1
|
Huang J, Alanís-Martínez I, Kumagai L, Dai Z, Zheng Z, Perez de Leon AA, Chen J, Deng X. Machine learning and analysis of genomic diversity of " Candidatus Liberibacter asiaticus" strains from 20 citrus production states in Mexico. FRONTIERS IN PLANT SCIENCE 2022; 13:1052680. [PMID: 36589083 PMCID: PMC9798433 DOI: 10.3389/fpls.2022.1052680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 11/23/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Huanglongbing (HLB, yellow shoot disease) is a highly destructive citrus disease associated with a nonculturable bacterium, "Candidatus Liberibacter asiaticus" (CLas), which is transmitted by Asian citrus psyllid (ACP, Diaphorina citri). In Mexico, HLB was first reported in Tizimin, Yucatán, in 2009 and is now endemic in 351 municipalities of 25 states. Understanding the population diversity of CLas is critical for HLB management. Current CLas diversity research is exclusively based on analysis of the bacterial genome, which composed two regions, chromosome (> 1,000 genes) and prophage (about 40 genes). METHODS AND RESULTS In this study, 40 CLas-infected ACP samples from 20 states in Mexico were collected. CLas was detected and confirmed by PCR assays. A prophage gene(terL)-based typing system (TTS) divided the Mexican CLas strains into two groups: Term-G including four strains from Yucatán and Chiapas, as well as strain psy62 from Florida, USA, and Term-A included all other 36 Mexican strains, as well as strain AHCA1 from California, USA. CLas diversity was further evaluated to include all chromosomal and prophage genes assisted by using machine learning (ML) tools to resolve multidimensional data handling issues. A Term-G strain (YTMX) and a Term-A strain (BCSMX) were sequenced and analyzed. The two Mexican genome sequences along with the CLas genome sequences available in GenBank were studied. An unsupervised ML was implemented through principal component analysis (PCA) on average nucleotide identities (ANIs) of CLas whole genome sequences; And a supervised ML was implemented through sparse partial least squares discriminant analysis (sPLS-DA) on single nucleotide polymorphisms (SNPs) of coding genes of CLas guided by the TTS. Two CLas Geno-groups, Geno-group 1 that extended Term-A and Geno-group 2 that extended Term-G, were established. CONCLUSIONS This study concluded that: 1) there were at least two different introductions of CLas into Mexico; 2) CLas strains between Mexico and USA are closely related; and 3) The two Geno-groups provide the basis for future CLas subspecies research.
Collapse
Affiliation(s)
- Jiaquan Huang
- Department of Plant Pathology, South China Agricultural University, Guangzhou, Guangdong, China
- Center for Biological Science and Technology, Advanced Institute of Natural Sciences, Beijing Normal University at Zhuhai, Zhuhai, Guangdong, China
| | - Iobana Alanís-Martínez
- National Station of Plant Epidemiology, Quarantine and Sanitation, SENASICA, Queretaro, Mexico
| | - Lucita Kumagai
- Plant Pest Diagnostic Center, California Department of Food and Agriculture, Sacramento, CA, United States
| | - Zehan Dai
- Department of Plant Pathology, South China Agricultural University, Guangzhou, Guangdong, China
| | - Zheng Zheng
- Department of Plant Pathology, South China Agricultural University, Guangzhou, Guangdong, China
| | - Adalberto A. Perez de Leon
- United States Department of Agriculture-Agricultural Research Service (USDA-ARS), San Joaquín Valley Agricultural Sciences Center, Parlier, CA, United States
| | - Jianchi Chen
- United States Department of Agriculture-Agricultural Research Service (USDA-ARS), San Joaquín Valley Agricultural Sciences Center, Parlier, CA, United States
| | - Xiaoling Deng
- Department of Plant Pathology, South China Agricultural University, Guangzhou, Guangdong, China
| |
Collapse
|
2
|
Ibrahim YE, Paredes-Montero JR, Al-Saleh MA, Widyawan A, He R, El Komy MH, Al Dhafer HM, Kitchen N, Gang DR, Brown JK. Characterization of the Asian Citrus Psyllid-‘Candidatus Liberibacter Asiaticus’ Pathosystem in Saudi Arabia Reveals Two Predominant CLas Lineages and One Asian Citrus Psyllid Vector Haplotype. Microorganisms 2022; 10:microorganisms10101991. [PMID: 36296267 PMCID: PMC9610752 DOI: 10.3390/microorganisms10101991] [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: 08/24/2022] [Revised: 09/16/2022] [Accepted: 10/01/2022] [Indexed: 11/16/2022] Open
Abstract
In Saudi Arabia (SA), the citrus greening disease is caused by ‘Candidatus Liberibacter asiaticus’ (CLas) transmitted by the Asian citrus psyllid (ACP) Diaphorina citri. The origin and route(s) of the ACP-CLas pathosystem invasion in SA have not been studied. Adult ACP were collected from citrus trees in SA and differentiated by analysis of the mitochondrial cytochrome oxidase I (mtCOI) and nuclear copper transporting protein (atox1) genes. A phylogenetic analysis of the Wolbachia spp. surface protein (wsp) gene was used to identify the ACP-associated Wolbachia spp. A phylogenetic analysis of the atox1 and mtCOI gene sequences revealed one predominant ACP haplotype most closely related to the Indian subcontinent founder populations. The detection and identification of CLas in citrus trees were carried out by polymerase chain reaction (PCR) amplification and sequencing of the 16S rDNA gene. The CLas-integrated prophage genomes were sequenced, annotated, and used to differentiate CLas populations. The ML and ASTRAL trees reconstructed with prophages type 1 and 2 genome sequences, separately and concatenated, resolved two major lineages, CLas-1 and -2. The CLas-1 clade, reported here for the first time, consisted of isolates from SA isolates and Pakistan. The CLas-2 sequences formed two groups, CLas-2-1 and -2-2, previously the ‘Asiatic’ and ‘Floridian’ strains, respectively. Members of CLas-2-1 originated from Southeast Asia, the USA, and other worldwide locations, while CLas-2-2 was identified only in Florida. This study provides the first snapshot into the status of the ACP-CLas pathosystem in SA. In addition, the results provide new insights into the pathosystem coevolution and global invasion histories of two ACP-CLas lineages with a predicted center of origin in South and Southeast Asia, respectively.
