Net greenhouse gas balance of fibre wood plantation on peat in Indonesia.

Tropical peatlands cycle and store large amounts of carbon in their soil and biomass1-5. Climate and land-use change alters greenhouse gas (GHG) fluxes of tropical peatlands, but the magnitude of these changes remains highly uncertain6-19. Here we measure net ecosystem exchanges of carbon dioxide, methane and soil nitrous oxide fluxes between October 2016 and May 2022 from Acacia crassicarpa plantation, degraded forest and intact forest within the same peat landscape, representing land-cover-change trajectories in Sumatra, Indonesia. This allows us to present a full plantation rotation GHG flux balance in a fibre wood plantation on peatland. We find that the Acacia plantation has lower GHG emissions than the degraded site with a similar average groundwater level (GWL), despite more intensive land use. The GHG emissions from the Acacia plantation over a full plantation rotation (35.2 ± 4.7 tCO2-eq ha-1 year-1, average ± standard deviation) were around two times higher than those from the intact forest (20.3 ± 3.7 tCO2-eq ha-1 year-1), but only half of the current Intergovernmental Panel on Climate Change (IPCC) Tier 1 emission factor (EF)20 for this land use. Our results can help to reduce the uncertainty in GHG emissions estimates, provide an estimate of the impact of land-use change on tropical peat and develop science-based peatland management practices as nature-based climate solutions.

Magnitude and Drivers of Oxic Methane Production in Small Temperate Lakes.

Methanogenesis is traditionally considered as a strictly anaerobic process. Recent evidence suggests instead that the ubiquitous methane (CH4) oversaturation found in freshwater lakes is sustained, at least partially, by methanogenesis in oxic conditions. Although this paradigm shift is rapidly gaining acceptance, the magnitude and regulation of oxic CH4 production (OMP) have remained ambiguous. Based on the summer CH4 mass balance in the surface mixed layer (SML) of five small temperate lakes (surface area, SA, of 0.008-0.44 km2), we show that OMP (range of 0.01 ± 0.01 to 0.52 ± 0.04 µmol L-1 day-1) is linked to the concentrations of chlorophyll-a, total phosphorus, and dissolved organic carbon. The stable carbon isotopic mass balance of CH4 (δ13C-CH4) indicates direct photoautotrophic release as the most likely source of oxic CH4. Furthermore, we show that the oxic CH4 contribution to the SML CH4 saturation and emission is an inverse function of the ratio of the sediment area to the SML volume in lakes as small as 0.06 km2. Given that global lake CH4 emissions are dominated by small lakes (SA of <1 km2), the large contribution of oxic CH4 production (up to 76%) observed in this study suggests that OMP can contribute significantly to global CH4 emissions.

The role of methanotrophy in the microbial carbon metabolism of temperate lakes.

Previous stable isotope and biomarker evidence has indicated that methanotrophy is an important pathway in the microbial loop of freshwater ecosystems, despite the low cell abundance of methane-oxidizing bacteria (MOB) and the low methane concentrations relative to the more abundant dissolved organic carbon (DOC). However, quantitative estimations of the relative contribution of methanotrophy to the microbial carbon metabolism of lakes are scarce, and the mechanism allowing methanotrophy to be of comparable importance to DOC-consuming heterotrophy remained elusive. Using incubation experiments, microscopy, and multiple water column profiles in six temperate lakes, we show that MOB play a much larger role than their abundances alone suggest because of their larger cell size and higher specific activity. MOB activity is tightly constrained by the local methane:oxygen ratio, with DOC-rich lakes with large hypolimnetic volume fraction showing a higher carbon consumption through methanotrophy than heterotrophy at the whole water column level. Our findings suggest that methanotrophy could be a critical microbial carbon consumption pathway in many temperate lakes, challenging the prevailing view of a DOC-centric microbial metabolism in these ecosystems.

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

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

Coupling of stable carbon isotopic signature of methane and ebullitive fluxes in northern temperate lakes.

Stable isotopic analysis is a popular method to understand the mechanisms sustaining methane (CH4) emissions in various aquatic environments. Yet, the general lack of concurrent measurements of isotopes and fluxes impedes our ability to establish a connection between the variation in the rates of CH4 emission and isotopic signature. Here, we examine the magnitude of CH4 ebullition (bubbling) and stable carbon isotopic signature (δ13C-CH4) of bubble CH4 in four northern temperate lakes and evaluate the in-lake processes shaping their variability. The ebullitive CH4 flux and bubble δ13C-CH4 varied from 0.01 to 37.0 mmol m-2 d-1 and between -71.0‰ and -50.9‰, respectively. The high emission lakes in general and high fluxing shallow zones within each lake consistently showed enriched δ13C-CH4 signature. Subsequently, in addition to the temperature dependence (1.4 ± 0.1 eV), the rates of ebullition strongly correlated with the variability of δ13C-CH4 across our study lakes. Our results suggest that higher ebullitive emissions are sustained by acetoclastic methanogenesis, likely fueled by fresh organic matter inputs. Further, the annual whole-lake estimate of bubble isotopic flux alone showed depleted δ13C-CH4 values (-64.6 ± 0.6‰ to -60.1 ± 3.2‰), yet the signature of the total CH4 emission (ebullition + diffusion) was relatively enriched (-60.7‰ to -52.6‰) due to high methanotrophic activity in the water column. We show that δ13C-CH4 signature of bubbles can be linked to the magnitude of ebullition itself, yet we suggest there is a need to account for different emission pathways and their isotopic signature to allocate CH4 source signature to northern lakes.

