Lake Microbial Communities Research Articles

Tire wear particles enhance horizontal gene transfer of antibiotic resistance genes in aquatic ecosystems

Microplastics (MPs) have introduced new surfaces for biofilm development and gene exchange among bacteria. We investigated Tire Wear Particles (TWPs) for their involvement in horizontal gene transfer (HGT), particularly in relation to associated metals in the matrices of TWPs. We employed red-fluorescently tagged E. coli strain as a donor with green-fluorescently tagged, broad-host-range plasmid pKJK5, resistant to trimethoprim. As a recipient, we utilized Pseudomonas sp. and a natural lake microbial community. HGT activity on TWPs was determined and compared with that on polystyrene (PS) (with and without metals), and chitosan, which was used as a natural surface. Exposure to TWPs significantly enhanced HGT frequency of antibiotic resistance gene (ARG) from donor to recipient compared to PS and chitosan, and metals of TWPs further promoted HGT. HGT frequency on TWPs with Pseudomonas sp. was found to be 10−3 at 30 °C. in the lake community, it was similarly high already at 25 °C suggesting a higher permissiveness of the natural microbial community towards ARG at lower temperatures. This study sheds light on the potential impact of TWPs in promoting HGT, forming the basis for health risk assessments of TWPs and more generally of MP pollution in various aquatic ecosystems.

Glacier Retreat Induces Contrasting Shifts in Bacterial Biodiversity Patterns in Glacial Lake Water and Sediment

Glacial lake ecosystems are experiencing rapid changes due to accelerated glacier retreat. As glaciers recede, their influence on downstream habitats diminishes, potentially affecting the biodiversity of glacial lake microbial communities. However, there remains a knowledge gap regarding how bacterial biodiversity patterns in glacial lakes are altered by diminishing glacial influence. Here, we investigated shifts in bacterial communities in paired water and sediment samples collected from seven glacial lakes on the Tibetan Plateau, using a space-for-time substitution approach to understand the consequences of glacier retreat. Our findings reveal that bacterial diversity in lake water increases significantly with a higher glacier index (GI), whereas sediment bacterial diversity exhibits a negative correlation with GI. Both the water and sediment bacterial communities display significant structural shifts along the GI gradient. Notably, reduced glacial influence decreases the complexity of bacterial co-occurrence networks in lake water but enhances the network complexity in sediment. This divergence in diversity and co-occurrence patterns highlights that water and sediment bacterial communities respond differently to changes in glacial influence in these lake ecosystems. This study provides insights into how diminishing glacial influence impacts the bacterial biodiversity in glacial lake water and sediments, revealing contrasting patterns between the two habitats. These findings emphasize the need for comprehensive monitoring to understand the implications of glacier retreat on these fragile ecosystems.

Lake microbiome composition determines community adaptability to warming perturbations

BackgroundMicrobial communities are crucial for ecosystems. A central goal of microbial ecological research is to simplify the biodiversity in natural environments and quantify the functional roles to explore how the ecosystems respond under different environmental conditions. However, the research on the stability and dynamics of lake microbes in response to repeated warming stress is limited.MethodsTo exclude confounding environmental factors, we conducted a 20-day repeated warming simulation experiment to examine the composition and function dynamics of lake microbial communities.ResultsExperimental warming significantly altered the community structure of bacteria instead of fungi. Microbial community structure, together with microbial biomass, jointly regulated the function of microbial communities. The plummeting of aerobic denitrifiers Pseudomonadaceae decreased by 99% (P < 0.001) after high temperature, leading to reduced microbial nitrogen metabolism on nitrogen respiration and nitrate respiration. Under warming conditions, the microbial community with higher adaptability showed more positive correlations and less competitive relationships in co-occurrence networks to acclimate to warming.ConclusionMicrobiome composition controlled carbon and nitrogen metabolism, thus determining lake microbial communities’ adaptability to heat stress. This study extended our insights on the lake microbial community response and adaptability under warming drivers.

