Journal Description
Applied Microbiology
Applied Microbiology
is an international, peer-reviewed, open access journal on application of microorganisms published quarterly online by MDPI.
- Open Access— free for readers, with article processing charges (APC) paid by authors or their institutions.
- High Visibility: indexed within Scopus, EBSCO, and other databases.
- Rapid Publication: manuscripts are peer-reviewed and a first decision is provided to authors approximately 16.3 days after submission; acceptance to publication is undertaken in 3.6 days (median values for papers published in this journal in the first half of 2024).
- Recognition of Reviewers: APC discount vouchers, optional signed peer review, and reviewer names published annually in the journal.
- Applied Microbiology is a companion journal of Microorganisms.
Latest Articles
Metatranscriptomic Analysis of Argentinian Kefirs Varying in Apparent Viscosity
Appl. Microbiol. 2024, 4(3), 1150-1164; https://doi.org/10.3390/applmicrobiol4030078 - 24 Jul 2024
Abstract
Comparative metatranscriptomics of the bacterial and yeast communities of two milk kefir beverages (MKAA1 and MKAA2) was carried out. They were obtained by fermentation with two different frozen stocks of the kefir grain CIDCA AGK1, differing in rheological features and production of organic
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Comparative metatranscriptomics of the bacterial and yeast communities of two milk kefir beverages (MKAA1 and MKAA2) was carried out. They were obtained by fermentation with two different frozen stocks of the kefir grain CIDCA AGK1, differing in rheological features and production of organic acids. We hypothesised that the differences in their physicochemical and rheological properties might be due to the microbial activity in each product. The dominance of lactic acid bacteria, yeast, and a marginal amount of acetic acid bacteria characterised the microbiome. The bacterial families Lactobacillaceae and Streptococcaceae accounted for almost all of the bacterial gene transcripts, with Lactobacillus helveticus, L. kefiranofaciens, L. gallinarum, and Lactococcus lactis being most frequent in the microbiome of the MKAA1 beverage and L. kefiranofaciens, Lc. Lactis, and Leuconostoc mesenteroides being the most prevalent in MKAA2. Dipodascaceae and Saccharomycetaceae were the leading yeast families, represented by Yarrowia lipolytica, Saccharomyces unisporus, and Kluyveromyces marxianus. MKAA1 and MKAA2 shared >75% KEGG Ortologs (KOs) in their bacteria and yeast libraries. The considerable decreases in total expressed genes (KEGG Ortologs) assigned to Lactobacillus helveticus and L. gallinarum might be related to the variations in the rheological features of the beverages, probably by compromising the interrelations with L. kefiranofaciens, which might explain the variations in the rheological features of the beverages.
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(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2023, 2024))
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Open AccessArticle
Genomic Characterization of Selected Escherichia coli Strains from Catfish (Clarias gariepinus) in Nigeria
by
Chibuzo Linda Ekwuazi, Frank C. Ogbo, Anna Stöger, Werner Ruppitsch and Adriana Cabal Rosel
Appl. Microbiol. 2024, 4(3), 1142-1149; https://doi.org/10.3390/applmicrobiol4030077 - 24 Jul 2024
Abstract
According to a report by the World Health Organization (WHO), each year, over 550 million individuals worldwide suffer from and 230,000 die from diarrheal illnesses, which accounts for more than half of the global foodborne disease burden. Among them, children face a heightened
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According to a report by the World Health Organization (WHO), each year, over 550 million individuals worldwide suffer from and 230,000 die from diarrheal illnesses, which accounts for more than half of the global foodborne disease burden. Among them, children face a heightened vulnerability, with approximately 220 million falling ill and 96,000 succumbing to these diseases annually. This work aimed to study the genomic characterization of selected E. coli strains from catfish (Clarias (C.) gariepinus) caught from the Onitsha North axis of the River Niger in Anambra state, Nigeria. A total of 50 fish were randomly purchased from different fishermen over a period of four months. Samples that comprised six different organs (skin, flesh, gills, gonads, guts, and liver) were screened for E. coli strains using cultural and biochemical methods. Multilocus sequence typing (MLST) and core genome (cg)MLST were performed using Ridom SeqSphere+ software. The aerobic plate count (APC) and coliform count ranged from 0.5 × 104 to 3.7 × 104 cfu/g and 0 to 3.0 × 104 cfu/g, respectively. Whole-genome sequencing (WGS) confirmed the presence of E. coli and Klebsiella quasipneumoniae isolates in our samples. We could identify only two serotypes (O102:H7 and O40:H4) of E. coli. Antimicrobial resistance genes (ARGs) and point mutations that conferred antibiotic resistance were extracted from the genome assemblies. Good hygiene is recommended to avoid the cross-contamination of raw C. gariepinus with ready-to-eat food.
