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Li Y, Chen S, Yu Z, Yao J, Jia Y, Liao C, Chen J, Wei Y, Guo R, He L, Ding K. A Novel Bacillus Velezensis for Efficient Degradation of Zearalenone. Foods 2024; 13:530. [PMID: 38397507 PMCID: PMC10888444 DOI: 10.3390/foods13040530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 02/03/2024] [Accepted: 02/06/2024] [Indexed: 02/25/2024] Open
Abstract
Zearalenone (ZEN) is considered one of the most serious mycotoxins contaminating grains and their by-products, causing significant economic losses in the feed and food industries. Biodegradation pathways are currently considered the most efficient solution to remove ZEN contamination from foods. However, low degradation rates and vulnerability to environmental impacts limit the application of biodegradation pathways. Therefore, the main research objective of this article was to screen strains that can efficiently degrade ZEN and survive under harsh conditions. This study successfully isolated a new strain L9 which can efficiently degrade ZEN from 108 food ingredients. The results of sequence alignment showed that L9 is Bacillus velezensis. Meanwhile, we found that the L9 degradation rate reached 91.14% at 24 h and confirmed that the primary degradation mechanism of this strain is biodegradation. The strain exhibits resistance to high temperature, acid, and 0.3% bile salts. The results of whole-genome sequencing analysis showed that, it is possible that the strain encodes the key enzyme, such as chitinase, carboxylesterases, and lactone hydrolase, that work together to degrade ZEN. In addition, 227 unique genes in this strain are primarily involved in its replication, recombination, repair, and protective mechanisms. In summary, we successfully excavated a ZEN-degrading, genetically distinct strain of Bacillus velezensis that provides a solid foundation for the detoxification of feed and food contamination in the natural environment.
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Affiliation(s)
- Yijia Li
- Luoyang Key Laboratory of Live Carrier Biomaterial and Animal Disease Prevention and Control, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China; (Y.L.); (S.C.); (Z.Y.); (J.Y.); (Y.J.); (C.L.); (J.C.); (Y.W.); (R.G.); (L.H.)
- Laboratory of Functional Microbiology and Animal Health, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471003, China
| | - Songbiao Chen
- Luoyang Key Laboratory of Live Carrier Biomaterial and Animal Disease Prevention and Control, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China; (Y.L.); (S.C.); (Z.Y.); (J.Y.); (Y.J.); (C.L.); (J.C.); (Y.W.); (R.G.); (L.H.)
- Laboratory of Functional Microbiology and Animal Health, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471003, China
- Ministry of Education Key Laboratory for Animal Pathogens and Biosafety, Zhengzhou 450000, China
| | - Zuhua Yu
- Luoyang Key Laboratory of Live Carrier Biomaterial and Animal Disease Prevention and Control, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China; (Y.L.); (S.C.); (Z.Y.); (J.Y.); (Y.J.); (C.L.); (J.C.); (Y.W.); (R.G.); (L.H.)
- Laboratory of Functional Microbiology and Animal Health, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471003, China
| | - Jie Yao
- Luoyang Key Laboratory of Live Carrier Biomaterial and Animal Disease Prevention and Control, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China; (Y.L.); (S.C.); (Z.Y.); (J.Y.); (Y.J.); (C.L.); (J.C.); (Y.W.); (R.G.); (L.H.)
- Laboratory of Functional Microbiology and Animal Health, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471003, China
| | - Yanyan Jia
- Luoyang Key Laboratory of Live Carrier Biomaterial and Animal Disease Prevention and Control, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China; (Y.L.); (S.C.); (Z.Y.); (J.Y.); (Y.J.); (C.L.); (J.C.); (Y.W.); (R.G.); (L.H.)
- Laboratory of Functional Microbiology and Animal Health, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471003, China
- Ministry of Education Key Laboratory for Animal Pathogens and Biosafety, Zhengzhou 450000, China
| | - Chengshui Liao
- Luoyang Key Laboratory of Live Carrier Biomaterial and Animal Disease Prevention and Control, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China; (Y.L.); (S.C.); (Z.Y.); (J.Y.); (Y.J.); (C.L.); (J.C.); (Y.W.); (R.G.); (L.H.)
- Laboratory of Functional Microbiology and Animal Health, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471003, China
| | - Jian Chen
- Luoyang Key Laboratory of Live Carrier Biomaterial and Animal Disease Prevention and Control, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China; (Y.L.); (S.C.); (Z.Y.); (J.Y.); (Y.J.); (C.L.); (J.C.); (Y.W.); (R.G.); (L.H.)
- Laboratory of Functional Microbiology and Animal Health, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471003, China
| | - Ying Wei
- Luoyang Key Laboratory of Live Carrier Biomaterial and Animal Disease Prevention and Control, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China; (Y.L.); (S.C.); (Z.Y.); (J.Y.); (Y.J.); (C.L.); (J.C.); (Y.W.); (R.G.); (L.H.)
- Laboratory of Functional Microbiology and Animal Health, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471003, China
| | - Rongxian Guo
- Luoyang Key Laboratory of Live Carrier Biomaterial and Animal Disease Prevention and Control, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China; (Y.L.); (S.C.); (Z.Y.); (J.Y.); (Y.J.); (C.L.); (J.C.); (Y.W.); (R.G.); (L.H.)
