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Dixit S, Kumar S, Sharma R, Banakar PS, Singh M, Keshri A, Tyagi AK. Rumen multi-omics addressing diet-host-microbiome interplay in farm animals: a review. Anim Biotechnol 2023; 34:3187-3205. [PMID: 35713100 DOI: 10.1080/10495398.2022.2078979] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
Continuous improvement in the living standards of developing countries, calls for an urgent need of high quality meat and dairy products. The farm animals have a micro-ecosystem in gastro-intestinal tract, comprising of a wide variety of flora and fauna which converts roughages and agricultural byproducts as well as nutrient rich concentrate sources into the useful products such as volatile fatty acids and microbial crude proteins. The microbial diversity changes according to composition of the feed, host species/breed and host's individual genetic makeup. From culture methods to next-generation sequencing technologies, the knowledge has emerged a lot to know-how of microbial world viz. their identification, enzymatic activities and metabolites which are the keys of ruminant's successful existence. The structural composition of ruminal community revealed through metagenomics can be elaborated by metatranscriptomics and metabolomics through deciphering their functional role in metabolism and their responses to the external and internal stimuli. These highly sophisticated analytical tools have made possible to correlate the differences in the feed efficiency, nutrients utilization and methane emissions to their rumen microbiome. The comprehensively understood rumen microbiome will enhance the knowledge in the fields of animal nutrition, biotechnology and climatology through deciphering the significance of each and every domain of residing microbial entity. The present review undertakes the recent investigations regarding rumen multi-omics viz. taxonomic and functional potential of microbial populations, host-diet-microbiome interactions and correlation with metabolic dynamics.
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Affiliation(s)
- Sonam Dixit
- Rumen Biotechnology Laboratory, Department of Animal Nutrition, National Dairy Research Institute, Karnal, India
| | - Sachin Kumar
- Rumen Biotechnology Laboratory, Department of Animal Nutrition, National Dairy Research Institute, Karnal, India
| | - Ritu Sharma
- Rumen Biotechnology Laboratory, Department of Animal Nutrition, National Dairy Research Institute, Karnal, India
| | - P S Banakar
- Rumen Biotechnology Laboratory, Department of Animal Nutrition, National Dairy Research Institute, Karnal, India
| | - Manvendra Singh
- Krishi Vigyan Kendra, Banda University of Agriculture and Technology, Banda, India
| | - Anchal Keshri
- Rumen Biotechnology Laboratory, Department of Animal Nutrition, National Dairy Research Institute, Karnal, India
| | - A K Tyagi
- Rumen Biotechnology Laboratory, Department of Animal Nutrition, National Dairy Research Institute, Karnal, India
- Animal Nutrition and Physiology, Indian Council of Agricultural Research, New Delhi, India
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Hernández R, Chaib De Mares M, Jimenez H, Reyes A, Caro-Quintero A. Functional and Phylogenetic Characterization of Bacteria in Bovine Rumen Using Fractionation of Ruminal Fluid. Front Microbiol 2022; 13:813002. [PMID: 35401437 PMCID: PMC8992543 DOI: 10.3389/fmicb.2022.813002] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 02/01/2022] [Indexed: 01/08/2023] Open
Abstract
Cattle productivity depends on our ability to fully understand and manipulate the fermentation process of plant material that occurs in the bovine rumen, which ultimately leads to the improvement of animal health and increased productivity with a reduction in environmental impact. An essential step in this direction is the phylogenetic and functional characterization of the microbial species composing the ruminal microbiota. To address this challenge, we separated a ruminal fluid sample by size and density using a sucrose density gradient. We used the full sample and the smallest fraction (5%), allowing the enrichment of bacteria, to assemble metagenome-assembled genomes (MAGs). We obtained a total of 16 bacterial genomes, 15 of these enriched in the smallest fraction of the gradient. According to the recently proposed Genome Taxonomy Database (GTDB) taxonomy, these MAGs belong to Bacteroidota, Firmicutes_A, Firmicutes, Proteobacteria, and Spirochaetota phyla. Fifteen MAGs were novel at the species level and four at the genus level. The functional characterization of these MAGs suggests differences from what is currently known from the genomic potential of well-characterized members from this complex environment. Species of the phyla Bacteroidota and Spirochaetota show the potential for hydrolysis of complex polysaccharides in the plant cell wall and toward the production of B-complex vitamins and protein degradation in the rumen. Conversely, the MAGs belonging to Firmicutes and Alphaproteobacteria showed a reduction in several metabolic pathways; however, they have genes for lactate fermentation and the presence of hydrolases and esterases related to chitin degradation. Our results demonstrate that the separation of the rumen microbial community by size and density reduced the complexity of the ruminal fluid sample and enriched some poorly characterized ruminal bacteria allowing exploration of their genomic potential and their functional role in the rumen ecosystem.
