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Interaction between Plants, Microorganisms, and Soils in Different Ecosystems: 2nd Edition

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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Plant Sciences".

Deadline for manuscript submissions: closed (20 September 2024) | Viewed by 9800

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Prof. Dr. Anna Gałązka

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Department of Agricultural Microbiology, Institute of Soil Science and Plant Cultivation—State Research Institute, Czartoryskich 8, 24-100 Puławy, Poland
Interests: microbiome and mycobiome of soil and plant rhizosphere; endorhizosphere; next generation sequencing; soil and plant biodiversity
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Dear Colleagues,

Plants are colonised by an extremely high number of organisms, which can reach cell density much greater than the number of cells in the plant itself. In addition, the number of genes of microorganisms inhabiting the rhizosphere significantly exceeds the number of plant genes. Plants act as a link between communities of microorganisms, insects, and other invertebrate and vertebrate animals occurring both above and below the soil surface. In the natural environment, abiotic and biotic factors have an indirect or direct impact on plants. The root system of a plant works like a factory that produces a huge amount of chemicals to communicate effectively with the microorganisms around it. At the same time, micro-organisms can use these compounds as an energy source. The variety of microorganisms associated with plant roots is enormous, amounting to tens of thousands of species. This complex microbial community, also called the second plant genome, is essential for plant health and productivity. Over the last few years, there has been significant progress in research into the structure and dynamics of the microbial sphere of the rhizosphere. It has been proven that plants shape the composition of microorganisms by synthesizing root secretions. On the other hand, microorganisms play a key role in the functioning of plants through their positive impact on their growth and development. In general, rhizosphere microorganisms promote plant growth directly by providing plants with minerals such as nitrogen and phosphorus and by synthesizing growth regulators, as well as indirectly, by inhibiting the development of various plant pathogens. Researchers use novel technologies including next-generation sequencing, the use of soil profiling and microprobes for genomics, transcriptomics and metabolomics studies to conduct informative studies in the soil rhizosphere, and the role of plants and microorganisms in these interactions.

This Special Issue intends to improve our understanding of the “Interaction between the Plant Rhizosphere and Soil Organisms”. Submissions could consist of research on topics including but not limited to:

Diversity of soil microorganisms;
Soil microorganisms in forest ecosystems;
Rhizosphere diversity;
Interaction between plants and their microbial communities;
Functions of rhizosphere microorganisms;
Microorganisms synthesizing plant growth regulators;
Biological plant protection;
Genetic diversity among soil microbial communities;
Novel bioactive compound isolation and identification in plants and soil.

We would like to take this opportunity to welcome the submission of research articles, reviews, as well as technical notes and communications, on these related topics.

Prof. Dr. Anna Gałązka
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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

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Keywords

microbiome and mycobiome of soil and tree rhizosphere
mycorrhizal fungi
next-generation sequencing
soil and tree biodiversity
interaction between plants and microorganisms

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Published Papers (7 papers)

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Research

24 pages, 7452 KiB

Open AccessArticle

Exploring the Rhizospheric Microbial Communities under Long-Term Precipitation Regime in Norway Spruce Seed Orchard

by Dagmar Zádrapová, Amrita Chakraborty, Petr Žáček, Jiří Korecký, Anirban Bhar and Amit Roy

Int. J. Mol. Sci. 2024, 25(17), 9658; https://doi.org/10.3390/ijms25179658 - 6 Sep 2024

Viewed by 568

Abstract

The rhizosphere is the hotspot for microbial enzyme activities and contributes to carbon cycling. Precipitation is an important component of global climate change that can profoundly alter belowground microbial communities. However, the impact of precipitation on conifer rhizospheric microbial populations has not been investigated in detail. In the present study, using high-throughput amplicon sequencing, we investigated the impact of precipitation on the rhizospheric soil microbial communities in two Norway Spruce clonal seed orchards, Lipová Lhota (L-site) and Prenet (P-site). P-site has received nearly double the precipitation than L-site for the last three decades. P-site documented higher soil water content with a significantly higher abundance of Aluminium (Al), Iron (Fe), Phosphorous (P), and Sulphur (S) than L-site. Rhizospheric soil metabolite profiling revealed an increased abundance of acids, carbohydrates, fatty acids, and alcohols in P-site. There was variance in the relative abundance of distinct microbiomes between the sites. A higher abundance of Proteobacteria, Acidobacteriota, Ascomycota, and Mortiellomycota was observed in P-site receiving high precipitation, while Bacteroidota, Actinobacteria, Chloroflexi, Firmicutes, Gemmatimonadota, and Basidiomycota were prevalent in L-site. The higher clustering coefficient of the microbial network in P-site suggested that the microbial community structure is highly interconnected and tends to cluster closely. The current study unveils the impact of precipitation variations on the spruce rhizospheric microbial association and opens new avenues for understanding the impact of global change on conifer rizospheric microbial associations. Full article

