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Abdullaeva Y, Ratering S, Rosado-Porto D, Ambika Manirajan B, Glatt A, Schnell S, Cardinale M. Domestication caused taxonomical and functional shifts in the wheat rhizosphere microbiota, and weakened the natural bacterial biocontrol against fungal pathogens. Microbiol Res 2024; 281:127601. [PMID: 38218094 DOI: 10.1016/j.micres.2024.127601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 12/14/2023] [Accepted: 01/02/2024] [Indexed: 01/15/2024]
Abstract
Modern crops might have lost some of their functional traits, required for interacting with beneficial microbes, as a result of the genotypic/phenotypic modifications that occurred during domestication. Here, we studied the bacterial and fungal microbiota in the rhizosphere of two cultivated wheat species (Triticum aestivum and T. durum) and their respective ancestors (Aegilops tauschii and T. dicoccoides), in three experimental fields, by using metabarcoding of 16S rRNA genes and ITS2, coupled with co-occurrence network analysis. Moreover, the abundance of bacterial genes involved in N- and P-cycles was estimated by quantitative PCR, and urease, alkaline phosphatase and phosphomonoesterase activities were assessed by enzymatic tests. The relationships between microbiota and environmental metadata were tested by correlation analysis. The assemblage of core microbiota was affected by both site and plant species. No significant differences in the abundance of potential fungal pathogens between wild and cultivated wheat species were found; however, co-occurrence analysis showed more bacterial-fungal negative correlations in the wild species. Concerning functions, the nitrogen denitrification nirS gene was consistently more abundant in the rhizosphere of A. tauschii than T. aestivum. Urease activity was higher in the rhizosphere of each wild wheat species in at least two of the research locations. Several microbiota members, including potentially beneficial taxa such as Lysobacter and new taxa such as Blastocatellaceae, were found to be strongly correlated to rhizospheric soil metadata. Our results showed that a functional microbiome shift occurred as a result of wheat domestication. Notably, these changes also included the reduction of the natural biocontrol potential of rhizosphere-associated bacteria against pathogenic fungi, suggesting that domestication disrupted the equilibrium of plant-microbe relationships that had been established during million years of co-evolution.
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Affiliation(s)
| | - Stefan Ratering
- Institute of Applied Microbiology, Justus-Liebig-University, Giessen, Germany
| | - David Rosado-Porto
- Institute of Applied Microbiology, Justus-Liebig-University, Giessen, Germany
| | | | - Andrea Glatt
- Institute of Applied Microbiology, Justus-Liebig-University, Giessen, Germany
| | - Sylvia Schnell
- Institute of Applied Microbiology, Justus-Liebig-University, Giessen, Germany.
| | - Massimiliano Cardinale
- Institute of Applied Microbiology, Justus-Liebig-University, Giessen, Germany; Department of Biological and Environmental Sciences and Technologies - DiSTeBA, University of Salento, Lecce, Italy.
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2
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Quiroga S, Rosado-Porto D, Ratering S, Rekowski A, Schulz F, Krutych M, Zörb C, Schnell S. Long-term detection of Hartmannibacter diazotrophicus on winter wheat and spring barley roots under field conditions revealed positive correlations on yield parameters with the bacterium abundance. FEMS Microbiol Ecol 2024; 100:fiae023. [PMID: 38366928 PMCID: PMC10939331 DOI: 10.1093/femsec/fiae023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 02/09/2024] [Accepted: 02/15/2024] [Indexed: 02/19/2024] Open
Abstract
Monitoring of bioinoculants once released into the field remains largely unexplored; thus, more information is required about their survival and interactions after root colonization. Therefore, specific primers were used to perform a long-term tracking to elucidate the effect of Hartmannibacter diazotrophicus on wheat and barley production at two experimental organic agriculture field stations. Three factors were evaluated: organic fertilizer application (with and without), row spacing (15 and 50 cm), and bacterial inoculation (H. diazotrophicus and control without bacteria). Hartmannibacter diazotrophicus was detected by quantitative polymerase chain reaction on the roots (up to 5 × 105 copies g-1 dry weight) until advanced developmental stages under field conditions during two seasons, and mostly in one farm. Correlation analysis showed a significant effect of H. diazotrophicus copy numbers on the yield parameters straw yield (increase of 453 kg ha-1 in wheat compared to the mean) and crude grain protein concentration (increase of 0.30% in wheat and 0.80% in barley compared to the mean). Our findings showed an apparently constant presence of H. diazotrophicus on both wheat and barley roots until 273 and 119 days after seeding, respectively, and its addition and concentration in the roots are associated with higher yields in one crop.
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Affiliation(s)
- Santiago Quiroga
- Institute of Applied Microbiology, IFZ, Justus-Liebig University Giessen, 35392 Giessen, Germany
| | - David Rosado-Porto
- Institute of Applied Microbiology, IFZ, Justus-Liebig University Giessen, 35392 Giessen, Germany
- Faculty of Basic and Biomedical Sciences, Simón Bolívar University, 080002 Barranquilla, Colombia
| | - Stefan Ratering
- Institute of Applied Microbiology, IFZ, Justus-Liebig University Giessen, 35392 Giessen, Germany
| | - Azin Rekowski
- Institute of Crop Science, Quality of Plant Products, 340e, University of Hohenheim, 70593 Stuttgart, Germany
| | - Franz Schulz
- Department of Agronomy and Plant Breeding II, Justus-Liebig University Giessen, 35394 Giessen, Germany
| | - Marina Krutych
- Institute of Applied Microbiology, IFZ, Justus-Liebig University Giessen, 35392 Giessen, Germany
| | - Christian Zörb
- Institute of Crop Science, Quality of Plant Products, 340e, University of Hohenheim, 70593 Stuttgart, Germany
| | - Sylvia Schnell
- Institute of Applied Microbiology, IFZ, Justus-Liebig University Giessen, 35392 Giessen, Germany
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Cardinale M, Schnell S. Is the plant microbiome transmitted from pollen to seeds? Front Microbiol 2024; 15:1343795. [PMID: 38414764 PMCID: PMC10897013 DOI: 10.3389/fmicb.2024.1343795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 01/29/2024] [Indexed: 02/29/2024] Open
Affiliation(s)
- Massimiliano Cardinale
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy
| | - Sylvia Schnell
- Institute of Applied Microbiology, Justus-Liebig-University Giessen, Giessen, Germany
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Alvarez-Zapata M, Franco-Vega A, Rondero AG, Guerra RS, Flores BIJ, Comas-García M, Ovalle CO, Schneider B, Ratering S, Schnell S, Martinez-Gutierrez F. Modulation of the Altered Intestinal Microbiota by Use of Antibiotics with a Novel Synbiotic on Wistar Rats. Probiotics Antimicrob Proteins 2023:10.1007/s12602-023-10204-0. [PMID: 38127241 DOI: 10.1007/s12602-023-10204-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/09/2023] [Indexed: 12/23/2023]
Abstract
The use of antibiotics unbalances the intestinal microbiota. Probiotics, prebiotics, and synbiotics are alternatives for these unbalances. The effects of a new synbiotic composed of probiotic Saccharomyces boulardii CNCM I-745 and fructans from Agave salmiana (fAs) as prebiotics were assessed to modulate the intestinal microbiota. Two probiotic presentations, the commercial probiotic (CP) and the microencapsulated probiotic (MP) to improve those effects, were used to prepare the synbiotics and feed Wistar rats subjected to antibiotics (AB). Eight groups were studied, including five controls and three groups to modulate the microbiota after the use of antibiotics: G5: AB + MP-synbiotic, G6: AB + CP-synbiotic, and G8: AB + fAs. All treatments were administered daily for 7 days. On days 7 and 21, euthanasia was performed, cecum tissue was recovered and used to evaluate histological analysis and to study microphotograph by TEM, and finally, bacterial DNA was extracted and 16S rRNA gene metabarcode sequencing was performed. Histological analysis showed less epithelial damage and more abundance of the intestinal microbiota in the groups G5, G6, and G8 in comparison with the AB control group after 7 days. Microphotograph of the cecum at 2 weeks post treatment showed that G5 and G6 presented beneficial effects in epithelial reconstruction. Interestingly, in the groups that used the synbiotic without AB (G3 and G4) in addition to contributing to the recovery of the autochthonous microbiota, it promotes the development of beneficial microorganisms; those results were also achieved in the groups that used the synbiotic with AB enhancing the bacterial diversity and regulating the impact of AB.
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Affiliation(s)
- Miguel Alvarez-Zapata
- Laboratorio de Antimicrobianos, Biopelículas y Microbiota, Facultad de Ciencias Químicas, U.A.S.L.P., Av. Dr. Manuel Nava No. 6 Zona Universitaria, CP 78210, San Luis Potosí, S.L.P., México
| | - Avelina Franco-Vega
- Laboratorio de Tecnologías Emergentes, Facultad de Ciencias Químicas, U.A.S.L.P., San Luis Potosí, México
| | - Adriana Ganem Rondero
- Laboratorio de Investigación y Posgrado en Tecnología Farmacéutica (L-322), Facultad de Estudios Superiores Cuautitlán, Universidad Nacional Autónoma de México, Mexico City, Estado de México, México
| | - Ruth Soria Guerra
- Laboratorio de Biotecnología de plantas, Facultad de Ciencias Químicas, U.A.S.L.P., San Luis Potosí, México
| | | | - Mauricio Comas-García
- Sección de Genómica Médica, Centro de Investigación en Biomedicina y Salud, U.A.S.L.P., San Luis Potosí, México
- Sección de Microscopía de Alta Resolución, Centro de Investigación en Biomedicina y Salud, U.A.S.L.P., San Luis Potosí, Mexico
- Facultad de Ciencias, U.A.S.L.P., San Luis Potosi, Mexico
| | | | - Belinda Schneider
- Institute of Applied Microbiology, Justus Liebig University Giessen, Giessen, Germany
| | - Stefan Ratering
- Institute of Applied Microbiology, Justus Liebig University Giessen, Giessen, Germany
| | - Sylvia Schnell
- Institute of Applied Microbiology, Justus Liebig University Giessen, Giessen, Germany
| | - Fidel Martinez-Gutierrez
- Laboratorio de Antimicrobianos, Biopelículas y Microbiota, Facultad de Ciencias Químicas, U.A.S.L.P., Av. Dr. Manuel Nava No. 6 Zona Universitaria, CP 78210, San Luis Potosí, S.L.P., México.
- Sección de Genómica Médica, Centro de Investigación en Biomedicina y Salud, U.A.S.L.P., San Luis Potosí, México.
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Sacharow J, Salehi-Mobarakeh E, Ratering S, Imani J, Österreicher Cunha-Dupont A, Schnell S. Control of Blumeria graminis f. sp. hordei on Barley Leaves by Treatment with Fungi-Consuming Protist Isolates. Curr Microbiol 2023; 80:384. [PMID: 37872440 PMCID: PMC10593611 DOI: 10.1007/s00284-023-03497-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 09/08/2023] [Indexed: 10/25/2023]
Abstract
The obligate biotrophic fungal pathogen Blumeria graminis causes the powdery mildew disease of cereals, which results in large crop losses. Control of B. graminis in barley is mainly achieved by fungicide treatment and by breeding resistant varieties. Vampyrellid amoebae, just like mycophagous protists, are able to consume a variety of fungi. To reveal the impact of some selected fungus-consuming protists on Blumeria graminis f. sp. hordei (Bgh), and to evaluate the possibility of using these protists as biological agents in the future, their feeding behaviour on B. graminis spores on barley leaves was investigated. An experiment was carried out with five different protist isolates (Leptophrys vorax, Platyreta germanica, Theratromyxa weberi U 11, Theratromyxa weberi G7.2 and Acanthamoeba castellanii) and four matched controls, including the food sources of the cultures and the medium. Ten-day-old leaves of barley (Hordeum vulgare cv. Golden Promise) were first inoculated with Blumeria graminis (f. sp. hordei race A6) spores, then treated with protists and fungal colonies on the leaf surfaces were counted under the microscope after 5 days. The isolates L. vorax, P. germanica, and T. weberi U11 did not show a significant reduction in the number of powdery mildew colonies whereas the isolates T. weberi G7.2 and A. castellanii significantly reduced the number of powdery mildew colonies on the leaf surfaces compared to their respective controls. This indicates that these two isolates are capable of reducing B. graminis colonies on barley leaves and are suitable candidates for further investigation for possible use as biological agents. Nevertheless, the susceptibility to dryness and the cell division rate should be considered during the optimisation of the next steps like application procedure and whole plant treatment.
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Affiliation(s)
- Julia Sacharow
- Institute of Applied Microbiology, IFZ, Justus-Liebig-University, Giessen, Germany
| | | | - Stefan Ratering
- Institute of Applied Microbiology, IFZ, Justus-Liebig-University, Giessen, Germany
| | - Jafargholi Imani
- Institute of Phytopathology, IFZ, Justus-Liebig-University, Giessen, Germany
| | | | - Sylvia Schnell
- Institute of Applied Microbiology, IFZ, Justus-Liebig-University, Giessen, Germany.
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Shi H, Ambika Manirajan B, Ratering S, Geissler-Plaum R, Schnell S. Robbsia betulipollinis sp. nov., Isolated from Pollen of Birch (Betula pendula). Curr Microbiol 2023; 80:234. [PMID: 37278851 DOI: 10.1007/s00284-023-03344-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 05/23/2023] [Indexed: 06/07/2023]
Abstract
One gram-negative strain designated Bb-Pol-6 T was isolated from birch (Betula pendula) pollen at Giessen area, Germany. The analysis of 16S rRNA gene-based phylogenies indicated the next-relative genera were Robbsia, Chitinasiproducens, Pararobbsia and Paraburkholderia (96-95.6%). Further comparative genome analysis and phylogenetic tree-based methods revealed its phylogenetic position under the genus Robbsia. The genome of strain Bb-Pol-6 T was 5.04 Mbp with 4401 predicted coding sequences and a G + C content of 65.31 mol%. Average amino acid identity, average nucleotide identity, digital DNA-DNA hybridization and percentage of conserved proteins values to Robbsia andropogonis DSM 9511 T were 68.0, 72.5, 22.7 and 65.85%, respectively. Strain Bb-Pol-6 T was rod-shaped, non-motile, facultative anaerobic and grew optimally at 28 °C and pH 6-7. Ubiquinone 8 was the major respiratory quinone and the major cellular fatty acids were C16:0, C19:0 cyclo ω7c, C17:0 cyclo ω7c and C17:1 ω6c. The dominant polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and an unidentified aminophospholipid. Based on the genomic physiological and phenotypic characteristics, strain Bb-Pol-6 T was considered a novel species under the genus Robbsia, for which the name Robbsia betulipollinis sp. nov. was proposed. The type strain is Bb-Pol-6 T (= LMG 32774 T = DSM 114812 T).
