Rhizobium and Phyllobacterium bacterial inoculants increase bioactive compounds and quality of strawberries cultivated in field conditions

Diversity and functional features of the root-associated bacteriome are dependent on grapevine susceptibility to Plasmopara viticola

BACKGROUND

Plant health depends on beneficial interactions between the roots and their microbiomes. Despite recent progress on the role of the grapevine microbiome, the taxonomic identity and functional traits of microbial taxa specific to healthy or Plasmopara viticola-diseased plants, as well as to the susceptible or resistant cultivar are unknown. Using metabarcoding and shotgun metagenomics sequencing, we investigated the effect of downy mildew on the root-associated microbiome (rhizospheric soil, rhizoplane and endosphere) of 41B-grafted susceptible cultivar (Chardonnay) and resistant interspecific hybrid (Voltis) at flowering and veraison stages. The impact of conventional treatment on the rhizomicrobiome assembly of Chardonnay was also evaluated.

RESULTS

Analyses revealed a core bacteriome shared between both susceptible and resistant cultivars. This also highlighted common functional traits between the rhizosphere and rhizoplane bacteriomes in both cultivars. A dysbiosis state was also evidenced by a loss of beneficial communities in the rhizosphere of the P. viticola-infected cultivar. Microbial genome assemblies showed functional differences between healthy and diseased plants, with a loss of Pseudomonas and Phyllobacterium taxa at veraison. This state was mainly characterized by a loss of genes involved in polyamine transport and metabolism in the susceptible cultivar. It was also marked by an increase in population evenness and total bacterial diversity, and the presence of pathogenic species in susceptible plants.

CONCLUSIONS

This study reveals distinct and overlapping bacterial communities and functional genes in the rhizospheric soil, rhizoplane and root endosphere of both susceptible and resistant grapevine cultivars to downy mildew. Microbial diversity and abundant taxa of grapevine roots are influenced by downy mildew and cultivar susceptibility. Common bacterial functions are shared among rhizocompartments of susceptible and resistant cultivars, revealing a dysbiosis state and functional signatures related to plant immunity, especially in the infected-susceptible plants.

Effect of microbial biostimulants on the antioxidant profile, antioxidant capacity and activity of enzymes influencing the quality level of raspberries (Rubus idaeus L.)

The influence of four microbial biostimulants containing various strains of Bacillus subtilis and/or Paenibacillus sp. on the quality of raspberries cv. Delniwa, Poemat, and Enrosadira cultivated in two consecutive seasons was investigated. The biostimulants influenced the antioxidant level, antioxidant capacity, phenolic acids and flavonoids profiles, enzymatic activity, and the degree of methylation and acetylation of the pectin in the raspberry fruits. The biostimulants had the greatest effect on the antioxidant content (16% - 20% increase) and capacity in the Delniwa raspberry fruits from the first season. A positive correlation was found between the activity of the β-galactosidase enzyme and ferric reducing power. In the second season, a decrease in the activity of pectin esterase and α-L-arabinofuranosidase and an increase in the degree of methylation of pectin were noted. Our results suggest that the changes in raspberry quality were related to the type of biostimulant applied.

Dynamic changes of endophytic bacteria in the bark and leaves of medicinal plant Eucommia ulmoides in different seasons

The bark and leaves of the Eucommia ulmoides Oliv. (E. ulmoides) have good medicinal value. Studies show endophytes play important roles in host medicinal plant secondary metabolite synthesis, with season being a key influencing factor. Therefore, we used 16 S rRNA to detect endophytic bacteria (EB) in E. ulmoides bark and leaves collected in winter, spring, summer, and autumn, and analyzed the contents of major active components respectively. The results showed that the species diversity and richness of EB of the E. ulmoides bark were higher than those of leaves in all seasons except fall. Among them, the higher species diversity and richness were found in the E. ulmoides bark in winter and spring. EB community structure differed significantly between medicinal tissues and seasons. Concurrently, the bark and leaves of E. ulmoides showed abundant characteristic EB across seasons. For active components, geniposidic acid showed a significant positive correlation with EB diversity and richness, while the opposite was true for aucubin. Additionally, some dominant EB exhibited close correlations with the accumulation of active components. Delftia, enriched in autumn, correlated significantly positively with aucubin. Notably, the impact of the same EB genera on active components differed across medicinal tissues. For example, Sphingomonas, enriched in summer, correlated significantly positively with pinoresinol diglucoside (PDG) in the bark, but with aucubin in the leaves. In summary, EB of E. ulmoides was demonstrated high seasonal dynamics and tissue specificity, with seasonal characteristic EB like Delftia and Sphingomonas correlating with the accumulation of active components in medicinal tissues.

