Microbial Diversity in Aquatic Systems

A special issue of Diversity (ISSN 1424-2818). This special issue belongs to the section "Microbial Diversity and Culture Collections".

Deadline for manuscript submissions: closed (15 May 2024) | Viewed by 25176

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Department of Biology and Environment, Centre for the Research and Technology of Agro-Environmental and Biological Sciences (CITAB), University of Trás-os-Montes and Alto Douro, Vila Real, Portugal
Interests: microbial ecology; environment microbiology; biodegradation; bioremediation; natural antibiotics; antifungals
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Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
Interests: microbiology; one health; antimicrobial resistance; biofilms; microbial genetics; infectious diseases
Special Issues, Collections and Topics in MDPI journals

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Department of Natural SciencesFaculty of Natural Sciences and Agricultural Sciences, Ovidius University of Constanta, University Street, Building B, 900 437 Constanta, Romania
Interests: environmental microbiology; aquatic microbiology; diversity of microbial activities and genomic variability

Special Issue Information

Dear Colleagues,

Microorganisms are in all environments, even in the harshest ones. In water, microorganisms have been isolated and studied almost since the advent of microbiology. Despite all the studies, the diversity of aquatic microorganisms is largely unknown, both in natural ecosystems such as rivers, wetlands, and lakes as well as in artificial ecosystems such as wastewater treatment plants. Recent studies have shown that the high microbial diversity in aquatic and semi-aquatic ecosystems, strongly dependent on physicochemical and anthropogenic factors, is associated with nutrient cycling, pollution abatement, and potential pathogens. In particular, antibiotic resistance, although highly associated with human health, has been overlooked in these environments, which can be important reservoirs of resistant strains. Additionally, the acquisition and spread of resistance genes among aquatic animal microbiota and other animal species will be considered.

This Special Issue “Microbial Diversity in Aquatic Systems” focuses on microbial diversity (genes, species, communities, ecological functions, and relationships with other organisms) in natural and artificial water environments. The issue will give an overview of microbial species in inland aquatic systems, their importance, metabolisms, ecological functions, relationships, and impact with/in other organisms.

Prof. Dr. Ana C. Sampaio
Prof. Dr. Patricia Poeta
Assoc. Prof. Dr. Florin Aonofriesei
Guest Editors

Manuscript Submission Information

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Keywords

  • Bacteria
  • Fungi
  • Algae
  • Lotic and lentic freshwater ecosystems
  • Wastewaters
  • Biodegradation
  • Ecosystem functions
  • Ecological indicators
  • Pathogen reservoirs
  • Antibiotic resistance

Published Papers (6 papers)