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Affiliation(s)
- Haoran Shi
- Institute of Applied Microbiology, Research Center for BioSystems, Land Use, and Nutrition (IFZ), Justus-Liebig University Giessen, 35392, Giessen, Germany
| | - Binoy Ambika Manirajan
- Institute of Applied Microbiology, Research Center for BioSystems, Land Use, and Nutrition (IFZ), Justus-Liebig University Giessen, 35392, Giessen, Germany
- School of Biosciences, Mahatma Gandhi University, Kerala, India
| | - Stefan Ratering
- Institute of Applied Microbiology, Research Center for BioSystems, Land Use, and Nutrition (IFZ), Justus-Liebig University Giessen, 35392, Giessen, Germany.
| | - Rita Geissler-Plaum
- Institute of Applied Microbiology, Research Center for BioSystems, Land Use, and Nutrition (IFZ), Justus-Liebig University Giessen, 35392, Giessen, Germany
| | - Sylvia Schnell
- Institute of Applied Microbiology, Research Center for BioSystems, Land Use, and Nutrition (IFZ), Justus-Liebig University Giessen, 35392, Giessen, Germany
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7
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Ferdian E, Marlevi D, Schollenberger J, Aristova M, Edelman ER, Schnell S, Figueroa CA, Nordsletten DA, Young AA. Cerebrovascular super-resolution 4D Flow MRI - Sequential combination of resolution enhancement by deep learning and physics-informed image processing to non-invasively quantify intracranial velocity, flow, and relative pressure. Med Image Anal 2023; 88:102831. [PMID: 37244143 DOI: 10.1016/j.media.2023.102831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 04/04/2023] [Accepted: 04/20/2023] [Indexed: 05/29/2023]
Abstract
The development of cerebrovascular disease is tightly coupled to regional changes in intracranial flow and relative pressure. Image-based assessment using phase contrast magnetic resonance imaging has particular promise for non-invasive full-field mapping of cerebrovascular hemodynamics. However, estimations are complicated by the narrow and tortuous intracranial vasculature, with accurate image-based quantification directly dependent on sufficient spatial resolution. Further, extended scan times are required for high-resolution acquisitions, and most clinical acquisitions are performed at comparably low resolution (>1 mm) where biases have been observed with regard to the quantification of both flow and relative pressure. The aim of our study was to develop an approach for quantitative intracranial super-resolution 4D Flow MRI, with effective resolution enhancement achieved by a dedicated deep residual network, and with accurate quantification of functional relative pressures achieved by subsequent physics-informed image processing. To achieve this, our two-step approach was trained and validated in a patient-specific in-silico cohort, showing good accuracy in estimating velocity (relative error: 15.0 ± 0.1%, mean absolute error (MAE): 0.07 ± 0.06 m/s, and cosine similarity: 0.99 ± 0.06 at peak velocity) and flow (relative error: 6.6 ± 4.7%, root mean square error (RMSE): 0.56 mL/s at peak flow), and with the coupled physics-informed image analysis allowing for maintained recovery of functional relative pressure throughout the circle of Willis (relative error: 11.0 ± 7.3%, RMSE: 0.3 ± 0.2 mmHg). Furthermore, the quantitative super-resolution approach is applied to an in-vivo volunteer cohort, effectively generating intracranial flow images at <0.5 mm resolution and showing reduced low-resolution bias in relative pressure estimation. Our work thus presents a promising two-step approach to non-invasively quantify cerebrovascular hemodynamics, being applicable to dedicated clinical cohorts in the future.
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Affiliation(s)
- E Ferdian
- University of Auckland, Auckland 1142 New Zealand
| | - D Marlevi
- Massachusetts Institute of Technology, Cambridge, MA 02139 USA
| | | | - M Aristova
- Northwestern University, Chicago, IL 60611, USA
| | - E R Edelman
- Massachusetts Institute of Technology, Cambridge, MA 02139 USA
| | - S Schnell
- Northwestern University, Chicago, IL 60611, USA; University of Greifswald, Greifswald 17489, Germany
| | - C A Figueroa
- University of Michigan, Ann Arbor, MI 48109, USA
| | - D A Nordsletten
- University of Michigan, Ann Arbor, MI 48109, USA; King's College London, London, SE1 7EH, UK
| | - A A Young
- University of Auckland, Auckland 1142 New Zealand; King's College London, London, SE1 7EH, UK
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Vega-Cárdenas M, Martínez-Gutierrez F, Lara-Ramírez EE, Reynaga-Hernandez E, Yañez-Estrada L, Ratering S, Schnell S, Godínez-Hernández CI, Vargas-Morales JM, Portales-Pérez DP. Agave fructans enhance the effects of fermented milk products on obesity biomarkers: a randomised trial. Benef Microbes 2023; 14:153-164. [PMID: 36856122 DOI: 10.3920/bm2022.0078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
Dysbiosis has been implicated in childhood obesity. Oral intake of fermented milk containing Lacticaseibacillus casei strain Shirota preserves gut microbiota (GM) diversity in children and adults. This study was a double-blind trial involving 37 overweight or obese children aged 6-10 years. Children were followed over a 6-week intervention period in which they received different fermented milk products containing L. casei Shirota: 10 in the first group received just L. casei Shirota; 13 received L. casei Shirota with 3 g/day of inulin (L. casei+inulin); and 14 received L. casei Shirota with 3 g/day of fructans from Agave salmiana (L. casei+fructans). Principal component analysis showed the relationship between microbial abundance, GM metabolites, and other obesity-related markers. Supplementation with probiotics and synbiotics improved the HDL-cholesterol levels of overweight and obese children, although no changes in body composition were detected. We observed an increase in butyrate or propionate concentrations in the L. casei+fructans group compared to the end of the intervention (P<0.03). A diminished level of ANGPTL4 within the L. casei+fructans group (P=0.04) was also found, but no differences when lipopolysaccharide-binding protein was evaluated. The FFAR2+ cell frequency decreased between baseline and at the end of 6-week intervention in L. casei+inulin (P=0.02) and L. casei+fructans groups (P=0.04). In contrast, the percentage of CD14+FFAR3+ frequency increased in the same groups (P=0.04). The L. casei Shirota with inulin or fructans modulates GM, which improves the lipid profile and changes at a molecular level, such as expression of FFAR3 and FFAR2, ANGPTL4, propionate, and butyrate. It, therefore, could be considered an interesting therapeutic possibility for treating childhood overweight and obesity. The study was registered at ClinicalTrials.gov (ID: NCT05423015).
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Affiliation(s)
- M Vega-Cárdenas
- Research Centre for Health Sciences and Biomedicine, Autonomous University of San Luis Potosí (UASLP), Av. Sierra Leona 550, Lomas de San Luis 78210, San Luis Potosí, SLP, Mexico
| | - F Martínez-Gutierrez
- Research Centre for Health Sciences and Biomedicine, Autonomous University of San Luis Potosí (UASLP), Av. Sierra Leona 550, Lomas de San Luis 78210, San Luis Potosí, SLP, Mexico.,Faculty of Chemical Sciences, UASLP, Av. Dr. Manuel Nava 6, Zona Universitaria 78210, San Luis Potosí, SLP, Mexico
| | - E E Lara-Ramírez
- Zacatecas Biomedical Research Unit, Mexican Social Security Institute (IMSS), Alameda Trinidad García de La Cadena 438, Zacatecas Centro 98000 Zacatecas, Zac, Mexico
| | - E Reynaga-Hernandez
- Faculty of Chemical Sciences, UASLP, Av. Dr. Manuel Nava 6, Zona Universitaria 78210, San Luis Potosí, SLP, Mexico
| | - L Yañez-Estrada
- Faculty of Medicine, UASLP, Av. Dr. Manuel Nava 6, Zona Universitaria 78210, San Luis Potosí, SLP, Mexico
| | - S Ratering
- Institute of Applied Microbiology, Justus Liebig University, Schubertstr. 81 35392, Giessen, Germany
| | - S Schnell
- Institute of Applied Microbiology, Justus Liebig University, Schubertstr. 81 35392, Giessen, Germany
| | - C I Godínez-Hernández
- Desert Zones Research Institute, UASLP, De Altair 200, Col del Llano, 78377, San Luis Potosí, SLP, Mexico
| | - J M Vargas-Morales
- Faculty of Chemical Sciences, UASLP, Av. Dr. Manuel Nava 6, Zona Universitaria 78210, San Luis Potosí, SLP, Mexico
| | - D P Portales-Pérez
- Research Centre for Health Sciences and Biomedicine, Autonomous University of San Luis Potosí (UASLP), Av. Sierra Leona 550, Lomas de San Luis 78210, San Luis Potosí, SLP, Mexico.,Faculty of Chemical Sciences, UASLP, Av. Dr. Manuel Nava 6, Zona Universitaria 78210, San Luis Potosí, SLP, Mexico
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9
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Orban A, Jerschow JJ, Birk F, Suarez C, Schnell S, Rühl M. Effect of bacterial volatiles on the mycelial growth of mushrooms. Microbiol Res 2023; 266:127250. [DOI: 10.1016/j.micres.2022.127250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 10/20/2022] [Accepted: 10/31/2022] [Indexed: 11/06/2022]
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10
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Rosado-Porto D, Ratering S, Moser G, Deppe M, Müller C, Schnell S. Soil metatranscriptome demonstrates a shift in C, N, and S metabolisms of a grassland ecosystem in response to elevated atmospheric CO2. Front Microbiol 2022; 13:937021. [PMID: 36081791 PMCID: PMC9445814 DOI: 10.3389/fmicb.2022.937021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 08/01/2022] [Indexed: 11/16/2022] Open
Abstract
Soil organisms play an important role in the equilibrium and cycling of nutrients. Because elevated CO2 (eCO2) affects plant metabolism, including rhizodeposition, it directly impacts the soil microbiome and microbial processes. Therefore, eCO2 directly influences the cycling of different elements in terrestrial ecosystems. Hence, possible changes in the cycles of carbon (C), nitrogen (N), and sulfur (S) were analyzed, alongside the assessment of changes in the composition and structure of the soil microbiome through a functional metatranscriptomics approach (cDNA from mRNA) from soil samples taken at the Giessen free-air CO2 enrichment (Gi-FACE) experiment. Results showed changes in the expression of C cycle genes under eCO2 with an increase in the transcript abundance for carbohydrate and amino acid uptake, and degradation, alongside an increase in the transcript abundance for cellulose, chitin, and lignin degradation and prokaryotic carbon fixation. In addition, N cycle changes included a decrease in the transcript abundance of N2O reductase, involved in the last step of the denitrification process, which explains the increase of N2O emissions in the Gi-FACE. Also, a shift in nitrate (NO3-) metabolism occurred, with an increase in transcript abundance for the dissimilatory NO3- reduction to ammonium (NH4+) (DNRA) pathway. S metabolism showed increased transcripts for sulfate (SO42-) assimilation under eCO2 conditions. Furthermore, soil bacteriome, mycobiome, and virome significantly differed between ambient and elevated CO2 conditions. The results exhibited the effects of eCO2 on the transcript abundance of C, N, and S cycles, and the soil microbiome. This finding showed a direct connection between eCO2 and the increased greenhouse gas emission, as well as the importance of soil nutrient availability to maintain the balance of soil ecosystems.
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Affiliation(s)
- David Rosado-Porto
- Institute of Applied Microbiology, Justus Liebig University, Giessen, Germany
- Faculty of Basic and Biomedical Sciences, Simón Bolívar University, Barranquilla, Colombia
| | - Stefan Ratering
- Institute of Applied Microbiology, Justus Liebig University, Giessen, Germany
| | - Gerald Moser
- Institute of Plant Ecology, Justus Liebig University, Giessen, Germany
| | - Marianna Deppe
- Institute of Plant Ecology, Justus Liebig University, Giessen, Germany
| | - Christoph Müller
- Institute of Plant Ecology, Justus Liebig University, Giessen, Germany
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Dublin, Ireland
| | - Sylvia Schnell
- Institute of Applied Microbiology, Justus Liebig University, Giessen, Germany
- *Correspondence: Sylvia Schnell
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11
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Brandau L, Jacksch S, Weis S, Schnell S, Egert M. Minority report: small-scale metagenomic analysis of the non-bacterial kitchen sponge microbiota. Arch Microbiol 2022; 204:363. [PMID: 35661258 PMCID: PMC9167186 DOI: 10.1007/s00203-022-02969-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 05/04/2022] [Accepted: 05/05/2022] [Indexed: 11/30/2022]
Abstract
Kitchen sponges are particularly well known to harbor a high number and diversity of bacteria, including pathogens. Viruses, archaea, and eukaryotes in kitchen sponges, however, have not been examined in detail so far. To increase knowledge on the non-bacterial kitchen sponge microbiota and its potential hygienic relevance, we investigated five used kitchen sponges by means of metagenomic shot-gun sequencing. Viral particles were sought to be enriched by a filter step during DNA extraction from the sponges. Data analysis revealed that ~ 2% of the sequences could be assigned to non-bacterial taxa. Each sponge harbored different virus (phage) species, while the present archaea were predominantly affiliated with halophilic taxa. Among the eukaryotic taxa, besides harmless algae, or amoebas, mainly DNA from food-left-overs was found. The presented work offers new insights into the complex microbiota of used kitchen sponges and contributes to a better understanding of their hygienic relevance.
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Affiliation(s)
- Lena Brandau
- Faculty of Medical and Life Sciences, Institute of Precision Medicine, Microbiology and Hygiene Group, Furtwangen University, Villingen-Schwenningen, Germany
| | - Susanne Jacksch
- Faculty of Medical and Life Sciences, Institute of Precision Medicine, Microbiology and Hygiene Group, Furtwangen University, Villingen-Schwenningen, Germany
| | - Severin Weis
- Faculty of Medical and Life Sciences, Institute of Precision Medicine, Microbiology and Hygiene Group, Furtwangen University, Villingen-Schwenningen, Germany
| | - Sylvia Schnell
- Research Centre for BioSystems, Land Use, and Nutrition (IFZ), Institute of Applied Microbiology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Markus Egert
- Faculty of Medical and Life Sciences, Institute of Precision Medicine, Microbiology and Hygiene Group, Furtwangen University, Villingen-Schwenningen, Germany.
