Evolutionary change in metabolic rate of Daphnia pulicaria in response to the invasive predator Bythotrephes longimanus

Metabolic rate is a trait that can be hypothesized to evolve in response to a change in predation. In the current study, we address this question by utilising an invasive event by the predatory zooplankton Bythotrephes longimanus in Lake Mendota, Wisconsin, US. This invasion dramatically impacted the prey Daphnia pulicaria, causing a ~60% decline in their biomass. Using a resurrection ecology approach, we compared the metabolic rate of D. pulicaria clones originating from prior to the Bythotrephes invasion with that of clones having evolved in the presence of Bythotrephes. We observed a 7.4% reduction in metabolic rate among post-invasive clones compared to pre-invasive clones. This change is in the opposite direction to what might be expected to evolve in response to increased predation. The evolution of a lower metabolic rate may instead be due to a habitat shift in the prey species into deeper and less productive waters and associated changes in the optimal metabolic rate.

Microbial cysteine degradation is a source of hydrogen sulfide in oxic freshwater lakes

The sulfur-containing amino acid cysteine is abundant in the environment including in freshwater lakes. Biological degradation of cysteine can result in hydrogen sulfide (H2S), a toxic and ecologically relevant compound that is a central player in biogeochemical cycling in aquatic environments, including freshwater lakes. Here, we investigated the ecological significance of cysteine in oxic freshwater lake environments, using model systems of isolated cultures, controlled growth experiments, and multi-omics. We screened bacterial isolates enriched from natural lake water for their ability to produce H2S when provided cysteine. In total, we identified 29 isolates that produced H2S and belonged to the phylum Proteobacteria Bacteroidetes, and Actinobacteria. To understand the genomic and genetic basis for cysteine degradation and H2S production, we further characterized 3 freshwater isolates using whole-genome sequencing, and quantitatively tracked cysteine and H2S levels over their growth ranges: Stenotrophomonas maltophila, Stenotrophomonas bentonitica (Gammaproteobacteria) and Chryseobacterium piscium (Bacteroidetes). We observed a decrease in cysteine and increase in H2S, and identified genes involved in cysteine degradation in all 3 genomes. Finally, to assess the presence of these organisms and genes in the environment, we surveyed a five-year time series of metagenomic data from the same isolation source at Lake Mendota and identified their presence throughout the time series. Overall, our study shows that sulfur-containing amino acids can drive microbial H2S production in oxic environments. Future considerations of sulfur cycling and biogeochemistry in oxic environments should account for H2S production from degradation of organosulfur compounds.

Lake thermal structure drives interannual variability in summer anoxia dynamics in a eutrophic lake over 37 years

The concentration of oxygen is fundamental to lake water quality and ecosystem functioning through its control over habitat availability for organisms, redox reactions, and recycling of organic material. In many eutrophic lakes, oxygen depletion in the bottom layer (hypolimnion) occurs annually during summer stratification. The temporal and spatial extent of summer hypolimnetic anoxia is determined by interactions between the lake and its external drivers (e.g., catchment characteristics, nutrient loads, meteorology) as well as internal feedback mechanisms (e.g., organic matter recycling, phytoplankton blooms). How these drivers interact to control the evolution of lake anoxia over decadal timescales will determine, in part, the future lake water quality. In this study, we used a vertical one-dimensional hydrodynamic–ecological model (GLM-AED2) coupled with a calibrated hydrological catchment model (PIHM-Lake) to simulate the thermal and water quality dynamics of the eutrophic Lake Mendota (USA) over a 37 year period. The calibration and validation of the lake model consisted of a global sensitivity evaluation as well as the application of an optimization algorithm to improve the fit between observed and simulated data. We calculated stability indices (Schmidt stability, Birgean work, stored internal heat), identified spring mixing and summer stratification periods, and quantified the energy required for stratification and mixing. To qualify which external and internal factors were most important in driving the interannual variation in summer anoxia, we applied a random-forest classifier and multiple linear regressions to modeled ecosystem variables (e.g., stratification onset and offset, ice duration, gross primary production). Lake Mendota exhibited prolonged hypolimnetic anoxia each summer, lasting between 50–60 d. The summer heat budget, the timing of thermal stratification, and the gross primary production in the epilimnion prior to summer stratification were the most important predictors of the spatial and temporal extent of summer anoxia periods in Lake Mendota. Interannual variability in anoxia was largely driven by physical factors: earlier onset of thermal stratification in combination with a higher vertical stability strongly affected the duration and spatial extent of summer anoxia. A measured step change upward in summer anoxia in 2010 was unexplained by the GLM-AED2 model. Although the cause remains unknown, possible factors include invasion by the predacious zooplankton Bythotrephes longimanus. As the heat budget depended primarily on external meteorological conditions, the spatial and temporal extent of summer anoxia in Lake Mendota is likely to increase in the near future as a result of projected climate change in the region.

