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17 pages, 2049 KiB

Open AccessArticle

Assessment of Soil Health Through Metagenomic Analysis of Bacterial Diversity in Russian Black Soil

by Olesya O. Galanova, Nikita A. Mitkin, Albina A. Danilova, Vsevolod V. Pavshintsev, Denis A. Tsybizov, Alexander M. Zakharenko, Kirill S. Golokhvast, Tatiana V. Grigoryeva, Maria I. Markelova and Aleksey A. Vatlin

Microorganisms 2025, 13(4), 854; https://doi.org/10.3390/microorganisms13040854 - 9 Apr 2025

Viewed by 894

Abstract

Soil health is a critical determinant of agricultural productivity and environmental sustainability. Traditional assessment methods often fail to provide a comprehensive understanding of soil microbial communities and their functions. This study addresses this challenge by employing metagenomic techniques to assess the functionality of soil microbiomes in Russian black soil, renowned for its high fertility. We utilized shotgun metagenomic sequencing to analyze soil samples from Western Siberia subjected to different degrees of agro-soil disturbance. We identified functional genes involved in carbon (accA, argG, acsA, mphE, miaB), phosphorus (phoB, ppa, pstB, pnp, phnJ), and nitrogen (queC, amiF, pyrG, guaA, guaB, napA) metabolic pathways and associated with changes in microbial diversity, in general, and higher representation of certain bacterial species—Bradyrhizobium spp. The results demonstrated significant differences in microbial composition and functional potential between tillage treatments. No-Till technology and conventional tillage practices promoted beneficial microbial communities and enhanced soil health compared to long-term fallow soil. This work underscores the potential of metagenomic analysis in providing a comprehensive understanding of soil health, marking a significant advancement in the field. Full article

(This article belongs to the Section Microbiomes)

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14 pages, 2067 KiB

Open AccessArticle

Genotypic and Phenotypic Characterization of Pseudomonas atacamensis EMP42 a PGPR Strain Obtained from the Rhizosphere of Echinocactus platyacanthus (Sweet Barrel)

by Leilani Itzel Salinas-Virgen, María Eugenia de la Torre-Hernández, José Félix Aguirre-Garrido, Francisco Martínez-Abarca and Hugo César Ramírez-Saad

Microorganisms 2024, 12(8), 1512; https://doi.org/10.3390/microorganisms12081512 - 24 Jul 2024

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Abstract

Plant growth-promoting rhizobacteria (PGPR) are a group of bacteria that associate with the rhizosphere of plants; one of the most abundant bacterial genera in this ecological niche is Pseudomonas, which is constantly expanding due to the emergence of new species such as Pseudomonas atacamensis, whose discovery in 2019 has led to the characterization of several strains from different environments but taxonomically related. The objective of this work was to phenotypically and molecularly characterize P. atacamensis strain EMP42, isolated from the rhizosphere of Echinocactus platyacanthus. The strain EMP42 is able to use different substrates and reduce oxidative stress in plants. It is capable of improving growth parameters such as the number of inflorescences and the height of the aerial body of Arabidopsis thaliana, as well as the germination and seedling survival of the cacti Echinocactus platyacanthus and Astrophytum capricorne. The genetic structure of P. atacamensis EMP42 consists of a closed chromosome of 6.14 Mbp, and 61.1% GC content. It has 5572 genes, including those associated with PGPR activities, such as the trpABCDE, SAP, phoABPRU and acsABC genes, among others, and three ncRNA loci, nine regulatory regions, five complete rRNA operons and three CRISPR-Cas loci, showing phylogenomic similarities with the reference strain P. atacamensis B21-026. Therefore, this study contributes to the understanding of genomic diversity within P. atacamensis and, particularly, highlights the potential application of strain EMP42 as a PGPR. Full article

(This article belongs to the Special Issue Genomics Approaches in Microbial Ecology)

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11 pages, 1392 KiB

Open AccessArticle

Endophytic Community Composition and Genetic-Enzymatic Features of Cultivable Bacteria in Vaccinium myrtillus L. in Forests of the Baltic-Nordic Region

by Ingrida Mažeikienė, Birutė Frercks, Daiva Burokienė, Irena Mačionienė and Alvija Šalaševičienė

