Fish Farm Sediments Research Articles

Spatial distribution of antibiotics and antibiotic resistance genes in tidal flat reclamation areas in China.

Tidal flat areas are important resources for land development and are becoming antibiotic resistance receivers that trigger major health concerns. The spatial distributions of forty-nine antibiotics, nine antibiotic resistance genes (ARGs), one mobile gene element (MGE) gene, and nine available metals in the soils and sediments along the coastlines of the Yellow Sea in China were quantified. Hierarchical linear model analysis was used to explore relationships between the antibiotics and ARGs across multiple effects resulting from human activities and environmental factors. Fish farm sediments and farmland soils showed high levels of quinolones (QNs) (maximum 637ng·g-1), sulfonamides (SAs) (maximum 221ng·g-1), and corresponding ARGs. Significant positive correlations (P from 5.47 × 10-14 to 0.0487) were observed between the antibiotics (QNs, SAs, and chlortetracycline) and their corresponding ARGs (qnrA, qnrD, aac(6')-Ib-cr, dfrA, sul2, and tetA), indicating the selective pressure from antibiotics in soils and sediments. Nine available metals had positive correlations with at least one ARG, indicating heavy metal pollution could enhance the ARGs. Sheep and poultry husbandry and marine aquaculture contribute the most to the antibiotic resistance in the coastlines. In conclusion, antibiotic pollutions have promoting effects at sub-inhibitory concentrations and more attention should be given to inhibit the enrichment of ARGs during tidal flat reclamation processes. The study also suggests the induction effects from metal pollutions, MGE spread, and the antibiotic pollutions from the usage in livestock and aquaculture.

Biogeochemical impacts of fish farming on coastal sediments: Insights into the functional role of cable bacteria.

Fish farming in sea cages is a growing component of the global food industry. A prominent ecosystem impact of this industry is the increase in the downward flux of organic matter, which stimulates anaerobic mineralization and sulfide production in underlying sediments. When free sulfide is released to the overlying water, this can have a toxic effect on local marine ecosystems. The microbially-mediated process of sulfide oxidation has the potential to be an important natural mitigation and prevention strategy that has not been studied in fish farm sediments. We examined the microbial community composition (DNA-based 16S rRNA gene) underneath two active fish farms on the Southwestern coast of Iceland and performed laboratory incubations of resident sediment. Field observations confirmed the strong geochemical impact of fish farming on the sediment (up to 150 m away from cages). Sulfide accumulation was evidenced under the cages congruent with a higher supply of degradable organic matter from the cages. Phylogenetically diverse microbes capable of sulfide detoxification were present in the field sediment as well as in lab incubations, including cable bacteria (Candidatus Electrothrix), which display a unique metabolism based on long-distance electron transport. Microsensor profiling revealed that the activity of cable bacteria did not exert a dominant impact on the geochemistry of fish farm sediment at the time of sampling. However, laboratory incubations that mimic the recovery process during fallowing, revealed successful enrichment of cable bacteria within weeks, with concomitant high sulfur-oxidizing activity. Overall our results give insight into the role of microbially-mediated sulfide detoxification in aquaculture impacted sediments.

The Depleted Carbon Isotopic Signature of Nematodes and Harpacticoids and Their Place in Carbon Processing in Fish Farm Sediments

Fish farm-originating organic matter can modify the processes in a benthic ecosystem. This was investigated in the sediments of the northern Adriatic Sea by δ13C signature of nematodes, harpacticoids, and sedimentary organic matter, and by pore water nutrients and bacterial composition. In a mesocosm experiment, 13C-labeled diatoms were added on top of sediment cores and 13C enrichment was measured as a proxy of diatom uptake by meiofauna. The δ13C signatures were depleted under fish farming cages compared to the reference site, as observed for sedimentary organic matter (-24.4‰ vs. -21.8‰), for nematodes (-22.5‰ vs. -17.7‰), and for harpacticoids (-25.3‰ vs. -20.8‰). The direct consumption of fish feed (-22.2‰) was not traced in meiofauna taxa. Nematodes from the farm site likely reflect a diet comprising sedimentary organic matter, as they were enriched by 2‰ relative to the sedimentary organic matter. The nematodes from the reference site were enriched by 4.2‰ relative to the sedimentary organic matter, which implies that they rely on more enriched food sources, like diatoms, which was confirmed by their uptake of 13C-labeled diatoms. The nematode assemblage incorporated more diatom 13C than harpacticoids, making them more important players in the carbon flux from diatoms to higher trophic levels at the reference site. Harpacticoids from the reference site were enriched by 1.1‰ compared to sedimentary organic matter, implying that this was their primary food source. Harpacticoids from the farm site were depleted by 0.9‰ relative to the sedimentary organic matter, indicating they are influenced by a very negative food source, potentially bacteria. Harpacticoids from both the cage and reference sites consumed 13C-labeled diatoms, which implies their diet might span a broad δ13C range, from bacteria to diatoms. Pore water nutrients with high DIC, PO43-, and NH4+ concentration indicated an elevated microbial degradation of organic compounds under the fish farm. DGGE analysis showed a 70% similarity between sediment bacteria communities from the fish farm and reference site. The study demonstrated that fish farm-originating organic matter enters the meiofauna food chain, and that nematodes and harpacticoids use different food sources under the fish farm and at the reference site.

