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Review

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

by
Ashim Kumar Das
1,
Da-Sol Lee
1,
Youn-Ji Woo
1,
Sharmin Sultana
2,
Apple Mahmud
3 and
Byung-Wook Yun
1,*
1
Department of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
2
Department of Crop, Soil and Environmental Sciences, Auburn University, Auburn, AL 36849, USA
3
Department of Agronomy, Gazipur Agricultural University, Gazipur, 1706, Bangladesh
*
Author to whom correspondence should be addressed.
Stresses 2025, 5(2), 30; https://doi.org/10.3390/stresses5020030
Submission received: 18 March 2025 / Revised: 26 April 2025 / Accepted: 29 April 2025 / Published: 2 May 2025
(This article belongs to the Section Plant and Photoautotrophic Stresses)
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Abstract

:
Soil microorganisms provide multifaceted benefits, including maintaining soil nutrient dynamics, improving soil structure, and instituting decomposition, all of which are important to soil health. Unpredictable weather events, including flooding from heavy rainfall, flash floods, and seawater intrusion, profoundly impact soil ecology, which is primarily challenged by flooding stress, and imbalances these microbial communities and their functions. This disturbance impairs the symbiotic exchanges between microbes and plants by limiting root exudates and habitats for microbes, as well as nutrient acquisition efficiency for plants. Therefore, this review comprehensively examines the changes in soil microbial communities that occur under flooding conditions. Flooding reduces soil oxygen (O2) levels, limiting aerobic microbes but promoting anaerobic ones, including potential pathogens. In flooded soil, O2 deficiency indirectly depends on the size of the soil particles and water turbidity during flooding. O2 depletion is critical in shaping microbial community adaptation, which is linked to variations in soil pH, nutrient concentrations, and redox status, and fresh and saline water vary differently in terms of the adaptation of microorganisms. Wet soil alters soil enzyme activity, which influences microbial community composition. Notably, three-month post-flooding conditions allow microbial communities to adapt and stabilize more effectively than once-weekly flooding frequency. Based on the presence of aboveground species, fungi are found to reduce under flooding conditions, while nematode numbers, surprisingly, increase. Direct and indirect impacts between soil microbes and physio-chemical properties indicate positive or negative feedback loops that influence the soil ecosystem. Over the years, beneficial microorganisms such as plant-growth-promoting microbes (PGPMs) have been identified as important in regulating soil nutrients and microbial communities in wetland environments, thereby enhancing soil health and promoting better plant growth and development. Overall, understanding the mechanisms of belowground ecosystems under flooding conditions is essential for optimizing agricultural practices and ensuring sustainable crop production in flood-prone areas.

1. Introduction

Since the inception of soil development on Earth, the existence of life has been intricately tied to the biosphere. Directly or indirectly, nearly all organisms depend on soil for essential resources such as nutrients, water, and habitat. Plants and animals, which rely on these resources, produce primary foods for humans, who cannot otherwise make their own food. Soil is predominantly a habitat for microorganisms, including bacteria, fungi, archaea, and other microbes, which play crucial roles in nutrient cycling, organic matter decomposition, and maintaining soil health [1]. However, this dynamic process faces significant challenges, with two major issues: adverse climatic conditions and a rapidly growing global population that is projected to reach 9.73 billion by 2050 [2]. While “Save Soil, Save Earth” is a global initiative, increasing arable land can be problematic, and soil continues to be degraded (by 2 billion ha of land, which is 38% of global cropland) through erosion, salinization, and compaction, which have long-term implications for agroecosystems [3,4,5,6,7]. These aforementioned issues further exacerbate the pressure on the soil to meet the growing food demands of overpopulation.
Maintaining soil health is closely linked to a diverse and abundant community of soil microorganisms, which enhance fertility, nutrient cycling, and soil structure, directly benefiting agricultural productivity (Figure 1) [8,9]. One of the most essential nutrients for all living organisms is nitrogen (N). Although atmospheric dinitrogen (N2) constitutes 78% of the atmosphere, it is unavailable for direct use by plants [10]. Consequently, a diverse range of soil microbes facilitates N availability through key processes such as N fixation, nitrification, denitrification, anammox, and ammonification, ensuring the continuity of the N cycle in ecosystems (Figure 1) [11]. Representative prokaryotes, including free-living, aerobic, anaerobic, phototrophic, and chemoorganotrophic microorganisms modulate N fixation [11]. Moreover, a group of rhizobia-based symbiotic microorganisms that fix N within the root nodules of legume plants is commonly known to meet N requirements and enhance crop yields [12]. These microbes convert N2 into ammonium (NH4+), a bioavailable form, through enzymatic processes driven by nitrogenase activity, significantly contributing to ecosystem N cycling [13]. Biological N fixation in cropland is estimated at 60 Tg N annually, which is 30% of global N fixation [14]. In addition to N, the solubilization of P and K by soil microorganisms is well studied, and ongoing research increasingly focuses on microbial activities that release essential micronutrients such as Ca, Mg, Fe, Mn, and Zn into the rhizosphere [15,16]. These processes often involve organic acid production, enzyme activity, and chelation processes. Furthermore, arbuscular mycorrhizal fungi (AMF) significantly improve plant uptake of water and essential nutrients, such as N, P, K, Ca, and minor elements. AMF utilize their extensive hyphal networks to access resources beyond the root zone, thereby facilitating nutrient acquisition and improving plant health (Figure 1) [17,18]. Impoverished soil hinders the infiltration and distribution of water and oxygen (O2) throughout its structure, which restricts space for roots and soil fauna, disrupting both aerobic and anaerobic processes. These challenges collectively impair nutrient turnover and availability, impact plant growth, and complicate pest and disease management, along with pollutant degradation [7,19]. Soil microorganisms play an imperative role in improving soil structure by secreting “glue-like” substances, including mucilage, extracellular polysaccharides, and fungal hyphae, which contribute to soil aggregation during the decomposition of organic matter [20]. This aggregation process helps to improve water and O2 distribution, facilitates root penetration, reduces nutrient runoff, and enriches soil biodiversity [7]. Therefore, maintaining soil health and its associated ecosystems is essential to prevent degradation, and this requires continuous monitoring, protection, and sustainable practices.
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 (a detailed discussion follows in the next section) [21]. Beyond the loss of human lives and property damage, flooding also has a direct impact on agriculture, particularly cropland damage [22,23]. The 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 the microbial community structure and disruption of the normal functions 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 [24]. Therefore, we aimed for a comprehensive and collective understanding of flooding and soil microorganisms, which has been absent previously [25,26,27]. Based on recent studies regarding microbial responses to flooding, we focused on how flooding, including freshwater and saline areas, reshapes microbial structures, the interconnected relationships of 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 floodwaters 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 likely to become ever more necessary with the expected increase in erratic precipitation patterns in the near future [28].

