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Hide and Seek of Soil Microbes—Who Is Where with Whom and Why?

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A special issue of Applied Sciences (ISSN 2076-3417). This special issue belongs to the section "Earth Sciences".

Deadline for manuscript submissions: closed (31 August 2021) | Viewed by 25696

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Special Issue Editors

Dr. Maraike Probst

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Guest Editor

Institute of Microbiology, University of Innsbruck, 6020 Innsbruck, Austria
Interests: molecular microbial ecology; microbial communities; microbial interactions; microbial evolution and adaptation; modeling of ecological data

Dr. Judith Ascher-Jenull

E-Mail Website
Guest Editor

Institute of Microbiology, University of Innsbruck, 6020 Innsbruck, Austria
Interests: molecular microbial ecology; soil microbial communities; fate and ecological relevance of soil DNA: extracellular DNA vs. intracellular DNA vs. total DNA (environmental DNA); optimization of environmental DNA extraction/quantification protocols; microbial decomposition of coarse woody debris; C-dynamics; climate effects on soil physicochemical and microbiological properties

Special Issue Information

Dear Colleagues,

Technical innovations boost soil scientists’ opportunities to observe soil ecosystems and ask big questions. Nevertheless, fundamental focus points include:

1) Experimental design and sampling strategy. Although addressed previously, there is more to uncover and more to take home. Spatial heterogeneity in particular is unfortunately rarely considered.

2) Microbial diversity. Ecological hypotheses involve the observation of species number. The current methodology does not necessarily provide this information. Likewise, the controversially discussed analysis of relative abundance data needs validation and scientific awareness.

3) Functions. Omics benefits soil science. However, understanding the soil ecosystem from a mechanistic point of view differs from what recent research has termed “function”. Functioning implies malfunctioning, thereby reducing the soil ecosystem to a system providing a service. For comprehension, coherent and precise definitions are indispensable. Moreover, the precious information provided by sophisticated methods warrants critical discussion to draw relevant conclusions.

Therefore, we aim at opening a vivid discussion on this non-exhaustive list of topics:

Adequate experimental design for representative study of soil ecosystems;
Possibilities and limitations of observing microbial diversity;
Possibilities and limitations of data analysis and their impact on ecological conclusions;
Microbial spatial heterogeneity (across different scales);
How to observe microbial niche partitioning and occupation?
Soil ecosystems, soil microbial communities, and their “function”. In what sense can microbes, microbial communities and ecosystems have a function?

Please note that we warmly welcome review articles on all above topics. We hope they will be both useful as a reference and a contribution to a better understanding between experts from different disciplines.

Dr. Maraike Probst
Dr. Judith Ascher-Jenull
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. Applied Sciences is an international peer-reviewed open access semimonthly 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 2400 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.

Published Papers (6 papers)

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Editorial

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4 pages, 215 KiB

Open AccessEditorial

Special Issue on ‘Hide and Seek of Soil Microbes—Who Is Where with Whom and Why?’

by Maraike Probst and Judith Ascher-Jenull

Appl. Sci. 2022, 12(15), 7693; https://doi.org/10.3390/app12157693 - 30 Jul 2022

Viewed by 925

Abstract

Our question posed for and used as title of the special issue ‘Hide and Seek of Soil Microbes’–Who is Where with Whom and Why [...] Full article

(This article belongs to the Special Issue Hide and Seek of Soil Microbes—Who Is Where with Whom and Why?)

Research

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13 pages, 1695 KiB

Open AccessArticle

Biological Diabrotica Management and Monitoring of Metarhizium Diversity in Austrian Maize Fields Following Mass Application of the Entomopathogen Metarhizium brunneum

by Maria Zottele, Johanna Mayerhofer, Hannah Embleton, Katharina Wechselberger, Jürg Enkerli and Hermann Strasser

