Delineation of ecologically distinct units of marine Bacteroidetes in the Northwestern Mediterranean Sea

Abstract

Bacteroidetes is one of the dominant phyla of ocean bacterioplankton, yet its diversity and population structure is poorly understood. To advance in the delineation of ecologically meaningful units within this group, we constructed near full-length 16S rRNA gene clone libraries from contrasting marine environments in the NW Mediterranean. Based on phylogeny and the associated ecological variables (depth and season), 24 different Bacteroidetes clades were delineated. By considering their relative abundance (from iTag amplicon sequencing studies), we described the distribution patterns of each of these clades, delimiting them as Ecologically Significant Taxonomic Units (ESTUs). Spatially, there was almost no overlap among ESTUs at different depths. In deep waters there was predominance of Owenweeksia, Leeuwenhoekiella, Muricauda-related genera, and some depth-associated ESTUs within the NS5 and NS2b marine clades. Seasonally, multi-annual dynamics of recurring ESTUs were present with dominance of some ESTUs within the NS4, NS5 and NS2b marine clades along most of the year, but with variable relative frequencies between months. A drastic change towards the predominance of Formosa-related ESTUs and one ESTU from the NS5 marine clade was typically present after the spring bloom. Even though there are no isolates available for these ESTUs to determine their physiology, correlation analyses identified the environmental preference of some of them. Overall, our results suggest that there is a high degree of niche specialisation within these closely related clades. This work constitutes a step forward in disentangling the ecology of marine Bacteroidetes, which are essential players in organic matter processing in the oceans.

Exploring Vitamin B1 Cycling and Its Connections to the Microbial Community in the North Atlantic Ocean

“…The resulting tree indicated that the NAAMES ASVs clustered into three distinct clades, and each of these clades included at least one closely related SAG for genome comparison (Figure 5). The phylogenetic placement of the NAAMES flavobacteria ASVs is consistent with previous research that has indicated that there is a high degree of niche specialization amongst these organisms (Diez-Vives et al, 2019). The SAGs were then queried for B1 synthesis capacity.…”

Bacterial Diversity in a Dynamic and Extreme Sub-Arctic Watercourse (Pasvik River, Norwegian Arctic)

“…Among the non-shared Bacteroidetes genera or groups, the NS5 marine group, Polaribacter, Pseudarcicella, and Fluviicola (a typical freshwater genus) characterized water samples, whereas Lutimonas and Maribacter were retrieved in sediments. A number of authors have reported on the dominance of flavobacterial phylotypes responding to phytoplankton blooms, with the succession of particular clades (including Ulvibacter spp., Polaribacter spp., and NS5 marine clades) and the progressive consumption of the algal-derived organic matter [44,45]. In this study, the NS5 marine group was found at very high percentages, also at inner stations, and its co-occurrence with some clades cited above was especially evident at the middle station 9w, suggesting that an algal bloom was present at sampling time.…”

Bacteroidetes contribute to the carbon and nutrient cycling of deep sea through breaking down diverse glycans

“…Bacteroidetes, globally distributed in human gut, coastal ocean, marine sediments and other environments, play key roles in the degradation of high molecular weight carbohydrates ( Cottrell Kirchman, 2000; Fernandez-Gomez et al, 2013; Thomas et al, 2011 ). As such, Bacteroidetes are recognized as one of the dominant phyla of ocean bacterioplankton ( Diez-Vives et al, 2019 ) and are the most important decomposer for algae derived carbohydrates, actively driving the ocean carbon and nutrient cycling ( Kruger et al, 2019; Unfried et al, 2018 ). As compared to studies of Bacteroidetes derived from the shallow ocean, very little research has been done on the deep-sea counterparts, likely due to the difficulties of sampling and cultivation.…”