- Laboratory of Functional Microbiology and Animal Health, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471003, China
| | - Lei He
- Luoyang Key Laboratory of Live Carrier Biomaterial and Animal Disease Prevention and Control, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China; (Y.L.); (S.C.); (Z.Y.); (J.Y.); (Y.J.); (C.L.); (J.C.); (Y.W.); (R.G.); (L.H.)
- Laboratory of Functional Microbiology and Animal Health, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471003, China
| | - Ke Ding
- Luoyang Key Laboratory of Live Carrier Biomaterial and Animal Disease Prevention and Control, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China; (Y.L.); (S.C.); (Z.Y.); (J.Y.); (Y.J.); (C.L.); (J.C.); (Y.W.); (R.G.); (L.H.)
- Laboratory of Functional Microbiology and Animal Health, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471003, China
- Ministry of Education Key Laboratory for Animal Pathogens and Biosafety, Zhengzhou 450000, China
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Frascella A, Sarrocco S, Jona Lasinio G, Pollice A, Emiliani G, Danti R, Barberini S, Della Rocca G. Characterization of Trichoderma species from forest ecosystems by high-throughput phenotypic microarray. Fungal Biol 2023; 127:1376-1383. [PMID: 37993248 DOI: 10.1016/j.funbio.2023.09.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 09/18/2023] [Accepted: 09/21/2023] [Indexed: 11/24/2023]
Abstract
The use of beneficial organisms for the biocontrol of soil-borne pathogens in forestry is still poor explored. In this work, the nutritional demands of 10 previously selected isolates of Trichoderma for the biocontrol of forest soil-borne pathogens have been tested by Phenotype Microarray technology, to investigate about their C-source utilization and exploring the possibility to obtain a microbial consortia (SynCom), an innovative strategy for the biocontrol of plant disease. All Trichoderma isolates tested in this study showed a high spore germination percentage within 3 d and evidenced nutritional preference regardless of the species they belong to, and unrelated to their soil of origin. Results of growth curve analysis and MANOVA test revealed that all isolates assimilate a broad range of substrates, generally preferring complex compounds such as monosaccharides related compounds, nitrogen compounds, carboxylic acids and esters. No evidence of competition for nutritional resources have been observed among isolates of this study. As a result, a combination of different isolates could be proposed to obtain a SynCom useful for the practice of phytopathogen biocontrol in forestry. The addition of i-erythritol, adenosine and turanose to a growth substrate could be suggested as stimulating compounds for the growth of the selected Trichoderma isolates.
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Affiliation(s)
- Arcangela Frascella
- Institute of BioEconomy, National Research Council, Via Madonna Del Piano, 10, Sesto Fiorentino (Florence) 50019, Italy
| | - Sabrina Sarrocco
- Department of Agriculture, Food and Environment, University of Pisa, Via Del Borghetto 80, Pisa 50124, Italy.
| | - Giovanna Jona Lasinio
- Department of Statistical Sciences, University of Rome "Sapienza", Piazzale Aldo Moro 5, Rome, Italy
| | - Alessio Pollice
- Department of Economics and Finance, University of Bari Aldo Moro, Largo Abbazia Santa Scolastica, Bari, Italy
| | - Giovanni Emiliani
- Institute of Sustainable Plant Protection, National Research Council, Via Madonna Del Piano, 10, Sesto Fiorentino (Florence) 50019, Italy
| | - Roberto Danti
- Institute of Sustainable Plant Protection, National Research Council, Via Madonna Del Piano, 10, Sesto Fiorentino (Florence) 50019, Italy
| | - Sara Barberini
- Institute of Sustainable Plant Protection, National Research Council, Via Madonna Del Piano, 10, Sesto Fiorentino (Florence) 50019, Italy
| | - Gianni Della Rocca
- Institute of Sustainable Plant Protection, National Research Council, Via Madonna Del Piano, 10, Sesto Fiorentino (Florence) 50019, Italy
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Castillo JA, Conde G, Claros M, Ortuño N. Diversity of cultivable microorganisms associated with Quinoa (Chenopodium quinoa) and their potential for plant growth-promotion. BIONATURA 2022. [DOI: 10.21931/rb/2022.07.02.61] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Quinoa (Chenopodium quinoa) has grown since ancestral times in the Andean mountains and Altiplano, which are the center of origin of this pseudo-cereal. The interaction of Quinoa with native microorganisms may have contributed to the success of this plant in very adverse climatic and soil conditions. This study addressed the microbial diversity associated with Quinoa plants growing in traditional lands. We employed a cultivable-dependent approach to characterize the communities and identify bacterial strains with potential application in agriculture. We identified bacterial isolates belonging to phyla Firmicutes, Actinobacteria, Bacteroidetes, and Proteobacteria. The genera Bacillus and Rhizobium/Agrobacterium were the predominant groups in the Quinoa bacterial communities, while various Trichoderma species were also found in the fungi group. The plant growth-promoting ability of selected bacterial strains was assessed by culturing them on media and the in planta test. We used different assays to test the capabilities of the isolates for nitrogen fixation, phosphorus solubilization, and production of the phytohormone indole-3-acetic acid. We inoculated Quinoa seeds with some Bacillus strains and then evaluated plant growth and grain production. Plants inoculated with bacterial strains usually show increased growth parameters and grain yield. Altogether, this work reveals that Quinoa harbors many diverse cultivable bacteria and fungi, which could be used as biological amendments to promote plant growth in a chemical-free way. Avoiding chemical fertilizers helps reduce environmental pollution and maintains the organic character of Quinoa production. International Quinoa markets highly appreciate the organic quality of Quinoa.
