Fish-farm impact on metazoan meiofauna in the Mediterranean Sea: Analysis of regional vs. habitat effects

Mangrove microbial community recovery and their role in early stages of forest recolonization within shrimp ponds

Shrimp farming is blooming worldwide, posing a severe threat to mangroves and its multiple goods and ecosystem services. Several studies reported the impacts of aquaculture on mangrove biotic communities, including microbiomes. However, little is known about how mangrove soil microbiomes would change in response to mangrove forest recolonization. Using genome-resolved metagenomics, we compared the soil microbiome of mangrove forests (both with and without the direct influence of shrimp farming effluents) with active shrimp farms and mangroves under a recolonization process. We found that the structure and composition of active shrimp farms microbial communities differ from the control mangrove forests, mangroves under the impact of the shrimp farming effluents, and mangroves under recolonization. Shrimp farming ponds microbiomes have lower microbial diversity and are dominated by halophilic microorganisms, presenting high abundance of multiple antibiotic resistance genes. On the other hand, control mangrove forests, impacted mangroves (exposed to the shrimp farming effluents), and recolonization ponds were more diverse, with a higher abundance of genes related to carbon mobilization. Our data also indicated that the microbiome is recovering in the mangrove recolonization ponds, performing vital metabolic functions and functionally resembling microbiomes found in those soils of neighboring control mangrove forests. Despite highlighting the damage caused by the habitat changes in mangrove soil microbiome community and functioning, our study sheds light on these systems incredible recovery capacity. Our study shows the importance of natural mangrove forest recovery, enhancing ecosystem services by the soil microbial communities even in a very early development stage of mangrove forest, thus encouraging mangrove conservation and restoration efforts worldwide.

Anthropogenic influence on the physico-chemical parameters of Dhamra estuary and adjoining coastal water of the Bay of Bengal

Estuaries receive the anthropogenic pollutants of their watershed area. Dhamra estuary, on the east coast of India, is such an estuary that receives a huge amount of pollutants, and it will eventually pose a threat to the ecological sensitive areas in its vicinity. Therefore, a study was carried out on physico-chemical parameters and chlorophyll-a to delineate the sources of variation during pre-monsoon and post-monsoon seasons. Surface water sampling was carried out from 12 stations in the estuarine and coastal area. Factor analysis and cluster analysis were applied to seasonal data to understand the sources of variation. From the study, it was observed that the chemical parameters are severely affected by anthropogenic influences such as sediment dredging, aquaculture effluent, and waste from industry and sewage from upstream. In the long run, this will affect the nearby nesting ground of vulnerable Olive Ridley turtles, high bio-diverse mangrove forests, and saltwater crocodile habitat.

Potentially combined effect of the invasive seaweed Caulerpa cylindracea (Sonder) and sediment deposition rates on organic matter and meiofaunal assemblages

The seaweed Caulerpa cylindracea (Sonder) is one of the most successful marine bioinvaders worldwide. Caulerpa cylindracea can influence the quantity and biochemical composition of sedimentary organic matter (OM). However, it is still unknown if the effects of C. cylindracea on both OM and small metazoans (i.e. meiofauna) can change according to different sediment deposition rates. To provide insights on this, we investigated the biochemical composition of sediments along with the abundance and composition of meiofaunal assemblages in sediments colonized and not-colonized by the seaweed C. cylindracea under different regimes of sediment deposition. Our results show that the presence of the invasive alga C. cylindracea could alter quantity, biochemical composition, and nutritional quality of organic detritus and influence the overall functioning of the benthic system, but also that the observed effects could be context-dependent. In particular, we show that the presence of C. cylindracea could have a positive effect on meiofaunal abundance wherever the sediment deposition rates are low, whereas the contextual presence of high to medium sedimentation rates can provoke an accumulation of sedimentary organic matter, less favourable bioavailability of food for the benthos, and consequent negative effects on meiofauna.

Sedimentary Organic Matter, Prokaryotes, and Meiofauna across a River-Lagoon-Sea Gradient

