Greenhouse gas emissions from African lakes are no longer a blind spot.

Natural lakes are thought to be globally important sources of greenhouse gases (CO2, CH4, and N2O) to the atmosphere although nearly no data have been previously reported from Africa. We collected CO2, CH4, and N2O data in 24 African lakes that accounted for 49% of total lacustrine surface area of the African continent and covered a wide range of morphology and productivity. The surface water concentrations of dissolved CO2 were much lower than values attributed in current literature to tropical lakes and lower than in boreal systems because of a higher productivity. In contrast, surface water-dissolved CH4 concentrations were generally higher than in boreal systems. The lowest CO2 and the highest CH4 concentrations were observed in the more shallow and productive lakes. Emissions of CO2 may likely have been substantially overestimated by a factor between 9 and 18 in African lakes and between 6 and 26 in pan-tropical lakes.

The possible occurrence of iron-dependent anaerobic methane oxidation in an Archean Ocean analogue.

In the ferruginous and anoxic early Earth oceans, photoferrotrophy drove most of the biological production before the advent of oxygenic photosynthesis, but its association with ferric iron (Fe3+) dependent anaerobic methane (CH4) oxidation (AOM) has been poorly investigated. We studied AOM in Kabuno Bay, a modern analogue to the Archean Ocean (anoxic bottom waters and dissolved Fe concentrations > 600 µmol L-1). Aerobic and anaerobic CH4 oxidation rates up to 0.12 ± 0.03 and 51 ± 1 µmol L-1 d-1, respectively, were put in evidence. In the Fe oxidation-reduction zone, we observed high concentration of Bacteriochlorophyll e (biomarker of the anoxygenic photoautotrophs), which co-occurred with the maximum CH4 oxidation peaks, and a high abundance of Candidatus Methanoperedens, which can couple AOM to Fe3+ reduction. In addition, comparison of measured CH4 oxidation rates with electron acceptor fluxes suggest that AOM could mainly rely on Fe3+ produced by photoferrotrophs. Further experiments specifically targeted to investigate the interactions between photoferrotrophs and AOM would be of considerable interest. Indeed, ferric Fe3+-driven AOM has been poorly envisaged as a possible metabolic process in the Archean ocean, but this can potentially change the conceptualization and modelling of metabolic and geochemical processes controlling climate conditions in the Early Earth.

Cyanobacterial Contribution to Travertine Deposition in the Hoyoux River System, Belgium.

Travertine deposition is a landscape-forming process, usually building a series of calcareous barriers differentiating the river flow into a series of cascades and ponds. The process of carbonate precipitation is a complex relationship between biogenic and abiotic causative agents, involving adapted microbial assemblages but also requiring high levels of carbonate saturation, spontaneous degassing of carbon dioxide and slightly alkaline pH. We have analysed calcareous crusts and water chemistry from four sampling sites along the Hoyoux River and its Triffoy tributary (Belgium) in winter, spring, summer and autumn 2014. Different surface textures of travertine deposits correlated with particular microenvironments and were influenced by the local water flow. In all microenvironments, we have identified the cyanobacterium Phormidium incrustatum (Nägeli) Gomont as the organism primarily responsible for carbonate precipitation and travertine fabric by combining morphological analysis with molecular sequencing (16S rRNA gene and ITS, the Internal Transcribed Spacer fragments), targeting both field populations and cultures to exclude opportunistic microorganisms responding favourably to culture conditions. Several closely related cyanobacterial strains were cultured; however, only one proved identical with the sequences obtained from the field population by direct PCR. This strain was the dominant primary producer in the calcareous deposits under study and in similar streams in Europe. The dominance of one organism that had a demonstrated association with carbonate precipitation presented a valuable opportunity to study its function in construction, preservation and fossilisation potential of ambient temperature travertine deposits. These relationships were examined using scanning electron microscopy and Raman microspectroscopy.

Emission and oxidation of methane in a meromictic, eutrophic and temperate lake (Dendre, Belgium).

