The under-ice microbiome of seasonally frozen lakes

Compared to the well-studied open water of the “growing” season, under-ice conditions in lakes are characterized by low and rather constant temperature, slow water movements, limited light availability, and reduced exchange with the surrounding landscape. These conditions interact with ice-cover duration to shape microbial processes in temperate lakes and ultimately influence the phenology of community and ecosystem processes. We review the current knowledge on microorganisms in seasonally frozen lakes. Specifically, we highlight how under-ice conditions alter lake physics and the ways that this can affect the distribution and metabolism of auto- and heterotrophic microorganisms. We identify functional traits that we hypothesize are important for understanding under-ice dynamics and discuss how these traits influence species interactions. As ice coverage duration has already been seen to reduce as air temperatures have warmed, the dynamics of the under-ice microbiome are important for understanding and predicting the dynamics and functioning of seasonally frozen lakes in the near future

Cryoconite holes on frozen lakes as source of interesting extremophilic and extremotolerant organisms

The key thought of this short communication is biodiversity evaluation of the photo-autotrophic inhabitants of lake cryoconite holes and point out their potencial as extremo-tolerant or even extremophilic organisms that deserve attention. Cyanobacterial diversity of these environments was investigated in cryoconites holes of 2 permanently and 1 sea-sonally ice-covered lakes at James Ross Island. Twelve species from different taxonomic groups, both coccal and filamentous (with and without heterocytes) cyanobacteria, were determined using a light microscope and morphological features of autorophic microorganisms. The results suggested relatively high diversity in such extreme environments and also indicated potential of lake cryoconites to serve as a reservoir of organism that can have special protection properties

Energetic and Environmental Constraints on the Community Structure of Benthic Microbial Mats in Lake Fryxell, Antarctica.

Ecological communities are regulated by the flow of energy through environments. Energy flow is typically limited by access to photosynthetically active radiation (PAR) and oxygen concentration (O2). The microbial mats growing on the bottom of Lake Fryxell, Antarctica, have well-defined environmental gradients in PAR and (O2). We analyzed the metagenomes of layers from these microbial mats to test the extent to which access to oxygen and light controls community structure. We found variation in the diversity and relative abundances of Archaea, Bacteria and Eukaryotes across three (O2) and PAR conditions: high (O2) and maximum PAR, variable (O2) with lower maximum PAR, and low (O2) and maximum PAR. We found distinct communities structured by the optimization of energy use on a millimeter-scale across these conditions. In mat layers where (O2) was saturated, PAR structured the community. In contrast, (O2) positively correlated with diversity and affected the distribution of dominant populations across the three habitats, suggesting that meter-scale diversity is structured by energy availability. Microbial communities changed across covarying gradients of PAR and (O2). The comprehensive metagenomic analysis suggests that the benthic microbial communities in Lake Fryxell are structured by energy flow across both meter- and millimeter-scales

Bacterioplankton seasonality in deep high-mountain lakes

Due to global warming, shorter ice cover duration might drastically affect the ecology of lakes currently undergoing seasonal surface freezing. Highmountain lakes show snow-rich ice covers that determine contrasting conditions between ice-off and ice-on periods. We characterized the bacterioplankton seasonality in a deep high-mountain lake ice-covered for half a year. The lake shows a rich core bacterioplankton community consisting of three components: (i) an assemblage stable throughout the year, dominated by Actinobacteria, resistant to all environmental conditions; (ii) an ice-on-resilient assemblage dominating during the ice-covered period, which is more diverse than the other components and includes a high abundance of Verrucomicrobia; the deep hypolimnion constitutes a refuge for many of the typical under-ice taxa, many of which recover quickly during autumn mixing; and (iii) an ice-off-resilient assemblage, which members peak in summer in epilimnetic waters when the rest decline, characterized by a dominance of Flavobacterium, and Limnohabitans. The rich core community and low random elements compared to other relatively small cold lakes can be attributed to its simple hydrological network in a poorly-vegetated catchment, the long water-residence time (ca. 4 years), and the long ice-cover duration; features common to many headwater deep high-mountain lakes

