Special Issue "Advances in Soil Microbiome"

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

Deadline for manuscript submissions: 31 March 2022.

Special Issue Editors

Dr. Ryan McClure
E-Mail Website
Guest Editor
Pacific Northwest National Laboratory, P.O. Box 999, MSIN: J4-18, Richland, WA 99352, USA
Interests: microbiology
Dr. Emily B. Graham
E-Mail Website
Guest Editor
1. Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, P.O. Box 999, Richland, WA 99352, USA
2. School of Biological Sciences, Washington State University, 2710 Crimson Way, Richland, WA 99354, USA
Interests: environmental science; microbial ecology; biogeochemistry; metabolomics; wildfire science
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The soil microbiome plays a critical role in cycling carbon in the ecosystem, and in promoting plant health. However, the complexity of the microbiome makes analysis of the involved communities, molecular processes, and emergent phenotypes difficult. This difficulty is compounded by the fact that while our analytical tools can be applied at the molecular scale in the laboratory, this is often not possible in natural soil, requiring either the use of nonsoil environments or the analysis of soil samples at a scale that is much greater than that of microbial interactions. In order to bridge these gaps, new tools are required that can mimic soil in the laboratory, as are new techniques to query soil directly and new modeling tools to apply what we learn in the laboratory to the field. The application of these new approaches will lead to novel insights into how interactions within soil communities and between species scale up to the emergent metaphenome of the soil. This Special Issue will cover some of the latest advances in both analytical and modeling techniques applied to the soil microbiome as well as new conclusions gained from these approaches that lead to a deeper understanding of how the soil microbiome drives plant health and carbon cycling in the ecosystem.

Dr. Ryan McClure
Dr. Emily B. Graham
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 papers will be 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 2200 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

  • soil
  • microbiology
  • rhizosphere
  • plant microbe
  • metaphenome

Published Papers (2 papers)

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Research

Article
Water Level Has Higher Influence on Soil Organic Carbon and Microbial Community in Poyang Lake Wetland Than Vegetation Type
Microorganisms 2022, 10(1), 131; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10010131 - 09 Jan 2022
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Abstract
Although microorganisms play a key role in the carbon cycle of the Poyang Lake wetland, the relationship between soil microbial community structure and organic carbon characteristics is unknown. Herein, high-throughput sequencing technology was used to explore the effects of water level (low and [...] Read more.
Although microorganisms play a key role in the carbon cycle of the Poyang Lake wetland, the relationship between soil microbial community structure and organic carbon characteristics is unknown. Herein, high-throughput sequencing technology was used to explore the effects of water level (low and high levels above the water table) and vegetation types (Persicaria hydropiper and Triarrhena lutarioriparia) on microbial community characteristics in the Poyang Lake wetland, and the relationships between soil microbial and organic carbon characteristics were revealed. The results showed that water level had a significant effect on organic carbon characteristics, and that soil total nitrogen, organic carbon, recombinant organic carbon, particle organic carbon, and microbial biomass carbon were higher at low levels above the water table. A positive correlation was noted between soil water content and organic carbon characteristics. Water level and vegetation type significantly affected soil bacterial and fungal diversity, with water level exerting a higher effect than vegetation type. The impacts of water level and vegetation type were higher on fungi than on bacteria. The bacterial diversity and evenness were significantly higher at high levels above the water table, whereas an opposite trend was noted among fungi. The bacterial and fungal richness in T. lutarioriparia community soil was higher than that in P. hydropiper community soil. Although both water level and vegetation type had significant effects on bacterial and fungal community structures, the water level had a higher impact than vegetation type. The bacterial and fungal community changes were the opposite at different water levels but remained the same in different vegetation soils. The organic carbon characteristics of wetland soil were negatively correlated with bacterial diversity but positively correlated with fungal diversity. Soil water content, soluble organic carbon, C/N, and microbial biomass carbon were the key soil factors affecting the wetland microbial community. Acidobacteria, Alphaproteobacteria, Verrucomicrobia, Gammaproteobacteria, and Eurotiomycetes were the key microbiota affecting the soil carbon cycle in the Poyang Lake wetland. Thus, water and carbon sources were the limiting factors for bacteria and fungi in wetlands with low soil water content (30%). Hence, the results provided a theoretical basis for understanding the microbial-driven mechanism of the wetland carbon cycle. Full article
(This article belongs to the Special Issue Advances in Soil Microbiome)
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Article
Community Profile and Drivers of Predatory Myxobacteria under Different Compost Manures
Microorganisms 2021, 9(11), 2193; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9112193 - 21 Oct 2021
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Abstract
Myxobacteria are unique predatory microorganisms with a distinctive social lifestyle. These taxa play key roles in the microbial food webs in different ecosystems and regulate the community structures of soil microbial communities. Compared with conditions under conventional management, myxobacteria abundance increases in the [...] Read more.
Myxobacteria are unique predatory microorganisms with a distinctive social lifestyle. These taxa play key roles in the microbial food webs in different ecosystems and regulate the community structures of soil microbial communities. Compared with conditions under conventional management, myxobacteria abundance increases in the organic soil, which could be related to the presence of abundant myxobacteria in the applied compost manure during organic conditions. In the present study,16S rRNA genes sequencing technology was used to investigate the community profile and drivers of predatory myxobacteria in four common compost manures. According to the results, there was a significant difference in predatory myxobacteria community structure among different compost manure treatments (p < 0.05). The alpha-diversity indices of myxobacteria community under swine manure compost were the lowest (Observed OTU richness = 13.25, Chao1 = 14.83, Shannon = 0.61), and those under wormcast were the highest (Observed OTU richness = 30.25, Chao1 = 31.65, Shannon = 2.62). Bacterial community diversity and Mg2+ and Ca2+ concentrations were the major factors influencing the myxobacteria community under different compost manure treatments. In addition, organic carbon, pH, and total nitrogen influenced the community profile of myxobacteria in compost manure. The interaction between myxobacteria and specific bacterial taxa (Micrococcales) in compost manure may explain the influence of bacteria on myxobacteria community structure. Further investigations on the in-situ community profile of predatory myxobacteria and the key microorganism influencing their community would advance our understanding of the community profile and functions of predatory microorganisms in the microbial world. Full article
(This article belongs to the Special Issue Advances in Soil Microbiome)
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