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Coastal Sediments

Project Leader

Project leader

Department of Molecular Ecology

Dr. Katrin Knittel

MPI for Marine Microbiology
Celsiusstr. 1
D-28359 Bremen




+49 421 2028-9990

Dr. Katrin Knittel

Our research

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.

In October 2021, we received a donation of 10,000 euros from the Andreas Rühl Foundation. The donation supports us in continuing the research described here.

We are very happy about this generous support!

Svalbard sampling area
Sampling area at 78° North: Svalbard © Max Planck Institute for Marine Microbiology
Sampling in the Arctic: In May 2023, researchers were in Svalbard for the last time so far to conduct on-site measurements and collect samples for research on bacterial carbon turnover in the Arctic seafloor. (© F. Aspetsberger/Max-Planck-Institute for Marine Microbiology)
Sampling in the Arctic, May 2023 (© F. Aspetsberger/Max-Planck-Institute for Marine Microbiology)

Research thanks to Goldschmidt donation: Bacterial carbon cycling in high-latitude coastal sediments

Read more about Chyrene Moncada's project

Read more about Chyrene Moncada's project

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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.

sand grains
A view through a binocular: sand grains © Max Planck Institute for Marine Microbiology
Microbes on a sand grain
Microbes on a sand grain (stained with SYBR green). © Max Planck Institute for Marine Microbiology

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.


Bacterial community composition
Bacterial community composition of Helgoland surface sediments. The bubbles’ diameters give read frequencies of 16S rRNA genes, bubbles’ colors indicate season of sampling. Each row displays one genus/family. © Max Planck Institute for Marine Microbiology

Polysaccharide degradation

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.).


Genomic organization of GH
Organization of carbohydrate-active enzymes and sulfatases in Verrucomicrobia long reads retrieved from Svalbard surface sediment incubated with the polysaccharide fucoidan. © Max Planck Institute for Marine Microbiology
Selfish bacteria
Laser scanning micrographs showing selfish bacteria in Svalbard sediments incubated with fluorescently labelled polysaccharides. Green, substrate signal; red, FISH probe-specific signal; blue, DAPI. © Max Planck Institute for Marine Microbiology

PhD Student

Department of Molecular Ecology

Chyrene Moncada

MPI for Marine Microbiology
Celsiusstr. 1
D-28359 Bremen




+49 421 2028-9550

Chyrene Moncada


Former members of project

Dr. David Probandt

Jannika Moye




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