the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
Benthic foraminifera and gromiids from oxygen-depleted environments – survival strategies, biogeochemistry and trophic interactions
Nicolaas Glock
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- Final revised paper (published on 17 Aug 2023)
- Supplement to the final revised paper
- Preprint (discussion started on 07 Mar 2023)
- Supplement to the preprint
Interactive discussion
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CC1: 'Comment on bg-2023-49', Frans Jorissen, 31 Mar 2023
The review paper of Glock addresses concerns an exciting and rapidly evolving field of research. It comes very timely, and presents a good overview and perfect starting point for all scientists that want to know more about foraminifera living in anaerobic environments.
However, this first version is not perfect yet, and in my opinion, several points need to be addressed:
1. The taxonomy used in this paper.
Although taxonomy is not a central topic here, in order to avoid confusion, justice should be done to the important recent advances, largely resulting from the contribution of molecular studies. One of the problems is the treatment of species of the genus In some parts of the text, the author talks about A. tepida, a species name that was often used in the past for a complex of cryptic and pseudocryptic species that has only be sorted out recently. On lines 189-200 the author gives more detailed information and says that in that case, the text concerns “Ammonia sp. (T6)”, which is an informal name of a phylotype previously placed in the A. tepida morphocomplex. According to the most recent revision of this group of species (Hayward et al., 2021, Micropaleontology, 67; p. 109-313) the correct name of this phylotype is Ammonia confertitesta. I think that in the whole text, the taxonomy of Ammonia should be standardized, according to the 2021 revision of Hayward and coauthors.
A very similar case concerns the morphospecies Uvigerina peregrina. Also here, we are very probably confronted with a pseudocryptic species complex, but in case, things haven’t been sorted out yet. The consequence is that is impossible to treat U. peregrina as a single biological species, as the author is doing. When the author writes (lines 86-87) “Also, the NO3 - storage in U. peregrina shows a high variability, depending on the environment.”, it is very well possible that different biological species are concerned, and that the differences in nitrate storage are species-specific and have nothing to do with the environmental conditions.
A very similar situation, of species complexes with a multitude of cryptic and pseudocryptic species can be expected in the genera Nonionella and Globobulimina.
Although there is no ready solution for this problem, the author should take it into account, and realise that different species may be designed by the same species name, or inversely, different species names may indicate the same biological species. The author should show in the text that he is aware of this potential problem, and some of the conclusions should be reconsidered and be formulated with somewhat more reserve.
2. The synonymising of microhabitat and metabolic categories.
Both in lines 146-165 and in figure 4, the author states that epifaunal taxa are aerobic, shallow infaunal taxa are facultative anaerobes whereas deep infauna are facultative aerobes. Although this is certainly partly true, this seems to be a major oversimplification, for which the author gives insufficient justification.
First, it is not evident that all “epifauna” have necessarily an aerobic metabolism. In cases where bottom waters are strongly hypoxic, some typically epifaunal taxa may very well be facultative anaerobes or even facultative aerobes. As an example, I think of Epistominella smithi from the California foreland basins and the Peruvian margin. This large-sized species, which has never been described from well oxygenated sites, can reach high densities in strongly hypoxic settings, and its morphology very strongly suggests an epifaunal lifestyle.
Next, it is not evident either that all shallow infaunal taxa are facultative anaerobes, some definitely are not. Representatives of the Ammonia tepida morphogroup (A. aberdoveyensis, A. confertitesta) are good examples. Until to date, all tests trying to show anaerobic metabolism were negative for these taxa. Nevertheless, they are found massively in deeper sediment layers in estuarine mudflats, were they may survive the most adverse conditions by dormancy. But I would definitely consider them as shallow infaunal taxa with an aerobic metabolism.
Third, I have the least problems with considering deep infaunal taxa as facultative aerobes. But there is actually not a lot of evidence for the fact this. You would expect this, but it would be good if the author could give some arguments to strengthen this point.
Finally, I strongly regret that the author doesn’t mention “intermediate infauna”. The maximum abundance of these taxa is systematically found in the nitrate maximum zone; Melonis barleeanus is a typical example. These taxa are interesting, because most of them do not store nitrate (maybe because there is no reason to do so when you live in the nitrate maximum), but appear to be capable to denitrify.
And a detail: the legend of figure 4 is way too long, and repeats the running text.
3. Chapter 5: Applications in paleoceanography
This chapter didn’t convince me. The texts are very concise, and repeatedly the reader refers to the paper of Hoogakker et al., who treats this topic in much more detail. As it is, this chapter doesn’t add anything useful. I think the author should delete it altogether and expand some of the topics that would become more robust with a more deep-going treatment.
4. Minor points:
The title: I think that it is somewhat overdone: I don’t understand the plural form of the first words, and I would say that a review is always a synthesis. I would recommend something like : “Foraminifera from anaerobic environments - survival strategies, biogeochemistry and ecology – an overview”.
The cartoons presented in figures 1 and 6: these drawings are very nice (although somewhat simplistic), would be perfect in a text for a larger public, but are in my opinion not suitable for a scientific review paper.
Tables 2 and 3: these two tables are really the heart of this review paper. First, it is essential that the authors make it very clear that these tables are exhaustive, that they contain ALL published info available today. For me this became only progressively clear when reading the text. Next, unlike table 3, which is perfect, table 2 is a mess, all taxa are mixed without any visible order. Like for table 3, the taxa should be presented in alphabetical order. Finally, the signs used to indicate the different studies from which the data are taken are certainly artistic, but also unreadable. My mind is totally unfit to memorise such symbols, and I think it will be the same with many of our colleagues.
On several places the author is going too quickly, simply backs up a statement with a reference, but doesn’t tell on what evidence the statement is based. Some examples:
Lines 118-119: “It is noteworthy that denitrifying foraminifera from the Peruvian OMZ show a metabolic preference of NO3 - over O2 as an electron acceptor (Glock et al., 2019c).”
