Put out the light, and then put out the light.

The Long-Term Relationship between Microbial Metabolism and Greenhouse Gases.

https://hal-amu.archives-ouvertes.fr/hal-03151740/document

Anaerobic oxidation of methane and associated microbiome in anoxic water of Northwestern Siberian lakes

Biogeochemical processes are often confined to very narrow zones in aquatic systems. Therefore, highly resolved in situ measurements are required to study these processes. Potentiometric solid-contact ion selective electrodes (SC-ISEs) are promising tools for such measurements. SC-ISEs show good performance in analyses under controlled experimental conditions. Very few sensor designs, however, can sustain the challenges of natural water matrices and external environmental conditions during in situ applications. We fabricated ammonium and pH selective SC-ISEs with functionalized multiwalled carbon nanotubes (f-MWCNT) as a solid contact. Their functionality was tested in the laboratory and applied in situ for vertical profiling in a eutrophic lake. Sensors were insensitive to strong redox changes, high sulfide concentrations, and bright daylight conditions during the application in the lake. In addition, sensors are easily fabricated and exhibit short response times (<10 s). The proposed design of SC-ISEs b...

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Robust Solid-Contact Ion Selective Electrodes for High-Resolution In Situ Measurements in Fresh Water Systems

Lakes and reservoirs contribute substantially to atmospheric concentrations of the potent greenhouse gas methane. Lake sediments produce large amounts of methane, which accumulate in the oxygen-depleted bottom waters of stratified lakes. Climate change and eutrophication may increase the number of lakes with methane storage in the future. Whether stored methane escapes to the atmosphere during annual lake overturn is a matter of controversy and depends critically on the response of the methanotroph assemblage. Here we show, by combining 16S rRNA gene and pmoA mRNA amplicon sequencing, qPCR, CARD-FISH and potential methane-oxidation rate measurements, that the methanotroph assemblage in a mixing lake underwent both a substantial bloom and ecological succession. As a result, methane oxidation kept pace with the methane supplied from methane-rich bottom water and most methane was oxidized. This aspect of freshwater methanotroph ecology represents an effective mechanism limiting methane transfer from lakes to the atmosphere.

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Growth and rapid succession of methanotrophs effectively limit methane release during lake overturn

Lakes are a significant source of atmospheric methane, although methane-oxidizing bacteria consume most methane diffusing upward from anoxic sediments. Diverse methane-oxidizing bacteria form an effective methane filter in the water column of stratified lakes, yet, niche partitioning of different methane-oxidizing bacteria along the oxygen–methane counter gradient remains poorly understood. In our study, we reveal vertical distribution patterns of active methane-oxidizing bacteria along the oxygen–methane counter gradient of four lakes, based on amplicon sequencing analysis of 16S rRNA and pmoA genes, and 16S rRNA and pmoA transcripts, and potential methane oxidation rates. Differential distribution patterns indicated that ecologically different methane-oxidizing bacteria occupied the methane-deficient and oxygen-deficient part above and below the oxygen–methane interface. The interface sometimes harbored additional taxa. Within the dominant Methylococcales, an uncultivated taxon (CABC2E06) occurred mainly under methane-deficient conditions, whereas Crenothrix-related taxa preferred oxygen-deficient conditions. Candidatus Methylomirabilis limnetica (NC10 phylum) abundantly populated the oxygen-deficient part in two of four lakes. We reason that the methane filter in lakes is structured and that methane-oxidizing bacteria may rely on niche-specific adaptations for methane oxidation along the oxygen–methane counter gradient. Niche partitioning of methane-oxidizing bacteria might support greater overall resource consumption, contributing to the high effectivity of the lacustrine methane filter.

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Niche partitioning of methane-oxidizing bacteria along the oxygen-methane counter gradient of stratified lakes.

