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Role of Microorganisms and Their Metabolites in Agriculture, Food and the Environment: 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 Microbiology".

Deadline for manuscript submissions: 20 January 2025 | Viewed by 7886

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Prof. Dr. Barbara Sokolowska

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1. Department of Microbiology, Prof. Wacław Dąbrowski Institute of Agricultural and Food Biotechnology—State Research Institute, 02-532 Warsaw, Poland
2. Institute of High Pressure Physics, Polish Academy of Sciences, 01-142 Warsaw, Poland
Interests: food microbiology; food safety; high pressure food processing; Alicyclobacillus acidoterrestris; bacteriophage; biopreservation; biocontrol; biobanking
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Dear Colleagues,

Even though people have been using microorganisms for thousands of years, they still surprise us with their possibilities.

The production of fermented foods is one of the oldest food processing technologies and has been known since ancient times. Nowadays, microorganisms are used in the production of foods not only as a strategy for food preservation but also for improving specific characteristics, such as flavor, aroma, texture and digestibility.

The antagonistic activity of microorganisms is widely used, both in biological plant protection to reduce environmental degradation due to the widespread use of fungicides and against food-borne pathogens to prevent disease.

In turn, the ability of microorganisms to adsorb, accumulate and degrade common and emerging pollutants has attracted the use of biological resources in treating contaminated food, feed and the environment.

This Special Issue will attempt to shed light on the molecular aspects and enhance the current research in the field of new high-throughput technologies, such as genomics, metagenomics, transcriptomics, metatranscriptomics and metabolomics, allowing a more thorough description of the microbial constituents of the different environments.

As volume 1 of the Special Issue “Role of Microorganisms and Their Metabolites in Agriculture, Food and the Environment” was successful, we reopen this issue again in the International Journal of Molecular Sciences (https://www.mdpi.com/journal/ijms, ISSN 1422-0067, IF 5.6, JCR Category Q1). This second Special Issue, “Role of Microorganisms and Their Metabolites in Agriculture, Food and the Environment: 2nd Edition”, welcomes original manuscripts and review articles addressing this hot topic.

Prof. Dr. Barbara Sokolowska
Guest Editor

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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

fermentation
biopreservation
biocontrol
biodegradation
bioremediation
bioaugmentation
omic-technologies

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Related Special Issue

Role of Microorganisms and Their Metabolites in Agriculture, Food and the Environment in International Journal of Molecular Sciences (11 articles)

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Research

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17 pages, 2257 KiB

Open AccessArticle

Impact of Agroforestry Practices on Soil Microbial Diversity and Nutrient Cycling in Atlantic Rainforest Cocoa Systems

by Sayure Mariana Raad Nahon, Felipe Costa Trindade, Caio Augusto Yoshiura, Gabriel Caixeta Martins, Isa Rebecca Chagas da Costa, Paulo Henrique de Oliveira Costa, Héctor Herrera, Diego Balestrin, Tiago de Oliveira Godinho, Bia Makiyama Marchiori and Rafael Borges da Silva Valadares

Int. J. Mol. Sci. 2024, 25(21), 11345; https://doi.org/10.3390/ijms252111345 - 22 Oct 2024

Viewed by 801

Abstract

Microorganisms are critical indicators of soil quality due to their essential role in maintaining ecosystem services. However, anthropogenic activities can disrupt the vital metabolic functions of these microorganisms. Considering that soil biology is often underestimated and traditional assessment methods do not capture its complexity, molecular methods can be used to assess soil health more effectively. This study aimed to identify the changes in soil microbial diversity and activity under different cocoa agroforestry systems, specially focusing on taxa and functions associated to carbon and nitrogen cycling. Soils from three different cocoa agroforestry systems, including a newly established agroforestry with green fertilization (GF), rubber (Hevea brasiliensis)–cocoa intercropping (RC), and cocoa plantations under Cabruca (cultivated under the shave of native forest) (CAB) were analyzed and compared using metagenomic and metaproteomic approaches. Samples from surrounding native forest and pasture were used in the comparison, representing natural and anthropomorphic ecosystems. Metagenomic analysis revealed a significant increase in Proteobacteria and Basidiomycota and the genes associated with dissimilatory nitrate reduction in the RC and CAB areas. The green fertilization area showed increased nitrogen cycling activity, demonstrating the success of the practice. In addition, metaproteomic analyses detected enzymes such as dehydrogenases in RC and native forest soils, indicating higher metabolic activity in these soils. These findings underscore the importance of soil management strategies to enhance soil productivity, diversity, and overall soil health. Molecular tools are useful to demonstrate how changes in agricultural practices directly influence the microbial community, affecting soil health. Full article

