Priming of a DNA metabarcoding approach for species identification and inventory in marine macrobenthic communities

Dissertação de mestrado em Molecular Genetics

Petroleum contamination impact on macrobenthic communities under the influence of an oil refinery: Integrating chemical and biological multivariate data

Petroleum contamination impact on macrobenthic communities in the northeast portion of Todos os Santos Bay was assessed combining in multivariate analyses, chemical parameters such as aliphatic and polycyclic aromatic hydrocarbon indices and concentration ratios with benthic ecological parameters. Sediment samples were taken in August 2000 with a 0.05 m(2) van Veen grab at 28 sampling locations. The predominance of n-alkanes with more than 24 carbons, together with CPI values close to one, and the fact that most of the stations showed UCM/resolved aliphatic hydrocarbons ratios (UCM:R) higher than two, indicated a high degree of anthropogenic contribution, the presence of terrestrial plant detritus, petroleum products and evidence of chronic oil pollution. The indices used to determine the origin of PAH indicated the occurrence of a petrogenic contribution. A pyrolytic contribution constituted mainly by fossil fuel combustion derived PAH was also observed. The results of the stepwise multiple regression analysis performed with chemical data and benthic ecological descriptors demonstrated that not only total PAH concentrations but also specific concentration ratios or indices such as >= C24:< C24, An/178 and Fl/Fl + Py, are determining the structure of benthic communities within the study area. According to the BIO-ENV results petroleum related variables seemed to have a main influence on macrofauna community structure. The PCA ordination performed with the chemical data resulted in the formation of three groups of stations. The decrease in macrofauna density, number of species and diversity from groups III to I seemed to be related to the occurrence of high aliphatic hydrocarbon and PAH concentrations associated with fine sediments. Our results showed that macrobenthic communities in the northeast portion of Todos os Santos Bay are subjected to the impact of chronic oil pollution as was reflected by the reduction in the number of species and diversity. These results emphasise the importance to combine in multivariate approaches not only total hydrocarbon concentrations but also indices, isomer pair ratios and specific compound concentrations with biological data to improve the assessment of anthropogenic impact on marine ecosystems. (c) 2008 Elsevier Ltd. All rights reserved.

Macrobenthic intertidal communities from wave to tide dominated beach environments. A case study in two Brazilian beaches

Modification showed by intertidal macrofaunal communities between two nearby sites that change from a wave to a tide dominated beach environment, was analyzed on the present study. At each site, eleven intertidal sampling stations were distributed along a transect, from the drift line to the spring low tide water level. Four macrofaunal samples one meter long-shore spaced were collected at, each station with an iron core of 0.05 m(2) surface area, taken to a depth of 20 cm. Major,differences on sediments between sites were the offshore decrease of mean particle size diameter and increase of kurtosis and water content at the tide dominated site. KIDS ordination showed major similarities between the lowest stations of this site, that represents the dissipative low tide-terrace portion of the beach. Two lower station of the wave dominated site presented similarities with this group. The other stations of the tide-dominated site, that represents the reflective high tide beach portion, grouped distant from the former. (canonical Correspondence Analysis (CCA) showed a similar spatial distribution of stations, suggesting the importance of environmental factors on the explanation of species distribution patterns. Sediment water content and water table depth, with the highest inertia value, seems to be the principal physical factor. Increase on water content affects the macrofaunal distribution by the expansion of typical infralitoral species, as was the case of Bathyporeiapus ruffoi, on the dissipative low tide terrace beach portion. A disrupted distribution with the lost of a gradate zonation along a physical gradient is one of the major modification presented by macrobenthic communities on the transition from a wave to a tide dominated beach environment.