Rapid shifts in methanotrophic bacterial communities mitigate methane emissions from a tropical hydropower reservoir and its downstream river.

Methane-oxidizing bacteria (MOB) present in the water column mitigate methane (CH4) emissions from hydropower complexes to the atmosphere. By creating a discontinuity in rivers, dams cause large environmental variations, including in CH4 and oxygen concentrations, between upstream, reservoir, and downstream segments. Although highest freshwater methanotrophic activity is often detected at low oxygen concentrations, CH4 oxidation in well-oxygenated downstream rivers below dams has also been reported. Here we combined DNA and RNA high-throughput sequencing with microscopic enumeration (by CARD-FISH) and biogeochemical data to investigate the abundance, composition, and potential activity of MOB taxa from upstream to downstream waters in the tropical hydropower complex Batang Ai (Malaysia). High relative abundance of MOB (up to 61% in 16S rRNA sequences and 19% in cell counts) and enrichment of stable isotopic signatures of CH4 (up to 0‰) were detected in the hypoxic hypolimnion of the reservoir and in the outflowing downstream river. MOB community shifts along the river-reservoir system reflected environmental sorting of taxa and an interrupted hydrologic connectivity in which downstream MOB communities resembled reservoir's hypolimnetic communities but differed from upstream and surface reservoir communities. In downstream waters, CH4 oxidation was accompanied by fast cell growth of particular MOB taxa. Our results suggest that rapid shifts in active MOB communities allow the mitigation of CH4 emissions from different zones of hydropower complexes, including in quickly re-oxygenated rivers downstream of dams.

Magnitude and drivers of integrated fluvial network greenhouse gas emissions across the boreal landscape in Québec.

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 CO2 and CH4 concentrations and gas exchange continuously along entire fluvial networks to derive the total fluvial CO2 and CH4 emissions in large (3000 to 30,000 km2) 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 CO2, and 4-1780 mg C m-2 yr-1 for CH4, 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.

Niche separation within aerobic methanotrophic bacteria across lakes and its link to methane oxidation rates.

Lake methane (CH4 ) emissions are largely controlled by aerobic methane-oxidizing bacteria (MOB) which mostly belong to the classes Alpha- and Gammaproteobacteria (Alpha- and Gamma-MOB). Despite the known metabolic and ecological differences between the two MOB groups, their main environmental drivers and their relative contribution to CH4 oxidation rates across lakes remain unknown. Here, we quantified the two MOB groups through CARD-FISH along the water column of six temperate lakes and during incubations in which we measured ambient CH4 oxidation rates. We found a clear niche separation of Alpha- and Gamma-MOB across lake water columns, which is mostly driven by oxygen concentration. Gamma-MOB appears to dominate methanotrophy throughout the water column, but Alpha-MOB may also be an important player particularly in well-oxygenated bottom waters. The inclusion of Gamma-MOB cell abundance improved environmental models of CH4 oxidation rate, explaining part of the variation that could not be explained by environmental factors alone. Altogether, our results show that MOB composition is linked to CH4 oxidation rates in lakes and that information on the MOB community can help predict CH4 oxidation rates and thus emissions from lakes.

Large-scale biogeography and environmental regulation of methanotrophic bacteria across boreal inland waters.

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.

The NSERC Canadian Lake Pulse Network: A national assessment of lake health providing science for water management in a changing climate.

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.

Modelling CO2 emissions from water surface of a boreal hydroelectric reservoir.

To quantify CO2 emissions from water surface of a reservoir that was shaped by flooding the boreal landscape, we developed a daily time-step reservoir biogeochemistry model. We calibrated the model using the measured concentrations of dissolved organic and inorganic carbon (C) in a young boreal hydroelectric reservoir, Eastmain-1 (EM-1), in northern Quebec, Canada. We validated the model against observed CO2 fluxes from an eddy covariance tower in the middle of EM-1. The model predicted the variability of CO2 emissions reasonably well compared to the observations (root mean square error: 0.4-1.3gCm-2day-1, revised Willmott index: 0.16-0.55). In particular, we demonstrated that the annual reservoir surface effluxes were initially high, steeply declined in the first three years, and then steadily decreased to ~115gCm-2yr-1 with increasing reservoir age over the estimated "engineering" reservoir lifetime (i.e., 100years). Sensitivity analyses revealed that increasing air temperature stimulated CO2 emissions by enhancing CO2 production in the water column and sediment, and extending the duration of open water period over which emissions occur. Increasing the amount of terrestrial organic C flooded can enhance benthic CO2 fluxes and CO2 emissions from the reservoir water surface, but the effects were not significant over the simulation period. The model is useful for the understanding of the mechanism of C dynamics in reservoirs and could be used to assist the hydro-power industry and others interested in the role of boreal hydroelectric reservoirs as sources of greenhouse gas emissions.

