A bulk of the criticism to commercial fisheries comes from the assumption that all fishing activities are based on trawling. The arguments are that all trawling caused an irreparable impact on the benthic communities, that trawlers are the "bulldozers or the sea", and so on. Of course, as with most things in life (including fisheries), nothing is totally dichotomic... while there is impact (as with any human activity) the extent depends on the specific benthos, the type of gear, the target species and so on.
While there is semi-pelagic trawling (meaning does not touch the bottom), this gear is not used for tuna, (not if you were to believe this terrible post!) Yet having started my fisheries life in trawlers in the south Atlantic, I was quite interested in reading this paper, as it will become the reference for any further studies or claims of the real impacts of trawling.
Is a thorough job, done by a quite amazing number of very well know scientists from 10 different universities and organisations (including FAO).
I quote the abstract here, but as always advised, go to the original!
Bottom trawling is the most widespread human activity affecting seabed habitats. Here, we collate all available data for experimental and comparative studies of trawling impacts on whole communities of seabed macroinvertebrates on sedimentary habitats and develop widely applicable methods to estimate depletion and recovery rates of biota after trawling. Depletion of biota and trawl penetration into the seabed are highly correlated. Otter trawls caused the least depletion, removing 6% of biota per pass and penetrating the seabed on average down to 2.4 cm, whereas hydraulic dredges caused the most depletion, removing 41% of biota and penetrating the seabed on average 16.1 cm. Median recovery times post-trawling (from 50 to 95% of unimpacted biomass) ranged between 1.9 and 6.4 y. By accounting for the effects of penetration depth, environmental variation, and uncertainty, the models explained much of the variability of depletion and recovery estimates from single studies. Coupled with large-scale, high-resolution maps of trawling frequency and habitat, our estimates of depletion and recovery rates enable the assessment of trawling impacts on unprecedented spatial scales.