Lines 125-126: “Larger amounts of O2 might supply this demand but also harm the cell.”
Lines 134-135: “The fact that some foraminifera prefer NO3 over O2 as electron acceptor (Glock et al., 2019c)”.
Line 147: “since they are also able to respire O2.”
In none of these cases the author explains on what evidence these statements are based. Many similar examples are present in the text.
In all these cases, I would like that the author explains what evidence these important conclusions are based on. Since this is a review paper, the author should not oblige the reader to find such important information in another paper.
Lines 116-117: I feel that there is a slight contradiction here. On lines 92-94 the author indicates that foraminifera can denitrify without bacterial symbionts, whereas from lines 110-117 I understand that complete denitrification is not possible without bacterial symbionts.
Lines 207-208: “it is likely that dormancy is a common survival strategy under anoxia for foraminiferal species that don´t have an anaerobic metabolism”. I agree that dormancy is a logical alternative in case of absence of anaerobic metabolism, like in the various species of the A. tepida morphogroup. However, on line 182, as examples of dormancy, the author mentions Bulimina marginata, Stainforthia fusiformis and Adercotryma glomerata. The first two species have been shown to concentrate intracellular nitrate, and Stainforthia sp. has been shown to be able to denitrify. This would mean that we have also indications of dormancy in species which can denitrify. What makes the addition ”that don’t have an anaerobic metabolism” in the line cited above, incorrect, or at least incomplete. The author has to clarify this!
Lines 225-227: “Intertidal foraminifera are often exposed to hypoxic or even anoxic conditions,
when water stagnates during low tide or if they are transported to deeper anoxic sediment layers by bioturbation (Rybarczyk et al., 1996; Cesbron et al., 2017)”. These lines suggest that the author is not very familiar with intertidal environments. Things are much worse: on most intertidal mudflats, oxygen penetration is less than 1 mm, so that all forams are confronted with anoxia.
Lines 211-231: It should perhaps be useful to explain here that Haynesina germanica is very often found together with taxa of the Ammonia tepida morphogroup (Ammonia aberdoveyensis or Ammonia confertitesta), taxa which don’t have the ability to keep the ingested chloroplasts active.
Lines 308-310: “It is remarkable that there is so much evidence for phagotrophy on or by benthic foraminifera under anaerobic conditions and future studies might shed more light on predator prey interactions of benthic foraminifera in O2 depleted environments.” I think this is very much exaggerated. As far as I can see, evidence for foraminiferal phagotrophy under anaerobic conditions is very scarce. It seems to be limited to (rather indirect) evidence of Orsi et al. (2020).
As a final remark, although I appreciated the review, and found it very useful, I also think it emphases what we (think to) know, but doesn’t talk too much about the things we don’t know (yet). It would be good if the author could from time to time indicate some unsolved resolved questions, and, if possible, research strategies to answer these questions.
Citation: https://doi.org/10.5194/bg-2023-49-CC1 -
AC1: 'Response letter to review by Frans Jorissen', Nicolaas Glock, 15 May 2023
Dear Frans Jorissen,
thanks a lot for your detailed constructive feedback to the manuscript. I revised the manuscript according to the revisions by all three reviewers. In the attachments, you can find a pdf with a detailed point by point response to all the points of revision. I reworked the part about the microhabitats to avoid overgeneralization and to provide more evidence for the hypotheses. The paleo-part has been deleted according to your suggestions and just condensed to a paragraph in the introductions.
The main changes related to the reviews by the other two reviewers is a complete rework of the "ecology" section with a focus change on trophic interactions of foraminifera under O2 depletion and an extention about the discussion of other survival strategies of foraminifera under O2 depletion (for example symbiosis or peroxisome proliferation. These changes can be found in detail in my point-by-point response letters to the other reviews.
Best regards,
Nicolaas Glock
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AC1: 'Response letter to review by Frans Jorissen', Nicolaas Glock, 15 May 2023
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RC1: 'Comment on bg-2023-49', Andy Gooday, 01 Apr 2023
This manuscript gives a very useful review of biology of foraminifera that live where oxygen is absent or scarce. I found the section on survival strategies(1.3), together with the data summarized in Tables 1-3 and the figures, very interesting and informative. Section 1.5 on the role of foraminifera in nutrient cycling and biogeochemistry is also useful (although see the comment below). However, sections 1.4 (Ecology) and the final section
Specific comments
line 79, Table 2. Since the paper is about foraminifera, you should mention somewhere in the text that gromiids are not foraminifera but a separate group of protists within the Rhizaria.
- 8. Section 1.4 Ecology.
This is a brief and selective section about feeding, not a review of foraminiferal ecology. I would change the title to ‘Trophic interactions in oxygen-depleted environments’ or something similar. At the beginning, you might want to cite a few general reviews of feeding and diets in foraminifera, such as those of Lipps (1973, cited elsewhere) and Gooday et al. (1993, 2008). This would provide some context for feeding and diets in general. I have several other comments.
1) The Sagami Bay habitat is not strongly hypoxic, at least in terms of bottom water, and the observations of Nomaki probably apply to more oxygenated settings as well, particularly for the shallow infaunal species (Uvigerina akitaensis and Bolivina spissa).
2) In lines 325-326, you say that predation (‘phagotrophy’) is the main type of interaction in aerobic communities. Is phagotrophy synonymous with predation? I thought it applied to any ingested particle, not necessarily prey?
3) The same sentence seems to imply that foraminifera are mainly predators, which to me gives the impression that they are carnivores (as discussed in lines 319-324). I don’t believe this is correct. It’s true that there is increasing evidence that some foraminifera eat metazoans or other foraminifera, at least sometimes (e.g., review of Culver and Buzas, 2003), but in general, most forams seem to feed most of the time at a low trophic level on algae such as diatoms, bacteria, and decaying organic material, and form a link to higher trophic levels (Gooday et al., 1993; Nomaki et al., 2008). By predation you seem to mean consumption of mainly algae, bacteria, and sediment/degraded material (as described by Nomaki et al., 2005), which I would call herbivory, bacterivery and deposit feeding. Also, lines 325-333 are apparently about benthic communities generally, not specifically about forams, but the meaning is not clear and may give the wrong impression. I found this whole paragraph rather confusing.
