Dynamics of primary production and sedimentation in a coastal ecosystem

Cyanophage Diversity and Community Structure in Dead Zone Sediments

Cyanophages are viruses that target cyanobacteria and directly control their abundance via viral lysis. Cyanobacteria are known to cause large blooms in water bodies, substantially contributing to oxygen depletion in bottom waters resulting in areas called dead zones.

Up to 20% of prokaryotic organisms in the oceans are estimated to die every day due to viral infection and lysis. Viruses can therefore alter microbial diversity, community structure, and biogeochemical processes driven by these organisms. Cyanophages are viruses that infect and lyse cyanobacterial cells, adding bioavailable carbon and nutrients into the environment. Cyanobacteria are photosynthesizing bacteria, with some species capable of N₂ fixation, which are known to form large blooms as well as resistant resting cells known as akinetes. Here, we investigated cyanophage diversity and community structure plus cyanobacteria in dead zone sediments. We sampled surface sediments and sequenced DNA and RNA, along an oxygen gradient—representing oxic, hypoxic, and anoxic conditions—in one of the world’s largest dead zones located in the Baltic Sea. Cyanophages were detected at all stations and, based on partial genome contigs, had a higher alpha diversity and different beta diversity in the hypoxic-anoxic sediments, suggesting that cyanobacteria in dead zone sediments and/or environmental conditions select for specific cyanophages. Some of these cyanophages can infect cyanobacteria with potential consequences for gene expression related to their photosystem and phosphate regulation. Top cyanobacterial genera detected in the anoxic sediment included Dolichospermum/Anabaena, Synechococcus, and Cyanobium. RNA transcripts classified to cyanobacteria were associated with numerous pathways, including anaerobic carbon metabolism and N₂ fixation. Cyanobacterial blooms are known to fuel oxygen-depleted ecosystems with phosphorus (so-called internal loading), and our cyanophage data indicate the potential for viral lysis of cyanobacteria which might explain the high nutrient turnover in these environments.

IMPORTANCE Cyanophages are viruses that target cyanobacteria and directly control their abundance via viral lysis. Cyanobacteria are known to cause large blooms in water bodies, substantially contributing to oxygen depletion in bottom waters resulting in areas called dead zones. Our knowledge of cyanophages in dead zones is very scarce, and so far, no studies have assembled partial cyanophage genomes and investigated their associated cyanobacteria in these dark and anoxic sediments. Here, we present the first study using DNA and RNA sequencing to investigate in situ diversity of cyanophages and cyanobacteria in dead zones. Our study shows that dead zone sediments contain different cyanophages compared to oxic sediments and suggest that these viruses are able to affect cyanobacterial photosystem and phosphate regulation. Furthermore, cyanophage-controlled lysis of cyanobacteria might also increase the turnover of carbon, phosphorus, and nitrogen in these oxygen-free environments at the bottom of the sea.

Spring and Late Summer Phytoplankton Biomass Impact on the Coastal Sediment Microbial Community Structure

Two annual Baltic Sea phytoplankton blooms occur in spring and summer. The bloom intensity is determined by nutrient concentrations in the water, while the period depends on weather conditions. During the course of the bloom, dead cells sink to the sediment where their degradation consumes oxygen to create hypoxic zones (< 2 mg/L dissolved oxygen). These zones prevent the establishment of benthic communities and may result in fish mortality. The aim of the study was to determine how the spring and autumn sediment chemistry and microbial community composition changed due to degradation of diatom or cyanobacterial biomass, respectively. Results from incubation of sediment cores showed some typical anaerobic microbial processes after biomass addition such as a decrease in NO₂^- + NO₃^- in the sediment surface (0-1 cm) and iron in the underlying layer (1-2 cm). In addition, an increase in NO₂^- + NO₃^- was observed in the overlying benthic water in all amended and control incubations. The combination of NO₂^- + NO₃^- diffusion plus nitrification could not account for this increase. Based on 16S rRNA gene sequences, the addition of cyanobacterial biomass during autumn caused a large increase in ferrous iron-oxidizing archaea while diatom biomass amendment during spring caused minor changes in the microbial community. Considering that OTUs sharing lineages with acidophilic microorganisms had a high relative abundance during autumn, it was suggested that specific niches developed in sediment microenvironments. These findings highlight the importance of nitrogen cycling and early microbial community changes in the sediment due to sinking phytoplankton before potential hypoxia occurs.

