Sediment changes upstream and downstream of the Altnahinch Dam in the River Bush in Northern Ireland: A preliminary study

The River Bush must reach a standard of good ecological potential (GEP) by 2015 due to the requirements of the water framework directive. The role of sediments within a water body is extremely important to all aspects of a river's regime. The aim of this research is to investigate the effects of Altnahinch Dam on sediment distribution in the River Bush (a heavily modified water body) with comparison made against the Glendun River (an unmodified water body). Samples collected from the rivers were analysed by physical (pebble count, sieve analysis) and statistical methods (ANOVA, GRADISTAT). An increase in fine sediments upstream of the dam provides evidence that the dam is impacting sediment distribution. Downstream effects are not shown to be significant. The output of this study also implies similar impacts at other drinking water storage impoundments. This research recommends that a sediment management plan be put in place for Altnahinch Dam and that further studies be carried-out concentrating on fine sediment distribution upstream of the dam. 

An ecotoxicological approach to assessing the impact of tanning industry effluent on river health

A study was conducted to investigate the sediment health and water quality of the River Sagana, Kenya, as impacted by the local tanning industry. Chemical analysis identified the main chemical pollutants (pentachlorophenols and chromium) while a bioassay addressed pollutant bioavailability. The bioassay, exploiting the luminescence response of a lux marked bacterial biosensor, was coupled to a dehydrogenase and Dapnia magna test to determine toxicity effects on sediments. Results highlighted the toxicity of the tannery effluent to the sediments at the point of discharge (64% of control bioluminescence) with gradual improvement downstream. There was a significant increase in dehydrogenase downstream, with the enzyme activity attaining a peak at 600 m, also indicating a gradual reduction of toxicity. Biological oxygen demand (19.56 mg L(-1)) dissolved oxygen (3.97 mg L(-1)) and high lethal dose value (85%) of D. magna also confirmed an initial stress at the point of discharge and recovery downstream. Optical density of surface water demonstrated an increase in suspended particulates and colour after the discharge point, eventually decreasing beyond 400 m. In conclusion, the study highlighted the importance of understanding the biogeochemistry of river systems impacted by industries discharging effluent into them and the invaluable role of a biosensor-based ecotoxicological approach to address effluent hazards, particularly in relation to river sediments.

PCB congener dynamics in a heavily industrialized river catchment

PCB congener concentrations in the water column of a highly industrialized river catchment, the Aire/Calder, in N.E. England were determined weekly on a routine basis, and 2 hourly through selected high flow (flood) events. Bed, suspended and floodplain sediment PCB congener concentrations were also determined along transects of the rivers investigated. Weekly monitoring revealed that the sum of 11 quantified (Sigma11) PCBs rose in concentration by two orders of magnitude during late summer compared to their winter minimum values. This rise was concurrent with sustained periods of low flow. SigmaPCB concentrations were rapidly diluted during high flow (flood) events. Suspended sediment was, on average, 13 times more contaminated with PCBs than bed sediment, with means of 4.0 and 53.8 ng/g, respectively, while floodplain samples had an intermediate concentration of 29.8 ng/g. Principle components analysis (PCA) of congener profiles showed that all three sediment types were similar, but that congener profiles differed considerably between sediment and whole-water samples. There was no change in the percentage contribution of individual PCB congeners apparent from weekly whole-water monitoring. However, the congener pattern in whole-waters changed systematically during high flow events. PCA showed that whole-water samples collected during high flow events had progressively more sediment characteristics, and then returned to whole-water characteristics on cessation of the event. The PCA evidence, dilution of PCB concentrations during events, and suspended sediments more contaminated than bed sediments, indicate that the major sources of PCBs in this catchment are current inputs from sewage treatment works, rather than remobilization of bed sediments.

Molecular pedigree reconstruction and estimation of evolutionary parameters in a wild Atlantic salmon river system with incomplete sampling: a power analysis

Background: Pedigree reconstruction using genetic analysis provides a useful means to estimate fundamental population biology parameters relating to population demography, trait heritability and individual fitness when combined with other sources of data. However, there remain limitations to pedigree reconstruction in wild populations, particularly in systems where parent-offspring relationships cannot be directly observed, there is incomplete sampling of individuals, or molecular parentage inference relies on low quality DNA from archived material. While much can still be inferred from incomplete or sparse pedigrees, it is crucial to evaluate the quality and power of available genetic information a priori to testing specific biological hypotheses. Here, we used microsatellite markers to reconstruct a multi-generation pedigree of wild Atlantic salmon (Salmo salar L.) using archived scale samples collected with a total trapping system within a river over a 10 year period. Using a simulation-based approach, we determined the optimal microsatellite marker number for accurate parentage assignment, and evaluated the power of the resulting partial pedigree to investigate important evolutionary and quantitative genetic characteristics of salmon in the system.

Results: We show that at least 20 microsatellites (ave. 12 alleles/locus) are required to maximise parentage assignment and to improve the power to estimate reproductive success and heritability in this study system. We also show that 1.5 fold differences can be detected between groups simulated to have differing reproductive success, and that it is possible to detect moderate heritability values for continuous traits (h(2) similar to 0.40) with more than 80% power when using 28 moderately to highly polymorphic markers.

