Molecular Microbiology Research 2024, Vol.14 http://microbescipublisher.com/index.php/mmr © 2024 MicroSci Publisher, an online publishing platform of Sophia Publishing Group. All Rights Reserved. Sophia Publishing Group (SPG), founded in British Columbia of Canada, is a multilingual publisher.
Molecular Microbiology Research 2024, Vol.14 http://microbescipublisher.com/index.php/mmr © 2024 MicroSci Publisher, an online publishing platform of Sophia Publishing Group. All Rights Reserved. Sophia Publishing Group (SPG), founded in British Columbia of Canada, is a multilingual publisher. Publisher MicroSci Publisher Editedby Editorial Team of Molecular Microbiology Research Email: edit@mmr.microbescipublisher.com Website: http://microbescipublisher.com/index.php/mmr Address: 11388 Stevenston Hwy, PO Box 96016, Richmond, V7A 5J5, British Columbia Canada Molecular Microbiology Research (ISSN 1927-5595) is an open access, peer reviewed journal published online by MicroSci Publisher. The journal publishes all the latest and outstanding research articles, letters and reviews in all areas of molecular microbiology, including original articles, reviews and brief reports in microbiology, bacteriology, mycology, molecular and cellular biology and virology at the level of gene expression and regulation, genetic transfer, cell biology and subcellular organization, pathogenicity and virulence, physiology and metabolism, cell-cell communication and signalling pathways as well as the interactions between the various cell systems of microorganisms including the interrelationship of DNA, RNA and protein biosynthesis. All the articles published in Molecular Pathogens are Open Access, and are distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. MicroSci Publisher uses CrossCheck service to identify academic plagiarism through the world’s leading plagiarism prevention tool, iParadigms, and to protect the original authors’ copyrights. MicroSci Publisher is an international Open Access publisher specializing in microbiology, bacteriology, mycology, molecular and cellular biology and virology registered at the publishing platform that is operated by Sophia Publishing Group (SPG), founded in British Columbia of Canada.
Molecular Microbiology Research (online), 2024, Vol. 14 ISSN 1927-5595 http://microbescipublisher.com/index.php/mmr © 2024 MicroSci Publisher, an online publishing platform of Sophia Publishing Group. All Rights Reserved. Sophia Publishing Group (SPG), founded in British Columbia of Canada, is a multilingual publisher. Latest Content 2024, Vol.14, No.3 【Scientific Review】 NrfA Enzyme: The Bridge Connecting Microbes and Environmental Nitrogen Dynamics 119-123 ManmanLi DOI: 10.5376/mmr.2024.14.0013 【Invited Review】 Strategic Engineering of Synthetic Microbial Communities (SynComs) for Optimizing Plant Health and Yield in Agriculture 124-130 Wenfei Zhang DOI: 10.5376/mmr.2024.14.0014 【Review Article】 Clean Water Starts with Decomposers: The Importance of Microbial Life in Aquatic Systems 131-140 Xing Zhao, Minsheng Lin DOI: 10.5376/mmr.2024.14.0015 【Research Insight】 TheRole of Aspergillus oryzae in Bilological Control Against Rice Pests 141-152 Jun Wang, Jie Zhang DOI: 10.5376/mmr.2024.14.0016 【Feature Review】 Application of Non-Rhizobial Endophytic Microbes in Rice Cultivation 153-161 Weisheng He, Juyi Bai, Danyan Ding DOI: 10.5376/mmr.2024.14.0017
Molecular Microbiology Research 2024, Vol.14, No.3, 119-123 http://microbescipublisher.com/index.php/mmr 119 Scientific Review Open Access NrfA Enzyme: The Bridge Connecting Microbes and Environmental Nitrogen Dynamics ManmanLi Hainan Institute of Tropical Agricultural Resources, Sanya, 572024, Hainan, China Corresponding email: lmm314.editor@gmail.com Molecular Microbiology Research, 2024, Vol.14, No.3 doi: 10.5376/mmr.2024.14.0013 Received: 15 Mar., 2024 Accepted: 26 Apr., 2024 Published: 12 May, 2024 Copyright © 2024 Li, This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Preferred citation for this article: Li M.M., 2024, NrfA enzyme: the bridge connecting microbes and environmental nitrogen dynamics, Molecular Microbiology Research, 14(3):119-123 (doi: 10.5376/mmr.2024.14.0013) The paper Diversity and ecology of NrfA-dependent ammonifying microorganisms was published on March 9, 2024, in the journal Trends in Microbiology. Authored by Aurélien Saghaï and Sara Hallin from the Swedish University of Agricultural Sciences, among others, this study focuses on NrfA-dependent ammonifying microorganisms. These are a diverse group of microorganisms that reduce nitrate to ammonia, significantly impacting nitrogen retention across various ecosystems. These organisms play a crucial role in the nitrogen cycle. The article discusses in detail their diversity, physiological roles, and ecological significance in terrestrial and aquatic environments. 