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A special issue of Agriculture (ISSN 2077-0472). This special issue belongs to the section "Agricultural Soils".

Deadline for manuscript submissions: closed (20 January 2023) | Viewed by 39270

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Dr. Tibor Szili-Kovács

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Guest Editor

Centre for Agricultural Research, Institute for Soil Sciences, Herman O. út 15., 1022 Budapest, Hungary
Interests: soil biology; microbial ecology; sodic soils; karst soils; long-term experiments; restoration ecology
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Dr. Tünde Takács

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Guest Editor

HUN-REN Centre for Agricultural Research, Institute for Soil Sciences, Herman O. út 15., H-1022 Budapest, Hungary
Interests: arbuscular mycorrhizal fungi (AMF); microbial inoculation; organic farming; long-term experiments; plant stress physiology; bioremediation/phytoremediation
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Rhizosphere is one of the most important hotspots in soils that harbor a huge number of microbial species, including archaea, bacteria and fungi. Root exudates serve as carbon and energy sources for heterotrophic microbes, and meanwhile have selective power to shape the microbial communities around root systems. Rhizosphere microbial activity can be one or two orders of magnitude higher than that of the surrounding bulk soil. Additionally, it is a very dynamic system and sensitive as well. Microbes in the rhizosphere could help plant nutrition and water uptake and plant growth promotion by hormone and siderophore production; in addition, they can protect plants against pathogenic microbes, while, in certain conditions, some of them become pathogenic also. Climate change, land use change and different management options are challenges to evaluate soil health in connection with the plant–microbe interactions. Rhizosphere microbial activity can be detected and measured in several ways. The newly developed methods, such as community-level physiological profiling, different enzyme activity measurements—alone or together with the microbiome diversity by next generation DNA sequencing—and other methodical approaches focusing on rhizosphere microbial activity in all types of agricultural soils, including grassland and pasture soils, are welcome to this Special Issue.

Dr. Tibor Szili-Kovács
Dr. Tünde Takács
Guest Editors

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Keywords

rhizosphere
microbial activity
functional diversity
community-level physiological profile
soil health
bacterial and fungal community
PGPR bacteria
root exudates
root colonization

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Published Papers (11 papers)

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Editorial

Jump to: Research

4 pages, 210 KiB

Open AccessEditorial

Advanced Research of Rhizosphere Microbial Activity

by Tibor Szili-Kovács and Tünde Takács

Agriculture 2023, 13(4), 911; https://doi.org/10.3390/agriculture13040911 - 21 Apr 2023

Cited by 1 | Viewed by 2139

Abstract

Soils are generally considered a complex and largely unexplored vital “black box” with thousands of microorganism taxa in their networks [...] Full article

(This article belongs to the Special Issue Advanced Research of Rhizosphere Microbial Activity)

Research

Jump to: Editorial

15 pages, 2890 KiB

Open AccessArticle

Screening and Identification of the Rhizosphere Fungal Communities Associated with Land Reclamation in Egypt

by Mostafa Nafaa, Samah Mohamed Rizk, Tahany Abdel-Ghafar Ahmed Aly, Mohamed Abdel-Salam Rashed, Diaa Abd El-Moneim, Abir Ben Bacha, Mona Alonazi and Mahmoud Magdy

Agriculture 2023, 13(1), 215; https://doi.org/10.3390/agriculture13010215 - 14 Jan 2023

