The Impact of Flooding on Soil Microbial Communities and Their Functions: A Review

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

The article reviews the impact of flood on soil microbial communities and the factors such as heavy rainfall, flash floods, and seawater intrusion. The authors describe microbial adaptations to the flooding conditions, examining both freshwater and saline environments, and discuss how understanding these dynamics is critical for sustainable agriculture and soil health management in flood-prone areas.

The introduction is currently divided into subsections. However, I suggest removing subsection titles, to create a more logical progression of its paragraphs. For example, after introducing the broader context (importance of soil) the article can move into discussing soil microbes' roles and then move to the specific context of flooding and climate change. Additionally in my opinion general background is covered more than needed, so it could be reduced. The novelty of the review in relation to recent research should be clearly stated. It should be mentioned what specific knowledge gap this article addresses.

Figure 1 description seems a little too informal and vague. It should be changed. For example, starting with a schematic representation of soil microbial functions critical for maintaining soil health and plant productivity.

Chapters 2-5 cover flooding effects on ecosystems, microbial adaptations (both freshwater and saline), impacts on microbial structure, soil health, and plant productivity. For clarity each chapter could use short introductory sentences explaining what will be discussed and how it connects to the previous section. The number of citations within some sections (for example microbial adaptation to saline conditions, microbial community structural changes) could be expanded. There’s limited direct comparison or critical analysis of differing results or interpretations from various sources. Many statements are presented authoritatively without acknowledgement of differing perspectives, while critical comparison would be beneficial. For example: “While Liu et al. (2020) reported a significant reduction in aerobic microbes, González Macé et al. (2016) found the opposite, noting recovery of aerobic populations over time. These conflicting outcomes suggest microbial responses may vary depending on flooding duration, plant species, or soil type.”

Some figures and tables are included, but additional summary tables could improve readability.

The description of Figure 2 is somewhat lengthy. A figure caption should be concise but informative. Clearly describe what’s visually represented, avoiding detailed explanations better suited to the main text. For example start with: Flooding-induced changes in soil microbial communities and associated ecosystem processes.

The description of Table 1 needs to be improved to inform readers about the table's content or purpose. For example: Summary of experimental studies assessing plant-growth-promoting microorganisms (PGPMs) and their effects on plant responses under flooding stress conditions.

The article is consistent with recent findings in the field. The review summarizes current knowledge, but it could be improved by discussing gaps, unanswered questions and promising research directions.

The conclusions could be somewhat rewritten to serve as a better ending for the manuscript. The main points should be stated more shortly, and knowledge gaps and suggestions for future studies parts expanded. Detailed repetitions from the rest of the manuscript should be avoided.

After corrections, the article should be reviewed again before it is considered for publication.

Comments on the Quality of English Language

The manuscript is quite well-written but it would benefit from an additional proofreading and editing by the authors and/ or an external specialist review to correct such issues as minor grammatical errors like awkward constructions or missing articles, consistency in tense usage, minor typographical errors or consistency in abbreviations (once defined, abbreviations should replace full terms to avoid redundancy). It would be useful if a native speaker would check the language as well.

Author Response

Dear Editor,

Thanks a lot for providing us the opportunity to submit the revised version of our manuscript entitled "Flooding Impacts’ on Soil Microbial Communities and their Functions: A Review" to the journal of Stresses. We are really grateful to you and the reviewers for giving valuable insights and comments for the improvement of our manuscript. We have corrected all the comments and suggestions provided by the reviewers. The changes done in the manuscript are highlighted with red color within the manuscript.

Point-by-point responses to the Reviewer comments

Reviewer 1

Comment 1: The article reviews the impact of flood on soil microbial communities and the factors such as heavy rainfall, flash floods, and seawater intrusion. The authors describe microbial adaptations to the flooding conditions, examining both freshwater and saline environments, and discuss how understanding these dynamics is critical for sustainable agriculture and soil health management in flood-prone areas.

Response: Thank you, Dear Reviewer, for your critical and insightful evaluation of our MS.

 

Comment 2: The introduction is currently divided into subsections. However, I suggest removing subsection titles, to create a more logical progression of its paragraphs. For example, after introducing the broader context (importance of soil) the article can move into discussing soil microbes' roles and then move to the specific context of flooding and climate change. Additionally in my opinion general background is covered more than needed, so it could be reduced. The novelty of the review in relation to recent research should be clearly stated. It should be mentioned what specific knowledge gap this article addresses.

