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Role of Microorganisms and Their Metabolites in Agriculture, Food and the Environment

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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: closed (31 January 2024) | Viewed by 24428

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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 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 deeper description of the microbial constituents of the different environments.

Prof. Dr. Barbara Sokolowska
Guest Editor

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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: 2nd Edition in International Journal of Molecular Sciences (7 articles)

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Editorial

Jump to: Research, Review

5 pages, 175 KiB

Open AccessEditorial

Editorial for Special Issue “Role of Microorganisms and Their Metabolites in Agriculture, Food and the Environment”

by Barbara Sokołowska

Int. J. Mol. Sci. 2024, 25(21), 11417; https://doi.org/10.3390/ijms252111417 - 24 Oct 2024

Viewed by 726

Abstract

Microorganisms and their metabolites play a crucial role in agriculture, food production, and environmental sustainability, offering solutions to challenges like soil degradation, pest management, and climate resilience [...] Full article

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

Research

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14 pages, 2020 KiB

Open AccessArticle

Enterobacteriaceae as a Key Indicator of Huanglongbing Infection in Diaphorina citri

by Xing-Zhi Duan, Guo-Sen Guo, Ling-Fei Zhou, Le Li, Ze-Min Liu, Cheng Chen, Bin-Hua Wang and Lan Wu

Int. J. Mol. Sci. 2024, 25(10), 5136; https://doi.org/10.3390/ijms25105136 - 9 May 2024

Viewed by 883

Abstract

Extensive microbial interactions occur within insect hosts. However, the interactions between the Huanglongbing (HLB) pathogen and endosymbiotic bacteria within the Asian citrus psyllid (ACP, Diaphorina citri Kuwayama) in wild populations remain elusive. Thus, this study aimed to detect the infection rates of HLB in the ACP across five localities in China, with a widespread prevalence in Ruijin (RJ, 58%), Huidong (HD, 28%), and Lingui (LG, 15%) populations. Next, microbial communities of RJ and LG populations collected from citrus were analyzed via 16S rRNA amplicon sequencing. The results revealed a markedly higher microbial diversity in the RJ population compared to the LG population. Moreover, the PCoA analysis identified significant differences in microbial communities between the two populations. Considering that the inter-population differences of Bray–Curtis dissimilarity in the RJ population exceeded those between populations, separate analyses were performed. Our findings indicated an increased abundance of Enterobacteriaceae in individuals infected with HLB in both populations. Random forest analysis also identified Enterobacteriaceae as a crucial indicator of HLB infection. Furthermore, the phylogenetic analysis suggested a potential regulatory role of ASV4017 in Enterobacteriaceae for ACP, suggesting its possible attractant activity. This research contributes to expanding the understanding of microbial communities associated with HLB infection, holding significant implications for HLB prevention and treatment. Full article

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

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23 pages, 6115 KiB

Open AccessArticle

Buckwheat (Fagopyrum esculentum) Hulls Are a Rich Source of Fermentable Dietary Fibre and Bioactive Phytochemicals

by Zhihong Zhang, Songtao Fan, Gary J. Duncan, Amanda Morris, Donna Henderson, Philip Morrice, Wendy R. Russell, Sylvia H. Duncan and Madalina Neacsu

Int. J. Mol. Sci. 2023, 24(22), 16310; https://doi.org/10.3390/ijms242216310 - 14 Nov 2023