(This article belongs to the Special Issue Role of Microorganisms and Their Metabolites in Agriculture, Food and the Environment: 2nd Edition)

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16 pages, 2606 KiB

Open AccessArticle

Enhancing the Growth of Chili Plants and Soil Health: Synergistic Effects of Coconut Shell Biochar and Bacillus sp. Strain Ya-1 on Rhizosphere Microecology and Plant Metabolism

by Shimeng Tan, Bao Wang, Qian Yun, Wanrong Yan, Tongbin Xiao and Zhixiang Zhao

Int. J. Mol. Sci. 2024, 25(20), 11231; https://doi.org/10.3390/ijms252011231 - 18 Oct 2024

Viewed by 610

Abstract

To mitigate soil degradation and decrease dependency on chemical inputs in agriculture, this study examined the joint effects of coconut shell biochar and Bacillus strain Ya-1 on soil fertility, rhizosphere bacterial communities, and the growth of chili (Capsicum annuum L.). A controlled pot experiment with four treatments was conducted: control (CK), biochar only (C), Bacillus strain Ya-1 only (B), and a combination of both (BC). The BC treatment significantly enhanced the soil carbon and available phosphorus contents by approximately 20% and the soil nitrogen content and pH by 18% and 0.3 units, respectively, compared to the control. It also increased microbial biomass carbon and nitrogen by 25% and 30%, respectively, indicating improved soil microbial diversity as shown by the highest Pielou evenness index and Shannon index values. The combined application of biochar and the Ya-1 strain resulted in a 15% increase in chili plant height and a 40% improvement in root dehydrogenase activity, suggesting enhanced nutrient uptake and metabolism. Metabolic profiling showed shifts in stress response and nutrient assimilation under different treatments. Collectively, these results indicate the potential of biochar and microbial inoculants to significantly promote soil and plant health, providing a sustainable strategy to improve agricultural productivity and reduce reliance on chemical inputs. Full article

(This article belongs to the Special Issue Role of Microorganisms and Their Metabolites in Agriculture, Food and the Environment: 2nd Edition)

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14 pages, 6550 KiB

Open AccessArticle

Electron-Transferring Flavoprotein and Its Dehydrogenase Required for Fungal Pathogenicity in Arthrobotrys oligospora

by Yonglan Liu, Zhangyu Li, Junjie Liu, Xiqi Zhang and Xin Wang

Int. J. Mol. Sci. 2024, 25(20), 10934; https://doi.org/10.3390/ijms252010934 - 11 Oct 2024

Viewed by 641

Abstract

Electron transfer flavoprotein (ETF) plays an important function in fatty acid beta oxidation and the amino acid metabolic pathway. It can provide pathogenicity to some opportunistic fungi via modulating cellular metabolite composition. Arthrobotrys oligospora is a typical invasion fungus to nematodes. Its ETF characterization is still unknown. Here, we showed that the mutations of A. oligospora ETF (Aoetfα and Aoetfβ) and its dehydrogenase (Aoetfdh) led to severe defects in mitochondrial integrity and blocked fatty acid metabolism. The pathogenicity-associated trap structures were completely suppressed when exposed to nematode-derived ascarosides and nutrition signals, including ammonia and urea. Compared to the wild-type strain, the nematode predatory activity was significantly reduced and delayed. But surprisingly, the rich nutrition could restore the massive trap and robust predatory activity in the mutant Aoetfβ beyond all induction cues. Moreover, the deletion of Aoetfβ has led to the accumulation of butyrate-like smell, which has a strong attraction to Caenorhabditis elegans nematodes. Ultimately, ETF and its dehydrogenase play a crucial role in nematode-trapping fungi, highlighting mitochondrial metabolite fluctuations that are connected to pathogenesis and further regulating the interactions between fungi and nematodes. Full article

(This article belongs to the Special Issue Role of Microorganisms and Their Metabolites in Agriculture, Food and the Environment: 2nd Edition)

