Methodologies for the analysis and interpretation of environmental datasets from areas interested by offshore activities

The exploitation of hydrocarbon reservoirs by the oil and gas industries represents one of the most relevant and concerning anthropic stressor in various marine areas worldwide and the presence of extractive structures can have severe consequences on the marine environment. Environmental monitoring surveys are carried out to monitor the effects and impacts of offshore energy facilities. Macrobenthic communities, inhabiting the soft-bottom, represent a key component of these surveys given their great responsiveness to natural and anthropic changes. A comprehensive collection of monitoring data from four Italian seas was used to investigate distributional pattern of macrozoobenthos assemblages confirming a high spatial variability in relation to the environmental variables analyzed. Since these datasets could represent a powerful tool for the industrial and scientific research, the steps and standardized procedures needed to obtain robust and comparable high-quality data were investigated and outlined. Over recent years, decommissioning of old platforms is a growing topic in this sector, involving many actors in the various decision-making processes. A Multi-Criteria Decision Analysis, specific for the Adriatic Sea, was developed to investigate the impacts of decommissioning of a gas platform on environmental and socio-economic aspects, to select the best decommissioning scenario. From the scenarios studied, the most impacting one has resulted to be total removal, affecting all the faunal component considered in the study. Currently, the European nations are increasing the production of energy from offshore wind farms with an exponential expansion. A comparative study of methodologies used five countries of the North Sea countries was carried out to investigate the best approaches to monitor the effects of wind farms on the benthic communities. In the foreseeable future, collaboration between industry, scientific communities, national and international policies are needed to gain knowledge concerning the effects of these industrial activities on the ecological status of the ecosystems.

Rapid Biodiversity Assessment and Monitoring Method for Highly Diverse Benthic Communities: A Case Study of Mediterranean Coralligenous Outcrops

Increasing anthropogenic pressures urge enhanced knowledge and understanding of the current state of marine biodiversity. This baseline information is pivotal to explore present trends, detect future modifications and propose adequate management actions for marine ecosystems. Coralligenous outcrops are a highly diverse and structurally complex deep-water habitat faced with major threats in the Mediterranean Sea. Despite its ecological, aesthetic and economic value, coralligenous biodiversity patterns are still poorly understood. There is currently no single sampling method that has been demonstrated to be sufficiently representative to ensure adequate community assessment and monitoring in this habitat. Therefore, we propose a rapid non-destructive protocol for biodiversity assessment and monitoring of coralligenous outcrops providing good estimates of its structure and species composition, based on photographic sampling and the determination of presence/absence of macrobenthic species. We used an extensive photographic survey, covering several spatial scales (100s of m to 100s of km) within the NW Mediterranean and including 2 different coralligenous assemblages: Paramuricea clavata (PCA) and Corallium rubrum assemblage (CRA). This approach allowed us to determine the minimal sampling area for each assemblage (5000 cm² for PCA and 2500 cm²for CRA). In addition, we conclude that 3 replicates provide an optimal sampling effort in order to maximize the species number and to assess the main biodiversity patterns of studied assemblages in variability studies requiring replicates. We contend that the proposed sampling approach provides a valuable tool for management and conservation planning, monitoring and research programs focused on coralligenous outcrops, potentially also applicable in other benthic ecosystems

Studies on the macrobenthic community of Cochin backwaters with special reference to culture of Eriopisa chilkensis (Gammaridae-Amphipoda)

