1 Introduction

Aquatic systems, encompassing freshwater bodies such as lakes, rivers, and reservoirs, are vital for sustaining biodiversity and providing essential ecosystem services. These systems are under increasing stress from anthropogenic activities, including pollution, eutrophication, and climate change, which significantly impact water quality and ecosystem health (Sehnal et al., 2021). The conservation and sustainable use of freshwater resources are of global importance, as microorganisms play a crucial role in maintaining water quality by participating in various ecological processes. Despite advances in understanding the diversity of freshwater microorganisms, a comprehensive understanding of their ecological roles remains incomplete.

Decomposers, particularly microbial communities, are fundamental to the functioning of aquatic ecosystems. They are involved in nutrient cycling, breaking down organic matter, and maintaining the balance of the ecosystem (Mamidala et al., 2021). Microorganisms, including bacteria, archaea, and protists, are key players in processes such as nitrogen cycling, oxygen production, and the degradation of pollutants (Sagova-Mareckova et al., 2020; Savenko and Prysiazhniuk, 2022). These microbial processes are essential for the self-cleaning capacity of water bodies, influencing the hydrological and gas regimes and ultimately determining water quality (Savenko and Prysiazhniuk, 2022). The microbial decomposition of organic matter, such as leaf detritus and animal tissues, further underscores the importance of decomposers in nutrient cycling and ecosystem health (Lobb et al., 2020; Liao et al., 2023).

This study highlights the critical role of microbial decomposers in aquatic systems and their impact on water quality. By synthesizing current research, we will elucidate the diversity and ecological functions of microbial communities in freshwater habitats, explore the mechanisms by which decomposers contribute to nutrient cycling and pollutant degradation, and assess the potential of microbial indicators for monitoring and managing water quality. Understanding the dynamic interactions between microbial communities and their aquatic environments is essential for developing effective strategies to preserve and enhance water quality in the face of ongoing environmental challenges.

2 Overview of Microbial Decomposers

2.1 Types of microbial decomposers

In aquatic systems, the primary microbial decomposers are bacteria and fungi. Bacteria are often the main decomposers in the pelagic zones of lakes and oceans, where they act as primary mineralizers (Wurzbacher et al., 2014). Fungi, on the other hand, dominate the decomposition of organic matter in streams and wetlands, and they are also active in lakes (Wurzbacher et al., 2014). Aquatic hyphomycetes, a group of fungi, are particularly important in freshwater ecosystems for their ability to produce extracellular enzymes that break down complex molecules in leaf litter (Mariz et al., 2021). Additionally, microbial communities associated with submerged detritus often include a mix of autotrophic and heterotrophic microbes, such as algae, protozoa, and fungi, which interact to enhance decomposition processes (Kuehn et al., 2014).

2.2 Characteristics of aquatic microbes

Aquatic microbes exhibit a range of characteristics that enable them to thrive in diverse environments. For instance, aquatic hyphomycetes can assimilate nutrients from stream water and immobilize them in decomposing leaf litter, thereby increasing its nutritional value for higher trophic levels (Mariz et al., 2021). The gut microbiome of freshwater isopods like Asellus aquaticus also demonstrates the complexity and robustness of microbial communities, with distinct microbiomes in different habitats and digestive organs. These microbes are closely related to lignocellulose degradation, highlighting their role in breaking down plant material (Liao et al., 2023). Furthermore, microbial eukaryotes in freshwater environments show high molecular diversity, with groups like Amoebozoa, Viridiplantae, and Cryptophyta being particularly diverse (Debroas et al., 2017).

2.3 Microbial diversity in aquatic environments

The diversity of microbial decomposers in aquatic environments is vast and varies significantly across different habitats. For example, bacterial communities in freshwater, intertidal wetland, and marine sediments show distinct taxonomic compositions, with freshwater sediments having the highest diversity (Wang et al., 2012). Fungal communities also exhibit significant diversity, with different species playing central roles in decomposition processes. The interactions between fungi and bacteria can further influence microbial diversity and ecosystem functioning, as bacteria can promote fungal diversity and stimulate colonization (Baudy et al., 2021). Additionally, the necrobiome of decomposing fish reveals a strong succession of microbial communities, with specific bacteria dominating at different stages of decomposition (Lobb et al., 2020). This succession highlights the dynamic nature of microbial communities and their functional roles in nutrient cycling.