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17 pages, 14403 KiB

Open AccessArticle

Maize Endophytic Plant Growth-Promoting Bacteria Peribacillus simplex Can Alleviate Plant Saline and Alkaline Stress

by Guoliang Li, Miaoxin Shi, Wenhao Wan, Zongying Wang, Shangwei Ji, Fengshan Yang, Shumei Jin and Jianguo Zhang

Int. J. Mol. Sci. 2024, 25(20), 10870; https://doi.org/10.3390/ijms252010870 - 10 Oct 2024

Viewed by 963

Abstract

Soil salinization is currently one of the main abiotic stresses that restrict plant growth. Plant endophytic bacteria can alleviate abiotic stress. The aim of the current study was to isolate, characterize, and assess the plant growth-promoting and saline and alkaline stress-alleviating traits of Peribacillus simplex M1 (P. simplex M1) isolates from maize. One endophytic bacterial isolate, named P. simplex M1, was selected from the roots of maize grown in saline–alkali soil. The P. simplex M1 genome sequence analysis of the bacteria with a length of 5.8 Mbp includes about 700 genes that promote growth and 16 antioxidant activity genes that alleviate saline and alkaline stress. P. simplex M1 can grow below 400 mM NaHCO₃ on the LB culture medium; The isolate displayed multiple plant growth-stimulating features, such as nitrogen fixation, produced indole-3-acetic acid (IAA), and siderophore production. This isolate had a positive effect on the resistance to salt of maize in addition to the growth. P. simplex M1 significantly promoted seed germination by enhancing seed vigor in maize whether under normal growth or NaHCO₃ stress conditions. The seeds with NaHCO₃ treatment exhibited higher reactive oxygen species (ROS) levels than the maize in P. simplex M1 inoculant on maize. P. simplex M1 can colonize the roots of maize. The P. simplex M1 inoculant plant increased chlorophyll in leaves, stimulated root and leaf growth, increased the number of lateral roots and root dry weight, increased the length and width of the blades, and dry weight of the blades. The application of inoculants can significantly reduce the content of malondialdehyde (MDA) and increase the activity of plant antioxidant enzymes (Catalase (CAT), Superoxide Dismutase (SOD), and Peroxidase (POD)), which may thereby improve maize resistance to saline and alkaline stress. Conclusion: P. simplex M1 isolate belongs to plant growth-promoting bacteria by having high nitrogen concentration, indoleacetic acid (IAA), and siderophore, and reducing the content of ROS through the antioxidant system to alleviate salt alkali stress. This study presents the potential application of P. simplex M1 as a biological inoculant to promote plant growth and mitigate the saline and alkaline effects of maize and other crops. Full article

(This article belongs to the Special Issue Role of Microorganisms and Their Metabolites in Agriculture, Food and the Environment: 2nd Edition)

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28 pages, 9935 KiB

Open AccessArticle

Biological Characterization and Genomic Analysis of Three Novel Serratia- and Enterobacter-Specific Virulent Phages

by Dziyana Shymialevich, Stanisław Błażejak, Paulina Średnicka, Hanna Cieślak, Agnieszka Ostrowska, Barbara Sokołowska and Michał Wójcicki

Int. J. Mol. Sci. 2024, 25(11), 5944; https://doi.org/10.3390/ijms25115944 - 29 May 2024

Viewed by 1278

Abstract

Due to the high microbiological contamination of raw food materials and the increase in the incidence of multidrug-resistant bacteria, new methods of ensuring microbiological food safety are being sought. One solution may be to use bacteriophages (so-called phages) as natural bacterial enemies. Therefore, the aim of this study was the biological and genomic characterization of three newly isolated Serratia- and Enterobacter-specific virulent bacteriophages as potential candidates for food biocontrol. Serratia phage KKP_3708 (vB_Sli-IAFB_3708), Serratia phage KKP_3709 (vB_Sma-IAFB_3709), and Enterobacter phage KKP_3711 (vB_Ecl-IAFB_3711) were isolated from municipal sewage against Serratia liquefaciens strain KKP 3654, Serratia marcescens strain KKP 3687, and Enterobacter cloacae strain KKP 3684, respectively. The effect of phage addition at different multiplicity of infection (MOI) rates on the growth kinetics of the bacterial hosts was determined using a Bioscreen C Pro growth analyzer. The phages retained high activity in a wide temperature range (from −20 °C to 60 °C) and active acidity values (pH from 3 to 12). Based on transmission electron microscopy (TEM) imaging and whole-genome sequencing (WGS), the isolated bacteriophages belong to the tailed bacteriophages from the Caudoviricetes class. Genomic analysis revealed that the phages have linear double-stranded DNA of size 40,461 bp (Serratia phage KKP_3708), 67,890 bp (Serratia phage KKP_3709), and 113,711 bp (Enterobacter phage KKP_3711). No virulence, toxins, or antibiotic resistance genes were detected in the phage genomes. The lack of lysogenic markers indicates that all three bacteriophages may be potential candidates for food biocontrol. Full article

