Search

Boreal rivers transport and process large amounts of organic and inorganic materials derived from their catchments, yet quantitative estimates and patterns of carbon (C) transport and emissions in these large rivers are scarce relative to those of high-latitude lakes and headwater streams. Here, we present the results of a large-scale survey of 23 major rivers in northern Québec sampled during the summer period of 2010, which aimed to determine the magnitude and spatial variability of different C species (carbon dioxide - CO 2 , methane - CH 4 , total carbon - TC, dissolved organic carbon - DOC and inorganic carbon - DIC), as well as to identify their main drivers. In addition, we constructed a first order mass balance of total riverine C emissions to the atmosphere (outgassing from the main river channel) and export to the ocean over summer. All rivers were supersaturated in pCO 2 and pCH 4 (partial pressure of CO 2 and CH 4 ), and the resulting fluxes varied widely among rivers, especially the CH 4 . There was a positive relationship between DOC and gas concentrations, suggesting a common watershed source of these C species. DOC concentrations declined as a function of % land surface covered by water (lentic + lotic systems) in the watershed, suggesting that lentic systems may act as a net sink of organic matter in the landscape. The C balance suggests that the export component is higher than atmospheric C emissions in the river channel. However, for heavily dammed rivers, C emissions to the atmosphere approaches the C export component. Such studies are highly important for the overall efforts to effectively quantify and incorporate major boreal rivers into whole-landscape C budgets, to determine the net role of these ecosystems as C sinks or sources, and to predict how these might shift under anthropogenic pressures and dynamic climate conditions., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 Elsevier B.V. All rights reserved.)

In this Perspective, we put forward an integrative framework to improve estimates of land-atmosphere carbon exchange based on the accumulation of carbon in the landscape as constrained by its lateral export through rivers. The framework uses the watershed as the fundamental spatial unit and integrates all terrestrial and aquatic ecosystems as well as their hydrologic carbon exchanges. Application of the framework should help bridge the existing gap between land and atmosphere-based approaches and offers a platform to increase communication and synergy among the terrestrial, aquatic, and atmospheric research communities that is paramount to advance landscape carbon budget assessments., (© 2023. The Author(s).)

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., (© The Author(s) 2022. Published by Oxford University Press on behalf of the National Academy of Sciences.)

During transit from soils to the ocean, microbial communities are modified and re-assembled, generating complex patterns of ecological succession. The potential effect of upstream assembly on downstream microbial community composition is seldom considered within aquatic networks. Here, we reconstructed the microbial succession along a land-freshwater-estuary continuum within La Romaine river watershed in Northeastern Canada. We captured hydrological seasonality and differentiated the total and reactive community by sequencing both 16 S rRNA genes and transcripts. By examining how DNA- and RNA-based assemblages diverge and converge along the continuum, we inferred temporal shifts in the relative importance of assembly processes, with mass effects dominant in spring, and species selection becoming stronger in summer. The location of strongest selection within the network differed between seasons, suggesting that selection hotspots shift depending on hydrological conditions. The unreactive fraction (no/minor RNA contribution) was composed of taxa with diverse potential origins along the whole aquatic network, while the majority of the reactive pool (major RNA contribution) could be traced to soil/soilwater-derived taxa, which were distributed along the entire rank-abundance curve. Overall, our findings highlight the importance of considering upstream history, hydrological seasonality and the reactive microbial fraction to fully understand microbial community assembly on a network scale., (© 2021. The Author(s).)

Theory predicts that population genetic structure and metacommunity structure are linked by the common processes of drift and migration, but how population genetic structure and metacommunity structure are related in nature is still unknown. Deeper understanding of the processes influencing both genetic and community diversity is vital for better predicting how environmental change will impact biodiversity patterns. We examined how crustacean zooplankton and rotifer species' metapopulation genetic structure and metacommunities respond to environmental and spatial variation both within and across four regions of boreal Canada. Metapopulation and metacommunity variation partitioning results were compared within and across the four regions. Metapopulations and metacommunities responded differently to environmental variation and spatial structure both within and across regions, as metapopulations were influenced by different environmental variables compared to metacommunities. At larger spatial scales both metapopulations and metacommunities exhibited greater spatial and environmental structuring, again responding to a different subset of environmental variables. Our findings suggest that even though both genetic and species diversity are linked by the same processes, regional variation in environmental characteristics and spatial structure influence resulting biodiversity patterns differently. To date, no other empirical research has explored relationships between entire metapopulation and metacommunity assemblages at large regional spatial scales., (© 2020 by the Ecological Society of America.)