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Affiliation(s)
- Ruth Hernández
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Maryam Chaib De Mares
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Hugo Jimenez
- Animal Microbiology Laboratory, Agrodiversity Department, Corporación Colombiana de Investigación Agropecuaria - AGROSAVIA, Bogotá, Colombia
| | - Alejandro Reyes
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia.,The Edison Family Center for Genome Science and Systems Biology, Washington University School of Medicine, Saint Louis, MO, United States
| | - Alejandro Caro-Quintero
- Departamento de Biología, Facultad de Ciencias, Universidad Nacional de Colombia, Bogotá, Colombia
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Microbial patterns in rumen are associated with gain of weight in beef cattle. Antonie Van Leeuwenhoek 2020; 113:1299-1312. [PMID: 32577920 DOI: 10.1007/s10482-020-01440-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 06/15/2020] [Indexed: 10/24/2022]
Abstract
Ruminal microorganisms play a pivotal role in cattle nutrition. The discovery of the main microbes or of a microbial community responsible for enhancing the gain of weight in beef cattle might be used in therapeutic approaches to increase animal performance and cause less environmental damages. Here, we examined the differences in bacterial and fungal composition of rumen samples of Braford heifers raised in natural grassland of the Pampa Biome in Brazil. We aimed to detect microbial patterns in the rumen that could be correlated with the gain of weight. We hypothesized that microorganisms important to digestion process are increased in animals with a higher gain of weight. The gain of weight of seventeen healthy animals was monitored for 60 days. Ruminal samples were obtained and the 16S and ITS1 genes were amplified and sequenced to identify the closest microbial relatives within the microbial communities. A predictive model based on microbes responsible for the gain of weight was build and further tested using the entire dataset., The main differential abundant microbes between groups included the bacterial taxa RFN20, Prevotella, Anaeroplasma and RF16 and the fungal taxa Aureobasidium, Cryptococcus, Sarocladium, Pleosporales and Tremellales. The predictive model detected some of these taxa associated with animals with the high gain of weight group, most of them being organisms that have been correlated to the production of substances that improve the ruminal digestion process. These findings provide new insights about cattle nutrition and suggest the use of these microbes to improve beef cattle breeding.
