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Functional Diversity of Soil Microbial Communities in Environments Shaped by...
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Functional Diversity of Soil Microbial Communities in Environments Shaped by Anthropogenic Activities

A special issue of Agronomy (ISSN 2073-4395). This special issue belongs to the section "Agroecology Innovation: Achieving System Resilience".

Deadline for manuscript submissions: 30 November 2025 | Viewed by 8192

Special Issue Editors

Dr. Franco Magurno

E-Mail Website
Guest Editor
Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Jagiellońska 28, 40-032 Katowice, Poland
Interests: mycorrhiza fungi; arbuscular mycorrhiza; mycorrhizal symbiosis; soil microorganism
Special Issues, Collections and Topics in MDPI journals
Dr. Zoltán Kende

E-Mail Website
Guest Editor
Institute of Agronomy, Hungarian University of Agriculture and Life Sciences, Páter Károly u.1, 2100 Gödöllő, Hungary
Interests: soil management; adaptable soil tillage; nutrient management; crop production; impacts of climate change
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The current geological epoch, i.e., the Anthropocene, is profoundly affected by the expansion of environments shaped by human activities such as agriculture, industry, urbanization, etc. As a consequence, the human population is facing, on the one hand, the consequences of more than half of the terrestrial ecosystems having turned into anthropogenic ecosystems, and on the other hand, the dependence on services provided by ecosystems of unknown functional mechanisms. Soil microbial communities are undoubtedly key players in vital ecosystem processes such as primary production, decomposition, nutrient cycling, and carbon storage. For a long time, taxonomic richness has been used as an indirect measure of the potential contribution of microbial communities in the functioning of ecosystems. In recent decades, this perspective has been challenged, and the diversity of functions performed by microbial communities has received increasing recognition as the missing link between biodiversity patterns and ecosystem functions.

In this Special Issue of Agronomy, we invite you to submit both original research and review-type contributions regarding the use of available tools (metatranscriptomic approach, enzymatic assay, etc.) for the assessment of changes in the functional diversity of soils under the pressure of any anthropogenic activity.

Dr. Franco Magurno
Dr. Zoltán Kende
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

  • soil microbial communities
  • functional diversity
  • anthropogenic activities
  • biodiversity
  • ecosystem functions
  • ecosystem processes

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Published Papers (5 papers)

