the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
| 01 Sep 2021
The response of desert biocrust bacterial communities to hydration-desiccation cycles
Abstract. Rain events in arid environments are highly unpredictable, interspersing extended periods of drought. Therefore, tracking changes in desert soil bacterial communities during hydration-desiccation cycles in the field, was seldom attempted. Here, we assessed rain-mediated dynamics of active community in the Negev Desert biological soil crust (biocrust), and evaluated the changes in bacterial composition, potential function, photosynthetic activity, and extracellular polysaccharide (EPS) production. We predicted that increased biocrust moisture would resuscitate the phototrophs, while desiccation would inhibit their activity. Our results show that hydration increased chlorophyll content, resuscitated the biocrust Cyanobacteria, enhanced EPS production, and induced potential phototrophic functions. However, decrease in the soil water content did not immediately decrease the phototrophs activity, though chlorophyll levels decreased. Moreover, while the Cyanobacteria relative abundance significantly increased, Actinobacteria, the former dominant taxa, significantly decreased in abundance. We propose that, following a rain event, the response of the active bacterial community lagged the soil moisture content due to the production of EPS which delayed the desiccation of the biocrust community.
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RC1: 'Comment on soil-2021-88', Anonymous Referee #1, 18 Oct 2021
General comments:
The manuscript entitled “The response of desert biocrust bacterial communities to hydration-desiccations cycles” is an interesting manuscript which focusing on the effects hydration-desiccations cycles on biocrust bacterial communities. The introduction sets scene very nicely and the authors also clearly show the need for studying hydration-desiccations cycle, but see comments below for several ideas that need justification and/or more details. Some parts of the approaches are not appropriate and need more clarification (see comments below about major concern). Although this paper focused on bacterial communities but the results did not provide typical diversity analysis such as alpha and beta diversity. Discussion and conclusion will need to be revised when the major concern has been addressed. Overall, I think that the manuscript idea is interesting and will be valuable for the scientific community. However, additional work is needed to address major concerns and improve several parts of this manuscript to be more transparency and justified.
Title
The title indicates what this research is about but it does not provide any information about key results. I would suggest revising the title to be more specific. What is the key result?
Abstract
Line 20: How does rain-mediated dynamics were assessed? Please explain experimental setup briefly? And provide brief details about bacterial communities measurement.
Line 20: What does active community mean? Active crust community? Active bacterial community? Please be more specific, it is unclear.
Line 22-24: Why focus only on phototrophs? What about other bacteria?
Line 27-28: When Cyanobacteria increased and Actinobacteria decreased, what does it really mean for biocrust?
Introduction
In general, hydration-desiccation cycles were introduced very nicely. However, this paper focused on bacterial communities, but very little information about biocrust bacterial communities was introduced. There are other studies which also focused on biocrust bacterial communities, please introduce them here. What have they done? What were the general bacterial composition? Were there any patterns that other researchers found about biocrust bacterial communities? Is there a reason why this paper should specifically focus on Cyanobacteria and Actinobacteria? Are these the only two phyla found in biocrust?
Line 48 “of soil respiration(Castillo-Monroy et al., 2011)” – add space before parenthesis
Line 50 “trace gases(Meier et al., 2021; ” – add space before parenthesis
Materials and Methods
There are many types of biocrusts. What kind of biocrusts were collected? Were they all the same biocrust types?
Line 86-87: Please provide a reference.
For section 2.6 Community analysis, please report the number of reads in each step (number of raw reads, filtered reads, after chimera removals, etc.).
What is the average number of reads per sample? And what is the range (min – max)?
MAJOR CONCERN! Since the length of the sequences are different because of different platform, please provide details about how the analysis were performed to account for this issue. This section is also crucial in case other researcher would like to follow or repeat the analysis. Please make sure that all the details required for the experiment are included. Currently, it is not sufficient.
Line 172-173: What is the criteria for picking out “genes of interest”?
Results
Generally, simple diversity analysis (alpha and beta diversity) should be provided for microbiome paper. However, only relative abundance plot was provided. I would suggest including alpha and beta diversity analysis to confirm significant differences that were found in relative abundances comparison.
Line 190-201: Statistical test must be provided, reporting p-value only is not sufficient. Please check how statistical test results should be reported. Please also indicate significant differences in figures. Currently, the plots do not have these information.
Line 209-210: In total, how many bacterial phyla were found in these data?
Line 212-216: Please use appropriate statistical results report format. Reporting p-value only is not sufficient.
Figure 3: MAJOR CONCERN! Unless the author provide detailed explanation about how different sequencing platform and primers were accounted for. I think the differences might have been because of different platform used.
Discussion
Line 250: What exactly is “cyanobacterial activity” that was measured? How do we know that it is cyanobacterial activity not other bacteria?
Line 276: Perhaps beta diversity might help confirming this claim.
Conclusion
This might change when different sequencing platforms were taken into account.
Citation: https://doi.org/10.5194/soil-2021-88-RC1 -
AC1: 'Reply on RC1', Capucine Baubin, 10 Jan 2022
Comment on soil-2021-88
Anonymous Referee #1Referee comment on "The response of desert biocrust bacterial communities to hydration- desiccation cycles" by Capucine Baubin et al., SOIL Discuss.,
https://doi.org/10.5194/soil-2021-88-RC1, 2021
General comments:The manuscript entitled “The response of desert biocrust bacterial communities to hydration-desiccations cycles” is an interesting manuscript which focusing on the effects hydration-desiccations cycles on biocrust bacterial communities. The introduction sets scene very nicely and the authors also clearly show the need for studying hydration- desiccations cycle, but see comments below for several ideas that need justification and/or more details. Some parts of the approaches are not appropriate and need more clarification (see comments below about major concern). Although this paper focused on bacterial communities but the results did not provide typical diversity analysis such as alpha and beta diversity. Discussion and conclusion will need to be revised when the major concern has been addressed. Overall, I think that the manuscript idea is interesting and will be valuable for the scientific community. However, additional work is needed to address major concerns and improve several parts of this manuscript to be more transparency and justified.
Title• The title indicates what this research is about but it does not provide any information about key results. I would suggest revising the title to be more specific. What is the key result?
The title was modified to “The function and composition of active bacterial communities diverge during hydration and desiccation of desert biocrust – a field study”
Abstract• Line 20: How does rain-mediated dynamics were assessed? Please explain experimental setup briefly? And provide brief details about bacterial communities measurement.
The abstract was rewritten adding details (ln 25-36): “Here, we assessed rain-mediated dynamics of active bacterial community in the Negev Desert biological soil crust (biocrust) by sampling before, during and after a heavy rainfall, and evaluating the changes in active bacterial composition with amplicon sequencing, potential function, photosynthetic activity, and extracellular polysaccharides (EPS) production. We predicted that rain would resuscitate the biocrust phototrophs (mainly Cyanobacteria), while desiccation would inhibit their activity. In contrast, the biocrust Actinobacteria would decline during rewetting and revive with desiccation. Our results showed that hydration increased chlorophyll content and EPS production. The biocrust rewetting also resuscitated Cyanobacteria, which replaced the former dominant phylum, Actinobacteria, boosting potential autotrophic functions. However, desiccation of the biocrust did not immediately change the bacterial composition or potential function, and was followed by a delayed decrease in chlorophyll and EPS levels. This dramatic shift in the community upon rewetting leads to modifications in the ecosystem services.”
