Dynamics of culturable mesophilic bacterial communities of three fresh herbs and their production environment

Gekenidis, Maria-Theresia; Gossin, Diane; Schmelcher, Mathias; Schöner, Ulrich; Remus-Emsermann, Mitja N. P.; Drissner, David

doi:10.1111/jam.13532

Cited by 17 publications

(23 citation statements)

References 81 publications

(149 reference statements)

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“…Pseudomonas koreensis P19E3 was isolated from healthy marjoram ( Origanum marjorana ) leaf material during an isolation survey on an organic herb farm (Boppelsen, Switzerland) in summer 2014 and classified by matrix-assisted laser desorption/ionization time of flight (MALDI-TOF) analysis (26) . Genomic DNA (gDNA) was isolated (Sigma GenElute kit), and PacBio SMRT sequencing was performed on an RS II machine (4 SMRT cells, P6-C4 chemistry) aiming to de novo assemble a complete genome as described (9) .…”

Section: Bacterial Strain Genomic Dna Extraction and Sequencingmentioning

confidence: 99%

“…A bacterial strain isolated during a screening of herbal plants for food spoiling and pathogenic bacteria was assigned to the species Pseudomonas koreensis by MALDI biotyping (26) . However, although PacBio long read sequencing was used, it was not possible to assemble the genome de novo into a single complete chromosome.…”

Section: Repeat Analysis For the Genus Pseudomonasmentioning

confidence: 99%

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Pushing the limits of de novo genome assembly for complex prokaryotic genomes harboring very long, near identical repeats

Schmid

Frei

Patrignani

et al. 2018

Preprint

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Generating a complete, de novo genome assembly for prokaryotes is often considered a solved problem. However, we here show that Pseudomonas koreensis P19E3 harbors multiple, near identical repeat pairs up to 70 kilobase pairs in length. Beyond long repeats, the P19E3 assembly was further complicated by a shufflon region. Its complex genome could not be de novo assembled with long reads produced by Pacific Biosciences' technology, but required very long reads from the Oxford Nanopore Technology. Another important factor for a full genomic resolution was the choice of assembly algorithm.Importantly, a repeat analysis indicated that very complex bacterial genomes represent a general phenomenon beyond Pseudomonas . Roughly 10% of 9331 complete bacterial and a handful of 293 complete archaeal genomes represented this dark matter for de novo genome assembly of prokaryotes. Several of these dark matter genome assemblies contained repeats far beyond the resolution of the sequencing technology employed and likely contain errors, other genomes were closed employing labor-intense steps like cosmid libraries, primer walking or optical mapping. Using very long sequencing reads in combination with assemblers capable of resolving long, near identical repeats will bring most prokaryotic genomes within reach of fast and complete de novo genome assembly.

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Section: Bacterial Strain Genomic Dna Extraction and Sequencingmentioning

confidence: 99%

Section: Repeat Analysis For the Genus Pseudomonasmentioning

confidence: 99%

Pushing the limits of de novo genome assembly for complex prokaryotic genomes harboring very long, near identical repeats

Schmid

Frei

Patrignani

et al. 2018

Preprint

View full text Add to dashboard Cite

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“…In general, humidity can be adjusted in the Litterbox system by changing the ratio of media to zeolite, whereas in the agar system humidity cannot be adjusted without the agar drying out. Moreover, in agar-based systems the bacterial load in the phyllosphere is usually around 10 8 cfu/g [9,64,65] , which is one to two magnitudes greater than under temperate environmental conditions which have been reported to be 10 6 -10 7 cfu/g [66,67] . Four-week-old plants grown on zeolite were smaller ( Figure 1C,D), had significantly fewer leaves ( Figure 1L) and were significantly lighter than plants grown on agar ( Figure 1K).…”

Section: Resultsmentioning

confidence: 93%

Litterbox - A gnotobiotic zeolite-clay system to investigate Arabidopsis-microbe interactions

