Special Issue "Microbial Communities in Water Environments: Dynamics and Interaction"

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

Deadline for manuscript submissions: 31 October 2021.

Special Issue Editor

Dr. Sandi Orlić
E-Mail Website
Guest Editor
Laboratory for Precipitation Processes, Division of Materials Chemistry, Ruđer Bošković Institute, Croatia
Interests: novel methods in aquatic microbial ecology; marine and lake microbial ecology; climate change and microbes

Special Issue Information

Dear Colleagues,

An aquatic microbial community can be defined as an assemblage of co-occurring and potentially interacting microbes present in a defined habitat in space and time. Despite their small size, microorganisms are key elements in the ecological dynamics of the biosphere. In recent years, with advances in molecular tools, such as high-throughput sequencing, the field of microbial communities in water environments has gained increasing attention, resulting in novel knowledge regarding microbial dynamics and interactions.

Dr. Sandi Orlić
Guest Editor

Manuscript Submission Information

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Keywords

  • bacteria
  • fungi
  • protozoa
  • viruses
  • next-generation sequencing
  • freshwater and marine environments
  • interactions
  • novel tools
  • climate change

Published Papers (8 papers)

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Research

Article
Microbial Detoxification of Dimethoate and Methomyl Residues in Aqueous Media
Water 2021, 13(8), 1117; https://doi.org/10.3390/w13081117 - 19 Apr 2021
Viewed by 475
Abstract
The extensive and random application of major organic pollutants, mainly pesticides, threatens ecosystems and human health. The present study was conducted to isolate and identify microorganisms from some water resources contaminated with pesticides. We investigated the ability of the identified microbes to grow [...] Read more.
The extensive and random application of major organic pollutants, mainly pesticides, threatens ecosystems and human health. The present study was conducted to isolate and identify microorganisms from some water resources contaminated with pesticides. We investigated the ability of the identified microbes to grow in water spiked with dimethoate and methomyl. We also evaluated the potential effect of the identified microbial isolates on dimethoate and methomyl biodegradation in water. In addition, the total detoxification of dimethoate and methomyl residues in water after treatment with the most effective microbial isolates was confirmed using toxicity tests and analyzing biochemical parameters and histopathological changes in the kidney and liver of treated rats. The microbial isolates were identified as Xanthomonas campestris pv. Translucens and Aspergillus fumigates. Results showed that X. campestris pv. Translucens and A. fumigatus grow in media supplemented with dimethoate and methomyl faster than in other media without both pesticides. About 97.8% and 91.2% of dimethoate and 95% and 87.8% of methomyl (initial concentration of both 5 mg L−1) were biodegraded within 32 days of incubation with X. campestris pv. Translucens and A. fumigatus, respectively. There was no remaining toxicity in rats treated with dimethoate- and methomyl-contaminated water with respect to biochemical parameters and histopathological changes. Collectively, the identified bacterial isolate showed high potential for the complete degradation of dimethoate and methomyl residues in water. Full article
(This article belongs to the Special Issue Microbial Communities in Water Environments: Dynamics and Interaction)
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Article
Succession of Microbial Community in a Small Water Body within the Alluvial Aquifer of a Large River
Water 2021, 13(2), 115; https://doi.org/10.3390/w13020115 - 06 Jan 2021
Viewed by 582
Abstract
Nitrogen is one of the essential elements limiting growth in aquatic environments. Being primarily of anthropogenic origin, it exerts negative impacts on freshwater ecosystems. The present study was carried out at the nitrate-vulnerable zone within the alluvial aquifer of the large lowland Drava [...] Read more.
Nitrogen is one of the essential elements limiting growth in aquatic environments. Being primarily of anthropogenic origin, it exerts negative impacts on freshwater ecosystems. The present study was carried out at the nitrate-vulnerable zone within the alluvial aquifer of the large lowland Drava River. The main aim was to investigate the ecosystem’s functionality by characterizing the bacterial and phytoplankton diversity of a small inactive gravel pit by using interdisciplinary approaches. The phytoplankton community was investigated via traditional microscopy analyses and environmental DNA (eDNA) metabarcoding, while the bacterial community was investigated by a molecular approach (eDNA). Variations in the algal and bacterial community structure indicated a strong correlation with nitrogen compounds. Summer samples were characterized by a high abundance of bloom-forming Cyanobacteria. Following the cyanobacterial breakdown in the colder winter period, Bacillariophyceae and Actinobacteriota became dominant groups. Changes in microbial composition indicated a strong correlation between N forms and algal and bacterial communities. According to the nitrogen dynamics in the alluvial aquifer, we emphasize the importance of small water bodies as potential buffer zones to anthropogenic nitrogen pressures and sentinels of the disturbances displayed as algal blooms within larger freshwater systems. Full article
