Biology subjects

Ham, J. H.

Publications and source records attributed to Ham, J. H..

4 recordsLinked to original sources

bioRxiv2024

Co-occurrence Networks and Topological Analyses Revealed Microbiome Structures in Soybean Roots from a Louisiana Soybean Field Severely Damaged by Prolonged High Temperatures and Drought Stress

Drought stress has a significant impact on agricultural productivity, affecting key crops such as soybeans, the second most widely cultivated crop in the United States. We conducted endophytic and rhizospheric microbial diversity analyses in soybean plants cultivated during the 2023 growing season, amid extreme weather conditions of prolonged high temperatures and drought in Louisiana. Specifically, we collected surviving and non-surviving soybean plants from two plots of a Louisiana soybean field severely damaged from the extreme heat and drought condition in 2023. We did not observe any significant difference in the microbial diversity of rhizosphere between surviving and non-surviving plants. However, we found obvious differences in the structure of endophytic microbial community in root tissues between the two plant conditions. Especially, the bacterial genera of Proteobacteria, Pseudomonas and Pantoea, were predominant in the surviving root tissues, while the bacterial genus Streptomyces was conspicuously dominant in the non-surviving (dead) root tissues. Co-occurrence patterns and network centrality analyses enabled us to discern the intricate characteristics of operational taxonomic units (OTUs) within endophytic and rhizospheric networks. Overall, this study advances our understanding of the intricate relationship between bacteria and plants under drought stress, paving the way for future research to investigate the importance of microbial diversity in drought affected regions such as Louisiana.

microbiology↗

bioRxiv2024

Characterization of the growth promotion and defense enhancement of soybean plants driven by seed treatment of multiple soybean-associated beneficial bacteria

We screened soybean-associated bacterial strains from soybean fields in Louisiana, USA, based on various biological activities beneficial for soybean growth and health. Furthermore, we constructed sets of synthetic bacterial community (SBC) containing multiple strains of soybean-associated beneficial bacteria (SABB) having different types of beneficial activities and tested their effects of seed treatment on soybean growth and disease resistance. We found that all three sets of SBC (i.e., Set-1, Set-2, and Set-3) tested promoted soybean growth and yield significantly through seed treatment, showing better performance than the most effective SABB strain Pseudomonas putida SABB7 alone and the commercial seed-treating product included for comparison. Our analysis of soybean microbiomes in the root endosphere and rhizosphere based on 16S rDNA sequence profiles revealed that Bradyrhizobium elkanii, a symbiotic bacterium of soybean, was enriched in both compartments by seed treatment with Set-2 or Set-m4, which were the best-performing bacterial mixture among the three SABB sets and the most effective subset of Set-2, respectively. In addition, the soybean gene expression profile determined by RNA-seq revealed that seed treatment with Set-2 or Set-m4 made soybean plants grown from the treated-seeds induce a higher level of defense-related genes upon infection by the fungal pathogen Rhizoctonia solani compared to those from untreated seeds. These experimental results strongly suggest that the beneficial effects of the bacterial mixtures on plant growth and defense through seed treatment are largely mediated by the change of soybean-associated microbiomes that enriches beneficial components such as B. elkanii and the defense-priming effect that induces robust defense responses upon pathogen infection. This study provides a valuable insight into the development of innovative and sustainable management strategies through seed treatment of beneficial microbes in a form of SBC for soybean and further other major crops. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=104 SRC="FIGDIR/small/575074v1_ufig1.gif" ALT="Figure 1"> View larger version (56K): org.highwire.dtl.DTLVardef@41f817org.highwire.dtl.DTLVardef@106c4b4org.highwire.dtl.DTLVardef@15c1555org.highwire.dtl.DTLVardef@7cbba4_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2023

qsmR encoding an IclR-family transcriptional factor is a core pathogenic determinant of Burkholderia glumae beyond the acyl-homoserine lactone-mediated quorum-sensing system