• Line 20: What does active community mean? Active crust community? Active bacterial community? Please be more specific, it is unclear.
To clarify, the sentence was changed to “active bacterial community”.
• Line 22-24: Why focus only on phototrophs? What about other bacteria?
Following the reviewer comment the sentence was modified (ln 24-27): “We predicted that the rain would resuscitate the biocrust phototrophs, mainly the Cyanobacteria, while desiccation would inhibit their activity. In contrast, the biocrust Actinobacteria would decline during rewetting and revive with desiccation.”
• Line 27-28: When Cyanobacteria increased and Actinobacteria decreased, what does it really mean for biocrust?
Following the reviewer comment we added a sentence explaining the reported changes (ln 31-32): “This dramatic shift in the community upon rewetting led to modifications in ecosystem services.”Introduction
• In general, hydration-desiccation cycles were introduced very nicely. However, this paper focused on bacterial communities, but very little information about biocrust bacterial communities was introduced. There are other studies which also focused on biocrust bacterial communities, please introduce them here. What have they done? What were the general bacterial composition? Were there any patterns that other researchers found about biocrust bacterial communities? Is there a reason why this paper should specifically focus on Cyanobacteria and Actinobacteria? Are these the only two phyla found in biocrust?
Following the reviewer comment we added the following information: “The harsh desert conditions shift primary production from plants toward oxygenic photosynthetic microorganism, mostly cyanobacteria (Xu et al., 2021). However, biocrusts are dominated by heterotrophic microorganisms, mainly the phyla Actinobacteria and Proteobacteria (Nunes da Rocha et al., 2015; Meier et al., 2021). Members of these phyla can meet their energy demands during the desert prolonged draughts by harvesting sunlight or atmospheric trace gases (Leung et al., 2020). Studies that focused on biocrust community shifts and cyanobacterial response to hydration-desiccation cycles were carried out under controlled conditions (Angel and Conrad, 2013; Oren et al., 2019; Karaoz et al., 2018).”• Line 48 “of soil respiration(Castillo-Monroy et al., 2011)” – add space before parenthesis Line 50 “trace gases(Meier et al., 2021; ” – add space before parenthesis
AddedMaterials and Methods
• There are many types of biocrusts. What kind of biocrusts were collected? Were they all the same biocrust types?
Following the reviewer comment the following sentence was added: “In this site, the biocrust was identified as type 2 and 3 in some places e.g., well-established cyanobacterial dominated biocrust (Veste et al., 2001; Büdel et al., 2009; Kidron et al., 2015).
• Line 86-87: Please provide a reference.
The reference “(www.data.lter-europe.net)” was added
• For section 2.6 Community analysis, please report the number of reads in each step (number of raw reads, filtered reads, after chimera removals, etc.).
The number of reads at each step were specified in Table S2. To clarify, the following text was modified:” The number of reads at each step can be found in Table S2.”
• What is the average number of reads per sample? And what is the range (min – max)?
The following was added to the text: ”At input, the average number of reads is 86 611 with a minimum number of 22 095 reads and a maximum number of 110 046 reads.”• MAJOR CONCERN! Since the length of the sequences are different because of different platform, please provide details about how the analysis were performed to account for this issue. This section is also crucial in case other researcher would like to follow or repeat the analysis. Please make sure that all the details required for the experiment are included. Currently, it is not sufficient.
The following was added to the text: “We note that the despite the differences in sequencing platforms and primers, the community composition obtained matched previous reports performed at the very same site (Meier et al., 2021; Angel and Conrad, 2013; Bay et al., 2021).”
• Line 172-173: What is the criteria for picking out “genes of interest”?
The text was modified to explain this more clearly: ” We selected these genes in accordance with previous reports (Meier et al., 2021; Bay et al., 2021) and associated them with each step in the KEGG database and built our own database (Table S3).”
Results• Generally, simple diversity analysis (alpha and beta diversity) should be provided for microbiome paper. However, only relative abundance plot was provided. I would suggest including alpha and beta diversity analysis to confirm significant differences that were found in relative abundances comparison.
Following the reviewer comment, the Alpha diversity (Shannon diversity index), and beta diversity (RDA) were added in the supplementary material (Figure S3 and S4, respectively) with the values and the associated statistics. The following text was added: These patterns were supported by the alpha and beta diversity analyses (Figure S3 and S4). The community diversity significantly differed before the rain (T[0]) and during (T[R]) and after the rain (T[1-3]) (Figure S3, p < -0.05, F-value = 10.96, Table S10 and S11). The diversity in the later timepoints (T[R, 1-3]) did not differ (p>0.04, Table S11). Similarly, the RDA showed that T[0] was separately clustered from the other time points (Figure S4, F-value : 5.75, Table S12 and S13).”• Line 190-201: Statistical test must be provided, reporting p-value only is not sufficient. Please check how statistical test results should be reported. Please also indicate significant differences in figures. Currently, the plots do not have these information.
Chi2 and F-values were added to the text. Statistical significance marks were added to the figures.
• Line 209-210: In total, how many bacterial phyla were found in these data?
Nine phyla were detected in the biocrust. This information was added to the text: “The community is mostly composed of the phyla Cyanobacteria, Actinobacteria, and Proteobacteria in addition to six other phyla (Figure 3; Table S6).”
• Line 212-216: Please use appropriate statistical results report format. Reporting p-value only is not sufficient.
Chi2 and F-values were added to the text.
• Figure 3: MAJOR CONCERN! Unless the author provide detailed explanation about how different sequencing platform and primers were accounted for. I think the differences might have been because of different platform used.
This was explained in the Materials and Methods section: “We note that the despite the differences in sequencing platforms and primers, the community composition obtained matched previous reports performed at the very same site (Meier et al., 2021; Angel and Conrad, 2013; Bay et al., 2021).”Discussion
• Line 250: What exactly is “cyanobacterial activity” that was measured? How do we know that it is cyanobacterial activity not other bacteria?
Chlorophyll content was measured as a proxy of cyanobacterial activity. The text was modified following the reviewer comment:” Though the chlorophyll content, a proxy of cyanobacterial activity, increased with soil moisture (Figure 2A), no significant changes were detected in the total organic carbon C or N (Figure S1 and S2; Table S4 and S5).”
• Line 276: Perhaps beta diversity might help confirming this claim.
Beta diversity helped to confirm the claim and therefore a reference to Figure S4 was added to the text.
Conclusion• This might change when different sequencing platforms were taken into account.
The main conclusion was not modified as despite the difference sequencing platforms the community matched previous reports describing the community at the same site (Meier et al., 2021; Angel and Conrad, 2013; Bay et al., 2021).Citation: https://doi.org/10.5194/soil-2021-88-AC1
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AC1: 'Reply on RC1', Capucine Baubin, 10 Jan 2022
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RC2: 'Comment on soil-2021-88', Anonymous Referee #2, 05 Dec 2021
Reviewer comments to Baubin et al. “The response of desert biocrust bacterial communities to
hydration-desiccation cycles”
General comments: In their manuscript, Baubin and coauthors investigated the presence of bacteria and the chorophyll concentrations as related to hydration-desiccation cycles in biological soil crusts. This is a very interesting and timely topic, as water is considered as one of the dominating factors influencing the microbial composition in biocrusts, and the scientific community just starts to understand the functional roles of different bacteria. However, the manuscript suffers from some major flaws and the results are only superficially analyzed, as described below. Thus, major reviewing is needed before the study can be published in SOIL.