Native freshwater lake microbial community response to an in situ experimental dilbit spill.

With the increase in crude oil transport throughout Canada, the potential for spills into freshwater ecosystems has increased and additional research is needed in these sensitive environments. Large enclosures erected in a lake were used as mesocosms for this controlled experimental dilbit (diluted bitumen) spill under ambient environmental conditions. The microbial response to dilbit, the efficacy of standard remediation protocols on different shoreline types commonly found in Canadian freshwater lakes, including a testing of a shoreline washing agent were all evaluated. We found that the native microbial community did not undergo any significant shifts in composition after exposure to dilbit or the ensuing remediation treatments. Regardless of the treatment, sample type (soil, sediment, or water), or type of associated shoreline, the community remained relatively consistent over a 3-month monitoring period. Following this, metagenomic analysis of polycyclic aromatic and alkane hydrocarbon degradation mechanisms also showed that while many key genes identified in PAH and alkane biodegradation were present, their abundance did not change significantly over the course of the experiment. These results showed that the native microbial community present in a pristine freshwater lake has the prerequisite mechanisms for hydrocarbon degradation in place, and combined with standard remediation practices in use in Canada, has the genetic potential and resilience to potentially undertake bioremediation.

Phylogenetic distance-decay patterns are not explained by local community assembly processes in freshwater lake microbial communities.

While water and sediment microbial communities exhibit pronounced spatio-temporal patterns in freshwater lakes, the underlying drivers are yet poorly understood. Here, we evaluated the importance of spatial and temporal variation in abiotic environmental factors for bacterial and microeukaryotic community assembly and distance-decay relationships in water and sediment niches in Hongze Lake. By sampling across the whole lake during both Autumn and Spring sampling time points, we show that only bacterial sediment communities were governed by deterministic community assembly processes due to abiotic environmental drivers. Nevertheless, consistent distance-decay relationships were found with both bacterial and microeukaryotic communities, which were relatively stable with both sampling time points. Our results suggest that spatio-temporal variation in environmental factors was important in explaining mainly bacterial community assembly in the sediment, possibly due lesser disturbance. However, clear distance-decay patterns emerged also when the community assembly was stochastic. Together, these results suggest that abiotic environmental factors do not clearly drive the spatial structuring of lake microbial communities, highlighting the need to understand the role of other potential drivers, such as spatial heterogeneity and biotic species interactions.

Spatio-temporal connectivity of the aquatic microbiome associated with cyanobacterial blooms along a Great Lake riverine-lacustrine continuum.

Lake Erie is subject to recurring events of cyanobacterial harmful algal blooms (cHABs), but measures of nutrients and total phytoplankton biomass seem to be poor predictors of cHABs when taken individually. A more integrated approach at the watershed scale may improve our understanding of the conditions that lead to bloom formation, such as assessing the physico-chemical and biological factors that influence the lake microbial community, as well as identifying the linkages between Lake Erie and the surrounding watershed. Within the scope of the Government of Canada's Genomics Research and Development Initiative (GRDI) Ecobiomics project, we used high-throughput sequencing of the 16S rRNA gene to characterize the spatio-temporal variability of the aquatic microbiome in the Thames River-Lake St. Clair-Detroit River-Lake Erie aquatic corridor. We found that the aquatic microbiome was structured along the flow path and influenced mainly by higher nutrient concentrations in the Thames River, and higher temperature and pH downstream in Lake St. Clair and Lake Erie. The same dominant bacterial phyla were detected along the water continuum, changing only in relative abundance. At finer taxonomical level, however, there was a clear shift in the cyanobacterial community, with Planktothrix dominating in the Thames River and Microcystis and Synechococcus in Lake St. Clair and Lake Erie. Mantel correlations highlighted the importance of geographic distance in shaping the microbial community structure. The fact that a high proportion of microbial sequences found in the Western Basin of Lake Erie were also identified in the Thames River, indicated a high degree of connectivity and dispersal within the system, where mass effect induced by passive transport play an important role in microbial community assembly. Nevertheless, some cyanobacterial amplicon sequence variants (ASVs) related to Microcystis, representing less than 0.1% of relative abundance in the upstream Thames River, became dominant in Lake St. Clair and Erie, suggesting selection of those ASVs based on the lake conditions. Their extremely low relative abundances in the Thames suggest additional sources are likely to contribute to the rapid development of summer and fall blooms in the Western Basin of Lake Erie. Collectively, these results, which can be applied to other watersheds, improve our understanding of the factors influencing aquatic microbial community assembly and provide new perspectives on how to better understand the occurrence of cHABs in Lake Erie and elsewhere.

