Bacterial, Phytoplankton, and Viral Distributions and Their Biogeochemical Contexts in Meromictic Lake Cadagno Offer Insights into the Proterozoic Ocean Microbial Loop

Saini, Jaspreet S; Hassler, Christel; Cable, Rachel N.; Fourquez, Marion; Danza, Francesco; Roman, Samuele; Tonolla, Mauro; Storelli, Nicola; Jacquet, Stéphan; Zdobnov, Evgeny M.; Duhaime, Melissa B.

doi:10.1128/mbio.00052-22

Cited by 11 publications

(20 citation statements)

References 101 publications

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“…The mixing zone is often reported as a hotspot for microbial processes due to the mixing of microbial communities and river compounds, , creating opportunities for high rates of carbon assimilation via distinct processes, including chemosynthesis using the energetic yields of oxidation of reduced compounds . Although our survey represents all available measurements in the Amazon River, we found other studies in different aquatic systems where rates vary from nanograms of carbon per hour in lakes. − High rates of DCF were observed in karstic systems, − which could be related to the high concentration of inorganic carbon and reduced compounds in soil and groundwater, creating opportunities for microbial growth using the energetic yields of redox reactions to promote chemosynthesis since HBP was observed at lower rates in these systems. , In river estuaries, turbulent mixing promotes an increase in DCF ,, and HBP, − which could also be associated with reduced compounds from bottom sediments meeting oxic surface waters.…”

Section: Resultsmentioning

confidence: 85%

Distinct Non-conservative Behavior of Dissolved Organic Matter after Mixing Solimões/Negro and Amazon/Tapajós River Waters

Harir

Schmitt‐Kopplin

et al. 2023

ACS EST Water

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Positive and negative electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry and 1H NMR revealed major compositional and structural changes of dissolved organic matter (DOM) after mixing two sets of river waters in Amazon confluences: the Solimões and Negro Rivers (S + N) and the Amazon and Tapajós Rivers (A + T). We also studied the effects of water mixing ratios and incubation time on the composition and structure of DOM molecules. NMR spectra demonstrated large-scale structural transformations in the case of S + N mixing, with gain of pure and functionalized aliphatic units and loss of all other structures after 1d incubation. A + T mixing resulted in comparatively minor structural alterations, with a major gain of small aliphatic biomolecular binding motifs. Remarkably, structural alterations from mixing to 1d incubation were in essence reversed from 1d to 5d incubation for both S + N and A + T mixing experiments. Heterotrophic bacterial production (HBP) in endmembers S, N, and S + N mixtures remained near 0.03 μgC L–1 h–1, whereas HBP in A, T, and A + T were about five times higher. High rates of dark carbon fixation took place at S + N mixing in particular. In-depth biogeochemical characterization revealed major distinctions between DOM biogeochemical changes and temporal evolution at these key confluence sites within the Amazon basin.

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Section: Resultsmentioning

confidence: 85%

Distinct Non-conservative Behavior of Dissolved Organic Matter after Mixing Solimões/Negro and Amazon/Tapajós River Waters

Harir

Schmitt‐Kopplin

et al. 2023

ACS EST Water

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“…Other meromictic lakes have been studied in detail for years using different molecular and ecological approaches. For instance, Lake Cadagno, a well-known lake displaying a strong stratification of planktonic microorganisms driving vertically contrasting rates of the metabolic processes (Camacho et al 2001;Tonolla et al 2017), is a representative example from which amplicon sequencing studies have subsequently been derived (Danza et al 2018;Saini et al 2022). Both phototrophic sulfur bacteria and sulfate-reducers (Desulfobacterota) are extremely abundant in these systems (Storelli et al 2013) and have also been studied in this lake (Danza et al 2017;Di Nezio et al 2021;Philippi et al 2021).…”

Section: Author Contributionmentioning

confidence: 99%

Vertical niche occupation and potential metabolic interplay of microbial consortia in a deeply stratified meromictic model lake

