Coral reef habitat maps derived from a high-spatial-resolution multi-spectral satellite image using object based image analysis

Coral reef maps at various spatial scales and extents are needed for mapping, monitoring, modelling, and management of these environments. High spatial resolution satellite imagery, pixel <10 m, integrated with field survey data and processed with various mapping approaches, can provide these maps. These approaches have been accurately applied to single reefs (10-100 km**2), covering one high spatial resolution scene from which a single thematic layer (e.g. benthic community) is mapped. This article demonstrates how a hierarchical mapping approach can be applied to coral reefs from individual reef to reef-system scales (10-1000 km**2) using object-based image classification of high spatial resolution images guided by ecological and geomorphological principles. The approach is demonstrated for three individual reefs (10-35 km**2) in Australia, Fiji, and Palau; and for three complex reef systems (300-600 km**2) one in the Solomon Islands and two in Fiji. Archived high spatial resolution images were pre-processed and mosaics were created for the reef systems. Georeferenced benthic photo transect surveys were used to acquire cover information. Field and image data were integrated using an object-based image analysis approach that resulted in a hierarchically structured classification. Objects were assigned class labels based on the dominant benthic cover type, or location-relevant ecological and geomorphological principles, or a combination thereof. This generated a hierarchical sequence of reef maps with an increasing complexity in benthic thematic information that included: 'reef', 'reef type', 'geomorphic zone', and 'benthic community'. The overall accuracy of the 'geomorphic zone' classification for each of the six study sites was 76-82% using 6-10 mapping categories. For 'benthic community' classification, the overall accuracy was 52-75% with individual reefs having 14-17 categories and reef systems 20-30 categories. We show that an object-based classification of high spatial resolution imagery, guided by field data and ecological and geomorphological principles, can produce consistent, accurate benthic maps at four hierarchical spatial scales for coral reefs of various sizes and complexities.

Habitat Map for Lizard Island reef, Australia derived from a photo-transect survey field data collected in December 2011 and September/October 2012

An object based image analysis approach (OBIA) was used to create a habitat map of the Lizard Reef. Briefly, georeferenced dive and snorkel photo-transect surveys were conducted at different locations surrounding Lizard Island, Australia. For the surveys, a snorkeler or diver swam over the bottom at a depth of 1-2m in the lagoon, One Tree Beach and Research Station areas, and 7m depth in Watson's Bay, while taking photos of the benthos at a set height using a standard digital camera and towing a surface float GPS which was logging its track every five seconds. The camera lens provided a 1.0 m x 1.0 m footprint, at 0.5 m height above the benthos. Horizontal distance between photos was estimated by fin kicks, and corresponded to a surface distance of approximately 2.0 - 4.0 m. Approximation of coordinates of each benthic photo was done based on the photo timestamp and GPS coordinate time stamp, using GPS Photo Link Software (www.geospatialexperts.com). Coordinates of each photo were interpolated by finding the gps coordinates that were logged at a set time before and after the photo was captured. Dominant benthic or substrate cover type was assigned to each photo by placing 24 points random over each image using the Coral Point Count excel program (Kohler and Gill, 2006). Each point was then assigned a dominant cover type using a benthic cover type classification scheme containing nine first-level categories - seagrass high (>=70%), seagrass moderate (40-70%), seagrass low (<= 30%), coral, reef matrix, algae, rubble, rock and sand. Benthic cover composition summaries of each photo were generated automatically in CPCe. The resulting benthic cover data for each photo was linked to GPS coordinates, saved as an ArcMap point shapefile, and projected to Universal Transverse Mercator WGS84 Zone 56 South. The OBIA class assignment followed a hierarchical assignment based on membership rules with levels for "reef", "geomorphic zone" and "benthic community" (above).

Pigment distribution in surface sediments of the North Atlantic Ocean

In an extended deep-sea study the response of the benthic community to seasonally varying sedimentation rates of organic matter were investigated at a fixed abyssal site in the NE Atlantic (BIOTRANS station or JGOFS station L2 at 47°N-20°W, water depth >4500 m) on four legs of METEOR expedition 21 between March and August 1992. The vertical flux at 3500 m depth and temporal variations in the chloroplastic pigment concentration, a measure of phytodetritus deposition, and of total adenylates and total phospholipids, measures of benthic biomass, and of activity of hydrolytic enzymes were observed. The flux patterns in moored sediment traps of total chlorophyll, POC and total flux showed an early sedimentation peak in March/April 1992, followed by low fluxes in May and intermediate ones from June to August. Thus 1992 differed from other years, in which one large flux peak after the spring phytoplankton bloom was observed. Unusually high concentrations of chloroplastic pigments were consistently observed in March 1992, reflecting the early sedimentation input. At the same time biomass of small benthic organisms (bacteria to meiobenthos) and activity of hydrolytic enzymes were higher compared to values from March 1985 and from the following months in 1992. In May and August 1992 pigment concentrations and biomass and activity parameters in the sediment were lower than during previously observed depositions of phytodetrital matter in summer. The data imply that the deep ocean benthic community reacts to small sedimentation events with transient increases in metabolic activity and only small biomass production. The coupling between pelagic and benthic processes is so close that interannual variability in surface water production is "mirrored" by deep-sea benthic processes.

