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Molecular and Microbial Ecology: Plastic Responses and Eco-Evolutionary Interactions with...
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Molecular and Microbial Ecology: Plastic Responses and Eco-Evolutionary Interactions with Environmental Stressors and Climate Change

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

Deadline for manuscript submissions: 31 July 2024 | Viewed by 5819

Special Issue Editors

Dr. Spiros Papakostas

E-Mail Website1 Website2
Guest Editor
Department of Genetics, Development, and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
Interests: molecular ecology; contemporary evolution; functional genomics; molecular systematics; population and evolutionary genomics; microbial ecology; eco-evolutionary dynamics
Dr. Nikolaos Monokrousos

E-Mail Website
Guest Editor
Laboratory of Soil Ecology, International Hellenic University, 57001 Thessaloniki, Greece
Interests: soil microbial ecology; soil nematodes; soil enzymes; plant–soil microbe interactions
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The need to understand the short-term plastic and contemporary adaptive responses of organisms to environmental stressors and fast-paced climate change has never been more urgent. Microbial communities are also increasingly recognized as an integral part of healthy, sustainable ecosystems (soil, air, water) with key roles in several ecosystem functions from nutrient cycling to greenhouse gas emissions, and the dynamics of organic matter turnover. It is thus of great importance to assess the relationship between genetic diversity at different levels and ecosystem functioning under conditions of rapid environmental change. In this Special Issue, we invite studies, reviews, and datasets of molecular and microbial ecology interest regardless of taxon that investigate and disentangle the plastic and evolutionary components of this relationship at either the macro-environment (soil, air, water) or the micro-environment (e.g., gut microbiota). Our goal is to provide in this issue a collection of high-quality articles that present novel insights into the ways that organisms and microbial communities respond to rapid changes to their environments.

Dr. Spiros Papakostas
Dr. Nikolaos Monokrousos
Guest Editors

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 2600 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

  • biodiversity
  • rapid local adaptation
  • eco-evolutionary dynamics
  • microbiome 
  • microbial communities and structure
  • metagenomics
  • population genomics
  • transcriptomics

Published Papers (4 papers)

