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Amrutha Lakshmi M, B R A, Manyam P, Javeedvali S, Khan AS, Palnam DW, Kandan A. Traditional to technological advancements in Ganoderma detection methods in oil palm. Folia Microbiol (Praha) 2024:10.1007/s12223-024-01177-w. [PMID: 38976188 DOI: 10.1007/s12223-024-01177-w] [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: 09/11/2023] [Accepted: 05/19/2024] [Indexed: 07/09/2024]
Abstract
Ganoderma sp., the fungal agent causing basal stem rot (BSR), poses a severe threat to global oil palm production. Alarming increases in BSR occurrences within oil palm growing zones are attributed to varying effectiveness in its current management strategies. Asymptomatic progression of the disease and the continuous monoculture of oil palm pose challenges for prompt and effective management. Therefore, the development of precise, early, and timely detection techniques is crucial for successful BSR management. Conventional methods such as visual assessments, culture-based assays, and biochemical and physiological approaches prove time-consuming and lack specificity. Serological-based diagnostic methods, unsuitable for fungal diagnostics due to low sensitivity, assay affinity, cross-contamination which further underscores the need for improved techniques. Molecular PCR-based assays, utilizing universal, genus-specific, and species-specific primers, along with functional primers, can overcome the limitations of conventional and serological methods in fungal diagnostics. Recent advancements, including real-time PCR, biosensors, and isothermal amplification methods, facilitate accurate, specific, and sensitive Ganoderma detection. Comparative whole genomic analysis enables high-resolution discrimination of Ganoderma at the strain level. Additionally, omics tools such as transcriptomics, proteomics, and metabolomics can identify potential biomarkers for early detection of Ganoderma infection. Innovative on-field diagnostic techniques, including remote methods like volatile organic compounds profiling, tomography, hyperspectral and multispectral imaging, terrestrial laser scanning, and Red-Green-Blue cameras, contribute to a comprehensive diagnostic approach. Ultimately, the development of point-of-care, early, and cost-effective diagnostic techniques accessible to farmers is vital for the timely management of BSR in oil palm plantations.
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Affiliation(s)
- M Amrutha Lakshmi
- Plant Pathology, ICAR-Indian Institute of Oil Palm Research, India, Andhra Pradesh.
| | - Ajesh B R
- Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Pradeep Manyam
- Acharya N. G, Ranga Agricultural University, Guntur, Andhra Pradesh, India
| | - Shaik Javeedvali
- Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Amjada S Khan
- Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Dauda Wadzani Palnam
- Crop Science Unit, Department of Agronomy, Federal University, Yobe State, Gashua, Nigeria
| | - A Kandan
- ICAR-National Bureau of Agricultural Insect Resources, Bangalore, India
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2
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Karunarathna SC, Patabendige NM, Lu W, Asad S, Hapuarachchi KK. An In-Depth Study of Phytopathogenic Ganoderma: Pathogenicity, Advanced Detection Techniques, Control Strategies, and Sustainable Management. J Fungi (Basel) 2024; 10:414. [PMID: 38921400 PMCID: PMC11204718 DOI: 10.3390/jof10060414] [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: 04/02/2024] [Revised: 05/06/2024] [Accepted: 05/14/2024] [Indexed: 06/27/2024] Open
Abstract
Phytopathogenic Ganoderma species pose a significant threat to global plant health, resulting in estimated annual economic losses exceeding USD (US Dollars) 68 billion in the agriculture and forestry sectors worldwide. To combat this pervasive menace effectively, a comprehensive understanding of the biology, ecology, and plant infection mechanisms of these pathogens is imperative. This comprehensive review critically examines various aspects of Ganoderma spp., including their intricate life cycle, their disease mechanisms, and the multifaceted environmental factors influencing their spread. Recent studies have quantified the economic impact of Ganoderma infections, revealing staggering yield losses ranging from 20% to 80% across various crops. In particular, oil palm plantations suffer devastating losses, with an estimated annual reduction in yield exceeding 50 million metric tons. Moreover, this review elucidates the dynamic interactions between Ganoderma and host plants, delineating the pathogen's colonization strategies and its elicitation of intricate plant defense responses. This comprehensive analysis underscores the imperative for adopting an integrated approach to Ganoderma disease management. By synergistically harnessing cultural practices, biological control, and chemical treatments and by deploying resistant plant varieties, substantial strides can be made in mitigating Ganoderma infestations. Furthermore, a collaborative effort involving scientists, breeders, and growers is paramount in the development and implementation of sustainable strategies against this pernicious plant pathogen. Through rigorous scientific inquiry and evidence-based practices, we can strive towards safeguarding global plant health and mitigating the dire economic consequences inflicted by Ganoderma infections.
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Affiliation(s)
- Samantha C. Karunarathna
- Center for Yunnan Plateau Biological Resources Protection and Utilization, College of Biological Resource and Food Engineering, Qujing Normal University, Qujing 655011, China;
- National Institute of Fundamental Studies, Hantane Road, Kandy 20000, Sri Lanka
| | | | - Wenhua Lu
- Center of Excellence in Microbial Diversity and Sustainable Utilization, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand;
| | - Suhail Asad
- School of Biology and Chemistry, Pu’er University, Pu’er 665000, China;
| | - Kalani K. Hapuarachchi
- College of Biodiversity Conservation, Southwest Forestry University, Kunming 650224, China
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3
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Darlis D, Jalloh MB, Chin CFS, Basri NKM, Besar NA, Ahmad K, Rakib MRM. Exploring the potential of Bornean polypore fungi as biological control agents against pathogenic Ganoderma boninense causing basal stem rot in oil palm. Sci Rep 2023; 13:10316. [PMID: 37365214 DOI: 10.1038/s41598-023-37507-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 06/22/2023] [Indexed: 06/28/2023] Open
Abstract
Basal stem rot due to a fungal pathogen, Ganoderma boninense, is one of the most devastating diseases in oil palm throughout the major palm oil producer countries. This study investigated the potential of polypore fungi as biological control agents against pathogenic G. boninense in oil palm. In vitro antagonistic screening of selected non-pathogenic polypore fungi was performed. Based on in planta fungi inoculation on oil palm seedlings, eight of the 21 fungi isolates tested (GL01, GL01, RDC06, RDC24, SRP11, SRP12, SRP17, and SRP18) were non-pathogenic. In vitro antagonistic assays against G. boninense revealed that the percentage inhibition of radial growth (PIRG) in dual culture assay for SRP11 (69.7%), SRP17 (67.3%), and SRP18 (72.7%) was relatively high. Percentage inhibition of diameter growth (PIDG) in volatile organic compounds (VOCs) in dual plate assay of SRP11, SRP17, and SRP18 isolates were 43.2%, 51.6%, and 52.1%, respectively. Molecular identification using the internal transcribed spacer gene sequences of SRP11, SRP17, and SRP18 isolates revealed that they were Fomes sp., Trametes elegans, and Trametes lactinea, respectively.
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Affiliation(s)
- Darwana Darlis
- Faculty of Sustainable Agriculture, Universiti Malaysia Sabah, 90000, Sandakan, Sabah, Malaysia
| | - Mohamadu Boyie Jalloh
- Faculty of Sustainable Agriculture, Universiti Malaysia Sabah, 90000, Sandakan, Sabah, Malaysia
| | - Clament Fui Seung Chin
- Faculty of Sustainable Agriculture, Universiti Malaysia Sabah, 90000, Sandakan, Sabah, Malaysia
| | | | - Normah Awang Besar
- Faculty of Tropical Forestry, Universiti Malaysia Sabah, 88400, Kota Kinabalu, Sabah, Malaysia
| | - Khairulmazmi Ahmad
- Department of Plant Protection, Faculty of Agriculture, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Mohd Rashid Mohd Rakib
- Faculty of Sustainable Agriculture, Universiti Malaysia Sabah, 90000, Sandakan, Sabah, Malaysia.
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4
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Alhawari AR, Saeidi T, Ismail I, Alsuwian T, Al-Gburi AJA. Health Control of Tree Trunk Utilizing Microwave Imaging and Reverse Problem Algorithms. ACS OMEGA 2023; 8:14387-14400. [PMID: 37125111 PMCID: PMC10134228 DOI: 10.1021/acsomega.2c07015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 03/16/2023] [Indexed: 05/03/2023]
Abstract
The voids in their trunk significantly affect tropical trees' health. Both the wood and timber industries may face substantial financial losses because of the lack of an effective technique to inspect the defected trees through deep zonal monitoring. Microwave imaging offers the advantages of mobility, processing time, compactness, and resolution over alternative imaging methods. An ultra-wide band (UWB) imaging system consisting of UWB antennas and a reverse problem algorithm is proposed. Several conditions, such as the size of trunk samples (16-30 cm), number of targets, size of voids, heterogeneity of media, and number of layers, are considered in experimental studies. Based on these studies, cylindrical wooden models with 100 and 140 mm diameters, one void at the center, and three voids in different locations were 3D printed. After proving the system's ability through simulation and measurements on 3D models, a rubber-wood trunk with a length of 75 cm was cut into smaller pieces. The images created utilizing the measured data showed that the system could detect voids in the rubber trunk. Furthermore, the system indicated a high percentage of reliability and repeatability.
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Affiliation(s)
- Adam R.
H. Alhawari
- Electrical
Engineering Department, College of Engineering, Najran University, Najran 66462, Kingdom
of Saudi Arabia
| | - Tale Saeidi
- Electrical
and Electronics Engineering Department, Faculty of Engineering and
Natural Sciences, İstinye University, Istanbul 34010, Turkey
| | - Idris Ismail
- Electrical
and Electronic Engineering Department of Universiti Teknologi PETRONAS, Bandar Seri Iskandar, Perak 32610, Malaysia
| | - Turki Alsuwian
- Electrical
Engineering Department, College of Engineering, Najran University, Najran 66462, Kingdom
of Saudi Arabia
| | - Ahmed Jamal Abdullah Al-Gburi
- Department
of Electronics and Computer Engineering (FKEKK), Center for Telecommunication
Research and Innovation (CeTRI), Universiti
Teknikal Malaysia Melaka (UTeM), Durian Tunggal, Malacca 76100, Malaysia
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5
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Haw YH, Lai KW, Chuah JH, Bejo SK, Husin NA, Hum YC, Yee PL, Tee CATH, Ye X, Wu X. Classification of basal stem rot using deep learning: a review of digital data collection and palm disease classification methods. PeerJ Comput Sci 2023; 9:e1325. [PMID: 37346512 PMCID: PMC10280561 DOI: 10.7717/peerj-cs.1325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 03/13/2023] [Indexed: 06/23/2023]
Abstract
Oil palm is a key agricultural resource in Malaysia. However, palm disease, most prominently basal stem rot caused at least RM 255 million of annual economic loss. Basal stem rot is caused by a fungus known as Ganoderma boninense. An infected tree shows few symptoms during early stage of infection, while potentially suffers an 80% lifetime yield loss and the tree may be dead within 2 years. Early detection of basal stem rot is crucial since disease control efforts can be done. Laboratory BSR detection methods are effective, but the methods have accuracy, biosafety, and cost concerns. This review article consists of scientific articles related to the oil palm tree disease, basal stem rot, Ganoderma Boninense, remote sensors and deep learning that are listed in the Web of Science since year 2012. About 110 scientific articles were found that is related to the index terms mentioned and 60 research articles were found to be related to the objective of this research thus included in this review article. From the review, it was found that the potential use of deep learning methods were rarely explored. Some research showed unsatisfactory results due to limitations on dataset. However, based on studies related to other plant diseases, deep learning in combination with data augmentation techniques showed great potentials, showing remarkable detection accuracy. Therefore, the feasibility of analyzing oil palm remote sensor data using deep learning models together with data augmentation techniques should be studied. On a commercial scale, deep learning used together with remote sensors and unmanned aerial vehicle technologies showed great potential in the detection of basal stem rot disease.
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Affiliation(s)
- Yu Hong Haw
- Department of Biomedical Engineering, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Khin Wee Lai
- Department of Biomedical Engineering, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Joon Huang Chuah
- Department of Electrical Engineering, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Siti Khairunniza Bejo
- Department of Biological and Agricultural Engineering, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Nur Azuan Husin
- Department of Biological and Agricultural Engineering, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Yan Chai Hum
- Department of Mechatronics and Biomedical Engineering, Universiti Tunku Abdul Rahman, Bandar Sungai Long, Cheras, Kajang, Selangor, Malaysia
| | - Por Lip Yee
- Department of Computer System and Technology, Universiti Malaya, Kuala Lumpur, Malaysia
| | | | - Xin Ye
- YLZ Eaccessy Information Technology Co., Ltd, Xiamen, China
| | - Xiang Wu
- School of Medical Information and Engineering, Xuzhou Medical University, Xuzhou, China
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6
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Mustafa IF, Hussein MZ, Idris AS, Hilmi NHZ, Fakurazi S. The effect of surfactant on fungitoxicity of dazomet-micelle nanodelivery system against Ganoderma boninense. CHEMICAL PAPERS 2023. [DOI: 10.1007/s11696-023-02760-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
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7
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Lim JA, Yaacob JS, Mohd Rasli SRA, Eyahmalay JE, El Enshasy HA, Zakaria MRS. Mitigating the repercussions of climate change on diseases affecting important crop commodities in Southeast Asia, for food security and environmental sustainability—A review. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2023. [DOI: 10.3389/fsufs.2022.1030540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Southeast Asia is a fertile land with a warm and humid climate which tends to accommodate various food crops. The development and advancement of the agricultural sector not only allows the countries in the region to feed the increasing population, but are also able to boost the nation's economy through exportation of the crops. Some of the well-known and economically-significant plant commodities found in the region include rice, oil palm, rubber, coconut, banana, sugarcane, pineapple, black pepper, maize, cocoa, durian, and jackfruit. Due to the high production of crops, Southeast Asia is able to stand among the top world producers of these commodities. Nevertheless, the widespread of pathogenic microorganisms has posed a serious threat to the industry over the years; with hundreds of millions of money wasted and total yield being lost due to the devastating diseases associated with each type of the plants. A lot of attention and effort have been continuously devoted to find effective plant management strategies to combat plant diseases, starting from traditional physical and chemical methods to the increasing discoveries on biological approaches made in recent decades. Due to the challenges and limitations faced by conventional approaches and the rising awareness toward the environment, more work has been focused on establishing the application of beneficial microorganisms to tackle plant diseases through direct mechanisms. Thus, by bringing the common plant commodities in Southeast Asia, their associated diseases and various physical, chemical and biological control measures together, this review aims to provide clearer insights and practical information to those who seek to limit the damages caused by plant diseases.
