1
|
Sha Y, Lin N, Zhang G, Zhang Y, Zhao J, Lu J, Zhu T, Zhang X, Li Q, Zhang H, Lin X, Li K, Bao Q, Li D. Identification and characterization of a novel chromosomal aminoglycoside 3'- O-phosphotransferase, APH(3')-Id, from Kluyvera intermedia DW18 isolated from the sewage of an animal farm. Front Microbiol 2023; 14:1224464. [PMID: 37700861 PMCID: PMC10493288 DOI: 10.3389/fmicb.2023.1224464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 07/17/2023] [Indexed: 09/14/2023] Open
Abstract
Background Aminoglycosides, as important clinical antimicrobials, are used as second-line drugs for treating multidrug-resistant tuberculosis or combined with β-lactam drugs for treating severe infections such as sepsis. Aminoglycoside-modifying enzyme (AME) is the most important mechanism of aminoglycoside resistance and deserves more attention. Methods The bacterium Kluyvera intermedia DW18 was isolated from the sewage of an animal farm using the conventional method. The agar dilution method was used to determine the minimum inhibitory concentrations (MICs) of antimicrobials. A novel resistance gene was cloned, and the enzyme was expressed. The kinetic parameters were measured by a SpectraMax M5 multifunctional microplate reader. Bioinformatic analysis was performed to reveal the genetic context of the aph(3')-Id gene and its phylogenetic relationship with other AMEs. Results A novel aminoglycoside 3'-O-phosphotransferase gene designated aph(3')-Id was identified in K. intermedia DW18 and shared the highest amino acid identity of 77.49% with the functionally characterized aminoglycoside 3'-O-phosphotransferase APH(3')-Ia. The recombinant plasmid carrying the novel resistance gene (pMD19-aph(3')-Id/E. coli DH5α) showed 1,024-, 512-, 128- and 16-fold increased MIC levels for kanamycin, ribostamycin, paromomycin and neomycin, respectively, compared with the reference strain DH5α. APH(3')-Id showed the highest catalytic efficiency for ribostamycin [kcat/Km of (4.96 ± 1.63) × 105 M-1/s-1], followed by paromomycin [kcat/Km of (2.18 ± 0.21) × 105 M-1/s-1], neomycin [kcat/Km of (1.73 ± 0.20) × 105 M-1/s-1], and kanamycin [kcat/Km of (1.10 ± 0.18) × 105 M-1/s-1]. Three conserved functional domains of the aminoglycoside phosphotransferase family and ten amino acid residues responsible for the phosphorylation of kanamycin were found in the amino acid sequence of APH(3')-Id. No mobile genetic element (MGE) was discovered surrounding the aph(3')-Id gene. Conclusion In this work, a novel aminoglycoside 3'-O-phosphotransferase gene designated aph(3')-Id encoded in the chromosome of the environmental isolate Kluyvera intermedia DW18 was identified and characterized. These findings will help clinicians select effective antimicrobials to treat infections caused by pathogens with this kind of resistance gene.