The loss of diatoms in the spring bloom

The sinking of diatoms towards the end of the spring bloom contributes to the loss of organic material below the mixer layer. Earlier work is reviewed. The study of Peinert et al . ( Neth. J. Sea Res. 16, 276 (1982)) in the Kieler Bucht was reworked assuming that the algal reproductive rate can be derived from the ratio of a radiocarbon measurement to stock in carbon. This method revealed a somewhat greater loss. The material of Marshall & Orr ( J. mar. biol. Ass. U.K. 16, 853 (1930)) was reworked with an estimate of the diatom sinking rate. It was assumed that the difference between the algal reproductive rate and the grazing rate was constant in the shortest intervals of time and depth. A method was developed to estimate production, the quantity grazed and the quantity sunk. During the spring outburst, diatoms are lost, probably by detrainment, but at the end of the outburst there is a sudden loss. The quantity grazed may have been estimated somewhat more precisely.

The importance of the planktonic ecosystem of the North Sea in the context of oil and gas development

Planktonic organisms are the primary source of food for the top level of the marine food chain, the fish. Yet only part of the plankton is ingested by fish, the remainder sediments to the bottom to provide food for benthic organisms (which may in turn be grazed by demersal fish) and to contribute to a detrital sink. Although the relative proportions of the plankton entering each of these compartments is still a matter of debate, some indication of its importance as a resource can be gauged from the North Sea fishery that has yielded 2-3 Mt per year since the mid-1960s. Calculations for the North Sea of the annual production of phytoplankton, zooplankton, fish and benthos as energy equivalents are contrasted with the annual energy yields of oil and gas. Since 1948 the plankton of the North Sea has been monitored at a depth of 10 m by the Continuous Plankton Recorder (CPR) survey. Results for two large areas which encompass the Brent, Beryl and Forties oilfields are presented. Between 1948 and 1982 the plankton of these areas showed similar large changes in population structure in both phytoplankton and zooplankton with almost tenfold changes in levels of biomass during this 35 year period. The development of oil-related activities is discussed in relation to the plankton time-series with comment on possible causes of the changes which are believed to be the result of natural variability.

Seasonal and Spatial Distribution of Extracellular Enzymatic Activities and Microbial Incorporation of Dissolved Organic Substrates in Marine Sediments

Seasonal and spatial distributions of extracellular enzymatic activities and microbial incorporations of dissolved organic substrates were followed in sediments of the brackish water Kiel Bight (Baltic Sea, Federal Republic of Germany). Enzymatic hydrolysis of polymeric organic compounds was determined by means of fluorogenic substrates (4-methylumbelliferyl-β- d -glucoside, l -leucine-4-methylcoumarinyl-7-amide hydrochloride); incorporation of dissolved organic substrates into microbial biomass was measured by using tritiated substances (acetate, leucine, and thymidine). Based on a recently developed core injection technique, substrates were injected in microliter portions into undisturbed sediment cores. Enzymatic and incorporation activities underwent strong seasonal variations related to the enrichment of organic material in the sediment surface following sedimentation events. The input of the phytoplankton bloom during autumn caused stimulation of both enzymatic hydrolysis of polymeric organic compounds and microbial incorporation of dissolved organic substrates. Following input by spring phytoplankton bloom, mainly incorporation activities were stimulated. In late spring the development of the benthic fauna obviously greatly influenced microbial activities. During summer individual periods of high microbial activities were observed which might be traced back to short-term sedimentation events. The high microbial incorporation of leucine and thymidine during winter demonstrated that the nutrient supply rather than temperature is the dominating factor determining microbial production. Stimulation of microbial activities arose from the sediment surface and spread out relatively quickly into deeper horizons. Generally, the sediments were characterized by distinct patterns of interrelationships between the individual parameters of microbial activities measured.