Controls and significance of priming effects in lake sediments.

Warming and eutrophication influence carbon (C) processing in sediments, with implications for the global greenhouse-gas budget. Temperature effects on sedimentary C loss are well understood, but the mechanism of change in turnover through priming with labile organic matter (OM) is not. Evaluating changes in the magnitude of priming as a function of warming, eutrophication, and OM stoichiometry, we incubated sediments with 13 C-labeled fresh organic matter (FOM, algal/cyanobacterial) and simulated future climate scenarios (+4°C and +8°C). We investigated FOM-induced production of CH4 and microbial community changes. C loss was primed by up to 17% in dominantly allochthonous sediments (ranging from 5% to 17%), compared to up to 6% in autochthonous sediments (-9% to 6%), suggesting that refractory OM is more susceptible to priming. The magnitude of priming was dependent on sediment OM stoichiometry (C/N ratio), the ratio of fresh labile OM to microbial biomass (FOM/MB), and temperature. Priming was strongest at 4°C when FOM/MB was below 50%. Addition of FOM was associated with activation and growth of bacterial decomposers, including for example, Firmicutes, Bacteroidetes, or Fibrobacteres, known for their potential to degrade insoluble and complex structural biopolymers. Using sedimentary C/N > 15 as a threshold, we show that in up to 35% of global lakes, sedimentation is dominated by allochthonous rather than autochthonous material. We then provide first-order estimates showing that, upon increase in phytoplankton biomass in these lakes, priming-enabled degradation of recalcitrant OM will release up to 2.1 Tg C annually, which would otherwise be buried for geological times.

Elucidating the picocyanobacteria salinity divide through ecogenomics of new freshwater isolates.

BACKGROUND: Cyanobacteria are the major prokaryotic primary producers occupying a range of aquatic habitats worldwide that differ in levels of salinity, making them a group of interest to study one of the major unresolved conundrums in aquatic microbiology which is what distinguishes a marine microbe from a freshwater one? We address this question using ecogenomics of a group of picocyanobacteria (cluster 5) that have recently evolved to inhabit geographically disparate salinity niches. Our analysis is made possible by the sequencing of 58 new genomes from freshwater representatives of this group that are presented here, representing a 6-fold increase in the available genomic data. RESULTS: Overall, freshwater strains had larger genomes (≈2.9 Mb) and %GC content (≈64%) compared to brackish (2.69 Mb and 64%) and marine (2.5 Mb and 58.5%) isolates. Genomic novelties/differences across the salinity divide highlighted acidic proteomes and specific salt adaptation pathways in marine isolates (e.g., osmolytes/compatible solutes - glycine betaine/ggp/gpg/gmg clusters and glycerolipids glpK/glpA), while freshwater strains possessed distinct ion/potassium channels, permeases (aquaporin Z), fatty acid desaturases, and more neutral/basic proteomes. Sulfur, nitrogen, phosphorus, carbon (photosynthesis), or stress tolerance metabolism while showing distinct genomic footprints between habitats, e.g., different types of transporters, did not obviously translate into major functionality differences between environments. Brackish microbes show a mixture of marine (salt adaptation pathways) and freshwater features, highlighting their transitional nature. CONCLUSIONS: The plethora of freshwater isolates provided here, in terms of trophic status preference and genetic diversity, exemplifies their ability to colonize ecologically diverse waters across the globe. Moreover, a trend towards larger and more flexible/adaptive genomes in freshwater picocyanobacteria may hint at a wider number of ecological niches in this environment compared to the relatively homogeneous marine system.

α-cyanobacteria possessing form IA RuBisCO globally dominate aquatic habitats.

