Microbial Ecology of Aquatic Habitats

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 (20 October 2021) | Viewed by 20870

Special Issue Editor


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Guest Editor
Department of Biological Applications and Technology, University Campus of Ioannina, Ioannina, Greece
Interests: aquatic microbial ecology; food webs; biogeography; diversity
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Microbes are important biological components of aquatic habitats with pivotal roles in biogeochemical processes and food webs structuring and with multiple interactions with other micro- or macroorganisms. Progress in microbiology and molecular techniques, in recent years, as well as improvements in field equipment and experimental approaches, shed light on their ecology but has also shown that there is still much to learn. Furthermore, all data accumulated so far needs organization and interpretation based on ecological theory. Thus, microbial ecologists continue to address questions related to the diversity, function, biogeography, and biological interactions of microbes in aquatic habitats, often associated with serious global or local environmental issues facing societies today. The Special Issue “Microbial Ecology of Aquatic Habitats” aims to present recent research on viruses, prokaryotes, and protists dynamics in marine and freshwater habitats, natural, artificial or engineered. Indicative topics of interest of this issue are:

  • Biodiversity and community assembly of microbes
  • Biogeography of microbes
  • Application of ecology theory to microbial ecology
  • Role of microbes on biogeochemical processes
  • Response of microbes to environmental stress
  • Microbes as trophic links in food webs
  • Mixotrophic protists
  • Ecology of viruses
  • Microbe-microbe and microbe-host interactions

Asst. Prof. Dr. Hera Karayanni
Guest Editor

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Keywords

  • Protists
  • Prokaryotes
  • Viruses
  • Mixotrophs
  • Community assembly
  • Microbial function
  • Interactions
  • Ecology theory

Published Papers (6 papers)