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Baharim MSA, Adnan NA, Mohd FA, Othman AN, Abdul Rahim H, Azis MHA, Seman IA, Izzuddin MA, Shahabuddin NA, Nordiana AA. A review of ganoderma Basal Stem Rot (BSR) disease detection and mapping using geospatial and advanced techniques. GEOCARTO INTERNATIONAL 2022; 37:8100-8126. [DOI: 10.1080/10106049.2021.1993350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 09/01/2021] [Accepted: 10/08/2021] [Indexed: 09/01/2023]
Affiliation(s)
- Mohd Sharul Aikal Baharim
- Centre of Studies Surveying Science and Geomatics, Faculty of Architecture, Planning & Surveying, Universiti Teknologi MARA, Shah Alam, Malaysia
| | - Nor Aizam Adnan
- Centre of Studies Surveying Science and Geomatics, Faculty of Architecture, Planning & Surveying, Universiti Teknologi MARA, Shah Alam, Malaysia
| | - Fazly Amri Mohd
- Centre of Studies Surveying Science and Geomatics, Faculty of Architecture, Planning & Surveying, Universiti Teknologi MARA Perlis, Arau, Malaysia
| | - Ainon Nisa Othman
- Centre of Studies Surveying Science and Geomatics, Faculty of Architecture, Planning & Surveying, Universiti Teknologi MARA, Shah Alam, Malaysia
| | - Haris Abdul Rahim
- Centre of Studies Surveying Science and Geomatics, Faculty of Architecture, Planning & Surveying, Universiti Teknologi MARA, Shah Alam, Malaysia
| | - Mohamad Haris Abd Azis
- Centre of Studies Surveying Science and Geomatics, Faculty of Architecture, Planning & Surveying, Universiti Teknologi MARA, Shah Alam, Malaysia
| | - Idris Abu Seman
- Malaysian Palm Oil Board (MPOB), Persiaran Institusi, Kajang, Selangor, Malaysia
| | | | | | - Abd Aziz Nordiana
- Malaysian Palm Oil Board (MPOB), Persiaran Institusi, Kajang, Selangor, Malaysia
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Wong WC, Tung HJ, Nurul Fadhilah M, Midot F, Lau SYL, Melling L, Astari S, Hadziabdic Đ, Trigiano RN, Goh YK, Goh KJ. Evidence for high gene flow, nonrandom mating, and genetic bottlenecks of Ganoderma boninense infecting oil palm ( Elaeis guineensis Jacq.) plantations in Malaysia and Indonesia. Mycologia 2022; 114:947-963. [PMID: 36239960 DOI: 10.1080/00275514.2022.2118512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Ganoderma boninense, the causal agent of basal stem rot (BSR) disease, has been recognized as a major economic threat to commercial plantings of oil palm (Elaeis guineensis Jacq.) in Southeast Asia, which supplies 86% of the world's palm oil. High genetic diversity and gene flow among regional populations of 417 G. boninense isolates collected from Sabah, Sarawak, and Peninsular Malaysia (Malaysia) and Sumatra (Indonesia) were demonstrated using 16 microsatellite loci. Three genetic clusters and different admixed populations of G. boninense across regions were detected, and they appeared to follow the spread of the fungus from the oldest (Peninsular Malaysia and Sumatra) to younger generations of oil palm plantings (Sabah and Sarawak). Low spatial genetic differentiation of G. boninense (FST = 0.05) among the sampling regions revealed geographically nonrestricted gene dispersal, but isolation by distance was still evident. Analysis of molecular variance (AMOVA) confirmed the little to no genetic differentiation among the pathogen populations and the three genetic clusters defined by STRUCTURE and minimum spanning network. Despite G. boninense being highly outcrossing and spread by sexual spores, linkage disequilibrium was detected in 7 of the 14 populations. Linkage disequilibrium indicated that the reproduction of the fungus was not entirely by random mating and genetic drift could be an important structuring factor. Furthermore, evidence of population bottleneck was indicated in the oldest oil palm plantations as detected in genetic clusters 2 and 3, which consisted mainly of Peninsular Malaysia and Sumatra isolates. The population bottleneck or founding event could have arisen from either new planting or replanting after the removal of large number of palm hosts. The present study also demonstrated that migration and nonrandom mating of G. boninense could be important for survival and adaptation to new palm hosts.
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Affiliation(s)
- W C Wong
- Biotechnology Section, Advanced Agriecological Research Sendirian Berhad, AAR-UNMC Biotechnology Research Centre, Jalan Broga, 43500 Semenyih, Selangor, Malaysia.,Pest and Disease Section, Applied Agricultural Resources Sendirian Berhad, No. 11 Jalan Teknologi 3/6, Taman Sains Selangor 1, Kota Damansara, 47810 Petaling Jaya, Selangor, Malaysia
| | - H J Tung
- Biotechnology Section, Advanced Agriecological Research Sendirian Berhad, AAR-UNMC Biotechnology Research Centre, Jalan Broga, 43500 Semenyih, Selangor, Malaysia.,Pest and Disease Section, Applied Agricultural Resources Sendirian Berhad, No. 11 Jalan Teknologi 3/6, Taman Sains Selangor 1, Kota Damansara, 47810 Petaling Jaya, Selangor, Malaysia
| | - M Nurul Fadhilah
- Pest and Disease Section, Applied Agricultural Resources Sendirian Berhad, No. 11 Jalan Teknologi 3/6, Taman Sains Selangor 1, Kota Damansara, 47810 Petaling Jaya, Selangor, Malaysia
| | - F Midot
- Molecular and Microbiology Division, Sarawak Tropical Peat Research Institute, Lot 6035, Kuching-Kota Samarahan Expressway, 94300, Kota Samarahan, Sarawak, Malaysia
| | - S Y L Lau
- Molecular and Microbiology Division, Sarawak Tropical Peat Research Institute, Lot 6035, Kuching-Kota Samarahan Expressway, 94300, Kota Samarahan, Sarawak, Malaysia
| | - L Melling
- Molecular and Microbiology Division, Sarawak Tropical Peat Research Institute, Lot 6035, Kuching-Kota Samarahan Expressway, 94300, Kota Samarahan, Sarawak, Malaysia
| | - S Astari
- Pest and Disease Section, Perseroan Terbatas Applied Agricultural Resources Indonesia, KLK Plantation Crop Research Centre, Jalan Harapan Utama No. 10, Rukun Tetangga 001 / Rukun Warga 001, Kelurahan Delima, Kecamatan Binawidya, Pekanbaru 28295, Riau, Indonesia
| | - Đ Hadziabdic
- Department of Entomology and Plant Pathology, The University of Tennessee, 370 Plant Biotechnology Building, 2505 E.J. Chapman Drive, Knoxville, Tennessee 37996
| | - R N Trigiano
- Department of Entomology and Plant Pathology, The University of Tennessee, 370 Plant Biotechnology Building, 2505 E.J. Chapman Drive, Knoxville, Tennessee 37996
| | - Y K Goh
- Pest and Disease Section, Applied Agricultural Resources Sendirian Berhad, No. 11 Jalan Teknologi 3/6, Taman Sains Selangor 1, Kota Damansara, 47810 Petaling Jaya, Selangor, Malaysia
| | - K J Goh
- Pest and Disease Section, Applied Agricultural Resources Sendirian Berhad, No. 11 Jalan Teknologi 3/6, Taman Sains Selangor 1, Kota Damansara, 47810 Petaling Jaya, Selangor, Malaysia
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Jazuli NA, Kamu A, Chong KP, Gabda D, Hassan A, Abu Seman I, Ho CM. A Review of Factors Affecting Ganoderma Basal Stem Rot Disease Progress in Oil Palm. PLANTS (BASEL, SWITZERLAND) 2022; 11:2462. [PMID: 36235329 PMCID: PMC9571826 DOI: 10.3390/plants11192462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 09/16/2022] [Accepted: 09/17/2022] [Indexed: 06/16/2023]
Abstract
In recent years, oil palm has grown on a major scale as it is a prominent commodity crop that contributes the most to almost every producing country's gross domestic product (GDP). Nonetheless, existing threats such as the Ganoderma basal stem rot (BSR) disease have been deteriorating the oil palm plantations and suitable actions to overcome the issue are still being investigated. The BSR disease progression in oil palm is being studied using the disease progression through the plant disease triangle idea. This concept looks at all potential elements that could affect the transmission and development of the disease. The elements include pathogenic, with their mode of infection in each studied factor.
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Affiliation(s)
- Nur Aliyah Jazuli
- Faculty of Science and Natural Resources, Universiti Malaysia Sabah, Kota Kinabalu 88400, Sabah, Malaysia
| | - Assis Kamu
- Faculty of Science and Natural Resources, Universiti Malaysia Sabah, Kota Kinabalu 88400, Sabah, Malaysia
| | - Khim Phin Chong
- Faculty of Science and Natural Resources, Universiti Malaysia Sabah, Kota Kinabalu 88400, Sabah, Malaysia
| | - Darmesah Gabda
- Faculty of Science and Natural Resources, Universiti Malaysia Sabah, Kota Kinabalu 88400, Sabah, Malaysia
| | - Affendy Hassan
- Faculty of Science and Natural Resources, Universiti Malaysia Sabah, Kota Kinabalu 88400, Sabah, Malaysia
| | | | - Chong Mun Ho
- Faculty of Science and Natural Resources, Universiti Malaysia Sabah, Kota Kinabalu 88400, Sabah, Malaysia
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11
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Yang HD, Ding Y, Wen TC, Hapuarachchi KK, Wei DP. Ganodermaovisporum sp. nov. (Polyporales, Polyporaceae) from Southwest China. Biodivers Data J 2022; 10:e80034. [PMID: 36761562 PMCID: PMC9848459 DOI: 10.3897/bdj.10.e80034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 06/02/2022] [Indexed: 02/06/2023] Open
Abstract
Background Ganoderma is a white-rot fungus with a cosmopolitan distribution and includes several economically important species. This genus has been extensively researched due to its beneficial medicinal properties and chemical constituents with potential nutritional and therapeutic values. Traditionally, species of Ganoderma were identified solely based on morphology; however, recent molecular studies revealed that many morphology-based species are conspecific. Furthermore, some type species are in poor condition, which hinders us from re-examining their taxonomic characteristics and obtaining their molecular data. Therefore, new species and fresh collections with multigene sequences are needed to fill the loopholes and to understand the biological classification system of Ganoderma. New information In a survey of Ganoderma in Guizhou Province, southwest China, we found a new species growing on soil and, herein, it was identified by both morphology and phylogenetic evidence. Hence, we propose a new species, Ganodermaovisporum sp. nov. This species is characterised by an annual, stipitate, laccate basidiome, with a red-brown to brownish-black pileus surface and pale white pores, duplex context, clavate pileipellis terminal cells, trimitic hyphal system, ellipsoid basidiospores with dark brown eusporium bearing coarse echinulae and an obtuse turgid appendix. Phylogenetic analyses confirmed that the novel species sisters to G.sandunense with high bootstrap support. Furthermore, the RPB2 sequence of G.sandunense is supplied for the first time. Notably, we re-examined the type specimen of G.sandunense and provide a more precise description of the duplex context, pileipellis terminal cells and basidia. All species collected are described and illustrated with coloured photographs. Moreover, we present an updated phylogeny for Ganoderma, based on nLSU, ITS, RPB2 and TEF1-α DNA sequence data and species relationships and classification are discussed.