Keywords. Plant growth-promoting bacteria, Microbial diversity, Rhizosphere bacteria, Andean Altiplano, Trichoderma
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Affiliation(s)
- José A. Castillo
- Fundación PROINPA, Av. Meneces Km. 4, El Paso, Cochabamba, Bolivia. 2 School of Biological Sciences and Engineering, Yachay Tech University, San Miguel de Urcuquí, Imbabura, Ecuador
| | | | - Mayra Claros
- Faculty of Agricultural and Livestock Sciences, Universidad Mayor de San Simón, Cochabamba, Bolivia
| | - Noel Ortuño
- Faculty of Agricultural and Livestock Sciences, Universidad Mayor de San Simón, Cochabamba, Bolivia
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Chen S, Daly P, Zhou D, Li J, Wang X, Deng S, Feng H, Wang C, Sheikh TMM, Chen Y, Xue T, Cai F, Kubicek CP, Wei L, Druzhinina IS. The use of mutant and engineered microbial agents for biological control of plant diseases caused by Pythium: Achievements versus challenges. FUNGAL BIOL REV 2022. [DOI: 10.1016/j.fbr.2022.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Screening and Identification of Trichoderma Strains isolated from Natural Habitats in China with Potential Agricultural Applications. BIOMED RESEARCH INTERNATIONAL 2022; 2021:7913950. [PMID: 34970627 PMCID: PMC8714372 DOI: 10.1155/2021/7913950] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 11/09/2021] [Accepted: 11/18/2021] [Indexed: 01/21/2023]
Abstract
Trichoderma spp. are widely distributed in natural habitats and have been evaluated as a potential biocontrol agent (BCA) for disease control and plant growth promotion. In this study, 1308 Trichoderma strains were obtained from the plant rhizosphere soil, above-ground plants, and decaying wood from natural habitats in China. Among them, 49 Trichoderma strains showed a good inhibitory effect, especially against Botrytis cinerea, Fusarium oxysporum, and Colletotrichum gloeosporioides with inhibition rate above 85% in the dual culture test. Among these 49 strains, the 13 strains with broad-spectrum inhibitory effects also significantly promoted the seed germination of five crops (rice, cucumber, tomato, melon, and pakchoi) and root growth of four crop seedlings (watermelon, tomato, eggplant, and chili). Furthermore, these strains showed effective colonization in the rhizosphere and root of cucumber. Trichoderma strains SC012 and NX043 showed the highest chitinase and β-1,3-glucanase activity among all strains. Based on the morphological characterization and phylogenetic analysis of the nuclear ribosomal internal transcribed spacer (ITS) and translation elongation factor 1 (tef1), twelve Trichoderma strains were identified as Trichoderma asperellum and one as Trichoderma afroharzianum. This study suggests that the 13 Trichoderma strains are promising BCAs and could be developed as biofertilizers and biological pesticides for agricultural applications.
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6
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Rahimi MJ, Cai F, Grujic M, Chenthamara K, Druzhinina IS. Molecular Identification of Trichoderma reesei. Methods Mol Biol 2021; 2234:157-175. [PMID: 33165788 DOI: 10.1007/978-1-0716-1048-0_14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Fungi comprise one of the most diverse groups of eukaryotes with many cryptic species that are difficult to identify. In this chapter, we detail a protocol for the molecular identification of the most industrially relevant species of Trichoderma-T. reesei. We first describe how a single spore culture should be isolated and used for the sequencing of the diagnostic fragment of the tef1 gene. Then, we provide two alternative methods that can be used for molecular identification and offer the diagnostic oligonucleotide hallmark of the tef1 sequence that is present in sequences of all T. reesei strains known to date and that is therefore suitable for reliable and straightforward identification.
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Affiliation(s)
- Mohammad J Rahimi
- Fungal Genomics Laboratory (FungiG), The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, China
- Institute of Chemical, Environmental and Bioscience Engineering (ICEBE), TU Wien, Vienna, Austria
| | - Feng Cai
- Fungal Genomics Laboratory (FungiG), The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, China
| | - Marica Grujic
- Institute of Chemical, Environmental and Bioscience Engineering (ICEBE), TU Wien, Vienna, Austria
| | - Komal Chenthamara
- Institute of Chemical, Environmental and Bioscience Engineering (ICEBE), TU Wien, Vienna, Austria
| | - Irina S Druzhinina
- Fungal Genomics Laboratory (FungiG), The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, China.
- Institute of Chemical, Environmental and Bioscience Engineering (ICEBE), TU Wien, Vienna, Austria.