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Research

Jump to: Review

15 pages, 1157 KiB  
Article
Bacillus Strains Isolated from Agroforestry Systems in the Amazon Promote Açaí Palm Seedling Growth When Inoculated as a Consortium
by Josinete Torres Garcias, Rosiane do Socorro dos Reis de Sousa, Suania Maria do Nascimento Sousa, Lucimar Di Paula dos Santos Madeira, Allana Laís Alves Lima, Jackeline Rosseti Mateus, Joyce Kelly do Rosário da Silva, Lucy Seldin, Hervé Louis Ghislain Rogez and Joana Montezano Marques
Agronomy 2025, 15(3), 569; https://doi.org/10.3390/agronomy15030569 - 25 Feb 2025
Viewed by 562
Abstract
The hypothesis that cultivating açaí in agroforestry systems (AFS) can recruit beneficial microorganisms to its rhizosphere was tested in this study. For this purpose, rhizospheric soil samples were collected from an AFS area. The colony-forming unit (CFU) counts of the soil samples were [...] Read more.
The hypothesis that cultivating açaí in agroforestry systems (AFS) can recruit beneficial microorganisms to its rhizosphere was tested in this study. For this purpose, rhizospheric soil samples were collected from an AFS area. The colony-forming unit (CFU) counts of the soil samples were 3.5 × 106 CFU/g, with no statistically significant differences between the plants (p < 0.05). Regarding PGPR characteristics, of the 44 isolated strains, 18% produced siderophores, 9% mineralized organic phosphate, 15% solubilized inorganic phosphate, and 7% produced indole-3-acetic acid (IAA) and antimicrobial substances. Strains AP4-03, AP1-33, and AP2-36 were affiliated with the genus Bacillus sp. and produced IAA at 1.45, 1.35, and 2.02 µg/mL, respectively. Furthermore, these strains were able to inhibit the growth of the fungus Pestalotiopsis by 69%, 67%, and 71%, respectively. Regarding the antifungal activity of bacterial extracts, inhibition zones of 23 mm (AP-03), 20 mm (AP-33), and 18 mm (AP-36), with 96% and 92% inhibition at 50 mg/mL (AP4-03 and AP1-33) and 100% inhibition at 41 mg/mL (AP2-36), were observed. Considering seedling germination, açaí palms inoculated with the strain AP1-33 statistically differed from the controls in terms of root length and hypocotyl length. Furthermore, treatments inoculated with the strain AP2-36 or all strains in the consortium differed when only the hypocotyl length was compared to the control. Thus, the analyzed strains showed potential to improve the initial development of açaí plants. Full article
(This article belongs to the Special Issue Functional Diversity of Soil Microbial Communities in Environments Shaped by Anthropogenic Activities)
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18 pages, 2293 KiB  
Article
Nodules of Medicago spp. Host a Diverse Community of Rhizobial Species in Natural Ecosystems
by Andrei Stefan, Jannick Van Cauwenberghe, Craita Maria Rosu, Catalina Stedel, Crystal Chan, Ellen L. Simms, Catalina Iticescu, Daniela Tsikou, Emmanouil Flemetakis and Rodica Catalina Efrose
Agronomy 2024, 14(9), 2156; https://doi.org/10.3390/agronomy14092156 - 21 Sep 2024
Cited by 2 | Viewed by 1657
Abstract
Biological nitrogen fixation by rhizobia-nodulated legumes reduces the dependence on synthetic nitrogen fertilizers. Identification of locally adapted rhizobia may uncover economically valuable strains for sustainable agriculture. This study investigated the diversity and symbiotic potential of rhizobia associated with three Medicago species from Eastern [...] Read more.
Biological nitrogen fixation by rhizobia-nodulated legumes reduces the dependence on synthetic nitrogen fertilizers. Identification of locally adapted rhizobia may uncover economically valuable strains for sustainable agriculture. This study investigated the diversity and symbiotic potential of rhizobia associated with three Medicago species from Eastern Romania’s ecosystems. Phenotypic screening ensured that only rhizobial species were retained for molecular characterization. 16S rDNA sequencing clustered the isolates into four distinct groups: Sinorhizobium meliloti, Sinorhizobium medicae, Rhizobium leguminosarum, and Mesorhizobium spp. The chromosomal genes (atpD, glnII, recA) and nifH phylogenies were congruent, while the nodA phylogeny grouped the Mesorhizobium spp. isolates with R. leguminosarum. Medicago sativa was the most sampled plant species, and only S. meliloti and R. leguminosarum were found in its nodules, while Medicago falcata nodules hosted S. meliloti and Mesorhizobium spp. Medicago lupulina was the only species that hosted all four identified rhizobial groups, including S. medicae. This study provides the first report on the Mesorhizobium spp. associated with M. falcata nodules. Additionally, R. leguminosarum and two Mesorhizobium genospecies were identified as novel symbionts for Medicago spp. Comparative analysis of Medicago-associated rhizobia from other studies revealed that differences in 16S rDNA sequence type composition were influenced by Medicago species identity rather than geographic region. Full article
(This article belongs to the Special Issue Functional Diversity of Soil Microbial Communities in Environments Shaped by Anthropogenic Activities)
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18 pages, 7149 KiB  
Article
Borrow Pit Disposal of Coal Mining Byproducts Improves Soil Physicochemical Properties and Vegetation Succession
by Jawdat Bakr, Agnieszka Kompała-Bąba, Wojciech Bierza, Damian Chmura, Agnieszka Hutniczak, Jacek Kasztowski, Bartosz Jendrzejek, Adrian Zarychta and Gabriela Woźniak
Agronomy 2024, 14(8), 1638; https://doi.org/10.3390/agronomy14081638 - 26 Jul 2024
Cited by 1 | Viewed by 1361
Abstract
The way of disposing of rock mineral material has a significant impact on subsequent spontaneous vegetation succession, soil properties, and respiration. We compared seven spontaneously vegetated samples from a large (2 km2) borrow pit used to dispose of the byproducts of [...] Read more.
The way of disposing of rock mineral material has a significant impact on subsequent spontaneous vegetation succession, soil properties, and respiration. We compared seven spontaneously vegetated samples from a large (2 km2) borrow pit used to dispose of the byproducts of a hard coal mine with seven plots from four coal mine spoil heap piles. We used BIOLOG EcoPlates to assess the microbial catabolic activity of the substrate. The substrate in the borrow pit was characterized by higher water content and lower temperature compared to the heap pile substrate. The borrow pit had a more diverse plant community structure. Higher Rao’s quadratic entropy, functional richness, and functional divergence were also calculated from plant functional traits in borrow pit samples. Although borrow pit samples showed higher total microbial biomass, bacteria/fungi ratio, and gram+/gram− ratio, and heap pile samples showed higher soil enzymatic activity, microbial functional diversity, and catabolic activity, these differences were not significant. Soil respiration from the borrow pit substrate was two folds higher. The borrow pit method of disposing of rock mineral material can be suggested to speed up spontaneous vegetation succession. This research provides new insights into the effects of burying hard coal byproducts in borrow pits and offers guidance for the management of hard coal mining. Full article
(This article belongs to the Special Issue Functional Diversity of Soil Microbial Communities in Environments Shaped by Anthropogenic Activities)
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15 pages, 3871 KiB  
Article
Glomus mongioiense, a New Species of Arbuscular Mycorrhizal Fungi from Italian Alps and the Phylogeny-Spoiling Issue of Ribosomal Variants in the Glomus Genus
by Franco Magurno, Sylwia Uszok, Karolina Bierza, Jawdat Bakr, Zoltan Kende, Mariana Bessa de Queiroz and Leonardo Casieri
Agronomy 2024, 14(7), 1350; https://doi.org/10.3390/agronomy14071350 - 21 Jun 2024
Cited by 2 | Viewed by 2232
Abstract
Glomus mongioiense, a new species of arbuscular mycorrhizal fungi (AMF) in the family Glomeraceae, was isolated from rhizosphere soil collected from a meadow in the Italian Alps. The novelty of the species and its relationship with other species of the same genus [...] Read more.
Glomus mongioiense, a new species of arbuscular mycorrhizal fungi (AMF) in the family Glomeraceae, was isolated from rhizosphere soil collected from a meadow in the Italian Alps. The novelty of the species and its relationship with other species of the same genus were obtained by morphological and phylogenetic (45S nrDNA + RPB1 gene) analyses. Two glomoid spore-producing AMF isolates from a saltmarsh of the Scottish Highlands and maritime sand dunes of the Baltic Sea in Poland, were also included in this study and later found to be conspecific with G. rugosae. Phylogenetic placement analysis using environmental sequences indicated that G. mongioiense sp. nov. seems to be a rare species. Furthermore, the molecular and phylogenetic analysis provided important insights into the presence of highly divergent ribosomal variants in several Glomus species, with potential negative implication in phylogeny and species recognition. Full article
(This article belongs to the Special Issue Functional Diversity of Soil Microbial Communities in Environments Shaped by Anthropogenic Activities)
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Review