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12
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Brandau L, Weis S, Weyland M, Berger FK, Schnell S, Schäfer KH, Egert M. RNA-based stable isotope probing provides no indication for rapid α-synuclein assimilation by murine gut bacteria. Access Microbiol 2022; 4:acmi000345. [PMID: 36003361 PMCID: PMC9394525 DOI: 10.1099/acmi.0.000345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 02/19/2022] [Indexed: 11/23/2022] Open
Abstract
In Parkinson’s disease (PD), α-synuclein is a key protein in the process of neurodegeneration. Besides motor symptoms, most PD patients additionally suffer from gastrointestinal tract (GIT) dysfunctions, even several years before the onset of motor disabilities. Studies have reported a dysbiosis of gut bacteria in PD patients compared to healthy controls and have suggested that the enteric nervous system (ENS) can be involved in the development of the disease. As α-synuclein was found to be secreted by neurons of the ENS, we used RNA-based stable isotope probing (RNA-SIP) to identify gut bacteria that might be able to assimilate this protein. The gut contents of 24 mice were pooled and incubated with isotopically labelled (13C) and unlabelled (12C) α-synuclein. After incubation for 0, 4 and 24 h, RNA was extracted from the incubations and separated by density gradient centrifugation. However, RNA quantification of density-resolved fractions revealed no incorporation of the 13C isotope into the extracted RNA, suggesting that α-synuclein was not assimilated by the murine gut bacteria. Potential reasons and consequences for follow-up-studies are discussed.
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Affiliation(s)
- Lena Brandau
- Faculty of Medical and Life Sciences, Institute of Precision Medicine, Microbiology and Hygiene Group, Furtwangen University, Jakob-Kienzle-Straße 17, Villingen-Schwenningen, Germany
| | - Severin Weis
- Faculty of Medical and Life Sciences, Institute of Precision Medicine, Microbiology and Hygiene Group, Furtwangen University, Jakob-Kienzle-Straße 17, Villingen-Schwenningen, Germany
| | - Maximilian Weyland
- Department of Informatics and Microsystem Technology, University of Applied Sciences Kaiserslautern, Working Group Enteric Nervous System, Amerikastraße 1, Zweibrücken, Germany
| | - Fabian K. Berger
- German National Reference Centre for Clostridioides (Clostridium) difficile, Homburg/Saar-Münster-Coesfeld, Germany
- Institute for Medical Microbiology and Hygiene, Saarland University, Kirrberger Straße 100, Homburg/Saar, Germany
| | - Sylvia Schnell
- Research Centre for BioSystems, Land Use, and Nutrition (IFZ), Institute of Applied Microbiology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Karl-Herbert Schäfer
- Department of Informatics and Microsystem Technology, University of Applied Sciences Kaiserslautern, Working Group Enteric Nervous System, Amerikastraße 1, Zweibrücken, Germany
| | - Markus Egert
- Faculty of Medical and Life Sciences, Institute of Precision Medicine, Microbiology and Hygiene Group, Furtwangen University, Jakob-Kienzle-Straße 17, Villingen-Schwenningen, Germany
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13
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Martinez-Martinez MU, Vázquez-Maldonado D, Ratering S, Godínez-Hernández C, Ortiz-Basurto RI, Soria-Guerra RE, Schneider B, Juárez-Flores BI, Portales-Pérez DP, Schnell S, Martinez-Gutierrez F. Fructans from Agave enhance probiotic yoghurt by modulating gut microbiota on children with overweight or obesity. FOOD BIOSCI 2022. [DOI: 10.1016/j.fbio.2021.101516] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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14
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Rosado-Porto D, Ratering S, Cardinale M, Maisinger C, Moser G, Deppe M, Müller C, Schnell S. Elevated Atmospheric CO 2 Modifies Mostly the Metabolic Active Rhizosphere Soil Microbiome in the Giessen FACE Experiment. Microb Ecol 2022; 83:619-634. [PMID: 34148108 PMCID: PMC8979872 DOI: 10.1007/s00248-021-01791-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 06/08/2021] [Indexed: 06/12/2023]
Abstract
Elevated levels of atmospheric CO2 lead to the increase of plant photosynthetic rates, carbon inputs into soil and root exudation. In this work, the effects of rising atmospheric CO2 levels on the metabolic active soil microbiome have been investigated at the Giessen free-air CO2 enrichment (Gi-FACE) experiment on a permanent grassland site near Giessen, Germany. The aim was to assess the effects of increased C supply into the soil, due to elevated CO2, on the active soil microbiome composition. RNA extraction and 16S rRNA (cDNA) metabarcoding sequencing were performed from bulk and rhizosphere soils, and the obtained data were processed for a compositional data analysis calculating diversity indices and differential abundance analyses. The structure of the metabolic active microbiome in the rhizospheric soil showed a clear separation between elevated and ambient CO2 (p = 0.002); increased atmospheric CO2 concentration exerted a significant influence on the microbiomes differentiation (p = 0.01). In contrast, elevated CO2 had no major influence on the structure of the bulk soil microbiome (p = 0.097). Differential abundance results demonstrated that 42 bacterial genera were stimulated under elevated CO2. The RNA-based metabarcoding approach used in this research showed that the ongoing atmospheric CO2 increase of climate change will significantly shift the microbiome structure in the rhizosphere.
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Affiliation(s)
- David Rosado-Porto
- Institute of Applied Microbiology, Justus Liebig University, Giessen, DE, Germany
- Faculty of Basic and Biomedical Sciences, Simón Bolívar University, Barranquilla, Colombia
| | - Stefan Ratering
- Institute of Applied Microbiology, Justus Liebig University, Giessen, DE, Germany
| | - Massimiliano Cardinale
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Via Prov.le Monteroni, 73100, Lecce, Italy
| | - Corinna Maisinger
- Institute of Applied Microbiology, Justus Liebig University, Giessen, DE, Germany
| | - Gerald Moser
- Institute of Plant Ecology, Justus Liebig University, Giessen, DE, Germany
| | - Marianna Deppe
- Institute of Plant Ecology, Justus Liebig University, Giessen, DE, Germany
| | - Christoph Müller
- Institute of Plant Ecology, Justus Liebig University, Giessen, DE, Germany
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Sylvia Schnell
- Institute of Applied Microbiology, Justus Liebig University, Giessen, DE, Germany.
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15
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Scansani S, van Wyk N, Nader KB, Beisert B, Brezina S, Fritsch S, Semmler H, Pasch L, Pretorius IS, von Wallbrunn C, Schnell S, Rauhut D. The film-forming Pichia spp. in a winemaker's toolbox: A simple isolation procedure and their performance in a mixed-culture fermentation of Vitis vinifera L. cv. Gewürztraminer must. Int J Food Microbiol 2022; 365:109549. [DOI: 10.1016/j.ijfoodmicro.2022.109549] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 12/17/2021] [Accepted: 01/13/2022] [Indexed: 01/21/2023]
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16
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Abdullaeva Y, Ratering S, Ambika Manirajan B, Rosado-Porto D, Schnell S, Cardinale M. Domestication Impacts the Wheat-Associated Microbiota and the Rhizosphere Colonization by Seed- and Soil-Originated Microbiomes, Across Different Fields. Front Plant Sci 2022; 12:806915. [PMID: 35095978 PMCID: PMC8789879 DOI: 10.3389/fpls.2021.806915] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 12/13/2021] [Indexed: 05/17/2023]
Abstract
The seed-transmitted microorganisms and the microbiome of the soil in which the plant grows are major drivers of the rhizosphere microbiome, a crucial component of the plant holobiont. The seed-borne microbiome can be even coevolved with the host plant as a result of adaptation and vertical transmission over generations. The reduced genome diversity and crossing events during domestication might have influenced plant traits that are important for root colonization by seed-borne microbes and also rhizosphere recruitment of microbes from the bulk soil. However, the impact of the breeding on seed-transmitted microbiome composition and the plant ability of microbiome selection from the soil remain unknown. Here, we analyzed both endorhiza and rhizosphere microbiome of two couples of genetically related wild and cultivated wheat species (Aegilops tauschii/Triticum aestivum and T. dicoccoides/T. durum) grown in three locations, using 16S rRNA gene and ITS2 metabarcoding, to assess the relative contribution of seed-borne and soil-derived microbes to the assemblage of the rhizosphere microbiome. We found that more bacterial and fungal ASVs are transmitted from seed to the endosphere of all species compared with the rhizosphere, and these transmitted ASVs were species-specific regardless of location. Only in one location, more microbial seed transmission occurred also in the rhizosphere of A. tauschii compared with other species. Concerning soil-derived microbiome, the most distinct microbial genera occurred in the rhizosphere of A. tauschii compared with other species in all locations. The rhizosphere of genetically connected wheat species was enriched with similar taxa, differently between locations. Our results demonstrate that host plant criteria for soil bank's and seed-originated microbiome recruitment depend on both plants' genotype and availability of microorganisms in a particular environment. This study also provides indications of coevolution between the host plant and its associated microbiome resulting from the vertical transmission of seed-originated taxa.
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Affiliation(s)
| | - Stefan Ratering
- Institute of Applied Microbiology, Justus-Liebig-University, Giessen, Germany
| | | | - David Rosado-Porto
- Institute of Applied Microbiology, Justus-Liebig-University, Giessen, Germany
| | - Sylvia Schnell
- Institute of Applied Microbiology, Justus-Liebig-University, Giessen, Germany
| | - Massimiliano Cardinale
- Institute of Applied Microbiology, Justus-Liebig-University, Giessen, Germany
- Department of Biological and Environmental Sciences and Technologies – DiSTeBA, University of Salento, Lecce, Italy
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17
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Weis S, Meisner A, Schwiertz A, Unger MM, Becker A, Faßbender K, Schnell S, Schäfer KH, Egert M. Association between Parkinson's disease and the faecal eukaryotic microbiota. NPJ Parkinsons Dis 2021; 7:101. [PMID: 34795317 PMCID: PMC8602383 DOI: 10.1038/s41531-021-00244-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 10/21/2021] [Indexed: 12/20/2022] Open
Abstract
Parkinson's disease (PD) is one of the most common neurodegenerative disease, and is so far not considered curable. PD patients suffer from several motor and non-motor symptoms, including gastrointestinal dysfunctions and alterations of the enteric nervous system. Constipation and additional intestinal affections can precede the classical motor symptoms by several years. Recently, we reported effects of PD and related medications on the faecal bacterial community of 34 German PD patients and 25 age-matched controls. Here, we used the same collective and analysed the V6 and V7 hypervariable region of PCR-amplified, eukaryotic 18S rRNA genes using an Illumina MiSeq platform. In all, 53% (18) of the PD samples and 72% (18) of the control samples yielded sufficient amplicons for downstream community analyses. The PD samples showed a significantly lower alpha and a different beta eukaryotic diversity than the controls. Most strikingly, we observed a significantly higher relative abundance of sequence affiliated with the Geotrichum genus in the PD samples (39.7%), when compared to the control samples (0.05%). In addition, we observed lower relative abundances of sequences affiliated with Aspergillus/Penicillium, Charophyta/Linum, unidentified Opisthokonta and three genera of minor abundant zooflagellates in the PD samples. Our data add knowledge to the small body of data about the eukaryotic microbiota of PD patients and suggest a potential association of certain gut eukaryotes and PD.
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Affiliation(s)
- Severin Weis
- Faculty of Medical and Life Sciences, Institute of Precision Medicine, Microbiology and Hygiene Group, Furtwangen University, Villingen-Schwenningen, Germany
| | - Alexandra Meisner
- Faculty of Medical and Life Sciences, Institute of Precision Medicine, Microbiology and Hygiene Group, Furtwangen University, Villingen-Schwenningen, Germany
| | | | - Marcus M Unger
- Department of Neurology, Saarland University, Homburg, Germany
| | - Anouck Becker
- Department of Neurology, Saarland University, Homburg, Germany
| | - Klaus Faßbender
- Department of Neurology, Saarland University, Homburg, Germany
| | - Sylvia Schnell
- Institute of Applied Microbiology, Justus-Liebig-University, Giessen, Germany
| | - Karl-Herbert Schäfer
- Working Group Enteric Nervous System (AGENS), University of Applied Sciences Kaiserslautern, Zweibrücken, Germany
| | - Markus Egert
- Faculty of Medical and Life Sciences, Institute of Precision Medicine, Microbiology and Hygiene Group, Furtwangen University, Villingen-Schwenningen, Germany.
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18
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Vítězová M, Lochman J, Zapletalová M, Ratering S, Schnell S, Vítěz T. Archaeal community dynamics in biogas fermentation at various temperatures assessed by mcrA amplicon sequencing using different primer pairs. World J Microbiol Biotechnol 2021; 37:188. [PMID: 34611812 DOI: 10.1007/s11274-021-03152-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 09/21/2021] [Indexed: 10/20/2022]
Abstract
In this study, the taxonomic and functional diversity of methanogenic archaea in two parallel 120 l fermenters operated at different temperatures and fed with maize silage was estimated by mcrA metabarcoding analysis using two typical primer pairs (ML and MLA) amplifying part of the functional methyl coenzyme M reductase (mcrA) gene. The alpha diversity indices showed that the ML primer pair detected a higher Operational Taxonomic Unit (OTU) abundance compared to the MLA primer pair and methanogen diversity was significantly lower in the 60 °C fermenters. The beta diversity analysis showed the methanogenic community clustered together at 50 °C and 40° and was statistically different from the 60 °C community. Similar, to alpha diversity, beta diversity was also significantly different between primer pairs. At all temperatures analysed, the primer pairs showed a different abundance of the different methanogenic OTUs, e.g. more OTUs relative to Methanoculleus sp. with the ML primer pair, and more OTUs corresponding to Methanobacterium sp. with the MLA primer pair. Moreover, OTUs corresponding to Methanosphaera sp. and Methanobrevibacter sp. were found only by using ML primer pair, while the MLA primer pair detected sequences corresponding to Methanothrix sp.