This thesis Entitled studies on the macrobenthic community of cochin backwaters with special reference to culture of eriopisa chilkensis (Gammaridae- amphipoda).Benthic organisms are usually studied for environmental impact assessment, pollution control and resource conservation. The benthic monitoring component has three major objectives: 1) characterize the benthic communities to assess the estuarine health, 2) determine seasonal and spatial variability in benthic communities, and 3) detect changes in the estuarine community through examination of changes in abundances of specific indicator taxa and other standard benthic indices.Cochin backwaters situated at the tip of the northern Vembanad lake is a tropical positive estuarine system. The backwaters of Kerala support as much biological productivity and diversity as tropical rain forest and are responsible for the rich fishery potential of Kerala. Backwaters also act as nursery grounds for commercially important prawns and fishes.The thesis has been subdivided into seven chapters. The first chapter gives a general introduction about the topic and also highlights the scope and purpose of the study. The second chapter covers the methodology adopted for the collection and analysis of water quality parameters, sediment and the macrobenthic fauna.Chapter 3 deals with hydrographic features, sediment characteristics and the spatial variation and abundance of macrobenthic fauna in the Cochin estuary.Chapter 4 explains the impact of organic enrichment on macrobenthic popUlation in the Cochin estuary and includes the comparison of the present data with the earlier work in this region.Chapter 5 deals with seasonal variability in abundance of macrobenthic species in the estuary. The study was conducted from 9 stations during three seasons (pre-monsoon, monsoon and post-monsoon) in 2003.Chapter 6 deals with Life history and Population Dynamics of Eriopisa chilkensis Chilton (Gammaridae-Amphipoda). The life cycle of the gammarid amphipod Eriopisa chilkensis from the Cochin estuary, south west coast of India was studied for the first time under laboratory conditions.

SPATIO-TEMPORAL AND FUNCTIONAL STRUCTURE OF THE AMPHIPOD COMMUNITIES OFF SANTOS, SOUTHWESTERN ATLANTIC

The amphipod fauna was employed to investigate a bottom environmental gradient in the continental shelf adjacent to Santos Bay. The constant flow of less saline water from the estuarine complex of the Santos and Sao Vicente rivers besides the seasonal intrusion of the cold saline South Atlantic Central Water (SACW) bring a highly dynamic water regime to the area. Density, distribution, diversity and functional structure of the communities were studied on a depth gradient from 10 to 100 m on two cruises in contrasting seasons, winter 2005 and summer 2006. Twenty-one sediment samples were taken with a 0.09m(2) box corer. Temperature and salinity were measured at each station and an additional surface sediment sample was obtained with the box corer for granulometric and chemical analyses. Sixty species were collected on each survey and higher density values were found in summer. A priori one-way Analysis of Similarities (ANOSIM) indicated the existence of three different groups of amphipods related to the depth gradient: the Coastal group, the Mixed Zone group and the Deep Zone group. The Coastal Zone in both cruises was inhabited by a community presenting low diversity and density, besides high dominance of the infaunal tube-dweller Ampelisca paria; the area around 30 m presented the highest values of all the ecological indicators and the species showed several life styles; the outer area, situated between 50 and 100 m depth in the SACW domain, presented a community characterized by lower diversity and high biomass and density values. A season-depth ANOSIM showed the influence of depth and season for the Coastal and Mixed Zone groups whereas no seasonal difference was obtained for the Deep Zone group. The synergistic effect of the SACW and depth in the first place, followed by physical changes in substrate, seem to be the main factors controlling the fauna's distribution. In addition, the estuarine waters from Santos Bay apparently had no effect on the establishment of the environmental gradient observed on the adjacent shelf. Diversity, distribution, functional groups and trophic conditions of superficial sediments are discussed in the light of the main oceanographic processes present on the southern Brazilian shelf.

Effects of harvesting callianassid (ghost) shrimps on subtropical benthic communities

The effects of harvesting of callianassid shrimp (Trypaea australiensis) on the abundance and composition of macrobenthic assemblages in unvegetated sediments of a subtropical coastal embayment in Queensland, Australia were examined using a combination of sampling and manipulative experiments. First, the abundance and composition of the benthic infauna in an area regularly used for the collection of shrimp for bait by recreational anglers was compared with multiple reference areas. Second, a BACI design, with multiple reference areas, was used to examine the short-term effects of harvesting on the benthic assemblages from an intensive commercialised fishing competition. Third, a large-scale, controlled manipulative experiment, where shrimp were harvested from 10,000 m(2) plots at intensities commensurate with those from recreational and commercial operators, was done to determine the impacts on different components of the infaunal assemblage. Only a few benthic taxa showed significant declines in abundance in response to the removal of ghost shrimp from the unvegetated sediments. There was evidence, however, of more subtle effects with changes in the degree of spatial variation (patchiness) of several taxa as a result of harvesting.. Groups such as capitellid polychaetes, gammarid amphipods and some bivalves were significantly more patchy in their distribution in areas subjected to harvesting than reference areas, at a scale of tens of metres. This scale corresponds to the patterns of movement and activity of recreational harvesters working in these areas. In contrast, patchiness in the abundance of ghost shrimp decreased significantly under harvesting at scales of hundreds of metres, in response to harvesters focussing their efforts on areas with greater numbers of burrow entrances, leading to a more even distribution of the animals. Controlled experimental harvesting caused declines in the abundance of soldier crabs (Mictyris longicarpus), polychaetes and amphipods and an increase in the spatial patchiness of polychaetes. Populations of ghost shrimp were, however, resilient to harvesting over extended periods of time. In conclusion, harvesting of ghost shrimp for bait by recreational and commercial fishers causes significant but localised impacts on a limited range of benthic fauna in unvegetated sediments, including changes in the degree of spatial patchiness in their distribution. (c) 2005 Elsevier B.V. All rights reserved.

