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Agronomy
Special Issues
Living Soils: The Role of Microorganisms in Heterogeneous Soil Microenvironments
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Living Soils: The Role of Microorganisms in Heterogeneous Soil Microenvironments

A special issue of Agronomy (ISSN 2073-4395). This special issue belongs to the section "Soil and Plant Nutrition".

Deadline for manuscript submissions: closed (30 September 2022) | Viewed by 21467

Special Issue Editors

Dr. Agnieszka Kuźniar

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Guest Editor
Department of Biology and Biotechnology of Microorganisms, Institute of Biological Sciences, Faculty of Natural Sciences and Health, The John Paul II Catholic University of Lublin, 20-950 Lublin, Poland
Interests: soil microorganisms; endophytes; bacteria–plant interaction; industrial biotechnology; beneficial microorganisms
Prof. Jolanta Jaroszuk-Ściseł

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Guest Editor
Department of Industrial and Environmental Microbiology, Faculty of Biology and Biotechnology, Institute of Biological Sciences, Maria Curie-Skłodowska University, 20-033 Lublin, Poland
Interests: direct and indirect (biotic elicitors of resistance) biocontrol mechanisms; biofertilizers; phytopathogens; saprotrophic and endophytic microorganisms; mycoparasitism; microbial polymers; cell wall degrading enzymes; microbial phytohormones
Prof. Dr. Magdalena Frąc

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Guest Editor
Institute of Agrophysics, Polish Academy of Sciences, 20-290 Lublin, Poland
Interests: soil microbiomes and mycobiomes; plant holobiont; soil health and quality; soil–plant–microbial interactions; environmental microbiology; agricultural microbiology; fungal ecology; microbial biodiversity; mycology; agricultural biotechnology
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Agnieszka Wolińska

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Guest Editor
Department of Biology and Biotechnology of Microorganisms Faculty of Science and Health, The John Paul II Catholic University of Lublin, Konstantynów 1 I Str., 20-708 Lublin, Poland
Interests: soil biodiversity; NGS; CLPP; soil biology; endophytes; microorganisms
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The word “soil” may have different contextual meanings. The simplest definition of soil is as follows: the natural material that plants grow in and which provides them with physical support, water, and nutrients. Soil engineers refer to this term as the finely divided and relatively loose “rock’’ material at the earth’s surface. Geologists call this layer the regolith. Archaeologists appreciate soil as a carrier of archaeological heritage. In sum, the most widely held opinion of soil is as a medium for plant growth and the provision of food and fiber directly, or through the intermediate stage, of animals. The development of microbiological tests and culture-independent techniques has allowed the definition of soil to be completed. It has been found that soil is also an ecological niche for soil microorganisms.

Soil biodiversity reflects the mix of living organisms in the soil. These organisms interact with one another, plants, and small animals, forming a web of biological activity. Soil is undoubtedly the most biologically diverse part of Earth. The soil food web includes beetles, springtails, mites, worms, spiders, ants, nematodes, fungi, and bacteria.

These microorganisms constitute an extremely diverse group of organisms in the soil which interact with each other and with different plants and animals in the ecosystem to form an even more complex web of biological activity. Soil microorganisms provide a wide range of essential properties for the sustainable functioning of all ecosystems. Furthermore, soil microorganisms, due to their huge gene pool, are also used as a potential resource in biochemical reactions, which recycle nutrients for plant growth. Soil microbiota plays an extremely important role in activating nutrient elements for plants—especially nitrogen fixation, phosphorus, and iron activation—as well as interactions and communication (plants–microorganisms), explaining the ecological equilibrium in soil. The balanced diversity of soil microorganisms is closely associated with soil health due to the diversity and activity of soil microorganisms. In addition, many studies have indicated that soil microbes can be used as biological fertilizers and/or soil improvers.

In this issue, we aim to summarize and present the role of microorganisms in heterogeneous soil microenvironments and also in bottom sediments, the importance of biodiversity of soil microorganisms, and their contribution to the improvement of soil health. This Special Issue is dedicated to increasing knowledge about gene pool microorganisms in soils, participation of microorganisms in the circulation of elements, humus formation, as well as production of substances stimulating plant growth. An important aspect of this Special Issue will be to present the use of modern techniques to analyze the structure, functions, and interactions of soil microbial communities.