Specific comments:
Sampling methodology: As the first sample was taken in June and the next ones were taken in January of the following year, it would be important to know the climatic conditions before the first sampling and also between the first and the follow-up samplings, as this information is necessary to thoroughly interpret the results. Information on the habitat, where these samples were taken, is missing. What was the surrounding vegetation, how was the geomorphology, what about fog and dew at the site? This information is necessary to the reader to interpret the results.
I see a major general problem in the presentation and discussion of the results. In this study, the RNA and thus the active organisms were investigated. Thus, the results do not give information on the community composition, but on the composition of active bacteria in biocrusts at different time points before, during and after a rain event. The argumentation thus has to be adopted throughout the manuscript.
Relative abundance at order level: In figure 3, it is hard to tell the colors apart from each other (e.g. Chitinophagales vs. Cytophagales). At the latter also a “p” is missing. It also seems that the sorting of the orders varies from one time point to the next. As an example, in T[R] it seems that “unclassified” is next to the Actinobacterial orders, whereas in T[1] to T[3] it is all the way at the bottom. In the text, only the changes from T[0] to T[1] are described, but the changes from T[R] to T[1] are largely ignored. This is unfortunate, as there are major changes that need to be interpreted (and look quite interesting)!
Temporal changes in microbial function: the results shown in figure 4 are hardly discussed at all. This is hard to understand, as they look quite interesting as well. It also would be good to include the statistical results in figure 4, as this will facilitate an interpretation of the results without the necessity to search in the supplement.
In the discussion (line 269 ff.) the authors wonder why the response to desiccation is slower than the response to hydration, but the results show that desiccation also happens much slower and thus it seems reasonable that the organisms stay active over longer time-spans. This then, indeed, could also be caused partly by EPS, but the argumentation has to be adopted accordingly. Looking at the statistics of the water contents (Table A4, A5) it seems highly questionable that the water content of T[0] versus T[R] and of T[R] and T[1] should not be significantly different. Thus, the statistics need to be thoroughly checked again!
There are multiple language problems throughout the text, which need to be fixed by a native speaker or professional language editing.
Technical corrections:
Line 35: The term biome does not completely fit for “arid environments”. Better write “drylands”
Line 42: Biocrusts are not only fixed by EPS, but also the organisms themselves, as e.g. fungal hyphae, entangle soil particles and thus stabilize the soil matrix.
Line 43: I don’t think that “desolate” is always the correct term for biocrust habitats. They could also stabilize the soil in regions where e.g. succession starts again.
Line 47: Biocrusts could be a main source of C and N and a strong contributor to soil respiration, but I would not say that this always is the case!
Line 52: It is critical to speak of cryptogams as a “seed bank”. They do not produce seeds and they mainly outlast as desiccated plants and not as seed-like structures or spores.
Line 121: The section is named “Chlorophyll concentration and water content”, but the calculation of the water content has been described before.
Line 178: please write the version, company and location of the company in brackets; the description, what R is, is not needed.
Line 187-189: It is written that at T1 the sampling site was greener than at any other sampling time, but in the referred figure, only pictures of T0 and T1 are shown. It would be very interesting to also see images of the other time points (T2, 3, 4)
Line 196: The term “However” does not make sense here, as also the other parameters, that were described before, behaved in the same manner.
Figure 2: It would be very helpful to include the statistical results in the figure (letters a, b, c…). The number of replicates should be added in the legend.
Line 263: Delete comma at end of line
Citation: https://doi.org/10.5194/soil-2021-88-RC2 -
AC2: 'Reply on RC2', Capucine Baubin, 10 Jan 2022
Comment on soil-2021-88
Anonymous Referee #2Referee comment on "The response of desert biocrust bacterial communities to hydration- desiccation cycles" by Capucine Baubin et al., SOIL Discuss.,
https://doi.org/10.5194/soil-2021-88-RC2, 2021
Reviewer comments to Baubin et al. “The response of desert biocrust bacterial communities to hydration-desiccation cycles”
General comments: In their manuscript, Baubin and coauthors investigated the presence of bacteria and the chorophyll concentrations as related to hydration-desiccation cycles in biological soil crusts. This is a very interesting and timely topic, as water is considered as one of the dominating factors influencing the microbial composition in biocrusts, and the scientific community just starts to understand the functional roles of different bacteria. However, the manuscript suffers from some major flaws and the results are only superficially analyzed, as described below. Thus, major reviewing is needed before the study can be published in SOIL.Specific comments:
• Sampling methodology: As the first sample was taken in June and the next ones were taken in January of the following year, it would be important to know the climatic conditions before the first sampling and also between the first and the follow-up samplings, as this information is necessary to thoroughly interpret the results. Information on the habitat, where these samples were taken, is missing. What was the surrounding vegetation, how was the geomorphology, what about fog and dew at the site? This information is necessary to the reader to interpret the results.
Following the reviewer’s comment we have added the requested information to the materials and methods section (ln 119-126):“The study was conducted in the long-term ecological research station in the Negev Desert Highlands (Avdat, 30°86'N, 34°46'E, Israel; Figure 1). In this site, the annual rainfall ranges from 20 to 180 mm (average of 90 mm) that extends from October to April (www.data.lter-europe.net). The soil in Avdat is mostly loess sediments in leveled Byzantian agricultural terraces cleared of rocks (Bruins, 2012). Vegetation cover is about 25% dominated by dwarf shrubs, mostly Haloxylon scoparium (Shelef and Groner, 2011). Dew and fog in the area were estimated at 0.1 - 0.2 mm per day (Kidron, 1999; Hill et al., 2020) and occur year round on approximately 200-250 days (Zangvil, 1996).”• I see a major general problem in the presentation and discussion of the results. In this study, the RNA and thus the active organisms were investigated. Thus, the results do not give information on the community composition, but on the composition of active bacteria in biocrusts at different time points before, during and after a rain event. The argumentation thus has to be adopted throughout the manuscript.
We have replaced “community” with “active bacterial community” throughout the manuscript.• Relative abundance at order level: In figure 3, it is hard to tell the colors apart from each other (e.g. Chitinophagales vs. Cytophagales). At the latter also a “p” is missing. It also seems that the sorting of the orders varies from one time point to the next. As an example, in T[R] it seems that “unclassified” is next to the Actinobacterial orders, whereas in T[1] to T[3] it is all the way at the bottom. In the text, only the changes from T[0] to T[1] are described, but the changes from T[R] to T[1] are largely ignored. This is unfortunate, as there are major changes that need to be interpreted (and look quite interesting)!