Collapse
Affiliation(s)
- Yuning Sha
- The Second Affiliated Hospital and Yuying Children’s Hospital, Wenzhou Medical University, Wenzhou, China
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Naru Lin
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Guozhi Zhang
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Yuan Zhang
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Jingxuan Zhao
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Junwan Lu
- Medical Molecular Biology Laboratory, School of Medicine, Jinhua Polytechnic, Jinhua, China
| | - Tingting Zhu
- The Second Affiliated Hospital and Yuying Children’s Hospital, Wenzhou Medical University, Wenzhou, China
| | - Xueya Zhang
- The Second Affiliated Hospital and Yuying Children’s Hospital, Wenzhou Medical University, Wenzhou, China
| | - Qiaoling Li
- The Second Affiliated Hospital and Yuying Children’s Hospital, Wenzhou Medical University, Wenzhou, China
| | - Hailin Zhang
- The Second Affiliated Hospital and Yuying Children’s Hospital, Wenzhou Medical University, Wenzhou, China
| | - Xi Lin
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Kewei Li
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Qiyu Bao
- The Second Affiliated Hospital and Yuying Children’s Hospital, Wenzhou Medical University, Wenzhou, China
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
- Medical Molecular Biology Laboratory, School of Medicine, Jinhua Polytechnic, Jinhua, China
| | - Dong Li
- The Second Affiliated Hospital and Yuying Children’s Hospital, Wenzhou Medical University, Wenzhou, China
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| |
Collapse
|
2
|
Ramzan M, Ayub F, Shah AA, Naz G, Shah AN, Malik A, Sardar R, Telesiński A, Kalaji HM, Dessoky ES, Elgawad HA. Synergistic Effect of Zinc Oxide Nanoparticles and Moringa oleifera Leaf Extract Alleviates Cadmium Toxicity in Linum usitatissimum: Antioxidants and Physiochemical Studies. FRONTIERS IN PLANT SCIENCE 2022; 13:900347. [PMID: 35982701 PMCID: PMC9380429 DOI: 10.3389/fpls.2022.900347] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 04/11/2022] [Indexed: 05/06/2023]
Abstract
Among heavy metals, cadmium (Cd) is one of the toxic metals, which significantly reduce the growth of plants even at a low concentration. Cd interacts with various plant mechanisms at the physiological and antioxidant levels, resulting in decreased plant growth. This research was conducted to exploit the potential of synergistic application of zinc oxide nanoparticles (ZnO NPs) and Moringa oleifera leaf extract in mitigation of Cd stress in linseed (Linum usitatissimum L.) plants. The main aim of this study was to exploit the role of M. oleifera leaf extract and ZnO NPs on Cd-exposed linseed plants. Cd concentrations in the root and shoot of linseed plants decreased after administration of MZnO NPs. Growth parameters of plants, antioxidant system, and physiochemical parameters decreased as the external Cd level increased. The administration of MZnO NPs to the Cd-stressed linseed plant resulted in a significant increase in growth and antioxidant enzymes. Furthermore, the antioxidative enzymes superoxide dismutase (SOD), peroxidase (POD), catalase (CAT), and ascorbate peroxidase (APX) exhibited a considerable increase in the activity when MZnO NPs were applied to Cd-stressed seedlings. The introduction of MZnO NPs lowered the levels of malondialdehyde (MDA) and hydrogen peroxide (H2O2) in the linseed plant grown in Cd-toxic conditions. The NPs decreased electrolyte leakage (EL) in Cd-stressed linseed leaves and roots. It was concluded that synergistic application of ZnO NPs and M. oleifera leaf extract alleviated Cd stress in linseed plants through enhanced activity of antioxidant enzymes. It is proposed that role of MZnO NPs may be evaluated for mitigation of numerous abiotic stresses.
