Article
Horticulture
Xorla Kanfra, Taye Obawolu, Andreas Wrede, Bernhard Strolka, Traud Winkelmann, Bernd Hardeweg, Holger Heuer
Summary: The study suggests that Tagetes can alleviate apple replant disease by altering the nematode community in the soil. Nematodes extracted from soil treated with Tagetes had less impact on plant growth compared to those extracted from grass-treated soil. This indicates the potential of using Tagetes as a control option for managing apple replant disease.
Article
Plant Sciences
Eduarda Kalena Kirsh de Ramos, Paulo Cesar Pazdiora, Leandro Jose Dallagnol, Jeronimo Vieira de Araujo Filho
Summary: This study identified and quantified major plant-parasitic nematodes infesting apple growing areas in southern Brazil, with Pratylenchus and Helicotylenchus being the most abundant genera. The abundance of nematodes was strongly influenced by annual mean temperature and annual precipitation, although bioclimatic variables did not impact their distribution. Pratylenchus zeae and P. penetrans were identified for the first time in apple plants in Brazil, suggesting the need for management strategies in infested orchards.
TROPICAL PLANT PATHOLOGY
(2022)
Article
Microbiology
Xorla Kanfra, Andreas Wrede, Julia Moll, Holger Heuer
Summary: This study revealed significant differences in nematode, fungal, and bacterial communities between apple replanted plots and control plots. Nematodes associated with replanting and specific genera of fungi and bacteria were found in replanted plots, while certain genera indicative of a healthy state were found in control plots.
Article
Microbiology
Felix Mahnkopp-Dirks, Viviane Radl, Susanne Kublik, Silvia Gschwendtner, Michael Schloter, Traud Winkelmann
Summary: Apple Replant Disease (ARD) is a widespread problem in the horticultural industry, affecting plant growth and fruit quality. This study used both culture-independent and culture-dependent approaches to investigate the endophytic root microbiome of apple plants in ARD-affected and unaffected soil. The results suggest that Streptomyces play a key role in the etiology of ARD in the field.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Plant Sciences
Y. N. Duan, S. R. Ma, X. S. Chen, X. Shen, C. M. Yin, Z. Q. Mao
Summary: Apple replant disease (ARD) caused by Fusarium proliferatum f. sp. malus domestica (Fpmd) MR5 is a fungal pathogen that leads to annual losses in apple production in China. In this study, the whole-genome sequence of the highly virulent Fpmd MR5 was obtained, revealing potential pathogenicity-related genes and specific virulence factor genes. These findings will contribute to further research on host-pathogen interactions and the development of disease management strategies.
Article
Biochemistry & Molecular Biology
Belnaser A. Busnena, Till Beuerle, Felix Mahnkopp-Dirks, Traud Winkelmann, Ludger Beerhues, Benye Liu
Summary: Apple replant disease leads to the production of phytoalexins in apple tree roots, which are exuded into the roots and culture medium, potentially influencing the soil microbiome.
Article
Horticulture
Annmarie-Deetja Rohr, Jannika Staudt, Katharina Cziborra, Annabel Fritz, Michaela Schmitz, Traud Winkelmann
Summary: Apple replant disease (ARD), caused by shifts in the soil microbiome, poses a global threat to apple fruit and tree production. Roots growth is severely reduced in ARD affected soils, but shoot growth remains unaffected as long as part of the root system is in healthy soil. Plants show a localized molecular response to ARD, and are able to partially counteract its negative effects by growing into unaffected soil regions.
SCIENTIA HORTICULTURAE
(2021)
Article
Environmental Sciences
Xiaolong He, Baoying Yin, Jiran Zhang, Shasha Zhou, Zhongyong Li, Xueying Zhang, Jizhong Xu, Bowen Liang
Summary: Apple replant disease (ARD) is a common soil-borne disease that affects apple plants. The study found that adding melatonin to the replant soil can enhance plant tolerance to ARD by up-regulating the expression of antioxidant enzyme-related genes and increasing ROS scavenging enzyme activity. Melatonin also improves nitrogen absorption and utilization, promotes soil enzyme activity and bacterial richness, and reduces harmful fungi in the rhizosphere soil. These findings provide new insights into how melatonin enhances ARD tolerance.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Horticulture
Zhenquan Fan, Qun Xia, Zhiqiang Zhao, Yanan Duan, Lei Zhao, Haiyan Wang, Weitao Jiang, Xuesen Chen, Chengmiao Yin, Zhiquan Mao
Summary: XERF-1, an endophytic fungus isolated from healthy roots of apple trees, showed strong competitive antagonism against ARD-related pathogenic Fusarium species. Treatment with XERF-1 fertilizer significantly improved the growth of Malus hupehensis Rehd. seedlings and reduced the abundance of harmful Fusarium species in the soil.