RuBisCO (ribulose 1,5-bisphosphate carboxylase/oxygenase) is one the most abundant enzymes on Earth. Virtually all food webs depend on its activity to supply fixed carbon. In aerobic environments, RuBisCO struggles to distinguish efficiently between CO2 and O2. To compensate, organisms have evolved convergent solutions to concentrate CO2 around the active site. The genetic engineering of such inorganic carbon concentrating mechanisms (CCMs) into plants could help facilitate future global food security for humankind. In bacteria, the carboxysome represents one such CCM component, of which two independent forms exist: α and ß. Cyanobacteria are important players in the planet's carbon cycle and the vast majority of the phylum possess a ß-carboxysome, including most cyanobacteria used as laboratory models. The exceptions are the exclusively marine Prochlorococcus and Synechococcus that numerically dominate open ocean systems. However, the reason why marine systems favor an α-form is currently unknown. Here, we report the genomes of 58 cyanobacteria, closely related to marine Synechococcus that were isolated from freshwater lakes across the globe. We find all these isolates possess α-carboxysomes accompanied by a form 1A RuBisCO. Moreover, we demonstrate α-cyanobacteria dominate freshwater lakes worldwide. Hence, the paradigm of a separation in carboxysome type across the salinity divide does not hold true, and instead the α-form dominates all aquatic systems. We thus question the relevance of ß-cyanobacteria as models for aquatic systems at large and pose a hypothesis for the reason for the success of the α-form in nature.

Integrated approach towards quantifying carbon dioxide and methane release from waste stabilization ponds.

Accurate estimations of gaseous emissions and carbon sequestration in wastewater processing are essential for the design, operation and planning of treatment infrastructure, particularly considering greenhouse gas reduction targets. In this study, we look at the interplay between biological productivity, hydrodynamics and evasion of carbon-based greenhouse gases (GHG) through diffusion and ebullition in order to provide direction for more accurate assessments of their emissions from waste stabilization ponds (WSPs). The ponds stratified in the day and mixed at night. Buoyancy flux contributed between 40 and 75% to turbulence in the water column during nocturnal cooling events, and the associated mixing lead to increasing carbon dioxide (CO2) and methane (CH4) concentrations by up to an order of magnitude in the surface. The onset of stratification and phytoplankton surface blooms, associated with high pH as well as low and variable CO2 partial pressure resulted in an overall reduction of CO2 efflux. Ebullition represented between 40 and 99% of the total CH4 efflux, and up to 95% of the integrated GHG release during wastewater treatment (in CO2 equivalents). Hydrodynamic conditions, diurnal variability and ebullition need to be accounted for reliable assessments of GHG emissions from WSPs. Our study is an important step towards gaining a deeper understanding in the functioning of these hot spots of carbon processing. The contribution of WSPs to atmospheric GHG budget is likely to increase with population growth unless their performance is improved in this regard.

Effects of phytoplankton blooms on fluxes and emissions of greenhouse gases in a eutrophic lake.

Lakes are important sources of greenhouse gases (GHGs) to the atmosphere. Factors controlling CO2, CH4 and N2O fluxes include eutrophication and warming, but the integrated influence of climate-warming-driven stratification, oxygen loss and resultant changes in bloom characteristics on GHGs are not well understood. Here we assessed the influence of contrasting meteorological conditions on stratification and phytoplankton bloom composition in a eutrophic lake, and tested for associated changes in GHGs inventories in both the shallow and deep waters, over three seasons (2010-2012). Atmospheric heatwaves had one of the most dramatic effects on GHGs. Indeed, cyanobacterial blooms that developed in response to heatwave events in 2012 enhanced both sedimentary CH4 concentrations (reaching up to 1mM) and emissions to the atmosphere (up to 8 mmol m-2 d-1). That summer, CH4 contributed 52% of the integrated warming potential of GHGs produced in the lake (in CO2 equivalents) as compared to between 34 and 39% in years without cyanobacterial blooms. High CH4 accumulation and subsequent emission in 2012 were preceded by CO2 and N2O consumption and under-saturation at the lake surface (uptakes at -30 mmol m-2 d-1 and -1.6 µmol m-2 d-1, respectively). Fall overturn presented a large efflux of N2O and CH4, particularly from the littoral zone after the cyanobacterial bloom. We provide evidence that, despite cooling observed at depth during hot summers, CH4 emissions increased via stronger stratification and surface warming, resulting in enhanced cyanobacterial biomass deposition and intensified bottom water anoxia. Our results, supported by recent literature reports, suggests a novel interplay between climate change effects on lake hydrodynamics that impacts both bloom characteristics and GHGs production in shallow eutrophic lakes. Given global trends of warming and enrichment, these interactive effects should be considered to more accurately predict the future global role of lakes in GHG emissions.