Macrobenthic abundance, biomass, productivity and production in the deep Arctic ocean

The few existing studies on macrobenthic communities of the deep Arctic Ocean report low standing stocks, and confirm a gradient with declining biomass from the slopes down to the basins as commonly reported for deep-sea benthos. In this study we have further investigated the relationship of faunal abundance (N), biomass (B) as well as community production (P) with water depth, geographical latitude and sea ice concentration. The underlying dataset combines legacy data from the past 20 years, as well as recent field studies selected according to standardized quality control procedures. Community P/B and production were estimated using the multi-parameter ANN model developed by Brey (2012). We could confirm the previously described negative relationship of water depth and macrofauna standing stock in the Arctic deep-sea. Furthermore, the sea-ice cover increasing with high latitudes, correlated with decreasing abundances of down to < 200 individuals/m**2, biomasses of < 65 mg C/m**2 and P of < 75 mg C/m**2/y. Stations under influence of the seasonal ice zone (SIZ) showed much higher standing stock and P means between 400 - 1400 mg C/m**2/y; even at depths up to 3700 m. We conclude that particle flux is the key factor structuring benthic communities in the deep Arctic ocean, explaining both the low values in the ice-covered Arctic basins and the high values along the SIZ.

(Table 1) Dominant species and total biomass of macrozoobenthos communities in the southwestern Kara Sea

The structure and distribution of the macrobenthic communities were studied in the southwestern Kara Sea. The material was collected in Baidaratskaya Bay in July 2007 and in a section running westward of the Yamal Peninsula in September 2007. The depths of the sampling stations ranged from 5 to 25 m in the Baidaratskaya Bay area and between 16 and 46 m in the Yamal section. A total of 212 benthic invertebrate species were recorded. In both areas, Bivalvia was the group with the highest biomass (54.88 g/m**2 in the Yamal section and 59.71 g/m**2 in the Baidaratskaya Bay area), while polychaetes were the group with the highest number of species (45 in the Yamal section and 64 the Baidaratskaya Bay area). Three major macrozoobenthic communities were recognized: the Astarte borealis community (20-46 m, the deepest sampling stations in both areas); the 'medium-depth' community (10-20 m, extremely mosaic, usually dominated by Serripes groenlandicus); and the Nephtys longosetosa community (depth smaller than 10 m, characterized by low biomass and the absence of large bivalves and echinoderms). The western Yamal shallow-water communities were shown to be generally similar to those of Baidaratskaya Bay. The comparison of these results with those of the benthos censuses performed in 1927-1945, 1975, and 1993 showed that the benthic communities in the southwestern Kara Sea remained relatively stable during the second half of the 20th century and the early 21st century.

Structural and functional vulnerability to elevated pCO2 in marine benthic communities

The effect of elevated pCO2/low pH on marine invertebrate benthic biodiversity, community structure and selected functional responses which underpin ecosystem services (such as community production and calcification) was tested in a medium-term (30 days) mesocosm experiment in June 2010. Standardised intertidal macrobenthic communities, collected (50.3567°N, 4.1277°W) using artificial substrate units (ASUs), were exposed to one of seven pH treatments (8.05, 7.8. 7.6, 7.4, 7.2, 6.8 and 6.0). Community net calcification/dissolution rates, as well as changes in biomass, community structure and diversity, were measured at the end of the experimental period. Communities showed significant changes in structure and reduced diversity in response to reduced pH: shifting from a community dominated by calcareous organisms to one dominated by non-calcareous organisms around either pH 7.2 (number of individuals and species) or pH 7.8 (biomass). These results were supported by a reduced total weight of CaCO3 structures in all major taxa at lowered pH and a switch from net calcification to net dissolution around pH 7.4 (Omega calc = 0.78, Omega ara = 0.5). Overall community soft tissue biomass did not change with pH and high mortality was observed only at pH 6.0, although molluscs and arthropods showed significant decreases in soft tissue. This study supports and refines previous findings on how elevated pCO2 can induce changes in marine biodiversity, underlined by differential vulnerability of different phyla. In addition, it shows significant elevated pCO2-/low pH-dependent changes in fundamental community functional responses underpinning changes in ecosystem services.

Investigação em ambientes marinhos naturalmente acidificados

Jornadas "Ciência nos Açores – que futuro?", Ponta Delgada, 7-8 de Junho de 2013.