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Research

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12 pages, 1568 KiB  
Article
Comparative Metagenomic Analysis of Marine eDNA Investigating the Production Crisis of Aquacultured Saccharina japonica
by Soyun Choi, Kwon Mo Yang, Dong Mun Choi, Yang Ho Choi, Xiuliang Wang, Lingxiu Wang, Xiaoyong Liu, Delin Duan, Hyun Park and Jeong Ha Kim
Diversity 2024, 16(4), 245; https://doi.org/10.3390/d16040245 - 19 Apr 2024
Viewed by 590
Abstract
Aquaculture farms cultivating Saccharina japonica are highly active in Wando, Korea, and Rongcheng, China. However, the yield of S. japonica significantly declined in the Rongcheng region in 2022 compared to previous records, whereas that in Wando remained at a normal level, presumably due [...] Read more.
Aquaculture farms cultivating Saccharina japonica are highly active in Wando, Korea, and Rongcheng, China. However, the yield of S. japonica significantly declined in the Rongcheng region in 2022 compared to previous records, whereas that in Wando remained at a normal level, presumably due to the presence of a pathogenic microbiome. We used environmental DNA (eDNA) metagenomic analysis to compare the microbial compositions of seawater from aquaculture farms in Wando and Rongcheng. Seawater samples were collected from one Korean site in Wando (WA) and two Chinese sites in Ailian Bay (AB) and Lidao Bay (LB). Metagenomic analysis focusing on the microbial 16S rRNA identified 38 phyla and 58 families of microbiomes in all regions. Potentially pathogenic bacterial groups associated with S. japonica in AB and LB were more abundant than in WA, suggesting their potential influence on mortality and the decline in the harvest yield of S. japonica. The microbial composition of WA was distinguished from those of the other two sites, which clustered together with higher similarity. Since the S. japonica aquaculture industry is important for both countries, this comparative eDNA monitoring is a valuable initiation towards the next step of problem-solving practices in coastal management in these two aquaculture systems. Full article
(This article belongs to the Special Issue Microbial Diversity in Aquatic Systems)
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11 pages, 2052 KiB  
Article
Community Composition and Antibiotic Resistance of Tap Water Bacteria Retained on Filtration Membranes
by Mirela Wolf-Baca and Agata Siedlecka
Diversity 2023, 15(3), 427; https://doi.org/10.3390/d15030427 - 14 Mar 2023
Cited by 1 | Viewed by 1671
Abstract
Community composition and antibiotic resistance of tap water bacteria are still not known well enough. This study fills the gaps in knowledge regarding this matter. To provide representativeness of collected samples, tap water bacteria were concentrated from huge amounts of water, using filtration [...] Read more.
Community composition and antibiotic resistance of tap water bacteria are still not known well enough. This study fills the gaps in knowledge regarding this matter. To provide representativeness of collected samples, tap water bacteria were concentrated from huge amounts of water, using filtration membranes monthly during the continuous, semi-annual study, covering winter and spring seasons. Biomass was investigated both using a culture-based method (for total and antibiotic-resistant culturable bacteria counts) and metagenomic DNA sequencing (for taxonomic identification of bacteria). The results showed that bacteria resistant to ceftazidime were the most prevalent among the studied resistance phenotypes, whereas bacteria resistant to amoxicillin, ciprofloxacin, and tetracycline were scarce. On average, 20,059 and 26,200 CFU/mL per month was counted in the winter and spring season, respectively, whereas in terms of antibiotic-resistant bacteria, average counts were 14,270 and 9435 CFU/mL per month in the winter and spring season, respectively. In terms of bacterial community composition, Cyanobacteria, Proteobacteria and Actinobacteria were the most abundant phyla, reaching up to 77.71%, 74.40% and 21.85%, respectively, which is supported by previous studies conducted on the same water supply network and other drinking water distribution systems across the world. No season-dependent variations were observed for culturable antibiotic-resistant bacteria or bacterial community composition. The prevalence of culturable antibiotic-resistant bacteria was not correlated with any of the identified taxa. Full article
(This article belongs to the Special Issue Microbial Diversity in Aquatic Systems)
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14 pages, 1692 KiB  
Article
Genomic Analysis of a Novel Heavy Metal Resistant Isolate from a Black Sea Contaminated Sediment with the Potential to Degrade Alkanes: Plantactinospora alkalitolerans sp. nov.
by Lorena Carro, Aysel Veyisoglu, Kiymet Guven, Peter Schumann, Hans-Peter Klenk and Nevzat Sahin
