Ice cover extent drives phytoplankton and bacterial community structure in a large north-temperate lake: implications for a warming climate

Metatranscriptomic analysis reveals dissimilarity in viral community activity between an ice-free and ice-covered winter in Lake Erie

Winter is a relatively under-studied season in freshwater ecology. The paucity of wintertime surveys has led to a lack of knowledge regarding microbial community activity during the winter in Lake Erie, a North American Great Lake. Viruses shape microbial communities and regulate biogeochemical cycles by acting as top-down controls, yet very few efforts have been made to examine active virus populations during the winter in Lake Erie. Furthermore, climate change-driven declines in seasonal ice cover have been shown to influence microbial community structure, but no studies have compared viral community activity between different ice cover conditions. We surveyed surface water metatranscriptomes for viral hallmark genes as a proxy for active virus populations and compared activity metrics between ice-covered and ice-free conditions from two sampled winters. Transcriptionally active viral communities were detected in both winters, spanning diverse phylogenetic clades of putative bacteriophage (Caudoviricetes), giant viruses (Nucleocytoviricota, or NCLDV), and RNA viruses (Orthornavirae). However, viral community activity metrics revealed pronounced differences between the ice-covered and ice-free winters. Viral community composition was distinct between winters and viral hallmark gene richness was reduced in the ice-covered relative to the ice-free conditions. In addition, the observed differences in viral communities correlated with microbial community activity metrics. Overall, these findings contribute to our understanding of the viral populations that are active during the winter in Lake Erie and suggest that viral community activity may be associated with ice cover extent.IMPORTANCEAs seasonal ice cover is projected to become increasingly rare on large temperate lakes, there is a need to understand how microbial communities might respond to changing ice conditions. Although it is widely recognized that viruses impact microbial community structure and function, there is little known regarding wintertime viral activity or the relationship between viral activity and ice cover extent. Our metatranscriptomic analyses indicated that viruses were transcriptionally active in the winter surface waters of Lake Erie. These findings also expanded the known diversity of viral lineages in the Great Lakes. Notably, viral community activity metrics were significantly different between the two sampled winters. The pronounced differences we observed in active viral communities between the ice-covered and ice-free samples merit further research regarding how viral communities will function in future, potentially ice-free, freshwater systems.

Microbial difference and its influencing factors in ice-covered lakes on the three poles

Most lakes in the world are permanently or seasonally covered with ice. However, little is known about the distribution of microbes and their influencing factors in ice-covered lakes worldwide. Here we analyzed the microbial community composition in the waters of 14 ice-covered lakes in the Hoh Xil region of northern Qing-Tibetan Plateau (QTP), and conducted a meta-analysis by integrating published microbial community data of ice-covered lakes in the tripolar regions (the Arctic, Antarctica and QTP). The results showed that there were significant differences in microbial diversity, community composition and distribution patterns in the ice-covered tripolar lakes. Microbial diversity and richness were lower in the ice-covered QTP lakes (including the studied lakes in the Hoh Xil region) than those in the Arctic and Antarctica. In the ice-covered lakes of Hoh Xil, prokaryotes are mainly involved in S-metabolic processes, making them more adaptable to extreme environmental conditions. In contrast, prokaryotes in the ice-covered lakes of the Arctic and Antarctica were predominantly involved in carbon/nitrogen metabolic processes. Deterministic (salinity and nutrients) and stochastic processes (dispersal limitation, homogenizing dispersal and drift) jointly determine the geographical distribution patterns of microorganisms in ice-covered lakes, with stochastic processes dominating. These results expand the understanding of microbial diversity, distribution patterns, and metabolic processes in polar ice-covered lakes.

A tale of two blooms: do ecological paradigms for algal bloom success and succession require revisiting?

Lake Erie algal bloom discussions have historically focused on cyanobacteria, with foundational "blooms like it hot" and "high nutrient" paradigms considered as primary drivers behind cyanobacterial bloom success. Yet, recent surveys have rediscovered winter-spring diatom blooms, introducing another key player in the Lake Erie eutrophication and algal bloom story which has been historically overlooked. These blooms (summer vs. winter) have been treated as solitary events separated by spatial and temporal gradients. However, new evidence suggests they may not be so isolated, linked in a manner that manifests as an algal bloom cycle. Equally notable are the emerging reports of cyanobacterial blooms in cold and/or oligotrophic freshwaters, which have been interpreted by some as shifts in classical bloom paradigms. These emerging bloom reports have led many to ask "what is a bloom?". Furthermore, questioning classic paradigms has caused others to wonder if we are overlooking additional factors which constrain bloom success. In light of emerging data and ideas, we revisited foundational concepts within the context of Lake Erie algal blooms and derived five key take-aways: 1) Additional bloom-formers (diatoms) need to be included in Lake Erie algal discussions, 2) The term "bloom" must be reinforced with a clear definition and quantitative metrics for each event, 3) Algal blooms should not be studied solitarily, 4) Shifts in physiochemical conditions serve as an alternative interpretation to potential shifts in ecological paradigms, 5) Additional factors which constrain bloom success and succession (i.e., pH and light) require consideration.

