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Microorganisms
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Advances in Microbial Ecology That Drives Biogeochemical Cycles: Environmental Impact
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Advances in Microbial Ecology That Drives Biogeochemical Cycles: Environmental Impact

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Environmental Microbiology".

Deadline for manuscript submissions: 30 September 2025 | Viewed by 4406

Special Issue Editor

Dr. Ajit Kumar Passari

E-Mail Website
Guest Editor
Department of Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), Mexico City 04510, Mexico
Interests: microbial biotechnology; anthropogenic activity; biogeochemical cycles; microbial community; climate change; carbon cycles

Special Issue Information

Dear Colleagues,

Human activity is increasingly impacting global carbon and nutrient biogeochemical cycles. Most of our knowledge about how this will affect carbon and nutrient biogeochemical cycles in ecosystems has come from modeling. Since the transfer of nutrients and carbon between pools is reductive and challenging, if not impossible, to quantify empirically, these models were obliged to employ this technique. Furthermore, the microbial component of the ecosystem is occasionally disregarded or ignored completely, even if some of these models take into account how primary producers respond to environmental change in terms of physiology, ecology, and biogeography. Biogeochemical processes are widely simulated with numerical models. Growing data and understandings of key regulators of microbial growth and activity, as well as microbial ecology in general, are opening up new avenues for improving the description and prediction of biogeochemical processes in environmental systems utilizing intelligent model approaches.

In the realm of environmental sciences and microbiology, the understanding of microbial ecology and its intricate connections with biogeochemical cycles is of paramount importance. This Special Issue, entitled “Advances in Microbial Ecology That Drives Biogeochemical Cycles: Environmental Impact”, aims to bring together the latest research and insights from scientists around the world.

Microbes play a crucial role in shaping the Earth's ecosystems and driving biogeochemical processes that influence the planet's climate, nutrient cycling, and overall environmental health. This Special Issue aims to showcase the latest research and advancements in this field. We welcome original research articles, reviews, and perspectives that cover a wide range of topics, including the following:

  • Studies on the diversity and function of microbial communities in different habitats, such as soil, water, and extreme environments.
  • Investigations into the mechanisms by which microbes interact with and transform elements within biogeochemical cycles.
  • Research on the impact of environmental changes (e.g., climate change, pollution, land use change) on microbial ecology and biogeochemical processes.
  • Novel techniques and approaches for studying microbial ecology and biogeochemical cycles on different scales.

By contributing to this Special Issue, researchers will have the opportunity to share their findings with a wide international audience and contribute to the advancement of our knowledge in this critical area of science. We look forward to receiving high-quality original research articles, reviews, and perspectives that will enhance our understanding of the complex relationships between microbial ecology and biogeochemical cycles.

Dr. Ajit Kumar Passari
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Microorganisms is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • microbial ecology
  • biogeochemical cycles
  • microbial community
  • environmental impact
  • nutrient cycling
  • carbon cycling
  • nitrogen cycling
  • climate change
  • anthropogenic stressors

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Published Papers (7 papers)