Particle flux in the NE Atlantic as recorded by sediment traps

Downward particle flux was measured using sediment traps at various depths over the Porcupine Abyssal Plain (water depth ab. 4850 m) for prolonged periods from 1989 to 1999. A strong seasonal pattern of flux was evident reaching a maximum in mid-summer. The composition of the material changed with depth, reflecting the processes of remineralisation and dissolution as the material sank through the water column. However, there was surprisingly little seasonal variation in its composition to reflect changes in the biology of the euphotic zone. Currents at the site have a strong tidal component with speeds almost always less than 15 cm/sec. In the deeper part of the water column they tend to be northerly in direction, when averaged over periods of several months. A model of upper ocean biogeochemistry forced by meteorology was run for the decade in order to provide an estimate of flux at 3000 m depth. Agreement with measured organic carbon flux is good, both in terms of the timings of the annual peaks and in the integrated annual flux. Interannual variations in the integrated flux are of similar magnitude for both the model output and sediment trap measurements, but there is no significant relationship between these two sets of estimates. No long-term trend in flux is evident, either from the model, or from the measurements. During two spring/summer periods, the marine snow concentration in the water column was assessed by time-lapse photography and showed a strong peak at the start of the downward pulse of material at 3000 m. This emphasises the importance of large particles during periods of maximum flux and at the start of flux peaks. Time lapse photographs of the seabed show a seasonal cycle of coverage of phytodetrital material, in agreement with the model output both in terms of timing and magnitude of coverage prior to 1996. However, after a change in the structure of the benthic community in 1996 no phytodetritus was evident on the seabed. The model output shows only a single peak in flux each year, whereas the measured data usually indicated a double peak. It is concluded that the observed double peak may be a reflection of lowered sediment trap efficiency when flux is very high and is dominated by large marine snow particles. Resuspension into the trap 100 m above the seabed, when compared to the primary flux at 3000 m depth (1800 mab) was lower during periods of high primary flux probably because of a reduction in the height of resuspension when the material is fresh. At 2 mab, the picture is more complex with resuspension being enhanced during the periods of higher flux in 1997, which is consistent with this hypothesis. However there was rather little relationship to flux at 3000 m in 1998. At 3000 m depth, the Flux Stability Index (FSI), which provides a measure of the constancy of the seasonal cycle of flux, exhibited an inverse relationship with flux, such that the highest flux of organic carbon was recorded during the year with the greatest seasonal variation.

Seawater carbonate chemistry and structural integrity of the coralline algae Lithothamnion glaciale in a laboratory experiment

The uptake of anthropogenic emission of carbon dioxide is resulting in a lowering of the carbonate saturation state and a drop in ocean pH. Understanding how marine calcifying organisms such as coralline algae may acclimatize to ocean acidification is important to understand their survival over the coming century. We present the first long-term perturbation experiment on the cold-water coralline algae, which are important marine calcifiers in the benthic ecosystems particularly at the higher latitudes. Lithothamnion glaciale, after three months incubation, continued to calcify even in undersaturated conditions with a significant trend towards lower growth rates with increasing pCO2. However, the major changes in the ultra-structure occur by 589 µatm (i.e. in saturated waters). Finite element models of the algae grown at these heightened levels show an increase in the total strain energy of nearly an order of magnitude and an uneven distribution of the stress inside the skeleton when subjected to similar loads as algae grown at ambient levels. This weakening of the structure is likely to reduce the ability of the alga to resist boring by predators and wave energy with severe consequences to the benthic community structure in the immediate future (50 years).