Do Changes in Current Flow as a Result of Arrays of Tidal Turbines Have an Effect on Benthic Communities?

Arrays of tidal energy converters have the potential to provide clean renewable energy for future generations. Benthic communities may, however, be affected by changes in current speeds resulting from arrays of tidal converters located in areas characterised by strong currents. Current speed, together with bottom type and depth, strongly influence benthic community distributions; however the interaction of these factors in controlling benthic dynamics in high energy environments is poorly understood. The Strangford Lough Narrows, the location of SeaGen, the world’s first single full-scale, grid-compliant tidal energy extractor, is characterised by spatially heterogenous high current flows. A hydrodynamic model was used to select a range of benthic community study sites that had median flow velocities between 1.5–2.4 m/s in a depth range of 25–30 m. 25 sites were sampled for macrobenthic community structure using drop down video survey to test the sensitivity of the distribution of benthic communities to changes in the flow field. A diverse range of species were recorded which were consistent with those for high current flow environments and corresponding to very tide-swept faunal communities in the EUNIS classification. However, over the velocity range investigated, no changes in benthic communities were observed. This suggested that the high physical disturbance associated with the high current flows in the Strangford Narrows reflected the opportunistic nature of the benthic species present with individuals being continuously and randomly affected by turbulent forces and physical damage. It is concluded that during operation, the removal of energy by marine tidal energy arrays in the far-field is unlikely to have a significant effect on benthic communities in high flow environments. The results are of major significance to developers and regulators in the tidal energy industry when considering the environmental impacts for site licences.

Comparative Metagenomic Analysis Of Coral Microbial Communities Using A Reference-independent Approach.

By comparing the SEED and Pfam functional profiles of metagenomes of two Brazilian coral species with 29 datasets that are publicly available, we were able to identify some functions, such as protein secretion systems, that are overrepresented in the metagenomes of corals and may play a role in the establishment and maintenance of bacteria-coral associations. However, only a small percentage of the reads of these metagenomes could be annotated by these reference databases, which may lead to a strong bias in the comparative studies. For this reason, we have searched for identical sequences (99% of nucleotide identity) among these metagenomes in order to perform a reference-independent comparative analysis, and we were able to identify groups of microbial communities that may be under similar selective pressures. The identification of sequences shared among the metagenomes was found to be even better for the identification of groups of communities with similar niche requirements than the traditional analysis of functional profiles. This approach is not only helpful for the investigation of similarities between microbial communities with high proportion of unknown reads, but also enables an indirect overview of gene exchange between communities.

The Role Of Edaphic Environment And Climate In Structuring Phylogenetic Pattern In Seasonally Dry Tropical Plant Communities.