Collapse
Affiliation(s)
- Musarrat Ramzan
- Department of Botany, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
- *Correspondence: Musarrat Ramzan
| | - Fazila Ayub
- Department of Botany, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Anis Ali Shah
- Department of Botany, Division of Science and Technology, University of Education, Lahore, Pakistan
- Anis Ali Shah
| | - Gul Naz
- Faculty of Science, Institute of Physics, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
- Gul Naz
| | - Adnan Noor Shah
- Department of Agricultural Engineering, Khwaja Fareed University of Engineering and Information Technology, Punjab, Pakistan
- Adnan Noor Shah
| | - Aqsa Malik
- Department of Botany, University of Narowal, Narowal, Pakistan
| | - Rehana Sardar
- Institute of Botany, University of the Punjab, Lahore, Pakistan
| | - Arkadiusz Telesiński
- Zachodniopomorski Uniwersytet Technologiczny w Szczecinie, West Pomeranian University of Technology, Szczecin, Poland
| | - Hazem M. Kalaji
- Department of Plant Physiology, Institute of Biology, Warsaw University of Life Science, Warsaw, Poland
- Institute of Technology and Life Sciences - National Research Institute, Raszyn, Poland
| | | | - Hamada Abd Elgawad
- Botany and Microbiology Department, Faculty of Science, Beni-Suef University, Beni-Suef, Egypt
| |
Collapse
|
3
|
Al-Saari N, Azmi NSA, Samsulrizal NH. Trichoderma Genes for Abiotic Stress Tolerance in Plants. Fungal Biol 2022. [DOI: 10.1007/978-3-030-91650-3_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
4
|
Vaish S, Gupta D, Mehrotra R, Mehrotra S, Basantani MK. Glutathione S-transferase: a versatile protein family. 3 Biotech 2020; 10:321. [PMID: 32656054 PMCID: PMC7320970 DOI: 10.1007/s13205-020-02312-3] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 06/19/2020] [Indexed: 12/20/2022] Open
Abstract
Glutathione-S transferase (GST) is a most ancient protein superfamily of multipurpose roles and evolved principally from gene duplication of an ancestral GSH binding protein. They have implemented in diverse plant functions such as detoxification of xenobiotic, secondary metabolism, growth and development, and majorly against biotic and abiotic stresses. The vital structural features of GSTs like highly divergent functional topographies, conserved integrated architecture with separate binding pockets for substrates and ligand, the stringent structural fidelity with high Tm values (50º-60º), and stress-responsive cis-regulatory elements in the promoter region offer this protein as most flexible plant protein for plant breeding approaches, biotechnological applications, etc. This review article summarizes the recent information of GST evolution, and their distribution and structural features with emphasis on the assorted roles of Ser and Cys GSTs with the signature motifs in their active sites, alongside their recent biotechnological application in the area of agriculture, environment, and nanotechnology have been highlighted.
Collapse
Affiliation(s)
- Swati Vaish
- Institute of Bioscience and Technology, Shri Ramswaroop Memorial University, Lucknow Deva Road, Barabanki, Uttar Pradesh 225003 India
| | - Divya Gupta
- Institute of Bioscience and Technology, Shri Ramswaroop Memorial University, Lucknow Deva Road, Barabanki, Uttar Pradesh 225003 India
| | - Rajesh Mehrotra
- Department of Biological Sciences, Birla Institute of Technology and Science, KK Birla Goa Campus, NH-17B, Zuarinagar, Goa 403726 India
| | - Sandhya Mehrotra
- Department of Biological Sciences, Birla Institute of Technology and Science, KK Birla Goa Campus, NH-17B, Zuarinagar, Goa 403726 India
| | - Mahesh Kumar Basantani
- Faculty of Bioscience, Institute of Bioscience and Technology, Shri Ramswaroop Memorial University, Lucknow-Deva Road, Barabanki, Uttar Pradesh India
| |
Collapse
|
5
|
Removal Efficiencies of Constructed Wetland Planted with Phragmites and Vetiver in Treating Synthetic Wastewater Contaminated with High Concentration of PAHs. SUSTAINABILITY 2020. [DOI: 10.3390/su12083357] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
This study aimed to evaluate the capability of horizontal subsurface flow constructed wetlands (HSFCWs) in treating contaminated wastewater with a high concentration of polycyclic aromatic hydrocarbons (PAHs) (Phenanthrene, Pyrene, and Benzo[a]Pyrene), using two plants, namely Phragmites and Vetiver. The investigated parameters were (1) PAHs uptake by the plants, (2) PAHs removal efficiencies, (3) accumulated PAHs in the soil of CWs, (4) shoot/root concentration factor, (5) translocation factor, and (6) PAHs correlation to lipid contains in the plants. During the treatment period, the results showed that the highest concentration of Phenanthrene in the shoot and the root systems of Phragmites, was 229.3 and 192 μg/g; Pyrene was 69.1 and 59.2 µg/g; and Benzo[a]Pyrene 25.1 and 20.2 µg/g, respectively. Meanwhile, in the Vetiver shoot and root systems were Phenanthrene 87.5 and 64.1 µg/g; Pyrene 63.2 and 42.1 µg/g; and Benzo[a]Pyrene 21.3 and 27.3 µg/g, respectively. The removal rates of Phenanthrene, Pyrene, and Benzo[a]Pyrene (PAHs compounds) by the CW planted with Phragmites were found to be 83%, 71%, and 81%, respectively, while the removal rates by CW planted with Vetiver were found to be 67%, 66%, and 73%, respectively. Moreover, the removal rates by unplanted CW were found to be 62%, 58%, and 55%, respectively. The results indicated that the HSFCW planted with Phragmites has an effective pathway to remove high concentrations of PAHs.
