Article
Biochemical Research Methods
Natalie J. Wu-Woods, Jacob T. Barlow, Florian Trigodet, Dustin G. Shaw, Anna E. Romano, Bana Jabri, A. Murat Eren, Rustem F. Ismagilov
Summary: This study introduces a microbial-enrichment method (MEM) that enables the removal of host DNA in human intestinal biopsies and allows for the characterization of low-abundance microbial taxa. The method provides deeper insights into the high-throughput characterization of the gut microbiome and demonstrates the construction of metagenome-assembled genomes from human intestinal biopsies.
Review
Microbiology
Chuan Wang, Lijian Jin
Summary: Microbial persisters refer to a subgroup of microorganisms that develop high tolerance to various antimicrobials. The research on persisters is still in its early stages, making it challenging to accurately distinguish persister cells from other drug tolerant ones. The existence of persisters is crucial for prolonged antibiotic exposure time and treatment failure, as well as the formation of antibiotic-resistant mutants. Further understanding of persisters is of great importance for effective prevention and control of chronic infections/inflammation.
CRITICAL REVIEWS IN MICROBIOLOGY
(2023)
Article
Microbiology
Julian C. B. Ponsford, Charley J. Hubbard, Joshua G. Harrison, Lois Maignien, C. Alex Buerkle, Cynthia Weinig
Summary: The composition of microbial communities associated with plants is influenced by the genetic background and ploidy level of the host. This study investigated the effects of genome duplication on rhizosphere bacterial communities in Arabidopsis thaliana and found that both the host genetic background and ploidy level affected the composition of the microbial communities. Additionally, the microbial communities derived from specific genetic backgrounds and ploidy levels had negative effects on plant growth. These findings suggest an interaction between host genetic background, ploidy level, and bacterial community assembly.
Article
Environmental Sciences
Jennifer M. Polinski, Mattie Rodrigue, Jason D. Meyer, Matthew J. Harke
Summary: This study focuses on hydrothermal vent plume waters above the Moytirra hydrothermal vent field and examines the biodiversity and metabolic activities of the microbial communities in the plume. The results reveal a rich diversity of microorganisms and suggest the importance of sulfur compounds as an energy source in these waters. The study also highlights the decreasing metabolic functions and quiescent stages of bacterial communities with distance from the vent source.
FRONTIERS IN MARINE SCIENCE
(2023)
Article
Biotechnology & Applied Microbiology
Mingyu Gan, Bingbing Wu, Gangfeng Yan, Gang Li, Li Sun, Guoping Lu, Wenhao Zhou
Summary: Enzyme-based host depletion and nanopore adaptive sequencing both significantly improved the microbial enrichment efficiency, resulting in increased diversity of microorganisms. The combined method showed the highest microbial enrichment efficiency compared to standard methods.
Article
Plant Sciences
Jing Guo, Boliang Wei, Jinliang Liu, David M. Eissenstat, Shuisheng Yu, Xiaofei Gong, Jianguo Wu, Xiaoyong He, Mingjian Yu
Summary: Plant species identity influences soil microbial communities directly by host specificity and root exudates, and indirectly by changing soil properties. The dominance of tree species and ectomycorrhizal woody plant species accounts for more of the variation among microbial communities than pine dominance alone. These findings indicate strong linkages between woody plant composition than soil microbial diversity.
Article
Microbiology
Jialin Hu, Grady Miller, Wei Shi
Summary: The study aimed to characterize drought-responsive bacteria and fungi in the roots and rhizosphere of different tall fescue cultivars. The bacterial and fungal communities in roots, rhizosphere and bulk soil were examined for abundance, diversity, and composition. The study revealed significant differences in microbial community composition and structure between non-irrigated and irrigated samples, as well as the impact of tall fescue cultivars on endophytic microbial communities.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Plant Sciences
Anthony Wenndt, Richard Boyles, Arlyn Ackerman, Sirjan Sapkota, Ace Repka, Rebecca Nelson
Summary: This study developed three novel phenotypes for evaluating the symptom manifestation of sorghum grain mold (SGM). Through investigating a diversity panel's genome, 19 significant single nucleotide polymorphisms associated with the symptom were identified. These findings provide insights into the genetic resistance to SGM.