4) What about dissolved organic matter (DOM)? This may also be important, including in Sagami Bay (Nomaki et al., 2011).
Culver S J, Buzas MA (2003). Predation on and by foraminifera. In Predator-Prey Interactions in the Fossil Record, ed. Patricia H. Kelley, Michael Kowalewski & Thor A. Hansen Kluwer Academic/Plenum Publishers, New York; pp. 7-32.
Gooday, AJ, Levin LA, Linke P, Heeger T. (1992b) The role of benthic foraminifera in deep-sea food webs and carbon cycling. In: Rowe GT and Pariente V (eds) Deep-Sea Food Chains and the Global Carbon Cycle. Kluwer Academic Publishers, p. 63-91.
Gooday, A.J., Nomaki, H. & H. Kitazato. 2008. Modern deep-sea benthic foraminifera: a brief review of their biodiversity and trophic diversity. In: Austin, W. E. N. & James, R. H. (eds) Biogeochemical Controls on Palaeoceanographic Environmental Proxies. Geological Society, London, Special Publications, 303, 97–119. DOI: 10.1144/SP303.8 0305-8719/08/
Nomaki, H., Ogawa, N.O., Ohkouchi, N., Suga, H., Toyofuku, T., Shimanaga, M., Nakatsuka, T., Kitazato, H., 2008. Benthic foraminifera as trophic links between phytodetritus and benthic metazoans: carbon and nitrogen isotopic evidence. Mar. Ecol. Prog. Ser. 357: 153–164, 2008
Nomaki, H., Ogawa, N.O., Takano, Y., Suga, H., Ohkouchi, N., Kitazato, H., 2011. Differing utilization of glucose and algal particulate matter by deep-sea benthic organisms of Sagami Bay, Japan. Mar. Ecol. Prog. Ser. 431, 11–24.
Section 1.5 Lines 376-379. Are the pristine shells live and those filled with phosphorite dead? Or are they dead in both cases? If the shells are dead, it might suggest that the phosphorite was deposited by some inorganic process. I thought that modern phosphorites in anoxic sediments were precipitated from interstitial porewater (e.g., Kolodny, 1981, Phosphorites. In: The Sea v. 7, The Oceanic Lithosphere). Please explain further or delete.
Subsection 1.5.1, p. 9-10. You finish this subsection rather abruptly with equations for estimating cell biovolume, denitrification rates, and P content. You precede these equations by presenting a regression between intracellular NO3- and cell volume (Fig. 7). It would make more sense to present Fig. 7 after you have outlined the equations, since the regression depends on equation 1. This would give the subsection a more logical structure.
Section 1.6.3. Obviously, this is a very extensive topic that a short paragraph cannot do justice to. If you want to keep it, then there are reviews that you could cite (e.g., Gooday 2003, Jorissen et al. 2007). The OMZ review of Levin (2003), which deals with benthos as whole but includes foraminifera, is also relevant. Please note that it’s not just the taxonomic composition that reflects oxygen concentrations. Other assemblage attributes, such as diversity and dominance, are also strongly influenced. However, I would agree that the problem of disentangling the relative effects of organic matter and oxygen on the composition, diversity, dominance etc of foraminiferal assemblages in hypoxic settings is an important point to make.
Gooday, A.J. (2003). Benthic foraminifera (Protista) as tools in deep-water palaeoceanography: a review of environmental influences on faunal characteristics. Advances in Marine Biology, 46, 1-90.
Levin, L.A. (2003) Oxygen minimum zone benthos: adaptation and community response to hypoxia. Oceanography and Marine Biology: An Annual Review 41: 1-45
Jorissen, F., Fontanier, C., and Thomas, E. 2007. Paleoceanographical proxies based on deep-sea benthic foraminiferal assemblage characteristics. in: Hillaire-Marcel, C., and de Vernal, A.: Proxies in Late Cenozoic Paleoceanography, Elsevier, Amsterdam, Boston, Heidelberg, London, New York, Oxford, Paris, San Diego, San Francisco, Singapore, Sydney, Tokyo, 263-325.
Editing suggestions
Some parts of the text are well written, but others are not and need careful editing, for which suggestions are made below.
Abstract and Introduction
Line 12. Delete ‘ongoing’
- ‘Since several species….’ (no need to repeat foraminifera)
23, 24. Delete the repetitions of ‘even’.
24-25. ‘Finally, since foraminifera can calcify under anaerobic conditions, I will briefly review proxies for O2 based on their shell composition and assemblage composition.
- ‘More than a decade later…..published…’
- ‘Nevertheless, advances in methods to analyse the metabolic rates, intracellular nitrate storage and molecular genetics of foraminifera has changed our understanding of strategies such as anaerobic metabolism that help them to withstand O2 depletion.’
- Are foraminifera really ‘microeukaryotes? This term would be more appropriate for eukaryotic microbes such as flagellates. Better to just call them ‘small eukaryotes’ or ‘meiofaunal eukaryotes’ (although not all are meiofaunal or particularly small).
- ‘….2021). As a result, G. hexagonus has…’
43-44. ‘Benthic foraminifera ….have also been established ..’
- However, I will touch on …..benthic foraminifer only briefly, since…’
48-52. ‘The first part of this paper reviews recent advances in our understanding of the diverse strategies that foraminifera use to withstand O2 depletion, focussing mainly on denitrification, dormancy and kleptoplasty. I also incorporate denitrification into the conceptual TROX model of Jorissen et al. (1995), which explains the sediment microhabitats of benthic foraminifera in terms of an interplay…..’
