Organic and inorganic geochemistry and archaeal community composition of hypersaline sediments from Orca Basin, RV Atlantis Expedition AT18-02

Among the most extreme habitats on Earth, dark, deep, anoxic brines host unique microbial ecosystems that remain largely unexplored. As the terminal step of anaerobic degradation of organic matter, methanogenesis is a potentially significant but poorly constrained process in deep-sea hypersaline environments. We combined biogeochemical and phylogenetic analyses as well as incubation experiments to unravel the origin of methane in hypersaline sediments of Orca Basin in the northern Gulf of Mexico. Substantial concentrations of methane (up to 3.4 mM) coexisted with high concentrations of sulfate (16-43 mM) in two sediment cores retrieved from the northern and southern parts of Orca Basin. The strong depletion of 13C in methane (-77 to -89 per mill) pointed towards a biological source. While low concentrations of competitive substrates limited the significance of hydrogenotrophic and acetoclastic methanogenesis, the presence of non-competitive methylated substrates (methanol, trimethylamine, dimethyl sulfide, dimethylsulfoniopropionate) supported the potential for methane generation through methylotrophic methanogenesis. Thermodynamic calculations demonstrated that hydrogenotrophic and acetoclastic methanogenesis were unlikely to occur under in situ conditions, while methylotrophic methanogenesis from a variety of substrates was highly favorable. Likewise, carbon isotope relationships between methylated substrates and methane supported methylotrophic methanogenesis as the major source of methane. Stable isotope tracer and radiotracer experiments with 13C bicarbonate, acetate and methanol as well as 14C-labeled methylamine indicated that methylotrophic methanogenesis was the predominant methanogenic pathway. Based on 16S rRNA gene sequences, halophilic methylotrophic methanogens related to the genus Methanohalophilus dominated the benthic archaeal community in the northern basin but also occurred in the southern basin. High abundances of methanogen lipid biomarkers such as intact polar and polyunsaturated hydroxyarchaeols were detected in sediments from the northern basin, with lower abundances in the southern basin. Strong 13C-depletion of saturated and monounsaturated hydroxyarchaeol were consistent with methylotrophic methanogenesis as the major methanogenic pathway. Collectively, the availability of methylated substrates, thermodynamic calculations, experimentally determined methanogenic activity as well as lipid and gene biomarkers strongly suggested methylotrophic methanogenesis as predominant pathway of methane formation in the presence of sulfate in Orca Basin sediments.

The ecology of southern California coastal salt marshes : a community profile /

Mode of access: Internet.

The ecology of the soft-bottom benthos of San Francisco Bay : a community profile /

Mode of access: Internet.

Forest ecology ; the forest environment, the forest community and the forest itself.

Includes bibliography.

Interpretation of the relationship between benthic fauna, geologic distributions, and methane seeps at Southern Hydrate Ridge, Oregon continental margin

Senior thesis written for Oceanography 445

Detecting the effects of physical disturbance on benthic assemblages in a subtropical estuary: A Beyond BACI approach

The effects of dredging on the benthic communities in the Noosa River, a subtropical estuary in SE Queensland, Australia, were examined using a 'Beyond BACF experimental design. Changes in the numbers and types of animals and characteristics of the sediments in response to dredging in the coarse sandy sediments near the mouth of the estuary were compared with those occurring naturally in two control regions. Samples were collected twice before and twice after the dredging operations, at multiple spatial scales, ranging from metres to kilometres. Significant effects from the dredging were detected on the abundance of some polychaetes and bivalves and two measures of diversity (numbers of polychaete families and total taxonomic richness). In addition, the dredging caused a significant increase in the diversity of sediment particle sizes found in the dredged region compared with elsewhere. Community composition in the dredged region was more similar to that in the control regions after dredging than before. Changes in the characteristics of the sedimentary environment as a result of the dredging appeared to lead to the benthic communities of the dredged region becoming more similar to those elsewhere in the estuary, so dredging in this system may have led to the loss or reduction in area of a specific type of habitat in the estuary with implications for overall patterns of biodiversity and ecosystem function. (c) 2006 Elsevier B.V. All rights reserved.

