scholarly journals Seasonal dynamics of methanotrophic bacteria in a boreal oil sands end-pit lake

2021 ◽  
Author(s):  
Emad A. Albakistani ◽  
Felix C. Nwosu ◽  
Chantel Furgason ◽  
Evan S. Haupt ◽  
Angela V. Smirnova ◽  
...  
Keyword(s):  
Microbial Ecology ◽  
Methane Oxidation ◽  
Oil Sands ◽  
Boreal Lakes ◽  
Model Organisms ◽  
Rrna Gene ◽  
Methanotrophic Bacteria ◽  
Pit Lake ◽  
Oxidation Activity ◽  
Stratified Lakes

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 × 10 4 cells mL −1 of water (median 0.5 × 10 3 ) 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 CH 4 /O 2 microniches created during thermal stratification. These data are consistent with temporal and spatial niche differentiation based on temperature, CH 4 and O 2 . 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.

scholarly journals Anaerobic Oxidation of Methane Coupled to Nitrite Reduction by Halophilic Marine NC10 Bacteria

2015 ◽  
Vol 81 (16) ◽  
pp. 5538-5545 ◽  
Author(s):  
Zhanfei He ◽  
Sha Geng ◽  
Chaoyang Cai ◽  
Shuai Liu ◽  
Yan Liu ◽  
...  
Keyword(s):  
16S Rrna ◽  
Methane Oxidation ◽  
Nitrite Reduction ◽  
Substrate Affinity ◽  
Rrna Gene ◽  
Anaerobic Oxidation Of Methane ◽  
Anaerobic Oxidation ◽  
Oxidation Activity ◽  
Optimal Salinity ◽  
Oxidation Of Methane

ABSTRACTAnaerobic oxidation of methane (AOM) coupled to nitrite reduction is a novel AOM process that is mediated by denitrifying methanotrophs. To date, enrichments of these denitrifying methanotrophs have been confined to freshwater systems; however, the recent findings of 16S rRNA andpmoAgene sequences in marine sediments suggest a possible occurrence of AOM coupled to nitrite reduction in marine systems. In this research, a marine denitrifying methanotrophic culture was obtained after 20 months of enrichment. Activity testing and quantitative PCR (qPCR) analysis were then conducted and showed that the methane oxidation activity and the number of NC10 bacteria increased correlatively during the enrichment period. 16S rRNA gene sequencing indicated that only bacteria in group A of the NC10 phylum were enriched and responsible for the resulting methane oxidation activity, although a diverse community of NC10 bacteria was harbored in the inoculum. Fluorescencein situhybridization showed that NC10 bacteria were dominant in the enrichment culture after 20 months. The effect of salinity on the marine denitrifying methanotrophic culture was investigated, and the apparent optimal salinity was 20.5‰, which suggested that halophilic bacterial AOM coupled to nitrite reduction was obtained. Moreover, the apparent substrate affinity coefficients of the halophilic denitrifying methanotrophs were determined to be 9.8 ± 2.2 μM for methane and 8.7 ± 1.5 μM for nitrite.

scholarly journals Vertical stratification patterns of methanotrophs and their genetic controllers in water columns of oxygen-stratified boreal lakes

2020 ◽  
Author(s):  
Antti J Rissanen ◽  
Taija Saarela ◽  
Helena Jäntti ◽  
Moritz Buck ◽  
Sari Peura ◽  
...  
Keyword(s):  
16S Rrna Gene Sequencing ◽  
Boreal Lakes ◽  
Vertical Stratification ◽  
Rrna Gene ◽  
Stratified Lakes ◽  
Oxygen Gradient ◽  
Variation Patterns ◽  
Water Columns ◽  
Water Layers ◽  
Rrna Gene Sequencing

ABSTRACT The vertical structuring of methanotrophic communities and its genetic controllers remain understudied in the water columns of oxygen-stratified lakes. Therefore, we used 16S rRNA gene sequencing to study the vertical stratification patterns of methanotrophs in two boreal lakes, Lake Kuivajärvi and Lake Lovojärvi. Furthermore, metagenomic analyses were done to assess the genomic characteristics of methanotrophs in Lovojärvi and a previously studied Lake Alinen Mustajärvi. The methanotroph communities were vertically structured along the oxygen gradient. Alphaproteobacterial methanotrophs preferred oxic water layers, while Methylococcales methanotrophs, consisting of putative novel genera and species, thrived especially at and below the oxic-anoxic interface and showed distinct depth variation patterns, which were not completely predictable by their taxonomic classification. Instead, genomic differences among Methylococcales methanotrophs explained their variable vertical depth patterns. Genes in COG categories L (Replication, recombination and repair) and S (Function unknown) were relatively high in metagenome-assembled-genomes representing Methylococcales thriving clearly below the oxic-anoxic interface, suggesting genetic adaptations for increased stress tolerance enabling living in the hypoxic/anoxic conditions. In contrast, genes in COG category N (Cell motility) were relatively high in metagenome-assembled-genomes of Methylococcales thriving at the oxic-anoxic interface, which suggests genetic adaptations for increased motility at the vertically fluctuating oxic-anoxic interface.

scholarly journals Genomic evidence for a chemical link between redox conditions and microbial community composition

2021 ◽  
Author(s):  
Jeffrey M Dick ◽  
Jingqiang Tan
Keyword(s):  
Microbial Communities ◽  
Microbial Ecology ◽  
Microbial Community Composition ◽  
16S Rrna Gene Sequencing ◽  
Hydrothermal Systems ◽  
Reference Sequence ◽  
Rrna Gene ◽  
Stratified Lakes ◽  
Chemical Variability ◽  
Rrna Gene Sequencing

Many microbial ecology studies use multivariate analyses to relate microbial abundances to independently measured physicochemical variables. However, genes and proteins are themselves chemical entities; in combination with genome databases, differences in microbial abundances therefore quantitatively encode for chemical variability. We combined community profiles from published 16S rRNA gene sequencing datasets with predicted microbial proteomes from the NCBI Reference Sequence (RefSeq) database to generate a two-dimensional chemical representation of microbial communities. This analysis demonstrates that environmental redox gradients within and between hydrothermal systems and stratified lakes and marine environments are reflected in predictable changes in the carbon oxidation state of inferred community proteomes. These findings have important implications for understanding the microbial communities in produced well fluids and streams affected by hydraulically fractured wells. Although redox measurements for these environments generally are not available, this analysis suggests that redox chemistry is likely to be a significant driver of the microbial ecology of these systems.

