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Pires GP, Fioresi VS, Canal D, Canal DC, Fernandes M, Brustolini OJB, de Avelar Carpinetti P, Ferreira A, da Silva Ferreira MF. Effects of trimer repeats on Psidium guajava L. gene expression and prospection of functional microsatellite markers. Sci Rep 2024; 14:9811. [PMID: 38684872 PMCID: PMC11059378 DOI: 10.1038/s41598-024-60417-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Accepted: 04/23/2024] [Indexed: 05/02/2024] Open
Abstract
Most research on trinucleotide repeats (TRs) focuses on human diseases, with few on the impact of TR expansions on plant gene expression. This work investigates TRs' effect on global gene expression in Psidium guajava L., a plant species with widespread distribution and significant relevance in the food, pharmacology, and economics sectors. We analyzed TR-containing coding sequences in 1,107 transcripts from 2,256 genes across root, shoot, young leaf, old leaf, and flower bud tissues of the Brazilian guava cultivars Cortibel RM and Paluma. Structural analysis revealed TR sequences with small repeat numbers (5-9) starting with cytosine or guanine or containing these bases. Functional annotation indicated TR-containing genes' involvement in cellular structures and processes (especially cell membranes and signal recognition), stress response, and resistance. Gene expression analysis showed significant variation, with a subset of highly expressed genes in both cultivars. Differential expression highlighted numerous down-regulated genes in Cortibel RM tissues, but not in Paluma, suggesting interplay between tissues and cultivars. Among 72 differentially expressed genes with TRs, 24 form miRNAs, 13 encode transcription factors, and 11 are associated with transposable elements. In addition, a set of 20 SSR-annotated, transcribed, and differentially expressed genes with TRs was selected as phenotypic markers for Psidium guajava and, potentially for closely related species as well.
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Affiliation(s)
- Giovanna Pinto Pires
- Centro de Ciências Agrárias e Engenharias, Departamento de Agronomia, Universidade Federal Do Espírito Santo, Alto Universitário, s/n, Alegre, ES, 29500-000, Brazil
| | - Vinicius Sartori Fioresi
- Centro de Ciências Agrárias e Engenharias, Departamento de Agronomia, Universidade Federal Do Espírito Santo, Alto Universitário, s/n, Alegre, ES, 29500-000, Brazil
| | - Drielli Canal
- Centro de Ciências Agrárias e Engenharias, Departamento de Agronomia, Universidade Federal Do Espírito Santo, Alto Universitário, s/n, Alegre, ES, 29500-000, Brazil
| | - Dener Cezati Canal
- Centro de Ciências Agrárias e Engenharias, Departamento de Agronomia, Universidade Federal Do Espírito Santo, Alto Universitário, s/n, Alegre, ES, 29500-000, Brazil
| | - Miquéias Fernandes
- Centro de Ciências Agrárias e Engenharias, Departamento de Agronomia, Universidade Federal Do Espírito Santo, Alto Universitário, s/n, Alegre, ES, 29500-000, Brazil
| | - Otávio José Bernardes Brustolini
- Laboratório Nacional de Computação Científica (LNCC). Av. Getulio Vargas, 333, Petrópolis, Rio de Janeiro, Quitandinha, 25651-076, Brazil
| | - Paola de Avelar Carpinetti
- Centro de Ciências Agrárias e Engenharias, Departamento de Agronomia, Universidade Federal Do Espírito Santo, Alto Universitário, s/n, Alegre, ES, 29500-000, Brazil
| | - Adésio Ferreira
- Centro de Ciências Agrárias e Engenharias, Departamento de Agronomia, Universidade Federal Do Espírito Santo, Alto Universitário, s/n, Alegre, ES, 29500-000, Brazil
| | - Marcia Flores da Silva Ferreira
- Centro de Ciências Agrárias e Engenharias, Departamento de Agronomia, Universidade Federal Do Espírito Santo, Alto Universitário, s/n, Alegre, ES, 29500-000, Brazil.