The plant pathogenic bacterium Burkholderia glumae causes bacterial panicle blight (BPB) in rice-growing areas worldwide. It has been widely accepted that an acyl-homoserine lactone (AHL)-type quorum sensing (QS) system encoded by tofI and tofR genes (TofIR QS) is a key regulatory mechanism underlying the bacterial pathogenesis of B. glumae. In addition, qsmR, which encodes an IclR-family regulatory protein, has been considered an important part of TofIR QS. However, the present study with three strains of B. glumae representing different pathogenic strains revealed that this currently accepted paradigm should be modified. We characterized the regulatory function of TofIR QS and qsmR in three different strains of B. glumae, 336gr-1 (virulent), 411gr-6 (hypervirulent) and 257sh-1 (avirulent). In 336gr-1, both TofIR QS and qsmR were critical for the pathogenesis, being consistent with previous studies. However, in the hypervirulent strain 411gr-6, TofIR QS only partially contributes to the virulence, whereas qsmR was critical for pathogenesis like in 336gr-1. Furthermore, we found that a single nucleotide polymorphism causing T50K substitution in the qsmR coding sequence was the cause of the non-pathogenic trait of the naturally avirulent strain 257sh-1. Subsequent analyses of gene expression and transcriptome revealed that TofIR QS is partially controlled by qsmR at the transcriptional level in both virulent strains. Further genetic tests of additional B. glumae strains showed that 11 out of 20 virulent strains retained the ability to produce toxoflavin even after removing the tofI/tofM/tofR QS gene cluster like 411gr-6. In contrast, all the virulent strains tested lost the function almost completely upon deletion of the qsmR gene. Taking these results together, qsmR, rather than TofIR QS, is a master regulator that determines the pathogenic trait of B. glumae thus a more appropriate pathogen target for successful management of BPB. Author summaryBacterial cell-to-cell communication, called quorum-sensing, systems mediated by homoserine lactone (HSL)-type signaling molecules play pivotal roles in the virulence-related functions of diverse plant and animal pathogenic Gram-negative bacteria. Burkholderia glumae is the chief causal agent for bacterial panicle blight, a devastating rice disease worldwide. In this pathogen, the HSL-type quorum-sensing system dependent on the tofI and tofR genes had long been thought to be the core regulatory/signaling system essential for virulence. However, we discovered in this study that a highly virulent strain of B. glumae, 411gr-6, retained its virulence even after the tofI/tofR-dependent quorum-sensing function was disabled. We also found that more than a half of the natural strains of this pathogen species tested in this study also exhibited their virulence function in the absence of the tofI/tofR-dependent quorum-sensing system. Then we characterized the qsmR gene as an essential regulatory/signaling element for the bacterial pathogenesis regardless of the genetic variations among the strains of B. glumae. This study indicates that the qsmR gene, rather than the tofI/tofR-dependent quorum-sensing system, should be considered as an essential master regulatory/signaling factor for the virulence of B. glumae and, thus, a promising target for suppressing bacterial panicle blight.

microbiology↗

bioRxiv2020

Low aflatoxin levels and flowering delay in Aspergillus flavus-resistant maize lines are correlated with increased corn earworm damage and enhanced seed fumonisin content

Preharvest mycotoxin contamination of field-grown crops is influenced not only by the host genotype, but also inoculum load, insect pressure and their confounding interactions with seasonal weather. In two field trials, we observed a preferred natural infestation of specific maize (Zea mays L.) genotypes by corn earworm (Helicoverpa zea Boddie) and investigated this unexpected interaction. These studies involved four maize lines with contrasting levels of resistance to Aspergillus flavus. The resistant lines had 7 to 14-fold greater infested ears than the susceptible lines. However, seed aflatoxin B1 levels, in mock- or A. flavus-inoculated ears were consistent with maize genotype resistance to A. flavus. Further, the corn earworm-infested ears had greater levels of fumonisin content in seeds than uninfested ears, indicating that the insect may have vectored native Fusarium verticillioides inoculum. The two maize lines with heavy infestation showed delayed flowering. The availability of young silk for egg-laying could have been a factor in the pervasive corn earworm damage of these lines. At the same time, H. zea larvae reared on AF-infused diet showed decreasing mass with increasing AF and >30% lethality at 250 ppb. In contrast, corn earworm was tolerant to fumonisin with no significant loss in mass even at 100 ppm, implicating the low seed aflatoxin content as a predominant factor for the prevalence of corn earworm infestation and the associated fumonisin contamination in A. flavus resistant lines. These results highlight the need for integrated strategies targeting mycotoxigenic fungi and their insect vectors to enhance the safety of crop commodities. IMPORTANCEAspergillus and Fusarium spp. not only cause ear rots in maize leading to crop loss, they can also contaminate the grain with carcinogenic mycotoxins. Incorporation of genetic resistance into breeding lines is an ideal solution for mycotoxin mitigation. However, the goal is fraught by a major problem. Resistance for AF or FUM accumulation is quantitative and contributed by several loci with small effects. Our work reveals that host phenology (flowering time) and insect vector-mycotoxin interactions can further confound breeding efforts. A host genotype even with demonstrable resistance can become vulnerable due to seasonal variation in flowering time or an outbreak of chewing insects. Incorporation of resistance to a single mycotoxin accumulation and not pairing it with insect resistance may not adequately ensure food safety. Diverse strategies including host-induced silencing of genes essential for fungal and insect pest colonization and broad-spectrum biocontrol systems need to be considered for robust mycotoxin mitigation.

plant biology↗