In benthic ecosystems, organic matter (OM), prokaryotes, and meiofauna represent a functional bottleneck in the energy transfer towards higher trophic levels and all respond to a variety of natural and anthropogenic disturbances. The relationships between OM and the different components of benthic communities are influenced by multiple environmental variables, which can vary across different habitats. However, analyses of these relationships have mostly been conducted by considering the different habitats separately, even though freshwater, transitional, and marine ecosystems, physically linked to each other, are not worlds apart. Here, we investigated the quantity and nutritional quality of sedimentary OM, along with the prokaryotic and meiofauna abundance, biomass, and biodiversity, in two sampling periods, corresponding to high vs. low freshwater inputs to the sea, along a river-to-sea transect. The highest values of sedimentary organic loads and their nutritional quality, prokaryotic and meiofaunal abundance, and biomass were consistently observed in lagoon systems. Differences in the prokaryotic Operational Taxonomic Units (OTUs) and meiofaunal taxonomic composition, rather than changes in the richness of taxa, were observed among the three habitats and, in each habitat, between sampling periods. Such differences were driven by either physical or trophic variables, though with differences between seasons. Overall, our results indicate that the apparent positive relationship between sedimentary OM, prokaryote and meiofaunal abundance, and biomass across the river-lagoon-sea transect under scrutiny is more the result of a pattern of specifically adapted prokaryotic and meiofaunal communities to different habitats, rather than an actually positive ‘response’ to OM enrichment. We conclude that the synoptic analysis of prokaryotes and meiofauna can provide useful information on the relative effect of organic enrichment and environmental settings across gradients of environmental continuums, including rivers, lagoons, and marine coastal ecosystems.

Concerns and Threats of Contamination on Aquatic Ecosystems

Aquatic ecosystems are the ultimate sinks for the contaminants. Water contamination is the outcome of human activities such as urbanization, industrialization, and agricultural activities. The overuse of pesticides and fertilizers and sewage from residential and industrial areas ultimately find its way to aquatic environment. Thus results in the degradation of the water quality and leads to the spread of infectious diseases such as dysentery, diarrhea, and jaundice. Contamination in aquatic environs is one of the leading types of pollution which has significant negative health issues and mortality. Water has a natural capacity to neutralize the contamination, but when contamination becomes uncontrolled, water will lose its self-generating capacity. Therefore, there is a need for regular monitoring and controlling of pollutant discharge into the nearby aquatic environs.

Benthic ecological quality assessment of the Bohai Sea, China using marine biotic indices

The coastal ecological environments are heavily affected by anthropogenic activities as well as global climate change. Macrofauna can be used as good indicators for benthic ecological quality status due to its relatively slow movement ability under disturbance and a variety of assessment approaches have been established based on the characteristics of macrofauna. The benthic ecological quality of the Bohai Sea, China, is increasingly threatened by anthropogenic activities. In order to accurately assess the benthic ecological quality status in this region, Shannon-Wiener diversity index, ABC curve, AMBI, M-AMBI and macrofaunal feeding evenness index were used. Results showed that the northern Laizhou Bay and Bohai Bay were under slight disturbance while Liaodong Bay, the central Bohai Sea and Bohai Strait were under moderate disturbance. Overall, the ecological quality indicated by the assessment results of AMBI, Shannon-Wiener diversity index and feeding evenness index were better than that by M-AMBI and the ABC curve.

Multiple human pressures in coastal habitats: variation of meiofaunal assemblages associated with sewage discharge in a post-industrial area

Marine ecosystems are globally threatened by human activities, but some areas, such as those affected by abandoned industrial plants, show an overlap of acute and chronic impacts, which determine a considerable deterioration of their health status. Here we report the results of a research conducted on coastal sewers that discharge their loads in the highly contaminated area of Bagnoli-Coroglio (Tyrrhenian Sea, Western Mediterranean). The sampling area is characterized by heavy industrial activities (a steel plant using coal, iron and limestone) started in 1905 and ceased in 1990, which left widespread heavy metals and hydrocarbon contamination. After taking into account the potential influence of sediment grain size ranges through their inclusion as covariates in the analysis, we tested the potential impact of sewage discharge on the total abundance and multivariate structure of meiofaunal assemblages, as well as on the abundance of single taxa. The organic matter was analysed in terms of total phytopigment and biopolymeric carbon concentrations. Nematoda, Copepoda (including their nauplii), and Tardigrada were the most abundant meiofaunal taxa at all sites, but nematodes did not show a consistent pattern relative to the sewage outfalls. However, the sewer located in the historically most contaminated area showed a minimal abundance of all taxa, including nematodes, while copepods were relatively less abundant at the two southernmost sewers. Comparing the north vs. south site of the sewers, higher meiofaunal abundances were observed in the southward part, likely as a result of the local circulation. The results of this study indicate the general adaptation of meiofauna to multiple stressors (sewage discharge, superimposed to chronic industrial contamination) and its likely modulation by other local processes. They also provide relevant baseline information for future restoration interventions that would take into account the spatial variation of target organisms as needed.