Water microecology is affected by seasons but not sediments: A spatiotemporal dynamics survey of bacterial community composition in Lake Changshou—The largest artificial lake in southwest China

This study aimed to evaluate the correlation between microecology of sediments and water as well as their spatial-temporal variations in Changshou Lake. The results demonstrated that microecology in the lake exhibits spatiotemporal heterogeneity, and microbial diversity of sediments was significantly higher than that of water body. Further, it was found that there was statistically insignificant positive correlation between microecology of sediments and that of water body. PCoA and community structure analysis revealed that the predominant phyla which exhibited significant spatial differences in sediments were Proteobacteria, Actinobacteria and Planctomycetes. While, the distribution of dominant bacteria Actinobacteria and Verrucomicrobia in water body showed significant seasonal differences. Microbial networks analysis indicated that there was a cooperative symbiotic relationship between lake microbial communities. Notably, the same bacterial genus had no significant positive correlation in sediment and water, which suggested that bacteria transport between sediment-water interface does not influence the microecological functions of lake water.

Tracking the upstream history of aquatic microbes in a boreal lake yields new insights on microbial community assembly.

Bacterial community structure can change rapidly across short spatial and temporal scales as environmental conditions vary, but the mechanisms underlying those changes are still poorly understood. Here, we assessed how a lake microbial community assembles by following its reorganization from the main tributary, which, when flowing into the lake, first traverses an extensive macrophyte-dominated vegetated habitat, before reaching the open water. Environmental conditions in the vegetated habitat changed drastically compared to both river and lake waters and represented a strong environmental gradient for the incoming bacteria. We used amplicon sequencing of the 16S rRNA gene and transcript to reconstruct the shifts in relative abundance of individual taxa and link this to their pattern in activity (here assessed with RNA:DNA ratios). Our results indicate that major shifts in relative abundance were restricted mostly to rare taxa (<0.1% of relative abundance), which seemed more responsive to environmental changes. Dominant taxa (>1% of relative abundance), on the other hand, traversed the gradient mostly unchanged with relatively low and stable RNA:DNA ratios. We also identified a high level of local recruitment and a seedbank of taxa capable of activating/inactivating, but these were almost exclusively associated with the rare biosphere. Our results suggest a scenario where the lake community results from a reshuffling of the rank abundance structure within the incoming rare biosphere, driven by selection and growth, and that numerical dominance is not a synonym of activity, growth rate, or environmental selection, but rather reflect mass effects structuring these freshwater bacterial communities.

Antarctic lake phytoplankton and bacteria from near-surface waters exhibit high sensitivity to climate-driven disturbance.

The McMurdo Dry Valleys (MDVs), Antarctica, represent a cold, desert ecosystem poised on the threshold of melting and freezing water. The MDVs have experienced dramatic signs of climatic change, most notably a warm austral summer in 2001-2002 that caused widespread flooding, partial ice cover loss and lake level rise. To understand the impact of these climatic disturbances on lake microbial communities, we simulated lake level rise and ice-cover loss by transplanting dialysis-bagged communities from selected depths to other locations in the water column or to an open water perimeter moat. Bacteria and eukaryote communities residing in the surface waters (5m) exhibited shifts in community composition when exposed to either disturbance, while microbial communities from below the surface were largely unaffected by the transplant. We also observed an accumulation of labile dissolved organic carbon in the transplanted surface communities. In addition, there were taxa-specific sensitivities: cryptophytes and Actinobacteria were highly sensitive particularly to the moat transplant, while chlorophytes and several bacterial taxa increased in relative abundance or were unaffected. Our results reveal that future climate-driven disturbances will likely undermine the stability and productivity of MDV lake phytoplankton and bacterial communities in the surface waters of this extreme environment.