2. Flooding Impacts on the Ecosystem

Water is essential for all agriculture and food systems and for sustainable development [29]. However, excessive water can have disastrous effects on people and the ecosystem. In lower-income countries where infrastructure systems, such as drainage and flood protection, are often underdeveloped, floods can cause severe damage and suffering [30]. It is estimated that 1.81 billion people (23% of the world’s population) are directly exposed to 1-in-100-year floods, with 1.24 billion of them residing in South and East Asia [31]. The Food and Agriculture Organization (FAO) recognized flooding as the second-largest disaster type (next to drought), costing USD 21 billion in crop and livestock losses from 2008 to 2018 [32]. Nonetheless, the frequency of flooding was higher than that of other disasters between 1998 and 2017 [33]. These effects emphasize that flooding can severely impact food security and disrupt the ecological balance with other climatic disasters.
Recent case studies and projections of flood-prone areas have explored the impacts of flooding on livelihoods, coupled with the surrounding ecosystems and agriculture. Meanwhile, Bangladesh, a country in the southeast region, is designated as the most vulnerable country on the planet to climate change [34,35]. Kamruzzaman et al. [36] reported that in Bangladesh, average temperatures are projected to rise by up to 3.76 °C, and annual precipitation could increase by 52.6%, reaching up to 3446.38 mm by the year 2100, according to CMIP6 global climate models. Moreover, a recent assessment of flood impact and future susceptibility management of the 2020 flooding incidents in the northeastern region of Bangladesh, conducted by Rahman et al. [37], demonstrated that 67.87% of cropland and 10.69 million people were affected. This alarming projection could have devastating consequences for the agriculture-based country of Bangladesh if not addressed proactively. Jointly with Bangladesh, its bordering country of India has already faced devastating floods that killed and displaced thousands of people due to erratic rainfall [38,39]. Similarly, Bhutan expects a 57% and 81% increase in rainfall in the near future (2040–2065) and into the far future (2075–2100), which poses a significant risk to agricultural production and ecosystems, as 75% of Bhutan’s population depends on agriculture [40]. Moreover, a flood hazard map assessment revealed that 87% of the Gwagwalada area in Nigeria is at risk of flooding, with profound socioeconomic impacts on the community across income, education, agriculture, sanitation, infrastructure, and property [41]. Additionally, major flooding events became more frequent in Pakistan from 1950 to 2023 [42], with 1.6 million hectares of farmland destroyed and economic losses estimated between USD 30 and 35 billion [43]. The above-mentioned findings concern near-future climatic uncertainties that could particularly influence the loss of agriculture and are challenging in terms of providing risk management support in advance. Moreover, accurately assessing climatic parameters remains a significant challenge in predicting future flooding risks.
While the effects of flooding are predominantly negative, there can also be indirect positive outcomes [44], including flooding resulting in a reduction in greenhouse gas emissions, nitrogen, and phosphorus leaching, and improved sedimentation [45]. However, these small benefits do not compensate for the overall economic losses. Moreover, a comprehensive assessment of flooding on agricultural land in Bangladesh, specifically focusing on rice and jute productivity from 1978–2000, revealed that flood-prone areas typically experienced higher agricultural productivity during normal floods, although extreme flooding led to yield reductions in subsequent months [46]. Floating agriculture is gaining importance in flood-prone areas of Bangladesh, where long-term waterlogging makes it difficult for farmers to continue agricultural production [47]. Similar to these findings, other flood adaptation measures require immediate attention in flood-prone areas, which could reduce the extensive losses caused by uncertain flooding events. To this end, the Consultative Group on International Agricultural Research (CGIAR) has suggested six individual management strategies to increase the productivity of flood-based farming systems, including water distribution, field water management, groundwater use, agronomic practices, multi-functional use, and internal governance [48]. By following these strategies, flood-prone areas can strengthen their flood resilience and minimize its negative impact.

3. Mechanisms of Flooding-Induced Changes in Soil Microbial Communities

Soil microorganisms regulate the belowground ecosystem to maintain soil health, which has a direct influence on aboveground biodiversity. Among the various climate-induced disasters, flooding in the form of heavy precipitation and flash floods has a primary and profound impact on complex soil ecosystems. Understanding the impact of flooding 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.