Dr. Agnieszka Kuźniar
Prof. Jolanta Jaroszuk-Ściseł
Prof. Dr. Magdalena Frąc
Dr. Agnieszka Wolińska
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. Agronomy 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 2600 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

  • biodiversity of soils
  • beneficial microorganisms
  • agricultural soils
  • non-agricultural soils
  • microbiological indicators of soil quality
  • microbial–plant interactions
  • culture-independent techniques
  • biocontrol mechanisms
  • biofertilizers
  • phytopathogenic fungi

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Published Papers (6 papers)

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Research

20 pages, 2198 KiB  
Article
(1→3)-α-D-glucooligosaccharides as Elicitors Influencing the Activity of Plant Resistance Pathways in Wheat Tissues
by Artur Nowak, Renata Tyśkiewicz, Adrian Wiater and Jolanta Jaroszuk-Ściseł
Agronomy 2022, 12(5), 1170; https://doi.org/10.3390/agronomy12051170 - 12 May 2022
Cited by 5 | Viewed by 4177
Abstract
Laetiporus sulphureus (Bull.: Fr.) Murrill is an arboreal species of the large-fruited Basidiomycota fungus from the Polyporales, family Laetiporaceae. The cell wall of this fungus is the source of many bioactive polymer compounds, including (1→3)-α-D-glucans. (1→3)-α-D-glucans can [...] Read more.
Laetiporus sulphureus (Bull.: Fr.) Murrill is an arboreal species of the large-fruited Basidiomycota fungus from the Polyporales, family Laetiporaceae. The cell wall of this fungus is the source of many bioactive polymer compounds, including (1→3)-α-D-glucans. (1→3)-α-D-glucans can be hydrolyzed to shorter compounds, (1→3)-α-D-glucooligosaccharides (GOS), with different degrees of polymerization (DP). The use of GOS obtained from L. sulphureus (1→3)-α-D-glucans, as an elicitor of plant resistance, may be important for biological protection used in sustainable agriculture. In the presented study, GOS influenced the activity of antioxidant enzymes (Catalase−CAT, Ascorbate Peroxidase−APX, Guaiacol Peroxidase−GPX, and Superoxide Dismutase−SOD), lignin and flavonoids producing phenylpropanoids pathways (Phenylalanine Ammonia-Lyase−PAL and Tyrosine Ammonia-Lyase−TAL), and pathogen-related proteins (with Glucanase−GLUC and Chitinase−CHIT activity) in wheat (Triticum aestivum L.) seedling tissues. Other than that, the application of GOS increased the fresh weight of wheat stems and roots by 1.5–2-times, compared to the water control. The GOS at a concentration of 0.05% most strongly increased the activity of APX and GPX, where a 2-fold (up to 6000 U) and a 3-fold (up to 180 U) increase in enzymatic activity in wheat stems was observed, compared to the control. Simultaneously, 0.1% GOS significantly increased the activity of PAL (80 U in stems and 50 U in roots) and TAL (60 U in stems and 50 U in roots), where a 4–5-fold increase in enzymatic activity was observed, both in comparison to the water control and commercial elicitors (chitosan−CHI and laminarin−LAM). No effect of GOS on GLUC activity was observed, but a 1.5–2-fold increase in CHIT activity in plant tissues was noted. The complexity of the influence of GOS on the level of marker enzymes indicates the potential of their application in agriculture. This work is the first report of the successful use of (1→3)-α-D-glucooligosaccharides as an elicitor inducing resistance in the cereal plant (wheat). Full article
(This article belongs to the Special Issue Living Soils: The Role of Microorganisms in Heterogeneous Soil Microenvironments)
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19 pages, 4054 KiB  
Article
Does the Use of an Intercropping Mixture Really Improve the Biology of Monocultural Soils?—A Search for Bacterial Indicators of Sensitivity and Resistance to Long-Term Maize Monoculture
by Agnieszka Wolińska, Anna Kruczyńska, Jacek Podlewski, Andrzej Słomczewski, Jarosław Grządziel, Anna Gałązka and Agnieszka Kuźniar
Agronomy 2022, 12(3), 613; https://doi.org/10.3390/agronomy12030613 - 28 Feb 2022
Cited by 15 | Viewed by 3224
Abstract
The choice of appropriate agricultural practices has a significant impact on soil quality, crop productivity, or soil microbial community. Ten representative soil samples were collected in Wierzchucin Królewski (Kujawsko-Pomorskie Province, NW Poland), an agricultural area belonging to the Potulicka Foundation Group. The cropping [...] Read more.
The choice of appropriate agricultural practices has a significant impact on soil quality, crop productivity, or soil microbial community. Ten representative soil samples were collected in Wierzchucin Królewski (Kujawsko-Pomorskie Province, NW Poland), an agricultural area belonging to the Potulicka Foundation Group. The cropping systems included a maize monoculture grown continuously for over 30 years and an intercropping mixture (Gorzow mixture) applied in 2020. The study aimed to determine the effect of the intercropping system on the quality and biodiversity of the studied soils and to identify bacterial indicators of sensitivity and resistance to long-term maize monoculture. Therefore, in this study, the impact of the intercrop mixture application on the chemical and biological soil properties and on the diversity of the bacterial community was evaluated by amplifying the 16S rRNA gene sequences and indicators of sensitivity and resistance to long-term maize monoculture were recommended. The results showed that intercropping had a positive effect on soil features and increased the richness and diversity of soil bacteria at the taxonomic level of genera compared to the maize monoculture. Massilia and Haliangium were proposed to be bacterial indicators of sensitivity, while Sphingomonas was recommended to be an indicator of resistance to long-term maize monoculture. Overall, our results evidenced that using an intercropping system may be a sustainable agricultural practice in this area and in north-western Poland. Full article