Media, ecology and conservation:using the media to protect the world's wildlife and ecosystems

The second book in The Converging World series, Media, Ecology and Conservation focuses on global connectivity and the role of new digital and traditional media in bringing people together to protect the world's endangered wildlife and conserve fragile and threatened habitats. New media offers opportunities for like-minded individuals, community groups, businesses and public organisations to learn and work cooperatively for the good of all species. One of the key themes of this book explores the important issue of how new information and communication technologies mediate the natural world, and our understanding of our place in it. By exploring the role of film, television, video, photography and the internet in animal conservation in the USA, India, Africa, Australia and the United Kingdom John Blewitt investigates the politics of media representation surrounding important controversies such as the trade in bushmeat, whaling and habitat destruction. The work and achievements of media/conservation activists are located within a cultural framework that simultaneously loves nature, reveres animals but too often ignores the uncomfortable realities of species extinction and animal cruelty.

Understanding anuran community dynamics in temporary wetlands: The interaction and importance of landscape and biotic processes

The major objective of this study was to determine the relative importance of landscape factors, local abiotic factors, and biotic interactions in influencing tadpole community structure in temporary wetlands. I also examined the influence of agricultural activities in South-central Florida by comparing tadpole communities in native prairie wetlands (a relatively unmodified habitat) at the Kissimmee Prairie Sanctuary (KPS) to tadpole communities in three agriculturally modified habitats found at MacArthur Agro-Ecology Research Center (MAERC). Environmental characteristics were measured in 24 isolated wetlands, and tadpoles were sampled using throw-traps and dipnets during the 1999 wet season (June–October). Landscape characteristics were expected to predominately influence all aspects of community structure because anurans associated with temporary wetland systems are likely to exist as metapopulations. Both landscape characteristics (wetland proximity to nearest woodland and the amount of woodland surrounding the wetland) and biotic interactions (fish predation) had the largest influence on tadpole community structure. Predatory fish influenced tadpole communities more than expected due to the ubiquity of wetlands, lack of topographic relief, and dispersal abilities of several fish species. Differences in tadpole community structure among habitat types were attributed to differences in woodland attributes and susceptibility to fish colonization. Furthermore, agricultural modification of prairie habitats in South-central Florida may benefit amphibian communities, particularly woodland-dwelling species that are unable to coexist with predatory fish. From a conservation standpoint, temporary wetlands proximal to woodland areas and isolated from permanent water sources appear to be most important to amphibians. In addition, the high tadpole densities attained in these wetlands suggest that these wetlands serve as biological hotspots within the landscape, and their benefits extend into the adjacent terrestrial matrix. Further research efforts are needed to quantify the biological productivity of these systems and determine spatial dynamics of anurans in surrounding terrestrial habitats. ^

Defining the role of floating periphyton mats in shaping food-web dynamics in the Florida Everglades

Expansive periphyton mats are a striking characteristic of the Florida Everglades. Floating periphyton mats are home to a diverse macroinvertebrate community dominated by chironomid and ceratopogonid larvae and amphipods that use the mat as both a food resource and refuge from predation. While this periphyton complex functions as a self-organizing system, it also serves as a base for trophic interactions with larger organisms. The purpose of my research was to quantify variation in the macroinvertebrate community inhabiting floating periphyton mats, describe the role of mats in shaping food-web dynamics, and describe how these trophic interactions change with eutrophication. ^ I characterized the macroinvertebrate community inhabiting periphyton through a wet-season by describing spatial variation on scales from 0.2 m to 3 km. Floating periphyton mats contained a diverse macroinvertebrate community, with greater taxonomic richness and higher densities of many taxa than adjacent microhabitats. Macroinvertebrate density increased through the wet season as periphyton mats developed. While some variation was noted among sites, spatial patterns were not observed on smaller scales. I also sampled ten sites representing gradients of hydroperiod and nutrient (P) levels. The density of macroinvertebrates inhabiting periphyton mats increased with increasing P availability; however, short-hydroperiod P-enriched sites had the highest macroinvertebrate density. This pattern suggests a synergistic interaction of top-down and bottom-up effects. In contrast, macroinvertebrate density was lower in benthic floc, where it was negatively correlated with hydroperiod. ^ I used two types of mesocosms (field cages and tanks) to manipulate large consumers (fish and grass shrimp) with inclusion/exclusion cages over an experimental P gradient. In most cases, periphyton mats served as an effective predation refuge. Macroinvertebrates were consumed more frequently in P-enriched treatments, where mats were also heavily grazed. Macroinvertebrate densities decreased with increasing P in benthic floc, but increased with enrichment in periphyton mats until levels were reached that caused disassociation of the mat. ^ This research documents several indirect trophic interactions that can occur in complex habitats, and emphasizes the need to characterize dynamics of all microhabitats to fully describe the dynamics of an ecosystem. ^

Distribution and ecology of amphibians and reptiles in a fragmented landscape, northeastern Bolivia

