Metagenomic and Metatranscriptomic Analyses of Diverse Watermelon Cultivars Reveal the Role of Fruit Associated Microbiome in Carbohydrate Metabolism and Ripening of Mature Fruits

Quality Changes and Fungal Microbiota Dynamics in Stored Jujube Fruits: Insights from High-Throughput Sequencing for Food Preservation

Postharvest rot is an urgent problem affecting the storage of winter jujube. Therefore, the development of new technologies for efficient and safe preservation is very important. This study aimed to elucidate the fungal microbiota found on the epidermis of jujube during the storage period using high-throughput sequencing, as well as to monitor the changes in quality indexes throughout this period. Through internal transcribed spacer (ITS) sequencing, we identified two phyla (Basidiomycota and Ascomycota) and six genera (Cryptococcus, Bulleromyces, Sporidiobolus, Alternaria, Pseudozyma, and Sporobolomyces), which potentially contribute to the spoilage and deterioration of jujube, referred to as "core fungal taxa". A high correlation was further found between preservation indices (including decay rate, firmness, and total soluble solids) and the growth of multiple core fungi over time. These findings will provide insights and a theoretical basis for further research on preservation techniques related to biological control during date fruit storage.

Bacterial diversity and composition on the rinds of specific melon cultivars and hybrids from across different growing regions in the United States

The goal of this study was to characterize the bacterial diversity on different melon varieties grown in different regions of the US, and determine the influence that region, rind netting, and variety of melon has on the composition of the melon microbiome. Assessing the bacterial diversity of the microbiome on the melon rind can identify antagonistic and protagonistic bacteria for foodborne pathogens and spoilage organisms to improve melon safety, prolong shelf-life, and/or improve overall plant health. Bacterial community composition of melons (n = 603) grown in seven locations over a four-year period were used for 16S rRNA gene amplicon sequencing and analysis to identify bacterial diversity and constituents. Statistically significant differences in alpha diversity based on the rind netting and growing region (p < 0.01) were found among the melon samples. Principal Coordinate Analysis based on the Bray-Curtis dissimilarity distance matrix found that the melon bacterial communities clustered more by region rather than melon variety (R2 value: 0.09 & R2 value: 0.02 respectively). Taxonomic profiling among the growing regions found Enterobacteriaceae, Bacillaceae, Microbacteriaceae, and Pseudomonadaceae present on the different melon rinds at an abundance of ≥ 0.1%, but no specific core microbiome was found for netted melons. However, a core of Pseudomonadaceae, Bacillaceae, and Exiguobacteraceae were found for non-netted melons. The results of this study indicate that bacterial diversity is driven more by the region that the melons were grown in compared to rind netting or melon type. Establishing the foundation for regional differences could improve melon safety, shelf-life, and quality as well as the consumers' health.

Microbiota and its antibiotic resistance profile in avocado Guatemalan fruits (Persea nubigena var. guatemalensis) sold at retail markets of Ibarra city, northern Ecuador

Introduction

Avocados are typically sold in unsanitary conditions at the retail markets in Ecuador, which can raise the risk of microbial contamination. These microorganisms could exhibit multi-antibiotic resistance (MAR), being a serious threat concern to human health. In this study, we aimed to evaluate the microbiota and its antibiotic resistance profile in avocado Guatemalan fruits (Persea nubigena var. guatemalensis), at ripe stage: immature, firm light green (ready to eat in 4 days), peel (AFPE) and pulp (AFPU), and mature intense green (ready to eat) peel (AMPE) and pulp (AMPU), to gain baseline information on the prevalence of MAR bacteria.

Methods

Culture-independent (16S rRNA metagenomics) and culture-dependent approach (to detect specific indicator microorganisms) were used. Moreover, antibiotic susceptibility of selected target indicator bacteria was assessed providing information about the antibiotic resistance (AR) among the groups.

Results

Based on 16S rRNA gene metagenomic analysis, over 99.78% of reads were classified as bacteria in all samples. Shannon diversity index varies from 1.22 to 2.22, with the highest bacterial population assigned to AFPE samples (1327 species). The highest microbial counts of indicator Staphylococcus spp. (STAPHY), Enterobacter spp. (ENT), and Listeria spp. (LIST), were detected in AMPE samples. Thirty percent of the selected STAPHYs, and 20.91% of Enterobacter (ENT) clones were resistant to various classes of antibiotics. The MAR index varies between 0.25 to 0.88 and was clone-, and fruit ripe stage-dependent.

Conclusions

The results indicated that ready to eat avocados contained detectable levels of MAR bacteria, including methicillin resistant (MR)-STAPHY, which may act as a potential vector for the spread of antibiotic resistance. To achieve the increase of the production and marketing of Fuerte cultivar in Ecuador, it is vitally important to consider valuable strategies to protect the fruits at the early ripe stage in future. Thus, it is crucial to set up efficient control measures and develop coordinated strategies to guarantee the microbiological quality of the food.

