Deposit-Feeding Sea Cucumbers Enhance Mineralization and Nutrient Cycling in Organically-Enriched Coastal Sediments

Background

Bioturbators affect multiple biogeochemical interactions and have been suggested as suitable candidates to mitigate organic matter loading in marine sediments. However, predicting the effects of bioturbators at an ecosystem level can be difficult due to their complex positive and negative interactions with the microbial community.

Methodology/Principal Findings

We quantified the effects of deposit-feeding sea cucumbers on benthic algal biomass (microphytobenthos, MPB), bacterial abundance, and the sediment–seawater exchange of dissolved oxygen and nutrients. The sea cucumbers increased the efflux of inorganic nitrogen (ammonium, NH₄ ⁺) from organically enriched sediments, which stimulated algal productivity. Grazing by the sea cucumbers on MPB (evidenced by pheopigments), however, caused a net negative effect on primary producer biomass and total oxygen production. Further, there was an increased abundance of bacteria in sediment with sea cucumbers, suggesting facilitation. The sea cucumbers increased the ratio of oxygen consumption to production in surface sediment by shifting the microbial balance from producers to decomposers. This shift explains the increased efflux of inorganic nitrogen and concordant reduction in organic matter content in sediment with bioturbators.

Conclusions/Significance

Our study demonstrates the functional role and potential of sea cucumbers to ameliorate some of the adverse effects of organic matter enrichment in coastal ecosystems.     

Distribution of capsulated bacterioplankton in the North Atlantic and North Sea

In laboratory experiments, bacterioplankton were incubated under different nutrient conditions, and the percentage of bacteria exhibiting a polysaccharidic capsule (capsulated bacteria) and that of CTC (cyanotetrazolium chloride)-positive and therefore metabolically highly active bacteria were determined. In these seawater cultures amended with nutrients more than 95% of the CTC-positive cells exhibited a capsule. During two cruises, one to the North Atlantic and one to the North Sea, we investigated the distribution of capsulated bacteria throughout the water column. Capsulated bacteria were generally more abundant in eutrophic surface waters than in deeper layers or more oligotrophic regions. In the upper 100 m of the North Atlantic, about 6–14% of the total bacterioplankton community was capsulated, while in the layers below 100 m depth, 97% of the bacteria lacked a visible capsule. The percentage of capsulated bacteria correlated with bacterial abundance and production, and chlorophyll a concentration. Also, the bioavailability of DOC (dissolved organic carbon), estimated by the ratio between bacterial production and DOC concentration, significantly correlated with the percentage of capsulated bacteria. In the North Sea, the contribution of capsulated bacteria to the total number of bacteria decreased from the surface (3 m depth) to the near-bottom (25–35 m) layers from 20% to 14% capsulated bacteria. In the nearshore area of the North Sea, about 27% of the bacteria exhibited a capsule. Overall, a pronounced decrease in the contribution of capsulated bacteria to the total bacterial abundance was detectable from the eutrophic coastal environment to the open North Atlantic. Using this epifluorescence-based technique to enumerate capsulated bacterioplankton thus allowed us to routinely assess the number of capsulated bacteria even in the oceanic water column. Based on the data obtained in this study we conclude that almost all metabolically highly active bacteria exhibit a capsule, but also some of the metabolically less active cells express a polysaccharide capsule detectable with this method.     

Identification of DNA-Synthesizing Bacterial Cells in Coastal North Sea Plankton

We describe a method for microscopic identification of DNA-synthesizing cells in bacterioplankton samples. After incubation with the halogenated thymidine analogue bromodeoxyuridine (BrdU), environmental bacteria were identified by fluorescence in situ hybridization (FISH) with horseradish peroxidase (HRP)-linked oligonucleotide probes. Tyramide signal amplification was used to preserve the FISH staining during the subsequent immunocytochemical detection of BrdU incorporation. DNA-synthesizing cells were visualized by means of an HRP-labeled antibody Fab fragment and a second tyramide signal amplification step. We applied our protocol to samples of prefiltered (pore size, 1.2 μm) North Sea surface water collected during early autumn. After 4 h of incubation, BrdU incorporation was detected in 3% of all bacterial cells. Within 20 h the detectable DNA-synthesizing fraction increased to >14%. During this period, the cell numbers of members of the Roseobacter lineage remained constant, but the fraction of BrdU-incorporating Roseobacter sp. cells doubled, from 24 to 42%. In Alteromonas sp. high BrdU labeling rates after 4 to 8 h were followed by a 10-fold increase in abundance. Rapid BrdU incorporation was also observed in members of the SAR86 lineage. After 4 h of incubation, cells affiliated with this clade constituted 8% of the total bacteria but almost 50% of the visibly DNA-synthesizing bacterial fraction. Thus, this clade might be an important contributor to total bacterioplankton activity in coastal North Sea water during periods of low phytoplankton primary production. The small size and low ribosome content of SAR86 cells are probably not indications of inactivity or dormancy.     

