Human pathogenic bacteria on plants

Obst und Gemüse wirken sich positiv auf die Gesundheit aus. Dazu tragen auch die mit Pflanzen assoziierten Mikro­organismen bei. Allerdings kann Obst oder Gemüse, wenn es mit humanpathogenen Keimen kontaminiert ist und roh verzehrt wird, auch Lebensmittelvergiftungen verursachen. In diesem Übersichtsartikel zeigen wir anhand einer Literaturstudie, wie humanpathogene Stämme von Escherichia coli oder Salmonella enterica auf Obst und Gemüse gelangen können und dass ein kom­plexes Zusammenspiel verschiedener biotischer und abiotischer Faktoren ihr Überleben im Boden und auf Pflanzen beeinflusst. Insbesondere mobile genetische Elemente, die durch horizontalen Gentransfer erhalten werden, tragen zur Diversität der pathogenen Eigenschaften, aber auch zur Anpassung an Habitate außerhalb des Darms bei. Wichtig für die erfolgreiche Etablierung von Humanpathogenen an der Pflanze ist deren Anhaftung und Aufnahme sowie die Reak­tion der Pflanze. Die komplexe Interaktion von Human­pathogenen und Pflanze wird wesentlich durch die genetische Ausstattung des Humanpathogens, vom Pflanzengenotyp und -mikrobiom, aber auch von einer Vielzahl von Umweltfaktoren bestimmt. Für das Überleben von Humanpathogenen ist insbesondere die Verfügbarkeit von Nährstoffen kritisch, um die sie mit der natürlichen Mikroflora konkurrieren.Empfehlungen für die Praxis setzen ein besseres Verständnis der Ökologie von Humanpathogenen im Boden und an Pflanzen, aber auch entlang der Produktkette voraus. Dafür sind die Entwicklung und Nutzung empfindlicher und spezifischer Nachweistechniken, die sowohl die mögliche Diversifizierung der Humanpathogene durch horizontalen Gentransfer als auch das Problem der Nichtkultivierbarkeit berücksichtigen, besonders dringlich. DOI: 10.5073/JfK.2015.09.01, https://doi.org/10.5073/JfK.2015.09.01Fruits and vegetables are beneficial for human health. A major contribution to this comes from the microorganisms associated with them. However, fruits and vegetables may cause food poisoning, when contaminated with human pathogens and eaten raw. In our review, based on a lite­rature survey, we show insights into the entry of Escherichia coli or Salmonella enterica into the fruit and vegetable environment via diverse routes and the complex interactions between various bio­tic and abiotic factors, which influence the survival of human pathogens in soil and on plants. In particular, mobile genetic elements acquired through horizontal gene transfer contri­bute to the diversity of pathogenic strains and to their adaptation to extra-intestinal habitats. For a successful establishment of human pathogens on plants, the attachment, internalization and the response of the plant are important. Mainly the genetic equipment of the human pathogen, the plant, and its microbiome determine the complex interaction between human pathogens and plants. However, also a multitude of environmental factors plays an important role. The availability of nutrients, for example, is fundamental for the survival of human pathogens and they have to compete for them with the indigenous plant and soil microorganisms. Recommendations for the practice require an improved understanding of the ecology of human pathogens in soil and on plants but also along the production chain. The development and use of sensitive and specific detection tools is essential and needs to consider the diversification of human pathogens through horizontal gene transfer as well as the problem of their non-cultivability under environmental stress conditions. DOI: 10.5073/JfK.2015.09.01, https://doi.org/10.5073/JfK.2015.09.0

Adaptions of Lichen Microbiota Functioning Under Persistent Exposure to Arsenic Contamination

Host-associated microbiota play an important role in the health and persistence of more complex organisms. In this study, metagenomic analyses were used to reveal microbial community adaptations in three lichen samples as a response to different arsenic concentrations at the sampling sites. Elevated arsenic concentrations at a former mining site expanded the spectrum and number of relevant functions in the lichen-associated microorganisms. Apparent changes affected the abundance of numerous detoxification-related genes, they were substantially enhanced in arsenic-polluted samples. Complementary quantifications of the arsenite S-adenosylmethionine methyltransferase (arsM) gene showed that its abundance is not strictly responding to the environmental arsenic concentrations. The analyzed samples contained rather low numbers of the arsM gene with a maximum of 202 gene copies μl-1 in total community DNA extracts. In addition, bacterial isolates were screened for the presence of arsM. Positive isolates were exposed to different As(III) and As(V) concentrations and tolerated up to 30 mM inorganic arsenic in fluid media, while no substantial biotransformations were observed. Obtained data deepens our understanding related to adaptions of whole microbial communities to adverse environmental conditions. Moreover, this study provides the first evidence that the integrity of bacteria in the lichen holobiont is maintained by acquisition of specific resistances

