Anne-Catherine Lehours

Production and consumption of methane in freshwater lake ecosystems

The atmospheric concentration of methane (CH(4)), a major greenhouse gas, is mainly controlled by the activities of methane-producing (methanogens) and methane-consuming (methanotrophs) microorganisms. Freshwater lakes are identified as one of the main CH(4) sources, as it was estimated that they contribute to 6-16% of natural CH(4) emissions. It is therefore critical to better understanding the biogeochemical cycling of CH(4) in these ecosystems. In this paper, the effects of environmental factors on methanogenic and methanotrophic rates are reviewed and an inventory of the methanogens and methanotrophs at the genus/species level in freshwater lakes is given. We focus on the anaerobic oxidation of methane, which is a still poorly known process but increasingly reported in freshwater lakes.

Phylogenetic Diversity of Archaea and Bacteria in the Anoxic Zone of a Meromictic Lake (Lake Pavin, France)

ABSTRACT The compositions of archaeal and bacterial populations at different depths (60 m [mixolimnion-chemocline interface], 70 m [chemocline-subchemocline interface], 90 m, and 92 m [the water-sediment interface]) in the anoxic zone of the water column in Lake Pavin, a freshwater permanently stratified mountain lake in France, were determined. Phylogenetic trees were constructed from sequences to assess archaeal and bacterial diversity at the four sites.

Unexpected and novel putative viruses in the sediments of a deep-dark permanently anoxic freshwater habitat.

Morphological diversity, abundance and community structure of viruses were examined in the deep and anoxic sediments of the volcanic Lake Pavin (France). The sediment core, encompassing 130 years of sedimentation, was subsampled every centimeter. High viral abundances were recorded and correlated to prokaryotic densities. Abundances of viruses and prokaryotes decreased with the depth, contrasting the pattern of virus-to-prokaryote ratio. According to fingerprint analyses, the community structure of viruses, bacteria and archaea gradually changed, and communities of the surface (0–10 cm) could be discriminated from those of the intermediate (11–27 cm) and deep (28–40 cm) sediment layers. Viral morphotypes similar to virions of ubiquitous dsDNA viruses of bacteria were observed. Exceptional morphotypes, previously never reported in freshwater systems, were also detected. Some of these resembled dsDNA viruses of hyperthermophilic and hyperhalophilic archaea. Moreover, unusual types of spherical and cubic virus-like particles (VLPs) were observed. Infected prokaryotic cells were detected in the whole sediment core, and their vertical distribution correlated with both viral and prokaryotic abundances. Pleomorphic ellipsoid VLPs were visible in filamentous cells tentatively identified as representatives of the archaeal genus Methanosaeta, a major group of methane producers on earth.

Diversity of Culturable Bacteria, from the Anaerobic Zone of the Meromictic Lake Pavin, Able to Perform Dissimilatory-Iron Reduction in Different in Vitro Conditions

A culture-dependent study was performed with the aim of assessing the carbon, electron and Fe(III) sources used for the dissimilatory Fe(III) reduction pathway and the diversity of culturable Fe(III)-reducers in the anoxic zone of the meromictic Lake Pavin. This metabolic pathway was investigated in enrichment cultures inoculated with water samples collected at 70 m depth in the anoxic zone of Lake Pavin. Combinations of different media, organic acids, and incubation gas phases were performed. The potential for Fe(III) reduction in the different growth conditions was assessed by measuring the accumulation of Fe(II) overtime. Bacterial community structure was determined in each growth conditions by Temporal Temperature gradient Gel Electrophoresis (TTGE) profiles of 16S rDNA genes and bands of interest in positive enrichments were sequenced. Comparisons of bacterial community structure between growth conditions revealed that the electron donor, the basal media as well as the Fe(III) source yielded to the selection of different bacterial populations, suggesting that Fe(III) reducers occupy different ecological niches in the anoxic zone of Lake Pavin. Facultative Fe(III) reducers, such as fermentative (e.g., Pseudomonas, Clostridium) and sulphate-reducing (e.g., Desulfovibrio sp.) bacteria, were retrieved in enrichments but well-known obligatory Fe(III) reducers (e.g., Geobacter) were not detected. A greater Fe(III) reduction was noted under H2:CO2 gas phase, suggesting that H2 is used as an electron donor for Fe(III) reduction. Acetate was not used as a precursor for this terminal electron-accepting process, and a high Fe(III) reduction was observed with fumarate provided as the electron donor and carbon sources suggesting that this metabolite may be energetically more beneficial for Fe(III)-reducers.

Members of candidate divisions OP11, OD1 and SR1 are widespread along the water column of the meromictic Lake Pavin (France)

The vertical distribution of OP11, OD1 and SR1 divisions in the oxycline and in the anoxic water column of Lake Pavin, a freshwater permanently stratified mountain lake in France, was determined by temporal temperature gel gradient electrophoresis and 16S rRNA clone libraries. Gradual changes in the community structure were noted in relation to environmental variables along the oxidized/reduced environment. In addition, a separate effort to identify members of these lineages in the oxic mixolimnion identified sequences affiliated to SR1 and OP11 divisions, indicating that they are more widespread than previously expected.

