Characterization of microbial communities from coastal waters using microarrays

Molecular methods, including DNA probes, were used to identify and enumerate pathogenic Vibrio species in the Chesapeake Bay; our data indicated that Vibrio vulnificus exhibits seasonal fluctuations in number. Our work included a characterization of total microbial communities from the Bay; development of microarrays that identify and quantify the diversity of those communities; and observation of temporal changes in those communities. To identify members of the microbial community, we amplified the 16S rDNA gene from community DNA isolated from a biofilm sample collected from the Chesapeake Bay in February, 2000. The resultant 75 sequences were 95% or more similar to 7 species including two recently described Shewanella species, baltica and frigidimarina, that have not been previously isolated from the Chesapeake. When the genera of bacteria from biofilm after culturing are compared to those detected by subcloning amplified 16S fragments from community DNA, the cultured sample exhibited a strong bias. In oysters collected in February, the most common bacteria were previously unknown. Based on our 16S findings, we are developing microarrays to detect these and other microbial species in these estuarine communities. The microarrays will detect each species using four distinct loci, with the multiple loci serving as an internal control. The accuracy of the microarray will be measured using sentinel species such as Aeromonas species, Escherichia coli, and Vibrio vulnificus. Using microarrays, it should be possible to determine the annual fluctuations of bacterial species (culturable and non-culturable, pathogenic and non-pathogenic). The data may be applied to understanding patterns of environmental change; assessing the health of the Bay; and evaluating the risk of human illness associated with exposure to and ingestion of water and shellfish.     

Temporal and spatial variations of nutrients in the Ten Mile Creek of South Florida, USA and effects on phytoplankton biomass

Water quality throughout south Florida has been a major concern for many years. Nutrient enrichment in the Indian River Lagoon (IRL) is a major surface water issue and is suggested as a possible cause of symptoms of ecological degradation. In 2005-06, water samples were collected weekly from seven sites along Ten Mile Creek (TMC), which drains into the Indian River Lagoon, to investigate and analyze spatial and temporal fluctuations of nutrients nitrogen (N) and phosphorus (P). The objective of this study was to understand the relationships among chlorophyll a concentration, nutrient enrichment and hydrological parameters in the surface water body.High median concentrations of total P (TP, 0.272 mg L(-1)), PO4-P (0.122 mg L(-1)), and dissolved total P (DTP, 0.179 mg L(-1)); and total N (TN, 0.988 mg L(-1)), NO3(-)-N (0.104 mg L(-1)), NH4+-N (0.103 mg L(-1)), and total Kjeldahl N (TKN, 0.829 mg L(-1)), were measured in TMC. The concentrations of TP, PO4-P, DTP, TN, NO3(-)-N, NH4+-N, and TKN were higher in summer and fall than in winter and spring. However, chlorophyll a and pheophytin concentrations during this period in TMC varied in the range of 0.000-60.7 and 0.000-17.4 microg L(-1), with their median values of 3.54 and 3.02 microg L(-1), respectively. The greatest mean chlorophyll a (10.3 microg L(-1)) and pheophytin (5.71 microg L(-1)) concentrations occurred in spring, while the lowest chlorophyll a (1.49 microg L(-1)) and pheophytin (1.97 mug L(-1)) in fall. High concentrations of PO4-P (>0.16 mg L(-1)), DTP (>0.24 mg L(-1)), NO3(-)-N (>0.15 mg L(-1)), NH4+-N (>0.12 mg L(-1)), and TKN (>0.96 mg L(-1)), occurred in the upstream of TMC, while high concentrations of chlorophyll a (>6.8 mug L(-l)) and pheophytin (>3.9 microg L(-l)) were detected in the downstream of TMC. The highest chlorophyll a (11.8 mug L(-l)) and pheophytin (6.06 microg L(-l)) concentrations, however, were associated with static and open water conditions. Hydrological parameters (total dissolved solid, electrical conductivity, salinity, pH, and water temperature) were positively correlated with chlorophyll a and pheophytin concentrations (P < 0.01) and these factors overshadowed the relationships between N and P concentrations and chlorophyll a under field conditions. Principal component analysis and the ratios of DIN/DP and TN/TP in the water suggest that N is the limiting nutrient factor for phytoplankton growth in the TMC and elevated N relative to P is beneficial to the growth of phytoplankton, which is supported by laboratory culture experiments under controlled conditions.     