Collapse
|
6
|
Debnath B, Islam W, Li M, Sun Y, Lu X, Mitra S, Hussain M, Liu S, Qiu D. Melatonin Mediates Enhancement of Stress Tolerance in Plants. Int J Mol Sci 2019; 20:E1040. [PMID: 30818835 PMCID: PMC6429401 DOI: 10.3390/ijms20051040] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Revised: 02/18/2019] [Accepted: 02/22/2019] [Indexed: 02/07/2023] Open
Abstract
Melatonin is a multifunctional signaling molecule, ubiquitously distributed in different parts of plants and responsible for stimulating several physiological responses to adverse environmental conditions. In the current review, we showed that the biosynthesis of melatonin occurred in plants by themselves, and accumulation of melatonin fluctuated sharply by modulating its biosynthesis and metabolic pathways under stress conditions. Melatonin, with its precursors and derivatives, acted as a powerful growth regulator, bio-stimulator, and antioxidant, which delayed leaf senescence, lessened photosynthesis inhibition, and improved redox homeostasis and the antioxidant system through a direct scavenging of reactive oxygen species (ROS) and reactive nitrogen species (RNS) under abiotic and biotic stress conditions. In addition, exogenous melatonin boosted the growth, photosynthetic, and antioxidant activities in plants, confirming their tolerances against drought, unfavorable temperatures, salinity, heavy metals, acid rain, and pathogens. However, future research, together with recent advancements, would support emerging new approaches to adopt strategies in overcoming the effect of hazardous environments on crops and may have potential implications in expanding crop cultivation against harsh conditions. Thus, farming communities and consumers will benefit from elucidating food safety concerns.
Collapse
Affiliation(s)
- Biswojit Debnath
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China.
- Department of Horticulture, Sylhet Agricultural University, Sylhet 3100, Bangladesh.
| | - Waqar Islam
- College of Geographical Sciences, Fujian Normal University, Fuzhou, Fujian 350007, China.
| | - Min Li
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China.
| | - Yueting Sun
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China.
| | - Xiaocao Lu
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China.
| | - Sangeeta Mitra
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China.
| | - Mubasher Hussain
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China.
| | - Shuang Liu
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China.
| | - Dongliang Qiu
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China.
