Cultivation-Independent Analysis of the Bacterial Community Associated With the Calcareous Sponge Clathrina clathrus and Isolation of Poriferisphaera corsica Gen. Nov., Sp. Nov., Belonging to the Barely Studied Class Phycisphaerae in the Phylum Planctomycetes

Abstract

Marine ecosystems serve as global carbon sinks and nutrient source or breeding ground for aquatic animals. Sponges are ancient parts of these important ecosystems and can be found in caves, the deep-sea, clear waters, or more turbid environments. Here, we studied the bacterial community composition of the calcareous sponge Clathrina clathrus sampled close to the island Corsica in the Mediterranean Sea with an emphasis on planctomycetes. We show that the phylum Planctomycetes accounts for 9% of the C. clathrus-associated bacterial community, a 5-fold enrichment compared to the surrounding seawater. Indeed, the use of C. clathrus as a yet untapped source of novel planctomycetal strains led to the isolation of strain KS4T. The strain represents a novel genus and species within the class Phycisphaerae in the phylum Planctomycetes and displays interesting cell biological features, such as formation of outer membrane vesicles and an unexpected mode of cell division.

Novel and Conventional Isolation Techniques to Obtain Planctomycetes from Marine Environments

“…No planctomycetes were obtained from the anemone Actinia equina in either sampling period. Planctomycetes have already been associated to different invertebrates, such as crustaceans, jellyfish, and sponges [5,8,9,11,[60][61][62]. Furthermore, in a recent study that characterized the gut microbiome of the mussel Mytilus galloprovincialis, [63] members of Fuerstiella sp., Phycisphaera sp., Blastopirella sp., and diverse unclassified planctomycetes were detected by metagenomic analysis.…”

“…Presently, aquatic environments exhibit the most known diversity in this phylum, with a vast predominance in marine environments [1]. Planctomycetes are associated with organisms such as macroalgae, plants, and invertebrates [3][4][5][6][7][8][9][10][11]. They are also found in diverse terrestrial environments such as peat bogs [12][13][14].…”

Volatiles of the Apicomplexan Alga Chromera velia and Associated Bacteria

“…The comparably low RpoB identity of 73.2 % of the planctomycete MAG with the next genome‐sequenced relative was indicative of a very distinct phylogenetic positioning. This conclusion was confirmed by the nearly complete 16S‐rRNA gene with a size of 1494 nt that showed a sequence identity of only 86.5 % with the closest related type strain Poriferisphera corsica DSM 103958 [22] . This value exactly matches the threshold for the delineation of different bacterial families, [15] which proposes that the uncultivated planctomycete from the phycosphere of C. velia CCAP 1602/1 might represent a novel family in the planctomycete order Phycisphaerales.…”

Mucisphaera calidilacus gen. nov., sp. nov., a novel planctomycete of the class Phycisphaerae isolated in the shallow sea hydrothermal system of the Lipari Islands

“…Our analysis classifies strain Pan265 T as a member of the class Phycisphaerae , more specifically of the family Phycisphaeraceae , which is currently the sole family in the order Phycisphaerales. The current closest relatives of the strain are Algisphaera agarilytica 06SJR6-2 T , Phycisphaera mikurensis FYK2301M01 T and Poriferisphaera corsica KS4 T (Fukunaga et al 2009 ; Kallscheuer et al 2020f ; Yoon et al 2014 ). Strain Pan265 T shares the highest 16S rRNA gene sequence similarity of 90.1% with A. agarilytica , which suggests this species as the current closest neighbour (Fig.…”