Friederike Trognitz

Metabolic potential of endophytic bacteria

Graphical abstract

Advances in Elucidating Beneficial Interactions Between Plants, Soil, and Bacteria

Abstract Survival of every organism on earth depends on its interactions with other organisms. For example, animals form associations with the intestinal microflora, while plants develop symbiotic associations with neighboring plants, microflora, and microfauna. Most of the associations between plants and microorganisms are mediated by organic compounds released by the plant. The plant root system acts as a factory and exudes enormous amount of chemicals to effectively communicate with the surrounding soil organisms. Bacteria on roots and in the rhizosphere can also utilize these organic compounds as a source of nutrients and enhance their population size and metabolic activities. In return, plant-associated bacteria improve plant growth and development by different mechanisms including nitrogen fixation, provision of nutrients, and mediating resistance against pathogens. Although plant–bacterial partnerships have been found effective to enhance biomass production, their importance and relevance in agricultural systems are still underestimated. A better understanding of beneficial interactions between plant, soil, and bacteria could be exploited to improve growth and health of food and feed crops. Plant growth-promoting mechanisms of bacteria might enhance biomass production in a more sustainable manner, even on marginal land. Furthermore, plant growth-promoting and/or pollutant-degrading activities of bacteria could be exploited to improve the efficiency of phytoremediation of organic and inorganic pollutants from the soil and water or to protect the food chain by decreasing the concentrations of pollutants in food crops.

Ecology and Genomic Insights into Plant-Pathogenic and Plant-Nonpathogenic Endophytes

Plants are colonized on their surfaces and in the rhizosphere and phyllosphere by a multitude of different microorganisms and are inhabited internally by endophytes. Most endophytes act as commensals without any known effect on their plant host, but multiple bacteria and fungi establish a mutualistic relationship with plants, and some act as pathogens. The outcome of these plant-microbe interactions depends on biotic and abiotic environmental factors and on the genotype of the host and the interacting microorganism. In addition, endophytic microbiota and the manifold interactions between members, including pathogens, have a profound influence on the function of the system plant and the development of pathobiomes. In this review, we elaborate on the differences and similarities between nonpathogenic and pathogenic endophytes in terms of host plant response, colonization strategy, and genome content. We furthermore discuss environmental effects and biotic interactions within plant microbiota that influence pathogenesis and the pathobiome.

Transcriptome Profiling of the Endophyte Burkholderia phytofirmans PsJN Indicates Sensing of the Plant Environment and Drought Stress

ABSTRACT It is widely accepted that bacterial endophytes actively colonize plants, interact with their host, and frequently show beneficial effects on plant growth and health. However, the mechanisms of plant-endophyte communication and bacterial adaption to the plant environment are still poorly understood. Here, whole-transcriptome sequencing of B. phytofirmans PsJN colonizing potato (Solanum tuberosum L.) plants was used to analyze in planta gene activity and the response of strain PsJN to plant stress. The transcriptome of PsJN colonizing in vitro potato plants showed a broad array of functionalities encoded in the genome of strain PsJN. Transcripts upregulated in response to plant drought stress were mainly involved in transcriptional regulation, cellular homeostasis, and the detoxification of reactive oxygen species, indicating an oxidative stress response in PsJN. Genes with modulated expression included genes for extracytoplasmatic function (ECF) group IV sigma factors. These cell surface signaling elements allow bacteria to sense changing environmental conditions and to adjust their metabolism accordingly. TaqMan quantitative PCR (TaqMan-qPCR) was performed to identify ECF sigma factors in PsJN that were activated in response to plant stress. Six ECF sigma factor genes were expressed in PsJN colonizing potato plants. The expression of one ECF sigma factor was upregulated whereas that of another one was downregulated in a plant genotype-specific manner when the plants were stressed. Collectively, our study results indicate that endophytic B. phytofirmans PsJN cells are active inside plants. Moreover, the activity of strain PsJN is affected by plant drought stress; it senses plant stress signals and adjusts its gene expression accordingly. IMPORTANCE In recent years, plant growth-promoting endophytes have received steadily growing interest as an inexpensive alternative to resource-consuming agrochemicals in sustainable agriculture. Even though promising effects are recurrently observed under controlled conditions, these are rarely reproducible in the field or show undesirably strong variations. Obviously, a better understanding of endophyte activities in plants and the influence of plant physiology on these activities is needed to develop more-successful application strategies. So far, research has focused mainly on analyzing the plant response to bacterial inoculants. This prompted us to study the gene expression of the endophyte Burkholderia phytofirmans PsJN in potato plants. We found that endophytic PsJN cells express a wide array of genes and pathways, pointing to high metabolic activity inside plants. Moreover, the strain senses changes in the plant physiology due to plant stress and adjusts its gene expression pattern to cope with and adapt to the altered conditions. In recent years, plant growth-promoting endophytes have received steadily growing interest as an inexpensive alternative to resource-consuming agrochemicals in sustainable agriculture. Even though promising effects are recurrently observed under controlled conditions, these are rarely reproducible in the field or show undesirably strong variations. Obviously, a better understanding of endophyte activities in plants and the influence of plant physiology on these activities is needed to develop more-successful application strategies. So far, research has focused mainly on analyzing the plant response to bacterial inoculants. This prompted us to study the gene expression of the endophyte Burkholderia phytofirmans PsJN in potato plants. We found that endophytic PsJN cells express a wide array of genes and pathways, pointing to high metabolic activity inside plants. Moreover, the strain senses changes in the plant physiology due to plant stress and adjusts its gene expression pattern to cope with and adapt to the altered conditions.