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Characterization and comprehensive analysis of the ecological interaction networks of bacterial communities in Paullinia cupana var. sorbilis by 16S rRNA gene metabarcoding. World J Microbiol Biotechnol 2019; 35:182. [DOI: 10.1007/s11274-019-2758-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 11/02/2019] [Indexed: 12/17/2022]
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Pyzik A, Ciezkowska M, Krawczyk PS, Sobczak A, Drewniak L, Dziembowski A, Lipinski L. Comparative analysis of deep sequenced methanogenic communities: identification of microorganisms responsible for methane production. Microb Cell Fact 2018; 17:197. [PMID: 30572955 PMCID: PMC6302309 DOI: 10.1186/s12934-018-1043-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 12/11/2018] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Although interactions between microorganisms involved in biogas production are largely uncharted, it is commonly accepted that methanogenic Archaea are essential for the process. Methanogens thrive in various environments, but the most extensively studied communities come from biogas plants. In this study, we employed a metagenomic analysis of deeply sequenced methanogenic communities, which allowed for comparison of taxonomic and functional diversity as well as identification of microorganisms directly involved in various stages of methanogenesis pathways. RESULTS A comprehensive metagenomic approach was used to compare seven environmental communities, originating from an agricultural biogas plant, cattle-associated samples, a lowland bog, sewage sludge from a wastewater treatment plant and sediments from an ancient gold mine. In addition to the native consortia, two laboratory communities cultivated on maize silage as the sole substrate were also analyzed. Results showed that all anaerobic communities harbored genes of all known methanogenesis pathways, but their abundance varied greatly between environments and that genes were encoded by different methanogens. Identification of microorganisms directly involved in different stages of methane production revealed that hydrogenotrophic methanogens, such as Methanoculleus, Methanobacterium, Methanobrevibacter, Methanocorpusculum or Methanoregula, predominated in most native communities, whereas acetoclastic Methanosaeta seemed to be the key methanogen in the wastewater treatment plant. Furthermore, in many environments, the methylotrophic pathway carried out by representatives of Methanomassiliicoccales, such as Candidatus Methanomethylophilus and Candidatus Methanoplasma, seemed to play an important role in methane production. In contrast, in stable laboratory reactors substrate versatile Methanosarcina predominated. CONCLUSIONS The metagenomic approach presented in this study allowed for deep exploration and comparison of nine environments in which methane production occurs. Different abundance of methanogenesis-related functions was observed and the functions were analyzed in the phylogenetic context in order to identify microbes directly involved in methane production. In addition, a comparison of two metagenomic analytical tools, MG-RAST and MetAnnotate, revealed that combination of both allows for a precise characterization of methanogenic communities.
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Affiliation(s)
- Adam Pyzik
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106, Warsaw, Poland
| | - Martyna Ciezkowska
- Laboratory of Environmental Pollution Analysis, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland
| | - Pawel S Krawczyk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106, Warsaw, Poland
| | - Adam Sobczak
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106, Warsaw, Poland.,Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106, Warsaw, Poland
| | - Lukasz Drewniak
- Laboratory of Environmental Pollution Analysis, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland
| | - Andrzej Dziembowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106, Warsaw, Poland.,Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106, Warsaw, Poland
| | - Leszek Lipinski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106, Warsaw, Poland.
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Khattab MS, Tawab AMAE, Fouad MT. Isolation and Characterization of Anaerobic Bacteria from Frozen
Rumen Liquid and its Potential Characterizations. INTERNATIONAL JOURNAL OF DAIRY SCIENCE 2016; 12:47-51. [DOI: 10.3923/ijds.2017.47.51] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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Zhang J, Hu Q, Xu C, Liu S, Li C. Key Microbiota Identification Using Functional Gene Analysis during Pepper (Piper nigrum L.) Peeling. PLoS One 2016; 11:e0165206. [PMID: 27768750 PMCID: PMC5074590 DOI: 10.1371/journal.pone.0165206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2016] [Accepted: 10/07/2016] [Indexed: 11/20/2022] Open
Abstract
Pepper pericarp microbiota plays an important role in the pepper peeling process for the production of white pepper. We collected pepper samples at different peeling time points from Hainan Province, China, and used a metagenomic approach to identify changes in the pericarp microbiota based on functional gene analysis. UniFrac distance-based principal coordinates analysis revealed significant changes in the pericarp microbiota structure during peeling, which were attributed to increases in bacteria from the genera Selenomonas and Prevotella. We identified 28 core operational taxonomic units at each time point, mainly belonging to Selenomonas, Prevotella, Megasphaera, Anaerovibrio, and Clostridium genera. The results were confirmed by quantitative polymerase chain reaction. At the functional level, we observed significant increases in microbial features related to acetyl xylan esterase and pectinesterase for pericarp degradation during peeling. These findings offer a new insight into biodegradation for pepper peeling and will promote the development of the white pepper industry.