Comunidades macrobentônicas da Reserva Biológica do Lago Piratuba (Amapá – Brasil)

Caracterizou-se a estrutura das comunidades macrobentônicas em diferentes áreas e períodos climáticos da Reserva Biológica do Lago Piratuba (Amapá - Brasil). As amostragens ocorreram nos meses de junho e novembro de 2005 (cinturão lacustre meridional- lagos Comprido de cima, Bacia, Lodão, Grande, Canal Tabaco e Comprido de. baixo e foz do rio Araguari) e 2006 (cinturão lacustre oriental - lagos Piratuba, Jussara, Escara, Trindade, Maresia e Boiado e Rego do Duarte e sete locais da costa (áreas vegetada e não vegetada). Em cada local foram coletadas quatro amostras, com tubo de PVC de 0,0079 m2 , enterrado 20 cm no sedimento. Após coletadas as amostras foram passadas em malha de nylon de 0,3 mm de abertura e os organismos retidos fixados em formalina a 5%. A estrutura das comunidades variou sazonalmente, com marcantes modificações na densidade, composição específica, número de espécies, equitabilidade e diversidade entre ocasiões de amostragem e entre lagos e costa. Foram identificados 54 táxons pertencentes aos filos: Annelida , Arthropoda , Mollusca e Nemertea . No período chuvoso foram registrados 36 táxons e o seco 42. Annelida foi o táxon mais abundante, representando sempre mais que 48% do total de organismos. Os lagos foram dominados por larvas de Insecta , Mollusca e Oligochaeta . Na costa Polychaeta e Crustácea dominaram. Registrou-se nos lagos 32 táxons e densidade média de 667 ind.m -2 . Na costa foram identificados 34 táxons e 1353 ind.m -2 .A área não vegetada da costa foi mais rica, densa e equitativa. O cinturão lacustre meridional e o cinturão lacustre oriental responderam de forma distinta as mudanças sazonais nos seus descritores. Foram identificados três sub-ambientes para a comunidade bentônica: ambiente dulcícola - maioria dos lagos do cinturão meridional, com a fauna predominante de insetos; ambiente de transição entre a região de água doce e a região costeira com fauna mista ( Polychaeta e Insecta ); e, costa, com espécimes de Polychaeta e Crustacea . Os fatores ambientais que melhor se correlacionaram com as variações espaço-temporais na estrutura das comunidades bentônicas foram pH, condutividade elétrica e turbidez da água.

Eficiência de diferentes abordagens metodológicas e caracterização das associações macrobentônicas estuarinas da zona costeira amazônica

As associações macrobentonicas estuarinas de regiões costeiras amazônicas foram caracterizadas usando diferentes aberturas de malha e profundidades de amostragem. As amostragens aconteceram na ilha de Algodoal e península de Ajuruteua (PA), nos períodos chuvoso e seco (junho e dezembro de 2007, respectivamente), nos habitats borda do mangue, mangue, areno-lamoso e arenoso. Em cada habitat foram coletadas oito amostras biológicas, utilizando tubo cilíndrico de 0,0079 m², assim como amostras para caracterização do substrato (textura, umidade e concentrações de matéria orgânica), e concentrações de clorofila a e feopigmentos. Cada amostra biológica foi dividida em três estratos (0-5, 5-10 e 10-20 cm), sendo cada estrato peneirado em malhas de 1,0, 0,5, 0,3 e 0,25 mm de abertura. Foram utilizadas técnicas univariadas (ANOVA) e multivariadas (MDS, ANOSIM, SIMPER e BIOENV) para a analise dos dados. A macrofauna foi composta por 68 táxons com dominância de Annelida (Tubificidae e Capitellidae). As malhas de 0,3 e 0,25 mm foram as mais eficientes na retenção de organismos e espécies, enquanto a malha de 1,0 mm perdeu quantidades significativas de organismos, sobretudo de Tubificidae. As amostras coletadas a 10 e 20 cm de profundidade não diferiram significativamente quanto numero de táxons e organismos. Foram observadas variações espaciais significativas na estrutura da macrofauna entre habitats em ambos os locais e ocasiões de amostragem, com densidade e riqueza superiores nos habitats lamosos. As variáveis ambientais mais correlacionas com a fauna foram a quantidade de argila, a concentração orgânica e o teor de umidade nos sedimentos. Foi possível concluir que: 1. A fauna bentônica na ilha de Algodoal e península de Ajuruteua foi composta por poucos táxons, sendo eles tipicamente estuarinas e de pequenas dimensões, dominada por Annelida; 2. para a caracterização da macrofauna bentônica e necessário a tomada de amostras somente ate a profundidade de 10 cm de sedimento e o peneiramento em malha de 0,3 mm de abertura; 3. os habitats lamosos tiveram geralmente maiores densidades e riqueza; 4. apenas na ilha de Algodoal se observou variação temporal na estrutura da macrofauna; 5. a quantidade de argila, feopigmentos e teor de umidade nos sedimentos foram os principais fatores responsáveis pela estruturação da fauna.