Multi-laboratory evaluation of the rapid genoserotyping array (SGSA) for the identification of Salmonella serovars

Salmonella serotyping is an essential first step for identification of isolates associated with disease outbreaks. The Salmonella genoserotyping array (SGSA) is a microarray-based alternative to standard serotyping designed to rapidly identify 57 of the most commonly reported serovars through detection of the genes encoding surface O and H antigens and reporting the corresponding serovar in accordance with the existing White-Kaufmann-Le Minor serotyping scheme. In this study, we evaluated the SGSA at 4 laboratories in 3 countries by testing 1874 isolates from human and non-human sources. The SGSA correctly identified 96.7% of isolates from the target 57 serovars. For the prevalent and clinically important Salmonella serovars Enteritidis and Typhimurium, test specificity and sensitivity were greater than 98% and 99%, respectively. Due to its high-throughput nature, the SGSA is a rapid and cost-effective alternative to standard serotyping for identifying the most prevalent serovars of Salmonella.

High-Quality Draft Genome Sequence of an Endophytic Pseudomonas viridiflava Strain with Herbicidal Properties against Its Host, the Weed Lepidium draba L.

ABSTRACT Here, we report the draft genome sequence of Pseudomonas viridiflava strain CDRTc14 a pectinolytic bacterium showing herbicidal activity, isolated from the root of Lepidium draba L. growing as a weed in an Austrian vineyard. The availability of this genome sequence allows us to investigate the genetic basis of plant–microbe interactions.

Comparative genome analysis of the vineyard weed endophyte Pseudomonas viridiflava CDRTc14 showing selective herbicidal activity

Microbes produce a variety of secondary metabolites to be explored for herbicidal activities. We investigated an endophyte Pseudomonas viridiflava CDRTc14, which impacted growth of its host Lepidium draba L., to better understand the possible genetic determinants for herbicidal and host-interaction traits. Inoculation tests with a variety of target plants revealed that CDRTc14 shows plant-specific effects ranging from beneficial to negative. Its herbicidal effect appeared to be dose-dependent and resembled phenotypically the germination arrest factor of Pseudomonas fluorescens WH6. CDRTc14 shares 183 genes with the herbicidal strain WH6 but the formylaminooxyvinylglycine (FVG) biosynthetic genes responsible for germination arrest of WH6 was not detected. CDRTc14 showed phosphate solubilizing ability, indole acetic acid and siderophores production in vitro and harbors genes for these functions. Moreover, genes for quorum sensing, hydrogen cyanide and ACC deaminase production were also found in this strain. Although, CDRTc14 is related to plant pathogens, we neither found a complete pathogenicity island in the genome, nor pathogenicity symptoms on susceptible plant species upon CDRTc14 inoculation. Comparison with other related genomes showed several unique genes involved in abiotic stress tolerance in CDRTc14 like genes responsible for heavy metal and herbicide resistance indicating recent adaptation to plant protection measures applied in vineyards.

Nutzung von Rhizobakterien und Endophyten zur biologischen Bekämpfung von Unkräutern und Ungräsern

Weeds cause severe yield losses in agriculture, with a maximum estimate of 34% of yield loss worldwide due to competition between the crops and the weeds for nutrition, light and humidity (OERKE, 2006). Invasive plants contribute partially to other problems. The pollen of common ragweed, Ambrosia artemisiifolia L., for example, is five times more allergenic than grass pollen; already ten pollen grains per m3 air can trigger allergy in sensitized patients, including rhinitis, conjunctivitis and asthma. This neophyte from America has extended the season of allergy in European patients to October. Common ragweed is currently most frequent in Hungary, France and Italy. In Austria, ragweed populations along roads have increased dramatically since 2000. The effective means to control this weed of the Asteraceae family are limited; a single plant can produce up to 6000 seeds which stay in the soil for 40 years. Control using selective herbicides is not possible within stands of the Asteraceae member sunflower. Efforts to use herbivore insects as biological control agents also failed due to the unavailability of insects specializing on this ragweed. The use of plant-associated rhizobacteria and endophytes as bio-herbicides offers a novel alternative to conventional methods. By analogy to experiences from other plant-microbe systems, the chances to find microbes of the desired characteristics are highest when isolating and testing specimens directly from ragweed plants. These organisms often have an extremely narrow host range that permits their use for the control of among several even closely related plant species growing together in a field.