| |
Collapse
|
7
|
Singha LP, Sinha N, Pandey P. Rhizoremediation prospects of Polyaromatic hydrocarbon degrading rhizobacteria, that facilitate glutathione and glutathione-S-transferase mediated stress response, and enhance growth of rice plants in pyrene contaminated soil. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2018; 164:579-588. [PMID: 30149357 DOI: 10.1016/j.ecoenv.2018.08.069] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 08/13/2018] [Accepted: 08/19/2018] [Indexed: 05/22/2023]
Abstract
Rhizoremediation is a strategy where pollutant degrading bacteria are augmented through plant roots using plant-microbe interaction. Therefore, for effective rhizoremediation of pyrene contaminated soil, bacterial strains were experimented for amelioration of stress response in host plant along with biodegradation ability. A total of 28 bacteria, having ability to degrade polycyclic aromatic hydrocarbons were isolated from contaminated sites and checked for their plant growth promoting attributes, such as indole acetic acid (IAA) production, phosphate solubilization, atmospheric nitrogen fixation and siderophore release. Among these isolates, Klebsiella pneumoniae AWD5 was found to degrade 60% of pyrene. While other isolates, i.e. Alcaligenes faecalis BDB4, Pseudomonas fragi DBC, Pseudomonas aeruginosa PDB1, Acinetobactor sp. PDB4 degraded 48.5%, 50.29%, 31.3% and 36% of pyrene, respectively, after 6 days of incubation. K. pneumoniae AWD5 produced 94.2 μg/ml IAA and 3.1 mM/mg/h unit of ACC deaminase, which was best among eighteen indole acetic acid producers and five of the 1-aminocyclopropane-1-carboxylate (ACC) deaminase producing isolates. P. aeruginosa PDB1 resulted in highest phosphate solubilization activity of 875.26 ng/ml of soluble phosphate among seven phosphate solubilizers. The isolates AWD5 and PDB1 both have shown a good amount of siderophore release (56.3% and 84.3% unit). There was 19.1% increase in shoot length of rice seedlings treated with PDB1 in presence of pyrene. Similarly, 26.5% increase in the root length of AWD5 treated rice was recorded in pyrene contaminated soil. Bacterial inoculation also induced and improved the stress response in host plant, in presence of pyrene, as suggested by the superoxide dismutase, glutathione and glutathione-S-transferase activities in rice.
Collapse
Affiliation(s)
| | - Nibedita Sinha
- Department of Microbiology, Assam University, Silchar 788011, India
| | - Piyush Pandey
- Department of Microbiology, Assam University, Silchar 788011, India.
| |
Collapse
|
8
|
Zhou D, Huang X, Guo J, dos‐Santos ML, Vivanco JM. Trichoderma gamsii affected herbivore feeding behaviour on Arabidopsis thaliana by modifying the leaf metabolome and phytohormones. Microb Biotechnol 2018; 11:1195-1206. [PMID: 30221488 PMCID: PMC6196387 DOI: 10.1111/1751-7915.13310] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 07/02/2018] [Accepted: 08/07/2018] [Indexed: 11/30/2022] Open
Abstract
Plants can re-programme their transcriptome, proteome and metabolome to deal with environmental and biotic stress. It has been shown that the rhizosphere microbiome has influence on the plant metabolome and on herbivore behaviour. In the present study, Trichoderma gamsii was isolated from Arabidopsis thaliana rhizosphere soil. The inoculation of roots of Arabidopsis thaliana with T. gamsii significantly inhibited the feeding behaviour of Trichoplusia ni and affected the metabolome as well as the content of phytohormones in Arabidopsis leaves. T. gamsii-treated plant leaves had higher levels of amino acids and lower concentrations of sugars. In addition, T. gamsii-treated plant leaves had more abscisic acid (ABA) and lower levels of salicylic acid (SA) and indole-3-acetic acid (IAA) in comparison with the untreated plants. Furthermore, the inoculation with T. gamsii on different signalling mutants showed that the induction of defences were SA-dependent. These findings indicate that T. gamsii has potential as a new type of biocontrol agent to promote plant repellence to insect attacks.
