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.

Recent progress in the identification and determination of freshwater phytoplankton in the natural environment

The biomass of the phytoplankton and its composition is one of the most important factors in water quality control. Determination of the phytoplankton assemblage is usually done by microscopic analysis (Utermöhl's method). Quantitative estimations of the biovolume, by cell counting and cell size measurements, are time-consuming and normally are not done in routine water quality control. Several alternatives have been tried: computer-based image analysis, spectral fluorescence signatures, flow cytometry and pigment fingerprinting aided by high performance liquid chromatography (HPLC). The latter method is based on the fact that each major algal group of taxa contains a specific carotenoid which can be used for identification and relative quantification of the taxa in the total assemblage. This article gives a brief comparative introduction to the different techniques available and presents some recent results obtained by HPLC-based pigment fingerprinting, applied to three lakes of different trophic status. The results show that this technique yields reliable results from different lake types and is a powerful tool for studying the distribution pattern of the phytoplankton community in relation to water depth. However, some restrictions should be taken into account for the interpretation of routine data.

Lune - 1992 surveys. Summary of results

This report summarises the routine monitoring surveys carried out in the River Lune and River Duddon estuaries during 1992. Data includes salinity, chloride, pH, nutrients and heavy metals.

River Lune juvenile fish stock assessment 1997 with particular reference to salmonids

This report presents data from the juvenile salmonid fish stock assessment which is part of the routine Environment Agency riverine monitoring programme. A total of 110 sites was electrofished throughout the Lune catchment between 15th July 1997 and 14th October 1997. These sites included 84 that had been previously sampled in the last comprehensive survey of the catchment, in 1991. The aim of this survey was to assess the distribution and abundance of juvenile salmon and trout in the River Lune catchment and to compare results with those of previous surveys.

Effects of photoperiod on growth of larvae and juveniles of the anemonefish Amphiprion melanopus

Rearing of anemonefishes is now relatively routine compared to the culture of cardinalfishes (Apogonidae) or angelfishes (Pomacanthidae). However, it is still a labor intensive, time intensive and expensive procedure. To reduce time and cost of rearing anemonefishes, experiments were undertaken to improve the methods for rearing Amphiprion melanopus. These experiments were conducted to determine the effect of the length of photoperiod on larval duration, growth to metamorphosis and early juvenile phase. Growth of larvae was significantly faster and the duration of the larval phase was significantly shorter, under a photoperiod of 16 hours light/8 hours dark, compared to the photoperiods of 12 hours light/12 hours dark and 24 hours light/0 hours dark.

The Ancillary Harvest of Atlantic Menhaden, Brevoortia tyrannus, Roe on the North Carolina Coast

Gravid Atlantic menhaden, Brevoortia tyrannus, are available along the central coast of North Carolina during the fall and are harvested by the purse-seine fleet from the port of Beaufort. Virtually all of the catch, sexually immature fish included, is reduces to fish meal, fish oil, and fish solubles; however, minor quantities of roe from ripening female menhaden are extracted for local consupmtion. Routine and selective port sampling information was used to characterize the seasonal and biostatistical nautre of the roe menhaden catches at Beaufort. Fishermen recognize two size classes of roe Atlantic menhaden: "forerunners," which are usually the smallest and earliest adult menhaden encountered in the Fall Fishery, and "mammy shad," which are the largest menhaden harvested and produce the greatest roe yields. Roe is extracted from femal fish at various points along the reduction process stream and by several techniques. Vessel cremen and factory personnel extract menhaden roe for personal and local consumption. Undetermined quantities of menhaden roe are channeled into local retail seafood markets. Wholesale prices are about $20 per gallon of roe, while retail prices are about $5 per pound. Carteret County, North Carolina, is probably the only area on the U.S. Atlantic and Gulf coasts where menhaden roe is sold in retail seafood markets. The potential of extracting menhaden roe for foreign markets is discussed

First Record of the Ragged-tooth Shark, Odontaspis ferox, off the U.S. Atlantic Coast

On 11 September 1994, a large shark was captured and later identified as the ragged-tooth shark, Odontaspis ferox (Risso). The shark was captured during routine bottom trawl survey operations onboard the NOAA R/V Albatross IV, approximately 25 n.mi. south-southeast of Cape Hatteras, N.C. (lat. 34° 51' N, long. 75° 26' W) with a “36 Yankee” bottom trawl towed at 3.5 knots. Average water depth at the time of capture was 173 m, bottom temperature was 17.8°C, and salinity was 36.41‰. Total length (cm), fork length (cm), weight (kg), and sex were recorded, the specimen was tagged, photographed, and returned live to t

The Atlantic and Gulf Menhaden Purse Seine Fisheries: Origins, Harvesting Technologies, Biostatistical Monitoring, Recent Trends in Fisheries Statistics, and Forecasting