Habitat loss and fragmentation have been implicated as driving forces behind recent waves of extinction. The regional landscape where this study occurred is a mosaic of forest and grassland, and therefore provides an ideal system with which to investigate the implications of habitat patchiness for the distribution and ecology of organisms. Here I describe patterns of amphibian and reptile distribution among and within habitats at the study site, investigate associations between habitat and community structure, describe nested subset patterns on forest islands, and quantify the relationship between body size and density across ecological scales and taxonomic groups. ^ Species richness did not vary across habitats, between forest island isolation classes or between island edges and cores. In contrast, species composition varied at all three ecological scales, reflecting differences in the distribution of both forest and open-habitat affiliated species. Species composition was associated with multivariate habitat profiles, with differences occurring along the isolation gradient of forest islands rather than the area gradient. The relationship between species composition and habitat was stronger for amphibians than for reptiles, a pattern that may be ascribed to physiological differences between the two groups. Analysis of nested subset pattern of community structure indicated that species composition of islands is nested as a function of isolation. Four species whose distribution on forest islands seems to be dispersal-limited drive the relationship between nestedness and isolation. Although there were several examples of shifts in body size across spatial scales and taxonomic groups, body size was not associated with density as predicted by theory, which may reflect differences between real and habitat islands, or differential responses of poikilothermic vertebrates to changes in density relative to homeotherms. ^ Taken together, the strongest result to emerge from this research is the importance of isolation, rather than area, on community structure in this system. Much evidence suggested that different ecological groups of species show distinct patterns of distribution both within and among habitat types. This suggests that species distributions at this site are not the result of 'neutral' processes at the community level, but rather reflect fundamental differences in the ecology of component species. ^

Relative significance of pelagic, benthic and allochthonous organic matter to microbial carbon cycling in a phosphorus-depleted subtropical estuary (Florida Bay)

Heterotrophic bacteria are important decomposers and transformers of primary production and provide an important link between detritus and the aquatic food web. In seagrass ecosystems, much of seagrass primary production is unavailable through direct grazing and must undergo microbial reworking before seagrass production can enter the aquatic food web. The goal of my dissertation research is to understand better the role heterotrophic bacteria play in carbon cycling in seagrass estuaries. My dissertation research focuses on Florida Bay, a seagrass estuary that has experienced recent changes in carbon source availability, which may have altered ecosystem function. My dissertation research investigates the importance of seagrass, algal and/or cyanobacterial, and allochthonous-derived organic matter to heterotrophic bacteria in Florida Bay and helps establish the carbon base of the estuarine food web. ^ A three tiered approach to the study of heterotrophic bacterial carbon cycling and trophic influences in Florida Bay was used: (1) Spatiotemporal observations of environmental parameters (hydrology, nutrients, extracellular enzymes, and microbial abundance, biomass, and production); (2) Microbial grazing experiments under different levels of top-down and bottom-up influence; and (3) Bulk and compound-specific (bacteria-biomarker fatty acid analysis) stable carbon isotope analysis. ^ In Florida Bay, spatiotemporal patterns in microbial extracellular enzyme (also called ectoenzyme) activities indicate that microorganisms hydrolyzed selectively fractions of the estuarine organic matter pool. The microbial community hydrolyzed organic acids, peptides, and phosphate esters and did not use storage and structural carbohydrates. Organic matter use by heterotrophic bacterioplankton in Florida Bay was co-regulated by bottom-up (resource availability) and top-down (grazer mediated) processes. A bacterial carbon budget based on bacterial, epiphytic, and seagrass production indicates that heterotrophic bacterial carbon cycles are supported primarily through epiphytic production with mixing from seagrass production. Stable carbon isotope analysis of bacteria biomarkers and carbon sources in Florida Bay corroborate the results of the bacterial carbon budget. These results support previous studies of aquatic consumers in Florida Bay, indicating that epiphytic/benthic algal and/or cyanobacterial production with mixing from seagrass-derived organic matter is the carbon base of the seagrass estuarine food web. ^

Ecology and distribution of diatoms in Biscayne Bay, Florida (USA): Implications for bioassessment and paleoenvironmental studies

