Microbial Communities in a Changing World: Composition, Metabolism, and Environmental Adaptation

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

Deadline for manuscript submissions: closed (28 February 2023) | Viewed by 10440

Special Issue Editor

LIMES Institute and West German Genome Center, University of Bonn, Bonn, Germany
Interests: microbial communities; computational models; genomics; metabolic modelling; microbiome; bioinformatics; data science
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

We as humans are facing grand societal challenges on many fronts today: climate change, food insecurity, pandemic outbreaks. The importance of microbial communities in a continuously changing world cannot be overstated: they are key players for safeguarding and restoring the health of the environment or of their host. Before we can fully exploit their potential, however, some fundamental aspects still need to be better understood. What are the mechanisms driving community assembly and resilience? What metabolic capability can a community achieve, and how does it occupy different metabolic niches? How does a community react and adapt to temporary or permanent changes in the surrounding environment?

This Special Issue aims at providing a cross-disciplinary overview of current knowledge and methods for microbiome research, collecting work targeting a better understanding of how microbial communities can help to address grand societal challenges (for example, sustainable agriculture or antibiotic resistance).

As the Guest Editor of this Special Issue, I invite you to submit research articles, review articles, and short communications related to the aforementioned challenges. Bottom-up or top-down approaches, exploratory or hypothesis-driven analyses are equally welcome, and interdisciplinary work combining experimental and computational methods is particularly appreciated.

Dr. Antonella Succurro
Guest Editor

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Keywords

  • Microbial Communities
  • Microbial Symbiosis
  • Microbiome-Host Interactions
  • Environmental Adaptation
  • Climate Change
  • Sustainable Agriculture
  • Antibiotic Resistance
  • Bioeconomy
  • Synthetic Communities

Published Papers (5 papers)