Bacterioplankton seasonality in deep high-mountain lakes

Due to global warming, shorter ice cover duration might drastically affect the ecology of lakes currently undergoing seasonal surface freezing. High-mountain lakes show snow-rich ice covers that determine contrasting conditions between ice-off and ice-on periods. We characterized the bacterioplankton seasonality in a deep high-mountain lake ice-covered for half a year. The lake shows a rich core bacterioplankton community consisting of three components: (i) an assemblage stable throughout the year, dominated by Actinobacteria, resistant to all environmental conditions; (ii) an ice-on-resilient assemblage dominating during the ice-covered period, which is more diverse than the other components and includes a high abundance of Verrucomicrobia; the deep hypolimnion constitutes a refuge for many of the typical under-ice taxa, many of which recover quickly during autumn mixing; and (iii) an ice-off-resilient assemblage, which members peak in summer in epilimnetic waters when the rest decline, characterized by a dominance of Flavobacterium, and Limnohabitans. The rich core community and low random elements compared to other relatively small cold lakes can be attributed to its simple hydrological network in a poorly-vegetated catchment, the long water-residence time (ca. 4 years), and the long ice-cover duration; features common to many headwater deep high-mountain lakes

Community dynamics and function of algae and bacteria during winter in central European great lakes

Abundant phytoplankton and bacteria were identified by microscopy and high-throughput 16S rRNA tag Illumina sequencing of samples from water- and ice phases collected during winter at two central European Great Lakes, Balaton and Fertő (Neusiedlersee). Bacterial reads at all sites were dominated (\u3e85%) by Bacteroidetes and Proteobacteria. Amongst phototrophs, microscopy and 16S sequencing revealed that both phytoplankton and cyanobacteria were represented, with a median of 1500 cyanobacterial sequence reads amongst 13 samples analyzed. The sequence analysis compared replicate Balaton and Fertő ice and water samples with an outgroup from three Hungarian soda lakes. In particular, both water and ice from Fertő contained high contributions from cyanobacteria. Two percent of total reads identified to the level of family in water at Fertő were dominated by a single operational taxonomic unit (OTU) of a cyanobacterium within the Rivulariaceae, which was largely absent from ice. Conversely, ice samples from both lakes yielded an abundant OTU assigned to a Flavobacterium sp. known to be associated with freshwater ice. Principal Coordinates Analysis (PCoA) revealed that the ice communities from all sites were similar to one another, and that the water communities did not cluster together. Fluorescence emission spectra obtained at 77 K confirmed the presence of intact cyanobacteria in Fertő water and ice. Photosynthetic characterization of phototrophs resident in water and ice analyzed by assay of acid-stable photosynthetic H14CO3– incorporation showed that communities from both phases were photosynthetically active, thus adding to growing recognition of ice-covered lakes as viable habitat for phototrophs

Environmental control on the distribution of metabolic strategies of benthic microbial mats in Lake Fryxell, Antarctica

naEcological theories posit that heterogeneity in environmental conditions greatly affects community structure and function. However, the degree to which ecological theory developed using plant- and animal-dominated systems applies to microbiomes is unclear. Investigating the metabolic strategies found in microbiomes are particularly informative for testing the universality of ecological theories because microorganisms have far wider metabolic capacity than plants and animals. We used metagenomic analyses to explore the relationships between the energy and physicochemical gradients in Lake Fryxell and the metabolic capacity of its benthic microbiome. Statistical analysis of the relative abundance of metabolic marker genes and gene family diversity shows that oxygenic photosynthesis, carbon fixation, and flavin-based electron bifurcation differentiate mats growing in different environmental conditions. The pattern of gene family diversity points to the likely importance of temporal environmental heterogeneity in addition to resource gradients. Overall, we found that the environmental heterogeneity of photosynthetically active radiation (PAR) and oxygen concentration ([O2]) in Lake Fryxell provide the framework by which metabolic diversity and composition of the community is structured, in accordance with its phylogenetic structure. The organization of the resulting microbial ecosystems are consistent with the maximum power principle and the species sorting model.© 2020 Dillon et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited

Temporal and spatial differences of the under-ice microbiome are linked to light transparency and chlorophyll-a

1openInternationalUnder-ice community dynamics are barely understood. Temporal and spatial studies are needed to fully understand the consequences of a declining ice cover on microbial biodiversity. Here, bacterial communities of different years (2015, 2017–2021) and layers (upper and lower euphotic layer, euphotic layer, hypolimnion) were assessed by Illumina sequencing of the 16S rRNA gene. Alpha- and beta-diversity of summer and under-ice hypolimnetic communities were similar, and a seasonal difference was found only when excluding summer hypolimnetic communities. Similarly, in non-metric multidimensional scaling (NMDS), summer and under-ice communities were different even though hypolimnetic communities were similar. Investigating under-ice conditions, the year 2017 showed highest under-ice light and chlorophyll-a while 2021 showed no under-ice light and lowest chlorophyll-a. Under-ice communities were not linked to layer differences implying that a spatial distinction under ice was less important than in summer, especially in years with little or no under-ice light. Most under-ice bacterial classes and ASVs showed direct and indirect dependencies on light availability and primary production. Similarly in NMDS with only under-ice communities, light transparency and primary production were important. In the future, ice conditions with less snow cover might lead to bacterial communities similar to that of high-light years (2017, 2018, 2020).openObertegger, U.Obertegger, U

First Insights into the Resilience of the Soil Microbiome of a Tropical Dry Forest in Puerto Rico

This study evaluated the effect that tree species traits and wet/dry periods display on soil microbial communities in a tropical dry forest in Puerto Rico. Understanding the ecological role of soil microorganisms in tropical dry forests and how they relate to different tree species is necessary to protect these fragile forest ecosystems. Thus, by using 454 pyrosequencing, we explored how microbial diversity was affected by dominant tree species during the wettest and driest periods at the Guánica Dry Forest. We found that 9 out of 17 phyla were more abundant during the dry period demonstrating that soil communities have adapted to historically low rainfall patterns. The most abundant phyla during both periods were Proteobacteria, Actinobacteria, and Bacteroidetes. During the dry period, Actinobacteria increased significantly (p < 0.0001), whereas Proteobacteria and Bacteroidetes decreased significantly (p < 0.0001; p < 0.001). Canonical correspondence analysis (CCA) also demonstrated that soil microbes are shaped by wet and dry periods, thus axis 1 of CCA explained 80% of the variation. This study offers baseline information in order to help elucidate how microbial diversity is affected by climate change in tropical areas and extrapolate this information to agricultural areas in order to develop better management practices

Microbial mitigation of greenhouse gas emissions from boreal lakes

The climate change crisis has drawn the attention of both the public and scientific community to the carbon cycle and particularly to the importance of greenhouse gases (GHG) carbon dioxide (CO2) and methane (CH4). CO2 has been a key component of Earth´s climate regulation throughout its geological history and is now the main driver of the current change in climate. CH4 has been responsible for a quarter of the cumulative radiative forcing observed so far. Recent studies suggest that lakes could be a major source of both CO2 and CH4. Boreal lakes are of special interest as they represent 27% of the global lake area, and their production of CO2 and CH4 are expected to increase in the future. This project aimed to investigate microbial processes with the potential to limit the emissions of GHGs from boreal lakes. For that purpose, the impact of an increase in phosphorus (P) concentration in the water on CH4 oxidation under the ice was investigated as well as the community composition of the methanotrophic guild. We also looked at the potential importance of chemolithoautotrophic microorganisms in fixing CO2 in the water column. Using a combination of geochemical analysis, genomic studies, and in vivo assays, we showed that P amendment has the potential to increase methane oxidation, possibly limiting the expected increase in CH4 emissions due to anthropogenic fertilization of boreal lakes. We also showed that methanotrophic community structure in boreal lakes is driven by CH4 concentration and that alphaproteobacterial methanotrophs might play an important role in removing CH4 from surface waters. Finally, we showed that dark carbon fixation is a common trait in boreal lakes and that it seems related to the iron cycle