1 Experimental Data Analysis The key findings of the experiment are mainly reflected in two aspects: First, in terms of diversity and ecological environment: (1) NrfA-dependent ammonifying microorganisms are widely present in both terrestrial and aquatic environments, with a rich variety of species and broad distribution. (2) These microorganisms demonstrate the capability to reduce nitrate, especially under oxygen-limited conditions, across various environments. The second aspect concerns physiological functions: (1) The NrfA enzyme is a key biocatalyst linking nitrate reduction to ammonia, through which these microorganisms contribute to nitrogen retention in the environment. (2) The NrfA enzyme, by acting in the space between the outer membranes of bacterial cells, can directly reduce nitrite to ammonia. Figure 1 presents a conceptual schematic of the inorganic nitrogen cycle, revealing the pathways of nitrogen transformation in the natural environment. The nitrogen cycle primarily includes: (1) atmospheric nitrogen fixation, (2) mineralization of organic nitrogen, (3) nitrification, (4) denitrification, (5) ammonification of nitrate, (6) anaerobic ammonium oxidation, and (7) assimilation of ammonia and nitrate. The products of each stage and some intermediate products are indicated by their chemical names in the diagram. Nitrogen is lost from ecosystems through leaching of nitrate and gaseous losses. This cyclic process is fundamental for understanding the flow of nitrogen in soil, water, and air and its impact on ecosystems. Figure 2 provides a detailed depiction of the dimeric structure of the NrfA enzyme in Escherichia coli and its role in the electron transport chain from formate to nitrite. Panel A shows the three-dimensional structure of the NrfA homodimer, each monomer containing five heme groups, along with calcium ions and iron atoms. Panel B illustrates the electron transfer during the respiratory nitrite ammonification process, involving NrfH or NrfBCD as electron carriers. Through this process, formate is oxidized on the cell membrane, generating proton motive force that drives electrons through the complex, ultimately achieving the reduction of nitrite. This complex reaction process is crucial for intracellular energy conversion and material cycling.
Molecular Microbiology Research 2024, Vol.14, No.3, 119-123 http://microbescipublisher.com/index.php/mmr 120 Figure 1 Schematic illustration of the inorganic nitrogen cycle Figure 2 Structure of NrfA and schematics of the enzyme complexes involved in the electron transport chain from formate to nitrite Figure 3 shows the maximum likelihood phylogenetic tree inferred from the alignment of 1 150 complete NrfA sequences within 1 121 genomic assemblies, based on 350 amino acid positions. Different bacterial phyla are identified by colored bands in the outer ring, with the color coding based on genomic classification databases. Phyla represented by fewer than 10 sequences are labeled as "Others" and shown in gray. Gray branches represent those sequences that contain a Cys-X-X-Cys-His variant at the first heme-binding site. Blue stars mark known bacterial isolates that can reduce nitrate or nitrite to ammonia, while yellow stars indicate bacterial isolates with a determined NrfA crystal structure. The scale bar represents the rate of amino acid substitution (WAG+R10). Outgroups are not shown. This phylogenetic tree reveals the rich diversity of NrfA sequences and their distribution across different bacterial phyla.
Molecular Microbiology Research 2024, Vol.14, No.3, 119-123 http://microbescipublisher.com/index.php/mmr 121 Figure 3 Maximum likelihood phylogeny of 1150 full-length NrfA sequences from 1121 genome assemblies inferred from the alignment of 350 amino acid positions
Molecular Microbiology Research 2024, Vol.14, No.3, 119-123 http://microbescipublisher.com/index.php/mmr 122 Figure 4 illustrates the distribution of nrfA sequence fragments from metagenomes across different biomes through a phylogenetic tree. Part A shows the distribution in aquatic environments, while Part B displays terrestrial biomes. Bacterial phyla are color-coded in the outer ring based on genomic classification databases. In the diagram, the size of the dots represents the proportion of sequences in the corresponding biome, providing a visual reference for quantitative analysis. This combination of categorization and quantification lays the foundation for studying the ecology and evolution of NrfA-dependent ammonifying microorganisms in various biomes. The scale represents the rate of amino acid substitution, a common metric for comparing gene sequence differences. Outgroup sequences distinctly different from other biomes are not shown in the diagram. Figure 4 Phylogenetic placement of the metagenomic nrfA sequence fragments across biomes 2 Analysis of Research Findings This study provides a comprehensive insight into how NrfA-dependent ammonifying microorganisms facilitate the nitrogen cycle. These microorganisms not only help retain nitrogen within ecosystems but also contribute to reducing greenhouse gas emissions by minimizing nitrate loss. 3 Evaluation of the Research This study is methodologically rigorous and addresses significant gaps in our understanding of nitrogen-cycling microorganisms. However, the research would benefit from broader geographic sampling to enhance the generalizability of the findings.