Cited by 5 | Viewed by 1839

Abstract

Pseudo-cereals such as buckwheat (Fagopyrum esculentum) are valid candidates to promote diet biodiversity and nutrition security in an era of global climate change. Buckwheat hulls (BHs) are currently an unexplored source of dietary fibre and bioactive phytochemicals. This study assessed the effects of several bioprocessing treatments (using enzymes, yeast, and combinations of both) on BHs’ nutrient and phytochemical content, their digestion and metabolism in vitro (using a gastrointestinal digestion model and mixed microbiota from human faeces). The metabolites were measured using targeted LC-MS/MS and GC analysis and 16S rRNA gene sequencing was used to detect the impact on microbiota composition. BHs are rich in insoluble fibre (31.09 ± 0.22% as non-starch polysaccharides), protocatechuic acid (390.71 ± 31.72 mg/kg), and syringaresinol (125.60 ± 6.76 mg/kg). The bioprocessing treatments significantly increased the extractability of gallic acid, vanillic acid, p-hydroxybenzoic acid, syringic acid, vanillin, syringaldehyde, p-coumaric acid, ferulic acid, caffeic acid, and syringaresinol in the alkaline-labile bound form, suggesting the bioaccessibility of these phytochemicals to the colon. Furthermore, one of the treatments, EC_2 treatment, increased significantly the in vitro upper gastrointestinal release of bioactive phytochemicals, especially for protocatechuic acid (p < 0.01). The BH fibre was fermentable, promoting the formation mainly of propionate and, to a lesser extent, butyrate formation. The EM_1 and EC_2 treatments effectively increased the content of insoluble fibre but had no effect on dietary fibre fermentation (p > 0.05). These findings promote the use of buckwheat hulls as a source of dietary fibre and phytochemicals to help meet dietary recommendations and needs. Full article

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

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14 pages, 3509 KiB

Open AccessArticle

Insight into the High-Efficiency Benzo(a)pyrene Degradation Ability of Pseudomonas benzopyrenica BaP3 and Its Application in the Complete Bioremediation of Benzo(a)pyrene

by Xingchen Dong, Siyi Wu, Zihuan Rao, Yaqian Xiao, Yan Long and Zhixiong Xie

Int. J. Mol. Sci. 2023, 24(20), 15323; https://doi.org/10.3390/ijms242015323 - 18 Oct 2023

Cited by 4 | Viewed by 2174

Abstract

Polycyclic aromatic hydrocarbons (PAHs) are common carcinogens. Benzo(a)pyrene is one of the most difficult high-molecular-weight (HMW) PAHs to remove. Biodegradation has become an ideal method to eliminate PAH pollutants from the environment. The existing research is mostly limited to low-molecular-weight PAHs; there is little understanding of HMW PAHs, particularly benzo(a)pyrene. Research into the biodegradation of HMW PAHs contributes to the development of microbial metabolic mechanisms and also provides new systems for environmental treatments. Pseudomonas benzopyrenica BaP3 is a highly efficient benzo(a)pyrene-degrading strain that is isolated from soil samples, but its mechanism of degradation remains unknown. In this study, we aimed to clarify the high degradation efficiency mechanism of BaP3. The genes encoding Rhd1 and Rhd2 in strain BaP3 were characterized, and the results revealed that rhd1 was the critical factor for high degradation efficiency. Molecular docking and enzyme activity determinations confirmed this conclusion. A recombinant strain that could completely mineralize benzo(a)pyrene was also proposed for the first time. We explained the mechanism of the high-efficiency benzo(a)pyrene degradation ability of BaP3 to improve understanding of the degradation mechanism of highly toxic PAHs and to provide new solutions to practical applications via synthetic biology. Full article

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

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20 pages, 1582 KiB

Open AccessArticle

The Effect of Plasma-Treated Water on Microbial Growth and Biosynthesis of Gamma-Decalactones by Yarrowia lipolytica Yeast

by Jolanta Małajowicz, Karen Khachatryan, Zdzisław Oszczęda, Piotr Karpiński, Agata Fabiszewska, Bartłomiej Zieniuk and Konrad Krysowaty

Int. J. Mol. Sci. 2023, 24(20), 15204; https://doi.org/10.3390/ijms242015204 - 15 Oct 2023

