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Microorganisms
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Microbes in Communities—Geobiological Processes, Symbioses, Applications 2.0
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Microbes in Communities—Geobiological Processes, Symbioses, Applications 2.0

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

Deadline for manuscript submissions: closed (31 December 2023) | Viewed by 6726

Special Issue Editors

Dr. Michael Hoppert

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Guest Editor
Institute of Microbiology and Genetics, University of Goettingen, Grisebachstraße 8, 37077 Göttingen, Germany
Interests: geomicrobiology (microbial marine symbioses, aerophytic biofilms); cytology of prokaryotes
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Joachim Reitner

E-Mail Website
Guest Editor
Geoscience Centre, Geobiology, University of Goettingen, Goldschmidtstraße 3, 37077 Göttingen, Germany
Interests: Geobiology of prebiotic and early life processes Biogeochemistry of biomineralisation; biofilms Microbial mats; Phylogeny and biogeochemistry of ancestral metazoans (sponges, cnidarians)
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue is a continuation of our previous Special Issue on the same topic, entitled "Microbes in Communities—Geobiological Processes, Symbioses, Applications".

All microorganisms, both prokaryotes and eukaryotes live in multi-species assemblages. Though these communities are nowadays easy to elucidate (in terms of species diversity) by next-generation sequencing, their functionality is difficult to understand. Scientific knowledge of the metabolic properties and flows of substrates and products is lagging behind the fast-growing metagenome data, revealing more and more microbial taxa of unknown function. Reasons for the occurrence of specific organisms, their interdependence between species, their fitness, and their adaptations are still largely unknown.

In this Issue, we aim to shed light on the functionality of microbial communities in geobiological processes at micro- and macroscales. This includes, but is not restricted to, communities involved in primary production and elemental cycling, mineral dissolution and precipitation, animal–microbe symbioses, the degradation of complex compounds, and bioremediation.

For this Special Issue, we invite academics to submit research papers and reviews describing the interrelations between community members in microbial consortia. Of particular interest are extreme habitats and model ecosystems with low diversity, in which few organisms are dominant and whose processes may be reconstructed. We are also looking for research that highlights key players and factors in complex communities like in soil, marine sediments, or animal microbiomes. We are also interested in the role of (bacterial) viruses in microbial communities.

All methodologies, like (functional) metagenomics, metabolome studies, in situ analyses of parameters (macro- to nanoscale), microbial biomarker tracing, and structure–functional microscopic techniques, are welcome.

Dr. Michael Hoppert
Prof. Dr. Joachim Reitner
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. 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.

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Published Papers (5 papers)