(This article belongs to the Special Issue Living Soils: The Role of Microorganisms in Heterogeneous Soil Microenvironments)
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16 pages, 2033 KiB  
Article
Seasonal Dynamics of Soil Bacterial Community under Long-Term Abandoned Cropland in Boreal Climate
by Alena Zhelezova, Timofey Chernov, Dmitry Nikitin, Azida Tkhakakhova, Natalia Ksenofontova, Aleksei Zverev, Olga Kutovaya and Mikhail Semenov
Agronomy 2022, 12(2), 519; https://doi.org/10.3390/agronomy12020519 - 19 Feb 2022
Cited by 8 | Viewed by 2882
Abstract
The collapse of collective farming in Russia after 1990 led to the abandonment of 23% of the agricultural area. Microbial biomass is a transit pool between fresh and soil organic matter; therefore, structural changes in soil microbial community determine the carbon cycle processes [...] Read more.
The collapse of collective farming in Russia after 1990 led to the abandonment of 23% of the agricultural area. Microbial biomass is a transit pool between fresh and soil organic matter; therefore, structural changes in soil microbial community determine the carbon cycle processes caused by self-restoration of arable lands after abandonment. Here, we assessed the influence of monthly changes in moisture and temperature on the bacterial community structure and abundance in Retisols under long-term abandoned cropland. Two periods with pronounced differences in bacterial properties were revealed: the growing period from March to September and the dormant period from October to February. The growing period was characterized by higher bacterial abundance and diversity compared to the dormant period. The relative abundances of the bacterial community dominants (Alpha-, Gamma- and Deltaproteobacteria, subgroup 6 of phylum Acidobacteria) did not change significantly over the year, either in total or active communities. The relative abundances of Bacteroidetes and Verrucomicrobia increased in the growing period, whereas Actinobacteria and Chloroflexi were more abundant in the dormant period. The microbial gene abundances positively correlated with soil and air temperature, but not with soil moisture. Thus, the seasonal dynamics of soil microbial communities are closely related to soil temperature and should be considered when assessing carbon cycles in abandoned lands. Full article
(This article belongs to the Special Issue Living Soils: The Role of Microorganisms in Heterogeneous Soil Microenvironments)
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24 pages, 3952 KiB  
Article
Optimization of Growing Medium and Preservation Methods for Plant Beneficial Bacteria, and Formulating a Microbial Biopreparation for Raspberry Naturalization
by Michał Pylak, Karolina Oszust and Magdalena Frąc
Agronomy 2021, 11(12), 2521; https://doi.org/10.3390/agronomy11122521 - 12 Dec 2021
Cited by 7 | Viewed by 4300
Abstract
The current study focuses on the optimization of bacterial growing medium composition, including the carbon and nitrogen source in different concentrations, the pH value of the medium and the temperature. Optimization was performed for four environmental bacterial isolates belonging to the genera Arthrobacter [...] Read more.
The current study focuses on the optimization of bacterial growing medium composition, including the carbon and nitrogen source in different concentrations, the pH value of the medium and the temperature. Optimization was performed for four environmental bacterial isolates belonging to the genera Arthrobacter, Pseudomonas and Rhodococcus, which were previously obtained from wild raspberries. These bacteria proved to be potent antagonists against certain fungal and fungal-like plant pathogens. Furthermore, three preservation methods and three sample preparation techniques were evaluated. In addition, a prebiotic supplementary blend based on previous research was tested. The research included a pot experiment to estimate the influence of bacterial cultures on the growth of plant shoots and roots, on the soil enzymatic activity and the content of macronutrients, minerals and nitrogen in the soil depending on the naturalization strategy. The best carbon and nitrogen source were chosen. The addition of a supplementary blend resulted in the increased growth of two bacterial isolates. Bacterial inoculum applied to the roots and watering resulted in increased shoot mass in objects infected with plant pathogens, although in plants without the pathogen infection, bacterial inoculum resulted in the decreased mass of plants. Naturalization strategy should be matched to the pathogens present at plantations. Full article