Collapse
Affiliation(s)
- Dongmei Zhou
- Department of Plant PathologyCollege of Plant ProtectionNanjing Agricultural UniversityNanjing210095China
- Department of Horticulture and Landscape ArchitectureCenter for Rhizosphere BiologyColorado State UniversityFort CollinsCO80523USA
- Institute of Plant ProtectionJiangsu Academy of Agricultural SciencesNanjingChina
| | - Xing‐Feng Huang
- Department of Horticulture and Landscape ArchitectureCenter for Rhizosphere BiologyColorado State UniversityFort CollinsCO80523USA
- Department of Chemical and Biological EngineeringColorado State UniversityFort CollinsCO80523USA
| | - Jianhua Guo
- Department of Plant PathologyCollege of Plant ProtectionNanjing Agricultural UniversityNanjing210095China
| | - Marcia L. dos‐Santos
- Department of Horticulture and Landscape ArchitectureCenter for Rhizosphere BiologyColorado State UniversityFort CollinsCO80523USA
- Plant Molecular Biology LaboratoryDepartment of Genetics – “Luiz de Queiroz” College of Agriculture – ESALQUniversity of Sao PauloPiracicabaSP13418‐900Brazil
| | - Jorge M. Vivanco
- Department of Horticulture and Landscape ArchitectureCenter for Rhizosphere BiologyColorado State UniversityFort CollinsCO80523USA
| |
Collapse
|
9
|
Fanelli F, Liuzzi VC, Logrieco AF, Altomare C. Genomic characterization of Trichoderma atrobrunneum (T. harzianum species complex) ITEM 908: insight into the genetic endowment of a multi-target biocontrol strain. BMC Genomics 2018; 19:662. [PMID: 30200883 PMCID: PMC6131884 DOI: 10.1186/s12864-018-5049-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 08/31/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND So far, biocontrol agent selection has been performed mainly by time consuming in vitro confrontation tests followed by extensive trials in greenhouse and field. An alternative approach is offered by application of high-throughput techniques, which allow extensive screening and comparison among strains for desired genetic traits. In the genus Trichoderma, the past assignments of particular features or strains to one species need to be reconsidered according to the recent taxonomic revisions. Here we present the genome of a biocontrol strain formerly known as Trichoderma harzianum ITEM 908, which exhibits both growth promoting capabilities and antagonism against different fungal pathogens, including Fusarium graminearum, Rhizoctonia solani, and the root-knot nematode Meloidogyne incognita. By genomic analysis of ITEM 908 we investigated the occurrence and the relevance of genes associated to biocontrol and stress tolerance, providing a basis for future investigation aiming to unravel the complex relationships between genomic endowment and exhibited activities of this strain. RESULTS The MLST analysis of ITS-TEF1 concatenated datasets reclassified ITEM 908 as T. atrobrunneum, a species recently described within the T. harzianum species complex and phylogenetically close to T. afroharzianum and T. guizhouense. Genomic analysis revealed the presence of a broad range of genes encoding for carbohydrate active enzymes (CAZYmes), proteins involved in secondary metabolites production, peptaboils, epidithiodioxopiperazines and siderophores potentially involved in parasitism, saprophytic degradation as well as in biocontrol and antagonistic activities. This abundance is comparable to other Trichoderma spp. in the T. harzianum species complex, but broader than in other biocontrol species and in the species T. reesei, known for its industrial application in cellulase production. Comparative analysis also demonstrated similar genomic organization of major secondary metabolites clusters, as in other Trichoderma species. CONCLUSIONS Reported data provide a contribution to a deeper understanding of the mode of action and identification of activity-specific genetic markers useful for selection and improvement of biocontrol strains. This work will also enlarge the availability of genomic data to perform comparative studies with the aim to correlate phenotypic differences with genetic diversity of Trichoderma species.
Collapse
Affiliation(s)
- Francesca Fanelli
- Institute of Sciences of Food Production, National Research Council, Bari, Italy
| | - Vania Cosma Liuzzi
- Institute of Sciences of Food Production, National Research Council, Bari, Italy
| | | | - Claudio Altomare
- Institute of Sciences of Food Production, National Research Council, Bari, Italy
| |
Collapse
|
10
|
Kashyap PL, Rai P, Srivastava AK, Kumar S. Trichoderma for climate resilient agriculture. World J Microbiol Biotechnol 2017; 33:155. [PMID: 28695465 DOI: 10.1007/s11274-017-2319-1] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 07/05/2017] [Indexed: 01/16/2023]
Abstract
Climate change is one of the biggest challenges of the twenty-first century for sustainable agricultural production. Several reports highlighted the need for better agricultural practices and use of eco-friendly methods for sustainable crop production under such situations. In this context, Trichoderma species could be a model fungus to sustain crop productivity. Currently, these are widely used as inoculants for biocontrol, biofertilization, and phytostimulation. They are reported to improve photosynthetic efficiency, enhance nutrient uptake and increase nitrogen use efficiency in crops. Moreover, they can be used to produce bio-energy, facilitate plants for adaptation and mitigate adverse effect of climate change. The technological advancement in high throughput DNA sequencing and biotechnology provided deep insight into the complex and diverse biotic interactions established in nature by Trichoderma spp. and efforts are being made to translate this knowledge to enhance crop growth, resistance to disease and tolerance to abiotic stresses under field conditions. The discovery of several traits and genes that are involved in the beneficial effects of Trichoderma spp. has resulted in better understanding of the performance of bioinoculants in the field, and will lead to more efficient use of these strains and possibly to their improvement by genetic modification. The present mini-review is an effort to elucidate the molecular basis of plant growth promotion and defence activation by Trichoderma spp. to garner broad perspectives regarding their functioning and applicability for climate resilient agriculture.
