Review
Plant Sciences
Wei Fang, Fang Liu, Zhaoyuan Wu, Zhigang Zhang, Kaimei Wang
Summary: Weeds have a significant impact on crop production and ecological health, while chemical herbicides have adverse effects on the environment and food safety. To address this, microbes have been explored as bioherbicides. Plant-associated bacteria (PAB) can inhibit weed growth through the production of various compounds. However, the performance of PAB-based herbicides is influenced by multiple factors and further research is needed to maximize their effectiveness.
Article
Agronomy
Elena A. Tsavkelova, Olga A. Churikova, Elena A. Volynchikova, Sofia S. Sapun, Maria R. Leontieva, Anna S. Speranskaya, Evgenii A. Konorov, Anastasia A. Krinitsina
Summary: Beneficial bacteria contribute significantly to the adaptive capacities of host plants. This study found a wide diversity of beneficial bacteria in the root system of lilacs. However, the endophytic community in the buds was limited and varied among different cultivars.
Article
Environmental Sciences
Yibo Liu, Baiyu Zhang, Ye Yao, Bo Wang, Yiqi Cao, Yanping Shen, Xiaohui Jia, Fukai Xu, Ziwei Song, Chengpeng Zhao, Hongjie Gao, Ping Guo
Summary: This study investigated the interaction between rhizosphere and endosphere bacteria and their impact on plant phytoextraction of arsenic and carbon fixation. Through various experiments and analyses, it was found that cooperative interactions occurred between bacteria in the rhizosphere and endosphere, promoting plant arsenic extraction and carbon fixation. This study revealed the mechanisms of these interactions and highlighted the potential of phytoextraction for achieving multiple environmental goals.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Microbiology
Claudia Sanchis-Lopez, Jean Paul Cerna-Vargas, Saray Santamaria-Hernando, Cayo Ramos, Tino Krell, Pablo Rodriguez-Palenzuela, Emilia Lopez-Solanilla, Jaime Huerta-Cepas, Jose J. Rodriguez-Herva
Summary: Chemosensory pathways in bacteria are crucial for environmental sensing and response, with a large diversity of ligand binding domains (LBDs) identified. Our study demonstrates the importance of environmental factors in shaping the evolution and selection of LBDs, especially in plant-associated bacteria. The presence of niche-specific LBD types suggests lifestyle adaptation is important in the selection of these signal transduction proteins.
Article
Multidisciplinary Sciences
Ruyi Fan, Fen Zhao, Zhou Gong, Yanke Chen, Bao Yang, Chen Zhou, Jie Zhang, Zhangmeng Du, Xuemin Wang, Ping Yin, Liang Guo, Zhu Liu
Summary: This study reports the crystal structure of Arabidopsis NPC4 and reveals that the C-terminal domain (CTD) plays a critical role in NPC4 activity. Through structure-guided biochemical studies, the authors elucidate the molecular mechanism of phospholipid hydrolysis by NPC4 and provide new insights into the phospholipase family members.
NATURE COMMUNICATIONS
(2023)
Article
Agronomy
Qiuxia Liu, Jinsong Wang, Ailian Wu, Anqi Sun, Erwei Dong, Yuan Wang, Xiaolei Huang, Hangwei Hu, Xiaoyan Jiao
Summary: This study evaluated the relative importance of bacterial and fungal communities in different compartments of sorghum plants in predicting grain yield and quality. The findings showed that the microbiome during the reproductive period had a greater impact on grain yield and protein content than during the vegetative period. The microbiomes in the root endosphere and rhizosphere were found to be more important in predicting sorghum grain yield and protein content. Both bacterial and fungal communities in these compartments played an equal role.
FIELD CROPS RESEARCH
(2023)
Article
Microbiology
Louis Berrios
Summary: The study analyzed the genomes of selected Burkholderia strains from humans and plants, revealing host-specific metabolic pathway potentials and convergent features related to pathogenic overlap between hosts.
ARCHIVES OF MICROBIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Alice Miral, Sylvain Fournet, Catherine Porte, Aurelie Sauvager, Josselin Montarry, Sophie Tomasi, Sylvain Tranchimand
Summary: Healthy food is a major challenge for the development of this century, with plant-parasitic nematodes causing significant damage to global crop yields. The use of chemical nematicides for control is no longer environmentally sustainable, and biocontrol methods, such as biopesticides derived from living organisms, offer a promising alternative. This study focuses on the underexploited ecological niche of lichen microecosystems to develop new plant protection products. The lichen-associated bacterial suspensions from Paenibacillus etheri are investigated for their potential as nematicides against two nematode species, and the effects of volatile organic compounds produced by the bacteria are evaluated.
