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Microorganisms
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Soil Microbiome: Biotic and Abiotic Interactions
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Soil Microbiome: Biotic and Abiotic Interactions

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

Deadline for manuscript submissions: closed (31 December 2021) | Viewed by 18278

Special Issue Editor

Prof. Dr. Eiko Kuramae

E-Mail Website
Guest Editor
1. Department of Microbial Ecology, Netherlands Institute of Ecology, 6708 PB Wageningen, The Netherlands
2. Ecology and Biodiversity, Institute of Environmental Biology, Utrecht University, 3584 CS Utrecht, The Netherlands
Interests: environmental genomics; soil microbial community ecology; N and C cycle interactions; soil–plant–microbe interactions; greenhouse gas mitigation
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Soil-borne microorganisms are an essential component of terrestrial ecosystems and key to many vital ecosystem functions. Abiotic and biotic interactions drive the activity of soil-borne microorganisms and shape their community structure and functionality. This implies an understanding of the relationships between genetic diversity and community structure, and between community structure and function and abiotic factors.

With this Special Issue of Microorganisms, we aim to present the state of the art and future directions in understanding the mechanisms underlying microbe–microbe and microbe–abiotic interactions in soil ecosystems. We kindly invite you to contribute with either original research articles or reviews covering new experimental and environmental (meta)omics approaches to identifying and quantifying the factors that determine community assembly, microbial metabolic roles within a soil community, microbe–microbe interactions, microbial community interactions (physiological, biochemical, genetic), and natural patterns of microbial distributions. We aim to cover a wide range of descriptive and experimental studies on soil microbiomes using classical and novel techniques.

Prof. Dr. Eiko Kuramae
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

  • metagenomics
  • metaproteomics
  • metabolomics
  • metatranscriptomics
  • environmental factors
  • soil aggregates
  • metabolic networks
  • context-dependent interactions
  • bioinformatics
  • modeling
  • facilitation/competition/resilience

Published Papers (6 papers)

