Browsing by Author "Sheremet, Andriy"

Now showing 1 - 3 of 3
  • Thumbnail Image
    ItemOpen Access
    Insights into communities, metabolic and ecological potential of the bacteria of two extreme acidic environments
    (2022-11-08) Sheremet, Andriy; Peter Dunfield; Lisa Stein, Michael F. Hynes
    This work examines the microbial communities in two extremely acidic habitats:the terrestrial environment of the Paint Pots Mound (Kootenay National Park, BritishColumbia, Canada) and the sediments of an ultra-acidic lake in the Smoking Hills (CapeBathurst, Northwest Territories, Canada) area. While the acidification of both locationsoriginates from the natural pyrite ore oxidation processes, the sites show a dramaticcontrast in microbial compositions, function, complexity, and diversity. The chemicalcomposition of the sites is suggestive of that of acid mine drainage (AMD) systems;however, the habitats of the Paint Pots and Smoking Hills are pristine, unlike the majorityof AMD, and therefore offer a unique opportunity in microbial ecology research.The microbial communities of the sites are explored using metagenomics andstable isotope probing. Microbial load and diversity in both locations were low. However,despite their high acidity, metal, and sulfate content similarities, the habitats hostedcontrasting microbial communities.The Paint Pots Mound environment is notable for the elevated abundance of suchlineages as WPS-2, AD3, Ca. Binatia, Elsterales, and atmospheric methane oxidizers ofthe genus Methylocapsa, compared to other habitats reported in the literature. Membersof the phylum WPS-2, also known as Eremiobacterota, dominated bare, nonvegetatedzones. Metabolically, it was proposed that these organisms were organoheterotrophs,using amino acids, peptides, and nucleotides for growth, and were, perhaps, adapted toscavenging or parasitizing and antimicrobial compound resistance. At the same time, themetagenomic data indicated the presence of multiple lineages of soluble and particulatemethane monooxygenase homologs. Such results aligned with the soil activity towardsoxidating methane, ethane, and propane. As a result of a DNA stable isotope probingexperiment, using 13 C labeled propane, it was established that 2-propanemonooxygenases were associated with propane oxidation, carried out by taxonomicallydiverse groups of organisms. The short-chain hydrocarbon oxidation activity in the PaintPots soil was comparable to the soils from natural gas seepage sites.In contrast, the prokaryotic community of the Smoking Hills lake sediments wasdominated by a single species of Acidithiobacillus ferrivorans SH11, constituting morethan 73% of the 16S rRNA gene amplicons. The site was characterized by low microbialcell count and lithoautotrophic metabolism, centered on iron and sulfur oxidation andCO 2 fixation via the Calvin–Benson–Bassham cycle. At the same time, the genomicfeatures of A. ferrivorans SH11 suggested these organisms were undergoing genomestreamlining. The genome of these organisms was characterized by increased genedensity and fractions of genes annotated with COG or Pfam, compared to culturedisolates. The degree of genome streamlining in these organisms living inside the Arcticcircle surpassed that of the uncultured Acidithiobacillus genomes recovered from hotsprings. A strong inverse relationship between genome size and a fraction of genesannotated with COG, observed for Acidithiobacillus genomes, was a common trendamong other genera in Proteobacteria.Therefore, as the Smoking Hills environment was dominated by an autotrophicorganism with a streamlined genome, the notable members of the Paint Pots Moundcommunity were mainly metabolically diverse heterotrophs.
  • Thumbnail Image
    ItemOpen Access
    Novel copper-containing membrane monooxygenases (CuMMOs) encoded by alkane-utilizing Betaproteobacteria
    (Nature Publishing Group, 2019-07-01) Rochman, Fauziah F.; Kwon, Miye; Khadka, Roshan; Tamas, Ivica; Lopez-Jauregui, Abraham; Sheremet, Andriy; Smirnova, Angela V.; Malmstrom, Rex; Yoon, Sukhwan; Woyke, Tanja; Dunfield, Peter F.; Verbeke, Tobin J.