3 Mechanisms of Decomposition in Aquatic Systems

3.1 Breakdown of organic matter

The breakdown of organic matter in aquatic systems is a fundamental process driven by microbial activity. Microbes, including bacteria and fungi, play a crucial role in decomposing both terrestrial and aquatic organic materials. For instance, bacteria from the family Burkholderiaceae have been identified as key decomposers of leaf litter and polystyrene in freshwater environments, highlighting their versatility in breaking down both natural and synthetic polymers (Vesamäki et al., 2022). Additionally, aquatic hyphomycetes are significant contributors to the decomposition of leaf litter in freshwater ecosystems, facilitating the turnover of organic matter and supporting detrital food webs (Pimentão et al., 2019). In marine environments, diverse microbial communities, including Cloacimonetes and Marinimicrobia, are responsible for degrading dissolved organic matter (DOM) and protein extracts, particularly under anoxic conditions (Suominen et al., 2019).

3.2 Nutrient recycling and mineralization

Nutrient recycling and mineralization are critical processes in aquatic ecosystems, ensuring the availability of essential nutrients for primary production. Microbial mineralization of organic compounds, such as lignin and cellulose, is essential for carbon recycling in food webs (Vesamäki et al., 2022). In coral reef ecosystems, microbial processes are central to the transformation and recycling of DOM, which acts as a key currency in nutrient cycling and ecosystem stability (Nelson et al., 2022). The presence of specific microbial taxa, such as Dechloromonas and Pseudomonas, in benthic environments further underscores the role of microbes in nutrient cycling, particularly in the presence of stressors like E. coli (Gu et al., 2021). These microbes contribute to the biogeochemical balance by mediating the turnover of nitrogen and other essential elements.

3.3 Microbial enzymes and their functions

Microbial enzymes are pivotal in the decomposition process, facilitating the breakdown of complex organic molecules into simpler compounds that can be assimilated by other organisms. In the decomposition of fish tissues, for example, the presence of hemolytic toxin genes in Aeromonas veronii suggests that these enzymes play a role in host cell lysis during early stages of decomposition (Lobb et al., 2020). Similarly, in oligotrophic streams, the performance of fungal decomposers, including their respiration, biomass accrual, and sporulation rates, is influenced by the quality of leaf litter, which in turn affects the enzymatic activity involved in decomposition (Pérez et al., 2021). The enzymatic capabilities of microbial communities in the Black Sea's sulphidic zone also highlight their role in organic matter degradation, particularly under anoxic conditions where streamlined microorganisms like Parcubacteria and Woesearchaeota exhibit high activity (Suominen et al., 2019).

4 Impact on Water Quality

4.1 Removal of organic pollutants

Microorganisms are essential in the degradation and recycling of organic pollutants in aquatic systems. They naturally control the flux of nutrients and degrade anthropogenic contaminants, thereby maintaining the ecological balance (Ribeiro et al., 2019). The use of high-throughput molecular technologies has shown that microbial communities can respond to extreme pollution conditions, such as oil spills, by altering their structure and function to degrade pollutants more effectively (Michán et al., 2021) (Figure 1). Additionally, metagenomic approaches have revealed new metabolic pathways in microbes that are crucial for the breakdown of organic pollutants, further highlighting their importance in water quality management (Grossart et al., 2019).

