A first inventory of the labile biochemicals found in Avignon groundwater: can we identify potential bacterial substrates?

Groundwater is a major source of water for irrigation of vegetables, especially in the Mediterranean basin. Contamination of aquifer by pathogens has been responsible for numerous disease outbreaks worldwide. Several studies reported that groundwater dissolved organic matter (DOM) can serve as a source of carbon and energy for heterotrophic metabolism of pathogens. In this study, we aimed to investigate the DOM composition of groundwater collected at Avignon. Six liters of groundwater were filtered (0.2 µm) and freeze-dried following appropriate cleaning procedure. The bulk analyses of powder sample were performed using 1D and 2D nuclear magnetic resonance spectroscopy and liquid chromatography coupled with mass spectroscopy. Several components were found at concentrations around 1 µM and comprise: (i) humic and fulvic acids originated from land-derived material or soils and, (ii) various acids, esters and alcohols of different sizes including acetate, lactate and formate, these may result from microbial metabolism. In conclusion, the Avignon groundwater DOM contains a heterogeneous mixture of dissolved organic components with a rather low potential bioreactivity based on the low level of labile biogeochemicals such as carbohydrates

Pseudomonas syringae on plants in Iceland has likely evolved for several million years outside the reach of processes that mix this bacterial complex across earth’s temperate zones

Funding Information: Funding: This research was funded by (i) the Campus France/ Partenariat Hubert Curien Jules Verne Franco-Icelandic Exchange Program project 40885YF, (ii) the Ranis Icelandic Research Fund project 206801–051 and (iii) French National Research Agency (ANR) project SPREE-17-CE32-0004-01. Publisher Copyright: © 2022 by the authors. Licensee MDPI, Basel, Switzerland.Here we report, for the first time, the occurrence of the bacteria from the species complex Pseudomonas syringae in Iceland. We isolated this bacterium from 35 of the 38 samples of angiosperms, moss, ferns and leaf litter collected across the island from five habitat categories (boreal heath, forest, subalpine and glacial scrub, grazed pasture, lava field). The culturable populations of P. syringae on these plants varied in size across 6 orders of magnitude, were as dense as 107 cfu g−1 and were composed of strains in phylogroups 1, 2, 4, 6, 7, 10 and 13. P. syringae densities were significantly greatest on monocots compared to those on dicots and mosses and were about two orders of magnitude greater in grazed pastures compared to all other habitats. The phylogenetic diversity of 609 strains of P. syringae from Iceland was compared to that of 933 reference strains of P. syringae from crops and environmental reservoirs collected from 27 other countries based on a 343 bp sequence of the citrate synthase (cts) housekeeping gene. Whereas there were examples of identical cts sequences across multiple countries and continents among the reference strains indicating mixing among these countries and continents, the Icelandic strains grouped into monophyletic lineages that were unique compared to all of the reference strains. Based on estimates of the time of divergence of the Icelandic genetic lineages of P. syringae, the geological, botanical and land use history of Iceland, and atmospheric circulation patterns, we propose scenarios whereby it would be feasible for P. syringae to have evolved outside the reach of processes that tend to mix this bacterial complex across the planet elsewhere.Here we report, for the first time, the occurrence of the bacteria from the species complex Pseudomonas syringae in Iceland. We isolated this bacterium from 35 of the 38 samples of angiosperms, moss, ferns and leaf litter collected across the island from five habitat categories (boreal heath, forest, subalpine and glacial scrub, grazed pasture, lava field). The culturable populations of P. syringae on these plants varied in size across 6 orders of magnitude, were as dense as 107 cfu g−1 and were com-posed of strains in phylogroups 1, 2, 4, 6, 7, 10 and 13. P. syringae densities were significantly greatest on monocots compared to those on dicots and mosses and were about two orders of magnitude greater in grazed pastures compared to all other habitats. The phylogenetic diversity of 609 strains of P. syringae from Iceland was compared to that of 933 reference strains of P. syringae from crops and environmental reservoirs collected from 27 other countries based on a 343 bp sequence of the citrate synthase (cts) housekeeping gene. Whereas there were examples of identical cts sequences across mul-tiple countries and continents among the reference strains indicating mixing among these countries and continents, the Icelandic strains grouped into monophyletic lineages that were unique compared to all of the reference strains. Based on estimates of the time of divergence of the Icelandic genetic lineages of P. syringae, the geological, botanical and land use history of Iceland, and atmospheric circulation patterns, we propose scenarios whereby it would be feasible for P. syringae to have evolved outside the reach of processes that tend to mix this bacterial complex across the planet elsewhere.Peer reviewe