- Next, I briefly discuss….’
- ‘foraminifera in marine…’
- You’ve already mentioned foraminifera as oxygen proxies in paleoceanography in lines 44-47
Section 1.3
60-65. You’ve already explained some of this paragraph in the Introduction. I think you can limit it to the first sentence (but please change ‘examples see’ to ‘see examples’).
- ‘first evidence emerged…’
- ‘can store substantial amounts of…’
- ‘of the presence..’
- ‘storage capacity’
108-109. ‘This indicates that foraminifera use other enzymes to catalyze these steps, or they rely on…., or…..’ (you can only use ‘either…or’ for two alternatives, not three)
- Woehle & Roy et al, 2022. Is this the same as Woehle et al 2022?
- Replace second ‘likely’ with ‘possibly’ or ‘probably’.
- Better to delete ‘Furthermore’ and start sentence with ‘The’.
149, 154. ‘epifaunal’ (not ‘Epifaunal’ – you are not starting a new sentence).
168 ‘its shallow infaunal…’ (not ‘their’)
- ‘certain circumstances’
182-186. These last two sentences can be simplified – ‘Research to measure denitrification rates in different benthic foraminiferal species continues. This will add to the scarce available data and contribute to estimates of the role of foraminifera in …….’
195-196. ‘some studies suggested that some foraminifera may become dormant when …’
- ‘putative anoxic habitats
- ‘had’ (not ‘has’)
- Delete ‘own’
- ‘fended’
247-248. Insert commas after brackets.’
- No comma after ‘test’
- Delete ‘rest’.
277-281. You could condense these two sentences as follows – ‘Several recent publications based on advances in molecular biological methods……have revealed some other metabolic adaptations of foraminifera that thrive under…..’
281-283. Again, this could be simplified - ‘In N. stella and B. argentea, Gomaa et al. (2021) found evidence for the expression of proteins, including pyruvate……hydrogenase, that are characteristic of anaerobic metabolism. The PFOR sequences…..’
- ‘already came from a study by Nardelli…’
297-299. This sentence more or less repeats the previous one in lines 295-296. I suggest you run together the next two sentences to say – ‘These processes (calcification and the ingestion of prey cells by phagocytosis) require bursts of high energy, which the authors suggest is generated by dephosphorylation of….to generate ATP.’
- ‘metatranscriptonomes’ (spelling)
303-304. ‘might serve as a ….’
305-307. ‘Orsi also found evidence for an anaerobic metabolism….’. I may not be understanding correctly, but isn’t anaerobic metabolism what you describe on line 300? If so, perhaps you should run these two sentences together – ‘Orsi et al. (2021) also found evidence that foraminifera on the Namibian shelf metabolize hydrolyzed…..’
- ‘conducted’ (not ‘made’)
Section 1.4.
Please see comments above.
Section 1.5
339-342. These two opening sentences more or less repeat lines 74-76. I would start this section instead with the third sentence (‘Pina-Ochoa et al. (2020b) pointed out the possible importance of….’).
- ‘due partly to their high abundances…’
- ’Globobuliminids’ is not a genus. If you want to use italics, then this should be ‘Some species of Globobulimina…’
- Add comma after ‘foraminifera’.
363-365. These equations are the subject of subsection 1.5.1, so perhaps they should not be mentioned here. Also, .’….to calculate estimated denitrification rates,…’
- ‘data’ (not ‘Data’).
372-373. ‘Hypotheses include…’ (Delete ‘about the use of the stored phosphate’ – you’ve said this already)
- ‘contain’ (not ‘bear’).
389-390. ‘…are typically shallow infaunal and …’
394-395. This could be reworded for clarity, e.g. – ‘Given this variation in NO3- storage capability, the reliability of estimates for the foraminiferal contribution to NO3- budgets depends crucially on the availability of data. The more data there is, the better …..’
- ‘…including the contribution of species with….’
404, 412. Maybe remove the comma at the beginning of the line. It looks odd.
Section 1.6
- ‘This section (not chapter) briefly discusses morphological and geochemical aspects of benthic foraminiferal tests, and foraminiferal assemblage attributes, that can be used……. A more extensive review will summarize…’
- ‘that live in deep infaunal microhabitats below….’ Also ‘spp., for example, are….’ (spp. is not in italics).
434-5. ‘Though, Globobuliminidae…..’ Delete this sentence. You already said this a few lines earlier. Also please note that although species of Globobulimina (and Praeglobobulimina) are large and are not flattened, none of them are actually spherical. I would say that members of this genus tend to have an ovate or globular shape, sometimes with a pointed proximal end.
- ‘is the porosity, including pore size and pore density, of foraminiferal tests.’
- ‘…characteristics began in the 1950s…’
- ‘…the first attempts were made to use the test porosity of PLANKTONIC foraminifera…’
- ‘Here, I focus on the…’
451-452. ‘…environments with ………and fossil specimens from periods of..’
- Delete comma after ‘known’
- ‘were identified as potential…’
481-482. ‘This offset depends on the vertical separation of the species within the sediment column…’
Table 2 caption. Foraminifera and gromiids (or Gromia, but not ‘gromiida’) are mentioned separately, which is correct, but in the table itself it might be clearer to put them in a separate section, just to be clear.
Table 3 caption line 1. ‘foraminifera’
Fig. 4 caption line 5. Delete ‘supply’.
Fig. 4 caption line 8. ‘..when they have to, although if the food supply is too low, they …’
Fig. 6 caption, bottom line. 'Foraminifera in hypoxic'
Citation: https://doi.org/10.5194/bg-2023-49-RC1 -
AC2: 'Response letter to review by Andy Gooday', Nicolaas Glock, 15 May 2023
Dear Andy Gooday,
thanks a lot for your detailed constructive feedback to the manuscript. I revised the manuscript according to the revisions by all three reviewers. In the attachments, you can find a pdf with a detailed point by point response to all of your points of revision. According to your suggestions, I reworked the "ecology" section with a focus change on trophic interactions of foraminifera under O2 depletion. The paleo-part has been deleted according to your remarks and the suggestions of another reviewer (Frans Jorissen) and just condensed to a paragraph in the introductions.