Collapse
Affiliation(s)
- Prem Lal Kashyap
- ICAR-Indian Institute of Wheat and Barley Research (IIWBR), Karnal, 132001, India. .,ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Mau, Uttar Pradesh, 275103, India.
| | - Pallavi Rai
- ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Mau, Uttar Pradesh, 275103, India
| | - Alok Kumar Srivastava
- ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Mau, Uttar Pradesh, 275103, India
| | - Sudheer Kumar
- ICAR-Indian Institute of Wheat and Barley Research (IIWBR), Karnal, 132001, India
| |
Collapse
|
11
|
El Amrani A, Dumas AS, Wick LY, Yergeau E, Berthomé R. "Omics" Insights into PAH Degradation toward Improved Green Remediation Biotechnologies. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:11281-91. [PMID: 26352597 DOI: 10.1021/acs.est.5b01740] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
This review summarizes recent knowledge of polycyclic aromatic hydrocarbons (PAHs) biotransformation by microorganisms and plants. Whereas most research has focused on PAH degradation either by plants or microorganisms separately, this review specifically addresses the interactions of plants with their rhizosphere microbial communities. Indeed, plant roots release exudates that contain various nutritional and signaling molecules that influence bacterial and fungal populations. The complex interactions of these populations play a pivotal role in the biodegradation of high-molecular-weight PAHs and other complex molecules. Emerging integrative approaches, such as (meta-) genomics, (meta-) transcriptomics, (meta-) metabolomics, and (meta-) proteomics studies are discussed, emphasizing how "omics" approaches bring new insight into decipher molecular mechanisms of PAH degradation both at the single species and community levels. Such knowledge address new pictures on how organic molecules are cometabolically degraded in a complex ecosystem and should help in setting up novel decontamination strategies based on the rhizosphere interactions between plants and their microbial associates.
Collapse
Affiliation(s)
- Abdelhak El Amrani
- University of Rennes 1 , CNRS/UMR 6553/OSUR, Ecosystems - Biodiversity - Evolution, 35042 Rennes Cedex, France
| | - Anne-Sophie Dumas
- University of Rennes 1 , CNRS/UMR 6553/OSUR, Ecosystems - Biodiversity - Evolution, 35042 Rennes Cedex, France
| | - Lukas Y Wick
- UFZ, Department of Environmental Microbiology, Helmholtz Centre for Environmental Research , Permoserstraße 15, D-04318 Leipzig, Germany
| | - Etienne Yergeau
- National Research Council Canada, Energy, Mining and Environment, Montreal, Quebec Canada
| | - Richard Berthomé
- Plant Genomics Research Unit, UMR INRA 1165 - CNRS 8114 - UEVE , 2, Gaston Crémieux St., CP5708, 91057 Evry Cedex, France
| |
Collapse
|
12
|
Tian YS, Jin XF, Fu XY, Zhao W, Han HJ, Zhu B, Liu M, Yao QH. Microarray analysis of differentially expressed gene responses to bisphenol A in Arabidopsis . J Toxicol Sci 2014; 39:671-9. [DOI: 10.2131/jts.39.671] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Affiliation(s)
- Yong-Sheng Tian
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences
- Shanghai Ruifeng Agricultural Science and Technology Co., Ltd
| | - Xiao-Fen Jin
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences
| | - Xiao-Yan Fu
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences
| | - Wei Zhao
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences
| | - Hong-Juan Han
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences
| | - Bo Zhu
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences
| | - Man- Liu