Activity of the botanical compound thymol against kiwifruit rot caused by Fusarium tricinctum and the underlying mechanisms

BACKGROUND

Kiwifruit rot is an important disease caused by different fungal pathogens, which can lead to huge economic loss in the kiwifruit industry. The aims of this study were to discover an effective botanical compound that significantly inhibits the pathogens causing kiwifruit rot, evaluate its control efficacy against this disease, and reveal the underlying mechanisms.

RESULTS

A strain of Fusarium tricinctum (GF-1), isolated from diseased kiwifruit, could cause fruit rot in both Actinidia chinensis var. chinensis and Actinidia chinensis var. deliciosa. Different botanical chemicals were used for antifungal activity test against GF-1 and thymol was the most effective one with a 50% effective concentration (EC₅₀ ) of 30.98 mg L^-1 . The minimal inhibitory concentration (MIC) of thymol against GF-1 was 90 mg L^-1 . Control efficacy of thymol against kiwifruit rot was evaluated and the results indicated that thymol could effectively decrease the occurrence and spread of kiwifruit rot. The mechanisms underlying the antifungal activity of thymol against F. tricinctum were investigated, and it showed that thymol could significantly damage the ultrastructure, destroy the plasma membrane integrity, and instantaneously increase energy metabolisms of F. tricinctum. Further investigations indicated that thymol could extend shelf life of kiwifruit by increasing their storability.

CONCLUSION

Thymol can effectively inhibit F. tricinctum that is one of the causal agents of kiwifruit rot. Multiple modes of action are involved in the antifungal activity. The results of this study indicate that thymol can be a promising botanical fungicide to control kiwifruit rot and provide useful references for thymol application in agriculture system. © 2023 Society of Chemical Industry.

Physiological, Nutritional and Transcriptomic Responses of Sturgeon (Acipenser schrenckii) to Complete Substitution of Fishmeal with Cottonseed Protein Concentrate in Aquafeed

This study estimated the effect of substituting fishmeal completely with cottonseed protein concentrate (CPC) in the diet of sturgeon (Acipenser schrenckii) on growth, digestive physiology, and hepatic gene expression. A control diet containing fishmeal and an experimental diet based on CPC was designed. The study was conducted for 56 days in indoor recirculating aquaculture systems. The results showed that weight gain, feed efficiency, and whole-body essential amino acids (EAAs) all decreased significantly in the experimental group, while whole-body non-essential amino acids (NEAAs) and serum transaminase activity increased (p < 0.05). The activity of digestive enzymes in the mid-intestine was significantly reduced (p < 0.05), and liver histology revealed fatty infiltration of hepatocytes. The hepatic transcriptome revealed an upregulation of genes linked to metabolism, including steroid biosynthesis, pyruvate metabolism, fatty acid metabolism, and amino acid biosynthesis. These findings indicate that fully replacing fishmeal with CPC harms A. schrenckii growth and physiology. This study provides valuable data for the development of improved aquafeeds and the use of molecular methods to evaluate the diet performance of sturgeon.

Combined Metabolome and Transcriptome Analysis Elucidates Sugar Accumulation in Wucai (Brassica campestris L.)

Wucai (Brassica campestris L.) is a leafy vegetable that originated in China, its soluble sugars accumulate significantly to improve taste quality during maturation, and it is widely accepted by consumers. In this study, we investigated the soluble sugar content at different developmental stages. Two periods including 34 days after planting (DAP) and 46 DAP, which represent the period prior to and after sugar accumulation, respectively, were selected for metabolomic and transcriptomic profiling. Differentially accumulated metabolites (DAMs) were mainly enriched in the pentose phosphate pathway, galactose metabolism, glycolysis/gluconeogenesis, starch and sucrose metabolism, and fructose and mannose metabolism. By orthogonal projection to latent structures-discriminant s-plot (OPLS-DA S-plot) and MetaboAnalyst analyses, D-galactose and β-D-glucose were identified as the major components of sugar accumulation in wucai. Combined with the transcriptome, the pathway of sugar accumulation and the interact network between 26 DEGs and the two sugars were mapped. CWINV4, CEL1, BGLU16, and BraA03g023380.3C had positive correlations with the accumulation of sugar accumulation in wucai. The lower expression of BraA06g003260.3C, BraA08g002960.3C, BraA05g019040.3C, and BraA05g027230.3C promoted sugar accumulation during the ripening of wucai. These findings provide insights into the mechanisms underlying sugar accumulation during commodity maturity, providing a basis for the breeding of sugar-rich wucai cultivars.

