RESUMO
The spatial and temporal changes in the bacterial communities associated with the Atlantic cod Gadus morhua were investigated using terminal restriction fragment length polymorphism (T-RFLP) analysis of 16S recombinant DNA (rDNA). Epidermal mucous was sampled from 366 cod caught in three harvest locations (Baltic, Icelandic, and North Seas) over three seasons (spring 2002, autumn 2002, and spring 2003), and an automated method for the high-throughput processing of environmental samples was developed using a Qiagen BioRobot. The analysis revealed that a diverse consortium of bacteria were found on fish; gamma-proteobacteria and Cytophaga-Flavobacter-Bacteroides (CFB) species were dominant. T-RFLP peak profiles suggested that operational taxonomic units (OTUs) related to Photobacterium sp., Psychrobacter sp., and Bacteroides sp. were common to all sites in all three seasons, but there were intersite variations in community composition. Cod caught from different seas had distinct reproducible bacterial assemblages. Whereas communities from fish caught in the Baltic and Icelandic Seas were relatively stable over the three seasons, those from fish from the North Sea changed significantly over time.
Assuntos
Bactérias/isolamento & purificação , Biodiversidade , Gadus morhua/microbiologia , Água do Mar/microbiologia , Animais , Oceano Atlântico , Bactérias/classificação , Bactérias/genética , DNA Bacteriano/genética , DNA Ribossômico/genética , Mucosa/microbiologia , Filogenia , Polimorfismo de Fragmento de Restrição , RNA Ribossômico 16S/genética , Estações do Ano , Análise de Sequência de DNARESUMO
The bacterial community inhabiting the mucus layer and surface of whiting was examined to determine whether the bacteria present are a reflection of the surrounding water or an indigenous bacterial flora is present. The outer mucus, mouth mucus and gut of four whiting harvested from a site in the Irish Sea and the surrounding water were examined by terminal restriction fragment length polymorphism (tRFLP) analysis of the 16S rRNA gene and clone library construction. The water community was the most diverse, with only a small number of shared water-mucus phylotypes present. The bacterial flora associated with the outer mucus layer were more diverse than that of the mouth mucus and gut. All three mucus layers were characterized by the presence of a dominant phylotype, identified as clone wom-1, highly similar to Photobacterium iliopiscarium. In addition to other Photobacterium phylotypes, members of the CFB and Clostridia groups were also detected. Subsequently, whiting from 11 different sites along the east and south coast of Ireland were compared by tRFLP analysis. Strikingly, the mucus layer of whiting at all sites was characterized by the presence and dominance of a TRF corresponding to the clone wom-1 which was virtually absent from the water column.
Assuntos
Bactérias/classificação , Bactérias/isolamento & purificação , Biodiversidade , Gadiformes/microbiologia , Muco/microbiologia , Água do Mar/microbiologia , Animais , Bactérias/genética , Análise por Conglomerados , Impressões Digitais de DNA , DNA Bacteriano/química , DNA Bacteriano/genética , DNA Ribossômico/química , DNA Ribossômico/genética , Intestinos/microbiologia , Irlanda , Dados de Sequência Molecular , Boca/microbiologia , Polimorfismo de Fragmento de Restrição , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Pele/microbiologiaRESUMO
Terminal restriction fragment length polymorphism (tRFLP) is a potentially high-throughput method for the analysis of complex microbial communities. Comparison of multiple tRFLP profiles to identify shared and unique components of microbial communities however, is done manually, which is both time consuming and error prone. This paper describes a freely accessible web-based program, T-Align (http://inismor.ucd.ie/~talign/), which addresses this problem. Initially replicate profiles are compared and used to generate a single consensus profile containing only terminal restriction fragments that occur in all replicate profiles. Subsequently consensus profiles representing different communities are compared to produce a list showing whether a terminal restriction fragment (TRF) is present in a particular sample and its relative fluorescence intensity. The use of T-Align thus allows rapid comparison of numerous tRFLP profiles. T-Align is demonstrated by alignment of tRFLP profiles generated from bacterioplankton communities collected from the Irish and Celtic Seas in November 2000. Ubiquitous TRFs and site-specific TRFs were identified using T-Align.
Assuntos
Bactérias/genética , Ecossistema , Técnicas Genéticas , Internet , Plâncton/genética , Polimorfismo de Fragmento de Restrição , Software , Primers do DNA , Especificidade da EspécieRESUMO
As well as serving valuable biodiversity conservation roles, functioning no-take fishery reserves protect a portion of the fishery stock as insurance against future over-fishing. So long as there is adequate compliance by the fishing community, it is likely that they will also sustain and even enhance fishery yields in the surrounding area. However, there are significant gaps in scientific knowledge that must be filled if no-take reserves are to be used effectively as fishery management tools. Unfortunately, these gaps are being glossed over by some uncritical advocacy. Here, we review the science, identify the most crucial gaps, and suggest ways to fill them, so that a promising management tool can help meet the growing challenges faced by coastal marine fisheries.