(This article belongs to the Special Issue Interaction between Plants, Microorganisms, and Soils in Different Ecosystems: 2nd Edition)

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18 pages, 2165 KiB

Open AccessArticle

Medicinal Plant Root Exudate Metabolites Shape the Rhizosphere Microbiota

by Peng Qu, Butian Wang, Meijun Qi, Rong Lin, Hongmei Chen, Chun Xie, Zhenwei Zhang, Junchao Qiu, Huabo Du and Yu Ge

Int. J. Mol. Sci. 2024, 25(14), 7786; https://doi.org/10.3390/ijms25147786 - 16 Jul 2024

Viewed by 824

Abstract

The interactions between plants and rhizosphere microbes mediated by plant root exudates are increasingly being investigated. The root-derived metabolites of medicinal plants are relatively diverse and have unique characteristics. However, whether medicinal plants influence their rhizosphere microbial community remains unknown. How medicinal plant species drive rhizosphere microbial community changes should be clarified. In this study involving high-throughput sequencing of rhizosphere microbes and an analysis of root exudates using a gas chromatograph coupled with a time-of-flight mass spectrometer, we revealed that the root exudate metabolites and microorganisms differed among the rhizosphere soils of five medicinal plants. Moreover, the results of a correlation analysis indicated that bacterial and fungal profiles in the rhizosphere soils of the five medicinal plants were extremely significantly or significantly affected by 10 root-associated metabolites. Furthermore, among the 10 root exudate metabolites, two (carvone and zymosterol) had opposite effects on rhizosphere bacteria and fungi. Our study findings suggest that plant-derived exudates modulate changes to rhizosphere microbial communities. Full article

(This article belongs to the Special Issue Interaction between Plants, Microorganisms, and Soils in Different Ecosystems: 2nd Edition)

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22 pages, 4649 KiB

Open AccessArticle

Genotype Combinations Drive Variability in the Microbiome Configuration of the Rhizosphere of Maize/Bean Intercropping System

by Giovanna Lanzavecchia, Giulia Frascarelli, Lorenzo Rocchetti, Elisa Bellucci, Elena Bitocchi, Valerio Di Vittori, Fabiano Sillo, Irene Ferraris, Giada Carta, Massimo Delledonne, Laura Nanni and Roberto Papa

Int. J. Mol. Sci. 2024, 25(2), 1288; https://doi.org/10.3390/ijms25021288 - 20 Jan 2024

Cited by 4 | Viewed by 1692

Abstract

In an intercropping system, the interplay between cereals and legumes, which is strongly driven by the complementarity of below-ground structures and their interactions with the soil microbiome, raises a fundamental query: Can different genotypes alter the configuration of the rhizosphere microbial communities? To address this issue, we conducted a field study, probing the effects of intercropping and diverse maize (Zea mays L.) and bean (Phaseolus vulgaris L., Phaseolus coccineus L.) genotype combinations. Through amplicon sequencing of bacterial 16S rRNA genes from rhizosphere samples, our results unveil that the intercropping condition alters the rhizosphere bacterial communities, but that the degree of this impact is substantially affected by specific genotype combinations. Overall, intercropping allows the recruitment of exclusive bacterial species and enhances community complexity. Nevertheless, combinations of maize and bean genotypes determine two distinct groups characterized by higher or lower bacterial community diversity and complexity, which are influenced by the specific bean line associated. Moreover, intercropped maize lines exhibit varying propensities in recruiting bacterial members with more responsive lines showing preferential interactions with specific microorganisms. Our study conclusively shows that genotype has an impact on the rhizosphere microbiome and that a careful selection of genotype combinations for both species involved is essential to achieve compatibility optimization in intercropping. Full article