BENTHIC MACROFAUNA STRUCTURE IN THE NORTHEAST AREA OF TODOS OS SANTOS BAY, BAHIA STATE, BRAZIL: PATTERNS OF SPATIAL AND SEASONAL DISTRIBUTION

Structure of intertidal and subtidal benthic macrofauna in the northeastern region of Todos os Santos Bay (TSB), northeast Brazil, was investigated during a period of two years. Relationships with environmental parameters were studied through uni- and multivariate statistical analyses, and the main distributional patterns shown to be especially related to sediment type and content of organic fractions (Carbon, Nitrogen, Phosphorus), on both temporal and spatial scales. Polychaete annelids accounted for more than 70% of the total fauna and showed low densities, species richness and diversity, except for the area situated on the reef banks. These banks constitute a peculiar environment in relation to the rest of the region by having coarse sediments poor in organic matter and rich in biodetritic carbonates besides an abundant and diverse fauna. The intertidal region and the shallower area nearer to the oil refinery RLAM, with sediments composed mainly of fine sand, seem to constitute an unstable system with few highly dominant species, such as Armandia polyophthalma and Laeonereis acuta. In the other regions of TSB, where muddy bottoms predominated, densities and diversity were low, especially in the stations near the refinery. Here the lowest values of the biological indicators occurred together with the highest organic compound content. In addition, the nearest sites (stations 4 and 7) were sometimes azoic. The adjacent Caboto, considered as a control area at first, presented low density but intermediate values of species diversity, which indicates a less disturbed environment in relation to the pelitic infralittoral in front of the refinery. The results of the ordination analyses evidenced five homogeneous groups of stations (intertidal; reef banks; pelitic infralittoral; mixed sediments; Caboto) with different specific patterns, a fact which seems to be mainly related to granulometry and chemical sediment characteristics.

Struttura dei popolamenti meiobentonici nella zona intertidale dell'Alto Adriatico a differenti gradi di antropizzazione

The present work is part of the European project THESEUS (Innovative technologies for safer Europeans coasts in a changing climate). The main goals are to provide adequate integrated methodologies for strategic planning of sustainable coastal defence. The present study investigates the structure and composition of meiobenthonic populations of the intertidal zone in four beaches along the Northern Adriatic coast of Emilia Romagna: Lido di Spina, Bellocchio, Lido di Dante e Cervia. The four sites are different for the level of human impacts and for the different management interventions against coastal erosion. The analysis of biotic and abiotic variables revealed different responses due mainly to site-specific characteristics of the investigated sites, in particular as regards the site of Bellocchio. The growing interest in ecosystems of sandy beaches has recently highlighted the importance of the ecological role of meiofauna, emphasizing the need to develop studies aimed to conservation as well as to the use of these organisms as descriptors of the environmental status. The present study showed that the response of the organisms of meiofauna was highly sensitive to the specific environmental conditions of the four sites considered. Therefore it appears to be possible to consider the response of meiofauna to environmental and anthropogenic stressors as supplementary information to the responses of macrobenthic communities, which have been, until now, widely recognized and used as syncretic indicators of the ecosystem status.