Response:

1. We appreciate your suggestions to improve our MS. We removed the subsections and kept maintaining the flow of importance of soil and the challenges of soil microorganisms under flooded soil.
2. According to your suggestion, we trimmed the general background from the introduction.
3. We would like to thank you again for identifying the most critical gaps in our MS. In this revised MS, we amended the novelty of the MS along with the previous knowledge gaps that we have addressed in our MS. We believe your valuable suggestions allow us to improve our MS. Please see in below;

“Since the late 20th century, many regions worldwide have experienced rising flood risks due to increased precipitation, with forecasts predicting a continued and substantial increase in these risks (detailed discussion in the next section) (Kundzewicz et al., 2014). Beyond the loss of human lives and property damages, flooding has a direct impact on agriculture, particularly cropland damage (D. Cressman et al., 1988; Nandy & Kumar, 2024). Soil is home to a vast and diverse array of microorganisms, which experience profound changes due to flooding-induced O₂ depletion, leading to anaerobic conditions. These conditions favor certain microbial groups, such as denitrifiers and methanogens, while being detrimental to others, which results in a shift in microbial community structure and a disruption in the normal function of soil biodiversity. These alterations have cascading effects on nutrient cycling, reducing nutrient availability for plant uptake and limiting crop productivity. Plant breeding programs also ignore the continuous shifting of microbial dynamics due to climate change, which needs to be revisited (Raza et al. 2025). Therefore, we aimed for a comprehensive and collective understanding of flooding and soil microorganisms that has been denied previously (Philippot et al. 2024; Filho et al. 2023; Xu et al. 2020). Based on the recent studies on microbial responses to flooding, we focused on how flooding, including freshwater and saline areas, reshapes microbial structures, the interconnected relation with soil nutrients, their adaptation strategies, and long-term soil health outcomes, an area that has remained a critical yet underexplored knowledge gap. Finally, how plant-growth-promoting microorganisms act as saviors for the plants when under flooding is also discussed briefly. Overall, this review will offer a holistic understanding of managing soil biodiversity to sustain crop production under excessive soil water conditions, which is an excepted challenge to intensify with the increase of erratic precipitation patterns near future (Panagos et al., 2022).“

 

Comment 3: Figure 1 description seems a little too informal and vague. It should be changed. For example, starting with a schematic representation of soil microbial functions critical for maintaining soil health and plant productivity.

Response: According to your suggestion, we revised the Figure 1 title. Please see in below;

“Figure 1. Schematic representation of key soil microbial functions that are critical for maintaining soil health and supporting plant productivity. These functions include nutrient cycling, organic matter decomposition, symbiotic interactions with host plants (nodulation in legumes), and the stimulation of nutrient mineralization processes, all of which contribute to a resilient and functional belowground ecosystem.”

 

Comment 4: Chapters 2-5 cover flooding effects on ecosystems, microbial adaptations (both freshwater and saline), impacts on microbial structure, soil health, and plant productivity. For clarity, each chapter could use short introductory sentences explaining what will be discussed and how it connects to the previous section. The number of citations within some sections (for example microbial adaptation to saline conditions, microbial community structural changes) could be expanded. There’s limited direct comparison or critical analysis of differing results or interpretations from various sources. Many statements are presented authoritatively without acknowledgement of differing perspectives, while critical comparison would be beneficial. For example: “While Liu et al. (2020) reported a significant reduction in aerobic microbes, González Macé et al. (2016) found the opposite, noting recovery of aerobic populations over time. These conflicting outcomes suggest microbial responses may vary depending on flooding duration, plant species, or soil type.”

Response:

1. Thank you for your critical evaluation. From sections 2-5, we revised these sections with a short introductory sentence that connects with the previous part. First, discussing the flooding impacts on the total ecosystem, in section 3, we connect how belowground ecosystems are important for maintaining soil health with the help of microorganisms, and then the flooding impacts on microorganisms.

“3. Mechanisms of flooding-induced changes in soil microbial communities

Soil microorganisms regulate the belowground ecosystem for maintaining soil health, which has a direct influence on aboveground biodiversity. Among various climate-induced disasters, flooding in the form of heavy precipitation and flash floods has a primary and profound impact on the complex soil ecosystem. Understanding the flooding impacts on soil microorganisms is crucial for developing sustainable strategies to protect soil biodiversity and ensure agricultural resilience under changing climatic conditions. This section examines how flooding induces a shift from aerobic to anaerobic soil conditions, emphasizing the factors influencing microbial adaptation, community restructuring, and interactions with key soil physio-chemical properties.” 

