Metagenomic analysis reveals adaptations to a cold-adapted lifestyle in a low-temperature acid mine drainage stream

Liljeqvist, Maria; Ossandon, Francisco J.; González, Carolina; Rajan, Sukithar; Stell, Adam L.; Valdés, Jorge Hernández; Holmes, David S.; Dopson, Mark

doi:10.1093/femsec/fiv011

Cited by 79 publications

(57 citation statements)

References 88 publications

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“…were found to be predominant at the late oxidation stage, which was usually characterized by low pH (<3.0) and a high concentration of metals [47,49,50], revealing their favorable adaptation of harsh environmental conditions and indispensability in such ecosystems [51]. Metagenomic as well as transcriptomic analyses deciphered significant variations in microbial community function [27,52,53].…”

Section: Microbial Community Function and Dynamics During Amd Generationmentioning

confidence: 99%

“…In summary, microbial-mediated AMD generation results in a low alpha-diversity of microbial community at the late stage. [27,52,53]. For example, previous metagenomics study of tailings acidification showed that the sulfur oxidation was mainly performed by Thiobacillus at the early stage and by Acidithiobacillus at the late stage [50].…”

Section: Microbial Community Function and Dynamics During Amd Generationmentioning

confidence: 99%

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Microbial Diversity and Community Assembly across Environmental Gradients in Acid Mine Drainage

et al. 2017

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Abstract:Microorganisms play an important role in weathering sulfide minerals worldwide and thrive in metal-rich and extremely acidic environments in acid mine drainage (AMD). Advanced molecular methods provide in-depth information on the microbial diversity and community dynamics in the AMD-generating environment. Although the diversity is relatively low and in general inversely correlated with the acidity, a considerable number of microbial species have been detected and described in AMD ecosystems. The acidophilic microbial communities dominated by iron/sulfur-oxidizing microbes vary widely in their composition and structure across diverse environmental gradients. Environmental conditions affect the microbial community assembly via direct and indirect interactions with microbes, resulting in an environmentally dependent biogeographic pattern. This article summarizes the latest studies to provide a better understanding of the microbial biodiversity and community assembly in AMD environments.

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Section: Microbial Community Function and Dynamics During Amd Generationmentioning

confidence: 99%

Section: Microbial Community Function and Dynamics During Amd Generationmentioning

confidence: 99%

Microbial Diversity and Community Assembly across Environmental Gradients in Acid Mine Drainage

et al. 2017

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“…In addition, a metagenomic study identified potential adaptations of acidophiles (including an At. ferrivorans -like population) to low temperatures in an acid mine drainage stream community in northern Sweden (Liljeqvist et al 2015). These adaptations include CSPs, several pathways for the production of compatible solutes, growth as a biofilm, and an anti-freeze protein.…”

Section: Introductionmentioning

confidence: 99%

“…Therefore, this study aims to elucidate the At. ferrivorans transcriptional response to cultivation at 8 °C, a temperature relevant in low temperature mining environments (Liljeqvist et al 2015), compared 20 °C, a temperature near to where it shows the highest growth rate.…”

Section: Introductionmentioning

confidence: 99%

Acidithiobacillus ferrivorans SS3 presents little RNA transcript response related to cold stress during growth at 8 °C suggesting it is a eurypsychrophile

