A pan-genomic approach reveals novel Sulfurimonas clade in the ferruginous meromictic Lake Pavin.

The permanently anoxic waters in meromictic lakes create suitable niches for the growth of bacteria using sulphur metabolisms like sulphur oxidation. In Lake Pavin, the anoxic water mass hosts an active cryptic sulphur cycle that interacts narrowly with iron cycling, however the metabolisms of the microorganisms involved are poorly known. Here we combined metagenomics, single-cell genomics, and pan-genomics to further expand our understanding of the bacteria and the corresponding metabolisms involved in sulphur oxidation in this ferruginous sulphide- and sulphate-poor meromictic lake. We highlighted two new species within the genus Sulfurimonas that belong to a novel clade of chemotrophic sulphur oxidisers exclusive to freshwaters. We moreover conclude that this genus holds a key-role not only in limiting sulphide accumulation in the upper part of the anoxic layer but also constraining carbon, phosphate and iron cycling.

Diversity of the Pacific Ocean coral reef microbiome.

Coral reefs are among the most diverse ecosystems on Earth. They support high biodiversity of multicellular organisms that strongly rely on associated microorganisms for health and nutrition. However, the extent of the coral reef microbiome diversity and its distribution at the oceanic basin-scale remains to be explored. Here, we systematically sampled 3 coral morphotypes, 2 fish species, and planktonic communities in 99 reefs from 32 islands across the Pacific Ocean, to assess reef microbiome composition and biogeography. We show a very large richness of reef microorganisms compared to other environments, which extrapolated to all fishes and corals of the Pacific, approximates the current estimated total prokaryotic diversity for the entire Earth. Microbial communities vary among and within the 3 animal biomes (coral, fish, plankton), and geographically. For corals, the cross-ocean patterns of diversity are different from those known for other multicellular organisms. Within each coral morphotype, community composition is always determined by geographic distance first, both at the island and across ocean scale, and then by environment. Our unprecedented sampling effort of coral reef microbiomes, as part of the Tara Pacific expedition, provides new insight into the global microbial diversity, the factors driving their distribution, and the biocomplexity of reef ecosystems.

Ecology of Endozoicomonadaceae in three coral genera across the Pacific Ocean.

Health and resilience of the coral holobiont depend on diverse bacterial communities often dominated by key marine symbionts of the Endozoicomonadaceae family. The factors controlling their distribution and their functional diversity remain, however, poorly known. Here, we study the ecology of Endozoicomonadaceae at an ocean basin-scale by sampling specimens from three coral genera (Pocillopora, Porites, Millepora) on 99 reefs from 32 islands across the Pacific Ocean. The analysis of 2447 metabarcoding and 270 metagenomic samples reveals that each coral genus harbored a distinct new species of Endozoicomonadaceae. These species are composed of nine lineages that have distinct biogeographic patterns. The most common one, found in Pocillopora, appears to be a globally distributed symbiont with distinct metabolic capabilities, including the synthesis of amino acids and vitamins not produced by the host. The other lineages are structured partly by the host genetic lineage in Pocillopora and mainly by the geographic location in Porites. Millepora is more rarely associated to Endozoicomonadaceae. Our results show that different coral genera exhibit distinct strategies of host-Endozoicomonadaceae associations that are defined at the bacteria lineage level.

Seasonal microbial dynamics in the ocean inferred from assembled and unassembled data: a view on the unknown biosphere.

In environmental metagenomic experiments, a very high proportion of the microbial sequencing data (> 70%) remains largely unexploited because rare and closely related genomes are missed in short-read assemblies. The identity and the potential metabolisms of a large fraction of natural microbial communities thus remain inaccessible to researchers. The purpose of this study was to explore the genomic content of unassembled metagenomic data and test their level of novelty. We used data from a three-year microbial metagenomic time series of the NW Mediterranean Sea, and conducted reference-free and database-guided analysis. The results revealed a significant genomic difference between the assembled and unassembled reads. The unassembled reads had a lower mean identity against public databases, and fewer metabolic pathways could be reconstructed. In addition, the unassembled fraction presented a clear temporal pattern, unlike the assembled ones, and a specific community composition that was similar to the rare communities defined by metabarcoding using the 16S rRNA gene. The rare gene pool was characterised by keystone bacterial taxa, and the presence of viruses, suggesting that viral lysis could maintain some taxa in a state of rarity. Our study demonstrates that unassembled metagenomic data can provide important information on the structure and functioning of microbial communities.

Seasonality of archaeal proteorhodopsin and associated Marine Group IIb ecotypes (Ca. Poseidoniales) in the North Western Mediterranean Sea.

The Archaea Marine Group II (MGII) is widespread in the world's ocean where it plays an important role in the carbon cycle. Despite recent discoveries on the group's metabolisms, the ecology of this newly proposed order (Candidatus Poseidoniales) remains poorly understood. Here we used a combination of time-series metagenome-assembled genomes (MAGs) and high-frequency 16S rRNA data from the NW Mediterranean Sea to test if the taxonomic diversity within the MGIIb family (Candidatus Thalassarchaeaceae) reflects the presence of different ecotypes. The MAGs' seasonality revealed a MGIIb family composed of different subclades that have distinct lifestyles and physiologies. The vitamin metabolisms were notably different between ecotypes with, in some, a possible link to sunlight's energy. Diverse archaeal proteorhodopsin variants, with unusual signature in key amino acid residues, had distinct seasonal patterns corresponding to changing day length. In addition, we show that in summer, archaea, as opposed to bacteria, disappeared completely from surface waters. Our results shed light on the diversity and the distribution of the euryarchaeotal proteorhodopsin, and highlight that MGIIb is a diverse ecological group. The work shows that time-series based studies of the taxonomy, seasonality, and metabolisms of marine prokaryotes is critical to uncover their diverse role in the ocean.