Cited by 2 | Viewed by 1921

Abstract

In recent years, the production of plasma-treated water (PTW) by low-temperature low-pressure glow plasma (LPGP) has been increasingly gaining in popularity. LPGP-treated water changes its physical and physiochemical properties compared to standard distilled water. In this study, a non-conventional lipolytic yeast species Yarrowia lipolytica was cultivated in culture media based on Nantes plasma water with heightened singlet oxygen content (Nantes PW) or in water treated with low-temperature, low-pressure glow plasma while in contact with air (PWTA) or nitrogen (PWTN). The research aimed to assess the influence of culture conditions on castor oil biotransformation to gamma-decalactone (GDL) and other secondary metabolites in media based on nanowater. The Nantes plasma water-based medium attained the highest concentration of gamma-decalactone (4.81 ± 0.51 g/L at 144 h of culture), maximum biomass concentration and biomass yield from the substrate. The amplified activity of lipases in the nanowater-based medium, in comparison to the control medium, is encouraging from the perspective of GDL biosynthesis, relying on the biotransformation of ricinoleic acid, which is the primary component of castor oil. Although lipid hydrolysis was enhanced, this step seemed not crucial for GDL concentration. Interestingly, the study validates the significance of oxygen in β-oxidation enzymes and its role in the bioconversion of ricinoleic acid to GDL and other lactones. Specifically, media with higher oxygen content (WPTA) and Nantes plasma water resulted in remarkably high concentrations of four lactones: gamma-decalactone, 3-hydroxy-gamma-decalactone, dec-2-en-4-olide and dec-3-en-4-olide. Full article

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

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17 pages, 2813 KiB

Open AccessArticle

A High-Quality Genome Sequence of the Penicillium oxalicum 5-18 Strain Isolated from a Poplar Plantation Provides Insights into Its Lignocellulose Degradation

by Shuang Hu, Rui Zhu, Xing-Ye Yu, Bao-Teng Wang, Hong-Hua Ruan and Feng-Jie Jin

Int. J. Mol. Sci. 2023, 24(16), 12745; https://doi.org/10.3390/ijms241612745 - 13 Aug 2023

Cited by 2 | Viewed by 1529

Abstract

Studies on the degradation of plant cell wall polysaccharides by fungal extracellular enzymes have attracted recent attention from researchers. Xylan, abundant in hemicellulose, that play great role in connection between cellulose and lignin, has seen interest in its hydrolytic enzymatic complex. In this study, dozens of fungus species spanning genera were isolated from rotting leaves based on their ability to decompose xylan. Among these isolates, a strain with strong xylanase-producing ability was selected for further investigation by genome sequencing. Based on phylogenetic analysis of ITS (rDNA internal transcribed spacer) and LSU (Large subunit 28S rDNA) regions, the isolate was identified as Penicillium oxalicum. Morphological analysis also supported this finding. Xylanase activity of this isolated P. oxalicum 5-18 strain was recorded to be 30.83 U/mL using the 3,5-dinitro-salicylic acid (DNS) method. Further genome sequencing reveals that sequenced reads were assembled into a 30.78 Mb genome containing 10,074 predicted protein-encoding genes. In total, 439 carbohydrate-active enzymes (CAZymes) encoding genes were predicted, many of which were associated with cellulose, hemicellulose, pectin, chitin and starch degradation. Further analysis and comparison showed that the isolate P. oxalicum 5-18 contains a diverse set of CAZyme genes involved in degradation of plant cell wall components, particularly cellulose and hemicellulose. These findings provide us with valuable genetic information about the plant biomass-degrading enzyme system of P. oxalicum, facilitating a further exploration of the repertoire of industrially relevant lignocellulolytic enzymes of P. oxalicum 5-18. Full article

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

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34 pages, 7474 KiB

Open AccessArticle

Newly Isolated Virulent Salmophages for Biocontrol of Multidrug-Resistant Salmonella in Ready-to-Eat Plant-Based Food

by Michał Wójcicki, Olga Świder, Paulina Średnicka, Dziyana Shymialevich, Tomasz Ilczuk, Łukasz Koperski, Hanna Cieślak, Barbara Sokołowska and Edyta Juszczuk-Kubiak

Int. J. Mol. Sci. 2023, 24(12), 10134; https://doi.org/10.3390/ijms241210134 - 14 Jun 2023

