Biogeochemical Niche of Magnetotactic Cocci Capable of Sequestering Large Polyphosphate Inclusions in the Anoxic Layer of the Lake Pavin Water Column

Magnetotactic bacteria (MTB) are microorganisms thriving mostly at oxic–anoxic boundaries of aquatic habitats. MTB are efficient in biomineralising or sequestering diverse elements intracellularly, which makes them potentially important actors in biogeochemical cycles. Lake Pavin is a unique aqueous system populated by a wide diversity of MTB with two communities harbouring the capability to sequester not only iron under the form of magnetosomes but also phosphorus and magnesium under the form of polyphosphates, or calcium carbonates, respectively. MTB thrive in the water column of Lake Pavin over a few metres along strong redox and chemical gradients representing a series of different microenvironments. In this study, we investigate the relative abundance and the vertical stratification of the diverse populations of MTB in relation to environmental parameters, by using a new method coupling a precise sampling for geochemical analyses, MTB morphotype description, and in situ measurement of the physicochemical parameters. We assess the ultrastructure of MTB as a function of depth using light and electron microscopy. We evidence the biogeochemical niche of magnetotactic cocci, capable of sequestering large PolyP inclusions below the oxic–anoxic transition zone. Our results suggest a tight link between the S and P metabolisms of these bacteria and pave the way to better understand the implication of MTB for the P cycle in stratified environmental conditions.

Depth-discrete metagenomics reveals the roles of microbes in biogeochemical cycling in the tropical freshwater Lake Tanganyika

Lake Tanganyika (LT) is the largest tropical freshwater lake, and the largest body of anoxic freshwater on Earth’s surface. LT’s mixed oxygenated surface waters float atop a permanently anoxic layer and host rich animal biodiversity. However, little is known about microorganisms inhabiting LT’s 1470 meter deep water column and their contributions to nutrient cycling, which affect ecosystem-level function and productivity. Here, we applied genome-resolved metagenomics and environmental analyses to link specific taxa to key biogeochemical processes across a vertical depth gradient in LT. We reconstructed 523 unique metagenome-assembled genomes (MAGs) from 34 bacterial and archaeal phyla, including many rarely observed in freshwater lakes. We identified sharp contrasts in community composition and metabolic potential with an abundance of typical freshwater taxa in oxygenated mixed upper layers, and Archaea and uncultured Candidate Phyla in deep anoxic waters. Genomic capacity for nitrogen and sulfur cycling was abundant in MAGs recovered from anoxic waters, highlighting microbial contributions to the productive surface layers via recycling of upwelled nutrients, and greenhouse gases such as nitrous oxide. Overall, our study provides a blueprint for incorporation of aquatic microbial genomics in the representation of tropical freshwater lakes, especially in the context of ongoing climate change, which is predicted to bring increased stratification and anoxia to freshwater lakes.

Siderite-based anaerobic iron cycle driven by autotrophic thermophilic microbial consortium

Using a sample from a terrestrial hot spring (pH 6.8, 60 °C), we enriched a thermophilic microbial consortium performing anaerobic autotrophic oxidation of hydrothermal siderite (FeCO3), with CO2/bicarbonate as the electron acceptor and the only carbon source, producing green rust and acetate. In order to reproduce Proterozoic environmental conditions during the deposition of banded iron formation (BIF), we incubated the microbial consortium in a bioreactor that contained an unmixed anoxic layer of siderite, perfectly mixed N2/CO2-saturated liquid medium and microoxic (2% O2) headspace. Long-term incubation (56 days) led to the formation of magnetite (Fe3O4) instead of green rust as the main product of Fe(II) oxidation, the precipitation of newly formed metabolically induced siderite in the anoxic zone, and the deposition of hematite (Fe2O3) on bioreactor walls over the oxycline boundary. Acetate was the only metabolic product of CO2/bicarbonate reduction. Thus, we have demonstrated the ability of autotrophic thermophilic microbial consortium to perform a short cycle of iron minerals transformation: siderite–magnetite–siderite, accompanied by magnetite and hematite accumulation. This cycle is believed to have driven the evolution of the early biosphere, leading to primary biomass production and deposition of the main iron mineral association of BIF.