Biogenic barium in Cretaceous-Paleogene sediments

One of the best-studied aspects of the K-Pg mass extinction is the decline and subsequent recovery of open ocean export productivity (e.g., the flux of organic matter from the surface to deep ocean). Some export proxies, including surface-to-deep water d13C gradients and carbonate sedimentation rates, indicate a global decline in export productivity triggered by the extinction. In contrast, benthic foraminiferal and other geochemical productivity proxies suggest spatially and temporally heterogeneous K-Pg boundary effects. Here we address these conflicting export productivity patterns using new and compiled measurements of biogenic barium. Unlike a previous synthesis, we find that the boundary effect on export productivity and the timing of recovery varied considerably between different oceanic sites. The northeast and southwest Atlantic, Southern Ocean, and Indian Ocean records saw export production plummet and remain depressed for 350 thousand to 2 million years. Biogenic barium and other proxies in the central Pacific and some upwelling or neritic Atlantic sites indicate the opposite, with proxies recording either no change or increased export production in the early Paleocene. Our results suggest that widespread declines in surface-to-deep ocean d13C do not record a global decrease in export productivity. Rather, independent proxies, including barium and other geochemical proxies, and benthic community structure, indicate that some regions were characterized by maintained or rapidly recovered organic flux from the surface ocean to the deep seafloor, while other regions had profound reductions in export productivity that persisted long into the Paleocene.

Of Marx and Makers: an Historical Perspective on Generative Justice

In Marxist frameworks “distributive justice” depends on extracting value through a centralized state. Many new social movements—peer to peer economy, maker activism, community agriculture, queer ecology, etc.—take the opposite approach, keeping value in its unalienated form and allowing it to freely circulate from the bottom up. Unlike Marxism, there is no general theory for bottom-up, unalienated value circulation. This paper examines the concept of “generative justice” through an historical contrast between Marx’s writings and the indigenous cultures that he drew upon. Marx erroneously concluded that while indigenous cultures had unalienated forms of production, only centralized value extraction could allow the productivity needed for a high quality of life. To the contrary, indigenous cultures now provide a robust model for the “gift economy” that underpins open source technological production, agroecology, and restorative approaches to civil rights. Expanding Marx’s concept of unalienated labor value to include unalienated ecological (nonhuman) value, as well as the domain of freedom in speech, sexual orientation, spirituality and other forms of “expressive” value, we arrive at an historically informed perspective for generative justice. 

The state and known impacts of fish species transferred to or within continental Africa

Fish introductions have been made from small fish ponds to the largest lakes in Africa. The primary intent of these introductions has been to sustain or increase fish production, although some introductions have been made to develop sport fisheries and to control unwanted organisms. Some of these introductions have fulfilled their objective in the short term, but several of these "successful" introductions have created uncertainties about their long term sustainability. Lates niloticus, Oreochromis niloticus, O. leucostictus, Tilapia melanopleura and T. zilli were introduced into lakes Victoria and Kyoga in 1950s and early 1960s. By the 1980s O. niloticus and O. niloticus dominated the fisheries of these lakes, virtually eliminating a number of endemic fish species. The loss of genetic diversity of the fish in the worlds second largest lake has also been accompanied by a loss of trophic diversity. The transformation of the fish community has, in Lake Victoria coincided with a profound eutrophication (algal blooms, fish kills, hypolimnetic anoxia) which might be related to alterations of the lake's food-web structure. In contrast, the introduction of a planktivore, Limnothrissa miodon into Lake Kivu and the Kariba reservoir has established highly successful fisheries with little documented effect on the pre-existing fish community or trophic ecology of the lakes. The highly endemised species-rich African Great lakes may be particularly sensitive to species introductions and require special consideration and caution when introductions are contemplated because species extinctions, introgressive hybridization and ecosystem alterations may occur following fish introductions.

Diversidade de macroalgas marinhas bentônicas dos recifes de Maracajaú, área de preservação ambiental dos recifes de corais, Rio Grande do Norte, Brasil