Quantifying metabolic rates in lakes and other aquatic ecosystems is a complex task, as methods are continually evolving and are not currently standardized. Recently, Peeters et al. presented a valuable simulated dataset that advances the field by comparing the strengths and limitations of individual and combined metabolic techniques. The authors conclude that calculating metabolic rates from point sampling and mass balancing of surface water oxygen concentration and isotope composition is flawed, because the technique does not capture sub-daily patterns of metabolic variability, which they argue invalidates past applications and interpretations. These conclusions are inconsistent with how the method has been used, and are based on a biased construction of scenarios and interpretation of model results, especially because their parameterization of the stable isotopic model employs input values that appear unrepresentative of most lake conditions. Here, we establish that 1) empirical evidence supports the isotopic approach's suitability to approximate daily or longer metabolic patterns in most lakes. 2) The authors' own simulations show agreement between metabolic estimates from point isotopic measurements and average metabolic rates under most scenarios. 3) The authors' invalidation of isotopic measurements are based on the most extreme model deviations observed in simulated hypereutrophic environments. While we welcome a critical evaluation of the isotopic approach, we argue that isotopic model uncertainty needs to be placed within an appropriate context. We emphasize that isotopic sampling and steady state metabolic modelling has a key role to play in constraining metabolic patterns in the global lake landscape, but that the research questions addressed with the method need to be commensurate with the limitations and uncertainties of the approach., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2020 Elsevier Ltd. All rights reserved.)

Increased incorporation of terrestrial organic matter (t-OM) into consumer biomass (allochthony) is believed to reduce growth capacity. In this study, we examined the relationship between crustacean zooplankton allochthony and production in a boreal lake that displays strong seasonal variability in t-OM inputs. Contrary to our hypotheses, we found no effect of allochthony on production at the community and the species levels. The high-frequency seasonal sampling (time-for-space) allowed for estimating the efficiency of zooplankton in converting this external carbon source to growth. From the daily t-OM inputs in the lake (57-3,027 kg C/d), the zooplankton community transferred 0.2% into biomass (0.01-2.36 kg C/d); this level was of the same magnitude as the carbon transfer efficiency for algal-derived carbon (0.4%). In the context of the boundless carbon cycle, which integrates inland waters as a biologically active component of the terrestrial landscape, the use of the time-for-space approach for the quantifying of t-OM trophic transfer efficiency by zooplankton is a critical step toward a better understanding of the effects of increasing external carbon fluxes on pelagic food webs., (© 2020 The Authors. Ecology published by Wiley Periodicals, Inc. on behalf of Ecological Society of America.)

Streams and rivers are now recognized to be sites of intense carbon (C) emissions, yet the lack of C emission estimates that integrate beyond individual river systems has slowed their inclusion in landscape C budgets. Here we apply empirical models of CO 2 and CH 4 concentrations and gas exchange continuously along entire fluvial networks to derive the total fluvial CO 2 and CH 4 emissions in large (3000 to 30,000 km 2 ) watersheds located across the boreal biome of Québec (Canada). We assess how total fluvial network C emissions vary with landscape and climate properties, and compare their magnitude to other components of the landscape C budget. The total fluvial network emissions expressed as per unit watershed area ranged from 0.7 to 29.2 g C m -2  yr -1 for CO 2 , and 4-1780 mg C m -2  yr -1 for CH 4 , and neither was related to watershed area or drainage density. Rather, watershed slope and terrestrial net productivity were major drivers of the integrated network fluvial emissions. We also show that steeper watersheds had a greater proportion of emissions relative to downstream export of C from the watershed. Integrated fluvial emissions are of the same magnitude as the terrestrial C sink, yet these two fundamental components of the boreal landscape C budget are not tightly coupled., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2020 Elsevier Ltd. All rights reserved.)

Aerobic anoxygenic phototrophic (AAP) bacteria are a phylogenetically diverse and ubiquitous group of prokaryotes that use organic matter but can harvest light using bacteriochlorophyll a. Although the factors regulating AAP ecology have long been investigated through field surveys, the few available experimental studies have considered AAPs as a group, thus disregarding the potential differential responses between taxonomically distinct AAP assemblages. Here, we used sequencing of the pufM gene to describe the diversity of AAPs in 10 environmentally distinct temperate lakes, and to investigate the taxonomic responses of AAP communities in these lakes when subjected to similar experimental manipulations of light and predator removal. The studied communities were clearly dominated by Limnohabitans AAP but presented a clear taxonomic segregation between lakes presumably driven by local conditions, which was maintained after experimental manipulations. Predation reduction (but not light exposure) caused significant compositional shifts across most assemblages, but the magnitude of these changes could not be clearly related to changes in bulk AAP abundances or taxonomic richness of AAP assemblages during experiments. Only a few operational taxonomic units, which differed taxonomically between lakes, were found to respond positively during experimental treatments. Our results highlight that different freshwater AAP communities respond differently to similar control mechanisms, highlighting that in-depth knowledge on AAP diversity is essential to understand the ecology and potential role of these photoheterotrophs., (© 2020 John Wiley & Sons Ltd.)