(This article belongs to the Special Issue Living Soils: The Role of Microorganisms in Heterogeneous Soil Microenvironments)
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16 pages, 859 KiB  
Article
The Cumulative Effect of Various Tillage Systems and Stubble Management on the Biological and Chemical Properties of Soil in Winter Wheat Monoculture
by Karol Kotwica, Barbara Breza-Boruta, Justyna Bauza-Kaszewska, Piotr Kanarek, Iwona Jaskulska and Dariusz Jaskulski
Agronomy 2021, 11(9), 1726; https://doi.org/10.3390/agronomy11091726 - 29 Aug 2021
Cited by 5 | Viewed by 2120
Abstract
Agricultural practices, including tillage systems and postharvest residue management, strongly affect a wide range of soil properties. Depending on the degree of soil inversion, both negative and beneficial changes of its structure, chemical composition, and biological activity may occur as a result of [...] Read more.
Agricultural practices, including tillage systems and postharvest residue management, strongly affect a wide range of soil properties. Depending on the degree of soil inversion, both negative and beneficial changes of its structure, chemical composition, and biological activity may occur as a result of these treatments. The three-year experiment was carried out on the soil under winter wheat (cv. Arktis) monoculture. The effect of various tillage systems and stubble management on the soil environment’s biological and chemical features was investigated. The total number of microorganisms (TNM); bacteria (B); actinobacteria(A); fungi (F); soil respiratory activity (SR); pH in 1 M KCl (pH); organic carbon content (OC); content of available phosphorus (Pa); potassium (Ka); magnesium (Mg); and content of total nitrogen (TN) and mineral nitrogen forms were determined in soil samples. It was shown that manure application was the factor with the greatest influence on soil properties. The manure fertilization resulted in a higher number of microorganisms in arable soil. Conventional tillage procedures combined with manure application increased the amounts of available forms of phosphorus, potassium, magnesium, and mineral nitrogen. Introduction of the chopped straw in the field enhanced the beneficial effect of manure on soil properties. Full article
(This article belongs to the Special Issue Living Soils: The Role of Microorganisms in Heterogeneous Soil Microenvironments)
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12 pages, 1104 KiB  
Article
The Reaction of Cellulolytic and Potentially Cellulolytic Spore-Forming Bacteria to Various Types of Crop Management and Farmyard Manure Fertilization in Bulk Soil
by Jakub Dobrzyński, Paweł Stanisław Wierzchowski, Wojciech Stępień and Ewa Beata Górska
Agronomy 2021, 11(4), 772; https://doi.org/10.3390/agronomy11040772 - 15 Apr 2021
Cited by 20 | Viewed by 2841
Abstract
The ecology of cellulolytic bacteria in bulk soil is still relatively unknown. There is still only a handful of papers on the abundance and diversity of this group of bacteria. Our study aimed to determine the impact of various crop management systems and [...] Read more.
The ecology of cellulolytic bacteria in bulk soil is still relatively unknown. There is still only a handful of papers on the abundance and diversity of this group of bacteria. Our study aimed to determine the impact of various crop management systems and farmyard manure (FYM) fertilization on the abundance of cellulolytic and potentially cellulolytic spore-forming bacteria (SCB). The study site was a nearly 100-year-old fertilization experiment, one of the oldest still active field trials in Europe. The highest contents of total carbon (TC) and total nitrogen (TN) were recorded in both five-year rotations. The abundances of SCB and potential SCB were evaluated using classical microbiological methods, the most probable number (MPN), and 16S rRNA Illumina MiSeq sequencing. The highest MPN of SCB was recorded in soil with arbitrary rotation without legumes (ARP) fertilized with FYM (382 colony-forming units (CFU) mL−1). As a result of the bioinformatic analysis, the highest values of the Shannon–Wiener index and the largest number of operational taxonomic units (OTUs) were found in ARP-FYM, while the lowest in ARP treatment without FYM fertilization. In all treatments, those dominant at the order level were: Brevibacillales (13.1–43.4%), Paenibacillales (5.3–36.9%), Bacillales (4.0–0.9%). Brevibacillaceae (13.1–43.4%), Paenibacillaceae (8.2–36.9%), and Clostridiaceae (5.4–11.9%) dominated at the family level in all tested samples. Aneurinibacillaceae and Hungateiclostridiaceae families increased their overall share in FYM fertilization treatments. The results of our research show that the impact of crop management types on SCB was negligible while the actual factor shaping SCB community was the use of FYM fertilization. Full article
(This article belongs to the Special Issue Living Soils: The Role of Microorganisms in Heterogeneous Soil Microenvironments)
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