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Affiliation(s)
- Monika Vítězová
- Department of Experimental Biology, Faculty of Science, Masaryk University, 62500, Brno, Czech Republic
| | - Jan Lochman
- Department of Biochemistry, Faculty of Science, Masaryk University, 62500, Brno, Czech Republic.
| | - Martina Zapletalová
- Department of Biochemistry, Faculty of Science, Masaryk University, 62500, Brno, Czech Republic
| | - Stefan Ratering
- Institute of Applied Microbiology, Justus Liebig University Giessen, 35392, Giessen, Germany
| | - Sylvia Schnell
- Institute of Applied Microbiology, Justus Liebig University Giessen, 35392, Giessen, Germany
| | - Tomáš Vítěz
- Department of Experimental Biology, Faculty of Science, Masaryk University, 62500, Brno, Czech Republic.,Department of Agricultural, Food and Environmental Engineering, Faculty of AgriSciences, Mendel University in Brno, 61300, Brno, Czech Republic
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19
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Alibrandi P, Schnell S, Perotto S, Cardinale M. Diversity and Structure of the Endophytic Bacterial Communities Associated With Three Terrestrial Orchid Species as Revealed by 16S rRNA Gene Metabarcoding. Front Microbiol 2020; 11:604964. [PMID: 33519751 PMCID: PMC7839077 DOI: 10.3389/fmicb.2020.604964] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 11/23/2020] [Indexed: 01/13/2023] Open
Abstract
The endophytic microbiota can establish mutualistic or commensalistic interactions within the host plant tissues. We investigated the bacterial endophytic microbiota in three species of Mediterranean orchids (Neottia ovata, Serapias vomeracea, and Spiranthes spiralis) by metabarcoding of the 16S rRNA gene. We examined whether the different orchid species and organs, both underground and aboveground, influenced the endophytic bacterial communities. A total of 1,930 operational taxonomic units (OTUs) were obtained, mainly Proteobacteria and Actinobacteria, whose distribution model indicated that the plant organ was the main determinant of the bacterial community structure. The co-occurrence network was not modular, suggesting a relative homogeneity of the microbiota between both plant species and organs. Moreover, the decrease in species richness and diversity in the aerial vegetative organs may indicate a filtering effect by the host plant. We identified four hub OTUs, three of them already reported as plant-associated taxa (Pseudoxanthomonas, Rhizobium, and Mitsuaria), whereas Thermus was an unusual member of the plant microbiota. Core microbiota analysis revealed a selective and systemic ascent of bacterial communities from the vegetative to the reproductive organs. The core microbiota was also maintained in the S. spiralis seeds, suggesting a potential vertical transfer of the microbiota. Surprisingly, some S. spiralis seed samples displayed a very rich endophytic microbiota, with a large number of OTUs shared with the roots, a situation that may lead to a putative restoring process of the root-associated microbiota in the progeny. Our results indicate that the bacterial community has adapted to colonize the orchid organs selectively and systemically, suggesting an active involvement in the orchid holobiont.
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Affiliation(s)
- Pasquale Alibrandi
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
- Institute of Applied Microbiology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Sylvia Schnell
- Institute of Applied Microbiology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Silvia Perotto
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Massimiliano Cardinale
- Institute of Applied Microbiology, Justus-Liebig-University Giessen, Giessen, Germany
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy
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20
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Rojas J, Ambika Manirajan B, Ratering S, Suarez C, Geissler-Plaum R, Schnell S. Spirosoma endbachense sp. nov., isolated from a natural salt meadow. Int J Syst Evol Microbiol 2020; 71. [PMID: 33300859 DOI: 10.1099/ijsem.0.004601] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative bacterium, designated I-24T, was isolated from soil of a natural salt meadow. Strain I-24T was aerobic, non-motile, rod-shaped, catalase-positive, oxidase-positive and grew optimally at pH 7 and 25 °C. Comparative 16S rRNA gene analysis indicated that strain I-24T has closest similarities to Spirosoma agri KCTC 52727T (95.9 %) and Spirosoma terrae KCTC 52035T (95.5 %). Strain I-24T contained summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c) and C16 : 1 ω5c as the major fatty acids, the predominant respiratory quinone was menaquinone MK-7, and the major polar lipids were phosphatidylethanolamine as well as an unidentified phosphoaminolipid. The draft genome of strain I-24T consists of 10 326 072 base pairs with 9153 predicted coding sequences and a G+C content of 47.7 mol%. Clear distinctions between strain I-24T and S. agri KCTC 52727T or S. terrae KCTC 52035T were shown in the pairwise average nucleotide identity results with values of 76.71 and 74.01 %, respectively. Moreover, the digital DNA-DNA relatedness values to these strains were 20.8 and 19.0 %. Based on its phenotypic, genotypic and chemotaxonomic characteristics, strain I-24T represents a novel species of the genus Spirosoma, for which the name Spirosoma endbachense sp. nov. is proposed. The type strain is I-24T (DSM 111055T=KCTC 72613T).
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Affiliation(s)
- Julian Rojas
- Institute of Applied Microbiology, Research Center for BioSystems, Land Use, and Nutrition (IFZ), Justus-Liebig University Giessen, 35392 Giessen, Germany
| | | | - Stefan Ratering
- Institute of Applied Microbiology, Research Center for BioSystems, Land Use, and Nutrition (IFZ), Justus-Liebig University Giessen, 35392 Giessen, Germany
| | - Christian Suarez
- Institute of Applied Microbiology, Research Center for BioSystems, Land Use, and Nutrition (IFZ), Justus-Liebig University Giessen, 35392 Giessen, Germany
| | - Rita Geissler-Plaum
- Institute of Applied Microbiology, Research Center for BioSystems, Land Use, and Nutrition (IFZ), Justus-Liebig University Giessen, 35392 Giessen, Germany
| | - Sylvia Schnell
- Institute of Applied Microbiology, Research Center for BioSystems, Land Use, and Nutrition (IFZ), Justus-Liebig University Giessen, 35392 Giessen, Germany
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21
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Schübel M, Hantke K, Garcia Varo J, Seiffert-Störiko A, Schulz S, Neumann-Staubitz P, Gewering T, Kruck D, Schnell S, Steinert M. Journal Club. Biospektrum 2020; 26:748-752. [PMID: 33250578 PMCID: PMC7686443 DOI: 10.1007/s12268-020-1502-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Affiliation(s)
- Marisa Schübel
- Fakultät für Biologie, LMU München, Großhaderner Straße 2, Planegg-Martinsried, D-82152 München, Deutschland
| | - Klaus Hantke
- Fakultät für Biologie, Universität Tübingen, Auf der Morgenstelle 28, D-72076 Tübingen, Deutschland
| | - Javier Garcia Varo
- Karlsruhe Institut für Technologie (KIT), Postfach 6980, D-76049 Karlsruhe, Deutschland
| | | | | | - Petra Neumann-Staubitz
- Institut für Mikrobiologie und Genetik, Universität Göttingen, Grisebachstraße 8, D-37077 Göttingen, Deutschland
| | - Theresa Gewering
- Max Planck Institut für Biophysik, Max-von-Laue-Straße 3, D-60438 Frankfurt a. M., Deutschland
| | - Daniela Kruck
- Fakultät Chemie, Universität Duisburg-Essen, Universitätsstraße 5, D-45141 Essen, Deutschland
| | - Sylvia Schnell
- Institut für Angewandte Mikrobiologie, Universität Gießen, IFZ, Heinrich-Buff-Ring 26-32, D-35392 Gießen, Deutschland
| | - Michael Steinert
- Institut für Mikrobiologie, TU Braunschweig, Spielmannstraße 7, D-38106 Braunschweig, Deutschland
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22
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Regalado-Rentería E, Aguirre-Rivera JR, Godínez-Hernández CI, García-López JC, Oros-Ovalle AC, Martínez-Gutiérrez F, Martinez-Martinez M, Ratering S, Schnell S, Ruíz-Cabrera MÁ, Juárez-Flores BI. Effects of Agave Fructans, Inulin, and Starch on Metabolic Syndrome Aspects in Healthy Wistar Rats. ACS Omega 2020; 5:10740-10749. [PMID: 32455193 PMCID: PMC7240812 DOI: 10.1021/acsomega.0c00272] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 04/27/2020] [Indexed: 05/10/2023]
Abstract
Healthy Wistar rats were supplemented during 20 weeks with commercial inulin (I) and Agave tequilana fructans (CAT), experimental fructans from A. tequilana (EAT) and A. salmiana (AS) mature stems, rice starch 10% (RS), and standard feed for rodents (C). Feed intake was kept steady, but with I, body weight and abdominal adipose tissue (6.01 g) decreased at the end. Glucose (mg/dL) (C, 120.52; I, 110.69; CAT, 105.75; EAT, 115.48; AS, 101.63; and RS, 121.82), total cholesterol (C, 89.89; I, 64.48; CAT, 68.04; EAT, 68.74; AS, 68.04; and RS, 82), and triglycerides (C, 84.03; I, 59.52; CAT, 68.56; EAT, 59.08; AS, 75.27; and RS, 81.8) kept being normal and without differences between fructans. At the end, there was a significant increase in lactic acid bacteria when the I and AS groups were compared to the C group (C, 9.18; I, 10.64; CAT, 10.34; EAT, 10.36; AS, 10.49; and RS, 9.62 log 10 CFU/g of feces). In addition, with fructans, there was an accelerated process in feces emptiness, Lieberkühn crypts kept their morphology, and there was an increment of goblet cells.
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Affiliation(s)
- Evelyn Regalado-Rentería
- Instituto
de Investigacion de Zonas Desérticas, Universidad Autónoma de San Luis Potosí, Altair200 Fracc. del Llano C.P., 78377 San Luis Potosí, S.L.P., México
| | - Juan Rogelio Aguirre-Rivera
- Instituto
de Investigacion de Zonas Desérticas, Universidad Autónoma de San Luis Potosí, Altair200 Fracc. del Llano C.P., 78377 San Luis Potosí, S.L.P., México
| | - César Iván Godínez-Hernández
- Instituto
de Investigacion de Zonas Desérticas, Universidad Autónoma de San Luis Potosí, Altair200 Fracc. del Llano C.P., 78377 San Luis Potosí, S.L.P., México
| | - Juan Carlos García-López
- Instituto
de Investigacion de Zonas Desérticas, Universidad Autónoma de San Luis Potosí, Altair200 Fracc. del Llano C.P., 78377 San Luis Potosí, S.L.P., México
| | - A. Cuauhtémoc Oros-Ovalle
- Hospital
Central “Dr. Ignacio Morones Prieto”, Av. Venustiano Carranza No. 2395, C.P., 78290 San Luis Potosí, S.L.P., México
| | - Fidel Martínez-Gutiérrez
- Facultad
de Ciencias Químicas, Universidad
Autónoma de San Luis Potosí, Av. Dr. Manuel Nava No. 6, C.P., 78290 San Luis Potosí, S.L.P., México
| | - Marco Martinez-Martinez
- Facultad
de Ciencias Químicas, Universidad
Autónoma de San Luis Potosí, Av. Dr. Manuel Nava No. 6, C.P., 78290 San Luis Potosí, S.L.P., México
| | - Stefan Ratering
- Institute
of Applied Microbiology, Justus-Liebig University,
IFZ, Heinrich-Buff-Ring, 26-32, 35392 Gießen, Germany
| | - Sylvia Schnell
- Institute
of Applied Microbiology, Justus-Liebig University,
IFZ, Heinrich-Buff-Ring, 26-32, 35392 Gießen, Germany
| | - Miguel Ángel Ruíz-Cabrera
- Facultad
de Ciencias Químicas, Universidad
Autónoma de San Luis Potosí, Av. Dr. Manuel Nava No. 6, C.P., 78290 San Luis Potosí, S.L.P., México
| | - Bertha Irene Juárez-Flores
- Instituto
de Investigacion de Zonas Desérticas, Universidad Autónoma de San Luis Potosí, Altair200 Fracc. del Llano C.P., 78377 San Luis Potosí, S.L.P., México
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Jacksch S, Thota J, Shetty S, Smidt H, Schnell S, Egert M. Metagenomic Analysis of Regularly Microwave-Treated and Untreated Domestic Kitchen Sponges. Microorganisms 2020; 8:microorganisms8050736. [PMID: 32423128 PMCID: PMC7284620 DOI: 10.3390/microorganisms8050736] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 05/08/2020] [Accepted: 05/08/2020] [Indexed: 01/04/2023] Open
Abstract
Kitchen sponges massively absorb and spread microorganisms, leading to contamination of kitchen appliances, surfaces, and food. Microwaving as an effective and widespread technique can rapidly reduce the microbial load of kitchen sponges. However, long-term effects of such treatments are largely unknown. Notably, it has been speculated that regularly applied domestic cleaning and disinfection may select for microbial communities with a higher pathogenic potential and/or malodorous properties. In this study, we distributed newly purchased polyurethane kitchen sponges to 20 participants, with the instruction to use them under normal household conditions for four weeks. Ten of the participants sanitized their sponges regularly by a standardized microwaving protocol, while the remaining ten sponges remained untreated. Metagenomic sequence data evaluation indicated that, in addition to bacteria, viruses, eukaryotes, and archaea were also part of the kitchen sponge microbiome. Comparisons of sanitized and untreated kitchen sponges indicated a trend towards a reduced structural microbial diversity while functional diversity increased. Microwave sanitization appeared to alter composition and metabolic properties of the microbial communities. Follow-up studies will have to show whether these changes are more positive or negative in terms of domestic hygiene, human health, and well-being.
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Affiliation(s)
- Susanne Jacksch
- Faculty of Medical and Life Sciences, Institute of Precision Medicine, Microbiology and Hygiene Group, Furtwangen University, 78054 Villingen-Schwenningen, Germany; (S.J.); (J.T.)
| | - Jyothi Thota
- Faculty of Medical and Life Sciences, Institute of Precision Medicine, Microbiology and Hygiene Group, Furtwangen University, 78054 Villingen-Schwenningen, Germany; (S.J.); (J.T.)
| | - Sudarshan Shetty
- Laboratory of Microbiology, Wageningen University & Research, 6708 WE Wageningen, The Netherlands; (S.S.); (H.S.)
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, 6708 WE Wageningen, The Netherlands; (S.S.); (H.S.)
| | - Sylvia Schnell
- Institute of Applied Microbiology, Research Centre for BioSystems, Land Use, and Nutrition (IFZ), Justus-Liebig-University Giessen, 35392 Giessen, Germany;
| | - Markus Egert
- Faculty of Medical and Life Sciences, Institute of Precision Medicine, Microbiology and Hygiene Group, Furtwangen University, 78054 Villingen-Schwenningen, Germany; (S.J.); (J.T.)
