Diversity and potential activity of methanotrophs in high methane-emitting permafrost thaw ponds

Lakes and ponds derived from thawing permafrost are strong emitters of carbon dioxide and methane to the atmosphere, but little is known about the methane oxidation processes in these waters. Here we investigated the distribution and potential activity of aerobic methanotrophic bacteria in thaw ponds in two types of eroding permafrost landscapes in subarctic Québec: peatlands and mineral soils. We hypothesized that methanotrophic community composition and potential activity differ regionally as a function of the landscape type and permafrost degradation stage, and locally as a function of depth-dependent oxygen conditions. Our analysis of pmoA transcripts by Illumina amplicon sequencing and quantitative PCR showed that the communities were composed of diverse and potentially active lineages. Type I methanotrophs, particularly Methylobacter, dominated all communities, however there was a clear taxonomic separation between the two landscape types, consistent with environmental control of community structure. In contrast, methanotrophic potential activity, measured by pmoA transcript concentrations, did not vary with landscape type, but correlated with conductivity, phosphorus and total suspended solids. Methanotrophic potential activity was also detected in low-oxygen bottom waters, where it was inversely correlated with methane concentrations, suggesting methane depletion by methanotrophs. Methanotrophs were present and potentially active throughout the water column regardless of oxygen concentration, and may therefore be resilient to future mixing and oxygenation regimes in the warming subarctic.

• Publication year

  2017

• Venue

  PLoS ONE

• Publication date

  2017-11-28

• Fields of study

  Medicine, Environmental Science

• Identifiers
  DOI 10.1371/journal.pone.0188223PMID 29182670PMCID 5705078
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• Methanotrophic potential activity was detected in low-oxygen bottom waters and was inversely related to methane concentrations across the water column.

  Confidence 0.90

  박진우 (dztg5apj7m) extraction뀨 (7c402c1b98) reviewKiller Whale (322360f1c1) reviewB (s683577b42) review
• Methanotrophic potential activity did not differ by landscape type but was associated with conductivity, phosphorus, and total suspended solids.

  Confidence 0.92

  박진우 (dztg5apj7m) extraction뀨 (7c402c1b98) reviewKiller Whale (322360f1c1) reviewB (s683577b42) review
• Methanotroph community composition separated between peatland and mineral-soil thaw ponds, consistent with landscape type control.

  Confidence 0.93

  박진우 (dztg5apj7m) extraction뀨 (7c402c1b98) reviewKiller Whale (322360f1c1) reviewB (s683577b42) review
• Type I methanotrophs, especially Methylobacter, dominated the transcript-based communities.

  Confidence 0.95

  박진우 (dztg5apj7m) extraction뀨 (7c402c1b98) reviewKiller Whale (322360f1c1) reviewB (s683577b42) review
• pmoA transcript profiling by Illumina amplicon sequencing and quantitative PCR identified diverse, potentially active methanotroph communities in the thaw ponds.

  Confidence 0.97

  박진우 (dztg5apj7m) extraction뀨 (7c402c1b98) reviewKiller Whale (322360f1c1) reviewB (s683577b42) review

• conductivity

  environmental variable, measurement

  Water electrical conductivity used as an environmental variable.

  Aliases: electrical conductivity

  박진우 (dztg5apj7m) extraction뀨 (7c402c1b98) reviewKiller Whale (322360f1c1) reviewB (s683577b42) review
• illumina amplicon sequencing

  method, sequencing approach

  A high-throughput sequencing approach used to profile pmoA transcript diversity.

  Aliases: Illumina sequencing, amplicon sequencing

  박진우 (dztg5apj7m) extraction뀨 (7c402c1b98) reviewKiller Whale (322360f1c1) reviewB (s683577b42) review
• landscape type

  environmental category, setting

  The broader thaw-pond setting distinguished as peatland or mineral-soil eroding permafrost landscape.

  Aliases: peatland vs mineral-soil landscape, landscape

  박진우 (dztg5apj7m) extraction뀨 (7c402c1b98) reviewKiller Whale (322360f1c1) reviewB (s683577b42) review
• low-oxygen bottom waters

  environmental compartment, water layer

  The deepest pond waters sampled under reduced oxygen conditions.

  Aliases: bottom waters, low oxygen bottom water

  박진우 (dztg5apj7m) extraction뀨 (7c402c1b98) reviewKiller Whale (322360f1c1) reviewB (s683577b42) review
• methane concentrations

  chemical measurement, concentration

  Dissolved methane levels measured in the pond water.

  Aliases: CH4 concentrations, methane levels

  박진우 (dztg5apj7m) extraction뀨 (7c402c1b98) reviewKiller Whale (322360f1c1) reviewB (s683577b42) review
• methanotrophic potential activity

  outcome, activity measure

  An inferred measure of methanotroph activity based on pmoA transcript concentration.

  Aliases: potential activity of methanotrophs, methanotroph activity

  박진우 (dztg5apj7m) extraction뀨 (7c402c1b98) reviewKiller Whale (322360f1c1) reviewB (s683577b42) review
• methylobacter

  genus, microbial taxon

  A genus of type I methanotrophic bacteria represented in the pmoA transcript communities.

  Aliases: Methylobacter spp.

  박진우 (dztg5apj7m) extraction뀨 (7c402c1b98) reviewKiller Whale (322360f1c1) reviewB (s683577b42) review
• phosphorus

  nutrient, measurement

  A nutrient concentration variable measured in pond water.

  Aliases: P

  박진우 (dztg5apj7m) extraction뀨 (7c402c1b98) reviewKiller Whale (322360f1c1) reviewB (s683577b42) review
• pmoa transcripts

  molecular marker, transcript

  Transcripts of the particulate methane monooxygenase alpha-subunit gene used here as a marker of methanotroph presence and activity.

  Aliases: pmoA transcript

  박진우 (dztg5apj7m) extraction뀨 (7c402c1b98) reviewKiller Whale (322360f1c1) reviewB (s683577b42) review
• quantitative pcr

  method, quantification method

  A targeted nucleic-acid quantification method used to estimate pmoA transcript abundance.

  Aliases: qPCR

  박진우 (dztg5apj7m) extraction뀨 (7c402c1b98) reviewKiller Whale (322360f1c1) reviewB (s683577b42) review
• total suspended solids

  water quality variable, measurement

  The concentration of suspended particulate matter in the water.

  Aliases: TSS

  박진우 (dztg5apj7m) extraction뀨 (7c402c1b98) reviewKiller Whale (322360f1c1) reviewB (s683577b42) review
• type i methanotrophs

  microbial group, functional group

  A functional group of aerobic methane-oxidizing bacteria within the Gammaproteobacteria.

  박진우 (dztg5apj7m) extraction뀨 (7c402c1b98) reviewKiller Whale (322360f1c1) reviewB (s683577b42) review
• water column

  environmental compartment, water body

  The vertical span of pond water from surface to bottom.

  Aliases: pond water column

  박진우 (dztg5apj7m) extraction뀨 (7c402c1b98) reviewKiller Whale (322360f1c1) reviewB (s683577b42) review

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