Effects of fish farming on microbial enzyme activities and densities: comparison between three Mediterranean sites

Diversities and Shifts of Microbial Communities Associated with Farmed Oysters (Crassostrea gigas) and Their Surrounding Environments in Laoshan Bay Marine Ranching, China

Pacific oysters (Crassostrea gigas) are widely cultured in Chinese marine ranching with high economic value. However, mass death of farmed oysters has occurred frequently in recent years because of diseases and environmental disturbance (e.g., high temperatures). In order to analyze the potential relationships between microorganisms and the death of farmed oysters, we compared the dynamics of bacterial and protist communities in oysters at different growth phases using high-throughput sequencing. The results showed that the microbial communities in farmed oysters significantly changed and were markedly different from microbes in natural oysters and the surrounding environments. The number of biomarker taxa among farmed oysters and their surrounding environments decreased gradually with the growth of oysters. During the mass death of farmed oysters, the microbial communities' abundance of ecological function genes changed, and the correlations among microorganisms disappeared. These results enrich our understanding of the dynamics of microbial communities in farmed oysters at different growth phases, illustrating the characteristics of interactions among microorganisms during the mass death of farmed oysters. Our study is beneficial to promote the healthy aquaculture of oysters.

An Integrated Monitoring Approach to the Evaluation of the Environmental Impact of an Inshore Mariculture Plant (Mar Grande of Taranto, Ionian Sea)

The results of an ex-ante survey aiming to assess the impact of a fish farm in the Mar Grande of Taranto (southern Italy, Mediterranean Sea) on the surrounding environment are reported. There, the implementation of an innovative IMTA plant was planned, with the goals of environment bioremediation and commercially exploitable biomass production. Analyses were conducted in February and July 2018. Both seawater and sediments were sampled at the four corners of the fish farm to detect the existing biological and physico-chemical features. The investigation was performed to identify the best area of the farming plant for positioning the bioremediating system, but also to obtain a data baseline, to compare to the environmental status after the bioremediating action. Data were also analyzed by canonical analysis of principal coordinates (CAP). All the measurements, in particular, microbiology and macrobenthic community characterization using AZTI's Marine Biotic Index (AMBI) and the Multivariate-AMBI (M-AMBI) indices, suggest that the effect of fish farm waste was concentrated and limited to a small portion of the investigated area in relation to the direction of the main current. A site named A3, which was found to be the most impacted by the aquaculture activities, especially during the summer season, was chosen to place the bioremediation system.

Biodeposition of oysters in an urbanized bay area alleviates the black-malodorous compounds in sediments by altering microbial sulfur and iron metabolism

The occurrence of the 'black-malodorous phenomenon' in a waterbody is a clear sign of a highly eutrophic bay, the formation of which is associated with microbial sulfur and iron metabolism in the sediments. Oyster farming restoration has been widely studied as an important method for treating eutrophication and related ecological problems. However, few studies focus on the ecosystem-level consequences of oyster farming concerning microbial sulfur and iron cycles in the sediment. Here, we compared the physicochemical features and microbial functions of oyster farms with those of reference areas using the Geochip5.0 technique. Our results showed a significant reduction of acid volatile sulfide (AVS) content associated with oyster farming, thus alleviating the black-malodorous status of Shenzhen Bay in China. Oyster farming created loose and porous sedimentary structures and stimulated the oxidation of black-odorous compounds. Moreover, we observed that the introduction of oysters changed microbial biodiversity significantly based on gyrB gene structure, with typical sulfur- and iron-cycling microbes being enriched. We also demonstrated that microbial abilities involved in sulfur and iron metabolism were greatly increased in oyster farming areas compared with reference areas. Under such circumstances, some cascading processes (AVS uptake and rates of organic matter turnover) were improved, which eventually contributed to black odor reduction. From the microecological perspective, we conclude that the biodeposition of oysters was the key factor for water retention and improvement of microbial metabolism. This study suggests that biodeposition shapes the microbial functional communities in adjacent territories and presumably alleviates the black-malodorous compounds in sediments.

