Dear authors
Thank you for your detailed responses to the reviewers comments. Please submit a revised manuscript. With best regards
Gwenaël Abril

Decision#2 on BG2018-278

Dear Authors

Because the first round of reviews of your paper was quiet detailed and comprehensive, I wanted to move forward its edition process based on my own reading. My conclusion is that your paper contains all the necessary data to reach your conclusions, that these conclusions are original and well within the scope of Biogeosciences, but that presentation and selection of the data must re-thought, and the text must be intensively re-worked in order to make your conclusion clear and understandable for all BG readers. Note that my evaluation is based only on text and figure and not sup. Material

One first big problem with your MS is your phrasing that often creates confusion. On many occasions, what should be a strong and precise message is diluted in very general statements using sophisticated expression likely of your own invention. In other occasions, the structures of sentences are very long and repetitive and something that could be clearly said in a few words is hardly expressed in a long and awkward sentence. The style of your text is really a major weakness of your paper because it dilutes the main messages in unnecessary superficial text, including the occurrence of some wrong or imprecise statements. Here an example: L500 “The observed reach-specific patterns of altered water quality and GHG dynamics provide an empirical evidence for ecosystem structural and functional responses to anthropogenic changes in hydrogeomorphic patches of the fluvial landscape, which have been emphasized in recent conceptual models integrating fluvial geomorphology and ecosystem processes at the valley to reach scales (Thorp et al., 2010).” This looks like a suite of savant words without real precise meaning and without referring to objective scientific facts to sustain the statements: what is a “reach-specific pattern”? What pattern? of increasing/decreasing what parameter? “water quality” and “dynamics” are very general terms that can be either positive of negative; “ecosystem structural and functional responses” ecosystem structure is a vast domain, be more precise : what ecological processes are your dealing with here? What responses? What is a “hydrogeomorphic patch”? sorry, I do not understand and I doubt this expression has been defined in the literature. What is a “reach scale”? how many km for the reach scale?… etc., etc. You use the term “reach” (upper reach, lower reach, river reach… etc.) throughout your MS without giving a clear definition for it. Other kind of problem with your style is illustrated by the following sentence from the abstract (there are many other cases in the MS) “The basin-wide surveys of three GHGs revealed distinct increases in the concentrations of three gases along the lower reach receiving urban tributaries enriched in GHGs and DOC”. Your are repeating 3 times “GHG” here and 2 times “three GHGs” although the meaning of the sentence is simply that urban tributaries are a source of GHG and DOC for the river. This kind of phrasing occurs all through your MS and makes it very hard to read and follow, because crucial new original finding are diluted in very general statements, without clearly hierarchizing what is new, what is specific from the study site, what can be generalized elsewhere, and, where and when a statement applies… You will find a list of problematic sentences below, because I am not English native, the list is probably not exhaustive, and I did not try to re-phrase all of them. Please consider seriously that your MS needs profound revision of the style, including detailed editing of language meaning, avoiding vague conceptual statements not based on precise scientific facts (eg “the parameter X increases downstream when the parameter Y decreases” and not “parameters X and Y evolve according to complex biogeochemical processes occurring from upper to lower reaches of river basin and tributaries…”). Simplifying and shortening sentences so it becomes easier for readers.

