Eric Viollier

Anaerobic lake sediments harbour fermentative micro-organisms that contribute to organic-matter degradation and dihydrogen (H ₂ ) turnover. Strain PP1C4 ^T was isolated from sediment of Lake Pavin, a permanently stratified meromictic lake characterized by active anaerobic microbial processes, including methanogenesis and characterized using a polyphasic taxonomic approach. Cells were strictly anaerobic, Gram-stain-negative, motile rods. Growth occurred at 19–37 °C (optimum, 30 °C), pH 7.0–9.0 (optimum, pH 7.0) and NaCl concentrations of 0–20 g l⁻¹ (optimum, 1 g l ⁻¹ ). Glucose fermentation produced propionate and butyrate as major organic end-products together with CO _₂ and H ₂ . Phylogenetic analysis placed PP1C4 ^T within the family Oscillospiraceae , with the highest 16S rRNA gene sequence similarity to ‘ Marasmitruncus massiliensis ’ Marseille-P3646 (95.2%). The genome was ∼3.4 Mb with a DNA G+C content of 45.6 mol%. Maximum blast -based average nucleotide identity and average amino acid identity values between PP1C4 ^T and the compared taxa were 71.53 and 69.30%, respectively, and in silico DNA–DNA hybridization values ranged from 18.0 to 24.3%. Based on the combined phylogenetic, genomic, phenotypic and chemotaxonomic evidence, strain PP1C4ᵀ represents a novel genus and species within the family Oscillospiraceae , for which the name Hydrogenimesophilus fermentans gen. nov., sp. nov. is proposed. The type strain is PP1C4 ^T (=DSM 118145 ^T =CIP 112512ᵀ).

River-dominated ocean margins (RiOMars), located at the land-ocean boundary, are susceptible to both land- and ocean-based stressors. Due to climate change, hydrological regimes are expected to change, with, for example, an increase in the intensity and frequency of river floods in the near future. To better understand the impact of these changes on the benthic ecosystem in RiOMars, we conducted eleven sampling campaigns in the Rhône River prodelta (Mediterranean Sea, France) between October 2023 and September 2024. We measured variations in total oxygen uptake (TOU), and benthic fluxes of dissolved inorganic carbon (DIC) and total alkalinity (AT), using ex-situ core incubations. Our results show integrated values of 26 ± 4, 54 ± 6, and 41 ± 5 mmol m-2 d-1 for TOU, and fluxes of DIC and AT, respectively, with strong variability throughout the year. Flood material derived from the western flank of the Rhône River likely contained relatively more labile organic matter (OM) compared to that of the rest of the catchment area. The lowest fluxes were observed after large flood depositions, likely containing large amounts of non-reactive OM, while high fluxes occurred after smaller flood depositions with, possibly, high labile OM content. The highest rates (DIC: 104 ± 8, AT: 81 ± 6, TOU: 35 ± 9 mmol m-2 d-1) occurred in spring and early summer due to the conceivable input of fresh, labile OM from riverine primary production. Our results thus highlight the relationships among river catchment area, the origin of flood material, seasonality, OM quality, and their effects on benthic flux rates.

Magnetotactic bacteria form a highly diverse group of microorganisms, yet early exploration of their diversity was largely centered on the Pseudomonadota. More recently, metagenomic studies have revealed that magnetotaxis, a form of chemotaxis guided by Earth’s magnetic field, is widespread in other deep-branching phyla for which little to no ecological or biological information is available beyond that inferred from their genomes. For most of them, the morphology, ultrastructure and magnetosome chain characteristics responsible for the magnetic guidance remain unknown. While screening extreme environments for novel magnetotactic species, we observed magnetotactic Bdellovibrionota in the anoxic and ferruginous sediments of the Fontaine Goyon spring (France). We characterized their cell morphology and ultrastructure using magnetic enrichment, a single-cell sorting approach, and high-resolution electron microscopy. Cells display the morphology typical of the few predatory bacteria described in this phylum, and biomineralize, on average, five irregularly faceted, bullet-shaped magnetite magnetosomes along the concave side of the cell. Metagenomic analysis of approximately 100 cells revealed a potentially predatory and heterotrophic lifestyle adapted to low-O2 conditions. It also suggests a flexible respiratory metabolism under varying redox conditions, using iron as an alternative terminal electron acceptor. Exploring the diversity of Bdellovibrionota in public databases, we found 21 metagenome-assembled-genomes containing magnetosome genes. None of them harbor the canonical mamK actin-like gene implicated in aligning magnetosomes in described magnetotactic models. Affiliated to an undescribed class, we propose a classification scheme for the magnetotactic Bdellovibrionota species representing the class Bdellonasia class nov., for which no species had been formally described.

An anaerobic, spore-forming, 3-hydroxybutyrate (3-HB)-producing bacterium, strain IPX_CK^T, was isolated from sediment of a meromictic lake located in Massif Central (France). Cells were rods, forming filamentous chains which were observed moving under the microscope. Strain IPX_CK^T utilized a wide variety of carbohydrates, but not raffinose, rhamnose and starch. Hydrogen (H₂), 3-HB, acetate and ethanol were the main fermentative end-products from growth in medium containing glucose. Strain IPX_CK^T grew optimally at 37 °C and pH 7. Its closest phylogenetic relative was Kineothrix alysoides (16S rRNA gene sequence identity 98.7%, isDDH 34.6%, ANIb 87.4%). The genomic DNA G+C content was 43.0 mol%. As for K. alysoides, whole-genome sequencing suggested that strain IPX_CK^T is capable of fixing nitrogen (N₂). However, strain IPX_CK^T carried a five-nif-gene-set (nifHDKEB), not present in K. alysoides. Genome sequence also showed a high number of encoded chemotaxis receptors (42 genes, the second highest in the family Lachnospiraceae after K. alysoides). Based on phenotypic, genomic, phylogenetic and chemotaxonomic analyses, it is proposed that a novel species, Kineothrix sedimenti sp. nov., be created, with strain IPX_CK^T (DSM 118044^T, CIP 112511^T) as the type strain.

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.

Summary: 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.