Genome Sequences and Metagenome-Assembled Genome Sequences of Microbial Communities Enriched on Phytoplankton Exometabolites

Genetic and physiological insights into the diazotrophic activity of a non-cyanobacterial marine diazotroph

Nitrogen (N₂ ) fixation, or diazotrophy, supports a large part of primary production in oceans. Culture-independent approaches highlighted the presence in abundance of marine non-cyanobacterial diazotrophs (NCD), but their ecophysiology remains elusive, mostly because of the low number of isolated NCD and because of the lack of available genetic tools for these isolates. Here, a dual genetic and functional approach allowed unveiling the ecophysiology of a marine NCD affiliated to the species Vibrio diazotrophicus. Physiological characterization of the first marine NCD mutant obtained so far was performed using a soft-gellan assay, demonstrating that a ΔnifH mutant is not able to grow in nitrogen-free media. Furthermore, we demonstrated that V. diazotrophicus produces a thick biofilm under diazotrophic conditions, suggesting biofilm production as an adaptive response of this NCD to cope with the inhibition of nitrogen fixation by molecular oxygen. Finally, the genomic signature of V. diazotrophicus is essentially absent from metagenomic data of Tara Ocean expeditions, despite having been isolated from various marine environments. We think that the genetically tractable V. diazotrophicus strain used in this study may serve as an ideal model to study the ecophysiology of these overlooked procaryotic group.

Metagenome-assembled genomes of phytoplankton microbiomes from the Arctic and Atlantic Oceans

BACKGROUND

Phytoplankton communities significantly contribute to global biogeochemical cycles of elements and underpin marine food webs. Although their uncultured genomic diversity has been estimated by planetary-scale metagenome sequencing and subsequent reconstruction of metagenome-assembled genomes (MAGs), this approach has yet to be applied for complex phytoplankton microbiomes from polar and non-polar oceans consisting of microbial eukaryotes and their associated prokaryotes.

RESULTS

Here, we have assembled MAGs from chlorophyll a maximum layers in the surface of the Arctic and Atlantic Oceans enriched for species associations (microbiomes) with a focus on pico- and nanophytoplankton and their associated heterotrophic prokaryotes. From 679 Gbp and estimated 50 million genes in total, we recovered 143 MAGs of medium to high quality. Although there was a strict demarcation between Arctic and Atlantic MAGs, adjacent sampling stations in each ocean had 51-88% MAGs in common with most species associations between Prasinophytes and Proteobacteria. Phylogenetic placement revealed eukaryotic MAGs to be more diverse in the Arctic whereas prokaryotic MAGs were more diverse in the Atlantic Ocean. Approximately 70% of protein families were shared between Arctic and Atlantic MAGs for both prokaryotes and eukaryotes. However, eukaryotic MAGs had more protein families unique to the Arctic whereas prokaryotic MAGs had more families unique to the Atlantic.

CONCLUSION

Our study provides a genomic context to complex phytoplankton microbiomes to reveal that their community structure was likely driven by significant differences in environmental conditions between the polar Arctic and warm surface waters of the tropical and subtropical Atlantic Ocean. Video Abstract.

Weekly Observations of Estuarine Microbial Assemblages during Summer in the Inner Part of Ariake Bay, Japan; Microbial Water-sediment Coupling in Turbid Shallow Waters

Estuarine microbial assemblages are altered by a number of environmental factors, and knowledge of these changes is essential for understanding the functions of microbes in estuarine ecosystems. The aims of the present study were to examine the relationship between microbial assemblages in the water column and sediment surface, and to identify the environmental factors that influence the short-term dynamics of microbial assemblages in these two zones in summer in the inner part of Ariake Bay. The microbial assemblage of each sample consisted of a mean of 71.1% operational taxonomic units (OTUs), which commonly occurred in the water column and sediment surface, although their relative composition markedly differed between the two zones. In the water column, spatiotemporal changes in microbial assemblages correlated with several environmental factors, such as the nitrogen content in suspended particles, turbidity, and salinity. On the other hand, temporal changes in the sediment’s microbial assemblages were governed by a single environmental factor, namely, the oxygen reduction potential. These results suggest that the composition of microbial assemblages in the water column and sediment surface differed even in highly turbid brackish waters with high sediment resuspension, and the environmental factors contributing to the change in the assemblage composition also differed between the water column and sediment.