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Affiliation(s)
- Hong-De Yang
- Key Laboratory of Forest Biotechnology in Yunnan, Southwest Forestry University, Kunming, ChinaKey Laboratory of Forest Biotechnology in Yunnan, Southwest Forestry UniversityKunmingChina,The Engineering Research Center of Southwest Bio–Pharmaceutical Resources Ministry of Education, Guizhou University, Guiyang, ChinaThe Engineering Research Center of Southwest Bio–Pharmaceutical Resources Ministry of Education, Guizhou UniversityGuiyangChina,Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, ThailandCenter of Excellence in Fungal Research, Mae Fah Luang UniversityChiang RaiThailand
| | - Yong Ding
- Key Laboratory of Forest Biotechnology in Yunnan, Southwest Forestry University, Kunming, ChinaKey Laboratory of Forest Biotechnology in Yunnan, Southwest Forestry UniversityKunmingChina
| | - Ting-Chi Wen
- The Engineering Research Center of Southwest Bio–Pharmaceutical Resources Ministry of Education, Guizhou University, Guiyang, ChinaThe Engineering Research Center of Southwest Bio–Pharmaceutical Resources Ministry of Education, Guizhou UniversityGuiyangChina,State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Guiyang, ChinaState Key Laboratory Breeding Base of Green Pesticide and Agricultural BioengineeringGuiyangChina,The Mushroom Research Centre, Guizhou University, Guiyang, ChinaThe Mushroom Research Centre, Guizhou UniversityGuiyangChina
| | - Kalani Kanchana Hapuarachchi
- The Engineering Research Center of Southwest Bio–Pharmaceutical Resources Ministry of Education, Guizhou University, Guiyang, ChinaThe Engineering Research Center of Southwest Bio–Pharmaceutical Resources Ministry of Education, Guizhou UniversityGuiyangChina,Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, ThailandCenter of Excellence in Fungal Research, Mae Fah Luang UniversityChiang RaiThailand,The Mushroom Research Centre, Guizhou University, Guiyang, ChinaThe Mushroom Research Centre, Guizhou UniversityGuiyangChina,State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, ChinaState Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou UniversityGuiyangChina
| | - De-Ping Wei
- The Engineering Research Center of Southwest Bio–Pharmaceutical Resources Ministry of Education, Guizhou University, Guiyang, ChinaThe Engineering Research Center of Southwest Bio–Pharmaceutical Resources Ministry of Education, Guizhou UniversityGuiyangChina,Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, ThailandCenter of Excellence in Fungal Research, Mae Fah Luang UniversityChiang RaiThailand,The Mushroom Research Centre, Guizhou University, Guiyang, ChinaThe Mushroom Research Centre, Guizhou UniversityGuiyangChina,State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, ChinaState Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou UniversityGuiyangChina,Department of Entomology and Plant Pathology, Faculty of Agriculture, Chiang Mai University, Chiang Mai, ThailandDepartment of Entomology and Plant Pathology, Faculty of Agriculture, Chiang Mai UniversityChiang MaiThailand
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12
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Panel Products Made of Oil Palm Trunk: A Review of Potency, Environmental Aspect, and Comparison with Wood-Based Composites. Polymers (Basel) 2022; 14:polym14091758. [PMID: 35566927 PMCID: PMC9104621 DOI: 10.3390/polym14091758] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 04/20/2022] [Accepted: 04/23/2022] [Indexed: 12/28/2022] Open
Abstract
Oil palm plantations have expanded rapidly in Southeast Asia, particularly in Indonesia and Malaysia. A lot of products, including food and other edible products, oleo-chemicals, cosmetics, personal and household care, pharmaceutical products, and biodiesels are derived from palm oil, thus making them one of the most economically important plants. After 25-30 years of age, the palms are felled and replaced due to declining oil production. Oil palm trunks (OPT) are considered significant waste products. The trunks remain on the plantation site for nutrient recycling or burning. This increases insect and fungi populations causing environmental problems for the new palm generation or air pollution due to the fire. Up till now, OPT has received less attention in research studies. Therefore, this review summarizes the utilization of OPT into products made of oil palm fibers mainly derived from OPT and its application as the substitution of wood panel products. Some research works have been carried out on oil palm fibers that are derived from OPT for exploiting their potential as raw material of composite panel products, which is the objective of this review. Areas of development are processed into various conventional composite panel products such as plywood and laminated board which are usually predominantly made of wood and bonded by synthetic resins, particleboard with binder, or binderless and cement board which is arranged with wood as a minor component. All of the products have been presented and described technically according to best knowledge of the authors and literature review.
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Lee CC, Koo VC, Lim TS, Lee YP, Abidin H. A multi-layer perceptron-based approach for early detection of BSR disease in oil palm trees using hyperspectral images. Heliyon 2022; 8:e09252. [PMID: 35445158 PMCID: PMC9014396 DOI: 10.1016/j.heliyon.2022.e09252] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 12/20/2021] [Accepted: 04/01/2022] [Indexed: 11/25/2022] Open
Abstract
Basal Stem Rot (BSR) disease caused by Ganoderma boninense is identified as the biggest threat in oil palm industry in Malaysia, resulting in significant yield losses. Effective BSR disease detection is important for plantation management to ensure stable palm oil production. Existing method is done by experience personnel, via visual inspection it is very time consuming. Rapid development of unmanned aerial vehicle (UAV) and machine learning has the potential to address this issue with higher efficiency. This paper proposed a new framework to automate BSR disease detection with UAV images to improve time efficiency and automate detection process. The proposed method has two steps, first hyperspectral image (HSI) pre-processing, followed by artificial neural network disease detection. Multilayer-Perceptron model is introduced to learn spectral features from different infection stages. The model is trained with ground truth collected by trained surveyors. The HSI sample size consists of 2 healthy trees, 5 Stage A (mild infection), 5 Stage B (moderate infection), and 3 Stage C (severe infection). Performance is examined with support vector machine (SVM), 1 dimensional convolutional network (1D CNN), and several vegetation indices, namely Normalized Difference Vegetation Index (NDVI), Normalized Difference Red Edge (NDRE), Optimised Soil-Adjusted Vegetation Index (OSAVI), and Merris Terrestrial Chlorophyll Index (MTCI). All machine learning algorithms can segregate infection stages, MLP modal had a highest overall accuracy 86.67%, compared to SVM and 1D CNN at 66.67% and 73.33%. Whereas for vegetation index, it can only detect Stage C tree, and not able to differentiate between Healthy, Stage A and Stage B tree. In term of computational cost, MLP modal had balance performance with moderate training time, but faster inference time. It demonstrates effectiveness on BSR disease detection, even at early infection stage.
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Affiliation(s)
- Chee Cheong Lee
- Faculty of Engineering and Technology, Multimedia University, 75450 Bukit Beruang, Melaka, Malaysia
| | - Voon Chet Koo
- Faculty of Engineering and Technology, Multimedia University, 75450 Bukit Beruang, Melaka, Malaysia
| | - Tien Sze Lim
- Faculty of Engineering and Technology, Multimedia University, 75450 Bukit Beruang, Melaka, Malaysia
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14
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Faizah R, Putranto RA, Raharti VR, Supena N, Sukma D, Budiani A, Wening S, Sudarsono S. Defense response changes in roots of oil palm (Elaeis guineensis Jacq.) seedlings after internal symptoms of Ganoderma boninense Pat. infection. BMC PLANT BIOLOGY 2022; 22:139. [PMID: 35331141 PMCID: PMC8944027 DOI: 10.1186/s12870-022-03493-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Accepted: 02/25/2022] [Indexed: 05/14/2023]
Abstract
BACKGROUND The development of basal stem rot (BSR) disease in oil palm is associated with lignin during vegetative growth and salicylic acid (SA) biosynthesis. The increase in the lignin content, SA accumulation, growth, and root biomass could indicate the resistance of oil palm seedlings to BSR disease. Therefore, although there are many studies on the interactions between the Ganoderma boninense and oil palm, research on evaluation of physiological processes, biochemistry, and molecules occurring during early internal symptoms of BSR in roots of oil palm (Elaeis guineensis Jacq.) are essential. RESULTS Ganoderma boninense inoculation indicated that C01, C02, and C05 seedlings were susceptible, while the other three seedlings, C03, C07, and C08, were resistant based on Ganoderma Disease Index (GDI). Infection by G. boninense in the most susceptible seedlings C05 reduced fresh weight of roots (FW) by 9.0%, and lignin content by 10.9%. The most resistant seedlings C08 were reduced by only 8.4%, and 0.2% regarding their fresh weight and lignin content, respectively. BSR disease induced SA accumulation in the most susceptible C08 and decreased peroxidase (PRX) enzyme (EC 1.11.1.7) activities in root tissues of oil palm seedlings except C07 and C08 where PRX activities remained high in the 4 months after planting. Infection with G. boninense also increased glutathione S-transferase U19-like (EgGSTU19) gene expression in the root tissues of susceptible seedlings, while laccase-24 (EgLCC24) gene expression was associated with resistance against BSR disease. Based on the relative expression of twelve genes, two genes are categorized as receptors (EgWAKL5, EgMIK1), two genes as biosynthesis signal transduction compound (EgOPR5, EgACO1), five genes as defense responses (EgROMT, EgSOT12, EgLCC24, EgGLT3, EgGSTU19), and one gene as trans-resveratrol di-O-methyltransferase-like (EgRNaseIII) predicted related to BSR infection. While two other genes remain unknown (EgUnk1, EgUnk2). CONCLUSIONS Ganoderma infection-induced SA accumulation and lignification in resistant accessions promote the seedlings root biomass. Oil palm seedlings have a synergistic physical, biochemical, and molecular defense mechanism to the BSR disease. The utilization of nucleotide-based molecular markers using EgLCC24 gene is able to detect resistant oil palm seedlings to G. boninense.
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Affiliation(s)
- Rokhana Faizah
- Plant Breeding and Biotechnology Study Program, Department of Agronomy and Horticulture, Faculty of Agriculture, Bogor Agricultural University (IPB University), Jl. Meranti, Dramaga Campus, Bogor, 16680, Indonesia.
- Indonesian Oil Palm Research Institute, Jl. Brigjen Katamso No. 51, Medan, North Sumatera, 20158, Indonesia.
| | - Riza Arief Putranto
- Indonesian Research Institute for Biotechnology and Bioindustry, Jl. Taman Kencana No. 1, Bogor, 16128, Indonesia
- PT Riset Perkebunan Nusantara (Nusantara Estate Crops Research), Jl. Salak no. 1A, Bogor, 16128, Indonesia
| | - Vivi Restu Raharti
- Department of Agrotechnology, Agriculture Faculty, Jenderal Soedirman University, Jl. Dr. Soeparno No. 63, Karangwangkal, North Purwokerto, Central Java, 53122, Indonesia
| | - Nanang Supena
- Indonesian Oil Palm Research Institute, Jl. Brigjen Katamso No. 51, Medan, North Sumatera, 20158, Indonesia
| | - Dewi Sukma
- Plant Breeding and Biotechnology Study Program, Department of Agronomy and Horticulture, Faculty of Agriculture, Bogor Agricultural University (IPB University), Jl. Meranti, Dramaga Campus, Bogor, 16680, Indonesia
| | - Asmini Budiani
- Indonesian Research Institute for Biotechnology and Bioindustry, Jl. Taman Kencana No. 1, Bogor, 16128, Indonesia
| | - Sri Wening
- Indonesian Oil Palm Research Institute, Jl. Brigjen Katamso No. 51, Medan, North Sumatera, 20158, Indonesia
| | - Sudarsono Sudarsono
- Plant Breeding and Biotechnology Study Program, Department of Agronomy and Horticulture, Faculty of Agriculture, Bogor Agricultural University (IPB University), Jl. Meranti, Dramaga Campus, Bogor, 16680, Indonesia
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15
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Santoso I, Fadhilah QG, Safitri SD, Handayani S, Maryanto AE, Yasman Y. Inhibition of the phytopathogenic fungi Curvularia lunata BM and Ganoderma sp. TB4 by antifungal compounds produced by Bacillus siamensis LDR grown on hanjeli (Coix lacryma-jobi L.) starch. PHARMACIA 2022. [DOI: 10.3897/pharmacia.69.e80180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Bacillus siamensis LDR was tested for its potential as a biocontrol agent against the phytopathogenic fungi Curvularia lunata BM and Ganoderma sp. TB4. Fermentation of B. siamensis LDR for the production of antifungal compound was performed in modified Czapex-Dox broth using hanjeli (Coix lacryma-jobi L.) starch as carbon source. The Bacillus siamensis LDR inoculum was 105 CFU/ mL, and fermentation was conducted for up to 16 days. Antibiosis assay conducted to test the antifungal activity of filtrate medium. The results showed inhibition of C. lunata BM and Ganoderma sp. TB4 were 47.08% and 85.99%, respectively on 14th day of fermentation. Antifungal assay of the crude extract from filtrate medium revealed growth inhibition of C. lunata BM (60.70%) and Ganoderma sp. TB4 (65.25%). Thin layer chromatography of the crude extract revealed pink-colored spots indicative of lipopeptide compounds. Analysis of the crude extract by ultraperformance liquid chromatography-mass spectrometry was tentatively identified as iturin A, bacillomycin F, and surfactin.
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Ganoderma zonatum Is the Causal Agent of Basal Stem Rot in Oil Palm in Colombia. J Fungi (Basel) 2022; 8:jof8030230. [PMID: 35330232 PMCID: PMC8953267 DOI: 10.3390/jof8030230] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 02/21/2022] [Accepted: 02/22/2022] [Indexed: 02/04/2023] Open
Abstract
Basal stem rot (BSR), caused by Ganoderma spp., is one of the most important emerging oil palm diseases in Colombia, and is restricted to two oil palm production areas in the country. To identify the causal agent of the disease, basidiocarp of oil palms affected by BSR were used to prepare isolates, and their pathogenicity was then assessed in pre-nursery plants. Four-month-old oil palm seedlings were inoculated with rubber wood (Hevea brasiliensis) blocks colonized with dikaryotic mycelia of Ganoderma. The incidence, severity, and symptoms of the pathogen were assessed. A multiregional analysis (ITS, rpb2, and tef1-α) was carried out to identify the isolates; all isolates were determined to be Ganoderma zonatum. Phylogenetic analyses with the three regions yielded concordant phylogenetic information and supported the distinction of the isolates with high bootstrap support. Seven isolates (CPBsZN-01-29, CPBsZN-02-30, CPBsZN-03-31, CPBsZN-04-34, CPBsZN-05-35, CPBsZN-06-36, and CPBsZN-07-38) were pathogenic in oil palm, with incidences greater than 90% and a maximum severity of 34%, and the highest severity index was found in isolates CPBsZN-03-31, CPBsZN-04-34, and CPBsZN-06-36. The pathogen was recovered from inoculated oil palms in all cases. This study reveals the pathogenic association of Ganoderma zonatum with BSR in Colombia.