Tapping Freshwaters for Methane and Energy.

Energy supply limits development through fuel constraints and climatic effects. Production of renewable energy is a central pillar of sustainability but will need to play an increasingly important role in energy generation in order to mitigate fossil-fuel based greenhouse-gas emissions. Global freshwaters represent a vast reservoir of biomass and biogenic CH4. Here we demonstrate the great potential for the optimized use of this nonfossil carbon as a source of energy that is replenishable within a human lifetime. The feasibility of up-scaled adsorption-driven technologies to capture and refine aqueous CH4 still awaits verification, yet recent estimates of global freshwater CH4 production imply that the worldwide energy demand could be satisfied by using the "biofuel" building up in lakes and wetlands. Biogenic CH4 is mostly generated from biomass produced through atmospheric CO2 uptake. Its exploitation in freshwaters can thus secure large amounts of carbon-neutral energy, helping to sustain the planetary equilibrium.

The biogeochemical variability of Arctic thermokarst ponds is reflected by stochastic and niche-driven microbial community assembly processes.

Shallow thermokarst ponds are a conspicuous landscape element of the Arctic Siberian tundra with high biogeochemical variability. Little is known about how microbes from the regional species pool assemble into local pond communities and how the resulting patterns affect functional properties such as dissolved organic carbon (DOC) remineralization and greenhouse gas (GHG) turnover. We analysed the pelagic microbiomes of 20 ponds in north-eastern Siberia in the context of their physico-chemical properties. Ponds were categorized as polygonal or trough according to their geomorphological origin. The diversity of bacteria and eukaryotic microbes was assessed by ribosomal gene tag sequencing. Null model analysis revealed an important role of stochastic assembly processes within ponds of identical origin, in particular for genotypes only occurring in few systems. Nevertheless, the two pond types clearly represented distinct niches for both the bacterial and eukaryotic microbial communities. Carbon dioxide concentration, indicative of heterotrophic microbial processes, varied greatly, especially in the trough ponds. Methane concentrations were lower in polygonal ponds and were correlated with the estimated abundance of methanotrophs. Thus, the overall functional variability of Arctic ponds reflects the stochastic assembly of their microbial communities. Distinct functional subcommunities can, nevertheless, be related to GHG concentrations.

Effects of climate change and episodic heat events on cyanobacteria in a eutrophic polymictic lake.

Mixing regime and CO2 availability may control cyanobacterial blooms in polymictic lakes, but the underlying mechanisms still remain unclear. We integrated detailed results from a natural experiment comprising an average-wet year (2011) and one with heat waves (2012), a long-term meteorological dataset (1960-2010), historical phosphorus concentrations and sedimentary pigment records, to determine the mechanistic controls of cyanobacterial blooms in a eutrophic polymictic lake. Intense warming in 2012 was associated with: 1) increased stability of the water column with buoyancy frequencies exceeding 40 cph at the surface, 2) high phytoplankton biomass in spring (up to 125 mg WW L-1), 3) reduced downward transport of heat and 4) depleted epilimnetic CO2 concentrations. CO2 depletion was maintained by intense uptake by phytoplankton (influx up to 30 mmol m-2 d-1) in combination with reduced, internal and external, carbon inputs during dry, stratified periods. These synergistic effects triggered bloom of buoyant cyanobacteria (up to 300 mg WW L-1) in the hot year. Complementary evidence from polynomial regression modelling using historical data and pigment record revealed that warming explains 78% of the observed trends in cyanobacterial biomass, whereas historical phosphorus concentration only 10% thereof. Together the results from the natural experiment and the long-term record indicate that effects of hotter and drier climate are likely to increase water column stratification and decrease CO2 availability in eutrophic polymictic lakes. This combination will catalyze blooms of buoyant cyanobacteria.

Greenhouse gas emissions from waste stabilisation ponds in Western Australia and Quebec (Canada).