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Affiliation(s)
- Jiachao Zhang
- College of Food Science and Technology, Hainan University, Haikou, 570228, P. R. China
| | - Qisong Hu
- College of Food Science and Technology, Hainan University, Haikou, 570228, P. R. China
| | - Chuanbiao Xu
- College of Food Science and Technology, Hainan University, Haikou, 570228, P. R. China
| | - Sixin Liu
- College of Materials and Chemical Engineering, Hainan University, Haikou, 570228, P. R. China
- * E-mail: (CL); (SL)
| | - Congfa Li
- College of Food Science and Technology, Hainan University, Haikou, 570228, P. R. China
- * E-mail: (CL); (SL)
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Sun H, Ni X, Song X, Wen B, Zhou Y, Zou F, Yang M, Peng Z, Zhu H, Zeng Y, Wang H, Fu X, Shi Y, Yin Z, Pan K, Jing B, Zeng D, Wang P. Fermented Yupingfeng polysaccharides enhance immunity by improving the foregut microflora and intestinal barrier in weaning rex rabbits. Appl Microbiol Biotechnol 2016; 100:8105-20. [DOI: 10.1007/s00253-016-7619-0] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 05/01/2016] [Accepted: 05/07/2016] [Indexed: 02/06/2023]
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Mootapally CS, Nathani NM, Patel AK, Jakhesara SJ, Joshi CG. Mining of Ruminant Microbial Phytase (RPHY1) from Metagenomic Data of Mehsani Buffalo Breed: Identification, Gene Cloning, and Characterization. J Mol Microbiol Biotechnol 2016; 26:252-60. [DOI: 10.1159/000445321] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 03/09/2016] [Indexed: 11/19/2022] Open
Abstract
Phytases have been widely used as animal feed supplements to increase the availability of digestible phosphorus, especially in monogastric animals fed cereal grains. The present study describes the identification of a full-length phytase gene of <i>Prevotella</i> species present in Mehsani buffalo rumen. The gene, designated as RPHY1, consists of 1,251 bp and is expressed into protein with 417 amino acids. A homology search of the deduced amino acid sequence of the RPHY1 phytase gene in a nonredundant protein database showed that it shares 92% similarity with the histidine acid phosphatase domain. Subsequently, the RPHY1 gene was expressed using a pET32a expression vector in <i>Escherichia coli </i>BL21 and purified using a His60 Ni-NTA gravity column. The mass of the purified RPHY1 was estimated to be approximately 63 kDa by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). The optimal RPHY1 enzyme activity was observed at 55°C (pH 5) and exhibited good stability at 5°C and within the acidic pH range. Significant inhibition of RPHY1 activity was observed for Mg<sup>2+</sup> and K<sup>+</sup> metal ions, while Ca<sup>2+</sup>, Mn<sup>2+</sup>, and Na<sup>+</sup> slightly inhibited enzyme activity. The RPHY1 phytase was susceptible to SDS, and it was highly stimulated in the presence of EDTA. Overall, the observed comparatively high enzyme activity levels and characteristics of the RPHY1 gene mined from rumen prove its promising candidature as a feed supplement enzyme in animal farming.