Second general problem is the choice of data you are presenting in the MS. The MS deals preliminary with CO2, CH4 and N2O (or GHGs); Ancillary parameters include, nutrients, oxygen, pH, CHla, alkalinity, DIC DOC concentration, 13C and 14C, UV absorbance, and fluorescence excitation. I found questionable the choice you made in showing these data in the figures and tables and in the supplementary material.
UV absorbance, and fluorescence excitation bring very little information to the paper, I wonder if these data are really necessary here (they could appear in a couple of sentences in the discussion as “unpublished data” avoiding long description in the Mat &Met. To the contrary, because your data include pCO2, and because pCO2 was measured with a headspace technique, the information on the entire carbonate system is necessary: provide TA values and calculated DIC values (from TA and pCO2). Values of these crucial parameters are not even mentioned in the text.
WWTP generally release DIC in the form of TA, it should be the case here, a detailed analysis of TA might be important for the paper.
In addition, if TA values are high, the buffer capacity of the carbonate system should be taken into consideration in order to calculated in situ pCO2 from pCO2 measured in a headspace. The henry’s law is not sufficient in the case of carbonate rich waters, because equilibrium between CO3= and HCO3- and between CO2 and HCO3- are displaced when creating the headspace (CO2 decreases, CO3= increases and HCO3- may increase or decrease depending on the conditions). Thus for alkaline waters, calculation of in-situ (pre-headspace) pCO2 must include the entire DIC and the changes in CO3=, HCO3- and CO2. In the headspace technique, the volume of water is finite; this is different from the equilibrator technique, where an infinite volume of water is equilibrated with a finite volume of air.
One of the reviewers pointed out the question of d13C-CO2 and I agree with her/him that stable isotopes studies must rely on data of d13C-DIC and not d13C-CO2. You mention in your revised MS a difference of about 10 to 11 per mil between d13C-DIC and d13C-CO2, referring to Mc Callister and del Giorgio. I haven’t read this paper, but almost all the literature reports d13C-DIC and not d13C-CO2. The problem is that the difference between d13C-DIC and d13C-CO2 and the value d13C-CO2 are strongly dependent on water temperature, pH, and alkalinity, because the fractionation between CO3=, HCO3- and CO2 depend on these parameters. To the contrary, d13C-DIC is a conservative notion that considers all the 12C and the 13C contained in the DIC of a sample, whatever the temperature and/or the pH and whatever the proportion of each chemical form.
You put a lot of emphasis in your MS on the importance and interest of using the dual isotopes approach; however, you apply this approach only to DOC in a very limited amount of samples. And in fact the dual isotope approach brings little information because of the contamination of WWTP with old DOM such as gasoline. If the paper deals mainly with GHG, one would expect the dual isotopes techniques to be applied to DIC or CH4… So be less ambitious when introducing the dual isotope approach because when applied to DOC here, it gives little information for the interpretation of the three gases
Inversely, discussion on 13C-CH4 data is relatively superficial and could be strengthened and be more quantitative. These values are quiet high and reveal strong oxidation, maybe up to 95% of the CH4 is oxidized

Alternative choices of data to be shown in figure and table in the main MS are necessary, reminding that the main topics is CO2, CH4 and N2O


Below the detailed comments on the MS

Repeating “GHG” >8 times in the abstract is awkward. Instead, specify at least the ranges of concentrations of each individual dissolved gas. Some key numerical values are missing in the abstract.

L35 not sure “body of research” is appropriate here
L40 specify that wetland are source of dissolved CO2 FOR RIVERS (not source of CO2 for the atmosphere as it suggests here)
L45 I guess you mean Abril et al. 2015 and not 2014
L49 change “natural” to “pristine”
L53 what’s the meaning of “concurrent” here? Please rephrase
L55 insert measured “simultaneously” CO2, CH4 and N2O and remove “together”
L56 what’s the meaning of “interrelated”? Please rephrase
L60 “comparison of three GHGs” do you mean “these three GHGs” or could be any other GHG?
L70 “measurements of multiple GHGs…” you are repeating what you already stated before
L83 “shifting balance between autotrophy and heterotrophy at diel to decadal scale” please be precise: shifting in favour of what? Favouring autotrophy or heterotrophy? All through the MS avoid the numerous sentence with such incomplete information.
L85 what is a “reach” ? I understand it is a portion of a river, but what is its typical length? Few meters, hundred meters, kilometres? The continuous use of this term all through the MS is really perturbing.

Although you repeated several times the necessity of measuring the three GHGs, nothing on the interests of measuring isotopes in the abstract.

L110 “we expected that the comparison of reach-specific spatial pattern of three GHGs and C isotopic composition in DOM, CO2 and CH4 … emerging concepts of anthropogenically created discontinuities in riverine metabolic processes and GHG emissions”. Long, awkward sentence. What is a “reach-specific spatial pattern”? Do you simply mean that the longitudinal (or spatial) distributions of dissolved gases are probably impacted by dams and urban areas? “metabolic processes” do you mean primary production and/or respiration? Or other food-web metabolic processes?
If later in the MS you refer to the river continuum concept, it would be interesting to mention it in the intro.