Figure 1 Application of high-throughput molecular technologies for the microbial biomonitoring of aquatic environments (Adopted from Michán et al., 2021)

4.2 Reduction of eutrophication

Eutrophication, caused by excessive nutrient inputs, leads to harmful algal blooms and oxygen depletion in water bodies. Microbial communities play a significant role in mitigating eutrophication by participating in nutrient cycling processes. For instance, bacteria and archaea are involved in nitrogen cycling, which helps in the removal of excess nutrients from the water (Sehnal et al., 2021). The presence and diversity of microbial communities can serve as bioindicators for monitoring eutrophication levels and implementing timely interventions (Sagova-Mareckova et al., 2020). Moreover, submerged macrophytes recruit unique microbial communities that drive functional zonation, aiding in the efficient conversion of nutrients and reducing the risk of eutrophication (Zhu et al., 2021).

4.3 Maintenance of oxygen levels

The maintenance of oxygen levels in aquatic systems is vital for the survival of aerobic organisms. Microbial communities contribute to this by participating in oxygen production and consumption processes. Photosynthetic microorganisms, such as cyanobacteria, produce oxygen as a byproduct of photosynthesis, thereby replenishing oxygen levels in the water (Sehnal et al., 2021). Conversely, microbial respiration processes consume oxygen, but the balance between these activities is crucial for maintaining stable oxygen levels. The resilience of microbial communities in adapting to environmental changes ensures the continuous regulation of oxygen levels, even under stress conditions (Mamidala et al., 2021). Understanding the dynamic relationship between aquatic microbiota and their environment is essential for monitoring and managing oxygen levels in aquatic ecosystems (Michán et al., 2021; Sehnal et al., 2021).

5 Interactions with Other Aquatic Organisms

5.1 Symbiotic relationships

Microbial symbionts are essential for the survival and health of many aquatic organisms. These symbionts help hosts cope with stress, defend against predators, pathogens, and parasites, and are often indispensable for the host's development or life cycle completion. Human activities, however, are altering these interactions, potentially impacting the health of the host and the ecosystem at large (Stock et al., 2021). For instance, fungi and bacteria interact in aquatic decomposer communities, where bacteria can promote fungal diversity by alleviating competition among fungi, leading to synergistic interactions that enhance ecosystem functioning (Baudy et al., 2021).

5.2 Food web dynamics

Microbial communities are fundamental components of aquatic food webs, contributing to biogeochemical processes and energy flow. During different productive periods, such as phytoplankton blooms, microbial interactions shift, with complex networks dominated by competition and mutualism during blooms and simpler networks during non-bloom periods (Trombetta et al., 2020). Additionally, parasitic fungi can significantly alter microbial interactions by transferring photosynthetic carbon to themselves and stimulating bacterial colonization on phytoplankton cells, thereby modifying the carbon flow and microbial community composition (Klawonn et al., 2021). The presence of microplastics also affects food web dynamics by interacting with microalgae, potentially altering their growth and photosynthetic activity, which can propagate throughout the food web and impact aquatic productivity (Nava and Leoni, 2020).

5.3 Impact on aquatic biodiversity

Microbial diversity is immense and plays a critical role in shaping community dynamics and ecosystem-scale biogeochemical transformations. Metagenomic approaches have provided insights into the discovery of new taxa and metabolisms, community assembly, and the influence of human activities on aquatic microbiomes (Grossart et al., 2019). The structure of microbial food webs can be significantly modified by climatic conditions, with warmer years favoring smaller organism interactions and intensifying trophic cascades, potentially shifting energy circulation from highly productive herbivorous food webs to less productive microbial food webs (Trombetta et al., 2020). Furthermore, the interactions between microplastics and aquatic organisms, such as fish and invertebrates, can have variable effects on feeding, growth, reproduction, and survival, with potential ramifications throughout the food web (Foley et al., 2021).

6 Technological Applications in Water Treatment

6.1 Bioremediation techniques

6.1.1 Principles of bioremediation

Bioremediation leverages the natural metabolic processes of microorganisms to degrade or detoxify pollutants in contaminated environments. This eco-friendly and cost-effective approach utilizes various microbes, including bacteria, fungi, and algae, to break down contaminants into less harmful substances. The process can be applied in situ (at the contamination site) or ex situ (off-site) using engineered bioreactors to optimize conditions for microbial activity (Dangi et al., 2018; Tekere, 2019; Koure et al., 2021; Sarhan, 2023).

