Our aim is to understand carbon cycling in coastal sandy sediments with a focus on heterotrophic bacterial communities that live in surface layers. Research questions address, for example, if seasonality in primary production is reflected in benthic bacterial community composition, the identification of main food sources for benthic heterotrohic bacteria (algae-derived or animal-derived carbon) or different degradation modes for polysaccharides by specific benthic taxa (selfish bacteria versus external hydrolyzers versus scavenging bacteria).
In the oceans, about one-fifth of primary production takes place at continental shelves (Jahnke, 2010), emphasizing the importance of these ecosystems for global carbon cycling. The first interaction of water column-derived organic matter with benthic microbial communities takes place in surface sediments which are acting as biological filters catalyzing central steps of elemental cycling.
Helgoland Roads (North Sea, German Bight) and Isfjorden (Svalbard, Arctic Ocean) are our main study sites. Bacterial communities in surface sediments were richer, more even and significantly different from communities in bottom waters (Probandt et al. 2017; Miksch et al., subm.). Planctomycetes, Verrucomicrobia and Actinobacteria are suggested as key bacteria for degradation of high molecular weight compounds and recalcitrant material that entered surface sediments from the water column.
Life on a sand grain
Marine sediments constitute the natural habitat for estimated 1.7 x 1028 bacteria and archaea (Whitman et al., 1998). In surface sediments, cell abundances are 108 to 109 per gram, and even for the subsurface seabed, more than 105 cells per gram have been reported.
More than 99% of the benthic microbial community lives attached to sand grains (Rusch et al., 2003). Resuspension of sediment grains exposes the microbial community to mechanical shearing stress and constantly changing environmental conditions. Based on 16S rRNA gene sequencing of environmental DNA extracted from several grams of sediment, North Sea surface sediments were found to accommodate up to 12,000 bacterial species (Probandt et al., 2017).
In this project we took the step from bulk sediments to single sand grains by taking a direct look at single sand grains to study the microbes in their micro-habitat (Probandt et al., 2018). Adapted protocols for hybridization or PCR of single sand grains without prior sonication or DNA extraction allows us to study the microbial community composition and structure in situ.
Each sand grain harbored a total of 104–105 cells consisting of a highly diverse bacterial community with several thousand species-level operational taxonomic units (OTU)0.97. Although bacterial communities differed between sand grains, a core community accounting for >50% of all OTUs was present on each sand grain (Probandt et al. 2018). Colonization was patchy, with exposed areas largely devoid of any epi-growth and protected areas more densely populated.
Benthic bacterial communities are seasonally stable
At high temporal resolution, we accessed the variability of benthic bacterial communities over two annual cycles at Helgoland (North Sea), and compared it with seasonality of communities in Isfjorden (Svalbard, 78°N) sediments, where primary production does not occur during winter.
Benthic community structure remained stable in both, temperate and polar sediments on the level of cell counts and 16S rRNA-based taxonomy (Miksch et al., submitted). Thus, phytodetrital input do not drive seasonal changes in benthic bacterial community structures of Svalbard and Helgoland sediments.
Even though Helgoland and Svalbard sampling sites showed no phytodetritus-driven changes of the benthic bacterial community structure, they harbored significantly different communities. The temporal stability of benthic bacterial communities is in stark contrast to the dynamic succession typical of coastal waters, suggesting that pelagic and benthic bacterial communities respond to phytoplankton productivity very differently.
Polysaccharides are major constituents of macroalgae and phytoplankton biomass. They make up a large fraction of the organic matter produced and degraded in the oceans. Yet, little is known about identity, organization and expression of genes responsible for benthic polysaccharide degradation.
As benthic bacterial communities in sandy surface sediments are seasonally stable and do not respond to changes in primary production/substrates they might respond by changes in transcript profiles. Therefore, we started to study expression profiles of carbohydrate-active enzymes (CAZymes), in particular of glycoside hydrolases, in surface sediments from Svalbard. At 78° N there is strong seasonality with respect to light and algae-derived organic matter production. Metatranscriptomics do show different polysaccharide utilization patterns for polar winter (December and February) compared to polar summer (May; Miksch, Knittel et al., in prep.). More detailed analysis will show if the diversity of glycoside hydrolases is more diverse or more even in winter and which are the major substrates for benthic heterotrophs. Based on SusCD transporter complexes that we find in the metagenomes/metatranscriptomes we aim to predict substrates used by the organisms.
In surface ocean waters, a relatively large fraction of up to one-fourth of bacteria is capable of polysaccharide degradation by using the selfish uptake mode (Reintjes et al., 2017) and external hydrolysis becomes more important in course of a spring phytoplankton bloom (Reintjes et al., 2020). Here, we study the importance of different polysaccharide degradation modes in Svalbard surface sediments. Sediment slurries were set-up and incubated with different fluorescently-labelled polysaccharides. Preliminary analysis show that only a minor fraction of bacteria is using the selfish uptake mode while extracellular degradation rates were high for complex and less complex subsrates tested (Knittel, Miksch et al., unpubl.).
Former members of project
Dr. David Probandt