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Arrizabalaga, H., Dufour, F., Kell, L., Merino, G., Ibaibarriaga, L., Chust, G., et al. (2015). Global habitat preferences of commercially valuable tuna. Deep Sea Research Part II: Topical Studies in Oceanography, 113, 102–112.
Résumé: In spite of its pivotal role in future implementations of the Ecosystem Approach to Fisheries Management, current knowledge about tuna habitat preferences remains fragmented and heterogeneous, because it relies mainly on regional or local studies that have used a variety of approaches making them difficult to combine. Therefore in this study we analyse data from six tuna species in the Pacific, Atlantic and Indian Oceans in order to provide a global, comparative perspective of habitat preferences. These data are longline catch per unit effort from 1958 to2007 for albacore, Atlantic bluefin, southern bluefin, bigeye, yellowfin and skipjack tunas. Both quotient analysis and Generalized Additive Models were used to determine habitat preference with respect to eight biotic and abiotic variables. Results confirmed that, compared to temperate tunas, tropical tunas prefer warm, anoxic, stratified waters. Atlantic and southern bluefin tuna prefer higher concentrations of chlorophyll than the rest. The two species also tolerate most extreme sea surface height anomalies and highest mixed layer depths. In general, Atlantic bluefin tuna tolerates the widest range of environmental conditions. An assessment of the most important variables determining fish habitat is also provided.
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Aubin, J., Callier, M., Rey-Valette, H., Mathe, S., Wilfart, A., Legendre, M., et al. (2019). Implementing ecological intensification in fish farming: definition and principles from contrasting experiences. Rev. Aquac., 11(1), 149–167.
Résumé: Ecological intensification is a new concept in agriculture that addresses the double challenge of maintaining a level of production sufficient to support needs of human populations and respecting the environment in order to conserve the natural world and human quality of life. This article adapts this concept to fish farming using agroecological principles and the ecosystem services framework. The method was developed from the study of published literature and applications at four study sites chosen for their differences in production intensity: polyculture ponds in France, integrated pig and pond polyculture in Brazil, the culture of striped catfish in Indonesia and a recirculating salmon aquaculture system in France. The study of stakeholders' perceptions of ecosystem services combined with environmental assessment through Life Cycle Assessment and Emergy accounting allowed development of an assessment tool that was used as a basis for co-building evolution scenarios. From this experience, ecological intensification of aquaculture was defined as the use of ecological processes and functions to increase productivity, strengthen ecosystem services and decrease disservices. It is based on aquaecosystem and biodiversity management and the use of local and traditional knowledge. Expected consequences for farming systems consist of greater autonomy, efficiency and better integration into their surrounding territories. Ecological intensification requires territorial governance and helps improve it from a sustainable development perspective.
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Aubin, J., Fontaine, C., Callier, M., & Roque d'orbcastel, E. (2018). Blue mussel (Mytilus edulis) bouchot culture in Mont-St Michel Bay: potential mitigation effects on climate change and eutrophication. Int. J. Life Cycle Assess., 23(5), 1030–1041.
Résumé: Bivalve production is an important aquaculture activity worldwide, but few environmental assessments have focused on it. In particular, bivalves' ability to extract nutrients from the environment by intensely filtering water and producing a shell must be considered in the environmental assessment. LCA of blue mussel bouchot culture (grown out on wood pilings) in Mont Saint-Michel Bay (France) was performed to identify its impact hotspots. The chemical composition of mussel flesh and shell was analyzed to accurately identify potential positive effects on eutrophication and climate change. The fate of mussel shells after consumption was also considered. Its potential as a carbon-sink is influenced by assumptions made about the carbon sequestration in wooden bouchots and in the mussel shell. The fate of the shells which depends on management of discarded mussels and household waste plays also an important role. Its carbon-sink potential barely compensates the climate change impact induced by the use of fuel used for on-site transportation. The export of N and P in mussel flesh slightly decreases potential eutrophication. Environmental impacts of blue mussel culture are determined by the location of production and mussel yields, which are influenced by marine currents and the distance to on-shore technical base. Bouchot mussel culture has low environmental impacts compared to livestock systems, but the overall environmental performances depend on farming practices and the amount of fuel used. Changes to the surrounding ecosystem induced by high mussel density must be considered in future LCA studies.