Zooplankton Community Responses to Oxygen Stress

Recent changes in climate and eutrophication have caused increases in oxygen depletion in both freshwater and marine ecosystems. However, the impact of oxygen stress on zooplankton, which is the major trophic link between primary producers and fish, remains largely unknown in lakes. Therefore, we studied 41 lakes with different trophic and oxygen conditions to assess the role of oxygen stress on zooplankton communities and carbon transfer between phytoplankton and zooplankton. Samples were collected from each lake at the peak of summer stratification from three depth layers (the epilimnion, metalimnion, and hypolimnion). Our results revealed that freshwater zooplankton were relatively tolerant to anoxic conditions and the greatest changes in community structure were found in lakes with the highest oxygen deficits. This caused a switch in dominance from large to small species and reduced the zooplankton biomass in lower, anoxic layers of water, but not in the upper layers of water where the oxygen deficits began. This upper anoxic layer could thus be a very important refuge for zooplankton to avoid predation during the day. However, the reduction of zooplankton in the lower water layers was the main factor that reduced the effectiveness of carbon transfer between the phytoplankton and zooplankton.

Depth-discrete metagenomics reveals the roles of microbes in biogeochemical cycling in the tropical freshwater Lake Tanganyika

Lake Tanganyika (LT) is the largest tropical freshwater lake, and the largest body of anoxic freshwater on Earth’s surface. LT’s mixed oxygenated surface waters float atop a permanently anoxic layer and host rich animal biodiversity. However, little is known about microorganisms inhabiting LT’s 1470 m deep water column and their contributions to nutrient cycling, which affect ecosystem-level function and productivity. Here, we applied genome-resolved metagenomics and environmental analyses to link specific taxa to key biogeochemical processes across a vertical depth gradient in LT. We reconstructed 523 unique metagenome-assembled genomes (MAGs) from 21 bacterial and archaeal phyla, including many rarely observed in freshwater lakes. We identified sharp contrasts in community composition and metabolic potential with an abundance of typical freshwater taxa in oxygenated mixed upper layers, and Archaea and uncultured Candidate Phyla in deep anoxic waters. Genomic capacity for nitrogen and sulfur cycling was abundant in MAGs recovered from anoxic waters, highlighting microbial contributions to the productive surface layers via recycling of upwelled nutrients, and greenhouse gases such as nitrous oxide. Overall, our study provides a blueprint for incorporation of aquatic microbial genomics in the representation of tropical freshwater lakes, especially in the context of ongoing climate change which is predicted to bring increased stratification and anoxia to freshwater lakes.

Study of macroinvertebrate in two intertidal soft bottoms: reference data in conditions of incipient anthropic impact

In this study, we analyzed the relation between the abundance of benthic macroinvertebrates and relevant environmental variables in two intertidal in Golfo Nuevo (Argentinean patagonia), one near a urban center (Mimosa Beach, PM) and the other at 20 km from that location (Cerro Avanzado Beach, CA). Within each beach, the environmental conditions were homogeneous (90% of similarity). Mean size grain values, anoxic layer depth, and percent organic matter were 117.6 µm, 4.95 cm and 0.76%, and 165.2 µm, 9.5 cm and 0.63%, for PM and CA respectively. Even though three families were the most abundant in both beaches (Tellinidae, Maldanidae and Opheliidae), nine families were exclusively observed in PM. This resulted in a higher biodiversity in PM (3.06) in relation to CA (1.77). When faunal composition was considered, the similarity between sites was notably low (lower than 82%) if compared with the environmental conditions. Granulometry and organic matter were the variables with the highest correlation with macroinvertebrates abundance. This is the first study of macroinvertebrates and their relationship with some environmental variables throughout the complete spatial extension of two beaches in Golfo Nuevo. This is of particular relevance if we consider that coastal regions of this gulf has been exposed to a sustained increase of anthropic activities in the last years and base- line information is scarce.