We present evidence that oxygenic primary production occurs in the virtually anoxic regions (i.e. regions where no oxygen was detected) of the eutrophic, pre-alpine Lake Rot (Switzerland). Chlorophyll-a measurements in combination with phytoplankton densities indicated the presence of oxygenic primary producers throughout the water column. While Chlorophyceae were present as the main class of oxygenic phototrophs above the oxycline, which extended from 8 down to 9.2 m, the phototrophic community in and below the oxycline was dominated by cyanobacteria. In-situ incubation experiments with H14CO3
 − conducted in August 2013 revealed an oxygenic primary production rate of 1.0 and 0.5 mg C m−3 h−1 in 9 and 10 m depth, respectively. However, measurements with optical trace oxygen sensors showed that oxygen concentrations were below the detection limit (20 nmol l−1) during the incubation period below 9.2 m. Potential oxygen consumption rates, which were 10–20 times higher than oxygen production rates, explain this absence of free oxygen. Our data show that oxygen production in the virtually anoxic zone corresponded to approximately 8 % of the oxygen flux driven by the concentration gradient in the oxycline. This provided an important source of electron acceptors for biogeochemical processes beyond the conventional redox boundary and in the apparently oxygen depleted zone of Lake Rot. This oxygenic primary production in the virtually anoxic zone could allow growth and activity of aerobic microorganisms adapted to low oxygen supply.

/pdf/oxygenic-primary-production-below-the-oxycline-and-its-1v2tfoppjy.pdf

Oxygenic primary production below the oxycline and its importance for redox dynamics

Aerobic methane-oxidizing bacteria (MOB) substantially reduce methane fluxes from freshwater sediments to the atmosphere. Their metalloenzyme methane monooxygenase (MMO) catalyses the first oxidation step converting methane to methanol. Its most prevalent form is the copper-dependent particulate pMMO, however, some MOB are also able to express the iron-containing, soluble sMMO under conditions of copper scarcity. So far, the link between copper availability in different forms and biological methane consumption in freshwater systems is poorly understood. Here, we present high-resolution profiles of MOB abundance and pMMO and sMMO functional genes in relation to copper, methane and oxygen profiles across the oxic-anoxic boundary of a stratified lake. We show that even at low nanomolar copper concentrations, MOB species containing the gene for pMMO expression are present at high abundance. The findings highlight the importance of copper as a micronutrient for MOB species and the potential usage of copper acquisition strategies, even under conditions of abundant iron, and shed light on the spatial distribution of these microorganisms.

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Aerobic methane oxidation under copper scarcity in a stratified lake.

In stratified lakes, methane-oxidizing bacteria (MOB) are strongly mitigating methane fluxes to the atmosphere by consuming methane entering the water column from the sediments. MOB communities in lakes are diverse and vertically structured, but their spatio-temporal dynamics along the water column as well as physico-chemical parameters and interactions with other bacterial species that drive the community assembly have so far not been explored in depth. Here, we present a detailed investigation of the MOB and bacterial community composition and a large set of physico-chemical parameters in a shallow, seasonally stratified, and sub-alpine lake. Four highly resolved vertical profiles were sampled in three different years and during various stages of development of the stratified water column. Non-randomly assembled MOB communities were detected in all compartments. We could identify methane and oxygen gradients and physico-chemical parameters like pH, light, available copper and iron, and total dissolved nitrogen as important drivers of the MOB community structure. In addition, MOB were well-integrated into a bacterial-environmental network. Partial redundancy analysis of the relevance network of physico-chemical variables and bacteria explained up to 84% of the MOB abundances. Spatio-temporal MOB community changes were 51% congruent with shifts in the total bacterial community and 22% of variance in MOB abundances could be explained exclusively by the bacterial community composition. Our results show that microbial interactions may play an important role in structuring the MOB community along the depth gradient of stratified lakes.

/pdf/environmental-and-microbial-interactions-shape-methane-ml1plxyw1x.pdf

Carole Guggenheim

Papers

Niche partitioning of methane-oxidizing bacteria along the oxygen-methane counter gradient of stratified lakes.

Oxygenic primary production below the oxycline and its importance for redox dynamics

Aerobic methane oxidation under copper scarcity in a stratified lake.

Environmental and Microbial Interactions Shape Methane-Oxidizing Bacterial Communities in a Stratified Lake.