SCIENTIA HORTICULTURAE
(2022)
Article
Plant Sciences
Haiyan Wang, Yuefan Sheng, Weitao Jiang, Fengbing Pan, Mei Wang, Xuesen Chen, Xiang Shen, Chengmiao Yin, Zhiquan Mao
Summary: This study investigates the effects of crop rotation on soil quality and seedling growth in an old apple orchard. It finds that rotating different crops can significantly improve soil quality and promote the growth of apple rootstock. The study also shows that certain crops have inhibitory effects on Fusarium species, and rotating crops can increase bacterial count and reduce fungal populations. In addition, crop rotation can enhance root respiration, enzyme activity, pH, and organic matter content, while decreasing soil bulk density.
HORTICULTURAL PLANT JOURNAL
(2022)
Article
Plant Sciences
Aurita Butkeviciute, Jonas Viskelis, Mindaugas Liaudanskas, Pranas Viskelis, Valdimaras Janulis
Summary: The study found variations in antioxidant activity and composition of phenolic compounds in different apple cultivars stored under different controlled atmosphere conditions, highlighting the importance of determining optimal storage conditions for providing consumers with high-quality apples.
Article
Forestry
Daniel A. Edge-Garza, Miguel Villamil-Castro, Dorrie Main, Craig Hardner
Summary: This communication addresses the issue of discrepant ssID information for 78 SNPs on the 8K IRSC apple SNP array and reports the correct NCBI ssIDs for these SNPs in order to accurately aggregate historical SNP data and prevent the perpetuation of misassigned sslDs in further publications.
TREE GENETICS & GENOMES
(2021)
Article
Soil Science
Xorla Kanfra, Andreas Wrede, Felix Mahnkopp-Dirks, Traud Winkelmann, Holger Heuer
Summary: Apple replant disease has a global impact on tree nurseries and apple production. Researchers have found that nematodes and co-extracted microbes trigger the symptoms, while pathogens or plant-parasitic nematodes cannot explain the early development of the disease. Studying nematode-microbe complexes can help understand the external biotic stress on apple roots and design mitigation measures.
APPLIED SOIL ECOLOGY
(2022)
Article
Horticulture
Wenwen Geng, Yi Lv, Yanan Duan, Haiyan Wang, Weitao Jiang, Rong Zhang, Ran Chen, Xuesen Chen, Xiang Shen, Chengmiao Yin, Zhiquan Mao
Summary: This study screened antagonistic Bacillus strains against apple replant disease pathogens and prepared a composite microbial culture. The results showed that the composite microbial culture significantly affected the growth of apple trees, soil bacteria, and enzyme activities, while reducing the abundance of soil fungi.
SCIENTIA HORTICULTURAE
(2022)
Article
Plant Sciences
Weitao Jiang, Ran Chen, Lei Zhao, Yanan Duan, Haiyan Wang, Zhubing Yan, Xiang Shen, Xuesen Chen, Chengmiao Yin, Zhiquan Mao
Summary: We isolated and identified a bacterium, Ochrobactrum haematophilum, from the rhizosphere soil of healthy replanted apple that produces IAA and degrades phloridzin. This bacterium can promote apple growth and degrade phenolic acids, providing a potential solution for the reduction of apple replant disease (ARD).
HORTICULTURAL PLANT JOURNAL
(2023)
Article
Allergy
Kathleen A. Lee-Sarwar, Yih-Chieh Chen, Yuan Yao Chen, Anita L. Kozyrskyj, Piush J. Mandhane, Stuart E. Turvey, Padmaja Subbarao, Hans Bisgaard, Jakob Stokholm, Bo Chawes, Soren J. Sorensen, Rachel S. Kelly, Jessica Lasky-Su, Robert S. Zeiger, George T. O'Connor, Megan T. Sandel, Leonard B. Bacharier, Avraham Beigelman, Vincent J. Carey, Benjamin J. Harshfield, Nancy Laranjo, Diane R. Gold, Scott T. Weiss, Augusto A. Litonjua
Summary: This study found associations between prenatal and early-life fecal microbiomes and childhood asthma phenotypes. Cesarean section was found to increase the risk of early asthma.