Seasonally dry tropical plant formations (SDTF) are likely to exhibit phylogenetic clustering owing to niche conservatism driven by a strong environmental filter (water stress), but heterogeneous edaphic environments and life histories may result in heterogeneity in degree of phylogenetic clustering. We investigated phylogenetic patterns across ecological gradients related to water availability (edaphic environment and climate) in the Caatinga, a SDTF in Brazil. Caatinga is characterized by semiarid climate and three distinct edaphic environments - sedimentary, crystalline, and inselberg -representing a decreasing gradient in soil water availability. We used two measures of phylogenetic diversity: Net Relatedness Index based on the entire phylogeny among species present in a site, reflecting long-term diversification; and Nearest Taxon Index based on the tips of the phylogeny, reflecting more recent diversification. We also evaluated woody species in contrast to herbaceous species. The main climatic variable influencing phylogenetic pattern was precipitation in the driest quarter, particularly for herbaceous species, suggesting that environmental filtering related to minimal periods of precipitation is an important driver of Caatinga biodiversity, as one might expect for a SDTF. Woody species tended to show phylogenetic clustering whereas herbaceous species tended towards phylogenetic overdispersion. We also found phylogenetic clustering in two edaphic environments (sedimentary and crystalline) in contrast to phylogenetic overdispersion in the third (inselberg). We conclude that while niche conservatism is evident in phylogenetic clustering in the Caatinga, this is not a universal pattern likely due to heterogeneity in the degree of realized environmental filtering across edaphic environments. Thus, SDTF, in spite of a strong shared environmental filter, are potentially heterogeneous in phylogenetic structuring. Our results support the need for scientifically informed conservation strategies in the Caatinga and other SDTF regions that have not previously been prioritized for conservation in order to take into account this heterogeneity.

Molecular Diversity Of Fungal And Bacterial Communities In The Marine Sponge Dragmacidon Reticulatum.

The present work aimed to investigate the diversity of bacteria and filamentous fungi of southern Atlantic Ocean marine sponge Dragmacidon reticulatum using cultivation-independent approaches. Fungal ITS rDNA and 18S gene analyses (DGGE and direct sequencing approaches) showed the presence of representatives of three order (Polyporales, Malasseziales, and Agaricales) from the phylum Basidiomycota and seven orders belonging to the phylum Ascomycota (Arthoniales, Capnodiales, Dothideales, Eurotiales, Hypocreales, Pleosporales, and Saccharomycetales). On the other hand, bacterial 16S rDNA gene analyses by direct sequencing approach revealed the presence of representatives of seven bacterial phyla (Cyanobacteria, Proteobacteria, Actinobacteria, Bacteroidetes, Lentisphaerae, Chloroflexi, and Planctomycetes). Results from statistical analyses (rarefaction curves) suggested that the sampled clones covered the fungal diversity in the sponge samples studied, while for the bacterial community additional sampling would be necessary for saturation. This is the first report related to the molecular analyses of fungal and bacterial communities by cultivation-independent approaches in the marine sponges D. reticulatum. Additionally, the present work broadening the knowledge of microbial diversity associated to marine sponges and reports innovative data on the presence of some fungal genera in marine samples.

Bee communities (Hymenoptera: Anthophila) of the "Cerrado" ecosystem in Sao Paulo State, Brazil

Five surveys of the bee communities in four "Cerrado" ecosystem reserves in Sao Paulo State were compared for species richness and similarity. These areas are fragment vegetation reser-reserves located in the Cerrado Corumbata Reserve (Corumbata), Jata Ecological Park (Luiz Antonio), Cajuru (Cajuru), and Vassununga State Park - ""Gleba de Cerrado de Pe-de-Gigante"" (Santa Rita do Passa Quatro). The methodology consisted of capturing bees foraging on flowers along transects, though with small differences between surveys. These ""cerrado"" areas have a large number of species of native bees, which are important pollinators in several Brazilian ecosystems. The community of bees varied among these different fragments. Based on 500 individuals (standardized by rarefaction), Cajuru, Corumbata 1 and Corumbata 2 were the areas with highest species richness, and Jata and Pe-de-Gigante had the lowest species richness in the bee communities. The bee faunas of Corumbata 2 and Pe-de-Gigante had the highest similarity, forming a group with the bee fauna of Cajuru. The bee faunas of Corumbata 1 and Jata were isolated from this group. We found that the bee species richness and similarity found in these ""cerrado"" areas cannot be explained by general factors such as the size of the fragment, the species richness of plants and the distance between the areas. Therefore, we suppose that local factors that differ among areas, such as interactions between populations, and competition and interference from surrounding areas influence and determine bee species richness and similarity in these reserves.