Impact of lime treatment on tailings dewatering and cap water quality under an oil sands end pit lake scenario

2021 ◽  
pp. 146699
Author(s):  
Nesma Eltoukhy Allam ◽  
Nikolas Romaniuk ◽  
Mike Tate ◽  
Mohamed N.A. Meshref ◽  
Bipro R. Dhar ◽  
...  
Keyword(s):  
Water Quality ◽  
Oil Sands ◽  
Pit Lake ◽  
Lime Treatment

scholarly journals Methylocella Species Are Facultatively Methanotrophic

2005 ◽  
Vol 187 (13) ◽  
pp. 4665-4670 ◽  
Author(s):  
Svetlana N. Dedysh ◽  
Claudia Knief ◽  
Peter F. Dunfield
Keyword(s):  
Methane Oxidation ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Methanotrophic Bacteria ◽  
Soluble Methane Monooxygenase ◽  
Cell Counts ◽  
Carbon Compounds ◽  
Methane Fluxes ◽  
The One ◽  
Pcr Targeting

ABSTRACT All aerobic methanotrophic bacteria described to date are unable to grow on substrates containing carbon-carbon bonds. Here we demonstrate that members of the recently discovered genus Methylocella are an exception to this. These bacteria are able to use as their sole energy source the one-carbon compounds methane and methanol, as well as the multicarbon compounds acetate, pyruvate, succinate, malate, and ethanol. To conclusively verify facultative growth, acetate and methane were used as model substrates in growth experiments with the type strain Methylocella silvestris BL2. Quantitative real-time PCR targeting the mmoX gene, which encodes a subunit of soluble methane monooxygenase, showed that copies of this gene increased in parallel with cell counts during growth on either acetate or methane as the sole substrate. This verified that cells possessing the genetic basis of methane oxidation grew on acetate as well as methane. Cloning of 16S rRNA genes and fluorescence in situ hybridization with strain-specific and genus-specific oligonucleotide probes detected no contaminants in cultures. The growth rate and carbon conversion efficiency were higher on acetate than on methane, and when both substrates were provided in excess, acetate was preferably used and methane oxidation was shut down. Our data demonstrate that not all methanotrophic bacteria are limited to growing on one-carbon compounds. This could have major implications for understanding the factors controlling methane fluxes in the environment.

The interplay of methane and ammonia as key oxygen consuming constituents in early stage development of Base Mine Lake, the first demonstration oil sands pit lake

2018 ◽  
Vol 93 ◽  
pp. 49-59 ◽  
Author(s):  
Florent F. Risacher ◽  
Patrick K. Morris ◽  
Daniel Arriaga ◽  
Corey Goad ◽  
Tara Colenbrander Nelson ◽  
...  
Keyword(s):  
Oil Sands ◽  
Early Stage ◽  
Pit Lake ◽  
Stage Development

scholarly journals Ample Arsenite Bio-Oxidation Activity in Bangladesh Drinking Water Wells: A Bonanza for Bioremediation?

2019 ◽  
Vol 7 (8) ◽  
pp. 246
Author(s):  
Zahid Hassan ◽  
Munawar Sultana ◽  
Sirajul I. Khan ◽  
Martin Braster ◽  
Wilfred F.M. Röling ◽  
...  
Keyword(s):  
Drinking Water ◽  
Ex Situ ◽  
Rrna Gene ◽  
Microbial Activities ◽  
16S Rrna Gene Sequences ◽  
Previous Survey ◽  
Oxidation Activity ◽  
Water Wells ◽  
Enriched Cultures ◽  
Biological Solutions

Millions of people worldwide are at risk of arsenic poisoning from their drinking water. In Bangladesh the problem extends to rural drinking water wells, where non-biological solutions are not feasible. In serial enrichment cultures of water from various Bangladesh drinking water wells, we found transfer-persistent arsenite oxidation activity under four conditions (aerobic/anaerobic; heterotrophic/autotrophic). This suggests that biological decontamination may help ameliorate the problem. The enriched microbial communities were phylogenetically at least as diverse as the unenriched communities: they contained a bonanza of 16S rRNA gene sequences. These related to Hydrogenophaga, Acinetobacter, Dechloromonas, Comamonas, and Rhizobium/Agrobacterium species. In addition, the enriched microbiomes contained genes highly similar to the arsenite oxidase (aioA) gene of chemolithoautotrophic (e.g., Paracoccus sp. SY) and heterotrophic arsenite-oxidizing strains. The enriched cultures also contained aioA phylotypes not detected in the previous survey of uncultivated samples from the same wells. Anaerobic enrichments disclosed a wider diversity of arsenite oxidizing aioA phylotypes than did aerobic enrichments. The cultivatable chemolithoautotrophic and heterotrophic arsenite oxidizers are of great interest for future in or ex-situ arsenic bioremediation technologies for the detoxification of drinking water by oxidizing arsenite to arsenate that should then precipitates with iron oxides. The microbial activities required for such a technology seem present, amplifiable, diverse and hence robust.

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