Despite the importance of coral reefs to humanity, these environments have been threatened throughout the world. Several factors contribute to the degradation of these ecosystems. The Maracajaú Reef Complex, in Rio Grande do Norte state is part of the Coral Reefs Environment Preservation Area in northeastern Brazil. This area has been receiving an increasing influx of tourism and the integrity of the local reefs is a matter of concern. In this study, the reef macroalgae communities were studied and compared within two areas distinguished by the presence or absence of tourism activities. Two sample sites were chosen: the first one, where diving activities are intense; and the other, where these practices do not occur. Samples were collected at both sites within a quadrate of 625 cm2 of area randomly thrown 5 times along a 10 meters transect line. Richness, Shannon-Hill diversity and Simpson dominance indices were determined based on biomass data. Similarity between sites was analyzed with Bray-Curtis similarity and distance index. Fifty-eight macroalgae species were observed, including 7 Chlorophyta, 13 Phaeophyta and 38 Rhodophyta. In the non-disturbed site, 49 species were found, while at the disturbed site, there were 42 species. Dictyotaceae and Corallinaceae were the most representative families at the non-disturbed site, and Rhodomelaceae and Dictyotaceae at the disturbed site. The non-disturbed site presented a higher biomass and the greatest richness and diversity indices. In the disturbed site the dominance index was greater and Caulerpa racemosa was the dominant species. The dendogram based on similarity index showed two major clusters, and an isolated element at the center that corresponds to a sample from the disturbed site. In the first cluster, samples from the non-impacted site were predominant and fleshy brown algae were more conspicuous. The second cluster was composed primarily of samples from the impacted site, where C. racemosa and red filamentous and erect calcareous algae associations (turf forming) were observed covering large extensions. These associations are represented by groups of algae adapted to environments where disturbances are frequent. They can grow rapidly on substrate where benthic community was removed and do not allow the establishment of other species. The results of the present study show that tourism activity is an impacting factor that has been causing shifts in macroalgae communities in the Maracajaú Reef Complex

Harmonised framework for ecological risk assessment of sediments from ports and estuarine zones of North and South Atlantic

This paper presents a harmonised framework of sediment quality assessment and dredging material characterisation for estuaries and port zones of North and South Atlantic. This framework, based on the weight-of-evidence approach, provides a structure and a process for conducting sediment/dredging material assessment that leads to a decision. The main structure consists of step 1 (examination of available data); step 2 (chemical characterisation and toxicity assessment); decision 1 (any chemical level higher than reference values? are sediments toxic?); step 3 (assessment of benthic community structure); step 4 (integration of the results); decision 2 (are sediments toxic or benthic community impaired?); step 5 (construction of the decision matrix) and decision 3 (is there environmental risk?). The sequence of assessments may be interrupted when the information obtained is judged to be sufficient for a correct characterisation of the risk posed by the sediments/dredging material. This framework brought novel features compared to other sediment/dredging material risk assessment frameworks: data integration through multivariate analysis allows the identification of which samples are toxic and/or related to impaired benthic communities; it also discriminates the chemicals responsible for negative biological effects; and the framework dispenses the use of a reference area. We demonstrated the successful application of this framework in different port and estuarine zones of the North (Gulf of Cadiz) and South Atlantic (Santos and Paranagua Estuarine Systems).

Integrated sediment quality assessment in Paranagua Estuarine System, Southern Brazil

Sediment quality from Paranagua Estuarine System (PES), a highly important port and ecological zone, was evaluated by assessing three lines of evidence: (1) sediment physical-chemical characteristics; (2) sediment toxicity (elutriates, sediment-water interface, and whole sediment); and (3) benthic community structure. Results revealed a gradient of increasing degradation of sediments (i.e. higher concentrations of trace metals, higher toxicity, and impoverishment of benthic community structure) towards inner PES. Data integration by principal component analysis (PCA) showed positive correlation between some contaminants (mainly As, Cr, Ni, and Pb) and toxicity in samples collected from stations located in upper estuary and one station placed away from contamination sources. Benthic community structure seems to be affected by both pollution and natural fine characteristics of the sediments, which reinforces the importance of a weight-of-evidence approach to evaluate sediments of PES. (C) 2008 Elsevier B.V. All rights reserved.

Development of site-specific sediment quality guidelines for North and South Atlantic littoral zones: Comparison against national and international sediment quality benchmarks

We aimed to develop site-specific sediment quality guidelines (SQGs) for two estuarine and port zones in Southeastern Brazil (Santos Estuarine System and Paranagua Estuarine System) and three in Southern Spain (Ria of Huelva, Bay of Cadiz, and Bay of Algeciras), and compare these values against national and traditionally used international benchmark values. Site-specific SQGs were derived based on sediment physical-chemical, toxicological, and benthic community data integrated through multivariate analysis. This technique allowed the identification of chemicals of concern and the establishment of effects range correlatively to individual concentrations of contaminants for each site of study. The results revealed that sediments from Santos channel, as well as inner portions of the SES, are considered highly polluted (exceeding SQGs-high) by metals, PAHs and PCBs. High pollution by PAHs and some metals was found in Sao Vicente channel. In PES, sediments from inner portions (proximities of the Ponta do Mix port's terminal and the Port of Paranagua) are highly polluted by metals and PAHs, including one zone inside the limits of an environmental protection area. In Gulf of Cadiz, SQGs exceedences were found in Ria of Huelva (all analysed metals and PAHs), in the surroundings of the Port of CAdiz (Bay of CAdiz) (metals), and in Bay of Algeciras (Ni and PAHs). The site-specific SQGs derived in this study are more restricted than national SQGs applied in Brazil and Spain, as well as international guidelines. This finding confirms the importance of the development of site-specific SQGs to support the characterisation of sediments and dredged material. The use of the same methodology to derive SQGs in Brazilian and Spanish port zones confirmed the applicability of this technique with an international scope and provided a harmonised methodology for site-specific SQGs derivation. (C) 2009 Elsevier B.V. All rights reserved.