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Tiwari S, Vis ML. Fine-tuning RNA extraction protocols for polysaccharide-rich freshwater red algae (Rhodophyta). MICROPUBLICATION BIOLOGY 2024; 2024:10.17912/micropub.biology.001180. [PMID: 38665313 PMCID: PMC11044696 DOI: 10.17912/micropub.biology.001180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 04/01/2024] [Accepted: 04/09/2024] [Indexed: 04/28/2024]
Abstract
Freshwater red algae are important primary producers, widely distributed, contributing significantly to nutrient cycling in aquatic ecosystems. Recent studies have focused on identifying the effect of different environmental conditions such as light on the gene expression in photosynthesis pathways. However, obtaining the necessary RNA quantity and quality for sequencing from these algae has been challenging. Although RNA extractions have been optimized for model organisms, RNA extraction for non-model organisms, such as gelatinous (polysaccharide-rich) red algae, requires considerable troubleshooting. The common freshwater red alga, Batrachospermum gelatinosum , was used to test protocols. The extraction efficiency of various sample disruption methods in combination with seven RNA extraction kits was compared. Using a 2-minute disruption procedure with a modification of TRIzol ™ Plus RNA Purification Kit (PureLink ™ RNA Mini Kit + Trizol ™ ) protocol resulted in significantly higher RIN scores (p < 0.05) and high RNA concentration, compared to other methods. The fine-tuned protocol yielded quality RNA (RIN>7) in high concentrations for subsequent sequencing.
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Affiliation(s)
- Sunil Tiwari
- Arizona State University, Tempe, Arizona, United States
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Singh VV, Naseer A, Sellamuthu G, Jakuš R. An Optimized and Cost-Effective RNA Extraction Method for Secondary Metabolite-Enriched Tissues of Norway Spruce ( Picea abies). PLANTS (BASEL, SWITZERLAND) 2024; 13:389. [PMID: 38337922 PMCID: PMC10857598 DOI: 10.3390/plants13030389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 01/21/2024] [Accepted: 01/26/2024] [Indexed: 02/12/2024]
Abstract
Since the development of next-generation sequencing techniques and with the growing interest in transcriptomic studies, there is a demand for high-throughput RNA extraction techniques. General RNA extraction protocols are unreliable when it comes to the quality and quantity of isolated RNA obtained from different tissue types of different plant species. Despite Norway spruce (Picea abies) being one of the most significant and commercially valuable tree species in European forests, only limited genetic research is available. In this study, we developed a cetyltrimethylammonium bromide (CTAB) protocol by modifying the original method. We compared this CTAB protocol with other widely used methods for extracting RNA from different tissues (needle, phloem, and root) of Norway spruce, known for its richness in polyphenols, polysaccharides, and secondary metabolites. The modified CTAB method proves to be superior to the kit-based and TRIzol-based methods for extracting RNA from the metabolite-rich tissues of Norway spruce, resulting in high RNA quality and integrity values (RIN~7-9). The modified CTAB RNA extraction method is rapid, cost-effective, and relatively simple in yielding the desired RNA quality from Norway spruce tissues. It is optimal for RNA sequencing and other downstream molecular applications.
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Affiliation(s)
- Vivek Vikram Singh
- Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Kamýcká 129, Praha-Suchdol, 165 00 Prague, Czech Republic; (A.N.); (G.S.); (R.J.)
| | - Aisha Naseer
- Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Kamýcká 129, Praha-Suchdol, 165 00 Prague, Czech Republic; (A.N.); (G.S.); (R.J.)
| | - Gothandapani Sellamuthu
- Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Kamýcká 129, Praha-Suchdol, 165 00 Prague, Czech Republic; (A.N.); (G.S.); (R.J.)
| | - Rastislav Jakuš
- Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Kamýcká 129, Praha-Suchdol, 165 00 Prague, Czech Republic; (A.N.); (G.S.); (R.J.)