- Correspondence: ; Tel.: +49-0-7720-307-4554
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24
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Weis S, Schnell S, Egert M. Towards safer stable isotope probing - effect of formamide on the separation of isotope-labeled and unlabeled Escherichia coli RNA by isopycnic density ultracentrifugation. Can J Microbiol 2020; 66:491-494. [PMID: 32134703 DOI: 10.1139/cjm-2019-0612] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
RNA-based stable isotope probing (RNA-SIP) is used in molecular microbial ecology to link the identity of microorganisms in a complex community with the assimilation of a distinct substrate. The technique is highly dependent on a reliable separation of isotopic-labeled RNA from unlabeled RNA by isopycnic density gradient ultracentrifugation. Here we show that 13C-labeled and unlabeled Escherichia coli RNA can be sufficiently separated by isopycnic ultracentrifugation even in the absence of formamide. However, a slightly lower starting density is needed to obtain a distribution pattern similar to that obtained when formamide was used. Hence, the commonly used addition of formamide to the centrifugation solution might not be needed to separate 13C-labeled RNA from unlabeled RNA, but this must be verified for more complex environmental mixtures of RNA. Clearly, an omission of formamide would increase the safety of RNA-SIP analyses.
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Affiliation(s)
- Severin Weis
- Faculty of Medical and Life Sciences, Institute of Precision Medicine, Microbiology and Hygiene Group, Furtwangen University, Villingen-Schwenningen, Germany
| | - Sylvia Schnell
- Institute of Applied Microbiology, Research Center for BioSystems, Land Use, and Nutrition (IFZ), Justus-Liebig-University Giessen, Germany
| | - Markus Egert
- Faculty of Medical and Life Sciences, Institute of Precision Medicine, Microbiology and Hygiene Group, Furtwangen University, Villingen-Schwenningen, Germany
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25
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Araya JP, González M, Cardinale M, Schnell S, Stoll A. Microbiome Dynamics Associated With the Atacama Flowering Desert. Front Microbiol 2020; 10:3160. [PMID: 32038589 PMCID: PMC6990129 DOI: 10.3389/fmicb.2019.03160] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 12/30/2019] [Indexed: 11/13/2022] Open
Abstract
In a desert, plants as holobionts quickly respond to resource pulses like precipitation. However, little is known on how environment and plants modulate the rhizosphere-associated microbiome. As a model species to represent the Atacama Desert bloom, Cistanthe longiscapa (Montiaceae family) was selected to study the influence of abiotic and biotic environment on the diversity and structure of the microbiota associated to its rhizosphere. We analyzed the rhizosphere and soil microbiome along a North-South precipitation gradient and between a dry and rainy year by using Illumina high−throughput sequencing of 16S rRNA gene fragments and ITS2 regions for prokaryotes and fungi, respectively. In the rhizosphere of C. longiscapa the microbiota clearly differs in composition and structure from the surrounding bulk soil. The fungal and bacterial communities respond differently to environmental conditions. The diversity and richness of fungal OTUs were negatively correlated with aridity, as predicted. The community structure was predominantly influenced by other soil characteristics (pH, organic matter content) but not by aridity. In contrast, diversity, composition, and structure of the bacterial community were not influenced by aridity or any other evaluated soil parameter. These findings coincide with the identification of mainly site-specific microbial communities, not shared along the sites. These local communities contain a group of OTUs, which are exclusive to the rhizosphere of each site and presumably vertically inherited as seed endophytes. Their ecological functions and dispersal mechanisms remain unclear. The analysis of co-occurrence patterns highlights the strong effect of the desert habitat over the soil- and rhizosphere-microbiome. The site-independent enrichment of only a small bacterial cluster consistently associated with the rhizosphere of C. longiscapa further supports this conclusion. In a rainy year, the rhizosphere microbiota significantly differed from bulk and bare soil, whereas in a dry year, the community structure of the former rhizosphere approximates to the one found in the bulk. In the context of plant–microbe interactions in desert environments, our study contributes new insights into the importance of aridity in microbial community structure and composition, discovering the influence of other soil parameters in this complex dynamic network, which needs further to be investigated.
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Affiliation(s)
| | - Máximo González
- Centro de Estudios Avanzados en Zonas Áridas, La Serena, Chile
| | - Massimiliano Cardinale
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy.,Institute of Applied Microbiology, Justus Liebig University Giessen, Giessen, Germany
| | - Sylvia Schnell
- Institute of Applied Microbiology, Justus Liebig University Giessen, Giessen, Germany
| | - Alexandra Stoll
- Centro de Estudios Avanzados en Zonas Áridas, La Serena, Chile.,Instituto de Investigación Multidisciplinario en Ciencia y Tecnología, Universidad de La Serena, La Serena, Chile
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26
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Suarez C, Ratering S, Weigel V, Sacharow J, Bienhaus J, Ebert J, Hirz A, Rühl M, Schnell S. Isolation of bacteria at different points of Pleurotus ostreatus cultivation and their influence in mycelial growth. Microbiol Res 2019; 234:126393. [PMID: 32036274 DOI: 10.1016/j.micres.2019.126393] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 12/01/2019] [Accepted: 12/07/2019] [Indexed: 12/14/2022]
Abstract
Pleurotus ostreatus is one of the most cultivated edible mushrooms worldwide and few approaches have been done to analyze bacterial influence during its cultivation. Therefore, bacteria from commercial spawn, mycelial-colonized straw and fruiting bodies from healthy productive samples were counted, isolated and tested for their mycelial growth promoting ability. Bacterial cell numbers at different steps of the process showed low bacterial cell numbers in spawn and in fruiting bodies inner tissue compared to the high concentration in mycelial-colonized straw. The majority of the 38 isolates belonged to phyla Firmicutes and Actinobacteria were identified as Bacillus, Paenibacillus and Micromonospora species. Similarly, 16S rRNA gene bacterial clones obtained from mycelial biomass DNA samples showed bacterial presence of various genera including Bacillus and Paenibacillus. In the mycelial growth promoting ability tests, 30 isolates negatively affected mycelial growth, two isolates showed no effect on mycelial growth, and six isolates promoted mycelial growth. Moreover, mycelial thickness was influenced in different ways by the bacterial growth. In general, nearly all isolates growth-preventing were isolated from healthy spawn and mycelial-colonized straw, whereas fruiting bodies were the best source for isolation of mycelial growth-promoting bacteria. Characterization of bacterial isolates revealed that growth-preventing isolates exhibited various enzymatic activities in comparison with positive influencing bacteria that exhibited none or weak enzymatic activities. In addition, the influence of volatile compounds being present in the headspace of bi-plate co-cultures on P. ostreatus mycelial growth was demonstrated. The effect of isolates, that promoted mycelial growth in co-cultivation, to reduce P. ostreatus spawn running time, was evaluated on sterilized rye seeds. Results showed that not all mycelial promoted isolates were able to significantly promote P. ostreatus colonization. However, isolate M46F identified as Micromonospora lupini significantly reduce spawn running time. This is one of few studies to estimate cultivable bacteria from healthy samples of P. ostreatus cultivation, to evaluate a bacterial effect on mycelial growth, to show that fruiting bodies are a good source for mycelia growth-promoting isolates, and the first to report a shorter P. ostreatus spawn running time due to bacterial inoculation.
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Affiliation(s)
- Christian Suarez
- Institute of Applied Microbiology, IFZ, Justus-Liebig University Giessen, 35392, Giessen, Germany.
| | - Stefan Ratering
- Institute of Applied Microbiology, IFZ, Justus-Liebig University Giessen, 35392, Giessen, Germany
| | - Victoria Weigel
- Institute of Applied Microbiology, IFZ, Justus-Liebig University Giessen, 35392, Giessen, Germany
| | - Julia Sacharow
- Institute of Applied Microbiology, IFZ, Justus-Liebig University Giessen, 35392, Giessen, Germany
| | - Jackeline Bienhaus
- Institute of Applied Microbiology, IFZ, Justus-Liebig University Giessen, 35392, Giessen, Germany
| | - Janine Ebert
- Institute of Applied Microbiology, IFZ, Justus-Liebig University Giessen, 35392, Giessen, Germany
| | - Anika Hirz
- Institute of Applied Microbiology, IFZ, Justus-Liebig University Giessen, 35392, Giessen, Germany
| | - Martin Rühl
- Institute of Food Chemistry and Food Biotechnology, Justus-Liebig University Giessen, 35392, Giessen, Germany
| | - Sylvia Schnell
- Institute of Applied Microbiology, IFZ, Justus-Liebig University Giessen, 35392, Giessen, Germany
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27
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Weis S, Schwiertz A, Unger MM, Becker A, Faßbender K, Ratering S, Kohl M, Schnell S, Schäfer KH, Egert M. Effect of Parkinson's disease and related medications on the composition of the fecal bacterial microbiota. NPJ Parkinsons Dis 2019; 5:28. [PMID: 31815177 PMCID: PMC6884491 DOI: 10.1038/s41531-019-0100-x] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 10/29/2019] [Indexed: 02/07/2023] Open
Abstract
Parkinson's disease (PD) is one of the most common neurodegenerative disorders. PD patients suffer from gastrointestinal dysfunctions and alterations of the autonomous nervous system, especially its part in the gut wall, i.e., the enteric nervous system (ENS). Such alterations and functional gastrointestinal deficits often occur years before the classical clinical symptoms of PD appear. Until now, only little is known about PD-associated changes in gut microbiota composition and their potential implication in PD development. In order to increase knowledge in this field, fecal samples of 34 PD patients and 25 healthy, age-matched control persons were investigated. Here, the V4 and V5 hypervariable region of bacterial 16S rRNA genes was PCR-amplified and sequenced using an Ion Torrent PGM platform. Within the PD group, we observed a relative decrease in bacterial taxa which are linked to health-promoting, anti-inflammatory, neuroprotective or other beneficial effects on the epithelial barrier, such as Faecalibacterium and Fusicatenibacter. Both taxa were lowered in PD patients with elevated levels of the fecal inflammation marker calprotectin. In addition, we observed an increase in shares of the Clostridiales family XI and their affiliated members in these samples. Finally, we found that the relative abundances of the bacterial genera Peptoniphilus, Finegoldia, Faecalibacterium Fusicatenibacter, Anaerococcus, Bifidobacterium, Enterococcus, and Ruminococcus were significantly influenced by medication with L-dopa and entacapone, respectively. Our data confirm previously reported effects of COMT inhibitors on the fecal microbiota of PD patients and suggest a possible effect of L-dopa medication on the relative abundance of several bacterial genera.
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Affiliation(s)
- Severin Weis
- Faculty of Medical and Life Sciences, Institute of Precision Medicine, Microbiology and Hygiene Group, Furtwangen University, Villingen-Schwenningen, Germany
| | | | - Marcus M. Unger
- Department of Neurology, Saarland University, Homburg, Germany
| | - Anouck Becker
- Department of Neurology, Saarland University, Homburg, Germany
| | - Klaus Faßbender
- Department of Neurology, Saarland University, Homburg, Germany
| | - Stefan Ratering
- Institute of Applied Microbiology, Justus-Liebig-University, Giessen, Germany
| | - Matthias Kohl
- Faculty of Medical and Life Sciences, Institute of Precision Medicine, Group for Statistics in Biology and Medicine, Furtwangen University, Villingen-Schwenningen, Germany
| | - Sylvia Schnell
- Institute of Applied Microbiology, Justus-Liebig-University, Giessen, Germany
| | - Karl-Herbert Schäfer
- Department of Biotechnology, ENS Working Group, University of Applied Sciences Kaiserslautern, Zweibrücken, Germany
| | - Markus Egert
- Faculty of Medical and Life Sciences, Institute of Precision Medicine, Microbiology and Hygiene Group, Furtwangen University, Villingen-Schwenningen, Germany
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28
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Soldan R, Mapelli F, Crotti E, Schnell S, Daffonchio D, Marasco R, Fusi M, Borin S, Cardinale M. Bacterial endophytes of mangrove propagules elicit early establishment of the natural host and promote growth of cereal crops under salt stress. Microbiol Res 2019; 223-225:33-43. [DOI: 10.1016/j.micres.2019.03.008] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 03/15/2019] [Accepted: 03/22/2019] [Indexed: 10/27/2022]
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29
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Cardinale M, Suarez C, Steffens D, Ratering S, Schnell S. Effect of Different Soil Phosphate Sources on the Active Bacterial Microbiota Is Greater in the Rhizosphere than in the Endorhiza of Barley (Hordeum vulgare L.). Microb Ecol 2019; 77:689-700. [PMID: 30259168 DOI: 10.1007/s00248-018-1264-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 09/16/2018] [Indexed: 06/08/2023]
Abstract
Phosphate is a macronutrient and often the limiting growing factor of many ecosystems. The aim of this work was to assess the effect of various phosphate sources on the active bacterial microbiota of barley rhizosphere and endorhiza. Barley was grown on poor soil supplemented with either Ca(H2PO4)2 (CaP), Gafsa rock phosphate (Gafsa), sodium hexaphytate (NaHex), or not amended (P0). RNA was extracted and cDNA synthesized via reverse transcription from both rhizosphere and endorhiza of barley roots; the obtained 16S rRNA cDNA was sequenced by Ion Torrent and analyzed with QIIME and co-occurrence network analysis. Phosphatase activity was measured in the rhizosphere. The phosphate source significantly affected alpha- and beta-diversities of the active microbiota, especially in the rhizosphere. CaP enriched the relative abundance of a broad range of taxa, while NaHex and Gafsa specifically enriched one dominant Massilia-related OTU. Co-occurrence network analysis showed that the most abundant OTUs were affected by phosphate source and, at the same time, were low connected to other OTUs (thus they were relatively "independent" from other bacteria); this indicates a successful adaptation to the specific abiotic conditions. In the rhizosphere, the phosphatase activities were correlated to several OTUs. Moreover, the phosphodiesterase/alk. phosphomonoesterase ratio was highly correlated to the dominance index of the microbiota and to the relative abundance of the dominant Massilia OTU. This study shows the differential response of the rhizosphere- and endorhiza bacterial microbiota of barley to various phosphate sources in soil, thus providing insights onto this largely unknown aspect of the soil microbiome ecology and plant-microbe interactions.