Sedimentary DNA records long‐term changes in a lake bacterial community in response to varying nutrient availability

AbstractMicrobial communities play important roles in lake ecosystems and are sensitive to environmental change. However, our understanding of their responses to long‐term change such as eutrophication is limited, as long‐term lake monitoring is rare, and traditional paleolimnological techniques (pigments and microfossils) are restricted to a low taxonomic resolution, or organisms with well‐preserved structures. Sedimentary DNA (sedDNA) is a promising technique to reconstruct past microbial communities in sediments, but taphonomic processes and the ability of sedDNA to record bacterial pelagic history accurately are largely unknown. Here, we sequenced the 16S rRNA gene in triplicate sediment cores from Esthwaite Water (English Lake District) which has concurrent long‐term monitoring and observational data. The sediment record spanned 113 years and included an episode of increased nutrient availability from the 1970s, followed by a more recent decline. Trends in bacterial community composition were broadly similar among the three sediment cores. Cyanobacterial richness in the sediment cores correlated significantly with that of cyanobacteria in a 65‐year microscopy‐based monitoring record, and some known pelagic bacterial taxa were detected in the sediment. sedDNA revealed distinct shifts in community composition in response to changing lake physicochemical conditions. The relative abundance of cyanobacteria closely reflected nutrient enrichment, and Proteobacteria, Bacteroidetes, and Verrucomicrobia were relatively more abundant in recent sediments, while Chloroflexi, Firmicutes, Acidobacteria, Nitrospirae, Spirochaetes, and Planctomycetes declined in more recent sediments. Following lake restoration efforts to reduce nutrient enrichment, the relative abundance of cyanobacteria returned to pre‐1970 levels, but the bacterial community did not fully recover from the period of intense eutrophication within the time scale of our study. These results suggest that sedDNA is a valuable approach to reconstruct lake microbial community composition over the 100‐year time scale studied, but an improved understanding of DNA deposition and degradation is required to further the application of sedDNA in paleolimnology.

Archaeal and bacterial ecological strategies in sediment denitrification under the influence of graphene oxide and different temperatures

As an emerging material, graphene oxide (GO) has been widely used in recent years and will inevitably enter into natural water bodies, and it may have an impact on lake microbial communities owing to its potential toxicity and denitrification-enhancing ability. This study simulated the effect of 0.1 g/L GO on denitrification in lake sediments under summer (28 °C) and winter temperatures (8 °C). GO promoted carbon source metabolism and denitrification. Phylogenetic bin-based null model analysis suggested that GO significantly altered the contribution of heterogeneous selection in bacterial and archaeal community assembly. The co-occurrence network indicated that bacterial communities responded to the enhancement of heterogeneous selection by strategies of enhancing positive correlation and shared niche, whereas archaeal communities adopted strategies of enhancing negative correlation and competition. Bacterial networks also emerged with more non-hub connector species that could drive changes in community structure. Our study contributed to the understanding of different ecological strategies adopted by bacterial and archaeal communities in response to changes in ecological selection driven by GO.

Microbial Community Structure Is Most Strongly Associated With Geographical Distance and pH in Salt Lake Sediments.