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Kirkman ER, Hilton S, Sethuraman G, Elias DMO, Taylor A, Clarkson J, Soh AC, Bass D, Ooi GT, McNamara NP, Bending GD. Diversity and Ecological Guild Analysis of the Oil Palm Fungal Microbiome Across Root, Rhizosphere, and Soil Compartments. Front Microbiol 2022; 13:792928. [PMID: 35222328 PMCID: PMC8874247 DOI: 10.3389/fmicb.2022.792928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 01/18/2022] [Indexed: 11/14/2022] Open
Abstract
The rhizosphere microbiome is a major determinant of plant health, which can interact with the host directly and indirectly to promote or suppress productivity. Oil palm is one of the world’s most important crops, constituting over a third of global vegetable oil production. Currently there is little understanding of the oil palm microbiome and its contribution to plant health and productivity, with existing knowledge based almost entirely on culture dependent studies. We investigated the diversity and composition of the oil palm fungal microbiome in the bulk soil, rhizosphere soil, and roots of 2-, 18-, and 35-year old plantations in Selangor, Malaysia. The fungal community showed substantial variation between the plantations, accounting for 19.7% of community composition, with compartment (root, rhizosphere soil, and bulk soil), and soil properties (pH, C, N, and P) contributing 6.5 and 7.2% of community variation, respectively. Rhizosphere soil and roots supported distinct communities compared to the bulk soil, with significant enrichment of Agaricomycetes, Glomeromycetes, and Lecanoromycetes in roots. Several putative plant pathogens were abundant in roots in all the plantations, including taxa related to Prospodicola mexicana and Pleurostoma sp. The mycorrhizal status and dependency of oil palm has yet to be established, and using 18S rRNA primers we found considerable between-site variation in Glomeromycotinian community composition, accounting for 31.2% of variation. There was evidence for the selection of Glomeromycotinian communities in oil palm roots in the older plantations but compartment had a weak effect on community composition, accounting for 3.9% of variation, while soil variables accounted for 9% of community variation. While diverse Mucoromycotinian fungi were detected, they showed very low abundance and diversity within roots compared to bulk soil, and were not closely related to taxa which have been linked to fine root endophyte mycorrhizal morphology. Many of the fungal sequences showed low similarity to established genera, indicating the presence of substantial novel diversity with significance for plant health within the oil palm microbiome.
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Affiliation(s)
- Eleanor R. Kirkman
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Sally Hilton
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Gomathy Sethuraman
- Crops for the Future Research Centre, Semenyih, Malaysia
- Faculty of Science, Institute of Biological Sciences, University of Malaya, Kuala Lumpur, Malaysia
| | - Dafydd M. O. Elias
- UK Centre for Ecology & Hydrology, Lancaster Environment Centre, Bailrigg, United Kingdom
| | - Andrew Taylor
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - John Clarkson
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Aik Chin Soh
- Crops for the Future Research Centre, Semenyih, Malaysia
| | - David Bass
- Department of Life Sciences, Natural History Museum, London, United Kingdom
- Centre for Environment, Fisheries and Aquaculture Science, Weymouth, United Kingdom
| | - Gin Teng Ooi
- Crops for the Future Research Centre, Semenyih, Malaysia
| | - Niall P. McNamara
- UK Centre for Ecology & Hydrology, Lancaster Environment Centre, Bailrigg, United Kingdom
| | - Gary D. Bending
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
- *Correspondence: Gary D. Bending,
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Bharudin I, Ab Wahab AFF, Abd Samad MA, Xin Yie N, Zairun MA, Abu Bakar FD, Abdul Murad AM. Review Update on the Life Cycle, Plant–Microbe Interaction, Genomics, Detection and Control Strategies of the Oil Palm Pathogen Ganoderma boninense. BIOLOGY 2022; 11:biology11020251. [PMID: 35205119 PMCID: PMC8869222 DOI: 10.3390/biology11020251] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/25/2022] [Accepted: 02/03/2022] [Indexed: 11/16/2022]
Abstract
Plant pathogens are key threats to agriculture and global food security, causing various crop diseases that lead to massive economic losses. Palm oil is a commodity export of economic importance in Southeast Asia, especially in Malaysia and Indonesia. However, the sustainability of oil palm plantations and production is threatened by basal stem rot (BSR), a devastating disease predominantly caused by the fungus Ganoderma boninense Pat. In Malaysia, infected trees have been reported in nearly 60% of plantation areas, and economic losses are estimated to reach up to ~USD500 million a year. This review covers the current knowledge of the mechanisms utilized by G. boninense during infection and the methods used in the disease management to reduce BSR, including cultural practices, chemical treatments and antagonistic microorganism manipulations. Newer developments arising from multi-omics technologies such as whole-genome sequencing (WGS) and RNA sequencing (RNA-Seq) are also reviewed. Future directions are proposed to increase the understanding of G. boninense invasion mechanisms against oil palm. It is hoped that this review can contribute towards an improved disease management and a sustainable oil palm production in this region.
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Affiliation(s)
- Izwan Bharudin
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, UKM, Bangi 43600, Malaysia; (A.F.F.A.W.); (M.A.A.S.); (N.X.Y.); (M.A.Z.); (F.D.A.B.); (A.M.A.M.)
- Fraser’s Hill Research Centre (PPBF), Faculty of Science & Technology, Universiti Kebangsaan Malaysia, UKM, Bangi 43600, Malaysia
- Correspondence:
| | - Anis Farhan Fatimi Ab Wahab
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, UKM, Bangi 43600, Malaysia; (A.F.F.A.W.); (M.A.A.S.); (N.X.Y.); (M.A.Z.); (F.D.A.B.); (A.M.A.M.)
- FGV Innovation Centre (Biotechnology), Pt. 23417 Lengkuk Teknologi, Bandar Enstek 71760, Malaysia
| | - Muhammad Asyraff Abd Samad
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, UKM, Bangi 43600, Malaysia; (A.F.F.A.W.); (M.A.A.S.); (N.X.Y.); (M.A.Z.); (F.D.A.B.); (A.M.A.M.)
| | - Ng Xin Yie
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, UKM, Bangi 43600, Malaysia; (A.F.F.A.W.); (M.A.A.S.); (N.X.Y.); (M.A.Z.); (F.D.A.B.); (A.M.A.M.)
| | - Madihah Ahmad Zairun
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, UKM, Bangi 43600, Malaysia; (A.F.F.A.W.); (M.A.A.S.); (N.X.Y.); (M.A.Z.); (F.D.A.B.); (A.M.A.M.)
- Plant Pathology & Biosecurity Unit, Biology & Sustainability Research Division, 6, Malaysian Palm Oil Board, Bandar Baru Bangi, Kajang 43000, Malaysia
| | - Farah Diba Abu Bakar
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, UKM, Bangi 43600, Malaysia; (A.F.F.A.W.); (M.A.A.S.); (N.X.Y.); (M.A.Z.); (F.D.A.B.); (A.M.A.M.)
| | - Abdul Munir Abdul Murad
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, UKM, Bangi 43600, Malaysia; (A.F.F.A.W.); (M.A.A.S.); (N.X.Y.); (M.A.Z.); (F.D.A.B.); (A.M.A.M.)
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19
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Analysis of rhizobacterial community associated with the occurrence of Ganoderma basal stem rot disease in oil palm by Illumina next-generation sequencing. Arch Microbiol 2021; 204:31. [DOI: 10.1007/s00203-021-02670-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 10/15/2021] [Accepted: 10/17/2021] [Indexed: 10/19/2022]
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20
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Shokrollahi N, Ho CL, Zainudin NAIM, Wahab MABA, Wong MY. Identification of non-ribosomal peptide synthetase in Ganoderma boninense Pat. that was expressed during the interaction with oil palm. Sci Rep 2021; 11:16330. [PMID: 34381084 PMCID: PMC8358039 DOI: 10.1038/s41598-021-95549-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 07/16/2021] [Indexed: 02/07/2023] Open
Abstract
Basal stem rot (BSR) of oil palm is a disastrous disease caused by a white-rot fungus Ganoderma boninense Pat. Non-ribosomal peptides (NRPs) synthesized by non-ribosomal peptide synthetases (NRPSs) are a group of secondary metabolites that act as fungal virulent factors during pathogenesis in the host. In this study, we aimed to isolate NRPS gene of G. boninense strain UPMGB001 and investigate the role of this gene during G. boninense-oil palm interaction. The isolated NRPS DNA fragment of 8322 bp was used to predict the putative peptide sequence of different domains and showed similarity with G. sinense (85%) at conserved motifs of three main NRPS domains. Phylogenetic analysis of NRPS peptide sequences demonstrated that NRPS of G. boninense belongs to the type VI siderophore family. The roots of 6-month-old oil palm seedlings were artificially inoculated for studying NRPS gene expression and disease severity in the greenhouse. The correlation between high disease severity (50%) and high expression (67-fold) of G. boninense NRPS gene at 4 months after inoculation and above indicated that this gene played a significant role in the advancement of BSR disease. Overall, these findings increase our knowledge on the gene structure of NRPS in G. boninense and its involvement in BSR pathogenesis as an effector gene.
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Affiliation(s)
- Neda Shokrollahi
- grid.11142.370000 0001 2231 800XDepartment of Plant Protection, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor Malaysia
| | - Chai-Ling Ho
- grid.11142.370000 0001 2231 800XDepartment of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor Malaysia
| | - Nur Ain Izzati Mohd Zainudin
- grid.11142.370000 0001 2231 800XDepartment of Biology, Faculty of Science, Universiti Putra Malaysia, 43400 Serdang, Selangor Malaysia
| | - Mohd As’wad Bin Abul Wahab
- grid.11142.370000 0001 2231 800XDepartment of Plant Protection, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor Malaysia
| | - Mui-Yun Wong
- grid.11142.370000 0001 2231 800XDepartment of Plant Protection, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor Malaysia ,grid.11142.370000 0001 2231 800XInstitute of Plantation Studies, Universiti Putra Malaysia, 43400 Serdang, Selangor Malaysia
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21
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Wong WC, Tung HJ, Fadhilah MN, Midot F, Lau SYL, Melling L, Astari S, Hadziabdic Đ, Trigiano RN, Goh KJ, Goh YK. Genetic diversity and gene flow amongst admixed populations of Ganoderma boninense, causal agent of basal stem rot in African oil palm ( Elaeis guineensis Jacq.) in Sarawak (Malaysia), Peninsular Malaysia, and Sumatra (Indonesia). Mycologia 2021; 113:902-917. [PMID: 34161196 DOI: 10.1080/00275514.2021.1884815] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
In 1911 and 1917, the first commercial plantings of African oil palm (Elaeis guineensis Jacq.) were made in Indonesia and Malaysia in Southeast Asia. In less than 15 years, basal stem rot (BSR) was reported in Malaysia. It took nearly another seven decades to identify the main causal agent of BSR as the fungus, Ganoderma boninense. Since then, research efforts have focused on understanding G. boninense disease epidemiology, biology, and etiology, but limited progress was made to characterize pathogen genetic diversity, spatial structure, pathogenicity, and virulence. This study describes pathogen variability, gene flow, population differentiation, and genetic structure of G. boninense in Sarawak (Malaysia), Peninsular Malaysia, and Sumatra (Indonesia) inferred by 16 highly polymorphic cDNA-SSR (simple sequence repeat) markers. Marker-inferred genotypic diversity indicated a high level of pathogen variability among individuals within a population and among different populations. This genetic variability is clearly the result of outcrossing between basidiospores to produce recombinant genotypes. Although our results indicated high gene flow among the populations, there was no significant genetic differentiation among G. boninense populations on a regional scale. It suggested that G. boninense genetic makeup is similar across a wide region. Furthermore, our results revealed the existence of three admixed genetic clusters of G. boninense associated with BSR-diseased oil palms sampled throughout Sarawak, Peninsular Malaysia, and Sumatra. We postulate that the population structure is likely a reflection of the high genetic variability of G. boninense populations. This, in turn, could be explained by highly successful outcrossing between basidiospores of G. boninense from Southeast Asia and introduced genetic sources from various regions of the world, as well as regional adaptation of various pathogen genotypes to different palm hosts. Pathogen variability and population structure could be employed to deduce the epidemiology of G. boninense, as well as the implications of plantation cultural practices on BSR disease control in different regions.