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21 pages, 976 KiB  
Review
Engineering Synthetic Microbial Communities: Diversity and Applications in Soil for Plant Resilience
by Arneeb Tariq, Shengzhi Guo, Fozia Farhat and Xihui Shen
Agronomy 2025, 15(3), 513; https://doi.org/10.3390/agronomy15030513 - 20 Feb 2025
Viewed by 1636
Abstract
Plants host a complex but taxonomically assembled set of microbes in their natural environment which confer several benefits to the host plant including stress resilience, nutrient acquisition and increased productivity. To understand and simplify the intricate interactions among these microbes, an innovative approach—Synthetic [...] Read more.
Plants host a complex but taxonomically assembled set of microbes in their natural environment which confer several benefits to the host plant including stress resilience, nutrient acquisition and increased productivity. To understand and simplify the intricate interactions among these microbes, an innovative approach—Synthetic Microbial Community (SynCom)—is practiced, involving the intentional co-culturing of multiple microbial taxa under well-defined conditions mimicking natural microbiomes. SynComs hold promising solutions to the issues confronted by modern agriculture stemming from climate change, limited resources and land degradation. This review explores the potential of SynComs to enhance plant growth, development and disease resistance in agricultural settings. Despite the promising potential, the effectiveness of beneficial microbes in field applications has been inconsistent. Computational simulations, high-throughput sequencing and the utilization of omics databases can bridge the information gap, providing insights into the complex ecological and metabolic networks that govern plant–microbe interactions. Artificial intelligence-driven models can predict complex microbial interactions, while machine learning algorithms can analyze vast datasets to identify key microbial taxa and their functions. We also discuss the barriers to the implementation of these technologies in SynCom engineering. Future research should focus on these innovative applications to refine SynCom strategies, ultimately contributing to the advancement of green technologies in agriculture. Full article
(This article belongs to the Special Issue Functional Diversity of Soil Microbial Communities in Environments Shaped by Anthropogenic Activities)
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