Temporal Changes in Microbial Communities Beneath Fish Farm Sediments Are Related to Organic Enrichment and Fish Biomass Over a Production Cycle

The marine fish farming industry is growing at a significant rate, yet a number of concerns still remain with regards to environmental impacts on the surrounding coastal sea and its biota. Here, we assessed the impact of intensive farming on benthic prokaryotic communities at a Mediterranean sea bass and sea bream intensive aquaculture site over a period of 10 months, in relation to the increase in fish biomass within the cage together with the organic matter enrichment in the sediments. We report positive relationships between prokaryotic abundance and both organic matter and fish biomass, and a contextual decrease in prokaryotic diversity below the cages. A significant shift in microbial community composition occurred in fish farm sediments (FF) over time, indicating a likely impact of ongoing aquaculture activity on prokaryotic communities. Among the dominant taxa at the impacted site, we found Epsilonproteobacteria and Bacteroidetes, which showed a general increase with fish biomass. Analyses on specialist taxa underlined significant contributions of Clostridiales and Bacteroidales in the farmed sediments. Finally, sea bream and sea bass gut microbiome-related taxa were detected during the sampling period. Our results indicate that prokaryotic community composition underneath the cages is related to fish biomass and organic enrichment over the course of production, and confirms that the study of benthic microbial communities at aquaculture sites represents a useful tool to assess the impact of intensive mariculture on the surrounding environment.

Terrestrial-marine continuum of sedimentary natural organic matter in a mid-latitude estuarine system

Humic acids (HA) have several environmental roles, but are particularly important in aquatic environments, being recognized as redox active natural organic matter (NOM) components. We examined NOM in recent sediments of a low-energy coastal environment which is free from inputs of dissolved terrestrial HA as their solubility is suppressed by bonding with Ca2+ ions. Our aim is to investigate the contribution of autochthonous versus terrestrial C sources to HA and their fractions along a river-coastal lagoon transect. Surface sediments were collected along the Aussa River (R), in the central basin of the Marano and Grado Lagoon (L) and within a secluded lagoon fish farm (FF). Extractable NOM components were obtained by extracting sediments first with 0.5 M NaOH (free NOM) and then with 0.1 M NaOH plus 0.1 M Na4P2O7 (bound NOM). Extracts were separated into non-humic and humic fractions by solid phase chromatography. Organic carbon (Corg), total nitrogen (Ntot), δ13C, and δ15N were determined with an Isotope Ratio Mass Spectrometer (Thermo Scientific Delta V Advantage) coupled with an Elemental Analyzer (Costech Instruments Elemental Combustion System). Fourier-transform infrared (FTIR) spectra were recorded with a FT-IR100 PerkinElmer Spectrometer. UV-vis spectra were recorded at pH 7 by a Varian Cary Spectrophotometer. Both NOM and HA display typical traits of terrestrial origin in river sediments and of a more marine (algal) origin in lagoon and fish farm sediments. This trend is evident in free HA, whereas bound HA seem more influenced by terrestrial inputs. A larger proportion (60–70%) of non-humic C was extracted by NaOH in all samples. Bound HA differ from free HA for their C/N ratios, which are higher and vary within a much narrower range. The changes in HA’s 13C isotopic composition, FTIR spectra, and spectroscopic parameters (SUVA254, SR, and aromaticity) highlight a progressive mixing of terrestrial and marine substrates that either undergo in situ humification or are transported as materials sorbed onto suspended mineral particles. Our results highlight the existence of a complex, but continuous pattern of terrestrial and marine contributions to C sequestration and humification even in transitional environments where allochthonous humic C inputs are restricted due to insolubilization of humic substances by Ca2+. Along the examined transect, the NOM and free and bound HA appear well differentiated. Terrestrial inputs contribute to the bound HA fraction via transported mineral particles in all the samples, no matter the environment encountered.