The spatial and temporal distribution of planktonic, sediment-associated and epiphytic diatoms among 58 sites in Biscayne Bay, Florida was examined in order to identify diatom taxa indicative of different salinity and water quality conditions, geographic locations and habitat types. Assessments were made in contrasting wet and dry seasons in order to develop robust assessment models for salinity and water quality for this region. We found that diatom assemblages differed between nearshore and offshore locations, especially during the wet season when salinity and nutrient gradients were steepest. In the dry season, habitat structure was primary determinant of diatom assemblage composition. Among a suite of physicochemical variables, water depth and sediment total phosphorus (STP) were most strongly associated with diatom assemblage composition in the dry season, while salinity and water total phosphorus (TP) were more important in the wet season. We used indicator species analysis (ISA) to identify taxa that were most abundant and frequent at nearshore and offshore locations, in planktonic, epiphytic and benthic habitats and in contrasting salinity and water quality regimes. Because surface water concentrations of salts, total phosphorus, nitrogen (TN) and organic carbon (TOC) are partly controlled by water management in this region, diatom-based models were produced to infer these variables in modern and retrospective assessments of management-driven changes. Weighted averaging (WA) and weighted averaging partial least squares (WA-PLS) regressions produced reliable estimates of salinity, TP, TN and TOC from diatoms (r2 = 0.92, 0.77, 0.77 and 0.71, respectively). Because of their sensitivity to salinity, nutrient and TOC concentrations diatom assemblages should be useful in developing protective nutrient criteria for estuaries and coastal waters of Florida.

Diel Patterns of Patch Reef Community Dynamics in a Caribbean Back-Reef System

Back-reef seascapes represent critical habitat for juvenile and adult fishes. Patch reef, seagrass, and mangrove habitats form a heterogeneous mosaic, often linked by species that use reefs as structure during the day and make foraging migrations into soft-bottom habitat at night. Artificial reefs are used to model natural patch reefs, however may not function equivalently as fish habitat. To study the relative value of natural and artificial patch reefs as fish habitat, these communities in the Sea of Abaco, Bahamas were compared using roving diver surveys and time-lapse photography. Diel turnover in fish abundance, recorded with time-lapse photography and illuminated by infrared light, was quantified across midday, dusk, and night periods to explore possible effects of reef type (artificial vs. natural) on these patterns. Diurnal communities on natural reefs exhibited greater fish abundance, species richness, and functional diversity compared to artificial reefs. Furthermore, both types of reef communities exhibited a significant shift across the diel period, characterized by a decline in total fish density at night, especially for grunts (Haemulidae). Cross-habitat foraging migrations by diurnal or nocturnal species, such as haemulids, are likely central drivers of this twilight turnover and can represent important energy and nutrient subsidies. Time-lapse surveys provided more consistent measures of reef fish assemblages for the smaller artificial reef habitats, yet underestimated abundance of certain taxa and species richness on larger patch habitats when compared to the roving diver surveys. Time-lapse photography complemented with infrared light represent a valuable non-invasive approach to studying behavior of focal species and their fine-scale temporal dynamics in shallow-reef communities.

Does landscape context affect habitat value? The importance of seascape ecology in back-reef systems

Seascape ecology provides a useful framework from which to understand the processes governing spatial variability in ecological patterns. Seascape context, or the composition and pattern of habitat surrounding a focal patch, has the potential to impact resource availability, predator-prey interactions, and connectivity with other habitats. For my dissertation research, I combined a variety of approaches to examine how habitat quality for fishes is influenced by a diverse range of seascape factors in sub-tropical, back-reef ecosystems. In the first part of my dissertation, I examined how seascape context can affect reef fish communities on an experimental array of artificial reefs created in various seascape contexts in Abaco, Bahamas. I found that the amount of seagrass at large spatial scales was an important predictor of community assembly on these reefs. Additionally, seascape context had differing effects on various aspects of habitat quality for the most common reef species, White grunt Haemulon plumierii. The amount of seagrass at large spatial scales had positive effects on fish abundance and secondary production, but not on metrics of condition and growth. The second part of my dissertation focused on how foraging conditions for fish varied across a linear seascape gradient in the Loxahatchee River estuary in Florida, USA. Gray snapper, Lutjanus griseus, traded food quality for quantity along this estuarine gradient, maintaining similar growth rates and condition among sites. Additional work focused on identifying major energy flow pathways to two consumers in oyster-reef food webs in the Loxahatchee. Algal and microphytobenthos resource pools supported most of the production to these consumers, and body size for one of the consumers mediated food web linkages with surrounding mangrove habitats. All of these studies examined a different facet of the importance of seascape context in governing ecological processes occurring in focal habitats and underscore the role of connectivity among habitats in back-reef systems. The results suggest that management approaches consider the surrounding seascape when prioritizing areas for conservation or attempting to understand the impacts of seascape change on focal habitat patches. For this reason, spatially-based management approaches are recommended to most effectively manage back-reef systems.