Simulation Model of Benthic Antarctic Assemblages (SIMBAA), link to PC-executable

SIMBAA is a spatially explicit, individual-based simulation model. It was developed to analyse the response of populations of Antarctic benthic species and their diversity to iceberg scouring. This disturbance is causing a high local mortality providing potential space for new colonisation. Traits can be attributed to model species, e.g. in terms of reproduction, dispersal, and life span. Physical disturbances can be designed in space and time, e.g. in terms of size, shape, and frequency. Environmental heterogeneity can be considered by cell-specific capacities to host a certain number of individuals. When grid cells become empty (after a disturbance event or due to natural mortality of of an individual), a lottery decides which individual from which species stored in a pool of candidates (for this cell) will recruit in that cell. After a defined period the individuals become mature and their offspring are dispersed and stored in the pool of candidates. The biological parameters and disturbance regimes decide on how long an individual lives. Temporal development of single populations of species as well as Shannon diversity are depicted in the main window graphically and primary values are listed. Examples for simulations can be loaded and saved as sgf-files. The results are also shown in an additional window in a dimensionless area with 50 x 50 cells, which contain single individuals depicted as circles; their colour indicates the assignment to the self-designed model species and the size represents their age. Dominant species per cell and disturbed areas can also be depicted. Output of simulation runs can be saved as images, which can be assembled to video-clips by standard computer programs (see GIF-examples of which "Demo 1" represents the response of the Antarctic benthos to iceberg scouring and "Demo 2" represents a simulation of a deep-sea benthic habitat).

Environmental controls on bioturbation processes in marine benthic habits

Through bioturbation, the macrofauna mediate chemical, physical and biological processes in marine benthic ecosystems. Because of the importance of bioturbation as ecosystem mediator, various studies have been conducted on bioturbation intensity and depth, and the relation of bioturbation processes to environmental condition and ecosystem state. This thesis builds on those previous studies, using a standard field and analytical protocol and by expanding the geographical scale to three climatic regions along Canada’s East Coast and Arctic margins, the Arctic Archipelago, the coastal Subarctic (Labrador Fjords), and the temperate continental climate zone (Gulf of Maine and adjacent Scotian shelf/slope). This Ph.D. study provides a comprehensive assessment of environmental influences on bioturbation along gradients in latitude and ocean depth. Bioturbation intensity, mixing depth, and bioturbation structures were studied in relation to the quantity and quality of potential food sources (organic matter) and substrate characteristics to gain an understanding of the environmental controls on bioturbation in these regions. The three main research chapters of this thesis are divided based on the contrasting climatic and geographical regions studied. The analytical approach included seabed sampling with a boxcorer, describing the sedimentary fabric and bioturbation structures by X-radiography, estimating bioturbation intensity and depth applying a biodiffusion model to particle tracer profiles of ²¹⁰Pbₓs, ²²⁸Thₓs, ²³⁴Thₓs, and chlorophyll-a, and analyzing benthic organic matter and substrate characteristics. Strong regional and cross-climatic relations of bioturbation processes with combinations of environmental factors were observed. In particular, bioturbation depth and the vertical extent of bioturbation structures responded to the environmental patterns observed and, therefore, represented potentially applicable predictors of environmental conditions and ecosystem state. The results of this Ph.D. study may be further extended to other geographical regions with similar environmental characteristics to predict the effects of benthic habitat alterations through environmental stresses on a global scale. Integrated with biological data produced by fellow CHONe scientists the presented data may provide valuable information about functional roles of macrofaunal species and community traits in marine benthic ecosystems along Canada’s extensive East Coast and Arctic margins.

A review on systematic and taxonomic of the Persian Gulf fish species, based on geographical distribution pattern and habitat diversity, using by GIS

