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A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Environmental Microbiology".

Deadline for manuscript submissions: closed (31 January 2025) | Viewed by 13575

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Special Issue Editor

Dr. Wen-Ching Chen

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Guest Editor

International Bachelor Program in Agribusiness, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung 40227, Taiwan
Interests: soil remediation; soil microbiology; pesticide; environmental toxicology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue aims to explore the pivotal role of microorganisms in enhancing agricultural productivity, sustainability and resilience. Microorganisms, including bacteria, fungi, viruses, archaea and protozoa, play diverse and crucial roles in agricultural ecosystems, influencing soil health, plant growth, nutrient cycling, disease suppression and the overall ecosystem functioning.

In this Special Issue, original research articles, reviews and perspectives are welcome. Research areas may include various aspects of microbial involvement in agriculture, including, but not limited to:

Crop–Microbe Interactions: Research focusing on the symbiotic and pathogenic interactions between crops and microorganisms, including beneficial associations such as mycorrhizal symbiosis, nitrogen-fixing bacteria and biocontrol agents against plant pathogens.
Microbial Biostimulants and Biofertilizers: Exploration of microbial-based products and formulations designed to enhance crop growth, nutrient uptake, stress tolerance and overall crop productivity in sustainable agricultural practices.
Microbial Control of Crop Diseases: Investigations into the mechanisms underlying microbial biocontrol agents' efficacy against phytopathogens and the development of novel strategies for managing crop diseases while minimizing environmental impacts.
Microbial Bioremediation: Studies assessing the potential of microorganisms to degrade pollutants, detoxify soil and mitigate environmental contamination in agricultural settings.
Microbial Diversity and Functional Genomics: Utilization of advanced molecular techniques and omics approaches to characterize microbial communities, identify key functional genes and decipher metabolic pathways relevant to agricultural ecosystems.

Dr. Wen-Ching Chen
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. Microorganisms 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 2700 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

bio-fertilizer
bio-pesticide
functional microbes
microbial ecology
plant growth-promoting microoganism
bio-remediation

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Published Papers (11 papers)

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Research

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20 pages, 5634 KiB

Open AccessArticle

Association Analysis of the Genomic and Functional Characteristics of Halotolerant Glutamicibacter endophyticus J2-5-19 from the Rhizosphere of Suaeda salsa

by Longhao Sun, Shanshan Sun, Tianyang Liu, Xinmin Lei, Ruiqi Liu, Junyi Zhang, Shanshan Dai, Jing Li and Yanqin Ding

Microorganisms 2025, 13(1), 208; https://doi.org/10.3390/microorganisms13010208 - 18 Jan 2025

Viewed by 730

Abstract

Halotolerant plant growth-promoting bacteria (HT-PGPB) have attracted considerable attention for their significant potential in mitigating salt stress in crops. However, the current exploration and development of HT-PGPB remain insufficient to meet the increasing demands of agriculture. In this study, an HT-PGPB isolated from coastal saline-alkali soil in the Yellow River Delta was identified as Glutamicibacter endophyticus J2-5-19. The strain was capable of growing in media with up to 13% NaCl and producing proteases, siderophores, and the plant hormone IAA. Under 4‰ salt stress, inoculation with strain J2-5-19 significantly increased the wheat seed germination rate from 37.5% to 95%, enhanced the dry weight of maize seedlings by 41.92%, and notably improved the development of maize root systems. Moreover, this work presented the first whole-genome of Glutamicibacter endophyticus, revealing that G. endophyticus J2-5-19 resisted salt stress by expelling sodium ions and taking up potassium ions through Na⁺/H⁺ antiporters and potassium uptake proteins, while also accumulating compatible solutes such as betaine, proline, and trehalose. Additionally, the genome contained multiple key plant growth-promoting genes, including those involved in IAA biosynthesis, siderophore production, and GABA synthesis. The findings provide a theoretical foundation and microbial resources for the development of specialized microbial inoculants for saline-alkali soils. Full article

(This article belongs to the Special Issue Microorganisms in Agriculture)

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13 pages, 1052 KiB

Open AccessArticle

Microorganism Strains, Environmentally Friendly and Biological Preparations Against Meloidogyne hapla Chitwood, 1949 and Their Impact on Fruit Quality and Tomato Crop Structure

by Svetlana Nikolaevna Nekoval, Arina Konstantinovna Churikova, Oksana Aleksandrovna Maskalenko, Zhanneta Zaurovna Tukhuzheva and Valentin Valentinovich Ivanov

