Giant sulfur bacteria (Beggiatoaceae) from sediments below the Benguela Upwelling System the host diverse microbiomes

Abstract

Due to their lithotrophic metabolisms, morphological complexity and conspicuous appearance, members of the Beggiatoaceae have been extensively studied for more than 100 years. These bacteria are known to be primarily sulfur-oxidizing autotrophs that commonly occur in dense mats at redox interfaces. Their large size and the presence of a mucous sheath allows these cells to serve as sites of attachment for communities of other microorganisms. But little is known about their individual niche preferences and attached microbiomes, particularly in marine environments, due to a paucity of cultivars and their prevalence in habitats that are difficult to access and study. Therefore, in this study, we compare Beggiatoaceae strain composition, community composition, and geochemical profiles collected from sulfidic sediments at four marine stations off the coast of Namibia. To elucidate community members that were directly attached and enriched in both filamentous Beggiatoaceae, namely Ca. Marithioploca spp. and Ca. Maribeggiatoa spp., and non-filamentous Beggiatoaceae, Ca. Thiomargarita spp., the two morphotypes were rinsed of sediment debris and pooled by morphotype for iTag sequencing. The Beggiatoaceae samples collected from a highly sulfidic site were enriched in strains of sulfur-oxidizing Campylobacterota, who may promote a more hospitable setting for the Beggiatoaceae who are known to have a lower tolerance for sulfide to oxygen ratios. Otherwise, specific Beggiatoaceae niche preferences were not elucidated by the methods employed in this study. We found just a few host-specific associations with the motile filamentous morphotypes. On the contrary, we detected 123 host specific enrichments with non-motile chain forming Beggiatoaceae. Potential metabolisms of the enriched strains include fermentation of host sheath, syntrophic exchange of H2 and acetate, inorganic sulfur metabolism, and nitrite oxidation. Surprisingly, we did not detect any enrichments of anaerobic ammonium oxidizing bacteria as previously suggested and postulate that less well-studied anaerobic ammonium oxidation pathways may be occurring instead.