Marine unconsolidated sediments constitute the largest ecosystems on earth in terms of spatial coverage, but there are still critical gaps in the science required to support conservation and ecosystem-based management. This is mainly due to the inaccessibility of these ecosystems in wave-exposed environments or deeper waters and the difficulty in observing biota in their three-dimensional sedimentary habitat. Currently, the physical driving processes of intertidal unconsolidated sediment ecosystems are much better understood than those of the subtidal ecosystems. However, these ecosystems are linked through water and sediment movement. This thesis, therefore, considers the continuum of unconsolidated sediment ecosystems across the entire continental shelf (i.e. intertidal to the shelf edge). The aim of this thesis was two-fold; (i) to advance the foundational understanding of biodiversity patterns and driving processes in unconsolidated sediment habitats, and (ii) to apply this knowledge in the development of a systematic conservation plan for marine unconsolidated sediment ecosystems. The South African west coast continental shelf was used as a case study in order to represent Eastern boundary upwelling regions. This study sought to investigate biodiversity patterns in macro-infaunal communities and determine their driving processes for incorporation into habitat classifications and the development of a habitat map. Systematic conservation plans require a map of biodiversity patterns and processes, and quantitative conservation targets to ensure representation of all biodiversity features including habitats.in marine protected areas. This thesis provided these key elements by classifying the unconsolidated sediment habitats and determining habitat-specific evidence-based conservation targets to support conservation of these important ecosystems. The application of these elements was then demonstrated in a systematic conservation plan for the unconsolidated sediment ecosystems of the South African west coast. Diversity patterns were examined using physical and macro-infauna data, ranging from the beach to the shelf edge (0-412 m). These data were analysed to develop two different habitat classifications, namely seascapes derived from geophysical and biophysical data, and biotopes derived from the combination of macro-infaunal and physical data. Multivariate analyses of 13 physical variables identified eight seascapes for the unconsolidated sediment samples from 48 sites on the South African west coast. These were based on depth, slope, sediment type, and upwelling-related processes (i.e. maximum chlorophyll concentration, sediment organic carbon content and austral summer bottom oxygen concentration). Latitude and bottom temperature were not considered major drivers of seascapes on the west coast because latitude closely reflected changes in upwelling-related processes and the temperature range was narrow across the shelf. This study revealed that productivity, a biophysical variable not usually included in geo-physical habitat classifications, played a significant role in the definition of seascapes on the South African west coast. It is therefore recommended that productivity be included in future seascape classifications to improve the utility of these classifications particularly in areas of variable productivity. Seascapes should, however, be tested against biological data to improve the understanding of key physical drivers of communities in unconsolidated sediment ecosystems. Macro-infaunal community distributions were determined along with their physical drivers for the unconsolidated sediments of the South African west coast. A total of 44 828 individuals from 469 taxa were identified from 48 sites representing 46.2 m2 of seafloor. Seven distinct macro-infaunal communities were defined through multivariate analyses and their key characteristic and distinguishing species were identified. These communities reflected five depth zones across the shelf, namely beach, inner shelf (10-42 m), middle shelf (60-142 m), outer shelf (150-357 m) and shelf edge (348-412 m). The processes driving the community structure of these depth zones were postulated to be tides, wave turbulence, seasonal hypoxia, habitat stability and homogeneity, and internal tides and/or shelf break upwelling, with drivers listed in order of increasing influence with depth. The middle shelf was further separated into three distinct communities based on sediment type, sediment organic carbon content and frequency of hypoxia. Variations in water turbulence, sediment grain size, upwelling-related variables and riverine sediment input were identified as the likely primary drivers of macro-infaunal community patterns. This chapter culminated in the development of a biotope classification based on the combination of macro-infaunal communities and their physical habitats (i.e. biotopes). South Africa has developed an expert-derived National Marine and Coastal Habitat (SANMC) Classification System which is used as a biodiversity surrogate in ecosystem assessment and spatial planning. This thesis tested the validity of this classification and the data derived Seascape classification against macro-infauna species abundance and biomass data in an effort to determine how well the different classifications represent macro-infaunal diversity of the west coast. These two classifications were also compared to the Biotope classification which combines macro-infaunal communities with their physical habitats. A canonical analysis of principle coordinates (CAP) was utilised to test the success with which each sample was allocated to the relevant habitat type in each classification. The total allocation success for each classification was used as a measure of effectiveness in terms of representing biodiversity patterns. Both classifications had similar allocation successes of 89-92 percent and 92-94 percent for the Seascape and National Habitat Classification respectively, but either over- or under-classified the macrofauna communities. The Biotope classification had the highest allocation success (98 percent), therefore it is the most accurate reflection of the macrofauna biodiversity patterns on the west coast. A key finding of this study was the increasing accuracy of classifications from physically- to expert- to biologically-derived habitat classifications. In this thesis, the Biotope classification was deemed the best representative of biodiversity patterns and was therefore used to produce the Biotope map for use in spatial assessment and planning. The distinct depth patterns that emerged in both the Seascape and Biotope classifications highlighted the need for further investigation of the relationship between depth and biodiversity. Despite variability in macro-infaunal communities, a general unifying pattern in biodiversity across the shelf was sought. Three relationships between depth and species richness have been described in the literature; namely a unimodal pattern, a positively linear relationship with depth, and no relationship between depth and species richness. These hypotheses were tested on the west coast. Two different species richness metrics were utilised to test the depth-diversity relationship, namely observed species density (spp.0.2m-2) and estimated species richness (spp.site-1). Observed species density increased from the beach to the shelf edge (350 m), then decreased to 412 m. The decline may have been due to difficulty in detecting species at greater depths as a result of sampling challenges. The inclusion of an innovative extrapolative method for estimating species richness (the capture-recapture heterogeneity model) within the Bayesian statistical framework mitigated the effects of species detection heterogeneity and revealed that species richness actually increased continuously across the shelf from beach to shelf edge. Thus the general relationship between depth and species richness is positively linear on the west coast of South Africa The new macro-infauna dataset and biotope map provided the opportunity to develop the first habitat-specific evidence-based conservation targets for unconsolidated sediments of the west coast. Species-Area Relationship (SAR) based conservation targets were developed for the biotopes using a modification of the generally accepted methodology. The accepted methodology has three steps (i) the estimation of total species richness for each habitat using the Bootstrap asymptotic estimator, (ii) the calculation of the slope of the species area curve (i.e. the z-value), and (iii) the calculation of targets representing 80 percent of the species. The inclusion of an innovative extrapolative species richness estimator, the Multi-species Site Occupancy Model (MSOM) provided better species richness estimation than the more conventional bootstrap species richness estimator, even though both are based on species accumulation. The MSOM, applied in the Bayesian statistical framework takes detectability of a species into account.