(This article belongs to the Special Issue Interaction between Plants, Microorganisms, and Soils in Different Ecosystems: 2nd Edition)

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19 pages, 4311 KiB

Open AccessArticle

The Inhibiting Effects of High-Dose Biochar Application on Soil Microbial Metagenomics and Rice (Oryza sativa L.) Production

by Nanyan Zhu, Qiaoqiao Yu, Lingqi Song and Haijun Sheng

Int. J. Mol. Sci. 2023, 24(20), 15043; https://doi.org/10.3390/ijms242015043 - 10 Oct 2023

Viewed by 1476

Abstract

Biochar is usually considered as an organic improver which can improve soil and increase crop yields. However, the unrestricted application of biochar to normal-fertility farmland will cause chemical stress on crops and affect agricultural production. At present, the effects and mechanisms of high-dose applications of biochar on rice (Oryza sativa L.) production and soil biological characteristics have not been fully studied. In this greenhouse pot experiment, combined with soil microbial metagenomics, three treatments in triplicates were conducted to explore the responses of rice production, soil chemical properties, and soil biological properties to high-dose applications of biochar (5%, w/w) prepared using peanut waste (peanut hulls and straw). The results show that peanut hulls, with a loose texture and pore structure, are a raw material with stronger effects for preparing biochar than peanut straw in terms of its physical structure. In a rice monoculture system, high-dose applications of biochar (5%, w/w) can slightly increase the grains per spike, while significantly inhibiting the spike number per pot and the percentage of setting. High-dose applications of biochar also have significant negative effects on the diversity and stability of soil bacterial and archaeal communities. Moreover, the microbial metabolism and nutrient cycling processes are also significantly affected by changing the soil carbon/nitrogen ratio. This study discusses the response mechanisms of rice production and soil biology to high-dose biochar applications, and complements the understanding of irrational biochar application on agricultural production and land sustainability. Full article

(This article belongs to the Special Issue Interaction between Plants, Microorganisms, and Soils in Different Ecosystems: 2nd Edition)

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22 pages, 3600 KiB

Open AccessArticle

Microbial Community Response to Various Types of Exogenous Organic Matter Applied to Soil

by Sylwia Siebielec, Anna Marzec-Grządziel, Grzegorz Siebielec, Aleksandra Ukalska-Jaruga, Monika Kozieł, Anna Gałązka, Marcin Przybyś, Piotr Sugier and Magdalena Urbaniak

Int. J. Mol. Sci. 2023, 24(19), 14559; https://doi.org/10.3390/ijms241914559 - 26 Sep 2023

Cited by 3 | Viewed by 1601

Abstract

Recycling of solid biowaste and manure would reduce the dependence of agriculture on synthetic products. Most of the available studies on the effects of exogenous organic matter (EOM) application to soil were focused on nutrients and crop yield, with much less attention to microbiological processes in soil, especially using modern molecular methods. The aim of this study was to evaluate the effects of various types of manure, sewage sludge and bottom sediment on the biochemical activity and biodiversity of soil and plant yield in a pot experiment. The soil was treated with a range of EOM types: six types of manure (cattle, pig, goat, poultry, rabbit and horse manure; two bottom sediments (from urban and rural systems); and two types of municipal sewage sludge. All EOMs stimulated dehydrogenases activity at a rate of 20 t ha⁻¹. Alkaline phosphatase was mostly stimulated by poultry manure and one of the sludges. In general, the two-fold greater rate of EOMs did not further accelerate the soil enzymes. The functional diversity of the soil microbiome was stimulated the most by cattle and goat manure. EOMs produce a shift in distribution of the most abundant bacterial phyla and additionally introduce exogenous bacterial genera to soil. Poultry and horse manure introduced the greatest number of new genera that were able to survive the strong competition in soil. EOMs differentiated plant growth in our study, which was correlated to the rate of nitrate release to soil. The detailed impacts of particular amendments were EOM-specific, but in general, no harm for microbial parameters was observed for manure and sludge application, regardless of their type. There was also no proof that the PAH and pesticide contents measured in manure or sludge had any effect on microbial activity and diversity. Full article