Molecular Microbiology Research 2024, Vol.14, No.3, 119-123 http://microbescipublisher.com/index.php/mmr 123 4 Conclusions NrfA-dependent ammonifying microorganisms are crucial in maintaining nitrogen within ecosystems, impacting environmental health and agricultural practices. Further research is needed to fully leverage their potential for effective nitrogen management across various biotic communities. 5 Access the Full Text Saghaï A., and Hallin S., 2024, Diversity and ecology of NrfA-dependent ammonifying microorganisms, Trends in Microbiology, 32(6): 602-613. DOI: 10.1016/j.tim.2024.02.007. Acknowledgments The authors sincerely thank the Trends in Microbiology journal for providing open access to their papers, especially the research on the diversity and ecology of NrfA-dependent ammonifying microorganisms by Aurélien Saghaï and Sara Hallin (2024). This has given us the opportunity to gain an in-depth understanding and share the latest findings in this field with our peers, contributing to the advancement of the scientific community.
Molecular Microbiology Research 2024, Vol.14, No.3, 124-130 http://microbescipublisher.com/index.php/mmr 124 Invited Review Open Access Strategic Engineering of Synthetic Microbial Communities (SynComs) for Optimizing Plant Health and Yield in Agriculture Wenfei Zhang Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, 571158, Hainan, China Corresponding email: wenfei2007@163.com Molecular Microbiology Research, 2024, Vol.14, No.3 doi: 10.5376/mmr.2024.14.0014 Received: 20 Mar., 2024 Accepted: 08 May, 2024 Published: 23 May, 2024 Copyright © 2024 Zhang, This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Preferred citation for this article: Zhang W.F., 2024, Strategic engineering of synthetic microbial communities (SynComs) for optimizing plant health and yield in agriculture, Molecular Microbiology Research, 14(3): 124-130 (doi: 10.5376/mmr.2024.14.0014) Abstract This comprehensive review encapsulates the current state of research on Synthetic Microbial Communities (SynComs) and their burgeoning role in agriculture. The paper aims to elucidate the conceptual framework and developmental milestones of SynComs, tracing their historical evolution from mere scientific inquiry to pivotal agricultural assets. By delving into the synthesis of current literature, this review presents an analytical digest of the advancements in SynCom development, their applications in enhancing plant health, and their integration with existing agricultural practices. The engineered microbial consortia are highlighted for their precise functionality, such as biofilm formation, secondary metabolite production, and induction of plant resistance, structured by ecological theories and phylogenetic organization. The document reviews evidence demonstrating the efficacy of SynComs in bolstering crop resilience, especially under challenging environmental conditions, with case studies exemplifying the protection of wheat against soilborne pathogens and the improvement of soybean yield. Furthermore, it explores the potential of SynCom integration with traditional breeding techniques and plant cultivation management, suggesting that SynComs can complement breeding programs and provide sustainable solutions to biotic stresses. The review concludes by underscoring the promise of SynComs in sustainable agriculture and proposing future research directions that address challenges in microbial colonization, stability, and the harmonization of SynComs with traditional farming methods. This work serves as a cornerstone for developing a new paradigm in precision agriculture where SynComs play a crucial role in crop management for enhanced productivity. Keywords Synthetic microbial communities; Plant health; Agricultural productivity; Microbial engineering; Crop resilience; Plant-microbe interactions; Precision agriculture; Sustainable farming practices 1 Introduction In recent years, the agricultural sector has witnessed a surge in interest toward a more sustainable and resilient approach to crop production and plant health management (Fang, 2024). One of the most promising frontiers in this quest is the exploration and application of Synthetic Microbial Communities (SynComs), which hold the potential to revolutionize the way we support plant growth and combat agricultural challenges. SynComs are engineered communities of microorganisms specifically designed to provide beneficial effects to plants, such as enhanced nutrient uptake, disease resistance, and stress tolerance (Marín et al., 2021). The significance of SynComs lies in their ability to mimic and enhance the natural plant-microbe interactions that are critical for plant health and soil fertility (Martins et al., 2023). By understanding and harnessing these relationships, SynComs can be strategically applied to improve agricultural productivity in a manner that is in harmony with the environment (Gopal and Gupta, 2016). This review aims to consolidate the current body of research regarding the development and application of SynComs with a focus on enhancing plant health and agricultural productivity. Our objectives are multifold and we intend to gain a deep understanding of the concept and historical development of SynComs, provide a