3.1. Flooding Leading to Soil Oxygen Reduction, Creating Anaerobic Environments

Excess water, inadequate drainage systems, and the presence of natural wetlands can significantly restrict O2 diffusion in the water-saturated pore spaces of soil [49]. Under warm soil conditions, where microbial respiration is spurred on, O2 depletion can occur rapidly, often within 24 h. This leads to a transition from fully aerobic to anaerobic conditions, whereby soil habitats face O2 deficiency [50]. In particular, the partial loss of O2 is called hypoxia, while the complete absence of O2 is termed anoxia [51]. This condition significantly restricts gas movements depending on soil pore sizes [52]. Large pores facilitate gas transportation, whereas small pores hinder it. The wetting of the soil increases the respiration of anaerobic microorganisms, which consume O2 along with the roots and other soil fauna [53]. Importantly, anaerobic microorganisms are responsible for producing greenhouse gases under wetland conditions, such as N2O and CH4 [54,55]. A recent study also noted the increase in CO2 levels associated with the enhancement of O2 depletion [56]. As flooding events are increasing globally, concerns have arisen regarding the potential for anaerobic microorganisms to amplify greenhouse gas emissions. Wet soil can also improve the availability of C and N substrates [57,58], thereby supporting microbial activity that enhances the soil’s O2 consumption rate [59]. The anaerobic process is also essential for specific organisms and the ecosystem, and it cannot be overlooked totally. The availability of O2 is crucial, both above and below the Earth’s surface. Therefore, a deeper understanding of O2 dynamics and their relationship with microbial processes is necessary, as these factors are interconnected and regulate soil biodiversity under flooding conditions. Beyond flooding analysis, it is essential to focus on how these factors balance soil ecosystems in the context of a continuously changing climate.

3.2. Adaptation of Microorganisms in Freshwater

Flooding dramatically alters the physical, chemical, and biological properties of soil, and favors to the selective microbial communities that can only survive under O2-depleted conditions [60]. Adaptations of microorganisms include traits such as endospore formation, the production of osmoprotectants, and specialized cell wall structures, all of which enhance microbial resistance and resilience to hydrological stress [61,62]. Different energy metabolism types also allow microbial survival under such conditions: for example, anaerobic and facultative respiration, fermentation, and microaerophilic systems [61,62,63]. The interplay between soil physicochemical properties and water availability is critical in shaping microbial community adaptation. Variables such as pH, nutrient concentrations, and redox status significantly influence microbial dynamics, establishing mechanisms that link water regimes to edaphic properties [64,65,66]. Additionally, denitrification increases dramatically under anaerobic conditions and in areas with a high nitrogen input, where microbes utilize nitrate (NO3−) as an alternative terminal electron acceptor, reducing it to nitrite, nitric oxide, nitrous oxide, or N2 gas [67].
O2 shifting beneath the Earth’s surface promotes microbial taxa with both anaerobic and occasionally aerobic respiratory capabilities, influencing the soil ecosystem either beneficially or detrimentally. Soil flooding mostly increases the abundance of anaerobic taxa, including Firmicutes, Desulfobacterota, methanogens, and Geobacteraceae [68,69,70,71]. Actinobacteria and Proteobacteria can survive in both aerobic and anaerobic conditions; however, studies have shown that their abundance decreased after 12 days of flooding in wheat-grown soil [68,69]. In particular, a few beneficial species of these microbial taxa decreased, including Spinghomonas, Streptomyces, Saccharimonadia, Massilia, and Flavobacterium, indicating that flooding negatively regulates beneficial microorganisms for plants. For example, Saccharimonadia species are commonly known for their nitrogen uptake efficiency and ability to enhance nutrient turnover [72,73], while Massilia and Flavobacterium species solubilize phosphate, produce siderophores, and produce plant growth-promoting hormones such as auxin and salicylic acid, as well as antifungal chitinases and hydrogen cyanide [74,75,76,77]. Liu et al. [71] found a decreased abundance of Chloroflexi, which is important for organic matter (OM) degradation, nitrogen removal, biofilm formation, and other beneficial processes [78,79]. Alongside the reduction of beneficial microbial taxa, soil flooding in wheat fields promotes the proliferation of harmful anaerobic taxa, such as Clostridium species [68], which increase under heavy rainfall and flooding conditions, leading to soft rot disease in vegetables [80]. In contrast, varying flooding regimes in bald cypress seedlings (under sterile and non-sterile conditions) promoted the growth of AMF. AMF suppresses the colonization of pathogenic oomycetes, thereby enhancing plant growth [81]. Recent findings elucidate the role of AMF symbiosis in enhancing the resilience of Medicago truncatula under waterlogged conditions [82]. Specifically, a transgenic line, ha1-2, which was unable to establish functional symbiosis with AMF due to a defective proton pump that is essential for phosphate transport from AMF to the plant, exhibited impaired symbiotic interactions compared to the wild-type plant, indicating the importance of AMF in supporting plant adaptation to waterlogged environments.