     

1. In section 4, we connect how the microbial changes under anaerobic conditions have long-term soil health and crop productivity.

“4. Flooding impact on long-term soil health and crop productivity

The changes in soil microbial structure and soil nutrient dynamics under frequent flooding events are intensively threatening beneficial microorganisms, which are essential for plant health, crop productivity, food security, and environmental sustainability (IPCC, 2022; Reed et al., 2022).”

 

1. In section 5, we connected how long-term negative effects of flooding can be mitigated with the help of plant growth-promoting microorganisms.
2. According to your suggestions, we added more citations based on the peer-reviewed research findings, meta-analysis, model study, and review article as well. (Line: 288-310; )
3. We apologize for the lack of critical interpretations and perspectives in our submitted MS. And thank you for mentioning to us to improve our MS. Based on your suggestions, we revised our MS, where we added more interpretations on the findings that we reviewed. We believe this improvement will enhance the readability of our MS. (Line: 288-310; 335-339; 347-354; and many more).

For example:

“Similar to this result, a meta-analysis of 109 fields with elevated precipitation has increased microbial biomass up to 18% (Xu et al., 2020), pointing to the increased soil water regulating total microbial growth. For instance, Unger et al. (Unger et al., 2009) observed a notable reduction in aerobic microbes, while González Macé et al. (González Macé et al., 2016) reported the opposite, noting recovery of aerobic populations over time, possibly due to adaptation depending on flooding depth and duration. Following a natural flood, Wagner et al. (Wagner et al., 2015) reported a decrease in Gram-negative bacterial composition, which is primarily rhizosphere-associated (Söderberg et al., 2004), indicating a cascading negative impact of flooding on plant health (Wright et al., 2015). In contrast, Gram-positive bacteria were less affected, while fungal biomass increased significantly (Figure 2). This increase may be attributed to fungi’s superior ability to degrade low-quality dead organic material (Berg & McClaugherty, 2008), which allows them to adapt to low O₂ conditions. However, contrary findings have also been reported, where fungal presence decreased in flooded soils (Unger et al., 2009). Further complexity arises in metal-contaminated flood-prone soils, where the microbial biomass carbon and soil organic carbon (SOC) ratios declined, indicating polluted soils are more detrimental for soil health (Szili-Kovács & Takács, 2024). In contrast, afforestation sharply increased the fungal residual carbon as well as showed a positive interaction with SOC in flooded Marshland, even in different soil layers (Tang et al., 2024). Overall, these conflicting outcomes suggest that microbial responses to flooding are influenced by multiple interacting factors, including flooding duration, plant species, and soil types and their properties.”

 

 

Comment 5: The description of Figure 2 is somewhat lengthy. A figure caption should be concise but informative. Clearly describe what’s visually represented, avoiding detailed explanations better suited to the main text. For example start with: Flooding-induced changes in soil microbial communities and associated ecosystem processes.

Response: According to your suggestion and suggestions from Reviewer 2, we revised the Figure 2 title. Please see in below;

“Figure 2. Flooding-induced changes in soil microbial communities and associated ecosystem processes (A). Excess water in the rhizosphere reduces oxygen availability, promoting anaerobic microbial respiration and altering microbial composition and soil physio-chemical properties (B). These shifts impact gas exchange, microbial biomass, and ecosystem functions depending on flood duration and soil conditions.”

 

Comment 6: The description of Table 1 needs to be improved to inform readers about the table's content or purpose. For example: Summary of experimental studies assessing plant-growth-promoting microorganisms (PGPMs) and their effects on plant responses under flooding stress conditions.

Response: According to your suggestion, we revised the Table 1 title. Please see in below;

“Table 1. Summary of experimental studies assessing plant-growth-promoting microorganisms (PGPMs) and their effects on plant responses under flooding stress conditions.”

 

Comment 7: Some figures and tables are included, but additional summary tables could improve readability.

Response: We are grateful for your efforts to improve our MS. Although we respect your suggestions, we revised this current MS by adding a precise summary of the peer-reviewed articles in the text; therefore, we do not feel an additional summary table is necessary in this case. We will consider your suggestion for our future work. So, it would be appreciated if you could consider this issue.