Watermelon domestication was shaped by stepwise selection and regulation of the metabolome

Although crop domestication has greatly aided human civilization, the sequential domestication and regulation of most quality traits remain poorly understood. Here, we report the stepwise selection and regulation of major fruit quality traits that occurred during watermelon evolution. The levels of fruit cucurbitacins and flavonoids were negatively selected during speciation, whereas sugar and carotenoid contents were positively selected during domestication. Interestingly, fruit malic acid and citric acid showed the opposite selection trends during the improvement. We identified a novel gene cluster (CGC1, cucurbitacin gene cluster on chromosome 1) containing both regulatory and structural genes involved in cucurbitacin biosynthesis, which revealed a cascade of transcriptional regulation operating mechanisms. In the CGC1, an allele caused a single nucleotide change in ClERF1 binding sites (GCC-box) in the promoter of ClBh1, which resulted in reduced expression of ClBh1 and inhibition of cucurbitacin synthesis in cultivated watermelon. Functional analysis revealed that a rare insertion of 244 amino acids, which arose in C. amarus and became fixed in sweet watermelon, in ClOSC (oxidosqualene cyclase) was critical for the negative selection of cucurbitacins during watermelon evolution. This research provides an important resource for metabolomics-assisted breeding in watermelon and for exploring metabolic pathway regulation mechanisms.

Characterization of the microbiota dynamics associated with Moniliophthora roreri, causal agent of cocoa frosty pod rot disease, reveals new viral species

Introduction

Theobroma cacao, the cocoa tree, is a target for pathogens, such as fungi from the genera Phytophthora, Moniliophthora, Colletotrichum, Ceratocystis, among others. Some cacao pathogens are restricted to specific regions of the world, such as the Cacao swollen shoot virus (CSSV) in West African countries, while others are expanding geographically, such as Moniliophthora roreri in the Americas. M. roreri is one of the most threatening cacao pathogens since it directly attacks the cacao pods driving a significant reduction in production, and therefore economic losses. Despite its importance, the knowledge about the microenvironment of this pathogen and the cocoa pods is still poorly characterized.

Methods

Herein we performed RNA sequencing of spores in differential stages of culture in a medium supplemented with cacao pod extract and mycelium collected of the susceptible variety ICT 7121 naturally infected by the pathogen to evaluate the diversity and transcriptional activity of microorganisms associated with the in vitro sporulation of M. roreri.

Results

Our data revealed a great variety of fungi and bacteria associated with M. roreri, with an exceptional diversity of individuals from the genus Trichoderma sp. Interestingly, the dynamics of microorganisms from different kingdoms varied proportionally, suggesting they are somehow affected by M. roreri culture time. We also identified three sequences similar to viral genomes from the Narnaviridae family, posteriorly confirmed by phylogenetic analysis as members of the genus Narnavirus. Screening of M. roreri public datasets indicated the virus sequences circulating in samples from Ecuador, suggesting a wide spread of these elements. Of note, we did not identify traces of the viral sequences in the M. roreri genome or DNA sequencing, restricting the possibility of these sequences representing endogenized elements.

Discussion

To the best of our knowledge, this is the first report of viruses infecting the fungus of the genus Moniliophthora and only the third description of viruses that are able to parasite elements from the Marasmiaceae family.

Microbiome-based biotechnology for reducing food loss post harvest

Microbiomes have an immense potential to enhance plant resilience to various biotic and abiotic stresses. However, intrinsic microbial communities respond to changes in their host's physiology and environment during plant's life cycle. The potential of the inherent plant microbiome has been neglected for a long time, especially for the postharvest period. Currently, close to 50% of all produced fruits and vegetables are lost either during production or storage. Biological control of spoilage and storage diseases is still lacking sufficiency. Today, novel multiomics technologies allow us to study the microbiome and its responses on a community level, which will help to advance current classic approaches and develop more effective and robust microbiome-based solutions for fruit and vegetable storability, quality, and safety.

New insights into engineered plant-microbe interactions for pesticide removal

Over the past decades, rapid industrialization along with the overutilization of organic pollutants/pesticides has altered the environmental circumstances. Moreover, various anthropogenic, xenobiotics and natural activities also affected plants, soil, and human health, in both direct and indirect ways. To counter this, several conventional methods are currently practiced, but are uneconomical, noxious, and is yet inefficient for large-scale application. Plant-microbe interactions are mediated naturally in an ecosystem and are practiced in several areas. Plant growth promoting rhizobacteria (PGPR) possess certain attributes affecting plant and soil consequently performing decontamination activity via a direct and indirect mechanism. PGPR also harbors indispensable genes stimulating the mineralization of several organic and inorganic compounds. This makes microbes potential candidates for contributing to sustainably remediating the harmful pesticide contaminants. There is a limited piece of information about the plant-microbe interaction pertaining predict and understand the overall interaction concerning a sustainable environment. Therefore, this review focuses on the plant-microbe interaction in the rhizosphere and inside the plant's tissues, along with the utilization augmenting the crop productivity, reduction in plant stress along with decontamination of pesticides/organic pollutants in soil for sustainable environmental management.