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(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2023, 2024))
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Open AccessArticle
Multiplex-PCR Detection of an Atypical Leuconostoc mesenteroides subsp. jonggajibkimchii Phenotype Dominating the Terminal Spoilage Microbial Association of a Fresh Greek Whey Cheese Stored at 4 °C in Vacuum
by
Nikoletta Sameli, Eleni Sioziou, Loulouda Bosnea, Spiros Paramithiotis and John Samelis
Appl. Microbiol. 2024, 4(3), 1124-1141; https://doi.org/10.3390/applmicrobiol4030076 - 24 Jul 2024
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A species-specific multiplex-PCR method and phenotypic tests were combined to evaluate biochemical and genotypic differences between 24 representative Leuconostoc mesenteroides diverse isolates previously found to dominate in spoiled, vacuum-packed Anthotyros whey cheeses stored at 4 °C for 40 days and identified by 16S
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A species-specific multiplex-PCR method and phenotypic tests were combined to evaluate biochemical and genotypic differences between 24 representative Leuconostoc mesenteroides diverse isolates previously found to dominate in spoiled, vacuum-packed Anthotyros whey cheeses stored at 4 °C for 40 days and identified by 16S rRNA gene sequencing. Based on their phenotypic (API 50 CHL) profiles, the 24 isolates comprised 6 multi-strain and 7 single-strain biotypes. Only two single-strain biotypes (L4A and L4B) produced slime (dextran) from sucrose, and only four biotypes (L2A–L2C, L3; 7 isolates) fermented L-arabinose; the remaining 15 isolates (biotypes L1A–L1F) were dextran-negative, oligofermenting Ln. mesenteroides variants, able to ferment D-xylose and grow at 37 °C. Based on their multiplex-PCR (rpoB, araA, dsr, and sorA) gene profiles in comparison with those of the type strains of the four Ln. mesenteroides subsp. cremoris (rpoB), dextranicum (rpoB/dsr), mesenteroides (rpoB/araA/dsr/sorA), and jonggajibkimchii (rpoB/araA/dsr), no isolate was assigned to the first two subspecies and only four isolates (L2A and L2C) to the subsp. mesenteroides. Ten isolates shared the subsp. jonggajibkimchii profile, while the other ten ones have a fifth atypical profile (rpoB/dsr/sorA), seemingly being closer to the subsp. dextranicum. Particularly the atypical biotype L1B representatives of the most prevalent psychrotrophic Ln. mesenteroides subsp. jonggajibkimchii (rpoB/araA/dsr) genotype at Anthotyros whey cheese spoilage deserve further biochemical and molecular characterization studies.
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Open AccessArticle
Interaction between Trichoderma sp., Pseudomonas putida, and Two Organic Amendments on the Yield and Quality of Strawberries (Fragaria x annanasa cv. San Andreas) in the Huaral Region, Peru
by
Lucero Huasasquiche, Thania Ccori, Leonela Alejandro, Héctor Cántaro-Segura, Tomás Samaniego and Richard Solórzano
Appl. Microbiol. 2024, 4(3), 1110-1123; https://doi.org/10.3390/applmicrobiol4030075 - 22 Jul 2024
Abstract
Strawberry cultivation holds significant economic and social promise within Peruvian fruit production. However, conventional management practices have led to the excessive use of agrochemicals in this crop. This study proposes an organic approach to strawberry production, integrating less environmentally harmful technologies. The aim
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Strawberry cultivation holds significant economic and social promise within Peruvian fruit production. However, conventional management practices have led to the excessive use of agrochemicals in this crop. This study proposes an organic approach to strawberry production, integrating less environmentally harmful technologies. The aim was to assess microbial inoculation by using Trichoderma sp. and Pseudomonas putida and the application of organic amendments on strawberry seedlings of the commercial cultivar “San Andreas”. A field experiment was established with evaluations in the vegetative and productive stages. Results indicate that the co-inoculation of Trichoderma sp. and Pseudomonas putida increased leaf area by 7%, and enhanced the aerial part’s fresh and dry biomass by 13% and 28%, respectively, compared to treatment without microbial inoculation. Concurrently, compost application increased the leaf number and aerial dry biomass by 22% and 19% at the end of the vegetative stage, respectively, compared to treatment without organic amendment. In addition, it reduced the days for flowering, maintaining the fruit’s physicochemical attributes. Regarding yield, the amendments application significantly enhanced fruit weight per plant by 40%, especially when applied together with Trichoderma sp., and co-inoculation increased the number of fruits per meter square by 22%. These findings highlight the potential of technologies such as microbial inoculation and organic amendments to enhance strawberry yields and to gradually reduce the use of synthetic fertilizers.