We sampled the water column of the Dendre stone pit lake (Belgium) in spring, summer, autumn and winter. Depth profiles of several physico-chemical variables, nutrients, dissolved gases (CO2, CH4, N2O), sulfate, sulfide, iron and manganese concentrations and δ13C-CH4 were determined. We performed incubation experiments to quantify CH4 oxidation rates, with a focus on anaerobic CH4 oxidation (AOM), without and with an inhibitor of sulfate reduction (molybdate). The evolution of nitrate and sulfate concentrations during the incubations was monitored. The water column was anoxic below 20 m throughout the year, and was thermally stratified in summer and autumn. High partial pressure of CO2 and CH4 and high concentrations of ammonium and phosphate were observed in anoxic waters. Important nitrous oxide and nitrate concentration maxima were also observed (up to 440 nmol L-1 and 80 µmol L-1, respectively). Vertical profiles of δ13C-CH4 unambiguously showed the occurrence of AOM. Important AOM rates (up to 14 µmol L-1 d-1) were observed and often co-occurred with nitrate consumption peaks, suggesting the occurrence of AOM coupled with nitrate reduction. AOM coupled with sulfate reduction also occurred, since AOM rates tended to be lower when molybdate was added. CH4 oxidation was mostly aerobic (∼80% of total oxidation) in spring and winter, and almost exclusively anaerobic in summer and autumn. Despite important CH4 oxidation rates, the estimated CH4 fluxes from the water surface to the atmosphere were high (mean of 732 µmol m-2 d-1 in spring, summer and autumn, and up to 12,482 µmol m-2 d-1 in winter).

Divergent biophysical controls of aquatic CO2 and CH4 in the World's two largest rivers.

Carbon emissions to the atmosphere from inland waters are globally significant and mainly occur at tropical latitudes. However, processes controlling the intensity of CO2 and CH4 emissions from tropical inland waters remain poorly understood. Here, we report a data-set of concurrent measurements of the partial pressure of CO2 (pCO2) and dissolved CH4 concentrations in the Amazon (n = 136) and the Congo (n = 280) Rivers. The pCO2 values in the Amazon mainstem were significantly higher than in the Congo, contrasting with CH4 concentrations that were higher in the Congo than in the Amazon. Large-scale patterns in pCO2 across different lowland tropical basins can be apprehended with a relatively simple statistical model related to the extent of wetlands within the basin, showing that, in addition to non-flooded vegetation, wetlands also contribute to CO2 in river channels. On the other hand, dynamics of dissolved CH4 in river channels are less straightforward to predict, and are related to the way hydrology modulates the connectivity between wetlands and river channels.

Pelagic photoferrotrophy and iron cycling in a modern ferruginous basin.

Iron-rich (ferruginous) ocean chemistry prevailed throughout most of Earth's early history. Before the evolution and proliferation of oxygenic photosynthesis, biological production in the ferruginous oceans was likely driven by photoferrotrophic bacteria that oxidize ferrous iron {Fe(II)} to harness energy from sunlight, and fix inorganic carbon into biomass. Photoferrotrophs may thus have fuelled Earth's early biosphere providing energy to drive microbial growth and evolution over billions of years. Yet, photoferrotrophic activity has remained largely elusive on the modern Earth, leaving models for early biological production untested and imperative ecological context for the evolution of life missing. Here, we show that an active community of pelagic photoferrotrophs comprises up to 30% of the total microbial community in illuminated ferruginous waters of Kabuno Bay (KB), East Africa (DR Congo). These photoferrotrophs produce oxidized iron {Fe(III)} and biomass, and support a diverse pelagic microbial community including heterotrophic Fe(III)-reducers, sulfate reducers, fermenters and methanogens. At modest light levels, rates of photoferrotrophy in KB exceed those predicted for early Earth primary production, and are sufficient to generate Earth's largest sedimentary iron ore deposits. Fe cycling, however, is efficient, and complex microbial community interactions likely regulate Fe(III) and organic matter export from the photic zone.

Vertical Distribution of Functional Potential and Active Microbial Communities in Meromictic Lake Kivu.

The microbial community composition in meromictic Lake Kivu, with one of the largest CH4 reservoirs, was studied using 16S rDNA and ribosomal RNA (rRNA) pyrosequencing during the dry and rainy seasons. Highly abundant taxa were shared in a high percentage between bulk (DNA-based) and active (RNA-based) bacterial communities, whereas a high proportion of rare species was detected only in either an active or bulk community, indicating the existence of a potentially active rare biosphere and the possible underestimation of diversity detected when using only one nucleic acid pool. Most taxa identified as generalists were abundant, and those identified as specialists were more likely to be rare in the bulk community. The overall number of environmental parameters that could explain the variation was higher for abundant taxa in comparison to rare taxa. Clustering analysis based on operational taxonomic units (OTUs at 0.03 cutoff) level revealed significant and systematic microbial community composition shifts with depth. In the oxic zone, Actinobacteria were found highly dominant in the bulk community but not in the metabolically active community. In the oxic-anoxic transition zone, highly abundant potentially active Nitrospira and Methylococcales were observed. The co-occurrence of potentially active sulfur-oxidizing and sulfate-reducing bacteria in the anoxic zone may suggest the presence of an active yet cryptic sulfur cycle.

