Microbial Geochemistry Reflecting Sulfur, Iron, Manganese, and Calcium Sources in the San Diego River Watershed, Southern California USA
Round 1
Reviewer 1 Report
The paper provides a descriptive overview of the local microbiological and geochemical reactions taking place along the San Diego River.
Line numbers along the text would have helped with the review report...
Results:
The sentence "The colorless sulfur oxidizers require suboxic water and the anoxyphotosynthetic purple and green sulfur bacteria require anoxic water that receives full sunlight." can use a reference.
Discussion:
The sentence "Stable isotopes of oxygen and deuterium are being studied currently by Trent Biggs and Chun-Ta Lai at SDSU to address the question of variable water sources (in preparation [51])." goes against the style of most journals, better removed.
What is LBB?
Author Response
The paper provides a descriptive overview of the local microbiological and geochemical reactions taking place along the San Diego River.
Line numbers along the text would have helped with the review report...
Results:
The sentence "The colorless sulfur oxidizers require suboxic water and the anoxyphotosynthetic purple and green sulfur bacteria require anoxic water that receives full sunlight." can use a reference.
Thank you so much for pointing me in this direction—I’ve done a lot of work in the field with these bacteria, but I didn’t pay much attention to the literature. Because of you, I started reading. In particular, the Sanchez and Van Gemerden papers were really useful. Sanchez et al. explained why our sulfuretum was under the bridge—the anoxys need low levels of light.
Discussion:
The sentence "Stable isotopes of oxygen and deuterium are being studied currently by Trent Biggs and Chun-Ta Lai at SDSU to address the question of variable water sources (in preparation [51])." goes against the style of most journals, better removed.
I fixed it according to their style.
What is LBB?
I spelled out leucoberbelin blue in the two places we discussed it, and I explained it is a redox dye. I shouldn’t have used an abbreviation for something that only showed up twice in a ms…
Author Response File: 
Author Response.docx
Reviewer 2 Report
The study by Robbins et al. on the microbial geochemistry of S, Fe, Mn and Ca in the San Diego River watershed uses an integrative approach with data from numerous different sources describing interdisciplinary properties and processes. I found the story the authors relay on the problem and its potential explanation compelling and I want to encourage its eventual publication.
I’m not sure if the authors didn’t use the template provided by the journal for manuscripts or whether the pdf of the manuscript was generated later and all page numbers and line numbers were removed. In either case, is very difficult to make page-by-page or line-by-line comments here. Therefore, I will restrict myself to some major key suggestions that hopefully will direct the authors on what I think is necessary prior to consideration for publication.
In its present state, the manuscript is fairly difficult to process. I didn’t necessarily find fault with many of the figures, the presented data and information in isolation. Rather, the problem lies in the organization of the manuscript. Information belonging in the methods can be found in the introduction, and information belonging in the introduction can be found in the discussion.
Introduction
In the first paragraph of page 2, we are being told that “This paper is a qualitative analysis of the S, Fe, Mn, and Ca cycles that were studied through a year and a half of monthly collections.” This could very well be the last paragraph of the introduction. The section titled “Study Area” should be part of the Methods, unless crucial overarching information is extracted and included in the introduction as further elaboration of the problem.
Materials and Methods
Despite the statement quoted above, it is not clear at all what the authors monitored, where and when, from the descriptions in Materials and Methods. After several readings, I was able to glean that microbiological samples were collected by them “during SDRPF sampling days” which, elsewhere we are told, were monthly over “a year and a half” but not which specific time period. The rest of the information seems to have been collected by others. A table of different types of information and their sources (literature, databases, sampling and processing) would resolve these questions. Also, a figure with the specific sampling locations of this study would also be very useful. Most crucially, how they are all synthesized to explain the problem is sorely needed. Appealing to a “qualitative analysis” shouldn’t imply a free-form discussion of data. There must be a method behind this analysis, and this method should be described in the Materials and Methods section.
Results and Discussion
The term “cycle” appears in text and figures, but doesn’t resemble at all what one would expect in either case. Diagrams showing the important reservoirs and processes connecting them, one for each element would be very useful in illustrating what the authors aim to convey. The authors have great visual evidence of those key processes for every element, and it’s a pity not to put it in a proper scientific framework. Overall, the scientific exploration of the data is wanting. I have a sense that data are merely being presented but not being processed sufficiently to test and explore various potential explanations. The authors should consider presenting their data in alternative graphical formats to better highlight what they describe in the text.
Author Response
The study by Robbins et al. on the microbial geochemistry of S, Fe, Mn and Ca in the San Diego River watershed uses an integrative approach with data from numerous different sources describing interdisciplinary properties and processes. I found the story the authors relay on the problem and its potential explanation compelling and I want to encourage its eventual publication.
What a nice word—compelling!