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Research

16 pages, 2412 KiB  
Article
Structural and Metabolic Profiling of Lycopersicon esculentum Rhizosphere Microbiota Artificially Exposed at Commonly Used Non-Steroidal Anti-Inflammatory Drugs
by Emoke Dalma Kovacs, Luminita Silaghi-Dumitrescu, Cecilia Roman and Di Tian
Microorganisms 2022, 10(2), 254; https://doi.org/10.3390/microorganisms10020254 - 24 Jan 2022
Cited by 3 | Viewed by 2184
Abstract
In this study, the effect of common non-steroidal anti-inflammatory drugs on Lycopersicon esculentum rhizosphere microbiota was monitored. The experiments were performed with artificially contaminated soil with ibuprofen (0.5 mg·kg−1), ketoprofen (0.2 mg·kg−1) and diclofenac (0.7 mg·kg−1). The [...] Read more.
In this study, the effect of common non-steroidal anti-inflammatory drugs on Lycopersicon esculentum rhizosphere microbiota was monitored. The experiments were performed with artificially contaminated soil with ibuprofen (0.5 mg·kg−1), ketoprofen (0.2 mg·kg−1) and diclofenac (0.7 mg·kg−1). The results evidenced that the rhizosphere microbiota abundance decreased especially under exposure to diclofenac (187–201 nmol·g−1 dry weight soil) and ibuprofen (166–183 nmol·g−1 dry weight soil) if compared with control (185–240 nmol·g−1 dry weight soil), while the fungal/bacteria ratio changed significantly with exposure to diclofenac (<27%) and ketoprofen (<18%). Compared with control samples, the average amount of the ratio of Gram-negative/Gram-positive bacteria was higher in rhizosphere soil contaminated with ibuprofen (>25%) and lower in the case of diclofenac (<46%) contamination. Carbon source consumption increased with the time of assay in case of the control samples (23%) and those contaminated with diclofenac (8%). This suggests that rhizosphere microbiota under contamination with diclofenac consume a higher amount of carbon, but they do not consume a larger variety of its sources. In the case of contamination with ibuprofen and ketoprofen, the consumption of carbon source presents a decreasing tendency after day 30 of the assay. Rhizosphere microbiota emitting volatile organic compounds were also monitored. Volatile compounds belonging to alcohol, aromatic compounds, ketone, terpene, organic acids, aldehyde, sulphur compounds, esters, alkane, nitrogen compounds, alkene and furans were detected in rhizosphere soil samples. Among these, terpene, ketone, alcohol, aromatic compounds, organic acids and alkane were the most abundant compound classes (>75%), but their percentage changed with exposure to diclofenac, ketoprofen and ibuprofen. Such changes in abundance, structure and the metabolic activity of Lycopersicon esculentum rhizosphere microbiota under exposure to common non-steroidal anti-inflammatory drugs suggest that there is a probability to also change the ecosystem services provided by rhizosphere microbiota. Full article
(This article belongs to the Special Issue Soil Microbiome: Biotic and Abiotic Interactions)
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17 pages, 1801 KiB  
Article
Highly Distinct Microbial Communities in Elevated Strings and Submerged Flarks in the Boreal Aapa-Type Mire
by Andrey L. Rakitin, Shahjahon Begmatov, Alexey V. Beletsky, Dmitriy A. Philippov, Vitaly V. Kadnikov, Andrey V. Mardanov, Svetlana N. Dedysh and Nikolai V. Ravin
Microorganisms 2022, 10(1), 170; https://doi.org/10.3390/microorganisms10010170 - 13 Jan 2022
Cited by 3 | Viewed by 2305
Abstract
Large areas in the northern hemisphere are covered by extensive wetlands, which represent a complex mosaic of raised bogs, eutrophic fens, and aapa mires all in proximity to each other. Aapa mires differ from other types of wetlands by their concave surface, heavily [...] Read more.
Large areas in the northern hemisphere are covered by extensive wetlands, which represent a complex mosaic of raised bogs, eutrophic fens, and aapa mires all in proximity to each other. Aapa mires differ from other types of wetlands by their concave surface, heavily watered by the central part, as well as by the presence of large-patterned string-flark complexes. In this paper, we characterized microbial diversity patterns in the surface peat layers of the neighboring string and flark structures located within the mire site in the Vologda region of European North Russia, using 16S rRNA gene sequencing. The microbial communities in raised strings were clearly distinct from those in submerged flarks. Strings were dominated by the Alpha- and Gammaproteobacteria. Other abundant groups were the Acidobacteriota, Bacteroidota, Verrucomicrobiota, Actinobacteriota, and Planctomycetota. Archaea accounted for only 0.4% of 16S rRNA gene sequences retrieved from strings. By contrast, they comprised about 22% of all sequences in submerged flarks and mostly belonged to methanogenic lineages. Methanotrophs were nearly absent. Other flark-specific microorganisms included the phyla Chloroflexi, Spirochaetota, Desulfobacterota, Beijerinckiaceae- and Rhodomicrobiaceae-affiliated Alphaproteobacteria, and uncultivated groups env.OPS_17 and vadinHA17 of the Bacteroidota. Such pattern probably reflects local anaerobic conditions in the submerged peat layers in flarks. Full article
(This article belongs to the Special Issue Soil Microbiome: Biotic and Abiotic Interactions)
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13 pages, 2067 KiB  
Article