Biostimulation of in situ microbial degradation processes in organically-enriched sediments mitigates the impact of aquaculture

Fish farm deposition, resulting in organic matter accumulation on bottom sediments, has been identified as among the main phenomena causing negative environmental impacts in aquaculture. An in situ bioremediation treatment was carried out in order to reduce the organic matter accumulation in the fish farm sediments by promoting the natural microbial biodegradation processes. To assess the effect of the treatment, the concentration of organic matter in the sediment and its microbial degradation, as well as the response of the benthic prokaryotic community, were investigated. The results showed a significant effect of the treatment in stimulating microbial degradation rates, and the consequent decrease in the concentration of biochemical components beneath the cages during the treatment. During the bioremediation process, the prokaryotic community in the fish farm sediment responded to the overall improvement of the sediment conditions by showing the decrease of certain anaerobic taxa (e.g. Clostridiales, Acidaminobacteraceae and Caldilinaceae). This suggested that the bioactivator was effective in promoting a shift from an anaerobic to an aerobic metabolism in the prokaryotic community. However, the larger importance of Lachnospiraceae (members of the gut and faecal microbiota of the farmed fishes) in treated compared to non-treated sediments suggested that the bioactivator was not efficient in reducing the accumulation of faecal bacteria from the farmed fishes. Our results indicate that bioremediation is a promising tool to mitigate the aquaculture impact in fish farm sediments, and that further research needs to be oriented to identifying more successful interventions able to specifically target also fish-faeces related microbes.

Persistent organic pollutants (POPs) in fresh water farm fish species from Punjab (India) and evaluation of their dietary intake for human risk assessment

ABSTRACTIn India, persistent organic pollutants (POPs) have been used extensively in both agricultural and industrial sectors, resulting in deterioration of terrestrial and aquatic environment. In the present study, analysis of POPs in fresh water ecosystem comprising samples of fish, sediments, and water was done from fish farms in Punjab, India. POP residues comprising lindane, p,p’-DDE, p,p’-DDD, endosulfan sulfate, and polychlorinated biphenyl (PCB) congeners (PCB-28, PCB-138, PCB-180) were detected in fish samples. Residues of p,p’ DDE and p,p’ DDD were recorded utmost in fish flesh with mean levels of 13.8 and 5.8 ng g−1, respectively. PCB residues were estimated in 20 fish samples with values in the range ND–46.3 ng g−1. The mean residue levels detected in this study were lower than the recommended maximum residue limits (MRLs) described by EU-MRLs, Italian-MRLs, FDA-2001, and FAO-1983. At the current levels of POP residues in fish flesh, the human health risk assessment based on both deterministic (mean residue levels) and probabilistic (95th percentile upper bound limit) approaches, reflected that cancer and non-cancer risks were within United States Environmental Protection Agency (USEPA) prescribed limits. The presence of POP residues in fish farm sediments and water elucidated the relationship between occurrence of POP residues in fish and its aquatic environment.

Utilization of Putative Enterobacter Isolate and Substrates for Microbial Fuel Cells

The current Philippine energy crisis reminds us of the importance of finding alternative energy sources. Microbial fuel cells (MFC) may contribute to the solution. MFCs utilizing marine sediments, rice straw, domestic sewage, and agricultural water have a large potential as an alternative energy source. The objectives of the project were to isolate the biological agent, determine the optimum waste substrates, and to develop a working microbial fuel cell using locally available materials as fuel source. Soil, sediment, and corn stover were collected. An improvised MFC was constructed with two compartments for the anode and cathode sections separated by an agar plug (5% w/v). Each compartment had 750 ml capacities. Several combinations of materials were determined. Triplicates of each material-isolate combination were used to determine voltage, amperage, and Columbic output. Thirty percent fish farm sediments produced the highest voltage and amperage. This treatment was able to produce power for 7 to 25 days after MFC setup. Addition of ammonium sulfate in this setup reduced electrical output. Other treatments also produced power but were not as comparable. This study showed that utilizing wastes as substrate for MFCs is feasible and may have practical use.