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Research

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18 pages, 6631 KiB  
Article
Diversity of Microbial Communities, PAHs, and Metals in Road and Leaf Dust of Functional Zones of Moscow and Murmansk
by Anna A. Vetrova, Olesya I. Sazonova, Anastasia A. Ivanova, Rostislav A. Streletskii, Dmitriy A. Sarzhanov, Maria V. Korneykova, Andrey I. Novikov, Viacheslav I. Vasenev, Kristina V. Ivashchenko, Marina V. Slukovskaya and Olga Gavrichkova
Microorganisms 2023, 11(2), 526; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms11020526 - 18 Feb 2023
Cited by 1 | Viewed by 1609
Abstract
The impact of geographical factors, functional zoning, and biotope type on the diversity of microbial communities and chemical components in the dust of urban ecosystems was studied. Comprehensive analyses of bacterial and fungal communities, polycyclic aromatic hydrocarbons (PAHs), and metals in road and [...] Read more.
The impact of geographical factors, functional zoning, and biotope type on the diversity of microbial communities and chemical components in the dust of urban ecosystems was studied. Comprehensive analyses of bacterial and fungal communities, polycyclic aromatic hydrocarbons (PAHs), and metals in road and leaf dust in three urban zones of Murmansk and Moscow with contrasting anthropogenic load were conducted. We found that the structure of bacterial communities affected the functional zoning of the city, biotope type, and geographical components. Fungal communities were instead impacted only by biotope type. Our findings revealed that the structure of fungal communities was mostly impacted by PAHs whereas bacterial communities were sensitive to metals. Bacteria of the genus Sphingomonas in road and leaf dust as indicators of the ecological state of the urban ecosystems were proposed. Full article
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11 pages, 7607 KiB  
Article
Fungus under a Changing Climate: Modeling the Current and Future Global Distribution of Fusarium oxysporum Using Geographical Information System Data
by Dalal Hussien M. Alkhalifah, Eman Damra, Moaz Beni Melhem and Wael N. Hozzein
Microorganisms 2023, 11(2), 468; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms11020468 - 13 Feb 2023
Cited by 10 | Viewed by 2114
Abstract
The impact of climate change on biodiversity has been the subject of numerous research in recent years. The multiple elements of climate change are expected to affect all levels of biodiversity, including microorganisms. The common worldwide fungus Fusarium oxysporum colonizes plant roots as [...] Read more.
The impact of climate change on biodiversity has been the subject of numerous research in recent years. The multiple elements of climate change are expected to affect all levels of biodiversity, including microorganisms. The common worldwide fungus Fusarium oxysporum colonizes plant roots as well as soil and several other substrates. It causes predominant vascular wilt disease in different strategic crops such as banana, tomato, palm, and even cotton, thereby leading to severe losses. So, a robust maximum entropy algorithm was implemented in the well-known modeling program Maxent to forecast the current and future global distribution of F. oxysporum under two representative concentration pathways (RCPs 2.6 and 8.5) for 2050 and 2070. The Maxent model was calibrated using 1885 occurrence points. The resulting models were fit with AUC and TSS values equal to 0.9 (±0.001) and 0.7, respectively. Increasing temperatures due to global warming caused differences in habitat suitability between the current and future distributions of F. oxysporum, especially in Europe. The most effective parameter of this fungus distribution was the annual mean temperature (Bio 1); the two-dimensional niche analysis indicated that the fungus has a wide precipitation range because it can live in both dry and rainy habitats as well as a range of temperatures in which it can live to certain limits. The predicted shifts should act as an alarm sign for decision makers, particularly in countries that depend on such staple crops harmed by the fungus. Full article
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19 pages, 3900 KiB  
Article
Response of Soil Bacterial Diversity, Predicted Functions and Co-Occurrence Patterns to Nanoceria and Ionic Cerium Exposure
by Jie Zhang, Hui-Sheng Meng, Yan-Meng Shang, Jamie R. Lead, Zhang-Zhen Guo and Jian-Ping Hong
Microorganisms 2022, 10(10), 1982; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10101982 - 06 Oct 2022
Cited by 1 | Viewed by 1389
Abstract
Release of nanoceria (nCeO2) into the environment has caused much concern about its potential toxicity, which still remains poorly understood for soil microorganisms. In this study, nanoceria and cerium (III) nitrate at different doses (10, 100 and 500 mg/kg) were applied [...] Read more.
Release of nanoceria (nCeO2) into the environment has caused much concern about its potential toxicity, which still remains poorly understood for soil microorganisms. In this study, nanoceria and cerium (III) nitrate at different doses (10, 100 and 500 mg/kg) were applied to bok choy (Brassica rapa subsp. chinensis), grown in potting soil, to investigate the responses of soil bacterial communities to nanoceria (NC) and ionic cerium (IC) applications. The results showed that bacterial richness was slightly increased in all cerium treatments relative to the negative control without cerium amendment (CK), but a significant increase was only found in IC500. The patterns of bacterial community composition, predicted functions and phenotypes of all NC treatments were significantly differentiated from IC and CK treatments, which was correlated with the contents of cerium, available potassium and phosphorus in soil. The co-occurrence network of bacterial taxa was more complex after exposure to ionic cerium than to nanoceria. The keystone taxa of the two networks were entirely different. Predicted functions analysis found that anaerobic and Gram-negative bacteria were enriched under nanoceria exposure. Our study implies that Proteobacteria and nitrifying bacteria were significantly enriched after exposure to nanoceria and could be potential biomarkers of soil environmental perturbation from nanoceria exposure. Full article
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13 pages, 1385 KiB  
Article
Effect of AM Fungi Inoculation on Litter Bacterial Community Characteristics under Heavy Metal Stress
by Tong Jia, Yu Wang, Xiaoxia Liang and Tingyan Guo
Microorganisms 2022, 10(2), 206; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10020206 - 19 Jan 2022
Cited by 7 | Viewed by 1617
Abstract
Because microorganisms are the primary driving force behind litter decomposition, they play an important role in maintaining ecosystem material and chemical cycling. Arbuscular mycorrhizal (AM) fungi can improve host plant tolerance to various environmental stressors, making their application in mining area remediation important. [...] Read more.
Because microorganisms are the primary driving force behind litter decomposition, they play an important role in maintaining ecosystem material and chemical cycling. Arbuscular mycorrhizal (AM) fungi can improve host plant tolerance to various environmental stressors, making their application in mining area remediation important. In this study, litter from the dominant plant species (Imperata cylindrica) in a copper tailings mining area was selected as the experimental material. We conducted a greenhouse-based heavy metal stress experiment to investigate how AM fungi affect litter microbial community characteristics and key ecological factors. Results showed that AM fungi species, heavy metal treatments, and their combined interaction had significant impacts on litter pH. Additionally, enzyme activities in litter were significantly affected by interactions between AM fungi species and heavy metal contaminates. Ralstonia was significantly positively correlated to lead (Pb) content, indicating that Ralstonia had a certain tolerance to Pb pollution. Sucrase and urease activity were increased when plants were inoculated with Rhizophagus irregularis under Pb stress. Furthermore, Microbacterium, Brevundimonas, and Pseudonocardia all may play important roles in litter decomposition, while a certain tolerance was observed in Kushneria and Roseivivax to heavy metal pollution when plants were inoculated with Glomus mosseae. Results showed that AM fungi affected litter bacterial community structure and function by influencing plant litter properties. By exploring interactions between AM fungi and bacterial communities in plant litter under heavy metal stress, we will better understand associative processes that promote the cycling of soil organic matter and nutrients contaminated by non-ferrous metal tailings. Full article
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11 pages, 1099 KiB  
Brief Report
Chemical and Microbial Characterization of Fermented Forest Litters Used as Biofertilizers
by Johann Marois, Thomas Z. Lerch, Ugo Dunant, Anne-Marie Farnet Da Silva and Pierre Christen
Microorganisms 2023, 11(2), 306; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms11020306 - 24 Jan 2023
Cited by 2 | Viewed by 1471
Abstract
The excessive use of chemicals in intensive agriculture has had a negative impact on soil diversity and fertility. A strategy for developing sustainable agriculture could rely on the use of microbial-based fertilizers, known as biofertilizers. An alternative to marketed products could be offered [...] Read more.
The excessive use of chemicals in intensive agriculture has had a negative impact on soil diversity and fertility. A strategy for developing sustainable agriculture could rely on the use of microbial-based fertilizers, known as biofertilizers. An alternative to marketed products could be offered to small farmers if they could produce their own biofertilizers using forest litters, which harbor one of the highest microbial diversities. The aim of this study is to characterize microbial communities of Fermented Forest Litters (FFL), assuming that the fermentation process will change both their abundance and diversity. We investigated two types of differing in the chemical composition of the initial litters used and the climatic context of the forest where they are originated from. The abundance and diversity of bacterial and fungal communities were assessed using quantitative PCR and molecular genotyping techniques. The litter chemical compositions were compared before and after fermentation using Infrared spectrometry. Results obtained showed that fermentation increased the abundance of bacteria but decreased that of fungi. Low pH and change in organic matter composition observed after fermentation also significantly reduced the α-diversity of both bacterial and fungal communities. The higher proportion of aliphatic molecules and lower C/N of the FFLs compared to initial litters indicate that FFLs should be rapidly decomposed once added into the soil. This preliminary study suggests that the agronomic interest of FFLs used as biofertilizers is probably more related to the contribution of nutrients easily assimilated by plants than to the diversity of microorganisms that compose it. Further studies must be conducted with sequencing techniques to identify precisely the microbial species likely to be beneficial to plant growth. Full article
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