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Miral A, Kautsky A, Alves-Carvalho S, Cottret L, Guillerm-Erckelboudt AY, Buguet M, Rouaud I, Tranchimand S, Tomasi S, Bartoli C. Rhizocarpon geographicum Lichen Discloses a Highly Diversified Microbiota Carrying Antibiotic Resistance and Persistent Organic Pollutant Tolerance. Microorganisms 2022; 10:1859. [PMID: 36144461 PMCID: PMC9503503 DOI: 10.3390/microorganisms10091859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 09/06/2022] [Accepted: 09/14/2022] [Indexed: 11/16/2022] Open
Abstract
As rock inhabitants, lichens are exposed to extreme and fluctuating abiotic conditions associated with poor sources of nutriments. These extreme conditions confer to lichens the unique ability to develop protective mechanisms. Consequently, lichen-associated microbes disclose highly versatile lifestyles and ecological plasticity, enabling them to withstand extreme environments. Because of their ability to grow in poor and extreme habitats, bacteria associated with lichens can tolerate a wide range of pollutants, and they are known to produce antimicrobial compounds. In addition, lichen-associated bacteria have been described to harbor ecological functions crucial for the evolution of the lichen holobiont. Nevertheless, the ecological features of lichen-associated microbes are still underestimated. To explore the untapped ecological diversity of lichen-associated bacteria, we adopted a novel culturomic approach on the crustose lichen Rhizocarpon geographicum. We sampled R. geographicum in French habitats exposed to oil spills, and we combined nine culturing methods with 16S rRNA sequencing to capture the greatest bacterial diversity. A deep functional analysis of the lichen-associated bacterial collection showed the presence of a set of bacterial strains resistant to a wide range of antibiotics and displaying tolerance to Persistent Organic Pollutants (POPs). Our study is a starting point to explore the ecological features of the lichen microbiota.
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Affiliation(s)
- Alice Miral
- CNRS, ISCR (Institut des Sciences Chimiques de Rennes)—UMR 6226, University of Rennes 1, 35000 Rennes, France
| | - Adam Kautsky
- IGEPP, INRAE, Institut Agro, University of Rennes 1, LIPME, INRAE, 35653 Le Rheu, France
| | - Susete Alves-Carvalho
- IGEPP, INRAE, Institut Agro, University of Rennes 1, LIPME, INRAE, 35653 Le Rheu, France
| | - Ludovic Cottret
- CNRS, Université de Toulouse, 31320 Castanet-Tolosan, France
| | | | - Manon Buguet
- CNRS, ISCR (Institut des Sciences Chimiques de Rennes)—UMR 6226, University of Rennes 1, 35000 Rennes, France
| | - Isabelle Rouaud
- CNRS, ISCR (Institut des Sciences Chimiques de Rennes)—UMR 6226, University of Rennes 1, 35000 Rennes, France
| | - Sylvain Tranchimand
- Ecole Nationale Supérieure de Chimie de Rennes, CNRS, ISCR (Institut des Sciences Chimiques de Rennes)—UMR 6226, University of Rennes 1, 35000 Rennes, France
| | - Sophie Tomasi
- CNRS, ISCR (Institut des Sciences Chimiques de Rennes)—UMR 6226, University of Rennes 1, 35000 Rennes, France
| | - Claudia Bartoli
- IGEPP, INRAE, Institut Agro, University of Rennes 1, LIPME, INRAE, 35653 Le Rheu, France
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Oren A, Garrity G. Valid publication of new names and new combinations effectively published outside the IJSEM. Int J Syst Evol Microbiol 2022; 72. [PMID: 35647792 DOI: 10.1099/ijsem.0.005331] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
| | - George Garrity
- Department of Microbiology & Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA
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Fiedler G, Gieschler S, Kabisch J, Grimmler C, Brinks E, Wagner N, Hetzer B, Franz CMAP, Böhnlein C. Pseudomonas rustica sp. nov., isolated from bulk tank raw milk at a German dairy farm. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005288] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Here we present the description of a novel
Pseudomonas
species, designated Pseudomonas rustica sp. nov., which was isolated from raw milk samples obtained from Germany. Results of initial 16S rRNA gene sequence analysis assigned the strain into the genus
Pseudomonas
and showed
Pseudomonas helmanticensis
,
Pseudomonas neuropathica