L150 change “reported” by “described”
L151 “in each SAMPLING, water SAMPLE…” rephrase
L153: we don’t care about the brand of the peristaltic pump
L157 we don’t care about the brand of the syringe, exetainer (L160), temperature and pressure sensor (L164)
L178 Your analysis of d13C in CO2 in a headspace without acidification is problematic. Instead, measurements of 13C-DIC should have been made.
L183-184 “The concentration of total suspended solid (TSS) was measured as the difference in the filter weight before and after drying at 60°C for 48 hours.” this procedure will give you the water content in the filter and filtered material, not the TSS. Did co-authors did not revise the MS?
L204: “subsamples of filtered water samples” please reword
You do not explain how d13C-CO2 and d13C-CH4 were measured: GC/C/IRMS?
L234 “tended to be lowest” please reword
L234 “particularly low: provide value”
L243 “of two gases” > of these two gases
L251 “points to” check English language
L252 “fraction” is a more usual word than “moieties”
L254 “three nutrients” which ones?
Nomenclature HR11… HR14… etc. are difficult to follow, indicating the characteristics of the river sections would help
L260… you mention correlations with parameters such as DO, pH, TA but the numerical values of these important parameters only appear in the supplementary material. Maybe an additional table could help
L279 “pointed to WWTP effluents driving the concentrations of…” revise English language
L280-283 you are repeating twice “GHGs” and “WWTP” in the same sentence, awkward sentence
L283 “increase abruptly along the most downstream reach after passing the WWTP located within a few km upstream” do you mean they “ rapidly increase immediately downstream of the WWTP”?
L284 what does “ending-up” mean here? End of what?
L285 “Corresponding to the large scatter of the box plots representing three GHG concentrations measured at the WWTP effluents and outlet site, two locations exhibited similar patterns of temporal variations in GHG concentrations” awkward and confusing sentence, please rephrase.
L290-298 specify if “high” and low” delta14C values correspond to “old” or “young” DOC
L296 unit is missing after -100
L300 “Concentrations of three GHGs (Fig. 8; Table S7) combined with d13C in CO2 and CH4 (Fig. 8; Table S8) collected along the lower Han River during a cruise expedition revealed clear tributary effects on the C isotopic composition of two GHGs sampled at the mainstem site” very awkward sentence. In addition it says almost nothing in terms of “results”
L303 “d13CO2 continued to increase toward the river mouth, with its values bracketed by those measured for the two upstream tributaries and a downstream tributary” to what figure does this refer to? Is “values bracketed by” correct English?
We would need d13C-DIC and DIC concentrations here
L308 remove “three”
L328 “lack of these natural source” do you mean the absence of floodplain? Not sure Richey 1988 considered wetlands as the “primary factor”.
L332 and at many other places: not sure “of three GHGs” is correct (it could be other gases), I would say either “the three GHGs” or “these three GHGs”
L335. “Spatial variations in three GHGs observed along the middle reach (Figs. 2 ␣ 4) suggest that complex interacting metabolic processes in water column and sediment influence the levels of three GHGs to varying degrees depending on gas and reservoir”
Avoid this type of sentences that says basically nothing. What “metabolic processes” ? be precise. “depending on gas and reservoir” Awkward wording. Again the use or “three GHGs” is confusing
“Lower values of pCO2 measured at all impoundment-affected sites including site HR11 downstream of the last dam (HR10) indicate an enhanced planktonic CO2 uptake, in agreement with enhanced photosynthesis and lowered pCO2 levels observed in some eutrophic impounded reaches of the Mississippi (Crawford et al., 2016), the Yangtze (Liu et al., 2016), and a Yellow River tributary (Ran et al., 2017)”
You repeat twice the “lower pCO2 here, rephrase, something like “in impoundments phytoplanktonic primary production is favoured (REF…) and pCO2 is lowered”
L343 what does “taper” mean?
L348 “which may be associated with terrestrial DOM components and their microbial transformation products”. Is it “may be associated” or does it reveal a degradation of terrestrial DOM to CO2?
L348 “However, the concurrence in the relatively high levels of pCO2 and DOC moieties of terrestrial origin at some middle reach sites that are less affected by impoundments (e.g., HR 7 and HR8) might have resulted in the observed significant correlations.” Confusing sentence. Please rephrase