Cited by 11 | Viewed by 3952

Abstract

Soil fungi are a wide range of microorganisms that play an essential role in enhancing the available nutrients in the soil for plants. In the current study, to study the fungal association with newly reclaimed land in Egypt, 22 composite soil samples were screened and characterized from citrus and olive orchard soil in contrast to a control soil that had never been cultivated (a nearby desert). The isolates were identified and tested for P solubilization and IAA production to highlight their potential as biofertilizers while the sampled soil was characterized. The physicochemical characteristics of the orchard’s soil sample had a high relative mean moisture content, and the C/N ratio were 45.24% and 16.8% compared with desert lands of 32.80% and 8.12%, respectively, while a higher pH was recorded for desert lands. A total of 272 fungal isolates yielded 27 filamentous fungal species. Based on ITS molecular identification, the 27 isolates belonged to phyla Ascomycota, from eight genera. Twelve species were positive in producing a phosphate clearance zone around the fungal colony growth, while ten species were able to release IAA in vitro with different tryptophan concentrations under different pH values. When known pathogenic fungi were excluded, Aspergillus tubingensis and A. fumigatus were the highest IAA producers and can solubilize phosphorus. The screening and identification of the fungal diversity of the newly reclaimed land provided insights into potential phosphate solubilizers and plant phytohormones producers (i.e., IAA). Overall, the obtained results can provide primary knowledge that indicates the great potential fungal ability to develop biofertilizers for application in improving the production of immature soil for agriculture reclamation processes and practices. Full article

(This article belongs to the Special Issue Advanced Research of Rhizosphere Microbial Activity)

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22 pages, 2302 KiB

Open AccessArticle

Functional Interpretation of Cross-Talking Pathways with Emphasis on Amino Acid Metabolism in Rhizosphere Microbiome of the Wild Plant Moringa oleifera

by Manal A. Tashkandi, Rewaa S. Jalal, Lina Baz, Mohammed Y. Refai, Ashwag Shami, Ruba Abdulrahman Ashy, Haneen W. Abuauf, Fatimah M. Alshehrei, Fawzia A. Alshubaily, Aminah A. Barqawi, Sahar Alshareef and Aala A. Abulfaraj

Agriculture 2022, 12(11), 1814; https://doi.org/10.3390/agriculture12111814 - 31 Oct 2022

Cited by 8 | Viewed by 2379

Abstract

The functional processes and mutual benefits of the wild plant Moringa oleifera and its rhizosphere microbiome were studied via metagenomic whole-genome shotgun sequencing (mWGS) in comparison with a bulk soil microbiome. The results indicated high gene abundance of the four KEGG categories, “Cellular Processes”, “Environmental Information Processing”, “Genetic Information Processing”, and “Metabolism”, in the rhizosphere microbiome. Most of the enriched enzymes in rhizobacteria are assigned to the pathway “Amino acids metabolism”, where soil-dwelling microbes use amino acids as a defense mechanism against phytopathogens, while promoting growth, colonizing the cohabiting commensal microbes and conferring tolerance against abiotic stresses. In the present study, it was proven that these beneficial microbes include Bacillus subtilis, Pseudomonas fluorescens, and Escherichia coli. Mineral solubilization in these rhizobacteria can make nutrients available for plant utilization. These rhizobacteria extensively synthesize and metabolize amino acids at a high rate, which makes nitrogen available in different forms for plants and microbes. Amino acids in the rhizosphere might stand mainly as an intermediate switcher for the direction of the soil nitrogen cycle. Indole acetic acid (IAA) was proven to be synthesized by these beneficial rhizobacteria via route indole-3-pyruvate (IPyA) of the pathway “Tryptophan metabolism”. This hormone might stand as a shuttle signaling molecule between M. oleifera and its rhizobacteria. Tryptophan is also metabolized to promote other processes with important industrial applications. Rhizobacteria were also proven to breakdown starch and sucrose into glucose, which is the primary metabolic fuel of living organisms. In conclusion, we assume that the metabolic processes in the rhizosphere microbiome of this wild plant can be eventually utilized in boosting the sustainability of agriculture applications and the plant’s ability to benefit from soil nutrients when they are not in the form available for plant root absorption. Full article

(This article belongs to the Special Issue Advanced Research of Rhizosphere Microbial Activity)

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13 pages, 2386 KiB

Open AccessArticle

16S Amplicon Sequencing of Nitrifying Bacteria and Archaea Inhabiting Maize Rhizosphere and the Influencing Environmental Factors

by Oluwatobi Esther Ayiti, Ayansina Segun Ayangbenro and Olubukola Oluranti Babalola