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11 pages, 1220 KiB  
Article
Selenium Metabolizing Capabilities of 12 Bacterial Strains Isolated from Urban Environmental Samples
by Masashi Kuroda, Iori Ishimoto, Chisato Kameoka, Toshiki Kawanishi, Ren Saito, Hajime Toki, Hiroya Yamagishi, Yuzuki Watanabe and Yukinori Tani
Microorganisms 2025, 13(7), 1675; https://doi.org/10.3390/microorganisms13071675 - 16 Jul 2025
Viewed by 215
Abstract
The role of bacterial selenium metabolism in non-polluted environments remains underexplored within the selenium biogeochemical cycle. In this study, selenium-metabolizing bacteria were isolated from urban environmental samples. Among 12 isolates, 10 were identified as Citrobacter spp., while the remaining 2 were Scandinavium hiltneri [...] Read more.
The role of bacterial selenium metabolism in non-polluted environments remains underexplored within the selenium biogeochemical cycle. In this study, selenium-metabolizing bacteria were isolated from urban environmental samples. Among 12 isolates, 10 were identified as Citrobacter spp., while the remaining 2 were Scandinavium hiltneri and Klebsiella aerogenes. The Citrobacter isolates demonstrated high selenium-removal efficiency, removing over 95% of 5 mM selenium from the aqueous phase within one week. In contrast, S. hiltneri K24-1 and K. aerogenes K24-4 removed only 19% and 69%, respectively. A detailed investigation of five representative isolates, C. freundii K21-1, S. hiltneri K24-1, C. braakii K24-2, K. aerogenes K24-4, and C. freundii K24-5, revealed that Citrobacter spp. efficiently reduced selenate directly to elemental selenium, with minimal accumulation of selenite intermediates. These results highlight Citrobacter spp. as key selenium reducers and suggest their potential as bioindicators of selenium metabolic capacity in the environment. Full article
(This article belongs to the Special Issue Advances in Microbial Ecology That Drives Biogeochemical Cycles: Environmental Impact)
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20 pages, 1946 KiB  
Article
Optimization of Growth Conditions of Desulfovibrio desulfuricans Strain REO-01 and Evaluation of Its Cd(II) Bioremediation Potential for Detoxification of Rare Earth Tailings
by Ping Zhang, Chaoyang Wei and Fen Yang
Microorganisms 2025, 13(7), 1511; https://doi.org/10.3390/microorganisms13071511 - 28 Jun 2025
Viewed by 337
Abstract
To promote environmentally sustainable remediation and resource recovery from ion-adsorption rare earth tailings (IRET), this study comprehensively investigated the previously isolated strain REO-01 by examining its sulfate-reducing performance, Cd(II) immobilization potential, and physiological and biochemical responses under varying environmental conditions. Strain REO-01 was [...] Read more.
To promote environmentally sustainable remediation and resource recovery from ion-adsorption rare earth tailings (IRET), this study comprehensively investigated the previously isolated strain REO-01 by examining its sulfate-reducing performance, Cd(II) immobilization potential, and physiological and biochemical responses under varying environmental conditions. Strain REO-01 was identified as a Gram-negative facultative anaerobe with strong sulfate-reducing activity and effective Cd(II) immobilization capacity. During a 96 h incubation period, the strain entered the exponential growth phase within 36 h, after which the OD600 values plateaued. Concurrently, the culture pH increased from 6.83 to 7.5, and the oxidation-reduction potential (ORP) declined to approximately −300 mV. Cd(II) concentrations decreased from 0.2 mM to 3.33 μM, corresponding to a removal efficiency exceeding 95%, while sulfate concentrations declined from 1500 mg/L to 640 mg/L, with a maximum reduction efficiency of 66.16%. The strain showed optimal growth at 25–40 °C and near-neutral pH (6–7), whereas elevated Cd(II) concentrations (≥0.2 mM) significantly inhibited cell growth. A sulfate concentration of 1500 mg/L was found to be optimal for cellular activity. Among the tested carbon sources, sodium lactate at 4.67 g/L yielded the most favorable results, reducing ORP to −325 mV, increasing pH to 7.6, and lowering Cd(II) and sulfate concentrations to 3.33 μM and 510 mg/L, respectively. These findings highlight the strong potential of strain REO-01 for simultaneous sulfate reduction and Cd(II) remediation, supporting its application in the in situ bioremediation and resource utilization of rare earth tailings. Full article
(This article belongs to the Special Issue Advances in Microbial Ecology That Drives Biogeochemical Cycles: Environmental Impact)
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18 pages, 3168 KiB  
Article
Ammonium-Generating Microbial Consortia in Paddy Soil Revealed by DNA-Stable Isotope Probing and Metatranscriptomics
by Chao-Nan Wang, Yoko Masuda and Keishi Senoo
Microorganisms 2025, 13(7), 1448; https://doi.org/10.3390/microorganisms13071448 - 21 Jun 2025
Viewed by 496
Abstract
Rice paddy fields are sustainable agricultural systems as soil microorganisms help maintain nitrogen fertility through generating ammonium. In these soils, dissimilatory nitrate reduction to ammonium (DNRA), nitrogen fixation, and denitrification are closely linked. DNRA and denitrification share the same initial steps and nitrogen [...] Read more.