Population structure, growth and production of the surf clam Donax hanleyanus (Bivalvia: Donacidae) from northern Argentinean beaches

The surf clams Mesodesma mactroides Reeve, 1854 and Donax hanleyanus Philippi, 1847 are the two dominating species in macrobenthic communities of sandy beaches off northern Argentina, with the latter now surpassing M. mactroides populations in abundance and biomass. Before stock decimation caused by exploitation (during the 1940s and 1950s) and mass mortality events (1995, 1999 and 2007) M. mactroides was the prominent primary consumer in the intertidal ecosystem and an important economic resource in Argentina. Since D. hanleyanus was not commercially fished and not affected by mass mortality events, it took over as the dominant species, but did never reach the former abundance of M. mactroides. Currently abundance and biomass of both surf clams are a multiple smaller than those of forty years ago, indicating the conservation status of D. hanleyanus and M. mactroides as endangered. Therefore the aim of this study is to analyse the population dynamics (population structure, growth and reproductive biology) of D. hanleyanus and M. mactroides, and to compare the results with historical data in order to detect possible differences within surf clam populations forty years ago and at present.

Ecological effects of rubble weir jetty construction at Murrells Inlet, South Carolina /

"June 1984"--Pt. 2.

An investigation on benthic macro-invertebrates species diversity as bio-indicators of environmental health in Bahrekan Bay

The purpose of this study was to evaluate benthic macro-invertebrates species diversity as bio-indicators of environmental health in Bahrekan bay (in the Northwest of Persian gulf). Seasonal sediments sampling along 5 transects, 15 stations at 4 replicates (3 replicates for macrobenthos and 1 replicate for sediment analysis) was done from November 2008 to August 2009 by 0.025 m2 Van Veen grab sampler. Physical and chemical parameters of water, grain size analysis, %TOM and Ni and Va concentrations of sediments were assessed through four seasons. Macrobenthic communities after staining and sorting, using stereomicroscope have been identified. Their density in every station and every season calculated. For using of AMBI index, identified macrobenthos according to their sensitivity to stressors and pollutants, categorized into 5 ecological groups and for using of Bentix index categorized into 3 ecological groups. The diversity indices and indicators that showing ecological status were calculated. Also, the differences between physiochemical parameters of sea water, sediments TOM% and grain size, diversity indices in stations and seasons were recorded (P=0.05). The correlation coefficient determined for all parameters. According to the results of grain size analysis, bottom grain size categorized as clay. Highest percent of TOM was belong to autumn (36.39±.075) and lowest was belong to summer (19.01±0.51). Also there was positive correlation (p=0.01) between %TOM and %Clay that showing sediments with lowest size containing highest amounts of organic matters. Ni concentrations in sediments (87.80±21.25)mg/kg showed the amounts over than standards levels but Va concentrations in sediments (53.54±17.60)mg/kg showed the amounts lower than standards level. The highest density of macrobenthos was recorded for summer (8254±485) N/m2 and the lowest density was recorded for spring (3775±172)N/m2. The highest annual density was belong to mollusca (81%) and then polycheates (13%), Others (4%) and crustaceae (2%). The highest diversity was recorded for winter (Simpson index: 0.13±0.01, H':3.47±0.06) and the lowest diversity recorded for autumn (Simpson index: 0.16±0.01, H':3.17±0.06). in all stations, the highest amount of Shanon index was belong to T2S3 station in summer (4.11± 0.32) and the lowest amount was belong to T1S1 station in autumn (2.42± 0.41). The annual mean of Simpson diversity index: (0.15 ±0.04) and Shanon diversity index (3.36±0.03), illustrated that macrobenthos in Bahrekan bay have a good variation. The results of Brilluin and N1 (Number of equally common species) indices confirm the results of Simpson index. For study on the regions that diversity has a little difference between stations, with use of Ni index, the degree of differences could be better ono recognizable. According to the results of AMBI index in all seasons (autumn: 0.46±0.03; summer: 0.22±0.01; annual mean:0.31±0.01) and standards (0.0