6.1.2 Applications in contaminated water bodies

Microbial bioremediation has been successfully applied to treat industrial wastewater, including effluents from textile mills and other industries contaminated with heavy metals and organic pollutants. Techniques such as bioaugmentation (adding specific strains of microbes) and biostimulation (enhancing the growth of indigenous microbes by adding nutrients) are commonly used to improve the efficiency of pollutant degradation (Gür et al., 2021; Saleem et al., 2022; Sarhan, 2023). Algae-based bioremediation is particularly effective for removing organic contaminants and emerging pollutants like pharmaceuticals from water bodies (Xiong et al., 2018; Rempel et al., 2021; Touliabah et al., 2022).

6.1.3 Case studies and success stories

Several case studies highlight the success of microbial bioremediation in various contexts. For instance, the use of microalgae and cyanobacteria has shown promising results in removing a wide range of organic pollutants from wastewater, making it a sustainable alternative to conventional treatment methods (Rempel et al., 2021; Touliabah et al., 2022). Additionally, the application of engineered bioreactors has enhanced the degradation of pollutants in industrial effluents, demonstrating the potential of bioremediation in large-scale water treatment (Arregui et al., 2019; Tekere, 2019) (Figure 2).

Figure 2 Schematic illustration of the potential sources of water contaminants and their bioremediation by laccases (Adopted from Arregui et al., 2019) Image caption: Emerging contaminants such as antibiotics, endocrine disruptors, dye-based pollutants and pharmaceutical drugs are often released into the environment causing harmful impacts and health problems to humans and other animals, water treatment with laccases and their biotechnological approaches generate less-toxic, inert or fully degraded compounds (Adopted from Arregui et al., 2019)

6.2 Constructed wetlands and biofilters

Constructed wetlands and biofilters are engineered systems that mimic natural wetlands to treat contaminated water. These systems utilize plants, soil, and microbial communities to remove pollutants through physical, chemical, and biological processes. The integration of microbial bioremediation within these systems enhances their efficiency in degrading organic and inorganic contaminants, providing a sustainable solution for water purification (Dangi et al., 2018; Saleem et al., 2022; Sarhan, 2023).

6.3 Innovations in microbial water purification

Recent advancements in microbial water purification include the development of genetically modified microorganisms and microbial consortia to enhance pollutant degradation. Techniques such as metabolic engineering and systems biology are being employed to optimize microbial pathways for more efficient bioremediation. Additionally, the immobilization of enzymes like laccases on novel biocatalytic materials has improved their stability and reusability, making them more effective for large-scale water treatment applications (Dangi et al., 2018; Xiong et al., 2018; Arregui et al., 2019).

7 Environmental and Ecological Considerations

7.1 Ecological balance and microbial communities

Microbial communities play a crucial role in maintaining the ecological balance of aquatic systems. These microorganisms are involved in nutrient cycling, decomposition of organic matter, and the overall productivity of the ecosystem. For instance, microbes are essential in the decomposition of detritus, contributing to nutrient recycling and supporting the food web from primary producers to higher trophic levels (Mamidala et al., 2021). Additionally, microbial biofilms on various surfaces within aquatic systems facilitate nutrient exchange and provide a habitat for diverse microbial taxa. The dynamic interactions within microbial communities, including competition and cooperation, are fundamental to the stability and functionality of aquatic ecosystems (Hurst, 2019).

7.2 Impact of climate change on microbial processes

Climate change poses significant threats to microbial processes in aquatic environments. Rising temperatures, altered precipitation patterns, and increased frequency of extreme weather events can disrupt microbial community structures and functions. For example, climate change can exacerbate eutrophication, leading to harmful algal blooms that alter microbial diversity and function (Sehnal et al., 2021). Furthermore, changes in water temperature and chemistry can affect the metabolic rates of microbes, influencing processes such as nitrogen cycling and organic matter decomposition (Sehnal et al., 2021; Kumar et al., 2022). The resilience of microbial communities to these changes is critical for the continued health and stability of aquatic ecosystems (Mamidala et al., 2021).

