General comments

This manuscript reports results from a comprehensive experimental investigation into the effects from two trawling gear types on Lanice conchilega habitats in the Vlakte van de Raan (Netherlands). Physical, biological and biogeochemical effects are well investigated and this work contributes significantly to the current evidence base, particularly regarding biochemical impacts from different gear types under varying environmental settings.

This paper matches well with the brief of the Biogeosciences journal, with other recent papers published in this journal on similar topics (e.g. Paradis, Pusceddu et al. (2019), De Borger, Tiano et al. (2021)). I would recommend the paper for publication after minor revisions.

General concerns:

• Reference sites: Reference site 2 seems to have significantly different grain size (Fig S1). Reference sites also have large variation in O2 consumption and species densities (Fig 6), as well as higher mean mixing rates (Table 2) and generally higher species densities when compared to treatment sites (Fig 6). Are these sites definitely representative of treatment sites? Information should be provided in the methods on how it was assured that all treatment sites and reference sites were generally environmentally representative of each other.
• Methods: It is not always clear how data analyses were undertaken e.g. Were the non-parametric tests undertaken in R and with what packages. How were the biological mixing models on bioturbation analysed, and with what software? Make sure sufficient detail is provided throughout the methods where necessary.
• Results: Some of the results seem superfluous. e.g SMP POC and TN; and backscatter testing between all pairwise combinations and factors. Throughout the manuscript, results should only be reported where they contribute to the narrative of the paper and are mentioned within the discussion. I realise it is tempting to report all results which were produced within the investigation but, results should be removed where they are superfluous to the narrative, discussions or conclusions.

Specific comments

L16: To add context it should be noted within the abstract that this is looking at “acute impacts by experimental disturbance from representative fishing gears”; or other similar phrasing conveying the same message.

L23: Taxon densities and species richness of what?

L35-36: It seems contradictory to say L. conchilega habitats are under “considerable threat” from bottom trawling, and then state that they have “biological resilience to bottom trawl impacts”.

L40: Alter to state “Bottom fishing affects carbon cycling on the seafloor” or “in seabed sediments”.

L42-43: again add “reduced mineralization of organic carbon in seabed sediments”.

L91: State the minimum distance experimental areas were separated by.

L92-93/Fig 1: It would be clearer if these three sampling stations (western, middle and eastern) were shown within the figure. E.g. with lined boxes.

L94: What was the size of the reference areas? How close were they to treatment areas?

L94: It would be good to give some descriptive information on how the different treatment and reference areas were determined to have similar/same environmental and biological settings.

L102: It would be clearer to move Table 1 to the supplementary material as it is overly detailed - simply put a descriptive sentence here (L102). E.g. that samples were collected between x-x hours before trawling and x-x hours after.  

L156-59: Here, and in other places within the methods (e.g. L141-146), you do not need to repeat the dates of sample collection if they are already reported in Table 1. If you want to add a brief descriptor in terms of time before/after trawling then try to be more general as suggested above (with reference to Table 1 for more detail).

L161: I think it would be clearer if this simply said “Two out of the three box cores were subsampled for sediment parameters from each treatment and reference station”.

L163: Did all of the sediment pass through 1mm? If not, was this fraction considered?

L179: Should be simplified to state “Pore water was collected from the same box cores as used for sediment parameter sampling”.

L293-295: The details of the results from all the different bio-mixing models do not seem to be reported. They should be present in a Supplementary table with the AIC scores for each model and the selected optimal model highlighted.

L230: LMMs were used to investigate what about the stated responses variables? Significant differences between T0 and T1 for each treatment separately? This needs to be explained better.

L250-253: There is no use/discussion of SPM POC and TN in the discussion. Remove from results as the information seems to be superfluous.

L269-270: Backscatter results seem overly explorative as much of the reported differences (or lack of differences) are not mentioned in the discussion. E.g. Why are you testing for differences between sites separate from the consideration of trawling impact?

L265: It is not clear where these statistical tests have been reported. The legends of Table S1 and Table S2 should be expanded so it is clear how statistical significance was determined.

L268-269: Again Fig 3 does not report the statistical tests. Where are these reported?