Microorganisms 2024, 12(12), 2586; https://doi.org/10.3390/microorganisms12122586 - 13 Dec 2024

Viewed by 513

Abstract

The primary aim of this research was to study the effectiveness of various strains of antagonist microorganisms and biological preparations against Meloidogyne hapla, in addition to their impact on the quality of tomato fruits and crop structure. Four microorganism strains and three registered environmentally safe nematicides were used in the experiment presented herein. The results showed that the strains Paecilomyces lilacinus F-22BK/6 and Arthrobotrys conoides F-22BK/4 had the greatest biological efficacy, reducing the number of galls on tomato plants by 91.8% and 88.4%, values comparable with the results of the chemical control Vydate 5G. The Metarhizium anisopliae F-22BK/2 and Arthrobotrys conoides F-22BK/4 treatments showed the best results, increasing the fruit weight by 8.6% and 9.9%, in addition to increasing the tomato yield by 5.0% and 13.3%. These strains contributed to an increase in sugar content, whereas the concentration of vitamin C was reduced in the Trichoderma viride F-294 and Fitoverm treatments, indicating a high level of oxidative stress in the latter treatments. The results of this study confirm the prospects of using biological nematicides against phytoparasitic nematodes, which will not only enable effective control of their population but also improve the quality of agricultural products, minimizing harm to the environment and human health. Full article

(This article belongs to the Special Issue Microorganisms in Agriculture)

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18 pages, 2488 KiB

Open AccessArticle

Individual and Combined Effects of Nanoplastics and Cadmium on the Rhizosphere Bacterial Community of Sedum alfredii Hance

by Yixiu Wang, Hongyan Cheng, Yuenan Li, Ruiyan Ning, Yonghui Lv, Qing Wang, Haibo Zhang and Na Liu

Microorganisms 2024, 12(12), 2471; https://doi.org/10.3390/microorganisms12122471 - 1 Dec 2024

Viewed by 830

Abstract

Nanoplastics (NPs) and cadmium (Cd) coexist in soil, but the combined effects of NPs and Cd on the rhizosphere bacterial community remain unknown. In this study, high-throughput sequencing and PICRUSt2 functional analysis were employed to explore the individual and combined effects of polystyrene (PS) NPs (low concentration [N1, 100 mg·kg⁻¹] and high concentration [N2, 1000 mg·kg⁻¹]) and Cd (low concentration [C1, 0.6 mg·kg⁻¹] and high concentration [C2, 4 mg·kg⁻¹]) on the diversity, structural composition, and function of the rhizosphere bacterial community associated with Sedum alfredii Hance. Individually, PS NPs and Cd significantly reduced the soil pH, while the combined treatments induced a more significant decrease in pH. In contrast, combined PS NPs and Cd significantly increased the diethylenetriaminepentaacetic acid–Cd (DTPA-Cd) and total Cd concentrations. Compared with individual treatments, C2N2 significantly increased DPTA-Cd by 4.08%. N1 had no significant effect on the Chao1, observed species, or Shannon indices, while N2 significantly reduced the richness and diversity of the rhizosphere bacteria and altered their community structure. Furthermore, adding PS NPs exacerbated the effect of Cd on rhizosphere bacterial communities. Compared with individual Cd treatments, C2N2 significantly reduced the relative abundances of Actinobacteriota, Bacteroidota, Crenarchaeota, and Myxococcota by 19.76%, 2.01%, 1.49%, and 2.00%, respectively, and significantly increased the relative abundance of Acidobacteriota by 16.05%. A cluster heat map showed that the combined treatments attenuated glycan biosynthesis and metabolic function and enhanced the metabolism of cofactors and vitamins. These findings illuminate rhizosphere processes under co-contamination with heavy metals and PS NPs, supporting the practical application of phytoremediation to alleviate combined Cd and PS NP pollution. Full article

(This article belongs to the Special Issue Microorganisms in Agriculture)

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16 pages, 4757 KiB

Open AccessArticle

Whole Genome Sequencing and Biocontrol Potential of Streptomyces luteireticuli ASG80 Against Phytophthora Diseases

by Gang Xu, Weihuai Wu, Liqian Zhu, Yanqiong Liang, Minli Liang, Shibei Tan, Helong Chen, Xing Huang, Chunping He, Ying Lu, Kexian Yi and Xiang Ma

Microorganisms 2024, 12(11), 2255; https://doi.org/10.3390/microorganisms12112255 - 7 Nov 2024