Figure 3 was fixed (“p” added to Cytophagales and Chitinophagales, Unclassified at the bottom of each bar, and a better colours distinctions for some orders, Proteobacteria in Figure 3 were grouped, coloured in shades of brown and put under the Actinobacteria group, the Chloroplast order was removed as it represented plants and the values in Table S and p-values were changed accordingly). In addition, the. In the manuscript, the changes explained are between T[0] (before rain) and T[R] (during rain) as they are the most pronounced changes. The differences between T[R] and T[1] are not significant, and therefore we did not focus on them afterwards. However, following the reviewer’s comment we added the following (ln 287-303): “Figure 3 shows the active bacterial community composition at the order level for each sampling point. The community is mostly composed of the phyla Cyanobacteria, Actinobacteria, and Proteobacteria in addition to six other phyla (Figure 3; Table S6). During the dry season (T[0]), biocrust community composition differed significantly from the community depicted during the rain event (T[R]) (Figure S3 and S4, Table S7). The differences were shown mostly in orders belonging to the Actinobacteria and Cyanobacteria phyla (Figure 3; p < 0.05, χ2 = 36.7 and χ2 = 49.8, respectively Table S7). The relative abundance of Cyanobacteria, dominated by the Cyanobacteriales, increased during the rain event(T[R]) (from 21% to 41%, Table S6; p < 0.05, χ2 = 49.8, Table S7). While the relative abundance of the Actinobacteria, dominated by Micrococcales, decreased during the rain event (T[R]) (from 52% to 20%, Table S6; p < 0.05, χ2 = 36.7, Table S7). While the biocrust water content decrease after the rain, In the following days , no major changes were detected in the biocrust community (Figure 3; Figure S3 and S4, Table S6 and S7). These patterns were supported by the alpha and beta diversity analyses (Figure S3 and S4). The community diversity significantly differed before the rain (T[0]) and during (T[R]) and after the rain (T[1-3]) (Figure S3, p < -0.05, F-value = 10.96, Table S10 and S11). The diversity in the later timepoints (T[R, 1-3]) did not differ (p>0.04, Table S11). Similarly, the RDA showed that T[0] was separately clustered from the other time points (Figure S4, F-value : 5.75, Table S12 and S13).”. We have also added “T[0]” and “T[R]” whenever “before rain” and “during rain” were written.• Temporal changes in microbial function: the results shown in figure 4 are hardly discussed at all. This is hard to understand, as they look quite interesting as well. It also would be good to include the statistical results in figure 4, as this will facilitate an interpretation of the results without the necessity to search in the supplement.
Following the reviewers comment we have added letters to Figure 4 to denoting the statistical results. We also added text to the results section (ln 418-424): “Figure 4 shows the predicted function based on the taxonomic composition using Piphillin displayed in copy number (CN). The values were significantly lower (p < 0.03; χ2 and p-values in Table A9) in the dry season (T[0]) compared to the hydrated soil (T[R]-[3]), except for light and energy sensing pathways (Figure 4; Table S8). The results suggest that the rain event enhanced activity of the biocrust communities including C and N fixation (phototrophy and organotrophy), as well as preparing for the eminent desiccation by activating stress response pathways (DNA repair and ROS-damage prevention) and persistent mechanisms (sporulation and DNA conservation) (Figure 4; Table S3).”
In addition, we added the following text to the discussion section (ln 449-460): “The increase of water content leads to a “metabolic window” (Leung et al., 2020) for quick energy reservation following the “pulse-reserve” paradigm proposed for plant adaptation to desert ecosystems (Noy-Meir, 1973). In this framework hydration of the biocrust community increased the potential activity of gene groups linked to assimilation of carbon and nitrogen (Figure 4; Table S9). We also detected an increase in the potential motility of the community upon hydration (Figure 4) that could facilitate cells interactions in the soil aqueous phase (Dechesne et al., 2010). Yet, while the community is exploiting of brief water abundance, it also prepares to the unavoidable desiccation and associated stresses, by increasing potential stress mitigation mechanisms like ROS damage prevention and DNA repair (Figure 4; Table S9). In addition, the community prepares to persist during the long draught through potential activation of sporulation and DNA conservation mechanisms (Figure 4; Table S9). These strategies correspond to reports of sizeable fractions of spore forming bacteria in desert biocrusts (Meier et al., 2021; Nunes da Rocha et al., 2015).”• In the discussion (line 269 ff.) the authors wonder why the response to desiccation is slower than the response to hydration, but the results show that desiccation also happens much slower and thus it seems reasonable that the organisms stay active over longer time- spans. This then, indeed, could also be caused partly by EPS, but the argumentation has to be adopted accordingly.
The representation of hydration and desiccation in Figure 2A might be misleading as the X axis is not linear. Soil water content decreased from 16% to 3% within three days of the rain event. Most of the desiccation occurred during the first day (decline of 16% to 6% in the soil water content). Likewise, Kidron and Tal 2012 reported that the biocrust rapidly desiccates because the soil surface, is in direct contact with the atmosphere and thus dries rapidly, immediately after a rain event in the desert (Kidron and Tal, 2012).
• Looking at the statistics of the water contents (Table A4, A5) it seems highly questionable that the water content of T[0] versus T[R] and of T[R] and T[1] should not be significantly different. Thus, the statistics need to be thoroughly checked again!
We have inverted the statistics of the water content and chlorophyll and have corrected the error. For better clarity, we have also added letters on Figure 2 to denote the significance the statistics in the figure.• There are multiple language problems throughout the text, which need to be fixed by a native speaker or professional language editing.
The revised manuscript was proofread by a native speaker.Technical corrections:
• Line 35: The term biome does not completely fit for “arid environments”. Better write “drylands”
Modified• Line 42: Biocrusts are not only fixed by EPS, but also the organisms themselves, as e.g. fungal hyphae, entangle soil particles and thus stabilize the soil matrix.
The sentence was modified (ln 47-50): “Biocrusts are soil surface matrices of phototrophic and heterotrophic microorganisms that bind soil particles, using extracellular polymeric substances in cyanobacterial biocrusts (Kidron et al., 2020; Belnap et al., 2016), or fungal hyphae in lichen and moss biocrusts (Pointing and Belnap, 2012).”• Line 43: I don’t think that “desolate” is always the correct term for biocrust habitats. They could also stabilize the soil in regions where e.g. succession starts again.
The word “desolate” was removed• Line 47: Biocrusts could be a main source of C and N and a strong contributor to soil respiration, but I would not say that this always is the case!
The sentence was modified as followed:” Desert biocrusts are the main source of carbon and nitrogen (Agarwal et al., 2014), and strong contributors to soil respiration (Castillo-Monroy et al., 2011).”• Line 52: It is critical to speak of cryptogams as a “seed bank”. They do not produce seeds and they mainly outlast as desiccated plants and not as seed-like structures or spores.
The sentence was modified as such: “To that end, photosynthetic members of the biocrust community either form a seed bank of species that can spring to life when soil water content increases (Murik et al., 2017; Lennon and Jones, 2011; Kedem et al., 2020) or cryptogams that desiccate and remain dormant until the next rain event (Péli et al., 2011).“• Line 121: The section is named “Chlorophyll concentration and water content”, but the calculation of the water content has been described before.
“water content” was removed from the title• Line 178: please write the version, company and location of the company in brackets; the description, what R is, is not needed.
The description was removed and the following was added :”(version 4.0.0, The R Core)”• Line 187-189: It is written that at T1 the sampling site was greener than at any other sampling time, but in the referred figure, only pictures of T0 and T1 are shown. It would be very interesting to also see images of the other time points (T2, 3, 4)
Pictures of the soil during the other time points were added to Figure 1• Line 196: The term “However” does not make sense here, as also the other parameters, that were described before, behaved in the same manner.