Impact of raking and bioturbation-mediated ecological manipulation on sediment-water phosphorus diagenesis: a mesocosm study supported with radioactive signature.

The study examined the impact of raking and fish bioturbation on modulating phosphorus (P) concentrations in the water and sediment under different trophic conditions. An outdoor experiment was set to monitor physicochemical and microbiological parameters of water and sediment influencing P diagenesis. A pilot study with radioactive 32P was also performed under the agency of raking and bacteria (Bacillus sp.). Raking was more effective in release of P under unfertilized conditions by significantly enhancing orthophosphate (35%) and soluble reactive phosphate (31.8%) over respective controls. Bioturbation increased total and available P in sediments significantly as compared to control. The rates of increase were higher in the unfertilized conditions (17.6-28.4% for total P and 12.2 to 23.2% for available P) than the fertilized ones (6.5-12.4% for total P and 9.1 to 15% for available P). The combined effects of raking and bioturbation on orthophosphate and soluble reactive phosphate were also stronger under unfertilized state (54.5 and 81.8%) than fertilized ones (50 and 70%). The tracer signature showed that coupled action of introduced bacteria and repeated raking resulted in 59.2, 23 and 16% higher counts of radioactive P than the treatments receiving raking once, repeated raking and bacteria inoculation, respectively. Raking alone or in sync with bioturbation exerted pronounced impact on P diagenesis through induction of coupled mineralization and nutrient release. It has significant implication for performing regular raking of fish-farm sediments and manipulation of bottom-grazing fish to regulate mineralization of organic matter and release of obnoxious gases from the system. Further, they synergistically can enhance the buffering capacity against organic overload and help to maintain aquatic ecosystem health.

Influence of tubificid worms on nutrient fluxes across water-sediment interface in fish farm settling ponds

Key-words: tubificids, phosphorus, ammonia, nitrate, fish farming, settling ponds The influence of tubificid worms on nutrient translocation from water to fish farm sediments accumulating in settling ponds was addressed under laboratory conditions. Small microcosms of 0.5 L were filled up with 35 g of sludge from a fish farm settling pond and 0.15 L of filtered settling pond water. The experimental set up consisted of one control line (no worms added), a second experimental line with 1 mg of tubificid worms·g −1 fresh sediment (550 individuals·m −2 ) and a third experimental line with 40 mg of tubificid worms·g −1 fresh sediment (22000 individuals·m −2 ). Nutrients translocation was determined by monitoring overlaying water concentration of ammonia, nitrate and phosphate for ten days. Results showed that abundances of 550 individuals·m −2 had no significant influence on the fluxes of nutrients here considered. However, the influence of higher abundances of tubificids (22000 individuals·m −2 ) was of significant extent on the translocation of nitrate and phosphate. Accordingly, bioturbation of tubificids caused 55% lower nitrate uptake by the sediment when compared to control conditions. Phosphorus released by the sediments of the control condition was ca. 90% higher than that recorded under abundances of tubificids (22000 individuals·m −2 ). Results obtained allowed us to estimate that fish farm settling ponds highly colonized by tubificid worms (22000 individuals·m −2 ) may contribute to decrease phosphorus discharge (in terms of soluble phosphorus) in ca. 5go f P·ton −1 of fish produced.

Characterization of a multiresistant mosaic plasmid from a fish farm Sediment Exiguobacterium sp. isolate reveals aggregation of functional clinic-associated antibiotic resistance genes.

The genus Exiguobacterium can adapt readily to, and survive in, diverse environments. Our study demonstrated that Exiguobacterium sp. strain S3-2, isolated from marine sediment, is resistant to five antibiotics. The plasmid pMC1 in this strain carries seven putative resistance genes. We functionally characterized these resistance genes in Escherichia coli, and genes encoding dihydrofolate reductase and macrolide phosphotransferase were considered novel resistance genes based on their low similarities to known resistance genes. The plasmid G+C content distribution was highly heterogeneous. Only the G+C content of one block, which shared significant similarity with a plasmid from Exiguobacterium arabatum, fit well with the mean G+C content of the host. The remainder of the plasmid was composed of mobile elements with a markedly lower G+C ratio than the host. Interestingly, five mobile elements located on pMC1 showed significant similarities to sequences found in pathogens. Our data provided an example of the link between resistance genes in strains from the environment and the clinic and revealed the aggregation of antibiotic resistance genes in bacteria isolated from fish farms.