Rice paddy fields are sustainable agricultural systems as soil microorganisms help maintain nitrogen fertility through generating ammonium. In these soils, dissimilatory nitrate reduction to ammonium (DNRA), nitrogen fixation, and denitrification are closely linked. DNRA and denitrification share the same initial steps and nitrogen gas, the end product of denitrification, can serve as a substrate for nitrogen fixation. However, the microorganisms responsible for these three reductive nitrogen transformations, particularly those focused on ammonium generation, have not been comprehensively characterized. In this study, we used stable isotope probing with 15NO3−, 15N2O, and 15N2, combined with 16S rRNA high-throughput sequencing and metatranscriptomics, to identify ammonium-generating microbial consortia in paddy soils. Our results revealed that several bacterial families actively contribute to ammonium generation under different nitrogen substrate conditions. Specifically, Geobacteraceae (N2O and +N2), Bacillaceae (+NO3− and +N2), Rhodocyclaceae (+N2O and +N2), Anaeromyxobacteraceae (+NO3− and +N2O), and Clostridiaceae (+NO3− and +N2) were involved. Many of these bacteria participate in key ecological processes typical of paddy environments, including iron or sulfate reduction and rice straw decomposition. This study revealed the ammonium-generating microbial consortia in paddy soil that contain several key bacterial drivers of multiple reductive nitrogen transformations and suggested their diverse functions in paddy soil metabolism. Full article
(This article belongs to the Special Issue Advances in Microbial Ecology That Drives Biogeochemical Cycles: Environmental Impact)
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22 pages, 3483 KiB  
Article
The Patterns and Environmental Factors of Diversity, Co-Occurrence Networks, and Assembly Processes of Protistan Communities in Bulk Soils of Forests
by Bing Yang, Lin Wu, Zhisong Yang, Zhihe Zhang, Wanju Feng, Weichao Zheng and Chi Xu
Microorganisms 2025, 13(6), 1249; https://doi.org/10.3390/microorganisms13061249 - 28 May 2025
Viewed by 437
Abstract
Understanding the maintenance of soil protists within forest ecosystems is crucial for comprehending ecosystem responses to climate change. A comprehensive analysis of soil samples from the Fengtongzhai National Reserve in China, utilizing high-throughput sequencing and network analysis, indicates that topsoil protistan communities predominantly [...] Read more.
Understanding the maintenance of soil protists within forest ecosystems is crucial for comprehending ecosystem responses to climate change. A comprehensive analysis of soil samples from the Fengtongzhai National Reserve in China, utilizing high-throughput sequencing and network analysis, indicates that topsoil protistan communities predominantly comprise consumers, parasites, and plant pathogens. The principal phyla identified include Stramenopiles, Alveolates, Rhizaria (SAR), Cercozoa, Apicomplexa, and Ciliophora, with Monocystis, Rhogostoma, Cercomonas, and Globisporangium as the most prevalent genera. Although α diversity metrics did not reveal significant differences across various forest types, β diversity demonstrated notable distinctions, primarily influenced by soil pH, organic carbon content, and moisture levels. Complex co-occurrence networks were particularly evident in deciduous broadleaved and evergreen broadleaved mixed forests. The stability of these networks was higher in plantation forests compared with natural forests, with no significant differences observed among the three natural forest types studied. This finding challenges the reliability of using soil protists as indicators for forest soil health assessments. Stochastic processes, especially ecological drift, play a significant role in shaping these communities. In conclusion, the findings suggest that the mechanisms underlying the enhanced stability of co-occurrence networks of soil protists in plantations require further investigation. Additionally, the specific responses of soil protists to forest type highlight the necessity of incorporating multidimensional indicators in the evaluation of forest soil health and the effectiveness of ecological restoration efforts. Full article
(This article belongs to the Special Issue Advances in Microbial Ecology That Drives Biogeochemical Cycles: Environmental Impact)
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15 pages, 1475 KiB  
Article
Nitrogen Fertilization Alleviates Microplastic Effects on Soil Protist Communities and Rape (Brassica napus L.) Growth
by Ge Wang, Maolu Wei, Qian Sun, Ting Shen, Miaomiao Xie and Dongyan Liu
Microorganisms 2025, 13(3), 657; https://doi.org/10.3390/microorganisms13030657 - 14 Mar 2025
Cited by 2 | Viewed by 859
Abstract
Agricultural plastic mulch enhances crop yields but leads to persistent microplastic contamination in soils. Concurrently, nitrogen (N) fertilization and atmospheric deposition profoundly reshape microbial ecosystems. This study examined the individual and interactive effects of polyethylene microplastics (PE, 1% w/w) and [...] Read more.
Agricultural plastic mulch enhances crop yields but leads to persistent microplastic contamination in soils. Concurrently, nitrogen (N) fertilization and atmospheric deposition profoundly reshape microbial ecosystems. This study examined the individual and interactive effects of polyethylene microplastics (PE, 1% w/w) and nitrogen addition (N, 180 kg ha−1 yr−1) on soil protist communities and rape (Brassica napus L.) productivity. High-throughput sequencing and soil–plant trait analyses revealed that PE alone reduced the soil water retention and the rape biomass while elevating the soil total carbon content, C/N ratios, and NH₄⁺-N/NO₃−-N levels. Conversely, N addition significantly boosted the rape biomass and the chlorophyll content, likely through enhanced nutrient availability. Strikingly, the combined PE_N treatment exhibited antagonistic interactions; protist diversity and functional group composition stabilized to resemble the control conditions, and the rape biomass under the PE_N treatment showed no difference from the CK (with basal fertilizer only), despite significant reductions under the PE treatment alone. Soil nutrient dynamics (e.g., the SWC and the C/N ratio) and the protist community structure collectively explained 96% of the biomass variation. These findings highlight the potential of nitrogen fertilization to mitigate microplastic-induced soil degradation, offering a pragmatic strategy to stabilize crop productivity in contaminated agricultural systems. This study underscores the importance of balancing nutrient management with pollution control to sustain soil health under global microplastic and nitrogen deposition pressures. Full article