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17 pages, 4950 KiB  
Article
Assessment of Microbial Community Composition Changes in the Presence of Phytoplankton-Derived Exudates in Two Contrasting Areas from Chilean Patagonia
by Valentina Valdés-Castro, Humberto E. González, Ricardo Giesecke, Camila Fernández and Verónica Molina
Diversity 2022, 14(3), 195; https://doi.org/10.3390/d14030195 - 07 Mar 2022
Cited by 5 | Viewed by 2350
Abstract
Patagonian fjords and channels in southern Chile are heterogeneous ecosystems characterized by the interaction of estuarine and marine waters influencing physical-chemical conditions and biological assemblages. Besides salinity, microbial communities from estuarine and marine origin are naturally subjected to changing organic matter quality and [...] Read more.
Patagonian fjords and channels in southern Chile are heterogeneous ecosystems characterized by the interaction of estuarine and marine waters influencing physical-chemical conditions and biological assemblages. Besides salinity, microbial communities from estuarine and marine origin are naturally subjected to changing organic matter quality and variable nutrient concentrations. In this study, we tackle the response of the bacterial community from estuarine and marine origins associated with two size classes (<0.7 µm and <1.6 µm) to the addition of sterile phytoplankton-derived exudates (PDE) compared to control conditions (no addition). Picoplanktonic cell abundance, active bacterial composition analyzed through 16S rRNA sequencing, changes in dissolved organic carbon (DOC) and δ13C were determined over 5 and 15 days after PDE addition. Our results showed that the active marine bacteria were richer and more diverse than their estuarine counterparts, and were dominated by Alphaproteobacteria and Gammaproteobacteria, respectively. PDE addition in both the fractions and the sample origin resulted in an enrichment throughout the incubation of Rhodobacteracea and Cryimorphaceae families, whereas Epsilonproteobacteria (Arcobacteraceae) were mainly favored in the estuarine experiments. Picoplankton abundance increased with time, but higher cell numbers were found in PDE treatments in both size classes (>2 × 105 cell mL−1). In all the experiments, DOC concentration decreased after eight days of incubation, but shifts in δ13C organic matter composition were greater in the estuarine experiments. Overall, our results indicate that despite their different origins (estuarine versus marine), microbial communities inhabiting the fjord responded to PDE with a faster effect on marine active bacteria. Full article
(This article belongs to the Special Issue Microbial Ecology of Aquatic Habitats)
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12 pages, 2104 KiB  
Article
A Comparison of DNA Metabarcoding and Microscopy Methodologies for the Study of Aquatic Microbial Eukaryotes
by Ioulia Santi, Panagiotis Kasapidis, Ioannis Karakassis and Paraskevi Pitta
Diversity 2021, 13(5), 180; https://doi.org/10.3390/d13050180 - 23 Apr 2021
Cited by 26 | Viewed by 2970
Abstract
The procedures and methodologies employed to study microbial eukaryotic plankton have been thoroughly discussed. Two main schools exist—one insisting on classic microscopy methodologies and the other supporting modern high-throughput sequencing (DNA metabarcoding). However, few studies have attempted to combine both these approaches; most [...] Read more.
The procedures and methodologies employed to study microbial eukaryotic plankton have been thoroughly discussed. Two main schools exist—one insisting on classic microscopy methodologies and the other supporting modern high-throughput sequencing (DNA metabarcoding). However, few studies have attempted to combine both these approaches; most studies implement one method while ignoring the other. This work aims to contribute to this discussion and examine the advantages and disadvantages of each methodology by comparing marine plankton community results from microscopy and DNA metabarcoding. The results obtained by the two methodologies do not vary significantly for Bacillariophyta, although they do for Dinoflagellata and Ciliophora. The lower the taxonomic level, the higher the inconsistency between the two methodologies for all the studied groups. Considering the different characteristics of microscopy-based identification and DNA metabarcoding, this work underlines that each method should be chosen depending on the aims of the study. DNA metabarcoding provides a better estimate of the taxonomic richness of an ecosystem while microscopy provides more accurate quantitative results regarding abundance and biomass. In any case, the combined use of the two methods, if properly standardized, can provide much more reliable and accurate results for the study of marine microbial eukaryotes. Full article
(This article belongs to the Special Issue Microbial Ecology of Aquatic Habitats)
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13 pages, 2437 KiB  
Article
Bacterial Composition and Diversity in Deep-Sea Sediments from the Southern Colombian Caribbean Sea
by Nelson Rivera Franco, Miguel Ángel Giraldo, Diana López-Alvarez, Jenny Johana Gallo-Franco, Luisa F. Dueñas, Vladimir Puentes and Andrés Castillo
Diversity 2021, 13(1), 10; https://doi.org/10.3390/d13010010 - 31 Dec 2020
Cited by 11 | Viewed by 3638
Abstract
Deep-sea sediments are considered an extreme environment due to high atmospheric pressure and low temperatures, harboring novel microorganisms. To explore marine bacterial diversity in the southern Colombian Caribbean Sea, this study used 16S ribosomal RNA (rRNA) gene sequencing to estimate bacterial composition and [...] Read more.
Deep-sea sediments are considered an extreme environment due to high atmospheric pressure and low temperatures, harboring novel microorganisms. To explore marine bacterial diversity in the southern Colombian Caribbean Sea, this study used 16S ribosomal RNA (rRNA) gene sequencing to estimate bacterial composition and diversity of six samples collected at different depths (1681 to 2409 m) in two localities (CCS_A and CCS_B). We found 1842 operational taxonomic units (OTUs) assigned to bacteria. The most abundant phylum was Proteobacteria (54.74%), followed by Bacteroidetes (24.36%) and Firmicutes (9.48%). Actinobacteria and Chloroflexi were also identified, but their dominance varied between samples. At the class-level, Alphaproteobacteria was most abundant (28.4%), followed by Gammaproteobacteria (24.44%) and Flavobacteria (16.97%). The results demonstrated that some bacteria were common to all sample sites, whereas other bacteria were unique to specific samples. The dominant species was Erythrobacter citreus, followed by Gramella sp. Overall, we found that, in deeper marine sediments (e.g., locality CCS_B), the bacterial alpha diversity decreased while the dominance of several genera increased; moreover, for locality CCS_A, our results suggest that the bacterial diversity could be associated with total organic carbon content. We conclude that physicochemical properties (e.g., organic matter content) create a unique environment and play an important role in shaping bacterial communities and their diversity. Full article