Integration of multi-omics technologies for crop improvement: Status and prospects

With the rapid development of next-generation sequencing (NGS), multi-omics techniques have been emerging as effective approaches for crop improvement. Here, we focus mainly on addressing the current status and future perspectives toward omics-related technologies and bioinformatic resources with potential applications in crop breeding. Using a large amount of omics-level data from the functional genome, transcriptome, proteome, epigenome, metabolome, and microbiome, clarifying the interaction between gene and phenotype formation will become possible. The integration of multi-omics datasets with pan-omics platforms and systems biology could predict the complex traits of crops and elucidate the regulatory networks for genetic improvement. Different scales of trait predictions and decision-making models will facilitate crop breeding more intelligent. Potential challenges that integrate the multi-omics data with studies of gene function and their network to efficiently select desirable agronomic traits are discussed by proposing some cutting-edge breeding strategies for crop improvement. Multi-omics-integrated approaches together with other artificial intelligence techniques will contribute to broadening and deepening our knowledge of crop precision breeding, resulting in speeding up the breeding process.

Debaryomyces nepalensis reduces fungal decay by affecting the postharvest microbiome during jujube storage

Microbial antagonists are effective and environmentally friendly in controlling postharvest diseases of fruit. The present study investigated the influence of D. nepalensis on epiphytic microbiome and postharvest decay of jujube. Results showed that D. nepalensis notably reduced fungal decay, maintained the fruit firmness and delayed discoloration. The epiphytic microbiome revealed that D. nepalensis changed the fungal communities, but few influence on bacterial communities were observed. D. nepalensis, as the dominant population in the treatment group, decreased the abundance of pathogenic fungi of Alternaria, Penicillium, Fusarium and Botrytis, while increased the beneficial bacteria of Pantoea. The canonical correspondence analysis revealed that Debaryomyces was negatively correlated with the decay rate, whereas Penicillium, Acremonium, Rhodosporidiobolus and Hansfordia were positively correlated. In conclusion, D. nepalensis altered the successional process of fungal and bacterial communities to reduce the decay rate of jujube during storage.

Novel Approaches for Sustainable Horticultural Crop Production: Advances and Prospects

Reduction of plant growth, yield and quality due to diverse environmental constrains along with climate change significantly limit the sustainable production of horticultural crops. In this review, we highlight the prospective impacts that are positive challenges for the application of beneficial microbial endophytes, nanomaterials (NMs), exogenous phytohormones strigolactones (SLs) and new breeding techniques (CRISPR), as well as controlled environment horticulture (CEH) using artificial light in sustainable production of horticultural crops. The benefits of such applications are often evaluated by measuring their impact on the metabolic, morphological and biochemical parameters of a variety of cultures, which typically results in higher yields with efficient use of resources when applied in greenhouse or field conditions. Endophytic microbes that promote plant growth play a key role in the adapting of plants to habitat, thereby improving their yield and prolonging their protection from biotic and abiotic stresses. Focusing on quality control, we considered the effects of the applications of microbial endophytes, a novel class of phytohormones SLs, as well as NMs and CEH using artificial light on horticultural commodities. In addition, the genomic editing of plants using CRISPR, including its role in modulating gene expression/transcription factors in improving crop production and tolerance, was also reviewed.

The endophytome (plant-associated microbiome): methodological approaches, biological aspects, and biotech applications

Similar to other organisms, plants establish interactions with a variety of microorganisms in their natural environment. The plant microbiome occupies the host plant's tissues, either internally or on its surfaces, showing interactions that can assist in its growth, development, and adaptation to face environmental stresses. The advance of metagenomics and metatranscriptomics approaches has strongly driven the study and recognition of plant microbiome impacts. Research in this regard provides comprehensive information about the taxonomic and functional aspects of microbial plant communities, contributing to a better understanding of their dynamics. Evidence of the plant microbiome's functional potential has boosted its exploitation to develop more ecological and sustainable agricultural practices that impact human health. Although microbial inoculants' development and use are promising to revolutionize crop production, interdisciplinary studies are needed to identify new candidates and promote effective practical applications. On the other hand, there are challenges in understanding and analyzing complex data generated within a plant microbiome project's scope. This review presents aspects about the complex structuring and assembly of the microbiome in the host plant's tissues, metagenomics, and metatranscriptomics approaches for its understanding, covering descriptions of recent studies concerning metagenomics to characterize the microbiome of non-model plants under different aspects. Studies involving bio-inoculants, isolated from plant microbial communities, capable of assisting in crops' productivity, are also reviewed.