L270: Again, where are these p-values and pairwise differences reported? They are not shown in Fig. 3

L284-287: It is not clear what this adds to the story of the paper. Remove to aid clarity.

L287: In the methods “Robust regression analysis” is only discussed in relation to Section 2.7.4 (Impact of Lanice conchilega). It is not clear why/how it is used here.

L288-290: Add “between T0 and T1” to the end of this sentence to aid clarity.

L299-303: There is a lot in the results, to keep the focus of the reader I would remove this more descriptive information if it is not used later in this paper. Its presence in the supplementary is sufficient.

L311: Restructure sentence so it starts “For all fishing treatments….”. Just so it is clear you are no longer talking about just Tickler.

L343: It is not clear why Fig 3 is specifically referenced here.

L347-349: Remove this sentence. There is no need to introduce the discussion by saying you are going to “discuss”.

L360-369: Is it not also possible that increased current speeds would transport trawl-induced resuspended sediment away from potential sampling equipment more quickly, therefore reducing likely SPM effect? Or is it considered that the sampling equipment were too close to the trawl disturbance for this to be an influencing factor?

L376: Remove statement about variation between northern and southern plots. It does not add anything to the messaging of the paper.

L389: Some mention should be made into the significant difference in anoxic sediment in the reference sites between T0 and T1, and how this may influence results of treatment sites.

L394: Remove discussion of reference sites – again it is not clear how this contributes to the discussion and messaging of the paper in general.

L396: I think it is important to reiterate here that it was not statistically significant.

L406-407: This is already mentioned in Section 4.2; no need to repeat here.

L408: Change to “Despite the lower impact of Chl a”

L471-472: Rephrase, to remove “environmental benefit”. Fishing cannot really be said to have environmental benefit. Perhaps change to say “there is potential for reduced environmental impact from pulse trawls due to its higher catch efficiency……”.

L745: Alter to state “Example sediment profile imagery…”

Tables: Table 2 and Table 3 should be combined. This would aid clarity and there is no need for them to be separated.

Technical corrections

L134: I assume this is meant to state T1 rather than T2.

References mentioned

De Borger, E., et al. (2021). "Impact of bottom trawling on sediment biogeochemistry: a modelling approach." Biogeosciences 18: 2539–2557.

Paradis, S., et al. (2019). "Organic matter contents and degradation in a highly trawled area during fresh particle inputs (Gulf of Castellammare, southwestern Mediterranean)." Biogeosciences 16(21): 4307-4320.

General comments

This contribution presents results from an intense in situ experiment, investigating into trawling effects inflicted by different trawling gears on a shallow, 10 m water depth, sandy sediment inhabited by the polychaete Lanice conchilega, which locally forms dense tube “lawns”, here termed biogenetic “reefs”. The investigation encompasses physical impact on sediment structure, biological and biogeochemical effects thereof. It is well conducted and the data are by enlarge well interpreted; thus, this study is an important contribution to literature. The shallow water setting in particular, the different disciplines involved as well as a substantial data set on biogeochemical aspects of the impact, will make it a valuable publication.  

It will contribute both to publications in Biogeosciences and in other journals on this growing body of evidence. I recommend the manuscript for publication subject to minor revisions.

Major points

1. Bioturbation results …
   
   Did you average D_B from different models? This would involve averaging D_B representative of different portions of the overall particle transport (D_B represents all of transport in model 2, however only parts of the overall transport in higher models)
   
   Please comment on this and add information. This becomes particularly important in the context of results discussed in line 296, i.e. “physical trawling enhances D_B”_.
   
   
   
   
2. SCOC …
   
   Could you please comment on the unusually high absolute values (see also recent database by Stratmann et al. 2022)?
   
   SCOC of >400 mmol m^-2 d^-1 at ~500 g WW m^-2 conchilega or ~700 mmol m^-2 d^-1 at ~1400 g WW m^-2 seem at least questionable! My reasoning is as follows. The later biomass could be responsible for around 100 mmol oxygen m^-2 d^-1, if biomass-specific respiration is around 2.5 mg O₂ g^-1 h^-1 as for smaller sized polychaetes (e.g. Bennett and Rakocinski 2020). However, who or which additional process in a lawn of Lanice conchilega could respire an additional 600 mmol m^-2 d^-1?
   
