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Lorenz Hiltner is recognized as the first scientist to coin the term \"rhizosphere\" in 1904. His scientific career and achievements are summarized in this essay. Most of his research he performed in the Bavarian Agriculture-Botanical Institute (later named the \"Bavarian Institute of Plant Growth and Plant Protection\") in Munich, where he was the director from 1902 to 1923. Beginning with intensive and thorough investigations on the germination and growth of different crop plants (legumes and nonlegumes) Hiltner became convinced, that root exudates of different plants support the development of different bacterial communities. His definition of the \"rhizosphere\" in the year 1904 centered on the idea, that plant nutrition is considerably influenced by the microbial composition of the rhizosphere. Hiltner observed bacterial cells even inside the rhizodermis of healthy roots. In analogy with fungal root symbionts, Hiltner named the bacterial community that is closely associated with roots \"bacteriorhiza.\" In his rhizosphere concept, Hiltner also envisioned, that beneficial bacteria are not only attracted by the root exudates but that there are also \"uninvited guests,\" that adjust to the specific root exudates. Based on his observations he hypothesized that \"the resistance of plants towards pathogenesis is dependent on the composition of the rhizosphere microflora.\" He even had the idea, that the quality of plant products may be dependent on the composition of the root microflora. In addition to his scientific achievements, Hiltner was very dedicated to applied work. Together with F. Nobbe he had the first patent on Rhizobium inoculants (Nitragin). He continuously improved formulations and the effectivity of the Rhizobium preparations and he also initiated seed dressing with sublimate for plant protection of seedlings. Thus, Hiltner tightly linked breakthroughs in basic research to improved rhizosphere management practices. In addition, he wrote a pioneering monograph on plant protection for everybody's practical use. His emphasis on understanding microbes in the context of their micro-habitat, the rhizosphere, made him a pioneer in microbial ecology. Even now, in the era of genome and postgenome analysis with our better understanding of plant nutrition and soil bacteriology, his ideas and contributions are as fresh as they were more than 100 years ago.

The biological control of plant pathogens is linked to the composition and activity of the plant microbiome. Plant-associated microbiomes co-evolved with land plants, leading to plant holobionts with plant-beneficial microbes but also with plant pathogens. A diverse range of plant-beneficial microbes assists plants to reach their optimal development and growth under both abiotic and biotic stress conditions. Communication within the plant holobiont plays an important role, and besides plant hormonal interactions, quorum-sensing signalling of plant-associated microbes plays a central role. Quorum-sensing (QS) autoinducers, such as N-acyl-homoserine lactones (AHL) of Gram-negative bacteria, cause a pronounced interkingdom signalling effect on plants, provoking priming processes of pathogen defence and insect pest control. However, plant pathogenic bacteria also use QS signalling to optimise their virulence; these QS activities can be controlled by quorum quenching (QQ) and quorum-sensing inhibition (QSI) approaches by accompanying microbes and also by plants. Plant growth-promoting bacteria (PGPB) have also been shown to demonstrate QQ activity. In addition, some PGPB only harbour genes for AHL receptors, so-called luxR-solo genes, which can contribute to plant growth promotion and biological control. The presence of autoinducer solo receptors may reflect ongoing microevolution processes in microbe–plant interactions. Different aspects of QS systems in bacteria–plant interactions of plant-beneficial and pathogenic bacteria will be discussed, and practical applications of bacteria with AHL-producing or -quenching activity; QS signal molecules stimulating pathogen control and plant growth promotion will also be presented.

Climate change is altering the dynamics of crop pests and diseases resulting in reduced crop yields. Using beneficial soil bacterial to increase crop health is a quickly developing area in sustainable agriculture, but it is unknown if climate change or interactions with other species could alter their effect. The plant growth-promoting rhizobacterium Acidovorax radicis N35 is known to increase barley ( Hordeum vulgare ) plant growth under laboratory conditions, and we tested the stability of the plant-bacterial interactions when exposed to elevated carbon dioxide (CO2) and ozone (O3) levels while infesting the aboveground leaves with cereal aphids ( Sitobion avenae ) and the soil with beneficial earthworms. Acidovorax radicis N35 increased plant growth and reduced insect growth – with greatest effect in a high-stress elevated O3 environment, but reduced effects under elevated CO2. Earthworms promoted both plant and insect growth, but inoculation with A. radicis N35 alleviated some of the earthworm-mediated increase in pest abundance, particularly in the ambient environment. The consistency of these beneficial effects highlights the potential of exploiting local species interactions for predicting and mitigating climate change effects in managed systems. We conclude that microbial bioprotectants have high potential for benefiting agriculture via plant-growth promotion and pest suppression.