Removed• Figure 2: It would be very helpful to include the statistical results in the figure (letters a, b, c…). The number of replicates should be added in the legend.
Letters were added to Figure 2, 4, S1, and S2• Line 263: Delete comma at end of line
RemovedCitation: https://doi.org/10.5194/soil-2021-88-AC2
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AC2: 'Reply on RC2', Capucine Baubin, 10 Jan 2022
Status: closed
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RC1: 'Comment on soil-2021-88', Anonymous Referee #1, 18 Oct 2021
General comments:
The manuscript entitled “The response of desert biocrust bacterial communities to hydration-desiccations cycles” is an interesting manuscript which focusing on the effects hydration-desiccations cycles on biocrust bacterial communities. The introduction sets scene very nicely and the authors also clearly show the need for studying hydration-desiccations cycle, but see comments below for several ideas that need justification and/or more details. Some parts of the approaches are not appropriate and need more clarification (see comments below about major concern). Although this paper focused on bacterial communities but the results did not provide typical diversity analysis such as alpha and beta diversity. Discussion and conclusion will need to be revised when the major concern has been addressed. Overall, I think that the manuscript idea is interesting and will be valuable for the scientific community. However, additional work is needed to address major concerns and improve several parts of this manuscript to be more transparency and justified.
Title
The title indicates what this research is about but it does not provide any information about key results. I would suggest revising the title to be more specific. What is the key result?
Abstract
Line 20: How does rain-mediated dynamics were assessed? Please explain experimental setup briefly? And provide brief details about bacterial communities measurement.
Line 20: What does active community mean? Active crust community? Active bacterial community? Please be more specific, it is unclear.
Line 22-24: Why focus only on phototrophs? What about other bacteria?
Line 27-28: When Cyanobacteria increased and Actinobacteria decreased, what does it really mean for biocrust?
Introduction
In general, hydration-desiccation cycles were introduced very nicely. However, this paper focused on bacterial communities, but very little information about biocrust bacterial communities was introduced. There are other studies which also focused on biocrust bacterial communities, please introduce them here. What have they done? What were the general bacterial composition? Were there any patterns that other researchers found about biocrust bacterial communities? Is there a reason why this paper should specifically focus on Cyanobacteria and Actinobacteria? Are these the only two phyla found in biocrust?
Line 48 “of soil respiration(Castillo-Monroy et al., 2011)” – add space before parenthesis
Line 50 “trace gases(Meier et al., 2021; ” – add space before parenthesis
Materials and Methods
There are many types of biocrusts. What kind of biocrusts were collected? Were they all the same biocrust types?
Line 86-87: Please provide a reference.
For section 2.6 Community analysis, please report the number of reads in each step (number of raw reads, filtered reads, after chimera removals, etc.).
What is the average number of reads per sample? And what is the range (min – max)?
MAJOR CONCERN! Since the length of the sequences are different because of different platform, please provide details about how the analysis were performed to account for this issue. This section is also crucial in case other researcher would like to follow or repeat the analysis. Please make sure that all the details required for the experiment are included. Currently, it is not sufficient.
Line 172-173: What is the criteria for picking out “genes of interest”?
Results
Generally, simple diversity analysis (alpha and beta diversity) should be provided for microbiome paper. However, only relative abundance plot was provided. I would suggest including alpha and beta diversity analysis to confirm significant differences that were found in relative abundances comparison.
Line 190-201: Statistical test must be provided, reporting p-value only is not sufficient. Please check how statistical test results should be reported. Please also indicate significant differences in figures. Currently, the plots do not have these information.
Line 209-210: In total, how many bacterial phyla were found in these data?
Line 212-216: Please use appropriate statistical results report format. Reporting p-value only is not sufficient.
Figure 3: MAJOR CONCERN! Unless the author provide detailed explanation about how different sequencing platform and primers were accounted for. I think the differences might have been because of different platform used.
Discussion
Line 250: What exactly is “cyanobacterial activity” that was measured? How do we know that it is cyanobacterial activity not other bacteria?
Line 276: Perhaps beta diversity might help confirming this claim.
Conclusion
This might change when different sequencing platforms were taken into account.
Citation: https://doi.org/10.5194/soil-2021-88-RC1 -
AC1: 'Reply on RC1', Capucine Baubin, 10 Jan 2022
Comment on soil-2021-88
Anonymous Referee #1Referee comment on "The response of desert biocrust bacterial communities to hydration- desiccation cycles" by Capucine Baubin et al., SOIL Discuss.,
https://doi.org/10.5194/soil-2021-88-RC1, 2021
General comments:The manuscript entitled “The response of desert biocrust bacterial communities to hydration-desiccations cycles” is an interesting manuscript which focusing on the effects hydration-desiccations cycles on biocrust bacterial communities. The introduction sets scene very nicely and the authors also clearly show the need for studying hydration- desiccations cycle, but see comments below for several ideas that need justification and/or more details. Some parts of the approaches are not appropriate and need more clarification (see comments below about major concern). Although this paper focused on bacterial communities but the results did not provide typical diversity analysis such as alpha and beta diversity. Discussion and conclusion will need to be revised when the major concern has been addressed. Overall, I think that the manuscript idea is interesting and will be valuable for the scientific community. However, additional work is needed to address major concerns and improve several parts of this manuscript to be more transparency and justified.
Title• The title indicates what this research is about but it does not provide any information about key results. I would suggest revising the title to be more specific. What is the key result?
The title was modified to “The function and composition of active bacterial communities diverge during hydration and desiccation of desert biocrust – a field study”
Abstract• Line 20: How does rain-mediated dynamics were assessed? Please explain experimental setup briefly? And provide brief details about bacterial communities measurement.
The abstract was rewritten adding details (ln 25-36): “Here, we assessed rain-mediated dynamics of active bacterial community in the Negev Desert biological soil crust (biocrust) by sampling before, during and after a heavy rainfall, and evaluating the changes in active bacterial composition with amplicon sequencing, potential function, photosynthetic activity, and extracellular polysaccharides (EPS) production. We predicted that rain would resuscitate the biocrust phototrophs (mainly Cyanobacteria), while desiccation would inhibit their activity. In contrast, the biocrust Actinobacteria would decline during rewetting and revive with desiccation. Our results showed that hydration increased chlorophyll content and EPS production. The biocrust rewetting also resuscitated Cyanobacteria, which replaced the former dominant phylum, Actinobacteria, boosting potential autotrophic functions. However, desiccation of the biocrust did not immediately change the bacterial composition or potential function, and was followed by a delayed decrease in chlorophyll and EPS levels. This dramatic shift in the community upon rewetting leads to modifications in the ecosystem services.”
• Line 20: What does active community mean? Active crust community? Active bacterial community? Please be more specific, it is unclear.
To clarify, the sentence was changed to “active bacterial community”.
• Line 22-24: Why focus only on phototrophs? What about other bacteria?
Following the reviewer comment the sentence was modified (ln 24-27): “We predicted that the rain would resuscitate the biocrust phototrophs, mainly the Cyanobacteria, while desiccation would inhibit their activity. In contrast, the biocrust Actinobacteria would decline during rewetting and revive with desiccation.”