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Research

13 pages, 2384 KiB  
Article
The Molecular Detection, Characterization, and Temperature Dependence of Wolbachia Infections in Field Populations of Aedes albopictus (Diptera: Culicidae) Mosquitoes in Greece
by Michail Misailidis, Nikolaos Kotsiou, Aristotelis Moulistanos, Sandra Gewehr, Antonios A. Augustinos, Spiros Mourelatos, Spiros Papakostas and Elena Drosopoulou
Diversity 2024, 16(1), 43; https://doi.org/10.3390/d16010043 - 09 Jan 2024
Viewed by 1016
Abstract
We investigated the prevalence and genetic diversity of Wolbachia pipientis strains in Aedes albopictus populations in Greece. Using a combination of PCR and Sanger sequencing techniques, we genotyped Wolbachia strains in 105 mosquitoes collected across eight different administrative regions in 2021. We found [...] Read more.
We investigated the prevalence and genetic diversity of Wolbachia pipientis strains in Aedes albopictus populations in Greece. Using a combination of PCR and Sanger sequencing techniques, we genotyped Wolbachia strains in 105 mosquitoes collected across eight different administrative regions in 2021. We found a high prevalence of Wolbachia in both male (90%) and female (97%) mosquitoes. Among the infected samples, 84% had double infections with both wAlbA and wAlbB strains, while 16% had infections with only wAlbB. Our comparison of the Multi-Locus Sequence Typing (MLST) profile, employing gatB–coxA–hcpA–ftsZ–fbpA genotyping, revealed a single MLST profile for each wAlbA and wAlbB strain in Greek populations. The same MLST profiles were also reported in populations from China, Russia, and Argentina, suggesting low levels of global diversity in wAlbA and wAlbB strains. Furthermore, our results indicated a significant association between temperature and the prevalence of single infections (p = 6.498 × 10−7), with higher temperatures correlating with an increased likelihood of single infections. Although male bias showed a tendency towards single infections, the effect was marginally non-significant (p = 0.053). These results were confirmed using a bootstrap-with-replacement analysis approach. Overall, our findings offer novel insights into the distribution and species diversity of Wolbachia strains in Greek Ae. albopictus populations, emphasizing the importance of understanding the short-term plastic and adaptive responses of these organisms to environmental stressors and rapid climate change. Full article
(This article belongs to the Special Issue Molecular and Microbial Ecology: Plastic Responses and Eco-Evolutionary Interactions with Environmental Stressors and Climate Change)
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15 pages, 3009 KiB  
Article
An Update of Knowledge of the Bacterial Assemblages Associated with the Mexican Caribbean Corals Acropora palmata, Orbicella faveolata, and Porites porites
by Joicye Hernández-Zulueta, Leopoldo Díaz-Pérez, Alex Echeverría-Vega, Gabriela Georgina Nava-Martínez, Miguel Ángel García-Salgado and Fabián A. Rodríguez-Zaragoza
Diversity 2023, 15(9), 964; https://doi.org/10.3390/d15090964 - 26 Aug 2023
Viewed by 1005
Abstract
In this study, the bacterial microbiota associated with apparently healthy corals of Acropora palmata, Orbicella faveolata, and Porites porites and the surrounding seawater and sediment were evaluated via the MiSeq Illumina sequencing of the V4 region of 16S rRNA at three [...] Read more.
In this study, the bacterial microbiota associated with apparently healthy corals of Acropora palmata, Orbicella faveolata, and Porites porites and the surrounding seawater and sediment were evaluated via the MiSeq Illumina sequencing of the V4 region of 16S rRNA at three reef sites in the Mexican Caribbean. Bacterial assemblages associated with apparently healthy corals and sediments showed no significant differences between sites. The colonies of A. palmata showed a dominance of families Amoebophilaceae, Spirochaetaceae, Myxococcaceae, and Cyclobacteriaceae. Meanwhile, the colonies of O. faveolata and P. porites revealed a high prevalence of the Rhodobacteraceae and Kiloniellaceae families. The families Rhodobacteraceae, Cryomorphaceae, Cyanobiaceae, and Flavobacteriaceae were predominant in seawater samples, while Pirellulaceae, Nitrosococcaceae, and Woeseiaceae were predominant in sediments. Variations in A. palmata bacterial assemblages were correlated with salinity, sea surface temperature, and depth. These variables, along with nitrate, phosphate, and ammonium concentrations, were also correlated with changes in the bacterial composition of P. porites, seawater, and sediments. However, none of the environmental variables were related to the bacterial taxa of O. faveolata. Aerobic chemoheterotrophy and fermentation, followed by nitrate reduction and ureolysis, were the metabolic functions with the highest occurrence in the bacterial assemblages associated with all substrates. Full article
(This article belongs to the Special Issue Molecular and Microbial Ecology: Plastic Responses and Eco-Evolutionary Interactions with Environmental Stressors and Climate Change)
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18 pages, 2154 KiB  