3.3. Adaptation of Microorganisms to Saline Water

Anaerobic conditions, when combined with salinity, significantly influence soil microbial communities. Coastal wetlands are home to several halotolerant bacterial taxa, including Gammaproteobacteria, Alphaproteobacteria, Bacteroidetes, and Verrucomicrobia [83]. These microbes contribute to soil health by sequestering toxic ions, producing phytohormones, and synthesizing antimicrobial compounds that suppress pathogen growth. They also contribute to nutrient transport and cycling, thereby supporting plant resilience under saline conditions. For example, tidal saltwater flooding in black mangroves has been shown to decrease nitrification and denitrification, while increasing nitrogen content in mangrove leaves [84]. This rise in nitrogen boosts leaf production and shoot growth. In regions with denser and taller mangroves, higher levels of mineralizable nitrogen are observed, likely due to the accumulation of organic nitrogen from long-term litter production, belowground biomass, and root turnover. Elevated soil moisture in these regions creates less toxic conditions, further promoting nitrogen retention [84]. These findings highlight the significant role of climatic fluctuations, such as sea-level rise, and hydrological stress in influencing nitrogen cycling. For example, the mangrove ecosystem is a unique ecosystem located along the coastlines in both tropical and sub-tropical regions [85]. Coastal tides in the mangroves have an enormous influence on soil microbial communities [86], where their relationship is interdependent [85]. Several beneficial microbes have been isolated from the rhizosphere of tree species in mangrove areas, including Stenotrophomonas maltophilia [87], Bacillus amyloliquefaciens NAR38.1 [88], Microbulbifer mangrovi DD-13T [89], Pseudomonas hussainii MB3 [90], and many more nitrogen-fixing [91] and phosphate-solubilizing microbes [92]. In contrast, a group of pathogenic microbial species was also isolated from the rhizosphere of mangroves [93,94]. However, in addition to identifying microbial species, investigating the influence of tidal fluctuations on microbial communities would be valuable for understanding how these communities respond to changes in soil oxygen dynamics. Such insights could enhance our understanding of saline water-induced climatic impacts on soil microbial ecology. Furthermore, a vast range of halotolerant microbes with proton-pumping capacity (Na+ and K+) have been tested in different media [95]. In particular, Halobacillus halophilus, a nutritionally enriched microbe found in salt marsh soil, has been found to grow across a wide range of salt concentrations [95]. Nonetheless, it is difficult to say whether all halotolerant microbes can grow in saline water conditions, as neither test has been performed until today. Overall, these findings indicate that saline water environments have a significant influence on soil microorganisms.

3.4. Impacts on Soil Microbial Structure and Biomass Under Flooded Conditions

Hydrological changes, for example, extreme dry or wet soil conditions, influence aboveground biomass and diversity, which, in turn, directly or indirectly alter soil microbial composition. Here, we explore the causes and impacts of such disturbances on the microbial community and soil ecosystems, particularly when anaerobic conditions are expected to drive these shifts through competition for nutrients, aboveground-derived carbon inputs, and other related factors. After reviewing the published studies, significant discrepancies were observed in the reported effects of flooding on soil microbial biomass, community composition, structure, and diversity. Soil microbial biomass refers to the total living microbial mass present in the soil, while the microbial community structure and diversity represent the composition and relative abundance of different microbial taxa within the soil ecosystem.
The proper functioning of soil microorganisms relies on enzyme activity, which is essential for organic matter decomposition and nutrient cycling [96]. Both microbial and plant-derived enzymes break down complex organic compounds like cellulose, chitin, and lignin into smaller molecules that can be utilized by microbes and plants [97]. O2 availability is a key factor influencing microbial community composition by altering soil enzyme activities [98]. González Macé et al. [99] reported that flooding significantly increased the activity of phenol oxidase, peroxidase, and 1,4-β-N-acetylglucosaminidase, particularly in plots under prolonged flooding. This suggests that long-term flooding promotes chitin and lignin degradation due to an accumulation of dead organic material. Thus, three months of post-flooding activity had a more pronounced effect on microbial biomass, compared to a one-week flooding period (Figure 2). Similar to this result, a meta-analysis of 109 fields with elevated precipitation identified increased microbial biomass of up to 18% [27], pointing to the increased soil water regulating total microbial growth. For instance, Unger et al. [62] observed a notable reduction in aerobic microbes, while González Macé et al. [99] reported the opposite, noting the recovery of aerobic populations over time, possibly due to adaptation, depending on flooding depth and duration. Following a natural flood, Wagner et al. [100] reported a decrease in Gram-negative bacterial composition, which is primarily rhizosphere-associated [101], indicating a cascading negative impact of flooding on plant health [102]. 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 [103], which allows them to adapt to low O2 conditions. However, contrary findings have also been reported, where the fungal presence decreased in flooded soils [62]. Further complexity arises in metal-contaminated flood-prone soils, where microbial biomass carbon and soil organic carbon (SOC) ratios have declined, indicating that polluted soils are more detrimental to soil health [104]. In contrast, afforestation sharply increased the fungal residual carbon, as well as showing a positive interaction with SOC in flooded marshland, even in the different soil layers [105]. 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. Beyond bacteria and fungi, nematodes exhibited a significant increase post-flooding [100]. This rise was likely driven by an abundance of dead plant and animal biomass, particularly in species-rich aboveground biomass, where plant roots may enhance soil porosity, promoting nematode growth.
Phospholipid fatty acid (PLFA) analysis is a widely used method for microbial community characterization, as it utilizes membrane phospholipids and helps to overcome the limitations of selective culturing [106]. This approach has been extensively applied to study soil microbial communities in flooded environments [107,108]. However, differences in PLFA composition and microbial biomass have been observed between greenhouse and field studies [109]. For instance, under stagnant flooding conditions in greenhouse experiments, microbial biomass was reduced [62], whereas field studies on flooded riparian wetland soils reported significantly higher microbial biomass, with a mean value of 29.36 nmol g−1 [110]. Field soils often support more diverse and resilient microbial communities, which may help these microbes better adapt to flooding than those in controlled conditions. However, some studies have also found no significant changes in total PLFA content concerning microbial biomass and community structure in flooded paddy soils [111,112]. Similarly, post-flood microbial diversity in sandy loam soil remained statistically unchanged (p > 0.05) [113]; even after a three-week recovery period, the microbial community structure closely resembled that of non-flooded soil. In cropland soil, its high organic matter and carbon content may contribute to microbial resilience to flooding [113]. These variations in soil microbial responses to flooding could be influenced by multiple factors, including soil type, water depth, aboveground biomass, and nutrient composition, which collectively regulate soil ecosystem dynamics.
Additionally, pronounced plant diversity intensified O2 limitations in flooded plots due to increased root biomass and root respiration. This led to greater microbial biomass and respiration [114,115,116]. A positive correlation between plant diversity and microbial biomass was observed in soils subjected to two months of flooding [100]. This positive interaction has a direct impact on soil health by enhancing nutrient cycling, soil structure, and ecosystem resilience. Moreover, soil bacterial community composition was found to be influenced by altitude, with low-elevation sites harboring greater bacterial diversity than high-elevation sites [117]. This difference may be attributed to longer flooding durations in low-elevation lakeshore wetlands, which could support a greater abundance of bacterial taxa, enabling them to adapt better to prolonged inundation. Flooding-induced shifts in microbial communities are interconnected with multiple environmental factors, and further in-depth studies are needed to identify and link these factors.