Article
Environmental Sciences
Patricia Soler, Laura Moreno-Mesonero, Andres Zornoza, V Javier Macian, Yolanda Moreno
Summary: The effectiveness of drinking water treatment is crucial for safe water consumption. This study evaluated the changes in eukaryotic microbiome before and after UV disinfection in a drinking water treatment plant (DWTP), and found a correlation between flow, nitrate levels and eukaryotic microbiome structure. Public health concern eukaryotic organisms were identified, and the presence of some human bacterial pathogens was statistically correlated with certain eukaryotic carriers, indicating a public health risk.
SCIENCE OF THE TOTAL ENVIRONMENT
(2021)
Article
Plant Sciences
Hannes Schmidt, Stefan Gorka, David Seki, Arno Schintlmeister, Dagmar Woebken
Summary: This study developed an analytical approach that combines gold-based in situ hybridization with NanoSIMS imaging to identify and localize individual bacteria on root surfaces and observe their metabolic activity. Experiments conducted on rice plants associated with the DS-1 strain showed heterogeneous patterns of N-15 enrichment in the rhizoplane bacteria involved in N2 fixation. This method can be used to investigate plant-microbe interactions and verify the in situ metabolic activity of plant-associated commercial strains or growth-promoting bacteria, aiding in the design of plant-microbe combinations for improved crop management.
Article
Plant Sciences
Svitlana Bilous, Artur Likhanov, Vira Boroday, Yurii Marchuk, Liubov Zelena, Oleksandr Subin, Andrii Bilous
Summary: Europe's forests, especially in Ukraine, are highly susceptible to climate change. Ensuring forest health is a top priority, and stakeholders are interested in understanding and utilizing the interactions between trees and their associated microorganisms. Endophytic bacteria isolated from unripe oak acorns have shown potential as biocontrol agents against phytopathogens, suggesting their use as biopesticides in forest management.
Review
Environmental Sciences
Sarah Gonzalez Henao, Thaura Ghneim-Herrera
Summary: This study critically analyzed 85 research articles published over the past 15 years, focusing on bacteria-assisted remediation strategies for the non-essential heavy metals arsenic, cadmium, and lead, and highlighted Klebsiella and Enterobacter as potential candidates for bioremediation and bacterial-assisted phytoremediation in contaminated soils.
FRONTIERS IN ENVIRONMENTAL SCIENCE
(2021)
Review
Microbiology
Bernard R. Glick, Elisa Gamalero
Summary: Studying how beneficial bacteria promote plant growth has shown that specific soil microorganism consortia interact to benefit plant growth. Plants attract beneficial microorganisms based on their root exudates, excluding potentially pathogenic ones, and these consortia not only promote plant growth but also protect plants from environmental stresses. By understanding beneficial bacterial microbiomes, it may be possible to develop synthetic microbiomes where compatible bacteria work together to promote plant growth under various natural conditions.
Article
Microbiology
Robert Radisch, Miroslav Patek, Barbora Kristkova, Margit Winkler, Vladimir Kren, Ludmila Martinkova
Summary: This review focuses on the contribution of enzymes to plant-bacteria interactions, specifically discussing substrate specificities, taxonomic and ecological distribution, and importance in selected plant symbionts. The data shows that these enzymes are abundant in Actinobacteria and Proteobacteria and play important roles in breaking through plant defenses, utilizing aldoximes or nitriles as nutrients, and potentially contributing to the synthesis of the phytohormone indole-3-acetic acid.
Review
Plant Sciences
Maha Chieb, Emma W. Gachomo
Summary: Climate change exacerbates the negative effects of abiotic stresses, such as drought, on plant growth and productivity. Plant colonization by plant growth-promoting rhizobacteria (PGPR) can enhance plant drought tolerance and improve plant growth and productivity.
Article
Neurosciences
Kylynda C. Bauer, Elisa M. York, Mihai S. Cirstea, Nina Radisavljevic, Charisse Petersen, Kelsey E. Huus, Eric M. Brown, Tahereh Bozorgmehr, Rebeca Berdun, Louis-Philippe Bernier, Amy H. Y. Lee, Sarah E. Woodward, Zakhar Krekhno, Jun Han, Robert E. W. Hancock, Victoria Ayala, Brian A. MacVicar, Barton Brett Finlay
Summary: Fecal-oral contamination promotes malnutrition pathology and cognitive impairment. In this study, the researchers found that continuous exposure to fecal commensals affected the morphology and transcriptional profile of microglial cells in malnourished mice, leading to altered neuroimmune responses and brain plasticity. Additionally, mitigating cognitive deficits in the malnourished mice was possible through supplementation with an omega-3 PUFA/antioxidant-associated diet, highlighting PUFA metabolism as a potential therapeutic target.