L358 what is a “low head dam”?
L361 “depth-dependent gradient” > vertical gradient?
L363-367 what does d13C-CH4 say about CH4 oxidation?
Conversion of DOC to CH4 is extremely speculative, (in fact here the correlation is indirect, as they both come from urban areas) because methonogenesis is marginal in the water column, and methanogenesis occurs in sediments using sediment OM and not water column DOC.
“based on the coupling between anaerobic organic matter degradation and methanogenesis” what coupling? This is meaningless. In fact, methanogenesis IS anaerobic organic matter degradation.
L374 “might be explained by the complex interactions between microbial N transformations in the oxygen-rich epilimnion and oxygen-poor hypolimnion” be precise, what processes?, nitrification, denitrification, DRNA, anamox? In addition the fact that N2O does not peak in reservoirs does not mean it is a result of “complex” processes, it might be very simple: no production of N2O…
L375 “a suite of related processes” related to what? “in stream metabolism” ok, but heterotrophic or autotrophic, respiration or primary production? Please be more precise.
L378 and later in the MS: the term “pulse” refer to temporal changes not spatial changes. It is not appropriate for describing local inputs due to urban areas
L379 “benthic sediment” is a truism
L384-388 how was this budget calculated? “was estimated to be consumed by phyto…” how?
“same reach” do you mean the same river section?
L390 “By directly measuring d13C in CO2 respired by bacterioplankton across a gradient of streams and lakes in Canada, McCallister and del Giorgio (2008) showed that the production of CO2 through bacterial degradation of terrigenous DOM decreased in sharp contrast to the increasing proportion of algal-derived DOC and CO2 with increasing levels of Chl a” It is hard to find the relevance of this observation on boreal lakes with that here in Korean rivers. If the question here is whether algae release (exudate DOC) that is further mineralized to CO2 by heterotrophic microbes, or does the algae directly respire in the dark, I think you will never answer this question. Out of the scope of the paper.
L398 “ranges of two gases” please specify which gases
L401 “point to” is not correct English
L405 “In contrast to the lacking or weak correlations indicative of anaerobic CH4 production in the impounded middle reach” I wonder what is a “correlation indicative of anaerobic CH4 production”? please rephrase.
What is a “correlation related to anaerobic metabolism”? please rephrase
L408 “eutrophication (indicated by significant positive correlation with PO4)” correlation of what parameter with PO4? Please rephrase
In general the ideas contained in this 4.1 section are ok and make sense, but the phrasing in English is hazardous which makes the message confusing


