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Microbial Diversity in Freshwater Ecosystems
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Microbial Diversity in Freshwater Ecosystems

A special issue of Water (ISSN 2073-4441). This special issue belongs to the section "Biodiversity and Functionality of Aquatic Ecosystems".

Deadline for manuscript submissions: 20 December 2026 | Viewed by 2281

Editor

Dr. Siddiq Akbar

E-Mail Website
Guest Editor
Department of Biology, Chemistry and Geography, University of Quebec Rimouski (UQAR), Rimouski, QC, Canada
Interests: microbial ecology; freshwater ecosystems; water quality; host-microbiome interactions; environmental stressors; antimicrobial resistance; cyanobacterial blooms

Special Issue Information

Dear Colleagues,

Freshwater ecosystems, including rivers, lakes, ponds, wetlands, and groundwater, harbor incredibly diverse microbes that play an important role in nutrient cycling, ecosystem functioning, and water quality maintenance. Microbial communities in these environments are highly dynamic and sensitive to natural variations, as well as anthropogenic influences such as pollution, climate change, eutrophication, and land-use change. Despite their ecological importance, microbial diversity in freshwater habitats remains underexplored compared to marine or terrestrial systems.

This Special Issue will bring together cutting-edge research that enhances our understanding of microbial diversity, community structure, and function in freshwater ecosystems across geographical and temporal scales. We welcome submissions on microbial ecology, metagenomics, bioinformatics, environmental microbiology, and biogeochemical interactions. Studies employing innovative methodologies to characterize microbial taxa, functional genes, or microbial responses to environmental stressors are particularly encouraged. Comparative analyses, novel methodological approaches, and applied perspectives on microbial indicators for freshwater health are also of interest.

By showcasing diverse research approaches and case studies, this Special Issue will highlight the ecological and applied significance of microbial diversity in shaping the health, resilience, and sustainability of freshwater ecosystems worldwide.

Dr. Siddiq Akbar
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 250 words) can be sent to the Editorial Office for assessment.

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-anonymized peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Water is an international peer-reviewed open access semimonthly 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 2600 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

  • freshwater microbial diversity
  • aquatic microbiome dynamics
  • microbial indicators of water quality
  • metagenomic profiling of freshwater
  • microbial responses to environmental stress

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Published Papers (3 papers)