    Copper-containing membrane monooxygenases (CuMMOs) are encoded by xmoCAB(D) gene clusters and catalyze the oxidation of methane, ammonia, or some short chain alkanes and alkenes. In a metagenome constructed from an oilsands tailings pond we detected an xmoCABD gene cluster with <59% derived amino acid identity to genes from known bacteria. Stable isotope probing experiments combined with a specific xmoA qPCR assay demonstrated that the bacteria possessing these genes were incapable of methane assimilation, but did grow on ethane and propane. Single-cell genomes (SAGs) from propane-enriched samples were therefore constructed and screened with the specific PCR assay to identify bacteria possessing the target gene cluster. Multiple SAGs of Betaproteobacteria belonging to the genera Rhodoferax and Polaromonas possessed close homologues of the metagenomic xmoCABD gene cluster. Unexpectedly, each of these two genera also possessed other xmoCABD paralogs, representing two additional lineages in phylogenetic analyses. Metabolic reconstructions from SAGs predicted that neither bacterium was capable of catabolic methane or ammonia oxidation, but that both were capable of higher n-alkane degradation. The involvement of the encoded CuMMOs in alkane oxidation was further suggested by reverse transcription PCR analyses, which detected elevated transcription of the xmoA genes upon enrichment of water samples with propane as the sole energy source. Enrichments, isotope incorporation studies, genome reconstructions, and gene expression studies therefore all agreed that the unknown xmoCABD operons did not encode methane or ammonia monooxygenases, but rather n-alkane monooxygenases. This study broadens the known diversity of CuMMOs and identifies non-nitrifying Betaproteobacteria as possessing these enzymes.
  • Thumbnail Image
    ItemOpen Access
    Seasonal dynamics of methanotrophic bacteria in a boreal oil sands end-pit lake
    (2021-11-29) Albakistani, Emad; Nwosu, Felix; Furgason, Chantel; Haupt, Evan; Smirnova, Angela; Verbeke, Tobin; Lee, Eun-Suk; Kim, Joong-Jae; Chan, Amelia; Ruhl, Ilona; Sheremet, Andriy; Rudderham, Sarah; Lindsay, Matthew; Dunfield, Peter
    Base Mine Lake (BML) is the first full-scale demonstration end pit lake for the oil sands mining industry in Canada. We examined aerobic methanotrophic bacteria over all seasons for five years in this dimictic lake. Methanotrophs comprised up to 58% of all bacterial reads in 16S rRNA gene amplicon sequencing analyses (median 2.8%), and up to 2.7 × 104 cells mL−1 of water (median 0.5 × 103) based on qPCR of pmoA genes. Methanotrophic activity and populations in the lake water were highest during fall turnover, and remained high through the winter ice-covered period into spring turnover. They declined during summer stratification, especially in the epilimnion. Three methanotroph genera (Methylobacter, Methylovulum, and Methyloparacoccus) cycled seasonally, based on both relative and absolute abundance measurements. Methylobacter and Methylovulum populations peaked in winter/spring, when methane oxidation activity was psychrophilic. Methyloparacoccus populations increased in the water column through summer and fall, when methane oxidation was mesophilic, and also predominated in the underlying tailings sediment. Other, less abundant genera grew primarily during summer, possibly due to distinct CH4/O2 microniches created during thermal stratification. These data are consistent with temporal and spatial niche differentiation based on temperature, CH4 and O2. This pit lake displays methane cycling and methanotroph population dynamics similar to natural boreal lakes. Importance statement: The study examined methanotrophic bacteria in an industrial end pit lake, combining molecular DNA methods (both quantitative and descriptive) with biogeochemical measurements. The lake was sampled over 5 years, in all four seasons, as often as weekly, and included sub-ice samples. The resulting multi-season and multi-year dataset is unique in its size and intensity, and allowed us to document clear and consistent seasonal patterns of growth and decline of three methanotroph genera (Methylobacter, Methylovulum, and Methyloparacoccus). Laboratory experiments suggested that one major control of this succession was niche partitioning based on temperature. The study helps to understand microbial dynamics in engineered end-pit lakes, but we propose that the dynamics are typical of boreal stratified lakes, and widely applicable in microbial ecology and limnology. Methane oxidising bacteria are important model organisms in microbial ecology, and have implications for global climate change.