• Line 27-28: When Cyanobacteria increased and Actinobacteria decreased, what does it really mean for biocrust?
Following the reviewer comment we added a sentence explaining the reported changes (ln 31-32): “This dramatic shift in the community upon rewetting led to modifications in ecosystem services.”Introduction
• In general, hydration-desiccation cycles were introduced very nicely. However, this paper focused on bacterial communities, but very little information about biocrust bacterial communities was introduced. There are other studies which also focused on biocrust bacterial communities, please introduce them here. What have they done? What were the general bacterial composition? Were there any patterns that other researchers found about biocrust bacterial communities? Is there a reason why this paper should specifically focus on Cyanobacteria and Actinobacteria? Are these the only two phyla found in biocrust?
Following the reviewer comment we added the following information: “The harsh desert conditions shift primary production from plants toward oxygenic photosynthetic microorganism, mostly cyanobacteria (Xu et al., 2021). However, biocrusts are dominated by heterotrophic microorganisms, mainly the phyla Actinobacteria and Proteobacteria (Nunes da Rocha et al., 2015; Meier et al., 2021). Members of these phyla can meet their energy demands during the desert prolonged draughts by harvesting sunlight or atmospheric trace gases (Leung et al., 2020). Studies that focused on biocrust community shifts and cyanobacterial response to hydration-desiccation cycles were carried out under controlled conditions (Angel and Conrad, 2013; Oren et al., 2019; Karaoz et al., 2018).”• Line 48 “of soil respiration(Castillo-Monroy et al., 2011)” – add space before parenthesis Line 50 “trace gases(Meier et al., 2021; ” – add space before parenthesis
AddedMaterials and Methods
• There are many types of biocrusts. What kind of biocrusts were collected? Were they all the same biocrust types?
Following the reviewer comment the following sentence was added: “In this site, the biocrust was identified as type 2 and 3 in some places e.g., well-established cyanobacterial dominated biocrust (Veste et al., 2001; Büdel et al., 2009; Kidron et al., 2015).
• Line 86-87: Please provide a reference.
The reference “(www.data.lter-europe.net)” was added
• For section 2.6 Community analysis, please report the number of reads in each step (number of raw reads, filtered reads, after chimera removals, etc.).
The number of reads at each step were specified in Table S2. To clarify, the following text was modified:” The number of reads at each step can be found in Table S2.”
• What is the average number of reads per sample? And what is the range (min – max)?
The following was added to the text: ”At input, the average number of reads is 86 611 with a minimum number of 22 095 reads and a maximum number of 110 046 reads.”• MAJOR CONCERN! Since the length of the sequences are different because of different platform, please provide details about how the analysis were performed to account for this issue. This section is also crucial in case other researcher would like to follow or repeat the analysis. Please make sure that all the details required for the experiment are included. Currently, it is not sufficient.
The following was added to the text: “We note that the despite the differences in sequencing platforms and primers, the community composition obtained matched previous reports performed at the very same site (Meier et al., 2021; Angel and Conrad, 2013; Bay et al., 2021).”
• Line 172-173: What is the criteria for picking out “genes of interest”?
The text was modified to explain this more clearly: ” We selected these genes in accordance with previous reports (Meier et al., 2021; Bay et al., 2021) and associated them with each step in the KEGG database and built our own database (Table S3).”
Results• Generally, simple diversity analysis (alpha and beta diversity) should be provided for microbiome paper. However, only relative abundance plot was provided. I would suggest including alpha and beta diversity analysis to confirm significant differences that were found in relative abundances comparison.
Following the reviewer comment, the Alpha diversity (Shannon diversity index), and beta diversity (RDA) were added in the supplementary material (Figure S3 and S4, respectively) with the values and the associated statistics. The following text was added: These patterns were supported by the alpha and beta diversity analyses (Figure S3 and S4). The community diversity significantly differed before the rain (T[0]) and during (T[R]) and after the rain (T[1-3]) (Figure S3, p < -0.05, F-value = 10.96, Table S10 and S11). The diversity in the later timepoints (T[R, 1-3]) did not differ (p>0.04, Table S11). Similarly, the RDA showed that T[0] was separately clustered from the other time points (Figure S4, F-value : 5.75, Table S12 and S13).”• Line 190-201: Statistical test must be provided, reporting p-value only is not sufficient. Please check how statistical test results should be reported. Please also indicate significant differences in figures. Currently, the plots do not have these information.
Chi2 and F-values were added to the text. Statistical significance marks were added to the figures.
• Line 209-210: In total, how many bacterial phyla were found in these data?
Nine phyla were detected in the biocrust. This information was added to the text: “The community is mostly composed of the phyla Cyanobacteria, Actinobacteria, and Proteobacteria in addition to six other phyla (Figure 3; Table S6).”
• Line 212-216: Please use appropriate statistical results report format. Reporting p-value only is not sufficient.
Chi2 and F-values were added to the text.
• Figure 3: MAJOR CONCERN! Unless the author provide detailed explanation about how different sequencing platform and primers were accounted for. I think the differences might have been because of different platform used.
This was explained in the Materials and Methods section: “We note that the despite the differences in sequencing platforms and primers, the community composition obtained matched previous reports performed at the very same site (Meier et al., 2021; Angel and Conrad, 2013; Bay et al., 2021).”Discussion
• Line 250: What exactly is “cyanobacterial activity” that was measured? How do we know that it is cyanobacterial activity not other bacteria?
Chlorophyll content was measured as a proxy of cyanobacterial activity. The text was modified following the reviewer comment:” Though the chlorophyll content, a proxy of cyanobacterial activity, increased with soil moisture (Figure 2A), no significant changes were detected in the total organic carbon C or N (Figure S1 and S2; Table S4 and S5).”
• Line 276: Perhaps beta diversity might help confirming this claim.
Beta diversity helped to confirm the claim and therefore a reference to Figure S4 was added to the text.
Conclusion• This might change when different sequencing platforms were taken into account.
The main conclusion was not modified as despite the difference sequencing platforms the community matched previous reports describing the community at the same site (Meier et al., 2021; Angel and Conrad, 2013; Bay et al., 2021).Citation: https://doi.org/10.5194/soil-2021-88-AC1
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AC1: 'Reply on RC1', Capucine Baubin, 10 Jan 2022
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RC2: 'Comment on soil-2021-88', Anonymous Referee #2, 05 Dec 2021
Reviewer comments to Baubin et al. “The response of desert biocrust bacterial communities to
hydration-desiccation cycles”
General comments: In their manuscript, Baubin and coauthors investigated the presence of bacteria and the chorophyll concentrations as related to hydration-desiccation cycles in biological soil crusts. This is a very interesting and timely topic, as water is considered as one of the dominating factors influencing the microbial composition in biocrusts, and the scientific community just starts to understand the functional roles of different bacteria. However, the manuscript suffers from some major flaws and the results are only superficially analyzed, as described below. Thus, major reviewing is needed before the study can be published in SOIL.
Specific comments:
Sampling methodology: As the first sample was taken in June and the next ones were taken in January of the following year, it would be important to know the climatic conditions before the first sampling and also between the first and the follow-up samplings, as this information is necessary to thoroughly interpret the results. Information on the habitat, where these samples were taken, is missing. What was the surrounding vegetation, how was the geomorphology, what about fog and dew at the site? This information is necessary to the reader to interpret the results.