OMICs, Epigenetics, and Genome Editing Techniques for Food and Nutritional Security

The incredible success of crop breeding and agricultural innovation in the last century greatly contributed to the Green Revolution, which significantly increased yields and ensures food security, despite the population explosion. However, new challenges such as rapid climate change, deteriorating soil, and the accumulation of pollutants require much faster responses and more effective solutions that cannot be achieved through traditional breeding. Further prospects for increasing the efficiency of agriculture are undoubtedly associated with the inclusion in the breeding strategy of new knowledge obtained using high-throughput technologies and new tools in the future to ensure the design of new plant genomes and predict the desired phenotype. This article provides an overview of the current state of research in these areas, as well as the study of soil and plant microbiomes, and the prospective use of their potential in a new field of microbiome engineering. In terms of genomic and phenomic predictions, we also propose an integrated approach that combines high-density genotyping and high-throughput phenotyping techniques, which can improve the prediction accuracy of quantitative traits in crop species.

Evolutionary gain of oligosaccharide hydrolysis and sugar transport enhanced carbohydrate partitioning in sweet watermelon fruits

How raffinose (Raf) family oligosaccharides, the major translocated sugars in the vascular bundle in cucurbits, are hydrolyzed and subsequently partitioned has not been fully elucidated. By performing reciprocal grafting of watermelon (Citrullus lanatus) fruits to branch stems, we observed that Raf was hydrolyzed in the fruit of cultivar watermelons but was backlogged in the fruit of wild ancestor species. Through a genome-wide association study, the alkaline alpha-galactosidase ClAGA2 was identified as the key factor controlling stachyose and Raf hydrolysis, and it was determined to be specifically expressed in the vascular bundle. Analysis of transgenic plants confirmed that ClAGA2 controls fruit Raf hydrolysis and reduces sugar content in fruits. Two single-nucleotide polymorphisms (SNPs) within the ClAGA2 promoter affect the recruitment of the transcription factor ClNF-YC2 (nuclear transcription factor Y subunit C) to regulate ClAGA2 expression. Moreover, this study demonstrates that C. lanatus Sugars Will Eventually Be Exported Transporter 3 (ClSWEET3) and Tonoplast Sugar Transporter (ClTST2) participate in plasma membrane sugar transport and sugar storage in fruit cell vacuoles, respectively. Knocking out ClAGA2, ClSWEET3, and ClTST2 affected fruit sugar accumulation. Genomic signatures indicate that the selection of ClAGA2, ClSWEET3, and ClTST2 for carbohydrate partitioning led to the derivation of modern sweet watermelon from non-sweet ancestors during domestication.

Unravelling the fruit microbiome: The key for developing effective biological control strategies for postharvest diseases

Fruit-based diets are recognized for their benefits to human health. The safety of fruit is a global concern for scientists. Fruit microbiome represents the whole microorganisms that are associated with a fruit. These microbes are either found on the surfaces (epiphytes) or in the tissues of the fruit (endophytes). The recent knowledge gained from these microbial communities is considered relevant to the field of biological control in prevention of postharvest fruit pathology. In this study, the importance of the microbiome of certain fruits and how it holds promise for solving the problems inherent in biocontrol and postharvest crop protection are summarized. Research needs on the fruit microbiome are highlighted. Data from DNA sequencing and "meta-omics" technologies very recently applied to the study of microbial communities of fruits in the postharvest context are also discussed. Various fruit parameters, management practices, and environmental conditions are the main determinants of the microbiome. Microbial communities can be classified according to their structure and function in fruit tissues. A critical mechanism of microbial biological control agents is to reshape and interact with the microbiome of the fruit. The ability to control the microbiome of any fruit is a great potential in postharvest management of fruits. Research on the fruit microbiome offers important opportunities to develop postharvest biocontrol strategies and products, as well as the health profile of the fruit.

Evolution of fungal community associated with ready-to-eat pineapple during storage under different temperature conditions

The international market of fresh-cut products has witnessed dramatic growth in recent years, stimulated by consumer's demand for healthy, nutritious and convenient foods. One of the main challenging issues for the quality and safety of these products is the potential microbial spoilage that can significantly reduce their shelf-life. The complete identification of fresh-cut product microbiota together with the evaluation of environmental factors impact on microbial composition is of primary importance. We therefore assessed the fungal communities associated with the spoilage of ready-to-eat (RTE) pineapple using a metagenetic amplicon sequencing approach, based on the ITS2 region. Our results revealed a significant variability on fungal species composition between the different batches of RTE pineapple. The initial microbiota composition was the main influencing factor and determined the progress of spoilage. Temperature and storage time were the secondary factors influencing spoilage and their impact was depending on the initial prevalent fungal species, which showed different responses to the various modifications. Our results strongly suggest that further large-scale sampling of RTE pineapple production should be conducted in order to assess the full biodiversity range of fungal community involved in the spoilage process and for unravelling the impact of important environmental factors shaping the initial microbiota.