The distribution and quality of water resources vary dramatically across Canada, and human impacts such as land-use and climate changes are exacerbating uncertainties in water supply and security. At the national level, Canada has no enforceable standards for safe drinking water and no comprehensive water-monitoring program to provide detailed, timely reporting on the state of water resources. To provide Canada's first national assessment of lake health, the NSERC Canadian Lake Pulse Network was launched in 2016 as an academic-government research partnership. LakePulse uses traditional approaches for limnological monitoring as well as state-of-the-art methods in the fields of genomics, emerging contaminants, greenhouse gases, invasive pathogens, paleolimnology, spatial modelling, statistical analysis, and remote sensing. A coordinated sampling program of about 680 lakes together with historical archives and a geomatics analysis of over 80,000 lake watersheds are used to examine the extent to which lakes are being altered now and in the future, and how this impacts aquatic ecosystem services of societal importance. Herein we review the network context, objectives and methods., (Copyright © 2019 The Authors. Published by Elsevier B.V. All rights reserved.)

Aerobic methanotrophic bacteria (methanotrophs) use methane as a source of carbon and energy, thereby mitigating net methane emissions from natural sources. Methanotrophs represent a widespread and phylogenetically complex guild, yet the biogeography of this functional group and the factors that explain the taxonomic structure of the methanotrophic assemblage are still poorly understood. Here, we used high-throughput sequencing of the 16S rRNA gene of the bacterial community to study the methanotrophic community composition and the environmental factors that influence their distribution and relative abundance in a wide range of freshwater habitats, including lakes, streams and rivers across the boreal landscape. Within one region, soil and soil water samples were additionally taken from the surrounding watersheds in order to cover the full terrestrial-aquatic continuum. The composition of methanotrophic communities across the boreal landscape showed only a modest degree of regional differentiation but a strong structuring along the hydrologic continuum from soil to lake communities, regardless of regions. This pattern along the hydrologic continuum was mostly explained by a clear niche differentiation between type I and type II methanotrophs along environmental gradients in pH, and methane concentrations. Our results suggest very different roles of type I and type II methanotrophs within inland waters, the latter likely having a terrestrial source and reflecting passive transport and dilution along the aquatic networks, but this is an unresolved issue that requires further investigation., (© 2019 John Wiley & Sons Ltd.)

Translating the ever-increasing wealth of information on microbiomes (environment, host or built environment) to advance our understanding of system-level processes is proving to be an exceptional research challenge. One reason for this challenge is that relationships between characteristics of microbiomes and the system-level processes that they influence are often evaluated in the absence of a robust conceptual framework and reported without elucidating the underlying causal mechanisms. The reliance on correlative approaches limits the potential to expand the inference of a single relationship to additional systems and advance the field. We propose that research focused on how microbiomes influence the systems they inhabit should work within a common framework and target known microbial processes that contribute to the system-level processes of interest. Here, we identify three distinct categories of microbiome characteristics (microbial processes, microbial community properties and microbial membership) and propose a framework to empirically link each of these categories to each other and the broader system-level processes that they affect. We posit that it is particularly important to distinguish microbial community properties that can be predicted using constituent taxa (community-aggregated traits) from those properties that cannot currently be predicted using constituent taxa (emergent properties). Existing methods in microbial ecology can be applied to more explicitly elucidate properties within each of these three categories of microbial characteristics and connect them with each other. We view this proposed framework, gleaned from a breadth of research on environmental microbiomes and ecosystem processes, as a promising pathway with the potential to advance discovery and understanding across a broad range of microbiome science.

Freshwater bacterioplankton communities are influenced by the inputs of material and bacteria from the surrounding landscape, yet few studies have investigated how different terrestrial inputs affect bacterioplankton. We examined whether the addition of soils collected under various tree species combinations differentially influences lake bacterial communities. Lake water was incubated for 6 days following addition of five different soils. We assessed the taxonomic composition (16S rRNA gene sequencing) and metabolic activity (Biolog Ecoplates) of lake bacteria with and without soil addition, and compared these to initial soil communities. Soil bacterial assemblages showed a strong influence of tree composition, but such community differences were not reflected in the structure of lake communities that developed during the experiment. Bacterial taxa showing the largest abundance increases during incubation were initially present in both lake water and across most soils, and were related to Cytophagales, Burkholderiales and Rhizobiales. No clear metabolic profiles based on inoculum source were found, yet soil-amended communities used 60% more substrate than non-inoculated communities. Overall, we show that terrestrial inputs influence aquatic communities by stimulating the growth and activity of certain ubiquitous taxa distributed across the terrestrial-aquatic continuum, yet different forest soils did not cause predictable changes in lake bacterioplankton assemblages.