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Research

21 pages, 8694 KB  
Article
Differences in Bacterial Communities of Deep and Shallow Subarctic Ice-Covered Lakes in the Northern Pole of Cold
by Yulia Zakharova, Maria Bashenkhaeva, Yuri Galachyants, Darya Petrova, Alena Firsova, Irina Tomberg, Ivan Mikhailov, Yekaterina Bedoshvili, Liubov Kopyrina and Yelena Likhoshway
Water 2026, 18(15), 1890; https://doi.org/10.3390/w18151890 - 3 Aug 2026
Viewed by 468
Abstract
The cold conditions of these habitats, as well as the morphometric features and origins of long-term ice-covered freshwater lakes, influence the structure and diversity of bacterial communities, which remain poorly understood. This study focused on long-term ice-covered lakes of contrasting origins (tectonic–glacial, glacial, [...] Read more.
The cold conditions of these habitats, as well as the morphometric features and origins of long-term ice-covered freshwater lakes, influence the structure and diversity of bacterial communities, which remain poorly understood. This study focused on long-term ice-covered lakes of contrasting origins (tectonic–glacial, glacial, and thermokarst), located in the highland subarctic region of Eastern Yakutia—an area that includes the Northern Hemisphere’s Pole of Cold, characterized by extremely low temperatures The differences in bacterial community diversity between deep lakes of tectonic–glacial origin and shallow lakes of glacial and thermokarst origin are shown by metabarcoding of the 16S rRNA gene. According to ANOVA, the water quality parameters were homogeneous between samples from the deep and shallow, and their effect on the bacterial community structure was insignificant. The deep lake communities were dominated by groups indicative of oligotrophic, stratified, and cold environments: Cyanobium_PCC−6307 (low-light picocyanobacteria), Methylacidiphilaceae (methanotrophs in oxygenated conditions), and the heterotrophic psychrotolerant genera Acinetobacter and Paenisporosarcina. Shallow lakes, by contrast, were enriched in taxa associated with high-light, well-mixed, and sediment-influenced conditions: SAR11 (Clade_III) (photoheterotrophic oligotrophs), Methylobacter (methanotrophs at neutral-pH), and taxa dominant in sediments (Gemmataceae и Terrimicrobium). The broadly distributed genera Candidatus_Planktophila, Ilumatobacter, and Polynucleobacter represent cosmopolitan freshwater generalists with diverse metabolic capabilities, explaining their consistent presence across both lake types. The novelty of this study lies in identifying a link between the structure of bacterial communities and the morphometric characteristics of lakes under conditions of homogeneous environmental parameters. Despite similar chemical compositions, opposite patterns were observed in deep and shallow lakes: in deep lakes, autochthonous taxa associated with stratification (low-light-tolerant cyanobacteria, aerobic methanotrophs) predominated, whereas sediment-associated and photoheterotrophic taxa dominated in shallow lakes, indicating a stronger connection between the benthos and the pelagic zone and a dependence on allochthonous carbon. Our results demonstrate that morphometry appears to be an important factor of the stability of microbial composition and carbon flux in permafrost regions. We revealed the heterogeneity of bacterial communities in subarctic lakes and identified dominant groups and key taxa, contributing to a better understanding of the ecological structure and functioning of lake ecosystems in cold regions and providing a basis for their monitoring. Full article
(This article belongs to the Special Issue Microbial Diversity in Freshwater Ecosystems)
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22 pages, 3783 KB  
Article
Seasonal Dynamics of Sediment Microbial Communities in Glacial Lakes
by Boyanka Angelova, Silvena Boteva, Ivan Traykov, Martin Tsvetkov and Anelia Kenarova
Water 2026, 18(5), 592; https://doi.org/10.3390/w18050592 - 28 Feb 2026
Cited by 2 | Viewed by 677
Abstract
High-altitude lakes are sensitive sentinels of climate change, and yet the microbial processes driving biogeochemical cycles under warming remain poorly understood. Seasonal dynamics of sediment microbial communities in four glacial lakes within the cirques of the Seven Rila Lakes (Rila Mountains, Bulgaria) were [...] Read more.
High-altitude lakes are sensitive sentinels of climate change, and yet the microbial processes driving biogeochemical cycles under warming remain poorly understood. Seasonal dynamics of sediment microbial communities in four glacial lakes within the cirques of the Seven Rila Lakes (Rila Mountains, Bulgaria) were investigated during June, August, and October 2024. Environmental monitoring showed pronounced seasonal variability with summer peaks in temperature, dissolved organic carbon and nitrogen, and increased inputs of labile organic matter. Multivariate analyses revealed strong seasonal structuring of microbial assemblages, with the largest shifts occurring between the early ice-free season and summer. Archaeal communities were dominated by Halobacteriota over time, whereas lake warming corresponded to a shift from early-season dominance of Actinomycetota and Bacillota to the summer prevalence of Pseudomonadota and Cyanobacteriota, as well as a proliferation of minor phyla Gemmatimonadota. At the genus level, summer enrichment of archaeal methanogen Methanosaeta and bacterial genera Paucibacter, Ca. Accumulibacter, Methylibium, Crenothrix, and Pseudanabaena was observed. Canonical correspondence analysis identified temperature and nutrient availability as the primary drivers of microbial community restructuring. Our results provide empirical evidence that warming and associated changes in organic matter inputs drive shifts in sediment microbial communities, with direct implications for carbon cycling and methane production. Additionally, the results highlight the sensitivity of high-altitude lakes to global warming and emphasize the critical role of microbial communities in modulating ecosystem responses to climate change. Full article
(This article belongs to the Special Issue Microbial Diversity in Freshwater Ecosystems)
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14 pages, 1847 KB  
Article
The Vertical Profile and Diversity Within the Bacterioplankton Assemblages in a Deep Freshwater Lake (Lake Biwa, Japan)
by Ola A. Olapade, Jeremy J. Piggott and Shin-ichi Nakano
Water 2026, 18(5), 546; https://doi.org/10.3390/w18050546 - 26 Feb 2026
Viewed by 553
Abstract
Holomictic mesotrophic lakes, characterized by oxygenated hypolimnion due to seasonal mixing of their water layers, host microbial assemblages with diversity and community compositions strongly shaped by the constant recycling of nutrients. However, other studies showed occurrences of hypolimnion-specific lineages, distinct from adjacent epilimnion [...] Read more.
Holomictic mesotrophic lakes, characterized by oxygenated hypolimnion due to seasonal mixing of their water layers, host microbial assemblages with diversity and community compositions strongly shaped by the constant recycling of nutrients. However, other studies showed occurrences of hypolimnion-specific lineages, distinct from adjacent epilimnion in such lakes. The study focused on Lake Biwa, a tectonic mesotrophic lake in Japan, to spatially elucidate bacterial assemblages between the epilimnion and oxygenated hypolimnion. 16S rRNA gene analysis revealed dominance of bacterial members belonging to Pseudomonadota, Bacillota and Bacteroidota throughout the water column, while other lineages such as Bdellovibrionota, Kapabacteria and WGS were not detected in the epilimnion and were solely hypolimnion-specific in their occurrences. This study serves to further corroborate earlier investigations that have shown bacterioplankton community differences in the vertical distribution of deep-water lakes. Full article
(This article belongs to the Special Issue Microbial Diversity in Freshwater Ecosystems)
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