L419: 14CDOC in a wide range of global river systems” Please rephrase
L423: “large fluctuations in d13CDOC along the upper to middle reaches from HR2 to HR11 do not present any consistent longitudinal trend of the stable C isotopic composition” Awkward sentence, please rephrase
L425 you use here the term “autochtonous”, do you mean phytoplankton in majority? d13C-DIC of phytoplankton varies a lot depending of the 13C signature of the DIC it has been using.
L416 “which deviated substantially from those of the headwater DOM dominated by allochthonous components”. Please be precise, mentioning what isotope and what are the respective values. What’s the meaning of “allochtonous component” here?
L428 “In addition, the distinct seasonal differences in isotopic signatures suggest that the age of DOM is generally younger at five mainstem sites across the river basin during the monsoon period (July 2014; modern -590 years B.P.) than in the dry season (May 2015; 180 - 675 years B.P.)” Do the isotopic values suggest they vary or do they simply show variation? Please rephrase. Provide the values of 14C together with the age.
L433: why “latitudinal” here? Are values plotted versus latitude?
L434 is WWTP DOC older or younger? Could the downstream trend in 14C originate from selective degradation of young C?
L438 “As suggested by Griffith and Raymond (2011), aged DOM moieties in WWTP effluents (765 - 905 years B.P.; Table S6) may not only leave clear isotopic signatures on DOM in downstream reaches, but also fuel the riverine heterotrophy by providing labile sources for biodegradation” Is it younger or older DOC being degraded? Please reword “may not leave clear”
L440 “might be related to a complex array of interacting processes such as organic matter degradation, photosynthesis by phytoplankton, and atmospheric gas exchange, which have usually been investigated as determinants of the isotopic composition of riverine DIC consisting of dissolved CO2, bicarbonate, and carbonate “ this is too general and confusing. Gas exchange fractionated because 12CO2 degases faster than 13CO2, uptake by phytoplankton fractionate because algae preferentially use 12C, leaving more 13C-DIC, and respiration releases DIC with a signature close to that of the OM source (not fractionation but mixing with 13C depleted DIC). It looks you only refer to Mc Callister and del Giorgio regarding 13C-DIC (or 13C CO2), but their study site is very different from yours
L447 “When the observed values of 13CCO2.. it follows then that other riverine processes than bacterial degradation of plant (predominantly C3 in the studied basin) and algal biomass might be involved in the upward shift of 13CCO2.” The interpretation is wrong here: algal biomass must be considered as a fractionating process during primary production rather than an input of DIC from degradation of algae. The production of algal biomass will increase de 13C-CO2 and 13C-DIC and is probably responsible for the observed trend, maybe with water-air isotopic equilibration.
“assuming and enrichment of 10%o...” this enrichment may vary between what and what values? (I guess between 5 and 15%o). In fact because you have alkalinity, you should be able to calculate the DIC and the concentration of all DIC species as well as the isotopic composition of each species and the total DIC. See Zhang J., Quay P. D. and Wilbour D. O. (1995) Carbon isotope fractionation during gas–water exchange and dissolution of CO2. Geochim. Cosmochim. Acta 59, 107–114.

L463 what does “flanked” mean here?
L467 Weir will enhance CO2 degassing and increase d13C-DIC
What is a “tributary-specific process”?
DOM from WWTP have old 14C signal because of a small contribution of fossil OM such as fuel and gasoline. However, these compounds represent a very marginal contribution to the total DOC. Thus the 14C signal as a tracer of source is hampered by this contamination. See Marwick et al. 2015
L473 why referring to “latitudinal” here? No latitude in figure 8
L478 “pulsating” or “pulse” refer to temporal dimension. Maybe you mean “hotspots” or “point source” here?
L483 “Down-river concentration decreases and 13C enrichment in CH4 are consistent with the underway measurements conducted using a cavity ring-down spectroscopy(CRDS) along a 15 km reach of the North Creek estuary in Australia, which displayed CH4 concentrations…. respectively (Maher et al., 2013).” Comparing river with an estuary is not necessarily appropriated because in estuaries, mixing with seawater occurs.
L489. You did not measure d15N-N2O so no need for this last sentence
Section 4.2 needs profound revision making clearer the question of 13C CO2 versus 13C DIC and the story of old/young DOM

L493: “5.implications” of what? strange title for a last section
Mentioning the river continuum concept here is too late. In addition, one may say that your study does not show a “limited validity” of the concept, to the contrary, it suggest that anthropogenic actions might alter it, but the concept continues being valid if we consider these impact as artificial.
498 “Borges and Abril 2011” is for estuaries, not adapted here
L499 “eutrophic reaches receiving wastewater” do you simply mean river sections receiving WW?
L500 awkward sentence, please rephrase
L506 “Reach-specific significance levels observed for the correlations between GHGs and DOC or its optical properties (Fig. 5; Table S4) imply that…” awkward sentence, please rephrase
L510, “pulse” refers to time, not to space
L511 replace biodegradation by respiration
L514 “gas-specific sets of significant correlations between gas concentrations and related water quality measurements shown for the lower reach” such sentence says basically nothing. What parameters, what gas?
L517 algal productivity will NOT favour CO2 production, to the contrary, it favours consumption
L522 “Urban tributary effects on metabolic processes in the eutrophic lower reach were also reflected in the lower-reach values of d13C in CO2 and CH4 resembling those measured in the tributaries”. This sentence is almost impossible to understand. What metabolic processes are you referring to?
L525 what “metabolic processes”?

Strange the term “hotspot” only appears here

Figures: why are time courses of monthly monitoring shown only in Fig6 and not before in the MS?
Fig2 I could not see the “Dashed horizontal lines”. What is the yellow area?