Comment 8: The article is consistent with recent findings in the field. The review summarizes current knowledge, but it could be improved by discussing gaps, unanswered questions and promising research directions.

Response: Thank you for your insightful evaluations. In the revised MS, we amended the knowledge gaps and promising research directions. Please see a few revised parts in the current MS.

“Nonetheless, it’s difficult to say that all halotolerant microbes can grow in saline water conditions, as neither test has been done till today. Overall, these findings indicate that saline water environments have a great influence on soil microorganisms.”  

“Therefore, when soil pH is thought to be a crucial factor for bacterial community structure (Qiqige et al., 2025), critical knowledge gaps remain regarding how the changes in soil pH influence microbial communities under varying flooding intensities. Similarly, the long-term stability of microbial functions under fluctuating redox conditions is not well understood.”

“Yet, the long-term plant-microbe-soil dynamics remain largely unexplored in different soil types and agroecosystems, which limits our ability to accurately assess its effects.”

 “However, understanding how fungi manage the trade-offs involved in forming networks with plant roots has long been a challenge. A recent breakthrough study by Oyarte Galvez et al. (Oyarte Galvez et al., 2025) revealed that symbiotic fungi regulate the network-level structure and flow dynamics of their networks to meet the nutrient demands of plants. Fungi achieve this by continuously transporting nutrients to the roots through widened hyphal tubes. This newly identified mechanism provides deeper insights into how beneficial fungal communities support soil health and enhance crop productivity under adverse climatic conditions.”

“Particularly, studying the responses of genetically modified ACCD-produced microbial strains and plants under flooding stress could provide the key to understanding their symbiotic interactions that regulate the acclimation process. Moreover, it is still unknown how the application of PGPMs could regulate the flooding effects on crop production in field conditions when all studies have been explored in the greenhouse.”

Comment 9: The conclusions could be somewhat rewritten to serve as a better ending for the manuscript. The main points should be stated more shortly, and knowledge gaps and suggestions for future studies parts expanded. Detailed repetitions from the rest of the manuscript should be avoided.

Response: According to your suggestions, we rewrote the conclusions part, focusing on the main points and suggestions for future studies.

“6. Conclusions

Climate change intensifies extreme precipitation events, resulting in more frequent flooding. Flooding alters the soil structure, nutrient availability, fertility, and biogeochemical cycles, together with the eroded topsoil and nutrients. Excess water levels highly influence the soil microbial communities due to the low O₂ conditions. However, moderate flooding may benefit nutrient cycling and enhance soil microbial biodiversity by increasing habitat diversity. Soil microorganisms are vital for the long-term sustainability of soil ecosystems. Flooding notably affects soil microorganisms by decreasing aerobic microbes and changing the overall microbial community composition, depending on the flood duration and intensity. Microorganisms in freshwater and saline environments adapt in various ways, such as growing on surfaces, forming communities, maintaining osmotic balance within their cells, accumulating compatible solutes and inorganic potassium to achieve osmotic equilibrium, and evolving their genomes. However, the mechanisms governing microbial community shifts and resilience in flooded soils are not fully elucidated. 

In parallel to microorganisms, long-term flooding can delay planting time, shorten the growing season, and lower crop yields. It also encourages pests and diseases, resulting in additional losses. Economic hardships for farmers and damage to agricultural infrastructure further obstruct future crop production. Importantly, PGPMs support plant growth under flooding conditions by lowering ethylene levels and improving nutrient uptake. However, microorganisms with ACCD enzyme activity possess both beneficial and detrimental effects on plants, which are yet to be well-understood. Besides, the mechanisms by which these microbes regulate plant physiology under complete submergence remain largely unexplored. Therefore, long-term monitoring is necessary to understand how microbial communities recover after flooding, the potential for microbial adaptation and resilience, and the management strategies to mitigate negative impacts on soil health and promote recovery after flood events.”

 

Comment 10: After corrections, the article should be reviewed again before it is considered for publication.

Response: We appreciate your valuable time and efforts.

Comment 11: The manuscript is quite well-written but it would benefit from an additional proofreading and editing by the authors and/ or an external specialist review to correct such issues as minor grammatical errors like awkward constructions or missing articles, consistency in tense usage, minor typographical errors or consistency in abbreviations (once defined, abbreviations should replace full terms to avoid redundancy). It would be useful if a native speaker would check the language as well.

