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Plant-associated microorganisms are involved in important functions related to growth, performance and health of their hosts. Understanding their modes of action is important for the design of promising microbial inoculants for sustainable agriculture. Plant-associated microorganisms are able to interact with their hosts and often exert specific functions toward potential pathogens; the underlying in vitro interactions are well studied. In contrast, in situ effects of inoculants, and especially their impact on the plant indigenous microbiome was mostly neglected so far. Recently, microbiome research has revolutionized our understanding of plants as coevolved holobionts but also of indigenous microbiome-inoculant interactions. Here we disentangle the effects of microbial inoculants on the indigenous plant microbiome and point out the following types of plant microbiome modulations: (i) transient microbiome shifts, (ii) stabilization or increase of microbial diversity, (iii) stabilization or increase of plant microbiome evenness, (iv) restoration of a dysbiosis/compensation or reduction of a pathogen-induced shift, (v) targeted shifts toward plant beneficial members of the indigenous microbiota, and (vi) suppression of potential pathogens. Therefore, we suggest microbiome modulations as novel and efficient mode of action for microbial inoculants that can also be mediated via the plant.

ABSTRACT 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.

Background Sugar loss due to storage rot has a substantial economic impact on the sugar industry. The gradual spread of saprophytic fungi such as Fusarium and Penicillium spp. during storage in beet clamps is an ongoing challenge for postharvest processing. Early detection of shifts in microbial communities in beet clamps is a promising approach for the initiation of targeted countermeasures during developing storage rot. In a combined approach, high-throughput sequencing of bacterial and fungal genetic markers was complemented with cultivation-dependent methods and provided detailed insights into microbial communities colonizing stored roots. These data were used to develop a multi-target qPCR technique for early detection of postharvest diseases. Results The comparison of beet microbiomes from six clamps in Austria and Germany highlighted regional differences; nevertheless, universal indicators of the health status were identified. Apart from a significant decrease in microbial diversity in decaying sugar beets ( p ≤ 0.01), a distinctive shift in the taxonomic composition of the overall microbiome was found. Fungal taxa such as Candida and Penicillium together with the gram-positive Lactobacillus were the main disease indicators in the microbiome of decaying sugar beets. In contrast, the genera Plectosphaerella and Vishniacozyma as well as a higher microbial diversity in general were found to reflect the microbiome of healthy beets. Based on these findings, a qPCR-based early detection technique was developed and confirmed a twofold decrease of health indicators and an up to 10,000-fold increase of disease indicators in beet clamps. This was further verified with analyses of the sugar content in storage samples. Conclusion By conducting a detailed assessment of temporal microbiome changes during the storage of sugar beets, distinct indicator species were identified that reflect progressing rot and losses in sugar content. The insights generated in this study provide a novel basis to improve current or develop next-generation postharvest management techniques by tracking disease indicators during storage. Electronic supplementary material The online version of this article (10.1186/s40168-019-0728-0) contains supplementary material, which is available to authorized users.

Postharvest food decay is one major issue for today’s food loss along the supply chain. Hot water treatment (HWT), a sustainable method to reduce pathogen-induced postharvest fruit decay, has been proven to be effective on a variety of crops. However, the microbiome response to HWT is still unknown, and the role of postharvest microbiota for fruit quality is largely unexplored. To study both, we applied a combined approach of metabarcoding analysis and real time qPCR for microbiome tracking. Overall, HWT was highly effective in reducing rot symptoms on apples under commercial conditions, and induced only slight changes to the fungal microbiota, and insignificantly affected the bacterial community. Pathogen infection, however, significantly decreased the bacterial and fungal diversity, and especially rare taxa were almost eradicated in diseased apples. Here, about 90% of the total fungal community was composed by co-occurring storage pathogens Neofabraea alba and Penicillium expansum. Additionally, the prokaryote to eukaryote ratio, almost balanced in apples before storage, was shifted to 0.6% bacteria and 99.4% fungi in diseased apples, albeit the total bacterial abundance was stable across all samples. Healthy stored apples shared 18 bacterial and 4 fungal taxa that were not found in diseased apples; therefore, defining a health-related postharvest microbiome. In addition, applying a combined approach of HWT and a biological control consortium consisting of Pantoea vagans 14E4, Bacillus amyloliquefaciens 14C9 and Pseudomonas paralactis 6F3, were proven to be efficient in reducing both postharvest pathogens. Our results provide first insights into the microbiome response to HWT, and suggest a combined treatment with biological control agents.

