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Microorganisms
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Microbial Communities in Aquifer Ecosystems
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Microbial Communities in Aquifer Ecosystems

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

Deadline for manuscript submissions: closed (31 March 2023) | Viewed by 8050

Special Issue Editor

Dr. Cassandre Sara Lazar

E-Mail Website
Guest Editor
Department of Biological Sciences, University of Quebec at Montreal, C.P. 8888, Succ. Centre-Ville, Montréal, QC H3C 3P8, Canada
Interests: the ecology of subsurface microorganisms; the relationships between microbial communities and their environment; the interactions of microbial populations with each other within a habitat
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Aquifers are major ecosystems in the terrestrial subsurface, harboring a vast diversity and abundance of microbial communities. These habitats function as open systems, with water flowing from the surface to the subsurface and eventually reaching the surface once more. The water flowing in these environments brings microbes and nutrients to the subsurface, fueling this ecosystem in various ways. Although the advent of high-throughput sequencing has developed the study of diversity, community structure, and function of these communities, it remains unclear what drives community assembly, which organisms constitute these communities (from all three domains of life, i.e., Archaea, Bacteria and Eukaryotes), or the impact of surface communities and environments on subsurface aquifer habitats.

Therefore, this special issue of Microorganisms invites you to send contributions pertaining to any aspect of microbial community studies in aquifer ecosystems, pristine or contaminated, shallow or deep, using molecular biology based genomic, and -omic, studies, as well as culture-based studies in microbiology, environmental microbiology, and microbial ecology. We encourage the submission of papers associating microbial community analyses with environmental parameters (e.g., geochemical, geological), as well as papers focusing on eukaryotic communities in aquifer habitats.

Dr. Cassandre Sara Lazar
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

  • aquifer ecosystem
  • terrestrial subsurface
  • microbial ecology
  • microbial community
  • ecosystem function
  • groundwater ecosystem

Published Papers (4 papers)