Salt lakes are globally significant microbial habitats, hosting substantial novel microbial diversity and functional capacity. Extremes of salinity and pH both pose major challenges for survival of microbial life in terrestrial and aquatic environments, and are frequently cited as primary influences on microbial diversity across a wide variety of environments. However, few studies have attempted to identify spatial and geochemical contributions to microbial community composition, functional capacity, and environmental tolerances in salt lakes, limiting exploration of novel halophilic and halotolerant microbial species and their potential biotechnological applications. Here, we collected sediment samples from 16 salt lakes at pH values that ranged from pH 4 to 9, distributed across 48,000 km2 of the Archaean Yilgarn Craton in southwestern Australia to identify associations between environmental factors and microbial community composition, and used a high throughput culturing approach to identify the limits of salt and pH tolerance during iron and sulfur oxidation in these microbial communities. Geographical distance between lakes was the primary contributor to variation in microbial community composition, with pH identified as the most important geochemical contributor to variation in microbial community composition. Microbial community composition split into two clear groups by pH: Bacillota dominated microbial communities in acidic saline lakes, whereas Euryarchaeota dominated microbial communities in alkaline saline lakes. Iron oxidation was observed at salinities up to 160 g L–1 NaCl at pH values as low as pH 1.5, and sulfur oxidation was observed at salinities up to 160 g L–1 NaCl between pH values 2–10, more than doubling previously observed tolerances to NaCl salinity amongst cultivable iron and sulfur oxidizers at these extreme pH values. OTU level diversity in the salt lake microbial communities emerged as the major indicator of iron- and sulfur-oxidizing capacity and environmental tolerances to extremes of pH and salinity. Overall, when bioprospecting for novel microbial functional capacity and environmental tolerances, our study supports sampling from remote, previously unexplored, and maximally distant locations, and prioritizing for OTU level diversity rather than present geochemical conditions.

Road Salt versus Urban Snow Effects on Lake Microbial Communities

Freshwater salinization is an ongoing concern for north temperate lakes; however, little is known about its impacts on microbial communities, particularly for bacteria. We tested the hypotheses that road de-icing salt induces changes in the microbial community structure of lake plankton, and that changes due to chloride would differ from those due to urban snowmelt because of additional chemicals in the snowmelt. In a laboratory incubator experiment, an overwintering plankton community in lake water was exposed for two weeks to either NaCl or municipal road snow with the same level of chloride. Microbial community structure as determined by 16S (prokaryotes) and 18S (eukaryotes) rRNA transcript analysis showed changes in response to the chloride-only enrichment, with some rare taxa becoming more prominent. Consistent with our hypothesis, the salt and the snow treatments induced different community changes. These results indicate that ecotoxicology assays based on a single salt addition may not reflect the in situ effects of salt-contaminated urban snow, and that the combined chemical effects of urban snowmelt require direct testing.

The relationship between land cover and microbial community composition in European lakes

Microbes are essential for element cycling and ecosystem functioning. However, many questions central to understanding the role of microbes in ecology are still open. Here, we analyze the relationship between lake microbiomes and the lakes' land cover. By applying machine learning methods, we quantify the covariance between land cover categories and the microbial community composition recorded in the largest amplicon sequencing dataset of European lakes available to date. Our results show that the aggregation of environmental features or microbial taxa before analysis can obscure ecologically relevant patterns. We observe a comparatively high covariation of the lakes' microbial community with herbaceous and open spaces surrounding the lake; nevertheless, the microbial covariation with land cover categories is generally lower than the covariation with physico-chemical parameters. Combining land cover and physico-chemical bioindicators identified from the same amplicon sequencing dataset, we develop analytical data structures that facilitate insights into the ecology of the lake microbiome. Among these, a list of the environmental parameters sorted by the number of microbial bioindicators we have identified for them points towards apparent environmental drivers of the lake microbial community composition, such as the altitude, conductivity, and area covered herbaceous vegetation surrounding the lake. Furthermore, the response map, a similarity matrix calculated from the Jaccard similarity of the environmental parameters' lists of bioindicators, allows us to study the ecosystem's structure from the standpoint of the microbiome. More specifically, we identify multiple clusters of highly similar and possibly functionally linked ecological parameters, including one that highlights the importance of the calcium-bicarbonate equilibrium for lake ecology. Taken together, we demonstrate the use of machine learning approaches in studying the interplay between microbial diversity and environmental factors and introduce novel approaches to integrate environmental molecular diversity into monitoring and water quality assessments.