Hardwater lakes are common in human-dominated regions of the world and often experience pollution due to agricultural and urban effluent inputs of inorganic and organic nitrogen (N). Although these lakes are landscape hotspots for CO2 exchange and food web carbon (C) cycling, the effect of N enrichment on hardwater lake food web functioning and C cycling patterns remains unclear. Specifically, it is unknown if different eutrophication scenarios (e.g., modest non point vs. extreme point sources) yield consistent effects on auto- and heterotrophic C cycling, or how biotic responses interact with the inorganic C system to shape responses of air-water CO2 exchange. To address this uncertainty, we induced large metabolic gradients in the plankton community of a hypereutrophic hardwater Canadian prairie lake by adding N as urea (the most widely applied agricultural fertilizer) at loading rates of 0, 1, 3, 8 or 18 mg N L-1 week-1 to 3240-L, in-situ mesocosms. Over three separate 21-day experiments, all treatments of N dramatically increased phytoplankton biomass and gross primary production (GPP) two- to six-fold, but the effects of N on autotrophs plateaued at ~3 mg N L-1. Conversely, heterotrophic metabolism increased linearly with N fertilization over the full treatment range. In nearly all cases, N enhanced net planktonic uptake of dissolved inorganic carbon (DIC), and increased the rate of CO2 influx, while planktonic heterotrophy and CO2 production only occurred in the highest N treatments late in each experiment, and even in these cases, enclosures continued to in-gas CO2. Chemical effects on CO2 through calcite precipitation were also observed, but similarly did not change the direction of net CO2 flux. Taken together, these results demonstrate that atmospheric exchange of CO2 in eutrophic hardwater lakes remains sensitive to increasing N loading and eutrophication, and that even modest levels of N pollution are capable of enhancing autotrophy and CO2 in-gassing in P-rich lake ecosystems.

Recent experimental evidence suggests that changes in the partial pressure of CO 2 (pCO 2 ), in concert with nutrient fertilisation, may result in increased primary production and shifted phytoplankton community composition that favours species lacking adaptations to low CO 2 environments. It is not clear whether these results apply in ambient freshwaters, which are already often supersaturated in CO 2 , and where phytoplankton structure and activity are under complex control of diverse local and regional factors. Here, we use a large-scale comparative study of 69 boreal lakes to explore the influence of existing CO 2 gradients (c. 50-2300 μatm) on phytoplankton community composition and biomass production. While community composition did not respond to pCO 2 gradients, gross primary production was enhanced, but only in lakes already supersaturated in CO 2 , demonstrating that environmental context is key in determining pCO 2 -phytoplankton interactions. We further argue that increased atmospheric CO 2 is unlikely to influence phytoplanktonic composition and production in northern lakes., (© 2017 John Wiley & Sons Ltd/CNRS.)

Seed banks are believed to contribute to compositional changes within and across microbial assemblages, but the application of this concept to natural communities remains challenging. Here we describe the core seed bank of a bacterial metacommunity from a boreal watershed, using the spatial distribution of bacterial operational taxonomic units (OTUs) across 223 heterogeneous terrestrial, aquatic and phyllosphere bacterial assemblages. Taxa were considered potential seeds if they transitioned from rare to abundant somewhere within the metacommunity and if they were ubiquitous and able to persist under unfavorable conditions, the latter assessed by checking their presence in three deeply sequenced samples (one soil, one river and one lake, 2.2-3 million reads per sample). We show that only a small fraction (13%) of all detected OTUs constitute a metacommunity seed bank that is shared between all terrestrial and aquatic communities, but not by phyllosphere assemblages, which seem to recruit from a different taxa pool. Our results suggest directional recruitment driven by the flow of water in the landscape, since most aquatic sequences were associated to OTUs found in a single deeply-sequenced soil sample, but only 45% of terrestrial sequences belonged to OTUs found in the two deeply-sequenced aquatic communities. Finally, we hypothesize that extreme rarity, and its interplay with water residence time and growth rates, may further constrain the size of the potential seed bank.

One of the major contemporary challenges in microbial ecology has been to discriminate the reactive core from the random, unreactive components of bacterial communities. In previous work we used the spatial abundance distributions of bacterioplankton across boreal lakes of Québec to group taxa into four distinct categories that reflect either hydrology-mediated dispersal along the aquatic network or environmental selection mechanisms within lakes. Here, we test whether this categorization derived from the spatial distribution of taxa is maintained over time, by analyzing the temporal dynamics of the operational taxonomic units (OTUs) within those spatially derived categories along an annual cycle in the oligotrophic lake Croche (Québec, Canada), and assessing the coherence in the patterns of abundance, occurrence, and environmental range of these OTUs over space and time. We report that the temporal dynamics of most taxa within a single lake are largely coherent with those derived from their spatial distribution over large spatial scales, suggesting that these properties must be intrinsic of particular taxa. We also identified a set of rare taxa cataloged as having a random occupancy based on their spatial distribution, but which showed clear seasonality and abundance peaks along the year, yet these comprised a very small fraction of the total rare OTUs. We conclude that the presence of most rare bacterioplankton taxa in boreal lakes is random, since both their temporal and spatial dynamics suggest links to passive downstream transport and persistence in freshwater networks, rather than environmental selection.