(This article belongs to the Special Issue Microbial Communities in Water Environments: Dynamics and Interaction)
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Article
The Horizontal Distribution of Siliceous Planktonic Radiolarian Community in the Eastern Indian Ocean
Water 2020, 12(12), 3502; https://doi.org/10.3390/w12123502 - 13 Dec 2020
Cited by 1 | Viewed by 538
Abstract
The plankton radiolarian community was investigated in the spring season during the two-month cruise ‘Shiyan1’ (10 April–13 May 2014) in the Eastern Indian Ocean. This is the first comprehensive plankton tow study to be carried out from 44 sampling stations across [...] Read more.
The plankton radiolarian community was investigated in the spring season during the two-month cruise ‘Shiyan1’ (10 April–13 May 2014) in the Eastern Indian Ocean. This is the first comprehensive plankton tow study to be carried out from 44 sampling stations across the entire area (80.00°–96.10° E, 10.08° N–6.00° S) of the Eastern Indian Ocean. The plankton tow samples were collected from a vertical haul from a depth 200 m to the surface. During the cruise, conductivity–temperature–depth (CTD) measurements were taken of temperature, salinity and chlorophyll a from the surface to 200 m depth. Shannon–Wiener’s diversity index (H’) and the dominance index (Y) were used to analyze community structure. There was a total of 168 plankton species, composed of Acantharia, Phaeodaria, Polycystina, Collodaria and Taxopodida (monospecific—Sticholonche zanclea, Hertwig is the only recognized species). Hence, it included both celestine-based and siliceous organisms, which are also described here for the first time from this region. Total radiolarians ranged from 5 to 5500 ind/m−3, dominated by co-occurrences of Sphaerozoum punctatum and Stichonche zanclea species at the south-equator zone (SEQ)-transect 80° E and equator zone (EQ)-transect Lati-0. The possible environmental variables were tested through RDA analysis; although no result was obtained for the full species dataset, the samples from the equatorial transect related strongly to mixed-layer chlorophyll a concentration and those of a north–south transect to surface silicate concentrations or mixed-layer nitrate were significantly correlated (p < 0.01) to the radiolarian community. Our results indicate that the silicate and chlorophyll-a concentrations are the two major factors affecting the radiolarian distribution along two of the investigated transects (southern equator and equator) in the study area. Full article
(This article belongs to the Special Issue Microbial Communities in Water Environments: Dynamics and Interaction)
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Article
Structural Characteristics and Driving Factors of the Planktonic Eukaryotic Community in the Danjiangkou Reservoir, China
Water 2020, 12(12), 3499; https://doi.org/10.3390/w12123499 - 12 Dec 2020
Viewed by 529
Abstract
Planktonic eukaryotes are widespread in aquatic ecosystems, and the study of their community composition and driving factors is of great significance to protecting and maintaining the balance of these ecosystems. This study evaluates five typical ecological sites in the Danjiangkou Reservoir—the water source [...] Read more.
Planktonic eukaryotes are widespread in aquatic ecosystems, and the study of their community composition and driving factors is of great significance to protecting and maintaining the balance of these ecosystems. This study evaluates five typical ecological sites in the Danjiangkou Reservoir—the water source for the project. This was done to comprehensively understand the composition of Danjiangkou Reservoir planktonic eukaryotes, and ensure the ecological balance of the water source for the South-to-North Water Diversion Project. The diversity of the planktonic eukaryotes in surface water and the factors driving changes in their abundance are analyzed with an 18S ribosomal DNA sequencing approach. Monitoring shows that the Danjiangkou Reservoir has good water quality. The Danjiangkou Reservoir planktonic eukaryote community is mainly composed of 11 phyla, of which Cryptomonadales is dominant, accounting for an average percentage of 65.19% of the community (47.2–84.90%). LEFSe analysis shows significant differences among samples in the abundances of 13 phyla, 20 classes, 23 orders, 26 families, and 27 genera, and there are also significant differences in the diversity of planktonic eukaryotes at different temporal and spatial scales. Redundancy analysis (RDA) show that water temperature, DO, SD, TN, and Chla are significant factors that affect the composition of the planktonic eukaryote community. Spearman rank correlation analysis combined with taxonomic difference analysis shows that Kathablepharidae and Choanoflagellida are not sensitive to environmental or physicochemical factors and that the interannual variations in their abundance are not significant. Network analysis shows that Protalveolata, Basidiomycota, P1-31, Bicosoecida, and Ochrophyta represent important nodes in the single-factor network, while Chytridiomycota, P1-31, Cryptomycota, Ochrophyta, Ichthyosporea, Bicosoecida, Protalveolata, and physicochemical factors (ORP, TN, WT, DO, SD, NH3-N, and NO3-N) represent important nodes in the two-factor network. Full article