The main changes related to the reviews by the other two reviewers are the rework of the section that discusses the microhabitats to avoid overgeneralization and to provide more evidence for the hypotheses and an extention about the discussion of other survival strategies of foraminifera under O2 depletion (for example symbiosis or peroxisome proliferation). These changes can be found in detail in my point-by-point response letters to the other reviews.
Best regards,
Nicolaas Glock
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RC2: 'Comment on bg-2023-49', Anonymous Referee #2, 05 Apr 2023
The manuscript by Glock is a good initial attempt to review current knowledge about benthic foraminifera inhabiting anoxic AND oxygen-depleted (hypoxic, dysoxic) habitats. In fact, roughly half of the situations described regard foraminifera living in low – perhaps even moderately high— oxygen conditions. Further, manuscript portions discuss gromiids / Gromia, which are not foraminifera. With these two things in mind, the present title must be changed in terms of “anaerobic” and “foraminifera”. In particular, the title must include low oxygen (or synonym) and “gromiids” or the contribution must be stricken of all discourse about low-oxygen habitats and the gromiids. Further, the use of plural (“Reviews and syntheses”) is grammatically incorrect. In my opinion, the title should also include “benthic” as there are only a few sentences about planktic foraminifers. The abstract too requires edits after considering the detailed comments that follow.
It is not clear why certain topics received much attention while other “survival strategies” for inhabiting oxygen-depleted habitats were effectively ignored (symbionts, for example).
In reality, there are few studies that have shown bonafide “complete denitrification” as Risgaard-Petersen et al. did in their 2006 paper. To date, the ‘omics have shown the process lacks the final step, so those studies technically have not shown “complete denitrification”. This point should be made clear and elaborated upon as necessary throughout the contribution.
The contribution should include a short synopsis where definitions of the terms used in the manuscript are defined. For instance, the term “anaerobic” typically refers to a physiological or metabolic process, not a habitat—meaning, “anaerobic environments” is unconventional phraseology. As the author likely knows, there are a plethora of terms designating environments with low concentrations of oxygen; these must be defined as the author interprets. For example, when one “low oxygen” concentration was presented, it was really quite high (60 uM), so it really is necessary that details be included.
There are a number of overgeneralizations that require literature support or the assertions much be curtailed. For example, lines 13-14 state that benthic foraminifera as a group can benefit from ocean deoxygenation. This is vastly overstated. While some species may compete well in very low oxygen to anoxia, there is little, if any, evidence to suggest the entire group will benefit from deoxygenation. A second example involves the genus Bolivina, which is considered a model “deep infaunal” taxon in Fig. 4 yet there is no universally accepted agreement that all Bolivina are deep infaunal / anaerobes. Lines 149-150 notes four genera that are designated “deep infaunal facultative anaerobes” yet all species of each of these genera have not been assessed in this context so this assertion is premature.
Other statements are incorrect. For example, lines 66-68 note that foraminifera are the only eukaryote to perform denitrification. This is not true—a number of fungi also perform denitrification, and this was first described in the 1990s (Shoun et al. 1992 FEMS Microbiology Letters). Also, the passage spanning lines 218 to 219 is simply wrong: Grzymski et al. (2003) – not Pillet et al., 2011— was the first to sequence foraminiferal kleptoplasts, documenting via molecular methods they were from diatoms. Further, the studies documenting kleptoplast morphology via TEM should not be discounted or belittled as diatom chloroplasts have distinctive morphologies. Molecular methods are not required to establish all facts.
The fact that there is strong natural variability in nitrate storage causes the estimations of rates and contributions (lines 364) to be merely statistical manipulations that may mean little. This should be elaborated upon.
Referring to lines 334-336, the author needs clarify why it is sensible to: (1) estimate the denitrification rate for species that are NOT documented to denitrify and (2) why it is sensible to think that the volume of a foraminiferal test reflects denitrification rate (think of the LBFs [Large Benthic Foraminifera] like Amphistegina—by this argument, it would have an extremely high denitrification rate, yet these species live on coral reefs which are not known for anoxic bottom waters).
The section on kleptoplasty is mostly about species living in shallow, aerated environments— if there is proof of these species inhabiting anoxic conditions, that should be presented in this Review. It should be noted that the experimental conditions used by LeKieffre et al. (2018) were aerated (lines 223-225) so discussing this paper in the context of uptake during anoxia is misleading. Further, Jauffrais et al. (2019) did not incubate in anoxia either (Lines 245-246).
The paragraph about kleptoplastidic foraminifers from aphotic anoxic zones are relevant to this Review as two species inhabit anoxic conditions: Nonionella stella from Santa Barbara Basin and Virgulinella fragilis from a few habitats (Venezuela, Japan, Namibia; unfortunately the New Zealand population has become decimated as eutrophication remediation has progressed). It is surprising that V. fragilis has not been discussed at all in this Review.
Why is Figure 2 a figure? It is merely an equation and should be included as such.
Figure 3 shows a common biogeochemical pathway, denitrification (do a Google search!)—why include it here as a figure? Further, given Orsi et al. and Gomaa et al. also documented this pathway for other foraminifera communities/species, why are these not cited as well as the Woehle et al. papers? If this figure is similar to a previously published image, copyright permission may be required.
The point of Fig, 6 is not clear. For example, bacterivory by benthic foraminifera was established in the 1960s (work of JJ Lee and colleagues), so this is nothing new. Foraminiferal preying on metazoans also is not new—see, e.g., Alan Be papers (1980s), Bowser on carnivory by Antarctic foraminifera (1990s), etc. If insist on only citing Dupuy then must add “e.g.,” as it is only an example. Term “bolivinids” should be capitalized without italics; same for “globobuliminids”.