Bacterial community composition in three freshwater reservoirs of different alkalinity and trophic status.

In order to investigate the factors controlling the bacterial community composition (BCC) in reservoirs, we sampled three freshwater reservoirs with contrasted physical and chemical characteristics and trophic status. The BCC was analysed by 16S rRNA gene amplicon 454 pyrosequencing. In parallel, a complete dataset of environmental parameters and phytoplankton community composition was also collected. BCC in the analysed reservoirs resembled that of epilimnetic waters of natural freshwater lakes with presence of Actinobacteria, Alpha- and Betaproteobacteria, Cytophaga-Flavobacteria-Bacteroidetes (CFB) and Verrucomicrobia groups. Our results evidenced that the retrieved BCC in the analysed reservoirs was strongly influenced by pH, alkalinity and organic carbon content, whereas comparatively little change was observed among layers in stratified conditions.

Carbon cycling of Lake Kivu (East Africa): net autotrophy in the epilimnion and emission of CO2 to the atmosphere sustained by geogenic inputs.

We report organic and inorganic carbon distributions and fluxes in a large (>2000 km2) oligotrophic, tropical lake (Lake Kivu, East Africa), acquired during four field surveys, that captured the seasonal variations (March 2007-mid rainy season, September 2007-late dry season, June 2008-early dry season, and April 2009-late rainy season). The partial pressure of CO2 (pCO2) in surface waters of the main basin of Lake Kivu showed modest spatial (coefficient of variation between 3% and 6%), and seasonal variations with an amplitude of 163 ppm (between 579±23 ppm on average in March 2007 and 742±28 ppm on average in September 2007). The most prominent spatial feature of the pCO2 distribution was the very high pCO2 values in Kabuno Bay (a small sub-basin with little connection to the main lake) ranging between 11,213 ppm and 14,213 ppm (between 18 and 26 times higher than in the main basin). Surface waters of the main basin of Lake Kivu were a net source of CO2 to the atmosphere at an average rate of 10.8 mmol m(-2) d(-1), which is lower than the global average reported for freshwater, saline, and volcanic lakes. In Kabuno Bay, the CO2 emission to the atmosphere was on average 500.7 mmol m(-2) d(-1) (∼46 times higher than in the main basin). Based on whole-lake mass balance of dissolved inorganic carbon (DIC) bulk concentrations and of its stable carbon isotope composition, we show that the epilimnion of Lake Kivu was net autotrophic. This is due to the modest river inputs of organic carbon owing to the small ratio of catchment area to lake surface area (2.15). The carbon budget implies that the CO2 emission to the atmosphere must be sustained by DIC inputs of geogenic origin from deep geothermal springs.

Disproportionate Contribution of Riparian Inputs to Organic Carbon Pools in Freshwater Systems.

A lack of appropriate proxies has traditionally hampered our ability to distinguish riverine organic carbon (OC) sources at the landscape scale. However, the dissection of C4 grasslands by C3-enriched riparian vegetation, and the distinct carbon stable isotope signature (δ13C) of these two photosynthetic pathways, provides a unique setting to assess the relative contribution of riparian and more distant sources to riverine C pools. Here, we compared δ13C signatures of bulk sub-basin vegetation (δ13CVEG) with those of riverine OC pools for a wide range of sites within two contrasting river basins in Madagascar. Although C3-derived carbon dominated in the eastern Rianala catchment, consistent with the dominant vegetation, we found that in the C4-dominated Betsiboka basin, riverine OC is disproportionately sourced from the C3-enriched riparian fringe, irrespective of climatic season, even though δ13CVEG estimates suggest as much as 96% of vegetation cover in some Betsiboka sub-basins may be accounted for by C4 biomass. For example, δ13C values for river bed OC were on average 6.9 ± 2.7‰ depleted in 13C compared to paired estimates of δ13CVEG. The disconnection of the wider C4-dominated basin is considered the primary driver of the under-representation of C4-derived C within riverine OC pools in the Betsiboka basin, although combustion of grassland biomass by fire is likely a subsidiary constraint on the quantity of terrestrial organic matter available for export to these streams and rivers. Our findings carry implications for the use of sedimentary δ13C signatures as proxies for past forest-grassland distribution and climate, as the C4 component may be considerably underestimated due to its disconnection from riverine OC pools.

Contrasting biogeochemical characteristics of the Oubangui River and tributaries (Congo River basin).