Lake Erie ice is a repository of organisms

Organism abundance and diversity were assessed in Lake Erie ice samples using sequences derived from a combined metagenomic and metatranscriptomic analysis. The 68,417 unique sequences were from Bacteria (77.5%), Eukarya (22.3%), and Archaea (0.2%) and indicated diverse species of organisms from 32 bacterial, 8 eukaryotic, and 2 archaeal taxonomic groups.

Rarefaction is currently the best approach to control for uneven sequencing effort in amplicon sequence analyses

Considering it is common to find as much as 100-fold variation in the number of 16S rRNA gene sequences across samples in a study, researchers need to control for the effect of uneven sequencing effort. How to do this has become a contentious question. Some have argued that rarefying or rarefaction is "inadmissible" because it omits valid data. A number of alternative approaches have been developed to normalize and rescale the data that purport to be invariant to the number of observations. I generated community distributions based on 12 published data sets where I was able to assess the ability of multiple methods to control for uneven sequencing effort. Rarefaction was the only method that could control for variation in uneven sequencing effort when measuring commonly used alpha and beta diversity metrics. Next, I compared the false detection rate and power to detect true differences between simulated communities with a known effect size using various alpha and beta diversity metrics. Although all methods of controlling for uneven sequencing effort had an acceptable false detection rate when samples were randomly assigned to two treatment groups, rarefaction was consistently able to control for differences in sequencing effort when sequencing depth was confounded with treatment group. Finally, the statistical power to detect differences in alpha and beta diversity metrics was consistently the highest when using rarefaction. These simulations underscore the importance of using rarefaction to normalize the number of sequences across samples in amplicon sequencing analyses.

IMPORTANCE

Sequencing 16S rRNA gene fragments has become a fundamental tool for understanding the diversity of microbial communities and the factors that affect their diversity. Due to technical challenges, it is common to observe wide variation in the number of sequences that are collected from different samples within the same study. However, the diversity metrics used by microbial ecologists are sensitive to differences in sequencing effort. Therefore, tools are needed to control for the uneven levels of sequencing. This simulation-based analysis shows that despite a longstanding controversy, rarefaction is the most robust approach to control for uneven sequencing effort. The controversy started because of confusion over the definition of rarefaction and violation of assumptions that are made by methods that have been borrowed from other fields. Microbial ecologists should use rarefaction.

Declines in ice cover are accompanied by light limitation responses and community change in freshwater diatoms

The rediscovery of diatom blooms embedded within and beneath the Lake Erie ice cover (2007-2012) ignited interest in psychrophilic adaptations and winter limnology. Subsequent studies determined the vital role ice plays in winter diatom ecophysiology as diatoms partition to the underside of ice, thereby fixing their location within the photic zone. Yet, climate change has led to widespread ice decline across the Great Lakes, with Lake Erie presenting a nearly "ice-free" state in several recent winters. It has been hypothesized that the resultant turbid, isothermal water column induces light limitation amongst winter diatoms and thus serves as a competitive disadvantage. To investigate this hypothesis, we conducted a physiochemical and metatranscriptomic survey that spanned spatial, temporal, and climatic gradients of the winter Lake Erie water column (2019-2020). Our results suggest that ice-free conditions decreased planktonic diatom bloom magnitude and altered diatom community composition. Diatoms increased their expression of various photosynthetic genes and iron transporters, which suggests that the diatoms are attempting to increase their quantity of photosystems and light-harvesting components (a well-defined indicator of light limitation). We identified two gene families which serve to increase diatom fitness in the turbid ice-free water column: proton-pumping rhodopsins (a potential second means of light-driven energy acquisition) and fasciclins (a means to "raft" together to increase buoyancy and co-locate to the surface to optimize light acquisition). With large-scale climatic changes already underway, our observations provide insight into how diatoms respond to the dynamic ice conditions of today and shed light on how they will fare in a climatically altered tomorrow.

