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Microorganisms
Special Issues
Microbial Ecology and Assembly Dynamics in the Aquaculture Environment
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Microbial Ecology and Assembly Dynamics in the Aquaculture Environment

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

Deadline for manuscript submissions: closed (30 June 2025) | Viewed by 2043

Special Issue Editor

Dr. Lior Guttman

E-Mail Website
Guest Editor
Israel Oceanographic and Limnological Research, The National Center for Mariculture, Eilat 8811201, Israel
Interests: aquaculture; microbial ecology; host-microbe interactions; sustainability; water quality
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Aquaculture provides more than half of the consumed fish. It is the fastest-growing industry for edible protein production, with an estimated yield of 87.5 million tons of edible animals for human consumption produced worldwide in 2020 (FAO, 2022). However, rapid growth should not harm production sustainability while ensuring a low environmental footprint, societal acceptance, and cost-effectiveness. The hypertrophic culture environment enriches microorganisms and facilitates their metabolism. Moreover, the various services provided by microbes in this environment, such as determining water quality and contributing to host health, nutrition, and resilience, make them key players in the various aquaculture practices and organisms. While being studied extensively in cultured plants and livestock, a knowledge gap exists concerning the forces that govern the ecology and dynamics of microbial assemblies in the aquaculture environment. Recent studies have associated microbial diversity with resilience and resistance; however, strengthening this association in aquaculture requires more evidential significance from experimental research.

This Special Issue of Microorganisms aims to publish novel research works with significant scientific merit in microbial ecology and dynamics in the aquaculture environment concerning host-microbe and microbe–environment interactions and their consequences on the performances and resilience of the culture and cultured organisms. Original research articles and comprehensive reviews that cover aquatic microbes, microbial diversity, host-microbe interactions, and aquaculture sustainability are welcome.

Dr. Lior Guttman
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

  • aquaculture
  • microbial ecology
  • host–microbe interactions
  • resilience
  • sustainability

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Published Papers (2 papers)

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Research

22 pages, 4008 KB  
Article
Dissolved Oxygen Decline in Northern Beibu Gulf Summer Bottom Waters: Reserve Management Insights from Microbiome Analysis
by Chunyan Peng, Ying Liu, Yuyue Qin, Dan Sun, Jixin Jia, Zongsheng Xie and Bin Gong
Microorganisms 2025, 13(8), 1945; https://doi.org/10.3390/microorganisms13081945 - 20 Aug 2025
Viewed by 342
Abstract
The Sanniang Bay (SNB) and Dafeng River Estuary (DFR) in the Northern Beibu Gulf, China, are critical habitats for the Indo-Pacific humpback dolphin (Sousa chinensis). However, whether and how the decreased dissolved oxygen (DO) has happened in bottom seawater remains poorly [...] Read more.
The Sanniang Bay (SNB) and Dafeng River Estuary (DFR) in the Northern Beibu Gulf, China, are critical habitats for the Indo-Pacific humpback dolphin (Sousa chinensis). However, whether and how the decreased dissolved oxygen (DO) has happened in bottom seawater remains poorly understood. This study investigated DO depletion and microbial community responses using a multidisciplinary approach. High-resolution spatiotemporal sampling (16 stations across four seasons) was combined with functional annotation of prokaryotic taxa (FAPROTAX) to characterize anaerobic metabolic pathways and quantitative PCR (qPCR) targeting dsrA and dsrB genes to quantify sulfate-reducing bacteria. Partial least-squares path modeling (PLS-PM) was employed to statistically link environmental variables (seawater properties and nutrients) to microbial community structure. Results revealed pronounced bottom DO declining to 5.44 and 7.09 mg L−1, a level approaching sub-optimal state (4.0–4.8 mg L−1) in September. Elevated chlorophyll-a (Chl-a) near the SDH coincided with anaerobic microbial enrichment, including sulfate reducers (dsrA/dsrB abundance: SNB > DFR). PLS-PM identified seawater properties (turbidity, DO, pH) and nitrogen as key drivers of anaerobic taxa distribution. Co-occurrence network analysis further demonstrated distinct microbial modules in SNB (phytoplankton-associated denitrifiers) and DFR (autotrophic sulfur oxidizers, nitrogen fixation, and denitrification). These findings highlight how environmental factors drive decreased DO, reshaping microbial networks and threatening coastal ecosystems. This work underscores the need for regulating aquaculture/agricultural runoff to limit eutrophication-driven hypoxia and temporarily restrict human activities in SNB during peak hypoxia (September–October). Full article
(This article belongs to the Special Issue Microbial Ecology and Assembly Dynamics in the Aquaculture Environment)
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19 pages, 3437 KB  
Article
The Performance of a Multi-Stage Surface Flow Constructed Wetland for the Treatment of Aquaculture Wastewater and Changes in Epiphytic Biofilm Formation
by Chuanxin Chao, Shen Gong and Yonghong Xie
Microorganisms 2025, 13(3), 494; https://doi.org/10.3390/microorganisms13030494 - 22 Feb 2025
Cited by 1 | Viewed by 1234
Abstract
Constructed wetlands play a critical role in mitigating aquaculture wastewater pollution. However, the comprehensive treatment performance of aquatic plants and microorganisms under various water treatment processes remains insufficiently understood. Here, a multi-stage surface flow constructed wetland (SFCW) comprising four different aquatic plant species, [...] Read more.
Constructed wetlands play a critical role in mitigating aquaculture wastewater pollution. However, the comprehensive treatment performance of aquatic plants and microorganisms under various water treatment processes remains insufficiently understood. Here, a multi-stage surface flow constructed wetland (SFCW) comprising four different aquatic plant species, along with aeration and biofiltration membrane technologies, was investigated to explore the combined effects of aquatic plants and epiphytic biofilms on wastewater removal efficiency across different vegetation periods and treatment processes. The results demonstrated that the total removal efficiency consistently exceeded 60% in both vegetation periods, effectively intercepting a range of pollutants present in aquaculture wastewater. Changes in the vegetation period influenced the performance of the SFCW, with the system’s ability to treat total nitrogen becoming more stable over time. The removal efficiency of the treatment pond planted with submerged plants was highest in July, while the pond planted with emergent plants showed an increased removal rate in November. The aeration pond played a significant role in enhancing dissolved oxygen levels, thereby improving phosphorus removal in July and nitrogen removal in November. Additionally, the α-diversity of epiphytic bacteria in the aeration and biofiltration ponds was significantly higher compared to other ponds. In terms of bacterial composition, the abundance of Firmicutes was notably higher in July, whereas Nitrospirota and Acidobacteriota exhibited a significant increase in November. Furthermore, the functional genes associated with sulfur metabolism, nitrogen fixation, and oxidative phosphorylation displayed significant temporal variations in the aeration pond, highlighting that both growth period changes and treatment processes influence the expression of functional genes within biofilms. Our findings suggest that the integration of water treatment processes in SFCWs enhances the synergistic effects between aquatic plants and microorganisms, helping to mitigate the adverse impacts of vegetation period changes and ensuring stable and efficient wastewater treatment performance. Full article
(This article belongs to the Special Issue Microbial Ecology and Assembly Dynamics in the Aquaculture Environment)
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