Conclusion: The methodologies and work flow described provide a robust approach for evaluating archived samples for pedigree-based research, even where only a proportion of the total population is sampled. The results demonstrate the feasibility of pedigree-based studies to address challenging ecological and evolutionary questions in free-living populations, where genealogies can be traced only using molecular tools, and that significant increases in pedigree assignment power can be achieved by using higher numbers of markers.

Genome analysis of a simultaneously predatory and prey-independent, novel Bdellovibrio bacteriovorus from the River Tiber, supports in silico predictions of both ancient and recent lateral gene transfer from diverse bacteria

BACKGROUND: Evolution equipped Bdellovibrio bacteriovorus predatory bacteria to invade other bacteria, digesting and replicating, sealed within them thus preventing nutrient-sharing with organisms in the surrounding environment. Bdellovibrio were previously described as "obligate predators" because only by mutations, often in gene bd0108, are 1 in ~1x10(7) of predatory lab strains of Bdellovibrio converted to prey-independent growth. A previous genomic analysis of B. bacteriovorus strain HD100 suggested that predatory consumption of prey DNA by lytic enzymes made Bdellovibrio less likely than other bacteria to acquire DNA by lateral gene transfer (LGT). However the Doolittle and Pan groups predicted, in silico, both ancient and recent lateral gene transfer into the B. bacteriovorus HD100 genome.

RESULTS: To test these predictions, we isolated a predatory bacterium from the River Tiber- a good potential source of LGT as it is rich in diverse bacteria and organic pollutants- by enrichment culturing with E. coli prey cells. The isolate was identified as B. bacteriovorus and named as strain Tiberius. Unusually, this Tiberius strain showed simultaneous prey-independent growth on organic nutrients and predatory growth on live prey. Despite the prey-independent growth, the homolog of bd0108 did not have typical prey-independent-type mutations. The dual growth mode may reflect the high carbon content of the river, and gives B. bacteriovorus Tiberius extended non-predatory contact with the other bacteria present. The HD100 and Tiberius genomes were extensively syntenic despite their different cultured-terrestrial/freshly-isolated aquatic histories; but there were significant differences in gene content indicative of genomic flux and LGT. Gene content comparisons support previously published in silico predictions for LGT in strain HD100 with substantial conservation of genes predicted to have ancient LGT origins but little conservation of AT-rich genes predicted to be recently acquired.

CONCLUSIONS: The natural niche and dual predatory, and prey-independent growth of the B. bacteriovorus Tiberius strain afforded it extensive non-predatory contact with other marine and freshwater bacteria from which LGT is evident in its genome. Thus despite their arsenal of DNA-lytic enzymes; Bdellovibrio are not always predatory in natural niches and their genomes are shaped by acquiring whole genes from other bacteria.

Storage of sediment-associated nutrients and contaminants in river channel and floodplain systems

Samples of fine-grained channel bed sediment and overbank floodplain deposits were collected along the main channels of the Rivers Aire (and its main tributary, the River Calder) and Swale, in Yorkshire, UK, in order to investigate downstream changes in the storage and deposition of heavy metals (Cr, Cu, Pb, Zn), total P and the sum of selected PCB congeners, and to estimate the total storage of these contaminants within the main channels and floodplains of these river systems. Downstream trends in the contaminant content of the <63 μm fraction of channel bed and floodplain sediment in the study rivers are controlled mainly by the location of the main sources of the contaminants, which varies between rivers. In the Rivers Aire and Calder, the contaminant content of the <63 μm fraction of channel bed and floodplain sediment generally increases in a downstream direction, reflecting the location of the main urban and industrialized areas in the middle and lower parts of the basin. In the River Swale, the concentrations of most of the contaminants examined are approximately constant along the length of the river, due to the relatively unpolluted nature of this river. However, the Pb and Zn content of fine channel bed sediment decreases downstream, due to the location of historic metal mines in the headwaters of this river, and the effect of downstream dilution with uncontaminated sediment. The magnitude and spatial variation of contaminant storage and deposition on channel beds and floodplains are also controlled by the amount of <63 μm sediment stored on the channel bed and deposited on the floodplain during overbank events. Consequently, contaminant deposition and storage are strongly influenced by the surface area of the floodplain and channel bed. Contaminant storage on the channel beds of the study rivers is, therefore, generally greatest in the middle and lower reaches of the rivers, since channel width increases downstream. Comparisons of the estimates of total storage of specific contaminants on the channel beds of the main channel systems of the study rivers with the annual contaminant flux at the catchment outlets indicate that channel storage represents <3% of the outlet flux and is, therefore, of limited importance in regulating that flux. Similar comparisons between the annual deposition flux of specific contaminants to the floodplains of the study rivers and the annual contaminant flux at the catchment outlet, emphasise the potential importance of floodplain deposition as a conveyance loss. In the case of the River Aire the floodplain deposition flux is equivalent to between ca. 2% (PCBs) and 36% (Pb) of the outlet flux. With the exception of PCBs, for which the value is ≅0, the equivalent values for the River Swale range between 18% (P) and 95% (Pb). The study emphasises that knowledge of the fine-grained sediment delivery system operating in a river basin is an essential prerequisite for understanding the transport and storage of sediment-associated contaminants in river systems and that conveyance losses associated with floodplain deposition exert an important control on downstream contaminant fluxes and the fate of such contaminants. © 2003 Elsevier Science Ltd. All rights reserved.