A combined microscopy and single-cell sequencing approach reveals the ecology, morphology, and phylogeny of uncultured lineages of zoosporic fungi

Environmental DNA analyses of fungal communities typically reveal a much larger diversity than can be ascribed to known species. Much of this hidden diversity lies within undescribed fungal lineages, especially the early diverging fungi (EDF). Although these EDF often represent new lineages even at the phylum level, they have never been cultured, making their morphology and ecology uncertain. One of the methods to characterize these uncultured fungi is a single-cell DNA sequencing approach. In this study, we established a large data set of single-cell sequences of EDF by manually isolating and photographing parasitic fungi on various hosts such as algae, protists, and micro-invertebrates, combined with subsequent long-read sequencing of the ribosomal DNA locus (rDNA). We successfully obtained rDNA sequences of 127 parasitic fungal cells, which clustered into 71 phylogenetic lineages belonging to seven phylum-level clades of EDF: Blastocladiomycota, Chytridiomycota, Aphelidiomycota, Rozellomycota, and three unknown phylum-level clades. Most of our single cells yielded novel sequences distinguished from both described taxa and existing metabarcoding data, indicating an expansive and hidden diversity of parasitic taxa of EDF. We also revealed an unexpected diversity of endobiotic Olpidium-like chytrids and hyper-parasitic lineages. Overall, by combining photographs of parasitic fungi with phylogenetic analyses, we were able to better understand the ecological function and morphology of many of the branches on the fungal tree of life known only from DNA sequences. IMPORTANCE Much of the diversity of microbes from natural habitats, such as soil and freshwater, comprise species and lineages that have never been isolated into pure culture. In part, this stems from a bias of culturing in favor of saprotrophic microbes over the myriad symbiotic ones that include parasitic and mutualistic relationships with other taxa. In the present study, we aimed to shed light on the ecological function and morphology of the many undescribed lineages of aquatic fungi by individually isolating and sequencing molecular barcodes from 127 cells of host-associated fungi using single-cell sequencing. By adding these sequences and their photographs into the fungal tree, we were able to understand the morphology of reproductive and vegetative structures of these novel fungi and to provide a hypothesized ecological function for them. These individual host-fungal cells revealed themselves to be complex environments despite their small size; numerous samples were hyper-parasitized with other zoosporic fungal lineages such as Rozellomycota.

Variability of Microbial Communities in Two Long-Term Ice-Covered Freshwater Lakes in the Subarctic Region of Yakutia, Russia

Although under-ice microbial communities are subject to a cold environment, low concentrations of nutrients, and a lack of light, they nevertheless take an active part in biogeochemical cycles. However, we still lack an understanding of how high their diversity is and how these communities are distributed during the long-term ice-cover period. Here, we assessed for the first time the composition and distribution of microbial communities during the ice-cover period in two subarctic lakes (Labynkyr and Vorota) located in the area of the lowest temperature in the Northern Hemisphere. The diversity distribution and abundance of main bacterial taxa as well as the composition of microalgae varied by time and habitat. The 16S rRNA gene sequencing method revealed, in general, a high diversity of bacterial communities where Proteobacteria (~ 45%) and Actinobacteria (~ 21%) prevailed. There were significant differences between the communities of the lakes: Chthoniobacteraceae, Moraxellaceae, and Pirellulaceae were abundant in Lake Labynkyr, while Cyanobiaceae, Oligoflexales, Ilumatobacteraceae, and Methylacidiphilaceae were more abundant in Lake Vorota. The most abundant families were evenly distributed in April, May, and June their contribution was different in different habitats. In April, Moraxellaceae and Ilumatobacteraceae were the most abundant in the water column, while Sphingomonadaceae was abundant both in water column and on the ice bottom. In May, the abundance of Comamonadaceae increased and reached the maximum in June, while Cyanobiaceae, Oxalobacteraceae, and Pirellulaceae followed. We found a correlation of the structure of bacterial communities with snow thickness, pH, N_min concentration, and conductivity. We isolated psychrophilic heterotrophic bacteria both from dominating and minor taxa of the communities studied. This allowed for specifying their ecological function in the under-ice communities. These findings will advance our knowledge of the under-ice microbial life.

Metatranscriptomic Sequencing of Winter and Spring Planktonic Communities from Lake Erie, a Laurentian Great Lake

Previous reports suggest planktonic and under-ice winter microbial communities in Lake Erie are dominated by diatoms. Here, we report the assembled metatranscriptomes of 79 Lake Erie surface water microbial communities spanning both the winter (28 samples) and spring (51 samples) months over spatial, temporal, and climatic gradients in 2019 through 2020.

