterotrophic consortia, Acidithiobacillus in the autotrophic-acidophilic consortium tolerant to As(III), Acidiphilium in the autotrophic-acidophilic consortium tolerant to As(V), and Thiomonas and Clostridium in the anaerobic consortium. This study is the first report of As tolerance microorganisms obtained from Copahue and reasserts the versatility and flexibility of the community of this natural extreme environment; also, it opens the door to the study of possible uses of these consortia in the design of biotechnological processes where the As concentration may fluctuate.

Microbial strains isolated from CO2-venting Kolumbo submarine volcano show enhanced co-tolerance to acidity and antibiotics

As ocean acidification intensifies, there is growing global concern about the impacts that future pH levels are likely to have on marine life and ecosystems. By analogy, a steep decrease of seawater pH with depth is encountered inside the Kolumbo submarine volcano (northeast Santorini) as a result of natural CO₂ venting, making this system ideal for ocean acidification research. Here, we investigated whether the increase of acidity towards deeper layers of Kolumbo crater had any effect on relevant phenotypic traits of bacterial isolates. A total of 31 Pseudomonas strains were isolated from both surface- (SSL) and deep-seawater layers (DSL), with the latter presenting a significantly higher acid tolerance. In particular, the DSL strains were able to cope with H⁺ levels that were 18 times higher. Similarly, the DSL isolates exhibited a significantly higher tolerance than SSL strains against six commonly used antibiotics and As(III). More importantly, a significant positive correlation was revealed between antibiotics and acid tolerance across the entire set of SSL and DSL isolates. Our findings imply that Pseudomonas species with higher resilience to antibiotics could be favored by the prospect of acidifying oceans. Further studies are required to determine if this feature is universal across marine bacteria and to assess potential ecological impacts.

Understanding Microbiome Stability in a Changing World

Microbiomes underpin biogeochemical processes, sustain the bases of food webs, and recycle carbon and nutrients. Thus, microbes are frontline players in determining ecosystem responses to environmental change.

Microbiomes underpin biogeochemical processes, sustain the bases of food webs, and recycle carbon and nutrients. Thus, microbes are frontline players in determining ecosystem responses to environmental change. My research team and I investigate the causes and consequences of microbiome stability. Our primary objective is to understand the responses of complex microbiomes to stressors associated with environmental change. This work is important because Earth is changing rapidly and drastically, and these changes are expected to have serious consequences for ecosystems, their inhabiting organisms, and their microbiomes. Therefore, we aim to understand the repercussions of alterations to microbiome structure and functions and to use this information to predict the responses of microbiomes to stressors. This research is critical to prepare for, respond to, and potentially moderate environmental change. We anticipate that the results of our research will contribute toward these goals and will broadly inform management or manipulation of microbiomes toward desired functions.