(This article belongs to the Special Issue Microbial Communities in Water Environments: Dynamics and Interaction)
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Article
Changes in Fungal Community Structure in Freshwater Canals across a Gradient of Urbanization
Water 2020, 12(7), 1917; https://doi.org/10.3390/w12071917 - 05 Jul 2020
Viewed by 853
Abstract
Fungi are an important, yet often, neglected component of the aquatic microflora, and is responsible for primary decomposition and further processing of organic matter. By comparison, the ecological roles of terrestrial fungi have been well-studied, but the diversity and function of fungi that [...] Read more.
Fungi are an important, yet often, neglected component of the aquatic microflora, and is responsible for primary decomposition and further processing of organic matter. By comparison, the ecological roles of terrestrial fungi have been well-studied, but the diversity and function of fungi that populate aquatic environments remain poorly understood. Here, the impact of urbanization on fungal diversity and community composition in the canal system of Suzhou was assessed by sequencing the internal transcribed spacer 1 (ITS1) region of the rRNA operon. It was amplified from environmental DNA that has been extracted from water samples and pre-deployed decomposing leaves collected from nine sampling locations (high, medium and low urbanization) over two seasons. The fungal diversity and community composition were determined by bioinformatic analysis of the large DNA sequence datasets generated to identify operational taxonomic units (OTUs) for phylogenetic assignment; over 1 million amplicons were sequenced from 36 samples. The alpha-diversity estimates showed high differences in fungal diversity between water and leaf samples, and winter versus summer. Higher numbers of fungal OTUs were identified in both water and leaf samples collected in the summer, and fungal diversity was also generally higher in water than on colonized leaves in both seasons. The fungal community on leaves was usually dominated by Ascomycetes, especially in winter, while water samples contained more diversity at phylum level with Chytridiomycetes often prominent, particularly in summer. At a genus level, a very high relative abundance of Alternaria on leaves was observed in winter at all locations, in contrast to very low abundance of this genus across all water samples. Fungal community composition also varied between sampling locations (i.e., urbanization); in cluster analysis, samples from high urbanization locations formed a distinct cluster, with medium and low urbanization samples clustering together or in some instances, separately. Redundancy analysis shed further light on the relationships between variation in fungal community composition and water physico-chemical properties. Fungal community diversity variation and correlation with different parameters is discussed in detail, but overall, the influence of season outweighed that of urbanization. This study is significant in cataloguing the impact of urbanization on fungal diversity to inform future restoration of urban canal systems on the importance of protecting the natural aquatic fungal flora. Full article
(This article belongs to the Special Issue Microbial Communities in Water Environments: Dynamics and Interaction)
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Article
Aquatic Macrophytes and Local Factors Drive Bacterial Community Distribution and Interactions in a Riparian Zone of Lake Taihu
Water 2020, 12(2), 432; https://doi.org/10.3390/w12020432 - 06 Feb 2020
Cited by 1 | Viewed by 816
Abstract
Aquatic macrophytes rhizosphere are biogeochemical cycling hotspots in freshwater ecosystems. However, little is known regarding the effect of aquatic macrophytes on bacterial community and interactions in the riparian zones. We investigated the bacterial community composition and network structures along a gradient of the [...] Read more.
Aquatic macrophytes rhizosphere are biogeochemical cycling hotspots in freshwater ecosystems. However, little is known regarding the effect of aquatic macrophytes on bacterial community and interactions in the riparian zones. We investigated the bacterial community composition and network structures along a gradient of the riparian zone as follows: The supralittoral and eulittoral zones with Phragmites australis, the eulittoral and infralittoral zones without P. australi. The bacterial communities in the four zones differed significantly based on taxonomic dissimilarity, but the two zones with P. australis exhibited phylogenetic closeness of the bacterial communities. The characteristics of the bacterial networks, such as connectivity, modularity, and topological roles of OTUs, were totally different between the P. australis and non-P. australis zones. Some bacterial phyla enriched in the P. australis zones were found to be putative keystone taxa in the networks, which might be involved in the regulation of bacterial interactions and plant growth. Moreover, the hydrological regime and particle size were shown to be determinants of the bacterial community and network structures in the riparian zones. In summary, our results show that the role of P. australis and local factors are crucial for constructing bacterial community and interactions in the riparian zones of lakes. Full article