Viewed by 1047

Abstract

Phytophthora-induced crop diseases, commonly known as “plant plagues”, pose a significant threat to global food security. In this study, strain ASG80 was isolated from sisal roots and demonstrated a broad-spectrum antagonistic activity against several Phytophthora species and fungal pathogens. Strain ASG80 was identified as Streptomyces luteireticuli via phylogenetic analysis, digital DNA–DNA hybridization (dDDH), and average nucleotide identity (ANI). Whole-genome sequencing identified 40 biosynthetic gene clusters (BGCs) related to secondary metabolite production, including antimicrobial compounds. Strain ASG80 extract exhibited broad-spectrum inhibitory activity against Phytophthora nicotianae, P. vignae, P. cinnamomi, and P. sojae. Pot experiments showed that strain ASG80 extract significantly reduced sisal zebra disease incidence, with an efficacy comparable to the fungicide metalaxyl. These findings suggest that strain ASG80 is a promising biocontrol agent with substantial potential for managing Phytophthora-related diseases in agriculture. Full article

(This article belongs to the Special Issue Microorganisms in Agriculture)

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21 pages, 12433 KiB

Open AccessArticle

Biocontrol Activity of Bacillus altitudinis CH05 and Bacillus tropicus CH13 Isolated from Capsicum annuum L. Seeds against Fungal Strains

by Merle Ariadna Espinosa Bernal, Mayra Paola Mena Navarro, Jackeline Lizzeta Arvizu Gómez, Carlos Saldaña, Miguel Ángel Ramos López, Aldo Amaro Reyes, Monserrat Escamilla García, Juan Ramiro Pacheco Aguilar, Victor Pérez Moreno, José Alberto Rodríguez Morales, Erika Álvarez Hidalgo, Jorge Nuñez Ramírez, José Luis Hernández Flores and Juan Campos Guillén

Microorganisms 2024, 12(10), 1943; https://doi.org/10.3390/microorganisms12101943 - 25 Sep 2024

Viewed by 1457

Abstract

In this study, seed-surface-associated bacteria from fresh fruits of Capsicum spp. were analyzed to explore potential isolates for biocontrol of phytopathogenic fungal strains. A total of 76 bacterial isolates were obtained from three different species of chili pepper (C. annuum L., C. pubescens R. & P., and C. chinense Jacq.), and two isolates were selected via mycelial growth inhibition assays based on their production of volatile organic compounds (VOCs) against six fungal strains. Genomic analysis identified these isolates as Bacillus altitudinis CH05, with a chromosome size of 3,687,823 bp and with 41.25% G+C, and Bacillus tropicus CH13, with a chromosome size of 5,283,706 bp and with 35.24% G+C. Both bacterial strains showed high mycelial growth inhibition capacities against Sclerotium rolfsii, Sclerotinia sp., Rhizoctonia solani, and Alternaria alternata but lower inhibition capacities against Colletotrichum gloesporoides and Fusarium oxysporum. VOC identification was carried out after 24 h of fermentation with 64 VOCs for B. altitudinis CH05 and 53 VOCs for B. tropicus CH13. 2,5-Dimethyl pyrazine and acetoin had the highest relative abundance values in both bacterial strains. Our findings revealed that seed-surface-associated bacteria on Capsicum spp. have the metabolic ability to produce VOCs for biocontrol of fungal strains and have the potential to be used in sustainable agriculture. Full article

(This article belongs to the Special Issue Microorganisms in Agriculture)

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19 pages, 2758 KiB

Open AccessArticle

Dose Effect of Polyethylene Microplastics Derived from Commercial Resins on Soil Properties, Bacterial Communities, and Enzymatic Activity

by Lesbia Gicel Cruz, Fo-Ting Shen, Chiou-Pin Chen and Wen-Ching Chen

Microorganisms 2024, 12(9), 1790; https://doi.org/10.3390/microorganisms12091790 - 29 Aug 2024

Viewed by 873

Abstract

Soils are the largest reservoir of microplastics (MPs) on earth. Since MPs can remain in soils for a very long time, their effects are magnified. In this study, different concentrations of polyethylene (PE) MPs derived from commercial resins (0%, 1%, 7%, and 14%, represented as MP_0, MP_1, MP_7, and MP_14) were added to soils to assess the changes in the soils’ chemical properties, enzyme activities, and bacterial communities during a 70-day incubation period. The results show that PE MP treatments with low concentrations differed from other treatments in terms of exchangeable Ca and Mg, whereas at high concentrations, the pH and availability of phosphate ions differed. Fluorescein diacetate (FDA), acid phosphatase (ACP), and N-acetyl-β-d-glucosaminidase (NAG) enzyme activities exhibited a dose-related trend with the addition of the PE MPs; however, the average FDA and ACP activities were significantly affected only by MP_14. Changes in the microbial communities were observed at both the phylum and family levels with all PE MP treatments. It was revealed that even a low dosage of PE MPs in soils can affect the functional microbes, and a greater impact is observed on those that can survive in polluted environments with limited resources. Full article