During the period from 2011 - 2015 with the aim of this study was to systematically review and in particular the revised classification of the Persian Gulf (and the Strait of Hormuz) and to obtain new information about the final confirmed list of fish species of Iranian waters of the Persian Gulf (and Hormuz Strait), samples of museums, surveys and sampling, and comparative study of all available sources and documentation was done. Classification systematic of sharks and batoids and bony fishes. Based on the results, the final list of approved fish of the Persian Gulf (including the Strait of Hormuz and Gulf of Oman border region) are 907 species in 157 families, of which 93 species of fish with 28 cartilaginous families (including 18 families with 60 species and 10 families with 34 species of shark and batoids); and 129 families with 814 species of bony fishes are. The presence of 11 new family with only one representative species in the area include Veliferidae, Zeidae, Sebastidae, Stomiidae, Dalatiidae, Zanclidae, Pempheridae, Lophiidae Kuhliidae, Etmoptridae and Chlorophthalmidae also recently introduced and approved. The two families based Creediidae Clinidae and their larvae samples for newly identified area. 62 families with mono-species and 25 families with more than 10 species are present including Gobiidae (53), Carangide (48), Labride (41), Blenniidae (34), Apogonidae (32) and Lutjanidae (31) of bony fishes, Carcharhinidae (26) of sharks and Dasyatidae (12) in terms of number of species of batoids most families to have their data partitioning. Also, 13 species as well as endemic species introduced the Persian Gulf and have been approved in terms of geographical expansion of the Persian Gulf are unique to the area.Two species of the family Poeciliidae and Cyprinodontidae have species of fresh water to the brackish coastal habitats have found a way;in addition to 11 types of families Carcharhinidae, Clupeidae, Chanidae, Gobidae, Mugilidae, Sparidae also as a species, with a focus on freshwater river basins in the south of the country have been found. In this study, it was found that out of 907 species have been reported from the study area, 294 species (32.4 %) to benthic habitats (Benthic habitats) and 613 species (67.6 %) in pelagic habitats (Pelagic habitats) belong. Coral reefs and rocky habitats in the range of benthic fish (129 species - 14.3 %) and reef associated fishes in the range of pelagic fishes (432 species – 47.8 %), the highest number and percentage of habitat diversity (Species habitats) have been allocated. As well as fish habitats with sea grass and algae beds in benthic habitat (17 species- 1.9 %) and pelagic - Oceanic (Open sea) in the whole pelagic fish (30 species – 3.3 %), the lowest number and percentage of habitat diversity into account. From the perspective of animal geography (Zoogeography) and habitat overlaps and similarities (Habitat overlapping) fish fauna of the Persian Gulf compared with other similar seas (tropical and subtropical, and warm temperate) in the Indian Ocean area - calm on the surface, based on the presence of certain species that the fish fauna of the Persian Gulf to the Red Sea and the Bay of Bengal (East Arabian Sea) compared to other regions in the Indian Ocean (Pacific) is closer (about 50%), and the Mediterranean (East area) and The Hawaiian Islands have the lowest overlap and similarity of habitat and species (about 10%).

Shelf and estuarine transport mechanisms affecting the supply of competent larvae in a suite of brachyuran crabs with different life histories

Supply of competent larvae to the benthic habitat is a major determinant of population dynamics in coastal and estuarine invertebrates with an indirect life cycle. Larval delivery may depend not only on physical transport mechanisms, but also on larval behavior and physiological progress to the competent stage. Yet, the combined analysis of such factors has seldom been attempted. We used time-series analyses to examine tide- and wind-driven mechanisms responsible for the supply of crab megalopae to an estuarine river under a major marine influence in SW Spain, and monitored the vertical distribution of upstream moving megalopae, their net flux and competent state. The species Panopeus africanus (estuarine), Brachynotus sexdentatus (euryhaline) and Nepinnotheres pinnotheres (coastal) comprised 80% of the whole sample, and responded in a similar way to tide and wind forcing. Tidal range was positively correlated to supply, with maxima 0 to 1 d after spring tides, suggesting selective tidal stream transport. Despite being extensively subjected to upwelling, downwind drift under the effect of westerlies, not Ekman transport, explained residual supply variation at our sampling area. Once in the estuary, net flux and competence state matched the expected trends. Net upstream flux increased from B. sexdentatus to P. africanus, favoring transport to a sheltered coastal habitat (N. pinnotheres), or to the upper estuary (P. africanus). Competence state was highest in N. pinnotheres, intermediate in B. sexdentatus and lowest in P. africanus, as expected if larvae respond to cues from adequate benthic habitat. P. africanus megalopae were found close to the bottom, not above, rendering slower upstream transport than anticipated.

Using siting algorithms in the design of marine reserve networks

Using benthic habitat data from the Florida Keys (USA), we demonstrate how siting algorithms can help identify potential networks of marine reserves that comprehensively represent target habitat types. We applied a flexible optimization tool-simulated annealing-to represent a fixed proportion of different marine habitat types within a geographic area. We investigated the relative influence of spatial information, planning-unit size, detail of habitat classification, and magnitude of the overall conservation goal on the resulting network scenarios. With this method, we were able to identify many adequate reserve systems that met the conservation goals, e.g., representing at least 20% of each conservation target (i.e., habitat type) while fulfilling the overall aim of minimizing the system area and perimeter. One of the most useful types of information provided by this siting algorithm comes from an irreplaceability analysis, which is a count of the number of, times unique planning units were included in reserve system scenarios. This analysis indicated that many different combinations of sites produced networks that met the conservation goals. While individual 1-km(2) areas were fairly interchangeable, the irreplaceability analysis highlighted larger areas within the planning region that were chosen consistently to meet the goals incorporated into the algorithm. Additionally, we found that reserve systems designed with a high degree of spatial clustering tended to have considerably less perimeter and larger overall areas in reserve-a configuration that may be preferable particularly for sociopolitical reasons. This exercise illustrates the value of using the simulated annealing algorithm to help site marine reserves: the approach makes efficient use of;available resources, can be used interactively by conservation decision makers, and offers biologically suitable alternative networks from which an effective system of marine reserves can be crafted.