Article
Biotechnology & Applied Microbiology
Yu Fen Goh, Henriette L. L. Roder, Siew Herng Chan, Muhammad Hafiz Ismail, Jonas S. S. Madsen, Kai Wei Kelvin Lee, Soren J. Sorensen, Michael Givskov, Mette Burmolle, Scott A. A. Rice, Diane McDougald
Summary: Mixed species biofilms exhibit increased tolerance to stresses. Grazing by Tetrahymena pyriformis significantly reduced the biofilms of single species K. pneumoniae and P. protegens, but P. aeruginosa biofilms were resistant. Rhamnolipids and the quorum sensing molecule PQS contribute to the protective mechanisms.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Critical Care Medicine
Mahmoud I. Abdel-Aziz, Jonathan Thorsen, Simone Hashimoto, Susanne J. H. Vijverberg, Anne H. Neerincx, Paul Brinkman, Wim van Aalderen, Jakob Stokholm, Morten Arendt Rasmussen, Michael Roggenbuck-Wedemeyer, Nadja H. Vissing, Martin Steen Mortensen, Asker Daniel Brejnrod, Louise J. Fleming, Clare S. Murray, Stephen J. Fowler, Urs Frey, Andrew Bush, Florian Singer, Gunilla Hedlin, Bjorn Nordlund, Dominick E. Shaw, Kian Fan Chung, Ian M. Adcock, Ratko Djukanovic, Charles Auffray, Aruna T. Bansal, Ana R. Sousa, Scott S. Wagers, Bo Lund Chawes, Klaus Bonnelykke, Soren Johannes Sorensen, Aletta D. Kraneveld, Peter J. Sterk, Graham Roberts, Hans Bisgaard, Anke H. Maitland-van der Zee
Summary: By analyzing the oropharyngeal microbiota of children with asthma or wheezing, four distinct clusters with unique clinical characteristics were identified, and the enrichment scores of transcriptomic pathways associated with exacerbation risk and airway remodeling varied among these clusters.
AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE
(2023)
Article
Biochemical Research Methods
Danesh Moradigaravand, Liguan Li, Arnaud Dechesne, Joseph Nesme, Roberto de la Cruz, Huda Ahmad, Manuel Banzhaf, Soren J. Sorensen, Barth F. Smets, Jan-Ulrich Kreft
Summary: Wastewater treatment plants (WWTPs) contain diverse microbial communities that receive antimicrobial residues and resistant strains, allowing for horizontal gene transfer (HGT) of antimicrobial resistance (AMR) determinants. This study used machine learning models to predict plasmid permissiveness in water cycle microbial communities, which is the ability of cells to receive a plasmid through conjugation. The results showed a moderate-to-strong correlation between predicted and experimental permissiveness, indicating the potential for assessing the risk of AMR pollution in wastewater systems.
Article
Microbiology
Mathilde Borg Dahl, Juergen Kreyling, Sebastian Petters, Haitao Wang, Martin Steen Mortensen, Lorrie Maccario, Soren J. Sorensen, Tim Urich, Robert Weigel
Summary: In temperate regions, climate warming has implications for soil microorganisms and soil nutrient dynamics during winter. This study investigated the winter climate change responses in the soil microbiome of European beech forests. The results suggest a strong link between changes in the microbiomes and changes in environmental processes, such as nitrogen dynamics.
ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Inga Kwiecien, Natalizia Miceli, Elzbieta Kedzia, Emilia Cavo, Maria Fernanda Taviano, Ludger Beerhues, Halina Ekiert
Summary: The growth and accumulation of metabolites of three Hypericum perforatum cultivars were studied in different culture conditions, and their extracts were tested for antioxidant and antimicrobial activity. The extracts from plants grown under the best conditions showed high antioxidant and antimicrobial activity.
Article
Plant Sciences
Hesham M. B. Sayed, Sara Nassar, David Kaufholdt, Ludger Beerhues, Benye Liu, Islam El-Awaad
Summary: This study identified various derivatives of xanthones and found 5 variants of xanthone 4-prenyltransferase in St. John's wort. These enzymes were heterologously expressed and their functions were determined, with HpPT4px-v1 being the preferred acceptor substrate. These findings provide insights into the prenylation of xanthones in plants and contribute to the identification of other xanthone-specific prenyltransferases.