Meiobenthic communities of seagrass beds (Zostera capricorni) and unvegetated sediments along the coast of New South Wales, Australia

Seagrass beds have higher biomass, abundance, diversity and productivity of benthic organisms than unvegetated sediments. However, to date most studies have analysed only the macrofaunal component and ignored the abundant meiofauna present in seagrass meadows. This study was designed to test if meiobenthic communities, especially the free-living nematodes, differed between seagrass beds and unvegetated sediments. Sediment samples from beds of the eelgrass Zostera capricorni and nearby unvegetated sediments were collected in three estuaries along the coast of New South Wales, Australia. Results showed that sediments below the seagrass were finer, with a higher content of organic material and were less oxygenated than sediments without seagrass. Univariate measures of the fauna (i.e. abundance, diversity and taxa richness of total meiofauna and nematode assemblages) did not differ between vegetated and unvegetated sediments. However multivariate analysis of meiofaunal higher taxa showed significant differences between the two habitats, largely due to the presence and absence of certain taxa. Amphipods, tanaidacea, ostracods, hydrozoans and isopods occurred mainly in unvegetated sediments, while kinorhyncs, polychaetes, gastrotrichs and turbellarians were more abundant in vegetated sediments. Regarding the nematode assemblages, 32.4% of the species were restricted to Z. capricorni and 25% only occurred in unvegetated sediments, this suggests that each habitat is characterized by a particular suite of species. Epistrate feeding nematodes were more abundant in seagrass beds, and it is suggested that they graze on the microphytobenthos which accumulates underneath the seagrass. Most of the genera that characterized these estuarine unvegetated sediments are also commonly found on exposed sandy beaches. This may be explained by the fact that Australian estuaries have very little input of freshwater and experience marine conditions for most of the year. This study demonstrates that the seagrass and unvegetated sediments have discrete meiofaunal communities, with little overlap in species composition. (C) 2010 Elsevier Ltd. All rights reserved.

Effects of drill cuttings discharge on meiofauna communities of a shelf break site in the southwest Atlantic

The present study investigates the effects of drill cutting discharges on the structure of meiofauna communities in an area of the shelf break at Campos Basin, Southeast Brazil. Drilling activities were operated, in a first phase, with water-based fluid and, in a second phase, with synthetic fluid paraffin-based (NAF-III). A total of 135 samples taken at a pre-drilling situation (MS1) and two post-drilling moments (MS2 and MS3-3 and 22 months post-drilling, respectively) were analyzed. Effects on meiofauna were dependent on two main factors: 1-the impact received during drilling operation, if water-based or synthetic/water-based drilling fluid and 2-the background state, if it already presented signs of previous drilling activities or not. Based on univariate and multivariate analysis, there were evidences that the most affected area after drilling was those under the influence of synthetic-based fluid and that already had signs of previous drillings activities. The region impacted only by water-based fluid was less affected and the only one that completely recovered after 22 months. Nematodes and copepods had different responses to the impact. While copepods flourish in the impacted area and recovered 22 months after drilling, nematodes were adversely affected shortly after drilling and the community structure only recovered where hydrocarbons had been depleted.

The Influence of Different Land Uses on the Structure of Archaeal Communities in Amazonian Anthrosols Based on 16S rRNA and amoA Genes

Soil from the Amazonian region is usually regarded as unsuitable for agriculture because of its low organic matter content and low pH; however, this region also contains extremely rich soil, the Terra Preta Anthrosol. A diverse archaeal community usually inhabits acidic soils, such as those found in the Amazon. Therefore, we hypothesized that this community should be sensitive to changes in the environment. Here, the archaeal community composition of Terra Preta and adjacent soil was examined in four different sites in the Brazilian Amazon under different anthropic activities. The canonical correspondence analysis of terminal restriction fragment length polymorphisms has shown that the archaeal community structure was mostly influenced by soil attributes that differentiate the Terra Preta from the adjacent soil (i.e., pH, sulfur, and organic matter). Archaeal 16S rRNA gene clone libraries indicated that the two most abundant genera in both soils were Candidatus nitrosphaera and Canditatus nitrosocaldus. An ammonia monoxygenase gene (amoA) clone library analysis indicated that, within each site, there was no significant difference between the clone libraries of Terra Preta and adjacent soils. However, these clone libraries indicated there were significant differences between sites. Quantitative PCR has shown that Terra Preta soils subjected to agriculture displayed a higher number of amoA gene copy numbers than in adjacent soils. On the other hand, soils that were not subjected to agriculture did not display significant differences on amoA gene copy numbers between Terra Preta and adjacent soils. Taken together, our findings indicate that the overall archaeal community structure in these Amazonian soils is determined by the soil type and the current land use.