In many of the situations where dredges are used to gather these species it will be as part of a bottom cultivation operation. The shellfish are often from artificial beds established by the operator. In other circumstances dredges may be used to gather immature shellfish from ephemeral beds to be relaid in more stable situations.

Dredging - Investigations into the effects of oyster dredging and the use of modified oyster dredges to harvest clams have been shown to have direct effects on the sediment and associated fauna. The top 10-15 cm may be removed by the action of the dredge, sediment plumes created, and tracks made on the seabed. The gravel fraction in the sediment can be reduced and sediments become more anoxic after dredging²¹. All infauna to that depth can be removed in the short term. Segmented worms appear to be the most badly affected group whereas bivalves tend to be redistributed nearby²¹. The suspended sediment may also have an indirect effect on species some distance from the dredging operation if they are smothered and there can be detrimental effects on eel grass beds.

A study looking at the effects of mussel dredging in a sheltered fjord in Denmark showed an increase in suspended particular matter but a return to initial conditions after 1 hour³². There was a significant decrease in oxygen levels as a result of the dredging but generally little change in nutrient levels except in the case of ammonia. This work suggests that water quality can be reduced by mussel dredging because of increasing nutrient loads, oxygen consumption and possibly phytoplankton production. The total annual release of suspended particles as a consequence of mussel dredging at this site was nevertheless considered to be relatively unimportant compared with the total annual wind-induced resuspension^{32, 54}. Similarly the nutrient load entering the system from land was more significant than that caused by mussel dredging. Changes in the benthic flora and fauna as a consequence of repeated mussel dredging³² were considered to have a more severe effect than suspension of sediments and increased nutrient loads caused by the action of the dredges⁵⁴.

Recovery of habitats and species from these forms of dredging can take place but the timescale will vary depending on the conditions at the site and the outcome will not necessarily be identical to pre-dredging conditions⁷⁸. Tracks are likely to become infilled, although at low energy sites this may be with fine sediment, creating some habitat variation²¹. Species do not recover immediately (one short-term study showed no change within 8 days). However, with time, opportunistic polychaetes (bristle worms) and the surviving bivalves are thought to be likely early colonisers. Active polychaetes such as Eteone longa and more stable habitat species, such as Cirriformia tentaculata, may follow although continual disturbance will prevent recovery of communities typical of stable habitats²¹.

Hand gathering - Laboratory experiments studying the effects of digging on the short-shelled clam or sand gaper, Mya arenaria, suggest that the negative effects are likely to be limited to removal of market size clams and shell breakage of remaining ones²⁶. Exposure of other clams, and the placing of spoil on clams in adjacent areas, may however increase the susceptibility of unharvested clams on the flats to predation, desiccation, or freezing, depending on the substrate. Mortality is likely to be greater on muddy substrates compared to medium fine sand as clams exposed on sandy surfaces were able to re-establish their normal living depths whereas those on mud reburrowed to abnormally shallow depths. This work suggests that breaking up clumps in the tailings in sandy areas will make little difference to their survival as burial of clams in these conditions will probably not result in mortality whereas reducing tailing piles in muddy areas is likely to improve survival of buried and exposed clams²⁶.

A summary table shows the potential effects of fishing on estuaries, mudflats and sandflats not covered by seawater at low tide.

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