Review
Biochemistry & Molecular Biology
Muhammad Noman, Temoor Ahmed, Usman Ijaz, Muhammad Shahid, Azizullah, Dayong Li, Irfan Manzoor, Fengming Song
Summary: Local microbial communities play a crucial role in enhancing plant health by providing nutrients, promoting growth, and enhancing resistance to diseases and stress. Microbiome engineering is an emerging biotechnological strategy that can improve crop yield and resilience, helping to address various environmental constraints.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Environmental Sciences
Lan Liu, Albert Barberan, Cheng Gao, Zhaochen Zhang, Meng Wang, Nina Wurzburger, Xin Wang, Ran Zhang, Junxiang Li, Jian Zhang
Summary: Urbanization has a significant impact on the biodiversity of soil microbial communities, with increased urbanization associated with slightly homogenized microbial communities. Soil prokaryotes and total fungi richness show a weak positive relationship with urbanization levels. Microbial phylotypes abundance demonstrate synchronous increases and decreases along urban gradients. Urbanization explains a portion of microbial variances in richness and community composition, although soil properties play a larger role in explaining the variances.
LAND DEGRADATION & DEVELOPMENT
(2022)
Article
Biotechnology & Applied Microbiology
Chenghang Du, Runlai Xu, Xuan Zhao, Ying Liu, Xiaohan Zhou, Wanqing Zhang, Xiaonan Zhou, Naiyue Hu, Yinghua Zhang, Zhencai Sun, Zhimin Wang
Summary: This study investigated the root-associated microbial community in different wheat cultivars and found their close relationships with nitrogen absorption characteristics, soil variables, and host characteristics. The root-associated microbiome has a significant impact on host nitrogen absorption.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2023)
Article
Plant Sciences
Meredith J. Persico, Suzanne M. Fleishman, David M. Eissenstat, Terrence H. Bell, Michela Centinari
Summary: In grapevine, the metabolic activity of absorptive roots changes as roots age, and this study investigates if nearby microbial assemblages shift as well. The study finds that microbial composition is distinct between young and old absorptive roots, particularly for fungi. However, there is little evidence of shifts in alpha diversity between young and old roots. The study suggests that considering root age may improve the interpretation of results regarding root functional traits and associated microbes.
PHYTOBIOMES JOURNAL
(2023)
Article
Chemistry, Multidisciplinary
Na Yang, Yujun Cheng, Seoyoung Kim, Bin Huang, Zuoji Liu, Jiawei Deng, Jing Wang, Changduk Yang, Feiyan Wu, Lie Chen
Summary: This study synthesized two new polymers through copolymerization, improving device performance by introducing the TPD block. The research achieved higher power conversion efficiency in organic solar cells by adding a third component to the binary system of PM6 and PM6-TPD.
Article
Biochemistry & Molecular Biology
Yuan Tian, Yang Liu, Liang Yue, Constantine Uwaremwe, Xia Zhao, Qin Zhou, Yun Wang, Ruoyu Wang
Summary: This study found that the combined application of Bacillus amyloliquefaciens inoculant and sucrose can improve the growth and quality of Rheum palmatum, stimulate uptake of plant nutrients, and alter the microbial community for biocontrol potential.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Agronomy
Marianne Koranda, Riikka Rinnan, Anders Michelsen
Summary: This study aims to understand the divergent effects of dwarf shrubs and mosses on soil microbial processes and soil carbon and nutrient availability in tundra heath. By analyzing soil samples from different plant species, the study found that shrub soils have high microbial biomass and phosphorus activity, while moss soils have high soil nitrogen availability and enzyme activity associated with a bacterial-dominated microbial community.
Article
Biochemical Research Methods
Frank Vogt, Gautam Shirsekar, Detlef Weigel
Summary: vcf2gwas is a convenient package that streamlines the traditional GWAS workflow and enhances reproducibility.