Agriculture 2022, 12(9), 1328; https://doi.org/10.3390/agriculture12091328 - 28 Aug 2022

Cited by 9 | Viewed by 2592

Abstract

Nitrifying bacteria and archaea are ubiquitous and can transform ammonia locked up in soil or manure into nitrate, a more soluble form of nitrogen. However, nitrifying bacteria and archaea inhabiting maize rhizosphere have not been fully explored. This study evaluates the diversity and abundance of nitrifying bacteria and archaea across different growth stages of maize using 16S amplicon sequencing. Moreover, the influence of environmental factors (soil physical and chemical properties) on the nitrifying communities was evaluated. Rhizosphere soil DNA was extracted using Nucleospin Soil DNA extraction kit and sequenced on Illumina Miseq platform. MG-RAST was used to analyze the raw sequences. The physical and chemical properties of the soil were measured using standard procedure. The results revealed 9 genera of nitrifying bacteria; Nitrospira, Nitrosospira, Nitrobacter, Nitrosovibrio, Nitrosomonas, Nitrosococcus, Nitrococcus, unclassified (derived from Nitrosomonadales), unclassified (derived from Nitrosomonadaceae) and 1 archaeon Candidatus Nitrososphaera. The Nitrospirae phyla group, which had the most nitrifying bacteria, was more abundant at the tasselling stage (67.94%). Alpha diversity showed no significant difference. However, the Beta diversity showed significant difference (p = 0.01, R = 0.58) across the growth stages. The growth stages had no significant effect on the diversity of nitrifying bacteria and archaea, but the tasselling stage had the most abundant nitrifying bacteria. A correlation was observed between some of the chemical properties and some nitrifying bacteria. The research outcome can be put into consideration while carrying out a biotechnological process that involves nitrifying bacteria and archaea. Full article

(This article belongs to the Special Issue Advanced Research of Rhizosphere Microbial Activity)

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23 pages, 4932 KiB

Open AccessFeature PaperArticle

Long-Term Fertilization Alters Mycorrhizal Colonization Strategy in the Roots of Agrostis capillaris

by Larisa Corcoz, Florin Păcurar, Victoria Pop-Moldovan, Ioana Vaida, Anca Pleșa, Vlad Stoian and Roxana Vidican

Agriculture 2022, 12(6), 847; https://doi.org/10.3390/agriculture12060847 - 12 Jun 2022

Cited by 9 | Viewed by 2223

Abstract

Long-term fertilization targets mycorrhizal fungi adapted to symbiotic exchange of nutrients, thus restricting their colonization potential and re-orienting the colonization strategies. The MycoPatt tool has a high applicability in quantifying the symbiotic process with the identification of mycorrhizal indices and projection of mycorrhizal patterns. Organic treatments increase the symbiotic process, visible in values of colonization frequency and intensity, with about 6% more than the native status of colonization. At the opposite pole, organic-mineral treatments decrease the colonization parameters by up to half of the organic treatment. All of the colonization parameters show significant correlations, except for the arbuscules/vesicle ratio (0.03). All the applied treatments, except for the organic one, record multiple root segments with a colonization degree lower than 10%. The application of treatments changes the strategy of native colonization from a transfer (40%) and storage (37%) to a predominant storage (50%) for organic treatment, and are mainly proliferative between 38–50% in mixed and mineral treatments. The high amount of mineral components increases also the presence of resistance conditions strategies. The use of mycorrhizal pattern maps, with the inclusion of colonization strategies, presents an important direction in understanding the evolution of mutual relations, and to explore in-depth the efficiency of the whole symbiotic process. Full article

(This article belongs to the Special Issue Advanced Research of Rhizosphere Microbial Activity)

