The impact of molecular biology on assessment of water quality: advantages and limitations of current techniques

The advent of molecular biology has had a dramatic impact on all aspects of biology, not least applied microbial ecology. Microbiological testing of water has traditionally depended largely on culture techniques. Growing understanding that only a small proportion of microbial species are culturable, and that many microorganisms may attain a viable but non-culturable state, has promoted the development of novel approaches to monitoring pathogens in the environment. This has been paralleled by an increased awareness of the surprising genetic diversity of natural microbial populations. By targeting gene sequences that are specific for particular microorganisms, for example genes that encode diagnostic enzymes, or species-specific domains of conserved genes such as 16S ribosomal RNA coding sequences (rrn genes), the problems of culture can be avoided. Technical developments, notably in the area of in vitro amplification of DNA using the polymerase chain reaction (PCR), now permit routine detection and identification of specific microorganisms, even when present in very low numbers. Although the techniques of molecular biology have provided some very powerful tools for environmental microbiology, it should not be forgotten that these have their own drawbacks and biases in sampling. For example, molecular techniques are dependent on efficient lysis and recovery of nucleic acids from both vegetative forms and spores of microbial species that may differ radically when growing in the laboratory compared with the natural environment. Furthermore, PCR amplification can introduce its own bias depending on the nature of the oligonucleotide primers utilised. However, despite these potential caveats, it seems likely that a molecular biological approach, particularly with its potential for automation, will provide the mainstay of diagnostic technology for the foreseeable future.

Advantages of using crest nets to sample presettlement larvae of reef fishes in the Caribbean Sea

Identifying the spatial and temporal patterns of larval fish supply and settlement is a key step in understanding the connectivity of meta-populations (Sale et al., 2005). Because of the potentially dispersive nature of the pelagic larval phase of most reef fishes, tracking cohorts from hatching to settlement is extremely difficult (but see Jones et al., 1999). However, for many studies it is sufficient to sample larvae immediately before settlement. Many coral reef fish species use mangrove and seagrass beds as nursery habitats (Nagelkerken et al., 2001; Mumby et al., 2004) and larvae of these species must pass over the reef crest in order to arrive at their preferred settlement habitats. The ability to sample this new cohort of larval fishes provides opportunities for researchers to explore the intricacies of the transition from larva to juvenile (Searcy and Sponaugle, 2001). Quantifying the potential settlers also provides valuable information about the spatial and temporal supply of presettlement larvae (Victor, 1986). Therefore a number of larval sampling methods were developed, one of which is the use of crest nets (Dufour and Galzin, 1993).

Advantages of liquid nitrogen freezing of Penaeus monodon over conventional plate freezing

Liquid nitrogen frozen products are biochemically and organoleptically superior to conventional plate frozen products but beneficial effect of liquid nitrogen freezing over conventional plate freezing can exist only up to 59 days at a commercial storage temperature of -18°C.