(This article belongs to the Special Issue Microbial Ecology of Aquatic Habitats)
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15 pages, 5463 KiB  
Article
Analysis of Microbial Communities and Pathogen Detection in Domestic Sewage Using Metagenomic Sequencing
by Muhammad Yasir
Diversity 2021, 13(1), 6; https://doi.org/10.3390/d13010006 - 25 Dec 2020
Cited by 26 | Viewed by 5792
Abstract
Wastewater contains diverse microbes, and regular microbiological screening at wastewater treatment plants is essential for monitoring the wastewater treatment and protecting environmental health. In this study, a metagenomic approach was used to characterize the microbial communities in the influent and effluent of a [...] Read more.
Wastewater contains diverse microbes, and regular microbiological screening at wastewater treatment plants is essential for monitoring the wastewater treatment and protecting environmental health. In this study, a metagenomic approach was used to characterize the microbial communities in the influent and effluent of a conventional domestic sewage treatment plant in the metropolitan city of Jeddah. Bacteria were the prevalent type of microbe in both the influent and effluent, whereas archaea and viruses were each detected at <1% abundance. Greater diversity was observed in effluent bacterial populations compared with influent, despite containing similar major taxa. These taxa consisted primarily of Proteobacteria, followed by Bacteroidetes and Firmicutes. Metagenomic analysis provided broad profiles of 87 pathogenic/opportunistic bacteria belonging to 47 distinct genera in the domestic sewage samples, with most having <1% abundance. The archaea community included 20 methanogenic genera. The virus-associated sequences were classified mainly into the families Myoviridae, Siphoviridae, and Podoviridae. Genes related to resistance to antibiotics and toxic compounds, gram-negative cell wall components, and flagellar motility in prokaryotes identified in metagenomes from both types of samples. This study provides a comprehensive understanding of microbial communities in influent and effluent samples of a conventional domestic sewage treatment plant and suggests that metagenomic analysis is a feasible approach for microbiological monitoring of wastewater treatment. Full article
(This article belongs to the Special Issue Microbial Ecology of Aquatic Habitats)
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16 pages, 3187 KiB  
Article
The Influence of Human Interference on Zooplankton and Fungal Diversity in Poyang Lake Watershed in China
by Haiming Qin, Xinyi Cao, Lanyue Cui, Qian Lv and Tingtao Chen
Diversity 2020, 12(8), 296; https://doi.org/10.3390/d12080296 - 28 Jul 2020
Cited by 15 | Viewed by 2893
Abstract
The Poyang water system in Jiangxi Province, China, is important for floodwater storage, diversity maintenance, and the economy of the Poyang Lake watershed. In recent years, pollution has destroyed the ecosystem and impacted human health and the related economy. The water quality of [...] Read more.
The Poyang water system in Jiangxi Province, China, is important for floodwater storage, diversity maintenance, and the economy of the Poyang Lake watershed. In recent years, pollution has destroyed the ecosystem and impacted human health and the related economy. The water quality of the Poyang Lake watershed and the impact of human interference must be assessed. Conventional analysis and high-throughput sequencing were used to evaluate the structure of both zooplankton and fungi in six sub-lakes of the Poyang Lake watershed under different anthropogenic influences. The sub-lakes included were Dahuchi Lake (in natural preserve, DHC), Shahu Lake (in natural reserve, SH), Nanhu Lake (out of natural preserve, NH), Zhelinhu Lake (artificial reservoir, ZLH), Sixiahu Lake (agricultural lake artificially isolated from Poyang Lake, SXH), and Qianhu Lake (urban lake, QH). The densities and biomass of the zooplankton in DHC, SH, NH were higher compared with those in SXH, ZLH and QH (p < 0.05). Zooplankton distribution of SXH was the most strongly associated with total nitrogen (TN), total phosphorus (TP) and chlorophyll a (Chl a), while QH was highly associated with pH, conductivity (Cond), and water temperature (WT). For fungal diversity, a large number of beneficial fungi, Basidiomycota (phylum level) and Massarina (genus level) were obtained from DHC (55.3% and 27.5%, respectively), SH (54.4% and 28.9%, respectively), and NH (48.6% and 1.4%, respectively), while a large number of pathogenic Chytridiomycota (at phylum level) were identified from SXH (21.0%), ZLH (5.5%), and QH (7.5%). Manmade pollutants have impacted the natural hydrology and water quality and promoted variation between the zooplankton and fungi in the six sub-lakes, reducing the relative abundance of beneficial fungi and increasing the number of pathogens in the environment, which threatens human health and economic production. Understanding the diversity among the zooplankton and fungi in the six sub-lakes of the Poyang Lake watershed may help guide future water management practices. Full article
(This article belongs to the Special Issue Microbial Ecology of Aquatic Habitats)
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8 pages, 962 KiB  
Brief Report
Experimental Warming Effects on Prokaryotic Growth and Viral Production in Coastal Waters of the Northwest Pacific during the Cold Season
by An-Yi Tsai, Gwo-Ching Gong and Vladimir Mukhanov
Diversity 2021, 13(9), 409; https://doi.org/10.3390/d13090409 - 27 Aug 2021
Cited by 3 | Viewed by 1927
Abstract
Climate warming can directly affect biological processes in marine environments. Here, we investigated if warming (+2 °C) can change dynamics in viral and prokaryotic populations in the cold seasons in natural seawaters. We monitored the changes in viral production and prokaryotic growth rate. [...] Read more.
Climate warming can directly affect biological processes in marine environments. Here, we investigated if warming (+2 °C) can change dynamics in viral and prokaryotic populations in the cold seasons in natural seawaters. We monitored the changes in viral production and prokaryotic growth rate. The prokaryotic average gross growth rates were 0.08 and 0.34 h−1 in November and 0.06 and 0.41 h−1 in December in the in situ and warming experiments, respectively. We found that warming water temperature resulted in a significant increase in prokaryotic growth rates. In warming experiments, the overall viral production rate was about 0.77–14.4 × 105 viruses mL−1 h−1, and a rough estimate of prokaryotic mortality was about 5.6–6.8 × 104 cells mL−1 h−1. Based on our estimation, burst sizes of about 21 and 14 viruses prokaryotes−1 were measured under the experimental warming period. Moreover, the results found that an increased water temperature in the subtropical western Pacific coastal waters increases prokaryotic growth rates, enhances viral production, and changes the carbon fluxes in the trophic interactions of microbes. Full article
(This article belongs to the Special Issue Microbial Ecology of Aquatic Habitats)
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