The impact of climate warming on the diurnal dynamics of the microbial loop: Ice cover vs. lack of ice cover on dystrophic lakes

One of the effects of warming is earlier retreat of the ice cover or a complete lack of ice cover on water bodies in the winter. However, there is still no information on how climate warming affects the 24-hour dynamics of the planktonic microbial loop in winter. The aim of this investigation was to assess the diurnal dynamics of the taxonomic composition and abundance of microbial communities in experimentally reproduced conditions (samples from under the ice, +2, +4 and +8 °C) and to analyse the relationships between components of the microbial loop in relation to physical and chemical parameters. Samples were taken in winter from three dystrophic reservoir. The biological and physicochemical parameters in the water were analysed at the start (day 0), 15 and end of the experiment (day 30) over a 24-hour cycle. The increase in temperature caused an increase in the numbers of predators (particularly testate amoebae and ciliates) and a reduction in the body size of individual populations. During the period with ice cover, marked dominance of mixotrophic testate amoeba (Hyalosphenia papilio) and ciliates (Paramecium bursaria) was observed, while the increase in temperature caused an increase in the proportion of bacterivorous ciliates (Cinetochilum margaritaceum).

Changes in the Community Structure of Under-Ice and Open-Water Microbiomes in Urban Lakes Exposed to Road Salts

Salinization of freshwater is increasingly observed in regions where chloride de-icing salts are applied to the roads in winter, but little is known about the effects on microbial communities. In this study, we analyzed the planktonic microbiomes of four lakes that differed in degree of urbanization, eutrophication and salinization, from an oligotrophic reference lake with no surrounding roads, to a eutrophic, salinized lake receiving runoff from a highway. We tested the hypothesis that an influence of road salts would be superimposed on the effects of season and trophic status. We evaluated the microbial community structure by 16S rRNA sequencing for Bacteria, and by four methods for eukaryotes: 16S rRNA chloroplast analysis, 18S rRNA sequencing, photosynthetic pigment analysis and microscopy. Consistent with our hypothesis, chloride and total nitrogen concentrations were among the most important statistical factors explaining the differences in taxonomic composition. These factors were positively correlated with the abundance of cryptophytes, haptophytes, and cyanobacteria. Ice-cover was also a major structuring factor, with clear differences between the winter communities and those of the open-water period. Nitrifying and methane oxidizing bacteria were more abundant in winter, suggesting the importance of anaerobic sediment processes and release of reduced compounds into the ice-covered water columns. The four methods for eukaryotic analysis provided complementary information. The 18S rRNA observations were strongly influenced by the presence of ribosome-rich ciliates, but revealed a much higher degree of taxonomic richness and greater separation of lakes, seasonal changes and potential salinity effects than the other methods.

Effects of sea ice and wind speed on phytoplankton spring bloom in central and southern Baltic Sea

In this study, the effects of sea ice and wind speed on the timing and composition of phytoplankton spring bloom in the central and southern Baltic Sea are investigated by a hydrodynamic-biogeochemical model and observational data. The modelling experiment compared the results of a reference run in the presence of sea ice with those of a run in the absence of sea ice, which confirmed that ecological conditions differed significantly for both the scenarios. It has been found that diatoms dominate the phytoplankton biomass in the absence of sea ice, whereas dinoflagellates dominate the biomass in the presence of thin sea ice. The study concludes that under moderate ice conditions (representing the last few decades), dinoflagellates dominate the spring bloom phytoplankton biomass in the Baltic Sea, whereas diatoms will be dominant in the future as a result of climate change i.e. in the absence of sea ice.

Winter Decomposition of Emergent Macrophytes Affects Water Quality under Ice in a Temperate Shallow Lake

Decomposition of emergent macrophytes is now recognized as an internal nutrient source for shallow lakes. Temperate lakes always experience seasonal ice cover in winter, but the influences of emergent macrophytes decomposition on water quality have rarely been examined under ice. Here, we conducted an incubation experiment to investigate winter decomposition of two common emergent macrophytes species (Typha orientalis and Phragmites australis) and its influences on water quality in the Hengshui Lake, North China. Mesocosms simulating a lake ice regime were incubated in the field for 120 days in winter and were treated with and without plant material addition. Water quality was monitored through dissolved oxygen (DO), dissolved organic carbon (DOC), total nitrogen (TN), total phosphorus (TP), ammonium nitrogen (NH4-N), and nitrate nitrogen (NO3-N). We found that both species were significantly decomposed in winter and that the majority of mass loss occurred in the first 10 days of decomposition when the water surface of mesocosms were already frozen. The concentrations of DO rapidly dropped to values close to zero after plant material submergence. At the end of incubation, the concentrations of DOC, TN, and NO3-N in the mesocosms with plant material addition were significantly higher than initial concentrations. In contrast, the concentrations of DOC, TN, TP, NO3-N, and NH4-N in the mesocosms without plant material addition were equal to or less than initial concentrations. Our research suggests that winter decomposition of emergent macrophytes produces negative influences on water quality under ice that lasts for the whole winter.