- Institute of Forest Ecology, Slovak Academy of Sciences, Štúrova 2, 960 53 Zvolen, Slovakia
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Canal D, Dos Santos PHD, de Avelar Carpinetti P, Silva MA, Fernandes M, Brustolini OJB, Ferreira A, da Silva Ferreira MF. Exploring the versatility of sesquiterpene biosynthesis in guava plants: a comparative genome-wide analysis of two cultivars. Sci Rep 2024; 14:574. [PMID: 38182724 PMCID: PMC10770072 DOI: 10.1038/s41598-023-51007-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Accepted: 12/29/2023] [Indexed: 01/07/2024] Open
Abstract
Psidium guajava L., a fruit crop belonging to the Myrtaceae family, is highly valued for its nutritional and medicinal properties. The family exhibits a diverse chemical profile of essential oils and serves as a valuable resource due to its ecological interactions, adaptability, and dispersal capacity. The Myrtaceae family has been extensively studied for its terpenoids. Genetic studies have focused on foliar terpene yield in species from the Eucalypteae and Melaleucaceae tribes. To understand the evolutionary trends in guava breeding, this study predicted terpene synthase genes (TPS) from different cultivars. Through this analysis, 43 full-length TPS genes were identified, and approximately 77% of them exhibited relative expression in at least one of the five investigated plant tissues (root, leaf, bud, flower, and fruit) of two guava cultivars. We identified intra-species variation in the terpene profile and single nucleotide polymorphisms (SNPs) in twelve TPS genes, resulting in the clustering of 62 genotypes according to their essential oil chemotypes. The high concentration of sesquiterpenes is supported by the higher number of TPS-a genes and their expression. The expansion for TPS sub-families in P. guajava occurred after the expansion of other rosids species. Providing insight into the origin of structural diversification and expansion in each clade of the TPS gene family within Myrtaceae. This study can provide insights into the diversity of genes for specialized metabolites such as terpenes, and their regulation, which can lead to a diverse chemotype of essential oil in different tissues and genotypes. This suggests a mode of enzymatic evolution that could lead to high sesquiterpene production, act as a chemical defense and contribute to the adaptive capacity of this species to different habitats.
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Affiliation(s)
- Drielli Canal
- Department of Agronomy, Center for Agricultural Sciences and Engineering, Federal University of Espírito Santo, Alto Universitário, s/n, Guararema, Alegre, ES, 29500-000, Brazil
| | - Pedro Henrique Dias Dos Santos
- Department of Agronomy, Center for Agricultural Sciences and Engineering, Federal University of Espírito Santo, Alto Universitário, s/n, Guararema, Alegre, ES, 29500-000, Brazil
| | - Paola de Avelar Carpinetti
- Department of Agronomy, Center for Agricultural Sciences and Engineering, Federal University of Espírito Santo, Alto Universitário, s/n, Guararema, Alegre, ES, 29500-000, Brazil
| | - Matheus Alves Silva
- Department of Agronomy, Center for Agricultural Sciences and Engineering, Federal University of Espírito Santo, Alto Universitário, s/n, Guararema, Alegre, ES, 29500-000, Brazil
| | - Miquéias Fernandes
- Department of Agronomy, Center for Agricultural Sciences and Engineering, Federal University of Espírito Santo, Alto Universitário, s/n, Guararema, Alegre, ES, 29500-000, Brazil
| | | | - Adésio Ferreira
- Department of Agronomy, Center for Agricultural Sciences and Engineering, Federal University of Espírito Santo, Alto Universitário, s/n, Guararema, Alegre, ES, 29500-000, Brazil
| | - Marcia Flores da Silva Ferreira
- Department of Agronomy, Center for Agricultural Sciences and Engineering, Federal University of Espírito Santo, Alto Universitário, s/n, Guararema, Alegre, ES, 29500-000, Brazil.
