Sampling Design and Statistical Methods for Environmental Biologists

The industrialization of the deep sea is expanding worldwide. Expanding oil and gas exploration activities in the absence of sufficient baseline data in these ecosystems has made environmental management challenging. Here, we review the types of activities that are associated with global offshore oil and gas development in water depths over 200 m, the typical impacts of these activities, some of the more extreme impacts of accidental oil and gas releases, and the current state of management in the major regions of offshore industrial activity including 18 exclusive economic zones. Direct impacts of infrastructure installation, including sediment resuspension and burial by seafloor anchors and pipelines, are typically restricted to a radius of approximately 100 m on from the installation on the seafloor. Discharges of water-based and low-toxicity oil-based drilling muds and produced water can extend over 2 km, while the ecological impacts at the population and community levels on the seafloor are most commonly on the order of 200-300 m from their source. These impacts may persist in the deep sea for many years and likely longer for its more fragile ecosystems, such as cold-water corals. This synthesis of information provides the basis for a series of recommendations for the management of offshore oil and gas development. An effective management strategy, aimed at minimizing risk of significant environmental harm, will typically encompass regulations of the activity itself (e.g. discharge practices, materials used), combined with spatial (e.g. avoidance rules and marine protected areas) and temporal measures (e.g. restricted activities during peak reproductive periods). Spatial management measures that encompass representatives of all of the regional deep-sea community types is important in this context. Implementation of these management strategies should consider minimum buffer zones to displace industrial activity beyond the range of typical impacts: at least 2 km from any discharge points and surface infrastructure and 200 m from seafloor infrastructure with no expected discharges. Although managing natural resources is, arguably, more challenging in deep-water environments, inclusion of these proven conservation tools contributes to robust environmental management strategies for oil and gas extraction in the deep sea.

/pdf/environmental-impacts-of-the-deep-water-oil-and-gas-industry-2rhh0p5l4b.pdf

Environmental Impacts of the Deep-Water Oil and Gas Industry: A Review to Guide Management Strategies

As a consequence of the decline of numerous commercial fish populations, an ecosystem-based approach to fisheries management, which includes the protection of essential fish habitat (EFH), has emerged. Cold-water coral (CWC) sites are recognized as biodiversity hotspots, but numerous examples of CWC destruction and degradation as a result of anthropogenic activities are well documented. However, although functional connections between CWCs and fish stocks are suspected, based on correlative evidence, proof of any close or direct relationship identifying CWCs as EFH is still lacking. Here, we provide evidence of the utilization of CWCs by fish larvae, mainly those of redfish (Sebastes spp). In multiyear surveys, fish larvae were consistently found closely associated with five species of sea pen (Octocorallia: Pennatulacea) in April and May. Prevalence and/or yields of fish larvae varied with coral host species, depth, location, and colony size. Evidence of the role of CWCs in the early life history of some...

Deep cold‐water corals as nurseries for fish larvae

Bottom trawling has widespread impacts on benthic communities and habitats. While the direct impacts of trawl disturbances on benthic communities have been extensively studied, the consequences from long-term chronic disturbances are less well understood. The response of benthic macrofauna to chronic otter-trawl disturbance from a Nephrops norvegicus (Norway lobster) fishery was investigated along a gradient of fishing intensity over a muddy fishing ground in the northeastern Irish Sea. Chronic otter trawling had a significant, negative effect on benthic infauna abundance, biomass, and species richness. Benthic epifauna abundance and species richness also showed a significant, negative response, while no such effect was evident for epibenthic biomass. Furthermore, chronic trawl disturbance led to clear changes in community composition of benthic infauna and epifauna. The results presented indicate that otter-trawl impacts are cumulative and can lead to profound changes in benthic communities, which may have far-reaching implications for the integrity of marine food webs. Studies investigating the short-term effects of fishing manipulations previously concluded that otter trawling on muddy substrates had only modest effects on the benthic biota. Hence, the results presented by this study highlight that data from experimental studies can not be readily extrapolated to an ecosystem level and that subtle cumulative effects may only become apparent when fishing disturbances are examined over larger spatial and temporal scales. Furthermore, this study shows that data on chronic effects of bottom trawling on the benthos will be vital in informing the recently advocated move toward an ecosystem approach in fisheries management. As bottom-trawl fisheries are expanding into ever deeper muddy habitats, the results presented here are an important step toward understanding the global ecosystem effects of bottom trawling.

Trawl disturbance on benthic communities: chronic effects and experimental predictions.