Freezing and thawing of lakes on the Nelson and King George Islands, Antarctic, using Sentinel 1A synthetic aperture radar images

This article aims to analyze the dynamics of freezing and thawing of Antarctic lakes located in ice-free areas on Nelson Island and Fildes Peninsula, where response to changes in air temperature and precipitation rates occur rapidly, during the period from July 2016 to December 2018. In these places, which are difficult to access, remote sensing is an important alternative, especially considering the use of active remote sensors such as the Synthetic Aperture Radar (SAR), which has less restriction regarding the presence of clouds over the study area. Three backscatter thresholds were defined (σ) for the identification of the physical state of the water of the lakes of the study region, applied in Sentinel 1A SAR (S1A) images under Horizontal Horizontal (HH) polarization and Interferometric Wide (IW) imaging mode. These images, along with the air temperature data obtained by the Interim Re-Analysis (ERA-Interim) atmospheric reanalysis model, provided the evidence for the interpretation of the freezing and thawing periods of the lakes. The thresholds applied for the definition of the physical state of the lake water were greater than - 14 dB for frozen water, between - 14 and - 17 dB for the surface, with up to 60% of their frozen area, and less than - 17 dB for open water. The temporal analysis revealed that the lakes start to thaw in October, become completely thawed in February, and freeze again in March. Nevertheless, it can be said that the S1A satellite allows a satisfactory identification of the liquid and solid phases of the water in the lakes of the study region.

Microbial communities of the Laurentian Great Lakes reflect connectivity and local biogeochemistry

The Laurentian Great Lakes are a vast, interconnected freshwater system spanning strong physicochemical gradients, thus constituting a powerful natural laboratory for addressing fundamental questions about microbial ecology and evolution. We present a comparative analysis of pelagic microbial communities across all five Laurentian Great Lakes, focusing on Bacterial and Archaeal picoplankton characterized via 16S rRNA amplicon sequencing. We collected samples throughout the water column from the major basins of each lake in spring and summer over 2 years. Two oligotypes, classified as LD12 (Alphaproteobacteria) and acI‐B1 (Actinobacteria), were among the most abundant in every sample. At the same time, microbial communities showed distinct patterns with depth during summer stratification. Deep hypolimnion samples were frequently dominated by a Chloroflexi oligotype that reached up to 19% relative abundance. Stratified surface communities differed between the colder, less productive upper lakes (Superior, Michigan, Huron) and warmer, more productive lower lakes (Erie, Ontario), in part due to an Actinobacteria oligotype (acI‐C2) that averaged 7.7% of sequences in the lower lakes but <0.2% in the upper lakes. Together, our findings suggest that both hydrologic connectivity and local selective pressures shape microbial communities in the Great Lakes and establish a framework for future investigations.

Loci Encoding Compounds Potentially Active against Drug-Resistant Pathogens amidst a Decreasing Pool of Novel Antibiotics

Carbapenem-resistant P. aeruginosa is difficult to treat and has been deemed by the World Health Organization as a priority one pathogen for which antibiotics are most urgently needed. Although metagenomics and bioinformatic studies suggest that natural bacteria remain a source of novel compounds, the identification of genes and their products specific to activity against MDR pathogens remains problematic. Here, we examine water-derived pseudomonads and identify gene clusters whose compounds inhibit CF-derived MDR pathogens, including carbapenem-resistant P. aeruginosa.

Since the discovery of penicillin, microbes have been a source of antibiotics that inhibit the growth of pathogens. However, with the evolution of multidrug-resistant (MDR) strains, it remains unclear if there is an abundant or limited supply of natural products to be discovered that are effective against MDR isolates. To identify strains that are antagonistic to pathogens, we examined a set of 471 globally derived environmental Pseudomonas strains (env-Ps) for activity against a panel of 65 pathogens including Achromobacter spp., Burkholderia spp., Pseudomonas aeruginosa, and Stenotrophomonas spp. isolated from the lungs of cystic fibrosis (CF) patients. From more than 30,000 competitive interactions, 1,530 individual inhibitory events were observed. While strains from water habitats were not proportionate in antagonistic activity, MDR CF-derived pathogens (CF-Ps) were less susceptible to inhibition by env-Ps, suggesting that fewer natural products are effective against MDR strains. These results advocate for a directed strategy to identify unique drugs. To facilitate discovery of antibiotics against the most resistant pathogens, we developed a workflow in which phylogenetic and antagonistic data were merged to identify strains that inhibit MDR CF-Ps and subjected those env-Ps to transposon mutagenesis. Six different biosynthetic gene clusters (BGCs) were identified from four strains whose products inhibited pathogens including carbapenem-resistant P. aeruginosa. BGCs were rare in databases, suggesting the production of novel antibiotics. This strategy can be utilized to facilitate the discovery of needed antibiotics that are potentially active against the most drug-resistant pathogens.