7.3 Conservation of microbial diversity

The conservation of microbial diversity is essential for the sustainability of aquatic ecosystems. Microbial diversity underpins the resilience of ecosystems to environmental stressors and disturbances. For instance, diverse microbial communities are better equipped to degrade pollutants and recycle nutrients, thereby maintaining water quality and ecosystem health. Conservation efforts should focus on protecting habitats from pollution, over-extraction of water, and other anthropogenic impacts that threaten microbial diversity. Additionally, integrating microbial indicators into routine water quality monitoring can enhance our understanding of ecosystem health and guide conservation strategies (Gu, 2019; Sagova-Mareckova et al., 2020). The use of advanced molecular techniques and bioinformatics can further aid in the assessment and conservation of microbial diversity in aquatic systems (Sagova-Mareckova et al., 2020).

8 Concluding Remarks

This study has highlighted the critical role of microbial life in maintaining the health and functionality of aquatic systems. Microbial communities, including bacteria, archaea, fungi, and protists, are essential for processes such as nutrient cycling, organic matter decomposition, and the maintenance of water quality. The integration of microorganisms into routine freshwater biomonitoring has revealed their potential as bioindicators, providing valuable insights into the ecological status of aquatic environments. Additionally, the decomposition of organic matter by microbial communities, such as the necrobiome of fish, underscores the importance of microbial succession in nutrient cycling and ecosystem health. The impact of environmental stressors, such as fungicides and antibiotics, on microbial decomposers has also been documented, highlighting the potential long-term effects on ecosystem functions.

Microbial life forms the backbone of aquatic ecosystems, driving essential processes that sustain life and maintain water quality. Microorganisms play a pivotal role in the decomposition of organic matter, transforming complex compounds into simpler forms that can be utilized by other organisms in the food web. They are also crucial in nutrient cycling, particularly in the transformation and removal of nitrogen compounds, which helps prevent the accumulation of harmful substances such as nitrates. The gut microbiota of aquatic organisms further exemplifies the importance of microbial communities in regulating host health and resilience to environmental pollutants. The dynamic interactions between microbial communities and their environment underscore the need for comprehensive monitoring and management practices that consider microbial diversity and function.

Future research should focus on expanding our understanding of microbial community dynamics in various aquatic habitats and under different environmental conditions. This includes investigating the effects of emerging pollutants, such as microplastics and pharmaceuticals, on microbial communities and their ecological functions. There is also a need to develop and implement advanced molecular and bioinformatic techniques to enhance the resolution and accuracy of microbial monitoring programs. Additionally, studies should explore the potential of microbial communities as bioindicators for early detection of ecological disturbances and water quality issues. Practical applications should aim to integrate microbial assessments into routine water quality monitoring and management strategies, ensuring the protection and sustainability of aquatic ecosystems.

Acknowledgments

We would like to express our gratitude to Professor Jin from the Institute of Life Science of Jiyang College of Zhejiang A&F University for his reading and feedback.

Conflict of Interest Disclosure

The authors affirm that this research was conducted without any commercial or financial relationships that could be construed as a potential conflict of interest.

References

Arregui L., Ayala M., Gómez-Gil X., Gutiérrez-Soto G., Hernández-Luna C., Santos M., Levin L., Rojo-Domínguez A., Romero-Martínez D., Saparrat M., Trujillo-Roldán M., and Valdez-Cruz N., 2019, Laccases: structure, function, and potential application in water bioremediation, Microbial Cell Factories, 18: 200.

https://doi.org/10.1186/s12934-019-1248-0

Baudy P., Zubrod J., Konschak M., Kolbenschlag S., Pollitt A., Baschien C., Schulz R., and Bundschuh M., 2021, Fungal-fungal and fungal-bacterial interactions in aquatic decomposer communities: bacteria promote fungal diversity, Ecology, 102(10): e03471.

