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An overview of 13 chapters that assess baseline conditions and status of habitats and biota in the Gulf of Mexico before the Deepwater Horizon oil spill in 2010. Brief summaries of water and sediment quality, energy flow—including natural oil and gas seeps, coastal and offshore habitats, major groups of biota and their diseases and mortalities, and commercial and recreational fisheries are provided. Biodiversity in the Gulf is high, but environmental impacts are numerous and varied and most occur within the coastal zone.

Water quality is determined by the interaction of physiographic setting with human activities and is measured as the degree of eutrophication—the clarity of water—and the levels of contaminants. The patterns and trends in the Gulf of Mexico water quality are highly variable in space and through time. Assessments conclude that water quality in the Gulf of Mexico coastal environments is highly influenced by human activities, and the primary cause of degraded water quality is excess nutrients. The resulting eutrophication has led to low dissolved oxygen and increased chlorophyll concentrations, diminished water clarity, and other secondary effects including toxic/nuisance algal blooms and loss of submerged aquatic vegetation. Overall, the ecological condition of the coastal northern Gulf of Mexico was judged as to , water quality was fair, and expressions of eutrophication were high.

The Gulf of Mexico includes a broad spectrum of depositional environments from the coast to deep water. Waves, tides, currents, and gravity are the primary mechanisms that move sediment. Most sediment originates from the adjacent land, primarily via fluvial transport. Direct precipitation of calcium carbonate and evaporate minerals takes place primarily on the Florida and Yucatán platforms and some coastal lagoons. The deep environments tend to be dominated by mud in a combination of terrigenous and biogenic sediments. The rate of accumulation and the volume of modern sediment on the shelf range widely. Generally, areas bounded by rivers receive the greatest volume of sediment at the highest rates of delivery. The Mississippi Delta is the extreme of this generality in that it covers almost the entire shelf. Tidal range on the Gulf is low, meaning that tidal currents are minimal except in the inlets. The estuaries tend to be shallow: thus, waves can be important in modifying sediment distribution. Sediment delivery is dominated by fluvial discharge, so climate and seasons are important factors.

Contaminants in coastal sediments are compared with continental shelf/slope and abyssal sediments. Early introductions of contaminants to sediments were due to agricultural pesticide use, increased populations in, and industrialization of, coastal areas, and oil and gas exploration and production post-World War II. Coastal estuaries were judged to be in good to poor condition with concentrations of metals and pesticides in more than 40 % and concentrations of PAHs and PCBs in less than 1 % of coastal sediments exceeding levels suspected of causing biological effects. Within bay systems, steep gradients in contaminant concentrations were observed near population centers, agricultural activities, and industrial complexes. Highest concentrations of DDT, PCBs, PAHs, Ag, As, Cd, Hg, Pb, Sn, and Zn were found in sediments near population centers, agricultural lands, and industrial/military complexes. Natural petroleum seepage is the major source of hydrocarbons in north central Gulf of Mexico continental shelf/slope sediments.

Oil and gas seeps are common worldwide; occur on land and beneath the ocean; are numerous in the Gulf of Mexico; and are biogenic, thermogenic, or mixed in origin. Seeps occur as gases, liquids, asphalts, and tars. Seeps are estimated to account for about 95 % of oil annually discharged to the Gulf of Mexico waters. Biogenic gas seeps have a microbial metabolic origin. Thermogenic hydrocarbons rise to the surface from more deeply buried source rock horizons or accumulations. The seepage of oil and gas into marine sediments initiates a complex biogeochemical cycle. A unique ecology has evolved in association with oil and gas seeps based on chemosynthesis and symbioses. Consortia of microbial species mediate the geological and biogeochemical processes that are essential for supporting what are commonly referred to as cold-seep communities. At these locations, bacteria oxidize hydrocarbons to carbon dioxide or bicarbonate ions, which favor the formation of hard ground substrate in otherwise mostly muddy environments. Thermogenic oil and gas seeps and biogenic gas seeps are pervasive and intrinsic features of the Gulf of Mexico. Thermogenic seeps will persist as long as oil and gas continue to migrate to the seafloor.

Urbanization and industrial development pressures have seriously impacted coastal ecosystems, including vegetated intertidal and subtidal marine habitats such as barrier strands and associated wetlands and seagrasses. These ecosystems provide a suite of services including carbon storage, pollution and nutrient abatement, soil formation, fisheries support, and flood and storm protection. Emphasis has been placed on vegetated marine habitats that occur immediately adjacent to the Gulf of Mexico, including barrier islands and beaches, salt marshes and mangroves, seagrasses, intertidal and subtidal flats, and reed marshes at the mouth of the Mississippi River. These habitats, their depositional environments, and the ecology of their dominant flora and fauna are described within the context of major marine and terrestrial ecoregions. The information and analysis in this chapter should better enable effective management and restoration of coastal habitats in the Gulf as environmental change continues to alter their structure and function and reshape their associated biotic assemblages.

Ecosystem components at the bottom of oceanic food webs (phytoplankton, zooplankton, mid-water fishes, and seafloor organisms) are tabulated and mapped. Sessile communities in hard bottom habitats, including the Flower Garden Banks National Marine Sanctuary, are also reviewed. Some of the foundation species have symbiotic bacteria that use methane as a source of energy and carbon, but others (the vestimentiferan worms) use sulfide for energy. The inner continental shelf habitats are supplied with nutrients from numerous rivers, and thus, the biota nearshore is supported by phytoplankton enriched in nitrate. The freshwater and nitrate supplied to the Louisiana coast by the Mississippi River are so large that they overwhelm the ecosystem, and a large zone of detrimental hypoxia forms consistently during summer months off Louisiana. The size of the hypoxic zone is directly proportional to river flow volume and the delivery of nitrate. The broad continental slope south of Texas and Louisiana is riddled with numerous basins that are tens of kilometers in diameter and hundreds of meters deep relative to the surrounding slope, but the habitats in each can vary from lakes of oil and salt surrounded by dense populations of mussels to simple depauperate mud-lined basins. Offshore of the continental shelf, the productivity and species composition of the plankton of the Gulf of Mexico ecosystem are controlled by the source water (Caribbean) and concomitant physical processes.

Four of the five top species in the Gulf of Mexico by value and poundage of landings are shellfish species. Gulf-wide, there are at least 49 officially recognized shellfish species: 28 are mollusks, 18 are crustaceans, and three are echinoderms. Of these, 16 shellfish species are taken within US waters, 46 from Mexico, and 6 from Cuba. The major focus is on the northern Gulf species of brown, pink, and white shrimp, Eastern oyster, and blue crab. All species are known to vary widely or fluctuate in population levels in accordance with varying environmental conditions from year to year. In addition, shrimp have also been affected by exogenous factors, such as rising fuel costs, market competition from imported shrimp, and fleet damage from hurricanes. Shrimp populations seem to be flourishing, while the shrimp fishery is in decline. The oyster fishery appears to be fairly stable overall, except for hurricane damage in some places and a decadal decline in stock assessment in Louisiana. Oyster reef habitat loss is a major concern. The blue crab fishery is quite variable from state to state with Louisiana showing continued growth and the largest fishery over the past two decades, while Texas shows a decrease. Gulf-wide, there is agreement that healthy bays and estuaries lead to more productive fisheries; thus, habitats need to be conserved or in some cases, restored.