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7
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Wang C, Zhuang WY. Carbon metabolic profiling of Trichoderma strains provides insight into potential ecological niches. Mycologia 2020; 112:213-223. [PMID: 32017669 DOI: 10.1080/00275514.2019.1698246] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Many Trichoderma species are cosmopolitan and widespread free-living fungi in various ecological environment, and many are economically important in the fields of agriculture and industry. However, carbon metabolism profiles of Trichoderma species have not been characterized in detail. In this study, Biolog FF MicroPlates were used to contrast carbon utilization and the differences among five Trichoderma species, each representing a unique phenotype. Their metabolic abilities varied greatly. Species producing cellulases and chitinases and with phosphate-solubilizing activities exhibited high efficiency of substrate utilization, whereas low efficiency was shown by saline-alkaline-tolerant species that metabolized simple carbon sources. Species producing cellulases at high levels may be specified to decompose and assimilate cellulose and hemicellulose in woody substrates, and those producing chitinases may have mycoparasitic roles. Species with plant growth-promoting traits are good at uptake of exudates from plant roots. Overall, metabolic models reflect nutritional adaptation of Trichoderma to diverse niches in nature.
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Affiliation(s)
- Chao Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, People's Republic of China.,University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Wen-Ying Zhuang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, People's Republic of China
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El Enshasy HA, Ambehabati KK, El Baz AF, Ramchuran S, Sayyed RZ, Amalin D, Dailin DJ, Hanapi SZ. Trichoderma: Biocontrol Agents for Promoting Plant Growth and Soil Health. Fungal Biol 2020. [DOI: 10.1007/978-3-030-48474-3_8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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9
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10
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De Marchi R, Koss M, Ziegler D, De Respinis S, Petrini O. Fungi in water samples of a full-scale water work. Mycol Prog 2018. [DOI: 10.1007/s11557-017-1372-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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11
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Raja H, Miller AN, Pearce CJ, Oberlies NH. Fungal Identification Using Molecular Tools: A Primer for the Natural Products Research Community. JOURNAL OF NATURAL PRODUCTS 2017; 80:756-770. [PMID: 28199101 PMCID: PMC5368684 DOI: 10.1021/acs.jnatprod.6b01085] [Citation(s) in RCA: 373] [Impact Index Per Article: 53.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Indexed: 05/17/2023]
Abstract
Fungi are morphologically, ecologically, metabolically, and phylogenetically diverse. They are known to produce numerous bioactive molecules, which makes them very useful for natural products researchers in their pursuit of discovering new chemical diversity with agricultural, industrial, and pharmaceutical applications. Despite their importance in natural products chemistry, identification of fungi remains a daunting task for chemists, especially those who do not work with a trained mycologist. The purpose of this review is to update natural products researchers about the tools available for molecular identification of fungi. In particular, we discuss (1) problems of using morphology alone in the identification of fungi to the species level; (2) the three nuclear ribosomal genes most commonly used in fungal identification and the potential advantages and limitations of the ITS region, which is the official DNA barcoding marker for species-level identification of fungi; (3) how to use NCBI-BLAST search for DNA barcoding, with a cautionary note regarding its limitations; (4) the numerous curated molecular databases containing fungal sequences; (5) the various protein-coding genes used to augment or supplant ITS in species-level identification of certain fungal groups; and (6) methods used in the construction of phylogenetic trees from DNA sequences to facilitate fungal species identification. We recommend that, whenever possible, both morphology and molecular data be used for fungal identification. Our goal is that this review will provide a set of standardized procedures for the molecular identification of fungi that can be utilized by the natural products research community.
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Affiliation(s)
- Huzefa
A. Raja
- Department
of Chemistry and Biochemistry, University
of North Carolina at Greensboro, Greensboro, North Carolina 27402, United States
| | - Andrew N. Miller
- Illinois
Natural History Survey, University of Illinois, Champaign, Illinois 61820, United States
| | - Cedric J. Pearce
- Mycosynthetix,
Inc., 505 Meadowland
Drive, Suite 103, Hillsborough, North Carolina 27278, United States
| | - Nicholas H. Oberlies
- Department
of Chemistry and Biochemistry, University
of North Carolina at Greensboro, Greensboro, North Carolina 27402, United States
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Dulla EL, Kathera C, Gurijala HK, Mallakuntla TR, Srinivasan P, Prasad V, Mopati RD, Jasti PK. Highlights of DNA Barcoding in identification of salient microorganisms like fungi. J Mycol Med 2016; 26:291-297. [PMID: 27402509 DOI: 10.1016/j.mycmed.2016.05.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 04/22/2016] [Accepted: 05/25/2016] [Indexed: 11/19/2022]
Abstract
Fungi, the second largest kingdom of eukaryotic life, are diverse and widespread. Fungi play a distinctive role in the production of different products on industrial scale, like fungal enzymes, antibiotics, fermented foods, etc., to give storage stability and improved health to meet major global challenges. To utilize algae perfectly for human needs, and to pave the way for getting a healthy relationship with fungi, it is important to identify them in a quick and robust manner with molecular-based identification system. So, there is a technique that aims to provide a well-organized method for species level identifications and to contribute powerfully to taxonomic and biodiversity research is DNA Barcoding. DNA Barcoding is generally achieved by the retrieval of a short DNA sequence - the 'barcode' - from a standard part of the genome and that barcode is then compared with a library of reference barcode sequences derived from individuals of known identity for identification.