The environment drives microbial trait variability in aquatic habitats.

A prerequisite to improve the predictability of microbial community dynamics is to understand the mechanisms of microbial assembly. To study factors that contribute to microbial community assembly, we examined the temporal dynamics of genes in five aquatic metagenome time-series, originating from marine offshore or coastal sites and one lake. With this trait-based approach we expected to find gene-specific patterns of temporal allele variability that depended on the seasonal metacommunity size of carrier-taxa and the variability of the milieu and the substrates to which the resulting proteins were exposed. In more detail, we hypothesized that a larger seasonal metacommunity size would result in increased temporal variability of functional units (i.e., gene alleles), as shown previously for taxonomic units. We further hypothesized that multicopy genes would feature higher temporal variability than single-copy genes, as gene multiplication can result from high variability in substrate quality and quantity. Finally, we hypothesized that direct exposure of proteins to the extracellular environment would result in increased temporal variability of the respective gene compared to intracellular proteins that are less exposed to environmental fluctuations. The first two hypotheses were confirmed in all data sets, while significant effects of the subcellular location of gene products was only seen in three of the five time-series. The gene with the highest allele variability throughout all data sets was an iron transporter, also representing a target for phage infection. Previous work has emphasized the role of phage-prokaryote interactions as a major driver of microbial diversity. Our finding therefore points to a potentially important role of iron transporter-mediated phage infections for the assembly and maintenance of diversity in aquatic prokaryotes.

Genomic ecology of Marine Group II, the most common marine planktonic Archaea across the surface ocean.

Planktonic Archaea have been detected in all the world's oceans and are found from surface waters to the deep sea. The two most common Archaea phyla are Thaumarchaeota and Euryarchaeota. Euryarchaeota are generally more common in surface waters, but very little is known about their ecology and their potential metabolisms. In this study, we explore the genomic ecology of the Marine Group II (MGII), the main marine planktonic Euryarchaeota, and test if it is composed of different ecologically relevant units. We re-analyzed Tara Oceans metagenomes from the photic layer and the deep ocean by annotating sequences against a custom MGII database and by mapping gene co-occurrences. Our data provide a global view of the distribution of Euryarchaeota, and more specifically of MGII subgroups, and reveal their association to a number of gene-coding sequences. In particular, we show that MGII proteorhodopsins were detected in both the surface and the deep chlorophyll maximum layer and that different clusters of these light harvesting proteins were present. Our approach helped describing the set of genes found together with specific MGII subgroups. We could thus define genomic environments that could theoretically describe ecologically meaningful units and the ecological niche that they occupy.

New insights into the pelagic microorganisms involved in the methane cycle in the meromictic Lake Pavin through metagenomics.

Advances in metagenomics have given rise to the possibility of obtaining genome sequences from uncultured microorganisms, even for those poorly represented in the microbial community, thereby providing an important means to study their ecology and evolution. In this study, metagenomic sequencing was carried out at four sampling depths having different oxygen concentrations or environmental conditions in the water column of Lake Pavin. By analyzing the sequenced reads and matching the contigs to the proxy genomes of the closest cultivated relatives, we evaluated the metabolic potential of the dominant planktonic species involved in the methane cycle. We demonstrated that methane-producing communities were dominated by the genus Methanoregula while methane-consuming communities were dominated by the genus Methylobacter, thus confirming prior observations. Our work allowed the reconstruction of a draft of their core metabolic pathways. Hydrogenotrophs, the genes required for acetate activation in the methanogen genome, were also detected. Regarding methanotrophy, Methylobacter was present in the same areas as the non-methanotrophic, methylotrophic Methylotenera, which could suggest a relationship between these two groups. Furthermore, the presence of a large gene inventory for nitrogen metabolism (nitrate transport, denitrification, nitrite assimilation and nitrogen fixation, for instance) was detected in the Methylobacter genome.

A strong link between marine microbial community composition and function challenges the idea of functional redundancy.

Marine microbes have tremendous diversity, but a fundamental question remains unanswered: why are there so many microbial species in the sea? The idea of functional redundancy for microbial communities has long been assumed, so that the high level of richness is often explained by the presence of different taxa that are able to conduct the exact same set of metabolic processes and that can readily replace each other. Here, we refute the hypothesis of functional redundancy for marine microbial communities by showing that a shift in the community composition altered the overall functional attributes of communities across different temporal and spatial scales. Our metagenomic monitoring of a coastal northwestern Mediterranean site also revealed that diverse microbial communities harbor a high diversity of potential proteins. Working with all information given by the metagenomes (all reads) rather than relying only on known genes (annotated orthologous genes) was essential for revealing the similarity between taxonomic and functional community compositions. Our finding does not exclude the possibility for a partial redundancy where organisms that share some specific function can coexist when they differ in other ecological requirements. It demonstrates, however, that marine microbial diversity reflects a tremendous diversity of microbial metabolism and highlights the genetic potential yet to be discovered in an ocean of microbes.