https://doi.org/10.1002/ecy.3471

Dangi A., Sharma B., Hill R., and Shukla P., 2018, Bioremediation through microbes: systems biology and metabolic engineering approach, Critical Studys in Biotechnology, 39: 79-98.

https://doi.org/10.1080/07388551.2018.1500997

Debroas D., Domaizon I., Humbert J., Jardillier L., Lepère C., Oudart A., and Taïb N., 2017, Overview of freshwater microbial eukaryotes diversity: a first analysis of publicly available metabarcoding data, FEMS Microbiology Ecology, 93(4): fix023.

https://doi.org/10.1093/femsec/fix023

Foley C., Feiner Z., Malinich T., and Höök T., 2018, A meta-analysis of the effects of exposure to microplastics on fish and aquatic invertebrates, The Science of the Total Environment, 631-632: 550-559.

https://doi.org/10.1016/j.scitotenv.2018.03.046

Grossart H., Massana R., McMahon K., and Walsh D., 2019, Linking metagenomics to aquatic microbial ecology and biogeochemical cycles, Limnology and Oceanography, 65(51): S2-S20.

https://doi.org/10.1002/lno.11382

Gu J., 2019, Microbial Ecotoxicology as an emerging research subject, Applied Environmental Biotechnology, 4(1): 1-4.

https://doi.org/10.26789/AEB.2019.01.001

Gu L., Wu J., and Hua Z., 2021, Benthic prokaryotic microbial community assembly and biogeochemical potentials in E. coli-Stressed aquatic ecosystems during plant decomposition, Environmental Pollution, 275: 116643.

https://doi.org/10.1016/j.envpol.2021.116643

Gür S., Bakhshpour M., and Denizli A., 2021, Applications of microbes in bioremediation of water pollutants, Recent Advances in Microbial Degradation, 19: 465-483.

https://doi.org/10.1007/978-981-16-0518-5_19

Hurst C., 2019, Understanding aquatic microbial communities, Advances in Environmental Microbiology, 7: 1-12.

https://doi.org/10.1007/978-3-030-16775-2_1

Klawonn I., Wyngaert S., Parada A., Arandia-Gorostidi N., Whitehouse M., Grossart H., and Dekas A., 2021, Characterizing the “fungal shunt”: Parasitic fungi on diatoms affect carbon flow and bacterial communities in aquatic microbial food webs, Proceedings of the National Academy of Sciences of the United States of America, 118(23): e2102225118.

https://doi.org/10.1073/pnas.2102225118

Kour D., Kaur T., Devi R., Yadav A., Singh M., Joshi D., Singh J., Suyal D., Kumar A., Rajput V., Yadav A., Singh K., Singh J., Sayyed R., Arora N., and Saxena A., 2021, Beneficial microbiomes for bioremediation of diverse contaminated environments for environmental sustainability: present status and future challenges, Environmental Science and Pollution Research, 28: 24917-24939.

https://doi.org/10.1007/s11356-021-13252-7

Kuehn K., Francoeur S., Findlay R., and Neely R., 2014, Priming in the microbial landscape: periphytic algal stimulation of litter-associated microbial decomposers, Ecology, 95(3): 749-762.

https://doi.org/10.1890/13-0430.1

Kumar A., Ng D., Bairoliya S., and Cao B., 2022, The dark side of microbial processes: accumulation of nitrate during storage of surface water in the dark and the underlying mechanism, Microbiology Spectrum, 10(1): e02232-21.

https://doi.org/10.1128/spectrum.02232-21

Liao A., Hartikainen H., and Buser C., 2023, Individual level microbial communities in the digestive system of the freshwater isopod Asellus aquaticus : complex, robust and prospective, Environmental Microbiology Reports, 15(3): 188-196.

https://doi.org/10.1111/1758-2229.13142

Lobb B., Hodgson R., Lynch M., Mansfield M., Cheng J., Charles T., Neufeld J., Craig P., and Doxey A., 2020, Time series resolution of the fish necrobiome reveals a decomposer succession involving toxigenic bacterial pathogens, mSystems, 5(2): 1-15.