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Affiliation(s)
- E L Dulla
- Department of Biotechnology, Sri Venkateswara University, Tirupati, Andhra Pradesh 517502, India
| | - C Kathera
- Jiangsu key laboratory for Molecular and Medicak Biotechnology, College of life sciences, Nanjing normal university, Nanjing, China
| | - H K Gurijala
- Department of Biotechnology, Sri Venkateswara University, Tirupati, Andhra Pradesh 517502, India; Department of Microbiology, Sri Venkateswara University, Tirupati, Andhra Pradesh 517502, India
| | - T R Mallakuntla
- Department of Microbiology, Sri Venkateswara University, Tirupati, Andhra Pradesh 517502, India
| | - P Srinivasan
- Department of Microbiology, Sri Venkateswara University, Tirupati, Andhra Pradesh 517502, India
| | - V Prasad
- Jiangsu key laboratory for Molecular and Medicak Biotechnology, College of life sciences, Nanjing normal university, Nanjing, China
| | - R D Mopati
- Department of Microbiology, Sri Venkateswara University, Tirupati, Andhra Pradesh 517502, India
| | - P K Jasti
- Department of Biotechnology, Sri Venkateswara University, Tirupati, Andhra Pradesh 517502, India.
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Elucidating the Diversity of Aquatic Microdochium and Trichoderma Species and Their Activity against the Fish Pathogen Saprolegnia diclina. Int J Mol Sci 2016; 17:ijms17010140. [PMID: 26805821 PMCID: PMC4730379 DOI: 10.3390/ijms17010140] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 12/25/2015] [Accepted: 01/12/2016] [Indexed: 11/17/2022] Open
Abstract
Animals and plants are increasingly threatened by emerging fungal and oomycete diseases. Amongst oomycetes, Saprolegnia species cause population declines in aquatic animals, especially fish and amphibians, resulting in significant perturbation in biodiversity, ecological balance and food security. Due to the prohibition of several chemical control agents, novel sustainable measures are required to control Saprolegnia infections in aquaculture. Previously, fungal community analysis by terminal restriction fragment length polymorphism (T-RFLP) revealed that the Ascomycota, specifically the genus Microdochium, was an abundant fungal phylum associated with salmon eggs from a commercial fish farm. Here, phylogenetic analyses showed that most fungal isolates obtained from salmon eggs were closely related to Microdochium lycopodinum/Microdochium phragmitis and Trichoderma viride species. Phylogenetic and quantitative PCR analyses showed both a quantitative and qualitative difference in Trichoderma population between diseased and healthy salmon eggs, which was not the case for the Microdochium population. In vitro antagonistic activity of the fungi against Saprolegnia diclina was isolate-dependent; for most Trichoderma isolates, the typical mycoparasitic coiling around and/or formation of papilla-like structures on S. diclina hyphae were observed. These results suggest that among the fungal community associated with salmon eggs, Trichoderma species may play a role in Saprolegnia suppression in aquaculture.
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Vos CMF, De Cremer K, Cammue BPA, De Coninck B. The toolbox of Trichoderma spp. in the biocontrol of Botrytis cinerea disease. MOLECULAR PLANT PATHOLOGY 2015; 16:400-12. [PMID: 25171761 PMCID: PMC6638538 DOI: 10.1111/mpp.12189] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Botrytis cinerea is a necrotrophic fungal pathogen causing disease in many plant species, leading to economically important crop losses. So far, fungicides have been widely used to control this pathogen. However, in addition to their detrimental effects on the environment and potential risks for human health, increasing fungicide resistance has been observed in the B. cinerea population. Biological control, that is the application of microbial organisms to reduce disease, has gained importance as an alternative or complementary approach to fungicides. In this respect, the genus Trichoderma constitutes a promising pool of organisms with potential for B. cinerea control. In the first part of this article, we review the specific mechanisms involved in the direct interaction between the two fungi, including mycoparasitism, the production of antimicrobial compounds and enzymes (collectively called antagonism), and competition for nutrients and space. In addition, biocontrol has also been observed when Trichoderma is physically separated from the pathogen, thus implying an indirect systemic plant defence response. Therefore, in the second part, we describe the consecutive steps leading to induced systemic resistance (ISR), starting with the initial Trichoderma-plant interaction and followed by the activation of downstream signal transduction pathways and, ultimately, the defence response resulting in ISR (ISR-prime phase). Finally, we discuss the ISR-boost phase, representing the effect of ISR priming by Trichoderma spp. on plant responses after additional challenge with B. cinerea.