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Auguet, J. C., Barberan, A., & Casamayor, E. O. (2010). Global ecological patterns in uncultured Archaea. Isme J, 4(2), 182–190.
Résumé: We have applied a global analytical approach to uncultured Archaea that for the first time reveals well-defined community patterns along broad environmental gradients and habitat types. Phylogenetic patterns and the environmental factors governing the creation and maintenance of these patterns were analyzed for c. 2000 archaeal 16S rRNA gene sequences from 67 globally distributed studies. The sequences were dereplicated at 97% identity, grouped into seven habitat types, and analyzed with both Unifrac (to explore shared phylogenetic history) and multivariate regression tree (that considers the relative abundance of the lineages or taxa) approaches. Both phylogenetic and taxon-based approaches showed salinity and not temperature as one of the principal driving forces at the global scale. Hydrothermal vents and planktonic freshwater habitats emerged as the largest reservoirs of archaeal diversity and consequently are promising environments for the discovery of new archaeal lineages. Conversely, soils were more phylogenetically clustered and archaeal diversity was the result of a high number of closely related phylotypes rather than different lineages. Applying the ecological concept of 'indicator species', we detected up to 13 indicator archaeal lineages for the seven habitats prospected. Some of these lineages (that is, hypersaline MSBL1, marine sediment FCG1 and freshwater plSA1), for which ecological importance has remained unseen to date, deserve further attention as they represent potential key archaeal groups in terms of distribution and ecological processes. Hydrothermal vents held the highest number of indicator lineages, suggesting it would be the earliest habitat colonized by Archaea. Overall, our approach provided ecological support for the often arbitrary nomenclature within uncultured Archaea, as well as phylogeographical clues on key ecological and evolutionary aspects of archaeal biology.
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Auguet, J. C., Borrego, C. M., Baneras, L., & Casamayor, E. O. (2008). Fingerprinting the genetic diversity of the biotin carboxylase gene (accC) in aquatic ecosystems as a potential marker for studies of carbon dioxide assimilation in the dark. Environ Microbiol, 10(10), 2527–2536.
Résumé: We designed and tested a set of specific primers for specific PCR amplification of the biotin carboxylase subunit gene (accC) of the Acetyl CoA carboxylase (ACCase) enzyme. The primer set yielded a PCR product of c. 460 bp that was suitable for denaturing gradient gel electrophoresis (DGGE) fingerprinting followed by direct sequencing of excised DGGE bands and sequence analysis. Optimization of PCR conditions for selective amplification was carried out with pure cultures of different bacteria and archaea, and laboratory enrichments. Next, fingerprinting comparisons were done in several aerobic and anaerobic freshwater planktonic samples. The DGGE fingerprints showed between 2 and 19 bands in the different samples, and the primer set provided specific amplification in both pure cultures and natural samples. Most of the samples had sequences grouped with bacterial accC, hypothetically related to the anaplerotic fixation of inorganic carbon. Some other samples, however, yielded accC gene sequences that clustered with Crenarchaeota and were related to the 3-hydroxypropionate/4-hydroxybutyrate cycle of autotrophic crenarchaeota. Such samples came from oligotrophic high mountain lakes and the hypolimnia of a sulfide-rich lake, where crenarchaeotal populations had been previously reported by 16S rRNA surveys. This study provided a fast tool to look for presence of accC genes in natural environments as potential marker for studies of carbon dioxide assimilation in the dark. After further refinement for better specificity against archaea, the new and novel primers could be very helpful to establish a target for crenarchaeota with implications for our understanding of archaeal carbon biogeochemistry.
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