Alkane Biodegradation Genes from Chronically Polluted Subantarctic Coastal Sediments and Their Shifts in Response to Oil Exposure

Although sediments are the natural hydrocarbon sink in the marine environment, the ecology of hydrocarbon-degrading bacteria in sediments is poorly understood, especially in cold regions. We studied the diversity of alkane-degrading bacterial populations and their response to oil exposure in sediments of a chronically polluted Subantarctic coastal environment, by analyzing alkane monooxygenase (alkB) gene libraries. Sequences from the sediment clone libraries were affiliated with genes described in Proteobacteria and Actinobacteria, with 67?% amino acid identity in average to sequences from isolated microorganisms. The majority of the sequences were most closely related to uncultured microorganisms from cold marine sediments or soils from high latitude regions, highlighting the role of temperature in the structuring of this bacterial guild. The distribution of alkB sequences among samples of different sites and years, and selection after experimental oil exposure allowed us to identify ecologically relevant alkB genes in Subantarctic sediments, which could be used as biomarkers for alkane biodegradation in this environment. 16?S rRNA amplicon pyrosequencing indicated the abundance of several genera for which no alkB genes have yet been described (Oleispira, Thalassospira) or that have not been previously associated with oil biodegradation (Spongiibacter-formerly Melitea-, Maribius, Robiginitomaculum, Bizionia and Gillisia). These genera constitute candidates for future work involving identification of hydrocarbon biodegradation pathway genes.     

A Polyphasic Approach To Study the Diversity and Vertical Distribution of Sulfur-Oxidizing Thiomicrospira Species in Coastal Sediments of the German Wadden Sea

Recently, four Thiomicrospira strains were isolated from a coastal mud flat of the German Wadden Sea (T. Brinkhoff and G. Muyzer, Appl. Environ. Microbiol. 63:3789–3796, 1997). Here we describe the use of a polyphasic approach to investigate the functional role of these closely related bacteria. Microsensor measurements showed that there was oxygen penetration into the sediment to a depth of about 2.0 mm. The pH decreased from 8.15 in the overlaying water to a minimum value of 7.3 at a depth of 1.2 mm. Further down in the sediment the pH increased to about 7.8 and remained constant. Most-probable-number (MPN) counts of chemolithoautotrophic sulfur-oxidizing bacteria revealed nearly constant numbers along the vertical profile; the cell concentration ranged from 0.93 × 10⁵ to 9.3 × 10⁵ cells per g of sediment. A specific PCR was used to detect the presence of Thiomicrospira cells in the MPN count preparations and to determine their 16S rRNA sequences. The concentration of Thiomicrospira cells did not decrease with depth. It was found that Thiomicrospira strains were not dominant sulfur-oxidizing bacteria in this habitat. Denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S ribosomal DNA fragments followed by hybridization analysis with a genus-specific oligonucleotide probe revealed the diversity of Thiomicrospira strains in the MPN cultures. Sequence analysis of the highest MPN dilutions in which the genus Thiomicrospira was detected revealed that there were four clusters of several closely related sequences. Only one of the 10 Thiomicrospira sequences retrieved was related to sequences of known isolates from the same habitat. Slot blot hybridization of rRNA isolated from different sediment layers showed that, in contrast to the concentration of Thiomicrospira cells, the concentration of Thiomicrospira-specific rRNA decreased rapidly in the region below the oxic layer of the sediment. This study revealed the enormous sequence diversity of closely related microorganisms present in one habitat, which so far has been found only by sequencing molecular isolates. In addition, it showed that most of the Thiomicrospira populations in the sediment studied were quiescent.     