Waste stabilisation ponds (WSPs) are highly enriched environments that may emit large quantities of greenhouse gases (GHG), including CO2, CH4 and N2O. However, few studies provide detailed reports on these emissions. In the present study, we investigated GHG emissions from WSPs in Western Australia and Quebec, Canada, and compared emissions to WSPs from other climatic regions and to other types of aquatic ecosystems. Surface water GHG concentrations were related to phytoplankton biomass and nutrients. The CO2 was either emitted or absorbed by WSPs, largely as a function of phytoplankton dynamics and strong stratification in these shallow systems, whereas efflux of CH4 and N2O to the atmosphere was always observed albeit with highly variable emission rates, dependent on treatment phase and time of the day. The total global warming potential index (GWP index, calculated as CO2 equivalent) of emitted GHG from WSPs in Western Australia averaged 12.8 mmol m(-2) d(-1) (median), with CO2, CH4 and N2O respectively contributing 0%, 96.7% and 3.3% of the total emissions, while in Quebec WSPs this index was 194 mmol m(-2) d(-1), with a relative contribution of 93.8, 3.0 and 3.2% respectively. The CO2 fluxes from WSPs were of the same order of magnitude as those reported in hydroelectric reservoirs and constructed wetlands in tropical climates, whereas CH4 fluxes were considerably higher compared to other aquatic ecosystems. N2O fluxes were in the same range of values reported for WSPs in subtropical climate.

Heat-Wave Effects on Oxygen, Nutrients, and Phytoplankton Can Alter Global Warming Potential of Gases Emitted from a Small Shallow Lake.

Increasing air temperatures may result in stronger lake stratification, potentially altering nutrient and biogenic gas cycling. We assessed the impact of climate forcing by comparing the influence of stratification on oxygen, nutrients, and global-warming potential (GWP) of greenhouse gases (the sum of CH4, CO2, and N2O in CO2 equivalents) emitted from a shallow productive lake during an average versus a heat-wave year. Strong stratification during the heat wave was accompanied by an algal bloom and chemically enhanced carbon uptake. Solar energy trapped at the surface created a colder, isolated hypolimnion, resulting in lower ebullition and overall lower GWP during the hotter-than-average year. Furthermore, the dominant CH4 emission pathway shifted from ebullition to diffusion, with CH4 being produced at surprisingly high rates from sediments (1.2-4.1 mmol m(-2) d(-1)). Accumulated gases trapped in the hypolimnion during the heat wave resulted in a peak efflux to the atmosphere during fall overturn when 70% of total emissions were released, with littoral zones acting as a hot spot. The impact of climate warming on the GWP of shallow lakes is a more complex interplay of phytoplankton dynamics, emission pathways, thermal structure, and chemical conditions, as well as seasonal and spatial variability, than previously reported.

Climate Effects on High Latitude Daphnia via Food Quality and Thresholds.

Climate change is proceeding rapidly at high northern latitudes and may have a variety of direct and indirect effects on aquatic food webs. One predicted effect is the potential shift in phytoplankton community structure towards increased cyanobacterial abundance. Given that cyanobacteria are known to be a nutritionally poor food source, we hypothesized that such a shift would reduce the efficiency of feeding and growth of northern zooplankton. To test this hypothesis, we first isolated a clone of Daphnia pulex from a permafrost thaw pond in subarctic Québec, and confirmed that it was triploid but otherwise genetically similar to a diploid, reference clone of the same species isolated from a freshwater pond in southern Québec. We used a controlled flow-through system to investigate the direct effect of temperature and indirect effect of subarctic picocyanobacteria (Synechococcus) on threshold food concentrations and growth rate of the high latitude clone. We also compared the direct effect of temperature on both Daphnia clones feeding on eukaryotic picoplankton (Nannochloropsis). The high latitude clone had a significantly lower food threshold for growth than the temperate clone at both 18 and 26°C, implying adaptation to lower food availability even under warmer conditions. Polyunsaturated fatty acids were present in the picoeukaryote but not the cyanobacterium, confirming the large difference in food quality. The food threshold for growth of the high latitude Daphnia was 3.7 (18°C) to 4.2 (26°C) times higher when fed Synechococcus versus Nannochloropsis, and there was also a significant negative effect of increased temperature and cyanobacterial food on zooplankton fatty acid content and composition. The combined effect of temperature and food quality on the performance of the high latitude Daphnia was greater than their effects added separately, further indicating the potentially strong indirect effects of climate warming on aquatic food web processes.