Widespread evidence that organic matter exported from terrestrial into aquatic ecosystems supports recipient food webs remains controversial. A pressing question is not only whether high terrestrial support is possible but also what the general conditions are under which it arises. We assemble the largest data set, to date, of the isotopic composition (δ 2 H, δ 13 C, and δ 15 N) of lake zooplankton and the resources at the base of their associated food webs. In total, our data set spans 559 observations across 147 lakes from the boreal to subtropics. By predicting terrestrial resource support from within-lake and catchment-level characteristics, we found that half of all consumer observations that is, the median were composed of at least 42% terrestrially derived material. In general, terrestrial support of zooplankton was greatest in lakes with large physical and hydrological connections to catchments that were rich in aboveground and belowground organic matter. However, some consumers responded less strongly to terrestrial resources where within-lake production was elevated. Our study shows that multiple mechanisms drive widespread cross-ecosystem support of aquatic consumers across Northern Hemisphere lakes and suggests that changes in terrestrial landscapes will influence ecosystem processes well beyond their boundaries.

Streams are typically supersaturated in carbon dioxide (CO 2 ) and methane (CH 4 ), and are recognized as important components of regional carbon (C) emissions in northern landscapes. Whereas there is consensus that in most of the systems the CO 2 emitted by streams represents C fixed in the terrestrial ecosystem, the pathways delivering this C to streams are still not well understood. We assessed the contribution of direct soil CO 2 injection versus the oxidation of soil-derived dissolved organic C (DOC) and CH 4 in supporting CO 2 supersaturation in boreal streams in Québec. We measured the concentrations of CO 2 , CH 4 and DOC in 43 streams and adjacent soil waters during summer base-flow period. A mass balance approach revealed that all three pathways are significant, and that the mineralization of soil-derived DOC and CH 4 accounted for most of the estimated stream CO 2 emissions (average 75% and 10%, respectively), and that these estimated contributions did not change significantly between the studied low order (≤3) streams. Whereas some of these transformations take place in the channel proper, our results suggest that they mainly occur in the hyporheic zones of the streams. Our results further show that stream CH 4 emissions can be fully explained by soil CH 4 inputs. This study confirms that these boreal streams, and in particular their hyporheic zones, are extremely active processors of soil derived DOC and CH 4 , not just vents for soil produced CO 2 ., (Copyright © 2016 Elsevier B.V. All rights reserved.)

Aquatic bacterial communities harbour thousands of coexisting taxa. To meet the challenge of discriminating between a 'core' and a sporadically occurring 'random' component of these communities, we explored the spatial abundance distribution of individual bacterioplankton taxa across 198 boreal lakes and their associated fluvial networks (188 rivers). We found that all taxa could be grouped into four distinct categories based on model statistical distributions (normal like, bimodal, logistic and lognormal). The distribution patterns across lakes and their associated river networks showed that lake communities are composed of a core of taxa whose distribution appears to be linked to in-lake environmental sorting (normal-like and bimodal categories), and a large fraction of mostly rare bacteria (94% of all taxa) whose presence appears to be largely random and linked to downstream transport in aquatic networks (logistic and lognormal categories). These rare taxa are thus likely to reflect species sorting at upstream locations, providing a perspective of the conditions prevailing in entire aquatic networks rather than only in lakes., (© 2016 John Wiley & Sons Ltd/CNRS.)

Disentangling the mechanisms shaping bacterioplankton communities across freshwater ecosystems requires considering a hydrologic dimension that can influence both dispersal and local sorting, but how the environment and hydrology interact to shape the biogeography of freshwater bacterioplankton over large spatial scales remains unexplored. Using Illumina sequencing of the 16S ribosomal RNA gene, we investigate the large-scale spatial patterns of bacterioplankton across 386 freshwater systems from seven distinct regions in boreal Québec. We show that both hydrology and local water chemistry (mostly pH) interact to shape a sequential structuring of communities from highly diverse assemblages in headwater streams toward larger rivers and lakes dominated by fewer taxa. Increases in water residence time along the hydrologic continuum were accompanied by major losses of bacterial richness and by an increased differentiation of communities driven by local conditions (pH and other related variables). This suggests that hydrology and network position modulate the relative role of environmental sorting and mass effects on community assembly by determining both the time frame for bacterial growth and the composition of the immigrant pool. The apparent low dispersal limitation (that is, the lack of influence of geographic distance on the spatial patterns observed at the taxonomic resolution used) suggests that these boreal bacterioplankton communities derive from a shared bacterial pool that enters the networks through the smallest streams, largely dominated by mass effects, and that is increasingly subjected to local sorting of species during transit along the hydrologic continuum.

Aerobic anoxygenic phototrophic (AAP) bacteria are photoheterotrophs that despite their low abundances have been hypothesized to play an ecologically and biogeochemically important role in aquatic systems. Characterizing this role requires a better understanding of the in situ dynamics and activity of AAP bacteria. Here we provide the first assessment of the single-cell activity of freshwater AAP bacteria and their contribution to total bacterial production across lakes spanning a wide trophic gradient, and explore the role of light in regulating AAP activity. The proportion of cells that were active in leucine incorporation and the level of activity per cell were consistently higher for AAP than for bulk bacteria across lakes. As a result, AAP bacteria contributed disproportionately more to total bacterial production than to total bacterial abundance. Interestingly, although environmentally driven patterns in activity did not seem to differ largely between AAP and bulk bacteria, their response to light did, and exposure to light resulted in increases in the proportion of active AAP bacteria with no clear effect on their cell-specific activity. This suggests that light may play a role in the activation of AAP bacteria, enabling these photoheterotrophs to contribute more to the carbon cycle than suggested by their abundance.