(This article belongs to the Special Issue Microorganisms in Agriculture)

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19 pages, 690 KiB

Open AccessArticle

Response of Arugula to Integrated Use of Biological, Inorganic, and Organic Fertilization

by Aleksandra Stanojković-Sebić, Vladimir Miladinović, Olivera Stajković-Srbinović and Radmila Pivić

Microorganisms 2024, 12(7), 1334; https://doi.org/10.3390/microorganisms12071334 - 29 Jun 2024

Cited by 2 | Viewed by 1485 | Correction

Abstract

This study evaluated the effects of solely and integrated application of inorganic (NPK), commercial organic (NC), and biological (MIX, mixed strains Ensifer meliloti and Azotobacter chroococcum) fertilizers on the chemical characteristics of arugula biomass and its yield, as well as changes in soil microbiological parameters after the experiment in relation to the control treatment (Ø). The experiment was performed in semi-controlled greenhouse conditions, in pots, from the 4th decade of March to the 2nd decade of September, in 2023, at three cutting times/swaths, during one agricultural season, with Vertisol soil. For soil characterization, the following parameters were analysed: granulometric composition using sieving and sedimentation procedure; soil acidity—potentiometrically; SOM—soil organic matter by Kotzmann method; total N using CNS analyser; available P—spectrophotometrically; available K—flame photometrically; total number of microorganisms on an agarized soil extract medium; fungi on a solid Czapek agar; actinomycetes on a solid Krasiljnikov agar with saccharose; Azotobacter spp. on a liquid Fyodorov medium with mannitol; ammonifiers on a liquid medium with asparagine; and dehydrogenase activity—spectrophotometrically. For plant characterization, the following parameters were determined: N and C, both on CNS analyser; P on spectrophotometer; K on flame photometer; air-dried yield biomass. A stimulative effect on all microbiological parameters was found in the treatment with integrated use of organic and biological fertilizer, except for fungi, which grew better in the treatments with separate inorganic and organic fertilizers. Generally, the stimulative impact on plant chemical parameters manifested in combined inorganic and biological, organic and biological, and inorganic and organic fertilization treatments, and was inhibited in treatment without fertilization, in all three swaths, which could also be stated for the plant yield. Positive influence of all fertilization treatments on chemical parameters was observed for the second swath in relation to the first and the third. The total yield in the NPK+MIX treatment was 121%, and in the NC+MIX treatment, it was 87% higher compared to the control (Ø). In general, integrated use of inorganic and biological, organic and biological, and inorganic and organic fertilizers, respectively, could be proposed as an optimal fertilization treatment in arugula cultivation. Full article

(This article belongs to the Special Issue Microorganisms in Agriculture)

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17 pages, 2682 KiB

Open AccessArticle

Innovative Microbial Immobilization Strategy for Di-n-Butyl Phthalate Biodegradation Using Biochar-Calcium Alginate-Waterborne Polyurethane Composites

by Xuan-Di Cao, Shih-Hao Jien, Chu-Wen Yang, Yi-Hsuan Lin and Chien-Sen Liao

Microorganisms 2024, 12(7), 1265; https://doi.org/10.3390/microorganisms12071265 - 22 Jun 2024

Cited by 1 | Viewed by 1188

Abstract

Di-n-butyl phthalate (DBP) is a prevalent phthalate ester widely used as a plasticizer, leading to its widespread presence in various environmental matrices. This study presents an innovative microbial immobilization strategy utilizing biochar, calcium alginate (alginate-Ca, (C₁₂H₁₄CaO₁₂)n), and waterborne polyurethane (WPU) composites to enhance the biodegradation efficiency of DBP. The results revealed that rice husk biochar, pyrolyzed at 300 °C, exhibits relatively safer and more stable physical and chemical properties, making it an effective immobilization matrix. Additionally, the optimal cultural conditions for Bacillus aquimaris in DBP biodegradation were identified as incubation at 30 °C and pH 7, with the supplementation of 0.15 g of yeast extract, 0.0625 g of glucose, and 1 CMC of Triton X-100. Algal biotoxicity results indicated a significant decrease in biotoxicity, as evidenced by an increase in chlorophyll a content in Chlorella vulgaris following DBP removal from the culture medium. Finally, microbial community analysis demonstrated that encapsulating B. aquimaris within alginate-Ca and WPU layers not only enhanced DBP degradation, but also prevented ecological competition from indigenous microorganisms. This novel approach showcases the potential of agricultural waste utilization and microbial immobilization techniques for the remediation of DBP-contaminated environments. Full article