Appl. Sci. 2021, 11(20), 9445; https://doi.org/10.3390/app11209445 - 12 Oct 2021

Cited by 6 | Viewed by 2044

Abstract

Inundative mass application of Metarhizium brunneum BIPESCO 5 (Hypocreales, Clavicipitaceae) is used for the biological control of Diabrotica v. virgifera (Coleoptera, Chrysomelidae). Long-term field trials were performed in three Austrian maize fields—with different cultivation techniques and infestation rates—in order to evaluate the efficacy of the treatment to control the pest larvae. In addition, the indigenous Metarhizium spp. population structure was assessed to compare the different field sites with BIPESCO 5 mass application. Annual application of the product Granmet-P^TM (Metarhizium colonized barley kernels) significantly increased the density of Metarhizium spp. in the treated soil above the upper natural background level of 1000 colony forming units per gram dry weight soil. Although a decrease in the pest population over time was not achieved in heavily infested areas, less damage occurred in treated field sites in comparison to control sites. The Metarhizium population structure was significantly different between the treated field sites. Results showed that inundative mass application should be repeated regularly to achieve good persistence of the biological control agent, and indicated that despite intensive applications, indigenous populations of Metarhizium spp. can coexist in these habitats. To date, crop rotation remains the method of choice for pest reduction in Europe, however continuous and preventive application of M. brunneum may also present an alternative for the successful biological control of Diabrotica. Full article

(This article belongs to the Special Issue Hide and Seek of Soil Microbes—Who Is Where with Whom and Why?)

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12 pages, 1789 KiB

Open AccessFeature PaperArticle

Micro-Landscape Dependent Changes in Arbuscular Mycorrhizal Fungal Community Structure

by Stavros D Veresoglou, Leonie Grünfeld and Magkdi Mola

Appl. Sci. 2021, 11(11), 5297; https://doi.org/10.3390/app11115297 - 7 Jun 2021

Cited by 3 | Viewed by 2607

Abstract

The roots of most plants host diverse assemblages of arbuscular mycorrhizal fungi (AMF), which benefit the plant hosts in diverse ways. Even though we understand that such AMF assemblages are non-random, we do not fully appreciate whether and how environmental settings can make them more or less predictable in time and space. Here we present results from three controlled experiments, where we manipulated two environmental parameters, habitat connectance and habitat quality, to address the degree to which plant roots in archipelagos of high connectance and invariable habitats are colonized with (i) less diverse and (ii) easier to predict AMF assemblages. We observed no differences in diversity across our manipulations. We show, however, that mixing habitats and varying connectance render AMF assemblages less predictable, which we could only detect within and not between our experimental units. We also demonstrate that none of our manipulations favoured any specific AMF taxa. We present here evidence that the community structure of AMF is less responsive to spatio-temporal manipulations than root colonization rates which is a facet of the symbiosis which we currently poorly understand. Full article

(This article belongs to the Special Issue Hide and Seek of Soil Microbes—Who Is Where with Whom and Why?)

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18 pages, 3069 KiB

Open AccessArticle

Can We Use Functional Annotation of Prokaryotic Taxa (FAPROTAX) to Assign the Ecological Functions of Soil Bacteria?

by Chakriya Sansupa, Sara Fareed Mohamed Wahdan, Shakhawat Hossen, Terd Disayathanoowat, Tesfaye Wubet and Witoon Purahong