Impact of mangrove forests degradation on biodiversity and ecosystem functioning

Mangroves are amongst the most productive marine ecosystems on Earth, providing a unique habitat opportunity for many species and key goods and services for human beings. Mangrove habitats are regressing at an alarming rate, due to direct anthropogenic impacts and global change. Here, in order to assess the effects of mangrove habitat degradation on benthic biodiversity and ecosystem functioning, we investigated meiofaunal biodiversity (as proxy of benthic biodiversity), benthic biomass and prokaryotic heterotrophic production (as proxies of ecosystem functioning) and trophic state in a disturbed and an undisturbed mangrove forests. We report here that disturbed mangrove area showed a loss of 20% of benthic biodiversity, with the local extinction of four Phyla (Cladocera, Kynorincha, Priapulida, Tanaidacea), a loss of 80% of microbial-mediated decomposition rates, of the benthic biomass and of the trophic resources. The results of this study strengthen the need to preserve mangrove forests and to restore those degraded to guarantee the provision of goods and services needed to support the biodiversity and functioning of wide portions of tropical ecosystems.

Can intensive fish farming for 20 years induce changes in benthic ecosystems on a scale of waterbody? An assessment from Cephalonia bay (Ionian Sea)

The environmental impacts of fish farming on benthic ecosystems beneath the fish cages have been widely addressed the past decades. However, the chronic release of nutrients can cause a shift in local primary productivity and a chronic increase in the sedimentation of organic material at a large spatial scale which could be reflected in benthic ecosystems. In this context, the indirect effects of aquaculture on the benthic ecosystem were studied in a semi-closed bay (Cephalonia, Ionian Sea) where a relatively large fish farm has been operating since 1982. Results from the present sampling were compared to historical data obtained in 1996 and 2001, in order to detect if nutrient release that could impact phytoplankton dynamics in the bay could indirectly alter benthic communities, as well. Macrofaunal communities have not shown deterioration but rather a small, yet statistically significant, improvement in diversity indices and ecological status indicators, and no significant change regarding bioturbation potential. This indicated that processes involved in nutrient consumption and transfer are highly effective in such an oligotrophic environment.

Limited impact of several years of pretreated wastewater discharge on fauna and vegetation in a mangrove ecosystem

It was hypothesized that mangroves, tropical wetlands, could be used for the finishing treatment of domestic wastewaters. Our aim was to determine if a nutrient-stressed mangrove could tolerate long-term discharges of pretreated wastewater (PW). Since 2008, in an in situ experimental system set up in Mayotte Island (Indian Ocean), domestic PW are discharged into two impacted areas (675 m²) dominated by different species of mangrove trees. Anthropogenic inputs during > 4.5 years led to an increase in vegetation growth associated with an increase in leaf pigment content, leaf surface and tree productivity. A marked increase in tree mortality was observed. There was no effect on crabs and meiofauna densities, but significant modifications of community structures. These effects may be directly linked to PW inputs, or indirectly to the modifications of the environment associated with higher tree growth. However, our results indicate that there was no major dysfunction the ecosystem.

Biodiversity loss and turnover in alternative states in the Mediterranean Sea: a case study on meiofauna

In the Mediterranean Sea hard-bottom macroalgal meadows may switch to alternative and less-productive barrens grounds, as a result of sea urchins overgrazing. Meiofauna (and especially nematodes) represent key components of benthic ecosystems, are highly-diversified, sensitive to environmental change and anthropogenic impacts, but, so-far, have been neglected in studies on regime shifts. We report here that sedimentary organic matter contents, meiofaunal taxa richness and community composition, nematode α- and β-biodiversity vary significantly between alternative macroalgal and barren states. The observed differences are consistent in six areas spread across the Mediterranean Sea, irrespective of barren extent. Our results suggest also that the low biodiversity levels in barren states are the result of habitat loss/fragmentation, which is associated also with a lower availability of trophic resources. Furthermore, differences in meiofaunal and nematode abundance, biomass and diversity between macroalgal meadow and barren states persist when the latter is not fully formed, or consists of patches interspersed in macroalgal meadows. Since barren grounds are expanding rapidly along the Mediterranean Sea and meiofauna are a key trophic component in marine ecosystems, we suggest that the extension and persistence of barrens at the expenses of macroalgal meadows could also affect resilience of higher trophic level.