(This article belongs to the Special Issue Microorganisms in Agriculture)

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15 pages, 4103 KiB

Open AccessArticle

Purpureocillium lilacinum SBF054: Endophytic in Phaseolus vulgaris, Glycine max, and Helianthus annuus; Antagonistic to Rhizoctonia solani; and Virulent to Euschistus heros

by Flávia Melo Moreira, Túlio Iglésias Machado, Caio Augusto Rosado Torres, Hebert Ribeiro de Souza, Matheus Felipe Celestino, Marco Antônio Silva, Giovana Cidade Gomes, Breno Beda dos Reis Cunha, Pedro de Luca Buffon dos Santos, Magno Rodrigues de Carvalho Filho, Marcelo Tavares de Castro and Rose Gomes Monnerat

Microorganisms 2024, 12(6), 1100; https://doi.org/10.3390/microorganisms12061100 - 29 May 2024

Viewed by 1417

Abstract

Microorganisms with multiple ecological functions can be a useful biotechnological resource in integrated pest- and disease-management programs. This work aimed to investigate the potential endophytic and virulent effects of a strain of Purpureocillium lilacinum on organic cultivation in Brazil. Specifically, the strain’s ability to establish itself as an endophyte in common bean, soybean, and sunflower plants when inoculated via seed was evaluated. Furthermore, its antifungal activity against phytopathogens and its pathogenicity and virulence against insects of the order Lepidoptera, Coleoptera, and Hemiptera were evaluated. Furthermore, the strain was evaluated for its biochemical and physiological characteristics. For virulence bioassays, the experiments were conducted under a factorial scheme (2 × 3), with the following factors: (a) fungal inoculation and control without inoculum and (b) types of inocula (blastospores, aerial conidia, and metabolites). The treatments were sprayed on insect species at different stages of development. In summary, it was found that the SBF054 strain endophytically colonized the common bean, with partial recovery from the root tissues of soybean and sunflower plants, 30 days after inoculation; suppressed 86% of Rhizoctonia solani mycelial growth in an in vitro assay; and controlled eggs, nymphs, and Euschistus heros adults. These multifunctional abilities are mainly attributed to the strain’s mechanisms of producing metabolites, such as organic acids, soluble nutrients, and hydrolytic enzymes. Full article

(This article belongs to the Special Issue Microorganisms in Agriculture)

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Review

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36 pages, 3143 KiB

Open AccessReview

Arbuscular Mycorrhizal Fungi: Boosting Crop Resilience to Environmental Stresses

by Wenjing Nie, Qinghai He, Hongen Guo, Wenjun Zhang, Lan Ma, Junlin Li and Dan Wen

Microorganisms 2024, 12(12), 2448; https://doi.org/10.3390/microorganisms12122448 - 28 Nov 2024

Cited by 1 | Viewed by 1771

Abstract

Amid escalating challenges from global climate change and increasing environmental degradation, agricultural systems worldwide face a multitude of abiotic stresses, including drought, salinity, elevated temperatures, heavy metal pollution, and flooding. These factors critically impair crop productivity and yield. Simultaneously, biotic pressures such as pathogen invasions intensify the vulnerability of agricultural outputs. At the heart of mitigating these challenges, Arbuscular Mycorrhizal Fungi (AM fungi) form a crucial symbiotic relationship with most terrestrial plants, significantly enhancing their stress resilience. AM fungi improve nutrient uptake, particularly that of nitrogen and phosphorus, through their extensive mycelial networks. Additionally, they enhance soil structure, increase water use efficiency, and strengthen antioxidant defense mechanisms, particularly in environments stressed by drought, salinity, extreme temperatures, heavy metal contamination, and flooding. Beyond mitigating abiotic stress, AM fungi bolster plant defenses against pathogens and pests by competing for colonization sites and enhancing plant immune responses. They also facilitate plant adaptation to extreme environmental conditions by altering root morphology, modulating gene expression, and promoting the accumulation of osmotic adjustment compounds. This review discusses the role of AM fungi in enhancing plant growth and performance under environmental stress. Full article

(This article belongs to the Special Issue Microorganisms in Agriculture)

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