3.5. Interconnected Influences Between Soil Microorganisms and Nutrients in Wetlands

Excess water in the soil significantly alters nutrient availability, which regulates the belowground ecosystem. Along with O2 depletion, changes in soil physicochemical properties, including macro- and micronutrients, influence various direct and indirect mechanisms that shape soil microbial composition (Figure 2). Under waterlogged conditions, N application has been shown to increase microbial abundance and bacterial diversity, while simultaneously compromising C-degrading enzyme activities, leading to reduced microbial respiration rates [118]. Moreover, the SOC and pH exhibit an antagonistic relationship under flooding conditions [110]. This opposite interaction starts with the introduction of nitrate (NO3−) and ferric iron (Fe3+) into the soil during flooding conditions, when they participate in redox reactions and consume large amounts of protons. This process leads to a rise in pH and a reduction in SOC [119]. In contrast, no significant changes in soil pH and its effects on bacterial communities were observed across spatial and inter-annual scales in lakeshore wetlands [117]. Therefore, while soil pH is thought to be a crucial factor in terms of bacterial community structure [120], critical knowledge gaps remain regarding how these 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.
Research shows that when agronomic fields are contaminated by mining drainage systems, soil pH levels start to decrease, but increased Fe and Mn appear together with Geobacteracea-related species, a Fe-reducing bacterial family [110,121]. Additionally, Fe(II)-oxidizing bacteria, such as Gallionellales, were found to increase under flooding conditions, contributing to the reduction in Fe(III) [69]. The increased availability of Fe and Mn involvement plays a critical role in facilitating heavy metal uptake (Cd, Cr, Cu, Pb, Zn, and Ni) by aboveground plant species. The release of heavy metals into the soil is responsible for Fe/Mn dissolution [122] by enhancing Fe/Mn-reducing activity [123]. This process is driven by an increase in Fe-reducing bacteria under long-term flooding conditions [124]. Moreover, a heavy-metal-contaminated flooding area could also increase the possibilities of metal availability in the soil [104]. These findings are alarming for crop production as flooded soils facilitate the mobilization and uptake of heavy metals by plant roots. Furthermore, the role of AMF and dark septate endophytes (DSE) is beneficial under extreme flooding events. Their colonization resulted in a six-fold increase in bald cypress seedling growth in non-sterile soil [81] and helped with an increase in soil C, N, S, Mg, and Zn [81]. However, P content has declined; since P is often a limiting nutrient in wetlands, plants rely on AMF and DSE symbiosis to enhance P acquisition. This suggests that in exchange for P, plants may allocate significant amounts of C to the soil, influencing microbial dynamics and nutrient cycling. In contrast, Liu et al. [71] reported that NO3-N and NH4-N have been found to negatively influence bacterial community composition in flooded environments (Figure 2). NO3-N and NH4-N can promote nitrate reduction and increase ammonium toxicity by favoring denitrifying and facultative anaerobic bacteria while suppressing aerobic bacterial communities. This suggests that flooding hinders the nitrogen balance, leading to functional shifts in microbial growth.

4. Impact of Flooding on Long-Term Soil Health and Crop Productivity

The changes seen 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 [125,126]. Such flooding has long-term detrimental effects on soil, soil biology, and overall health, which are harmful to microscopic and macroscopic soil-dwelling organisms. The negative impacts of flooding hinder the breakdown of plant residues, disrupt the recycling of nutrients, and ultimately limit crop growth [127]. Flood-induced soil erosion takes nutrient-rich topsoil containing essential elements like phosphorus, nitrogen, and carbon, all of which are essential for crop growth [128,129]. Additionally, the use of heavy machinery after flooding leads to soil compaction [22], which reduces water infiltration and air space, limiting water absorption and causing rain runoff to wash away the topsoil and nutrients, thereby hindering root development and plant growth in subsequent seasons [130,131]. Prolonged wet conditions are responsible for the nutrient imbalances resulting from leaching, immobilization, and the accumulation of toxic compounds that may persist post-flooding. Flooding also spreads waterborne and soilborne pathogens from one area to another, increasing the risk of disease transmission to plants, animals, and humans. This highlights the need for effective biosecurity measures in flood-prone areas, including improved water management systems and early detection strategies for pathogens. 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 [132,133,134,135]. In anaerobic conditions, flooding encourages the growth of denitrifying microbes, which thrive in low-oxygen environments and contribute to nitrogen cycling in the soil [99]. This type of nutrient balance is essential for the survival of crops and microorganisms during prolonged flooding events. In some instances, flooding can enhance the soil structure by redistributing particles and 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 [136,137]. Importantly, the decomposition of carbon-rich debris in flooded fields also enriches soil fertility. However, such long-term benefits depend on the intensity and duration of flooding, as well as the existing soil ecosystem [135].
From a long-term perspective, flooding can delay planting schedules, shorten the growing season, and reduce crop yields [138]. Standing water creates favorable conditions for pests and disease outbreaks, directly impacting crop yields in subsequent seasons [130]. Significant crop losses due to flooding may also cause economic hardship for farmers, impacting their income and their ability to invest in future crop production [139]. Additionally, floodwaters can damage irrigation systems, drainage channels, farm roads, and other infrastructure, hindering future agricultural operations [140,141]. 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 global economic losses in the field crops, exceeding 1.5 billion annually [130,142,143]. Moreover, yield losses were estimated to be from 20 to 50% when soils were inundated with water for more than 10 days [144]. In contrast, flooding helps replenish groundwater, enrich soil nutrients, and improve soil structure [46], which could facilitate crop yields. Floodwater can carry and deposit nutrient-rich sediments containing nitrogen and phosphorus, enhancing soil fertility and providing essential minerals for plant growth [145,146]. However, long-term plant-microbe-soil dynamics remain largely unexplored in different soil types and agroecosystems, which limits our ability to accurately assess the effect of flooding.