Fig. 7 presents a subset of data, only those that fit some threshold. The important question is What does this regression look like when including the data that was excluded?? Remove one of the “from” in “from from” of the caption. Figure captions are generally far too long.
Grammatical and other minor specifics:
The first person singular (“I”) is used in many places (e.g., lines 43, 46, 51, 52), which is unconventional for scientific literature, which typically is in the third person plural.
Line 11: “artificial fertilizer” is a peculiar phrase. Most would say “eutrophication”.
Line 15 notes that certain foraminifera are “unique amongst eukaryotes” without elaboration of details. Again, this is an overstatement without supporting details. Such phraseology must be used with caution.
What is “heterotrophic denitrification”? First use: line 17.
Line 34 would read better if it was changed to “Nevertheless, much has changed in our perspective about…” (less “wordy”).
Line 50 equates organic matter to food. This is an arguable point as organic matter may be refactory, etc and otherwise not necessarily “food”.
Line 51 notes that there is scarce knowledge of the ecological interactions of benthic foraminifera from low oxygen to anoxic habitats. This, simply, is not true. Indeed, in Section 3, (lines 285-310) the authors notes that there is much to review on the ecology (although this discussion is about trophics).
Line 52 would read better as “…role of foraminifera in marine biogeochemical…”
The statement spanning lines 58-59 is redundant with the section header, so it should be omitted.
Line 61 would be better as “metabolism of benthic foraminifera.”
Line 76 mentioned gromids, which are not foraminifera. If discussion of this group remains, the title much include this taxon name.
Line 77 states the presence or size of the intracellular nitrate, but nitrate cannot be “sized”. Better alternatives include concentration, amount or magnitude.
Line 92 cites Bernhard et al. 2012a when Bernhard et al. 2012b should be cited.
Line 94 incorrectly infers that bacteria are “killed” by antibiotics, when in reality bacterial activities are inhibited when exposed to the appropriate antibiotics.
Line 108 states that genomes were obtained by Gomaa et al. (2021) but this is not the case and may not be the case in Orsi et al. (2020) either.
Why is a publication listed with two author names plus “et al.” (line 113)? There is no need of this given there are no other 2022 papers with Woehle and Roy as the first two authors.
Line 122 requires a literature citation(s) for the sentence ending “…strong reactivity”.
Line 133 should remove “denitrifying” as that word appears later in the sentence.
Line 139 should cite the original literature that documented “epifauna, shallow infauna, and deep infauna” foraminifera (Bruce Corliss Nature 1985).
Line 146 and elsewhere, the use of the verb “prefer” (or preference) should be avoided as foraminifers do not have conscious thought.
On line 150, the species of Globobulimina that are considered to be deep infuanal / facultative aerobes are not listed.
Use of “basically” on line 151 is colloquial and superfluous; the term should be omitted.
The phrase “competitional stress” (line 153) is unconventional. Perhaps the intention was “competitive stress”?
The references are often placed at the end of a sentence when the papers do not all show the same thing. This approach should be avoided. For example, the sentence spanning lines 155-158 should have Schmiedl and Mackensen (2006) cited after “shallow infaunal lifestyle”, not at the end as that paper did not assess denitrification or nitrate storage.
The statement on line 159 is awkward because “used” can mean “utilized”, but it seems the intent here is more like “accustomed”. A suggested edit is “that typically occur at the sediment-water interface or on elevated surfaces.”
Line 164 should read “spp. may denitrify under”.
Line 167 should read “…if they must, due to their…”
Line 170 should read “research still continues…”
Throughout, “chapters” should be called “sections”.
The sentence spanning lines 169-171 is poorly worded as published papers have already determined denitrification rates, meaning the wording cannot include any literature citations.
The order of subsections in Section 2.1 is illogical as it starts discussing an active process (denitrification), then discusses a inactive process (dormancy), and then discusses an active process again (kleptoplasty).
Line 183 should read “well-aerated condition. They interpreted this…” (two changes)
The paragraph spanning lines 189 to 200 consistently italicizes “sp.”, which is incorrect. This should never be italicized. Line 201 italicizes “spp.” incorrectly.
Line 197 should read “…acids, which was not the case…”
It Is not clear why paragraph spanning lines 201-209 is included in the dormancy section. If there is a connection to dormancy, this must be explicitly stated.
Line 206 should read “…could not be fended off” (although this is a rather colloquial statement). Further, this statement should cite the original publication that showed the transition from endobionts to parasites to necrophagy (i.e., Bernhard et al. 2010 Paleoceanography).
Line 214 should read “…this research originated in the 1970’s (Lopez…”
Line 232 must spell the genera name properly: Nonionella, for N. stella. The genus for N. labradorica is Nonionellina (not the same as Nonionella). Further, Powers et al. (2022) Frontiers in Mar. Sci Sect on Mar Microbiol and Ecol. should be cited in the string of citations on line 234.
The spelling of Grymsky on line 241 must be corrected (it is Grzymski).
Line 242 should read “…calculated that the required amount…”
Line 248 should read “… Gomaa et al. (2021) support observations of Grzymski et al (2002).”
It is surprising that Powers et al. (2022 Frontiers) is not discussed at all in this Review. ‘
Line 261 should write out the genus name for B. argentea (Bolivina).
Line 268 should read “…observation was made by…”
For line 270, the term “presumably” should be inserted to read “Presumably living foraminifera…”.
Line 276 “Though this requires…energy.” is not a sentence. Please rewrite.
Please correct spelling of “metatranskriptome” on line 279.
Line 281 should read “…found evidence of another anaerobic metabolism…” (as denitrification is an anaerobic metabolism).
Line 282-283 should include Gomaa et al. (2021) as these processes were also documented.
