Particle-associated bacteria in seawater dominate the colony-forming microbiome on ZoBell marine agar

Abstract

Planktonic particle-associated bacteria comprise particle-attached and motile free-living cells. These groups were obtained by settlement in Imhoff cones. Dilution plating on marine agar 2216 (ZoBell marine agar) and microscopic counts indicated a cultivability of 0.7% (0.4–1.2%) of bacteria in coastal seawater collected at Helgoland Roads, North Sea. Particle-associated bacteria presented a minority population in seawater, but had a larger cultivability of 25% (0.9–100%) for populations collected by settlement of particles and 5.7% (0.9–24%) for populations collected by filtration. Partial 16S rRNA gene sequences indicated that 84% of the cultured taxa were either enriched in particle-associated microbiomes or only found in these microbiomes, including Sulfitobacter and other Rhodobacteraceae, Pseudoalteromonas, Psychromonas, Arcobacter and many Flavobacteriaceae. Illumina-based 16S rRNA V3V4 amplicon sequences of plate communities revealed that nearly all operational taxonomic units had a cultivated and described strain in close phylogenetic proximity. This suggested that decades of strain isolation from seawater on ZoBell marine agar had achieved a very good coverage of cultivable genera abundant in nature. The majority belonged to particle-associated bacteria, complementing observations that abundant free-living seawater bacteria often require cultivation conditions closer to their natural habitat like liquid cultivation in oligotrophic medium.

Proteomic insight into arabinogalactan utilization by particle-associated Maribacter sp. MAR_2009_72

“…Plating sea and sediment pore water on arabinogalactan medium showed a large microbiome with the capacity to utilize arabinogalactan for growth. Together with the recent finding that particle-associated bacteria dominate the readily culturable fraction of seater microbiomes (Heins and Harder 2023 ) this observation indicates that arabinogalactan is a common carbon source for particle-associated bacteria.…”

“…MAR_2009_72 (Kappelmann et al 2018 , Heins et al 2021a ). Strains of the genus Maribacter are rarely isolated from sea water, but they are more abundant in particle fractions (Nedashkovskaya et al 2004 , Heins and Harder 2023 , Lu et al 2023 , Sidhu et al 2023 ). Abundances of up to 4% were detected in the oxic surface layer of sandy sediments (Probandt et al 2018 , Miksch et al 2021 ).…”

Seasonal dynamics of a glycan-degrading flavobacterial genus in a tidally-mixed coastal temperate habitat

“…Indeed, one of the eight validly described species, Z. amurskyensis KMM 3526 T , was isolated from seawater in Amursky Bay, Sea of Japan (Nedashkovskaya et al, 2004). Zobellia representatives were also previously grown from seawater and particles larger than 10 µm during a phytoplankton spring bloom off Helgoland (Heins and Harder, 2023). Our analysis of long-term observation data revealed recurring associations of Zobellia with individual eukaryotic OTUs in the particle-associated fraction.…”

Seasonal dynamics of a glycan‐degrading flavobacterial genus in a tidally mixed coastal temperate habitat

“…Indeed, one of the eight validly described species, Z. amurskyensis KMM 3526 T , was isolated from seawater in Amursky Bay, Sea of Japan (Nedashkovskaya et al, 2004). Zobellia representatives were also previously grown from seawater and particles larger than 10 μm during a phytoplankton spring bloom off Helgoland (Heins & Harder, 2023). Our analysis of long‐term observation data revealed recurring associations of Zobellia with individual eukaryotic OTUs in the particle‐associated fraction.…”