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(This article belongs to the Special Issue Applied Microbiology of Foods 2.0)
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Open AccessArticle
Assessing the Microbial Impact on the Performance of Bentonite Clay at Different Thermo-Hydro-Geochemical Conditions
by
Julia Mitzscherling, Anja M. Schleicher, Steffi Genderjahn, Marie Bonitz and Dirk Wagner
Appl. Microbiol. 2024, 4(3), 1091-1109; https://doi.org/10.3390/applmicrobiol4030074 - 20 Jul 2024
Abstract
Because of its swelling capacity, compacted bentonite clay is a suitable buffer material in deep geological repositories for high-level nuclear waste. However, this only applies if the swelling capacity is maintained. Accordingly, bentonites have to be stable to changing temperature, humidity, infiltrating fluids
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Because of its swelling capacity, compacted bentonite clay is a suitable buffer material in deep geological repositories for high-level nuclear waste. However, this only applies if the swelling capacity is maintained. Accordingly, bentonites have to be stable to changing temperature, humidity, infiltrating fluids or microbial activity. In batch experiments, we investigated combined microbial and thermo-hydro-geochemical effects on the swelling capacity of uncompacted bentonite MX-80. Bentonite was exposed to fluids of different ionic strength and the bacterium Stenotrophomonas bentonitica. Bacterial growth was monitored by counting colony-forming units while the swelling capacity of bentonite was evaluated using in situ XRD at varied temperatures and humidity. The presence of bentonite prolonged the survival of S. bentonitica. However, electron microscopy, XRD and ICP-OES analyses showed neither an interaction of S. bentonitica with bentonite, nor significant changes in the swelling capacity or element composition. The swelling capacity and diffraction peak intensity were, however, strongly reduced by the ionic strength of the fluid and the exposure time. The study highlights that bentonite is affected by thermo-hydro-geochemical and microbial processes to different degrees and that the complexity of different co-occurring factors in potential nuclear waste repositories is important to consider in safety assessments.
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(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2023, 2024))
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Open AccessArticle
A Comparison of the Microbial Populations in a Culture-Dependent and a Culture-Independent Analysis of Industrial Water Samples
by
Douglas B. McIlwaine, Mackenzie Moore, Alexsandra Corrigan, Benjamin Niemaseck and Danika Nicoletti
Appl. Microbiol. 2024, 4(3), 1079-1090; https://doi.org/10.3390/applmicrobiol4030073 - 15 Jul 2024
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Culture-dependent and culture-independent microbiological methods are two approaches used to study microbial community composition. Culture-dependent methods have been the standard method used for many years but have limited utility with unculturable microorganisms. Culture-independent methods, including molecular techniques, enable direct analysis of microbial DNA
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Culture-dependent and culture-independent microbiological methods are two approaches used to study microbial community composition. Culture-dependent methods have been the standard method used for many years but have limited utility with unculturable microorganisms. Culture-independent methods, including molecular techniques, enable direct analysis of microbial DNA without requiring cultivation. Both culture-dependent and -independent methods have roles in advancing our understanding of microbiology, and a combination of these approaches often yields a comprehensive depiction of the microbial diversity within a dynamic system. Bacterial activity reaction tests (BARTs) are a common culture-dependent test used to identify bacteria growing in industrial water samples. In this study, next-generation sequencing (NGS) was used to identify the taxa growing in BARTs and compared with the BART reaction patterns. Additionally, several water samples were analyzed by both BART and NGS analysis to determine whether the bacteria found in the water were also present in the BARTs. The results showed overall agreement between NGS and BARTs, though, in some cases, the most abundant taxa found in the water samples differed from those in the BARTs. This highlights the need for further study into the microbial community dynamics of culture-dependent tests to determine whether they are representative of the original sample.
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Open AccessArticle
Production of Poly(3-Hydroxybutyrate-Co-3-Hydroxyvalerate) by Bacillus megaterium LVN01 Using Biogas Digestate
by
Amanda Lucía Mora Martínez, María Yepes-Pérez, Karent Alexandra Carrero Contreras and Paola Eliana Zapata Moreno
Appl. Microbiol. 2024, 4(3), 1057-1078; https://doi.org/10.3390/applmicrobiol4030072 - 9 Jul 2024
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The Bacillus megaterium LVN01 species native to Colombia has demonstrated the ability to metabolize different coproducts or industrial waste (such as fique juice, cane molasses, and residual glycerol) and accumulate polyhydroxybutyrate (PHB), giving it potential in the bioplastics industry. In this research, the
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The Bacillus megaterium LVN01 species native to Colombia has demonstrated the ability to metabolize different coproducts or industrial waste (such as fique juice, cane molasses, and residual glycerol) and accumulate polyhydroxybutyrate (PHB), giving it potential in the bioplastics industry. In this research, the potential of liquid digestate as a carbon source for the production of PHA polymers in fermentation processes with this bacterial strain was evaluated. Favorably, it was found that B. megaterium utilizes the nutrients from this residual substrate to multiply appropriately and efficiently synthesize poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV). Bench-scale aerobic batch fermentation, under the operational conditions of this research [volume: 3 L; temperature: 30.8 °C; agitation: 400 rpm; pH: 7.0 ± 0.2; dissolved oxygen: 100% saturation; antifoam: 10% (v/v)], generated maximum values of dry cell weight (DCW) (0.56 g cell L−1) at 60 h, while the maximum PHBV yield (360 mg PHBV L−1) occurred at 16 h, which is very favorable for sustainable degradable bioplastics production. Additionally, GC–MS and NMR analyses confirmed that the PHBV copolymer synthesized by B. megaterium is made up of the monomers 3-hydroxybutyrate (3HB) and 3-hydroxyvalerate (3HV). Furthermore, the thermal properties determined by TGA (Tonset = 283.1 °C; Tendset = 296.98 °C; Td = 290.114 °C) and DSC (Tm = °C 155.7 °C; ΔHf = 19.80 J g−1; Xcr = 18.17%) indicate that it is a thermally stable biopolymer with low percentages of crystallinity, providing flexibility that facilitates molding, adaptation, and application in various industrial sectors.