https://doi.org/10.1128/mSystems.00145-20

Mamidala S., Balakrishna C., Yeshdas B., Ravinder B., Mahesh R., Bhanu P.C., Kummari, S., and Rajender B., 2021, A study on resilience of microbes in aquatic environment, Journal of Entomology and Zoology Studies, 9(2): 1403-1410.

https://doi.org/10.22271/J.ENTO.2021.V9.I2Q.8659

Mariz J., Franco-Duarte R., Cássio F., Pascoal C., and Fernandes I., 2021, Aquatic hyphomycete taxonomic relatedness translates into lower genetic divergence of the nitrate reductase gene, Journal of Fungi, 7(12): 1066.

https://doi.org/10.3390/jof7121066

Michán C., Blasco J., and Alhama J., 2021, High‐throughput molecular analyses of microbiomes as a tool to monitor the wellbeing of aquatic environments, Microbial Biotechnology, 14: 870-885.

https://doi.org/10.1111/1751-7915.13763

Nava V., and Leoni B., 2020, A critical study of interactions between microplastics, microalgae and aquatic ecosystem function, Water Research, 188: 116476.

https://doi.org/10.1016/j.watres.2020.116476

Nelson C., Kelly L., and Haas A., 2022, Microbial interactions with dissolved organic matter are central to coral reef ecosystem function and resilience, Annual study of Marine Science, 15: 431-460.

https://doi.org/10.1146/annurev-marine-042121-080917

Pérez J., Ferreira V., Graça M., and Boyero L., 2021, Litter quality is a stronger driver than temperature of early microbial decomposition in oligotrophic streams: a microcosm study, Microbial Ecology, 82: 897-908.

https://doi.org/10.1007/s00248-021-01858-w

Pimentão A., Pascoal C., Castro B., and Cássio F., 2019, Fungistatic effect of agrochemical and pharmaceutical fungicides on non-target aquatic decomposers does not translate into decreased fungi- or invertebrate-mediated decomposition, The Science of the Total Environment, 172: 135676.

https://doi.org/10.1016/j.scitotenv.2019.135676

Rempel A., Gutkoski J., Nazari M., Biolchi G., Cavanhi V., Treichel H., and Colla L., 2021, Current advances in microalgae-based bioremediation and other technologies for emerging contaminants treatment, The Science of the Total Environment, 772: 144918.

https://doi.org/10.1016/j.scitotenv.2020.144918.

Ribeiro H., Martins A., Gonçalves M., Guedes M., Tomasino M., Dias N., Dias A., Mucha A., Carvalho M., Almeida C., Ramos S., Almeida J., Silva E., and Magalhães C., 2019, Development of an autonomous biosampler to capture in situ aquatic microbiomes, PLoS ONE, 14(5): e0216882.

https://doi.org/10.1371/journal.pone.0216882

Sagova-Mareckova M., Boenigk J., Bouchez A., Čermáková K., Chonova T., Cordier T., Eisendle U., Eleršek T., Fazi S., Fleituch T., Frühe L., Gajdošová M., Graupner N., Haegerbaeumer A., Kelly A., Kopecký J., Leese F., Nõges P., Orlić S., Panksep K., Pawłowski J., Petrusek A., Piggott J., Rusch J., Salis R., Schenk J., Šimek K., Šťovíček A., Strand D., Vasquez M., Vrålstad T., Zlatkovic S., Zupančič M., and Stoeck T., 2020, Expanding ecological assessment by integrating microorganisms into routine freshwater biomonitoring, Water Research, 191: 116767.

https://doi.org/10.1016/j.watres.2020.116767

Saleem A., Naureen I., Tasleem G., Anwar R., Mairaj M., Muddassar H., and Rana N., 2022, Microbial assisted bioremediation of polluted water, Haya: The Saudi Journal of Life Sciences, 7(4): 116-127.

