Marine-freshwater prokaryotic transitions require extensive changes in the predicted proteome

Background The adaptation of a marine prokaryote to live in freshwater environments or vice versa is generally believed to be an unusual and evolutionary demanding process. However, the reasons are not obvious given the similarity of both kinds of habitats. Results We have found major differences at the level of the predicted metaproteomes of marine and freshwater habitats with more acidic values of the isoelectric points (pI) in marine microbes. Furthermore, by comparing genomes of marine-freshwater phylogenetic relatives, we have found higher pI values (basic shift) in the freshwater ones. This difference was sharper in secreted > cytoplasmic > membrane proteins. The changes are concentrated on the surface of soluble proteins. It is also detectable at the level of total amino acid composition and involves similarly core and flexible genome- encoded proteins. Conclusions The marked changes at the level of protein amino acid composition and pI provide a tool to predict the preferred habitat of a culture or a metagenome-assembled genome (MAG). The exact physiological explanation for such variations in the pIs and electrostatic surface potentials is not known yet. However, these changes might reflect differences in membrane bioenergetics derived from the absence of significant Na+ concentrations in most freshwater habitats. In any case, the changes in amino acid composition in most proteins imply that a long evolutionary time is required to adapt from one type of habitat to the other

The “Dark Side” of Picocyanobacteria: Life as We Do Not Know It (Yet)

Picocyanobacteria of the genus Synechococcus (together with Cyanobium and Prochlorococcus) have captured the attention of microbial ecologists since their description in the 1970s. These pico-sized microorganisms are ubiquitous in aquatic environments and are known to be some of the most ancient and adaptable primary producers. Yet, it was only recently, and thanks to developments in molecular biology and in the understanding of gene sequences and genomes, that we could shed light on the depth of the connection between their evolution and the history of life on the planet. Here, we briefly review the current understanding of these small prokaryotic cells, from their physiological features to their role and dynamics in different aquatic environments, focussing particularly on the still poorly understood ability of picocyanobacteria to adapt to dark conditions. While the recent discovery of Synechococcus strains able to survive in the deep Black Sea highlights how adaptable picocyanobacteria can be, it also raises more questions—showing how much we still do not know about microbial life. Using available information from brackish Black Sea strains able to perform and survive in dark (anoxic) conditions, we illustrate how adaptation to narrow ecological niches interacts with gene evolution and metabolic capacity

Extreme fluctuations in ambient salinity select for bacteria with a hybrid “salt-in”/”salt-out” osmoregulation strategy

Abundant microbial biofilms inhabit underwater freshwater springs of the Dead Sea. Unlike the harsh (i.e., over 35% total dissolved salts) yet stable environment of the basin, the flow rate of the springs changes with random amplitude and duration, resulting in drastic shifts in salinity, pH, and oxygen concentrations. This requires the organisms to continuously adapt to new environmental conditions. Osmotic regulation is energetically expensive; therefore, the response of the biofilm organisms to rapid and drastic changes in salinity is interesting. For this purpose, we studied the metagenome of an enrichment culture obtained from a green biofilm-covered rock positioned in a spring. We obtained metagenome-assembled genomes (MAGs) of Prosthecochloris sp. (Chlorobiales), Flexistipes sp. (Deferribacterales), Izemoplasma (Izemoplasmatales), Halomonas sp. (Oceanospirillales), and Halanaerobium (Halanaerobiales). The MAGs contain genes for both the energetically cheaper “salt-in” and more expensive “salt-out” strategies. We suggest that the dynamic response of these bacteria utilizes both osmoregulation strategies, similar to halophilic archaea. We hypothesize that the frequent, abrupt, and variable-in-intensity shifts in salinity, typical of the Dead Sea spring system, select for microorganisms with scalable adaptation strategies

Reconstruction of Diverse Verrucomicrobial Genomes from Metagenome Datasets of Freshwater Reservoirs