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16 pages, 1887 KiB

Open AccessArticle

Combined Use of Sewage Sludge and Plant Growth-Promoting Rhizobia Improves Germination, Biochemical Response and Yield of Ridge Gourd (Luffa acutangula (L.) Roxb.) under Field Conditions

by Vinod Kumar, Ebrahem M. Eid, Dhafer A. Al-Bakre, Samy M. Abdallah, Ivan Širić, Željko Andabaka, Pankaj Kumar, Madhumita Goala, Bashir Adelodun, Jogendra Singh, Sonika Kumari, Archana Bachheti, Ashish Kumar Arya and Kyung-Sook Choi

Agriculture 2022, 12(2), 173; https://doi.org/10.3390/agriculture12020173 - 26 Jan 2022

Cited by 4 | Viewed by 4210

Abstract

This research investigated the combined use of sewage sludge (SS) and plant growth-promoting rhizobia (PGPR) for Ridge gourd (Luffa acutangula (L.) Roxb.) cultivated under field conditions. The different treatments of SS and PGPR such as 0% (soil as control), 5% SS, 5% SS + PGPR, 10% SS, and 10% SS + PGPR were applied to assess their impacts on seedling growth, biochemical response, and yield performance of Ridge gourd. The results showed that the highest seedling emergence (92.3 ± 2.1%), fresh biomass (9.6 ± 0.3 g), growth rate (1.4 ± 0.1 g/day), seedling length (15.5 ± 0.3 cm), root length (10.4 ± 0.3 cm), total chlorophyll (3.2 ± 0.1 mg/g), crop yield (13.8 ± 0.1 kg/plant), and average crop yield per harvest (2.8 ± 0.1 kg/plant) were observed in 10% SS + PGPR treatment. The enzyme activities of superoxide dismutase (SOD; µg/g) and catalase (CAT: µg/g) were significantly lowered after PGPR inoculation in higher SS treatments. The results of principal component (PC) and Euclidian clustered distance analyses showed a positive influence of SS dose on soil nutrient availability and Ridge gourd’s growth, biochemical responses, and yield performance. Moreover, the elemental analysis showed that the bioaccumulation factor (BAF < 0.90) and health risk index (HRI < 0.40) of selected metal elements (Cd, Cr, Cu, Fe, Mn, and Zn) were within the permissible limits, indicating consumption of Ridge gourd fruits was safe. The outcomes of this study suggest the potential use of SS and PGPR for improved Ridge gourd production and contribution towards sustainable development goal (SDG) 12 on responsible consumption and production of vegetable crops. Full article

(This article belongs to the Special Issue Advanced Research of Rhizosphere Microbial Activity)

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11 pages, 1019 KiB

Open AccessArticle

Structure and Function of the Soil Rhizosphere Fungal Communities in Medicinal Plants—A Preliminary Study

by Itaii Applebaum, Mareeswaran Jeyaraman, Chen Sherman, Tirza Doniger and Yosef Steinberger

Agriculture 2022, 12(2), 152; https://doi.org/10.3390/agriculture12020152 - 21 Jan 2022

Cited by 8 | Viewed by 3049

Abstract

Plants regulate their rhizosphere microbiome, which partly comprises the fungal community. We conducted a study in order to determine the effect that five medicinal plant species (Origanum syriacum, Salvia fruticosa, Teucrium capitatum, Myrtus communis and Pistacia lentiscus) have on the fungal community in their rhizosphere. We measured abiotic parameters and used sequencing to determine the structure of the rhizosphere fungal community, both taxonomically, as phyla and genera, and functionally, as trophic modes. Our data shows that the rhizosphere fungal communities were significantly different, both taxonomically and functionally. The rhizosphere of M. communis had a significant relative abundance of saprotrophs and a lower relative abundance of symbiotrophs than the control soil and the rhizosphere of T. capitatum. The relative abundance of the genus Aureobasidium was significantly higher in the rhizosphere of P. lentiscus than in the control and for all other rhizospheres, but that of S. fruiticosa. The relative abundance of genus Alternaria was lower in the rhizospheres of S. fruticosa and M. communis than in the control soil. Our results highlight the potential use of these plants in agroforestry, as a means to influence the soil fungi population. Full article