Ferric Iron Reduction by Fermentative Strain BS2 Isolated From an Iron-Rich Anoxic Environment (Lake Pavin, France)

A facultatively Fe-reducing strain BS2 related to Clostridium saccarobutylicum was isolated from the anoxic zone of iron-rich Lake Pavin. A comparative study was performed on the growth, fermentative profile and heat production of BS2 on glucose in presence and absence of Fe(III). Fe(III) availability led to an optimization of glucose uptake and higher maintenance of strain BS2 in the growth media. Given the prevailing conditions (e.g., scarcity of metabolizable organic matter) in the anoxic zone of Lake Pavin, Fe(III) reduction by this facultative Fe(III) reducer may confer ecological benefits to strain BS2. Moreover, in presence of Fe(III), there was a modification of the fermentative balance that may influence the terminal-accepting processes in this layer.

Methanobacterium lacus sp. nov., isolated from the profundal sediment of a freshwater meromictic lake

An autotrophic, hydrogenotrophic methanogen, designated strain 17A1(T), was isolated from the profundal sediment of the meromictic Lake Pavin, France. The cells of the novel strain, which were non-motile, Gram-staining-negative rods that measured 2-15 µm in length and 0.2-0.4 µm in width, grew as filaments. Strain 17A1(T) grew in a mineral medium and its growth was stimulated by the addition of yeast extract, vitamins, acetate or rumen fluid. Penicillin, vancomycin and kanamycin reduced growth but did not completely inhibit it. Growth occurred at 14-41 °C (optimum 30 °C), at pH 5.0-8.5 (optimum pH 6.5) and with 0-0.4 M NaCl (optimum 0.1 M). The novel strain utilized H(2)/CO(2) and methanol/H(2) as substrates but not formate, acetate, methylamine/H(2), isobutanol or 2-propanol. Its genomic DNA G+C content was 37.0 mol%. In phylogenetic analyses based on 16S rRNA gene sequences, strain 17A1(T) appeared to be a member of the genus Methanobacterium, with Methanobacterium beijingense 8-2(T) (96.3% sequence similarity) identified as the most closely related established species. Based on phenotypic and phylogenetic data, strain 17A1(T) represents a novel species of methanogen within the genus Methanobacterium, for which the name Methanobacterium lacus sp. nov. is proposed. The type strain is 17A1(T) (=DSM 24406(T)=JCM 17760(T)).

The hydrological context determines the beta-diversity of aerobic anoxygenic phototrophic bacteria in European Arctic seas but does not favor endemism

Despite an increasing number of studies over the last 15 years, aerobic anoxygenic photoheterotrophic (AAP) bacteria remain a puzzling functional group in terms of physiology, metabolism, and ecology. To contribute to a better knowledge of their environmental distribution, the present study aims at analyzing their diversity and structure at the boundary between the Norwegian, Greenland, and Barents Seas. The polymorphism of a marker gene encoding a sub-unit of the photosynthetic apparatus (pufM gene) was analyzed and attempted to be related to environmental parameters. The Atlantic or Arctic origin of water masses had a strong impact on the AAP bacterial community structure whose populations mostly belonged to the Alpha- and Gammaproteobacteria. A majority (>60%) of pufM sequences were affiliated to the Gammaproteobacteria reasserting that this class often represents the major component of the AAP bacterial community in oceanic regions. Two alphaproteobacterial groups dominate locally suggesting that they can constitute key players in this marine system transiently. We found that temperature is a major determinant of alpha diversity of AAP bacteria in this marine biome with specific clades emerging locally according to the partitioning of water masses. Whereas we expected specific AAP bacterial populations in this peculiar and newly explored ecosystem, most pufM sequences were highly related to sequences retrieved elsewhere. This observation highlights that the studied area does not favor AAP bacteria endemism but also opens new questions about the truthfulness of biogeographical patterns and on the extent of AAP bacterial diversity.

Lake Pavin Paleolimnology and Event Stratigraphy

In this chapter we present an up-to-date database of sedimentary sequences retrieved from Lake Pavin during the last 50 years in both oxic and anoxic waters. The detailed history of this mid Holocene crater lake can be reconstructed from the correlation of radiocarbon dated sedimentary sequences retrieved from the deep central basin, a subaquatic plateau and littoral environments. High-resolution measurements of sediment composition (diffuse spectral refl ectance, XRF core scanning) combined with the analysis of organic matter composition and preliminary pollen and diatom assemblages investigations on selected sediment cores are used to reconstruct (i) the evolution since ca. 7000 cal BP of Lake Pavin limnology together with its radiocarbon reservoir effect and (ii) the impact of a wide range of subaquatic slope failure events. Such a multidisciplinary approach of Lake Pavin basin fi ll revealed contrasted sedimentation patterns just after the volcanic eruption and following the development of a dense vegetation cover along the slopes of the crater. Pavin sedimenta-tion is rapidly and largely dominated by organic rich and fi nely laminated diatomite formation , but several short periods of enhanced mineral inputs might refl ect the infl uence of wetter periods, such as the Little Ice Age. Over the last millennium two large subaquatic mass wasting events are also identifi ed and may have signifi cantly impacted its limnology.

Unexpectedly high bacteriochlorophyll a concentrations in neotropical tank bromeliads

The contribution of bacteriochlorophyll a (BChl a) to photosynthetically driven electron transport is generally low in aquatic and terrestrial systems. Here, we provide evidence that anoxygenic bacterial phototrophy is widespread and substantial in water retained by tank bromeliads of a primary rainforest in French Guiana. An analysis of the water extracted from 104 randomly selected tank bromeliads using infrared fluorimetry suggested the overall presence of abundant anoxygenic phototrophic bacterial populations. We found that purple bacteria dominated these populations responsible for unusually high BChl a/chlorophyll a ratios (>50%). Our data suggest that BChl a-based phototrophy in tank bromeliads can have significant effects on the ecology of tank-bromeliad ecosystems and on the carbon and energy fluxes in Neotropical forests.