Special Issue "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: 31 December 2021.

Special Issue Editor

Prof. Dr. Eiko Kuramae
E-Mail Website
Guest Editor
Department of Microbial Ecology – Netherlands Institute of Ecology (NIOO-KNAW) Wageningen; Ecology and Biodiversity Group, Utrecht University, 3508 TB Utrecht, The Netherlands
Interests: environmental genomics; soil microbial community ecology; N and C cycle interactions; soil–plant–microbe interactions; greenhouse gas mitigation
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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

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Keywords

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

Published Papers (3 papers)

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Research

Article
The Impact of the Inoculation of Phosphate-Solubilizing Bacteria Pantoea agglomerans on Phosphorus Availability and Bacterial Community Dynamics of a Semi-Arid Soil
Microorganisms 2021, 9(8), 1661; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9081661 - 04 Aug 2021
Viewed by 664
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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Article
Seasonal Variations in Soil Microbiota Profile of Termite (Syntermes wheeleri) Mounds in the Brazilian Tropical Savanna
Microorganisms 2020, 8(10), 1482; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms8101482 - 27 Sep 2020
Cited by 1 | Viewed by 886
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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Article
Response of Barley Plants to Drought Might Be Associated with the Recruiting of Soil-Borne Endophytes
Microorganisms 2020, 8(9), 1414; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms8091414 - 14 Sep 2020
Cited by 1 | Viewed by 1311
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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