Lake thermal structure drives inter-annual variability in summer anoxia dynamics in a eutrophic lake over 37 years

The concentration of oxygen is fundamental to lake water quality and ecosystem functioning through its control over habitat availability for organisms, redox reactions, and recycling of organic material. In many eutrophic lakes, oxygen depletion in the bottom layer (hypolimnion) occurs annually during summer stratification. The temporal and spatial extent of summer hypolimnetic anoxia is determined by interactions between the lake and its external drivers (e.g., catchment characteristics/nutrient loads, meteorology), as well as internal feedback mechanisms (e.g., organic matter recycling, phytoplankton blooms). How these drivers interact to control the evolution of lake anoxia over decadal time scales will determine, in part, the future lake water quality. In this study, we used a vertical one-dimensional hydrodynamic-ecological model (GLM-AED2) coupled with a calibrated hydrological catchment model (PIHM-Lake) to simulate the thermal and water quality dynamics of the eutrophic Lake Mendota (USA) over a 37-year period. The calibration and validation of the lake model consisted of a global sensitivity evaluation as well as the application of an evolutionary optimization algorithm to improve the fit between observed and simulated data. By quantifying stability indices (Schmidt Stability, Birgean Work, stored internal heat), we identified spring mixing and summer stratification periods, and quantified the energy required for stratification and mixing. To qualify which external and internal factors were most important in driving the inter-annual variation in summer anoxia, we applied a random-forest classifier and multiple linear regression to modeled ecosystem variables (e.g., stratification onset and offset, ice duration, gross primary production.) Lake Mendota exhibited prolonged hypolimnetic anoxia each summer, lasting between 50–60 days. The summer heat budget, as well as the timing of thermal stratification, were the most important predictors of the spatial and temporal extent of summer anoxia periods in Lake Mendota. An earlier onset of thermal stratification in combination with a higher vertical stability strongly affected the duration and spatial extent of summer anoxia. As the heat budget depended primarily on external meteorological conditions, the spatial and temporal extent of summer anoxia in Lake Mendota is likely to increase in the near future as a result of projected climate change in the region.

Wide Distribution of Phage That Infect Freshwater SAR11 Bacteria

ABSTRACT Fonsibacter (LD12 subclade) is among the most abundant bacterioplankton in freshwater ecosystems. These bacteria belong to the order Pelagibacterales (SAR11) and are related to Pelagibacter (marine SAR11), which dominates many marine habitats. Although a few Pelagibacter phage (Pelagiphage) have been described, no phage that infect Fonsibacter have been reported. In this study, we describe two groups of Podoviridae phage that infect Fonsibacter. A complete Fonsibacter genome containing a prophage was reconstructed from metagenomic data. A circularized and complete genome related to the prophage, referred to as uv-Fonsiphage-EPL (lysogenic strategy), shows high similarity to marine Pelagiphage HTVC025P. Additionally, we reconstructed three complete genomes and one draft genome of phage related to marine Pelagiphage HTVC010P and predicted a lytic strategy. The similarity in codon usage and cooccurrence patterns of HTVC010P-related phage and Fonsibacter suggested that these phage infect Fonsibacter. Similar phage were detected in Lake Mendota, Wisconsin, where Fonsibacter is also present. A search of related phage revealed the worldwide distribution of some genotypes in freshwater ecosystems, suggesting their substantial role in shaping indigenous microbial assemblages and influence on biogeochemical cycling. However, the uv-Fonsiphage-EPL and one group of HTVC010P-related phage have a more limited distribution in freshwater ecosystems. Overall, the findings provide insights into the genomic features of phage that infect Fonsibacter and expand understanding of the ecology and evolution of these important bacteria. IMPORTANCE Fonsibacter represents a significant microbial group of freshwater ecosystems. Although the genomic and metabolic features of these bacteria have been well studied, no phage infecting them has been reported. In this study, we reconstructed complete genomes of Fonsibacter and infecting phage and revealed their close relatedness to the phage infecting marine SAR11 members. Also, we illustrated that phage that infect Fonsibacter are widely distributed in freshwater habitats. In summary, the results contribute new insights into the ecology and evolution of Fonsibacter and phage.