- Shanghai Ruifeng Agricultural Science and Technology Co., Ltd
| | - Quan-Hong Yao
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences
| |
Collapse
|
13
|
Ahammed GJ, Choudhary SP, Chen S, Xia X, Shi K, Zhou Y, Yu J. Role of brassinosteroids in alleviation of phenanthrene-cadmium co-contamination-induced photosynthetic inhibition and oxidative stress in tomato. JOURNAL OF EXPERIMENTAL BOTANY 2013; 64. [PMID: 23201830 PMCID: PMC3528031 DOI: 10.1093/jxb/ers323] [Citation(s) in RCA: 110] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Heavy metal pollution often occurs together with organic contaminants. Brassinosteroids (BRs) induce plant tolerance to several abiotic stresses, including phenanthrene (PHE) and cadmium (Cd) stress. However, the role of BRs in PHE+Cd co-contamination-induced stress amelioration is unknown. Here, the interactive effects of PHE, Cd, and 24-epibrassinolide (EBR; a biologically active BR) were investigated in tomato plants. The application of Cd (100 µM) alone was more phytotoxic than PHE applied alone (100 µM); however, their combined application resulted in slightly improved photosynthetic activity and pigment content compared with Cd alone after a 40 d exposure. Accumulation of reactive oxygen species and membrane lipid peroxidation were induced by PHE and/or Cd; however, the differences in effect were insignificant between Cd and PHE+Cd. The foliar application of EBR (0.1 µM) to PHE- and/or Cd-stressed plants alleviated photosynthetic inhibition and oxidative stress by causing enhancement of the activity of the enzymes and related transcript levels of the antioxidant system, secondary metabolism, and the xenobiotic detoxification system. Additionally, PHE and/or Cd residues were significantly decreased in both the leaves and roots after application of EBR, more specifically in PHE+Cd-stressed plants when treated with EBR, indicating a possible improvement in detoxification of these pollutants. The findings thus suggest a potential interaction of EBR and PHE for Cd stress alleviation. These results advocate a positive role for EBR in reducing pollutant residues for food safety and also strengthening phytoremediation.
Collapse
Affiliation(s)
- Golam Jalal Ahammed
- Department of Horticulture, Zijingang Campus, Zhejiang University, Yuhangtang Road 866, Hangzhou 310058, People’s Republic of China
- * To whom correspondence should be addressed. E-mail: or
| | - Sikander Pal Choudhary
- Department of Horticulture, Zijingang Campus, Zhejiang University, Yuhangtang Road 866, Hangzhou 310058, People’s Republic of China
| | - Shuangchen Chen
- Department of Horticulture, Zijingang Campus, Zhejiang University, Yuhangtang Road 866, Hangzhou 310058, People’s Republic of China
| | - Xiaojian Xia
- Department of Horticulture, Zijingang Campus, Zhejiang University, Yuhangtang Road 866, Hangzhou 310058, People’s Republic of China
| | - Kai Shi
- Department of Horticulture, Zijingang Campus, Zhejiang University, Yuhangtang Road 866, Hangzhou 310058, People’s Republic of China
| | - Yanhong Zhou
- Department of Horticulture, Zijingang Campus, Zhejiang University, Yuhangtang Road 866, Hangzhou 310058, People’s Republic of China
| | - Jingquan Yu
- Department of Horticulture, Zijingang Campus, Zhejiang University, Yuhangtang Road 866, Hangzhou 310058, People’s Republic of China
- Key Laboratory of Horticultural Plants Growth, Development and Quality Improvement, Ministry of Agriculture, Yuhangtang Road 866, Hangzhou 310058, People’s Republic of China
- * To whom correspondence should be addressed. E-mail: or
| |
Collapse
|