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Research

19 pages, 3327 KiB  
Article
The Impact of Warming on Assembly Processes and Diversity Patterns of Bacterial Communities in Mesocosms
by Qian Yang, Yifeng Yan, Jinhe Huang, Zhaolei Wang, Mingjun Feng, Haowu Cheng, Peiyu Zhang, Huan Zhang, Jun Xu and Min Zhang
Microorganisms 2023, 11(11), 2807; https://doi.org/10.3390/microorganisms11112807 - 19 Nov 2023
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Abstract
Bacteria in lake water bodies and sediments play crucial roles in various biogeochemical processes. In this study, we conducted a comprehensive analysis of bacterioplankton and sedimentary bacteria community composition and assembly processes across multiple seasons in 18 outdoor mesocosms exposed to three temperature [...] Read more.
Bacteria in lake water bodies and sediments play crucial roles in various biogeochemical processes. In this study, we conducted a comprehensive analysis of bacterioplankton and sedimentary bacteria community composition and assembly processes across multiple seasons in 18 outdoor mesocosms exposed to three temperature scenarios. Our findings reveal that warming and seasonal changes play a vital role in shaping microbial diversity, species interactions, and community assembly disparities in water and sediment ecosystems. We observed that the bacterioplankton networks were more fragile, potentially making them susceptible to disturbances, whereas sedimentary bacteria exhibited increased stability. Constant warming and heatwaves had contrasting effects: heatwaves increased stability in both planktonic and sedimentary bacteria communities, but planktonic bacterial networks became more fragile under constant warming. Regarding bacterial assembly, stochastic processes primarily influenced the composition of planktonic and sedimentary bacteria. Constant warming intensified the stochasticity of bacterioplankton year-round, while heatwaves caused a slight shift from stochastic to deterministic in spring and autumn. In contrast, sedimentary bacteria assembly is mainly dominated by drift and remained unaffected by warming. Our study enhances our understanding of how bacterioplankton and sedimentary bacteria communities respond to global warming across multiple seasons, shedding light on the complex dynamics of microbial ecosystems in lakes. Full article
(This article belongs to the Special Issue Microbes in Communities—Geobiological Processes, Symbioses, Applications 2.0)
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12 pages, 1281 KiB  
Article
Real-Time and Rapid Respiratory Response of the Soil Microbiome to Moisture Shifts
by Montana L. Smith, Karl K. Weitz, Allison M. Thompson, Janet K. Jansson, Kirsten S. Hofmockel and Mary S. Lipton
Microorganisms 2023, 11(11), 2630; https://doi.org/10.3390/microorganisms11112630 - 26 Oct 2023
Viewed by 872
Abstract
Microbial response to changing environmental factors influences the fate of soil organic carbon, and drought has been shown to affect microbial metabolism and respiration. We hypothesized that the access of microbes to different carbon pools in response to dry–rewet events occurs sequentially at [...] Read more.
Microbial response to changing environmental factors influences the fate of soil organic carbon, and drought has been shown to affect microbial metabolism and respiration. We hypothesized that the access of microbes to different carbon pools in response to dry–rewet events occurs sequentially at different rates. We amended desiccated soils with 13C-labeled glucose and measured the rates of 12CO2 and 13CO2 respiration in real time after rewetting. Using these differentiated 12CO2 and 13CO2 respiration rate soils after rewetting, we were able to deduce when microbes are accessing different pools of carbon. Immediately upon rewetting, respiration of 12CO2 occurred first, with negligible 13CO2 respiration. Appreciable metabolism and respiration of the added 13C glucose did not occur until 15 min after rewetting. We conclude that, while all carbon pools are being accessed in the first 9 h after rewetting, the rate and timing at which new and existing carbon pools are being accessed varies. Within this study, using stable isotope-labeled substrates to discern which carbon pools are metabolized first uniquely illustrates how microorganisms access different carbon pools which has implications into understanding how carbon metabolism can further affect climate, carbon sequestration, and soil health. Full article
(This article belongs to the Special Issue Microbes in Communities—Geobiological Processes, Symbioses, Applications 2.0)
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22 pages, 2306 KiB  
Article
Large-Scale Integration of Amplicon Data Reveals Massive Diversity within Saprospirales, Mostly Originating from Saline Environments
by Rafaila Nikola Mourgela, Antonios Kioukis, Mohsen Pourjam and Ilias Lagkouvardos
Microorganisms 2023, 11(7), 1767; https://doi.org/10.3390/microorganisms11071767 - 6 Jul 2023
Viewed by 1252
Abstract
The order Saprospirales, a group of bacteria involved in complex degradation pathways, comprises three officially described families: Saprospiraceae, Lewinellaceae, and Haliscomenobacteraceae. These collectively contain 17 genera and 31 species. The current knowledge on Saprospirales diversity is the product of [...] Read more.
