Obtaining high biomass yields of specific microorganisms for culture-independent approaches is a challenge faced by scientists studying organism's recalcitrant to laboratory conditions and culture. This difficulty is highly decreased when studying magnetotactic bacteria (MTB) since their unique behaviour allows their enrichment and purification from other microorganisms present in aquatic environments. Here, we use Lake Pavin, a permanently stratified lake in the French Massif Central, as a natural laboratory to optimize collection and concentration of MTB that thrive in the water column and sediments. A method is presented to separate MTB from highly abundant abiotic magnetic particles in the sediment of this crater lake. For the water column, different sampling approaches are compared such as in situ collection using a Niskin bottle and online pumping. By monitoring several physicochemical parameters of the water column, we identify the ecological niche where MTB live. Then, by focusing our sampling at the peak of MTB abundance, we show that the online pumping system is the most efficient for fast recovering of large volumes of water at a high spatial resolution, which is necessary considering the sharp physicochemical gradients observed in the water column. Taking advantage of aerotactic and magnetic MTB properties, we present an efficient method for MTB concentration from large volumes of water. Our methodology represents a first step for further multidisciplinary investigations of the diversity, metagenomic and ecology of MTB populations in Lake Pavin and elsewhere, as well as chemical and isotopic analyses of their magnetosomes.
Dziani Dzaha is a maar the age of which is close to 4000 years. While its water is thought to have originated from seawater it is now considered as an extreme environment due to its hypersaline and alkaline characteristics. Those extreme features have led to the simplification of the trophic network. Cyanobacteria account for up to 95% of the photosynthetic biomass. The main biogeochemical processes, i.e. photosynthesis, bacterial sulfate reduction and methanogenesis could explain the current water composition. As far as we know, this ecosystem could be unique on Earth, extending the nature and chemical limits of aquatic inland ecosystems.
Abstract. Iron and manganese are poorly soluble elements in oxic and alkaline solutions, whereas they are much more soluble under anoxic conditions. As a result, the formation of authigenic mineral phases rich in Fe and/or Mn has traditionally been viewed as diagnostic of global or local anoxic conditions. Here we reveal that some specific cyanobacteria of very small size (< 2 µm, i.e., picocyanobacteria) can biomineralize abundant, authigenic Fe(III)-, Mn(IV)- and Si-rich amorphous phases under oxic conditions in an alkaline lake in Mexico. The resulting biominerals cluster as small globules arranged as rings around the division septum of cyanobacterial cells. These rings are enveloped within an organic, likely polysaccharidic envelope and are partially preserved, at least morphologically, upon sedimentation. Based on their 16S rDNA sequence, these cyanobacteria were affiliated with the Synechococcales order. The high Fe and Mn enrichment of the biominerals questions the systematic inference of anoxic conditions based on their detection. Moreover, this process scavenges iron from the water column, an overlooked biological contribution to the Fe cycle. Finally, it reveals a new case of controlled biomineralization of Si-rich phases by bacteria.
Abstract. The dissolved organic carbon (DOC) reservoir holds a critical role in the C cycle of marine and fresh water environments because of its large size and involvement in many biogeochemical reactions. Despite poor constraints, its importance in ancient Earth’s C cycles is also commonly invoked. However, DOC remains rarely quantified and characterized in modern stratified analogs. Here, we investigated the DOC reservoirs of four redox-stratified alkaline crater lakes from Mexico. To achieve this, we analyzed the concentrations and isotopic compositions of DOC throughout the four water columns and compared them with existing data on dissolved inorganic and particulate organic C reservoirs (DIC and POC). The four lakes have high DOC concentrations with important variability between and within the lakes (averaging 2 ± 4 mM; 1SD, n=28; representing from ~ 15 to 160 times the amount of POC). δ13CDOC signatures also span a broad range of values from -29.3 to -8.7 ‰ (with as much as 12.5 ‰ variation within a single lake). The prominent DOC peaks (up to 21 mM), together with their associated isotopic variability, are interpreted to reflect oxygenic and/or anoxygenic primary productivity through the release of excess fixed-carbon in three of the lakes (Atexcac, La Preciosa and La Alberca de los Espinos). By contrast, the variability of [DOC] and δ13CDOC in Lake Alchichica was mainly explained by partial degradation of organic matter and accumulation of DOC in anoxic waters. Overall, DOC records detailed metabolic functioning such as active DIC-uptake and DIC-concentrating mechanism that cannot be inferred from DIC and POC analyses alone but that are critical to understand carbon fluxes from the environment to the biomass. Extrapolating our results to the geological record, we suggest that anaerobic oxidation of DOC may have caused the very negative C isotope excursions in the Neoproterozoic, but it is unlikely that a large oceanic DOC reservoir overweight the associated DIC reservoir. Overall, this study shows how the analysis of DOC in modern lakes deepens our understanding of the C cycle in stratified environments and how it can help to size boundary conditions to the Earth’s past oceans.
Abstract Studies on microbial communities, and their associated organic biomarkers, that are found thriving in the aphotic euxinic waters in modern stratified ecosystems are scarce compared to those undertaken in euxinic photic zones. The Dziani Dzaha (Mayotte, Indian Ocean) is a tropical, saline, alkaline crater lake that has recently been presented as a modern analog of Proterozoic Oceans due to its thalassohaline classification (having water of marine origin) and specific biogeochemical characteristics. Continuous intense photosynthetic production and microbial mineralization keep most of the water column permanently aphotic and anoxic preventing the development of a euxinic (sulfidic and anoxic) photic zone despite a high sulfide/sulfate ratio and the presence of permanent or seasonal haloclines. In this study, the molecular composition of the organic matter in Lake Dziani Dzaha was investigated and compared to the microbial diversity evaluated through 16S rRNA gene amplicon sequencing, over two contrasting seasons (rainy vs. dry) that influence water column stratification. Depth profiles of organic biomarker concentrations (chlorophyll‐a and lipid biomarkers) and bacterial and archaeal OTU abundances appeared to be strongly dependent on the presence of aphotic haloclines and euxinia. OTU abundances revealed the importance of specific haloalkaliphilic bacterial and archaeal assemblages in phytoplanktonic biomass recycling and the biogeochemical functioning of the lake, suggesting new haloalkaline non‐phototrophic anaerobic microbial precursors for some of the lipid biomarkers. Uncultured Firmicutes from the family Syntrophomonadaceae (Clostridiales), and Bacteroidetes from the ML635J‐40 aquatic group, emerged as abundant chemotrophic bacterial members in the anoxic or euxinic waters and were probably responsible for the production of short‐chain n ‐alkenes, wax esters, diplopterol, and tetrahymanol. Halocline‐dependent euxinia also had a strong impact on the archaeal community which was dominated by Woesearchaeota in the sulfide‐free waters. In the euxinic waters, methanogenic Euryarchaeota from the Methanomicrobia, Thermoplasmata, and WSA2 classes dominated and were likely at the origin of common hydrocarbon biomarkers of methanogens (phytane, pentamethyl‐eicosenes, and partially hydrogenated squalene).