Response: We appreciate your suggestions. The manuscript has been thoroughly revised and checked by native English speakers.

 

Author Response File: Author Response.pdf

Reviewer 2 Report

Comments and Suggestions for Authors

1. Lines 34-67. The authors should expand the literature review to include a more comprehensive range of studies on the effects of flooding on soil microbial communities. This could include meta-analyses, recent reviews, and primary research articles from different regions and ecosystems. Additionally, they should discuss the broader context of how flooding impacts soil health and plant-microbe interactions, including potential long-term effects and mitigation strategies.
2. Lines 185-234. The authors should reorganize this section to provide a more coherent and logical flow. They could start with the initial impact of flooding on soil oxygen levels, followed by the subsequent effects on microbial communities, nutrient cycling, and plant-microbe interactions.
3. Lines 520-616. The manuscript mentions the potential benefits of PGPMs but does not provide specific instances or mechanisms by which these microorganisms mitigate flooding stress. The authors should provide more detailed examples and case studies of PGPMs in action. They could discuss specific strains of bacteria or fungi that have been shown to enhance plant growth under flooding conditions, along with the mechanisms by which they achieve this.
4. Lines 89–91. The manuscript broadly categorizes flooding as "short-term" (one week) or "long-term" (three months) but lacks explicit definitions of hydrological parameters (e.g., water depth, frequency, soil saturation level). For example, Figure 2 contrasts "waterlogging" and "submergence" but does not clarify how these terms differ operationally. Standardizing definitions (e.g., following FAO or IPCC guidelines) and providing detailed experimental conditions in cited studies would improve reproducibility and cross-study comparisons.
5. The manuscript cites non-peer-reviewed sources and heavily relies on review articles rather than primary research for critical claims (e.g., flood-induced soil erosion impacts, Line 489). For instance, the statement about global economic losses (Line 511) lacks a primary reference. Replacing these with peer-reviewed studies or meta-analyses would bolster credibility.

Comments on the Quality of English Language

The manuscript is fluent in language.

Author Response

Dear Editor,

Thanks a lot for providing us the opportunity to submit the revised version of our manuscript entitled "Flooding Impacts’ on Soil Microbial Communities and their Functions: A Review" to the journal of Stresses. We are really grateful to you and the reviewers for giving valuable insights and comments for the improvement of our manuscript. We have corrected all the comments and suggestions provided by the reviewers. The changes done in the manuscript are highlighted with red color within the manuscript.

Point-by-point responses to the Reviewer comments

Reviewer 2

Comment 1: Lines 34-67. The authors should expand the literature review to include a more comprehensive range of studies on the effects of flooding on soil microbial communities. This could include meta-analyses, recent reviews, and primary research articles from different regions and ecosystems. Additionally, they should discuss the broader context of how flooding impacts soil health and plant-microbe interactions, including potential long-term effects and mitigation strategies.

Response: Thank you, Dear Reviewer, for your critical and insightful evaluation of our MS. According to your suggestions, we have revised the current MS. We have included more studies based on meta-analysis, primary research articles, and reviews as well. Besides, we improved the discussion of the flooding impacts on soil health and long-term effects, and mitigation strategies. We believe this revised version will give more clearer understanding with a broader context. Thank you again for pointing out the lack of our MS and giving us a chance to improve it.

Comment 2: Lines 185-234. The authors should reorganize this section to provide a more coherent and logical flow. They could start with the initial impact of flooding on soil oxygen levels, followed by the subsequent effects on microbial communities, nutrient cycling, and plant-microbe interactions.

Response: According to your suggestions, we maintained the logical flow by providing more precise discussion of the flooding impact on oxygen level and its impact on the belowground ecosystems. Please see sections 2-5.

Comment 3: Lines 520-616. The manuscript mentions the potential benefits of PGPMs but does not provide specific instances or mechanisms by which these microorganisms mitigate flooding stress. The authors should provide more detailed examples and case studies of PGPMs in action. They could discuss specific strains of bacteria or fungi that have been shown to enhance plant growth under flooding conditions, along with the mechanisms by which they achieve this.

Response: We appreciate your critical evaluation and efforts to improve our MS. We believe understanding the specific mechanisms by which PGPMs elevate the plant tolerance is important. Here, we improved the current version by providing more in-depth discussion.  Please see below some examples how we tried to improve it.