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Open AccessArticle
Isolation of Diverse Phosphate- and Zinc-Solubilizing Microorganisms from Different Environments
by
Samira Islas-Valdez, Antisar Afkairin, Benjamin Rovner and Jorge M. Vivanco
Appl. Microbiol. 2024, 4(3), 1042-1056; https://doi.org/10.3390/applmicrobiol4030071 - 7 Jul 2024
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This study addresses the challenge of finding novel ways to solubilize phosphorus and zinc for agricultural purposes. The aim was to isolate PSMs (phosphorous-solubilizing microbes) and ZnSMs (zinc-solubilizing microbes) from different environments (e.g., soil amendments, land uses, and crop rotation systems) and evaluate
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This study addresses the challenge of finding novel ways to solubilize phosphorus and zinc for agricultural purposes. The aim was to isolate PSMs (phosphorous-solubilizing microbes) and ZnSMs (zinc-solubilizing microbes) from different environments (e.g., soil amendments, land uses, and crop rotation systems) and evaluate their ability to solubilize different insoluble P sources (e.g., β-tricalcium phosphate (β-TCP), calcium-phytate (CaP), and rock phosphate (RP)) and Zn sources (e.g., zinc carbonate (ZnC), zinc oxide (ZnO), and zinc phosphate (ZnP)). Here, 25 isolates capable of solubilizing either P or Zn sources were isolated and classified by species using 16S rRNA and ITS-region sequencing. Notably, Aspergillus awamori, Fusarium circinatum, Fusarium longifundum, and Mucor circinelloides, isolated from cultivated soils and soil amendments, emerged as the most efficient PSMs and ZnSMs. Mucor circinelloides exhibited the highest solubilization ability for broths containing β-TCP, CaP, RP, ZnO, and ZnP, with log2-fold changes of 3.7, 1.8, 8.9, 7.8, and 2.4, respectively, compared to the control. For ZnC and ZnO, Aspergillus awamori displayed the highest Zn solubilization, with a 2.1 and 3.0 log2-fold change. The study highlights the potential of these strains as biofertilizers and underscores the role of Mucor and Fusarium genera in zinc solubilization.
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Open AccessArticle
The Development of Novel Edible Films from Single-Cell Protein Produced by the Biotechnological Valorization of Cheese Whey
by
Danai Ioanna Koukoumaki, Seraphim Papanikolaou, Zacharias Ioannou, Konstantinos Gkatzionis and Dimitris Sarris
Appl. Microbiol. 2024, 4(3), 1030-1041; https://doi.org/10.3390/applmicrobiol4030070 - 3 Jul 2024
Cited by 1
Abstract
The production of value-added products from microorganisms, such as single-cell protein (SCP), through the valorization of agricultural byproducts enhances circular economy while offering alternative solutions for waste treatment. In this study, SCP was obtained through the biotechnological treatment and valorization of cheese whey,
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The production of value-added products from microorganisms, such as single-cell protein (SCP), through the valorization of agricultural byproducts enhances circular economy while offering alternative solutions for waste treatment. In this study, SCP was obtained through the biotechnological treatment and valorization of cheese whey, the main byproduct of the dairy industry, for the development of novel edible films. To the best of the authors’ knowledge, this is the first report examining SCP as a biopolymer for edible film production. Specifically, Kluyveromyces marxianus, which has gained QPS and GRAS status, strain EXF-5288 cultivated in deproteinized cheese whey (DCW) lactose (10.0 g/L) in a 3 L fed-batch bioreactor, resulting in a SCPmax of 2.63 g/L with a protein content of up to 49.1% w/w. The addition of increased glycerol concentrations (30, 40, and 50% w/w of dry cells) as plasticizers was examined to develop SCP-based edible films. Regarding physicochemical characterization, increased glycerol concentration significantly increased moisture content (MC%) and solubility (S%), but there was not a significant difference in other parameters. Regarding wettability, SCP-based films could be described as oleophilic surfaces since the degree of oil contact angle (OCA) ranged between 46.7° ± 1.3 and 54.0° ± 0.5. The proposed holistic approach could contribute to the development of sustainable packaging materials through waste treatment.