Distribution and Contamination Status of Trace Metals in the Mediterranean Coastal Sediments,Egypt

Trace metals concentrations in sediments from the Egyptian Mediterranean coast were determined to evaluate the levels of contamination. The highest concentrations of metals were generally found in the middle region of the coast. Sediment pollution assessment was carried out using Enrichment Factor (EF), Geoaccumulation Factor (Igeo), Contamination Factor (CF), Modified Degree of Contamination (mCd), and Pollution Load Index (PLI). Association of adverse effects to aquatic life was determined using the classification of sediments according to three sets of sediment quality guidelines. The mean EF values were found to fall in the following sequence: Cr > Pb > Ni > Zn > Cu > Mn. The results demonstrated that the EF of metals in the sediments of the middle region was lower than those recorded in the western region and Rafah Station at the eastern region; the difference in the EF levels was significantly correlated with Fe concentrations along the study area. Based on the average Igeo of target elements, the Egyptian Mediterranean coast could be considered not polluted with Cr, Cu, Mn, Ni, Pb, and Zn (Igeo ≤ 0). The modified degree of contamination was >1.5, indicating zero to very low contamination. The calculated PLI were less than 1, indicating only baseline levels of pollution. There were small differences between the results obtained with the three used SQGs. Highly significant correlations were found between the concentrations of Fe, Mn, Co, Cr, and Ni, suggesting similar sources and/or similar geochemical processes controlling the occurrence of these metals in the sediments.     

Small-Scale Distribution of Bacteria,Enzymatic Activities,and Organic Matter in Coastal Sediments

apd: 9 February 2001     

Distribution patterns of mesozooplankton biomass in the North Sea

During spring 1986 and winter 1987, zooplankton samples were collected over the entire North Sea by means of a multi-closing net-system. Before taxonomic treatment, wet weight estimates and carbon content conversions were carried out. From this data set, 4 962 522 tons zooplankton biomass (dry weight) were estimated for the whole North Sea during the spring survey. High biomasses (more than 100 mg C/m³) were located in areas between the Orkneys and the Shetlands, off the mouth of the Firth of Forth, the Channel and the river Rhine. Considerable zooplankton biomass was also found parallel to the Danish west coast. Furthermore, a narrow tongue of high biomass (partly greater than 200 mg C/m³) intruded from the north, between 1 °E and 4 °E, into the northern North Sea, turning to the east at 56°N, and continuing into deeper water layers to form a left turning “helix” of high biomass in the central part of the North Sea. During the winter survey the carbon content of the zooplankton stock was a factor 10 lower than in summer. Altogether, 519340 tons of zooplankton biomass (dry weight) were estimated in winter. Centres of relatively high biomass were located off the mouth of the rivers Rhine, Weser and Elbe and off the British east coast moving in a cyclic way across the Dogger Bank into the central North Sea. A further maximum of zooplankton abundance was found in the Skagerrak region. However, an intrusion of zooplankton from the shelf edge into the North Sea was not observed in winter. A qualitative analysis of species composition showed that small copepods dominated the zooplankton in the southern and eastern North Sea. The “eddy” of high biomass in the northern North Sea observed in spring, however, was mostly shaped by the large copepodCalanus finmarchicus (70–90%). The distribution of zooplankton biomass in the North Sea is discussed in relation to the hydrographic conditions and to the biology of the dominant species.     

Introduction to the Treatment of Polluted Sediments

This paper overviews the large variety of remediation options for polluted sediments that are currently available. These include physico-chemical and biological techniques that can be applied in situ or ex site.     

Denitrification and Ammonia Formation in Anaerobic Coastal Sediments

Simultaneous determinations of nitrogen gas production, ammonia, and particulate organic nitrogen formation in the coastal sediments of Mangoku-Ura, Simoda Bay, and Tokyo Bay were made by using the ¹⁵N-label tracer method. The rate of nitrogen gas production in the sediment surface layer was about 10⁻² μg atom of N per g per h, irrespective of the location of the sediments examined. [¹⁵N]ammonia and -particulate organic nitrogen accounted for 20 to 70% of the three products, and after several hours of incubation, the major fraction of nondenitrified ¹⁵N in Mangoku-Ura and Simoda Bay sediments was recovered as ammonia. In Tokyo Bay sediments, particulate organic nitrogen was produced at a greater rate than was ammonia. The reduction rate data suggest that the pathway of nitrate reduction to ammonia is important in coastal sediments.     