5. Plant-Growth-Promoting Microorganism Roles in Plants Under Flooding Conditions

The long-term impact of soil flooding profoundly affects soil microbial communities and its detrimental impact on standing crops cannot be overlooked. Waterlogging or complete submergence creates O2 limitation, altering plant physiology and triggering adaptive mechanisms to mitigate stress [147]. More importantly, it disrupts ATP production during oxidative phosphorylation in mitochondria, a critical process for energy generation. Mitochondria synthesize ATP, enabling the plant’s cells to use it. In a double-membrane mitochondrion, the outer membrane separates the protons from the cytosol, and the inner membrane surrounds the matrix. The area between the membranes is called the intermembrane space. ATP is generated at the inner membrane of the mitochondria through oxidative phosphorylation, involving several membrane protein complexes in the electron transport chain (ETC). Nutrients provide high-energy electrons in the form of NADH; the electrons pass through the ETC and are ultimately accepted by O2 in the final step, which is reduced to H2O. While the series of electrons are passing, protein complexes pump protons from the matrix into the intermembrane space. This continuous pumping creates a proton gradient, where the positively charged protons are attracted to the more negatively charged matrix. The protons re-enter the matrix through the ATP synthase protein complex, where they catalyze the phosphorylation of ADP to ATP [148].
To sustain ATP production under O2-limited conditions, plants shift from aerobic respiration to anaerobic fermentation [149]. While this shift compensates for ATP deficiency, it also leads to the accumulation of acetaldehyde and ethanol, which contribute to oxidative stress [150]. Due to the low O2 levels, impaired mitochondrial function elevates reactive oxygen species (ROS) production in the cell [151,152]. As a result, ROS and stress markers such as malondialdehyde (MDA) accumulate. To attenuate ROS-induced damage, plants enhance their antioxidant defenses by producing enzymatic and non-enzymatic antioxidants [153,154]. When the entire plant remains underwater, it closes its stomata to minimize transpiration and gas exchange, leading to carbon dioxide depletion and affecting the photosynthetic efficiency [155]. Moreover, the increased water turbidity limits light penetration and causes O2 deficiency in the shoots [156]. In both submergence and waterlogging conditions, the submerged roots experience declining hydraulic conductivity and impaired aquaporin function, reducing water uptake [157]. However, plants also exhibit structural adaptations in response to waterlogging. The formation of aerenchyma and adventitious roots facilitates O2 transport and enhances gas diffusion between aerated tissues and submerged roots [158]. Ethylene plays a crucial role in regulating these responses, as its diffusion is restricted underwater, leading to its rapid accumulation in plant tissues [159]. Over the years, multiple reports have indicated that ethylene is linked to metabolic acclimation in plants under low O2 conditions [160,161].
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) [9]. 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 [162,163]. 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 its first challenges due to flooding stress, whereby microorganisms and plants both compromise their normal physiological activities (Table 1) [164,165,166]. A recent model study identified several PGPMs isolated from waterlogged greenhouse soil that exhibited plant growth-promoting traits, including phosphorus and potassium solubilization and ammonia and organic acid production, as well as amylase and cellulase activity [167]. 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 [165], 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 [168,169,170]. Therefore, we here discuss the recent progress of PGPMs-based studies in plant physiology under inundated soil conditions.
AMF are symbiotic fungi that colonize plant roots and are widely distributed in terrestrial ecosystems, including wetlands and flood-prone areas [171]. AMF have the potential to improve nutrient uptake and strengthen antioxidant responses in plants, thereby improving their growth and adaptability to various environmental stresses [172]. Several studies have demonstrated that inoculation with AMF can improve plant physiology when under waterlogging stress. Waterlogging stress with the treatment of Diversispora spurca in Citrus junos and Poncirus trifoliata enhanced root system architecture and morphology, with improved stem and root growth [173,174]. Compared to uninoculated plants, AMF (D. spurca) inoculated plants exhibit increased antioxidant enzymes such as SOD and CAT, and reduced MDA levels, indicating stress resilience against oxidative stress. Similarly, the inoculation with Funneliformis mosseae of Prunus persica yielded similar results under inundation, demonstrating enhanced root growth and chlorophyll content, accompanied by an increased accumulation of proline, an osmolyte involved in antioxidant defense [175].
Table 1. Summary of experimental studies assessing plant-growth-promoting microorganisms (PGPMs) and their effects on plant responses under flooding stress conditions.
Table 1. Summary of experimental studies assessing plant-growth-promoting microorganisms (PGPMs) and their effects on plant responses under flooding stress conditions.
PlantsMicrobesGroupsFlooding TypesDurationStress ConditionImpact on Plant PhysiologyImpact on Ethylene Response/GeneImpact on Soil MicroorganismsReferences
Lycopersicon esculentumEnterobacter cloacae UW4,
E. cloacae CAL2,
Pseudomonas putida ATCC17399/pRKACC or
P. putida ATCC17399/pRK415		BacteriaWaterlogging9 daysPotACC deaminase-producing PGPR improved root growth, reduced shoot damage, and increased chlorophyll contentReduced ethylene mitigated leaf epinasty and flooding-induced damageFacilitated the proliferation of PGPR[176]
Ocimum sanctumFd2, Achromobacter xylosoxidans (GenBank Accession No. JQ975414),
Bac5, Serratia ureilytica (GenBank Accession No. JQ975415),
Oci9, Herbaspirillum seropedicae (GenBank Accession No. JQ975416) and
Oci13, Ochrobactrum rhizosphaerae (GenBank Accession No. JQ522946).		BacteriaWaterlogging15 daysPotReduced ROS production, increased root weight, shoot height, chlorophyll, and nutrient uptakeACC deaminase-containing rhizobacteria reduced ethylene levels by degrading ACC, facilitating improved growth and yieldPromoted beneficial rhizobacterial activity, especially of strains like Achromobacter xylosoxidans and Serratia ureilytica[177]
Cicer arietinumMesorhizobium ciceri LMS-1BacteriaWaterlogging7 daysPotEnhanced growth under normal conditions. No significant improvements of LMS-1 (pRKACC) inoculated chickpea under waterlogging stressLMS-1 (pRKACC) expressed an exogenous ACC deaminase gene (acdS) and reduced ethylene levelsEnhanced colonization of Mesorhizobium ciceri LMS-1 (pRKACC),
increasing nodulation efficiency and nitrogen fixation		[178]