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Ferragut F, Vega CG, Mauroy A, Conceição-Neto N, Zeller M, Heylen E, Uriarte EL, Bilbao G, Bok M, Matthijnssens J, Thiry E, Badaracco A, Parreño V. Molecular detection of bovine Noroviruses in Argentinean dairy calves: Circulation of a tentative new genotype. INFECTION GENETICS AND EVOLUTION 2016; 40:144-150. [PMID: 26940636 PMCID: PMC7185671 DOI: 10.1016/j.meegid.2016.02.034] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Revised: 02/11/2016] [Accepted: 02/25/2016] [Indexed: 11/27/2022]
Abstract
Bovine noroviruses are enteric pathogens detected in fecal samples of both diarrheic and non-diarrheic calves from several countries worldwide. However, epidemiological information regarding bovine noroviruses is still lacking for many important cattle producing countries from South America. In this study, three bovine norovirus genogroup III sequences were determined by conventional RT-PCR and Sanger sequencing in feces from diarrheic dairy calves from Argentina (B4836, B4848, and B4881, all collected in 2012). Phylogenetic studies based on a partial coding region for the RNA-dependent RNA polymerase (RdRp, 503 nucleotides) of these three samples suggested that two of them (B4836 and B4881) belong to genotype 2 (GIII.2) while the third one (B4848) was more closely related to genotype 1 (GIII.1) strains. By deep sequencing, the capsid region from two of these strains could be determined. This confirmed the circulation of genotype 1 (B4848) together with the presence of another sequence (B4881) sharing its highest genetic relatedness with genotype 1, but sufficiently distant to constitute a new genotype. This latter strain was shown in silico to be a recombinant: phylogenetic divergence was detected between its RNA-dependent RNA polymerase coding sequence (genotype GIII.2) and its capsid protein coding sequence (genotype GIII.1 or a potential norovirus genotype). According to this data, this strain could be the second genotype GIII.2_GIII.1 bovine norovirus recombinant described in literature worldwide. Further analysis suggested that this strain could even be a potential norovirus GIII genotype, tentatively named GIII.4. The data provides important epidemiological and evolutionary information on bovine noroviruses circulating in South America. Molecular prevalence of bovine Noroviruses in Argentina is reported. Newborn calves positive to Norovirus presented diarrhea. Phylogenetic inferences of the strains detected were performed and genotype–genogroups were determined for each strain. A tentative new genotype is reported. This is the first report of bovine Noroviruses from Argentina, one of the main meat and dairy farming countries worldwide.
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Affiliation(s)
- Fátima Ferragut
- Enteric Viruses Section, Virology Institute, Veterinary and Agronomic Research Centre, National Institute of Agricultural Technology (INTA), Castelar CC25 (CP 1712), Buenos Aires, Argentina
| | - Celina G Vega
- Enteric Viruses Section, Virology Institute, Veterinary and Agronomic Research Centre, National Institute of Agricultural Technology (INTA), Castelar CC25 (CP 1712), Buenos Aires, Argentina
| | - Axel Mauroy
- Veterinary Virology and Animal Viral Diseases, Fundamental and Applied Research for Animal and Health Centre, Faculty of Veterinary Medicine, University of Liège, Liège B-4000, Belgium
| | - Nádia Conceição-Neto
- KU Leuven - University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Viral Metagenomics, B-3000, Leuven, Belgium
| | - Mark Zeller
- KU Leuven - University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Viral Metagenomics, B-3000, Leuven, Belgium
| | - Elisabeth Heylen
- KU Leuven - University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Viral Metagenomics, B-3000, Leuven, Belgium
| | - Enrique Louge Uriarte
- Animal Health Section, Animal Production Area, EEA INTA Balcarce, Balcarce CP 7620, Buenos Aires, Argentina
| | - Gladys Bilbao
- Veterinary College, UNCPBA, Tandil CP 7000, Buenos Aires, Argentina
| | - Marina Bok
- Enteric Viruses Section, Virology Institute, Veterinary and Agronomic Research Centre, National Institute of Agricultural Technology (INTA), Castelar CC25 (CP 1712), Buenos Aires, Argentina
| | - Jelle Matthijnssens
- KU Leuven - University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Viral Metagenomics, B-3000, Leuven, Belgium
| | - Etienne Thiry
- Veterinary Virology and Animal Viral Diseases, Fundamental and Applied Research for Animal and Health Centre, Faculty of Veterinary Medicine, University of Liège, Liège B-4000, Belgium
| | - Alejandra Badaracco
- Enteric Viruses Section, Virology Institute, Veterinary and Agronomic Research Centre, National Institute of Agricultural Technology (INTA), Castelar CC25 (CP 1712), Buenos Aires, Argentina
| | - Viviana Parreño
- Enteric Viruses Section, Virology Institute, Veterinary and Agronomic Research Centre, National Institute of Agricultural Technology (INTA), Castelar CC25 (CP 1712), Buenos Aires, Argentina.
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