The order Saprospirales, a group of bacteria involved in complex degradation pathways, comprises three officially described families: Saprospiraceae, Lewinellaceae, and Haliscomenobacteraceae. These collectively contain 17 genera and 31 species. The current knowledge on Saprospirales diversity is the product of traditional isolation methods, with the inherited limitations of culture-based approaches. This study utilized the extensive information available in public sequence repositories combined with recent analytical tools to evaluate the global evidence-based diversity of the Saprospirales order. Our analysis resulted in 1183 novel molecular families, 15,033 novel molecular genera, and 188 K novel molecular species. Of those, 7 novel families, 464 novel genera, and 1565 species appeared in abundances at ≥0.1%. Saprospirales were detected in various environments, such as saline water, freshwater, soil, various hosts, wastewater treatment plants, and other bioreactors. Overall, saline water was the environment showing the highest prevalence of Saprospirales, with bioreactors and wastewater treatment plants being the environments where they occurred with the highest abundance. Lewinellaceae was the family containing the majority of the most prevalent species detected, while Saprospiraceae was the family with the majority of the most abundant species found. This analysis should prime researchers to further explore, in a more targeted way, the Saprospirales proportion of microbial dark matter. Full article
(This article belongs to the Special Issue Microbes in Communities—Geobiological Processes, Symbioses, Applications 2.0)
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17 pages, 3624 KiB  
Article
A Morphometric Approach to Understand Prokaryoplankton: A Study in the Sicily Channel (Central Mediterranean Sea)
by Giovanna Maimone, Maurizio Azzaro, Francesco Placenti, Rodolfo Paranhos, Anderson Sousa Cabral, Franco Decembrini, Renata Zaccone, Alessandro Cosenza, Alessandro Ciro Rappazzo, Bernardo Patti, Gualtiero Basilone, Angela Cuttitta, Rosalia Ferreri, Salvatore Aronica and Rosabruna La Ferla
Microorganisms 2023, 11(4), 1019; https://doi.org/10.3390/microorganisms11041019 - 13 Apr 2023
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Abstract
A new understanding of plankton ecology has been obtained by studying the phenotypic traits of free-living prokaryotes in the Sicily Channel (Central Mediterranean Sea), an area characterised by oligotrophic conditions. During three cruises carried out in July 2012, January 2013 and July 2013, [...] Read more.
A new understanding of plankton ecology has been obtained by studying the phenotypic traits of free-living prokaryotes in the Sicily Channel (Central Mediterranean Sea), an area characterised by oligotrophic conditions. During three cruises carried out in July 2012, January 2013 and July 2013, the volume and morphology of prokaryotic cells were assessed microscopically using image analysis in relation to environmental conditions. The study found significant differences in cell morphologies among cruises. The largest cell volumes were observed in the July 2012 cruise (0.170 ± 0.156 µm3), and the smallest in the January 2013 cruise (0.060 ± 0.052 µm3). Cell volume was negatively limited by nutrients and positively by salinity. Seven cellular morphotypes were observed among which cocci, rods and coccobacilli were the most abundant. Cocci, although they prevailed numerically, always showed the smallest volumes. Elongated shapes were positively related to temperature. Relationships between cell morphologies and environmental drivers indicated a bottom-up control of the prokaryotic community. The morphology/morphometry-based approach is a useful tool for studying the prokaryotic community in microbial ecology and should be widely applied to marine microbial populations in nature. Full article
(This article belongs to the Special Issue Microbes in Communities—Geobiological Processes, Symbioses, Applications 2.0)
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17 pages, 3145 KiB  
Article
Neotropical Frog Foam Nest’s Microbiomes
by Felipe Augusto Correia Monteiro, Saulo Gonçalves de Santiago Bezerra, Luzia Gabrielle Zeferino de Castro, Francisca Andrea da Silva Oliveira, Leonardo Ribeiro Oliveira Normando, Vânia Maria Maciel Melo and Denise Cavalcante Hissa
Microorganisms 2023, 11(4), 900; https://doi.org/10.3390/microorganisms11040900 - 30 Mar 2023
Viewed by 1989
Abstract
Amphibian foam nests are unique microenvironments that play a crucial role in the development of tadpoles. They contain high levels of proteins and carbohydrates, yet little is known about the impact of their microbiomes on tadpole health. This study provides a first characterization [...] Read more.
Amphibian foam nests are unique microenvironments that play a crucial role in the development of tadpoles. They contain high levels of proteins and carbohydrates, yet little is known about the impact of their microbiomes on tadpole health. This study provides a first characterization of the microbiome of foam nests from three species of Leptodactylids (Adenomera hylaedactyla, Leptodactylus vastus, and Physalaemus cuvieri) by investigating the DNA extracted from foam nests, adult tissues, soil, and water samples, analyzed via 16S rRNA gene amplicon sequencing to gain insight into the factors driving its composition. The results showed that the dominant phyla were proteobacteria, bacteroidetes, and firmicutes, with the most abundant genera being Pseudomonas, Sphingobacterium, and Paenibacillus. The foam nest microbiomes of A. hylaedactyla and P. cuvieri were more similar to each other than to that of L. vastus, despite their phylogenetic distance. The foam nests demonstrated a distinct microbiome that clustered together and separated from the microbiomes of the environment and adult tissue samples. This suggests that the peculiar foam nest composition shapes its microbiome, rather than vertical or horizontal transference forces. We expanded this knowledge into amphibian foam nest microbiomes, highlighting the importance of preserving healthy foam nests for amphibian conservation. Full article
(This article belongs to the Special Issue Microbes in Communities—Geobiological Processes, Symbioses, Applications 2.0)
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