Rumex palustrisP. putida UW4BacteriaSubmergence72 h and 17 daysPotDecreased leaf elongation, reduced shoot weight, and root weightDecreased ethylene production and altered flood escape strategiesEnhanced bacterial populations around plant roots[179]
Vigna radiataStreptomyces sp. GMKU 336BacteriaWaterlogging21 daysPotIncreased shoot and root elongation, biomass, leaf area, chlorophyll content, adventitious root formation, and survival rateReduced ethylene biosynthesisEnhanced colonization by endophytic Streptomyces sp. in plant root[180]
Sesamum indicumPseudomonas veronii KJBacteriaWaterlogging10 daysPotImproved shoot and root length, biomass, chlorophyll content, and photosynthetic efficiencyReduced ethylene levelEnhanced colonization by Pseudomonas veronii KJ in rhizosphere[181]
Triticum aestivumTrichoderma asperellum MAP1FungiWaterlogging5 daysPotIncreased growth, photosynthetic efficiency, chlorophyll content, reduced electrolyte leakage, MDA, H2O2, and enhanced antioxidant enzymeReduced ethylene biosynthesis and ethylene signaling genesPromoted colonization of Trichoderma asperellum MAP1 and influenced rhizosphere dynamics[182]
Oryza sativaBacillus sp. (AR-ACC1),
Microbacterium sp. (AR-ACC2),
Methylophaga sp. (AR-ACC3),
Paenibacillus sp. (ANR-ACC3)		BacteriaSubmergence7 daysPotEnhanced germination rates, seedling vigor index, improved root and shoot length, and total chlorophyll contentReduced ethylene levelPromoted colonization of ACC deaminase-producing
PGPR in the rhizosphere		[183]
Oryza sativa ssp. japonicaPhomopsis liquidambaris B3FungiWaterlogging9 daysHydroponicImproved root aerenchyma formation, chlorophyll content, soluble sugar accumulation, root respiration, and energy metabolism while increasing radial oxygen lossInduced ethylene-mediated root aerenchyma formationInteraction with rhizosphere microbial communities
influenced nutrient dynamics and energy metabolism		[184]
Zea maysSpergillus nomiae (MA1),
Aspergillus fumigatus (MA4)		FungiWaterlogging7 daysPotImproved root and shoot length, biomass, chlorophyll content, antioxidant enzyme activity, soluble sugar content, reduced ROS production, and enhanced stomatal activityReduced ethylene productionEnhanced colonization of fungal endophytes[185]
However, the wetland plants Lythrum salicaria and Taxodium distichum were inoculated with various AMF types, which did not induce significant physiological changes [81,186], suggesting that the response to AMF may be species-specific and may also be influenced by fungal identity. Beyond AMF, other fungal endophytes have also been shown to alleviate flooding stress. For instance, Phomopsis liquidambaris B3, an ethylene-producing fungus, promoted aerenchyma formation in rice by increasing ethylene production. This facilitated O2 transport from the aerated tissue to the root, thereby enhancing carbohydrate metabolism and improving plant growth [184]. 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. [187] 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.
ACC-deaminase (ACCD) is an enzyme produced by PGPMs that converts ethylene into α-ketobutyrate and reduces ethylene synthesis in plants [188]. ACCD-producing fungi have also been employed to mitigate flooding stress by reducing ethylene accumulation (Figure 2). Inoculation with ACCD-producing Aspergillus nomiae and Aspergillus fumigatus in maize promoted shoot and root growth, increasing biomass under waterlogging conditions [185]. The reduction in endogenous ACC levels led to decreased ethylene-mediated aerenchyma formation, suggesting that microbial ACC levels are responsible for gas exchange through aerenchyma. However, altered hormonal balance, for instance, caused elevated IAA and GA3 levels while lowering ABA levels, inducing adventitious root formation and enhanced nutrient and water uptake [189]. Moreover, reduced ethylene levels alleviated ROS stress and increased CAT and POD activity, thereby mitigating oxidative stress by improving chlorophyll content and photosynthetic efficiency. Similarly, another ACCD-and IAA-producing endophyte, Trichoderma asperellum MAP1, enhanced wheat growth by increasing antioxidant enzyme activity and reducing ROS-induced stress [182]. These beneficial effects are inherent in the symbiotic relationship between ACCD-producing microbes and plants, which takes place in the rhizosphere. Here, plant root exudates such as flavonoids, sugar, and amino acids are attracted by the PGPMs, allowing microbial colonization in the root cells [190,191]. This colonization helps to regulate redox homeostasis in plants under anaerobic stress conditions.
Among a billion microorganisms, plant growth-promoting rhizobacteria (PGPR) interact symbiotically with plants by facilitating nitrogen fixation, phosphate solubilization, and antioxidant regulation [162]. Several bacterial strains, including Enterobacter cloacae UW4, Pseudomonas putida UW4 [176], Achromobacter xylosoxidans [177], and Pseudomonas veronii KJ [181], have been found to mitigate ethylene-induced stress in various plant species under waterlogging conditions. ACCD-producing PGPR reduces plant ROS accumulation and promotes antioxidant enzyme activity, leading to increased chlorophyll content, improved root biomass, and enhanced stress tolerance. The beneficial effects of ACCD-producing PGPR have also been observed under complete submergence stress. Four bacterial strains, including Bacillus sp. AR-ACC1, Microbacterium sp. AR-ACC2, Methylophaga sp. AR-ACC3, and Paenibacillus sp. ANR-ACC3 were applied to rice seedlings, and the growth parameters were evaluated under submergence stress compared to uninoculated seedlings [183]. Treatment of Microbacterium sp. AR-ACC2, Methylophaga sp. AR-ACC3, and Paenibacillus sp. ANR-ACC3 improved the germination rates and root and shoot length, demonstrating the potential of ACCD-producing PGPR to mitigate the detrimental effects of low O2. However, seedlings inoculated with Bacillus sp. AR-ACC1 showed no significant growth promotion or inhibition compared to uninoculated seedlings. This result pinpoints the fact that symbiotic associations do not always confer resilience to plants, as their effectiveness is often species- or strain-specific.
Some studies suggest that ACCD-producing PGPR does not confer any noteworthy improvement under submergence conditions. For example, when the ACCD-producing Mesorhizobium ciceri LMS-1 (pRKACC)-transformed strain was applied to chickpea (Cicer arietinum) plants 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 [178]. A riparian plant, Rumex palustris, treated with an ACCD-producing bacterium P. putida UW4, led to an impeded ethylene-mediated hyponastic growth response [179]. Compared to the ACCD-deficient mutant, shoot elongation and dry weight were reduced. This study suggests that while the 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 [192], the PGPM-induced flooding tolerance may be attributed to microbial characteristics rather than the ACCD enzyme activity alone. These findings demonstrate 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 the symbiotic interactions that regulate the acclimation process. Moreover, it is still unknown how the application of PGPMs could regulate flooding’s effects on crop production in field conditions when all studies have been conducted in the greenhouse.