Molecular Microbiology Research 2024, Vol.14, No.3, 124-130 http://microbescipublisher.com/index.php/mmr 125 comprehensive summary of the progress made in this field, examine the potential for integration with traditional breeding techniques, and discuss the ways in which SynComs can be combined with plant cultivation management to unlock new possibilities in agriculture. The integration of SynComs into agricultural systems offers a window into a future where plants can thrive with reduced chemical inputs, where soil health is actively managed through microbial interventions, and where crop yields can be sustained or enhanced despite the growing challenges of climate change. It is through this lens that we will explore the current landscape of SynComs research and its implications for the future of plant health and agricultural productivity. 2 The Concept of Synthetic Microbial Communities (SynComs) 2.1 Definition and engineering of SynComs Synthetic Microbial Communities, commonly referred to as SynComs, represent a significant breakthrough in the intersection of microbial ecology and agricultural biotechnology. These are intentionally constructed consortia of microbial species, meticulously selected and engineered to perform specific functions beneficial to plant health and productivity (Gopal and Gupta, 2016). SynComs are not random assemblages but are designed to emulate and optimize the natural beneficial traits observed in plant-associated microbiomes. The key functions these microbial consortia are engineered for include biofilm formation, which can protect plant roots, the production of secondary metabolites, which can deter pathogens or attract beneficial insects, and the induction of plant resistance mechanisms, enhancing the plant’s innate ability to fend off diseases (Marín et al., 2021). The rationale behind the precise composition of a SynCom lies in the desired outcome or function intended for the plant host. For instance, one SynCom may be tailored to improve nitrogen fixation, directly influencing the nutritional uptake of the plant, while another may be designed to induce systemic resistance to specific pathogens, thereby fortifying the plant’s defensive capabilities. Martins et al. (2023) describe these communities as meticulously engineered based on an understanding of how specific microbial species interact with each other and with their plant hosts, demonstrating the purpose-driven nature of SynComs . 2.2 Design of SynComs based on ecological theories of plant-microbiome interactions The design of SynComs is not merely an act of biological engineering but is deeply rooted in ecological theories. These theories propose that plant-associated microbial communities are not arbitrary in their composition; rather, they possess a defined phylogenetic structure which is the result of complex community assembly rules. These rules dictate the interactions, co-existence, and functions of microbes within the community, which, in turn, impact the health and growth of the plant. SynComs are therefore constructed by simulating these natural organizational patterns, ensuring that the synthetic communities can integrate seamlessly into the plant’s ecosystem and perform their functions effectively. According to Martins et al. (2023), the creation of SynComs takes into account the intricate network of interactions within the rhizosphere, the region of soil in the immediate vicinity of plant roots. In this densely populated microbial hub, the selection of species for inclusion in a SynCom is guided by their known roles and interactions in the natural soil microbiome. By aligning with ecological theories, designers of SynComs can anticipate how these microbes will behave in conjunction with the plant and its native microbiome, establishing a stable and supportive environment that promotes plant health and growth . In summary, the development of SynComs marks a proactive stride towards harnessing microbial processes for agricultural advancement. It is a prime example of how scientific knowledge, especially the understanding of ecological and phylogenetic principles, can lead to practical applications that enhance the sustainability and productivity of crop systems.