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Affiliation(s)
- Massimiliano Cardinale
- Institute of Applied Microbiology, Justus-Liebig-University Giessen, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany.
| | - Christian Suarez
- Institute of Applied Microbiology, Justus-Liebig-University Giessen, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| | - Diedrich Steffens
- Institute of Plant Nutrition, Justus-Liebig-University Giessen, Heinrich-Buff-Ring 26-32, Giessen, 35392, Germany
| | - Stefan Ratering
- Institute of Applied Microbiology, Justus-Liebig-University Giessen, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| | - Sylvia Schnell
- Institute of Applied Microbiology, Justus-Liebig-University Giessen, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
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30
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Kaplan H, Ratering S, Felix-Henningsen P, Schnell S. Stability of in situ immobilization of trace metals with different amendments revealed by microbial 13C-labelled wheat root decomposition and efflux-mediated metal resistance of soil bacteria. Sci Total Environ 2019; 659:1082-1089. [PMID: 31096323 DOI: 10.1016/j.scitotenv.2018.12.441] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Revised: 12/14/2018] [Accepted: 12/28/2018] [Indexed: 05/16/2023]
Abstract
The aim of the present study was to prove the long-term efficiency of the amendments zerovalent iron grit, zeolite, and Divergan® for trace metal remediation in heavily contaminated soils and to attain a recovery of microbial functionality and diversity by remediation. For immobilization of the trace metals the amendments zerovalent iron grit, natural zeolite, and Divergan® were used. Trace metal total and mobile contents were determined and bacterial communities were assessed after a SIP experiment with 13C-labelled wheat root by Ion-Torrent Sequencing targeting the bacterial 16S rRNA gene and two trace metal resistant genes for copper and cadmium (copA and czcA gene). The results show that the remediation effect of the three amendments is still stable after five years. The mobile trace metal contents were significantly (≤0.001) reduced in all treatments, except the Cu content in the zeolite treatment. A higher diversity in active metabolizing and growing soil bacteria was observed in remediated soils as compared to the non-remediated control, especially for the Divergan® treatment. The bacterial genera Kribbella, Glycomyces, Inquilinus, Nocardioides, and Lysobacter are the most significantly enriched genera in the 13C fractions of the treated samples. The occurrence of bacterial families, which could be identified carrying efflux-mediated metal resistance genes for Cd/Zn and Cu, were reduced in the remediated soils as compared to the non-remediated control. The most abundant bacterial family for the copA and the czcA gene is Xanthomonadaceae. The pH-value and the trace metal concentration could be identified as key drivers of bacterial community composition, and functions in trace metal contaminated soils and remediated soils.
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Affiliation(s)
- Hülya Kaplan
- Institute of Applied Microbiology, Research Centre for Biosystems, Land Use and Nutrition (IFZ), Justus Liebig University, 35392 Giessen, Germany; Institute of Soil Science and Soil Conservation, Research Centre for Biosystems, Land Use and Nutrition (IFZ), Justus Liebig University, 35392 Giessen, Germany.
| | - Stefan Ratering
- Institute of Applied Microbiology, Research Centre for Biosystems, Land Use and Nutrition (IFZ), Justus Liebig University, 35392 Giessen, Germany.
| | - Peter Felix-Henningsen
- Institute of Soil Science and Soil Conservation, Research Centre for Biosystems, Land Use and Nutrition (IFZ), Justus Liebig University, 35392 Giessen, Germany.
| | - Sylvia Schnell
- Institute of Applied Microbiology, Research Centre for Biosystems, Land Use and Nutrition (IFZ), Justus Liebig University, 35392 Giessen, Germany.
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31
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Auerbach R, Ratering S, Bokelmann K, Gellermann C, Brämer T, Baumann R, Schnell S. Bioleaching of valuable and hazardous metals from dry discharged incineration slag. An approach for metal recycling and pollutant elimination. J Environ Manage 2019; 232:428-437. [PMID: 30500707 DOI: 10.1016/j.jenvman.2018.11.028] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 10/15/2018] [Accepted: 11/07/2018] [Indexed: 06/09/2023]
Abstract
Recycling of process wastes will be in future an essential step to meet the demands for valuable metals of a growing market. Depending on their particle sizes incineration slags are already used to recover metals but particle size fractions below 4 mm are still difficult to recycle. Therefore, different particle size fractions (mesh size 2 and 4 mm, high energy grinded) of dry discharged slags were used for bioleaching with and without the pure cultures Acidithiobacillus ferrooxidans or Leptospirillum ferrooxidans or a mixture of Acidithiobacillus thiooxidans and Acidithiobacillus ferrooxidans in batch cultures. Regarding Al, Cr, Cu, Ni, Mn and the rare earth elements Ce, La and Er, bioleaching was significantly more successful with iron oxidizing bacteria compared to abiotic controls. Metal mobilization for Al, Cu, Mn, Cr and Er with bacteria was between 70 and 100% and for Ce, Ni and La around 50% almost after 7 days, making an industrial application for the high concentrated metals like Al and Cu feasible. In addition to the recovery of valuable metals, a reduction in cost of landfilling was identified. After treatment of the slag with the microorganisms, concentrations of harmful substances in the residues could be reduced and thus a classification in lower safety levels regarding the LAGA or EU regulations was calculated.
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Affiliation(s)
- Romy Auerbach
- Institute of Applied Microbiology, Justus-Liebig University, IFZ, Heinrich-Buff-Ring 26-32, Gießen, Germany; Fraunhofer ISC, Fraunhofer Project Group IWKS, Alzenau and Hanau, Germany
| | - Stefan Ratering
- Institute of Applied Microbiology, Justus-Liebig University, IFZ, Heinrich-Buff-Ring 26-32, Gießen, Germany.
| | - Katrin Bokelmann
- Fraunhofer ISC, Fraunhofer Project Group IWKS, Alzenau and Hanau, Germany
| | - Carsten Gellermann
- Fraunhofer ISC, Fraunhofer Project Group IWKS, Alzenau and Hanau, Germany
| | - Thilo Brämer
- Fraunhofer ISC, Fraunhofer Project Group IWKS, Alzenau and Hanau, Germany
| | - Renate Baumann
- Institute of Applied Microbiology, Justus-Liebig University, IFZ, Heinrich-Buff-Ring 26-32, Gießen, Germany
| | - Sylvia Schnell
- Institute of Applied Microbiology, Justus-Liebig University, IFZ, Heinrich-Buff-Ring 26-32, Gießen, Germany
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32
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Abstract
The RNA-SIP technology allows for linking the structure and function of complex microbial communities, that is, the identification of microbial key players involved in distinct degradation and assimilation processes under in situ conditions. Being dependent on RNA, this technique is particularly suited for environments with high numbers of very active, that is, significantly RNA-expressing microorganisms, such as intestinal tract samples. We use RNA-SIP for the identification of bacteria involved in the degradation and assimilation of prebiotic carbohydrates in order to better understand the functionality of these medically and economically important nutrients in human and animal intestinal environments.
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Affiliation(s)
- Severin Weis
- Faculty of Medical and Life Sciences, Institute of Precision Medicine, Microbiology and Hygiene Group, Furtwangen University, Villingen-Schwenningen, Germany.,Institute of Applied Microbiology, Research Center for BioSystems, Land Use, and Nutrition (IFZ), Justus-Liebig-University Giessen, Giessen, Germany
| | - Sylvia Schnell
- Institute of Applied Microbiology, Research Center for BioSystems, Land Use, and Nutrition (IFZ), Justus-Liebig-University Giessen, Giessen, Germany
| | - Markus Egert
- Faculty of Medical and Life Sciences, Institute of Precision Medicine, Microbiology and Hygiene Group, Furtwangen University, Villingen-Schwenningen, Germany.
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Ambika Manirajan B, Suarez C, Ratering S, Rusch V, Geissler-Plaum R, Cardinale M, Schnell S. Spirosoma pollinicola sp. nov., isolated from pollen of common hazel (Corylus avellana L.). Int J Syst Evol Microbiol 2018; 68:3248-3254. [DOI: 10.1099/ijsem.0.002973] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Binoy Ambika Manirajan
- 1Institute of Applied Microbiology, Research Center for BioSystems, Land Use, and Nutrition (IFZ), Justus-Liebig-University, Giessen, 35392, Germany
| | - Christian Suarez
- 1Institute of Applied Microbiology, Research Center for BioSystems, Land Use, and Nutrition (IFZ), Justus-Liebig-University, Giessen, 35392, Germany
| | - Stefan Ratering
- 1Institute of Applied Microbiology, Research Center for BioSystems, Land Use, and Nutrition (IFZ), Justus-Liebig-University, Giessen, 35392, Germany
| | - Volker Rusch
- 2Institute for Integrative Biology, Old Herborn University Foundation, Herborn, Germany
| | - Rita Geissler-Plaum
- 1Institute of Applied Microbiology, Research Center for BioSystems, Land Use, and Nutrition (IFZ), Justus-Liebig-University, Giessen, 35392, Germany
| | - Massimiliano Cardinale
- 1Institute of Applied Microbiology, Research Center for BioSystems, Land Use, and Nutrition (IFZ), Justus-Liebig-University, Giessen, 35392, Germany
| | - Sylvia Schnell
- 1Institute of Applied Microbiology, Research Center for BioSystems, Land Use, and Nutrition (IFZ), Justus-Liebig-University, Giessen, 35392, Germany
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Auerbach R, Bokelmann K, Stauber R, Schnell S, Ratering S, Werner A, Haseneder R, Vostal R, Bertau M, Gellermann C. Bioleaching zum Recycling von Sekundärrohstoffen. CHEM UNSERER ZEIT 2018. [DOI: 10.1002/ciuz.201800829] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Romy Auerbach
- Fraunhofer-Projektgruppe Wertstoffkreisläufe und Ressourcenstrategie IWKS; Alzenau und Hanau
| | - Katrin Bokelmann
- Fraunhofer-Projektgruppe Wertstoffkreisläufe und Ressourcenstrategie IWKS; Alzenau und Hanau
| | - Rudolf Stauber
- Fraunhofer-Projektgruppe Wertstoffkreisläufe und Ressourcenstrategie IWKS; Alzenau und Hanau
| | - Sylvia Schnell
- Justus-Liebig-Universität Gießen; Institut für Angewandte Mikrobiologie; Gießen
| | - Stefan Ratering
- Justus-Liebig-Universität Gießen; Institut für Angewandte Mikrobiologie; Gießen
| | - Arite Werner
- TU-Bergakademie Freiberg; Institut für Thermische Verfahrenstechnik, Umwelt- und Naturstoffverfahrenstechnik
| | - Roland Haseneder
- TU-Bergakademie Freiberg; Institut für Thermische Verfahrenstechnik, Umwelt- und Naturstoffverfahrenstechnik
| | - Radek Vostal
- TU-Bergakademie Freiberg; Institut für Technische Chemie
| | - Martin Bertau
- TU-Bergakademie Freiberg; Institut für Technische Chemie
| | - Carsten Gellermann
- Fraunhofer-Projektgruppe Wertstoffkreisläufe und Ressourcenstrategie IWKS; Alzenau und Hanau
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35
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Auerbach R, Bokelmann K, Gabor E, Hofmann B, Stauber R, Schnell S, Ratering S. UFOPLAN: Effizienzsteigerung bei der Rückgewinnung von NE-Metallen und SEE aus festen Verbrennungsrückständen mittels Bioleaching und -flotation. CHEM-ING-TECH 2018. [DOI: 10.1002/cite.201855045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- R. Auerbach
- Fraunhofer Projektgruppe IWKS; Trenn- und Sortiertechnologien; Rodenbacher Chaussee 4 63457 Hanau Deutschland
| | - K. Bokelmann
- Fraunhofer Projektgruppe IWKS; Trenn- und Sortiertechnologien; Rodenbacher Chaussee 4 63457 Hanau Deutschland
| | - E. Gabor
- BRAIN AG; Green- and Urban Mining; Darmstädter Straße 34 - 36 64673 Zwingenberg Deutschland
| | - B. Hofmann
- BRAIN AG; Green- and Urban Mining; Darmstädter Straße 34 - 36 64673 Zwingenberg Deutschland
| | - R. Stauber
- Fraunhofer Projektgruppe IWKS; Trenn- und Sortiertechnologien; Rodenbacher Chaussee 4 63457 Hanau Deutschland
| | - S. Schnell
- Justus-Liebig-Universität Gießen; Institut für Angewandte Mikrobiologie; Heinrich-Buff-Ring 26 - 32 35392 Gießen Deutschland
| | - S. Ratering
- Justus-Liebig-Universität Gießen; Institut für Angewandte Mikrobiologie; Heinrich-Buff-Ring 26 - 32 35392 Gießen Deutschland
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Manirajan BA, Maisinger C, Ratering S, Rusch V, Schwiertz A, Cardinale M, Schnell S. Diversity, specificity, co-occurrence and hub taxa of the bacterial–fungal pollen microbiome. FEMS Microbiol Ecol 2018; 94:5033679. [DOI: 10.1093/femsec/fiy112] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 05/31/2018] [Indexed: 01/05/2023] Open
Affiliation(s)
- Binoy Ambika Manirajan
- Institute of Applied Microbiology, Research Center for BioSystems, Land Use, and Nutrition (IFZ), Justus-Liebig-University Giessen, Giessen, Germany
| | - Corinna Maisinger
- Institute of Applied Microbiology, Research Center for BioSystems, Land Use, and Nutrition (IFZ), Justus-Liebig-University Giessen, Giessen, Germany
| | - Stefan Ratering
- Institute of Applied Microbiology, Research Center for BioSystems, Land Use, and Nutrition (IFZ), Justus-Liebig-University Giessen, Giessen, Germany
| | - Volker Rusch
- Institut für Integrative Biologie, Stiftung Old Herborn University, Herborn, Germany
| | - Andreas Schwiertz
- MVZ Institut für Mikroökologie GmbH, D-35745 Herborn, Auf den Lüppen 8, Germany,
| | - Massimiliano Cardinale
- Institute of Applied Microbiology, Research Center for BioSystems, Land Use, and Nutrition (IFZ), Justus-Liebig-University Giessen, Giessen, Germany
| | - Sylvia Schnell
- Institute of Applied Microbiology, Research Center for BioSystems, Land Use, and Nutrition (IFZ), Justus-Liebig-University Giessen, Giessen, Germany
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Egert M, Weis S, Schnell S. RNA-based stable isotope probing (RNA-SIP) to unravel intestinal host-microbe interactions. Methods 2018; 149:25-30. [PMID: 29857194 DOI: 10.1016/j.ymeth.2018.05.022] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 05/23/2018] [Accepted: 05/25/2018] [Indexed: 12/15/2022] Open
Abstract
The RNA-SIP technology, introduced into molecular microbial ecology in 2002, is an elegant technique to link the structure and function of complex microbial communities, i.e. to identify microbial key-players involved in distinct degradation and assimilation processes under in-situ conditions. Due to its dependence of microbial RNA, this technique is particularly suited for environments with high numbers of very active, i.e. significantly RNA-expressing, bacteria. So far, it was mainly used in environmental studies using microbiotas from soil or water habitats. Here we outline and summarize our application of RNA-SIP for the identification of bacteria involved in the degradation and assimilation of prebiotic carbohydrates in intestinal samples of human and animal origin. Following an isotope label from a prebiotic substrate into the RNA of distinct bacterial taxa will help to better understand the functionality of these medically and economically important nutrients in an intestinal environment.