Here we explore strategies of resource utilization and allocation of algal versus terrestrially derived carbon (C) by lake bacterioplankton. We quantified the consumption of terrestrial and algal dissolved organic carbon, and the subsequent allocation of these pools to bacterial growth and respiration, based on the δ(13)C isotopic signatures of bacterial biomass and respiratory carbon dioxide (CO2). Our results confirm that bacterial communities preferentially remove algal C from the terrestrially dominated organic C pool of lakes, but contrary to current assumptions, selectively allocate this autochthonous substrate to respiration, whereas terrestrial C was preferentially allocated to biosynthesis. The results provide further evidence of a mechanism whereby inputs of labile, algal-derived organic C may stimulate the incorporation of a more recalcitrant, terrestrial C pool. This mechanism resulted in a counterintuitive pattern of high and relatively constant levels of allochthony (~76%) in bacterial biomass across lakes that otherwise differ greatly in productivity and external inputs.

Freshwater ecosystems are strongly influenced by both climate and the surrounding landscape, yet the specific pathways connecting climatic and landscape drivers to the functioning of lake ecosystems are poorly understood. Here, we hypothesize that the links that exist between spatial patterns in climate and landscape properties and the spatial variation in lake carbon (C) cycling at regional scales are at least partly mediated by the movement of terrestrial dissolved organic carbon (DOC) in the aquatic component of the landscape. We assembled a set of indicators of lake C cycling (bacterial respiration and production, chlorophyll a, production to respiration ratio, and partial pressure of CO2 ), DOC concentration and composition, and landscape and climate characteristics for 239 temperate and boreal lakes spanning large environmental and geographic gradients across seven regions. There were various degrees of spatial structure in climate and landscape features that were coherent with the regionally structured patterns observed in lake DOC and indicators of C cycling. These different regions aligned well, albeit nonlinearly along a mean annual temperature gradient; whereas there was a considerable statistical effect of climate and landscape properties on lake C cycling, the direct effect was small and the overall effect was almost entirely overlapping with that of DOC concentration and composition. Our results suggest that key climatic and landscape signals are conveyed to lakes in part via the movement of terrestrial DOC to lakes and that DOC acts both as a driver of lake C cycling and as a proxy for other external signals., (© 2015 John Wiley & Sons Ltd.)

Northern forests are important ecosystems for carbon (C) cycling and lakes within them process and bury large amounts of organic-C. Current burial estimates are poorly constrained and may discount other shifts in organic-C burial driven by global change. Here we analyse a suite of northern lakes to determine trends in organic-C burial throughout the Anthropocene. We found burial rates increased significantly over the last century and are up to five times greater than previous estimates. Despite a correlation with temperature, warming alone did not explain the increase in burial, suggesting the importance of other drivers including atmospherically deposited reactive nitrogen. Upscaling mean lake burial rates for each time period to global northern forests yields up to 4.5 Pg C accumulated in the last 100 years--20% of the total burial over the Holocene. Our results indicate that lakes will become increasingly important for C burial under future global change scenarios.

There is now evidence that aerobic anoxygenic phototrophic (AAP) bacteria are widespread across aquatic systems, yet the factors that determine their abundance and activity are still not well understood, particularly in freshwaters. Here we describe the patterns in AAP abundance, cell size and pigment content across wide environmental gradients in 43 temperate and boreal lakes of Québec. AAP bacterial abundance varied from 1.51 to 5.49 x 105 cells mL-1, representing <1 to 37% of total bacterial abundance. AAP bacteria were present year-round, including the ice-cover period, but their abundance relative to total bacterial abundance was significantly lower in winter than in summer (2.6% and 7.7%, respectively). AAP bacterial cells were on average two-fold larger than the average bacterial cell size, thus AAP cells made a greater relative contribution to biomass than to abundance. Bacteriochlorophyll a (BChla) concentration varied widely across lakes, and was not related to AAP bacterial abundance, suggesting a large intrinsic variability in the cellular pigment content. Absolute and relative AAP bacterial abundance increased with dissolved organic carbon (DOC), whereas cell-specific BChla content was negatively related to chlorophyll a (Chla). As a result, both the contribution of AAP bacteria to total prokaryotic abundance, and the cell-specific BChla pigment content were positively correlated with the DOC:Chla ratio, both peaking in highly colored, low-chlorophyll lakes. Our results suggest that photoheterotrophy might represent a significant ecological advantage in highly colored, low-chlorophyll lakes, where DOC pool is chemically and structurally more complex.