Article
Cell Plasticity of Marine Mediterranean Diazotrophs to Climate Change Factors and Nutrient Regimes
by Víctor Fernández-Juárez, Elisa H. Zech, Elisabet Pol-Pol and Nona S. R. Agawin
Diversity 2023, 15(3), 316; https://doi.org/10.3390/d15030316 - 21 Feb 2023
Viewed by 1218
Abstract
Ocean acidification and warming are current global challenges that marine diazotrophs must cope with. Little is known about the effects of pH and temperature changes at elevated CO2 levels in combination with different nutrient regimes on N2 fixers, especially on heterotrophic [...] Read more.
Ocean acidification and warming are current global challenges that marine diazotrophs must cope with. Little is known about the effects of pH and temperature changes at elevated CO2 levels in combination with different nutrient regimes on N2 fixers, especially on heterotrophic bacteria. Here, we selected four culturable diazotrophs, i.e., cyanobacteria and heterotrophic bacteria, found in association with the endemic Mediterranean seagrass Posidonia oceanica. We tested different pH (from pH 4 to 8) and temperature levels (from 12 to 30 °C), under different nutrient concentrations of both phosphorus, P (0.1 µM and 1.5 mM), and iron, Fe (2 nM and 1 µM). We also tested different CO2 concentrations (410 and 1000 particles per million (ppm)) under different P/Fe and temperature values (12, 18, and 24 °C). Heterotrophic bacteria were more sensitive to changes in pH, temperature, and CO2 than the cyanobacterial species. Cyanobacteria were resistant to very low pH levels, while cold temperatures stimulated the growth in heterotrophic bacteria but only under nutrient-limited conditions. High CO2 levels (1000 ppm) reduced heterotrophic growth only when cultures were nutrient-limited, regardless of temperature. In contrast, cyanobacteria were insensitive to elevated CO2 levels, independently of the nutrient and temperature levels. Changes in N2 fixation were mainly controlled by changes in growth. In addition, we suggest that alkaline phosphatase activity (APA) and reactive oxidative species (ROS) can be used as biomarkers to assess the plasticity of these communities to climate change factors. Unlike other studies, the novelty of this work lies in the fact that we compared the responses of cyanobacteria vs. heterotrophic bacteria, studying which changes occur at the cell plasticity level. Our results suggest that the responses of diazotrophs to climate change may depend on their P and Fe status and lifestyle, i.e., cyanobacteria or heterotrophic bacteria. Full article
(This article belongs to the Special Issue Molecular and Microbial Ecology: Plastic Responses and Eco-Evolutionary Interactions with Environmental Stressors and Climate Change)
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14 pages, 1322 KiB  
Article
Drying Shapes Aquatic Fungal Community Assembly by Reducing Functional Diversity
by Rebeca Arias-Real, Pilar Hurtado, Giulia Gionchetta and Cayetano Gutiérrez-Cánovas
Diversity 2023, 15(2), 289; https://doi.org/10.3390/d15020289 - 16 Feb 2023
Cited by 1 | Viewed by 1859
Abstract
Aquatic fungi are highly diverse organisms that play a critical role in global biogeochemical cycles. Yet it remains unclear which assembly processes determine their co-occurrence and assembly patterns over gradients of drying intensity, which is a common stressor in fluvial networks. Although aquatic [...] Read more.
Aquatic fungi are highly diverse organisms that play a critical role in global biogeochemical cycles. Yet it remains unclear which assembly processes determine their co-occurrence and assembly patterns over gradients of drying intensity, which is a common stressor in fluvial networks. Although aquatic fungi possess drying-specific adaptations, little is known about how functional similarity influences co-occurrence probability and which functional traits are sorted by drying. Using field data from 15 streams, we investigated how co-occurrence patterns and assembly processes responded to drying intensity. To do so, we determined fungal co-occurrence patterns, functional traits that best explain species co-occurrence likelihood, and community assembly mechanisms explaining changes in functional diversity over the drying gradient. Our results identified 24 species pairs with positive co-occurrence probabilities and 16 species pairs with negative associations. The co-occurrence probability was correlated with species differences in conidia shape and fungal endophytic capacity. Functional diversity reduction over the drying gradient is generally associated with non-random abiotic filtering. However, the assembly processes changed over the drying gradient, with random assembly prevailing at low drying intensity and abiotic filtering gaining more importance as drying intensifies. Collectively, our results can help anticipate the impacts of global change on fungal communities and ecosystem functioning. Full article
(This article belongs to the Special Issue Molecular and Microbial Ecology: Plastic Responses and Eco-Evolutionary Interactions with Environmental Stressors and Climate Change)
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