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.

Biogeochemical niche of phosphorus sequestrating magnetotactic bacteria in Lake Pavin, a freshwater feruginous environment.

<p>Phosphorus (P) is essential to life but a limiting nutrient in many ecosystems. Understanding the role of microorganisms in P cycling, especially the processes of P uptake and storage, is a major environmental issue.  Only few models are known to highly sequestrate phosphorus and mostly in marine environments. We thus need to improve our knowledge about other model of sequestration and especially in freshwater environments.</p><p>Freshwater magnetotactic bacteria (MTB) affiliated to the Magnetococcaceae family have been identified within the water column of Lake Pavin in France [3]. Similarly, to the marine Thiomarguarita and Beggiatoa [1, 2], they accumulate intracellular polyphosphates (PolyP) to a uniquely high extent, up to 90% of their cell volume. In contradiction with the marine Thiomarguarita and Beggiatoa, the Magnetococcaceae accumulate PolyP in anoxic conditions. They represent the major population of MTB and are located right under the oxic-anoxic interface in a zone of strong chemical and redox gradients. These gradients allow the study of the impact of varying chemical conditions on microbial physiology.</p><p>We aim at characterizing Magnetococcaceae distribution as a function of depth and therefore of different chemical parameters, but also at determining the drivers of PolyP accumulation. </p><p>Here, we combine a variety of methods to analyse these MTB and their potential appartenance to a specific ecological niche in the water column. We measured the physico-chemical parameters of the water column (O<sub>2</sub>, pH, redox, conductivity, FDOM, turbidity, etc.). We used a new sampling system that allowed us to reach a better spatial resolution [4], from 1 m to 20 cm. We were therefore able to better estimate the impact of the chemical parameters on the MTB. We then sampled the water to measure the geochemical parameters using ICP-OES and to characterize MTB via optical and electronic microscopy. Optical microscopy helped identify the main populations of MTB and their concentrations, while electronic microscopy permitted the characterization of the different magnetosome organisation and PolyP accumulation capacities. Multivariate statistics were finally performed on all data.</p><p>Multivariate statistics identified several parameters positively and significantly correlated to the Magnetococcaceae. These parameters are different from the ones correlated to other MTB of the water column. We therefore show that the Magnetococcaceae live into a specific niche with specific biogeochemical parameters. These correlated parameters include dissolved lithium concentration, mass percentage of nitrogen, magnesium and particulate P. Phosporus  and magnesium are linked to the formation of PolyP, lithium represent a cofactor for phosphate transport [5] and nitrogen might be linked to nitrate transportation by the MTB [6].</p><p>Genomic analyses will be done in the future to allow further comprehension on molecular mecanisms and PolyP formation.</p><p> </p><p>[1] Brock J, Schulz-Vogt HN. (2011) ISME Journal <strong>5</strong>, 497-506. [2] Mubmann M et al. (2007) PLoS Biology <strong>5</strong>(9), e230. [3] Rivas-Lamelo S et al. (2017) Geochem. Persp. Let. <strong>5</strong>, 35–41. [4] Busigny et al., submitted to Environmental Microbiology. [5] Jakobsson E et al. (2017) J. Membr. Biol. <strong>250</strong>,587-604. [6] Li et al. (2020) Geophys. Res. Biogeosciences.</p>

Metabolic marker gene mining provides insight in globalmcrAdiversity and, coupled with targeted genome reconstruction, sheds further light on metabolic potential of theMethanomassiliicoccales

Over the past years, metagenomics has revolutionized our view of microbial diversity. Moreover, extracting near-complete genomes from metagenomes has led to the discovery of known metabolic traits in unsuspected lineages. Genome-resolved metagenomics relies on assembly of the sequencing reads and subsequent binning of assembled contigs, which might be hampered by strain heterogeneity or low abundance of a target organism. Here we present a complementary approach, metagenome marker gene mining, and use it to assess the global diversity of archaeal methane metabolism through themcrAgene. To this end, we have screened 18,465 metagenomes for the presence of reads matching a database representative of all known mcrA proteins and reconstructed gene sequences from the matching reads. We use our mcrA dataset to assess the environmental distribution of theMethanomassiliicoccalesand reconstruct and analyze a draft genome belonging to the ‘Lake Pavin cluster’, an uncultivated environmental clade of theMethanomassiliicoccales. Analysis of the ‘Lake Pavin cluster’ draft genome suggests that this organism has a more restricted capacity for hydrogenotrophic methylotrophic methanogenesis than previously studiedMethanomassiliicoccales, with only genes for growth on methanol present. However, the presence of the soluble subunits of methyltetrahydromethanopterin:CoM methyltransferase (mtrAH)provide hypothetical pathways for methanol fermentation, and aceticlastic methanogenesis that await experimental verification. Thus, we show that marker gene mining can enhance the discovery power of metagenomics, by identifying novel lineages and aiding selection of targets for in-depth analyses. Marker gene mining is less sensitive to strain heterogeneity and has a lower abundance threshold than genome-resolved metagenomics, as it only requires short contigs and there is no binning step. Additionally, it is computationally cheaper than genome resolved metagenomics, since only a small subset of reads needs to be assembled. It is therefore a suitable approach to extract knowledge from the many publicly available sequencing projects.

Metabolic marker gene mining provides insight in global mcrA diversity and, coupled with targeted genome reconstruction, sheds light on metabolic versatility of theMethanomassiliicoccales

Over the past years, metagenomics has revolutionized our view of microbial diversity. Moreover, extracting near-complete genomes from metagenomes has led to the discovery of known metabolic traits in unsuspected lineages. Genome-resolved metagenomics relies on assembly of the sequencing reads and subsequent binning of assembled contigs, which might be hampered by strain heterogeneity or low abundance of a target organism. Here we present a complementary approach, metagenome marker gene mining, and use it to assess the global diversity of archaeal methane metabolism through the mcrA gene. To this end, we have screened 18,465 metagenomes for the presence of reads matching a database representative of all known mcrA proteins and reconstructed gene sequences from the matching reads. We use our mcrA dataset to assess the environmental distribution of theMethanomassiliicoccalesand reconstruct and analyze a draft genome belonging to the ‘Lake Pavin cluster’, an understudied environmental clade of theMethanomassiliicoccales. Thus, we show that marker gene mining can enhance the discovery power of metagenomics, by identifying novel lineages and aiding selection of targets for in-depth analyses. Marker gene mining is less sensitive to strain heterogeneity and has a lower abundance threshold than genome-resolved metagenomics, as it only requires short contigs and there is no binning step. Additionally, it is computationally cheaper than genome resolved metagenomics, since only a small subset of reads needs to be assembled. It is therefore a suitable approach to extract knowledge from the many publicly available sequencing projects.