“Microorganisms are known as a feasible and promising substitute for sustainable agricultural practices by maintaining the proper ecological functions. These microorganisms are referred to as “plant-growth-promoting microorganisms” (PGPMs) (Trivedi et al., 2021). PGPMs, including bacteria, fungi, and other microorganisms, play a crucial role in plant growth and stress tolerance through nitrogen fixation, phosphate solubilization, and the production of bioactive compounds. Additionally, PGPMs produce various plant growth regulators to enhance plant growth and development, such as cytokinin, IAA, and GA (Backer et al., 2018; Maheshwari et al., 2023). In particular, the application or presence of PGPMs in the rhizosphere supports crop production by maintaining a symbiotic relationship with plants. Together with substantial progress in utilizing PGPMs in plant development under stress conditions, the belowground ecosystem faces the first challenges due to flooding stress, where microorganisms and plants both compromise their normal physiological activities (Table 1) (Ali & Kim, 2018; Kumar et al., 2024; Martínez-Arias et al., 2022). A recent model study identified several PGPMs isolated from the waterlogged greenhouse soil that exhibited plant growth-promoting traits, including phosphorus and potassium solubilization, ammonia and organic acid production, as well as amylase and cellulase activity (Senko et al., 2024). These results suggest that when such PGPMs establish associations with plants in the rhizosphere, they can exchange essential nutrients and confer biocontrol properties, thereby enhancing plant tolerance under anaerobic conditions. Although the importance of PGPMs under waterlogged conditions is being increasingly studied (Ali & Kim, 2018), the mechanisms by which these microbes regulate plant physiology under complete submergence remain largely unexplored. Similarly, a comprehensive understanding of PGPMs under flooding conditions, supported by recent findings, is still lacking (Tyagi et al., 2024; Verma et al., 2024; Zhang et al., 2025). Therefore, we here discuss the recent progress on PGPMs-based studies in plant physiology under inundated soils.”

 

“This facilitated O₂ transport from the aerated tissue to the root, thereby enhancing carbohydrate metabolism and improving plant growth (Hu et al., 2022). At this point, it is clear that AMF contributes largely to plant resilience to flooding through antioxidant stimulation, osmolyte accumulation, and improved nutrient uptake. However, understanding how fungi manage the trade-offs involved in forming networks with plant roots has long been a challenge. A recent breakthrough study by Oyarte Galvez et al. (Oyarte Galvez et al., 2025) revealed that symbiotic fungi regulate the network-level structure and flow dynamics of their networks to meet the nutrient demands of plants. Fungi achieve this by continuously transporting nutrients to the roots through widened hyphal tubes. This newly identified mechanism provides deeper insights into how beneficial fungal communities support soil health and enhance crop productivity under adverse climatic conditions.”

 

“Some studies suggest that ACCD-producing PGPR does not confer noteworthy improvement under submergence conditions. For example, when the ACCD-producing Mesorhizobium ciceri LMS-1 (pRKACC) transformed strain was applied to chickpea (Cicer arietinum) under waterlogging conditions, despite its beneficial effect on nodulation under control conditions, no significant differences in plant growth and nodulation were observed under waterlogging stress (Nascimento et al., 2012). A riparian plant Rumex palustris treated with an ACCD-producing bacterium P. putida UW4, led to an impeded ethylene-mediated hyponastic growth response (Ravanbakhsh et al., 2017). Compared to the ACCD-deficient mutant, shoot elongation and dry weight were reduced. This study suggests that while ACCD-mediated ethylene reduction generally alleviates flooding stress, it can also interfere with plant-specific submergence adaptation mechanisms, potentially leading to growth inhibition. Although ethylene accumulation is a key factor under low O₂ conditions, its role is not always directly linked to enhancing plant resilience. Furthermore, as PGPMs also produce other advantageous phytohormones in addition to ACCD (Spaepen & Vanderleyden, 2011), the PGPMs-induced flooding tolerance may be attributed to microbial characteristics rather than the ACCD enzyme activity alone. These findings exhibit that microbial strategies for mitigating flooding stress must consider the complex interactions between plant species, microbial traits, and environmental conditions. These discrepancies in ACCD-mediated ethylene regulation during plant development under low O₂ conditions need to be clarified (Figure 2). Particularly, studying the responses of genetically modified ACCD-produced microbial strains and plants under flooding stress could provide the key to understanding their symbiotic interactions that regulate the acclimation process. Moreover, it is still unknown how the application of PGPMs could regulate the flooding effects on crop production in field conditions when all studies have been explored in the greenhouse.”

