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.

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.

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, the 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 in 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 the 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 in TZAR102 and increases in the abundance of Stenotrophomonas and Sphingomonas in MI82 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 type II polyketides and 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.

Bacterial contamination of raw diffusion juice poses unique challenges during the sugar extraction process. This study profiled bacterial communities by using full-length 16S rRNA amplicon sequencing and quantified the carbohydrate concentrations in raw diffusion juice samples received from sugar factory regions across the USA and Canada. Juice samples were collected at four time points during the 2021 and 2022 processing campaigns. Firmicutes was the dominant phylum from the raw diffusion juice samples collected during both campaigns and comprised 85.5% of total bacterial abundance. Lactic acid bacteria such as Leuconostoc and Lactobacillus were among the core genera which also dominated the bacterial community in raw diffusion juice. Positive correlations in the abundance of functionally and taxonomically related bacterial communities were identified. During the 2021 campaign, 44 bacterial genera were differentially abundant in raw diffusion juice extracted from sugarbeet roots in Periods 1 to 4. This number declined sixfold during the 2022 campaign to three genera. The concentration of raffinose in raw diffusion juice positively correlated to the relative abundance of Leuconostoc . Furthermore, an in vitro assay was performed to assess the growth dynamics of Leuconostoc mesenteroides in sucrose or raffinose-rich medium and observed the rapid consumption of both carbohydrates by this bacterium. This finding is important for deciphering microbial growth dynamics in raw diffusion juice that can be useful in minimizing sugar loss during the factory processing. IMPORTANCE: Findings additionally provide baseline information that can be used to develop mitigation strategies that reduce losses due to microbial contamination of sucrose processing streams.

Sugar beet is a major source of consumable sugar in domestic and industrial applications in the United States. Sugar beet roots are stored for up to 280 days under cold ambient temperature conditions in the Red River Valley (RRV) of Minnesota and North Dakota. During this period, storage rots often develop that can reduce the sucrose content and processing quality of the roots. Knowledge of the pathogens responsible for this sucrose loss is limited but crucial for devising management strategies. This study was conducted to re-examine and identify storage pathogens infecting sugar beet roots in outdoor nonventilated piles in the RRV of Minnesota and North Dakota and characterize their prevalence and geographic distribution. In the first year of the study, more than 50 roots exhibiting storage rot were collected from an outdoor nonventilated pile (ONVP) in Minnesota. In successive years, 150 storage rot and damaged symptomatic roots were collected from five geographically distinct ONVPs with three located in Minnesota and two located in North Dakota. Penicillium spp., Geotrichum candidum, and Mucor spp. were common filamentous fungal species identified, whereas Pichia membranifaciens was the dominant yeast identified in both years of the study. Leuconostoc mesenteroides and Gluconobacter cerinus were common bacterial isolates in both years of the study. Most of the bacterial isolates obtained from ONVP-4 (North Dakota) (63%) and ONVP-5 (North Dakota) (99%) during the second year of the study were identified as L. mesenteroides. This study identified fungal and bacterial species associated with storage diseases of sugar beet roots in the RRV of Minnesota and North Dakota, which is pivotal for implementing management strategies to minimize postharvest sucrose losses during sugar beet storage.

The worldwide distribution of plant seeds can disseminate beneficial and plant-pathogenic microorganisms. This phenomenon is of particular concern where seed production is geographically isolated from crop production, as is the case with spinach in the United States. We aimed to characterize the structure and function of spinach seed microbiomes in commercial spinach seed lots originating from Europe and New Zealand. The seed lots we analyzed were infested with Peronospora effusa and Verticillium dahliae, only infested with V. dahliae, or not infested with either of these pathogens. The microbial taxonomic composition and gene function (assessed by gene ontology [GO] terms) of spinach seeds were highly influenced by geographic origin and the status of pathogen infestation. Through taxonomic profiling, we found that potentially plant-beneficial bacterial genera such as Pseudomonas and Pantoea were the most abundant taxa both in infested and noninfested seeds, and Stenotrophomonas was observed in seed lots infested with P. effusa and V. dahliae. Many potential plant pathogens that are not known to be associated with spinach seed were also discovered by metagenomic analysis, including Sclerotinia sclerotiorum, Botrytis cinerea, Bipolaris sorokiniana, Fusarium pseudograminearum, Alternaria brassicae, A. solani, Parastagonospora nodorum, and Pyrenophora teres f. teres. Our analysis of the function of prokaryotic genes in de novo assembled metagenomes revealed distinct GO terms associated with the geographic origin of seed lots. This work provides an important first step toward identifying spinach seedborne microorganisms that could be utilized to improve plant health and plant pathogens that could be inadvertently carried to new locations.