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Gong D, Li B, Wu B, Fu D, Li Z, Wei H, Guo S, Ding G, Wang B. The Integration of the Metabolome and Transcriptome for Dendrobium nobile Lindl. in Response to Methyl Jasmonate. Molecules 2023; 28:7892. [PMID: 38067620 PMCID: PMC10707931 DOI: 10.3390/molecules28237892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 11/23/2023] [Accepted: 11/28/2023] [Indexed: 12/18/2023] Open
Abstract
Dendrobium nobile Lindl., as an endangered medicinal plant within the genus Dendrobium, is widely distributed in southwestern China and has important ecological and economic value. There are a variety of metabolites with pharmacological activity in D. nobile. The alkaloids and polysaccharides contained within D. nobile are very important active components, which mainly have antiviral, anti-tumor, and immunity improvement effects. However, the changes in the compounds and functional genes of D. nobile induced by methyl jasmonate (MeJA) are not clearly understood. In this study, the metabolome and transcriptome of D. nobile were analyzed after exposure to MeJA. A total of 377 differential metabolites were obtained through data analysis, of which 15 were related to polysaccharide pathways and 35 were related to terpenoids and alkaloids pathways. Additionally, the transcriptome sequencing results identified 3256 differentially expressed genes that were discovered in 11 groups. Compared with the control group, 1346 unigenes were differentially expressed in the samples treated with MeJA for 14 days (TF14). Moreover, the expression levels of differentially expressed genes were also significant at different growth and development stages. According to GO and KEGG annotations, 189 and 99 candidate genes were identified as being involved in terpenoid biosynthesis and polysaccharide biosynthesis, respectively. In addition, the co-expression analysis indicated that 238 and 313 transcription factors (TFs) may contribute to the regulation of terpenoid and polysaccharide biosynthesis, respectively. Through a heat map analysis, fourteen terpenoid synthetase genes, twenty-three cytochrome P450 oxidase genes, eight methyltransferase genes, and six aminotransferase genes were identified that may be related to dendrobine biosynthesis. Among them, one sesquiterpene synthase gene was found to be highly expressed after the treatment with MeJA and was positively correlated with the content of dendrobine. This study provides important and valuable metabolomics and transcriptomic information for the further understanding of D. nobile at the metabolic and molecular levels and provides candidate genes and possible intermediate compounds for the dendrobine biosynthesis pathway, which lays a certain foundation for further research on and application of Dendrobium.
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Affiliation(s)
- Daoyong Gong
- College of Bioengineering, Chongqing University, Chongqing 400045, China;
- Institute of Medicinal Plant Development, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100193, China; (B.W.); (H.W.); (S.G.); (G.D.)
| | - Biao Li
- Institute of Medicinal Plant Development, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100193, China; (B.W.); (H.W.); (S.G.); (G.D.)
| | - Bin Wu
- Institute of Medicinal Plant Development, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100193, China; (B.W.); (H.W.); (S.G.); (G.D.)
| | - Deru Fu
- Steinhardt School of Culture, Education, and Human Development, New York University, New York, NY 10003, USA;
| | - Zesheng Li
- Dehong Tropical Agriculture Research Institute of Yunnan, Ruili 678600, China;
| | - Haobo Wei
- Institute of Medicinal Plant Development, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100193, China; (B.W.); (H.W.); (S.G.); (G.D.)
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Shunxing Guo
- Institute of Medicinal Plant Development, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100193, China; (B.W.); (H.W.); (S.G.); (G.D.)
| | - Gang Ding
- Institute of Medicinal Plant Development, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100193, China; (B.W.); (H.W.); (S.G.); (G.D.)
| | - Bochu Wang
- College of Bioengineering, Chongqing University, Chongqing 400045, China;
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Sasi S, Krishnan S, Kodackattumannil P, Shamisi AA, Aldarmaki M, Lekshmi G, Kottackal M, Amiri KMA. DNA-free high-quality RNA extraction from 39 difficult-to-extract plant species (representing seasonal tissues and tissue types) of 32 families, and its validation for downstream molecular applications. PLANT METHODS 2023; 19:84. [PMID: 37568159 PMCID: PMC10416385 DOI: 10.1186/s13007-023-01063-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 07/24/2023] [Indexed: 08/13/2023]
Abstract