Molecular Microbiology Research 2024, Vol.14, No.3, 124-130 http://microbescipublisher.com/index.php/mmr 126 3 Historical Overview of the SynCom Concept 3.1 Evolution of the SynCom concept alongside microbial ecology The journey of Synthetic Microbial Communities (SynComs) is closely tied to the advancements in microbial ecology. Initially, the study of microbial communities was challenged by the complexity and variability of the environment. As microbial ecology progressed, the introduction of SynComs became a revolutionary approach. This allowed for a more controlled and systematic exploration of microbial functions and their contributions to plant health. SynComs simplified the complex interactions in natural microbial assemblages, thereby providing a clearer picture of the contributions and dynamics within microbial communities. This transition marked a significant shift from studying individual microbe-plant interactions to understanding the collective impact of microbial consortia. 3.2 Insights into plant-microbe regulation mechanisms through SynComs SynComs have bridged the gap in understanding the intricate regulation mechanisms between plants and their associated microbiomes. By employing a reductionist approach, researchers have been able to construct simplified versions of microbial communities to study the core interactions that govern the plant-microbiome relationship. This method has provided valuable functional and mechanistic insights, revealing how plants may influence the composition and function of their microbiomes and vice versa. Through studies employing SynComs, scientists like Liu et al. (2019) have demonstrated that plants can recruit specific microbial species from the environment, which in turn can modulate the plant's health and growth. This research underscores the potential of SynComs to dissect complex biological interactions into more manageable and observable phenomena, offering a clearer understanding of the symbiotic relationships at play . 4 Research Progress in SynComs 4.1 Exploring plant root microbiomes: diverse methodologies for comprehensive understanding In 2021, Marín et al. detail three investigative strategies for studying the root microbiome in plants (Figure 1). The Reductionist Approach, also known as Bottom-up, starts with the analysis of single microbial strains through culture-dependent techniques, offering precise insights into individual plant-microbe interactions with the benefit of simpler experimentation and high certainty in identifying specific microbial species. In contrast, the Holistic Approach or Top-down method delves into the complexities of wild microbial communities by utilizing culture-independent 'omics' techniques. While this approach embraces the dynamic nature of the rhizosphere, it trades off specificity for broader ecological insights, discerning patterns through correlational rather than causal analyses. Bridging these methodologies is the Synthetic Community (SynCom) Experimentation. This intermediate method combines the clarity of the Reductionist Approach with the encompassing perspective of the Holistic Approach. SynCom experiments deploy specially designed microbial communities of known composition, allowing researchers to manage experimental complexity more effectively and gain deeper understanding of microbe-microbe and plant-microbe interactions (Marín et al., 2021). Framework of Marín et al. (2021) demonstrates the necessary balance between experimental complexity, certainty in microbial identification, and the depth of insights when researching plant root microbiomes. Their schematic underscores the need for both targeted and comprehensive strategies to fully grasp the intricate web of interactions in the microbiome that significantly influence plant health. 4.2 Recent studies highlighting SynComs' role in crop resiliency and environmental stress adaptation The development of Synthetic Microbial Communities (SynComs) represents a significant advancement in agricultural biotechnology. Research has increasingly focused on how these engineered communities can bolster crop resilience, especially under challenging environmental conditions. In a pivotal study, Souza et al. (2020) detailed the design of SynComs that bolstered plant traits linked to improved stress tolerance, demonstrating a notable enhancement in crop resiliency.
Molecular Microbiology Research 2024, Vol.14, No.3, 124-130 http://microbescipublisher.com/index.php/mmr 127 Figure 1 Different approaches to understand the role of the root microbiome in plants. Schematic representation of information processing strategies (top-down and bottom-up) and the approaches that stand on the edges of them (reductionist and holistic) (Adopted from Marín et al., 2021) This body of work underpins a new paradigm in which the deliberate assembly of microbial species can be tailored to address specific agricultural challenges. By employing SynComs, scientists are able to invoke precise microbiome functions, such as enhanced stress response mechanisms in plants, which are crucial for maintaining productivity amidst climatic and environmental adversities. 