The phylum Verrucomicrobia contains freshwater representatives which remain poorly studied at the genomic, taxonomic, and ecological levels. In this work we present eighteen new reconstructed verrucomicrobial genomes from two freshwater reservoirs located close to each other (Tous and Amadorio, Spain). These metagenomeassembled genomes (MAGs) display a remarkable taxonomic diversity inside the phylum and comprise wide ranges of estimated genome sizes (from 1.8 to 6 Mb). Among all Verrucomicrobia studied we found some of the smallest genomes of the Spartobacteria and Opitutae classes described so far. Some of the Opitutae family MAGs were small, cosmopolitan, with a general heterotrophic metabolism with preference for carbohydrates, and capable of xylan, chitin, or cellulose degradation. Besides, we assembled large copiotroph genomes, which contain a higher number of transporters, polysaccharide degrading pathways and in general more strategies for the uptake of nutrients and carbohydrate-based metabolic pathways in comparison with the representatives with the smaller genomes. The diverse genomes revealed interesting features like green-light absorbing rhodopsins and a complete set of genes involved in nitrogen fixation. The large diversity in genome sizes and physiological properties emphasize the diversity of this clade in freshwaters enlarging even further the already broad eco-physiological range of these microbesFR-V was supported by grant “VIREVO” CGL2016-76273-P [AEI/FEDER, EU], (cofunded with FEDER funds)Acciones de dinamización “REDES DE EXCELENCIA” CONSOLIDERCGL2015- 71523-REDC from the Spanish Ministerio de Economía, Industria y Competitividad and PROMETEO II/2014/012 “AQUAMET” from Generalitat ValencianaValenciana.MMwas supported by the Czech Academy of Sciences (Postdoc program PPPLZ application number L200961651)RG was supported by the Grant Agency of the Czech Republic by the research grant -04828SThe authors would like to thank Ana-Belén Martin- Cuadrado, Riccardo Rosselli, and Rafael González-Serrano for assistance with sampling and filtratio

Microorganisms of Lake Baikal : the deepest and most ancient lake on Earth

Lake Baikal (Russia) is the largest (by volume) and deepest lake on Earth. The lake remains relatively pristine due to the low population density around its basin. Being very distant from any marine water body but having a remarkable number of similarities to oceans (depth, oxygen content, oligotrophy) provides a unique model of pelagic microbiota that is submitted to marine-like conditions minus the salt content of the water. It is also a model of lakes located at high latitudes and submitted to yearly ice cover (from January to April). The analysis by different approaches has indeed provided a view of the microbiota of this lake. It contains novel microbes that are closely related to marine groups not known to be present in freshwater like Chloroflexi or Pelagibacter. The deep water mass contains large communities of chemolithotrophs that use ammonia generated in the photic zone or methane from the sediments

DataSheet_1_Extreme fluctuations in ambient salinity select for bacteria with a hybrid “salt-in”/”salt-out” osmoregulation strategy.zip

Abundant microbial biofilms inhabit underwater freshwater springs of the Dead Sea. Unlike the harsh (i.e., over 35% total dissolved salts) yet stable environment of the basin, the flow rate of the springs changes with random amplitude and duration, resulting in drastic shifts in salinity, pH, and oxygen concentrations. This requires the organisms to continuously adapt to new environmental conditions. Osmotic regulation is energetically expensive; therefore, the response of the biofilm organisms to rapid and drastic changes in salinity is interesting. For this purpose, we studied the metagenome of an enrichment culture obtained from a green biofilm-covered rock positioned in a spring. We obtained metagenome-assembled genomes (MAGs) of Prosthecochloris sp. (Chlorobiales), Flexistipes sp. (Deferribacterales), Izemoplasma (Izemoplasmatales), Halomonas sp. (Oceanospirillales), and Halanaerobium (Halanaerobiales). The MAGs contain genes for both the energetically cheaper “salt-in” and more expensive “salt-out” strategies. We suggest that the dynamic response of these bacteria utilizes both osmoregulation strategies, similar to halophilic archaea. We hypothesize that the frequent, abrupt, and variable-in-intensity shifts in salinity, typical of the Dead Sea spring system, select for microorganisms with scalable adaptation strategies.</p