Meiofauna distribution in a mangrove forest exposed to shrimp farm effluents (New Caledonia)

Meiofauna abundance, biomass and individual size were studied in mangrove sediments subjected to shrimp farm effluents in New Caledonia. Two strategies were developed: i) meiofauna examination during the active (AP) and the non-active (NAP) periods of the farm in five mangrove stands characteristics of the mangrove zonation along this coastline, ii) meiofauna examination every two months during one year in the stand the closest to the pond (i.e. Avicennia marina). Thirteen taxonomic groups of meiofauna were identified, with nematodes and copepods being the most abundant ones. Meiofauna abundance and biomass increased from the land side to the sea side of the mangrove probably as a result of the increased length of tidal immersion. Abundance of total meiofauna was not significantly different before and after the rearing period. However, the effluent-receiving mangrove presented twice the meiofauna abundance and biomass than the control one. Among rare taxa, mites appeared extremely sensitive to this perturbation.

Trophic status and meiofauna biodiversity in the Northern Adriatic Sea: Insights for the assessment of good environmental status

The Descriptor 5 (Eutrophication) of the EU Marine Strategy Framework Directive aims at preventing the negative effects of eutrophication. However, in coastal systems all indicators based on water column parameters fail in identifying the trophic status and its effects on biodiversity and ecosystem functioning. We investigated benthic trophic status, in terms of sedimentary organic matter quantity, composition and quality, along with meiofaunal abundance, richness of taxa and community composition in three coastal sites (N Adriatic Sea) affected by different levels of anthropogenic stressors. We show that, on the basis of organic matter quantity and composition, the investigated areas can be classified from oligo-to mesotrophic, whereas using meiofauna as a descriptor, their environmental quality ranged from sufficient to moderately impacted. Our results show that the benthic trophic status based on organic matter variables, is not sufficient to provide a sound assessment of the environmental quality in marine coastal ecosystems. However, data reported here indicate that the integration of the meiofaunal variable allows providing robust assessments of the marine environmental status.

High Meiofaunal and Nematodes Diversity around Mesophotic Coral Oases in the Mediterranean Sea

Although the mesophotic zone of the Mediterranean Sea has been poorly investigated, there is an increasing awareness about its ecological importance for its biodiversity, as fish nursery and for the recruitment of shallow water species. Along with coastal rocky cliffs, isolated coralligenous concretions emerging from muddy bottoms are typical structures of the Mediterranean Sea mesophotic zone. Coralligenous concretions at mesophotic depths in the South Tyrrhenian Sea were investigated to assess the role of these coralligenous oases in relation to the biodiversity of surrounding soft sediments. We show here that the complex structures of the coralligenous concretions at ca. 110 m depth influence the trophic conditions, the biodiversity and assemblage composition in the surrounding sediments even at considerable distances. Coral concretions not only represent deep oases of coral biodiversity but they also promote a higher biodiversity of the fauna inhabiting the surrounding soft sediments. Using the biodiversity of nematodes as a proxy of the total benthic biodiversity, a high turnover biodiversity within a 200 m distance from the coralligenous concretions was observed. Such turnover is even more evident when only rare taxa are considered and seems related to specific trophic conditions, which are influenced by the presence of the coralligenous structures. The presence of a high topographic complexity and the trophic enrichment make these habitats highly biodiverse, nowadays endangered by human activities (such as exploitation of commercial species such as Corallium rubrum, or trawling fisheries, which directly causes habitat destruction or indirectly causes modification in the sedimentation and re-suspension rates). We stress that the protection of the coralligenous sea concretions is a priority for future conservation policies at the scale of large marine ecosystems and that a complete census of these mesophotic oases of biodiversity should be a priority for future investigations in the Mediterranean Sea.

A meta-analysis approach to the effects of fish farming on soft bottom polychaeta assemblages in temperate regions

Marine fish farms could cause environmental disturbances on the sediment due to uneaten food and fish faeces that impact the marine benthos. Polychaete assemblages are considered good indicators of environmental perturbations. The present study aimed to establish groups of polychaetes as potential indicators of fish farm pollution. This study was carried out in ten fish farms along the Spanish coast. Changes in polychaete assemblage were analyzed with meta-analysis and multivariate techniques. Abundance, richness and diversity showed significant decreases under fish farm conditions. Distribution patterns of polychaetes responded to combinations of physicochemical variables. The main ones are sulfide concentration, silt and clays percentage, and stable nitrogen isotope ratio. The results showed that some families are tolerant, Capitellidae, Dorvilleidae, Glyceridae, Nereididae, Oweniidae and Spionidae; while others are sensitive to fish farm pollution, Magelonidae, Maldanidae, Nephtyidae, Onuphidae, Paralacydoniidae, Paraonide, Sabellidae and also Cirratulidae in spite of being reported as a tolerant family.

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.