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Affiliation(s)
- Christine M F Vos
- Centre of Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20, 3001, Leuven, Belgium; Department of Plant Systems Biology, VIB, Technologiepark 927, 9052, Gent, Belgium
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Linde T, Hansen N, Lübeck M, Lübeck P. Fermentation in 24-well plates is an efficient screening platform for filamentous fungi. Lett Appl Microbiol 2014; 59:224-30. [DOI: 10.1111/lam.12268] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Revised: 04/04/2014] [Accepted: 04/04/2014] [Indexed: 11/26/2022]
Affiliation(s)
- T. Linde
- Section for Sustainable Biotechnology; Aalborg University; Copenhagen SV Denmark
| | - N.B. Hansen
- Section for Sustainable Biotechnology; Aalborg University; Copenhagen SV Denmark
| | - M. Lübeck
- Section for Sustainable Biotechnology; Aalborg University; Copenhagen SV Denmark
| | - P.S. Lübeck
- Section for Sustainable Biotechnology; Aalborg University; Copenhagen SV Denmark
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16
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Greetham D, Wimalasena T, Kerruish DWM, Brindley S, Ibbett RN, Linforth RL, Tucker G, Phister TG, Smart KA. Development of a phenotypic assay for characterisation of ethanologenic yeast strain sensitivity to inhibitors released from lignocellulosic feedstocks. J Ind Microbiol Biotechnol 2014; 41:931-45. [PMID: 24664516 DOI: 10.1007/s10295-014-1431-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Accepted: 02/26/2014] [Indexed: 12/16/2022]
Abstract
Inhibitors released by the breakdown of plant cell walls prevent efficient conversion of sugar into ethanol. The aim of this study was to develop a fast and reliable inhibitor sensitivity assay for ethanologenic yeast strains. The assay comprised bespoke 96-well plates containing inhibitors in isolation or combination in a format that was compatible with the Phenotypic Microarray Omnilog reader (Biolog, hayward, CA, USA). A redox reporter within the assay permits analysis of inhibitor sensitivity in aerobic and/or anaerobic conditions. Results from the assay were verified using growth on spot plates and tolerance assays in which maintenance of viability was assessed. The assay allows for individual and synergistic effects of inhibitors to be determined. It was observed that the presence of both acetic and formic acid significantly inhibited the yeast strains assessed, although this impact could be partially mitigated by buffering to neutral pH. Scheffersomyces stipitis, Candida spp., and Pichia guilliermondii demonstrated increased sensitivity to short chain weak acids at concentrations typically present in lignocellulosic hydrolysates. S. cerevisiae exhibited robustness to short chain weak acids at these concentrations. However, S. stipitis, Candida spp., and P. guilliermondii displayed increased tolerance to HMF when compared to that observed for S. cerevisiae. The results demonstrate that the phenotypic microarray assay developed in the current study is a valuable tool that can be used to identify yeast strains with desirable resistance to inhibitory compounds found in lignocellulosic hydrolysates.
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Affiliation(s)
- D Greetham
- Bioenergy and Brewing Science, School of Biosciences, Sutton Bonington Campus, University of Nottingham, Loughborough, Leicestershire, LE12 6RD, UK,
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17
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Enhancing the Sustainability of Quinoa Production and Soil Resilience by Using Bioproducts Made with Native Microorganisms. AGRONOMY-BASEL 2013. [DOI: 10.3390/agronomy3040732] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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18
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Zhao J, Li C, Wang W, Zhao C, Luo M, Mu F, Fu Y, Zu Y, Yao M. Hypocrea lixii, novel endophytic fungi producing anticancer agent cajanol, isolated from pigeon pea (Cajanus cajan [L.] Millsp.). J Appl Microbiol 2013; 115:102-13. [PMID: 23495919 DOI: 10.1111/jam.12195] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Revised: 03/01/2013] [Accepted: 03/11/2013] [Indexed: 11/30/2022]
Abstract
AIMS The aim was to isolate, identify and characterize endophytes from pigeon pea (Cajanus cajan [L.] Millsp.), as novel producer of cajanol and its in vitro cytotoxicity assay. METHODS AND RESULTS Isolation, identification and characterization of novel endophytes producing cajanol from the roots of pigeon pea were investigated. The endophytes were identified as Hypocrea lixii by morphological and molecular methods. Cajanol produced by endophytes were quantified by liquid chromatography-tandem mass spectrometry (LC-MS/MS). R-18 produced the highest levels of cajanol (322·4 ± 10·6 μg l(-1) or 102·8 ± 6·9 μg g(-1) dry weight of mycelium) after incubation for 7 days. The cytotoxicity towards human lung carcinoma cells (A549) of fungal cajanol was investigated in vitro. CONCLUSIONS First, a novel endophyte Hypocrea lixii, producing anticancer agent cajanol, was isolated from the host pigeon pea (Cajanus cajan [L.] Millsp.). Fungal cajanol possessed stronger cytotoxicity activity towards A549 cells in time- and dose-dependent manners. SIGNIFICANCE AND IMPACT OF THE STUDY This endophyte is a potential handle for scientific and commercial exploitation, and it could provide a promising alterative approach for large-scale production of cajanol to satisfy new anticancer drug development.
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Affiliation(s)
- J Zhao
- State Engineering Laboratory for Bio-Resource Eco-Utilization, Northeast Forestry University, Harbin, China
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19
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Assessing DNA barcoding as a tool for species identification and data quality control. PLoS One 2013; 8:e57125. [PMID: 23431400 PMCID: PMC3576373 DOI: 10.1371/journal.pone.0057125] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Accepted: 01/17/2013] [Indexed: 11/19/2022] Open
Abstract
In recent years, the number of sequences of diverse species submitted to GenBank has grown explosively and not infrequently the data contain errors. This problem is extensively recognized but not for invalid or incorrectly identified species, sample mixed-up, and contamination. DNA barcoding is a powerful tool for identifying and confirming species and one very important application involves forensics. In this study, we use DNA barcoding to detect erroneous sequences in GenBank by evaluating deep intraspecific and shallow interspecific divergences to discover possible taxonomic problems and other sources of error. We use the mitochondrial DNA gene encoding cytochrome b (Cytb) from turtles to test the utility of barcoding for pinpointing potential errors. This gene is widely used in phylogenetic studies of the speciose group. Intraspecific variation is usually less than 2.0% and in most cases it is less than 1.0%. In comparison, most species differ by more than 10.0% in our dataset. Overlapping intra- and interspecific percentages of variation mainly involve problematic identifications of species and outdated taxonomies. Further, we detect identical problems in Cytb from Insectivora and Chiroptera. Upon applying this strategy to 47,524 mammalian CoxI sequences, we resolve a suite of potentially problematic sequences. Our study reveals that erroneous sequences are not rare in GenBank and that the DNA barcoding can serve to confirm sequencing accuracy and discover problems such as misidentified species, inaccurate taxonomies, contamination, and potential errors in sequencing.