   
   
   
3. The reference stations are not ideal in that they represent extremes in some measures and do not represent an expected average background (high oxygen demand, high faunal density, intense bioturbation). It is necessary to address this issue for it obviously raises the questions if the trawling effects can be and are at all compared to the references, or if they are only compared between T0 and T1 on trawling plots. Does the statistical analyses take care of this? It is hard to see this easily.

Specific comments

L 41: “maximize” does not seem the right word here. Alterations of sediment structure implies changes of (possibly steady-state) diagenetic conditions. “Impairing biogeochemical processes”?

L 61: the sentence would be more straightforward if it read: “With respect to sensitivity to direct impact and recovery potential, coarse sediment ecosystems characterized by high levels of natural disturbance typically display more resistance and resilience to bottom fishing …”

Fig 1: The insert dimensions are MUCH smaller (~1.8 km wide) than the square indicating the location on the left map in Figure 1 (~20 km wide). This is a bit misleading and could be changed by reducing the square’s size.

Tab 1: This table could easily move to supplements. It contains only background information that is not necessary for understanding the main text.

L 125: “wide” should be “width”

L 154: The total number of 69 box cores cannot be understood without the information that at R3 only T1 was sampled! A total would be 72 (2 times 3 replicates at 9+3 plots/reference station, i.e. 6 x 12=72). Not sampling R3 for T0 reduces this number by 3. Right? Reword to include that R3 only T1 was sampled.

L 171-177: Following these details describing the model “family” there is no information in lines 193 and thereafter as to why only D_B is reported.

Was there no non-local effect visible in the modeling results? Maybe report (some) of these results as well in the supplement. And consider the information in D_B as mentioned in the major points above.

L 187: incubation on board or at land, how much time to settle after coring impact?

2.7.3. (SPI and benthic sample analysis) after reading this and not acquainted with the specific analyses, my impression is that this allows to separate effects of T0 or T1 and temperature at the same station for the mentioned parameters?  Add some information explaining what the described procedure yields, please.  

Tables S1 and S2 have much too little information their respective legends. Please add.

L 268-270: if all these statistical results are provided with reference to Figure 3, they should be shown there. I cannot find that statistical information in Fig 3!

L 280 and thereafter: Some of the results reported here are somewhat superfluous for they display commonly known relations of sediment grain size and other sediment related parameters (coarser grain size is associated with less fines, more fine material usually correlates with more chlorophyll). Thus the passage could be a bit shorter.

Figures 6 and 7: why is SCOC (fig.7) called oxygen consumption in Fig 6? Are those not the same values as in Fig 7?

L 348: the passage “to physical, biogeochemical, and ecological characteristics” ios again mentioned in line 357 as “simultaneously investigates acute beam trawl impacts on biological (Rabaut et al., 2008), physical (Depestele et al., 2016) and biogeochemical dynamics”. I suggest removing it in line 348.

L 375 and thereafter: This is  a lot of text for little change seen or measured! Can it be reduced?

L 396: Did D_B really increase? It may well be so, however, an increased burial with more random mixing of sediments is not always the case. Increased mineralization of labile material may counteract overall burial. A more cautious wording, such as “it may result in altered OM diagenesis and nutrient cycling”, is warranted.

L 406: this is an unnecessary repletion of the bathymetry discussion above

L 420: Lanice additionally extends its tubes up to 20 cm below the surface. Therefore the subsequent sentence (line 22) sentence should state “… to organisms without pronounced protruding sediment surface structures.”    

L 464: This is a bit of discussion and maybe should not be in conclusions.

L 479: “removal of sedimentary carbon”; this is why above there should be no statement of enhanced D’B’ increasing burial!

Technical corrections

 L 525 “(Blackburn 1988)”  does not belong in this Breakman et al. 2010 citation       

Literatur

Bennett AD and Rakocinski CF (2020) Respiration by the Opportunistic Spionid Polychaete Streblospio gynobranchiata during Adjustment to and Recovery from Moderate Hypoxia. Diversity, 12, 73; doi:10.3390/d12020073