Cited by 7 | Viewed by 2903

Abstract

Due to irrational antibiotic stewardship, an increase in the incidence of multidrug resistance of bacteria has been observed recently. Therefore, the search for new therapeutic methods for pathogen infection treatment seems to be necessary. One of the possibilities is the utilization of bacteriophages (phages)—the natural enemies of bacteria. Thus, this study is aimed at the genomic and functional characterization of two newly isolated phages targeting MDR Salmonella enterica strains and their efficacy in salmonellosis biocontrol in raw carrot–apple juice. The Salmonella phage vB_Sen-IAFB3829 (Salmonella phage strain KKP 3829) and Salmonella phage vB_Sen-IAFB3830 (Salmonella phage strain KKP 3830) were isolated against S. I (6,8:l,-:1,7) strain KKP 1762 and S. Typhimurium strain KKP 3080 host strains, respectively. Based on the transmission electron microscopy (TEM) and whole-genome sequencing (WGS) analyses, the viruses were identified as members of tailed bacteriophages from the Caudoviricetes class. Genome sequencing revealed that these phages have linear double-stranded DNA and sizes of 58,992 bp (vB_Sen-IAFB3829) and 50,514 bp (vB_Sen-IAFB3830). Phages retained their activity in a wide range of temperatures (from −20 °C to 60 °C) and active acidity values (pH from 3 to 11). The exposure of phages to UV radiation significantly decreased their activity in proportion to the exposure time. The application of phages to the food matrices significantly reduced the level of Salmonella contamination compared to the control. Genome analysis showed that both phages do not encode virulence or toxin genes and can be classified as virulent bacteriophages. Virulent characteristics and no possible pathogen factors make examined phages feasible to 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)

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17 pages, 3544 KiB

Open AccessArticle

Valorisation of Whey Permeate in Sequential Bioprocesses towards Value-Added Products–Optimisation of Biphasic and Classical Batch Cultures of Kluyveromyces marxianus

by Karolina Drężek, Maria Krystyna Sobczyk, Zoltán Kállai, Anna Detman, Paula Bardadyn and Jolanta Mierzejewska

Int. J. Mol. Sci. 2023, 24(8), 7560; https://doi.org/10.3390/ijms24087560 - 20 Apr 2023

Cited by 1 | Viewed by 2378

Abstract

Whey permeate is categorised as hazardous wastewater for aquatic environments, mainly due to its high lactose content. Therefore, it must be valorised before being released into the environment. One pathway for whey permeate management is its use in biotechnological processes. Herein, we present roads for whey permeate valorisation with the K. marxianus WUT240 strain. The established technology is based on two bioprocesses. During first, 2.5 g/L 2-phenylethanol and fermented plant oils enriched with different flavourings are obtained after 48 h biphasic cultures at 30 °C. The second process leads to a maximum of 75 g ethanol/L (Y_P/S = 0.53 g/g) after 96 h at 30 °C. Moreover, established whey permeate valorisation pathways reduced its biochemical oxygen demand and chemical oxygen demand values by 12- to 3-fold, respectively. Together, the present study reports a complete, effective, and environmentally friendly whey permeate management strategy while simultaneously enabling the acquisition of valuable compounds with substantial application potential. Full article

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

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14 pages, 3177 KiB

Open AccessArticle

Efficient Knocking Out of the Organophosphorus Insecticides Degradation Gene opdB in Cupriavidus nantongensis X1^T via CRISPR/Cas9 with Red System

by Yufei Zhang, Yuehan Geng, Shengyang Li, Taozhong Shi, Xin Ma, Rimao Hua and Liancheng Fang

Int. J. Mol. Sci. 2023, 24(6), 6003; https://doi.org/10.3390/ijms24066003 - 22 Mar 2023