English

The aims of this study were to help the development of the models describing denitrification in the recirculation aquaculture systems and to contribute to the knowledge on the role of heterotrophic bacteria in aquaculture nutrient removal systems in mudflats along the coast. Six aerobic denitrifying strains were isolated by bromothymol blue (BTB) plate technique from the fish farm sediments in mudflat along the coast. The strain DF-1 was selected for the aerobic denitrification studies as it was highly effective in removing nitrite compared with other strains; it lowered the nitrite nitrogen (nitrite-N) concentration from 10 mg/L to zero in 20 h. The aerobic denitrification by the strain DF-1 occurred at significantly higher rates of nitrite-N degradation than the positive controls (sterile screening media) under different pH, temperature, and various concentrations of nitrite and salinity. The rate of nitrite-N degradation was 99.3, 97.7, 99.5, 96.5, and 91.8% when sucrose, glucose, sodium acetate, sodium succinate and potassium sodium tartrate, respectively, were used as the carbon source. The strain DF-1 contained the nirK gene as indicated by the amplification of nitrite reductase. The strain DF-1 was identified asKlebsiella oxytoca by the morphological observation and 16SrRNA gene analysis.   Key words: Coastal pollution, high nitrogen risk, aerobic denitrification, Klebsiella oxytoca, nitrite nitrogen degradation rate, aquaculture.

Exchange of nutrients and oxygen across the sediment–water interface below a Sparus aurata marine fish farm in the north-western Mediterranean Sea

This study analyzes the effects of aquaculture activities in open seawater in the north-western coastal waters of the Mediterranean Sea. It is the first of its kind to be based on benthic flux data gathered in situ below fish farms for this particular area. Samples were collected on four sampling campaigns over a 1-year cycle under a Sparus aurata fish farm facility where benthic fluxes were measured in situ using light and dark benthic chambers. Bottom water and sediment samples were also collected. Data were compared to those for a nearby control station. Significant differences were found (ANOVA, p < 0.05) between concentrations of organic matter (OM), total phosphorus and redox potentials in sediments located under the cages and those of the control station. The consumption of dissolved oxygen (DO) by sediment and positive ammonium (NH 4 + ) fluxes was stimulated by OM content, with correlations of r = −0.60 (p < 0.01) and r = 0.70 (p < 0.01), respectively. The OM content of sediments was found to be consistently higher under the cages than at the control station, with the highest value (1.8 ± 0.7 %) under the cages observed during the early summer; values of DO and NH 4 + fluxes were −64 ± 17 and 12.7 ± 1.0 mmol m−2 day−1, respectively. PO 4 3– fluxes were consistently higher in the fish farm sediments (between 0.58 and 0.98 mmol m−2 day−1) than those observed at the control station. Nitrate (NO 3 − ) fluxes were found to be consistently negative due to denitrification occurring in the sediments and were related to the concentration of NO 3 − in bottom waters (r = 0.92, p < 0.01). Si fluxes were shown to be associated with water temperature (r = 0.59, p < 0.05). The results imply that sediments located below cages accumulate organic matter originating from aquaculture activities, especially during summer months when this activity increases. Sediments undergo biogeochemical changes that mainly affect fluxes of DO, NH 4 + and soluble reactive phosphorus, although these do not seem to have a significant impact on the quality of the water column due to the hydrodynamic characteristics of the area.

Comparison of Sulphate-reducing Bacterial Communities in Japanese Fish Farm Sediments with Different Levels of Organic Enrichment

