Editorial: Metagenomic insights into microbial communities in fruits and vegetable plants

Plant pathogens, particularly viruses and viroids, are highly destructive accounting for about approximately 50% of the diseases worldwide and over 30 billion USD in annual economic losses (Rodríguez-Verástegui et al. 2022). For example, when infected, citrus tristeza virus (CTV), destroyed over 100 million citrus trees (Folimonova et al. 2022), and tomato brown rugose fruit virus (ToBRFV) caused yield loss up to 70% (Oladokun et al., 2019). Current import practices rely on strict phytosanitary customs in which conventional detection methods are tested by visual inspection and traditional bioassays such as enzyme-linked immunosorbent assays (ELISA). The concern with ELISA assays is that they are time-consuming, with high false negative rates and cross-reaction with closely related species. Although PCR-based assays are the gold standard for detection of known viruses, they require a priori genomic information and therefore cannot be applied to novel viruses. To address these difficulties, high-throughput sequencing (HTS) technology offers the best methodology for collective identification of known and novel viruses.Despite its advantages, HTS-based virus diagnosis is dependent on bioinformatic expertise and computational infrastructure which has limited its widespread adaptation. Morgante et al.developed Viroscope that addresses the analytical challenges of HTS via an advanced Cloud service that leverages HTS for highly sensitive identification of low-abundance viruses and viroids.High-throughput sequencing (HTS) has numerous applications including pathogen detection and virome characterization. This article summarizes the current status of HTS in Mexico for use in identification of plant viruses and viroids and describes how it has revolutionized the field of plant virology in the country. Plant virology research in Mexico began in the mid-1900s and has expanded in scope and complexity as new technologies become available. Until recently, diagnostic techniques were limited to detection of known viruses, however, HTS does not require prior knowledge of the target. Since the introduction of this method less than a decade ago, 86 viruses/viroids have been detected in key crops such as corn, beans, grapes, and tomatoes in Mexico. This has led to an improved understanding of the virome of these crops and has made it possible to describe and characterize previously unknown viruses. The authors theorize that HTS will enable researchers to develop a comprehensive understanding of viral populations, including complex co-infections that impact disease epidemiology (Pacheco-Upon pathogenic microbes' interactions with plants, the associated microbial community might dynamically change. For instance, plant associated microorganisms are actively involved in the plant's nutritional metabolism and they can enable plants to take up essential nutrients such as nitrogen, potassium and phosphorus from the soil. In response to infection by the pathogen, plants are directly enriched with more beneficial microorganisms, which are of crucial significance for improving plant disease resistance. However, some microorganisms are suppressed by high-dominant pathogens, which may grow faster and cause disease. This paper details research into understanding the plant microbiomes composition and abundance when disrupted by disease-causing pathogens in the host. Several pathogen species cause diseases in crop plants such as wheat. The wheat stripe rust disease is a high threat to wheat production worldwide and is caused by the airborne fungus Puccinia striiformis. Goa et al unravel the responses of wheat microbial communities in different niches, the phyllosphere and rhizosphere, to P. striiformis infection. The authors have identified variations in certain microbial communities across a diverse set of wheat varieties. The highly disease resistant varieties show a greater optimization of microbial community functions that enhance disease resistance.In an agriculture field, continuous application of chemical fertilizers promotes soil accumulation of excess nutrients, and disrupts the diversity, composition, and metabolic functions of soil microbial communities, which are negatively correlated with crop yield (Zhou et al., 2023). The pepino (Solanum muricatum) is a perennial herbaceous species within the Solanaceae family. Its fruit has nutritional value, a significant level of minerals: calcium, phosphorus, potassium and ascorbic acid: vitamin C, and plausible potential health benefits such as anti-inflammatory, anticancer, and diabetes-management properties. In recent years it has emerged as a high-value crop. Research on the influence of varying nitrogen fertilizer on pepino rhizosphere soil biochemical properties, plant growth, and fruit quality has been evaluated. Utilizing various nitrogen rates such as N300, N225, N150, N75, and N0, determined nitrogen application rates 150 ~ 225 Kg-ha-1 is best for pepino production. Importantly, nitrogen fertilization indirectly elevates pepino productivity by stimulating urease and nitrate reductase activities, and enhancing microbiota: Nitrosomonas, Opitutus, Ensifer, Mesorhizobium and so on, to facilitate soil nutrient mobilization for plant growth and fruit nutrients (Su et al.).Rhizosphere microbiomes include a diverse community of bacteria, fungi, and several other microbes. It is pivotal in plant health, nutrient cycling, and soil ecosystem stability. Microbes help plants access nutrients and fight pathogens while plants provide microbes with energy, significantly boosting plant health, growth, and disease resistance. Radish (Raphanus sativus L) is an economically important vegetable crop and relies on its root-associated microbiome for stress resilience and nutrient acquisition (Kravchenko et al. 2022). Studies have shown that biodegradable mulches such as polybutylene adipate terephthalate/polylactic acid (PBAT/PLA) and humic acid (HA)-modified PBAT/PLA films are increasingly used in sustainable agriculture and to enrich microbial activity. However, their effects on plant rhizosphere microbial community structure and function have not been studied systematically. One of the research articles reported on the combined 16S rRNA/ITS sequencing and KEGG pathway analysis to characterize the Alpine radish rhizosphere microbiome and evaluate how PBAT/PLA biodegradable multi-film modulates microbial community structure and shifts microbial metabolic activity. The results revealed that the incorporation of HA into PBAT/PLA biodegradable mulch films has dual benefits in both enriching functional microbial taxa and stimulating metabolic pathways essential for adaptation (Zhong et al.).A study on Xylella fastidiosa subsp. pauca (Xfp), the causal agent of olive quick decline, used transcriptomic data from diseased trees to understand the interactions between plant host and bacterial pathogen during the infection process. This research identified a gene transcript, cvaC-1, generated during active bacterial multiplication, that could serve as a valuable target for diagnostic tests. RT-qPCRs designed to target cvaC-1 were even able to detect the pathogen early in the infection process, when pathogen levels are still very low and difficult to detect with existing diagnostic tests. In addition to being able to detect the pathogen early in the infection process, RT-qPCRs targeting cvaC-1 have the benefit of differentiating between actively growing and dormant, or nonviable, bacterial fragments. This finding addresses the diagnostic challenge caused by Xfp due to nonviable fragments of the bacterium remaining detectable in plants (Serena Amoia et al.).