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(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2023, 2024))
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Open AccessArticle
Evaluation of qPCR for the Selective Detection of Enteric Adenovirus Followed by Sequence-Based Genetic Characterization of F Strains Circulating in Brazil
by
Lilian Gonçalves do Nascimento, Sylvia Kahwage Sarmento, Reinaldo Röpke Junior and Tulio Machado Fumian
Appl. Microbiol. 2024, 4(3), 1016-1029; https://doi.org/10.3390/applmicrobiol4030069 - 27 Jun 2024
Abstract
Human adenovirus (HAdV) F40/41 is an important pathogen in pediatric acute gastroenteritis cases. However, the diversity of study designs and diagnostic methods often leads to misinterpretations of their impact. Our study explored the genetic diversity of HAdV-F40/41 in Brazil using a specific qPCR
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Human adenovirus (HAdV) F40/41 is an important pathogen in pediatric acute gastroenteritis cases. However, the diversity of study designs and diagnostic methods often leads to misinterpretations of their impact. Our study explored the genetic diversity of HAdV-F40/41 in Brazil using a specific qPCR assay for HAdV species F, combined with a phylogenetic analysis of the partial hexon and fiber genes. Our results demonstrated that HAdV-F41 strains predominated and exhibited higher diversity than HAdV-F40 strains. Based on the hexon gene, Brazilian HAdV-F41 strains were grouped into two genome type clusters (GTC), further divided into subclusters, with most strains clusteringto GTC2. The partial shaft region of the fiber gene exhibited higher conservation among HAdV-F41. The specific qPCR assay for HAdV species F identified HAdV-F in an additional 31.5% (34/108) of previously uncharacterized HAdV-positive samples detected using a non-specific HAdV qPCR assay. Both assays strongly correlated in detecting HAdV-F, and the specific qPCR assay for enteric types can enhance HAdV surveillance, especially when sequencing is not possible. Our study provides novel insights regarding the genetic diversity of HAdV-F species in Brazil.
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(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2023, 2024))
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Open AccessReview
Beneficial Plant–Microbe Interactions and Stress Tolerance in Maize
by
Saroj Burlakoti, Ananta R. Devkota, Shital Poudyal and Amita Kaundal
Appl. Microbiol. 2024, 4(3), 1000-1015; https://doi.org/10.3390/applmicrobiol4030068 - 25 Jun 2024
Abstract
Beneficial microbes are crucial for improving crop adaptation and growth under various stresses. They enhance nutrient uptake, improve plant immune responses, and help plants tolerate stresses like drought, salinity, and heat. The yield potential of any crop is significantly influenced by its associated
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Beneficial microbes are crucial for improving crop adaptation and growth under various stresses. They enhance nutrient uptake, improve plant immune responses, and help plants tolerate stresses like drought, salinity, and heat. The yield potential of any crop is significantly influenced by its associated microbiomes and their potential to improve growth under different stressful environments. Therefore, it is crucial and exciting to understand the mechanisms of plant–microbe interactions. Maize (Zea mays L.) is one of the primary staple foods worldwide, in addition to wheat and rice. Maize is also an industrial crop globally, contributing 83% of its production for use in feed, starch, and biofuel industries. Maize requires significant nitrogen fertilization to achieve optimal growth and yield. Maize plants are highly susceptible to heat, salinity, and drought stresses and require innovative methods to mitigate the harmful effects of environmental stresses and reduce the use of chemical fertilizers. This review summarizes our current understanding of the beneficial interactions between maize plants and specific microbes. These beneficial microbes improve plant resilience to stress and increase productivity. For example, they regulate electron transport, downregulate catalase, and upregulate antioxidants. We also review the roles of plant growth-promoting rhizobacteria (PGPR) in enhancing stress tolerance in maize. Additionally, we explore the application of these microbes in maize production and identify major knowledge gaps that need to be addressed to utilize the potential of beneficial microbes fully.
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(This article belongs to the Special Issue Current Trends in the Applications of Probiotics and Other Beneficial Microbes)
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Open AccessArticle
Obtaining Novel Vitamin B12 Production Strains Acetobacter malorum HFD 3141 and Acetobacter orientalis HFD 3031 from Home-Fermented Sourdough
by
Lisa Stumpf, Stefan Schildbach and Aidan Coffey
Appl. Microbiol. 2024, 4(3), 986-999; https://doi.org/10.3390/applmicrobiol4030067 - 23 Jun 2024
Abstract
Vitamin B12 is a critical nutrient in vegan and vegetarian lifestyles as plant-based vitamin sources are rare. Traditional fermented foods could be enriched by adding vitamin B12-producing bacteria to offer non-animal vitamin sources. The aim was to isolate a vitamin
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Vitamin B12 is a critical nutrient in vegan and vegetarian lifestyles as plant-based vitamin sources are rare. Traditional fermented foods could be enriched by adding vitamin B12-producing bacteria to offer non-animal vitamin sources. The aim was to isolate a vitamin B12 producer that is capable of producing the human-active vitamin even at low pH values so that it can be used in fruit juice fortification. Therefore, fermented foods (homemade and industrial) and probiotics were screened for vitamin B12 production strains. A modified microbiological vitamin B12 assay based on Lactobacillus delbrueckii subsp. lactis DSM 20355 was used to identify vitamin B12-containing samples and the presence of vitamin B12-producing strains. The screening resulted in isolating several positive strains for vitamin B12 formation derived from sourdough. Mass spectrometry confirmed the biosynthesis of solely the human physiologically active form. Species identification carried out by the German Strain Collection of Microorganisms and Cell Cultures resulted in two species: Acetobacter orientalis and Acetobacter malorum, of which two isolates were further characterised. The potential for cobalamin biosynthesises in food matrixes was demonstrated for A. malorum HFD 3141 and A. orientalis HFD 3031 in apple juice at different pH values (2.85–3.80). The isolates synthesised up to 18.89 µg/L and 7.97 µg/L vitamin B12 at pH 3.80. The results of this study suggest that acetic acid bacteria (AAB) and fermented acetic acid foods are promising resources for vitamin B12 and its producers, which might have been overlooked in the past.