Including variability in air temperature warming scenarios in a lake simulation model highlights uncertainty in predictions of cyanobacteria

Despite growing evidence that climate change will increase temperature variability and the frequency of temperature extremes, many modeling studies that analyze the effects of warming scenarios on cyanobacteria in lakes examine uniform warming temperature scenarios without including any variability. Here, we used the one-dimensional hydrodynamic General Lake Model coupled to Aquatic EcoDynamics modules (GLM-AED) to simulate 11 years of nitrogen-fixing and non-nitrogen-fixing cyanobacterial biomass in Lake Mendota (Madison, WI, USA). We developed climate scenarios with either uniform (constant) warming or variable warming based on random sampling of daily air temperatures from either a normal or Poisson probability distribution. We found that while the median cyanobacterial biomass among repeated simulations for each of the years was similar regardless of whether or not air temperature variability was included in the climate scenarios, the randomly-sampled air temperature distribution scenarios exhibited much greater variability in the year-to-year cyanobacterial biomass estimates. Our results suggest that including temperature variability in climate scenarios may substantially change our understanding of how climate warming may alter cyanobacterial blooms over yearly to decadal time scales. To more effectively predict the range of possible future cyanobacterial dynamics, both the magnitude and variability of warming must be considered when developing climate scenarios for lake modeling studies.

Wide distribution of phage that infect freshwater SAR11 bacteria

Fonsibacter (LD12 subclade) are among the most abundant bacterioplankton in freshwater ecosystems. These bacteria belong to the order Pelagibacterales (SAR11) and are related to Pelagibacter (marine SAR11) that dominate many marine habitats. Although a handful of Pelagibacter phage (Pelagiphage) have been described, no phage that infect Fonsibacter have been reported. In this study, a complete Fonsibacter genome containing a prophage was reconstructed from metagenomic data. A circularized and complete genome related to the prophage, referred to as uv-Fonsiphage-EPL, shows high similarity to marine Pelagiphage HTVC025P. Additionally, we reconstructed three complete and one draft genome of phage related to marine Pelagiphage HTVC010P, and predicted a lytic strategy. The similarity in codon usage and co-occurrence patterns of HTVC010P-related phage and Fonsibacter suggested that these phage infect Fonsibacter. Similar phage were detected in Lake Mendota, Wisconsin, where Fonsibacter is also present. A search of related phage revealed the worldwide distribution of some genotypes in freshwater ecosystems, suggesting their substantial role in shaping indigenous microbial assemblages and influence on biogeochemical cycling. However, the uv-Fonsiphage-EPL and one lineage of HTVC010P-related phage have a more limited distribution in freshwater ecosystems. Based on this, and their close phylogenetic relatedness with Pelagiphage, we predict that they transitioned from saline into freshwater ecosystems comparatively recently. Overall, the findings provide insights into the genomic features of phage that infect Fonsibacter, and expand understanding of the ecology and evolution of these important bacteria.

Evaluation of Low-Cost, Automated Lake Ice Thickness Measurements

Climate change is expected to decrease ice coverage and thickness globally while increasing the variability of ice coverage and thickness on midlatitude lakes. Ice thickness affects physical, biological, and chemical processes as well as safety conditions for scientists and the general public. Measurements of ice thickness that are both temporally frequent and spatially extensive remain a technical challenge. Here new observational methods using repurposed soil moisture sensors that facilitate high spatial–temporal sampling of ice thickness are field tested on Lake Mendota in Wisconsin during the winter 2015/16 season. Spatial variability in ice thickness was high, with differences of 10 cm of ice column thickness over 1.05 km of horizontal distance. When observational data were compared with manual measurements and model output from both the Freshwater Lake (FLake) model and General Lake Model (GLM), ice thickness from sensors matches manual measurements, whereas GLM and FLake results showed a thinner and thicker ice layer, respectively. The FLake-modeled ice column temperature effectively remained at 0°C, not matching observations. We also show that daily ice dynamics follows the expected linear function of ice thickness growth/melt, improving confidence in sensor accuracy under field conditions. We have demonstrated a new method that allows low-cost and high-frequency measurements of ice thickness, which will be needed both to advance winter limnology and to improve on-ice safety.