Municipal waste compost as an alternative to cattle manure for supplying potassium to lowland rice

The importance of the use of potassium in agriculture is increasing in South Asia for making most productive use of the nutrient in terms of economic returns. Nutrient supply traditionally by cattle manure is constrained by its insufficient availability. Municipal waste compost may be an alternative source of nutrient supplements. Field experiments were conducted at the Experimental Farm of Calcutta University, West Bengal, India during the wet seasons of 1997, 1998 and 1999 on flooded lowland rice. Potassium fractions in municipal waste compost and cattle manure were determined by sequential extraction and also the potassium uptake by rice to compare the effectiveness of municipal waste compost with traditional manure. Potassium was significantly bound to the organic matter in municipal waste compost. Potassium uptake by rice grain and straw increased significantly with the combined application of organics and fertilizers and it was higher in grain than in straw. Water-soluble and non-exchangeable potassium contents of municipal waste compost and cattle manure were highly correlated with the uptake of potassium by straw and grain. Exchangeable and residual potassium were also significantly correlated with the uptake of potassium by straw and grain of rice. Much higher uptake of K in rice straw and rain resulted from applying the manures in conjunction with fertilizers than when applied singly.     

Assessing inter-laboratory comparability and limits of determination for the analysis of cyclic volatile methyl siloxanes in whole Rainbow Trout (Oncorhynchus mykiss)

Cyclic volatile methyl siloxanes (cVMS) are high volume production chemicals used in a wide range of industrial and consumer products. Three cVMS compounds (D4, D5, and D6) have and are undergoing environmental risk evaluations in several countries and have been proposed for legal regulation in Canada. As interest in monitoring concentrations of these chemicals in the environment increase, there is a need to evaluate the analytical procedures for cVMS in biological matrices in order to assess the quality of data produced. The purpose of this study was to determine laboratory testing performance for measuring residues of D4, D5, and D6 in a standard set of fish homogenate samples and to estimate limits of determination for each substance. The samples sent to each laboratory consisted of homogenized whole body tissues of hatchery raised rainbow trout which were fed food fortified with D4, D5, and D6 (dosed) and trout that were fed standard food rations (control). The participants analyzed each sample using their analytical method of choice using their own standards and procedures for quantification and quality control. With a few exceptions, participating laboratories generated comparable results for D4, D5, and D6 in both the dosed and control samples having z-scores between 2 and −2. Method detection limits for the whole fish matrix were on average 2.4 ng g⁻¹ ww for D4, 2.3 ng g⁻¹ ww for D5, and 1.8 ng g⁻¹ ww for D6.     

Rapid prenatal diagnosis of Patau's syndrome in a fetus with an abdominal wall defect by 72 hour culture of cells from amniotic fluid

A woman in the 32nd week of pregnancy was referred for investigation because of fetal abnormalities, including an abdominal wall defect, detected by ultrasonography. In view of the increased risk of chromosome abnormality, amniocentesis was performed to enable informed decisions about the management of the pregnancy and delivery to be taken. Cells from the liquor were inoculated into standard lymphocyte culture medium and incubated for 72 h. Slides with a high mitotic index and good quality metaphases, comparable to those from a blood culture, were obtained after harvesting. Cytogenetic analysis showed the karyotype to be 46,XY,—14,+t(13ql4q), which is consistent with Patau's syndrome. This technique appears to be an option for rapid karyotyping in cases of abdominal wall defect, where a chromosomal abnormality is suspected.     