I’m not sure if the authors didn’t use the template provided by the journal for manuscripts or whether the pdf of the manuscript was generated later and all page numbers and line numbers were removed. In either case, is very difficult to make page-by-page or line-by-line comments here. Therefore, I will restrict myself to some major key suggestions that hopefully will direct the authors on what I think is necessary prior to consideration for publication.
In its present state, the manuscript is fairly difficult to process. I didn’t necessarily find fault with many of the figures, the presented data and information in isolation. Rather, the problem lies in the organization of the manuscript. Information belonging in the methods can be found in the introduction, and information belonging in the introduction can be found in the discussion.
Thank you so much for your great review. I'm embarrassed; when I worked for the Federal government, we had a full review process (4 people)--they would have caught the deficiencies (i.e., not enough analysis of the data; results in the discussion section). Thus I appreciate you forcing us back to work. My best excuse is that we were so excited to actually get all that data in one place; it looked perfect us...
Introduction
In the first paragraph of page 2, we are being told that “This paper is a qualitative analysis of the S, Fe, Mn, and Ca cycles that were studied through a year and a half of monthly collections.” This could very well be the last paragraph of the introduction. The section titled “Study Area” should be part of the Methods, unless crucial overarching information is extracted and included in the introduction as further elaboration of the problem.
I moved Study Area into Methods (looks better there). We did a better job of explaining all the moving parts in our protocols. I added all the sites to Figure 1--this makes the paper so much easier to understand--thank you.
Materials and Methods
Despite the statement quoted above, it is not clear at all what the authors monitored, where and when, from the descriptions in Materials and Methods. After several readings, I was able to glean that microbiological samples were collected by them “during SDRPF sampling days” which, elsewhere we are told, were monthly over “a year and a half” but not which specific time period. The rest of the information seems to have been collected by others.
You are entirely correct—I clarified all of this.
A table of different types of information and their sources (literature, databases, sampling and processing) would resolve these questions. Also, a figure with the specific sampling locations of this study would also be very useful.
I added all the sites to Figure 1—having these all on one map made it so much easier to discuss the important issues. Thanks for forcing me to do this.
Most crucially, how they are all synthesized to explain the problem is sorely needed. Appealing to a “qualitative analysis” shouldn’t imply a free-form discussion of data. There must be a method behind this analysis, and this method should be described in the Materials and Methods section.
As I said, I tightened this section.
Results and Discussion
The term “cycle” appears in text and figures, but doesn’t resemble at all what one would expect in either case. Diagrams showing the important reservoirs and processes connecting them, one for each element would be very useful in illustrating what the authors aim to convey. The authors have great visual evidence of those key processes for every element, and it’s a pity not to put it in a proper scientific framework. Overall, the scientific exploration of the data is wanting. I have a sense that data are merely being presented but not being processed sufficiently to test and explore various potential explanations. The authors should consider presenting their data in alternative graphical formats to better highlight what they describe in the text.
I removed the cycle concept for you. I still think that "rocks to water to bacteria" is a cycle. But I understand your concern too because in your cyclic diagrams, processes repeat over and over (which is the dictionary definition, after all). According to that, then our sulfuretum is the only place where we focus on the fact that reduction and oxidation switch back and forth. But we changed to everything to "sources and sinks" in accordance to your idea. And we changed the title to “Microbial geochemistry reflecting S, Fe, Mn, and Ca sources in the San Diego River watershed”
Here is further explanation of my review comment and a response to the author(s)' question.
I wasn't questioning what the authors perceive as cycles. I was stating that maps with data on them (Fig. 4, 6 and 8) don't constitute depictions of cycles, as the authors state in the legends.
A brief search of scientific sources on the internet yielded some good pictorials of examples of cycle depictions:
1) A figure (https://water.usgs.gov/nrp/microbiology/resources/Home/res_pic_cont2_big.jpg) found on this USGS page (https://water.usgs.gov/nrp/microbiology/research/contaminant/contaminant.html)
2) Another (global this time) figure (https://www.nature.com/scitable/content/ne0000/ne0000/ne0000/ne0000/15185899/f1_lower_ksm.jpg) found in this knowledge page (https://www.nature.com/scitable/knowledge/library/earth-s-ferrous-wheel-15180940)
What these figures do is they highlight the key reservoirs and the processes connecting them. I can see from the text in the manuscript (and the authors comment on that as well below) that "rock and water to organism" are the key reservoirs of the cycles they depict. The maps shown in Fig. 4, 6 and 8, don't show them and, most importantly, their interconnectedness clearly. I think that cycle diagrams will depict what the authors think much better than the maps.
I fiddled with a couple of different diagrams and never could create one that talked to me. I think that the figures showing sources and sinks are powerful diagrams on their own.
Just to be clear: keep the maps. They depict geospatial data perfectly. Just don't call them cycles, because they aren't really cycles.
Author Response File: Author Response.docx
Round 2
Reviewer 2 Report
I have read the authors' letter with their detailed responses, and I got the impression that they addressed my comments and suggestions satisfactorily and to the best their study could accommodate. I think that their manuscript is much improved as a result.
