The Majority of Active Rhodobacteraceae in Marine Sediments Belong to Uncultured Genera: A Molecular Approach to Link Their Distribution to Environmental Conditions

Abstract

General studies on benthic microbial communities focus on fundamental biogeochemical processes or the most abundant constituents. Thereby, minor fractions such as the Rhodobacteraceae are frequently neglected. Even though this family belongs to the most widely distributed bacteria in the marine environment, their proportion on benthic microbial communities is usually within or below the single digit range. Thus, knowledge on these community members is limited, even though their absolute numbers might exceed those from the pelagic zone by orders of magnitudes. To unravel the distribution and diversity of benthic, metabolically active Rhodobacteraceae , we have now analyzed an already existing library of bacterial 16S rRNA transcripts. The dataset originated from 154 individual sediment samples comprising seven oceanic regions and a broad variety of environmental conditions. Across all samples, a total of 0.7% of all 16S rRNA transcripts was annotated as Rhodobacteraceae. Among those, Sulfitobacter , Paracoccus , and Phaeomarinomonas were the most abundant cultured representatives, but the majority (78%) was affiliated to uncultured family members. To define them, the 45 most abundant Rhodobacteraceae -OTUs assigned as “uncultured” were phylogenetically assembled in new clusters. Their next relatives particularly belonged to different subgroups other than the Roseobacter group, reflecting a large part of the hidden diversity within the benthic Rhodobacteraceae with unknown functions. The general composition of active Rhodobacteraceae communities was found to be specific for the geographical location, exhibiting a decreasing richness with sediment depth. One-third of the Rhodobacteraceae -OTUs significantly responded to the prevailing redox regime, suggesting an adaption to anoxic conditions. A possible approach to predict their physiological properties is to identify the metabolic capabilities of their nearest relatives. Those need to be proven by physiological experiments, as soon an isolate is available. Because many uncultured members of these subgroups likely thrive under anoxic conditions, in future research, a molecular-guided cultivation strategy can be pursued to isolate novel Rhodobacteraceae from sediments.

Evidence That Microorganisms at the Animal-Water Interface Drive Sea Star Wasting Disease

“…Several studies have observed the proliferation of copiotrophic taxa longitudinally during SSW, including genera within the families Flavobacteriaceae , Rhodobacteriacaea ( Lloyd and Pespeni, 2018 ), Actinobacteria, and genera in the orders Altermonadales ( Nuñez-Pons et al, 2018 ), Vibrionales and Oceanospiralles ( Hoj et al, 2018 ). These taxonomic groups are amongst the most active constituents of bacterioplankton and major players in marine OM degradation, some of which have facultative anaerobic metabolisms ( Pinhassi et al, 2004 ; Choi et al, 2010 ; Buchan et al, 2014 ; Thiele et al, 2017 ; Pohlner et al, 2019 ). While it is tempting to ascribe pathogenicity traits to groups that are enriched on disease-affected tissues (based on members of the same family or genus causing pathology), or infer their role in community dysbiosis (i.e., the microbial boundary effect), this is not possible in the absence of demonstrated pathogenicity or strain-level assignment ( Hewson, 2019 ).…”

Microbial and nutrient dynamics in mangrove, reef, and seagrass waters over tidal and diurnal time scales

“…Draconibacterium (phylum Bacteroidetes) is another genus that contains marine sediment-derived bacteria, providing merit to the detection of this bacterium when water was shallowest (Du et al 2014, Gwak et al 2015. The Rhodobacteraceae (Alphaproteobacteria) are some of the most widely spread bacteria in the ocean and a study analyzing distribution and classification of Rhodobacteraceae found that onethird of the detected Rhodobacteraceae correlated to sediment parameters, indicating there are specific sediment-associated Rhodobacteraceae (Pohlner et al 2019). Rhodobacteraceae strains have been isolated from mangrove sediments (Yu et al 2018, Ren et al 2019.…”

Evidence that non-pathogenic microorganisms drive sea star wasting disease through boundary layer oxygen diffusion limitation

“…(Hoj et al, 2018). These taxonomic groups are amongst the most active constituents of bacterioplankton and major players in marine OM degradation, some of which have facultative anaerobic metabolisms (Pinhassi et al, 2004;Choi et al, 2010;Buchan et al, 2014;Thiele et al, 2017;Pohlner et al, 2019). While it is tempting to ascribe pathogenicity traits to groups that are enriched on disease-affected tissues (based on members of the same family or genus causing pathology), or infer their role in community dysbiosis (i.e.…”