Taxonomic and functional analyses of intact microbial communities thriving in extreme, astrobiology-relevant, anoxic sites

Background: Extreme terrestrial, analogue environments are widely used models to study the limits of life and to infer habitability of extraterrestrial settings. In contrast to Earth’s ecosystems, potential extraterrestrial biotopes are usually characterized by a lack of oxygen. Methods: In the MASE project (Mars Analogues for Space Exploration), we selected representative anoxic analogue environments (permafrost, salt-mine, acidic lake and river, sulfur springs) for the comprehensive analysis of their microbial communities. We assessed the microbiome profile of intact cells by propidium monoazide-based amplicon and shotgun metagenome sequencing, supplemented with an extensive cultivation effort. Results: The information retrieved from microbiome analyses on the intact microbial community thriving in the MASE sites, together with the isolation of 31 model microorganisms and successful binning of 15 high-quality genomes allowed us to observe principle pathways, which pinpoint specific microbial functions in the MASE sites compared to moderate environments. The microorganisms were characterized by an impressive machinery to withstand physical and chemical pressures. All levels of our analyses revealed the strong and omnipresent dependency of the microbial communities on complex organic matter. Moreover, we identified an extremotolerant cosmopolitan group of 34 poly-extremophiles thriving in all sites. Conclusions: Our results reveal the presence of a core microbiome and microbial taxonomic similarities between saline and acidic anoxic environments. Our work further emphasizes the importance of the environmental, terrestrial parameters for the functionality of a microbial community, but also reveals a high proportion of living microorganisms in extreme environments with a high adaptation potential within habitability borders

The impact of the pathogen Rhizoctonia solani and its beneficial counterpart Bacillus amyloliquefaciens on the indigenous lettuce microbiome

Lettuce belongs to the most commonly raw eaten food worldwide and its microbiome plays an important role for both human and plant health. Yet, little is known about the impact of potentially occurring pathogens and beneficial inoculants of the indigenous microorganisms associated with lettuce. To address this question we studied the impact of the phytopathogenic fungus Rhizoctonia solani and the biological control agent Bacillus amyloliquefaciens FZB42 on the indigenous rhizosphere and phyllosphere community of greenhouse-grown lettuce at two plant stages. The rhizosphere and phyllosphere gammaproteobacterial microbiomes of lettuce plants showed clear differences in their overall and core microbiome composition as well as in corresponding diversity indices. The rhizosphere was dominated by Xanthomonadaceae (48%) and Pseudomonadaceae (37%) with Rhodanobacter, Pseudoxanthomonas, Dokdonella, Luteimonas, Steroidobacter, Thermomonas as core inhabitants, while the dominating taxa associated to phyllosphere were Pseudomonadaceae (54%), Moraxellaceae (16%) and Enterobacteriaceae (25%) with Alkanindiges, Pantoea and a group of Enterobacteriaceae unclassified at genus level. The preferential occurrence of enterics in the phyllosphere was the most significant difference between both habitats. Additional enhancement of enterics on the phyllosphere was observed in bottom rot diseased lettuce plants, while Acinetobacter and Alkanindiges were identified as indicators of healthy plants. Interestingly, the microbial diversity was enhanced by treatment with both the pathogen, and the co-inoculated biological control agent. The highest impact and bacterial diversity was found by Rhizoctonia inoculation, but FZB42 lowered the impact of Rhizoctonia on the microbiome. This study shows that the indigenous microbiome shifts as a consequence to pathogen attack but FZB42 can compensate these effects, which supports their role as biocontrol agent and suggests a novel mode of action

Biotic Stress Shifted Structure and Abundance of <i>Enterobacteriaceae</i> in the Lettuce Microbiome