Background Microbiome assembly was identified as an important factor for plant growth and health, but this process is largely unknown, especially for the fruit microbiome. Therefore, we analyzed strawberry plants of two cultivars by focusing on microbiome tracking during the different growth stages and storage using amplicon sequencing, qPCR, and microscopic approaches. Results Strawberry plants carried a highly diverse microbiome, therein the bacterial families Sphingomonadaceae (25%), Pseudomonadaceae (17%), and Burkholderiaceae (11%); and the fungal family Mycosphaerella (45%) were most abundant. All compartments were colonized by high number of bacteria and fungi (107–1010 marker gene copies per g fresh weight), and were characterized by high microbial diversity (6049 and 1501 ASVs); both were higher for the belowground samples than in the phyllosphere. Compartment type was the main driver of microbial diversity, structure, and abundance (bacterial: 45%; fungal: 61%) when compared to the cultivar (1.6%; 2.2%). Microbiome assembly was strongly divided for belowground habitats and the phyllosphere; only a low proportion of the microbiome was transferred from soil via the rhizosphere to the phyllosphere. During fruit development, we observed the highest rates of microbial transfer from leaves and flowers to ripe fruits, where most of the bacteria occured inside the pulp. In postharvest fruits, microbial diversity decreased while the overall abundance increased. Developing postharvest decay caused by Botrytis cinerea decreased the diversity as well, and induced a reduction of potentially beneficial taxa. Conclusion Our findings provide insights into microbiome assembly in strawberry plants and highlight the importance of microbe transfer during fruit development and storage with potential implications for food health and safety.

Sugar beets (Beta vulgaris), which are one of the major sources for sugar, alternative energy, and fuel, are affected by several fungal pathogens at harvest time. In order to identify correlations between the microbiome of field-grown sugar beets and their health status before harvest, we studied 2,200 antifungal antagonists together with 73 amplicon datasets obtained with 16S rRNA gene fragments as well as the fungal internal transcribed spacer region in samples from 13 different field sites in Austria and Germany. Overall, a substantial loss of microbial diversity (bacteriome H’: 8 versus 6.5; mycobiome H’: 4.5 versus 3.5) as well as a substantially different taxonomic composition was observed in root rot-affected sugar beets when compared with healthy beets. The Gram-positive Lactobacillales as well as distinct fungal taxa such as Candida, Penicillium, and Fusarium were identified as indicators of root rot on the microbiome level. In contrast, higher microbial diversity as well as distinct fungal genera assigned to Vishniacozyma and Plectosphaerella were associated with the microbiome of healthy plants. The taxonomic shifts in the fungal microbiome were accompanied by trophic specialization; pathotrophic and symbiotrophic fungi were replaced by saprotrophic fungi in diseased sugar beets. Moreover, samples with high proportions of antagonistic bacteria were not vulnerable to shifts in the fungal microbiome. The overall findings show implications between microbial antagonists and plant health as well as key taxa that are indicative for the health status in beets. They provide the basis for the development of improved disease management systems and preventive counteractions.

Recently, it was shown that long-term plant breeding does not only shape plant characteristics but also impacts plant-associated microbiota substantially. This requires a microbiome-integrative breeding approach, which was not yet shown. Here we investigate this for the Styrian oil pumpkin (Cucurbita pepo L. subsp. pepo var. styriaca Greb.) by analyzing the microbiome of six genotypes (the complete pedigree of a three-way cross-hybrid, consisting of three inbred lines and one open pollinating cultivar) in the seed and rhizosphere as well as the progeny seeds. Using high-throughput amplicon sequencing targeting the 16S rRNA and the ITS1 genes, the bacterial and fungal microbiomes were accessed. Seeds were found to generally carry a significantly lower microbial diversity compared to the rhizosphere and soil as well as a different microbial composition, with an especially high fraction of Enterobacteriaceae (40–83%). Additionally, potential plant-beneficial bacterial taxa, including Bacillaceae, Burkholderiaceae, and Pseudomonadaceae, were found to be enriched in progeny seeds. Between genotypes, more substantial changes can be observed for seed microbiomes compared to the rhizosphere. Moreover, rhizosphere communities were assembled for the most part from soil. Interestingly, bacterial signatures are mainly linked from seed to seed, while fungal communities are shaped by the soil and rhizosphere. Our findings provide a deep look into the rhizosphere and seed microbiome assembly of pumpkin-associated communities and represent the first steps into microbiome-driven breeding for plant-beneficial microbes.