Diurnal Variation of Cell Proliferation in Three Bacterial Taxa from Coastal North Sea Waters

Pulse-labeling with bromodeoxyuridine (BrdU) in combination with fluorescence in situ hybridization was applied to quantify the percentage of proliferating cells in coastal North Sea waters. In order to assess diurnal variability, we sampled eight or nine times, respectively, within 3 consecutive days at two seasons. Bacteria affiliated with the Roseobacter, SAR86, and NOR5 lineages constituted on average 19% ± 3%, 8% ± 2%, and 6% ± 1% of all cells in May 2002 and 17% ± 3%, 10% ± 2%, and 11% ± 3% in August. The relative abundances of the three populations either remained stable, or they changed very gradually during the observation periods. On average, 38 and 39% of all Bacteria exhibited DNA de novo synthesis in May and August, respectively. The fractions of proliferating cells in bacteria of the SAR86 (May, 59%; August, 72%) and the Roseobacter (48 and 53%) lineages were significantly above the community average. A substantial cell proliferation of population NOR5 (34%) was only encountered in August, concomitant with a dinoflagellate bloom. Significant short-term fluctuations of DNA-synthesizing cells were observed in Roseobacter during May and in NOR5 during August, hinting at a pronounced (temporal or spatial) mesoscale patchiness of growth rates in these populations. Since the BrdU proliferation assay is susceptible to misinterpretation, we also modeled the expected number of labeled cells at increasing BrdU incubation times in a slowly growing bacterial population. We suggest that the absence of visible DNA synthesis in marine bacterioplankton cells after DNA pulse-labeling must not be interpreted as an indication of cell “inactivity.”     

Detection of Animal Viruses in Coastal Seawater and Sediments

Animal viruses, predominantly enteroviruses, were detected in shallow water at bottom depths and in clastic marine sediments. Viruses accumulated in sandy and slimy deposits of the sea bottom near the shore and could be easily released into water by means of simple mechanical shaking.     

Estimates of Denitrification and Nitrification in Coastal and Estuarine Sediments

Denitrification and nitrification in sediments of Tama Estuary and Odawa Bay, Japan, were investigated by the combined use of a continuous-flow sediment-water system and a ¹⁵N tracer technique. At Odawa Bay, the nitrification rate was comparable to the nitrate reduction rate, and 70% of the N₂ evolved originated from nitrogenous oxides (nitrate and nitrite) which were produced by the action of nitrifying bacteria in the sediments. At Tama Estuary, the nitrate reduction rate was 11 to 17 times higher than the nitrification rate, and nitrogenous oxides derived from ammonium accounted for only 6 to 9% of the N₂ evolution by denitrification.     

Pathogenic and Nonpathogenic Acanthamoeba spp. in Thermally Polluted Discharges and Surface Waters1

During spring and autumn, the total number of amoebae and the number of Acanthamoeba species able to grow at 37°C were determined in six thermally polluted factory discharges and the surrounding surface waters. The isolated Acanthamoeba strains were studied for growth in axenic medium, cytopathic effect in Vero cell cultures, and virulence in mice. Although more amoebae were isolated in autumn, the number of Acanthamoeba species was lower than in spring, when the percent of pathogenic strains among the isolates was highest. Higher concentrations of amoebae were found in warm discharges, and more virulent strains occurred in thermal discharges than in surface waters.     

