Gautier Calmin

University of Applied Sciences Western Switzerland, Engineering and Architecture, Adjunct

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Molecular Identification of Microbial Communities in the Recycled Nutrient Solution of a Tomato Glasshouse SoilLess Culture

The Open Horticulture Journal, 2008

This study aimed to assess microbial community diversity in recycled nutrient solutions used in s... more This study aimed to assess microbial community diversity in recycled nutrient solutions used in soil-less glasshouse cultivation of tomato. One hundred bacterial strains, twenty oomycetes and 6 fungi were isolated and identified through genomic DNA isolation, PCR amplification of the ribosomal DNA region and database interrogations. Similarities of ITS regions with known species ranged from 95% to 100%. This artificial ecosystem was shown to be microbiologically diverse, since recovered isolate were close to 35 bacterial species, 11 oomycete species and 3 fungal species. Bacteria belonged almost exclusively to-Proteobacteria and Firmicutes, with most represented genera being Bacillus, Acinetobacter, Klebsiella and Serratia. A few bacterial sequences grouped with clones similar to plant and human pathogens, while other isolates could be protective bacteria such as Pseudomonas fluorescens. Oomycetes isolated mostly belonged to the genus Pythium (19 isolates) and were phylogenetically related to common cosmopolitan soil inhabitants or phytopathogenic Pythium species. The six fungal isolates were in 2 genera, Rhizopus and Caesia; Rhizopus isolates were closely related to the post harvest pathogen Rhizopus stolonifer. This original work adds to the efforts of assessing microorganism diversity in recycled nutrient solutions commonly used in glasshouse vegetable production; microbial diversity was high and included potential plant pathogens. This study demonstrated the existence of a wide cultivable microbial community in the nutrient solution before recycling and recirculation and supported the necessity for disinfecting nutrient solutions used in soil-less cultivation systems, during the recycling process, in order to ensure crop sanitation and avoiding plant disease spreading.

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Metatranscriptomic and metagenomic description of the bacterial nitrogen metabolism in waste water wet oxidation effluents

Heliyon, 2017

Anaerobic digestion is a common method for reducing the amount of sludge solids in used waters an... more Anaerobic digestion is a common method for reducing the amount of sludge solids in used waters and enabling biogas production. The wet oxidation process (WOX) improves anaerobic digestion by converting carbon into methane through oxidation of organic compounds. WOX produces effluents rich in ammonia, which must be removed to maintain the activity of methanogens. Ammonia removal from WOX could be biologically operated by aerobic granules. To this end, granulation experiments were conducted in 2 bioreactors containing an activated sludge (AS). For the first time, the dynamics of the microbial community structure and the expression levels of 7 enzymes of the nitrogen metabolism in such active microbial communities were followed in regard to time by metagenomics and metatranscriptomics. It was shown that bacterial communities adapt to the wet oxidation effluent by increasing the expression level of the nitrogen metabolism, suggesting that these biological activities could be a less cost...

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Metagenomes and Metatranscriptomes of Activated Sludge from a Sewage Plant, with or without Aerobic Granule Enrichment

Genome Announcements

We report here the metagenomes and metatranscriptomes of activated sludge bioreactors, enriched o... more We report here the metagenomes and metatranscriptomes of activated sludge bioreactors, enriched or not enriched with aerobic granules, at an initial state and after 1 month of incubation. Data showed that the added granular biomass expressed higher levels of expression of genes involved in ammonia elimination.

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Assessing Efficacy of Ultra-Filtration and Bio-Filtration Systems Used in Soilless Production Through Molecular Detection of Pythium Oligandrum and Bacillus Subtilis as Model Organisms