Article
Medicine, General & Internal
Arjun Baghela, Olga M. Pena, Amy H. Lee, Beverlie Baquir, Reza Falsafi, Andy An, Susan W. Farmer, Andrew Hurlburt, Alvaro Mondragon-Cardona, Juan Diego Rivera, Andrew Baker, Uriel Trahtemberg, Maryam Shojaei, Carlos Eduardo Jimenez-Canizales, Claudia C. dos Santos, Benjamin Tang, Hjalmar R. Bouma, Gabriela V. Cohen Freue, Robert E. W. Hancock
Summary: This study used machine learning and data mining techniques to analyze gene expression profiles of septic shock patients, and identified distinct signatures associated with disease severity, organ dysfunction, and mortality. The patients were also classified into five endotypes based on gene expression differences and specific pathways/mechanisms. The findings provide a method for triaging and treating early sepsis patients.
Article
Multidisciplinary Sciences
Milad Ebadi, Claire McCague, Ophelia Vallee, Patrick K. Taylor, Amy H. Y. Lee, Majid Bahrami
Summary: This study investigated antiviral filtration used in personal protective equipment and HVAC systems, finding that coating compositions of NaCl and Tween 20 showed strong antiviral properties, effectively reducing viral activity within a short period of time.
SCIENTIFIC REPORTS
(2022)
Article
Microbiology
Renan N. D. Almeida, Michael Greenberg, Cedoljub Bundalovic-Torma, Alexandre Martel, Pauline W. Wang, Maggie A. Middleton, Syama Chatterton, Darrell Desveaux, David S. Guttman
Summary: The study investigates the virulence and host specificity of Pseudomonas syringae strains on common bean and demonstrates the power of machine learning in predicting host specific adaptation. The results show that PG3 strains have higher host specificity than PG2 strains, and a machine learning model based on whole genome data can accurately predict virulence. The study strengthens the hypothesis of different lifestyles between PG2 and other P. syringae strains.
Article
Microbiology
Angela Zou, Kerry Nadeau, Xuejian Xiong, Pauline W. Wang, Julia K. Copeland, Jee Yeon Lee, James St Pierre, Maxine Ty, Billy Taj, John H. Brumell, David S. Guttman, Shayan Sharif, Doug Korver, John Parkinson
Summary: This study systematically investigated the composition and function of the chicken gut microbiome in response to AGPs. Results revealed nuanced impacts of AGPs, dependent on age of bird, diet, and intestinal site sampled.
Article
Gastroenterology & Hepatology
Qiaochu Lin, Meggie Kuypers, Zhewei Liu, Julia K. Copeland, Donny Chan, Susan J. Robertson, Jean Kontogiannis, David S. Guttman, E. Kate Banks, Dana J. Philpott, Thierry Mallevaey
Summary: This study demonstrates that iNKT cells have minimal influence on regulating commensal bacteria in the gut at steady state.
Article
Multidisciplinary Sciences
Katharine Sedivy-Haley, Travis Blimkie, Reza Falsafi, Amy Huei-Yi Lee, Robert E. W. Hancock
Summary: Salmonella is an intracellular pathogen that causes significant morbidity and mortality. The ability of Salmonella to grow inside macrophages is important for its virulence. Different types of macrophages have different effects on the growth of Salmonella. Endotoxin-primed macrophages show similar levels of resistance to Salmonella as classically activated macrophages after 2 hours of infection, but become susceptible like alternatively activated macrophages at later time points. The JAK-STAT pathway plays an important role in the resistance of macrophages to Salmonella, and early activation of this pathway is crucial for M1 macrophage resistance.
Review
Plant Sciences
Clare Breit-McNally, Bradley Laflamme, Racquel A. Singh, Darrell Desveaux, David S. Guttman
Summary: A key aspect of innate immunity in plants involves the recognition of pathogen effector virulence proteins by host Nucleotide-Binding Leucine-Rich Repeat Receptors (NLRs). The ZAR1 NLR has the remarkable ability to recognize at least six different families of effectors from two bacterial genera. This broad recognition is achieved through interactions with two families of Receptor-Like Cytoplasmic Kinases (RLCKs): ZED1-Related Kinases (ZRKs) and PBS1-Like Kinases (PBLs).