I see a major general problem in the presentation and discussion of the results. In this study, the RNA and thus the active organisms were investigated. Thus, the results do not give information on the community composition, but on the composition of active bacteria in biocrusts at different time points before, during and after a rain event. The argumentation thus has to be adopted throughout the manuscript.
Relative abundance at order level: In figure 3, it is hard to tell the colors apart from each other (e.g. Chitinophagales vs. Cytophagales). At the latter also a “p” is missing. It also seems that the sorting of the orders varies from one time point to the next. As an example, in T[R] it seems that “unclassified” is next to the Actinobacterial orders, whereas in T[1] to T[3] it is all the way at the bottom. In the text, only the changes from T[0] to T[1] are described, but the changes from T[R] to T[1] are largely ignored. This is unfortunate, as there are major changes that need to be interpreted (and look quite interesting)!
Temporal changes in microbial function: the results shown in figure 4 are hardly discussed at all. This is hard to understand, as they look quite interesting as well. It also would be good to include the statistical results in figure 4, as this will facilitate an interpretation of the results without the necessity to search in the supplement.
In the discussion (line 269 ff.) the authors wonder why the response to desiccation is slower than the response to hydration, but the results show that desiccation also happens much slower and thus it seems reasonable that the organisms stay active over longer time-spans. This then, indeed, could also be caused partly by EPS, but the argumentation has to be adopted accordingly. Looking at the statistics of the water contents (Table A4, A5) it seems highly questionable that the water content of T[0] versus T[R] and of T[R] and T[1] should not be significantly different. Thus, the statistics need to be thoroughly checked again!
There are multiple language problems throughout the text, which need to be fixed by a native speaker or professional language editing.
Technical corrections:
Line 35: The term biome does not completely fit for “arid environments”. Better write “drylands”
Line 42: Biocrusts are not only fixed by EPS, but also the organisms themselves, as e.g. fungal hyphae, entangle soil particles and thus stabilize the soil matrix.
Line 43: I don’t think that “desolate” is always the correct term for biocrust habitats. They could also stabilize the soil in regions where e.g. succession starts again.
Line 47: Biocrusts could be a main source of C and N and a strong contributor to soil respiration, but I would not say that this always is the case!
Line 52: It is critical to speak of cryptogams as a “seed bank”. They do not produce seeds and they mainly outlast as desiccated plants and not as seed-like structures or spores.
Line 121: The section is named “Chlorophyll concentration and water content”, but the calculation of the water content has been described before.
Line 178: please write the version, company and location of the company in brackets; the description, what R is, is not needed.
Line 187-189: It is written that at T1 the sampling site was greener than at any other sampling time, but in the referred figure, only pictures of T0 and T1 are shown. It would be very interesting to also see images of the other time points (T2, 3, 4)
Line 196: The term “However” does not make sense here, as also the other parameters, that were described before, behaved in the same manner.
Figure 2: It would be very helpful to include the statistical results in the figure (letters a, b, c…). The number of replicates should be added in the legend.
Line 263: Delete comma at end of line
Citation: https://doi.org/10.5194/soil-2021-88-RC2 -
AC2: 'Reply on RC2', Capucine Baubin, 10 Jan 2022
Comment on soil-2021-88
Anonymous Referee #2Referee comment on "The response of desert biocrust bacterial communities to hydration- desiccation cycles" by Capucine Baubin et al., SOIL Discuss.,
https://doi.org/10.5194/soil-2021-88-RC2, 2021
Reviewer comments to Baubin et al. “The response of desert biocrust bacterial communities to hydration-desiccation cycles”
General comments: In their manuscript, Baubin and coauthors investigated the presence of bacteria and the chorophyll concentrations as related to hydration-desiccation cycles in biological soil crusts. This is a very interesting and timely topic, as water is considered as one of the dominating factors influencing the microbial composition in biocrusts, and the scientific community just starts to understand the functional roles of different bacteria. However, the manuscript suffers from some major flaws and the results are only superficially analyzed, as described below. Thus, major reviewing is needed before the study can be published in SOIL.Specific comments:
• Sampling methodology: As the first sample was taken in June and the next ones were taken in January of the following year, it would be important to know the climatic conditions before the first sampling and also between the first and the follow-up samplings, as this information is necessary to thoroughly interpret the results. Information on the habitat, where these samples were taken, is missing. What was the surrounding vegetation, how was the geomorphology, what about fog and dew at the site? This information is necessary to the reader to interpret the results.
Following the reviewer’s comment we have added the requested information to the materials and methods section (ln 119-126):“The study was conducted in the long-term ecological research station in the Negev Desert Highlands (Avdat, 30°86'N, 34°46'E, Israel; Figure 1). In this site, the annual rainfall ranges from 20 to 180 mm (average of 90 mm) that extends from October to April (www.data.lter-europe.net). The soil in Avdat is mostly loess sediments in leveled Byzantian agricultural terraces cleared of rocks (Bruins, 2012). Vegetation cover is about 25% dominated by dwarf shrubs, mostly Haloxylon scoparium (Shelef and Groner, 2011). Dew and fog in the area were estimated at 0.1 - 0.2 mm per day (Kidron, 1999; Hill et al., 2020) and occur year round on approximately 200-250 days (Zangvil, 1996).”• I see a major general problem in the presentation and discussion of the results. In this study, the RNA and thus the active organisms were investigated. Thus, the results do not give information on the community composition, but on the composition of active bacteria in biocrusts at different time points before, during and after a rain event. The argumentation thus has to be adopted throughout the manuscript.
We have replaced “community” with “active bacterial community” throughout the manuscript.• Relative abundance at order level: In figure 3, it is hard to tell the colors apart from each other (e.g. Chitinophagales vs. Cytophagales). At the latter also a “p” is missing. It also seems that the sorting of the orders varies from one time point to the next. As an example, in T[R] it seems that “unclassified” is next to the Actinobacterial orders, whereas in T[1] to T[3] it is all the way at the bottom. In the text, only the changes from T[0] to T[1] are described, but the changes from T[R] to T[1] are largely ignored. This is unfortunate, as there are major changes that need to be interpreted (and look quite interesting)!