Pollen allergies have been rapidly increasing over the last decades. Many allergenic proteins and non-allergenic adjuvant compounds of pollen are involved in the plant defense against environmental or microbial stress. The first aim of this study was to analyze and compare the colonizing microbes on allergenic pollen. The second aim was to investigate detectable correlations between pollen microbiota and parameters of air pollution or pollen allergenicity. To reach these aims, bacterial and fungal DNA was isolated from pollen samples of timothy grass (Phleum pratense, n = 20) and birch trees (Betula pendula, n = 55). With this isolated DNA, a terminal restriction fragment length polymorphism analysis was performed. One result was that the microbial diversity on birch tree and timothy grass pollen samples (Shannon/Simpson diversity indices) was partly significantly correlated to allergenicity parameters (Bet v 1/Phl p 5, pollen-associated lipid mediators). Furthermore, the microbial diversity on birch pollen samples was correlated to on-site air pollution (nitrogen dioxide (NO2), ammonia (NH3), and ozone (O3)). What is more, a significant negative correlation was observed between the microbial diversity on birch pollen and the measured NO2 concentrations on the corresponding trees. Our results showed that the microbial composition of pollen was correlated to environmental exposure parameters alongside with a differential expression of allergen and pollen-associated lipid mediators. This might translate into altered allergenicity of pollen due to environmental and microbial stress.

Caries is associated with shifts of microbiota in dental biofilms and primarily driven by frequent sucrose consumption. Data on environmentally induced in vivo microbiota shifts are scarce therefore we investigated the influence of frequent sucrose consumption on the oral biofilm. Splint systems containing enamel slabs were worn for 3 × 7 days with 7-day intervals to obtain oral biofilm samples. After a three-month dietary change of sucking 10 g of sucrose per day in addition to the regular diet, biofilm was obtained again at the end of the second phase. The microbiota was analysed using Illumina MiSeq amplicon sequencing (v1-v2 region). In addition, roughness of the enamel surface was measured with laser scanning microscopy. The sucrose phase resulted in significant differences in beta-diversity and significantly decreased species richness. It was marked by a significant increase in abundance of streptococci, specifically Streptococcus gordonii , Streptococcus parasanguinis and Streptococcus sanguinis . Enamel surface roughness began to increase, reflecting initial impairment of dental enamel surface. The results showed that frequent sucrose consumption provoked compositional changes in the microbiota, leading to an increase of non-mutans streptococci, hence supporting the extended ecological plaque hypothesis and emphasizing the synergy of multiple bacterial species in the development of caries.

The Alphaproteobacterium Rhizobium radiobacter F4 ( Rr F4) was originally characterized as an endofungal bacterium in the beneficial endophytic Sebacinalean fungus Piriformospora indica . Although attempts to cure P. indica from Rr F4 repeatedly failed, the bacterium can easily be grown in pure culture. Here, we report on Rr F4’s genome and the beneficial impact the free-living bacterium has on plants. In contrast to other endofungal bacteria, the genome size of Rr F4 is not reduced. Instead, it shows a high degree of similarity to the plant pathogenic R. radiobacter (formerly: Agrobacterium tumefaciens ) C58, except vibrant differences in both the tumor-inducing (pTi) and the accessor (pAt) plasmids, which can explain the loss of Rr F4’s pathogenicity. Similar to its fungal host, Rr F4 colonizes plant roots without host preference and forms aggregates of attached cells and dense biofilms at the root surface of maturation zones. Rr F4-colonized plants show increased biomass and enhanced resistance against bacterial leaf pathogens. Mutational analysis showed that, similar to P. indica , resistance mediated by Rr F4 was dependent on the plant’s jasmonate-based induced systemic resistance (ISR) pathway. Consistent with this, Rr F4- and P. indica -induced pattern of defense gene expression were similar. In clear contrast to P. indica , but similar to plant growth-promoting rhizobacteria, Rr F4 colonized not only the root outer cortex but also spread beyond the endodermis into the stele. On the basis of our findings, Rr F4 is an efficient plant growth-promoting bacterium.