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20
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Bourne CR, Wakeham N, Bunce RA, Berlin KD, Barrow WW. Classifying compound mechanism of action for linking whole cell phenotypes to molecular targets. J Mol Recognit 2012; 25:216-23. [PMID: 22434711 PMCID: PMC3703735 DOI: 10.1002/jmr.2174] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Drug development programs have proven successful when performed at a whole cell level, thus incorporating solubility and permeability into the primary screen. However, linking those results to the target within the cell has been a major setback. The Phenotype Microarray system, marketed and sold by Biolog, seeks to address this need by assessing the phenotype in combination with a variety of chemicals with known mechanism of action (MOA). We have evaluated this system for usefulness in deducing the MOA for three test compounds. To achieve this, we constructed a database with 21 known antimicrobials, which served as a comparison for grouping our unknown MOA compounds. Pearson correlation and Ward linkage calculations were used to generate a dendrogram that produced clustering largely by known MOA, although there were exceptions. Of the three unknown compounds, one was definitively placed as an antifolate. The second and third compounds' MOA were not clearly identified, likely because the unique MOA was not represented within the database. The availability of the database generated in this report for Staphylococcus aureus ATCC 29213 will increase the accessibility of this technique to other investigators. From our analysis, the Phenotype Microarray system can group compounds with clear MOA, but the distinction of unique or broadly acting MOA at this time is less clear.
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Affiliation(s)
- Christina R. Bourne
- Department of Veterinary Pathobiology, Oklahoma State University, 250 McElroy Hall, Stillwater OK 74078
| | - Nancy Wakeham
- Department of Veterinary Pathobiology, Oklahoma State University, 250 McElroy Hall, Stillwater OK 74078
| | - Richard A. Bunce
- Department of Chemistry, Oklahoma State University, 107 Physical Sciences 1, Stillwater OK 74078
| | - K. Darrell Berlin
- Department of Chemistry, Oklahoma State University, 107 Physical Sciences 1, Stillwater OK 74078
| | - William W. Barrow
- Department of Veterinary Pathobiology, Oklahoma State University, 250 McElroy Hall, Stillwater OK 74078
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21
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Atanasova L, Druzhinina IS. Review: Global nutrient profiling by Phenotype MicroArrays: a tool complementing genomic and proteomic studies in conidial fungi. J Zhejiang Univ Sci B 2010; 11:151-68. [PMID: 20205302 DOI: 10.1631/jzus.b1000007] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Conidial fungi or molds and mildews are widely used in modern biotechnology as producers of antibiotics and other secondary metabolites, industrially important enzymes, chemicals and food. They are also important pathogens of animals including humans and agricultural crops. These various applications and extremely versatile natural phenotypes have led to the constantly growing list of complete genomes which are now available. Functional genomics and proteomics widely exploit the genomic information to study the cell-wide impact of altered genes on the phenotype of an organism and its function. This allows for global analysis of the information flow from DNA to RNA to protein, but it is usually not sufficient for the description of the global phenotype of an organism. More recently, Phenotype MicroArray (PM) technology has been introduced as a tool to characterize the metabolism of a (wild) fungal strain or a mutant. In this article, we review the background of PM applications for fungi and the methodic requirements to obtain reliable results. We also report examples of the versatility of this tool.
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Affiliation(s)
- Lea Atanasova
- Research Area of Gene Technology and Applied Biochemistry, Institute of Chemical Engineering, Vienna University of Technology, A-1060 Vienna, Austria
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22
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Biology and biotechnology of Trichoderma. Appl Microbiol Biotechnol 2010; 87:787-99. [PMID: 20461510 PMCID: PMC2886115 DOI: 10.1007/s00253-010-2632-1] [Citation(s) in RCA: 292] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2010] [Revised: 04/16/2010] [Accepted: 04/17/2010] [Indexed: 01/01/2023]
Abstract
Fungi of the genus Trichoderma are soilborne, green-spored ascomycetes that can be found all over the world. They have been studied with respect to various characteristics and applications and are known as successful colonizers of their habitats, efficiently fighting their competitors. Once established, they launch their potent degradative machinery for decomposition of the often heterogeneous substrate at hand. Therefore, distribution and phylogeny, defense mechanisms, beneficial as well as deleterious interaction with hosts, enzyme production and secretion, sexual development, and response to environmental conditions such as nutrients and light have been studied in great detail with many species of this genus, thus rendering Trichoderma one of the best studied fungi with the genome of three species currently available. Efficient biocontrol strains of the genus are being developed as promising biological fungicides, and their weaponry for this function also includes secondary metabolites with potential applications as novel antibiotics. The cellulases produced by Trichoderma reesei, the biotechnological workhorse of the genus, are important industrial products, especially with respect to production of second generation biofuels from cellulosic waste. Genetic engineering not only led to significant improvements in industrial processes but also to intriguing insights into the biology of these fungi and is now complemented by the availability of a sexual cycle in T. reesei/Hypocrea jecorina, which significantly facilitates both industrial and basic research. This review aims to give a broad overview on the qualities and versatility of the best studied Trichoderma species and to highlight intriguing findings as well as promising applications.