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Connor R. Fitzpatrick, Julia Copeland, Pauline W. Wang, David S. Guttman, Peter M. Kotanen, Marc T. J. Johnson
Summary: The root microbiome consists of distinct epiphytic and endophytic habitats, with differences in abiotic and biotic factors driving diversity and composition differences between these habitats. Our study found significant differences in bacterial community between the rhizosphere and endosphere, with higher connectivity observed among core bacterial members in the endosphere. Taxonomic assortativity was higher in the endosphere, with positive co-occurrence more likely among bacteria within the same phylum and negative co-occurrence more likely between bacterial taxa from different phyla. Drought had limited effects on network properties but increased the proportion of shared co-occurrences between rhizosphere and endosphere networks.
MOLECULAR PLANT-MICROBE INTERACTIONS
(2023)
Review
Parasitology
Wenna Lee, Amanda D. Barbosa, Peter J. Irwin, Andrew Currie, Tobias R. Kollmann, Miles Beaman, Amy H. Lee, Charlotte L. Oskam
Summary: Tick-borne diseases pose a growing global health concern, and the immunological responses and inter-individual variations after tick bite remain unclear. By integrating clinical metadata and biological host data using advanced computational tools, we can gain a better understanding of tick-associated illnesses. This review emphasizes the importance of integrative system biology approaches for comprehending the complex pathobiology of tick-borne diseases.
TRENDS IN PARASITOLOGY
(2023)
Article
Multidisciplinary Sciences
Arjun Baghela, Andy An, Peter Zhang, Erica Acton, Jeff Gauthier, Elsa Brunet-Ratnasingham, Travis Blimkie, Gabriela Cohen Freue, Daniel Kaufmann, Amy H. Y. Lee, Roger C. Levesque, Robert E. W. Hancock
Summary: Severely-afflicted COVID-19 patients can exhibit sepsis-like disease manifestations, and the diagnostic tools used in managing sepsis may also be applicable to COVID-19 patients. This study analyzed the blood transcriptome of COVID-19 patients and identified gene expression signatures that are associated with severity and potential therapeutic opportunities. The expression of sepsis gene expression signatures in severely-afflicted COVID-19 patients indicates the importance of considering severe sepsis classification and using these signatures for mechanistic characterization, diagnosis, and guidance of treatment using repurposed drugs.
SCIENTIFIC REPORTS
(2023)
Review
Medicine, General & Internal
Wing Yin Venus Lau, Patrick K. Taylor, Fiona S. L. Brinkman, Amy H. Y. Lee
Summary: Novel therapeutics are urgently needed to manage bacterial infections as antimicrobial resistance (AMR) increases. Antivirulence therapeutics, which aim to weaken bacterial virulence and minimize the risk of AMR development, offer an alternative approach to antibiotics. Pathogen-associated genes (PAGs) that are unique to pathogens may play a crucial role in virulence or host association and represent potential drug targets. This review discusses the current advances in antivirulence drug research, including PAG identification, and emphasizes the importance of integrating bioinformatic/genomic-based methods for discovering novel virulence factors and developing effective antivirulence drugs.
Article
Microbiology
Tatiana Ruiz-Bedoya, Pauline W. Wang, Darrell Desveaux, David S. Guttman
Summary: This study investigates whether non-virulent strains can contribute to the emergence of collective virulence through the secretion of effectors as public goods. The researchers found that, although individually unfit, a metaclone consisting of 36 coisogenic strains of Pseudomonas syringae could collectively exhibit the same level of virulence as the wild-type strain on Arabidopsis thaliana, suggesting the role of effectors in driving cooperation-based virulence. Furthermore, independently evolved effector suits and transferred effector alleles were found to drive this cooperative behavior.
NATURE MICROBIOLOGY
(2023)
Article
Immunology
Andy Y. An, Arjun Baghela, Peter Zhang, Reza Falsafi, Amy H. Lee, Uriel Trahtemberg, Andrew J. Baker, Claudia C. dos Santos, Robert E. W. Hancock
Summary: Transcriptional evidence showed persistent immune dysfunction in both severe COVID-19 and non-COVID-19 septic patients, associated with increased mortality. This highlights the potential for immunomodulatory therapies targeting common mechanisms of immune dysfunction in both diseases.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Multidisciplinary Sciences
Amanda Formosa, Erica Acton, Amy Lee, Paul Turgeon, Shehla Izhar, Pamela Plant, Jim N. Tsoporis, Sabri Soussi, Uriel Trahtemberg, Andrew Baker, Claudia C. dos Santos
Summary: The COVID-19 pandemic has increased the urgency for studying the host gene response and miRNAs have been identified as potential biomarkers and therapeutic agents. This study used NanoString technology and RT-qPCR to identify suitable reference genes for miRNA expression studies in critically ill COVID-19 patients, concluding that miR-186-5p and miR-148b-3p are appropriate reference genes.