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Diversity
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Occurrence and Molecular Biology of Water Bacteria and Protozoa
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Occurrence and Molecular Biology of Water Bacteria and Protozoa

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 (1 October 2024) | Viewed by 9360

Special Issue Editor

Dr. Laura Moreno-Mesonero

E-Mail Website
Guest Editor
Research Institute of Water and Environmental Engineering (IIAMA) and Advanced Centre for Food Microbiology (CAMA), Universitat Politècnica de València (UPV), Camino de Vera s/n, 46022 Valencia, Spain
Interests: water; food; qPCR; amplicon sequencing; bacteria; amoebae; molecular techniques; metagenomics; bioinformatics

Special Issue Information

Dear Colleagues,

The presence of bacteria and protozoa is commonplace in water environments. Since water plays a central role in our lives, its microbial quality is normally controlled, especially in facets involving human contact or ingestion. Depending on the source of water, its use and the regulations in each country differ. Moreover, due to water scarcity, water reuse is becoming increasingly frequent, posing a health threat if not properly controlled. Since only a small fraction of bacteria can be cultured, molecular methods for their detection are much needed, especially for pathogenic bacteria, in different water sources. In addition, both bacteria and protozoa have been responsible for waterborne outbreaks worldwide, so information on their occurrence in different water sources is critical to preventing these events.

This Special Issue seeks to further the scientific knowledge on the occurrence and molecular biology of bacteria and protozoa in aquatic environments, making it possible to advance our understanding of the microbiome of different types of water with a particular emphasis on potential pathogenic microbes. We invite authors to contribute their original research, reviews and opinion articles to this issue.

Dr. Laura Moreno-Mesonero
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. Diversity 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 2100 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

  • waterborne pathogens
  • microbiome
  • molecular techniques
  • drinking water
  • wastewater
  • water reuse
  • source water
  • microbial water quality

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Published Papers (4 papers)