Diversity 2022, 14(11), 947; https://doi.org/10.3390/d14110947 - 4 Nov 2022
Cited by 3 | Viewed by 1806
Abstract
Microorganisms that grow in poorly studied environments are of special interest when new biotechnological applications are searched. The Melet river offshore sediments at the Black Sea have been described to contain an important number of contaminants from upstream industries which have been accumulating [...] Read more.
Microorganisms that grow in poorly studied environments are of special interest when new biotechnological applications are searched. The Melet river offshore sediments at the Black Sea have been described to contain an important number of contaminants from upstream industries which have been accumulating for years. Bacteria of such habitats must be adapted to the presence of those compounds and in some cases, are able to use them as carbon sources. In the analysis of some samples recovered from this environment, an actinobacterial strain was isolated, named as S1510T, and its taxonomic position was determined using a combination of phenotypic and genotypic properties. Strain S1510T presented phenotypic properties typical of members of the family Micromonosporaceae and was assigned to the Plantactinospora genus, based on the phylogenetic analyses of the 16S rRNA gene and whole-genome sequences. Low dDDH (digital DNA-DNA hybridization) values with other members of the genus confirmed that Plantactinospora sp. S1510T represents a novel species, and is proposed with the new name Plantactinospora alkalitolerans. The strain presented characteristics not previously described for other species in the genus, such as its high tolerance to alkaline pHs, the presence of genes related to the production and degradation of alkanes (oleABCD, ssuAD, almA), the degradation of several aromatic compounds, and the tolerance to high heavy metal concentrations. In addition, Plantactinospora sp. S1510T presents several bioclusters to produce nonribosomal peptide-synthetases, terpenes, polyketide synthases, and bacteriocins, that possess low similarities with known compounds. Full article
(This article belongs to the Special Issue Microbial Diversity in Aquatic Systems)
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17 pages, 2072 KiB  
Article
16S rRNA–Based Analysis Reveals Differences in the Bacterial Community Present in Tissues of Choromytilus chorus (Mytilidae, Bivalvia) Grown in an Estuary and a Bay in Southern Chile
by Tamara Valenzuela, Joaquin I. Rilling, Giovanni Larama, Jacquelinne J. Acuña, Marco Campos, Nitza G. Inostroza, Macarena Araya, Katherine Altamirano, So Fujiyoshi, Kyoko Yarimizu, Fumito Maruyama and Milko A. Jorquera
Diversity 2021, 13(5), 209; https://doi.org/10.3390/d13050209 - 14 May 2021
Cited by 1 | Viewed by 2722
Abstract
Microbiota associated with bivalves have drawn considerable attention because studies have suggested their relevance to the fitness and growth of marine bivalves. Although the mussel Choromytilus chorus is a valuable resource for Chilean aquaculture and fisheries, its microbiota is still unknown. In this [...] Read more.
Microbiota associated with bivalves have drawn considerable attention because studies have suggested their relevance to the fitness and growth of marine bivalves. Although the mussel Choromytilus chorus is a valuable resource for Chilean aquaculture and fisheries, its microbiota is still unknown. In this study, the composition and predicted functions of the bacterial community in tissues of C. chorus specimens grown in an estuary (Nehuentue) and a bay (Hueihue) were investigated. Using 16S rRNA genes as targets, the bacterial abundance in tissues was estimated by quantitative PCR and sequenced via Illumina MiSeq. The abundances of bacteria ranged from 103 to 105 copies of 16S rRNA genes g−1 tissue. In the Nehuentue estuary, the bacterial communities in the tissues were dominated by the Tenericutes phylum, whereas the Tenericutes and Proteobacteria phyla dominated in mussels from Hueihue Bay. Higher numbers of operational taxonomic units (OTUs) were observed in tissues from the Nehuentue Estuary than in those from Hueihue Bay. Differences in bacterial community compositions in tissues between both locations were confirmed by nonmetric multidimensional scaling (nMDS) and Venn diagram analysis. In addition, linear discriminant analysis effect size (LEfSe) revealed that the Mollicutes class and Actynomycetales order were key phylotypes in tissues from the Nehuentue Estuary and Hueihue Bay, respectively. Our analysis also predicted a high abundance of sequences assigned to heterotrophy; however, relatively high functional diversity was also found in tissues from Hueihue Bay. This work represents our first attempt to elucidate the C. chorus microbiota in contrasting Chilean aquatic environments. Full article
(This article belongs to the Special Issue Microbial Diversity in Aquatic Systems)
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Review