Article
Microbiology
Shiraz A. Shah, Ling Deng, Jonathan Thorsen, Anders G. Pedersen, Moira B. Dion, Josue L. Castro-Mejia, Ronalds Silins, Fie O. Romme, Romain Sausset, Leon E. Jessen, Eric Olo Ndela, Mathis Hjelmso, Morten A. Rasmussen, Tamsin A. Redgwell, Cristina Leal Rodriguez, Gisle Vestergaard, Yichang Zhang, Bo Chawes, Klaus Bonnelykke, Soren J. Sorensen, Hans Bisgaard, Francois Enault, Jakob Stokholm, Sylvain Moineau, Marie-Agnes Petit, Dennis S. Nielsen
Summary: Deep sequencing of faecal viromes from 647 healthy infants identified over 230 previously unknown gut virus families, expanding our understanding of the diversity in the human infant gut virome. The findings highlight the importance of the gut microbiome in infancy for the development of the immune system and long-term protection against chronic diseases. This study provides valuable insights into the viral diversity in the infant gut virome and expands phage taxonomy, serving as a resource for future research.
NATURE MICROBIOLOGY
(2023)
Article
Plant Sciences
Yongming Duan, Min Han, Maja Grimm, Jasper Schierstaedt, Jafargholi Imani, Massimiliano Cardinale, Marie Le Jean, Joseph Nesme, Soren J. Sorensen, Adam Schikora
Summary: This study investigated the response of barley to three different beneficial bacteria, as well as the influence of soil-borne Ensifer meliloti on seed microbiome. The results showed distinct colonization patterns of the bacteria in the rhizosphere and induction of systemic resistance against foliar fungal pathogens. Transcriptome analysis revealed the regulation of ion- and stress-related genes in plants upon bacterial encounter. The study also found an effect of bacterial inoculation on the composition of seed endophytes. These findings contribute to the understanding of the interaction between ISR-triggering bacteria and crop plants, which is crucial for sustainable agriculture.
Article
Multidisciplinary Sciences
Sarah Camara-Wilpert, David Mayo-Munoz, Jakob Russel, Robert D. Fagerlund, Jonas S. Madsen, Peter C. Fineran, Soren J. Sorensen, Rafael Pinilla-Redondo
Summary: Many bacteria use CRISPR-Cas systems to fight against mobile genetic elements like bacteriophages and plasmids. In response, these invasive elements have developed anti-CRISPR proteins to block host immunity. We have discovered a new type of CRISPR-Cas inhibition strategy based on small non-coding RNA anti-CRISPRs. These RNAs mimic the repeats found in CRISPR arrays and are encoded as individual repeat units in viral genomes. They strongly inhibit the type I-F CRISPR-Cas system by interacting with specific Cas proteins, leading to the formation of abnormal Cas subcomplexes.
Review
Plant Sciences
Belnaser A. Busnena, Ludger Beerhues, Benye Liu
Summary: This review summarizes the current research on biphenyls and dibenzofurans phytoalexins in the rosaceous subtribe Malinae, including apple and pear. A total of 46 biphenyls and 41 dibenzofurans have been detected in 44 species, and they exhibit varying inhibitory activity against phytopathogenic microorganisms. The formation, distribution, and function of these phytoalexins in Malinae species require further investigation.
Article
Genetics & Heredity
Angela M. Sanchez-Salazar, Tanvi Taparia, Asmus K. Olesen, Jacquelinne J. Acuna, Soren J. Sorensen, Milko A. Jorquera
Summary: Plant microbiomes play a vital role in the healthy development of plants. The interactions between microbes and plant hosts depend on various factors including plant genotype, plant compartment, phenological stage, and soil properties. Moreover, plant microbiomes contain a diverse pool of mobile genes encoded on plasmids, the functions of which are still poorly understood.
Article
Multidisciplinary Sciences
Yichao Wu, Chengxia Fu, Caroline L. Peacock, Soren J. Sorensen, Marc A. Redmile-Gordon, Ke-Qing Xiao, Chunhui Gao, Jun Liu, Qiaoyun Huang, Zixue Li, Peiyi Song, Yongguan Zhu, Jizhong Zhou, Peng Cai
Summary: Cooperative interactions between free-living and biofilm-forming bacteria are found to drive spatial segregation and enable species coexistence in a microfluidic chip environment, promoting their respective dominance in segregated microhabitats. This active spatial segregation is induced by cooperative interactions, improving the fitness of both biofilm and planktonic populations. The study also shows that free-living Arthrobacter induces surface colonization and receives benefits from public goods secreted by biofilm-forming strains.
NATURE COMMUNICATIONS
(2023)
Article
Microbiology
Lorrie Maccario, Ana F. Silva, Joseph Nesme, Cristina I. Amador, Soren J. Sorensen, Vaughn S. Cooper, Henriette L. Roder
Summary: We present the draft genomes of seven bacterial strains from two wastewater facilities in Denmark, two of which potentially belong to new groups within the Pseudomonas and Pseudochrobactrum genera. These genomes serve as valuable references for studying bacterial interactions and horizontal gene transfer in bacterial communities.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2023)