Proteome and strain analysis of cyanobacterium Candidatus “Phormidium alkaliphilum” reveals traits for success in biotechnology

SummaryCyanobacteria encompass a diverse group of photoautotrophic bacteria with important roles in nature and biotechnology. Here we characterized Candidatus “Phormidium alkaliphilum,” an abundant member in alkaline soda lake microbial communities globally. The complete, circular whole-genome sequence of Ca. “P. alkaliphilum” was obtained using combined Nanopore and Illumina sequencing of a Ca. “P. alkaliphilum” consortium. Strain-level diversity of Ca. “P. alkaliphilum” was shown to contribute to photobioreactor robustness under different operational conditions. Comparative genomics of closely related species showed that adaptation to high pH was not attributed to specific genes. Proteomics at high and low pH showed only minimal changes in gene expression, but higher productivity in high pH. Diverse photosystem antennae proteins, and high-affinity terminal oxidase, compared with other soda lake cyanobacteria, appear to contribute to the success of Ca. “P. alkaliphilum” in photobioreactors and biotechnology applications.

Lake microbial communities are not resistant or resilient to repeated large-scale natural pulse disturbances.

Opportunities to study community-level responses to extreme natural pulse disturbances in unaltered ecosystems are rare. Lake sediment records that span thousands of years can contain well-resolved sediment pulses, triggered by earthquakes. These palaeorecords provide a means to study repeated pulse disturbances and processes of resistance (insensitivity to disturbance) and ecological resilience (capacity to regain structure, function and process). In this study, sedimentary DNA was extracted from a sediment core from Lake Paringa (New Zealand) that is situated in a near natural catchment. Metabarcoding and inferred functions were used to assess the lake microbial community over the past 1100years - a period that included four major earthquakes. Microbial community composition and function differed significantly between highly perturbed (postseismic, ~50years) phases directly after the earthquakes and more stable (interseismic, ~250years) phases, indicating a lack of community resistance. Although community structure differed significantly in successive postseismic phases, function did not, suggesting potential functional redundancy. Significant differences in composition and function in successive interseismic phases demonstrate that communities are not resilient to large-scale natural pulse disturbances. The clear difference in structure and function, and high number of indicator taxa (responsible for driving differences in communities between phases) in the fourth interseismic phase probably represents a regime shift, possibly due to the two-fold increase in sediment and terrestrial biospheric organic carbon fluxes recorded following the fourth earthquake. Large pulse disturbances that enhance sediment inputs into lake systems may produce an underappreciated mechanism that destabilises lake ecosystem processes.

Characterization of microbial response to petroleum hydrocarbon contamination in a lacustrine ecosystem

Microbiomes of freshwater basins intended for human use remain poorly studied, with very little known about the microbial response to in situ oil spills. Lake Pertusillo is an artificial freshwater reservoir in Basilicata, Italy, and serves as the primary source of drinking water for more than one and a half million people in the region. Notably, it is located in close proximity to one of the largest oil extraction plants in Europe. The lake suffered a major oil spill in 2017, where approximately 400 tons of crude oil spilled into the lake; importantly, the pollution event provided a rare opportunity to study how the lacustrine microbiome responds to petroleum hydrocarbon contamination. Water samples were collected from Lake Pertusillo 10 months prior to and 3 months after the accident. The presence of hydrocarbons was verified and the taxonomic and functional aspects of the lake microbiome were assessed. The analysis revealed specialized successional patterns of lake microbial communities that were potentially capable of degrading complex, recalcitrant hydrocarbons, including aromatic, chloroaromatic, nitroaromatic, and sulfur containing aromatic hydrocarbons. Our findings indicated that changes in the freshwater microbial community were associated with the oil pollution event, where microbial patterns identified in the lacustrine microbiome 3 months after the oil spill were representative of its hydrocarbonoclastic potential and may serve as effective proxies for lacustrine oil pollution.

