@article{pal_saxena_kumar_verma_kumar_shukla_pandey_white_verma_2024, title={Seed endophytic bacterium<i> Lysinibacillus</i> sp. (ZM1) from maize (Zea mays L.) shapes its root architecture through modulation of auxin biosynthesis and nitrogen metabolism}, volume={212}, ISSN={["1873-2690"]}, DOI={10.1016/j.plaphy.2024.108731}, abstractNote={Seed endophytic bacteria have been shown to promote the growth and development of numerous plants. However, the underlying mechanism still needs to be better understood. The present study aims to investigate the role of a seed endophytic bacterium Lysinibacillus sp. (ZM1) in promoting plant growth and shaping the root architecture of maize seedlings. The study explores how bacteria-mediated auxin biosynthesis and nitrogen metabolism affect plant growth promotion and shape the root architecture of maize seedlings. The results demonstrate that ZM1 inoculation significantly enhances root length, root biomass, and the number of seminal roots in maize seedlings. Additionally, the treated seedlings exhibit increased shoot biomass and higher levels of photosynthetic pigments. Confocal laser scanning microscopy (CLSM) analysis revealed extensive colonization of ZM1 on root hairs, as well as in the cortical and stellar regions of the root. Furthermore, LC-MS analysis demonstrated elevated auxin content in the roots of the ZM1 treated maize seedlings compared to the uninoculated control. Inoculation with ZM1 significantly increased the levels of endogenous ammonium content, GS, and GOGAT enzyme activities in the roots of treated maize seedlings compared to the control, indicating enhanced nitrogen metabolism. Furthermore, inoculation of bacteria under nitrogen-deficient conditions enhanced plant growth, as evidenced by increased root shoot length, fresh and dry weights, average number of seminal roots, and content of photosynthetic pigments. Transcript analysis indicated upregulation of auxin biosynthetic genes, along with genes involved in nitrogen metabolism at different time points in roots of ZM1-treated maize seedlings. Collectively, our findings highlight the positive impact of Lysinibacillus sp. ZM1 inoculation on maize seeds by improving root architecture through modulation of auxin biosynthesis and affecting various nitrogen metabolism related parameters. These findings provide valuable insights into the potential utilization of seed endophytic bacteria as biofertilizers to enhance plant growth and yield in nutrient deficient soils.}, journal={PLANT PHYSIOLOGY AND BIOCHEMISTRY}, author={Pal, Gaurav and Saxena, Samiksha and Kumar, Kanchan and Verma, Anand and Kumar, Deepak and Shukla, Pooja and Pandey, Ashutosh and White, James and Verma, Satish K.}, year={2024}, month={Jul} }
 @article{molo_white_cornish_gell_baars_singh_carbone_isakeit_wise_woloshuk_et al._2022, title={Asymmetrical lineage introgression and recombination in populations of Aspergillus flavus: Implications for biological control}, volume={17}, ISSN={["1932-6203"]}, url={https://doi.org/10.1371/journal.pone.0276556}, DOI={10.1371/journal.pone.0276556}, abstractNote={Aspergillus flavusis an agriculturally important fungus that causes ear rot of maize and produces aflatoxins, of which B1is the most carcinogenic naturally-produced compound. In the US, the management of aflatoxins includes the deployment of biological control agents that comprise two nonaflatoxigenicA.flavusstrains, either Afla-Guard (member of lineage IB) or AF36 (lineage IC). We used genotyping-by-sequencing to examine the influence of both biocontrol agents on native populations ofA.flavusin cornfields in Texas, North Carolina, Arkansas, and Indiana. This study examined up to 27,529 single-nucleotide polymorphisms (SNPs) in a total of 815A.flavusisolates, and 353 genome-wide haplotypes sampled before biocontrol application, three months after biocontrol application, and up to three years after initial application. Here, we report that the two distinctA.flavusevolutionary lineages IB and IC differ significantly in their frequency distributions across states. We provide evidence of increased unidirectional gene flow from lineage IB into IC, inferred to be due to the applied Afla-Guard biocontrol strain. Genetic exchange and recombination of biocontrol strains with native strains was detected in as little as three months after biocontrol application and up to one and three years later. There was limited inter-lineage migration in the untreated fields. These findings suggest that biocontrol products that include strains from lineage IB offer the greatest potential for sustained reductions in aflatoxin levels over several years. This knowledge has important implications for developing new biocontrol strategies.}, number={10}, journal={PLOS ONE}, author={Molo, Megan S. and White, James B. and Cornish, Vicki and Gell, Richard M. and Baars, Oliver and Singh, Rakhi and Carbone, Mary Anna and Isakeit, Thomas and Wise, Kiersten A. and Woloshuk, Charles P. and et al.}, editor={Nierman, William C.Editor}, year={2022}, month={Oct} }
 @article{carbone_white_miadlikowska_arnold_miller_magain_u'ren_lutzoni_2019, title={T-BAS Version 2.1: Tree-Based Alignment Selector Toolkit for Evolutionary Placement of DNA Sequences and Viewing Alignments and Specimen Metadata on Curated and Custom Trees}, volume={8}, ISSN={2576-098X}, url={http://dx.doi.org/10.1128/MRA.00328-19}, DOI={10.1128/MRA.00328-19}, abstractNote={The Tree-Based Alignment Selector (T-BAS) toolkit combines phylogenetic-based placement of DNA sequences with alignment and specimen metadata visualization tools in an integrative pipeline for analyzing microbial biodiversity. The release of T-BAS version 2.1 makes available reference phylogenies, supports multilocus sequence placements and permits uploading and downloading trees, alignments, and specimen metadata.}, number={29}, journal={Microbiology Resource Announcements}, publisher={American Society for Microbiology}, author={Carbone, Ignazio and White, James B. and Miadlikowska, Jolanta and Arnold, A. Elizabeth and Miller, Mark A. and Magain, Nicolas and U'Ren, Jana M. and Lutzoni, François}, editor={Cuomo, Christina A.Editor}, year={2019}, month={Jul} }
 @article{carbone_white_miadlikowska_arnold_miller_kauff_u'ren_may_lutzoni_2016, title={T-BAS: Tree-Based Alignment Selector toolkit for phylogenetic-based placement, alignment downloads and metadata visualization: an example with the Pezizomycotina tree of life}, volume={33}, ISSN={1367-4803 1460-2059}, url={http://dx.doi.org/10.1093/bioinformatics/btw808}, DOI={10.1093/bioinformatics/btw808}, abstractNote={Abstract}, number={8}, journal={Bioinformatics}, publisher={Oxford University Press (OUP)}, author={Carbone, Ignazio and White, James B. and Miadlikowska, Jolanta and Arnold, A. Elizabeth and Miller, Mark A. and Kauff, Frank and U'Ren, Jana M. and May, Georgiana and Lutzoni, François}, year={2016}, month={Dec}, pages={btw808} }