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Affiliation(s)
- W C Wong
- Applied Agricultural Resources Sdn. Bhd., AAR-UNMC Biotechnology Research Centre, Jalan Broga, 43500 Semenyih, Selangor, Malaysia.,Advanced Agriecological Research Sdn. Bhd., No. 11 Jalan Teknologi 3/6, Taman Sains Selangor 1, Kota Damansara, 47810 Petaling Jaya, Selangor Darul Ehsan, Malaysia
| | - H J Tung
- Applied Agricultural Resources Sdn. Bhd., AAR-UNMC Biotechnology Research Centre, Jalan Broga, 43500 Semenyih, Selangor, Malaysia.,Advanced Agriecological Research Sdn. Bhd., No. 11 Jalan Teknologi 3/6, Taman Sains Selangor 1, Kota Damansara, 47810 Petaling Jaya, Selangor Darul Ehsan, Malaysia
| | - M Nurul Fadhilah
- Advanced Agriecological Research Sdn. Bhd., No. 11 Jalan Teknologi 3/6, Taman Sains Selangor 1, Kota Damansara, 47810 Petaling Jaya, Selangor Darul Ehsan, Malaysia
| | - F Midot
- Sarawak Tropical Peat Research Institute, Lot 6035, Kuching-Kota Samarahan Expressway, 94300, Kota Samarahan, Sarawak, Malaysia
| | - S Y L Lau
- Sarawak Tropical Peat Research Institute, Lot 6035, Kuching-Kota Samarahan Expressway, 94300, Kota Samarahan, Sarawak, Malaysia
| | - L Melling
- Sarawak Tropical Peat Research Institute, Lot 6035, Kuching-Kota Samarahan Expressway, 94300, Kota Samarahan, Sarawak, Malaysia
| | - S Astari
- PT Applied Agricultural Resources Indonesia, Kompleks Taman Anggrek Block D1, Jl Tuanku Tambusai, Pekanbaru, Riau, Indonesia, 28291
| | - Đ Hadziabdic
- Department of Entomology and Plant Pathology, University of Tennessee, 370 Plant Biotechnology Building, 2505 E J Chapman Drive, Knoxville, Tennessee 37996
| | - R N Trigiano
- Department of Entomology and Plant Pathology, University of Tennessee, 370 Plant Biotechnology Building, 2505 E J Chapman Drive, Knoxville, Tennessee 37996
| | - K J Goh
- Advanced Agriecological Research Sdn. Bhd., No. 11 Jalan Teknologi 3/6, Taman Sains Selangor 1, Kota Damansara, 47810 Petaling Jaya, Selangor Darul Ehsan, Malaysia
| | - Y K Goh
- Advanced Agriecological Research Sdn. Bhd., No. 11 Jalan Teknologi 3/6, Taman Sains Selangor 1, Kota Damansara, 47810 Petaling Jaya, Selangor Darul Ehsan, Malaysia
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Ganoderma boninense Disease Detection by Near-Infrared Spectroscopy Classification: A Review. SENSORS 2021; 21:s21093052. [PMID: 33925576 PMCID: PMC8123893 DOI: 10.3390/s21093052] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 04/16/2021] [Accepted: 04/20/2021] [Indexed: 11/16/2022]
Abstract
Ganoderma boninense (G. boninense) infection reduces the productivity of oil palms and causes a serious threat to the palm oil industry. This catastrophic disease ultimately destroys the basal tissues of oil palm, causing the eventual death of the palm. Early detection of G. boninense is vital since there is no effective treatment to stop the continuing spread of the disease. This review describes past and future prospects of integrated research of near-infrared spectroscopy (NIRS), machine learning classification for predictive analytics and signal processing towards an early G. boninense detection system. This effort could reduce the cost of plantation management and avoid production losses. Remarkably, (i) spectroscopy techniques are more reliable than other detection techniques such as serological, molecular, biomarker-based sensor and imaging techniques in reactions with organic tissues, (ii) the NIR spectrum is more precise and sensitive to particular diseases, including G. boninense, compared to visible light and (iii) hand-held NIRS for in situ measurement is used to explore the efficacy of an early detection system in real time using ML classifier algorithms and a predictive analytics model. The non-destructive, environmentally friendly (no chemicals involved), mobile and sensitive leads the NIRS with ML and predictive analytics as a significant platform towards early detection of G. boninense in the future.
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Current strategies and perspectives in detection and control of basal stem rot of oil palm. Saudi J Biol Sci 2021; 28:2840-2849. [PMID: 34012325 PMCID: PMC8116965 DOI: 10.1016/j.sjbs.2021.02.016] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 01/28/2021] [Accepted: 02/01/2021] [Indexed: 01/31/2023] Open
Abstract
The rapid expansion of oil palm (OP) has led to its emergence as a commodity of strategic global importance. Palm oil is used extensively in food and as a precursor for biodiesel. The oil generates export earnings and bolsters the economy of many countries, particularly Indonesia and Malaysia. However, oil palms are prone to basal stem rot (BSR) caused by Ganoderma boninense which is the most threatening disease of OP. The current control measures for BSR management including cultural practices, mechanical and chemical treatment have not proved satisfactory. Alternative control measures to overcome the G. boninense problem are focused on the use of biological control agents and many potential bioagents were identified with little proven practical application. Planting OP varieties resistant to G. boninense could provide the ideal long-term solution to basal stem rot. The total resistance of palms to G. boninense has not yet been reported, and few examples of partial resistances have been observed. Importantly, basidiospores are now recognized as the method by which the disease is spread, and control methods require to be revaluated because of this phenomenon. Many methods developed to prevent the spread of the disease effectively are only tested at nursery levels and are only reported in national journals inhibiting the development of useful techniques globally. The initial procedures employed by the fungus to infect the OP require consideration in terms of the physiology of the growth of the fungus and its possible control. This review assesses critically the progress that has been made in BSR development and management in OP.
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Determining Soil Microbial Communities and Their Influence on Ganoderma Disease Incidences in Oil Palm ( Elaeis guineensis) via High-Throughput Sequencing. BIOLOGY 2020; 9:biology9120424. [PMID: 33260913 PMCID: PMC7760618 DOI: 10.3390/biology9120424] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/23/2020] [Accepted: 11/25/2020] [Indexed: 01/04/2023]
Abstract
Simple Summary Biological and physicochemical soil factors involved in the incidence of the basal stem rot (BSR) disease in an oil palm (Elaeis guineensis) plantation in Malaysia were characterized. Blenheim soil with a low BSR disease incidence and Bernam soil with high BSR disease incidence were analyzed and observed to have differences in composition and diversity of soil prokaryotic and eukaryotic communities. Blenheim soil with a high pH and calcium was shown to have higher prokaryotic and eukaryotic diversity compared to Bernam soil. High abundances of rare metabolically diverse and versatile bacterial taxa, bacterial taxa that increased with the introduction of biocontrol agents, potential disease-suppressive bacteria, and bacterivorous flagellates were observed in Blenheim soil. In contrast, Bernam soil was predominantly characterized by potential disease-inducible bacterial taxa. A combination of both abiotic and biotic elements might be essential in driving disease-suppressive soil microbiome toward Ganoderma BSR in Blenheim soil. Abstract Basal stem rot (BSR), caused by Ganoderma boninense, is the most devastating oil palm disease in South East Asia, costing US$500 million annually. Various soil physicochemical parameters have been associated with an increase in BSR incidences. However, very little attention has been directed to understanding the relationship between soil microbiome and BSR incidence in oil palm fields. The prokaryotic and eukaryotic microbial diversities of two coastal soils, Blenheim soil (Typic Quartzipsamment—calcareous shell deposits, light texture) with low disease incidence (1.9%) and Bernam soil (Typic Endoaquept—non-acid sulfate) with high disease incidence (33.1%), were determined using the 16S (V3–V4 region) and 18S (V9 region) rRNA amplicon sequencing. Soil physicochemical properties (pH, electrical conductivity, soil organic matter, nitrogen, phosphorus, cation exchange capacity, exchangeable cations, micronutrients, and soil physical parameters) were also analyzed for the two coastal soils. Results revealed that Blenheim soil comprises higher prokaryotic and eukaryotic diversities, accompanied by higher pH and calcium content. Blenheim soil was observed to have a higher relative abundance of bacterial taxa associated with disease suppression such as Calditrichaeota, Zixibacteria, GAL15, Omnitrophicaeota, Rokubacteria, AKYG587 (Planctomycetes), JdFR-76 (Calditrichaeota), and Rubrobacter (Actinobacteria). In contrast, Bernam soil had a higher proportion of other bacterial taxa, Chloroflexi and Acidothermus (Actinobacteria). Cercomonas (Cercozoa) and Calcarisporiella (Ascomycota) were eukaryotes that are abundant in Blenheim soil, while Uronema (Ciliophora) and mammals were present in higher abundance in Bernam soil. Some of the bacterial taxa have been reported previously in disease-suppressive and -conducive soils as potential disease-suppressive or disease-inducible bacteria. Furthermore, Cercomonas was reported previously as potential bacterivorous flagellates involved in the selection of highly toxic biocontrol bacteria, which might contribute to disease suppression indirectly. The results from this study may provide valuable information related to soil microbial community structures and their association with soil characteristics and soil susceptibility to Ganoderma.
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Biocontrol and Plant-Growth-Promoting Traits of Talaromyces apiculatus and Clonostachys rosea Consortium against Ganoderma Basal Stem Rot Disease of Oil Palm. Microorganisms 2020; 8:microorganisms8081138. [PMID: 32731441 PMCID: PMC7463586 DOI: 10.3390/microorganisms8081138] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 07/20/2020] [Accepted: 07/24/2020] [Indexed: 12/04/2022] Open
Abstract
Basal stem rot (BSR) disease caused by Ganoderma boninense basidiomycetous fungus is the most economically important disease in oil palms in South East Asia. Unfortunately, there is no single most effective control measure available. Tremendous efforts have been directed in incorporation of environmentally friendly biocontrol approaches in minimizing BSR disease. This study investigated the performance of two potential biocontrol agents (BCAs), AAT0115 and AAB0114 strains recovered from oil palm on suppression of BSR in planta, and also assessed their plant-growth-promoting (PGP) performance. ITS rRNA-sequence phylogeny discriminated the two ascomycetous Talaromyces apiculatus (Ta) AT0115 and Clonostachys rosea (Cr) AAB0114 biocontrol species with PGP characteristics. In vitro studies have demonstrated both Ta and Cr are capable of reducing linear mycelial growth of G. boninense. Inoculation of individual Cr and Ta—as well as Cr+Ta consortium—induced a significant increment in leaf area and bole girth of oil-palm seedlings five months post-inoculation (MPI) under nursery conditions. At five months post-inoculation, shoot and root biomass, and nutrient contents (nitrogen, phosphorus, potassium, calcium, magnesium and boron) were significantly higher in Ta-inoculated seedlings compared to control treated with non-Ta-inoculated maize. Chlorophyll and carotenoids contents in rapidly growing oil-palm seedlings challenged with Cr, Ta or a combination of both were not negatively affected. Cr, Ta and Cr+Ta consortium treated seedlings had 4.9–60% BSR disease reduction compared to the untreated control. Co-inoculation of Cr and Ta resulted in increased BSR control efficiencies by 18–26% (compared with Cr only) and 48–55% (compared with Ta only). Collectively, Cr and Ta, either individually or in consortium showed potential as BSR biocontrol agents while also possess PGP traits in oil palm.
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Maluin FN, Hussein MZ, Azah Yusof N, Fakurazi S, Idris AS, Zainol Hilmi NH, Jeffery Daim LD. Chitosan-Based Agronanofungicides as a Sustainable Alternative in the Basal Stem Rot Disease Management. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:4305-4314. [PMID: 32227887 DOI: 10.1021/acs.jafc.9b08060] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The rise of environmental and health concerns due to the excessive use of the conventional fungicide urges the search for sustainable alternatives of agronanofungicides where the latter is aimed to enhance plant uptake and minimize the volatilization, leaching, and runoff of fungicides. With this in mind, fungicides of hexaconazole and/or dazomet were encapsulated into chitosan nanoparticles for the formulation of chitosan-based agronanofungicides. In the present study, chitosan nanoparticles (2 nm), chitosan-hexaconazole nanoparticles (18 and 168 nm), chitosan-dazomet nanoparticles (7 and 32 nm), and chitosan-hexaconazole-dazomet nanoparticles (5 and 58 nm) were synthesized and used as potent antifungal agents in combating the basal stem rot (BSR) disease caused by Ganoderma boninense in which they were evaluated via an artificial inoculation of oil palm seedlings with the rubber woodblock, which was fully colonized with the fungal Ganoderma boninense mycelium. The results revealed that chitosan nanoparticles could act as dual modes of action, which are themselves as a biocide or as a nanocarrier for the existing fungicides. In addition, the particle size of the chitosan-based agronanofungicides plays a crucial role in suppressing and controlling the disease. The synergistic effect of the double-fungicide system of 5 nm chitosan-hexaconazole-dazomet nanoparticles can be observed as the system showed the highest disease reduction with 74.5%, compared to the untreated infected seedlings.
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Affiliation(s)
- Farhatun Najat Maluin
- Institute of Advanced Technology, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Mohd Zobir Hussein
- Institute of Advanced Technology, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Nor Azah Yusof
- Institute of Advanced Technology, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
- Department of Chemistry, Faculty of Science, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Sharida Fakurazi
- Department of Human Anatomy, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Abu Seman Idris
- Malaysian Palm Oil Board (MPOB), 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Nur Hailini Zainol Hilmi
- Malaysian Palm Oil Board (MPOB), 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Leona Daniela Jeffery Daim
- Sime Darby Technology Centre Sdn. Bhd., UPM-MTDC Technology Centre III, Universiti Putra Malaysia, 1st Floor, Block B, Lebuh Silikon, 43400 Serdang, Selangor, Malaysia
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An Overview of the Oil Palm Industry: Challenges and Some Emerging Opportunities for Nanotechnology Development. AGRONOMY-BASEL 2020. [DOI: 10.3390/agronomy10030356] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The increase in the world’s oil demand due to the rise of the global population urges more research into the production of sustainable vegetable oilseeds, among which palm oil is the most suitable candidate as it is the most efficient oilseed crop in the world. In an effort to drive the oil palm industry in the areas of food safety and security nanotechnology could offer a sustainable alternative. However, the utilization of nanotechnology in the oil palm industry is still limited. In this review, we aim to encourage the researchers to fully utilize nanotechnology as an alternative solution to tackle the challenges faced by the oil palm industry. Moreover, we also aim to highlight the opportunities for nanotechnology development in oil palm-based related research. The major points are as follows: (1) Nanosensing enables real-time monitoring of plantation status and crop progression, including soil, water and nutrient management, early pest/disease detection, and the spreading of pests/diseases. The use of nanosensing conveniently extends into advanced breeding topics, such as the development of disease-tolerant plants; (2) Nanotechnology could be the answer for the development of integrated management of pest and disease. Active agricultural ingredients can be entrapped or encapsulated into nanocarrier systems to improve their solubility, stability, enhance their efficient delivery to site-specific targets, with longer shelf life, and consequently improved efficacy; (3) Valuable nanomaterials can be isolated and generated from oil palm biomass waste. The utilization of oil palm biomass waste could overcome the issue of the massive production of waste in the oil palm industry and palm oil mills, where oil only accounts for 10% of the biomass, while 90% is comprised of the generated biowastes. (4) Palm oil can be utilized as a green alternative as a capping and stabilizing agent in the biosynthesis of metallic and non-metallic nanoparticles. In addition, nanoemulsion formulations using palm oil in drug delivery systems offer advantages such as low toxicity, enhance bioavailability and solubility of the drugs, apart from being inexpensive and environmentally friendly.