4.3 Case studies: protection against soilborne pathogens, nutrient efficiency, and plant growth promotion Several case studies have underlined the effectiveness of SynComs in protecting crops against soilborne pathogens. Yin et al. (2022) illustrated how wheat crops benefitted from SynComs sourced from rhizosphere soil, which offered protection against fungal pathogens, thereby reducing the dependency on chemical fungicides . Beyond pathogen defense, SynComs have been recognized for their role in optimizing nutrient uptake and utilization. Wang et al. (2021) reported that certain functionally assembled SynComs could substantially improve nutrient efficiency and yields in soybean crops. Such findings suggest that SynComs could lead to reduced fertilizer use, contributing to more sustainable agricultural practices. Additionally, there is an emerging interest in the use of SynComs derived from compost-derived microbes. Tsolakidou et al. (2018) explored this domain, revealing that these specialized microbial pools could consistently enhance plant growth and health . These developments highlight the versatile nature of SynComs in various agricultural contexts, from boosting growth to ensuring crop survival under biotic and abiotic stressors. The research progress in SynComs indicates a promising trend towards developing more resilient agricultural systems that can withstand the test of changing global environmental conditions. The potential of SynComs to revolutionize crop management practices is immense, paving the way for a future where sustainable and resilient agriculture is the norm. 5 Integration with Traditional Plant Breeding 5.1 How SynCom principles assist in traditional plant breeding The integration of Synthetic Microbial Communities (SynComs) with traditional breeding techniques represents a pioneering approach to enhancing crop production and resilience. Traditional breeding has focused primarily on
Molecular Microbiology Research 2024, Vol.14, No.3, 124-130 http://microbescipublisher.com/index.php/mmr 128 the genetic manipulation of plant genomes to select for desirable traits. However, the principles of SynComs extend this paradigm by considering the microbial environment's role in expressing these traits. According to Souza et al. (2020), plant-associated microbiomes significantly influence phenotypic traits, such as disease resistance, yield, and stress tolerance. By strategically using SynComs, breeders can now target these microbiome-influenced traits. This approach could lead to a new era of breeding strategies where the selected microbial consortia are used to steer the expression of plant genotypes, thereby facilitating the breeding of crops with improved performance and adaptability to a range of environmental conditions. 5.2 Breeding for specific plant traits influenced by the microbiome The precise targeting of plant traits influenced by the microbiome is an innovative use of SynComs in traditional plant breeding. This process involves identifying key microbial species that interact with plant genomes to affect specific traits. For example, certain microbes can enhance nutrient uptake, promote growth under stress conditions, or increase resistance to pathogens. By incorporating SynComs into the breeding process, it is possible to promote these beneficial interactions and select for plants that not only possess the genetic capacity for these traits but also have an optimized microbiome that ensures their expression in various environments. Souza et al. (2020) suggest that designing SynComs for improved crop resiliency can serve as a blueprint for breeding programs looking to exploit the full potential of the plant microbiome . This presents an opportunity for breeders to develop crops that are better equipped to thrive in suboptimal conditions, ultimately leading to sustainable agriculture and enhanced food security. 5.3 New strategies in plant breeding: microbiome selection Although plants are stationary, they have evolved unique strategies to cope with biotic and abiotic stresses through symbiosis with microbes. Plants not only select their required microbiomes from the soil but also carry a diverse microbial community in their seeds, which serves as a primary source for microbial inoculation in crop cultivation. Gopal and Gupta (2016) discussed in detail how plant microbiomes help maintain plant health and provide crucial genetic diversity, a potential that has yet to be utilized in traditional breeding strategies. Undoubtedly, selecting microbiomes will become a strategy for the next generation of plant breeding. Gopal and Gupta (2016) introduced a novel plant breeding approach through microbiome selection, developing new generation crops that rely less on inorganic inputs, are resistant to pests and diseases, and can adapt to climate changes. The authors suggest that future plant breeding strategies should consider the plant and its microbial symbionts as co-propagated partners (Gopal and Gupta, 2016). 6 Combination with Plant Cultivation Management 6.1 Sustainable application of SynComs in plant disease stress management The integration of Synthetic Microbial Communities (SynComs) into plant cultivation management offers a sustainable solution to mitigate biotic stresses faced by crops. SynComs have been engineered to enhance plant resilience against a range of pathogens by optimizing the plant's own defense mechanisms. Utilizing SynComs as a part of an integrated disease management strategy can reduce reliance on chemical pesticides, thereby minimizing environmental impact and preserving beneficial soil microbiota. This approach aligns with sustainable agriculture principles, focusing on maintaining long-term soil health and crop productivity. As outlined by Pradhan et al. (2022), the strategic application of SynComs can combat biotic stresses by reinforcing the plant's innate immune responses and inducing systemic resistance. 6.2 Application of SynComs in seed treatment Applying SynComs to seeds represents a significant advance in agricultural practices. This method effectively engineers the seedling microbiota from the very start of plant development, potentially leading to healthier and more resilient plants. The inoculation of seeds with SynComs has been demonstrated to alter the recruitment and assembly of microbial communities in both the seedlings and the surrounding rhizosphere. By doing so, it can create a more favorable microbiological environment that supports growth and combats pathogenic organisms.