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(This article belongs to the Special Issue Current Trends in the Applications of Probiotics and Other Beneficial Microbes)
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Open AccessReview
Changes in the Skin Microbiome Following Dermatological Procedures: A Scoping Review
by
Jeremy R. Ellis, Eron J. Powell, Luke M. Tomasovic, Rachel L. Marcheskie, Vishruth Girish, Anmol Warman and Darshan Sivaloganathan
Appl. Microbiol. 2024, 4(2), 972-985; https://doi.org/10.3390/applmicrobiol4020066 - 18 Jun 2024
Abstract
The skin microbiome consists of bacteria, fungi, viruses, and mites, which play a crucial role in maintaining skin health and immune function. Imbalances in this microbial community, known as dysbiosis, are implicated in various dermatological conditions. While skincare products are known to influence
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The skin microbiome consists of bacteria, fungi, viruses, and mites, which play a crucial role in maintaining skin health and immune function. Imbalances in this microbial community, known as dysbiosis, are implicated in various dermatological conditions. While skincare products are known to influence the skin microbiome, the effects of dermatological procedures have not been extensively studied. Here, we perform a scoping review to outline the studies investigating the impacts of dermatological interventions on the skin microbiome. Phototherapy emerged as the most studied intervention, encompassing UV phototherapy, light therapy, laser therapy, and photodynamic therapy. Chemical interventions, such as chemical peels, micropigmentation, and debridement, have comparatively limited studies describing their impacts on the skin microbiome. To date, no studies have been done on a wide variety of common dermatological procedures such as cryotherapy, skin grafts, and dermabrasion, which may have stronger likelihoods of affecting the skin microbiome. This underscores the need for further research on the influences of dermatological procedures, especially chemical and physical interventions, on the skin microbiome. More comprehensive pre-clinical and clinical studies are essential not only for understanding the long-term consequences of these procedures, but also for optimizing patient outcomes in dermatological care.
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(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2023, 2024))
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Open AccessArticle
Valorisation of Spent Yeast Fermentation Media through Compositional-Analysis-Directed Supplementation
by
Laura Murphy, Ciara D. Lynch and David J. O’Connell
Appl. Microbiol. 2024, 4(2), 959-971; https://doi.org/10.3390/applmicrobiol4020065 - 12 Jun 2024
Abstract
Spent fermentation media from bioprocessing represent a significant waste stream, and interest in recycling them as part of the developing circular bioeconomy is growing. The potential to reuse yeast spent culture media (YSM) to feed secondary bacterial fermentations producing recombinant protein was investigated
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Spent fermentation media from bioprocessing represent a significant waste stream, and interest in recycling them as part of the developing circular bioeconomy is growing. The potential to reuse yeast spent culture media (YSM) to feed secondary bacterial fermentations producing recombinant protein was investigated in this study. Elemental and amino acid compositional analysis using inductively coupled plasma mass spectrometry (ICP-MS) and LC-MS/MS identified significant differences in the concentrations of 6 elements and 18/20 amino acids in YSM compared with rich microbiological media (LB). Restoration of levels of magnesium and sodium through addition of their salts and amino acids from tryptone supplementation led to the expression of equivalent titres of recombinant proteins by E. coli (0.275 g/L), compared to that in LB media (0.296 g/L) and BMMY media (0.294 g/L) in shake flask culture. When this supplementation strategy was employed in a bioreactor system, we observed a significant increase in recombinant protein titre using the supplemented YSM (2.29 (±0.02) g/L) over that produced using LB media (1.29 (±0.09) g/L). This study demonstrates through highly sensitive compositional analysis and identification of supplementation strategies the potential to valorise spent media from yeast fermentations that underpin industrial processes of significant scale, creating a circular approach to waste stream management.