Lakes are a major component of boreal landscapes, and whereas lake CO2 emissions are recognized as a major component of regional C budgets, there is still much uncertainty associated to lake CH4 fluxes. Here, we present a large-scale study of the magnitude and regulation of boreal lake summer diffusive CH4 fluxes, and their contribution to total lake carbon (C) emissions, based on in situ measurements of concentration and fluxes of CH4 and CO2 in 224 lakes across a wide range of lake type and environmental gradients in Québec. The diffusive CH4 flux was highly variable (mean 11.6 ± 26.4 SD mg m(-2)  d(-1) ), and it was positively correlated with temperature and lake nutrient status, and negatively correlated with lake area and colored dissolved organic matter (CDOM). The relationship between CH4 and CO2 concentrations fluxes was weak, suggesting major differences in their respective sources and/or regulation. For example, increasing water temperature leads to higher CH4 flux but does not significantly affect CO2 flux, whereas increasing CDOM concentration leads to higher CO2 flux but lower CH4 flux. CH4 contributed to 8 ± 23% to the total lake C emissions (CH4  + CO2 ), but 18 ± 25% to the total flux in terms of atmospheric warming potential, expressed as CO2 -equivalents. The incorporation of ebullition and plant-mediated CH4 fluxes would further increase the importance of lake CH4 . The average Q10 of CH4 flux was 3.7, once other covarying factors were accounted for, but this apparent Q10 varied with lake morphometry and was higher for shallow lakes. We conclude that global climate change and the resulting shifts in temperature will strongly influence lake CH4 fluxes across the boreal biome, but these climate effects may be altered by regional patterns in lake morphometry, nutrient status, and browning., (© 2014 John Wiley & Sons Ltd.)

Methanogenesis has traditionally been assumed to occur only in anoxic environments, yet there is mounting, albeit indirect, evidence of methane (CH4) production in oxic marine and freshwaters. Here we present the first direct, ecosystem-scale demonstration of methanogenesis in oxic lake waters. This methanogenesis appears to be driven by acetoclastic production, and is closely linked to algal dynamics. We show that oxic water methanogenesis is a significant component of the overall CH4 budget in a small, shallow lake, and provide evidence that this pathway may be the main CH4 source in large, deep lakes and open oceans. Our results challenge the current global understanding of aquatic CH4 dynamics, and suggest a hitherto unestablished link between pelagic CH4 emissions and surface-water primary production. This link may be particularly sensitive to widespread and increasing human influences on aquatic ecosystem primary productivity.

Dissolved organic matter (DOM) is a master variable in aquatic systems. Modern fluorescence techniques couple measurements of excitation emission matrix (EEM) spectra and parallel factor analysis (PARAFAC) to determine fluorescent DOM (FDOM) components and DOM quality. However, the molecular signatures associated with PARAFAC components are poorly defined. In the current study we characterized river water samples from boreal Québec, Canada, using EEM/PARAFAC analysis and ultrahigh resolution mass spectrometry (FTICR-MS). Spearman's correlation of FTICR-MS peak and PARAFAC component relative intensities determined the molecular families associated with 6 PARAFAC components. Molecular families associated with PARAFAC components numbered from 39 to 572 FTICR-MS derived elemental formulas. Detailed molecular properties for each of the classical humic- and protein-like FDOM components are presented. FTICR-MS formulas assigned to PARAFAC components represented 39% of the total number of formulas identified and 59% of total FTICR-MS peak intensities, and included significant numbers compounds that are highly unlikely to fluoresce. Thus, fluorescence measurements offer insight into the biogeochemical cycling of a large proportion of the DOM pool, including a broad suite of unseen molecules that apparently follow the same gradients as FDOM in the environment.

The trophic interactions between bacteria and their main predators, the heterotrophic nanoflagellates (HNFs), play a key role in the structuring and functioning of aquatic microbial food webs. Grazing regulation of bacterial communities, both of biomass and community structure, have been frequently reported. Additionally, bottom-up responses of the HNF at the population level (numerical responses) have also been extensively described. However, the functional response of HNF at the single-cell level has not been well explored. In this study, we concurrently measured the physiological structure of bacterial communities and HNF single-cell activities during re-growth cultures of natural aquatic communities. We found that changes in the abundance and proportion of the preferred, highly active bacterial prey, caused by the feeding activity of their predators (HNF), induced a negative feedback effect on the single-cell activity of these HNF. These shifts in the specific cellular activity of HNF occur at a much shorter time scale than population level shifts in flagellate abundance, and offer a complementary mechanism to explain not only the tight coupling between bacteria and HNF, but also the relative constancy of bacterial abundance in aquatic ecosystems.

The importance of terrestrial-derived organic matter for lake zooplankton communities remains debated, partly because little is known about the basic pathways by which allochthonous carbon is transferred to zooplankton, and whether these vary among the major taxonomic and functional groups. We quantified allochthony of three zooplankton groups (Cladocera, Calanoida, and Cyclopoida) across 18 lakes in Quebec, spanning broad gradients of dissolved organic matter (DOM) and lake trophy, using a multi-isotope (delta2H + delta13C), multi-source (terrestrial, phytoplanktonic, benthic) approach. All three zooplankton groups had significant levels of allochthony, but differed greatly in their respective patterns across lakes. Allochthony in Calanoida and Cyclopoida was linked to detrital food chains based on particulate organic matter (POM) and on DOM, respectively, whereas in Cladocera it appeared related to both pathways; not surprisingly this latter group had the highest mean allochthony (0.31; compared to 0.18 in Cyclopoida and 0.16 in Calanoida). This study highlights the complexity of the pathways of delivery and transfer of terrestrial organic matter in freshwaters, and underscores the role that microbial food webs play in this transfer.

