The effects of chemical pollution on the bioturbation potential of estuarine intertidal mudflats

Bioturbation by benthic infauna has important implications for the fate of contaminants as well as for changes to the sediment structure, chemistry and transport characteristics. There is an extensive literature dealing with the influence of sedimentary variables on the structure and function of infaunal marine and estuarine organisms but less is known of the converse, the influence of biota on sedimentary structure. Although some work has been carried out regarding spatial and temporal patterns of bioturbation, little attention has been given to the effects of pollution. The paper gives a framework of animal sediment relationships in an intertidal environment and discusses the general role of macrofauna in structuring and modifying sedimentary features. A brief outline of the various techniques used for quantifying the degree of bioturbation is given and some of these techniques have then been used to demonstrate the effect of a petrochemical discharge on the bioturbation potential of intertidal communities in the Humber estuary, eastern England. These studies indicate an increase in bioturbation with increasing distance from the source of pollution, not only because of differences in abundance, animal size and depth of activity but also because of the difference in species composition between the communities. As a means of interpreting the responses, the species present have been broadly classified in terms of their feeding strategy and sediment modification potential. The paper concludes by discussing the potential impact, in terms of effect on sediment transport, of selectively removing the different guilds (by pollution). Received: 8 February 1999 / Received in revised form: 10 May 1999 / Accepted: 14 May 1999     

The effects of manipulation of sedimentary iron and organic matter on sediment biogeochemistry and seagrasses in a subtropical carbonate environment

The microbial metabolism of organic matter (OM) in seagrass beds can create sulfidic conditions detrimental to seagrass growth; iron (Fe) potentially has ameliorating effects through titration of the sulfides and the precipitation of iron-sulfide minerals into the sediment. In this study, the biogeochemical effects of Fe availability and its interplay with sulfur and OM on sulfide toxicity, phosphorous (P) availability, seagrass growth and community structure were tested. The availability of Fe and OM was manipulated in a 2 × 2 factorial experiment arranged in a Latin square, with four replicates per treatment. The treatments included the addition of Fe, the addition of OM, the addition of both Fe and OM as well as no addition. The experiment was conducted in an oligotrophic, iron-deficient seagrass bed. Fe had an 84.5% retention efficiency in the sediments with the concentration of Fe increasing in the seagrass leaves over the course of the experiment. Porewater chemistry was significantly altered with a dramatic decrease in sulfide levels in Fe addition plots while sulfide levels increased in the OM addition treatments. Phosphorus increased in seagrass leaves collected in the Fe addition plots. Decreased sulfide stress was evidenced by heavier δ³⁴S in leaves and rhizomes from plots to which Fe was added. The OM addition negatively affected seagrass growth but increased P availability; the reduced sulfide stress in Fe added plots resulted in elevated productivity. Fe availability may be an important determinant of the impact that OM has on seagrass vitality in carbonate sediments vegetated with seagrasses.     

Heavy metal pollution in surface water and sediment: A preliminary assessment of an urban river in a developing country

The concentration and chemical fractionation of globally alarming six heavy metals (Cr, Ni, Cu, As, Cd and Pb) were measured in surface water and sediment of an urban river in Bangladesh. The decreasing trend of metals were observed in water as Cr > Cu > As > Ni > Pb > Cd and in sediment as Cr > Ni > Cu > Pb > As > Cd. The level of studied metals exceeded the safe limits of drinking water, indicated that water from this river is not safe for drinking and/or cooking purposes. However, the investigated metals showed low mobility except for Cd and Pb which could pose a severe threat to the aquatic environment. Contamination factor (CF) and geoaccumulation index (I_geo) demonstrated that most of the sediment samples were moderately to heavily contaminated by Cr, As, Cd and Pb. The pollution load index (PLI) values were above one (>1) indicates progressive deterioration of the sediment quality. The extent of pollution by heavy metals in the river Korotoa implies that the condition is much frightening to the biota and inhabitants in the vicinity of the river as well.     

Perspectives on measurement of denitrification in the field including recommended protocols for acetylene based methods

Of the biogeochemical processes, denitrification has perhaps been the most difficult to study in the field because of the inability to measure the product of the process. The last decade of research, however, has provided both acetylene and¹⁵N based methods as well as undisturbed soil core andin situ soil cover sampling approaches to implementing these methods. All of these methods, if used appropriately, give comparable results. Thus, we now have several methods, each with advantages for particular sites or objectives, that accurately measure denitrification in nature. Because of the general usefulness of the acetylene methods, updated protocols for the following three methods are given: gas-phase recirculation soil cores; static soil cores; and the denitrifying enzyme assay also known as the phase 1 assay. Despite the availability of these and other methods, denitrification budgets remain difficult to accurately establish in most environments because of the high spatial and temporal variability inherent in denitrification. Appropriate analysis of those data includes a distribution analysis of the data, and if highly skewed as is typically the case, the most accurate method to estimate the mean and the population variance is the UMVUE method (uniformly minimum variance unbiased estimator). Geostatistical methods have also been employed to improve spatial and temporal estimates of denitrification. These have occasionally been successful for spatial analysis but in the attempt described here for temporal analysis the approach was not useful.Discussions of the importance of denitrification have always focused on quantifying the process and whether particular measured quantities are judged to be a significant amount of nitrogen. A second line of evidence discussed here is the extant genetic record that results from natural selection. These analysis lead to the conclusion that strong selection for denitrification must currently be occurring, which implies that the process is of general significance in soils.     