Tracking multiple pathways of waste from a northern bluefin tuna farm in a marine-coastal area

Aquaculture of bluefin tuna in Mediterranean coastal waters has generated growing concern about the negative environmental effects. In the present isotopic study we examined the dispersal and fate of organic matter derived from a Mediterranean tuna farm in the surrounding environment. An overall enrichment in the heavy nitrogen isotope was found in the feed and in farmed tunas, indicating the input of isotopically traceable organic matter in the system. Waste was clearly traceable in the water column up to 1000 m from the cages, while only slight accumulation occurred in the sediment just below the cages. Waste was isotopically shown also to contribute to the diet of demersal and benthopelagic wild fish collected around the cages. As a result, waste undertook multiple pathways. In the water column its was diluted and dispersed due to hydrodynamism, which prevented great accumulation of aquaculture-derived organic matter in sediments. In addition, biological constraints such as benthopelagic and demersal fish further prevented organic matter accumulation through the benthic trophic route.

Long-term monitoring of fish farms: application of Nematode/Copepod index to oligotrophic conditions

Interannual variability (2003-2008) of meiofaunal assemblages were analyzed in sediments beneath fish cages (Impact group) and in areas not affected by aquaculture activities (Control group). Organisms responded with spatial and seasonal variation in meiofauna assemblages, with an abrupt increase of abundances in locations beneath fish cages throughout the study period. This increase was greater during the last sampling year (2008) and mainly due to high abundances of nematodes. Univariate analyses showed differences between control and impacted sites at both sites, however, only significant variations were found in Los Gigantes, which are consistent with seasonal meiofauna variations throughout the study period. These results are partially explained by differences in current velocity between both sampling areas. The Ne/Co index showed the same trend and it seems to be a reliable index in sediment slightly affected by aquaculture wastes. This index is especially recommended in oligotrophic areas (e.g. Canary Islands) where meiofaunal assemblages are poorly represented in terms of abundances.

Trophic status of earthen ponds used for semi-intensive shrimp (Litopenaeus stylirostris, Stimpson, 1874) farming in New Caledonia (Pacific Ocean)

We have investigated temporal variability in the quantity and biochemical composition of sediment organic matter along with variables proxies of water eutrophication (e.g., inorganic nutrient and chlorophyll-a) at two shrimp farms located in the Southern coast of New Caledonia and characterised by clear differences in shrimp feeding practices and levels of initial trophic conditions. The results of our study reveal that the trophic status of the water column increased during the rearing cycle at both sites, determining a general, though moderated, eutrophication. However, the water column trophic descriptors did not allow to discriminate differences in the trophic status among the investigated sites or between sites in the same farming plant, even if they were subjected to different feeding practices and largely different initial characteristics of the sediment. Temporal variations in biopolymeric C and phytopigment sedimentary contents (used as proxies of benthic eutrophication) varied inconsistently among sites. The multivariate analyses did not identify significant temporal patterns in the benthic trophic status, but allowed discriminating the four investigated sites. The semi-intensive shrimp farming significantly contributed to changing the water column and sediments trophic status of the earthen ponds, but the extent of those changes was not consistently observed in all ponds. In any of the investigated ponds the trophic status exceeded concerning thresholds over which hypoxia or anoxia could occur. We conclude that the established semi-intensive practices adopted so far for shrimp farming activities in the earthen ponds of New Caledonia are able to maintain the status of the ponds below the eutrophication levels over which dystrophic crises could sharply abate most of the reared biomass.

Impacts of marine aquaculture at large spatial scales: evidences from N and P catchment loading and phytoplankton biomass

While several studies point at off-shore aquaculture as a possible source of impacts on the local marine environment, very few have analysed its effects at large scales such as at the bay, gulf or basin levels. Similar analyses are hampered by the multiple sources of disturbance that may concomitantly affect a given area. The present paper addresses these issues taking the Gulf of Castellammare (Southern Tyrrhenian Sea) as an example. Nitrogen (N) and phosphorous (P) loads were calculated for the period 1970-2007, and compared to chlorophyll-a concentration as measured inside and outside the Gulf over the same period. Results indicate that N and P catchment loading has constantly decreased because of improved environmental management. Nevertheless, nutrient concentration in the Gulf has steadily increased since the establishment of aquaculture facilities in 1999. Chlorophyll-a concentration followed this trend, showing a marked increase from 2001 onwards. In the same period, chlorophyll-a concentrations measured inside and outside the Gulf have significantly diverged. As all the other possible causes can be ruled out, aquaculture remains the sole explanation for the observed situation. This paper demonstrates for the first time ever that off-shore aquaculture may affect the marine ecosystem well beyond the local scale and provides an additional element of concern to be kept into consideration when allocating oceans' space for new fish-farming activities.