With its genesis in New England during the 1800's, the purse seine fishery for Atlantic menhaden, Brevoortia tyrannus, expanded south and by the early 1900's ranged the length of the eastern seaboard. The purse seine fishery for Gulf menhaden. B. patronus, is of relatively recent development, exploitation of the stock beginning in the late 1940's. Landings from both fisheries annually comprise 35-40% of the total U. S. fisheries landings, ranking menhaden first in terms of volume landed. Technological advances in harvesting methods, fish-spotting capabilities, and vessel designs accelerated after World War II, resulting in larger, faster, and wider-ranging carrier vessels, improved speed and efficiency of the harvest, and reduction in labor requirements. Chief products of the menhaden industry are fish meal, fish oil, and solubles, but research into new product lines is underway. Since 1955 on the Atlantic coast and 1964 on the Gulf coast, the NMFS has monitored the fisheries for biostatistical data. Annual data summaries of numbers-of-fish-at-age harvested, catch tonnage, and fishing effort of the fleet form the basis of routine stock assessments and annual catch forecasts to industry for the upcoming fishing season. After landings declined in the 1960's, the Atlantic menhaden stock has recovered through the 1970's and 1980's. Exceptional year classes of Gulf menhaden in recent years account for record landings during the 1980's.

Life history and production of Capitella capitata (Polychaeta: Capitellidae) in Río de la Plata Estuary (Argentina)

A benthic survey was carried out from November 1998 to December 1999 in the tidal flats of Bahía Samborombón (Río de la Plata estuary, Argentina), in order to study the population structure, reproductive aspects, growth and secondary production of Capitella capitata (Fabricius, 1780). Growth was analyzed using ELEFAN routine, and the secondary production was estimated by Hynes and Coleman's method (1968). C. capitata did not present periods of very important recruitments throughout the year; however, the abundance of smallest size classes was higher during summer and autumn. The summer cohort showed a growth rate (K) of 2.05 and a seasonal growth oscillation (C) of 0.6, pointing out that worms grew very slowly during winter months. The life span of this cohort was 13 months. The autumn cohort showed a lower growth rate (K= 1.5) and its growth was lowest during winter. The life span was 15 months for this cohort. C. capitata in Punta Rasa presented an extended reproductive period, with absence of activity during winter months. The type of eggs and larvae suggest that C. capitata has benthic larval development in the study area, destining its reproductive effort to the production of a low number of eggs, and assuring larvae survival through incubation in brooding tubes. The annual mean biomass in Punta Rasa was 0.117 g m-2 (AFDW), with a mean secondary production of 0.23 g m-2 y-1 and a P/B ratio of 1.96 y-1. The relatively low density, biomass production and P/B ratio of C. capitata in Punta Rasa can be considered as reference values for this species inhabiting undisturbed or moderately disturbed areas.

Genetic evidence of two sibling species within the Contracoecum ogmorhini Johnson & Mawson 1941 complex (Nematoda; Anisakidae) from otariid seals in boreal and austral regions

Genetic variation of Contracaecum ogmorhini (sensu lato) populations from different otariid seals of the northern and southern hemisphere was studied on the basis of 18 enzyme loci as well as preliminary sequence analysis of the mitochondrial cyt b gene (260 bp). Samples were collected from Zalophus californianus in the boreal region and from Arctocephalus pusillus pusillus, A. pusillus doriferus and A. australis from the austral region. Marked genetic heterogeneity was found between C. ogmorhini (sensu lato) samples from the boreal and austral region, respectively. Two loci (Mdh-2 and NADHdh) showed fixed differences and a further three loci (Iddh, Mdh-1 and 6Pgdh) were highly differentiated between boreal and austral samples. Their average genetic distance was DNei = 0.36 at isozyme level. At mitochondrial DNA level, an average proportion of nucleotide substitution of 3.7% was observed. These findings support the existence of two distinct sibling species, for which the names C. ogmorhini (sensu stricto) and C. margolisi n. sp., respectively, for the austral and boreal taxon, are proposed. A description for C. margolisi n. sp. is provided. No diagnostic morphological characters have so far been detected; on the other hand, two enzyme loci, Mdh-2 and NADHdh, fully diagnostic between the two species, can be used for the routine identification of males, females and larval stages. Mirounga leonina was found to host C. ogmorhini (s.s.) inmixed infections with C. osculatum (s.l.) (of which C. ogmorhini (s.l.) was in the past considered to be a synonym) and C. miroungae; no hybrid genotypes were found,confirming the reproductive isolation of these three anisakid species. The hosts and geographical range so far recorded for C. margolisi n. sp. and C. ogmorhini (s.s.) are given.