Differential response of blueberry to the application of bacterial inoculants to improve yield, organoleptic qualities and concentration of bioactive compounds

The application of bacterial biofortifiers is an increasingly common technique. In recent years, some strains have been shown to improve the nutraceutical qualities of crops. This work analyses the impact of biofortification with 3 bacterial strains of the genera Rhizobium, Paenibacillus and Lactiplantibacillus on the nutritional characteristics and organic composition of blueberry in Portugal. Paenibacillus sp. VMFR46 treatment showed increase of 71.36 % and 79.88 % in total production. Biofortified treatments were able to increase Brix degree, maturity index (up to 48.05 % for cv. Legacy and up to 26.04 % for cv. Duke) and CIEL*a*b* index respect to uninoculated control. In this way, (poly)phenolic compounds concentration increased in biofortified treatment, and their (poly)phenolic profile was modified, some compounds such as myricetin aglycone or myricetin derivative are exclusive of the fruits from biofortified plants, with increases in (poly)phenolic concentrations related with R. laguerreae PEPV16 or Paenibacillus sp. VMFR46 inoculation in cv. Legacy. These modifications resulted in the improvement of the nutraceutical characteristics of the fruits obtained.

Schizotrophic Sclerotinia sclerotiorum-Mediated Root and Rhizosphere Microbiome Alterations Activate Growth and Disease Resistance in Wheat

Sclerotinia sclerotiorum, a widespread pathogen of dicotyledons, can grow endophytically in wheat, providing protection against Fusarium head blight and stripe rust and enhancing wheat yield. In this study, we found that wheat seed treatment with strain DT-8, infected with S. sclerotiorum hypovirulence-associated DNA virus 1 (SsHADV-1) and used as a "plant vaccine" for brassica protection, could significantly increase the diversity of the fungal and bacterial community in rhizosphere soil, while the diversity of the fungal community was obviously decreased in the wheat root. Interestingly, the relative abundance of potential plant growth-promoting rhizobacteria (PGPR) and biocontrol agents increased significantly in the DT-8-treated wheat rhizosphere soil. These data might be responsible for wheat growth promotion and disease resistance. These results may provide novel insights for understanding the interaction between the schizotrophic microorganism and the microbiota of plant roots and rhizosphere, screening and utilizing beneficial microorganisms, and further reducing chemical pesticide utilization and increasing crop productivity. IMPORTANCE Fungal pathogens are seriously threatening food security and natural ecosystems; efficient and environmentally friendly control methods are essential to increase world crop production. S. sclerotiorum, a widespread pathogen of dicotyledons, can grow endophytically in wheat, providing protection against Fusarium head blight and stripe rust and enhancing wheat yield. In this study, we discovered that S. sclerotiorum treatment increased the diversity of the soil fungal and bacterial community in rhizosphere soil, while the diversity of the fungal community was obviously decreased in the wheat root. More importantly, the relative abundance of potential PGPR and bio-control agents increased significantly in the S. sclerotiorum-treated wheat rhizosphere soil. The importance of this work is that schizotrophic S. sclerotiorum promotes wheat growth and enhances resistance against fungal diseases via changes in the structure of the root and rhizosphere microbiome.

The Friend Within: Endophytic Bacteria as a Tool for Sustainability in Strawberry Crops

Strawberry (Fragaria x ananassa, Duch.) is an important crop worldwide. However, since it is a highly demanding crop in terms of the chemical conditions of the substrate, a large part of strawberry production implies the application of large amounts of fertilizers in the production fields. This practice can cause environmental problems, in addition to increases in the fruit's production costs. In this context, applying plant growth-promoting bacteria in production fields can be an essential strategy, especially thanks to their ability to stimulate plant growth via different mechanisms. Therefore, this study aimed to test in vitro and in vivo the potential of bacteria isolated from strawberry leaves and roots to directly promote plant growth. The isolates were tested in vitro for their ability to produce auxins, solubilize phosphate and fix nitrogen. Isolates selected in vitro were tested on strawberry plants to promote plant growth and increase the accumulation of nitrogen and phosphorus in the leaves. The tested isolates showed an effect on plant growth according to biometric parameters. Among the tested isolates, more expressive results for the studied variables were observed with the inoculation of the isolate MET12M2, belonging to the species Brevibacillus fluminis. In general, bacterial inoculation induced strain-dependent effects on strawberry growth. In vitro and in vivo assays showed the potential use of the B. fluminis MET12M2 isolate as a growth promoter for strawberries.