   

 

Comment 4: 4.    Lines 89–91. The manuscript broadly categorizes flooding as "short-term" (one week) or "long-term" (three months) but lacks explicit definitions of hydrological parameters (e.g., water depth, frequency, soil saturation level). For example, Figure 2 contrasts "waterlogging" and "submergence" but does not clarify how these terms differ operationally. Standardizing definitions (e.g., following FAO or IPCC guidelines) and providing detailed experimental conditions in cited studies would improve reproducibility and cross-study comparisons.

Response: We apologize for the mistake. We revised this issue in the current MS, combining suggestions from both you and Reviewer 1. We revised the figure title and figure as well as the text. Please see in below.

Figure 2. Flooding-induced changes in soil microbial communities and associated ecosystem processes (A). Excess water in the rhizosphere reduces oxygen availability, promoting anaerobic microbial respiration and altering microbial composition and soil physio-chemical properties (B). These shifts impact gas exchange, microbial biomass, and ecosystem functions depending on flood duration and soil conditions.

 

Comment 5: The manuscript cites non-peer-reviewed sources and heavily relies on review articles rather than primary research for critical claims (e.g., flood-induced soil erosion impacts, Line 489). For instance, the statement about global economic losses (Line 511) lacks a primary reference. Replacing these with peer-reviewed studies or meta-analyses would bolster credibility.

Response: According to your queries, we revised the current version.

“Although flooding causes negative impacts on soil health, it has some advantages too. It restores soil moisture, supplies nutrients, and supports the growth of microbes suited to anaerobic conditions (Szejgis et al., 2024; Talbot et al., 2018; Tockner & Stanford, 2002; Tonkin et al., 2018). In anaerobic conditions, flooding encourages the growth of denitrifying microbes, which thrive in low-oxygen environments and contribute to nitrogen cycling in the soil (González Macé et al., 2016). This type of nutrient balance is essential for the survival of crops and microorganisms during prolonged flooding conditions. In some instances, flooding can enhance soil structure by redistributing particles, improving water infiltration and aeration after the water recedes. Nitrogen-fixing blue-green algae grow in submerged fields, and alternating oxygen-reduction and oxidation cycles enhance soil fertility (Brammer, 1988; Hofer & Messerli, 2006). Importantly, the decomposition of carbon-rich debris in flooded fields also enriches soil fertility. However, the long-term benefits depend on the intensity and duration of flooding as well as the existing soil ecosystem (Szejgis et al., 2024).

In a long-term perspective, flooding can delay planting schedules, shorten the growing season, and reduce crop yields (Dar et al., 2017). Standing water creates favorable conditions for pests and disease outbreaks, directly impacting crop yields in subsequent seasons (Kaur et al., 2020). Significant crop losses due to flooding may also cause economic hardship for farmers, impacting their income and ability to invest in future crop production (Rahaman, 2017). Additionally, floodwaters can damage irrigation systems, drainage channels, farm roads, and other infrastructure, hindering future agricultural operations (Tasleem et al., 2023; Wilbanks et al., 2013). Mitigation strategies such as improving drainage, reducing tillage, residue retention, and cover cropping could minimize the damage. Recent reports exhibited that flooding already accounts for the global economic losses in the field crops, exceeding 1.5 billion annually (Kaur et al., 2020; Ploschuk et al., 2022; Wu et al., 2019). Moreover, yield losses were estimated from 20 to 50% when soils were inundated with water for more than 10 days (Hossain & Uddin, 2011). In contrast, flooding helps replenish groundwater, enrich soil nutrients, and improve soil structure (Banerjee, 2010), which could facilitate crop yields. Floodwaters can carry and deposit nutrient-rich sediment containing nitrogen and phosphorus, enhancing soil fertility and providing essential minerals for plant growth (Gao et al., 2024; WMO, 2006). Yet, the long-term plant-microbe-soil dynamics remain largely unexplored in different soil types and agroecosystems, which limits our ability to accurately assess its effects.”

 

Comment 6: The manuscript is fluent in language.

Response: Thank you for your valuable time and efforts on our MS.

 

Author Response File: Author Response.pdf