Microbial Ecology and Biogeochemical Functions in Sediment and Aquatic Environments

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

Deadline for manuscript submissions: 31 December 2026 | Viewed by 452

Editors


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Guest Editor
1. Department of Civil, Environmental & Construction Engineering, Texas Tech University, Lubbock, TX 79409, USA
2. Geosyntec Consultants, Atlanta, GA, USA
Interests: mercury; methylmercury; genomic; anammox; biogeochemistry; trace metal; heavy metal pollution; metagenomics; Meta-Omics; wastewater treatment; microbial ecology; sediments
School of Civil Engineering, Shandong University, Jinan, China
Interests: plastisphere; pharmaceuticals and personal care products; water environment protection; antibiotic resistance genes; micro/nanoplastics; microbial ecology
Special Issues, Collections and Topics in MDPI journals

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Guest Editor
Department of Environment and Food, School of Chemical Engineering, Ocean, and Life Sciences, Dalian University of Technology, Panjin 124221, China
Interests: microbial bioenergy; microbial waste valorization; microbial environmental engineering; microbial oilfield sustainability; resource recovery; AI for microbial energy & environment
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Bacterial communities in sediment and aquatic environments—including freshwater, marine, and estuarine systems—play central roles in microbial ecology and biogeochemical cycling. Diverse bacterial groups contribute to the degradation of organic matter, nutrient and carbon cycling, greenhouse gas production, and the transformation of contaminants, including both trace metals and organic pollutants.

Microbial processes are closely linked to the cycling and fate of trace metals such as iron (Fe), arsenic (As), and mercury (Hg), as well as organic pollutants such as hydrocarbons, pesticides, pharmaceuticals, and other emerging contaminants. Through redox reactions, methylation, immobilization, mobilization, and biodegradation, bacterial communities can influence contaminants’ mobility, toxicity, persistence, and bioavailability. In turn, trace metals, organic pollutants, and other environmental stressors can shape microbial communities’ structure, diversity, ecological interactions, and functional potential in sediments and water columns.

This Special Issue highlights the advances in microbial ecology and biogeochemical functions in relation to sediment and aquatic environments, paying special attention to microbial responses to trace metal and organic pollution, contaminant transformation, and interactions among microbial communities, pollutants, and environmental gradients. We welcome original research and review articles using field observations, laboratory experiments, molecular approaches, omics technologies, isotopic tracing, bioinformatics, or ecosystem modeling.

Dr. Yongli Wang
Dr. Sheng Liu
Dr. Guandong Su
Guest Editors

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Keywords

  • microbial ecology
  • bacterial communities
  • organic pollutant transformation
  • sediment environments
  • aquatic environments
  • trace metals
  • biogeochemistry
  • community dynamics

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Published Papers (1 paper)

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Review

28 pages, 5883 KB  
Review
Engineered Nanomaterials, Microbial Community Responses, and Fe-Mediated Regulation of As and Cd Fate in the Flooded Rice Rhizosphere: A Mechanistic Synthesis
by Yinghui Gu, Yimeng Ren, Xiaodan Wang, Kai Song and Lihui Zhang
Microorganisms 2026, 14(6), 1336; https://doi.org/10.3390/microorganisms14061336 - 14 Jun 2026
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Abstract
The flooded rice rhizosphere is a continuous reactive interface composed of sediment, porewater, root-surface oxic microdomains, and iron plaque, where redox processes and Fe cycling regulate Cd/As speciation, bioavailability, and plant accumulation. Engineered nanomaterials (ENMs) have shown potential for reducing Cd/As uptake in [...] Read more.
The flooded rice rhizosphere is a continuous reactive interface composed of sediment, porewater, root-surface oxic microdomains, and iron plaque, where redox processes and Fe cycling regulate Cd/As speciation, bioavailability, and plant accumulation. Engineered nanomaterials (ENMs) have shown potential for reducing Cd/As uptake in rice, but the coupled roles of microbial community responses, iron-plaque gating, and cross-interface elemental migration remain insufficiently integrated. This review synthesizes the current evidence on ENM transformation and partitioning at flooded rhizosphere microinterfaces, focusing on front-end speciation changes, root-surface retention, microbial functional regulation, and plant sequestration or transport. Correlative evidence suggests that rhizosphere microorganisms are associated with altered redox conditions, Fe cycling, As methylation potential, and metabolite secretion, which may influence Cd/As partitioning and cross-interface migration. However, direct causal validation of the complete ENM transformation–microbial response–Fe cycling–Cd/As flux–grain accumulation sequence within a single integrated system remains lacking. We further discuss how elevated CO2, micro-/nanoplastics, Fe/DOM dynamics, and water management regimes may modify this framework, and we identify Sb as a theoretical boundary case because direct ENM–rice evidence remains limited. Finally, we highlight the need to integrate spatial tracing and imaging methods, including persistent luminescence tracing, LA-ICP-MS, NanoSIMS, and µ-XRF/µ-XANES, with metaomics to connect particle localization, microbial function, and contaminant fate. Full article
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