Article
Ecology
Or Shalev, Haim Ashkenazy, Manuela Neumann, Detlef Weigel
Summary: Plants are protected not only by their own immunity but also by commensal microbes. In interaction between a pathogenic Pseudomonas strain and naturally co-occurring commensals, non-pathogenic Pseudomonas were found to provide plant protection. Different bacterial genes linked to plant protection in each lineage were discovered through genome-wide association, highlighting iron acquisition and biofilm formation as prominent mechanisms of plant protection.
Article
Multidisciplinary Sciences
J. Grey Monroe, Thanvi Srikant, Pablo Carbonell-Bejerano, Claude Becker, Mariele Lensink, Moises Exposito-Alonso, Marie Klein, Julia Hildebrandt, Manuela Neumann, Daniel Kliebenstein, Mao-Lun Weng, Eric Imbert, Jon Agren, Matthew T. Rutter, Charles B. Fenster, Detlef Weigel
Summary: This study challenges the prevailing paradigm that mutations occur randomly by demonstrating that mutations occur less frequently in functionally constrained regions of the genome in Arabidopsis. It also shows that epigenomic and physical features explain the majority of the variance in the genome-wide pattern of mutation bias surrounding genes. The findings suggest that mutation bias is the primary force driving patterns of sequence evolution in natural accessions.
Article
Ecology
Or Shalev, Talia L. Karasov, Derek S. Lundberg, Haim Ashkenazy, Pratchaya Pramoj Na Ayutthaya, Detlef Weigel
Summary: The community structure in the plant-associated microbiome is influenced by interactions between the host and microbes, as well as among different microbes. In this study, the researchers found that commensal Pseudomonas strains can induce a host response that selectively inhibits specific pathogenic strains, providing plant protection. The extent of this protection depends on the genetic variation of the host plant.
NATURE ECOLOGY & EVOLUTION
(2022)
Editorial Material
Biology
Michael B. Eisen, Anna Akhmanova, Timothy E. Behrens, Jorn Diedrichsen, Diane M. Harper, Mihaela D. Iordanova, Detlef Weigel, Mone Zaidi
Summary: eLife is changing its editorial process to prioritize public reviews and assessments of preprints.
Article
Biochemistry & Molecular Biology
Fernando A. Rabanal, Maike Graff, Christa Lanz, Katrin Fritschi, Victor Llaca, Michelle Lang, Pablo Carbonell-Bejerano, Ian Henderson, Detlef Weigel
Summary: By comparing the assembly methods of long-read and high-fidelity reads, researchers found that contig breaks in long-read assembly are mainly caused by centromeres and rDNA clusters, while unfilled gaps in high-fidelity assembly are primarily composed of relatively short repetitive segments. This approach demonstrates its value in research by enabling the reconstruction of gapless genome regions.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Plant Sciences
Julieta L. Mateos, Sabrina E. Sanchez, Martina Legris, David Esteve-Bruna, Jeanette C. Torchio, Ezequiel Petrillo, Daniela Goretti, Noel Blanco-Tourinan, Danelle K. Seymour, Markus Schmid, Detlef Weigel, David Alabadi, Marcelo J. Yanovsky
Summary: Plants undergo transcriptome reprograming to adapt to daily and seasonal fluctuations in light and temperature conditions. The proper spliceosome assembly, which requires the methylosome complex, is crucial for efficient pre-mRNA splicing. PICLN, a part of the methylosome complex, plays a key role in regulating pre-mRNA splicing and mediating plant adaptation to environmental conditions.