Figure 3 was fixed (“p” added to Cytophagales and Chitinophagales, Unclassified at the bottom of each bar, and a better colours distinctions for some orders, Proteobacteria in Figure 3 were grouped, coloured in shades of brown and put under the Actinobacteria group, the Chloroplast order was removed as it represented plants and the values in Table S and p-values were changed accordingly). In addition, the. In the manuscript, the changes explained are between T[0] (before rain) and T[R] (during rain) as they are the most pronounced changes. The differences between T[R] and T[1] are not significant, and therefore we did not focus on them afterwards. However, following the reviewer’s comment we added the following (ln 287-303): “Figure 3 shows the active bacterial community composition at the order level for each sampling point. The community is mostly composed of the phyla Cyanobacteria, Actinobacteria, and Proteobacteria in addition to six other phyla (Figure 3; Table S6). During the dry season (T[0]), biocrust community composition differed significantly from the community depicted during the rain event (T[R]) (Figure S3 and S4, Table S7). The differences were shown mostly in orders belonging to the Actinobacteria and Cyanobacteria phyla (Figure 3; p < 0.05, χ2 = 36.7 and χ2 = 49.8, respectively Table S7). The relative abundance of Cyanobacteria, dominated by the Cyanobacteriales, increased during the rain event(T[R]) (from 21% to 41%, Table S6; p < 0.05, χ2 = 49.8, Table S7). While the relative abundance of the Actinobacteria, dominated by Micrococcales, decreased during the rain event (T[R]) (from 52% to 20%, Table S6; p < 0.05, χ2 = 36.7, Table S7). While the biocrust water content decrease after the rain, In the following days , no major changes were detected in the biocrust community (Figure 3; Figure S3 and S4, Table S6 and S7). These patterns were supported by the alpha and beta diversity analyses (Figure S3 and S4). The community diversity significantly differed before the rain (T[0]) and during (T[R]) and after the rain (T[1-3]) (Figure S3, p < -0.05, F-value = 10.96, Table S10 and S11). The diversity in the later timepoints (T[R, 1-3]) did not differ (p>0.04, Table S11). Similarly, the RDA showed that T[0] was separately clustered from the other time points (Figure S4, F-value : 5.75, Table S12 and S13).”. We have also added “T[0]” and “T[R]” whenever “before rain” and “during rain” were written.• Temporal changes in microbial function: the results shown in figure 4 are hardly discussed at all. This is hard to understand, as they look quite interesting as well. It also would be good to include the statistical results in figure 4, as this will facilitate an interpretation of the results without the necessity to search in the supplement.
Following the reviewers comment we have added letters to Figure 4 to denoting the statistical results. We also added text to the results section (ln 418-424): “Figure 4 shows the predicted function based on the taxonomic composition using Piphillin displayed in copy number (CN). The values were significantly lower (p < 0.03; χ2 and p-values in Table A9) in the dry season (T[0]) compared to the hydrated soil (T[R]-[3]), except for light and energy sensing pathways (Figure 4; Table S8). The results suggest that the rain event enhanced activity of the biocrust communities including C and N fixation (phototrophy and organotrophy), as well as preparing for the eminent desiccation by activating stress response pathways (DNA repair and ROS-damage prevention) and persistent mechanisms (sporulation and DNA conservation) (Figure 4; Table S3).”
In addition, we added the following text to the discussion section (ln 449-460): “The increase of water content leads to a “metabolic window” (Leung et al., 2020) for quick energy reservation following the “pulse-reserve” paradigm proposed for plant adaptation to desert ecosystems (Noy-Meir, 1973). In this framework hydration of the biocrust community increased the potential activity of gene groups linked to assimilation of carbon and nitrogen (Figure 4; Table S9). We also detected an increase in the potential motility of the community upon hydration (Figure 4) that could facilitate cells interactions in the soil aqueous phase (Dechesne et al., 2010). Yet, while the community is exploiting of brief water abundance, it also prepares to the unavoidable desiccation and associated stresses, by increasing potential stress mitigation mechanisms like ROS damage prevention and DNA repair (Figure 4; Table S9). In addition, the community prepares to persist during the long draught through potential activation of sporulation and DNA conservation mechanisms (Figure 4; Table S9). These strategies correspond to reports of sizeable fractions of spore forming bacteria in desert biocrusts (Meier et al., 2021; Nunes da Rocha et al., 2015).”• In the discussion (line 269 ff.) the authors wonder why the response to desiccation is slower than the response to hydration, but the results show that desiccation also happens much slower and thus it seems reasonable that the organisms stay active over longer time- spans. This then, indeed, could also be caused partly by EPS, but the argumentation has to be adopted accordingly.
The representation of hydration and desiccation in Figure 2A might be misleading as the X axis is not linear. Soil water content decreased from 16% to 3% within three days of the rain event. Most of the desiccation occurred during the first day (decline of 16% to 6% in the soil water content). Likewise, Kidron and Tal 2012 reported that the biocrust rapidly desiccates because the soil surface, is in direct contact with the atmosphere and thus dries rapidly, immediately after a rain event in the desert (Kidron and Tal, 2012).
• Looking at the statistics of the water contents (Table A4, A5) it seems highly questionable that the water content of T[0] versus T[R] and of T[R] and T[1] should not be significantly different. Thus, the statistics need to be thoroughly checked again!
We have inverted the statistics of the water content and chlorophyll and have corrected the error. For better clarity, we have also added letters on Figure 2 to denote the significance the statistics in the figure.• There are multiple language problems throughout the text, which need to be fixed by a native speaker or professional language editing.
The revised manuscript was proofread by a native speaker.Technical corrections:
• Line 35: The term biome does not completely fit for “arid environments”. Better write “drylands”
Modified• Line 42: Biocrusts are not only fixed by EPS, but also the organisms themselves, as e.g. fungal hyphae, entangle soil particles and thus stabilize the soil matrix.
The sentence was modified (ln 47-50): “Biocrusts are soil surface matrices of phototrophic and heterotrophic microorganisms that bind soil particles, using extracellular polymeric substances in cyanobacterial biocrusts (Kidron et al., 2020; Belnap et al., 2016), or fungal hyphae in lichen and moss biocrusts (Pointing and Belnap, 2012).”• Line 43: I don’t think that “desolate” is always the correct term for biocrust habitats. They could also stabilize the soil in regions where e.g. succession starts again.
The word “desolate” was removed• Line 47: Biocrusts could be a main source of C and N and a strong contributor to soil respiration, but I would not say that this always is the case!
The sentence was modified as followed:” Desert biocrusts are the main source of carbon and nitrogen (Agarwal et al., 2014), and strong contributors to soil respiration (Castillo-Monroy et al., 2011).”• Line 52: It is critical to speak of cryptogams as a “seed bank”. They do not produce seeds and they mainly outlast as desiccated plants and not as seed-like structures or spores.
The sentence was modified as such: “To that end, photosynthetic members of the biocrust community either form a seed bank of species that can spring to life when soil water content increases (Murik et al., 2017; Lennon and Jones, 2011; Kedem et al., 2020) or cryptogams that desiccate and remain dormant until the next rain event (Péli et al., 2011).“• Line 121: The section is named “Chlorophyll concentration and water content”, but the calculation of the water content has been described before.
“water content” was removed from the title• Line 178: please write the version, company and location of the company in brackets; the description, what R is, is not needed.
The description was removed and the following was added :”(version 4.0.0, The R Core)”• Line 187-189: It is written that at T1 the sampling site was greener than at any other sampling time, but in the referred figure, only pictures of T0 and T1 are shown. It would be very interesting to also see images of the other time points (T2, 3, 4)
Pictures of the soil during the other time points were added to Figure 1• Line 196: The term “However” does not make sense here, as also the other parameters, that were described before, behaved in the same manner.
Removed• Figure 2: It would be very helpful to include the statistical results in the figure (letters a, b, c…). The number of replicates should be added in the legend.
Letters were added to Figure 2, 4, S1, and S2• Line 263: Delete comma at end of line
RemovedCitation: https://doi.org/10.5194/soil-2021-88-AC2
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AC2: 'Reply on RC2', Capucine Baubin, 10 Jan 2022
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