The Oubangui is a major tributary of the Congo River. We describe the biogeochemistry of contrasting tributaries within its central catchment, with watershed vegetation ranging from wooded savannahs to humid rainforest. Compared to a 2-year monitoring record on the mainstem Oubangui, these tributaries show a wide range of biogeochemical signatures, from highly diluted blackwaters (low turbidity, pH, conductivity, and total alkalinity) in rainforests to those more typical for savannah systems. Spectral analyses of chromophoric dissolved organic matter showed wide temporal variations in the Oubangui compared to spatio-temporal variations in the tributaries, and confirm that different pools of dissolved organic carbon are mobilized during different hydrological stages. δ(13)C of dissolved inorganic carbon ranged between -28.1‰ and -5.8‰, and was strongly correlated to both partial pressure of CO2 and to the estimated contribution of carbonate weathering to total alkalinity, suggesting an important control of the weathering regime on CO2 fluxes. All tributaries were oversaturated in dissolved greenhouse gases (CH4, N2O, CO2), with highest levels in rivers draining rainforest. The high diversity observed underscores the importance of sampling that covers the variability in subcatchment characteristics, to improve our understanding of biogeochemical cycling in the Congo Basin.

Vertical distribution of ammonia-oxidizing crenarchaeota and methanogens in the epipelagic waters of Lake Kivu (Rwanda-Democratic Republic of the Congo).

Four stratified basins in Lake Kivu (Rwanda-Democratic Republic of the Congo) were sampled in March 2007 to investigate the abundance, distribution, and potential biogeochemical role of planktonic archaea. We used fluorescence in situ hybridization with catalyzed-reported deposition microscopic counts (CARD-FISH), denaturing gradient gel electrophoresis (DGGE) fingerprinting, and quantitative PCR (qPCR) of signature genes for ammonia-oxidizing archaea (16S rRNA for marine Crenarchaeota group 1.1a [MCG1] and ammonia monooxygenase subunit A [amoA]). Abundance of archaea ranged from 1 to 4.5% of total DAPI (4',6-diamidino-2-phenylindole) counts with maximal concentrations at the oxic-anoxic transition zone (∼50-m depth). Phylogenetic analysis of the archaeal planktonic community revealed a higher level of richness of crenarchaeal 16S rRNA gene sequences (21 of the 28 operational taxonomic units [OTUs] identified [75%]) over euryarchaeotal ones (7 OTUs). Sequences affiliated with the kingdom Euryarchaeota were mainly recovered from the anoxic water compartment and mostly grouped into methanogenic lineages (Methanosarcinales and Methanocellales). In turn, crenarchaeal phylotypes were recovered throughout the sampled epipelagic waters (0- to 100-m depth), with clear phylogenetic segregation along the transition from oxic to anoxic water masses. Thus, whereas in the anoxic hypolimnion crenarchaeotal OTUs were mainly assigned to the miscellaneous crenarchaeotic group, the OTUs from the oxic-anoxic transition and above belonged to Crenarchaeota groups 1.1a and 1.1b, two lineages containing most of the ammonia-oxidizing representatives known so far. The concomitant vertical distribution of both nitrite and nitrate maxima and the copy numbers of both MCG1 16S rRNA and amoA genes suggest the potential implication of Crenarchaeota in nitrification processes occurring in the epilimnetic waters of the lake.

How Daphnia copes with excess carbon in its food.

Animals that maintain near homeostatic elemental ratios may get rid of excess ingested elements from their food in different ways. C regulation was studied in juveniles of Daphnia magna feeding on two Selenastrum capricornutum cultures contrasting in P content (400 and 80 C:P atomic ratios). Both cultures were labelled with (14)C in order to measure Daphnia ingestion and assimilation rates. No significant difference in ingestion rates was observed between P-low and P-rich food, whereas the net assimilation of (14)C was higher in the treatment with P-rich algae. Some Daphnia were also homogeneously labelled over 5 days on radioactive algae to estimate respiration rates and excretion rates of dissolved organic C (DOC). The respiration rate for Daphnia fed with high C:P algae (38.7% of body C day(-1)) was significantly higher than for those feeding on low C:P algae (25.3% of body C day(-1)). The DOC excretion rate was also higher when animals were fed on P-low algae (13.4% of body C day(-1)) than on P-rich algae (5.7% of body C day(-1)). When corrected for respiratory losses, total assimilation of C did not differ significantly between treatments (around 60% of body C day(-1)). Judging from these experiments, D. magna can maintain its stoichiometric balance when feeding on unbalanced diets (high C:P) primarily by disposing of excess dietary C via respiration and excretion of DOC.