Establishment of anaerobic,reducing conditions in lake sediment after deposition of acidic,aerobic sediment by a major storm

Hurricane Danny resulted in the rapid deposition of 10cm of oxidized, acidic sediment in the Contrary Creek arm of Lake Anna, Virginia. Several biological and geochemical parameters were monitored with time to ascertain how long it took the newly-deposited lake sediments to attain the anaerobic, circumneutral, actively sulfate-reducing state normally observed in this portion of the lake. The sediment platinum-electrode potential dropped from 350 mV to 100 mV within the first week after the storm. The pH of the pore water increased from 4.5 to 5.8 within three weeks, and titratable alkalinity was detected within two weeks and three weeks at 3 cm and 1 cm depths, respectively. Accumulation of reduced products of sulfate reduction (acid volatile sulfide) began by three to four weeks after the storm event. Both methanogens and sulfate reducers were present in high and approximately equal numbers in the freshly deposited material. The rapid neutralization of the acidity in the fresh sediment prior to the onset of sulfate reduction suggests that reactions other than sulfate reduction caused the initial increase in pH and alkalinity in this system.     

Fate of elemental sulfur in an intertidal sediment

Abstract: Sediment from a tidal flat at Wedderwarden, near the mouth of the Weser estuary, northern Germany, was amended with elemental sulfur, and concentrations of metabolic end products were monitored. The production of both sulfate and sulfide was consistent with disproportionation as the most important fate of the added elemental sulfur. A population of bacteria conducting active elemental sulfur disproportionation was also enriched from the sediment. In the enrichments, containing both elemental sulfur and Fe oxides as a sulfide 'scrub', sulfide and sulfate were produced in a ratio of     , somewhat lower than the predicted ratio of     . The mismatch between predicted and observed production ratios is explained by the channelling of electrons into autotrophic or mixotrophic CO₂ fixation rather than sulfide formation. The production of organic carbon, in the correct amount to explain the observed sulfide to sulfate production ratio, was verified by organic carbon analysis. Finally, rates of sulfate reduction were identical in the elemental sulfur amended sediment, and in control sediment with no added sulfur. Hence, the heterotrophic bacterial community was completely unaffected by an active metabolism conducting elemental sulfur disproportionation.     

Inhibition of nitrous oxide reduction by a component of Hamilton Harbour sediment

Abstract: A component of Hamilton Harbour sediment prevented nitrous oxide (N₂O) reduction in denitrification assays with a mixed population of endogenous bacteria and a pure culture (HH1) isolated from the sediment. A 5% (v/v) concentration of sediment in nutrient broth caused near maximum inhibition of N₂O reduction. Sediment taken from a site closer to pollution sources (Site 906) was twice as inhibitory (as measured by N₂O accumulation) as sediment from Site 910, further from pollution sources. N₂O persistence was associated with the particulate sediment fraction only. Several heavy metals were tested at in situ concentrations, and ionic cadmium (Cd) and chromium (Cr) caused N₂O accumulation. Ashed sediment did not cause N₂O accumulation, but did decrease initial nitrate reduction rates with HH1.     

A procedure for detecting structural domains in proteins.

A procedure is described for detecting domains in proteins of known structure. The method is based on the intuitively simple idea that each domain should contain an identifiable hydrophobic core. By applying the algorithm described in the companion paper (Swindells MB, 1995, Protein Sci 4:93-102) to identify distinct cores in multi-domain proteins, one can use this information to determine both the number and the location of the constituent domains. Tests have shown the procedure to be effective on a number of examples, even when the domains are discontinuous along the sequence. However, deficiencies also occur when hydrophobic cores from different domains continue through the interface region and join one another.     

Automatic recognition of hydrophobic clusters and their correlation with protein folding units.

A method is described to objectively identify hydrophobic clusters in proteins of known structure. Clusters are found by examining a protein for compact groupings of side chains. Compact clusters contain seven or more residues, have an average of 65% hydrophobic residues, and usually occur in protein interiors. Although smaller clusters contain only side-chain moieties, larger clusters enclose significant portions of the peptide backbone in regular secondary structure. These clusters agree well with hydrophobic regions assigned by more intuitive methods and many larger clusters correlate with protein domains. These results are in striking contrast with the clustering algorithm of J. Heringa and P. Argos (1991, J Mol Biol 220:151-171). That method finds that clusters located on a protein's surface are not especially hydrophobic and average only 3-4 residues in size. Hydrophobic clusters can be correlated with experimental evidence on early folding intermediates. This correlation is optimized when clusters with less than nine hydrophobic residues are removed from the data set. This suggests that hydrophobic clusters are important in the folding process only if they have enough hydrophobic residues.