Methanogenesis is the predominant terminal process of polymer degradation in anaerobic marine sediments depleted of sulfate; however, characterization of a marine consortium has not been previously reported. A marine methanogenic consortium consisting of fermentative, hydrogen-producing acetogenic and methanogenic bacteria is described. An acetotrophic methane-producing strain of bacteria was isolated. This isolate expresses three distinct morphovars: individual cocci, cell aggregates and communal cysts. Individual cocci are 1.9 µm in diameter and are nonmotile, but have fimbria-like structures. Cells have a thin protein cell wall. Acetate, methanol, methylamine, dimethylamine and trimethylamine are substrates for growth; formate and hydrogen are not. Sodium chloride and magnesium concentrations found in seawater are required for optimum growth. RNA homology values indicated that this isolate is a new species. Methanosarcina acetivorans is the proposed specific epithet. This is the first report of an acetotrophic methane-producing species indigenous to marine sediments. A method is described for mass culturing this and other acetotrophic methanogens using a pH auxostat. A strictly methylotrophic methane-producing strain was also isolated and is described. Only trimethylamine, dimethylamine, methylamine and methanol were substrates for growth. Cells were nonmotile, irregular cocci 1 µm in diameter and had a thin protein cell wall. Sodium chloride and magnesium concentrations found in seawater were required for optimum growth. Biotin was the only organic supplement required for growth in mineral medium. Fe was required for growth; Ni and Co were stimulatory. This isolate is a new genus based on RNA homology. Methanococcoides is the proposed genus and Methanococcoides methylutens is the specific epithet. Population studies suggest that this species is uniquely adapted for methylated amine degradation in marine sediments. The phylogenetic relationships of M. acetivorans, M. methylutens and other acetotrophic and methylotrophic species were determined by RNA and DNA homology techniques. Phylogenetic and physiological results in this study indicated that the population of methanogenic bacteria in marine sediments is both unique and equally diverse as the population of freshwater methanogenic species. / Ph. D.

In 1970 the Arrow oil spill off Cape Breton contaminated 305 kilometres of shoreline. Aerial and land surveys have demonstrated that natural weathering has occurred throughout this period, but it was relatively slow, especially in sheltered areas like Black Duck Cove lagoon. This study analyzed the microbial hydrocarbon degradation potential in the lagoon sediments using direct and culture-based techniques. Mineralization of hydrocarbon substrates (hexadecane, octacosane and naphthalene) indicated the presence of an active degradative microbial community, however, genes from known bacterial hydrocarbon degradation pathways (alkB, ndoB, phnAc) were not detected by direct extraction of sediment DNA and PCR amplification. Sediment enrichment cultures had increased mineralization rates for naphthalene and hexadecane, and a hexadecane-degrading pure culture, Rhodococcus sp. BDC14, with a typical alkB gene was isolated. PCR analysis of total community DNA extracted directly from the enrichments indicated the presence of the Alcanivorax borkumensis alkB1 genotype. The results demonstrated that there were notable differences between culture-based and direct molecular analytical techniques in characterizing the contaminated sediments.

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