Forests 2021, 12(12), 1647; https://doi.org/10.3390/f12121647 - 27 Nov 2021

Cited by 9 | Viewed by 2643

Abstract

Regardless of their growth locations and species diversity, plants have endophytic bacterial communities. Bilberry (Vaccinium myrtillus L.) is valuable for human health because of its antioxidant properties, and the plant has adapted to stressful growing conditions in forests. Here, we aimed to describe the composition of the community of endophytic microorganisms in bilberry leaves and to determine whether the diversity of endophytic bacteria varies depending on the geographical location of the plants. In this study, we evaluated the significance of endophytes in the host plant and the potential use of such bacteria. Twenty-five culturable bacterial isolates were identified in V. myrtillus leaves based on 16S rRNA gene sequencing and phylogenetic analysis. For the first time, we report upon the diversity of endophytic communities coexisting in bilberry leaves in different geographical locations of the Nordic-Baltic region. Under harsh conditions, the bilberry plants had a greater diversity of bacteria. The bacterial families Bacillaceae, Paenibacillaceae and Micrococcaceae were the most common endophytes in leaves of bilberry. Strains of Staphylococcaceae, Lactobacillaceae, Pseudomonaceae, Corynebacteriaceae and Planococcaceae were identified in samples from Finland and Norway. Plant growth-promoting genes (acdS and AcPho) and/or enzymatic activity were identified in many isolates. Full article

(This article belongs to the Section Forest Biodiversity)

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13 pages, 2044 KiB

Open AccessArticle

Understanding the Role of Trichoderma reesei Vib1 in Gene Expression during Cellulose Degradation

by Xiuzhen Chen, Bingran Song, Minglu Liu, Lina Qin and Zhiyang Dong

J. Fungi 2021, 7(8), 613; https://doi.org/10.3390/jof7080613 - 29 Jul 2021

Cited by 9 | Viewed by 3180

Abstract

Vib1, a member of the Ndt80/PhoG-like transcription factor family, has been shown to be essential for cellulase production of Trichoderma reesei. Here, we combined transcriptomic and genetic analyses to gain mechanistic insights into the roles of Vib1 during cellulose degradation. Our transcriptome analysis showed that the vib1 deletion caused 586 genes with decreased expression and 431 genes with increased expression on cellulose. The downregulated genes were enriched for Gene Ontology terms associated with carbohydrate metabolism, transmembrane transport, oxidoreductase activity, and transcription factor activity. Of the 258 genes induced by cellulose, 229 showed no or decreased expression in Δvib1 on cellulose, including almost all (hemi)cellulase genes, crucial sugar transporter genes (IDs:69957, 3405), and the genes encoding main transcriptional activators Xyr1 and Ace3. Additionally, Vib1 also regulated the expression of genes involved in secondary metabolism. Further comparison of the transcriptomes of Δvib1 and Δxyr1 in cellulose revealed that the genes regulated by Vib1 had much overlap with Xyr1 targets especially for the gene set induced by cellulose, presumably whose expression requires the cooperativity between Vib1 and Xyr1. Genetic evidence indicated that Vib1 regulates cellulase gene expression partially via Xyr1. Our results will provide new clues for strain improvement. Full article

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20 pages, 4452 KiB

Open AccessFeature PaperArticle

Protein Kinase C Alpha Cellular Distribution, Activity, and Proximity with Lamin A/C in Striated Muscle Laminopathies

by Hannah A. Nicolas, Anne T. Bertrand, Sarah Labib, Musfira Mohamed-Uvaize, Pierrette M. Bolongo, Wen Yu Wu, Zofia T. Bilińska, Gisèle Bonne, Marie-Andrée Akimenko and Frédérique Tesson

Cells 2020, 9(11), 2388; https://doi.org/10.3390/cells9112388 - 31 Oct 2020

Cited by 5 | Viewed by 4326

Abstract

Striated muscle laminopathies are cardiac and skeletal muscle conditions caused by mutations in the lamin A/C gene (LMNA). LMNA codes for the A-type lamins, which are nuclear intermediate filaments that maintain the nuclear structure and nuclear processes such as gene expression. Protein kinase C alpha (PKC-α) interacts with lamin A/C and with several lamin A/C partners involved in striated muscle laminopathies. To determine PKC-α’s involvement in muscular laminopathies, PKC-α’s localization, activation, and interactions with the A-type lamins were examined in various cell types expressing pathogenic lamin A/C mutations. The results showed aberrant nuclear PKC-α cellular distribution in mutant cells compared to WT. PKC-α activation (phos-PKC-α) was decreased or unchanged in the studied cells expressing LMNA mutations, and the activation of its downstream targets, ERK 1/2, paralleled PKC-α activation alteration. Furthermore, the phos-PKC-α-lamin A/C proximity was altered. Overall, the data showed that PKC-α localization, activation, and proximity with lamin A/C were affected by certain pathogenic LMNA mutations, suggesting PKC-α involvement in striated muscle laminopathies. Full article

(This article belongs to the Collection Lamins and Laminopathies)

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