Cabello‐Yeves,

Picazo,

Roda‐Garcia

et al. 2023

Limnology & Oceanography

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The microbial ecology of meromictic lakes assessed with “omics” is still poorly studied compared to other aquatic systems. Here, a combination of metagenomics, high resolution sampling and detailed physical–chemical data gathering allowed to study the planktonic prokaryotic assemblages and metabolic capabilities in the crenogenic meromictic Lake El Tobar (Spain), a model lake for such purposes. This system presents a specific stratification comprising a freshwater layer and a halocline linked to the oxycline, driving to the euxinic hypersaline waters of the deep monimolimnion. The different strata showed a highly diverse and vertically distributed microbiome with their metabolic capacities fitting/influencing the physical–chemical environment. Overall, up to 338 novel genomes were found from metagenome assembled genomes. Picocyanobacteria and methanotrophs were abundant in the upper part of the oxycline. Anoxygenic phototrophs (Chlorobium, Thiohalocapsa, Chromatiaceae, Rhodospirillum, and Rhodobacteraceae spp.) dominated the 12.5–14 m anoxic waters with dim light availability. Sulfate reducers (Desulfobacterota and Firmicutes) inhabited low redox horizons from 13.5 to the bottom (18 m). The potential microbial synergistic performance increases toward the monimolimnion. Among these, a microbial assemblage mostly composed of Spirochaetota, Cloacimonadota, Omitrophota, Firmicutes, Marinisomatota, Nanoarchaeota, and Patescibacteria in hypersaline waters of 14–18 m (conductivities of 118–213 mS cm−1), is potentially capable of performing mixed‐acid fermentations, even including hydrogen and butanol biosynthesis of biotechnological interest. This metagenomics study shows how microbial lifestyles may be determinant in the interplay of environmental gradients, and exemplifies the potential interactions between the microbial guilds thereby.

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“…1) Ecosystem functioning (i.e., cell density as a proxy for primary production) is better explained by trait diversity metrics that integrate all available individual-based traits (morphological, physiological, and metabolic) rather than by taxonomic diversity metrics based on rRNA gene sequencing 33,44 . 2) In deep layers of the lake, competition for light drives increasing niche partitioning in pigment-related traits (i.e., increasing trait evenness 38 ), while limitation for essential nutrients mediates decreasing fitness differences in metabolic traits (i.e., trait convergence 45 ), as compared to the upper layers of the lake.…”

Section: Introductionmentioning

confidence: 99%

Single-cell trait diversity explains niche and fitness differences in aquatic microbial communities

Fontana,

Schmitz,

Daniels

et al. 2024

Preprint

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Two fundamental questions in ecology are how biodiversity is maintained and how it affects ecosystem functioning. Until now, it has been difficult to study the above mechanisms in natural microbial communities, yet they are important drivers of biogeochemical ecosystem functions. Here, we use a new approach to define and measure biodiversity in complex lake microbial communities (Lake Cadagno, Switzerland) based on the cell-to-cell variation in multiple functionally relevant phenotypic traits. We use stable isotope probing coupled to correlative imaging using confocal laser scanning microscopy (CLSM) and nanometer-scale secondary ion mass spectrometry (NanoSIMS) to obtain morphological (size), physiological (pigments) and metabolic (carbon and nitrogen isotope uptake and sulfur content) traits for a large number of individual cells along the environmental gradient found across lake depth. We show that cell-to-cell trait variation is significantly correlated with cell densities as a proxy for ecosystem functioning, whereas genetic diversity measured at the level of 16S and 18S is not. Our single-cell analysis provides evidence for a simultaneous increase in niche partitioning (measured as increased evenness in pigment composition) and decrease in fitness differences (measured as decreased variability in sulfur content) due to light limitation and competition for nutrients in deep layers of the lake. This leads to a negative relationship between niche and fitness differences. Our results suggest that niche and fitness differences in natural microbial communities can be understood at the level of single-cell traits, providing a mechanistic understanding of the relationship between microbial diversity and ecosystem functioning.

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Bacterial, Phytoplankton, and Viral Distributions and Their Biogeochemical Contexts in Meromictic Lake Cadagno Offer Insights into the Proterozoic Ocean Microbial Loop

Cited by 11 publications

References 101 publications

Distinct Non-conservative Behavior of Dissolved Organic Matter after Mixing Solimões/Negro and Amazon/Tapajós River Waters

Distinct Non-conservative Behavior of Dissolved Organic Matter after Mixing Solimões/Negro and Amazon/Tapajós River Waters

Vertical niche occupation and potential metabolic interplay of microbial consortia in a deeply stratified meromictic model lake

Single-cell trait diversity explains niche and fitness differences in aquatic microbial communities

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