Peat-Inhabiting Verrucomicrobia of the Order Methylacidiphilales Do Not Possess Methanotrophic Capabilities
by Svetlana N. Dedysh, Alexey V. Beletsky, Anastasia A. Ivanova, Olga V. Danilova, Shahjahon Begmatov, Irina S. Kulichevskaya, Andrey V. Mardanov and Nikolai V. Ravin
Microorganisms 2021, 9(12), 2566; https://doi.org/10.3390/microorganisms9122566 - 11 Dec 2021
Cited by 9 | Viewed by 2677
Abstract
Methanotrophic verrucomicrobia of the order Methylacidiphilales are known as extremely acidophilic, thermophilic or mesophilic bacteria that inhabit acidic geothermal ecosystems. The occurrence of verrucomicrobial methanotrophs in other types of acidic environments remains an open question. Notably, Methylacidiphilales-affiliated 16S rRNA gene sequences are [...] Read more.
Methanotrophic verrucomicrobia of the order Methylacidiphilales are known as extremely acidophilic, thermophilic or mesophilic bacteria that inhabit acidic geothermal ecosystems. The occurrence of verrucomicrobial methanotrophs in other types of acidic environments remains an open question. Notably, Methylacidiphilales-affiliated 16S rRNA gene sequences are commonly retrieved from acidic (pH 3.5–5.5) peatlands. In this study, we compared the patterns of verrucomicrobial diversity in four acidic raised bogs and six neutral fens located in European North Russia. Methylacidiphilales-like 16S rRNA gene reads displaying 83–86% similarity to 16S rRNA gene sequences of currently described verrucomicrobial methanotrophs were recovered exclusively from raised bogs. Laboratory incubation of peat samples with 10% methane for 3 weeks resulted in the pronounced increase of a relative abundance of alphaproteobacterial methanotrophs, while no response was detected for Methylacidiphilales-affiliated bacteria. Three metagenome-assembled genomes (MAGs) of peat-inhabiting Methylacidiphilales bacteria were reconstructed and examined for the presence of genes encoding methane monooxygenase enzymes and autotrophic carbon fixation pathways. None of these genomic determinants were detected in assembled MAGs. Metabolic reconstructions predicted a heterotrophic metabolism, with a potential to hydrolyze several plant-derived polysaccharides. As suggested by our analysis, peat-inhabiting representatives of the Methylacidiphilales are acidophilic aerobic heterotrophs, which comprise a sister family of the methanotrophic Methylacidiphilaceae. Full article
(This article belongs to the Special Issue Soil Microbiome: Biotic and Abiotic Interactions)
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19 pages, 2512 KiB  
Article
The Impact of the Inoculation of Phosphate-Solubilizing Bacteria Pantoea agglomerans on Phosphorus Availability and Bacterial Community Dynamics of a Semi-Arid Soil
by Ilhem Saadouli, Amor Mosbah, Raoudha Ferjani, Panagiota Stathopoulou, Ioannis Galiatsatos, Elias Asimakis, Ramona Marasco, Daniele Daffonchio, George Tsiamis and Hadda-Imene Ouzari
Microorganisms 2021, 9(8), 1661; https://doi.org/10.3390/microorganisms9081661 - 04 Aug 2021
Cited by 16 | Viewed by 3072
Abstract
The bacterial genus Pantoea has been widely evaluated as promising bacteria to increase phosphorus (P) availability in soil. The aim of this study was to characterize the phosphate solubilizing (PS) activity of a Pantoea agglomerans strain and to evaluate the impact of its [...] Read more.
The bacterial genus Pantoea has been widely evaluated as promising bacteria to increase phosphorus (P) availability in soil. The aim of this study was to characterize the phosphate solubilizing (PS) activity of a Pantoea agglomerans strain and to evaluate the impact of its application in a semi-arid soil on phosphate availability and structure of the bacterial communities as a whole. An incubation experiment under close-to-natural soil environmental conditions was conducted for 15 days at 30 °C. High-throughput sequencing of the bacterial 16S rRNA gene was used to characterize and to compare the bacterial community structure of P. agglomerans-inoculated soil with non-inoculated control. Furthermore, a qPCR-based method was developed for detection and quantification of the functional genes related to the expression of mineral phosphate solubilization (MPS) phenotype in P. agglomerans. The results showed that in vitro solubilization of Ca3(PO4)2 by P. agglomerans strain was very efficient (980 mg/L), and it was associated with a drop in pH due to the secretion of gluconic acid; these changes were concomitant with the detection of gdh and pqqC genes. Moreover, P. agglomerans inoculum application significantly increased the content of available P in semi-arid soil by 69%. Metagenomic analyses showed that P. agglomerans treatment modified the overall edaphic bacterial community, significantly impacting its structure and composition. In particular, during P. agglomerans inoculation the relative abundance of bacteria belonging to Firmicutes (mainly Bacilli class) significantly increased, whereas the abundance of Actinobacteria together with Acidobacteria and Chloroflexi phyla decreased. Furthermore, genera known for their phosphate solubilizing activity, such as Aneurinibacillus, Lysinibacillus, Enterococcus, and Pontibacter, were exclusively detected in P. agglomerans-treated soil. Pearson’s correlation analysis revealed that changes in soil bacterial community composition were closely affected by soil characteristics, such as pH and available P. This study explores the effect of the inoculation of P. agglomerans on the bacterial community structure of a semi-arid soil. The effectiveness in improving the phosphate availability and modification in soil bacterial community suggested that P. agglomerans represent a promising environmental-friendly biofertilizer in arid and semi-arid ecosystems. Full article