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Affiliation(s)
- Markus Egert
- Faculty of Medical and Life Sciences, Institute of Precision Medicine, Microbiology and Hygiene Group, Furtwangen University, Villingen-Schwenningen, Germany.
| | - Severin Weis
- Faculty of Medical and Life Sciences, Institute of Precision Medicine, Microbiology and Hygiene Group, Furtwangen University, Villingen-Schwenningen, Germany; Institute of Applied Microbiology, Research Center for BioSystems, Land Use, and Nutrition (IFZ), Justus-Liebig-University Giessen, Germany
| | - Sylvia Schnell
- Institute of Applied Microbiology, Research Center for BioSystems, Land Use, and Nutrition (IFZ), Justus-Liebig-University Giessen, Germany
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38
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Rahman MM, Flory E, Koyro HW, Abideen Z, Schikora A, Suarez C, Schnell S, Cardinale M. Consistent associations with beneficial bacteria in the seed endosphere of barley (Hordeum vulgare L.). Syst Appl Microbiol 2018; 41:386-398. [PMID: 29567394 DOI: 10.1016/j.syapm.2018.02.003] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Revised: 02/19/2018] [Accepted: 02/19/2018] [Indexed: 11/25/2022]
Abstract
The importance of the plant microbiome for host fitness has led to the concept of the "plant holobiont". Seeds are reservoirs and vectors for beneficial microbes, which are very intimate partners of higher plants with the potential to connect plant generations. In this study, the endophytic seed microbiota of numerous barley samples, representing different cultivars, geographical sites and harvest years, was investigated. Cultivation-dependent and -independent analyses, microscopy, functional plate assays, greenhouse assays and functional prediction were used, with the aim of assessing the composition, stability and function of the barley seed endophytic bacterial microbiota. Associations were consistently detected in the seed endosphere with Paenibacillus, Pantoea and Pseudomonas spp., which were able to colonize the root with a notable rhizocompetence after seed germination. In greenhouse assays, enrichment with these bacteria promoted barley growth, improved mineral nutrition and induced resistance against the fungal pathogen Blumeria graminis. We demonstrated here that barley, an important crop plant, was consistently associated with beneficial bacteria inside the seeds. The results have relevant implications for plant microbiome ecology and for the holobiont concept, as well as opening up new possibilities for research and application of seed endophytes as bioinoculants in sustainable agriculture.
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Affiliation(s)
- Md Mahafizur Rahman
- Institute of Applied Microbiology, Research Center for BioSystems, Land Use, and Nutrition (IFZ), Justus-Liebig-University Giessen, Heinrich-Buff-Ring 26-32, D-35392 Giessen, Germany
| | - Elias Flory
- Institute of Applied Microbiology, Research Center for BioSystems, Land Use, and Nutrition (IFZ), Justus-Liebig-University Giessen, Heinrich-Buff-Ring 26-32, D-35392 Giessen, Germany
| | - Hans-Werner Koyro
- Institute of Plant Ecology, Research Center for BioSystems, Land Use, and Nutrition (IFZ), Justus-Liebig-University Giessen, Heinrich-Buff-Ring 26-32, D-35392 Giessen, Germany
| | - Zainul Abideen
- Institute of Plant Ecology, Research Center for BioSystems, Land Use, and Nutrition (IFZ), Justus-Liebig-University Giessen, Heinrich-Buff-Ring 26-32, D-35392 Giessen, Germany; Institute of Sustainable Halophyte Utilization, University of Karachi, Karachi 75270, Pakistan
| | - Adam Schikora
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institut Federal Research Centre for Cultivated Plants (JKI), Messeweg 11/12, D-38104 Brauschweig, Germany
| | - Christian Suarez
- Institute of Applied Microbiology, Research Center for BioSystems, Land Use, and Nutrition (IFZ), Justus-Liebig-University Giessen, Heinrich-Buff-Ring 26-32, D-35392 Giessen, Germany
| | - Sylvia Schnell
- Institute of Applied Microbiology, Research Center for BioSystems, Land Use, and Nutrition (IFZ), Justus-Liebig-University Giessen, Heinrich-Buff-Ring 26-32, D-35392 Giessen, Germany
| | - Massimiliano Cardinale
- Institute of Applied Microbiology, Research Center for BioSystems, Land Use, and Nutrition (IFZ), Justus-Liebig-University Giessen, Heinrich-Buff-Ring 26-32, D-35392 Giessen, Germany.
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39
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Martinez-Gutierrez F, Ratering S, Juárez-Flores B, Godinez-Hernandez C, Geissler-Plaum R, Prell F, Zorn H, Czermak P, Schnell S. Potential use of Agave salmiana as a prebiotic that stimulates the growth of probiotic bacteria. Lebensm Wiss Technol 2017. [DOI: 10.1016/j.lwt.2017.05.044] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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40
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Suarez C, Ratering S, Schäfer J, Schnell S. Ancylobacter pratisalsi sp. nov. with plant growth promotion abilities from the rhizosphere of Plantago winteri Wirtg. Int J Syst Evol Microbiol 2017; 67:4500-4506. [PMID: 28945527 DOI: 10.1099/ijsem.0.002320] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-negative bacterium, designated E130T, was isolated from rhizospheric soil of Plantago winteri Wirtg. from a natural salt meadow as part of an investigation on rhizospheric bacteria from salt-resistant plant species and evaluation of their plant growth-promoting abilities. Cells were rods, non-motile, aerobic, and oxidase and catalase positive, grew in a temperature range of between 4 and 37 °C, and in the presence of 0.5-5 % NaCl (w/v). Based on 16S rRNA gene sequence analysis, strain E130T is affiliated within the genus Ancylobacter, sharing the highest similarity with Ancylobacter rudongensis DSM 17131T (97.6 %), Ancylobacter defluvii CCUG 63806T (97.5 %) and Ancylobacter dichloromethanicus DSM 21507T (97.4 %). The DNA G+C content of strain E130T was 65.1 mol%. Its respiratory quinones were Q-9 and Q-10 and its major polar lipids comprised phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine and unidentified phospholipid. Major fatty acids of the strains E130T were C12 : 0, C16 : 0, C18 : 1ω7c and C19 : 0cycloω8c. The DNA-DNA relatedness of E130T to A. rudongensis DSM 17131T, A. defluvii CCUG 63806T and A. dichloromethanicus DSM 21507T was 29.2, 21.2 and 32.2 % respectively. On the basis of our polyphasic taxonomic study the new isolate represents a novel species, for which the name Ancylobacter pratisalsi sp. nov. is proposed. The type strain is E130T (LMG 29367T=DSM 102029T).
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Affiliation(s)
- Christian Suarez
- Institute of Applied Microbiology, Justus-Liebig University Giessen, 35392 Giessen, Germany
| | - Stefan Ratering
- Institute of Applied Microbiology, Justus-Liebig University Giessen, 35392 Giessen, Germany
| | - Johanna Schäfer
- Institute of Applied Microbiology, Justus-Liebig University Giessen, 35392 Giessen, Germany
| | - Sylvia Schnell
- Institute of Applied Microbiology, Justus-Liebig University Giessen, 35392 Giessen, Germany
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41
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Cardinale M, Kaiser D, Lueders T, Schnell S, Egert M. Microbiome analysis and confocal microscopy of used kitchen sponges reveal massive colonization by Acinetobacter, Moraxella and Chryseobacterium species. Sci Rep 2017; 7:5791. [PMID: 28725026 PMCID: PMC5517580 DOI: 10.1038/s41598-017-06055-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 06/07/2017] [Indexed: 12/22/2022] Open
Abstract
The built environment (BE) and in particular kitchen environments harbor a remarkable microbial diversity, including pathogens. We analyzed the bacterial microbiome of used kitchen sponges by 454–pyrosequencing of 16S rRNA genes and fluorescence in situ hybridization coupled with confocal laser scanning microscopy (FISH–CLSM). Pyrosequencing showed a relative dominance of Gammaproteobacteria within the sponge microbiota. Five of the ten most abundant OTUs were closely related to risk group 2 (RG2) species, previously detected in the BE and kitchen microbiome. Regular cleaning of sponges, indicated by their users, significantly affected the microbiome structure. Two of the ten dominant OTUs, closely related to the RG2-species Chryseobacterium hominis and Moraxella osloensis, showed significantly greater proportions in regularly sanitized sponges, thereby questioning such sanitation methods in a long term perspective. FISH–CLSM showed an ubiquitous distribution of bacteria within the sponge tissue, concentrating in internal cavities and on sponge surfaces, where biofilm–like structures occurred. Image analysis showed local densities of up to 5.4 * 1010 cells per cm3, and confirmed the dominance of Gammaproteobacteria. Our study stresses and visualizes the role of kitchen sponges as microbiological hot spots in the BE, with the capability to collect and spread bacteria with a probable pathogenic potential.
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Affiliation(s)
- Massimiliano Cardinale
- Institute of Applied Microbiology, Research Center for BioSystems, Land Use, and Nutrition (IFZ), Justus-Liebig-University Giessen, Giessen, Germany
| | - Dominik Kaiser
- Faculty of Medical and Life Sciences, Institute of Precision Medicine (IPM), Microbiology and Hygiene Group, Furtwangen University, Villingen-Schwenningen, Germany
| | - Tillmann Lueders
- Institute of Groundwater Ecology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Sylvia Schnell
- Institute of Applied Microbiology, Research Center for BioSystems, Land Use, and Nutrition (IFZ), Justus-Liebig-University Giessen, Giessen, Germany
| | - Markus Egert
- Faculty of Medical and Life Sciences, Institute of Precision Medicine (IPM), Microbiology and Hygiene Group, Furtwangen University, Villingen-Schwenningen, Germany.
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42
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Wu C, Schnell S, Vakil P, Honarmand AR, Ansari SA, Carr J, Markl M, Prabhakaran S. In Vivo Assessment of the Impact of Regional Intracranial Atherosclerotic Lesions on Brain Arterial 3D Hemodynamics. AJNR Am J Neuroradiol 2017; 38:515-522. [PMID: 28057635 DOI: 10.3174/ajnr.a5051] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 10/26/2016] [Indexed: 11/07/2022]
Abstract
BACKGROUND AND PURPOSE Intracranial atherosclerosis induces hemodynamic disturbance, which is not well-characterized, particularly in cerebral flow redistribution. We aimed to characterize the impact of regional stenotic lesions on intracranial hemodynamics by using 4D flow MR imaging. MATERIALS AND METHODS 4D flow MR imaging was performed in 22 symptomatic patients (mean age, 68.4 ± 14.2 years) with intracranial stenosis (ICA, n = 7; MCA, n = 9; basilar artery, n = 6) and 10 age-appropriate healthy volunteers (mean age, 60.7 ± 8.1 years). 3D blood flow patterns were visualized by using time-integrated pathlines. Blood flow and peak velocity asymmetry indices were compared between patients and healthy volunteers in 4 prespecified arteries: ICAs, MCAs, and anterior/posterior cerebral arteries. RESULTS 3D blood flow pathlines demonstrated flow redistribution across cerebral arteries in patients with unilateral intracranial stenosis. For patients with ICA stenosis compared with healthy volunteers, significantly lower flow and peak velocities were identified in the ipsilateral ICA (P = .001 and P = .001) and MCA (P < .001 and P = .001), but higher flow, in the ipsilateral PCA (P < .001). For patients with MCA stenosis, significantly lower flow and peak velocities were observed in the ipsilateral ICA (P = .009 and P = .045) and MCA (P < .001 and P = .005), but significantly higher flow was found in the ipsilateral posterior cerebral artery (P = .014) and anterior cerebral artery (P = .006). The asymmetry indices were not significantly different between patients with basilar artery stenosis and the healthy volunteers. CONCLUSIONS Regional intracranial atherosclerotic lesions not only alter distal arterial flow but also significantly affect ipsilateral collateral arterial hemodynamics.