Recycling and fluxes of carbon gases in a stratified boreal lake following experimental carbon addition

Partly anoxic stratified humic lakes are important sources of methane (CH4) and carbon dioxide (CO2) to the atmosphere. We followed the fate of CH4 and CO2 in a small boreal stratified lake, Alinen Mustajärvi, during 2007–2009. In 2008 and 2009 the lake received additions of dissolved organic carbon (DOC) with stable carbon isotope ratio (δ13C) around 16‰ higher than that of local allochthonous DOC. Carbon transformations in the water column were studied by measurements of δ13C of CH4 and of the dissolved inorganic carbon (DIC). Furthermore, CH4 and CO2 production, consumption and emissions were estimated. Methane oxidation was estimated by a diffusion gradient method. The amount, location and δ13C of CH4-derived biomass and CO2 in the water column were estimated from the CH4 oxidation pattern and from measured δ13C of CH4. Release of CH4 and CO2 to the atmosphere increased during the study. Methane production and almost total consumption of CH4 mostly in the anoxic water layers, was equivalent to the input from primary production (PP). δ13C of CH4 and DIC showed that hydrogenotrophic methanogenesis was the main source of CH4 to the water column, and methanogenic processes in general were the reasons for the 13C-enriched DIC at the lake bottom. CH4 and DIC became further 13C-enriched in the anoxic layer of the water column during the years of DOC addition. Even gradient diffusion measurements showed active CH4 oxidation in the anoxic portion of the water column; there was no clear 13C-enrichment of CH4 as generally used to estimate CH4 oxidation strength. Increase in δ13C-CH4 was clear between the metalimnion and epilimnion where the concentration of dissolved CH4 and the oxidation of CH4 were small. Thus, 13C-enrichment of CH4 does not reveal the main location of methanotrophy in a lake having simultaneous anaerobic and aerobic oxidation of CH4. Overall the results show that organic carbon is processed efficiently to CH4 and CO2 and recycled in the anoxic layer of stratified boreal lakes by CH4 oxidation. In spite of this, increased DOC input led to increased greenhouse gas release, mainly as CO2 but also as CH4. Due to the predominantly anaerobic CH4 oxidation, a relatively small amount of CH4-derived biomass was produced, while a large amount of CH4-derived CO2 was produced in the anoxic bottom zone of the lake.

Anaerobic Microbial Communities in Lake Pavin, a Unique Meromictic Lake in France

ABSTRACT The Bacteria and Archaea from the meromictic Lake Pavin were analyzed in samples collected along a vertical profile in the anoxic monimolimnion and were compared to those in samples from the oxic mixolimnion. Nine targeted 16S rRNA oligonucleotide probes were used to assess the distribution of Bacteria and Archaea and to investigate the in situ occurrence of sulfate-reducing bacteria and methane-producing Archaea involved in the terminal steps of the anaerobic degradation of organic material. The diversity of the complex microbial communities was assessed from the 16S rRNA polymorphisms present in terminal restriction fragment (TRF) depth patterns. The densities of the microbial community increased in the anoxic layer, and Archaea detected with probe ARCH915 represented the largest microbial group in the water column, with a mean Archaea/Eubacteria ratio of 1.5. Terminal restriction fragment length polymorphism (TRFLP) analysis revealed an elevated archaeal and bacterial phylotype richness in anoxic bottom-water samples. The structure of the Archaea community remained rather homogeneous, while TRFLP patterns for the eubacterial community revealed a heterogeneous distribution of eubacterial TRFs.

Monitoring the influence of toxic compounds on microbial denitrifying biofilm processes

Microelectrode measurements were conducted to obtain nitrate, pH and redox potential profiles within anoxic denitrifying biofilms. The influence of a toxic organic compound (acid orange 7) on biofilm microprofiles was also monitored using microelectrodes. The data provide evidence that the denitrifying biofilms were stratified into an anoxic layer and an anaerobic layer. The anaerobic zone might provide a niche for the biodegradation of recalcitrant organic compounds in biofilms. It was found that acid orange 7 and its biodegradation byproducts had only a slight impact on biofilm nitrate, pH and redox potential profiles.