(This article belongs to the Special Issue Interaction between Plants, Microorganisms, and Soils in Different Ecosystems: 2nd Edition)

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15 pages, 1198 KiB

Open AccessArticle

Variability of Functional Groups of Rhizosphere Fungi of Norway Spruce (Picea abies (L.) H.Karst.) in the Boreal Range: The Wigry National Park, Poland

by Jolanta Behnke-Borowczyk, Robert Korzeniewicz, Adrian Łukowski, Marlena Baranowska, Radosław Jagiełło, Bartosz Bułaj, Maria Hauke-Kowalska, Janusz Szmyt, Jerzy M. Behnke, Piotr Robakowski and Wojciech Kowalkowski

Int. J. Mol. Sci. 2023, 24(16), 12628; https://doi.org/10.3390/ijms241612628 - 10 Aug 2023

Cited by 2 | Viewed by 1291

Abstract

Rhizosphere microbial communities can influence plant growth and development. Natural regeneration processes take place in the tree stands of protected areas, which makes it possible to observe the natural changes taking place in the rhizosphere along with the development of the plants. This study aimed to determine the diversity (taxonomic and functional) of the rhizosphere fungal communities of Norway spruce growing in one of four developmental stages. Our research was based on the ITS region using Illumina system sequencing. Saprotrophs dominated in the studied rhizospheres, but their percentage share decreased with the age of the development group (for 51.91 from 43.13%). However, in the case of mycorrhizal fungi, an opposite trend was observed (16.96–26.75%). The most numerous genera were: saprotrophic Aspergillus (2.54–3.83%), Penicillium (6.47–12.86%), Pyrenochaeta (1.39–11.78%), pathogenic Curvularia (0.53–4.39%), and mycorrhizal Cortinarius (1.80–5.46%), Pseudotomentella (2.94–5.64%) and Tomentella (4.54–15.94%). The species composition of rhizosphere fungal communities was favorable for the regeneration of natural spruce and the development of multi-generational Norway spruce stands. The ratio of the abundance of saprotrophic and mycorrhizal fungi to the abundance of pathogens was high and promising for the durability of the large proportion of spruce in the Wigry National Park and for forest ecosystems in general. Full article

(This article belongs to the Special Issue Interaction between Plants, Microorganisms, and Soils in Different Ecosystems: 2nd Edition)

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17 pages, 3624 KiB

Open AccessArticle

Tree Root-Associated Microbial Communities Depend on Various Floor Management Systems in an Intensive Apple (Malus × domestica Borkh.) Orchard

by Kamila Łucja Bokszczanin, Sebastian Przybyłko, Karolina Molska-Kawulok and Dariusz Wrona

Int. J. Mol. Sci. 2023, 24(12), 9898; https://doi.org/10.3390/ijms24129898 - 8 Jun 2023

Cited by 2 | Viewed by 1580

Abstract

Regenerative 3agriculture prioritizes soil health to build up organic soil carbon and nitrogen stocks while supporting the active and diverse soil biota that is a prerequisite for maintaining crop productivity and quality in sustainable food production. This study aimed at unravelling the impact of organic and inorganic soil maintenance systems in a ‘Red Jonaprince’ apple (Malus × domestica Borkh.) orchard on soil microbiota biodiversity and soil physico-chemical properties. During our study, we compared seven floor management systems in terms of microbial community diversity. Fungal and bacterial communities on all taxonomic levels differed largely between systems that augmented organic matter (organic) and other tested inorganic regimes. The dominant phylum of the soil in all management systems was Ascomycota. The operational taxonomic units (OTUs) within the Ascomycota were largely identified as members of Sordariomycetes, followed by Agaricomycetes, and both dominated in organic systems versus inorganic. The most prominent phyla, Proteobacteria, accounted for 43% of all assigned bacteria OTUs. Gammaproteobacteria, Bacteroidia, and Alphaproteobacteria were predominant in organic samples, while Acidobacteriae, Verrucomicrobiae, and Gemmatimonadetes were more abundant in inorganic mulches. Full article

(This article belongs to the Special Issue Interaction between Plants, Microorganisms, and Soils in Different Ecosystems: 2nd Edition)

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