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26 pages, 466 KiB  
Review
Vibrio spp.: Life Strategies, Ecology, and Risks in a Changing Environment
by Ana Sampaio, Vanessa Silva, Patrícia Poeta and Florin Aonofriesei
Diversity 2022, 14(2), 97; https://doi.org/10.3390/d14020097 - 29 Jan 2022
Cited by 36 | Viewed by 13116
Abstract
Vibrios are ubiquitous bacteria in aquatic systems, especially marine ones, and belong to the Gammaproteobacteria class, the most diverse class of Gram-negative bacteria. The main objective of this review is to update the information regarding the ecology of Vibrio species, and contribute to [...] Read more.
Vibrios are ubiquitous bacteria in aquatic systems, especially marine ones, and belong to the Gammaproteobacteria class, the most diverse class of Gram-negative bacteria. The main objective of this review is to update the information regarding the ecology of Vibrio species, and contribute to the discussion of their potential risk in a changing environment. As heterotrophic organisms, Vibrio spp. live freely in aquatic environments, from marine depths to the surface of the water column, and frequently may be associated with micro- and macroalgae, invertebrates, and vertebrates such as fish, or live in symbiosis. Some Vibrio spp. are pathogenic to humans and animals, and there is evidence that infections caused by vibrios are increasing in the world. This rise may be related to global changes in human behavior (increases in tourism, maritime traffic, consumption of seafood, aquaculture production, water demand, pollution), and temperature. Most likely in the future, Vibrio spp. in water and in seafood will be monitored in order to safeguard human and animal health. Regulators of the microbiological quality of water (marine and freshwater) and food for human and animal consumption, professionals involved in marine and freshwater production chains, consumers and users of aquatic resources, and health professionals will be challenged to anticipate and mitigate new risks. Full article
(This article belongs to the Special Issue Microbial Diversity in Aquatic Systems)
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13 pages, 341 KiB  
Review
Molecular Diversity of Methicillin-Resistant and -Susceptible Staphylococcus aureus Detected in Animals: A Focus on Aquatic Animals
by Vanessa Silva, Andreia Monteiro, Maria Porto, Ana Sampaio, Luís Maltez, José Eduardo Pereira, Florin Aonofriesei, José Luis Capelo, Gilberto Igrejas and Patrícia Poeta
Diversity 2021, 13(9), 417; https://doi.org/10.3390/d13090417 - 30 Aug 2021
Cited by 2 | Viewed by 3400
Abstract
Staphylococcus aureus (S. aureus) are one of the best-known opportunistic pathogens capable of causing different types of infections in animals. Furthermore, it has the ability to acquire resistance to various antibiotics very easily. Methicillin-resistant S. aureus (MRSA) are currently of great [...] Read more.
Staphylococcus aureus (S. aureus) are one of the best-known opportunistic pathogens capable of causing different types of infections in animals. Furthermore, it has the ability to acquire resistance to various antibiotics very easily. Methicillin-resistant S. aureus (MRSA) are currently of great concern as they are the leading cause of infections in humans and animals, with a major impact on health and the economy. Several studies already demonstrate that the spread of MRSA is constantly increasing due to its ability to form reservoirs in humans, animals and the environment. In fact, several works have already identified the presence of these bacteria in animals, including domestic animals, farm animals and even wild animals. Furthermore, the incidence of various S. aureus strains in aquatic animals has also been reported by different authors, although it is still a rarely discussed topic. Some of these strains have previously been associated with humans and other animals. Strain 398 is the strain that manages to infect a wider spectrum of hosts, having been identified in several different species. Aside from this strain, many others have yet to be identified. In addition, many of these strains have virulence factors and antibiotic resistance genes that worsen the situation. The present work is a review of studies that intend to investigate the epidemiology of this agent in samples of aquatic animals from different origins, in order to better understand its distribution, prevalence and the molecular lineages associated with these species. Full article
(This article belongs to the Special Issue Microbial Diversity in Aquatic Systems)
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