Greenhouse Gas Emissions from Freshwater Reservoirs: What Does the Atmosphere See?

Freshwater reservoirs are a known source of greenhouse gas (GHG) to the atmosphere, but their quantitative significance is still only loosely con- strained. Although part of this uncertainty can be attributed to the difficulties in measuring highly variable fluxes, it is also the result of a lack of a clear accounting methodology, particularly about what constitutes new emissions and potential new sinks. In this paper, we review the main processes involved in the generation of GHG in reservoir systems and propose a simple approach to quantify the reservoir GHG footprint in terms of the net changes in GHG fluxes to the atmosphere induced by damming, that is, 'what the atmosphere sees.' The approach takes into account the pre-impoundment GHG balance of the landscape, the temporal evolution of reservoir GHG emission profile as well as the natural emissions that are displaced to or away from the reservoir site resulting from hydrological and other changes. It also clarifies the portion of the reservoir carbon burial that can potentially be considered an offset to GHG emissions.

Large increases in carbon burial in northern lakes during the Anthropocene.

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.

Large-scale patterns in summer diffusive CH4 fluxes across boreal lakes, and contribution to diffusive C emissions.

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.

Oxic water column methanogenesis as a major component of aquatic CH4 fluxes.

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.

Browning of boreal freshwaters coupled to carbon-iron interactions along the aquatic continuum.

The color of freshwaters, often measured as absorbance, influences a number of ecosystem services including biodiversity, fish production, and drinking water quality. Many countries have recently reported on increasing trends of water color in freshwaters, for which drivers are still not fully understood. We show here with more than 58000 water samples from the boreal and hemiboreal region of Sweden and Canada that absorbance of filtered water (a420) co-varied with dissolved organic carbon (DOC) concentrations (R²  = 0.85, P<0.0001), but that a420 relative to DOC is increased by the presence of iron (Fe). We found that concentrations of Fe significantly declined with increasing water retention in the landscape, resulting in significantly lower Fe concentrations in lakes compared to running waters. The Fe loss along the aquatic continuum corresponded to a proportional loss in a420, suggesting a tight biogeochemical coupling between colored dissolved organic matter and Fe. Since water is being flushed at increasing rates due to enhanced runoff in the studied regions, diminished loss of Fe along the aquatic continuum may be one reason for observed trends in a420, and in particular in a420/DOC increases. If trends of increased Fe concentrations in freshwaters continue, water color will further increase with various effects on ecosystem services and biogeochemical cycles.

THE INFLUENCE OF SUBMERGED MACROPHYTES ON SEDIMENTARY DIATOM ASSEMBLAGES(1).

Submerged macrophytes are a central component of lake ecosystems; however, little is known regarding their long-term response to environmental change. We have examined the potential of diatoms as indicators of past macrophyte biomass. We first sampled periphyton to determine whether habitat was a predictor of diatom assemblage. We then sampled 41 lakes in Quebec, Canada, to evaluate whether whole-lake submerged macrophyte biomass (BiomEpiV) influenced surface sediment diatom assemblages. A multivariate regression tree (MRT) was used to construct a semiquantitative model to reconstruct past macrophyte biomass. We determined that periphytic diatom assemblages on macrophytes were significantly different from those on wood and rocks (ANOSIM R = 0.63, P < 0.01). A redundancy analysis (RDA) of the 41-lake data set identified BiomEpiV as a significant (P < 0.05) variable in structuring sedimentary diatom assemblages. The MRT analysis classified the lakes into three groups. These groups were (A) high-macrophyte, nutrient-limited lakes (BiomEpiV ≥525 µg · L(-1) ; total phosphorus [TP] <35 µg · L(-1) ; 23 lakes); (B) low-macrophyte, nutrient-limited lakes (BiomEpiV <525 µg · L(-1) ; TP <35 µg · L(-1) ; 12 lakes); and (C) eutrophic lakes (TP ≥35 µg · L(-1) ; six lakes). A semiquantitative model correctly predicted the MRT group of the lake 71% of the time (P < 0.001). These results suggest that submerged macrophytes have a significant influence on diatom community structure and that sedimentary diatom assemblages can be used to infer past macrophyte abundance.

Some misconceptions about the spurious correlation problem in the ecological literature.

It is a common misconception that correlations between variables that share a common term are statistically invalid. Although the idea that such relationships are wholly or partially spurious was rejected decades ago by statisticians, ecologists continue mistakenly to exclude legitimate hypotheses on this basis. Besides directing attention to the statistical literature on the subject, we briefly reconsider the problem from 3 viewpoints: first, the confusion between spurious correlation and spurious inference, second, the problem of concept familiarity and definition, with particular reference to the self-thinning rule for plants, and third, a legitimate concern with measurement error of shared variable components.