Changes in bacterial endophyte community following aspergillus flavus infection in resistant and susceptible maize kernels

Aspergillus flavus (A. flavus) mediated aflatoxin contamination in maize is a major global economic and health concern. As A. flavus is an opportunistic seed pathogen, identification of factors contributing to kernel resistance will be of great importance in the development of novel mitigation strategies. Using V3–V4 bacterial rRNA sequencing and seeds of A. flavus resistant maize breeding lines TZAR102 and MI82 and a susceptible line, SC212, we investigated kernel specific changes of bacterial endophytes during infection. A total of 81 bacterial genera belonging to 10 phyla were detected. Bacteria belonging to the phylum Tenericutes comprised 86-99% of detected phyla followed by Proteobacteria (14%), and others (<5%) that changed with treatments and/or genotypes. Higher basal levels (without infection) of Streptomyces, and Microbacterium and increases in the abundance of Stenotrophomonas and Sphingomonas in the resistant lines following infection may suggest their role in resistance. Functional profiling of bacteria using 16S rRNA sequencing data revealed the presence of bacteria associated with the production of putative antifungal type II polyketides, sesquiterpenoids in the resistant vs. susceptible lines. Future characterization of endophytes predicted to possess antifungal/ anti-aflatoxigenic properties will aid in their development as effective biocontrol agents or microbiome markers for maize aflatoxin resistance

Relationship Between Climatic Factors and Distribution of Pratylenchus spp. in the Dryland Wheat-Production Areas of Eastern Washington

Field surveys were conducted by collecting soil samples to estimate nematode densities in soil from winter wheat, spring wheat, spring barley, and spring legumes (lentil, chickpea, and pea) fields during 2010 and 2011. Pratylenchus spp. were observed in 60% of sampled fields. However, nematodes were detected in nearly all of the survey fields in high numbers where crops were grown every year. To identify climatic variables associated with density of Pratylenchus spp. in soil, correlation and regression analyses were performed using climate data of survey sites from 1979 to 2010. Fifty-seven climate variables were significantly correlated with densities of Pratylenchus spp. All precipitation variables were significantly positively correlated with nematode abundance. Summer maximum air temperature was negatively correlated and winter minimum air temperature was positively correlated with nematode densities. In addition, both years’ nematode densities were significantly correlated with cropping intensity. Five multivariate regression models for 2010 and seven models for 2011 nematode abundance levels were developed. The majority of the climate variables selected in the models were related to precipitation. Knowledge of root-lesion nematode distribution in the dryland region of eastern Washington and associated climate variables may be helpful to determine risk and apply management practices to minimize crop damage

Corrigendum: An In vitro Study of Bio-Control and Plant Growth Promotion Potential of Salicaceae Endophytes

[This corrects the article DOI: 10.3389/fmicb.2017.00386.]

Salicaceae Endophytes: Growth Promotion Potential in Rice (Oryza sativa L.) and Maize (Zea mays L.) and Bio-Control of Plant Pathogen

Thesis (Ph.D.)--University of Washington, 2016-08Abstract Salicaceae plants; poplar (Populus trichocarpa) and willow (Salix sitchensis) are hosts of many endophyte species. Salicaceae endophytes colonize the plant endosphere and confer various growth benefits to host plants. First three studies were conducted focusing on how these endophytes colonize and support the growth of major food crops; rice and maize under nutrient limited conditions. Fourth study was conducted to investigate the biocontrol and other growth promoting traits of these endophytes. The first study was conducted to determine the growth promoting potential of Salicaceae endophytes to rice under nitrogen (N) limited conditions. Rice seedlings were inoculated with endophytes and grown in the N limited conditions in the greenhouse for about four months. Endophyte inoculated rice plants were taller, and had higher biomass and tiller numbers over mock inoculated control plants. Furthermore, colonizing performance of these endophytes in rice seedlings was verified through fluorescent microscopy, and counting in planta endophyte density. Rice seedlings were considerably colonized by these endophytes. The second study was conducted to determine the growth potential of Salicaceae endophytes in maize and rice plants in N limited conditions. Endophyte inoculated plants were grown in the greenhouse, and plant physical characters such as plant height and biomass were recorded as growth response. Endophyte inoculated plants outperformed the mock inoculated plants but response was variable depending on crop genotypes or inoculated endophytes. In addition, through 15N dilution assay, evidence of N fixing activity was observed in rice. The third study was conducted to determine the colonization performance of poplar bacterial and yeast endophytes in rice and maize. Bacterial strains; WP5 (Rahnella sp.), and WP9 (Burkholderia sp.) labeled with green fluorescent protein, and yeast strain, WP1 were introduced in rice and maize seedlings aseptically. The in planta density of endophytes were determined by counting colony forming units and colonization pattern was observed using microscopy. These endophytes were found competent to colonize both rice and maize seedlings. They were observed in leaves and roots, and localized mostly in the intercellular spaces of root cortex and leaf mesophyll tissues. Higher in planta population of endophytes were observed in leaves and stems in majority of the colonization assays. Positive growth response was observed in endophytes inoculated rice and maize plants as compared to mock-inoculated control plants. The fourth study was conducted to investigate the biocontrol potential of Salicaceae endophytes over a soil borne plant pathogen, Rhizoctonia solani AG-8. These endophytes were also examined to delineate their other plant growth promoting features including N fixing activity, indole-3- acetic acid (IAA) and siderophore biosynthesis, and phosphate solubulization. Endophyte strains; Burkholderia, Rahnella, Pseudomonas, and Curtobacterium displayed antagonistic activity against R. solani AG-8. Burkholderia spp. showed relatively stronger antagonistic effect than other endophytes, perhaps very useful to explore as biocontrol measures to manage different soil borne plant pathogens. From nucleotide sequence analysis of Burkholderia spp., a 56-kb ofc gene cluster responsible for biosynthesis of anti-fungal glycolipopeptide, occidiofungin was detected in all species. Furthermore, these endophytes were found potential to support plant growth through multiple mechanisms such as N fixation, IAA and siderophore production, and phosphate solubilization besides protection from invading plant pathogens