Ontogenesis and functional morphology of the digestive system of the freshwater prawn, Macrobrachium amazonicum (Decapoda: Palaemonidae)

The appropriate feeding regime for larvae and post-larvae of crustacean decapods is essential for successful larval culture. Reports on the development and morphology of the mouthparts and foregut of these crustaceans have aided in the selection of appropriate larval foodstuffs and consequently increased larval survival and growth rate during development. In the present study, the functional morphology of foregut and mouthparts was investigated in larvae and post-larvae of the freshwater prawn M. amazonicum (Heller, 1862). From observations gathered on both the outer and inner feeding apparati the first stage larvae have obligatory lecithotrophy and feeding behaviour is initiated after molting to the second stage. The foregut of the larvae undergoes diverse morphological changes during larval development and the larval foregut of this species is primarily a mixing organ due to the absence of gastric mills and similar structures. After metamorphosis into post-larvae, drastic morphological changes occur in the foregut and mouthparts to adapt the animals to feed on the greater diversity of foods that are available in their new benthic habitat.

Long-term trends in invertebrate–habitat relationships under protected and fished conditions

Few studies examine the long-term effects of changing predator size and abundance on the habitat associations of resident organisms despite that this knowledge is critical to understand the ecosystem effects of fishing. Marine reserves offer the opportunity to determine ecosystem-level effects of manipulated predator densities, while parallel monitoring of adjacent fished areas allows separating these effects from regional-scale change. Relationships between two measures of benthic habitat structure (reef architecture and topographic complexity) and key invertebrate species were followed over 17 years at fished and protected subtidal rocky reefs associated with two southern Australian marine reserves. Two commercially harvested species, the southern rock lobster (Jasus edwardsii) and blacklip abalone (Haliotis rubra) were initially weakly associated with habitat structure across all fished and protected sites. The strength of association with habitat for both species increased markedly at protected sites 2 years after marine reserve declaration, and then gradually weakened over subsequent years. The increasing size of rock lobster within reserves apparently reduced their dependency on reef shelters as refuges from predation. Rising predation by fish and rock lobster in the reserves corresponded with weakening invertebrate–habitat relationships for H. rubra and sea urchins (Heliocidaris erythrogramma). These results emphasise that animal–habitat relationships are not necessarily stable through time and highlight the value of marine reserves as reference sites. Our work shows that fishery closures to enhance populations of commercially important and keystone species should be in areas with a range of habitat features to accommodate shifting ecological requirements with ontogenesis.

Physical, chemical and biological characteristics of disturbed and undisturbed Arctic lakes, Northwest Territories

1. Global warming is predicted to cause changes in permafrost cover and stability in the Arctic. Zones of high ion concentration in regions of ice-rich permafrost are a reservoir of chemicals that can potentially be transferred to fresh waters during thawing. Consequently, input of enriched runoff from the thaw and sediment and vegetation from the landscape could alter lakes by affecting their geochemistry and biological production. 2. Three undisturbed lakes and five lakes disturbed by retrogressive permafrost thaw slumps were sampled during late summer of 2006 to assess the potential effects of thermokarst shoreline slumping on water and sediment chemistry, the underwater light regime, and benthic macrophyte biomass and community structure. 3. Undisturbed lakes had sediments rich in organic material and selected micronutrients, while disturbed lakes had sediments richer in calcium, magnesium and strontium, greater transparency of the water column, and a well-developed submerged macrophyte community. 4. It is postulated that enriched runoff chemistry may alter nutrient availability at the sediment-water interface and also the degradation of organic material, thus affecting lake transparency and submerged macrophytes. The results suggest that retrogressive permafrost slumping can significantly affect food webs in arctic tundra lakes through an increase in macrophyte biomass and development of a more complex benthic habitat.