Fish farm sediments receive a large amount of organic matter from uneaten food and fecal material. This nutrient enrichment, or organic pollution, causes the accumulation of sulphide in the sediment from the action of sulphate-reducing bacteria (SRB). We investigated the effect of organic enrichment around coastal fish farms comparing the SRB community structure in these sediments. Sediment samples with different levels of organic pollution classified based upon the contents of acid-volatile sulphide and chemical oxygen demand were collected at three stations on the coast of western Japan. The SRB community composition was assessed using PCR amplification, cloning, sequencing and phylogenetic analysis of the dissimilatory sulphite reductase β-subunit gene (dsrB) fragments using directly extracted sediment DNA. Sequencing of the cloned PCR products of dsrB showed the existence of different SRB groups in the sediments. The majority of dsrB sequences were associated with the families Desulfobacteraceae and Desulfobulbaceae. Clones related to the phylum Firmicutes were also detected from all sediment samples. Statistical comparison of sequences revealed that community compositions of SRB from polluted sediments significantly differed from those of moderately polluted sediments and unpolluted sediments (LIBSHUFF, p<0.05), showing a different distribution of SRB in the fish farm sediments. There is evidence showing that the organic enrichment of sediments influences the composition of SRB communities in sediments at marine fish farms.

Abundance of sulphate-reducing bacteria in fish farm sediments along the coast of Japan and South Korea

The abundance of sulphate-reducing bacteria (SRB) was investigated in the coastal marine sediments along the coast of Japan and South Korea. Sediment samples were collected from fish and shellfish farms between 2006 and 2008. As non-fish farming reference sites, sediments were also collected from highly eutrophic bays, a highly sulphidogenic saline lake, and the deep sea. A quantitative real-time PCR analysis that targeted the gene coding for a portion of the α-subunit of dissimilatory sulphite reductase (dsrA) was performed to assess the abundance of the SRB in the sediments. Between 2.8 × 107 and 2.5 × 109 copies of the dsrA gene per gram dry sediment were detected. There was no relationship between dsrA gene copy number and total bacterial count in the sediments, whereas organic matter contents (particulate organic carbon and nitrogen, ignition loss and chemical oxygen demand) and acid-volatile sulphide contents were significantly correlated with the dsrA copy number. The data presented demonstrate that organic enrichment of sediment may influence the abundance of SRB communities in coastal marine sediments and that the cell density of SRB may be used as a biological indicator for assessing pollution levels in sediments of marine fish farms.

Biofilm formation and proteolytic activities of Pseudoalteromonas bacteria that were isolated from fish farm sediments

SummaryIn order to save natural resources and supply good fishes, it is important to improve fish‐farming techniques. The survival rate of fish fry appears to become higher when powders of foraminifer limestone are submerged at the bottom of fish‐farming fields, where bacterial biofilms often grow. The observations suggest that forming biofilms can benefit to keep health status of breeding fishes. We employed culture‐based methods for the identification and characterization of biofilm‐forming bacteria and assessed the application of their properties for fish farming. Fifteen bacterial strains were isolated from the biofilm samples collected from fish farm sediments. The 16S rRNA gene sequences indicated that these bacteria belonged to the genera, Pseudoalteromonas (seven strains), Vibrio (seven strains) and Halomonas (one strain). It was found that Pseudoalteromonas strains generally formed robust biofilms in a laboratory condition and produced extracellular proteases in a biofilm‐dependent manner. The results suggest that Pseudoalteromonas bacteria, living in the biofilm community, contribute in part to remove excess proteineous matters from the sediment sludge of fish farms.

Comparison of bacterial communities in fish farm sediments along an organic enrichment gradient

Aquaculture is of major industrial importance world wide and this has led to concerns over the impact of fish farming on previously pristine marine environments. Fish farm sediments receive a large amount of organic matter due to uneaten food and fecal materials. This organic enrichment of sediment influences the biogeochemical process and benthic microbial communities. This study was performed to investigate the effect of pollution from marine fish farms on the bacterial community structure in the underlying sediments. Sediment samples were collected at four stations along an organic enrichment gradient on the coast of Wakasa Bay in southern Fukui Prefecture, Japan between April 2004 and December 2006. Sagami Bay sediments were also used as a non-fish farming reference site. The bacterial community composition was assessed using PCR amplification, cloning, sequencing, and phylogenetic analysis of 16S rDNA using directly extracted sediment DNA. Most of the clones sequenced fell into six major lineages of the domain Bacteria: γ-, δ-, ε-Proteobacteria, Acidobacteria/ Holophaga, Bacteroidetes, and Planctomycetes. Although there were no significant differences in the bacterial community structures among the sediment samples except for Sagami Bay, a minor change in the composition of 16S rDNA operational taxonomy units (OTUs) between sites was recognized. 16S rDNA sequences related to the γ-Proteobacteria were recovered with relatively higher frequencies from unpolluted sediments than from polluted sediments. In contrast, the most abundant clone sequences from polluted sediment samples were grouped with δ-Proteobacteria. Our data suggests organic enrichment of sediment may influence the composition of bacterial communities; and the δ-Proteobacteria were found and selected for within polluted fish farm sediments.