<div><p>Lettuce cultivars are not only amongst the most popular vegetables eaten raw, they are also involved in severe pathogen outbreaks world-wide. While outbreaks caused by <i>Enterobacteriaceae</i> species are well-studied, less is known about their occurrence in natural environments as well as the impact of biotic stress. Here, we studied the ecology of the human health-relevant bacterial family <i>Enterobacteriaceae</i> and assessed the impact of biotic disturbances by a soil-borne phytopathogenic fungus and <i>Gastropoda</i> on their structure and abundance in mesocosm and pot experiments. Using a polyphasic approach including network analyses of 16S rRNA gene amplicon libraries, quantitative PCR and complementary fluorescence <i>in situ</i> hybridization (FISH) microscopy we found substantial yet divergent <i>Enterobacteriaceae</i> communities. A similar spectrum of 14 genera was identified from rhizo- and phyllospheres but the abundance of <i>Enterobacteriaceae</i> was on average 3fold higher in phyllosphere samples. Both stress factors shifted the bacterial community of the leaf habitat, characterized by increases of species abundance and diversity. For the rhizosphere, we observed significant structural shifts of <i>Enterobacteriaceae</i> communities but also a high degree of resilience. These results could be confirmed by FISH microscopy but it was difficult to visualize phyllosphere communities. Additional inoculation experiments with <i>Escherichia coli</i> as model revealed their presence below the wax layer as well as in the endosphere of leaves. The observed presence influenced by stress factors and the endophytic life style of <i>Enterobacteriaceae</i> on lettuce can be an important aspect in relation to human health.</p></div

Amplicon sequencing of <i>Gammaproteobacteria</i> revealed the relative abundance of <i>Enterobacteriaceae</i> associated with <i>L</i>. <i>sativa</i> var. <i>capitata</i> phyllosphere samples of the healthy control (C_P) and plants showing symptoms of bottom rot caused by <i>R</i>. <i>solani</i> (RS_P).

<p>Asterisks: significant differences (p < 0.05) between C_P and RS_P.</p

Enterobacteriaceae dominate the core microbiome and contribute to the resistome of arugula (Eruca sativa Mill.)

Abstract Background Arugula is a traditional medicinal plant and popular leafy green today. It is mainly consumed raw in the Western cuisine and known to contain various bioactive secondary metabolites. However, arugula has been also associated with high-profile outbreaks causing severe food-borne human diseases. A multiphasic approach integrating data from metagenomics, amplicon sequencing, and arugula-derived bacterial cultures was employed to understand the specificity of the indigenous microbiome and resistome of the edible plant parts. Results Our results indicate that arugula is colonized by a diverse, plant habitat-specific microbiota. The indigenous phyllosphere bacterial community was shown to be dominated by Enterobacteriaceae, which are well-equipped with various antibiotic resistances. Unexpectedly, the prevalence of specific resistance mechanisms targeting therapeutic antibiotics (fluoroquinolone, chloramphenicol, phenicol, macrolide, aminocoumarin) was only surpassed by efflux pump assignments. Conclusions Enterobacteria, being core microbiome members of arugula, have a substantial implication in the overall resistome. Detailed insights into the natural occurrence of antibiotic resistances in arugula-associated microorganisms showed that the plant is a hotspot for distinctive defense mechanisms. The specific functioning of microorganisms in this unusual ecosystem provides a unique model to study antibiotic resistances in an ecological context

Fluorescence <i>in situ</i> hybridization coupled with confocal laser scanning microscopy images.

<p>A) <i>Gammaproteobacteria</i> (yellow) and <i>Betaproteobacteria</i> (pink) form large colonies on the lateral roots of young lettuce plantlets, where they do not share their space, moreover it seems they exclude each other. B) We revealed increased gammaproteobacterial (yellow) colonization close to stomata which could be also detected on <i>R</i>. <i>solani</i> infected lettuce. C) Punctiform extensive colonization behavior of <i>Escherichia coli</i> K12 (yellow) on inoculated lettuce patches within the inner compartments of the leafy green. D) Physical damage to the leaves affects the epicuticular wax-layer (black arrow) and the cuticle cells (white arrow), and supports endophytic colonization of enterobacteria (yellow). E) Transport of bacteria (red) within a vascular bundle (white marker) and F) trough stoma.</p