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Affiliation(s)
- C Wu
- From the Department of Biomedical Engineering (C.W., M.M.), McCormick School of Engineering, Northwestern University, Chicago, Illinois .,Departments of Radiology (C.W., S.S., P.V., A.R.H., S.A.A., J.C., M.M.).,Philips Healthcare (C.W.), Gainesville, Florida
| | - S Schnell
- Departments of Radiology (C.W., S.S., P.V., A.R.H., S.A.A., J.C., M.M.)
| | - P Vakil
- Departments of Radiology (C.W., S.S., P.V., A.R.H., S.A.A., J.C., M.M.)
| | - A R Honarmand
- Departments of Radiology (C.W., S.S., P.V., A.R.H., S.A.A., J.C., M.M.)
| | - S A Ansari
- Departments of Radiology (C.W., S.S., P.V., A.R.H., S.A.A., J.C., M.M.).,Neurological Surgery (S.A.A.)
| | - J Carr
- Departments of Radiology (C.W., S.S., P.V., A.R.H., S.A.A., J.C., M.M.)
| | - M Markl
- From the Department of Biomedical Engineering (C.W., M.M.), McCormick School of Engineering, Northwestern University, Chicago, Illinois.,Departments of Radiology (C.W., S.S., P.V., A.R.H., S.A.A., J.C., M.M.)
| | - S Prabhakaran
- Neurology (S.P.), Feinberg School of Medicine, Northwestern University, Chicago, Illinois
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Ambika Manirajan B, Ratering S, Rusch V, Schwiertz A, Geissler-Plaum R, Cardinale M, Schnell S. Bacterial microbiota associated with flower pollen is influenced by pollination type, and shows a high degree of diversity and species-specificity. Environ Microbiol 2016; 18:5161-5174. [DOI: 10.1111/1462-2920.13524] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 09/04/2016] [Indexed: 11/27/2022]
Affiliation(s)
- Binoy Ambika Manirajan
- Institute of Applied Microbiology, Research Center for BioSystems, Land Use, and Nutrition (IFZ), Justus-Liebig-University; Giessen Germany
| | - Stefan Ratering
- Institute of Applied Microbiology, Research Center for BioSystems, Land Use, and Nutrition (IFZ), Justus-Liebig-University; Giessen Germany
| | - Volker Rusch
- Institut für Integrative Biologie, Stiftung Old Herborn University; Herborn Germany
| | | | - Rita Geissler-Plaum
- Institute of Applied Microbiology, Research Center for BioSystems, Land Use, and Nutrition (IFZ), Justus-Liebig-University; Giessen Germany
| | - Massimiliano Cardinale
- Institute of Applied Microbiology, Research Center for BioSystems, Land Use, and Nutrition (IFZ), Justus-Liebig-University; Giessen Germany
| | - Sylvia Schnell
- Institute of Applied Microbiology, Research Center for BioSystems, Land Use, and Nutrition (IFZ), Justus-Liebig-University; Giessen Germany
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Auerbach R, Bokelmann K, Stauber R, Schnell S, Ratering S. Bioleaching of Metals and Rare Earth Elements from Secondary Raw Materials Using Acidophilic Bacteria and Fungi. CHEM-ING-TECH 2016. [DOI: 10.1002/cite.201650166] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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45
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Garcia J, Barker A, Murphy I, Jarvis K, Powell A, Schnell S, Collins J, Carr J, Markl M. ASSESSMENT OF AORTIC MORPHOMETRY AND PEAK VELOCITY BASED ON 4D FLOW MRI. Can J Cardiol 2015. [DOI: 10.1016/j.cjca.2015.07.639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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46
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Cardinale M, Ratering S, Suarez C, Zapata Montoya AM, Geissler-Plaum R, Schnell S. Paradox of plant growth promotion potential of rhizobacteria and their actual promotion effect on growth of barley (Hordeum vulgare L.) under salt stress. Microbiol Res 2015; 181:22-32. [PMID: 26640049 DOI: 10.1016/j.micres.2015.08.002] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Revised: 07/28/2015] [Accepted: 08/01/2015] [Indexed: 10/23/2022]
Abstract
From the rhizosphere of two salt tolerant plant species, Hordeum secalinum and Plantago winteri growing in a naturally salt meadow, 100 strains were isolation on enrichment media for various plant growth-promoting (PGP) functions (ACC deaminase activity, auxin synthesis, calcium phosphate mobilization and nitrogen fixation). Based on the taxonomic affiliation of the isolated bacteria and their enrichment medium 22 isolates were selected to test their growth promotion effect on the crop barley (Hordeum vulgare) under salt stress in pot experiment. In parallel the isolates were characterized in pure culture for their plant growth-promoting activities. Surprisingly the best promotors did not display a promising set of PGP activities. Isolates with multiple PGP-activities in pure culture like Microbacterium natoriense strain E38 and Pseudomonas brassicacearum strain E8 did not promote plant growth. The most effective isolate was strain E108 identified as Curtobacterium flaccumfaciens, which increased barley growth up to 300%. In pure culture strain E108 showed only two out of six plant growth promoting activities and would have been neglected. Our results highlight that screening based on pure culture assays may not be suitable for recognition of best plant growth promotion candidates and could preclude the detection of both new PGPR and new plant promotion mechanisms.
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Affiliation(s)
- Massimiliano Cardinale
- Institute of Applied Microbiology, Justus-Liebig-University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Stefan Ratering
- Institute of Applied Microbiology, Justus-Liebig-University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Christian Suarez
- Institute of Applied Microbiology, Justus-Liebig-University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Ana Maria Zapata Montoya
- Institute of Applied Microbiology, Justus-Liebig-University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Rita Geissler-Plaum
- Institute of Applied Microbiology, Justus-Liebig-University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Sylvia Schnell
- Institute of Applied Microbiology, Justus-Liebig-University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany.
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Kampmann K, Ratering S, Geißler-Plaum R, Schmidt M, Zerr W, Schnell S. Changes of the microbial population structure in an overloaded fed-batch biogas reactor digesting maize silage. Bioresour Technol 2014; 174:108-117. [PMID: 25463789 DOI: 10.1016/j.biortech.2014.09.150] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 09/19/2014] [Accepted: 09/23/2014] [Indexed: 06/04/2023]
Abstract
Two parallel, stable operating biogas reactors were fed with increasing amounts of maize silage to monitor microbial community changes caused by overloading. Changes of microorganisms diversity revealed by SSCP (single strand conformation polymorphism) indicating an acidification before and during the pH-value decrease. The earliest indicator was the appearance of a Methanosarcina thermophila-related species. Diversity of dominant fermenting bacteria within Bacteroidetes, Firmicutes and other Bacteria decreased upon overloading. Some species became dominant directly before and during acidification and thus could be suitable as possible indicator organisms for detection of futurity acidification. Those bacteria were related to Prolixibacter bellariivorans and Streptococcus infantarius subsp. infantarius. An early detection of community shifts will allow better feeding management for optimal biogas production.
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Affiliation(s)
- Kristina Kampmann
- Institute of Applied Microbiology, Justus-Liebig University, Gießen, Germany
| | - Stefan Ratering
- Institute of Applied Microbiology, Justus-Liebig University, Gießen, Germany.
| | - Rita Geißler-Plaum
- Institute of Applied Microbiology, Justus-Liebig University, Gießen, Germany
| | - Michael Schmidt
- Landesbetrieb Hessisches Landeslabor (LHL), Standort Bad Hersfeld, Bad Hersfeld, Germany
| | - Walter Zerr
- Landesbetrieb Hessisches Landeslabor (LHL), Standort Bad Hersfeld, Bad Hersfeld, Germany
| | - Sylvia Schnell
- Institute of Applied Microbiology, Justus-Liebig University, Gießen, Germany
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Theophel K, Schacht VJ, Schlüter M, Schnell S, Stingu CS, Schaumann R, Bunge M. The importance of growth kinetic analysis in determining bacterial susceptibility against antibiotics and silver nanoparticles. Front Microbiol 2014; 5:544. [PMID: 25426104 PMCID: PMC4226228 DOI: 10.3389/fmicb.2014.00544] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Accepted: 09/30/2014] [Indexed: 11/20/2022] Open
Abstract
Routine antibiotics susceptibility testing still relies on standardized cultivation-based analyses, including measurement of inhibition zones in conventional agar diffusion tests and endpoint turbidity-based measurements. Here, we demonstrate that common off-line monitoring and endpoint determination after 18–24 h could be insufficient for reliable growth-dependent evaluation of antibiotic susceptibility. Different minimal inhibitory concentrations were obtained in 20- and 48 h microdilution plate tests using an Enterococcus faecium clinical isolate (strain UKI-MB07) as a model organism. Hence, we used an on-line kinetic assay for simultaneous cultivation and time-resolved growth analysis in a 96-well format instead of off-line susceptibility testing. Growth of the Enterococcus test organism was delayed up to 30 h in the presence of 0.25 μg mL-1 of vancomycin and 8 μg mL-1 of fosfomycin, after which pronounced growth was observed. Despite the delayed onset of growth, treatment with fosfomycin, daptomycin, fusidic acid, cefoxitin, or gentamicin resulted in higher maximum growth rates and/or higher final optical density values compared with antibiotic-free controls, indicating that growth stimulation and hormetic effects may occur with extended exposure to sublethal antibiotic concentrations. Whereas neither maximum growth rate nor final cell density correlated with antibiotic concentration, the lag phase duration for some antibiotics was a more meaningful indicator of dose-dependent growth inhibition. Our results also reveal that non-temporal growth profiles are only of limited value for cultivation-based antimicrobial silver nanoparticle susceptibility testing. The exposure to Ag(0) nanoparticles led to plasma membrane damage in a concentration-dependent manner and induced oxidative stress in Enterococcus faecium UKI-MB07, as shown by intracellular ROS accumulation.
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Affiliation(s)
- Karsten Theophel
- Institute of Applied Microbiology, Research Center for BioSystems, Land Use, and Nutrition, Justus Liebig University of Giessen Giessen, Germany
| | - Veronika J Schacht
- Institute of Applied Microbiology, Research Center for BioSystems, Land Use, and Nutrition, Justus Liebig University of Giessen Giessen, Germany
| | - Michael Schlüter
- Institute of Applied Microbiology, Research Center for BioSystems, Land Use, and Nutrition, Justus Liebig University of Giessen Giessen, Germany
| | - Sylvia Schnell
- Institute of Applied Microbiology, Research Center for BioSystems, Land Use, and Nutrition, Justus Liebig University of Giessen Giessen, Germany
| | - Catalina-Suzana Stingu
- Institute for Medical Microbiology and Epidemiology of Infectious Diseases, University of Leipzig Leipzig, Germany
| | - Reiner Schaumann
- Institute for Medical Microbiology and Epidemiology of Infectious Diseases, University of Leipzig Leipzig, Germany
| | - Michael Bunge
- Institute of Applied Microbiology, Research Center for BioSystems, Land Use, and Nutrition, Justus Liebig University of Giessen Giessen, Germany
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Suarez C, Ratering S, Geissler-Plaum R, Schnell S. Hartmannibacter diazotrophicus gen. nov., sp. nov., a phosphate-solubilizing and nitrogen-fixing alphaproteobacterium isolated from the rhizosphere of a natural salt-meadow plant. Int J Syst Evol Microbiol 2014; 64:3160-3167. [DOI: 10.1099/ijs.0.064154-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A phosphate-mobilizing, Gram-negative bacterium was isolated from rhizospheric soil of Plantago winteri from a natural salt meadow as part of an investigation of rhizospheric bacteria from salt-resistant plant species and evaluation of their plant-growth-promoting abilities. Cells were rods, motile, strictly aerobic, oxidase-positive and catalase-negative. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain E19T was distinct from other taxa within the class
Alphaproteobacteria
. Strain E19T showed less than 93.5 % 16S rRNA gene sequence similarity with members of the genera
Rhizobium
(≤93.5 %),
Labrenzia
(≤93.1 %),
Stappia
(≤93.1 %),
Aureimonas
(≤93.1 %) and
Mesorhizobium
(≤93.0 %) and was most closely related to
Rhizobium rhizoryzae
(93.5 % 16S rRNA gene sequence similarity to the type strain). The sole respiratory quinone was Q-10, and the polar lipids comprised phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, an aminolipid and an unidentified phospholipid. Major fatty acids were C18 : 1ω7c (71.4 %), summed feature 2 (C14 : 0 3-OH and/or iso-C16 : 1; 8.3 %), C20 : 0 (7.9 %) and C16 : 0 (6.1 %). The DNA G+C content of strain E19T was 59.9±0.7 mol%. The capacity for nitrogen fixation was confirmed by the presence of the nifH gene and the acetylene reduction assay. On the basis of the results of our polyphasic taxonomic study, the new isolate represents a novel genus and species, for which the name Hartmannibacter diazotrophicus gen. nov., sp. nov. is proposed. The type strain of Hartmannibacter diazotrophicus is E19T ( = LMG 27460T = KACC 17263T).
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Affiliation(s)
- Christian Suarez
- Institute of Applied Microbiology, IFZ, Justus-Liebig University Giessen, 35392 Giessen, Germany
| | - Stefan Ratering
- Institute of Applied Microbiology, IFZ, Justus-Liebig University Giessen, 35392 Giessen, Germany
| | - Rita Geissler-Plaum
- Institute of Applied Microbiology, IFZ, Justus-Liebig University Giessen, 35392 Giessen, Germany
| | - Sylvia Schnell
- Institute of Applied Microbiology, IFZ, Justus-Liebig University Giessen, 35392 Giessen, Germany
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50
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Suarez C, Ratering S, Geissler-Plaum R, Schnell S. Rheinheimera hassiensis sp. nov. and Rheinheimera muenzenbergensis sp. nov., two species from the rhizosphere of Hordeum secalinum. Int J Syst Evol Microbiol 2014; 64:1202-1209. [DOI: 10.1099/ijs.0.061200-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two motile, Gram-staining-negative, aerobic, rod-shaped bacteria designated strains E48T and E49T were isolated from the rhizosphere of Hordeum secalinum from a natural salt meadow near Münzenberg, Germany. 16S rRNA gene sequence similarity analysis revealed that strains E48T and E49T shared similarities of 97.6 % with
Rheinheimera pacifica
KMM 1406T and 98.5 % with
Rheinheimera nanhaiensis
E407-8T, respectively. Major fatty acids of strain E48T were C16 : 0, summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH) and C17 : 1ω8c, and of strain E49T were C16 : 0, summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH) and C18 : 1ω7c. The DNA G+C contents were 50.5 mol% (E48T) and 50.0 mol% (E49T). Strains E48T and E49T grew at 4–37 °C (optimum 28 °C) and with 0–6 % NaCl (optimum 0–3 %) and 0–5 % NaCl (optimum 0–3 %), respectively. The potential for nitrogen fixation by strains E48T and E49T was evaluated by molecular techniques and the acetylene reduction assay. The DNA–DNA hybridization, physiological and molecular data demonstrated that strains E48T and E49T represent two novel species of the genus
Rheinheimera
, and therefore the names Rheinheimera hassiensis sp. nov. (type strain E48T = LMG 27268T = KACC 17070T) and Rheinheimera muenzenbergensis sp. nov. (type strain E49T = LMG 27269T = KACC 17071T) are proposed.
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Affiliation(s)
- Christian Suarez
- Institute of Applied Microbiology, IFZ, Justus-Liebig University Giessen, 35392 Giessen, Germany
| | - Stefan Ratering
- Institute of Applied Microbiology, IFZ, Justus-Liebig University Giessen, 35392 Giessen, Germany
| | - Rita Geissler-Plaum
- Institute of Applied Microbiology, IFZ, Justus-Liebig University Giessen, 35392 Giessen, Germany
| | - Sylvia Schnell
- Institute of Applied Microbiology, IFZ, Justus-Liebig University Giessen, 35392 Giessen, Germany
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