Identification of key gene networks controlling organic acid and sugar metabolism during watermelon fruit development by integrating metabolic phenotypes and gene expression profiles

The organoleptic qualities of watermelon fruit are defined by the sugar and organic acid contents, which undergo considerable variations during development and maturation. The molecular mechanisms underlying these variations remain unclear. In this study, we used transcriptome profiles to investigate the coexpression patterns of gene networks associated with sugar and organic acid metabolism. We identified 3 gene networks/modules containing 2443 genes highly correlated with sugars and organic acids. Within these modules, based on intramodular significance and Reverse Transcription Quantitative polymerase chain reaction (RT-qPCR), we identified 7 genes involved in the metabolism of sugars and organic acids. Among these genes, Cla97C01G000640, Cla97C05G087120 and Cla97C01G018840 (r² = 0.83 with glucose content) were identified as sugar transporters (SWEET, EDR6 and STP) and Cla97C03G064990 (r² = 0.92 with sucrose content) was identified as a sucrose synthase from information available for other crops. Similarly, Cla97C07G128420, Cla97C03G068240 and Cla97C01G008870, having strong correlations with malic (r² = 0.75) and citric acid (r² = 0.85), were annotated as malate and citrate transporters (ALMT7, CS, and ICDH). The expression profiles of these 7 genes in diverse watermelon genotypes revealed consistent patterns of expression variation in various types of watermelon. These findings add significantly to our existing knowledge of sugar and organic acid metabolism in watermelon.

Microbiome approaches provide the key to biologically control postharvest pathogens and storability of fruits and vegetables

Microbes play an important role in plants and interact closely with their host starting from sprouting seeds, continuing during growth and after harvest. The discovery of their importance for plant and postharvest health initiated a biotechnological development of various antagonistic bacteria and fungi for disease control. Nevertheless, their application often showed inconsistent effects. Recently, high-throughput sequencing-based techniques including advanced microscopy reveal fruits and vegetables as holobionts. At harvest, all fruits and vegetables harbor a highly abundant and specific microbiota including beneficial, pathogenic and spoilage microorganisms. Especially, a high microbial diversity and resilient microbial networks were shown to be linked to fruit and vegetable health, while diseased products showed severe dysbiosis. Field and postharvest handling of fruits and vegetables was shown to affect the indigenous microbiome and therefore has a substantial impact on the storability of fruits and vegetables. Microbiome tracking can be implemented as a new tool to evaluate and assess all postharvest processes and contribute to fruit and vegetable health. Here, we summarize current research advancements in the emerging field of postharvest microbiomes and elaborate its importance. The generated knowledge provides profound insights into postharvest microbiome dynamics and sets a new basis for targeted, microbiome-driven and sustainable control strategies.

Hormonal and metabolites responses in Fusarium wilt-susceptible and -resistant watermelon plants during plant-pathogen interactions

BACKGROUND

Fusarium oxysporum f. sp. niveum (FON) causes Fusarium wilt in watermelon. Several disease-resistant watermelon varieties have been developed to combat Fusarium wilt. However, the key metabolites that mount defense responses in these watermelon varieties are unknown. Herein, we analyzed hormones, melatonin, phenolic acids, and amino acid profiles in the leaf tissue of FON zero (0)-resistant (PI-296341, Calhoun Grey, and Charleston Grey) and -susceptible (Sugar Baby) watermelon varieties before and after infection.

RESULTS

We found that jasmonic acid-isoleucine (JA-Ile) and methyl jasmonate (MeJA) were selectively accumulated in one or more studied resistant varieties upon infection. However, indole-3-acetic acid (IAA) was only observed in the FON 0 inoculated plants of all varieties on the 16th day of post-inoculation. The melatonin content of PI-296341 decreased upon infection. Conversely, melatonin was only detected in the FON 0 inoculated plants of Sugar Baby and Charleston Grey varieties. On the 16th day of post-inoculation, the lysine content in resistant varieties was significantly reduced, whereas it was found to be elevated in the susceptible variety.

CONCLUSIONS

Taken together, Me-JA, JA-Ile, melatonin, and lysine may have crucial roles in developing defense responses against the FON 0 pathogen, and IAA can be a biomarker of FON 0 infection in watermelon plants.