Article
Multidisciplinary Sciences
Derek S. Lundberg, Roger de Pedro Jove, Pratchaya Pramoj Na Ayutthaya, Talia L. Karasov, Or Shalev, Karin Poersch, Wei Ding, Anita Bollmann-Giolai, Ilja Bezrukov, Detlef Weigel
Summary: Sphingomonas is a highly abundant bacterial genus in the phyllosphere of wild Arabidopsis thaliana, but its interaction with plants is poorly understood. Genomic analysis reveals high intergenomic diversity and adaptability of Sphingomonas, indicating frequent biotic interactions. However, plant-protective phenotypes are rare among Sphingomonas isolates.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Julia M. Kreiner, Sergio M. Latorre, Hernan A. Burbano, John R. Stinchcombe, Sarah P. Otto, Detlef Weigel, Stephen I. Wright
Summary: This study uses genome analysis of the common waterhemp to demonstrate the significant impact of modern agriculture and agricultural intensification on the evolution of agricultural weeds. The strong selection pressure and changes in allele frequency trajectories since the 1960s have influenced the success of this weed in the 21st century, with human-mediated range shifts playing a role.
Article
Cell Biology
Agustin L. Arce, Regina Mencia, Damian A. Cambiagno, Patricia L. Lang, Chang LIu, Hernan A. Burbano, Detlef Weigel, Pablo A. Manavella
Summary: Transposons are mobile elements that are silenced in order to protect genome integrity. In plants, transposable element-derived inverted repeats (IRs) are often found near genes and affect gene expression. However, the molecular mechanisms of this regulation are still unclear in most cases.
Article
Genetics & Heredity
Anjar Tri Wibowo, Javier Antunez-Sanchez, Alexander Dawson, Jonathan Price, Cathal Meehan, Travis Wrightsman, Maximillian Collenberg, Ilja Bezrukov, Claude Becker, Moussa Benhamed, Detlef Weigel, Jose Gutierrez-Marcos
Summary: Clonal propagation is commonly used in commercial plant breeding and biotechnology programs to minimize genetic variation. However, clonal plants often show stable phenotypic changes, known as somaclonal variation. Studies have linked this variation to epigenetic modifications induced during regeneration.
Article
Biotechnology & Applied Microbiology
Sonja Kersten, Fernando A. Rabanal, Johannes Herrmann, Martin Hess, Zev N. Kronenberg, Karl Schmid, Detlef Weigel
Summary: Rapid adaptation of weeds to herbicide applications in agriculture through resistance development, particularly the grass Alopecurus myosuroides, is a common phenomenon. Target-site resistances (TSRs) are important for this adaptive response. In this study, we used PacBio HiFi reads to sequence long-range amplicons and resolved them into haplotypes using the PacBio amplicon analysis (pbaa) algorithm in pools of individuals. We recovered most haplotypes from previously sequenced individuals and found common TSR mutations originating from independent soft sweeps in new populations.
PLANT BIOTECHNOLOGY JOURNAL
(2023)
Letter
Biotechnology & Applied Microbiology
Herve Vanderschuren, Patience Chatukuta, Detlef Weigel, Devang Mehta
NATURE BIOTECHNOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Sami Saarenpaeae, Or Shalev, Haim Ashkenazy, Vanessa Carlos, Derek Severi Lundberg, Detlef Weigel, Stefania Giacomello
Summary: The interactions between microorganisms and their multicellular host are crucial for understanding plant or animal tissues. However, current technology hinders the study of spatial interactions between the host and its colonizing microorganisms. In this study, we introduce spatial metatranscriptomics (SmT), a sequencing-based approach that allows simultaneous characterization of host transcriptome and microbiome at a high spatial resolution. The SmT technique was applied to outdoor-grown Arabidopsis thaliana leaves and revealed tissue-scale hotspots of bacteria and fungi. By analyzing networks, we investigated the spatial interactions between microorganisms from different kingdoms, as well as the host response to microbial hotspots. SmT provides a valuable approach for studying the interplay between host and microbiome.
NATURE BIOTECHNOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Thanvi Srikant, Wei Yuan, Kenneth Wayne Berendzen, Adrian Contreras-Garrido, Hajk-Georg Drost, Rebecca Schwab, Detlef Weigel
Summary: A systematic analysis of the requirement for MET1 in different A. thaliana accessions reveals that CG methylation plays a dual role in gene expression. For many genes, CG methylation appears to canalize expression levels, masking regulatory divergence. However, for a smaller subset of genes, CG methylation increases expression diversity beyond genetically encoded differences.