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Microorganisms
Special Issues
Microbial Food Webs
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Microbial Food Webs

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

Deadline for manuscript submissions: closed (31 January 2026) | Viewed by 4528

Special Issue Editor

Dr. Wuchang Zhang

E-Mail Website
Guest Editor
CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
Interests: marine biology; planktonic ecology; microzooplankton; microbial food web

Special Issue Information

Dear Colleagues,

A microbial food web is an integrative component of the ecosystems in both pelagic and benthic zones, including both marine and freshwater habitats. Organisms that constitute the microbial food web include grazers such as ciliates and flagellates, small autotrophic protists and autotrophic and heterotrophic prokaryotes. In recent years, due to the development of observing technology and omics, knowledge of microbial food webs is exploding. In this Special Issue on microbial food webs, we encourage the submission of manuscripts in the scope of taxonomy, abundance and comparative studies of these organisms. Experimental work, field investigations and modelling studies are equally welcome. Insights about the influence of the global changes are especially valued. If possible, some efforts of alleviating global warming using microbial food webs will be discussed in this Special Issue. New technologies in microbial food web research could be introduced.

Dr. Wuchang Zhang
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-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 food web
  • ciliates
  • flagellates
  • prokaryote
  • taxonomy
  • ecology
  • global change

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Published Papers (3 papers)

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Research

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23 pages, 4799 KB  
Article
Spatiotemporal Dynamics of Mesozooplankton Trophic Structure and Food Web Configuration in the Vicinity of Daya Bay Nuclear Power Plant
by Yanjiao Lai, Bingqing Liu and Mianrun Chen
Microorganisms 2026, 14(1), 203; https://doi.org/10.3390/microorganisms14010203 - 15 Jan 2026
Cited by 1 | Viewed by 512
Abstract
Mesozooplankton play a pivotal role in marine pelagic food webs, mediating energy and matter transfer between primary producers and higher trophic levels. Daya Bay, a semi-enclosed bay located in the northern South China Sea, has undergone significant environmental changes due to anthropogenic activities, [...] Read more.
Mesozooplankton play a pivotal role in marine pelagic food webs, mediating energy and matter transfer between primary producers and higher trophic levels. Daya Bay, a semi-enclosed bay located in the northern South China Sea, has undergone significant environmental changes due to anthropogenic activities, such as thermal discharge from nuclear power plants and eutrophication. This study examined the mesozooplankton community structure, feeding preferences, and food web organization through four seasonal cruises (May 2022, February 2023, August 2023, and November 2023), employing stable isotope analysis and a Bayesian Isotopic Mixing Model. Results indicate that mesozooplankton abundance and diversity were lower in regions affected by thermal discharge, suggesting a suppressive effect of elevated temperatures. Seasonal shifts in dominant species were observed: Penilia avirostris and Dolioletta gegenbauri dominated the community in spring, while Noctiluca scintillans blooms occurred in summer and winter. Isotopic analysis revealed distinct trophic strategies: copepods exhibited omnivorous habits, whereas cladocerans and tunicates showed stronger herbivorous tendencies. N. scintillans functioned as a high-trophic omnivore, preying on copepod larvae and competing for food resources. Overall, the mesozooplankton community was characterized by an omnivory-dominated trophic network, which enhanced resilience yet remains sensitive to anthropogenic disturbances. This study clarifies how human-induced environmental changes reshape trophic pathways in subtropical coastal waters, providing a valuable reference for long-term monitoring and ecosystem management in Daya Bay. Full article
(This article belongs to the Special Issue Microbial Food Webs)
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19 pages, 23704 KB  
Article
Morphology and Molecular Phylogeny of Four Anaerobic Ciliates (Protista, Ciliophora, Armophorea), with Report of a New Species and a Unique Arrangement Pattern of Dikinetids in Family Metopidae
by Song Li, Wenbao Zhuang, Xiaochen Feng, Alan Warren and Jun Gong
Microorganisms 2025, 13(2), 240; https://doi.org/10.3390/microorganisms13020240 - 23 Jan 2025
Cited by 7 | Viewed by 2962
Abstract
The diversity of anaerobic ciliates is greatly underestimated owing to the limitation in sampling and cultivation when compared with their aerobic counterparts. In this study, four anaerobic ciliates, viz. Brachonella abnormalis sp. nov., Brachonella contorta (Levander, 1894) Jankowski, 1964, Metopus contortus (Quennerstedt, 1867) [...] Read more.
The diversity of anaerobic ciliates is greatly underestimated owing to the limitation in sampling and cultivation when compared with their aerobic counterparts. In this study, four anaerobic ciliates, viz. Brachonella abnormalis sp. nov., Brachonella contorta (Levander, 1894) Jankowski, 1964, Metopus contortus (Quennerstedt, 1867) Kahl, 1932, and Metopus major Kahl, 1932, were investigated by live observation, protargol staining and 18S rRNA gene sequencing. B. abnormalis sp. nov. can be separated from its congeners by a combination of the following features: bullet-shaped cell with a life size of about 130–190 × 90–120 μm, dikinetids distributed along dorsal dome kineties, highly developed adoral zone comprised of 87–107 polykinetids, making about 450° spiralization around the long axis. The present work demonstrates that two known species, M. contortus and M. major, have a special trait never previously reported, viz. short, regularly arranged preoral dome dikinetids. Species with short, regularly arranged dome dikinetids appear in divergent clades in SSU rRNA gene trees, which may infer that this trait evolved several times. Phylogenetic analyses based on SSU rRNA gene sequence data also support the monophyly of the genus Brachonella and the paraphyly of the order Metopida, respectively. Full article
(This article belongs to the Special Issue Microbial Food Webs)
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Review