(This article belongs to the Special Issue Advances in Microbial Ecology That Drives Biogeochemical Cycles: Environmental Impact)
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22 pages, 5186 KiB  
Article
Microbial Metabolic Limitations and Their Relationships with Sediment Organic Carbon Across Lake Salinity Gradient in Tibetan Plateau
by Weizhen Zhang, Jianjun Wang, Yun Li, Chao Song, Yongqiang Zhou, Xianqiang Meng and Ruirui Chen
Microorganisms 2025, 13(3), 629; https://doi.org/10.3390/microorganisms13030629 - 11 Mar 2025
Viewed by 900
Abstract
Inland lakes, contributing substantially to the global storage of sediment organic carbon (SOC), are subject to marked changes in salinity due to climate warming. The imbalance in the supply of resources, such as carbon, nitrogen, and phosphorus, in sediments leads to microbial metabolic [...] Read more.
Inland lakes, contributing substantially to the global storage of sediment organic carbon (SOC), are subject to marked changes in salinity due to climate warming. The imbalance in the supply of resources, such as carbon, nitrogen, and phosphorus, in sediments leads to microbial metabolic limitations (MMLs). This, in turn, triggers the secretion of extracellular enzymes by microorganisms to mine for deficient resources by decomposing complex organic carbon. This process is a rate-limiting step in the degradation of organic carbon and, as a result, has the potential to regulate organic carbon stocks. However, the general understanding of MML patterns and their relationships with SOC content along lake salinity gradients remains elusive. This study examined 25 lakes on the Tibetan Plateau with salinity ranging from 0.13‰ to 31.06‰, analyzing MMLs through enzymatic stoichiometry. The results showed that sediment microbial metabolism was mainly limited by carbon and nitrogen, with stronger limitations at higher salinity. Water salinity and sediment pH were the main factors influencing microbial limitations, either directly or indirectly, through their effects on nutrients and microbial diversity. Additionally, the SOC content was negatively correlated with microbial carbon limitation, a relationship weakened when salinity and pH were controlled. These findings suggest that the decrease in SOC with increased salinity or pH could be driven by stronger microbial carbon limitations, offering insights into the impact of salinity changes on SOC stocks in inland lakes due to climate change. Full article
(This article belongs to the Special Issue Advances in Microbial Ecology That Drives Biogeochemical Cycles: Environmental Impact)
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25 pages, 4079 KiB  
Systematic Review
Microorganisms in Macroalgae Cultivation Ecosystems: A Systematic Review and Future Prospects Based on Bibliometric Analysis
by Yinglong Chen, Pengbing Pei, Muhammad Aslam, Muhamad Syaifudin, Ran Bi, Ping Li and Hong Du
Microorganisms 2025, 13(5), 1110; https://doi.org/10.3390/microorganisms13051110 - 12 May 2025
Viewed by 663
Abstract
Microorganisms play an essential role in the biogeochemical processes of macroalgal cultivation ecosystems by participating in a complex network of interactions, significantly influencing the growth and development of macroalgae. This study used bibliometric analysis and VOSviewer based on Web of Science data to [...] Read more.
Microorganisms play an essential role in the biogeochemical processes of macroalgal cultivation ecosystems by participating in a complex network of interactions, significantly influencing the growth and development of macroalgae. This study used bibliometric analysis and VOSviewer based on Web of Science data to provide an overview by tracing the developmental footprint of the technology. Countries, institutions, authors, keywords, and key phrases were tracked and mapped accordingly. From 1 January 2003 to 31 December 2023, 619 documents by 2516 authors from 716 institutions in 51 countries were analyzed. Keyword co-occurrence network analysis revealed five main areas of research on microbes in macroalgal cultivation ecosystems: (1) identification of microbial species and functional genes, (2) biogeochemical cycling of carbon in microbial communities, (3) microbial influences on macroalgae growth and development, (4) bioactivities, and (5) studies based on database. Thematic evolution and map research emphasized the centrality of microbial diversity research in this direction. Over time, the research hotspots and the core scientific questions of the microorganisms in the macroalgal cultivation ecosystems have evolved from single-organism interactions to the complex dynamics of microbial communities. The application of high-throughput techniques had become a hotspot, and the adoption of systems biology approaches had further facilitated the integrated analysis of microbial community composition and function. Our results provide valuable guidance and information for future researches on algal–bacterial interactions and microbe-driven carbon cycling in coastal ecosystems. Full article
(This article belongs to the Special Issue Advances in Microbial Ecology That Drives Biogeochemical Cycles: Environmental Impact)
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