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Research

17 pages, 2473 KiB  
Article
Environmental Compatibility and Genome Flexibility of Klebsiella oxytoca Isolated from Eight Species of Aquatic Animals
by Shuo Sun, Tingting Gu, Yafei Ou, Yongjie Wang, Lu Xie and Lanming Chen
Diversity 2024, 16(1), 30; https://doi.org/10.3390/d16010030 - 2 Jan 2024
Cited by 3 | Viewed by 2152
Abstract
Klebsiella oxytoca is an emerging pathogen that can cause life-threatening infectious diseases in humans. Recently, we firstly reported for the first time the presence of K. oxytoca in edible aquatic animals. In this study, we further investigated its bacterial environmental fitness and genome [...] Read more.
Klebsiella oxytoca is an emerging pathogen that can cause life-threatening infectious diseases in humans. Recently, we firstly reported for the first time the presence of K. oxytoca in edible aquatic animals. In this study, we further investigated its bacterial environmental fitness and genome evolution signatures. The results revealed that K. oxytoca isolates (n = 8), originating from eight species of aquatic animals, were capable of growing under a broad spectrum of environmental conditions (pH 4.5–8.5, 0.5–6.5% NaCl), with different biofilm formation and swimming mobility profiles. The genome sequences of the K. oxytoca isolates were determined (5.84–6.02 Mb, 55.07–56.06% GC content). Strikingly, numerous putative mobile genetic elements (MGEs), particularly genomic islands (GIs, n = 105) and prophages (n = 24), were found in the K. oxytoca genomes, which provided the bacterium with specific adaptation traits, such as resistance, virulence, and material metabolism. Interestingly, the identified prophage-related clusters were derived from Burkholderia spp., Enterobacter spp., Klebsiella spp., Pseudomonas spp., and Haemophilus spp., suggesting phage transmission across Klebsiella and the other four genera. Many strain-specific (n = 10–447) genes were present in the K. oxytoca genomes, whereas the CRISPR-Cas protein-encoding gene was absent, indicating likely active horizontal gene transfer (HGT) and considerable genome variation in K. oxytoca evolution. Overall, the results of this study are the first to demonstrate the environmental compatibility and genome flexibility of K. oxytoca of aquatic animal origins. Full article
(This article belongs to the Special Issue Occurrence and Molecular Biology of Water Bacteria and Protozoa)
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14 pages, 2745 KiB  
Article
Evaluation of the Influence of Habitat Heterogeneity and Human Activities on the Distribution of Microbial Diversity in a High Elevation Drop River
by Haiming Qin, Xinyue Jia, Lu Wang, Ziyue Wang, Xinlei Chen, Yaowei Wang, Minfang Sun, Qin Qi and Yuewei Yang
Diversity 2023, 15(6), 698; https://doi.org/10.3390/d15060698 - 23 May 2023
Cited by 1 | Viewed by 1419
Abstract
The aim of this work was to investigate the microbial diversity characteristics and driving factors in a high elevation drop river and to analyze the potential risks of river microorganisms to human health. In March 2019, we analyzed the microbial diversity characteristics in [...] Read more.
The aim of this work was to investigate the microbial diversity characteristics and driving factors in a high elevation drop river and to analyze the potential risks of river microorganisms to human health. In March 2019, we analyzed the microbial diversity characteristics in surface water and sludge from the Huotong River using high-throughput sequencing. The Huotong River is of great importance to the production and life of the people living along this river. The sampling points were set at the estuary of the river, on a downstream section of the river, on an upstream section of the main river, at one tributary flowing through a town, at one tributary with a barrage, and at the source of one tributary. The results showed significant differences in bacterial diversity in different areas of the river. For example, actinomycetes were less abundant in water samples from the headwaters of tributaries and more abundant upriver. The results revealed that different intensities of human activities had significant different effects on functional flora. Anthropogenic disturbance and human activities reduced the abundance of probiotic bacteria and increased the abundance of pathogenic bacteria in the river. The changes in functional floral diversity may pose potential threats to human health. Full article
(This article belongs to the Special Issue Occurrence and Molecular Biology of Water Bacteria and Protozoa)
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15 pages, 1692 KiB  
Article
From Source to Tap: Tracking Microbial Diversity in a Riverbank Filtration-Based Drinking Water Supply System under Changing Hydrological Regimes
by Márta Vargha, Eszter Róka, Norbert Erdélyi, Kitti Németh, Zsuzsanna Nagy-Kovács, Péter B. Kós and Attila I. Engloner
Diversity 2023, 15(5), 621; https://doi.org/10.3390/d15050621 - 2 May 2023
Cited by 5 | Viewed by 2436
Abstract
In drinking water supply, riverbank filtration (RBF) is an efficient and cost-effective way of eliminating pathogens and micropollutants using a combination of biotic and abiotic processes. Microbial communities in the hyporheic zone both contribute to and are shaped by these processes. Microbial water [...] Read more.
In drinking water supply, riverbank filtration (RBF) is an efficient and cost-effective way of eliminating pathogens and micropollutants using a combination of biotic and abiotic processes. Microbial communities in the hyporheic zone both contribute to and are shaped by these processes. Microbial water quality at the point of consumption is in turn influenced by the source water microbiome, water treatment and distribution system. Understanding microbial community shifts from source to tap and the factors behind them is instrumental in maintaining safe drinking water delivery. To this end, microbial communities of an RBF-based drinking water supply system were investigated by metabarcoding in a one-year sampling campaign. Samples were collected from the river, RBF wells, treated water, and a consumer’s tap. Metabarcoding data were analysed in the context of physicochemical and hydrological parameters. Microbial diversity as well as cell count decreased consistently from the surface water to the tap. While Proteobacteria were dominant throughout the water supply system, typical river water microbiome phyla Bacteroidota, Actinobacteria, and Verrucomicrobiota were replaced by Nitrospira, Patescibacteria, Chloroflexi, Acidobacteriota, Methylomicrobilota, and the archaeal phylum Nanoarcheota in well water. Well water communities were differentiated by water chemistry, in wells with high concentration groundwater derived iron, manganese, and sulphate, taxa related to iron and sulphur biogeochemical cycle were predominant, while methane oxidisers characterised the more oxic wells. Chlorine-resistant and filtration-associated taxa (Acidobacteria, Firmicutes, and Bdellovibrionota) emerged after water treatment, and no potentially pathogenic taxa were identified at the point of consumption. River discharge had a distinct impact on well water microbiome indicative of vulnerability to climate change. Low flow conditions were characterised by anaerobic heterotrophic taxa (Woesarchaeales, Aenigmarchaeales, and uncultured bacterial phyla MBNT15 and WOR-1), implying reduced efficiency in the degradation of organic substances. High flow was associated the emergence of typical surface water taxa. Better understanding of microbial diversity in RBF water supply systems contributes to preserving drinking water safety in the future changing environment. Full article
(This article belongs to the Special Issue Occurrence and Molecular Biology of Water Bacteria and Protozoa)
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9 pages, 736 KiB  
Communication
Bacteria Release from Microplastics into New Aquatic Environments
by Ioanna Nikolopoulou, Odysseas Piperagkas, Stefanos Moschos and Hera Karayanni
Diversity 2023, 15(1), 115; https://doi.org/10.3390/d15010115 - 13 Jan 2023
Cited by 6 | Viewed by 2521
Abstract
Microplastics are considered the most common waste in aquatic ecosystems, and studying them along with their interactions with biota are considered a priority. Here, results on the role of microplastics in the dispersion of microbes from terrestrial to aquatic ecosystems are presented. Data [...] Read more.
Microplastics are considered the most common waste in aquatic ecosystems, and studying them along with their interactions with biota are considered a priority. Here, results on the role of microplastics in the dispersion of microbes from terrestrial to aquatic ecosystems are presented. Data were obtained from microcosm experiments in which microplastics (plastic bags (BA), polyethylene bottles (BO), acrylic beads (BE), and cigarette butts (BU)) with their attached natural bacterial communities were inoculated in filtered and autoclaved lake water. The bacterial abundance on microplastics was estimated before inoculation using a protocol for the enumeration of sediment bacteria and ranged between 1.63 (BA) and 203.92 (BE) × 103 cells mm−2. Bacteria were released in the new medium, and their growth rates reached 5.8 d−1. In the attached communities, Beta- (21.4%) and Alphaproteobacteria (18.6%) were the most abundant classes, while in the free-living communities Gammaproteobacteria dominated (48.07%). Abundant OTUs (≥1%) of the free-living communities were associated with the genera Acinetobacter, Pseudomonas, Ecidovorax, Delftia, Comamonas, Sphingopyxis, and Brevundimonas and members of the FCB group. Members of these genera are known to degrade natural or man-made organic compounds and have recently emerged as opportunistic pathogens. Thus, besides trophic transmission, microplastics can directly release bacteria in the environment, which could affect the health of humans, animals, and ecosystems. Full article
(This article belongs to the Special Issue Occurrence and Molecular Biology of Water Bacteria and Protozoa)
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