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Shao J, Wang L, Liu Y, Qi Q, Wang B, Lu S, Liu C. Identification of milRNAs and their target genes in Ganoderma lucidum by high-throughput sequencing and degradome analysis. Fungal Genet Biol 2020; 136:103313. [DOI: 10.1016/j.fgb.2019.103313] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 08/09/2019] [Accepted: 11/15/2019] [Indexed: 12/15/2022]
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Ramzi AB, Che Me ML, Ruslan US, Baharum SN, Nor Muhammad NA. Insight into plant cell wall degradation and pathogenesis of Ganoderma boninense via comparative genome analysis. PeerJ 2019; 7:e8065. [PMID: 31879570 PMCID: PMC6927665 DOI: 10.7717/peerj.8065] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Accepted: 10/20/2019] [Indexed: 12/20/2022] Open
Abstract
Background G. boninense is a hemibiotrophic fungus that infects oil palms (Elaeis guineensis Jacq.) causing basal stem rot (BSR) disease and consequent massive economic losses to the oil palm industry. The pathogenicity of this white-rot fungus has been associated with cell wall degrading enzymes (CWDEs) released during saprophytic and necrotrophic stage of infection of the oil palm host. However, there is a lack of information available on the essentiality of CWDEs in wood-decaying process and pathogenesis of this oil palm pathogen especially at molecular and genome levels. Methods In this study, comparative genome analysis was carried out using the G. boninense NJ3 genome to identify and characterize carbohydrate-active enzyme (CAZymes) including CWDE in the fungal genome. Augustus pipeline was employed for gene identification in G. boninense NJ3 and the produced protein sequences were analyzed via dbCAN pipeline and PhiBase 4.5 database annotation for CAZymes and plant-host interaction (PHI) gene analysis, respectively. Comparison of CAZymes from G. boninense NJ3 was made against G. lucidum, a well-studied model Ganoderma sp. and five selected pathogenic fungi for CAZymes characterization. Functional annotation of PHI genes was carried out using Web Gene Ontology Annotation Plot (WEGO) and was used for selecting candidate PHI genes related to cell wall degradation of G. boninense NJ3. Results G. boninense was enriched with CAZymes and CWDEs in a similar fashion to G. lucidum that corroborate with the lignocellulolytic abilities of both closely-related fungal strains. The role of polysaccharide and cell wall degrading enzymes in the hemibiotrophic mode of infection of G. boninense was investigated by analyzing the fungal CAZymes with necrotrophic Armillaria solidipes, A. mellea, biotrophic Ustilago maydis, Melampsora larici-populina and hemibiotrophic Moniliophthora perniciosa. Profiles of the selected pathogenic fungi demonstrated that necrotizing pathogens including G. boninense NJ3 exhibited an extensive set of CAZymes as compared to the more CAZymes-limited biotrophic pathogens. Following PHI analysis, several candidate genes including polygalacturonase, endo β-1,3-xylanase, β-glucanase and laccase were identified as potential CWDEs that contribute to the plant host interaction and pathogenesis. Discussion This study employed bioinformatics tools for providing a greater understanding of the biological mechanisms underlying the production of CAZymes in G. boninense NJ3. Identification and profiling of the fungal polysaccharide- and lignocellulosic-degrading enzymes would further facilitate in elucidating the infection mechanisms through the production of CWDEs by G. boninense. Identification of CAZymes and CWDE-related PHI genes in G. boninense would serve as the basis for functional studies of genes associated with the fungal virulence and pathogenicity using systems biology and genetic engineering approaches.
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Affiliation(s)
- Ahmad Bazli Ramzi
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Muhammad Lutfi Che Me
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Ummul Syafiqah Ruslan
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
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Midot F, Lau SYL, Wong WC, Tung HJ, Yap ML, Lo ML, Jee MS, Dom SP, Melling L. Genetic Diversity and Demographic History of Ganoderma boninense in Oil Palm Plantations of Sarawak, Malaysia Inferred from ITS Regions. Microorganisms 2019; 7:E464. [PMID: 31623251 PMCID: PMC6843275 DOI: 10.3390/microorganisms7100464] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 10/07/2019] [Accepted: 10/14/2019] [Indexed: 12/13/2022] Open
Abstract
Ganoderma boninense causes basal stem rot (BSR) and is responsible for substantial economic losses to Southeast Asia's palm oil industry. Sarawak, a major producer in Malaysia, is also affected by this disease. Emergence of BSR in oil palm planted on peat throughout Sarawak is alarming as the soil type was previously regarded as non-conducive. Phylogenetic analysis indicated a single species, G. boninense as the cause of BSR in Sarawak. Information on evolutionary and demographic history for G. boninense in Sarawak inferred through informative genes is lacking. Hence, a haplotype study on single nucleotide polymorphisms in internal transcribed spacers (SNPs-ITS) of G. boninense was carried out. Sequence variations were analysed for population structure, phylogenetic and phylogeographic relationships. The internal transcribed spacers (ITS) region of 117 isolates from four populations in eight locations across Sarawak coastal areas revealed seven haplotypes. A major haplotype, designated GbHap1 (81.2%), was found throughout all sampling locations. Single nucleotide polymorphisms were observed mainly in the ITS1 region. The genetic structure was not detected, and genetic distance did not correlate with geographical distance. Haplotype network analysis suggested evidence of recent demographic expansion. Low genetic differences among populations also suggested that these isolates belong to a single G. boninense founder population adapting to oil palm as the host.
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Affiliation(s)
- Frazer Midot
- Sarawak Tropical Peat Research Institute, Lot 6035, Kuching-Kota Samarahan Expressway, 94300 Kota Samarahan, Sarawak, Malaysia.
| | - Sharon Yu Ling Lau
- Sarawak Tropical Peat Research Institute, Lot 6035, Kuching-Kota Samarahan Expressway, 94300 Kota Samarahan, Sarawak, Malaysia.
| | - Wei Chee Wong
- Applied Agricultural Resources Sdn. Bhd. (AAR) - University of Nottingham Malaysia Campus (UNMC) Biotechnology Research Centre, Jalan Broga, 43500 Semenyih, Selangor Darul Ehsan, Malaysia.
| | - Hun Jiat Tung
- Applied Agricultural Resources Sdn. Bhd. (AAR) - University of Nottingham Malaysia Campus (UNMC) Biotechnology Research Centre, Jalan Broga, 43500 Semenyih, Selangor Darul Ehsan, Malaysia.
| | - Mui Lan Yap
- Sarawak Tropical Peat Research Institute, Lot 6035, Kuching-Kota Samarahan Expressway, 94300 Kota Samarahan, Sarawak, Malaysia.
| | - Mei Lieng Lo
- Sarawak Tropical Peat Research Institute, Lot 6035, Kuching-Kota Samarahan Expressway, 94300 Kota Samarahan, Sarawak, Malaysia.
| | - Mui Sie Jee
- Sarawak Tropical Peat Research Institute, Lot 6035, Kuching-Kota Samarahan Expressway, 94300 Kota Samarahan, Sarawak, Malaysia.
| | - Simon Peter Dom
- Sarawak Tropical Peat Research Institute, Lot 6035, Kuching-Kota Samarahan Expressway, 94300 Kota Samarahan, Sarawak, Malaysia.
| | - Lulie Melling
- Applied Agricultural Resources Sdn. Bhd. (AAR) - University of Nottingham Malaysia Campus (UNMC) Biotechnology Research Centre, Jalan Broga, 43500 Semenyih, Selangor Darul Ehsan, Malaysia.
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Yeong TJ, Pin Jern K, Yao LK, Hannan MA, Hoon STG. Applications of Photonics in Agriculture Sector: A Review. Molecules 2019; 24:E2025. [PMID: 31137897 PMCID: PMC6571790 DOI: 10.3390/molecules24102025] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 05/10/2019] [Accepted: 05/12/2019] [Indexed: 11/17/2022] Open
Abstract
The agricultural industry has made a tremendous contribution to the foundations of civilization. Basic essentials such as food, beverages, clothes and domestic materials are enriched by the agricultural industry. However, the traditional method in agriculture cultivation is labor-intensive and inadequate to meet the accelerating nature of human demands. This scenario raises the need to explore state-of-the-art crop cultivation and harvesting technologies. In this regard, optics and photonics technologies have proven to be effective solutions. This paper aims to present a comprehensive review of three photonic techniques, namely imaging, spectroscopy and spectral imaging, in a comparative manner for agriculture applications. Essentially, the spectral imaging technique is a robust solution which combines the benefits of both imaging and spectroscopy but faces the risk of underutilization. This review also comprehends the practicality of all three techniques by presenting existing examples in agricultural applications. Furthermore, the potential of these techniques is reviewed and critiqued by looking into agricultural activities involving palm oil, rubber, and agro-food crops. All the possible issues and challenges in implementing the photonic techniques in agriculture are given prominence with a few selective recommendations. The highlighted insights in this review will hopefully lead to an increased effort in the development of photonics applications for the future agricultural industry.
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Affiliation(s)
- Tan Jin Yeong
- Institute of Power Engineering, College of Engineering, Universiti Tenaga Nasional, Kajang 43000, Selangor, Malaysia.
| | - Ker Pin Jern
- Institute of Power Engineering, College of Engineering, Universiti Tenaga Nasional, Kajang 43000, Selangor, Malaysia.
| | - Lau Kuen Yao
- Institute of Power Engineering, College of Engineering, Universiti Tenaga Nasional, Kajang 43000, Selangor, Malaysia.
| | - M A Hannan
- Institute of Power Engineering, College of Engineering, Universiti Tenaga Nasional, Kajang 43000, Selangor, Malaysia.
| | - Shirley Tang Gee Hoon
- Microbiology Unit, Department of Pre-clinical, International Medical School, Management and Science University, University Drive, Off Persiaran Olahraga, Seksyen 13, Shah Alam 40100, Selangor, Malaysia.
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Fowotade SA, Yusof NA, Abdullah J, Sulaiman Y, Abd Rahman SF. Enhanced electrochemical sensing of secondary metabolites in oil palms for early detection of Ganoderma boninense based on novel nanoparticle-chitosan functionalized multi-walled carbon nanotube platform. SENSING AND BIO-SENSING RESEARCH 2019. [DOI: 10.1016/j.sbsr.2019.100274] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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33
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Rani E, Mohshim SA, Ahmad MZ, Goodacre R, Alang Ahmad SA, Wong LS. Polymer Pen Lithography-Fabricated DNA Arrays for Highly Sensitive and Selective Detection of Unamplified Ganoderma Boninense DNA. Polymers (Basel) 2019; 11:polym11030561. [PMID: 30960545 PMCID: PMC6474127 DOI: 10.3390/polym11030561] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 03/19/2019] [Accepted: 03/22/2019] [Indexed: 01/18/2023] Open
Abstract
There is an increasing demand for lithography methods to enable the fabrication of diagnostic devices for the biomedical and agri-food sectors. In this regard, scanning probe lithography methods have emerged as a possible approach for this purpose, as they are not only convenient, robust and accessible, but also enable the deposition of “soft” materials such as complex organic molecules and biomolecules. In this report, the use of polymer pen lithography for the fabrication of DNA oligonucleotide arrays is described, together with the application of the arrays for the sensitive and selective detection of Ganoderma boninense, a fungal pathogen of the oil palm. When used in a sandwich assay format with DNA-conjugated gold nanoparticles, this system is able to generate a visually observable result in the presence of the target DNA. This assay is able to detect as little as 30 ng of Ganoderma-derived DNA without any pre-amplification and without the need for specialist laboratory equipment or training.
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Affiliation(s)
- Ekta Rani
- Manchester Institute of Biotechnology and School of Chemistry, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
| | - Siti Akhtar Mohshim
- Department of Chemistry, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia.
- Biotechnology and Nanotechnology Research Centre, Malaysian Agricultural Research and Development Institute, Serdang 43400, Selangor, Malaysia.
| | - Muhammad Zamharir Ahmad
- Biotechnology and Nanotechnology Research Centre, Malaysian Agricultural Research and Development Institute, Serdang 43400, Selangor, Malaysia.
| | - Royston Goodacre
- Manchester Institute of Biotechnology and School of Chemistry, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
| | - Shahrul Ainliah Alang Ahmad
- Department of Chemistry, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia.