(This article belongs to the Special Issue Microbial Communities in Water Environments: Dynamics and Interaction)
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Article
The Impact of a Fish Cannery Wastewater Discharge on the Bacterial Community Structure and Sanitary Conditions of Marine Coastal Sediments
Water 2019, 11(12), 2566; https://doi.org/10.3390/w11122566 - 05 Dec 2019
Cited by 1 | Viewed by 1068
Abstract
The effects of fish cannery discharge (FCD) on bacteria in marine coastal sediments were investigated. Redox potentials were measured, and granulometry was determined by wet ASTM sieving, and with the Sedigraph method. Prokaryotic abundance (PA) was determined by epifluorescence microscopy (DAPI staining), and [...] Read more.
The effects of fish cannery discharge (FCD) on bacteria in marine coastal sediments were investigated. Redox potentials were measured, and granulometry was determined by wet ASTM sieving, and with the Sedigraph method. Prokaryotic abundance (PA) was determined by epifluorescence microscopy (DAPI staining), and faecal indicator bacteria (FIB) enumerated with the multiple test tube and most probable number method. Total lipids were determined gravimetrically, and sterols analysed by GC/MSD. Bacterial community composition was determined after total DNA isolation, Illumina MiSeq amplification, and SILVAngs processing pipeline. The FCD was rich in lipids, heterotrophic prokaryotes and FIB. The bacterial community of the FCD was dominated by Firmicutes and Gammaproteobacteria and many potentially pathogenic bacteria. Highly porosusgravelly sands clogged with fish remains transitioned to less permeable sandy muds away from the FCD. All sediments were anoxic with extremely negative potentials around the outfall. High surface PA and FIB spread 300 m from the outfall. Gammaproteobacteria and Deltaproteobacteria appeared in all sediments. Sulfurovum and Anaerolineaceae characterized the most polluted locations where gammaproteobacterial Woeseiaceae/JTB255 marine benthic group declined. Gammaproteobacteria and Bacteroidetes characterized surface sediments, while Chloroflexi and Deltaproteobacteria prevailed in deeper layers. The FCD enriched sediments in lipids and allochthonous bacteria degrading sanitary quality, lowering the permeability, redox potential, and bacterial diversity. Full article
(This article belongs to the Special Issue Microbial Communities in Water Environments: Dynamics and Interaction)
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Article
Tintinnid Ciliate Communities in Pre- and Post-Winter Conditions in the Southern Adriatic Sea (NE Mediterranean)
Water 2019, 11(11), 2329; https://doi.org/10.3390/w11112329 - 07 Nov 2019
Cited by 1 | Viewed by 904
Abstract
The Southern Adriatic Sea is a dynamic region under the influence of diverse physical forces that modify sea water properties as well as plankton dynamics, abundance, and distribution in an intricate way. The most pronounced being: winter vertical convection, lateral exchanges between coastal [...] Read more.
The Southern Adriatic Sea is a dynamic region under the influence of diverse physical forces that modify sea water properties as well as plankton dynamics, abundance, and distribution in an intricate way. The most pronounced being: winter vertical convection, lateral exchanges between coastal and open sea waters, and the ingression of water masses of different properties into the Adriatic. We investigated the distribution and abundance of tintinnid species in this dynamic environment in pre- and post-winter conditions in 2015/2016. A strong ingression of the saline Levantine Intermediate Water, supported by the cyclonic mode of the North Ionian Gyre in 2015 and 2016, in December was associated with a high diversity of oceanic species. An unusual spatial distribution of neritic-estuarine species Codonellopsis schabi was observed in deeper layers along the analyzed transect, which emphasizes the strong influence of physical processes on deep water biology in the South Adriatic. A shift of population toward greater depths (mesopelagic) and modification of deep sea community structure was recorded in April as a consequence of the winter convection-driven sinking of tintinnids. Our findings indicate that tintinnid abundance and composition is heavily influenced by physical conditions and they are good indicators of the impact of physical forces, including climate changes, on marine environment. Full article
(This article belongs to the Special Issue Microbial Communities in Water Environments: Dynamics and Interaction)
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