Cited by 5 | Viewed by 2418

Abstract

Cupriavidus nantongensis X1^T is a type strain of the genus Cupriavidus, that can degrade eight kinds of organophosphorus insecticides (OPs). Conventional genetic manipulations in Cupriavidus species are time-consuming, difficult, and hard to control. The clustered regularly interspaced short palindromic repeat (CRISPR)/associated protein 9 (Cas9) system has emerged as a powerful tool for genome editing applied in prokaryotes and eukaryotes due to its simplicity, efficiency, and accuracy. Here, we combined CRISPR/Cas9 with the Red system to perform seamless genetic manipulation in the X1^T strain. Two plasmids, pACasN and pDCRH were constructed. The pACasN plasmid contained Cas9 nuclease and Red recombinase, and the pDCRH plasmid contained the dual single-guide RNA (sgRNA) of organophosphorus hydrolase (OpdB) in the X1^T strain. For gene editing, two plasmids were transferred to the X1^T strain and a mutant strain in which genetic recombination had taken place, resulting in the targeted deletion of opdB. The incidence of homologous recombination was over 30%. Biodegradation experiments suggested that the opdB gene was responsible for the catabolism of organophosphorus insecticides. This study was the first to use the CRISPR/Cas9 system for gene targeting in the genus Cupriavidus, and it furthered our understanding of the process of degradation of organophosphorus insecticides in the X1^T strain. Full article

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

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Review

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20 pages, 2440 KiB

Open AccessReview

Microbial Consortia for Plant Protection against Diseases: More than the Sum of Its Parts

by Tomasz Maciag, Edmund Kozieł, Piotr Rusin, Katarzyna Otulak-Kozieł, Sylwia Jafra and Robert Czajkowski

Int. J. Mol. Sci. 2023, 24(15), 12227; https://doi.org/10.3390/ijms241512227 - 31 Jul 2023

Cited by 21 | Viewed by 3621

Abstract

Biological plant protection presents a promising and exciting alternative to chemical methods for safeguarding plants against the increasing threats posed by plant diseases. This approach revolves around the utilization of biological control agents (BCAs) to suppress the activity of significant plant pathogens. Microbial BCAs have the potential to effectively manage crop disease development by interacting with pathogens or plant hosts, thereby increasing their resistance. However, the current efficacy of biological methods remains unsatisfactory, creating new research opportunities for sustainable plant cultivation management. In this context, microbial consortia, comprising multiple microorganisms with diverse mechanisms of action, hold promise in terms of augmenting the magnitude and stability of the overall antipathogen effect. Despite scientific efforts to identify or construct microbial consortia that can aid in safeguarding vital crops, only a limited number of microbial consortia-based biocontrol formulations are currently available. Therefore, this article aims to present a complex analysis of the microbial consortia-based biocontrol status and explore potential future directions for biological plant protection research with new technological advancements. Full article

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

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20 pages, 2876 KiB

Open AccessReview

Involvement of Bacterial and Fungal Extracellular Products in Transformation of Manganese-Bearing Minerals and Its Environmental Impact

by Bence Farkas, Hana Vojtková, Zuzana Farkas, Domenico Pangallo, Peter Kasak, Antonio Lupini, Hyunjung Kim, Martin Urík and Peter Matúš

Int. J. Mol. Sci. 2023, 24(11), 9215; https://doi.org/10.3390/ijms24119215 - 24 May 2023

Cited by 2 | Viewed by 1976

Abstract

Manganese oxides are considered an essential component of natural geochemical barriers due to their redox and sorptive reactivity towards essential and potentially toxic trace elements. Despite the perception that they are in a relatively stable phase, microorganisms can actively alter the prevailing conditions in their microenvironment and initiate the dissolution of minerals, a process that is governed by various direct (enzymatic) or indirect mechanisms. Microorganisms are also capable of precipitating the bioavailable manganese ions via redox transformations into biogenic minerals, including manganese oxides (e.g., low-crystalline birnessite) or oxalates. Microbially mediated transformation influences the (bio)geochemistry of manganese and also the environmental chemistry of elements intimately associated with its oxides. Therefore, the biodeterioration of manganese-bearing phases and the subsequent biologically induced precipitation of new biogenic minerals may inevitably and severely impact the environment. This review highlights and discusses the role of microbially induced or catalyzed processes that affect the transformation of manganese oxides in the environment as relevant to the function of geochemical barriers. Full article

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

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