- Institute of Advanced Technology, Universiti Putra Malaysia, UPM Serdang 43400, Selangor, Malaysia.
| | - Lu Shin Wong
- Manchester Institute of Biotechnology and School of Chemistry, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
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Brinkmann N, Schneider D, Sahner J, Ballauff J, Edy N, Barus H, Irawan B, Budi SW, Qaim M, Daniel R, Polle A. Intensive tropical land use massively shifts soil fungal communities. Sci Rep 2019; 9:3403. [PMID: 30833601 PMCID: PMC6399230 DOI: 10.1038/s41598-019-39829-4] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Accepted: 01/30/2019] [Indexed: 12/02/2022] Open
Abstract
Soil fungi are key players in nutrient cycles as decomposers, mutualists and pathogens, but the impact of tropical rain forest transformation into rubber or oil palm plantations on fungal community structures and their ecological functions are unknown. We hypothesized that increasing land use intensity and habitat loss due to the replacement of the hyperdiverse forest flora by nonendemic cash crops drives a drastic loss of diversity of soil fungal taxa and impairs the ecological soil functions. Unexpectedly, rain forest conversion was not associated with strong diversity loss but with massive shifts in soil fungal community composition. Fungal communities clustered according to land use system and loss of plant species. Network analysis revealed characteristic fungal genera significantly associated with different land use systems. Shifts in soil fungal community structure were particularly distinct among different trophic groups, with substantial decreases in symbiotrophic fungi and increases in saprotrophic and pathotrophic fungi in oil palm and rubber plantations in comparison with rain forests. In conclusion, conversion of rain forests and current land use systems restructure soil fungal communities towards enhanced pathogen pressure and, thus, threaten ecosystem health functions.
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Affiliation(s)
- Nicole Brinkmann
- Forest Botany and Tree Physiology, University of Goettingen, Göttingen, Germany.
| | - Dominik Schneider
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, University of Goettingen, Göttingen, Germany
| | - Josephine Sahner
- Forest Botany and Tree Physiology, University of Goettingen, Göttingen, Germany
| | - Johannes Ballauff
- Forest Botany and Tree Physiology, University of Goettingen, Göttingen, Germany
| | - Nur Edy
- Forest Botany and Tree Physiology, University of Goettingen, Göttingen, Germany
- Department of Agrotechnology, Faculty of Agriculture, Tadulako University, Palu, Indonesia
| | - Henry Barus
- Department of Agrotechnology, Faculty of Agriculture, Tadulako University, Palu, Indonesia
| | - Bambang Irawan
- Department of Forestry, University of Jambi, Jambi, Indonesia
| | - Sri Wilarso Budi
- Department of Silviculture, Faculty of Forestry, Bogor Agriculture University, Bogor, Indonesia
| | - Matin Qaim
- Department of Agricultural Economics and Rural Development, University of Goettingen, Göttingen, Germany
| | - Rolf Daniel
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, University of Goettingen, Göttingen, Germany
| | - Andrea Polle
- Forest Botany and Tree Physiology, University of Goettingen, Göttingen, Germany
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Surendran A, Siddiqui Y, Ali NS, Manickam S. Inhibition and kinetic studies of cellulose- and hemicellulose-degrading enzymes of Ganoderma boninense by naturally occurring phenolic compounds. J Appl Microbiol 2018; 124:1544-1555. [PMID: 29405525 DOI: 10.1111/jam.13717] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 01/01/2018] [Accepted: 01/25/2018] [Indexed: 11/28/2022]
Abstract
AIM Ganoderma sp, the causal pathogen of the basal stem rot (BSR) disease of oil palm, secretes extracellular hydrolytic enzymes. These play an important role in the pathogenesis of BSR by nourishing the pathogen through the digestion of cellulose and hemicellulose of the host tissue. Active suppression of hydrolytic enzymes secreted by Ganoderma boninense by various naturally occurring phenolic compounds and estimation of their efficacy on pathogen suppression is focused in this study. METHODS AND RESULTS Ten naturally occurring phenolic compounds were assessed for their inhibitory effect on the hydrolytic enzymes of G. boninense. The enzyme kinetics (Vmax and Km ) and the stability of the hydrolytic enzymes were also characterized. The selected compounds had shown inhibitory effect at various concentrations. Two types of inhibitions namely uncompetitive and noncompetitive were observed in the presence of phenolic compounds. Among all the phenolic compounds tested, benzoic acid was the most effective compound suppressive to the growth and production of hydrolytic enzymes secreted by G. boninense. The phenolic compounds as inhibitory agents can be a better replacement for the metal ions which are known as conventional inhibitors till date. The three hydrolytic enzymes were stable in a wide range of pH and temperature. CONCLUSION These findings highlight the efficacy of the applications of phenolic compounds to control Ganoderma. SIGNIFICANCE AND IMPACT OF THE STUDY The study has proved a replacement for chemical controls of G. boninense with naturally occurring phenolic compounds.
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Affiliation(s)
- A Surendran
- Institute of Tropical Agriculture and food Security, The Laboratory of Climate-Smart Food Crop Production, University Putra Malaysia, Serdang, Malaysia
| | - Y Siddiqui
- Institute of Tropical Agriculture and food Security, The Laboratory of Climate-Smart Food Crop Production, University Putra Malaysia, Serdang, Malaysia
| | - N S Ali
- Department of Plant Protection, Faculty of Agriculture, University Putra Malaysia, Serdang, Selangor, Malaysia
| | - S Manickam
- Department of Chemical and Environmental Engineering, University of Nottingham Malaysia Campus, Semenyih, Selangor, Malaysia
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Shuhada SN, Salim S, Nobilly F, Zubaid A, Azhar B. Logged peat swamp forest supports greater macrofungal biodiversity than large-scale oil palm plantations and smallholdings. Ecol Evol 2017; 7:7187-7200. [PMID: 28944010 PMCID: PMC5606887 DOI: 10.1002/ece3.3273] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 06/11/2017] [Accepted: 06/25/2017] [Indexed: 12/11/2022] Open
Abstract
Intensive land expansion of commercial oil palm agricultural lands results in reducing the size of peat swamp forests, particularly in Southeast Asia. The effect of this land conversion on macrofungal biodiversity is, however, understudied. We quantified macrofungal biodiversity by identifying mushroom sporocarps throughout four different habitats; logged peat swamp forest, large‐scale oil palm plantation, monoculture, and polyculture smallholdings. We recorded a total of 757 clusters of macrofungi belonging to 127 morphospecies and found that substrates for growing macrofungi were abundant in peat swamp forest; hence, morphospecies richness and macrofungal clusters were significantly greater in logged peat swamp forest than converted oil palm agriculture lands. Environmental factors that influence macrofungi in logged peat swamp forests such as air temperature, humidity, wind speed, soil pH, and soil moisture were different from those in oil palm plantations and smallholdings. We conclude that peat swamp forests are irreplaceable with respect to macrofungal biodiversity. They host much greater macrofungal biodiversity than any of the oil palm agricultural lands. It is imperative that further expansion of oil palm plantation into remaining peat swamp forests should be prohibited in palm oil producing countries. These results imply that macrofungal distribution reflects changes in microclimate between habitats and reduced macrofungal biodiversity may adversely affect decomposition in human‐modified landscapes.
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Affiliation(s)
- Siti Noor Shuhada
- Department of Forest Production Faculty of Forestry Universiti Putra Malaysia Serdang Selangor Malaysia
| | - Sabiha Salim
- Department of Forest Production Faculty of Forestry Universiti Putra Malaysia Serdang Selangor Malaysia
| | - Frisco Nobilly
- Department of Animal Science Faculty of Agriculture Universiti Putra Malaysia Serdang Selangor Malaysia
| | - Akbar Zubaid
- Faculty of Science and Technology School of Environmental and Natural Resource Sciences National University of Malaysia Bangi Selangor Malaysia
| | - Badrul Azhar
- Department of Forest Production Faculty of Forestry Universiti Putra Malaysia Serdang Selangor Malaysia.,Biodiversity Unit Institute of Bioscience Universiti Putra Malaysia Serdang Selangor Malaysia
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Shao J, Chen H, Yang D, Jiang M, Zhang H, Wu B, Li J, Yuan L, Liu C. Genome-wide Identification and Characterization of Natural Antisense Transcripts by Strand-specific RNA Sequencing in Ganoderma lucidum. Sci Rep 2017; 7:5711. [PMID: 28720793 PMCID: PMC5515960 DOI: 10.1038/s41598-017-04303-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 05/12/2017] [Indexed: 12/13/2022] Open
Abstract
Ganoderma lucidum is a white-rot fungus best-known for its medicinal and ligninolytic activities. To discover the underlying genes responsible for these activities, we identified and characterized the natural antisense transcripts (NATs) using strand-specific (ss) RNA-seq data obtained from the mycelia, primordia and fruiting bodies. NATs were identified using a custom pipeline and then subjected to functional enrichment and differential expression analyses. A total of 1613 cis- and 244 trans- sense and antisense transcripts were identified. Mapping to GO terms and KEGG pathways revealed that NATs were frequently associated with genes of particular functional categories in particular stages. ssRT-qPCR experiments showed that the expression profiles of 30 of 50 (60%) transcripts were highly correlated with those of the RNA-seq results (r ≥ 0.9). Expression profiles of 22 of 25 (88%) pairs of NATs and STs were highly correlated (p ≤ 0.01), with 15 having r ≥ 0.8 and 4 having r ≤ -0.8. Six lignin-modifying genes and their NATs were analyzed in detail. Diverse patterns of differential expression among different stages and positive and negative correlations were observed. These results suggested that NATs were implicated in gene expression regulation in a function-group and developmental-stage specific manner through complex mechanisms.
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Affiliation(s)
- Junjie Shao
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, P.R. China
| | - Haimei Chen
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, P.R. China
| | - Dan Yang
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, P.R. China
| | - Mei Jiang
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, P.R. China
| | - Hui Zhang
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, P.R. China
| | - Bin Wu
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, P.R. China
| | - Jianqin Li
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, P.R. China
| | - Lichai Yuan
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, P.R. China
| | - Chang Liu
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, P.R. China.
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Yahya MS, Syafiq M, Ashton-Butt A, Ghazali A, Asmah S, Azhar B. Switching from monoculture to polyculture farming benefits birds in oil palm production landscapes: Evidence from mist netting data. Ecol Evol 2017; 7:6314-6325. [PMID: 28861235 PMCID: PMC5574735 DOI: 10.1002/ece3.3205] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 05/31/2017] [Accepted: 06/06/2017] [Indexed: 11/26/2022] Open
Abstract
Monoculture farming is pervasive in industrial oil palm agriculture, including those RSPO plantations certified as sustainably managed. This farming practice does not promote the maintenance of farmland biodiversity. However, little scientific attention has been given to polyculture farming in oil palm production landscapes. Polyculture farming is likely to increase the floristic diversity and stand structural complexity that underpins biodiversity. Mist nets were used to sample birds at 120 smallholdings in Peninsular Malaysia. At each site, 12 vegetation structure characteristics were measured. We compared bird species richness, abundance, and composition between monoculture and polyculture smallholdings and used predictive models to examine the effects of habitat quality on avian biodiversity. Bird species richness was significantly greater in polyculture than that of monoculture smallholdings. The number of fallen and standing, dead oil palms were also important positive predictors of species richness. Bird abundance was also strongly increased by standing and dead oil palms and decreased with oil palm stand height. Our results indicate that polyculture farming can improve bird species richness in oil palm production landscapes. In addition, key habitat variables that are closely associated with farming practices, such as the removal of dead trees, should and can be managed by oil palm growers in order to promote biodiversity. To increase the sustainability of oil palm agriculture, it is imperative that stakeholders modify the way oil palms are currently planted and managed. Our findings can guide policy makers and certification bodies to promote oil palm production landscapes that will function more sustainably and increase existing biodiversity of oil palm landscapes.
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Affiliation(s)
- Muhammad S Yahya
- Department of Forest Management Faculty of Forestry Universiti Putra Malaysia Selangor Malaysia
| | - Muhamad Syafiq
- Department of Forest Management Faculty of Forestry Universiti Putra Malaysia Selangor Malaysia
| | - Adham Ashton-Butt
- Institute for Life Sciences University of Southampton Southampton UK
| | - Amal Ghazali
- Department of Forest Management Faculty of Forestry Universiti Putra Malaysia Selangor Malaysia
| | - Siti Asmah
- Department of Forest Management Faculty of Forestry Universiti Putra Malaysia Selangor Malaysia
| | - Badrul Azhar
- Department of Forest Management Faculty of Forestry Universiti Putra Malaysia Selangor Malaysia.,Biodiversity Unit Institute of Bioscience Universiti Putra Malaysia Selangor Malaysia
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Akanbi FS, Yusof NA, Abdullah J, Sulaiman Y, Hushiarian R. Detection of Quinoline in G. boninense-Infected Plants Using Functionalized Multi-Walled Carbon Nanotubes: A Field Study. SENSORS (BASEL, SWITZERLAND) 2017; 17:E1538. [PMID: 28671561 PMCID: PMC5539608 DOI: 10.3390/s17071538] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 06/01/2017] [Accepted: 06/05/2017] [Indexed: 12/19/2022]
Abstract
Carbon nanotubes (CNTs) reinforced with gold nanoparticles (AuNPs) and chitosan nanoparticles (CTSNPs) were anchored on a screen-printed electrode to fabricate a multi-walled structure for the detection of quinoline. The surface morphology of the nanocomposites and the modified electrode was examined by an ultra-high resolution field emission scanning electron microscope (FESEM), and Fourier-transform infrared (FT-IR) spectroscopy was used to confirm the presence of specific functional groups on the multi-walled carbon nanotubes MWCNTs. Cyclic voltammetry (CV) and linear sweep voltammetry (LSV) were used to monitor the layer-by-layer assembly of ultra-thin films of nanocomposites on the surface of the electrode and other electrochemical characterizations. Under optimized conditions, the novel sensor displayed outstanding electrochemical reactivity towards the electro-oxidation of quinoline. The linear range was fixed between 0.0004 and 1.0 μM, with a limit of detection (LOD) of 3.75 nM. The fabricated electrode exhibited high stability with excellent sensitivity and selectivity, specifically attributable to the salient characteristics of AuNPs, CTSNPs, and MWCNTs and the synergistic inter-relationship between them. The newly developed electrode was tested in the field. The Ipa increased with an increase in the amount of quinoline solution added, and the peak potential deviated minimally, depicting the real capability of the newly fabricated electrode.
