François Darchambeau

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

ABSTRACT 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.

The age of river‐transported carbon: A global perspective

The role played by river networks in regional and global carbon (C) budgets is receiving increasing attention. Despite the potential of radiocarbon measurements (Δ14C) to elucidate sources and cycling of different riverine C pools, there remain large regions for which no data are available and no comprehensive attempts to synthesize the available information and examine global patterns in the 14C content of different riverine C pools. Here we present new 14C data on particulate and dissolved organic C (POC and DOC) from six river basins in tropical and subtropical Africa and compiled >1400 literature Δ14C data and ancillary parameters from rivers globally. Our analysis reveals a consistent pattern whereby POC is progressively older in systems carrying higher sediment loads, coinciding with a lower organic carbon content. At the global scale, this pattern leads to a proposed global median Δ14C signature of −203‰, corresponding to an age of ~1800 years B.P. For DOC exported to the coastal zone, we predict a modern (decadal) age (Δ14C = +22 to +46‰), and paired data sets confirm that riverine DOC is generally more recent in origin than POC—in contrast to the situation in ocean environments. Weathering regimes complicate the interpretation of 14C ages of dissolved inorganic carbon, but the available data favor the hypothesis that in most cases, more recent organic C is preferentially mineralized.

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.

LakeMIP Kivu: evaluating the representation of a large, deep tropical lake by a set of one-dimensional lake models

The African great lakes are of utmost importance for the local economy (fishing), as well as being essential to the survival of the local people. During the past decades, these lakes experienced fast changes in ecosystem structure and functioning, and their future evolution is a major concern. In this study, for the first time a set of one-dimensional lake models are evaluated for Lake Kivu (2.28°S; 28.98°E), East Africa. The unique limnology of this meromictic lake, with the importance of salinity and subsurface springs in a tropical high-altitude climate, presents a worthy challenge to the seven models involved in the Lake Model Intercomparison Project (LakeMIP). Meteorological observations from two automatic weather stations are used to drive the models, whereas a unique dataset, containing over 150 temperature profiles recorded since 2002, is used to assess the models performance. Simulations are performed over the freshwater layer only (60 m) and over the average lake depth (240 m), since salinity increases with depth below 60 m in Lake Kivu and some lake models do not account for the influence of salinity upon lake stratification. All models are able to reproduce the mixing seasonality in Lake Kivu, as well as the magnitude and seasonal cycle of the lake enthalpy change. Differences between the models can be ascribed to variations in the treatment of the radiative forcing and the computation of the turbulent heat fluxes. Fluctuations in wind velocity and solar radiation explain inter-annual variability of observed water column temperatures. The good agreement between the deep simulations and the observed meromictic stratification also shows that a subset of models is able to account for the salinity- and geothermal-induced effects upon deep-water stratification. Finally, based on the strengths and weaknesses discerned in this study, an informed choice of a one-dimensional lake model for a given research purpose becomes possible.

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.

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. δ13C 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.

Primary production in a tropical large lake: The role of phytoplankton composition

Phytoplankton biomass and primary production in tropical large lakes vary at different time scales, from seasons to centuries. We provide a dataset made of 7 consecutive years of phytoplankton biomass and production in Lake Kivu (Eastern Africa). From 2002 to 2008, bi-weekly samplings were performed in a pelagic site in order to quantify phytoplankton composition and biomass, using marker pigments determined by HPLC. Primary production rates were estimated by 96 in situ (14)C incubations. A principal component analysis showed that the main environmental gradient was linked to a seasonal variation of the phytoplankton assemblage, with a clear separation between diatoms during the dry season and cyanobacteria during the rainy season. A rather wide range of the maximum specific photosynthetic rate (PBm) was found, ranging between 1.15 and 7.21 g carbong(-1)chlorophyll ah(-1), and was best predicted by a regression model using phytoplankton composition as an explanatory variable. The irradiance at the onset of light saturation (Ik) ranged between 91 and 752 μE m(-2)s(-1) and was linearly correlated with the mean irradiance in the mixed layer. The inter-annual variability of phytoplankton biomass and production was high, ranging from 53 to 100 mg chlorophyll am(-2) (annual mean) and from 143 to 278 g carbon m(-2)y(-1), respectively. The degree of seasonal mixing determined annual production, demonstrating the sensitivity of tropical lakes to climate variability. A review of primary production of other African great lakes allows situating Lake Kivu productivity in the same range as that of lakes Tanganyika and Malawi, even if mean phytoplankton biomass was higher in Lake Kivu.

Lake Kivu: Limnology and biogeochemistry of a tropical great lake

We review available data on archaea, bacteria and small eukaryotes in anattempt to provide a general picture of microbial diversity, abundances and microbedrivenprocesses in Lake Kivu surface and intermediate waters (ca. 0–100 m). Thevarious water layers present contrasting physical and chemical properties andharbour very different microbial communities supported by the vertical redoxstructure. For instance, we found a clear vertical segregation of archaeal and bacterialassemblages between the oxic and the anoxic zone of the surface waters. Thepresence of speci fi c bacterial (e.g. Green Sulfur Bacteria) and archaeal (e.g.ammonia-oxidising archaea) communities and the prevailing physico-chemicalconditions point towards the redoxcline as the most active and metabolically diversewater layer. The archaeal assemblage in the surface and intermediate water columnlayers was mainly composed by the phylum Crenarchaeota , by the recently de fi nedphylum Thaumarchaeota and by the phylum Euryarchaeota . In turn, the bacterialassemblage comprised mainly ubiquitous members of planktonic assemblages offreshwater environments ( Actinobacteria , Bacteroidetes and Betaproteobacteria among others) and other less commonly retrieved phyla (e.g. Chlorobi , Clostridiumand Deltaproteobacteria ). The community of small eukaryotes (

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 11213 ppm and 14213 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.

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.