ITERATIVE EVALUATION OF A LAKE WATER QUALITY MANAGEMENT PROGRAM1

ABSTRACT: Local governments often face environmental problems that cross political boundaries. The onus for solution usually falls on the moat severely affected jurisdiction, others do nothing until impacted. Resolution of these problems requires cooperation across political boundaries which means that local governments must be persuaded first that there is a problem, and second that action is required to solve it. This paper presents a method to supply low cost, credible information that can be used to achieve consensus on problem solution. A case study of a lake water quality management problem is described. Formative evaluation techniques was adapted to provide a minimum of evidence which was then used to persuade less impacted local jurisdictions to cooperate in the problem solution.     

Assessment of the effectiveness of scup bycatch-reduction regulations in the Loligo squid fishery

Discard reduction is a component of the statutory requirements of the Sustainable Fisheries Act. One species of concern is scup, Stenotomus chrysops, discarded in the Loligo pealei fishery. Initially, regulations were imposed restricting the fishery in time and space to avoid areas and times associated with high scup discarding. Modified gear was required in 2003 on any boat fishing in areas otherwise closed to the fishery to reduce scup discarding. The purpose of this study was to evaluate the success of the 2003 net regulations and the potential influence of time-area closures (GRAs) in achieving a reduction in scup discarding. The regulations are based on three expectations. (1) Reduction in discarding in the Loligo squid fishery will materially reduce total scup discarding. (2) Exclusion of Loligo squid fishing vessels from the GRAs will result in these vessels fishing in areas that inherently produce fewer scup discards without equivalently increasing discarding in other sensitive species. (3) The use of a square-mesh large-mesh section in the extension will reduce scup discarding to the extent that otherwise would be achieved if the boats fished outside the GRAs without the economic cost imposed by redeploying the fleet. Analysis of the NMFS-NEFSC observer database offers no support for the belief that Expectation 1 has been met. Squid catches were too low to sustain a directed fishery in the northern GRA during this study. Thus, had this area been open, limited scup discarding would have occurred. In this study, squid catches averaged 1025 kg tow(-1) in the southern GRA. Thus, had the GRA been open, Loligo fishing would have taken place. Yet, in the 34 tows taken by two vessels, not a single scup was caught. Redeployment of the fleet clearly increased scup discarding in 2003. Thus, Expectation 2 was not met. Field tests demonstrated that the implemented net modification can produce reduced catches of mostly smaller-sized finfish without impairing squid catch, but the data also indicate that this result may not be routinely achieved. Thus, Expectation 3 was not completely met. Implementation of the 2003 net regulation was likely premature, in that the specification was not adequate to guarantee the desired results. The history of the scup discarding issue in the Loligo squid fishery demonstrates that discard reduction cannot be accomplished without adequate prior evaluation of the sources of discards, without the requisite and concomitant experimental evaluation of the results of regulatory reform, and without adequate commercial-scale testing of prospective reforms prior to implementation.     

Use of cluster and principal component analyses to profile areas in California where ground water has been contaminated by pesticides

An empirical approach to profiling areas of ground water contamination by pesticides was devised that did not rely upon determining the level of vulnerability between land areas and that did not assume any particular pathway for ground water contamination. Climatic and soil data were obtained for 1-square mile sections of land in California where pesticide residues had been found in well water samples and the detection was attributed to legal agricultural applications. These sections were designated as known contaminated (KC) sections. Climate and soil data were also obtained for sections which lacked either well sampling data or a positive pesticide detection. These sections were designated as candidate sections. Statistical procedures were used to cluster groups of KC sections first with respect to climate characteristics and then with respect to soil characteristics. Principal components analysis (PCA) was used to construct a statistical profile of soil variables for each cluster of KC sections. A method based on the PCA was developed to compare the similarity of soil profiles derived for each KC section cluster to individual candidate sections. Since the profiling scheme was based only on data from KC sections, candidate sections that did not match any KC cluster profile could only be considered dissimilar to contaminated sections, receiving a status of not-classified. This profiling method is flexible and it can be revised to incorporate updated well sampling information.