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The Rhizosphere of Coffea Arabica in Its Native Highland Forests of Ethiopia Provides a Niche for a Distinguished Diversity of Trichoderma. DIVERSITY-BASEL 2010. [DOI: 10.3390/d2040527] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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24
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Lorito M, Woo SL, Harman GE, Monte E. Translational research on Trichoderma: from 'omics to the field. ANNUAL REVIEW OF PHYTOPATHOLOGY 2010; 48:395-417. [PMID: 20455700 DOI: 10.1146/annurev-phyto-073009-114314] [Citation(s) in RCA: 259] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Structural and functional genomics investigations are making an important impact on the current understanding and application of microbial agents used for plant disease control. Here, we review the case of Trichoderma spp., the most widely applied biocontrol fungi, which have been extensively studied using a variety of research approaches, including genomics, transcriptomics, proteomics, metabolomics, etc. Known for almost a century for their beneficial effects on plants and the soil, these fungi are the subject of investigations that represent a successful case of translational research, in which 'omics-generated novel understanding is directly translated in to new or improved crop treatments and management methods. We present an overview of the latest discoveries on the Trichoderma expressome and metabolome, of the complex and diverse biotic interactions established in nature by these microbes, and of their proven or potential importance to agriculture and industry.
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Affiliation(s)
- Matteo Lorito
- Dipartimento di Arboricoltura, Botanica e Patologia Vegetale (ArBoPaVe), Università di Napoli Federico II, Portici, Napoli, Italy 80138.
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25
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Alberto F, Navarro D, de Vries R, Asther M, Record E. Technical advance in fungal biotechnology: development of a miniaturized culture method and an automated high-throughput screening. Lett Appl Microbiol 2009; 49:278-82. [DOI: 10.1111/j.1472-765x.2009.02655.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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26
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Bochner BR. Global phenotypic characterization of bacteria. FEMS Microbiol Rev 2009; 33:191-205. [PMID: 19054113 PMCID: PMC2704929 DOI: 10.1111/j.1574-6976.2008.00149.x] [Citation(s) in RCA: 293] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2008] [Revised: 10/06/2008] [Accepted: 10/24/2008] [Indexed: 11/30/2022] Open
Abstract
The measure of the quality of a systems biology model is how well it can reproduce and predict the behaviors of a biological system such as a microbial cell. In recent years, these models have been built up in layers, and each layer has been growing in sophistication and accuracy in parallel with a global data set to challenge and validate the models in predicting the content or activities of genes (genomics), proteins (proteomics), metabolites (metabolomics), and ultimately cell phenotypes (phenomics). This review focuses on the latter, the phenotypes of microbial cells. The development of Phenotype MicroArrays, which attempt to give a global view of cellular phenotypes, is described. In addition to their use in fleshing out and validating systems biology models, there are many other uses of this global phenotyping technology in basic and applied microbiology research, which are also described.
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27
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Kubicek CP, Komon-Zelazowska M, Druzhinina IS. Fungal genus Hypocrea/Trichoderma: from barcodes to biodiversity. J Zhejiang Univ Sci B 2008; 9:753-63. [PMID: 18837102 DOI: 10.1631/jzus.b0860015] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Hypocrea/Trichoderma is a genus of soil-borne or wood-decaying fungi containing members important to mankind as producers of industrial enzymes and biocontrol agents against plant pathogens, but also as opportunistic pathogens of immunocompromised humans and animals, while others can cause damage to cultivated mushroom. With the recent advent of a reliable, BarCode-aided identification system for all known taxa of Trichoderma and Hypocrea, it became now possible to study some of the biological fundamentals of the diversity in this fungal genus in more detail. In this article, we will therefore review recent progress in (1) the understanding of the geographic distribution of individual taxa; (2) mechanisms of speciation leading to development of mushroom diseases and facultative human mycoses; and (3) the possible correlation of specific traits of secondary metabolism and molecular phylogeny.
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Affiliation(s)
- Christian P Kubicek
- Institute of Chemical Engineering, Research Area Gene Technology and Applied Biochemistry, Vienna University of Technology, Getreidemarkt 9/E1665, A-1060 Vienna, Austria.
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Abstract
The ability to test hundreds to thousands of cellular phenotypes in a single experiment has opened up new avenues of investigation and exploration and led to important discoveries in very diverse applications of microbiological research and development. The information provided by global phenotyping is complementary to, and often more easily interpretable than information provided by global molecular analytical methods such as gene chips and proteomics. This report summarizes advances presented by scientists brought together to share their experiences and knowledge gained with high-throughput phenotyping.
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