Miebach

Schlechter

Clemens

et al. 2020

Preprint

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Plants are colonised by millions of microorganisms representing thousands of species with varying effects on plant growth and health. The microbial communities found on plants are compositionally consistent and their overall positive effect on the plant is well known. However, the effects of individual microbiota members on plant hosts and vice versa , as well as the underlying mechanisms remain largely unknown. Here, we describe 'Litterbox', a highly controlled system to investigate plant-microbe interactions. Plants were grown gnotobiotically on zeolite-clay, an excellent soil replacement that retains enough moisture to avoid subsequent watering. Plants grown on zeolite phenotypically resemble plants grown under environmental conditions. Further, bacterial densities on leaves in the Litterbox system resembled those in temperate environments. A PDMS sheet was used to cover the zeolite, thereby significantly lowering the bacterial load in the zeolite and rhizosphere. This reduced the likelihood of potential systemic responses in leaves induced by microbial rhizosphere colonisation. We present results of example experiments studying the transcriptional responses of leaves to defined microbiota members and the spatial distribution of bacteria on leaves. We anticipate that this versatile and affordable plant growth system will promote microbiota research and help in elucidating plant-microbe interactions and their underlying mechanisms. Introduction:Plants offer three different habitats to microbes: the endosphere, the rhizosphere, and the phyllosphere. The endosphere encompasses the habitat formed by internal tissues of plants, whereas the rhizosphere and phyllosphere encompass the surfaces of belowground and aboveground plant organs, respectively. Plants host remarkably diverse and complex, yet structured, microbial communities, collectively referred to as the plant microbiota [1][2][3] . Due to the microbiota's diversity and complexity, it is not surprising that the traditional view of host-microbe interactions focussing on plant pathogens, nitrogen-fixing rhizobacteria, and phosphate-mobilizing mycorrhizal fungi, has recently shifted to a holistic view considering the plant and its associated microbiota as a metaorganism or holobiont [4][5][6] . It is widely recognised that members of the microbiota assist in nutrient uptake, promote growth, and protect against biotic and abiotic stresses [7][8][9][10][11][12][13][14] . To harness these positive impacts of plant-associated microbiota, the use of synthetic microbiota has been proposed [15][16][17] . The prospect of using synthetic microbial communities to promote sustainable agriculture is leading to a growing appreciation of plant microbiota research.Generally, plant microbiota research aims to understand 1) plant-microbe and microbe-microbe interactions ranging from the individual microorganism to the microbial community resolution, 2) the underlying molecular mechanisms of these interactions, and 3) their contribution to microbial community structure. Thus far...

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“…[4][5][6][7]10 Potential contamination sources include: irrigation water, soil, fertiliser, farm workers, and equipment used around a farm. 11,12 Unwanted contamination can result in diseases detrimental to plant health or produce unwanted pathogens that are harmful to humans. Furthermore, leafy greens are often consumed raw or with minimal processing.…”

Section: Introductionmentioning

confidence: 99%

“…Which does not remove or kill unwanted contamination. 4,[10][11][12][13][14] In some cases, contamination can lead to outbreaks that can cause severe illnesses. [15][16][17] Unwanted leaf contamination is of an increased concern with increasing produce demand, large-scale production, and distribution.…”

Section: Introductionmentioning

confidence: 99%

Comparison of Replica Leaf Surface Materials for Phyllosphere Microbiology

Soffe¹,

Altenhuber²,

Bernach³

et al. 2018

Preprint

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Artificial surfaces are routinely used instead of leaves to enable a reductionist approach in phyllosphere microbiology, the study of microorganisms residing on plant leaf surfaces. For instance, flat surfaces such as nutrient agar, enable the influence of nutrient supply on microorganisms to be investigated. In contrast microstructured surfaces, such as isolated leaf cuticles or reconstituted leaf waxes enable the influence of physicochemical properties to be investigated. However, interest in replica leaf surfaces as an artificial surface is growing. As replica surfaces offer an improved representation of the complex topography of leaf surfaces. The use of replica leaf surfaces has to date primarily been focused on replicating the superhydrophobic surfaces of leaves. Whereas in this paper, we investigate potential replica surface materials for phyllosphere microbiology studies. Using a test pattern, we investigated the resolution, the degradation characteristics in environmental conditions, surface energy, and bacterial survival characteristics for each potential replica material. Our results indicate that PDMS is the most suitable material for producing replica leaf surfaces. Due to the high resolution achieved through replica molding, extended stability, hydrophobic properties, and bacterial survival characteristics comparable to isolated leaf cuticles. Our experiments highlight the importance of considering the inherent material properties, when selecting a replica leaf surface for phyllosphere microbiology studies. A replica leaf produced in PDMS offers a control surface that can be used for investigating microbe-microbe and microbe-plant interactions in the phyllosphere. Thus, in turn enabling mitigation strategies against pathogens to either the plant host or humans to be developed.

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Dynamics of culturable mesophilic bacterial communities of three fresh herbs and their production environment

Cited by 17 publications

References 81 publications

Pushing the limits of de novo genome assembly for complex prokaryotic genomes harboring very long, near identical repeats

Pushing the limits of de novo genome assembly for complex prokaryotic genomes harboring very long, near identical repeats

Litterbox - A gnotobiotic zeolite-clay system to investigate Arabidopsis-microbe interactions

Comparison of Replica Leaf Surface Materials for Phyllosphere Microbiology

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