IMPORTANCE Carbapenem-resistant P. aeruginosa is difficult to treat and has been deemed by the World Health Organization as a priority one pathogen for which antibiotics are most urgently needed. Although metagenomics and bioinformatic studies suggest that natural bacteria remain a source of novel compounds, the identification of genes and their products specific to activity against MDR pathogens remains problematic. Here, we examine water-derived pseudomonads and identify gene clusters whose compounds inhibit CF-derived MDR pathogens, including carbapenem-resistant P. aeruginosa.

Microbial life under ice: Metagenome diversity and in situ activity of Verrucomicrobia in seasonally ice-covered Lakes

Northern lakes are ice-covered for a large part of the year, yet our understanding of microbial diversity and activity during winter lags behind that of the ice-free period. In this study, we investigated under-ice diversity and metabolism of Verrucomicrobia in seasonally ice-covered lakes in temperate and boreal regions of Quebec, Canada using 16S rRNA sequencing, metagenomics and metatranscriptomics. Verrucomicrobia, particularly the V1, V3 and V4 subdivisions, were abundant during ice-covered periods. A diversity of Verrucomicrobia genomes were reconstructed from Quebec lake metagenomes. Several genomes were associated with the ice-covered period and were represented in winter metatranscriptomes, supporting the notion that Verrucomicrobia are metabolically active under ice. Verrucomicrobia transcriptome analysis revealed a range of metabolisms potentially occurring under ice, including carbohydrate degradation, glycolate utilization, scavenging of chlorophyll degradation products, and urea use. Genes for aerobic sulfur and hydrogen oxidation were expressed, suggesting chemolithotrophy may be an adaptation to conditions where labile carbon may be limited. The expression of genes for flagella biosynthesis and chemotaxis was detected, suggesting Verrucomicrobia may be actively sensing and responding to winter nutrient pulses, such as phytoplankton blooms. These results increase our understanding on the diversity and metabolic processes occurring under ice in northern lakes ecosystems.© 2018 Society for Applied Microbiology and John Wiley & Sons Ltd.

Microbial Community Dynamics During Lake Ice Freezing

Many freshwater environments experience dramatic seasonal changes with some systems remaining ice-covered for most of the winter. Freshwater systems are also highly sensitive to environmental change. However, little is known about changes in microbial abundance and community composition during lake ice formation and times of persistent ice cover. The goal of this study is to characterize temporal dynamics of microbial communities during ice formation and persistent ice cover. Samples were collected in triplicate, five days per week from surface water in the Keweenaw Waterway between November and April. Environmental conditions along with microbial abundance and microbial community composition was determined. Distinct community composition was found between ice-free and ice-covered time periods with significantly different community composition between months. The microbial community underwent dramatic shifts in microbial abundance and diversity during the transitions into and out of ice cover. The richness of the microbial community increased during times of ice cover. Relatives of microbes involved in nitrogen cycling bloomed during times of ice cover as sequences related to known nitrifying taxa were significantly enriched during ice cover. These results help to elucidate how microbial abundance and diversity change over drastic seasonal transitions and how ice cover may affect microbial abundance and diversity.

Terrestrial Origin for Abundant Riverine Nanoscale Ice-Nucleating Particles

Ice-nucleating particles (INPs) associated with fresh waters are a neglected, but integral component of the water cycle. Abundant INPs were identified from surface waters of both the Maumee River and Lake Erie with ice nucleus spectra spanning a temperature range from -3 to -15 °C. The majority of river INPs were submicron in size and attributed to biogenic macromolecules, inferred from the denaturation of ice-nucleation activity by heat. In a watershed dominated by row-crop agriculture, higher concentrations of INPs were found in river samples compared to lake samples. Further, ice-nucleating temperatures differed between river and lake samples, which indicated different populations of INPs. Seasonal analysis of INPs that were active at warmer temperatures (≥-10 °C; INP_-10) showed their concentration to correlate with river discharge, suggesting a watershed origin of these INPs. A terrestrial origin for INPs in the Maumee River was further supported by a correspondence between the ice-nucleation signatures of river INPs and INPs derived from the soil fungus Mortierella alpina. Aerosols derived from turbulence features in the river carry INP_-10, although their potential influence on regional weather is unclear. INP_-10 contained within aerosols generated from a weir spanning the river, ranged in concentration from 1 to 11 INP m^-3, which represented a fold-change of 3.2 over average INP_-10 concentrations sampled from aerosols at control locations.