and
Pseudomonas atagonensis
to be its closest relatives. Further studies including sequence analysis of the rpoB gene, multi-gene phylogenetic tree reconstruction, whole-genome sequence comparisons, cellular fatty acid analysis and chemotaxonomic characterization showed a clear separation from the known
Pseudomonas
species. Isolate MBT-4T was closely related to
Pseudomonas helmanticensis
, 'Pseudomonas crudilactis' and
Pseudomonas neuropathica
with average nucleotide identities based on blast values of 88.8, 88.8 and 88.6%, respectively. Therefore, the strain can be classified into the
Pseudomonas koreensis
subgroup of the
Pseudomonas fluorescens
group. The G+C content of strain MBT-4T was 58.9 mol%. The strain was catalase- and oxidase-positive, while the β-galactosidase reaction was negative. Growth occurred between 4 and 30 °C and at pH values from pH 6.0 to 8.0. In conclusion, strain MBT-4T belongs to a novel species, for which the name Pseudomonas rustica sp. nov. is proposed. The type strain is MBT-4T (=DSM 112348T=LMG 32241T) and strain MBT-17 is also a representative of this species.
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Affiliation(s)
- Gregor Fiedler
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Hermann-Weigmann-Straße 1, 24103 Kiel, Germany
| | - Stefanie Gieschler
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Hermann-Weigmann-Straße 1, 24103 Kiel, Germany
| | - Jan Kabisch
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Hermann-Weigmann-Straße 1, 24103 Kiel, Germany
| | - Christina Grimmler
- Department of Safety and Quality of Meat, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, E.-C.-Baumann-Straße 20, 95326 Kulmbach, Germany
| | - Erik Brinks
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Hermann-Weigmann-Straße 1, 24103 Kiel, Germany
| | - Natalia Wagner
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Hermann-Weigmann-Straße 1, 24103 Kiel, Germany
| | - Birgit Hetzer
- Department of Food Technology and Bioprocess Engineering, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Haid-und-Neu-Straße 9, 76131 Karlsruhe, Germany
| | - Charles M. A. P. Franz
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Hermann-Weigmann-Straße 1, 24103 Kiel, Germany
| | - Christina Böhnlein
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Hermann-Weigmann-Straße 1, 24103 Kiel, Germany
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Atanasov KE, Galbis DM, Gallego J, Serpico A, Bosch M, Altabella T, Ferrer A. Pseudomonas germanica sp. nov., isolated from Iris germanica rhizomes. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005268] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Through bacterial plant–endophyte extraction from rhizomes of Iris germanica plant, a Gram-stain-negative, aerobic, catalase- and oxidase-positive gammaproteobacterial strain, referred to as FIT28T, was isolated. FIT28T shows vigorous growth on nutrient rich media within the temperature range of 4–35 °C, with optimal growth at 28 °C, a wide pH tolerance from pH 5 to 11, and salt tolerance up to 6 % (w/v) NaCl. Colonies are white-yellow and quickly become mucoid. The results of analysis of the 16S rRNA gene sequence placed the strain within the genus
Pseudomonas
, and multilocus sequence analysis (MLSA) using 16S rRNA, rpoB, gyrB and rpoD concatenated sequences revealed that the closest relatives of FIT28T are
Pseudomonas zeae
OE48.2T, '
Pseudomonas crudilactis
' UCMA 17988,
Pseudomonas tensinigenes
ZA5.3T,
Pseudomonas helmanticensis
OHA11T,
Pseudomonas baetica
a390T,
Pseudomonas iridis
P42T,
Pseudomonas atagonensis
PS14T and
Pseudomonas koreensis
Ps 9-14T, within the
Pseudomonas koreensis
subgroup of the
Pseudomonas fluorescens
lineage. The genome size of FIT28T is about 6.7 Mb with 59.09 mol% DNA G+C content. Average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values calculated from the genomic sequences of FIT28T, and the closely related
P. zeae
OE48.2T are 95.23 and 63.4 %, respectively. Biochemical, metabolic and chemotaxonomic studies further support our proposal that Pseudomonas germanica sp. nov., should be considered a novel species of the genus
Pseudomonas
. Hence, the type strain FIT28T (=LMG 32353T=DSM 112698T) has been deposited in public cell-type culture centres.