Appl. Sci. 2021, 11(2), 688; https://doi.org/10.3390/app11020688 - 12 Jan 2021

Cited by 125 | Viewed by 10217

Abstract

FAPROTAX is a promising tool for predicting ecological relevant functions of bacterial and archaeal taxa derived from 16S rRNA amplicon sequencing. The database was initially developed to predict the function of marine species using standard microbiological references. This study, however, has attempted to access the application of FAPROTAX in soil environments. We hypothesized that FAPROTAX was compatible with terrestrial ecosystems. The potential use of FAPROTAX to assign ecological functions of soil bacteria was investigated using meta-analysis and our newly designed experiments. Soil samples from two major terrestrial ecosystems, including agricultural land and forest, were collected. Bacterial taxonomy was analyzed using Illumina sequencing of the 16S rRNA gene and ecological functions of the soil bacteria were assigned by FAPROTAX. The presence of all functionally assigned OTUs (Operation Taxonomic Units) in soil were manually checked using peer-reviewed articles as well as standard microbiology books. Overall, we showed that sample source was not a predominant factor that limited the application of FAPROTAX, but poor taxonomic identification was. The proportion of assigned taxa between aquatic and non-aquatic ecosystems was not significantly different (p > 0.05). There were strong and significant correlations (σ = 0.90–0.95, p < 0.01) between the number of OTUs assigned to genus or order level and the number of functionally assigned OTUs. After manual verification, we found that more than 97% of the FAPROTAX assigned OTUs have previously been detected and potentially performed functions in agricultural and forest soils. We further provided information regarding taxa capable of N-fixation, P and K solubilization, which are three main important elements in soil systems and can be integrated with FAPROTAX to increase the proportion of functionally assigned OTUs. Consequently, we concluded that FAPROTAX can be used for a fast-functional screening or grouping of 16S derived bacterial data from terrestrial ecosystems and its performance could be enhanced through improving the taxonomic and functional reference databases. Full article

(This article belongs to the Special Issue Hide and Seek of Soil Microbes—Who Is Where with Whom and Why?)

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Review

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21 pages, 1598 KiB

Open AccessFeature PaperReview

Methods for Studying Bacterial–Fungal Interactions in the Microenvironments of Soil

by Edoardo Mandolini, Maraike Probst and Ursula Peintner

Appl. Sci. 2021, 11(19), 9182; https://doi.org/10.3390/app11199182 - 2 Oct 2021

Cited by 6 | Viewed by 5186

Abstract

Due to their small size, microorganisms directly experience only a tiny portion of the environmental heterogeneity manifested in the soil. The microscale variations in soil properties constrain the distribution of fungi and bacteria, and the extent to which they can interact with each other, thereby directly influencing their behavior and ecological roles. Thus, to obtain a realistic understanding of bacterial–fungal interactions, the spatiotemporal complexity of their microenvironments must be accounted for. The objective of this review is to further raise awareness of this important aspect and to discuss an overview of possible methodologies, some of easier applicability than others, that can be implemented in the experimental design in this field of research. The experimental design can be rationalized in three different scales, namely reconstructing the physicochemical complexity of the soil matrix, identifying and locating fungi and bacteria to depict their physical interactions, and, lastly, analyzing their molecular environment to describe their activity. In the long term, only relevant experimental data at the cell-to-cell level can provide the base for any solid theory or model that may serve for accurate functional prediction at the ecosystem level. The way to this level of application is still long, but we should all start small. Full article

(This article belongs to the Special Issue Hide and Seek of Soil Microbes—Who Is Where with Whom and Why?)

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17 pages, 1177 KiB

Open AccessReview

Thermodynamics of Soil Microbial Metabolism: Applications and Functions

by Nieves Barros

Appl. Sci. 2021, 11(11), 4962; https://doi.org/10.3390/app11114962 - 28 May 2021

Cited by 19 | Viewed by 3674

Abstract

The thermodynamic characterization of soils would help to study and to understand their strategies for survival, as well as defining their evolutionary state. It is still a challenging goal due to difficulties in calculating the thermodynamic state variables (enthalpy, Gibbs energy, and entropy) of the reactions taking place in, and by, soils. Advances in instrumentation and methodologies are bringing options for those calculations, boosting the interest in this subject. The thermodynamic state variables involve considering the soil microbial functions as key channels controlling the interchange of matter and energy between soil and the environment, through the concept of microbial energy use efficiency. The role of microbial diversity using the energy from the soil organic substrates, and, therefore, the who, where, with whom, and why of managing that energy is still unexplored. It could be achieved by unraveling the nature of the soil organic substrates and by monitoring the energy released by the soil microbial metabolism when decomposing and assimilating those substrates. This review shows the state of the art of these concepts and the future impact of thermodynamics on soil science and on soil ecology. Full article

(This article belongs to the Special Issue Hide and Seek of Soil Microbes—Who Is Where with Whom and Why?)

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