Seasonal dynamics of the bacterioplankton community in a large, shallow, highly dynamic freshwater lake

The spatiotemporal shifts of the bacterioplankton community can mirror their transition of functional traits in an aquatic ecosystem. However, the spatiotemporal variation of the bacterioplankton community composition structure (BCCS) within a large, shallow, highly dynamic freshwater lake is still poorly understood. Here, we examined the seasonal and spatial variability of the BCCs within Poyang Lake by sequencing the 16S rRNA gene amplicon to explore how hydrological changes affect the BCCs. Principal coordinate analysis showed that the BCCs varied significantly among four sampling seasons, but not spatially. The seasonal changes of the BCCs were mainly attributed to the differences between autumn and spring–winter. Higher α diversity indices were observed in autumn. Redundancy analysis indicated that the BCCs co-variated with water level, pH, temperature, total phosphorus, ammoniacal nitrogen, electrical conductivity, total nitrogen, and turbidity. Among them, water level was the key determinant separating autumn BCCs from the BCCs in other seasons. A significantly lower relative abundance of Burkholderiales (betI and betVII) and a higher relative abundance of Actinomycetales (acI, acTH1, and acTH2) were found in autumn than in other seasons. Overall, our results suggest that water level changes associated with pH, temperature, and nutrient status shaped the seasonal patterns of the BCCs within Poyang Lake.

Evaluating RADARSAT-2 for the Monitoring of Lake Ice Phenology Events in Mid-Latitudes

Lake ice is an important component in understanding the local climate as changes in temperature have an impact on the timing of key ice phenology events. In recent years, there has been a decline in the in-situ monitoring of lake ice events in Canada and microwave remote sensing imagery from synthetic aperture radar (SAR) is more widely used due to the high spatial resolution and response of backscatter to the freezing and melting of the ice surface. RADARSAT-2 imagery was used to develop a threshold-based method for determining lake ice events for mid-latitude lakes in Central Ontario from 2008 to 2017. Estimated lake ice phenology events are validated with ground-based observations and are compared against the Moderate Resolution Imaging Spectroradiometer (MODIS band 2). The threshold-based method was found to accurately identify 12 out of 17 freeze events and 13 out of 17 melt events from 2015–2017 when compared to ground-based observations. Mean absolute errors for freeze events ranged from 2.5 to 10.0 days when compared to MODIS imagery while the mean absolute error for water clear of ice (WCI) ranged from 1.5 to 7.1 days. The method is important for the study of mid-latitude lake ice due to its unique success in detecting multiple freeze and melting events throughout the ice season.

Diversity and Cyclical Seasonal Transitions in the Bacterial Community in a Large and Deep Perialpine Lake

High-throughput sequencing (HTS) was used to analyze the seasonal variations in the bacterioplankton community composition (BCC) in the euphotic layer of a large and deep lake south of the Alps (Lake Garda). The BCC was analyzed throughout two annual cycles by monthly samplings using the amplification and sequencing of the V3-V4 hypervariable region of the 16S rRNA gene by the MiSeq Illumina platform. The dominant and most diverse bacterioplankton phyla were among the more frequently reported in freshwater ecosystems, including the Proteobacteria, Cyanobacteria, Bacteroidetes, Verrucomicrobia, Actinobacteria, and Planctomycetes. As a distinctive feature, the development of the BCC showed a cyclical temporal pattern in the two analyzed years and throughout the euphotic layer. The recurring temporal development was controlled by the strong seasonality in water temperature and thermal stratification, and by cyclical temporal changes in nutrients and, possibly, by the remarkable annual cyclical development of cyanobacteria and eukaryotic phytoplankton hosting bacterioplankton that characterizes Lake Garda. Further downstream analyses of operational taxonomic units associated to cyanobacteria allowed confirming the presence of the most abundant taxa previously identified by microscopy and/or phylogenetic analyses, as well as the presence of other small Synechococcales/Chroococcales and rare Nostocales never identified so far in the deep lakes south of the Alps. The implications of the high diversity and strong seasonality are relevant, opening perspectives for the definition of common and discriminating patterns characterizing the temporal and spatial distribution in the BCC, and for the application of the new sequencing technologies in the monitoring of water quality in large and deep lakes.