Macrofauna abundance and sediment characteristics during R/V Senckenberg cruise west of Sylt in september 2010

The continuously influence of human impacts on the seafloor and benthic habitats demands the knowledge of clearly defined habitats to assess recent conditions and to monitor future changes. In this study, a benthic habitat dominated by sorted bedforms was mapped in 2010 using biological, sedimentological and acoustic data. This approach reveals the first interdisciplinary analysis of macrofauna communities in sorted bedforms in the German Bight. The study area covered 4 km², and was located ca. 3.5 km west of island of Sylt. Sorted bedforms formed as sinuous depressions with an east west orientation. Inside these depressions coarse sand covers the seafloor, while outside predominantly fine to medium sand was found. Based on the hydroacoustic data, two seafloor classes were identified. Acoustic class 1 was linked to coarse sand (type A) found inside these sorted bedforms, whereas acoustic class 2 was related to mainly fine to medium sands (type B). The two acoustic classes and sediment types corresponded with the macrofauna communities 1 and 2. The Aoinides paucibranchiata-Goniadella bobretzkii community on coarse sand and the Spiophanes bombyx - Magelona johnstonii community on fine sand. A transitional community 3 (Scoloplos armiger - Ophelia community), with species found in communities 1 and 2, could not be detected by hydroacoustic methods. This study showed the limits of the used acoustic methods, which were unable to detect insignificant differences in the fauna composition of sandy areas.

Eocene-Oligocene diatoms in the western Indian Ocean

The occurrence of diatom species in the Eocene-Oligocene sections of Ocean Drilling Program (ODP) Leg 115 sites and Deep Sea Drilling Project (DSDP) Sites 219 and 236 in the low-latitude Indian Ocean are investigated. Diatoms are generally rare and poorly preserved in the Paleogene sequences we studied. The best-preserved assemblages are found close to ash layers in early Oligocene sediments. The low-latitude diatom zonation established for the Atlantic region by Fenner in 1984 is fully applicable to the Paleogene sequences of the western Indian Ocean. Correlation of the diatom zones to the calcareous nannofossil stratigraphy of the sites places the Coscinodiscus excavatus Zone of Fenner within calcareous nannofossil Subzone CP16b. For the Mascarene Plateau and the Chagos Ridge, the times when the sites studied, together with the areas upslope from them, subsided to below the euphotic zone are deduced from changes in the relative abundance between the group of benthic, shallow-water species and Grammatophora spp. vs. the group of fully planktonic diatom species. The Eocene section of Site 707, on the Mascarene Plateau, is characterized by the occurrence of benthic diatoms (approximately 10% of the diatom assemblage). These allochthonous diatoms must have originated from shallow-water environments around volcanic islands that existed upslope from ODP Site 707 in Eocene times. In Oligocene and younger sediments of Sites 707 and 706, occurrences of benthic diatoms are rare and sporadic and interpreted as reworked from older sediments. This indicates that the area upslope from these two Mascarene Plateau sites had subsided below the euphotic zone by the early Oligocene. Only Grammatophora spp., for which a neritic but not benthic habitat is assumed, continues to be abundant throughout the Oligocene sequences. The area of the Madingley Rise sites (Sites 709-710) and nearby shallower areas subsided below the euphotic zone already in middle Eocene times, as benthic diatoms are almost absent from these Eocene sections. Only sites located on abyssal plains, and which intermittently received turbidite sediments (e.g., Sites 708 and 711), contain occasionally single, benthic diatoms of Oligocene age. The occurrence of the freshwater diatom Aulacosira granulata in a few samples of late early Oligocene and late Oligocene age at Sites 707, 709, and 714 is interpreted as windblown. Their presence indicates at least seasonally arid conditions for these periods in the source areas of eastern Africa and India. Three new species and two new combinations are defined: Chaetoceros asymmetricus Fenner sp. nov.; Hemiaulus gracilis Fenner, sp. nov.; Kozloviella meniscosa Fenner, sp. nov.; Cestodiscus demergitus (Fenner) Fenner comb, nov.; and Rocella princeps (Jouse) Fenner comb. nov.

Aggregation dynamics and foraging behaviour of striped red mullet Mullus surmuletus in the western Mediterranean Sea

Habitat-related heterogeneity of striped red mullet Mullus surmuletus heterospecific foraging assemblages was examined off the coast of Spain. Video-based focal-follows conducted on 122 M. surmuletus assemblages (446 total individuals) revealed an array of attendant species (n = 7) with composition linked to benthic habitat complexity; bare sandy substrata were characterized by homospecific groups of M. surmuletus, while habitats with rock and vegetation attracted a variety of scrounging labrids and sparids. Although the nature of the relationship between M. surmuletus and attendants requires further exploration, the present study indicates that substratum composition can be a driving factor explaining the dynamics of this heterospecific assemblage.