Distribution of sulfate-reducing bacteria in fish farm sediments on the coast of southern Fukui Prefecture, Japan

The distribution of sulfate-reducing bacteria (SRB) was investigated in the sediments below fish cages used for torafugu (Takifugu rubripes) aquaculture along the coast of southern Fukui Prefecture, Japan. A quantitative competitive PCR targeting the gene coding for a portion of the α-subunit of the dissimilatory (bi)sulfite reductase (dsrA) gene was used to determine the distribution of SRB in the sediments. In unpolluted fish farm sediments, SRB were detected at levels of 0.5–8.4×108 cells g−1 dry sediment; whereas higher densities of SRB were found in sediments rich in organic matter and sulfide at levels of 0.8–4.4×109 cells g−1 dry sediment as determined by competitive PCR. We detected differences in SRB densities in fish farm sediments with different pollution levels, or organic contamination and sulfide content, suggesting SRB cell density may be used as an indicator of pollution levels in fish farm sediments as an adjunct to chemical analyses such as measurements of chemical oxygen demand (COD) or chemically determined total sulfide (TS).

The succession of microbial community in the organic rich fish-farm sediment during bioremediation by introducing artificially mass-cultured colonies of a small polychaete, Capitella sp. I

We monitored seasonal changes of the abundance and composition of microorganisms in the fish-farm sediment in Kusuura Bay, Amakusa, Japan, using the quinone profiling technique, during bioremediation by introducing cultured colonies of polychaete, Capitella sp. I. In November 2004, approximately 9.2 million cultured worms were transferred to the fish-farm sediment, which increased rapidly, and reached 458.5 gWW/m 2 (528,000 indiv./m 2) in March 2005. During this fast-increasing period of Capitella, the microbial quinone content of the surface sediment (0–2 cm) also increased markedly, and reached 237 μmol/m 2 in January 2005, although the water temperature decreased to the lowest levels in the year. Particularly, the mole fraction of ubiquinone-10 in total quinones in the sediment, indicating the presence of α subclass of Proteobacteria, increased by 9.3%. These facts suggest that the bacterial growth was enhanced markedly by the biological activities of worms in the sediment, and the bacteria played an important role in the decomposition of the organic matter in the sediment.

Stimulation of sulfate reduction rates in Mediterranean fish farm sediments inhabited by the seagrass Posidonia oceanica

Sulfate reduction rates and biogeochemical parameters of fish farm sediments across the Mediterranean were investigated in the order to evaluate the potential effects of organic matter inputs on habitat quality for the common seagrass Posidonia oceanica. Four study sites were selected in Spain, Italy, Greece and Cyprus to represent the Mediterranean basin. P. oceanica was found in immediate vicinity of all the farms, which were located at physically exposed sites about 1 km from the shore lines. Organic matter accumulation, sulfate reduction rates and sulfur pools were measured in depth profiles along transects from the farms in both bare and vegetated sediments. Results show that although the organic matter accumulation was minor at the sites (POC < 2.8% DW), the sulfate reduction rates were high, in particular at the largest farm in Italy (up to 212 mmol m−2 d−1), similar to rates found at shallower, temperate fish farm sites, where higher sedimentation rates can be expected. Sulfate reducing bacteria in these low-organic, carbonate-rich Mediterranean sediments respond strongly to organic matter loadings and cause habitat degradation. Sulfate reduction rates measured in the P. oceanica sediments were among the highest recorded (7.8–42.0 mmol m−2 d−1) similar to rates found in degrading meadows impacted by organic matter loadings. As sulfate reduction rates were correlated with the sedimentation rates along the transects rather than organic matter pools this suggests mineralization processes were controlled by organic matter loading in fish farm sediments. The vegetated sediments near the net cages were more reduced due to accumulation of sulfides compared to control sites, which is a possible contributing factor to the observed seagrass decline in the farm surroundings. It is recommended that Mediterranean fish farms are placed in areas with rapid dispersal of particulate waste products to minimize organic matter loading of the sediments and thereby preserve habitat quality for benthic fauna and flora.