A combinatory approach using metabolomics and gut microbiome analysis techniques was performed to unravel the nature and specificity of metabolic profiles related to gut ecology in obesity. This study focused on gut and liver metabolomics of two different mouse strains, the C57BL/6J (C57J) and the C57BL/6N (C57N) fed with high-fat diet (HFD) for 3 weeks, causing diet-induced obesity in C57N, but not in C57J mice. Furthermore, a 16S-ribosomal RNA comparative sequence analysis using 454 pyrosequencing detected significant differences between the microbiome of the two strains on phylum level for Firmicutes , Deferribacteres and Proteobacteria that propose an essential role of the microbiome in obesity susceptibility. Gut microbial and liver metabolomics were followed by a combinatory approach using Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) and ultra performance liquid chromatography time of tlight MS/MS with subsequent multivariate statistical analysis, revealing distinctive host and microbial metabolome patterns between the C57J and the C57N strain. Many taurine-conjugated bile acids (TBAs) were significantly elevated in the cecum and decreased in liver samples from the C57J phenotype likely displaying different energy utilization behavior by the bacterial community and the host. Furthermore, several metabolite groups could specifically be associated with the C57N phenotype involving fatty acids, eicosanoids and urobilinoids. The mass differences based metabolite network approach enabled to extend the range of known metabolites to important bile acids (BAs) and novel taurine conjugates specific for both strains. In summary, our study showed clear alterations of the metabolome in the gastrointestinal tract and liver within a HFD-induced obesity mouse model in relation to the host–microbial nutritional adaptation.

Quorum sensing auto-inducers of the -acyl homoserine lactone (AHL) type produced by Gram-negative bacteria have different effects on plants including stimulation on root growth and/or priming or acquirement of systemic resistance in plants. In this communication the influence of AHL production of the plant growth promoting endophytic rhizosphere bacterium N35 on barley seedlings was investigated. N35 produces 3-hydroxy-C10-homoserine lactone (3-OH-C10-HSL) as the major AHL compound. To study the influence of this QS autoinducer on the interaction with barley, the -biosynthesis gene was deleted. The comparison of inoculation effects of the N35 wild type and the mutant resulted in remarkable differences. While the N35 wild type colonized plant roots effectively in microcolonies, the mutant occurred at the root surface as single cells. Furthermore, in a mixed inoculum the wild type was much more prevalent in colonization than the mutant documenting that the mutation affected root colonization. Nevertheless, a significant plant growth promoting effect could be shown after inoculation of barley with the wild type and the mutant in soil after 2 months cultivation. While N35 wild type showed only a very weak induction of early defense responses in plant RNA expression analysis, the mutant caused increased expression of flavonoid biosynthesis genes. This was corroborated by the accumulation of several flavonoid compounds such as saponarin and lutonarin in leaves of root inoculated barley seedlings. Thus, although the exact role of the flavonoids in this plant response is not clear yet, it can be concluded, that the synthesis of AHLs by has implications on the perception by the host plant barley and thereby contributes to the establishment and function of the bacteria-plant interaction.

Background Improving drought tolerance of tree seedlings by plant growth-promoting microorganisms (PGPMs) is a promising approach for nature-based forest restoration. Identifying suitable microorganisms requires a robust selection, including efficient in planta screenings. Results We sampled at two forest sites in southern Germany with drought legacies and within a dry period to enhance the probability of isolating drought-tolerant microbes. Metabarcoding of the resident soil community revealed a broad on-site diversity with the potential for diverse plant growth-promoting and stress-resistance traits. We isolated 1,292 bacteria and 59 fungi from fine roots of Norway spruce and European beech. 429 isolates were identified to the Genus level. The most abundant genera were Paraburkholderia (121) and Bacillus (43) in bacteria and Penicillium (8) and Umbelopsis (8) in fungi. Isolates were scored in vitro for abiotic stress tolerance and plant growth-promoting traits, revealing diverse plant growth-promoting abilities for 31 bacteria and a particularly high stress tolerance for 8 fungi. Importantly, an axenic 24-well plate system was developed to investigate the influence of bacteria on spruce seedlings under drought conditions. The system allowed direct comparison of inoculation effects on seedling growth and survival with or without drought application. Six bacterial strains significantly promoted plant growth under well-watered conditions, while two bacterial strains improved survival and root length under drought. Conclusions This study represents one of the first larger scale screenings for PGPMs isolated from forest soils on tree seedlings under drought and may contribute to finding nature-based drought mitigation strategies.