COVID-19 symptoms at hospital admission vary with age and sex: results from the ISARIC prospective multinational observational study

Background: The ISARIC prospective multinational observational study is the largest cohort of hospitalized patients with COVID-19. We present relationships of age, sex, and nationality to presenting symptoms. Methods: International, prospective observational study of 60 109 hospitalized symptomatic patients with laboratory-confirmed COVID-19 recruited from 43 countries between 30 January and 3 August 2020. Logistic regression was performed to evaluate relationships of age and sex to published COVID-19 case definitions and the most commonly reported symptoms. Results: ‘Typical’ symptoms of fever (69%), cough (68%) and shortness of breath (66%) were the most commonly reported. 92% of patients experienced at least one of these. Prevalence of typical symptoms was greatest in 30- to 60-year-olds (respectively 80, 79, 69%; at least one 95%). They were reported less frequently in children (≤ 18 years: 69, 48, 23; 85%), older adults (≥ 70 years: 61, 62, 65; 90%), and women (66, 66, 64; 90%; vs. men 71, 70, 67; 93%, each P < 0.001). The most common atypical presentations under 60 years of age were nausea and vomiting and abdominal pain, and over 60 years was confusion. Regression models showed significant differences in symptoms with sex, age and country. Interpretation: This international collaboration has allowed us to report reliable symptom data from the largest cohort of patients admitted to hospital with COVID-19. Adults over 60 and children admitted to hospital with COVID-19 are less likely to present with typical symptoms. Nausea and vomiting are common atypical presentations under 30 years. Confusion is a frequent atypical presentation of COVID-19 in adults over 60 years. Women are less likely to experience typical symptoms than men

Écologie des populations bactériennes associées aux eucaryotes photosynthétiques: de la rhizosphère à la phycosphère

Diplôme : HD

Outils de biologie moléculaire pour la caractérisation des populations bactériennes des biofilms

National audienc

Exploring diversity of cultivable aerobic endospore-forming bacteria: from pasteurization to procedures without heat-shock selection

International audienceThe assessment of the diversity of populations with low abundances in soil, as are most of the aerobic endospore-forming bacteria, is a real challenge in modern studies of microbial ecology. Besides the culture-independent approaches reported in De Vos, Studying the bacterial diversity of the soil by culture-independent approaches. In: Logan NA (ed) Endospore forming soil bacteria (Soil Biology 27). Springer, Heidelberg, 2011, doi:10.1007/978-3-642-19577-3, cultivation-based methods are still useful, as they allow the description of novel bacterial species, as well as extensive biological studies and biotechnological exploitation of the isolated strains. The common traditional approach to isolation, through spore selection followed by growth in selective conditions, is a very efficient strategy and can give much information on cultivable populations living in soils and other environments. To enlarge our view of the diversity of endospore-formers in soils, this chapter reviews the use and evaluation of methods with and without spore selection, including immunocapture or selective media in combination with molecular techniques

Ratio of root-adhering soil (RAS) to root tissue (RT) dry masses (RAS/RT ratio), i.e. rhizosphere soil aggregation

International audienc

Bacterial exopolysaccharides and productivity of salt affected soils: I. Diversity of exopolysaccharide-producing bacteria isolated from the rhizosphere of wheat (<em>Triticum aestivum</em> L.) grown in normal and saline Pakistani soils

International audienceThis study was conducted to isolate and identify the EPS-producing bacteria associated with the roots of three wheat lines grown in saline and non-saline soils. Results indicated the presence of various EPS-producing bacterial genera in unplanted saline and non-saline soil, rhizosphere and rhizoplane of the three wheat fines. Bacillus sp. were more variable in unplanted saline than non-saline soil. In contrast to uniform distribution of Bacillus sp. in unplanted soils, other EPS-producing bacterial genera isolated from rhizosphere and rhizoplane were more numerous and diversified. Frequent occurrence of Microbacterium sp. in the soil and rhizosphere of the plants invoke the desire for more research work to explore the role of this bacterium in the saline environment