An Integrative, Multiparametric Approach for the Comprehensive Assessment of Microbial Quality and Pollution in Aquaculture Systems

As the aquaculture sector significantly expanded worldwide in the past decades, the concept of sustainable aquaculture has developed with the challenge of not only maximizing benefits but also minimizing the negative impacts on the environment assuring, at the same time, food security. In this framework, monitoring and improving the microbiological water quality and animal health are a central topic. In the present study, we evaluated the seawater microbiological quality in a mariculture system located in a Mediterranean coastal area (Northern Ionian Sea, Italy). We furnished, for the first time, a microbial inventory based on conventional culture-based methods, integrated with the 16S rRNA gene metabarcoding approach for vibrios identification and diversity analyses, and further implemented with microbial metabolic profiling data obtained from the Biolog EcoPlate system. Microbiological pollution indicators, vibrios diversity, and microbial metabolism were determined in two different times of the year (July and December). All microbial parameters measured in July were markedly increased compared to those measured in December. The presence of potentially pathogenic vibrios is discussed concerning the risk of fish disease and human infections. Thus, the microbial inventory here proposed might represent a new multiparametric approach for the suitable surveillance of the microbial quality in a mariculture system. Consequently, it could be useful for ensuring the safety of both the reared species and the consumers in the light of sustainable, eco-friendly aquaculture management.

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.

Seasonal dynamics of the coastal bacterioplankton at intensive fish-farming areas of the Yellow Sea, China revealed by high-throughput sequencing

Marine aquaculture areas are facing stressed environmental challenges, especially the degradation of coastal ecosystems. Here a coordinated time-series study was used to investigate the coastal bacterioplankton biodiversity dynamics of the Yellow Sea, China. Bacterial 16S rRNA gene sequencing revealed a temporal pattern of decreasing of diversity in summer. Functional prediction indicated that metabolic pathways related to the adenosine triphosphate (ATP)-binding cassette transporters and other membrane transporters were significantly enriched in May, while the genetic information processing category was most abundant in March. The May microbiomes showed most significant positive correlation with phosphate concentration, while the August and November microbiomes correlated with temperature and chemical oxygen demand (COD) most, and the March microbiomes showed significant correlation with Cu²⁺ level, pH and salinity. The correlations between representative bacteria and environmental parameters revealed in this study may provide insights into the potential influences of human aquaculture activities, on the biodiversity of coastal bacterioplankton.

Effects of microplastics on trophic parameters, abundance and metabolic activities of seawater and fish gut bacteria in mesocosm conditions

Plastic pollution is an emerging threat with severe implications on animals' and environmental health. Nevertheless, interactions of plastic particles with both microbial structure and metabolism are a new research challenge that needs to be elucidated yet. To improve knowledge on the effects played by microplastics on free-living and fish gut-associated microbial community in aquatic environments, a 90-day study was performed in three replicated mesocosms (control-CTRL, native polyvinyl chloride-MPV and weathered polyvinyl chloride-MPI), where sea bass specimens were hosted. In CTRL mesocosm, fish was fed with no-plastic-added food, whilst in MPV and MPI food was supplemented with native or exposed to polluted waters polyvinylchloride pellets, respectively. Particulate organic carbon (POC) and nitrogen, total and culturable bacteria, extracellular enzymatic activities, and microbial community substrate utilization profiles were analyzed. POC values were lower in MPI than MPV and CRTL mesocosms. Microplastics did not affect severely bacterial metabolism, although enzymatic activities decreased and microbes utilized a lower number of carbon substrates in MPI than MPV and CTRL. No shifts in the bacterial community composition of fish gut microflora were observed by denaturing gradient gel electrophoresis fingerprinting analysis.

Extracellular DNA amplicon sequencing reveals high levels of benthic eukaryotic diversity in the central Red Sea