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Affiliation(s)
- Fowotade Sulayman Akanbi
- Department of Chemistry, Faculty of Science, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia.
- Department of Science Laboratory Technology, Hussaini Adamu Federal Polytechnic, A2 Kazaure, Nigeria.
| | - Nor Azah Yusof
- Department of Chemistry, Faculty of Science, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia.
- Institute of Advanced Technology, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia.
| | - Jaafar Abdullah
- Department of Chemistry, Faculty of Science, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia.
| | - Yusran Sulaiman
- Department of Chemistry, Faculty of Science, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia.
| | - Roozbeh Hushiarian
- La Trobe Institute for Molecular Science, La Trobe University, Victoria 3086, Australia.
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Ahmadi P, Muharam FM, Ahmad K, Mansor S, Abu Seman I. Early Detection of Ganoderma Basal Stem Rot of Oil Palms Using Artificial Neural Network Spectral Analysis. PLANT DISEASE 2017; 101:1009-1016. [PMID: 30682927 DOI: 10.1094/pdis-12-16-1699-re] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Ganoderma boninense is a causal agent of basal stem rot (BSR) and is responsible for a significant portion of oil palm (Elaeis guineensis) losses, which can reach US$500 million a year in Southeast Asia. At the early stage of this disease, infected palms are symptomless, which imposes difficulties in detecting the disease. In spite of the availability of tissue and DNA sampling techniques, there is a particular need for replacing costly field data collection methods for detecting Ganoderma in its early stage with a technique derived from spectroscopic and imagery data. Therefore, this study was carried out to apply the artificial neural network (ANN) analysis technique for discriminating and classifying fungal infections in oil palm trees at an early stage using raw, first, and second derivative spectroradiometer datasets. These were acquired from 1,016 spectral signatures of foliar samples in four disease levels (T1: healthy, T2: mildly-infected, T3: moderately infected, and T4: severely infected). Most of the satisfactory results occurred in the visible range, especially in the green wavelength. The healthy oil palms and those which were infected by Ganoderma at an early stage (T2) were classified satisfactorily with an accuracy of 83.3%, and 100.0% in 540 to 550 nm, respectively, by ANN using first derivative spectral data. The results further indicated that the sensitive frond number modeled by ANN provided the highest accuracy of 100.0% for frond number 9 compared with frond 17. This study showed evidence that employment of ANN can predict the early infection of BSR disease on oil palm with a high degree of accuracy.
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Affiliation(s)
- Parisa Ahmadi
- Department of Agriculture Technology, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - Farrah Melissa Muharam
- Department of Agriculture Technology, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia; Geospatial Information Science Research Centre, Faculty of Engineering, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia; and Institute of Plantation Studies, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - Khairulmazmi Ahmad
- Department of Plant Pathology, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - Shattri Mansor
- Department of Civil Engineering, Faculty of Engineering, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia; and Geospatial Information Science Research Centre, Faculty of Engineering, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - Idris Abu Seman
- Malaysian Palm Oil Board (MPOB), No. 6, Persiaran Institut, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
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Kamarudin AN, Lai KS, Lamasudin DU, Idris AS, Balia Yusof ZN. Enhancement of Thiamine Biosynthesis in Oil Palm Seedlings by Colonization of Endophytic Fungus Hendersonia toruloidea. FRONTIERS IN PLANT SCIENCE 2017; 8:1799. [PMID: 29089959 PMCID: PMC5651052 DOI: 10.3389/fpls.2017.01799] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2017] [Accepted: 10/03/2017] [Indexed: 05/18/2023]
Abstract
Thiamine, or vitamin B1 plays an indispensable role as a cofactor in crucial metabolic reactions including glycolysis, pentose phosphate pathway and the tricarboxylic acid cycle in all living organisms. Thiamine has been shown to play a role in plant adaptation toward biotic and abiotic stresses. The modulation of thiamine biosynthetic genes in oil palm seedlings was evaluated in response to root colonization by endophytic Hendersonia toruloidea. Seven-month-old oil palm seedlings were inoculated with H. toruloidea and microscopic analyses were performed to visualize the localization of endophytic H. toruloidea in oil palm roots. Transmission electron microscopy confirmed that H. toruloidea colonized cortical cells. The expression of thiamine biosynthetic genes and accumulation of total thiamine in oil palm seedlings were also evaluated. Quantitative real-time PCR was performed to measure transcript abundances of four key thiamine biosynthesis genes (THI4, THIC, TH1, and TPK) on days 1, 7, 15, and 30 in response to H. toruloidea colonization. The results showed an increase of up to 12-fold in the expression of all gene transcripts on day 1 post-inoculation. On days 7, 15, and 30 post-inoculation, the relative expression levels of these genes were shown to be downregulated. Thiamine accumulation was observed on day 7 post-colonization and subsequently decreased until day 30. This work provides the first evidence for the enhancement of thiamine biosynthesis by endophytic colonization in oil palm seedlings.
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Affiliation(s)
- Amirah N. Kamarudin
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Malaysia
- Ganoderma and Diseases Research Group, Biology Division, Malaysian Palm Oil Board, Kajang, Malaysia
| | - Kok S. Lai
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Dhilia U. Lamasudin
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Abu S. Idris
- Ganoderma and Diseases Research Group, Biology Division, Malaysian Palm Oil Board, Kajang, Malaysia
| | - Zetty N. Balia Yusof
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Malaysia
- *Correspondence: Zetty N. Balia Yusof,
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Tan B, Daim L, Ithnin N, Ooi T, Md-Noh N, Mohamed M, Mohd-Yusof H, Appleton D, Kulaveerasingam H. Expression of phenylpropanoid and flavonoid pathway genes in oil palm roots during infection by Ganoderma boninense. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.plgene.2016.07.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Arango M, Martínez G, Torres G. Advances in the Interpretation of Tomographic Images as an Early Detection Method of Oil Palm Affected by Basal Stem Rot in Colombia. PLANT DISEASE 2016; 100:1559-1563. [PMID: 30686235 DOI: 10.1094/pdis-12-15-1473-re] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Basal stem rot, one of the most important diseases of oil palm in Southeast Asia, has also been identified in Colombia. The increase in disease incidence in the last decade has attracted the attention of producers and researchers. In the search for a procedure that allows for the early identification of diseased palm, Cenipalma evaluated the use of electrical impedance tomography to identify the different stages of development of basal stem rot. The tomograms were compared with transversal sections of healthy and diseased oil palm trees. Following Cenipalma's preliminary studies on early diagnosis of basal stem rot with tomography, the present study improved upon the technique by analyzing the tomograms of 209 diseased palm trees (confirmed by symptomatology), 346 asymptomatic palm trees, and 132 healthy palm trees. The minimum and maximum electric impedance values as well as the ratio between these values was recorded. The range of 1 to 95 Ω was used to represent the internal damage. The ratios averaged 5.1 for diseased, 1.9 for asymptomatic, and 1.5 for healthy palm trees. With the range and the ratio criteria established, it was possible to identify the disease in 100% of asymptomatic sampled palm trees. This study demonstrated that electrical impedance tomography is a powerful tool for early detection of basal stem rot, which can be used to establish an early disease management program.
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Affiliation(s)
- M Arango
- Pests and Diseases Program, Colombian Oil Palm Research Centre, Cenipalma. Bogota, Colombia
| | - G Martínez
- Pests and Diseases Program, Colombian Oil Palm Research Centre, Cenipalma. Bogota, Colombia
| | - G Torres
- Pests and Diseases Program, Colombian Oil Palm Research Centre, Cenipalma. Bogota, Colombia
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Hushiarian R, Yusof NA, Abdullah AH, Ahmad SAA, Dutse SW. Facilitating the indirect detection of genomic DNA in an electrochemical DNA biosensor using magnetic nanoparticles and DNA ligase. ACTA ACUST UNITED AC 2015. [DOI: 10.1016/j.ancr.2015.10.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Kües U, Nelson DR, Liu C, Yu GJ, Zhang J, Li J, Wang XC, Sun H. Genome analysis of medicinal Ganoderma spp. with plant-pathogenic and saprotrophic life-styles. PHYTOCHEMISTRY 2015; 114:18-37. [PMID: 25682509 DOI: 10.1016/j.phytochem.2014.11.019] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Revised: 11/03/2014] [Accepted: 11/06/2014] [Indexed: 06/04/2023]
Abstract
Ganoderma is a fungal genus belonging to the Ganodermataceae family and Polyporales order. Plant-pathogenic species in this genus can cause severe diseases (stem, butt, and root rot) in economically important trees and perennial crops, especially in tropical countries. Ganoderma species are white rot fungi and have ecological importance in the breakdown of woody plants for nutrient mobilization. They possess effective machineries of lignocellulose-decomposing enzymes useful for bioenergy production and bioremediation. In addition, the genus contains many important species that produce pharmacologically active compounds used in health food and medicine. With the rapid adoption of next-generation DNA sequencing technologies, whole genome sequencing and systematic transcriptome analyses become affordable approaches to identify an organism's genes. In the last few years, numerous projects have been initiated to identify the genetic contents of several Ganoderma species, particularly in different strains of Ganoderma lucidum. In November 2013, eleven whole genome sequencing projects for Ganoderma species were registered in international databases, three of which were already completed with genomes being assembled to high quality. In addition to the nuclear genome, two mitochondrial genomes for Ganoderma species have also been reported. Complementing genome analysis, four transcriptome studies on various developmental stages of Ganoderma species have been performed. Information obtained from these studies has laid the foundation for the identification of genes involved in biological pathways that are critical for understanding the biology of Ganoderma, such as the mechanism of pathogenesis, the biosynthesis of active components, life cycle and cellular development, etc. With abundant genetic information becoming available, a few centralized resources have been established to disseminate the knowledge and integrate relevant data to support comparative genomic analyses of Ganoderma species. The current review carries out a detailed comparison of the nuclear genomes, mitochondrial genomes and transcriptomes from several Ganoderma species. Genes involved in biosynthetic pathways such as CYP450 genes and in cellular development such as matA and matB genes are characterized and compared in detail, as examples to demonstrate the usefulness of comparative genomic analyses for the identification of critical genes. Resources needed for future data integration and exploitation are also discussed.
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Affiliation(s)
- Ursula Kües
- University of Göttingen, Büsgen-Institute, Department for Molecular Wood Biotechnology and Technical Mycology, Büsgenweg 2, D-37077 Göttingen, Germany
| | - David R Nelson
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, 858 Madison Ave., Memphis, TN 38163, USA
| | - Chang Liu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, 151 Malianwa North Road, Haidian District, Beijing 100193, China.
| | - Guo-Jun Yu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China; Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), Wuhan University, Wuhan, China
| | - Jianhui Zhang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, 151 Malianwa North Road, Haidian District, Beijing 100193, China
| | - Jianqin Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, 151 Malianwa North Road, Haidian District, Beijing 100193, China
| | - Xin-Cun Wang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, 151 Malianwa North Road, Haidian District, Beijing 100193, China
| | - Hui Sun
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China; Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), Wuhan University, Wuhan, China
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Hushiarian R, Yusof NA, Abdullah AH, Ahmad SAA, Dutse SW. A novel DNA nanosensor based on CdSe/ZnS quantum dots and synthesized Fe3O4 magnetic nanoparticles. Molecules 2014; 19:4355-68. [PMID: 24722589 PMCID: PMC6271521 DOI: 10.3390/molecules19044355] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2014] [Revised: 04/01/2014] [Accepted: 04/03/2014] [Indexed: 11/26/2022] Open
Abstract
Although nanoparticle-enhanced biosensors have been extensively researched, few studies have systematically characterized the roles of nanoparticles in enhancing biosensor functionality. This paper describes a successful new method in which DNA binds directly to iron oxide nanoparticles for use in an optical biosensor. A wide variety of nanoparticles with different properties have found broad application in biosensors because their small physical size presents unique chemical, physical, and electronic properties that are different from those of bulk materials. Of all nanoparticles, magnetic nanoparticles are proving to be a versatile tool, an excellent case in point being in DNA bioassays, where magnetic nanoparticles are often used for optimization of the hybridization and separation of target DNA. A critical step in the successful construction of a DNA biosensor is the efficient attachment of biomolecules to the surface of magnetic nanoparticles. To date, most methods of synthesizing these nanoparticles have led to the formation of hydrophobic particles that require additional surface modifications. As a result, the surface to volume ratio decreases and nonspecific bindings may occur so that the sensitivity and efficiency of the device deteriorates. A new method of large-scale synthesis of iron oxide (Fe3O4) nanoparticles which results in the magnetite particles being in aqueous phase, was employed in this study. Small modifications were applied to design an optical DNA nanosensor based on sandwich hybridization. Characterization of the synthesized particles was carried out using a variety of techniques and CdSe/ZnS core-shell quantum dots were used as the reporter markers in a spectrofluorophotometer. We showed conclusively that DNA binds to the surface of ironoxide nanoparticles without further surface modifications and that these magnetic nanoparticles can be efficiently utilized as biomolecule carriers in biosensing devices.
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Affiliation(s)
- Roozbeh Hushiarian
- Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
| | - Nor Azah Yusof
- Department of Chemistry, Faculty of Science, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
| | - Abdul Halim Abdullah
- Department of Chemistry, Faculty of Science, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
| | - Shahrul Ainliah Alang Ahmad
- Department of Chemistry, Faculty of Science, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
| | - Sabo Wada Dutse
- Department of Chemistry, Faculty of Science, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
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