(This article belongs to the Special Issue Soil Microbiome: Biotic and Abiotic Interactions)
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14 pages, 5095 KiB  
Article
Seasonal Variations in Soil Microbiota Profile of Termite (Syntermes wheeleri) Mounds in the Brazilian Tropical Savanna
by Helena Ipe Pinheiro Guimaraes, Renata Henrique Santana, Rafaella Silveira, Otavio Henrique Bezerra Pinto, Betania Ferraz Quirino, Cristine Chaves Barreto, Mercedes Maria da Cunha Bustamante and Ricardo Henrique Krüger
Microorganisms 2020, 8(10), 1482; https://doi.org/10.3390/microorganisms8101482 - 27 Sep 2020
Cited by 9 | Viewed by 2347
Abstract
Eusocial animals, such as the termites, often build a nest-like structure called a mound that provides shelter with stable internal conditions and protection against predators. Termites are important components of the Brazilian Cerrado biota. This study aimed to investigate the bacterial community composition [...] Read more.
Eusocial animals, such as the termites, often build a nest-like structure called a mound that provides shelter with stable internal conditions and protection against predators. Termites are important components of the Brazilian Cerrado biota. This study aimed to investigate the bacterial community composition and diversity of the Syntermes wheeleri termite-mound soil using culture-independent approaches. We considered the vertical profile by comparing two different mound depths (mound surface and 60 cm) and seasonality with samplings during the rainy and dry seasons. We compared the mound soil microbiota to the adjacent soil without the influence of the mound to test the hypothesis that the Cerrado soil bacterial community was more diverse and more susceptible to seasonality than the mound soil microbiota. The results support the hypothesis that the Cerrado soil bacterial community is more diverse than the mound soil and also has a higher variability among seasons. The number of observed OTUs (Operational Taxonomic Units) was used to express bacterial richness, and it indicates that soil moisture has an effect on the community distribution and richness of the Cerrado samples in comparison to mound samples, which remain stable across seasons. This could be a consequence of the protective role of the mound for the termite colony. The overall community taxonomic profile was similar between soil samples, especially when compared to the taxonomic composition of the Syntermes wheeleri termite’s gut, which might be explained by the different characteristics and functionality between the soil and the gut microbial community. Full article
(This article belongs to the Special Issue Soil Microbiome: Biotic and Abiotic Interactions)
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18 pages, 5653 KiB  
Article
Response of Barley Plants to Drought Might Be Associated with the Recruiting of Soil-Borne Endophytes
by Luhua Yang, Peter Schröder, Gisle Vestergaard, Michael Schloter and Viviane Radl
Microorganisms 2020, 8(9), 1414; https://doi.org/10.3390/microorganisms8091414 - 14 Sep 2020
Cited by 11 | Viewed by 3874
Abstract
Mechanisms used by plants to respond to water limitation have been extensively studied. However, even though the inoculation of beneficial microbes has been shown to improve plant performance under drought stress, the inherent role of soil microbes on plant response has been less [...] Read more.
Mechanisms used by plants to respond to water limitation have been extensively studied. However, even though the inoculation of beneficial microbes has been shown to improve plant performance under drought stress, the inherent role of soil microbes on plant response has been less considered. In the present work, we assessed the importance of the soil microbiome for the growth of barley plants under drought stress. Plant growth was not significantly affected by the disturbance of the soil microbiome under regular watering. However, after drought stress, we observed a significant reduction in plant biomass, particularly of the root system. Plants grown in the soil with disturbed microbiome were significantly more affected by drought and did not recover two weeks after re-watering. These effects were accompanied by changes in the composition of endophytic fungal and bacterial communities. Under natural conditions, soil-derived plant endophytes were major colonizers of plant roots, such as Glycomyces and Fusarium, whereas, for plants grown in the soil with disturbed microbiome seed-born bacterial endophytes, e.g., Pantoea, Erwinia, and unclassified Pseudomonaceae and fungal genera normally associated with pathogenesis, such as Gibberella and Gaeumannomyces were observed. Therefore, the role of the composition of the indigenous soil microbiota should be considered in future approaches to develop management strategies to make plants more resistant towards abiotic stress, such as drought. Full article
(This article belongs to the Special Issue Soil Microbiome: Biotic and Abiotic Interactions)
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