(This article belongs to the Special Issue Role of Microorganisms and Their Metabolites in Agriculture, Food and the Environment: 2nd Edition)

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Review

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24 pages, 3580 KiB

Open AccessReview

Wastewater Treatment with Bacterial Representatives of the Thiothrix Morphotype

by Maria V. Gureeva, Maria S. Muntyan, Nikolai V. Ravin and Margarita Yu. Grabovich

Int. J. Mol. Sci. 2024, 25(16), 9093; https://doi.org/10.3390/ijms25169093 - 22 Aug 2024

Viewed by 1351

Abstract

Bacteria of the Thiothrix morphotype, comprising the genera Thiothrix, Thiolinea and Thiofilum, are frequently encountered in domestic and industrial wastewater treatment systems, but they are usually not clearly differentiated due to the marked similarity in their morphologies. Methods ranging from light microscopy, FISH and PCR to modern high-throughput sequencing are used to identify them. The development of these bacteria in wastewater treatment systems has both advantages and disadvantages. On the one hand, the explosive growth of these bacteria can lead to activated sludge bulking or clogging of the treatment system’s membranes, with a consequent decrease in the water treatment efficiency. On the other hand, members of the Thiothrix morphotype can improve the quality of granular sludge and increase the water treatment efficiency. This may be due to their capacity for sulfide oxidation, denitrification combined with the oxidation of reduced sulfur compounds, enhanced biological phosphate removal and possibly denitrifying phosphate removal. The recently obtained pangenome of the genus Thiothrix allows the explanation, at the genomic level, of the experimental results of various studies. Moreover, this review summarizes the data on the factors affecting the proliferation of representatives of the Thiothrix morphotype. Full article

(This article belongs to the Special Issue Role of Microorganisms and Their Metabolites in Agriculture, Food and the Environment: 2nd Edition)

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15 pages, 1030 KiB

Open AccessReview

Microbial β C-S Lyases: Enzymes with Multifaceted Roles in Flavor Generation

by Mathieu Schwartz, Nicolas Poirier, Jade Moreno, Alena Proskura, Mélanie Lelièvre, Jean-Marie Heydel and Fabrice Neiers

Int. J. Mol. Sci. 2024, 25(12), 6412; https://doi.org/10.3390/ijms25126412 - 11 Jun 2024

Viewed by 1340

Abstract

β C-S lyases (β-CSLs; EC 4.4.1.8) are enzymes catalyzing the dissociation of β carbon–sulfur bonds of cysteine S-conjugates to produce odorant metabolites with a free thiol group. These enzymes are increasingly studied for their role in flavor generation in a variety of food products, whether these processes occur directly in plants, by microbial β-CSLs during fermentation, or in the mouth under the action of the oral microbiota. Microbial β-CSLs react with sulfur aroma precursors present in beverages, vegetables, fruits, or aromatic herbs like hop but also potentially with some precursors formed through Maillard reactions in cooked foods such as meat or coffee. β-CSLs from microorganisms like yeasts and lactic acid bacteria have been studied for their role in the release of polyfunctional thiols in wine and beer during fermentation. In addition, β-CSLs from microorganisms of the human oral cavity were shown to metabolize similar precursors and to produce aroma in the mouth with an impact on retro-olfaction. This review summarizes the current knowledge on β-CSLs involved in flavor generation with a focus on enzymes from microbial species present either in the fermentative processes or in the oral cavity. This paper highlights the importance of this enzyme family in the food continuum, from production to consumption, and offers new perspectives concerning the utilization of β-CSLs as a flavor enhancer. Full article

(This article belongs to the Special Issue Role of Microorganisms and Their Metabolites in Agriculture, Food and the Environment: 2nd Edition)

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