The plant endosphere world - bacterial life within plants

The plant endosphere is colonized by complex microbial communities and microorganisms, which colonize the plant interior at least part of their lifetime and are termed endophytes. Their functions range from mutualism to pathogenicity. All plant organs and tissues are generally colonized by bacterial endophytes and their diversity and composition depend on the plant, the plant organ and its physiological conditions, the plant growth stage as well as on the environment. Plant-associated microorganisms, and in particular endophytes, have lately received high attention, because of the increasing awareness of the importance of host-associated microbiota for the functioning and performance of their host. Some endophyte functions are known from mostly lab assays, genome prediction and few metagenome analyses; however, we have limited understanding on in planta activities, particularly considering the diversity of micro-environments and the dynamics of conditions. In our review, we present recent findings on endosphere environments, their physiological conditions and endophyte colonization. Furthermore, we discuss microbial functions, the interaction between endophytes and plants as well as methodological limitations of endophyte research. We also provide an outlook on needs of future research to improve our understanding on the role of microbiota colonizing the endosphere on plant traits and ecosystem functioning.

Profiling the composition and metabolic activities of microbial community in fermented grain for the Chinese strong-flavor Baijiu production by using the metatranscriptome, high-throughput 16S rRNA and ITS gene sequencings

The composition and function of microbial community analyzed by sequencing 16S rRNA/ITS gene amplicons (DNA level) were compared with those derived by using metatranscriptome sequencing (RNA level) from the same fermented grain (FG) sample, which obtained from the key fermentation time point during the Chinese strong-flavor Baijiu (CSFB) production process. The results showed that the fungi with the highest relative abundance was Saccharomyces (RNA: 83.15%, DNA: 89.74%) at the two levels. The most abundant bacterium was Kroppenstedtia (37.09%) detected only at the DNA level, while it was Streptococcus (93.75%) at the RNA level, indicating that the structures of prokaryotic communities at the two levels were quite different. For the microbial functions, a large proportion of genes of FG microorganisms related to "Metabolism" function were observed both by using PICRUSt2 analysis (DNA level) and metatranscriptome analysis (RNA level), and especially enriched in "Carbohydrate metabolism". While the proportions of genes involved in some functions were different, such as "Replication and repair", "Membrane transport" and "Environmental adaptation", with high proportions of genes involved in at the DNA level when compared those at the RNA level. Furthermore, Saccharomyces cerevisiae was the most active microbe in the top15 pathways, followed by Torulaspora dellbrueckii. During the conversion of starch to ethanol, S. cerevisiae showed high metabolic capacity, and cooperated with other microorganisms to convert pyruvate to acetaldehyde directly or through acetyl-CoA and acetate, and then acetaldehyde to ethanol. As far as we know, this is a first study to profile the microbial community and metabolic features in FG of CSFB by using a combination of DNA- and RNA- based technologies. Our findings could provide useful insights for further understanding the active microbial function, metabolic pathways and fermentation mechanism in the FG ecosystem during CSFB fermentation.

The Nexus Between Plant and Plant Microbiome: Revelation of the Networking Strategies

The diversity of plant-associated microbes is enormous and complex. These microbiomes are structured and form complex interconnected microbial networks that are important in plant health and ecosystem functioning. Understanding the composition of the microbiome and their core function is important in unraveling their networking strategies and their potential influence on plant performance. The network is altered by the host plant species, which in turn influence the microbial interaction dynamics and co-evolution. We discuss the plant microbiome and the complex interplay among microbes and between their host plants. We provide an overview of how plant performance is influenced by the microbiome diversity and function.

Formulating bacterial endophyte: Pre-conditioning of cells and the encapsulation in amidated pectin beads

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Endophytic activity of pre-conditioned and encapsulated cells in amidated pectin beads

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Hydroxyectoine-added cells within pectin amidated beads increase endophytismus

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Radish yields increased through the application of encapsulated K. radicincitans cells

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Entrapped cells chemoattraction towards radish visualized by multispectral imaging

Despite the benefits of bacterial endophytes, recent studies on the mostly Gram-negative bacteria lack of regard for formulation strategies. The encapsulation into biopolymeric materials such as amidated pectins hydrogels is a suitable alternative. Here, this research aimed at supporting the capability of the plant growth-promoting bacteria Kosakonia radicincitans DSM16656^T to endophytically colonize plant seedlings. In this approach, the pre-conditioned cells through osmoadaptation and hydroxyectoine accumulation were used. In general, pre-osmoadapted and hydroxyectoine-supplemented bacteria cells formulated in amidated pectin dried beads increased the endophytic activity by 10-fold. Moreover, plant promotion in radish plants enhanced by 18.9% and 20.7% for a dry matter of tuber and leaves. Confocal microscopy studies with GFP-tagged bacteria revealed that bacterial aggregates formed during the activation of beads play an essential role in early colonization stages. This research encourages the integration of fermentation and formulation strategies in a bioprocess engineering approach for exploiting endophytic bacteria.