(This article belongs to the Special Issue Advanced Research of Rhizosphere Microbial Activity)

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9 pages, 1604 KiB

Open AccessEditor’s ChoiceArticle

Field Inoculation of Arbuscular Mycorrhizal Fungi Improves Fruit Quality and Root Physiological Activity of Citrus

by Ming-Ao Cao, Peng Wang, Abeer Hashem, Stephan Wirth, Elsayed Fathi Abd_Allah and Qiang-Sheng Wu

Agriculture 2021, 11(12), 1297; https://doi.org/10.3390/agriculture11121297 - 20 Dec 2021

Cited by 19 | Viewed by 4789

Abstract

Soil arbuscular mycorrhizal (AM) fungi form a mutualistic symbiosis with plant roots and produce many benefits on host plants under potted conditions, while field inoculation of AM fungi on citrus (a woody plant) has been rarely reported. The present study aimed to analyze the changes in mycorrhizal growth, root vitality, and fruit quality of Citrus reticulata Blanco var. Ponkan mandarin cv. Jinshuigan grafted on Poncirus trifoliata L. after inoculation with a mix of AM fungi (Diversispora versiformis, Funneliformis mosseae, and Rhizophagus intraradices) and single F. mosseae. After the second year of AM fungal inoculations, root mycorrhizal colonization (%), root vitality, hyphal length in soil, and easily extractable glomalin-related soil protein content were significantly increased, while difficult-to-extract glomalin-related soil protein content was decreased. Two mycorrhizal fungal inoculation treatments collectively improved fruit quality parameters such as polar diameter, equatorial diameter, the weight of single fruits, fruit peel, and sarcocarp, coloration value, and soluble solids content. Our study, therefore, suggested that field inoculation with AM fungi improved root physiological activities in terms of mycorrhizal growth and root vitality and thus improved fruit quality. The effect of mixed-AM treatment was more significant than that of F. mosseae alone. Full article

(This article belongs to the Special Issue Advanced Research of Rhizosphere Microbial Activity)

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12 pages, 3938 KiB

Open AccessArticle

Spatial Distribution and Influencing Factors of Soil Fungi in a Degraded Alpine Meadow Invaded by Stellera chamaejasme

by Yongmei Liu, Fan Zhao, Lei Wang, Wei He, Jianhong Liu and Yongqing Long

Agriculture 2021, 11(12), 1280; https://doi.org/10.3390/agriculture11121280 - 16 Dec 2021

Cited by 5 | Viewed by 2844

Abstract

Alpine meadow degradation causes a notable decrease in palatable grasses and an increase in forbs and toxic plants in recent decades. Stellera chamaejasme is one of the most serious toxic weeds, which exerts an increasing threat on alpine meadow in Qinghai–Tibetan Plateau. Combined DNA sequencing with geostatistics was applied to analyze a typical degraded meadow invaded by S. chamaejasme in Qinghai Province, China. The study aimed to determine the spatial variation of soil fungi and its interrelationship with the plant–soil environment. Alpha diversity and relative abundance of fungal phyla and classes showed moderate or strong spatial dependency and were structured in patches of 19–318 m, and taxonomic composition exhibited much higher spatial variability than alpha diversity. Compared to plant cover, the matching of patch size showed a closer spatial link between soil properties and fungal community. Community coverage, SOM, TN, TP, and TK positively correlated to fungal diversity and taxonomic composition; no direct correlation was found between S. chamaejasme coverage and fungal community. The result suggested significant but weak association between plant–soil properties and soil fungal community at local scale. Patchy pattern of S. chamaejasme may disturb spatial variations of soil properties and fungal community, since S. chamaejasme in higher coverage corresponded to lower TK content, which contributed to a decrease in fungal diversity indirectly. Full article