The Composition of Root-Associated Bacteria and Fungi of Astragalus mongholicus and Their Relationship With the Bioactive Ingredients

Astragalus membranaceus (Fisch.) Bge. var. mongholicus, which is used in traditional Chinese medicine, contains several bioactive ingredients. The root-associated microbial communities play a crucial role in the production of secondary metabolites in plants. However, the correlation of root-associated bacteria and fungi with the bioactive ingredients production in A. mongholicus has not been elucidated. This study aimed to examine the changes in soil properties, root bioactive ingredients, and microbial communities in different cultivation years. The root-associated bacterial and fungal composition was analyzed using high-throughput sequencing. The correlation between root-associated bacteria and fungi, soil properties, and six major bioactive ingredients were examined using multivariate correlation analysis. Results showed that soil properties and bioactive ingredients were distinct across different cultivation years. The composition of the rhizosphere microbiome was different from that of the root endosphere microbiome. The bacterial community structure was affected by the cultivation year and exhibited a time-decay pattern. Soil properties affected the fungal community composition. It was found that 18 root-associated bacterial operational taxonomic units (OTUs) and four fungal OTUs were positively and negatively correlated with bioactive ingredient content, respectively. The abundance of Stenotrophomonas in the rhizosphere was positively correlated with astragaloside content. Phyllobacterium and Inquilinus in the endosphere were positively correlated with the calycosin content. In summary, this study provided a new opportunity and theoretical reference for improving the production and quality of in A. mongholicus, which thus increase the pharmacological value of A. mongholicus.

Complex microbial communities inhabiting natural Cordyceps militaris and the habitat soil and their predicted functions

Cordyceps militaris is a traditional Chinese medicinal food that is challenging to quality maintaining while mass cultivation. Many studies have found that abundant microbes inhabit Ophiocordyceps sinensis and perform important functions for their host. In this study, our objective was to reveal the microbial communities that inhabit C. militaris and analyze their potential functions. High-throughput sequencing of 16S rRNA and ITS genes was used to compare the diversity and composition of the bacterial and fungal communities associated with naturally occurring C. militaris collected from Yunnan Province, southwestern China. The diversity and richness of the microbial communities and the number of function genes of the bacteria were significantly higher in the habitat soil than in the fruiting body. The sclerotia and stromata samples shared the same microbiota and functions. The main bacterial phyla were Proteobacteria, Acidobacteria, Bacteroidetes and Actinobacteria, and Ascomycota was the main fungal phylum. The growth-promoting bacteria Herbaspirillum and the plant probiotic Phyllobacterium, which may enhance C. militaris quality and facilitate its cultivation, were detected in the fruiting body samples. Genes related to metabolism were more abundant in the soil bacteria, while membrane transport genes were more abundant in the endophytic bacteria of C. militaris. Our study is the first to reveal the unexpectedly high diversity of the microbial communities and the bacterial functions inhabiting the natural C. militaris using high-throughput sequencing, and our results provide insights into mining the functions of microorganisms in the development and quality of C. militaris.

Rhizobium laguerreae Improves Productivity and Phenolic Compound Content of Lettuce (Lactuca sativa L.) under Saline Stress Conditions

Lettuce (Lactuca sativa L.) is a widely consumed horticultural species. Its significance lies in a high polyphenolic compound content, including phenolic acids and flavonols. In this work, we have probed the ability of Rhizobium laguerreae HUTR05 to promote lettuce growth, under in vitro and greenhouse conditions (both non-saline and saline conditions). This strain has shown several in vitro plant growth promotion mechanisms, as well as capacity to colonize lettuce seedlings roots. We have analyzed the effect of the rhizobacterium inoculation on mineral and bioactive compounds in lettuce, under greenhouse conditions, and found a rise in the content of certain phenolic acids and flavonoids, such as derivatives of caffeoyl acid and quercetin. The genome analysis of the strain has shown the presence of genes related to plant growth-promoting rhizobacteria (PGPR) mechanisms, defense from saline stress, and phenolic compound metabolism (such as naringenin-chalcone synthase or phenylalanine aminotransferase).