Molecular Microbiology Research 2024, Vol.14, No.3, 124-130 http://microbescipublisher.com/index.php/mmr 129 Arnault et al. (2023) illustrate the effectiveness of this technique in shaping seedling microbiota, thereby influencing subsequent plant-microbe interactions that are crucial for plant development . 6.3 Impact of SynComs on planting and rhizosphere microbial communities The deployment of SynComs has a profound impact on the microbial communities associated with planted crops and their rhizosphere. By deliberately assembling and introducing beneficial microbial consortia, SynComs can significantly alter the diversity and function of the microbiome in favor of the plant's health. The targeted modification of microbial communities through SynComs can lead to improved nutrient uptake, enhanced stress tolerance, and suppression of harmful pathogens. This modification is not only beneficial for the individual plant but can also have positive implications for the overall agricultural ecosystem, promoting a more robust and sustainable cultivation practice as described by Arnault et al. (2023) in their exploration of seed microbiota engineering. In conclusion, the combination of SynComs with plant cultivation management is a promising area that aligns well with the emerging needs for sustainable agriculture. The continued research and application of SynComs in this manner not only advance our understanding of plant-microbe interactions but also pave the way for innovative strategies to bolster crop resilience and productivity. 7 Discussion and Prospects 7.1 Prospects of SynComs as a strategy to enhance plant health and agricultural productivity Synthetic Microbial Communities (SynComs) have emerged as a cutting-edge strategy with significant potential to enhance plant health and boost agricultural productivity. The synergy among the microbial species within these communities can be harnessed to form a stable and efficacious tool for improving crop resilience and yields. Studies have shown that SynComs can successfully increase the natural defense mechanisms of plants, leading to healthier crops that can withstand various environmental stresses (Yin et al., 2022; Martins et al., 2023). This synergy is crucial not just for plant growth but also for enabling the sustainable intensification of agriculture needed to meet the global food demand. 7.2 Future research directions including challenges in microbial colonization and stability Despite their promise, the application of SynComs in agriculture faces significant challenges, especially in the aspects of microbial colonization and stability. Future research should prioritize developing methodologies that enhance the successful colonization of beneficial microbes in the plant microbiome. Additionally, ensuring the long-term stability of these communities within the plant's ecosystem is essential to provide enduring benefits (Tsolakidou et al., 2018; Souza et al., 2020). Research should also investigate the resilience of SynComs against competing native microflora and their ability to adapt to different plant varieties and environmental conditions (Wang et al., 2021). 7.3 Sustainable integration of SynComs with traditional agricultural practices Integrating SynComs with conventional agricultural practices offers a sustainable path to improve crop management. Traditional practices and the innovative use of SynComs can complement each other, creating a holistic approach to agriculture. SynComs can be applied in tandem with traditional soil and seed treatments to engineer robust seedling microbiomes, thus enhancing the plants' capacity to regulate their rhizosphere microbiota (Arnault et al., 2023). This integration can result in improved nutrient uptake, better stress tolerance, and ultimately, higher yields. Moreover, aligning SynComs with sustainable agricultural practices could contribute to reducing the reliance on chemical inputs, promoting biodiversity, and preserving ecological balances (Shayanthan et al., 2022; Pradhan et al., 2022). In conclusion, SynComs hold the key to unlocking a new era of sustainable agriculture. With focused research on overcoming current challenges and strategic integration with traditional farming techniques, SynComs have the potential to revolutionize how we cultivate crops, leading to a more resilient and productive agricultural landscape.
Molecular Microbiology Research 2024, Vol.14, No.3, 124-130 http://microbescipublisher.com/index.php/mmr 130 Funding This research was funded by the Hainan Provincial Natural Science Foundation of China (321RC545, 320MS040); The Innovation Platform for Academicians of Hainan Province (YSPTZX202130); National Key Research and Development Program of China (2021YF C3201600). Acknowledgments I extend my thanks to the two anonymous peer reviewers for their valuable feedback on this manuscript. Conflict of Interest Disclosure The author affirms that this research was conducted without any commercial or financial relationships that could be construed as a potential conflict of interest. References Arnault G., Marais C., Préveaux A., Briand M., Poisson A., Sarniguet A., Barret M., and Simonin M., 2023, Seedling microbiota engineering using bacterial synthetic community inoculation on seeds, bioRxiv, 100(4): fiae027. https://doi.org/10.1101/2023.11.24.568582 Fang X.J., 2024, Harnessing genetic populations in plant breeding: innovative strategies for construction and application, International Journal of