The present study aims to characterize the benthic eukaryotic biodiversity patterns at a coarse taxonomic level in three areas of the central Red Sea (a lagoon, an offshore area in Thuwal and a shallow coastal area near Jeddah) based on extracellular DNA. High-throughput amplicon sequencing targeting the V9 region of the 18S rRNA gene was undertaken for 32 sediment samples. High levels of alpha-diversity were detected with 16,089 operational taxonomic units (OTUs) being identified. The majority of the OTUs were assigned to Metazoa (29.2%), Alveolata (22.4%) and Stramenopiles (17.8%). Stramenopiles (Diatomea) and Alveolata (Ciliophora) were frequent in a lagoon and in shallower coastal stations, whereas metazoans (Arthropoda: Maxillopoda) were dominant in deeper offshore stations. Only 24.6% of total OTUs were shared among all areas. Beta-diversity was generally lower between the lagoon and Jeddah (nearshore) than between either of those and the offshore area, suggesting a nearshore-offshore biodiversity gradient. The current approach allowed for a broad-range of benthic eukaryotic biodiversity to be analysed with significantly less labour than would be required by other traditional taxonomic approaches. Our findings suggest that next generation sequencing techniques have the potential to provide a fast and standardised screening of benthic biodiversity at large spatial and temporal scales.

Impact of aquaculture on benthic virus-prokaryote interactions in the Mediterranean Sea

We investigated the effects of organic enrichment due to the biodeposition from fish farms on benthic prokaryotic and viral abundance and production, viral-induced prokaryotic mortality, enzymatic activities and bacterial diversity. We compared four areas across the Mediterranean Sea, from Cyprus to Spain, and two different habitats: sediments covered by the seagrass Posidonia oceanica and soft-bottom unvegetated sediments. In several cases, the sediments beneath the cages showed higher prokaryotic and viral abundance and production, and higher rates of organic matter decomposition. However, the differences between impact and control sediments were not consistent at all regions and habitats. Benthic bacterial diversity was always lower below the cages, where high viral-induced bacterial mortality rates were also observed. The δ- and γ-Proteobacteria dominated in both impacted and control sediments, but the relative importance of sulphate-reducing δ-Proteobacteria increased beneath the cages. We conclude that aquaculture can have a significant impact on benthic prokaryotes and viruses, by stimulating prokaryotic metabolism and viral infections, reducing bacterial diversity and altering assemblage composition. However, these impacts vary depending upon the sediment type and the habitat characteristics.

Evaluation of microbiological accumulation capability of the commercial sponge Spongia officinalis var. adriatica (Schmidt) (Porifera, Demospongiae)

This study was carried out to evaluate the microbiological accumulation capability of the demosponge Spongia officinalis var. adriatica. Six microbiological parameters were researched in two sampling periods in the water and in reared sponge samples coming from sites with different degrees of microbial contamination: an off-shore fish farm displaced off the Apulian coast (Southern Adriatic Sea) and a no-impacted area displaced into the Marine Protected Area of Porto Cesareo (Apulian coast-Ionian Sea). We detected the density of culturable heterotrophic bacteria by spread plate on marine agar, total culturable bacteria at 37 degrees C on Plate Count Agar and vibrios on thiosulphate-citrate-bile-sucrose-salt (TCBS) agar. Total and fecal coliforms as well as fecal streptococci concentrations were detected by the MPN method. Bacterial densities were always higher in the sponge homogenates compared with the corresponding seawater in the sampling points and in both sampling periods. As regard vibrios, total culturable bacteria at 37 degrees C and fecal streptococci concentrations, the highest values were observed in the sponge samples coming from the off-shore fish farm during the summer period. The ability of Spongia officinalis var. adriatica to accumulate the microbial pollution indicators suggests that this species can be employed as a bioindicator for monitoring water quality.

Response of the bacterial community to in situ bioremediation of organic-rich sediments

A field trial experiment was carried out to assess the potential of bioremediation for mobilisation of carbon in organic-rich sediments. Both bioaugmentation (bio-fixed microorganisms) and biostimulation (oxygen release compounds--ORC) protocols have been tested and the response of the bacterial community has been described to assess the baseline for bioremediation potential. Multifactorial ANOVA revealed that bioaugmentation protocol had an effect in stimulate mobilisation processes and significantly enhanced extra-cellular enzymatic activity rates. In contrast biostimulation treatment did not have an effect on mobilisation rates but contributed to enhance bacterial efficiency through a maximization of the bacterial production:enzymatic activity ratio. Average calculation of net mobilised carbon showed that 23% increase of mobilised pool was accounted for bioaugmentation in summer. Although biostimulation accounted for a smaller increase in mobilised carbon (<10%), the use of ORC resulted in an increased mineralisation and net carbon loss via respiration. Based on our results, a conceptual model for application of bioremediation to face the problem of sediment eutrophication is discussed.