RAD-tag sequencing is a promising method for conducting genome-wide evolutionary studies. However, to date, only a handful of studies empirically tested its applicability above the species level. In this communication, we use RAD tags to contribute to the delimitation of species within a diverse genus of deep-sea octocorals, Chrysogorgia, for which few classical genetic markers have proved informative. Previous studies have hypothesized that single mitochondrial haplotypes can be used to delimit Chrysogorgia species. On the basis of two lanes of Illumina sequencing, we inferred phylogenetic relationships among 12 putative species that were delimited using mitochondrial data, comparing two RAD analysis pipelines (Stacks and PyRAD). The number of homologous RAD loci decreased dramatically with increasing divergence, as >70% of loci are lost when comparing specimens separated by two mutations on the 700-nt long mitochondrial phylogeny. Species delimitation hypotheses based on the mitochondrial mtMutS gene are largely supported, as six out of nine putative species represented by more than one colony were recovered as discrete, well-supported clades. Significant genetic structure (correlating with geography) was detected within one putative species, suggesting that individuals characterized by the same mtMutS haplotype may belong to distinct species. Conversely, three mtMutS haplotypes formed one well-supported clade within which no population structure was detected, also suggesting that intraspecific variation exists at mtMutS in Chrysogorgia. Despite an impressive decrease in the number of homologous loci across clades, RAD data helped us to fine-tune our interpretations of classical mitochondrial markers used in octocoral species delimitation, and discover previously undetected diversity.

https://hal.archives-ouvertes.fr/hal-01064545/document

Use of RAD sequencing for delimiting species

Publisher Summary This chapter discusses the taxonomy, phylogeny, biogeography, ecology, and reproductive biology of deep-sea octocorals and also focuses on gorgonian octocorals because they are the predominant octocoral group in the deep sea. The most widely accepted taxonomic scheme for octocorals divides the subclass into four orders: (1) helioporacea, (2) alcyonacea, (3) gorgonacea, and (4) pennatulacea. The distinctions between most orders and suborders are blurred by intermediate taxa that resulted in a continuum of colonial organization and skeletal structure. The major areas of study of deep-sea gorgonians and sources of species descriptions are also summarized. Octocorals have been known from deep water in the North Atlantic, although the Challenger expedition showed that octocorals could be found in the depths of all oceans. Knowledge of deep-water octocorals of the Indo-West Pacific region is meagre and contrasts with the wealth of information on shallow-water taxa. The distribution of the three major deep-sea families' discussed are––chrysogorgiidae, isididae, and primnoidae. Deep-sea octocoral colonies are often large so it offers a wide range of biogenic habitats to other invertebrate species. The chapter also focuses on those invertebrate species that are found most frequently on the octocoral host. Reproduction, growth, age, food habits, and conservation issues are also considered.

Biology of deep-water octocorals.

The cumulative impacts (i.e. collective, multi-year effects) of seasonal commercial shrimp trawling on habitat and macrofaunal community structure were investigated for two mud-bottom fishing grounds and adjacent untrawled areas in the Gulf of Maine. Habitat structure on mud-bottom fishing grounds did not differ significantly from that in similar untrawled areas. Moreover, sediment resuspension associated with shrimp trawling did not appear to result in net loss of deposited material on fishing grounds, but there is evidence that trawling may alter sediment mixing regimes. Visual inspection of the sediment surface in trawled areas revealed minimal evidence of fishing gear disturbance (such as door, bobbin, or net marks), but biological disturbance features, including numerous large burrows, pits, and dense aggregations of the brittle star Ophiura sarsi, were present in both trawled and untrawled areas. Macrofaunal communities on the two fishing grounds exhibited different responses to shrimp trawling, which were attributed to disparities in levels of fishing activity during the 2000-2001 shrimp season. The results suggest that seasonal shrimp trawling produced at least short-term changes (<3 months) in macrofaunal community structure, but did not appear to result in long-term cumulative changes. Resilience to trawling disturbance may be due in part to high levels of biological disturbance generated by benthic megafauna, such as lobsters and fish. By burrowing, pit-digging, and possibly foraging, these animals rework sediments to a depth of 16-17 cm, creating a natural level of disturbance that appears to maintain macrofaunal communities in a perpetually low successional state, so potentially minimizing trawling impacts.

/pdf/an-investigation-of-the-cumulative-impacts-of-shrimp-22j4abqqu0.pdf

An investigation of the cumulative impacts of shrimp trawling on mud-bottom fishing grounds in the Gulf of Maine: effects on habitat and macrofaunal community structure

Two new species belonging to the precious coral genus Corallium were collected during a series of exploratory cruises to the New England and Corner Rise Seamounts in 2003―2005. One red species, Corallium bathyrubrum sp. nov., and one white species, C. bayeri sp. nov., are described. Corallium bathyrubrum is the first red Corallium to be reported from the western Atlantic. An additional species, C. niobe Bayer, 19 6 4 originally described from the Straits of Florida, was also collected and its description augmented.

/pdf/precious-corals-coralliidae-from-north-western-atlantic-18hz8los5o.pdf

Anne Simpson

Papers

Biology of deep-water octocorals.

An investigation of the cumulative impacts of shrimp trawling on mud-bottom fishing grounds in the Gulf of Maine: effects on habitat and macrofaunal community structure

Precious Corals (Coralliidae) from North-Western Atlantic Seamounts