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(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2023, 2024))
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Open AccessArticle
Predicting Microbiome Growth Dynamics under Environmental Perturbations
by
George Sun and Yi-Hui Zhou
Appl. Microbiol. 2024, 4(2), 948-958; https://doi.org/10.3390/applmicrobiol4020064 - 10 Jun 2024
Abstract
MicroGrowthPredictor is a model that leverages Long Short-Term Memory (LSTM) networks to predict dynamic changes in microbiome growth in response to varying environmental perturbations. In this article, we present the innovative capabilities of MicroGrowthPredictor, which include the integration of LSTM modeling with a
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MicroGrowthPredictor is a model that leverages Long Short-Term Memory (LSTM) networks to predict dynamic changes in microbiome growth in response to varying environmental perturbations. In this article, we present the innovative capabilities of MicroGrowthPredictor, which include the integration of LSTM modeling with a novel confidence interval estimation technique. The LSTM network captures the complex temporal dynamics of microbiome systems, while the novel confidence intervals provide a robust measure of prediction uncertainty. We include two examples—one illustrating the human gut microbiota composition and diversity due to recurrent antibiotic treatment and the other demonstrating the application of MicroGrowthPredictor on an artificial gut dataset. The results demonstrate the enhanced accuracy and reliability of the LSTM-based predictions facilitated by MicroGrowthPredictor. The inclusion of specific metrics, such as the mean square error, validates the model’s predictive performance. Our model holds immense potential for applications in environmental sciences, healthcare, and biotechnology, fostering advancements in microbiome research and analysis. Moreover, it is noteworthy that MicroGrowthPredictor is applicable to real data with small sample sizes and temporal observations under environmental perturbations, thus ensuring its practical utility across various domains.
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(This article belongs to the Special Issue Microbiome in Ecosystem 3.0)
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Open AccessArticle
Evaluation of Solid-State Fermentation Conditions from Pineapple Peel Waste for Release of Bioactive Compounds by Aspergillus niger spp.
by
A. Danitza Casas-Rodríguez, Juan A. Ascacio-Valdés, Miriam Desirée Dávila-Medina, Miguel A. Medina-Morales, Liliana Londoño-Hernández and Leonardo Sepúlveda
Appl. Microbiol. 2024, 4(2), 934-947; https://doi.org/10.3390/applmicrobiol4020063 - 8 Jun 2024
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Currently, agroindustrial waste can be used to obtain bioactive compounds. The solid-state fermentation is an alternative for the valorization of these waste and to be able to release bioactive compounds that may be of interest to different industrial sectors. The aim of this
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Currently, agroindustrial waste can be used to obtain bioactive compounds. The solid-state fermentation is an alternative for the valorization of these waste and to be able to release bioactive compounds that may be of interest to different industrial sectors. The aim of this study was to evaluate solid-state fermentation conditions using pineapple peel waste as the substrate with Aspergillus niger spp., to release bioactive compounds using a Plackett–Burman exploratory design. Temperature, humidity, inoculum, NaNO3, MgSO4, KCl, and KH2PO4 conditions in the fermentation process were evaluated. The antioxidant capacity was determined, and the main compounds of the fermentation extracts were identified. The results revealed that the Aspergillus niger HT3 strain reached a hydrolyzable tannin release of 10.00 mg/g, While Aspergillus niger Aa20 reached a condensed tannin release of 82.59 mg/g. The KH2PO4 affects the release of condensed tannins with A. niger Aa20, and MgSO4 affects the release of hydrolyzable tannins with A. niger HT3. In addition, a positive antioxidant activity was demonstrated for the DPPH, ABTS, and FRAP technique. The main compounds in the fermented pineapple peel were 3-feruloylquinic acid, caffeic acid, lariciresinol, and 3-hydroxyphloretin 2′-O-xylosyl-glucoside, among others. The solid-state fermentation process is a biotechnological alternative for the release of bioactive compounds.
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Open AccessArticle
16S rRNA Analysis of Electrogenic Bacterial Communities from Soil Microbial Fuel Cells
by
Ana Rumora, Liliana Hopkins, Kayla Yim, Melissa F. Baykus, Luisa Martinez and Luis Jimenez
Appl. Microbiol. 2024, 4(2), 918-933; https://doi.org/10.3390/applmicrobiol4020062 - 5 Jun 2024
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Electrogenic bacteria present in bioelectrical devices such as soil microbial fuel cells (SMFCs) are powered by the oxidation of organic and inorganic compounds due to microbial activity. Fourteen soils randomly selected from Bergen Community College or areas nearby, located in the state of
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Electrogenic bacteria present in bioelectrical devices such as soil microbial fuel cells (SMFCs) are powered by the oxidation of organic and inorganic compounds due to microbial activity. Fourteen soils randomly selected from Bergen Community College or areas nearby, located in the state of New Jersey, USA, were used to screen for the presence of electrogenic bacteria. SMFCs were incubated at 35–37 °C. Of the 14 samples, 11 generated electricity and enriched electrogenic bacteria. The average optimal electricity production by the top 3 SMFCs was 152 microwatts. The highest electrical production was produced by SMFC-B1C and SMFC-B1B, with 162 and 152 microwatts, respectively. Microbial DNA was extracted from the biofilm grown on the anodes, followed by PCR analysis of the 16S rRNA V3–V4 region. Next-generation sequencing was performed to determine the structure and diversity of the electrogenic microbial community. The top 3 MFCs with the highest electricity production showed a bacterial community predominantly composed of bacteria belonging to the Bacillota and Pseudomonadota phyla with a significant presence of Euryarcheota members of methanogenic archaea. SMFC-B1C showed a more diverse electrogenic community, followed by SMFC-B1B and SMFC-B1. When analyzing the top 10 bacteria in the SMFCs, 67 percent belonged to the class Clostridia, indicating that anaerobic conditions were required to enrich electrogenic bacterial numbers and optimize electrical production. The ongoing optimization of SMFCs will provide better production of electricity and continuous enhancement of microbial activity to sustain longer operational times and higher levels of electrogenesis. The characterization of electrogenic microbial communities will provide valuable information to understand the contribution of different populations to the production of electricity in bioelectrical devices.
