title: Multiple approaches to enhance the cultivability of bacteria associated with the marine sponge Haliclona (gellius) sp.
abstract: Three methods were examined to cultivate bacteria associated with the marine sponge Haliclona (gellius) sp.: agar plate cultures, liquid cultures, and floating filter cultures. A variety of oligotrophic media were employed, including media with aqueous and organic sponge extracts, bacterial signal molecules, and siderophores. More than 3,900 isolates were analyzed, and 205 operational taxonomic units (OTUs) were identified. Media containing low concentrations of mucin or a mixture of peptone and starch were most successful for the isolation of diversity, while the commonly used marine broth did not result in a high diversity among isolates. The addition of antibiotics generally led to a reduced diversity on plates but yielded different bacteria than other media. In addition, diversity patterns of isolates from agar plates, liquid cultures, and floating filters were significantly different. Almost 89% of all isolates were Alphaproteobacteria; however, members of phyla that are less commonly encountered in cultivation studies, such as Planctomycetes, Verrucomicrobia, and Deltaproteobacteria, were isolated as well. The sponge-associated bacteria were categorized into three different groups. The first group represented OTUs that were also obtained in a clone library from previously analyzed sponge tissue (group 1). Furthermore, we distinguished OTUs that were obtained from sponge tissue (in a previous study) but not from sponge isolates (group 2), and there were also OTUs that were not obtained from sponge tissue but were obtained from sponge isolates (group 3). The 17 OTUs categorized into group 1 represented 10 to 14% of all bacterial OTUs that were present in a large clone library previously generated from Haliclona (gellius) sp. sponge tissue, which is higher than previously reported cultivability scores for sponge-associated bacteria. Six of these 17 OTUs were not obtained from agar plates, which underlines that the use of multiple cultivation methods is worthwhile to increase the diversity of the cultivable microorganisms from sponges.
authors.affiliation: University of California Berkeley, Department of Chemical Engineering, 201 Gilman Hall, Berkeley, California 94720, USA. detmer.sipkema@wur.nl
authors.forename: Detmer
authors.initials: D
authors.lastname: Sipkema
authors.forename: Klaske
authors.initials: K
authors.lastname: Schippers
authors.forename: Wouter J
authors.initials: WJ
authors.lastname: Maalcke
authors.forename: Yu
authors.initials: Y
authors.lastname: Yang
authors.forename: Sina
authors.initials: S
authors.lastname: Salim
authors.forename: Harvey W
authors.initials: HW
authors.lastname: Blanch
mesh_terms: D020561:Alphaproteobacteria / Q000145:classification / Q000235:genetics / Q000254:growth & development / Q000302:isolation & purification; D000818:Animals; D001419:Bacteria / Q000145:classification / Q000235:genetics / Q000254:growth & development* / Q000302:isolation & purification*; D047129:Haliclona / Q000382:microbiology*; D008969:Molecular Sequence Data; D010802:Phylogeny; D016133:Polymerase Chain Reaction