It is now widely accepted that boreal rivers and streams are regionally significant sources of carbon dioxide (CO2), yet their role as methane (CH4) emitters, as well as the sensitivity of these greenhouse gas (GHG) emissions to climate change, are still largely undefined. In this study, we explore the large-scale patterns of fluvial CO2 and CH4 partial pressure (pCO2 , pCH4) and gas exchange (k) relative to a set of key, climate-sensitive river variables across 46 streams and rivers in two distinct boreal landscapes of Northern Québec. We use the resulting models to determine the direction and magnitude of C-gas emissions from these boreal fluvial networks under scenarios of climate change. River pCO2 and pCH4 were positively correlated, although the latter was two orders of magnitude more variable. We provide evidence that in-stream metabolism strongly influences the dynamics of surface water pCO2 and pCH4 , but whereas pCO2 is not influenced by temperature in the surveyed streams and rivers, pCH4 appears to be strongly temperature-dependent. The major predictors of ambient gas concentrations and exchange were water temperature, velocity, and DOC, and the resulting models indicate that total GHG emissions (C-CO2 equivalent) from the entire network may increase between by 13 to 68% under plausible scenarios of climate change over the next 50 years. These predicted increases in fluvial GHG emissions are mostly driven by a steep increase in the contribution of CH4 (from 36 to over 50% of total CO2 -equivalents). The current role of boreal fluvial networks as major landscape sources of C is thus likely to expand, mainly driven by large increases in fluvial CH4 emissions., (© 2013 John Wiley & Sons Ltd.)

Methane (CH4) is an important greenhouse gas because it has 25 times the global warming potential of carbon dioxide (CO2) by mass over a century. Recent calculations suggest that atmospheric CH4 emissions have been responsible for approximately 20% of Earth's warming since pre-industrial times. Understanding how CH4 emissions from ecosystems will respond to expected increases in global temperature is therefore fundamental to predicting whether the carbon cycle will mitigate or accelerate climate change. Methanogenesis is the terminal step in the remineralization of organic matter and is carried out by strictly anaerobic Archaea. Like most other forms of metabolism, methanogenesis is temperature-dependent. However, it is not yet known how this physiological response combines with other biotic processes (for example, methanotrophy, substrate supply, microbial community composition) and abiotic processes (for example, water-table depth) to determine the temperature dependence of ecosystem-level CH4 emissions. It is also not known whether CH4 emissions at the ecosystem level have a fundamentally different temperature dependence than other key fluxes in the carbon cycle, such as photosynthesis and respiration. Here we use meta-analyses to show that seasonal variations in CH4 emissions from a wide range of ecosystems exhibit an average temperature dependence similar to that of CH4 production derived from pure cultures of methanogens and anaerobic microbial communities. This average temperature dependence (0.96 electron volts (eV)), which corresponds to a 57-fold increase between 0 and 30°C, is considerably higher than previously observed for respiration (approximately 0.65 eV) and photosynthesis (approximately 0.3 eV). As a result, we show that both the emission of CH4 and the ratio of CH4 to CO2 emissions increase markedly with seasonal increases in temperature. Our findings suggest that global warming may have a large impact on the relative contributions of CO2 and CH4 to total greenhouse gas emissions from aquatic ecosystems, terrestrial wetlands and rice paddies.

Metabolic plasticity and functional redundancy are fundamental properties of microbial communities, which shape their response to environmental forcing, and also mediate the relationship between community composition and function. Yet, the actual quantification of these emergent community properties has been elusive, and we thus do not know how they vary across bacterial communities, and their relationship to environmental gradients and to each other. Here we present an experimental framework that allows us to simultaneously quantify metabolic plasticity and functional redundancy in freshwater bacterioplankton communities, and to explore connections that may exists between them. We define metabolic plasticity as the rate of change in single-cell properties (cell wall integrity, cell size, single-cell activity) relative to changes in community composition. Likewise, we define functional redundancy as the rate of change in carbon substrate uptake capacities relative to changes in community composition. We assessed these two key community attributes in transplant experiments where bacterioplankton from various aquatic habitats within the same watershed were transplanted from their original water to waters from other systems that differ in their main resources. Our results show that metabolic plasticity is an intrinsic property of bacterial communities, whereas the expression of functional redundancy appears to be more dependent on environmental factors. Furthermore, there was an overall strong positive relationship between the level of functional redundancy and of metabolic plasticity, suggesting no trade-offs between these community attributes but rather a possible co-selection. The apparent continuum in the expression of both functional redundancy and plasticity among bacterial communities and the link between them, in turn suggest that the link between community diversity and function may also vary along a continuum, from being very tight, to being weak, or absent.