Bioaccumulation and effects of TBT on molluscs from southern Portugal

Tese de dout. Ciências e Tecnologias do Ambiente, Faculdade de Ciências do Mar e do Ambiente, Univ. do Algarve, 2004

Diversidade de macroalgas marinhas bentônicas dos recifes de Maracajaú, área de preservação ambiental dos recifes de corais, Rio Grande do Norte, Brasil

Despite the importance of coral reefs to humanity, these environments have been threatened throughout the world. Several factors contribute to the degradation of these ecosystems. The Maracajaú Reef Complex, in Rio Grande do Norte state is part of the Coral Reefs Environment Preservation Area in northeastern Brazil. This area has been receiving an increasing influx of tourism and the integrity of the local reefs is a matter of concern. In this study, the reef macroalgae communities were studied and compared within two areas distinguished by the presence or absence of tourism activities. Two sample sites were chosen: the first one, where diving activities are intense; and the other, where these practices do not occur. Samples were collected at both sites within a quadrate of 625 cm2 of area randomly thrown 5 times along a 10 meters transect line. Richness, Shannon-Hill diversity and Simpson dominance indices were determined based on biomass data. Similarity between sites was analyzed with Bray-Curtis similarity and distance index. Fifty-eight macroalgae species were observed, including 7 Chlorophyta, 13 Phaeophyta and 38 Rhodophyta. In the non-disturbed site, 49 species were found, while at the disturbed site, there were 42 species. Dictyotaceae and Corallinaceae were the most representative families at the non-disturbed site, and Rhodomelaceae and Dictyotaceae at the disturbed site. The non-disturbed site presented a higher biomass and the greatest richness and diversity indices. In the disturbed site the dominance index was greater and Caulerpa racemosa was the dominant species. The dendogram based on similarity index showed two major clusters, and an isolated element at the center that corresponds to a sample from the disturbed site. In the first cluster, samples from the non-impacted site were predominant and fleshy brown algae were more conspicuous. The second cluster was composed primarily of samples from the impacted site, where C. racemosa and red filamentous and erect calcareous algae associations (turf forming) were observed covering large extensions. These associations are represented by groups of algae adapted to environments where disturbances are frequent. They can grow rapidly on substrate where benthic community was removed and do not allow the establishment of other species. The results of the present study show that tourism activity is an impacting factor that has been causing shifts in macroalgae communities in the Maracajaú Reef Complex

Molecular mechanisms controlling physiological plasticity in marine mussels under the influence of natural and anthropogenic stress factors

Marine mussels are exceptionally well-adapted to live in transitional habitats where they are exposed to fluctuating environmental parameters and elevated levels of natural and anthropogenic stressors throughout their lifecycle. However, there is a dearth of information about the molecular mechanisms that assist in dealing with environmental changes. This project aims to investigate the molecular mechanisms governing acclimatory and stress responses of the Mediterranean mussel (Mytilus galloprovincialis) by addressing relevant life stages and environmental stressors of emerging concern. The experimental approach consisted of two phases to explore (i) the physiological processes at early life history and the consequences of plastic pollution and (ii) the adult physiology processes under natural habitats. As the first phase, I employed a plastic leachate (styrene monomer), and polystyrene microplastics to understand the modulation of cytoprotective mechanisms during the early embryo stages. Results revealed the onset of transcriptional impairments of genes involved in MXR-related transporters and other physiological processes induced by styrene and PS-MPs. In the second phase, as a preliminary analysis, microbiota profile of adult mussels at the tissue scale and its surrounding water was explored to understand microbiota structures that may reflect peculiar adaptations to the respective tissue functions. The broader experiment has been implemented to understand the variability of transcriptional profiles in the mussel digestive glands in the natural setting. All the genes employed in this study have shown possibilities to use as molecular biomarker responses throughout the year for monitoring the physiology of mussels living in a particular environment and, in turn, more properly detecting changes in the environment. As a whole, my studies provide insights into the interactions between environmental parameters, and intrinsic characters, and physiology of marine bivalves, and it could help to interpretation of responses correctly under stress conditions and climate change scenarios.