BACKGROUND High-purity RNA serves as the basic requirement for downstream molecular analysis of plant species, especially the differential expression of genes to various biotic and abiotic stimuli. But, the extraction of high-quality RNA is usually difficult from plants rich in polysaccharides and polyphenols, and their presence usually interferes with the downstream applications. The aim of the study is to optimize the extraction of high-quality RNA from diverse plant species/tissues useful for downstream molecular applications. RESULTS Extraction of RNA using commercially available RNA extraction kits and routine hexadecyltrimethylammonium bromide (CTAB) methods did not yield good quality DNA-free RNA from Prosopis cineraria, Conocarpus erectus, and Phoenix dactylifera. A reliable protocol for the extraction of high-quality RNA from mature leaves of these difficult-to-extract trees was optimized after screening nine different methods. The DNase I-, and proteinase K treatment-free modified method, consisting of extraction with CTAB method followed by TRIzol, yielded high-quality DNA-free RNA with an A260/A280 and A260/A230 ratios > 2.0. Extraction of RNA from Conocarpus, the most difficult one, was successful by avoiding the heat incubation of ground tissue in a buffer at 65 oC. Pre-warming of the buffer for 5-10 min was sufficient to extract good-quality RNA. RNA integrity number of the extracted RNA samples ranged between 7 and 9.1, and the gel electrophoresis displayed intact bands of 28S and 18S RNA. A cDNA library constructed from the RNA of P. cineraria was used for the downstream applications. Real-time qPCR analysis using the cDNA from P. cineraria RNA confirmed the quality. The extraction of good quality RNA from samples of the desert-growing P. cineraria (> 20-years-old) collected in alternate months of the year 2021 (January to December covering winter, spring, autumn, and the very dry and hot summer) proved the efficacy of the protocol. The protocol's broad applicability was further validated by extracting good-quality RNA from 36 difficult-to-extract plant species, including tissues such as roots, flowers, floral organs, fruits, and seeds. CONCLUSIONS The modified DNase I and Proteinase K treatment-free protocol enables to extract DNA-free, high-quality, intact RNA from a total of 39 difficult-to-extract plant species belonging to 32 angiosperm families is useful to extract good-quality RNA from dicots and monocots irrespective of tissue types and growing seasons.
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Affiliation(s)
- Shina Sasi
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, P.O. Box 15551, Al Ain, United Arab Emirates
| | - Saranya Krishnan
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, P.O. Box 15551, Al Ain, United Arab Emirates
| | - Preshobha Kodackattumannil
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, P.O. Box 15551, Al Ain, United Arab Emirates
| | - Aysha Al Shamisi
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, P.O. Box 15551, Al Ain, United Arab Emirates
| | - Maitha Aldarmaki
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, P.O. Box 15551, Al Ain, United Arab Emirates
| | - Geetha Lekshmi
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, P.O. Box 15551, Al Ain, United Arab Emirates
| | - Martin Kottackal
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, P.O. Box 15551, Al Ain, United Arab Emirates.
| | - Khaled M A Amiri
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, P.O. Box 15551, Al Ain, United Arab Emirates.
- Department of Biology, College of Science, United Arab Emirates University, P.O. Box 15551, Al Ain, United Arab Emirates.
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Cárdenas Espinosa MJ, Schmidgall T, Wagner G, Kappelmeyer U, Schreiber S, Heipieper HJ, Eberlein C. An optimized method for RNA extraction from the polyurethane oligomer degrading strain Pseudomonas capeferrum TDA1 growing on aromatic substrates such as phenol and 2,4-diaminotoluene. PLoS One 2021; 16:e0260002. [PMID: 34780548 PMCID: PMC8592408 DOI: 10.1371/journal.pone.0260002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 10/30/2021] [Indexed: 11/18/2022] Open
Abstract
Bacterial degradation of xenobiotic compounds is an intense field of research already for decades. Lately, this research is complemented by downstream applications including Next Generation Sequencing (NGS), RT-PCR, qPCR, and RNA-seq. For most of these molecular applications, high-quality RNA is a fundamental necessity. However, during the degradation of aromatic substrates, phenolic or polyphenolic compounds such as polycatechols are formed and interact irreversibly with nucleic acids, making RNA extraction from these sources a major challenge. Therefore, we established a method for total RNA extraction from the aromatic degrading Pseudomonas capeferrum TDA1 based on RNAzol® RT, glycogen and a final cleaning step. It yields a high-quality RNA from cells grown on TDA1 and on phenol compared to standard assays conducted in the study. To our knowledge, this is the first report tackling the problem of polyphenolic compound interference with total RNA isolation in bacteria. It might be considered as a guideline to improve total RNA extraction from other bacterial species.
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Affiliation(s)
| | - Tabea Schmidgall
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Georg Wagner
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Uwe Kappelmeyer
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Stephan Schreiber
- Department Molecular Systems Biology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Hermann J. Heipieper
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Christian Eberlein
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
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