et al. 2016

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Acidithiobacillus ferrivorans is an acidophilic bacterium that represents a substantial proportion of the microbial community in a low temperature mining waste stream. Due to its ability to grow at temperatures below 15 °C, it has previously been classified as ‘psychrotolerant’. Low temperature-adapted microorganisms have strategies to grow at cold temperatures such as the production of cold acclimation proteins, DEAD/DEAH box helicases, and compatible solutes plus increasing their cellular membrane fluidity. However, little is known about At. ferrivorans adaptation strategies employed during culture at its temperature extremes. In this study, we report the transcriptomic response of At. ferrivorans SS3 to culture at 8 °C compared to 20 °C. Analysis revealed 373 differentially expressed genes of which, the majority were of unknown function. Only few changes in transcript counts of genes previously described to be cold adaptation genes were detected. Instead, cells cultured at cold (8 °C) altered the expression of a wide range of genes ascribed to functions in transcription, translation, and energy production. It is, therefore, suggested that a temperature of 8 °C imposed little cold stress on At. ferrivorans, underlining its adaptation to growth in the cold as well as suggesting it should be classified as a ‘eurypsychrophile’.Electronic supplementary materialThe online version of this article (doi:10.1007/s00792-016-0882-2) contains supplementary material, which is available to authorized users.

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“…Thus, due to the dominance of bacteria in the biofilms obtained, these results suggest that the bacteria present at Site B and/or Site C (which was not evaluated for its proportions of eukaryotes, archaea, and bacteria) are the most likely candidates for the removal of aqueous Cu from the water column, if bioremediation was occurring. A low proportion of eukaryotes in an acidic, alkaline, and/or metals-rich environment does not appear to be unusual, although studies of these environments often focus on microbial community structures and thus the eukaryotic proportion is not evaluated or reported (Bier et al, 2014;Tsitko et al, 2014;Liljeqvist et al, 2015). It is possible that the biofilm collection period of 18 days may have affected the final composition of the communities through succession limitations (i.e., limited colonization of eukaryotes).…”

Section: Discussionmentioning

confidence: 99%

Microbiome Analysis Across a Natural Copper Gradient at a Proposed Northern Canadian Mine Site

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Osachoff

et al. 2016

Front. Environ. Sci.

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Due to the environmental persistence, bioaccumulation, and toxicity of metals released by mining activities, mitigation methods are crucial to minimize impacts on aquatic environments. Bioremediation is one mitigation strategy used to reduce the potential for metal accumulation and toxicity in aquatic organisms. At a potential mine site in Yukon, Canada, elevated copper (Cu) concentrations and low pH are found in a water course near a naturally mineralized area; however, Cu concentrations and acidity are greatly reduced downstream. Physicochemical processes do not appear to explain this natural remediation and it is suggested that unique microbial communities may be responsible through Cu immobilization. To investigate the role of microbes in sequestering or transforming Cu in the water, biofilm samples were collected from five sites along a natural copper gradient: upstream of Cu introduction, on a Cu-rich tributary, 30 m downstream of Cu introduction, where Cu levels were reduced, and 2 and 7 km further downstream, where Cu concentrations were low. Taxonomic profiles of microbial communities (microbiomes) were compiled using DNA sequencing of 16S rRNA gene amplicons. Clear relationships between total Cu concentrations, pH and the microbiomes were evident. In the most Cu-affected samples, communities were dominated by bacteria from the Gallionellaceae family. Metagenomic sequencing profiled the genes present in microbiomes from the most Cu-contaminated sampling location and the area immediately upstream and showed that microbes in this area are well adapted to tolerate heavy metals. This study provides fundamental knowledge of microbial communities at a potential mine site and characterizes the genes likely involved in providing tolerance to an acidic and metals-rich environment. These results inform hypotheses for future experiments to support the development of bioremediation approaches that incorporate the use of native microorganisms at mining sites.

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Metagenomic analysis reveals adaptations to a cold-adapted lifestyle in a low-temperature acid mine drainage stream

Cited by 79 publications

References 88 publications

Microbial Diversity and Community Assembly across Environmental Gradients in Acid Mine Drainage

Microbial Diversity and Community Assembly across Environmental Gradients in Acid Mine Drainage

Acidithiobacillus ferrivorans SS3 presents little RNA transcript response related to cold stress during growth at 8 °C suggesting it is a eurypsychrophile

Microbiome Analysis Across a Natural Copper Gradient at a Proposed Northern Canadian Mine Site

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