Tomato RNA-seq Data Mining Reveals the Taxonomic and Functional Diversity of Root-Associated Microbiota

Next-generation approaches have enabled researchers to deeply study the plant microbiota and to reveal how microbiota associated with plant roots has key effects on plant nutrition, disease resistance, and plant development. Although early "omics" experiments focused mainly on the species composition of microbial communities, new "meta-omics" approaches such as meta-transcriptomics provide hints about the functions of the microbes when interacting with their plant host. Here, we used an RNA-seq dataset previously generated for tomato (Solanum lycopersicum) plants growing on different native soils to test the hypothesis that host-targeted transcriptomics can detect the taxonomic and functional diversity of root microbiota. Even though the sequencing throughput for the microbial populations was limited, we were able to reconstruct the microbial communities and obtain an overview of their functional diversity. Comparisons of the host transcriptome and the meta-transcriptome suggested that the composition and the metabolic activities of the microbiota shape plant responses at the molecular level. Despite the limitations, mining available next-generation sequencing datasets can provide unexpected results and potential benefits for microbiota research.

Whole metagenome sequencing of cecum microbiomes in Ethiopian indigenous chickens from two different altitudes reveals antibiotic resistance genes

We analyzed the whole genomes of cecum microbiomes of Ethiopian indigenous chickens from two distinct geographical zones: Afar (AF) district (Dulecha, 730 m above sea level) and Amhara (AM) district (Menz Gera Midir, 3300 m). Through metagenomic analysis we found that microbial populations were mainly dominated by Bacteroidetes and Firmicutes. We identified 2210 common genes in the two groups. LEfSe showed that the distribution of Coprobacter, Geobacter, Cronobacter, Alloprevotella, and Dysgonomonas were more abundant in AF than AM. Analyses using KEGG, eggNOG, and CAZy databases indicated that the pathways of metabolism, genetic information processing, environmental information processing, and cellular process were significantly enriched. Functional abundance was found to be associated with the nutrient absorption and microbial localization of indigenous chickens. We also investigated antibiotic resistant genes and found antibiotics like LSM, cephalosporin, and tetracycline were significantly more abundant in AF than AM.

Advances and Challenges in Metatranscriptomic Analysis

Sequencing-based analyses of microbiomes have traditionally focused on addressing the question of community membership and profiling taxonomic abundance through amplicon sequencing of 16 rRNA genes. More recently, shotgun metagenomics, which involves the random sequencing of all genomic content of a microbiome, has dominated this arena due to advancements in sequencing technology throughput and capability to profile genes as well as microbiome membership. While these methods have revealed a great number of insights into a wide variety of microbiomes, both of these approaches only describe the presence of organisms or genes, and not whether they are active members of the microbiome. To obtain deeper insights into how a microbial community responds over time to their changing environmental conditions, microbiome scientists are beginning to employ large-scale metatranscriptomics approaches. Here, we present a comprehensive review on computational metatranscriptomics approaches to study microbial community transcriptomes. We review the major advancements in this burgeoning field, compare strengths and weaknesses to other microbiome analysis methods, list available tools and workflows, and describe use cases and limitations of this method. We envision that this field will continue to grow exponentially, as will the scope of projects (e.g. longitudinal studies of community transcriptional responses to perturbations over time) and the resulting data. This review will provide a list of options for computational analysis of these data and will highlight areas in need of development.

Evaluation of microbial communities in peels of Brazilian tropical fruits by amplicon sequence analysis

Elucidation of the distinctive microbial taxonomic profiles of tropical fruit peels is the indispensable component of investigations aimed at the detection of microorganisms responsible for the post-harvest loss. The objective of the present work was to dissect the bacterial and fungal community of five tropical fruit peels (banana, guava, mango, papaya, and passion fruit) in wild (non-cultivated) and conventionally produced samples from Brazil. To that end, 16S rRNA-encoding gene and ITS rDNA amplicon analysis of the five tropical fruit peels were performed to discriminate the bacterial and fungal communities, respectively. The result showed that bacterial communities of the five types of fruit peels were by far more diversified than that of fungal communities, independent of the type of production system involved. Among the investigated fruits, non-cultivated papaya peels hosted the most diversified bacterial community while the least bacterial community diversity was found in the conventionally produced papaya fruit peels. The gene amplicon analysis clearly discriminated the bacterial community into their respective classes, while fungal communities were better classified in their phyla, yet with clearer component discrimination of fungal community based on the type of cultivation system practiced. Conventionally produced banana and non-cultivated passion fruit peels were characteristically dominated by fungal and bacterial groups, respectively. Overall, in conventionally produced fruit peels, bacterial community was mainly composed of Proteobacteria, Actinobacteria, and Bacilli. The result provided a broad microbial diversity profile that could be used as an important input for seeking alternative fruit spoilage control and post-harvest treatments.