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 erosion of topsoil and nutrients. Excess water levels highly influence the soil’s microbial communities due to lowered 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 the number of aerobic microbes and changing the overall microbial community composition, depending on the flood duration and intensity. Microorganisms in freshwater and saline environments adapt to flooding 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 their resilience in flooded soils are not fully elucidated.
In parallel with 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 exert both beneficial and detrimental effects on plants, which are yet to be fully understood. In addition, 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 to encourage the development of management strategies to mitigate negative impacts on soil health and promote recovery after flood events.

Author Contributions

Conceptualization, A.K.D.; writing—original draft preparation, A.K.D., D.-S.L., Y.-J.W. and A.M.; visualization, A.K.D. and Y.-J.W.; writing—review and editing, A.K.D., S.S. and B.-W.Y.; supervision and project administration, B.-W.Y. All authors have read and agreed to the published version of the manuscript.

Funding

We cordially acknowledge the Basic Science Research Program through the National Research Foundation of Korea (NRF), aided by the Ministry of Education (RS-2023-00245922), which supported this study.

Data Availability Statement

Not applicable.

Acknowledgments

We are grateful to the Global Korea Scholarship (GKS) of the Government of the Republic of Korea for supporting the post-graduate students.

Conflicts of Interest

The authors declare no conflicts of interest.

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Stresses 05 00030 g001
Figure 1. Schematic representation of the 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.
Figure 1. Schematic representation of the 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.
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Figure 2. Flooding-induced changes in soil microbial communities and the 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. Pink arrows indicate increased ethylene production, the crossed O2 symbol represents oxygen deficiency, and dashed lines denote either inhibition or activation.
Figure 2. Flooding-induced changes in soil microbial communities and the 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. Pink arrows indicate increased ethylene production, the crossed O2 symbol represents oxygen deficiency, and dashed lines denote either inhibition or activation.
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Das, A.K.; Lee, D.-S.; Woo, Y.-J.; Sultana, S.; Mahmud, A.; Yun, B.-W. The Impact of Flooding on Soil Microbial Communities and Their Functions: A Review. Stresses 2025, 5, 30. https://doi.org/10.3390/stresses5020030

AMA Style

Das AK, Lee D-S, Woo Y-J, Sultana S, Mahmud A, Yun B-W. The Impact of Flooding on Soil Microbial Communities and Their Functions: A Review. Stresses. 2025; 5(2):30. https://doi.org/10.3390/stresses5020030

Chicago/Turabian Style

Das, Ashim Kumar, Da-Sol Lee, Youn-Ji Woo, Sharmin Sultana, Apple Mahmud, and Byung-Wook Yun. 2025. "The Impact of Flooding on Soil Microbial Communities and Their Functions: A Review" Stresses 5, no. 2: 30. https://doi.org/10.3390/stresses5020030

APA Style

Das, A. K., Lee, D.-S., Woo, Y.-J., Sultana, S., Mahmud, A., & Yun, B.-W. (2025). The Impact of Flooding on Soil Microbial Communities and Their Functions: A Review. Stresses, 5(2), 30. https://doi.org/10.3390/stresses5020030

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