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27 pages, 1297 KB  
Review
The Trophic Cascade Effects of Marine Mesozooplankton: Theory, Dynamics, and Responses to Global Change
by Mianrun Chen
Microorganisms 2026, 14(3), 697; https://doi.org/10.3390/microorganisms14030697 - 19 Mar 2026
Viewed by 473
Abstract
Marine mesozooplankton (0.2–20 mm), as a critical trophic link between primary producers and higher trophic levels, are pivotal drivers of trophic cascades regulating pelagic ecosystem structure and function. This review synthesizes recent advances in understanding mesozooplankton-mediated trophic cascades (MMTC), with a focus on [...] Read more.
Marine mesozooplankton (0.2–20 mm), as a critical trophic link between primary producers and higher trophic levels, are pivotal drivers of trophic cascades regulating pelagic ecosystem structure and function. This review synthesizes recent advances in understanding mesozooplankton-mediated trophic cascades (MMTC), with a focus on selective feeding mechanisms, and presents an original, integrated quantitative framework that fills gaps in quantification and prediction of MMTC. This framework includes the following: a dual-pathway conceptual model distinguishing density-mediated and trait-mediated cascades; a three-level grazing rate correction model addressing long-standing underestimations of mesozooplankton direct grazing rate on phytoplankton; a comprehensive Cascade Strength Index for quantifying cascade intensity; an extended numerical model—NPMZ model (Nutrient–Phytoplankton–Microzooplankton–Mesozooplankton) for simulating MMTC dynamics and their biogeochemical impacts. The review further elucidates the spatiotemporal heterogeneity of MMTC and its implications for plankton community size structure and biological carbon pump efficiency. It also systematically assess the combined impacts of global change drivers (ocean warming, acidification, eutrophication) on MMTC and their ecological consequences. This review advances the theoretical framework of marine trophic cascade research by establishing a unified quantitative paradigm for MMTC and provides mechanistic insights and predictive tools for understanding how climate change modulates pelagic food web dynamics and marine ecosystem services. Moreover, the proposed integrated research paradigm combining molecular tools, multi-factor experiments, and high-resolution numerical modeling offers a critical roadmap for future MMTC research in the Anthropocene. This provides a scientific basis for the conservation and adaptive management of marine ecosystems under global change. Full article
(This article belongs to the Special Issue Microbial Food Webs)
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