Abstract
Niche concept is a core tenet of ecology that has recently been applied in marine microbial research to describe the partitioning of taxa based either on adaptations to specific conditions across environments or on adaptations to specialised substrates. In this study, we combine spatiotemporal dynamics and predicted substrate utilisation to describe species-level niche partitioning within the NS5 Marine Group. Despite NS5 representing one of the most abundant marine flavobacterial clades from across the world’s oceans, our knowledge on their phylogenetic diversity and ecological functions is limited. Using novel and database-derived 16S rRNA gene and ribosomal protein sequences, we delineate the NS5 into 35 distinct species-level clusters, contained within four novel candidate genera. One candidate species, “Arcticimaribacter forsetii AHE01FL”, includes a novel cultured isolate, for which we provide a complete genome sequence—the first of an NS5—along with morphological insights using transmission electron microscopy. Assessing species’ spatial distribution dynamics across the Tara Oceans dataset, we identify depth as a key influencing factor, with 32 species preferring surface waters, as well as distinct patterns in relation to temperature, oxygen and salinity. Each species harbours a unique substrate-degradation potential along with predicted substrates conserved at the genus-level, e.g. alginate in NS5_F. Successional dynamics were observed for three species in a time-series dataset, likely driven by specialised substrate adaptations. We propose that the ecological niche partitioning of NS5 species is mainly based on specific abiotic factors, which define the niche space, and substrate availability that drive the species-specific temporal dynamics.
Highlights
An ecological niche is defined as a specific set of conditions that allow a population to perform its evolutionarily adapted function and as a result, persist or grow [1, 2]
MAGs belonging to the NS5 were identified by 16S rRNA gene phylogeny (Supplementary Material 1) and assigned to taxonomic groups in the Genome Taxonomy Database (GTDB) (Release 89) using the with 100 of the highest quality NS5 sequences in the SILVA database were used for phylogenetic tree reconstruction
Seven species-representative MAGs retrieved from Fram Strait metagenomes were identified as members of the NS5 marine group through 16S rRNA gene analysis and assigned to four different genera within the GTDB database (MED-G11, acid stain (DAPI) revealed similar peak counts for both NS5_A, 1.70 × 104 cells ml−1, and NS5_F, 1.76 × 104 cells ml−1 (Supplementary Fig. S4)
Summary
An ecological niche is defined as a specific set of conditions (environmental and biotic interactions) that allow a population to perform its evolutionarily adapted function and as a result, persist or grow [1, 2]. Microbial populations exhibit distinct dynamics that are driven by temporally derived shifts, such as seasons [6] This is evident with heterotrophic microbes in the Bacteroidetes phylum, that show recurrent and potentially predictable, seasonal dynamics driven by substrate availability [7, 13, 14]. From these studies, it is clear that conditions and resources influence microbial populations, to what extent do these determine niches?
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