Physicochemical Drivers of Microbial Community Structure in Sediments of Lake Hazen, Nunavut, Canada

The Arctic is undergoing rapid environmental change, potentially affecting the physicochemical constraints of microbial communities that play a large role in both carbon and nutrient cycling in lacustrine environments. However, the microbial communities in such Arctic environments have seldom been studied, and the drivers of their composition are poorly characterized. To address these gaps, we surveyed the biologically active surface sediments in Lake Hazen, the largest lake by volume north of the Arctic Circle, and a small lake and shoreline pond in its watershed. High-throughput amplicon sequencing of the 16S rRNA gene uncovered a community dominated by Proteobacteria, Bacteroidetes, and Chloroflexi, similar to those found in other cold and oligotrophic lake sediments. We also show that the microbial community structure in this Arctic polar desert is shaped by pH and redox gradients. This study lays the groundwork for predicting how sediment microbial communities in the Arctic could respond as climate change proceeds to alter their physicochemical constraints.

Environmental Pseudomonads Inhibit Cystic Fibrosis Patient-Derived Pseudomonas aeruginosa

Pseudomonas aeruginosa is an opportunistic pathogen which is evolving resistance to many currently used antibiotics. While much research has been devoted to the roles of pathogenic P. aeruginosa in cystic fibrosis (CF) patients, less is known of its ecological properties. P. aeruginosa dominates the lungs during chronic infection in CF patients, yet its abundance in some environments is less than that of other diverse groups of pseudomonads. Here, we sought to determine if clinical isolates of P. aeruginosa are vulnerable to environmental pseudomonads that dominate soil and water habitats in one-to-one competitions which may provide a source of inhibitory factors. We isolated a total of 330 pseudomonads from diverse habitats of soil and freshwater ecosystems and competed these strains against one another to determine their capacity for antagonistic activity. Over 900 individual inhibitory events were observed. Extending the analysis to P. aeruginosa isolates revealed that clinical isolates, including ones with increased alginate production, were susceptible to competition by multiple environmental strains. We performed transposon mutagenesis on one isolate and identified an ∼14.8-kb locus involved in antagonistic activity. Only two other environmental isolates were observed to carry the locus, suggesting the presence of additional unique compounds or interactions among other isolates involved in outcompeting P. aeruginosa. This collection of strains represents a source of compounds that are active against multiple pathogenic strains. With the evolution of resistance of P. aeruginosa to currently used antibiotics, these environmental strains provide opportunities for novel compound discovery against drug-resistant clinical strains.

IMPORTANCE We demonstrate that clinical CF-derived isolates of P. aeruginosa are susceptible to competition in the presence of environmental pseudomonads. We observed that many diverse environmental strains exhibited varied antagonistic profiles against a panel of clinical P. aeruginosa isolates, suggesting the presence of distinct mechanisms of inhibition among these ecological strains. Understanding the properties of these antagonistic events offers the potential for discoveries of antimicrobial compounds or metabolic pathways important to the development of novel treatments for P. aeruginosa infections.

Unanticipated Geochemical and Microbial Community Structure under Seasonal Ice Cover in a Dilute, Dimictic Arctic Lake

Despite most lakes in the Arctic being perennially or seasonally frozen for at least 40% of the year, little is known about microbial communities and nutrient cycling under ice cover. We assessed the vertical microbial community distribution and geochemical composition in early spring under ice in a seasonally ice-covered lake in southwest Greenland using amplicon-based sequencing that targeted 16S rRNA genes and using a combination of field and laboratory aqueous geochemical methods. Microbial communities changed consistently with changes in geochemistry. Composition of the abundant members responded strongly to redox conditions, shifting downward from a predominantly heterotrophic aerobic community in the suboxic waters to a heterotrophic anaerobic community in the anoxic waters. Operational taxonomic units (OTUs) of Sporichthyaceae, Comamonadaceae, and the SAR11 Clade had higher relative abundances above the oxycline and OTUs within the genus Methylobacter, the phylum Lentisphaerae, and purple sulfur bacteria (PSB) below the oxycline. Notably, a 13-fold increase in sulfide at the oxycline was reflected in an increase and change in community composition of potential sulfur oxidizers. Purple non-sulfur bacteria were present above the oxycline and green sulfur bacteria and PSB coexisted below the oxycline, however, PSB were most abundant. For the first time we show the importance of PSB as potential sulfur oxidizers in an Arctic dimictic lake.