Line 287 discusses a study with 60 uM O2, which is very high from many “hypoxia” perspectives.
Line 292 should read “cancellata and Chilostomella”.
Consider using the typical term for deposit feeders (detritivore) on line 293.
Line 294 must include “e.g.,” in the beginning of the ctations as there are additional studies of carnivory by foraminifers.
Line 298 uses the term “thrive” (used earlier in the manuscript too) yet there is no documentation that this species is truly abundant in the setting being discussed.
“Predator prey” must be hyphenated on line 310.
The sentence spanning lines 312-313 should be omitted as it is highly redundant.
The use of “not exotic” on line 314 requires explanation. Exotic to what?
Line 316 should use either “established” or “suggested” instead of “pointed out” which is colloquial. Consider replacing one of the “some” on line 317 (“In some environments, such as some habitats…” (possible replacements are “certain”, “selected”).
It would be good to add other publications on line 318 that have calculated the contribution of foraminifera to total denitrification such as Choquel et al., Glud et al., etc. While it is understood that the author is promoting his publications, it gets a bit much sometimes.
“keyplayers” is two words (line 318).
The text spanning lines 327 to 330 should explain why diagenetic models are being discussed. Most people will be interested in biogeochemical modeling vs diagenetic models.
Line 337: change capitalized “D” in “Data” to lower case.
The observation that foraminifera have served as a nucleating site for phosphorites (lines 348 to 350) does not necessarily indicate their active use of precursors as there is known presence of other mineral associations in foraminifer tests (e.g., pyrite framboids).
The single sentence spanning lines 356 to 361 must be broken into two or three sentences.
In section 4.1, the author does not address the very large variability of vacuole volume in cytoplasm from varied foraminifers (see Fig 2 in LeKieffre et a 2018 Mar Micropaleo).
The Section on paleoceanography (Sect 4) needs to be shortened as an “in prep” manuscript (Hoogakker et al.) is cited in most sentences (appears at least 5 times over ~75 lines). Such passages are irritating—just leave that information to the Hoogakker team to present. Further, most of this discussion is about environments with oxygen, which is not anoxia, impacting the decision to change the title or focus of the Review, as discussed earlier in this critique.
Do not italicize family names (line 399) and do not italicize “spp.” (line 397 and as noted earlier).
Line 399 is not a sentence. Please rewrite.
The format “C. spp.” is not allowed (line 416). Here, the genus name must be fully written.
Line 424: is 11 years still considered “recent”?
Aside from citing Erez, newer references should be cited regarding foraminiferal calcification mechanisms (e.g., works by Toyofuku and/or de Nooijer).
The list of 22 publications in one sentence (lines 432-435) is excessive and not the approach used in other places earlier in the manuscript.
Statement on line 439 should read “This offset is referred to as…” because that notation was used in the McCorkle paper from decades ago—the terminology is not new. Line 441 should cite McCorkle papers also, not solely the new publications.
“Height difference” (line 442) is a peculiar way to discuss what I believe the author intends, which is depth of calcification.
Line 445 should present values for “lower [O2] range”.
Line 454 should read “…this index are ongoing , with recent developments… Tetard et al. (2021) and Kranner et al. (2022).” (five changes)
Line 450 uses the phrase “appears obvious” which is rather rude. Hindsight is 20-20 vision, correct? Meaning of course things seem obvious now but no one / few thought foraminifera could be anaerobes back then. The author is urged to rewrite this.
Line 464 should be singular as there is only one author.
The proper way to cite one’s grant in Acks (line 467 is “…(DFG) through Heisenberg grant GL 999/3-1 to N.G.” (Initials can be used if the grant recipient is an author of the manuscript).
Species names must be italicized in the cited literature section.
Journal name is missing from van Dijk et al. 2019 (and most would alphabetize that under V). Same for de Frietas (should appear in the D’s).
Proper citation for Glock et al 2012b is:
Glock, N., Schönfeld, J., Mallon, J. (2012). The Functionality of Pores in Benthic Foraminifera in View of Bottom Water Oxygenation: A Review. In: Altenbach, A., Bernhard, J., Seckbach, J. (eds) Anoxia. Cellular Origin, Life in Extreme Habitats and Astrobiology, vol 21. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-1896-8_28
Line 583: do not capitalize “auriculata”
Why is Glock et al. (2019) PNAS repeated twice in the Literature citated section (2019a and 2019b)?
The citation for Grzymski et al. (2002) has added seven extraneous authors. Why? The author list is Grzymski, Schofield, Falkowski and Bernhard.
The “o” in Jorgensen has a slash through it (Scandinavian letter).
Line 849 should read “pH”, not “PH”.
Names in Table 1 must be alphabetized. Terms must be defined (“specific denitrification” is truly a rate presented on a per volume basis).
Table 2 should remove gromiida unless the title changes. And, proper: Gromiida, or “gromids”
Italicize ‘H’ in Haynesina in Table 3. “Labrospira cf. subglobosa” should read “Labrospira cf L. subglobosa” (add first letter of genus name italicized and without italics for “cf”).
Citation: https://doi.org/10.5194/bg-2023-49-RC2 -
AC3: 'Response letter to review by Anonymous Reviewer #2', Nicolaas Glock, 15 May 2023
Dear Anonymous Reviewer,
thanks a lot for your detailed constructive feedback to the manuscript. I revised the manuscript according to the revisions by all three reviewers. In the attachments, you can find a pdf with a detailed point by point response to all of your points of revision. According to your suggestions, I extended the discussion of other survival strategies of foraminifera under O2 depletion (for example symbiosis or peroxisome proliferation) and carefully adapted and corrected a significant part of the manuscript.