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Affiliation(s)
- Kostadin Evgeniev Atanasov
- Department of Biology, Healthcare and the Environment, Plant Physiology Section, Faculty of Pharmacy and Food Sciences, University of Barcelona, Barcelona, Spain
- Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Bellaterra, Barcelona, Spain
| | - David Miñana Galbis
- Department of Biology, Healthcare and the Environment, Microbiology Section, Faculty of Pharmacy and Food Sciences, University of Barcelona, Barcelona, Spain
| | - Julia Gallego
- Applied Microbiology and Biotechnology Unit, LEITAT Technological Center, Terrassa, Spain
| | - Annabel Serpico
- Applied Microbiology and Biotechnology Unit, LEITAT Technological Center, Terrassa, Spain
| | - Montserrat Bosch
- Applied Microbiology and Biotechnology Unit, LEITAT Technological Center, Terrassa, Spain
| | - Teresa Altabella
- Department of Biology, Healthcare and the Environment, Plant Physiology Section, Faculty of Pharmacy and Food Sciences, University of Barcelona, Barcelona, Spain
- Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Bellaterra, Barcelona, Spain
| | - Albert Ferrer
- Department of Biochemistry and Physiology, Faculty of Pharmacy and Food Sciences, University of Barcelona, Barcelona, Spain
- Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Bellaterra, Barcelona, Spain
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He AL, Li HR, Li HP, Gou JY, Chen J, Zhao Q, Zhang JL. Taxonomic description of Pseudomonas rhizovicinus sp. nov., isolated from the rhizosphere of a desert shrub Haloxylon ammodendron. Antonie van Leeuwenhoek 2021; 114:1443-1452. [PMID: 34272636 DOI: 10.1007/s10482-021-01612-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Accepted: 06/30/2021] [Indexed: 11/30/2022]
Abstract
A Gram-negative aerobic bacterium, strain M30-35 T, was isolated from the rhizosphere of Haloxylon ammodendron in Tengger desert, Gansu province, northwest China. Our previous research indicated that strain M30-35 T can promote the growth of ryegrass (Lolium perenne L.). In this study, strain M30-35 T was subjected to a polyphasic taxonomic study. Phylogenetic analysis of the 16S rRNA gene and two other housekeeping genes (gyrB, rpoD) showed that strain M30-35 T is a member of Pseudomonas anguilliseptica group. The average nucleotide identity (ANI) scores for strains KMM 3042 T and FR1439T were 76.5% and 83.7%, respectively, and DNA-DNA hybridization (DDH) were 21.6% and 26.6%, respectively, and the rates were less than the threshold range for species determination. The dominant cellular fatty acids of strain M30-35 T were C16:0 (22.7%), summed feature 3 (C16:1ω7c and/or C16:1ω6c; 18.5%), summed feature 8 (C18:1ω7c and/or C18:1ω6c; 23.1%). The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phospholipid and aminophospholipid and the predominant respiratory quinone was ubiquinone (Q9). On the basis of above data, it can be concluded that strain M30-35 T represents a novel species in the genus Pseudomonas, for which the name Pseudomonas rhizovicinus sp. nov. is proposed. The type strain is M30-35 T (= MCCC 1K03247T = KCTC 52664 T).
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Affiliation(s)
- Ao-Lei He
- Center for Grassland Microbiome, State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730000, People's Republic of China
| | - Hui-Ru Li
- Center for Grassland Microbiome, State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730000, People's Republic of China
| | - Hui-Ping Li
- Center for Grassland Microbiome, State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730000, People's Republic of China
| | - Jing-Yi Gou
- Center for Grassland Microbiome, State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730000, People's Republic of China
| | - Jia Chen
- Center for Grassland Microbiome, State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730000, People's Republic of China
| | - Qi Zhao
- Center for Grassland Microbiome, State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730000, People's Republic of China.
| | - Jin-Lin Zhang
- Center for Grassland Microbiome, State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730000, People's Republic of China.
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