Electrogenic and hydrocarbonoclastic biofilm at the oil-water interface as microbial responses to oil spill

The oil-water interface formed during an oil spill represents a challenging environment for pelagic communities living in aquatic ecosystems. At this anoxic barrier, we report the formation of a microbial hydrocarbonoclastic biofilm capable of electron transfer along the water column. This biofilm generated a membrane of surface-active compounds that allowed the spontaneous separation of electrical charges, causing the establishment of an anodic and a cathodic region and, as a result, the spontaneous creation of a liquid microbial fuel cell. Such floating biofilm was connected to the water column underneath by floating filaments that could contribute to oxygen reduction at distance. The filaments revealed an unusual lipid content induced by anoxic conditions, with prominent ultrastructural features similar to myelin found in oligodendrocytes of the vertebrate nervous system. Furthermore, these filaments showed an interesting cross-reactivity towards different epitopes of the myelin basic protein (MBP) and Claudin 11 (O4) of human oligodendrocytes. The presence of a network of filaments similar to myelin suggests the probable existence of evolutionary connections between very distant organisms. Collectively these results suggest a possible mechanism for how lake microbial communities can adapt to oil spills while offering an interesting starting point for technological developments of liquid microbial fuel cells related to the study of hydrocarbon-water interfaces.The data that support the findings of this study are openly available in figshare at https://figshare.com/s/72bc73ae14011dc7920d.

Landscape Setting Drives the Microbial Eukaryotic Community Structure in Four Swedish Mountain Lakes over the Holocene.

On the annual and interannual scales, lake microbial communities are known to be heavily influenced by environmental conditions both in the lake and in its terrestrial surroundings. However, the influence of landscape setting and environmental change on shaping these communities over a longer (millennial) timescale is rarely studied. Here, we applied an 18S metabarcoding approach to DNA preserved in Holocene sediment records from two pairs of co-located Swedish mountain lakes. Our data revealed that the microbial eukaryotic communities were strongly influenced by catchment characteristics rather than location. More precisely, the microbial communities from the two bedrock lakes were largely dominated by unclassified Alveolata, while the peatland lakes showed a more diverse microbial community, with Ciliophora, Chlorophyta and Chytrids among the more predominant groups. Furthermore, for the two bedrock-dominated lakes—where the oldest DNA samples are dated to only a few hundred years after the lake formation—certain Alveolata, Chlorophytes, Stramenopiles and Rhizaria taxa were found prevalent throughout all the sediment profiles. Our work highlights the importance of species sorting due to landscape setting and the persistence of microbial eukaryotic diversity over millennial timescales in shaping modern lake microbial communities.

Whole Genome Sequence and Experimental Proteome of &lt;i&gt;Candidatus&lt;/i&gt; 'Phormidium Alkaliphilum', an Abundant and Widespread Cyanobacterium With Applications in Biotechnology

Cyanobacteria encompass a diverse group of photoautotrophic bacteria with important roles in nature and biotechnology. Here we introduce Candidatus “Phormidium alkaliphilum”, an abundant member of alkaline soda lake microbial communities across the globe. Multiple, independent studies have reported successful colonization of photobioreactors for biotechnology applications by Ca. “P. alkaliphilum” and closely related cyanobacteria. The complete, circular whole genome sequence of Ca. “P. alkaliphilum” was obtained using combined Nanopore and Illumina sequencing of a consortium abundant in Ca. “P. alkaliphilum”. Strain heterogeneity of the Ca. “P. alkaliphilum” population was shown to contribute to photobioreactor robustness under different operational conditions. Comparative genomics of closely related Phormidium species showed that adaption to high pH and alkalinity could not be attributed to specific genes. Proteomics showed high pH (11.2) provoked only minimal changes in gene expression in Ca. “P. alkaliphilum”, compared to control cultures at pH 9. Diversity of photosystem antennae proteins, a high affinity terminal oxidase and ecophysiological flexibility contributed to success of Ca. “P. alkaliphilum” in photobioreactors and biotechnology, compared to other soda lake cyanobacteria.