A survey of root lesion and cereal cyst nematodes in the dryland wheat production areas of eastern Washington and resistance of pacific Northwest wheat varieties

Root lesion nematodes (Pratylenchus neglectus and P. thornei) and cereal cyst nematode (Heterodera avenae) are important parasites of wheat worldwide. Three studies were conducted focusing on the distribution of root lesion and cereal cyst nematodes in eastern Washington and the resistance response of spring wheat varieties to the cereal cyst nematode. The first study was conducted to estimate nematode densities in soils cropped to winter and spring cereals and spring legumes. P. neglectus and P. thornei were observed in nearly 60 percent of the sampled fields. H. avenae was observed in approximately 12 percent of the sampled fields; however, it was detected from about 45 percent of sampled fields in the annual cropping zone. Multivariate regression models were developed to determine the explanatory weather variables for Pratylenchus densities in soil. The majority of the weather variables selected in the models were precipitation variables. The second study was conducted at the Cook Agronomy Farm to determine the spatial distribution of Pratylenchus spp. in relation to crop rotation, soil and terrain attributes. Pratylenchus spp. were detected in more than 85% of the sampled sites. Classification and regression trees were developed to derive the relationship between soil and terrain variables and nematode densities. An aggregated pattern was observed, and soil organic carbon was identified as one of the most important variables to explain nematode densities. Molecular identification of Pratylenchus spp. in region-wide surveys of eastern Washington and at the Cook Agronomy Farm was conducted using species-specific primers targeting P. neglectus and P. thornei through conventional PCR. P. thornei was observed more frequently than P. neglectus in both region-wide surveys and Cook Farm, but some locations showed both species. The third field experiment was conducted to evaluate the resistance of Pacific Northwest spring wheat varieties and wheat entries carrying different Cre genes to H. avenae. Spring wheat genotypes with Cre1 gene had fewer numbers of H. avenae white females than other genotypes. However, all of the tested spring wheat varieties appear to be susceptible to H. avenae

Bacterial Endophyte Colonization and Distribution within Plants

The plant endosphere contains a diverse group of microbial communities. There is general consensus that these microbial communities make significant contributions to plant health. Both recently adopted genomic approaches and classical microbiology techniques continue to develop the science of plant-microbe interactions. Endophytes are microbial symbionts residing within the plant for the majority of their life cycle without any detrimental impact to the host plant. The use of these natural symbionts offers an opportunity to maximize crop productivity while reducing the environmental impacts of agriculture. Endophytes promote plant growth through nitrogen fixation, phytohormone production, nutrient acquisition, and by conferring tolerance to abiotic and biotic stresses. Colonization by endophytes is crucial for providing these benefits to the host plant. Endophytic colonization refers to the entry, growth and multiplication of endophyte populations within the host plant. Lately, plant microbiome research has gained considerable attention but the mechanism allowing plants to recruit endophytes is largely unknown. This review summarizes currently available knowledge about endophytic colonization by bacteria in various plant species, and specifically discusses the colonization of maize plants by Populus endophytes

Crustacean Meal Elicits Expression of Growth and Defense-Related Genes in Roots of Lettuce and Tomato