https://doi.org/10.36348/sjls.2022.v07i04.001

Sarhan A., 2023, Microbial bioremediation: effective strategy for removal of pollutants from contaminated industrial water of textile mills plants. an overview, International Journal of Pharmaceutical and Bio-Medical Science, 3(10): 536-542.

https://doi.org/10.47191/ijpbms/v3-i10-06

Savenko N., and Prysiazhniuk N., 2022, Role of microorganisms of the aquatic environment in the formation of the ecological and sanitary state of water bodies, Tehnologìâ Virobnictva ì Pererobki Produktìv Tvarinnictva, 2: 78-84.

https://doi.org/10.33245/2310-9289-2022-175-2-78-84

Sehnal L., Brammer-Robbins E., Wormington A., Bláha L., Bisesi J., Larkin I., Martyniuk C., Simonin M., and Adamovsky O., 2021, Microbiome composition and function in aquatic vertebrates: small organisms making big impacts on aquatic animal health, Frontiers in Microbiology, 12: 567408.

https://doi.org/10.3389/fmicb.2021.567408

Stock W., Callens M., Houwenhuyse S., Schols R., Goel N., Coone M., Theys C., Delnat V., Boudry A., Eckert E., Laspoumaderes C., Grossart H., Meester L., Stoks R., Sabbe K., and Decaestecker E., 2021, Human impact on symbioses between aquatic organisms and microbes, Aquatic Microbial Ecology, 87: 113-138.

https://doi.org/10.3354/AME01973

Suominen S., Dombrowski N., Damsté J., and Villanueva L., 2019, A diverse uncultivated microbial community is responsible for organic matter degradation in the Black Sea sulphidic zone, Environmental Microbiology, 23: 2709-2728.

https://doi.org/10.1111/1462-2920.14902

Tekere M., 2019, Microbial bioremediation and different bioreactors designs applied, Biotechnology and Bioengineering, 14: 1-19.

https://doi.org/10.5772/intechopen.83661

Touliabah H., El-sheekh M., Ismail M., and El-Kassas H., 2022, A study of microalgae- and cyanobacteria-based biodegradation of organic pollutants, Molecules, 27(3): 1141.

https://doi.org/10.3390/molecules27031141

Trombetta T., Vidussi F., Roques C., Scotti M., and Mostajir B., 2020, Marine microbial food web networks during phytoplankton bloom and non-bloom periods: warming favors smaller organism interactions and intensifies trophic cascade, Frontiers in Microbiology, 11: 502336.

https://doi.org/10.3389/fmicb.2020.502336

Vesamäki J., Nissinen R., Kainz M., Pilecky M., Tiirola M., and Taipale S., 2022, Decomposition rate and biochemical fate of carbon from natural polymers and microplastics in boreal lakes, Frontiers in Microbiology, 13: 1041242.

https://doi.org/10.3389/fmicb.2022.1041242

Wang Y., Sheng H.F., He Y., Wu J.Y., Jiang Y.X., Tam N., and Zhou H.W., 2012, Comparison of the levels of bacterial diversity in freshwater, intertidal wetland, and marine sediments by using millions of illumina tags, Applied and Environmental Microbiology, 78: 8264-8271.

https://doi.org/10.1128/AEM.01821-12

Wurzbacher C., Rösel S., Rychła A., and Grossart H., 2014, Importance of saprotrophic freshwater fungi for pollen degradation, PLoS ONE, 9(4): e94643.

https://doi.org/10.1371/journal.pone.0094643

Xiong J., Kurade M., and Jeon B., 2018, Can microalgae remove pharmaceutical contaminants from water? Trends in Biotechnology, 36(1): 30-44.

https://doi.org/10.1016/j.tibtech.2017.09.003

Zhu H.Z., Jiang M.Z., Zhou N., Jiang C.Y, and Liu S.J., 2021, Submerged macrophytes recruit unique microbial communities and drive functional zonation in an aquatic system, Applied Microbiology and Biotechnology, 105: 7517-7528.

https://doi.org/10.1007/s00253-021-11565-8