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Open AccessReview
The Industrial Fermentation Process and Clostridium Species Used to Produce Biobutanol
by
David T. Jones
Appl. Microbiol. 2024, 4(2), 894-917; https://doi.org/10.3390/applmicrobiol4020061 - 31 May 2024
Abstract
The fermentation route for producing biobutanol from renewable plant biomass was used extensively during the last century. The key factors affecting performance in the standard batch industrial fermentation process are highlighted. Four species of Clostridium were utilized for the industrial production of solvents,
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The fermentation route for producing biobutanol from renewable plant biomass was used extensively during the last century. The key factors affecting performance in the standard batch industrial fermentation process are highlighted. Four species of Clostridium were utilized for the industrial production of solvents, and although they share many features in common, they also exhibit significant differences. The salient features of the existing industrial species and strains are reviewed. These include their suitability for the type of process and fermentation substrate used. The strains are also assessed with respect to their potential for future applications.
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(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2023, 2024))
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Open AccessArticle
Trichoderma: Population Structure and Genetic Diversity of Species with High Potential for Biocontrol and Biofertilizer Applications
by
Adnan Ismaiel, Dilip K. Lakshman, Prashant P. Jambhulkar and Daniel P. Roberts
Appl. Microbiol. 2024, 4(2), 875-893; https://doi.org/10.3390/applmicrobiol4020060 - 27 May 2024
Abstract
Certain Trichoderma isolates provide biofertilizer, biocontrol, and other plant-beneficial activities while inhabiting the soil or internal plant tissue, and their use in agricultural systems can contribute to sustainable food production. It is thought that colonization of soil or internal plant tissue is fundamental
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Certain Trichoderma isolates provide biofertilizer, biocontrol, and other plant-beneficial activities while inhabiting the soil or internal plant tissue, and their use in agricultural systems can contribute to sustainable food production. It is thought that colonization of soil or internal plant tissue is fundamental for biocontrol and biofertilizer applications. Our collective analyses of prior surveys, where the tef1α sequence was almost exclusively used to identify Trichoderma species, showed that isolates from the Harzianum complex clade, the T. asperellum/T. asperelloides group, T. virens, T. hamatum, and T. atroviride were prevalent in soil and/or as endophytes. Population structure and genetic diversity based on the genetic markers tef1α, rpb2, and ITS were investigated, and new lineages with statistical bootstrap support within T. atroviride, T. asperellum, T. hamatum, and T. virens populations were found. The nearest relatives of some of these species were also revealed. Choosing isolates from among more than 500 known Trichoderma species for use in non-targeted evaluation screens for biocontrol or biofertilizer applications is time-consuming and expensive. Preferentially selecting isolates from T. atroviride, T. asperellum/T. asperelloides, T. hamatum, the T. harzianum complex clade, T. virens, and possibly nearest relatives may speed the identification of candidates for commercialization due to the demonstrated ability of these species to successfully inhabit the soil and internal plant tissue. To our knowledge, this is the first report where dominant soil and endophytic Trichoderma species were identified from past survey data and population structure and genetic diversity analyses conducted.
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(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2023, 2024))
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Open AccessArticle
The Detection of Propionate Utilization by Bacteria Isolated from a Plastic Recycling Site
by
Shuyan Wu, Pornchanok Subharat, Faith Palevich, John Mills and Gale Brightwell
Appl. Microbiol. 2024, 4(2), 856-874; https://doi.org/10.3390/applmicrobiol4020059 - 23 May 2024
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(1) The study aims to utilize a reported approach for culturing mesophilic bacteria from a plastic waste environment; (2) The work revived mesophilic microbial population from an aged PET recycling site using a culture-based approach, and determined the purified isolates in genus level
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(1) The study aims to utilize a reported approach for culturing mesophilic bacteria from a plastic waste environment; (2) The work revived mesophilic microbial population from an aged PET recycling site using a culture-based approach, and determined the purified isolates in genus level in 16S identification; (3) A total of 59 bacterial isolates were obtained, in which microbial species, including Pseudomonas spp, Rhodococcus spp, and Burkholderia spp were identified as abundance. It was observed that the surviving microbes favoured sodium propionate as a short-chain carbon source for growth, rather than the intended plastic substrate, PET. The preference of sodium propionate utilization by several bacterial isolates, including 5601W (detected as Rhodococcus spp.), 5601Y, 7801, and 7802 (detected as Burkholderia spp.), was confirmed through growth curve analysis and cell enumeration conducted in a medium where sodium propionate served as the sole carbon source.; (4) The microbial demonstration revealed the metabolic complex of microbial communities in the environment and indicated the challenges associated with bacterial isolation from environments with accumulated plastic waste.
Full article
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