Increase in phenolic compounds of Coriandrum sativum L. after the application of a Bacillus halotolerans biofertilizer

BACKGROUND

There is an urgent need for a new sustainable way of satisfying the increasing demand for food worldwide. One of the main challenges is replacing chemical fertilizers with biofertilizers, which include plant root-associated beneficial microorganisms. The present study reports, for the first time, the effects of SCCPVE07 bacterial strain with respect to improving not only plant development, but also the nutritional content and bioactive compounds content of Coriandrum sativum L., one of the most economically important crops, even for plant growth under salinity stress.

RESULTS

Innoculated coriander plants (C. sativum L.) showed an increase in potassium, carbon, calcium and iron content. A significant improvement in phenolic compounds contents was also observed. The contents of 5-O-caffeoylquinic acid, cinnamic acid, 4-methoxy-cinnamic acid hexoside, K-3-O rutinoside, Q-3-O-rutinoside, Q-3-O-glucoside and Q-3-O-glucuronide were significantly enhanced. Moreover, an efficient bacterial root colonization and a noted growth promotion were demonstrated. Bacterial genome was sequenced and analysed. Gene coding related to Plant growth promotion (PGP) mechanisms and proteins involved in plant defence from salinity or in the metabolism of phenolic compounds, such as quercetin 2,3-dioxygenase and phenolic acid decarboxylase, were identified.

CONCLUSION

The results obtained in the present study show, for the first time, the beneficial effects of the inoculation of a bacterial Bacillus halotolerans biofertilizer on coriander crops with respect to increasing the content in bioactive compounds and plant development. © 2020 Society of Chemical Industry.

Is the Application of Plant Probiotic Bacterial Consortia Always Beneficial for Plants? Exploring Synergies between Rhizobial and Non-Rhizobial Bacteria and Their Effects on Agro-Economically Valuable Crops

The overgrowth of human population and the demand for high-quality foods necessitate the search for sustainable alternatives to increase crop production. The use of biofertilizers, mostly based on plant probiotic bacteria (PPB), represents a reliable and eco-friendly solution. This heterogeneous group of bacteria possesses many features with positive effects on plants; however, how these bacteria with each other and with the environment when released into a field has still barely been studied. In this review, we focused on the diversity of root endophytic rhizobial and non-rhizobial bacteria existing within plant root tissues, and also on their potential applications as consortia exerting benefits for plants and the environment. We demonstrated the benefits of using bacterial inoculant consortia instead of single-strain inoculants. We then critically discussed several considerations that farmers, companies, governments, and the scientific community should take into account when a biofertilizer based on those PPBs is proposed, including (i) a proper taxonomic identification, (ii) the characterization of the beneficial features of PPB strains, and (iii) the ecological impacts on plants, environment, and plant/soil microbiomes. Overall, the success of a PPB consortium depends on many factors that must be considered and analyzed before its application as a biofertilizer in an agricultural system.

Microbial inoculants: reviewing the past, discussing the present and previewing an outstanding future for the use of beneficial bacteria in agriculture

More than one hundred years have passed since the development of the first microbial inoculant for plants. Nowadays, the use of microbial inoculants in agriculture is spread worldwide for different crops and carrying different microorganisms. In the last decades, impressive progress has been achieved in the production, commercialization and use of inoculants. Nowadays, farmers are more receptive to the use of inoculants mainly because high-quality products and multi-purpose elite strains are available at the market, improving yields at low cost in comparison to chemical fertilizers. In the context of a more sustainable agriculture, microbial inoculants also help to mitigate environmental impacts caused by agrochemicals. Challenges rely on the production of microbial inoculants for a broader range of crops, and the expansion of the inoculated area worldwide, in addition to the search for innovative microbial solutions in areas subjected to increasing episodes of environmental stresses. In this review, we explore the world market for inoculants, showing which bacteria are prominent as inoculants in different countries, and we discuss the main research strategies that might contribute to improve the use of microbial inoculants in agriculture.