Acta Horticulturae

ABSTRACT The majority of greenhouse crops are grown on artificial substrates in hydroponic system... more ABSTRACT The majority of greenhouse crops are grown on artificial substrates in hydroponic systems. Re-circulating nutrient systems offer an advantageous alternative for controlling nutrient solutions leaching from greenhouses into the environment, which represents an environmental issue in greenhouse production areas. However, the potential for the rapid spread of root diseases, and other diseases, is the main hindrance to the general adoption of re-circulating nutrient systems by the greenhouse industry. In this study, the total bacterial, fungal and oomycete communities present in re-circulating nutrient solutions, were monitored using selective media and direct viable counts. Sequence analysis of 126 main representatives of these three communities showed for Eubacteria the presence of 11 genera of γ-Proteobacteria, 3 genera of Firmicutes, one genus of Actinobacteria and one genus of Flavobacteria. For the fungi, recovered strains belonged to Rhizopus and to Postia. Twenty strains belonged to the Stramenopile lineage, 19 of them to the genus Pythium (Oomycota) and one to the genus Splachnidium (Phaeophyceae). In addition, the efficacy of ultra-filtration and bio-filtration for eliminating oomycete and bacterial pathogens, artificially added in the re-circulating nutrient solution was assessed, by using a tangential ultrafiltration system, a slow sand filter and a rockwool granule filter. The oomycete Pythium oligandrum and the bacterium Bacillus subtilis were used as model organisms because of their easy culture, their lack of pathogenicity and their similarity with common oomycete and bacterial plant pathogens. Using real time PCR and species specific oligonucleotides showed that ultrafiltration is highly effective in removing P. oligandrum and B. subtilis. No P. oligandrum or B. subtilis were detected by real time PCR in filtrated nutrient solutions. Passage of nutrient solution through the slow sand filters also resulted in complete removal of P. oligandrum but was less effective for B. subtilis removal.

Metagenome-Assembled Genome Sequence of Rhodopseudomonas palustris Strain ELI 1980, Commercialized as a Biostimulant

Genome Announcements

We report here the draft genome sequence of strain ELI 1980 of Rhodopseudomonas palustris , comme... more

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Whole-Genome Sequence ofPseudomonas xanthomarinaStrain UASWS0955, a Potential Biological Agent for Agricultural and Environmental Uses

Genome Announcements, 2016

We report here the whole-genome shotgun sequence of the strain UASWS0955 of the speciesPseudomona... more We report here the whole-genome shotgun sequence of the strain UASWS0955 of the speciesPseudomonas xanthomarina, isolated from sewage sludge. This genome was obtained with an Illumina MiniSeq and is the second genome registered for this species, which is considered as a promising resource for agriculture and bioremediation of contaminated soils.

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Whole-Genome Sequence ofMesorhizobium hungaricumsp. nov. Strain UASWS1009, a Potential Resource for Agricultural and Environmental Uses

Genome Announcements, 2016

We report here the whole-genome shotgun sequences of the strain UASWS1009 of the speciesMesorhizo... more We report here the whole-genome shotgun sequences of the strain UASWS1009 of the speciesMesorhizobium hungaricumsp. nov., which are different from any other knownMesorhizobiumspecies. This is the first genome registered for this new species, which could be considered as a potential resource for agriculture and environmental uses.

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Whole-Genome Sequence ofPseudomonas graminisStrain UASWS1507, a Potential Biological Control Agent and Biofertilizer Isolated in Switzerland

Genome Announcements, 2016

We report here the whole-genome shotgun sequence of the strain UASWS1507 of the speciesPseudomona... more We report here the whole-genome shotgun sequence of the strain UASWS1507 of the speciesPseudomonas graminis, isolated in Switzerland from an apple tree. This is the first genome registered for this species, which is considered as a potential and valuable resource of biological control agents and biofertilizers for agriculture.

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Whole-Genome Sequence ofEnteractinococcus helveticumsp. nov. Strain UASWS1574 Isolated from Industrial Used Waters

Genome Announcements, 2016

We report here the whole-genome shotgun sequences of the strain UASWS1574 of the undescribed Ente... more

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A New and Improved Automated Technology for Early Sex Determination of Ginkgo biloba

Random amplified polymorphic DNA (RAPD) technique with male associated decamer primer S1478 was u... more Random amplified polymorphic DNA (RAPD) technique with male associated decamer primer S1478 was used to amplify DNA from 72 leaf samples collected from Ginkgo biloba trees with known sexual determinism in the canton of Geneva, Switzerland. This marker was found to be male-specific and was lacking in all female plants. Automated random polymorphic DNA analysis (ARPA), a new automated technology developed in the frame of this work, proved highly effective in distinguishing males and females with 100% efficiency and successful in male and female discrimination from a collection of young seedlings derived from a sexual cross. Our findings provide unambiguous evidence that ARPA combined with the male-associated decamer primer S1478 could be considered an efficient, rapid, and easy method to make an early sex determination in the dioecious tree Ginkgo biloba.