Powdered crab and lobster shells (crustacean meal) obtained from fisheries are used as soil amendments to promote plant health and defense. In this study, a commercial crustacean meal amendment used to promote the health of lettuce, tomato, and other crop plants was applied to roots of lettuce and tomato seedlings. Gene expression profiling of the treated roots was assessed by RNA sequencing (RNA-seq) at 24 h after application relative to a 0 h time point. The RNA-seq analyses revealed upregulation of different types of genes in both tomato and lettuce roots at 24 h. Gene ontology analyses revealed increased expression of genes associated with oxidoreductases/metal ion binding in tomato roots at 24 h, while there was predominantly increased expression of genes associated with cell wall organization, lyases, and hydrolases in lettuce roots at 24 h. The types of defense-related genes expressed were also markedly different. In tomato roots, the most highly induced gene (log2 fold change 13.84, P ≤ 0.001) encoded a defense-associated miraculin-like protein, but transcripts of a similar gene were not induced in lettuce roots. Interestingly, phenylpropanoid pathway genes relating to cell wall biogenesis and lignification were significantly upregulated in both lettuce and tomato roots, suggesting that strengthening of plant cell walls is a common response to crustacean meal application. This research provides insight into gene expression patterns in the roots of lettuce and tomato in response to crustacean meal, improving our understanding of how this amendment could aid in plant health. [Graphic: see text] The author(s) have dedicated the work to the public domain under the Creative Commons CC0 “No Rights Reserved” license by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law, 2022

Increased Biomass of Nursery-Grown Douglas-Fir Seedlings upon Inoculation with Diazotrophic Endophytic Consortia

Douglas-fir (Pseudotsuga menziesii) seedlings are periodically challenged by biotic and abiotic stresses. The ability of endophytes to colonize the interior of plants could confer benefits to host plants that may play an important role in plant adaptation to environmental changes. In this greenhouse study, nursery-grown Douglas-fir seedlings were inoculated with diazotrophic endophytes previously isolated from poplar and willow trees and grown for fifteen months in nutrient-poor conditions. Inoculated seedlings had significant increases in biomass (48%), root length (13%) and shoot height (16%) compared to the control seedlings. Characterization of these endophytes for symbiotic traits in addition to nitrogen fixation revealed that they can also solubilize phosphate and produce siderophores. Colonization was observed through fluorescent microscopy in seedlings inoculated with gfp- and mkate-tagged strains. Inoculation with beneficial endophytes could prove to be valuable for increasing the production of planting stocks in forest nurseries

Transcriptomic and Metabolomic Analysis Provides Insights into the Fruit Quality and Yield Improvement in Tomato under Soilless Substrate-Based Cultivation

The effects of soilless substrate-based versus soil cultivation on overall fruit quality and yield in tomato (Solanum lycopersicum) were studied using the tomato cv. Zhonghua Lvbao. Experiments for tomato soilless cultivation were carried out under greenhouse conditions. Plant growth, fruit quality and yield, and physiologic traits were observed. RNA-seq and RT-PCR, as well as metabolomic analyses were performed to examine the expressed genes and metabolites under soilless substrate cultivation. The results showed that the plant height, stem diameter, and chlorophyll contents of tomato under substrate-based cultivation were increased by 37.3%, 19.8%, and 15.3%, respectively, compared with soil cultivation system. Leaf photosynthetic and transpiration rates, stomatal conductance, and root vitality of tomato, under substrate-based cultivation, increased by 29.0%, 21.2%, 43.9%, and 84.5%, respectively, compared with soil cultivation. The yield reached 7177.5 kg/667 m2, and the relative yield increased by 10.1%, compared with soil cultivation. The contents of total soluble sugar, soluble solids, and vitamin C increased by 35.7%, 19.7%, and 18.2%, respectively, higher than those of soil cultivation in tomato fruits, while nitrate content and titratable acid decreased by 29.4% and 11.8%, respectively. Therefore, substrate-based-cultivation can increase production and improve tomato fruit quality and taste. We examined the expressed genes and metabolites to explore the molecular mechanism of plant growth and overall fruit quality improvement in substrate-based cultivation. A total of 476 differentially expressed genes were identified by transcriptomes profiling, of which 321 and 155 were significantly up- and down-regulated, respectively. The results of metabolomics analysis showed that 441 metabolites were detected, where 24 and 36 metabolites were up- and down-regulated, respectively. By combining analyses of transcriptomic and metabolic groups, genes and metabolites related to the fruit quality were mainly concentrated in the vitamin B6/ascorbic acid/aldonic acidmetabolism, and glycerophospholipid metabolic pathways. Therefore, substrate-based cultivation can elevate vitamin and soluble sugar contents and the expression of fruit flavor related genes, which lays an initial background for exploring the mechanism of substrate-based cultivation, in order to improve the quality of tomato in the future