Distinct compositions of free-living, particle-associated and benthic communities of theRoseobactergroup in the North Sea

Abstract

The Roseobacter group is one of the predominant lineages in the marine environment. While most investigations focus on pelagic roseobacters, the distribution and metabolic potential of benthic representatives is less understood. In this study, the diversity of the Roseobacter group was characterized in sediment and water samples along the German/Scandinavian North Sea coast by 16S rRNA gene analysis and cultivation-based methods. Molecular analysis indicated an increasing diversity between communities of the Roseobacter group from the sea surface to the seafloor and revealed distinct compositions of free-living and attached fractions. Culture media containing dimethyl sulfide (DMS), dimethyl sulfonium propionate (DMSP) or dimethyl sulfoxide (DMSO) stimulated growth of roseobacters showing highest most probable numbers (MPN) in DMSO-containing dilutions of surface sediments (2.1 × 10(7) roseobacters cm(-3)). Twenty roseobacters (12 from sediments) were isolated from DMSP- and DMS-containing cultures. Sequences of the isolates represented 0.04% of all Bacteria and 4.7% of all roseobacters in the pyrosequencing dataset from sediments. Growth experiments with the isolate Shimia sp. SK013 indicated that benthic roseobacters are able to switch between aerobic and anaerobic utilization of organic sulfur compounds. This response to changing redox conditions might be an adaptation to specific environmental conditions on particles and in sediments.

The Biogeographical Distribution of Benthic Roseobacter Group Members along a Pacific Transect Is Structured by Nutrient Availability within the Sediments and Primary Production in Different Oceanic Provinces

“…Furthermore, while the Pacific transect includes deep-sea sediments distinct from landmasses, exhibiting low nutrient contents, most other benthic studies were performed in coastal, nutrient-rich sediments (Buchan et al, 2005 ). However, the relative amount of Roseobacter -affiliated OTUs in our 16S rRNA transcript library of up to 3% is comparable to proportions found in coastal sediments from the North Sea and cold seeps in the Nankai Trough, both around 2% of all 16S rRNA genes (Li et al, 1999 ; Kanukollu et al, 2016 ), as well as in volcanic sediments of the Sea of Okhotsk (Inagaki et al, 2003 ) and Antarctic Shelf sediments (Bowman and McCuaig, 2003 ). Differences in abundance between coastal and open ocean sites are not only visible at the seafloor.…”

“…The Roseobacter group does not only differ numerically between benthic and pelagic systems, but also in the community structure (Stevens et al, 2005 ). In a recent study on the distribution of the Roseobacter group in coastal North Sea sediments and water samples, we have shown that the diversity within the group increases from the sea surface to the seafloor revealing specific compositions of free-living and attached fractions (Kanukollu et al, 2016 ).…”

“…However, direct quantifications of the Roseobacter group at the sediment surface of North Sea tidal flats by CARD-FISH showed that their cell numbers exceed those in the pelagic environment by a factor of 1000 (Lenk et al, 2012 ). In reports on other coastal sediments, the Roseobacter group accounts for 1 to 4% of the entire bacterial community (Buchan et al, 2005 ; Kanukollu et al, 2016 ) or even 10% in brackish river sediments (González et al, 1999 ). Assuming that surface sediments contain approximately 10 9 cells × cm −3 , their absolute abundance is still orders of magnitudes higher than in corresponding water samples, which usually exhibit 10 6 cells × ml −1 (Kallmeyer et al, 2012 ).…”

Differences in free-living and particle-associated bacterial communities and their spatial variation in Kongsfjorden, Arctic

“…Abundance of members of RCA cluster are often highest during phytoplankton blooms and are mainly found associated with organic and inorganic marine particles/surfaces . Recent studies have shown that members of Sulfitobacter and Loktanella genera prefer particle‐associated lifestyle and are involved in the degradation of dimethylsulfoniopropionate (DMSP) . In the present study, members of SAR116 clade (class Alphaproteobacteria ) were enriched in the PA fractions.…”

Seasonal Changes in Microbial Dissolved Organic Sulfur Transformations in Coastal Waters

“…also metabolise DMSP [65]. Growth experiments with a Roseobacter isolate also revealed its potential plasticity in metabolism, by demonstrating a shift from DMS oxidation and DMSP degradation under aerobic conditions to DMSO (and nitrate) reduction under anaerobic conditions [66]. Alternatively, Thume et al [67] have recently reported that a new sulfur metabolite dimethylsulfoxonium propionate (DMSOP) is synthesized by several DMSP-producing phytoplankton and marine bacteria, which is further metabolized (by marine bacteria) to DMSO.…”