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Whole-Genome Sequences of Seven Strains ofBacillus cereusIsolated from Foodstuff or Poisoning Incidents: TABLE 1

Genome Announcements, 2016

We present here the whole shotgun genome sequences of seven strains ofBacillus cereusisolated fro... more

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Real time PCR diagnostic of Phytophthora alni and its three subspecies

Whole-Genome Sequence of Bradyrhizobium elkanii Strain UASWS1015, a Highly Ammonia-Tolerant Nitrifying Bacterium

Genome announcements, Jan 10, 2016

Bradyrhizobium elkanii UASWS1015 was isolated from a sewage plant in Switzerland. Its genome indi... more Bradyrhizobium elkanii UASWS1015 was isolated from a sewage plant in Switzerland. Its genome indicates that it is fully equipped for ammonia assimilation and aromatic compound degradation, and it displays a large type IV secretion system, which characterizes plant-associated microbes. Totally deprived of toxins, it could be considered for agricultural and environmental uses.

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Detection and diagnosis of Phytophthora ramorum with specipfic hybridization real time PCR probes

Gnomoniopsis smithogilvyi causes chestnut canker symptoms in Castanea sativa shoots in Switzerland

Fungal genetics and biology : FG & B, Jan 5, 2016

A screening of Castanea sativa scions for grafting for the presence of endophytes showed that the... more A screening of Castanea sativa scions for grafting for the presence of endophytes showed that the opportunistic fungal pathogen Gnomoniopsis smithogilvyi was the most abundant member of the endophytic flora. This fungus is known as a pathogen affecting chestnut fruits in Italy and Australia. Here, we present evidence that it causes cankers very similar to the ones due to Cryphonectria parasitica infection on twigs and scions of chestnut trees. We found natural infections of G. smithogilvyi in healthy grafted plants as well as in scions from chestnut trees. The identity of the fungus isolated from asymptomatic tissues was verified by applying Koch's postulates and corroborated by DNA sequencing of four different gene regions. In contrast to C. parasitica that appears on the bark as yellow to orange pycnidia, stromata and slimy twisted tendrils, G. smithogilvyi forms orange to red and black pycnidia, gray stromata and cream-colored to beige slimy twisted tendrils on the bark. Thes...

Phylogenetic Analysis and Real Time PCR Detection of a New Peronospora Species Responsible for Downy Mildew Disease of Sweet Basil and Sage

Acta Horticulturae, 2007

Whole-Genome Sequence of Pseudomonas putida Strain UASWS0946, a Highly Ammonia-Tolerant Nitrifying Bacterium Isolated from Sewage Sludge Aerobic Granules

Genome Announcements, 2015

We report here the genome ofPseudomonas putidastrain UASWS0946, a highly ammonia-tolerant nitrify... more

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Whole-Genome Sequences of 15 Strains of Staphylococcus aureus subsp. aureus Isolated from Foodstuff and Human Clinical Samples: Table 1

Genome Announcements, 2015

The whole-genome sequences of 15 strains of Staphylococcus aureus (10 strains isolated from foods... more The whole-genome sequences of 15 strains of Staphylococcus aureus (10 strains isolated from foodstuff samples in Switzerland and five from human clinical samples) were obtained by Illumina sequencing. Most strains fit within the known diversity for the species, but one (SA-120) possessed a higher G؉C content and a higher number of genes than usual.

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Direct PCR for DNA barcoding in the genera Phytophthora and Pythium

Biotechnology & Biotechnological Equipment

Assessing efficacy of ultra-filtration and slow filtration in soil-less production by molecular detection of Pythium oligandrum and Bacillus subtilis as model organisms

Archives Des Sciences Journal

Greenhouse crops are mainly grown on artificial substrates in soil-less systems. Re-circulating n... more Greenhouse crops are mainly grown on artificial substrates in soil-less systems. Re-circulating nutrient systems offer an advantageous alternative for controlling nutrient solutions leaching from greenhouses into the environment, which represents an environmental issue in greenhouse production areas. However, the potential for the rapid spread of plant pathogens, is the main hindrance to the general adoption of re-circulating nutrient systems by the greenhouse industry. Here we assessed by real time PCR the efficacy of filtration for eliminating oomycete and bacterial pathogens, artificially added in the recirculating nutrient solution, by using a tangential ultra-filtration system, a slow sand filter (SSF) and a slow Rockwool granule filter (SRF). The oomycete Pythium oligandrum and the bacterium Bacillus subtilis were used as model organisms because of their easy culture, their lack of pathogenicity and their similarity with common oomycete and bacterial plant pathogens. Using rea...

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