Interactions between Methane Oxidation and Nitrification in Coastal Sediments

Galveston Bay sediments exhibit substantial spatial and seasonal variability in rates of nitrification and aerobic methane oxidation. We examined the biogeochemical and microbiological controls on these processes using aerobic enrichment slurries. Potential aerobic methane and ammonia oxidation rates from unamended control slurries were compared to rates in slurries amended with methane, ammonium, or methane + ammonium. Bacterial community composition was monitored using denaturing gradient gel electrophoresis (DGGE) analysis of PCR amplified ribosomal and functional gene DNA. Potential methane and ammonia oxidation rates increased over time in sediments amended with methane and ammonium, respectively. The highest potential methane oxidation rates occurred in treatments receiving both ammonium and methane suggesting that methanotrophs in the enrichment cultures were nitrogen limited. The highest ammonia oxidation rates occurred in treatments amended with ammonium only. Treatments receiving both ammonium and methane exhibited ammonia oxidation rates and porewater ammonium concentrations similar to those measured in the unamended control suggesting that methanotrophs may have inhibited ammonia oxidation by sequestering available ammonia. Sequence analysis revealed a decrease in general bacterial community diversity over time and a shift in ammonia-oxidizing bacterial composition corresponding with methane availability. However, methanotroph community composition similarities between treatments with different relative methane oxidation rates suggest that changes in physiological activity, as well as shifts in community composition, contributed to the observed patterns in potential rates.     

Coastal peat-beds and peatlands of the southern North Sea: their past,present and future

Peat layers are well represented in the Holocene coastal deposits of the southern North Sea and provide evidence as to the extent and nature of the fens and bogs that occupied the region in the mid and late Holocene. While natural processes contributed to their demise, without human interference extensive areas of peatland would remain. We review the characteristics of the vegetation of these peatlands along with the processes that influenced their development. Spatial and temporal trends are explored through the use of palaeogeographic maps from three areas: the East Anglian Fenland, the Romney Marsh area and the Netherlands. The palaeoecological evidence indicates that eutrophic vegetation promoted by rising relative sea level (RSL) dominated in the mid Holocene, with a trend towards the development of oligotrophic and ombrotrophic vegetation in the late Holocene as the rate of RSL rise declined. Nevertheless, areas of eutrophic vegetation appear capable of long-term stability with areas of fen woodland and herbaceous fen persisting at some locations for several thousand years in the mid and late Holocene. Areas of active peat growth in the region are now largely confined to small remnants within agricultural settings. To retain their characteristic biodiversity these remnants have been managed using traditional practices, although their small size and fragmented distribution limits their biodiversity value. Biodiversity concerns and the ecosystem services peatlands provide, notably carbon sequestration and flood attenuation, underlie recent restoration projects. These efforts are likely to receive additional impetus as a consequence of rising water levels, given projected rates of RSL rise. Future large-scale restoration can be informed by a greater understanding of the processes that formed and sustained coastal peatlands in the past. We identify advances in palaeoenvironmental research that could enhance restoration efforts and help maximise the ecosystem services delivered through such projects.     

Incorporation of Glucose under Anoxic Conditions by Bacterioplankton from Coastal North Sea Surface Waters

It has been hypothesized that the potential for anaerobic metabolism might be a common feature of bacteria in coastal marine waters (L. Riemann and F. Azam, Appl. Environ. Microbiol. 68: 5554-5562, 2002). Therefore, we investigated whether different phylogenetic groups of heterotrophic picoplankton from the coastal North Sea were able to take up a simple carbon source under anoxic conditions. Oxic and anoxic incubations (4 h) or enrichments (24 h) of seawater with radiolabeled glucose were performed in July and August 2003. Bacteria with incorporated substrate were identified by using a novel protocol in which we combined fluorescence in situ hybridization and microautoradiography of cells on membrane filters. Incorporation of glucose under oxic and anoxic conditions was found in α-Proteobacteria, γ-Proteobacteria, and the Cytophaga-Flavobacterium cluster of the Bacteroidetes at both times, but not in marine Euryarchaeota. In July, the majority of cells belonging to the α-proteobacterial Roseobacter clade showed tracer incorporation both in oxic incubations and in oxic and anoxic enrichments. In August, only a minority of the Roseobacter cells, but most bacteria affiliated with Vibrio spp., were able to incorporate the tracer under either condition. A preference for glucose uptake under anoxic conditions was observed for bacteria related to Alteromonas and the Pseudoalteromonas-Colwellia group. These genera are commonly considered to be strictly aerobic, but facultatively fermentative strains have been described. Our findings suggest that the ability to incorporate substrates anaerobically is widespread in pelagic marine bacteria belonging to different phylogenetic groups. Such bacteria may be abundant in fully aerated coastal marine surface waters.