(This article belongs to the Special Issue Advanced Research of Rhizosphere Microbial Activity)

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17 pages, 2797 KiB

Open AccessArticle

In Vitro Evaluation and Genome Mining of Bacillus subtilis Strain RS10 Reveals Its Biocontrol and Plant Growth-Promoting Potential

by Sajid Iqbal, Nimat Ullah and Hussnain Ahmed Janjua

Agriculture 2021, 11(12), 1273; https://doi.org/10.3390/agriculture11121273 - 15 Dec 2021

Cited by 32 | Viewed by 5013

Abstract

Recently, crop management has involved excessive use of chemical fertilizers and pesticides, compromising public health and environmental integrity. Rhizobacteria, which can enhance plant growth and protect plants from phytopathogen, are eco-friendly and have been attracting increasing attention. In the current study, Bacillus subtilis RS10 isolated from the rhizosphere region of Cynodon dactylon, inhibited the growth of indicator strains and exhibited in vitro plant growth-promoting traits. A whole-genome analysis identified numerous biosynthetic gene clusters encoding antibacterial and antifungal metabolites including bacillibactin, bogorol A, fengycin, bacteriocin, type III polyketides (PKs), and bacilysin. The plant growth-promoting conferring genes involved in nitrogen metabolism, phosphate solubilization, hydrogen sulfide, phytohormones, siderophore biosynthesis, chemotaxis and motility, plant root colonization, lytic enzymes, and biofilm formation were determined. Furthermore, genes associated with abiotic stresses such as high salinity and osmotic stress were identified. A comparative genome analysis indicated open pan-genome and the strain was identified as a novel sequence type (ST-176). In addition, several horizontal gene transfer events were found which putatively play a vital role in the evolution and new functionalities of a strain. In conclusion, the current study demonstrates the potential of RS10 antagonism against important pathogens and plant growth promotion, highlighting its application in sustainable agriculture. Full article

(This article belongs to the Special Issue Advanced Research of Rhizosphere Microbial Activity)

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16 pages, 5539 KiB

Open AccessEditor’s ChoiceArticle

Effect of Plant-Growth-Promoting Fungi on Eggplant (Solanum melongena L.) in New Reclamation Land

by Xuqing Li, Dingyi Li, Jianli Yan, Ya Zhang, Hong Wang, Jingze Zhang, Temoor Ahmed and Bin Li

Agriculture 2021, 11(11), 1036; https://doi.org/10.3390/agriculture11111036 - 22 Oct 2021

Cited by 18 | Viewed by 3872

Abstract

Land reclamation may expand the supply of usable land for food security. Immature soil is not suitable for plant growth and needs to be amended by the addition of organic matter and plant growth-promoting (PGP) microorganisms. However, the effects of different PGP fungi on plant growth in immature soil are largely unexplored. In order to obtain beneficial soil microorganisms with a good PGP ability in new reclamation land, 162 fungal isolates were isolated from different abandoned wastelands, four isolates of which were obtained in this study by the screening of P solubilization, siderophore production, and indole acetic acid (IAA) production. The result of this study revealed that isolate HZ123 had the highest ability to solubilize P and produce siderophores and IAA, followed by HZ23, HZ10, and HZ06. Based on the results of morphological and molecular analyses, isolate HZ06 was identified as Penicillium oxalicum, isolates HZ23 and HZ10 were identified as Aspergillus brunneoviolaceus, and isolate HZ123 was identified as Aspergillustubingensis. Furthermore, the results of in vivo PGP assays demonstrated that isolate HZ123 has a minimal negative effect on the growth of eggplant; however, the other three isolates, particularly isolate HZ06, caused the greatest increase in eggplant biomasses. Overall, these results indicate that isolate HZ06 has great potential as a PGP fungus to develop biofertilizer for application in eggplant production in immature soil from new reclamation land. Full article

(This article belongs to the Special Issue Advanced Research of Rhizosphere Microbial Activity)

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