The main changes related to the reviews by the other two reviewers are the rework of the section that discusses the microhabitats to avoid overgeneralization and to provide more evidence for the hypotheses of this section and a rework the "ecology" section with a focus change on trophic interactions of foraminifera under O2 depletion. The paleo-part has been deleted according to your remarks and the suggestions of another reviewer (Frans Jorissen) and just condensed to a paragraph in the introductions. These changes can be found in detail in my point-by-point response letters to the other two reviews.
Best regards,
Nicolaas Glock
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AC3: 'Response letter to review by Anonymous Reviewer #2', Nicolaas Glock, 15 May 2023
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RC3: 'Comment on bg-2023-49', Andy Gooday, 05 Apr 2023
Unfortunately, the first paragraph of my comment posted on April 1st was incomplete. It should have read as follows –
This manuscript gives a very useful review of biology of foraminifera that live where oxygen is absent or scarce. I found the section on survival strategies(1.3), together with the data summarized in Tables 1-3 and the figures, very interesting and informative. Section 1.5 on the role of foraminifera in nutrient cycling and biogeochemistry is also useful (although see the comment below). However, sections 1.4 and 1.6 need some thought. Section 1.4 is headed 'ecology' but that's misleading. It's actually a very brief and rather confusing treatment of diets/feeding. The final section about palaeoceanography is rather superficial and somewhat redundant, since a more detailed review is on the way.
Citation: https://doi.org/10.5194/bg-2023-49-RC3 -
AC4: 'Reply on RC3', Nicolaas Glock, 15 May 2023
Dear Andy Gooday,
thanks a lot for this remark. I copied the missing text to my response letter, which I uploaded as a pdf in the response to your first comment. All comments are addressed together in this response letter.
With best regards,
Nicolaas Glock
Citation: https://doi.org/10.5194/bg-2023-49-AC4
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AC4: 'Reply on RC3', Nicolaas Glock, 15 May 2023
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EC1: 'Comment on bg-2023-49', Lisa Levin, 28 May 2023
Thank you for your very thorough consideration of the reviews. Please proceed by posting your revision. In making this revision please try to:
1. be absolutely clear about the definition of anoxia (zero oxygen), and make clear that even a very small amount of oxygen (< 1 micromolar) is very different than zero for organisms like Foraminifera. Explain the range of concentrations considered to be hypoxic or suboxic or oxygen depleted - always with oxygen present. e.g., why is Sagami Bay oxygen depleted?
2. avoid alphabeticsal order of subsections as in Survival strategies 2.1 suggest DNF, klepto, defining “other” ( fermentation) and dormancy
3. mention the wide range of vacuole volume
4. avoid use of first person in text (unless you have an strong reason for this),
Citation: https://doi.org/10.5194/bg-2023-49-EC1 -
AC5: 'Reply on EC1', Nicolaas Glock, 09 Jun 2023
Dear Lisa Levin,
thank you for your thorough evaluation of the reviews and the response letters. I will now upload the revised manuscript. Below you can find a point by point response for your points of revision:
Editor: Thank you for your very thorough consideration of the reviews. Please proceed by posting your revision. In making this revision please try to:
- be absolutely clear about the definition of anoxia (zero oxygen), and make clear that even a very small amount of oxygen (< 1 micromolar) is very different than zero for organisms like Foraminifera. Explain the range of concentrations considered to be hypoxic or suboxic or oxygen depleted - always with oxygen present. e.g., why is Sagami Bay oxygen depleted?
Reply: Done. The following part has been added to the introduction to define terms, such as hypoxia and anoxia:
“For the discussion about life in habitats, where O2 is scarce or absent it is important to define the range of O2 concentration for terms such as anoxia, hypoxia, suboxic or oxic conditions. The concentration range for these terms varies with literature. To avoid confusion, this review will use the following definitions from literature:
Anoxia usually indicate the complete absence of O2 ([O2] = 0 µM; Diaz, 2016)
Suboxic conditions indicate habitats, where O2 is low enough that denitrification and Mn- and Fe-reduction but sulfide concentrations are still low, due to the absence of sulfate reduction ([O2] ~ 1-10 µM; Oakley et al., 2007)
Hypoxia in aquatic environments indicate habitats where O2 is present but the O2 saturation is less than 30%, since most fish cannot survive below 30% saturation ([O2] < 62.5 µM Levin et al., 2009).
Low O2 or O2 depleted habitats will summarize all environments that fulfil one of the above definitions(i.e. every environment where [O2] is < 62.5 µM).”
To address, why Sagami Bay is oxygen depleted, the concerning section has been rewritten as follows:
“There are a few studies that specifically focused on trophic interactions of foraminifera in environments where O2 is scarce or absent. Early observations have been documented by Nomaki et al. (2006), who conducted an in situ feeding experiment at central Sagami Bay (1450 m), Japan, using 13C labeled algae and bacteria. Bottom water O2 concentration at this location is usually less than 60 µM and O2 penetration depth into sediments varies between 3 and 10 mm indicating that infaunal foraminifera in this habitat are regularly exposed to hypoxia and anoxia (Glud et al., 2005).”
Editor: 2. avoid alphabeticsal order of subsections as in Survival strategies 2.1 suggest DNF, klepto, defining “other” ( fermentation) and dormancy
Reply: Done. “Other” has now been defined: “Other strategies: Fermentation, utilization of high energy phosphates and peroxisome proliferation”
Editor: 3. mention the wide range of vacuole volume
Reply: Done. Following sentence has been added to the revised MS (section 4.1):
“In addition, the NO3- is most likely stored in seawater vacuoles and the vacuole volume of foraminifera can have a large variability (LeKieffre et al., 2018).”
Editor: 4. avoid use of first person in text (unless you have an strong reason for this).
Reply: Done. Use of first person is now avoided.
Citation: https://doi.org/10.5194/bg-2023-49-AC5
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AC5: 'Reply on EC1', Nicolaas Glock, 09 Jun 2023
Peer review completion
The requested paper has a corresponding corrigendum published. Please read the corrigendum first before downloading the article.
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