The diversity of the antimicrobial resistome of lake Tanganyika increases with the water depth

The presence of antimicrobial resistance genes (ARGs) in the microbiome of freshwater communities is a consequence of thousands of years of evolution but also of the pressure exerted by anthropogenic activities, with potential negative impact on environmental and human health. In this study, we investigated the distribution of ARGs in Lake Tanganyika (LT)'s water column to define the resistome of this ancient lake. Additionally, we compared the resistome of LT with that of Lake Baikal (LB), the oldest known lake with different environmental characteristics and a lower anthropogenic pollution than LT. We found that richness and abundance of several antimicrobial resistance classes were higher in the deep water layers in both lakes. LT Kigoma region, known for its higher anthropogenic pollution, showed a greater richness and number of ARG positive MAGs compared to Mahale. Our results provide a comprehensive understanding of the antimicrobial resistome of LT and underscore its importance as reservoir of antimicrobial resistance. In particular, the deepest water layers of LT are the main repository of diverse ARGs, mirroring what was observed in LB and in other aquatic ecosystems. These findings suggest that the deep waters might play a crucial role in the preservation of ARGs in aquatic ecosystems

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

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

Isolation and characterisation of monoclonal picocyanobacterial strains from contrasting New Zealand lakes

Freshwater picocyanobacteria form the base of microbial food webs in many lakes worldwide but have received less attention than other phytoplankton. Little is known about their potential response to environmental changes such as increased nutrient loading and climate change, due partly to the lack of available cultured and sequenced strains. Here, we isolated 25 monoclonal picocyanobacterial strains from 6 New Zealand lakes with contrasting trophic states. The use of MLA medium instead of BG11 proved highly successful for the rapid isolation of picocyanobacteria. Strains were characterised by sequencing of the 16S ribosomal RNA gene, spectrophotometry, and high-performance liquid chromatography. 16S rRNA gene analysis placed most strains within the cluster 5 picocyanobacterial lineage (sub-cluster 5.2, family: Synechococcaceae). Phylogenetic analysis showed that 12 isolates from Lakes Wakatipu, Hayes, Johnson, and Ellesmere/Te Waihora clustered with strains from a range of Northern Hemisphere locations, suggesting global dispersal of these strains. Pigment characterisation revealed that pink and brown cultures from oligotrophic and some eutrophic lakes were rich in phycoerythrin, while green cultures from eutrophic and hypertrophic lakes were rich in phycocyanin. This diverse group of freshwater cluster 5 picocyanobacterial cultures will provide a new resource to study how these critically important microbes function and respond to changing environmental stressors

TEP production under oxidative stress of the picocyanobacterium Synechococcus

Transparent exopolymer particles (TEP) are mainly acidic polysaccharides directly or indirectly formed by phytoplankton and bacteria. These particles are often colonized by picoplankton and considered a hot spot for microbial activity. Recent studies suggested an important role of Synechococcus in TEP production found in lakes and prompted us to further investigate this issue using monoclonal xenic cultures of Synechococcus. We tested TEP production under oxidative stress in two treatments, one with hydrogen peroxide and another treated with ultraviolet radiation (UVR) and high photosynthetic active radiation (PAR), compared with an unstressed control. Our results showed a cell-normalized TEP production, ranging from 12 to 238 ng C cell-1 among strains, not only under stress but also in the control with non-limiting nutrients. Our data prove that freshwater communities of Synechococcus and their associated heterotrophic microflora, are capable of producing TEP even during growth phase. The oxidative stress induced extra production of TEP up to 400 ng C cell-1 in one of our phycocyanin-type (PC) strain. The phycoerythrin-type (PE) strains increased TEP production, particularly under UV-PAR stress, whereas the PC strains did it under H2O2 stress. This study provides new perspectives on the potential role of freshwater Synechococcus in TEP production