Water quality monitoring in the Mersey

This is the Water Quality Monitoring in the Mersey Estuary report produced by the Environment Agency in 2001. This report focuses on the Water Quality Monitoring Programme held in the Mersey Estuary. Since the mid-1960s water samples have been collected at approximately monthly intervals along the length of the estuary between Warrington and New Brighton and in later years further off-shore. This data-set provides an invaluable resource to determine how the very large capital spending of recent years has resulted in the dramatic improvements in water quality that we are now able to record. Initially, the interest was focused on parameters such as dissolved oxygen, BOD, nutrients and suspended solids. Over the last decades, as analytical methods have improved, toxic metals and persistent organic compounds have been included in the routine monitoring programme at a limited number of sites. Moreover, with the introduction of the European Water Framework Directive monitoring programmes it was an opportune time to review the Mersey monitoring strategy. This revised monitoring programme required data from several other components (water, sediments, flora, fauna, fish and birds. This report also contains information about Routine monthly surveys, Special surveys, Chloralkali Directive, UKNMP, British Geological Survey, EDMAR and NERC Environmental Diagnostics Thematic Programme.

Intensive biological survey of the Glaze Brook catchment May 1981

This is the Intensive biological survey of the Glaze Brook catchment May 1981 report produced by the North West Water Authority in 1981. The aim of this report is to identify those pollution problems not identified during the routine biological water quality surveys, and to check the suitability of the routine biological sampling point. This report looks at an intensive biological water quality survey of the Glaze Brook catchment which was carried out by Biol. (S) on 13th-15th May, 1981. Kick samples of invertebrates were taken at 5 sites and all invertebrates were identified and counted in the field. The most significant water quality observations in the report were from: Borsdane brook, Pennington brook, Glaze brook, Amberswood brook, Cunningham brook, Old Mill brook, Shakerley brook, Astley brook and Shaw brook.

River Gowy rapid corridor survey July 1995. Ecology South Mersey

This is the River Gowy rapid corridor survey July 1995: Ecology South Mersey report produced by the National Rivers Authority North West Region in 1995. This report looks at the survey carried out by the South Mersey Ecology Team prior to routine deweeding operations on the main River Gowy at the end of July, 1995. The survey covered Flood Defence Stretch References RGOW03 to RGOW16. These stretches were further divided into a series of 43 stretches, each one being approximately 500m in length for ease o f mapping by Ecology. Recommendations for each length have been cross-referenced with the Bill of Quantities where possible, e.g. retention o f margins. In Flood Defence stretch RGOW03, the South West Winter Wetland forms an important habitat for birds. In stretches RGOW04 to RGOW05, the Gowy Meadows and Ditches have been designated a Grade A, Site of Biological Importance, by Cheshire County Council due to the nature of the acidic grassland and diverse ditches. In stretches RGOWIO to RGOW11 the left bank forms Hockenhull Platts, Grade A Site of Biological Importance and County Trust Reserve. In stretches RGOW15 to RGOW16, the area from Mill Farm to the Shropshire Union Canal is a Grade A Site of Biological Importance. These sites are very sensitive and detailed recommendations for working practices can be found in the relevant sections o f the survey.

The Kent estuary 1992 surveys. Summary of results

This is the Kent estuary 1992 surveys: Summary of results produced by the National Rivers Authority in 1993. The report summarises routine and baseline water quality surveys carried out on the Kent estuary during 1992. Baseline surveys are designed to respond to regional, national, and European requirements. During 1992 baseline surveys were carried out in June and December. Unfortunately, in June, samples could only be taken from stations 3, 7 and 8. For ease of interpretation the results have been presented in graph form, including the maximum and minimum parameter concentration and the appropriate Environmental Quality Standards (EQS). The parameters measured in this survey were physical parameters (temperature, BOD, dissolved oxygen, Ph, salinity, conductivity); nutrients (ammonia, phosphate, and nitrate); metals (Mercury, Nickel, Arsenic, Cadmium, Chromium, Cooper, Boron, and Zinc) and organic compounds.

Diel movements of fishes linked to benthic seascape structure in a Caribbean coral reef ecosystem

Many common fishes associated with Caribbean coral reef ecosystems use resources from more than 1 patch type during routine daily foraging activities. Few studies have provided direct evidence of connectivity across seascapes, and the importance of benthic seascape structure on movement behavior is poorly known. To address this knowledge gap, we coupled hydro-acoustic technology to track fish with seafloor mapping and pattern analysis techniques from landscape ecology to quantify seascape structure. Bluestriped grunts Haemulon sciurus and schoolmaster snapper Lutjanus apodus were tracked over 24 h periods using boat-based acoustic telemetry. Movement pathways, and day and night activity spaces were mapped using geographical information system (GIS) tools, and seafloor structure within activity spaces was mapped from high-resolution aerial photography and quantified using spatial pattern metrics. For both fish species, night activity spaces were significantly larger than day activity spaces. Fish exhibited a daytime preference for seascapes with aggregate coral reef and colonized bedrock, then shifted to night activity spaces with lower complexity soft sediment including sand, seagrass, and scattered coral/rock. Movement path complexity was negatively correlated with seascape complexity. This demonstrates direct connectivity across multiple patch types and represents the first study to apply quantitative landscape ecology techniques to examine the movement ecology of marine fish. The spatially explicit approach facilitates understanding to the linkages between biological processes and the heterogeneity of the landscape. Such studies are essential for identifying ecologically relevant spatial scales, delineating essential fish habitat and designing marine protected areas.