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Research

22 pages, 5780 KiB  
Article
Linking Groundwater to Surface Discharge Ecosystems: Archaeal, Bacterial, and Eukaryotic Community Diversity and Structure in Quebec (Canada)
by Benjamin Groult, Vicky St-Jean and Cassandre Sara Lazar
Microorganisms 2023, 11(7), 1674; https://doi.org/10.3390/microorganisms11071674 - 27 Jun 2023
Viewed by 1232
Abstract
Aquifer systems are composed of water flowing from surface recharge areas, to the subsurface and back to the surface in discharge regions. Groundwater habitats harbor a large microbial biomass and diversity, potentially contributing to surface aquatic ecosystems. Although this contribution has been widely [...] Read more.
Aquifer systems are composed of water flowing from surface recharge areas, to the subsurface and back to the surface in discharge regions. Groundwater habitats harbor a large microbial biomass and diversity, potentially contributing to surface aquatic ecosystems. Although this contribution has been widely studied in marine environments, very little is known about the connection between underground and surface microbial communities in freshwater settings. Therefore, in this study, we used amplicon sequencing to analyze the archaeal, bacterial, and eukaryotic community diversity and structure in groundwater and surface water samples, spanning the vast regions of the Laurentides and Lanaudières in the Quebec province (Canada). Our results show significant differences between subsurface and surface taxa; with more fungi, Amoebozoa, and chemolithoautotrophic prokaryotes involved in nitrogen-, sulfur-, and iron-cycling dominating the underground samples; while algae, ciliates, methanogens, and Actinobacteria dominate the surface discharge waters. Microbial source tracking suggested that only a small portion of the microbial communities in the groundwater contributed to the surface discharge communities. However, many taxa were shared between both habitats, with a large range of functional diversity, likely explaining their survival in both subsurface and surface water ecosystems. Full article
(This article belongs to the Special Issue Microbial Communities in Aquifer Ecosystems)
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16 pages, 3098 KiB  
Article
Effect of Snowmelt on Groundwater Bacterial Community Composition and Potential Role of Surface Environments as Microbial Seed Bank in Two Distinct Aquifers from the Region of Quebec, Canada
by Karine Villeneuve, Valérie Turcotte-Blais and Cassandre Sara Lazar
Microorganisms 2023, 11(6), 1526; https://doi.org/10.3390/microorganisms11061526 - 8 Jun 2023
Viewed by 983
Abstract
Events of groundwater recharge are associated with changes in the composition of aquifer microbial communities but also abiotic conditions. Modification in the structure of the community can be the result of different environmental condition favoring or hindering certain taxa, or due to the [...] Read more.
Events of groundwater recharge are associated with changes in the composition of aquifer microbial communities but also abiotic conditions. Modification in the structure of the community can be the result of different environmental condition favoring or hindering certain taxa, or due to the introduction of surface-derived taxa. Yet, in both cases, the local hydrogeochemical settings of the aquifer is likely to affect the amount of variation observed. Therefore, in our study, we used 16S rRNA gene sequencing to assess how microbial communities change in response to snowmelt and the potential connectivity between subsurface and surface microbiomes in two distinct aquifers located in the region of Vaudreuil–Soulanges (Québec, Canada). At both sites, we observed an increase in groundwater level and decrease in temperature following the onset of snow melt in March 2019. Bacterial community composition of each aquifer was significantly different (p < 0.05) between samples collected prior and after groundwater recharge. Furthermore, microbial source tracking results suggested a low contribution of surface environments to the groundwater microbiome except for in the months associated with recharge (March 2019 and April 2019). Overall, despite differences in soil permeability between both sites, the period of snow melt was followed by important changes in the composition of microbial communities from aquifers. Full article
(This article belongs to the Special Issue Microbial Communities in Aquifer Ecosystems)
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30 pages, 3945 KiB  
Article
From the Mountain to the Valley: Drivers of Groundwater Prokaryotic Communities along an Alpine River Corridor
by Alice Retter, Johannes Christoph Haas, Steffen Birk, Christine Stumpp, Bela Hausmann, Christian Griebler and Clemens Karwautz
Microorganisms 2023, 11(3), 779; https://doi.org/10.3390/microorganisms11030779 - 17 Mar 2023
Cited by 2 | Viewed by 1742
Abstract
Rivers are the “tip of the iceberg”, with the underlying groundwater being the unseen freshwater majority. Microbial community composition and the dynamics of shallow groundwater ecosystems are thus crucial, due to their potential impact on ecosystem processes and functioning. In early summer and [...] Read more.
Rivers are the “tip of the iceberg”, with the underlying groundwater being the unseen freshwater majority. Microbial community composition and the dynamics of shallow groundwater ecosystems are thus crucial, due to their potential impact on ecosystem processes and functioning. In early summer and late autumn, samples of river water from 14 stations and groundwater from 45 wells were analyzed along a 300 km transect of the Mur River valley, from the Austrian alps to the flats at the Slovenian border. The active and total prokaryotic communities were characterized using high-throughput gene amplicon sequencing. Key physico-chemical parameters and stress indicators were recorded. The dataset was used to challenge ecological concepts and assembly processes in shallow aquifers. The groundwater microbiome is analyzed regarding its composition, change with land use, and difference to the river. Community composition and species turnover differed significantly. At high altitudes, dispersal limitation was the main driver of groundwater community assembly, whereas in the lowland, homogeneous selection explained the larger share. Land use was a key determinant of the groundwater microbiome composition. The alpine region was more diverse and richer in prokaryotic taxa, with some early diverging archaeal lineages being highly abundant. This dataset shows a longitudinal change in prokaryotic communities that is dependent on regional differences affected by geomorphology and land use. Full article
(This article belongs to the Special Issue Microbial Communities in Aquifer Ecosystems)
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16 pages, 1463 KiB  
Article
Comparing the Efficacy of MALDI-TOF MS and Sequencing-Based Identification Techniques (Sanger and NGS) to Monitor the Microbial Community of Irrigation Water
by Botond Bendegúz Surányi, Benjamin Zwirzitz, Csilla Mohácsi-Farkas, Tekla Engelhardt and Konrad J. Domig
Microorganisms 2023, 11(2), 287; https://doi.org/10.3390/microorganisms11020287 - 21 Jan 2023
Cited by 4 | Viewed by 3548
Abstract
In order to intensify and guarantee the agricultural productivity and thereby to be able to feed the world’s rapidly growing population, irrigation has become very important. In parallel, the limited water resources lead to an increase in usage of poorly characterized sources of [...] Read more.
In order to intensify and guarantee the agricultural productivity and thereby to be able to feed the world’s rapidly growing population, irrigation has become very important. In parallel, the limited water resources lead to an increase in usage of poorly characterized sources of water, which is directly linked to a higher prevalence of foodborne diseases. Therefore, analyzing the microorganisms or even the complete microbiome of irrigation water used for food production can prevent the growing numbers of such cases. In this study, we compared the efficacy of MALDI-TOF Mass spectrometry (MALDI TOF MS) identification to 16S rRNA gene Sanger sequencing of waterborne microorganisms. Furthermore, we analyzed the whole microbial community of irrigation water using high-throughput 16S rRNA gene amplicon sequencing. The identification results of MALDI-TOF MS and 16S rRNA gene Sanger sequencing were almost identical at species level (66.7%; 64.3%). Based on the applied cultivation techniques, Acinetobacter spp., Enterobacter spp., Pseudomonas spp., and Brevundimonas spp. were the most abundant cultivable genera. In addition, the uncultivable part of the microbiome was dominated by Proteobacteria followed by Actinobacteria, Bacteroidota, Patescibacteria, and Verrucomicrobiota. Our findings indicate that MALDI-TOF MS offers a fast, reliable identification method and can act as an alternative to 16S rRNA gene Sanger sequencing of isolates. Moreover, the results suggest that MALDI-TOF MS paired with 16S rRNA gene amplicon sequencing have the potential to support the routine monitoring of the microbiological quality of irrigation water. Full article
(This article belongs to the Special Issue Microbial Communities in Aquifer Ecosystems)
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