Horticulture, 14(3): 105-110. https://doi.org/10.5376/ijh.2024.14.0012 Gopal M., and Gupta, A., 2016, Microbiome selection could spur next-generation plant breeding strategies, Frontiers in Microbiology, 7. https://doi.org/10.3389/fmicb.2016.01971 Liu Y., Qin Y., and Bai Y., 2019, Reductionist synthetic community approaches in root microbiome research, Current opinion in microbiology, 49: 97-102. https://doi.org/10.1016/j.mib.2019.10.010 Marín O., González B., and Poupin M., 2021, From microbial dynamics to functionality in the rhizosphere: a systematic review of the opportunities with synthetic microbial communities, Frontiers in Plant Science, 12. https://doi.org/10.3389/fpls.2021.650609 Martins S., Pasche J., Silva H., Selten G., Savastano N., Abreu L., Bais H., Garrett K., Kraisitudomsook N., Pieterse C., and Cernava T., 2023, The use of synthetic microbial communities (SynComs) to improve plant health, Phytopathology. https://doi.org/10.1094/PHYTO-01-23-0016-IA Pradhan S., Tyagi R., and Sharma S., 2022, Combating biotic stresses in plants by synthetic microbial communities: principles, applications and challenges, Journal of Applied Microbiology, 133: 2742-2759. https://doi.org/10.1111/jam.15799 Shayanthan A., Ordoñez P., and Oresnik, I., 2022, The role of synthetic microbial communities (SynCom) in Sustainable Agriculture, 4. https://doi.org/10.3389/fagro.2022.896307 Souza, R., Armanhi, J., and Arruda, P., 2020, From microbiome to traits: designing synthetic microbial communities for improved crop resiliency, Frontiers in Plant Science, 11. https://doi.org/10.3389/fpls.2020.01179 Tsolakidou M., Stringlis I., Fanega-Sleziak N., Papageorgiou S., Tsalakou A., and Pantelides I., 2018, Rhizosphere-enriched microbes as a pool to design synthetic communities for reproducible beneficial outputs, bioRxiv. https://doi.org/10.1101/488064 Wang C., Li Y., Li M., Zhang K., Ma W., Zheng L., Xu H., Cui B., Liu R., Yang Y., Zhong Y., and Liao H., 2021, Functional assembly of root-associated microbial consortia improves nutrient efficiency and yield in soybean, Journal of integrative plant biology. https://doi.org/10.1111/jipb.13073 Wang Z., Hu X., Solanki M., and Pang F., 2023, A synthetic microbial community of plant core microbiome can be a potential biocontrol tool, Journal of agricultural and food chemistry. https://doi.org/10.1021/acs.jafc.2c08017 Yin C., Hagerty C., and Paulitz T., 2022, Synthetic microbial consortia derived from rhizosphere soil protect wheat against a soilborne fungal pathogen, Frontiers in Microbiology, 13. https://doi.org/10.3389/fmicb.2022.908981
Molecular Microbiology Research 2024, Vol.14, No.3, 131-140 http://microbescipublisher.com/index.php/mmr 131 Review Article Open Access Clean Water Starts with Decomposers: The Importance of Microbial Life in Aquatic Systems Xing Zhao, Minsheng Lin Tropical Microbial Resources Research Center, Hainan Institute of Tropical Agricultural Resources, Sanya, 572025, Hainan, China Corresponding author: minsheng.lin@hitar.org Molecular Microbiology Research, 2024, Vol.14, No.3 doi: 10.5376/mmr.2024.14.0015 Received: 08 Apr., 2024 Accepted: 20 May, 2024 Published: 06 Jun., 2024 Copyright © 2024 Zhao and Lin, This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Preferred citation for this article: Zhang X., and Lin M.S., 2024, Clean water starts with decomposers: the importance of microbial life in aquatic systems, Molecular Microbiology Research, 14(3): 131-140 (doi: 10.5376/mmr.2024.14.0015) Abstract Microbial communities, including bacteria and fungi, are essential for the decomposition of organic matter and nutrient cycling in aquatic environments. The absence of sunlight, as seen in underground water storage or under floating solar panels, can significantly alter microbial activity, leading to the accumulation of nitrates due to increased nitrification rates and decreased nitrate assimilation. Additionally, the presence of periphytic algae can stimulate microbial decomposers, enhancing the breakdown of plant litter and organic matter. The study also highlighted the functional variability among aquatic fungal decomposers, which can influence higher trophic levels and overall ecosystem functioning. Furthermore, microbial communities respond to various environmental stressors, such as pollution and changes in water quality, which can affect their composition and function. The findings underscore the importance of microbial decomposers in maintaining water quality in aquatic systems. Microbial communities play a pivotal role in nutrient cycling, organic matter decomposition, and responding to environmental changes. These insights highlight the need for monitoring microbial activity and composition to ensure the health and sustainability of aquatic ecosystems. Keywords Microbial decomposers; Water quality; Nutrient cycling; Organic matter decomposition, Aquatic ecosystems; Microbial communities; Environmental stressors 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
Molecular Microbiology Research 2024, Vol.14, No.3, 131-140 http://microbescipublisher.com/index.php/mmr 132 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 (Wanget 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).
Molecular Microbiology Research 2024, Vol.14, No.3, 131-140 http://microbescipublisher.com/index.php/mmr 133 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). 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).
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