Collapse
Affiliation(s)
- Yasser E. Ibrahim
- Plant Protection Department, College of Food and Agriculture Sciences, King Saud University, Riyadh 11451, Saudi Arabia
- Correspondence: author:
| | - Jorge R. Paredes-Montero
- School of Plant Sciences, The University of Arizona, Tucson, AZ 85721, USA
- Department of Biology, Saginaw Valley State University, Saginaw, MI 48710, USA
- Facultad de Ciencias de la Vida, Escuela Superior Politécnica del Litoral, ESPOL, Campus Gustavo Galindo Km 30.5 Vía Perimetral, P.O. Box 09-01-5863, Guayaquil 090902, Ecuador
| | - Mohammed A. Al-Saleh
- Plant Protection Department, College of Food and Agriculture Sciences, King Saud University, Riyadh 11451, Saudi Arabia
| | - Arya Widyawan
- Plant Protection Department, College of Food and Agriculture Sciences, King Saud University, Riyadh 11451, Saudi Arabia
| | - Ruifeng He
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164, USA
| | - Mahmoud H. El Komy
- Plant Protection Department, College of Food and Agriculture Sciences, King Saud University, Riyadh 11451, Saudi Arabia
| | - Hathal M. Al Dhafer
- Plant Protection Department, College of Food and Agriculture Sciences, King Saud University, Riyadh 11451, Saudi Arabia
| | - Noel Kitchen
- School of Plant Sciences, The University of Arizona, Tucson, AZ 85721, USA
| | - David R. Gang
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164, USA
| | - Judith K. Brown
- School of Plant Sciences, The University of Arizona, Tucson, AZ 85721, USA
| |
Collapse
|
3
|
Biological Features and In Planta Transcriptomic Analyses of a Microviridae Phage (CLasMV1) in " Candidatus Liberibacter asiaticus". Int J Mol Sci 2022; 23:ijms231710024. [PMID: 36077424 PMCID: PMC9456138 DOI: 10.3390/ijms231710024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 08/29/2022] [Accepted: 08/30/2022] [Indexed: 11/27/2022] Open
Abstract
“Candidatus Liberibacter asiaticus” (CLas) is the causal agent of citrus Huanglongbing (HLB, also called citrus greening disease), a highly destructive disease threatening citrus production worldwide. A novel Microviridae phage (named CLasMV1) has been found to infect CLas, providing a potential therapeutic strategy for CLas/HLB control. However, little is known about the CLasMV1 biology. In this study, we analyzed the population dynamics of CLasMV1 between the insect vector of CLas, the Asian citrus psyllid (ACP, Diaphorina citri Kuwayama) and the holoparasitic dodder plant (Cuscuta campestris Yunck.); both acquired CLasMV1-infected CLas from an HLB citrus. All CLas-positive dodder samples were CLasMV1-positive, whereas only 32% of CLas-positive ACP samples were identified as CLasMV1-positive. Quantitative analyses showed a similar distribution pattern of CLasMV1 phage and CLas among eight citrus cultivars by presenting at highest abundance in the fruit pith and/or the center axis of the fruit. Transcriptome analyses revealed the possible lytic activity of CLasMV1 on CLas in fruit pith as evidenced by high-level expressions of CLasMV1 genes, and CLas genes related to cell wall biogenesis and remodeling to maintain the CLas cell envelope integrity. The up-regulation of CLas genes were involved in restriction–modification system that could involve possible phage resistance for CLas during CLasMV1 infection. In addition, the regulation of CLas genes involved in cell surface components and Sec pathway by CLasMV1 phage could be beneficial for phage infection. This study expanded our knowledge of CLasMV1 phage that will benefit further CLas phage research and HLB control.
Collapse
|
4
|
Mushtaq S, Shafiq M, Ashraf T, Haider MS, Atta S, Almaary KS, Elshikh MS. Enumeration of citrus endophytic bacterial communities based on illumine metagenomics technique. PLoS One 2022; 17:e0263144. [PMID: 35417473 PMCID: PMC9007379 DOI: 10.1371/journal.pone.0263144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 03/03/2022] [Indexed: 02/01/2023] Open
Abstract
Citrus is a valuable crop in Pakistan. It is rich in vitamin C, other nutrients and antioxidants. Huanglongbing (HLB) caused by a bacterium “Candidatus liberibacter asiaticus” (CLas), africanus and americanus has an influence on citrus production around the world. Beside HLB there exist several other bacterial species in citrus groves in Pakistan. The structure and diversity of bacterial species in various ecosystems can be quickly examined using NGS. This approach is considerably quicker and more precise than outdated methods. Healthy or citrus greening infected leaf samples of Grapefruit (Citrus paradisi), C. aurantifolia, and C. reticulata Blanco were used for diversity analysis. In this study high throughput, NGS technique was used to access the population of both cultivable and non-cultivable bacterial endophytes from citrus leaves, by using PCR amplicons of 16S rDNA sequences (V5–V7 regions) with Illumina Hi seq. As a result, a total number of 68,722 sequences were produced from the test samples. According to the NGS-based diversity classification, the most common genera of exploited bacterial endophytes were Proteobacteria, Firmicutes, Bacteroides, Cyanobacteria, and Actinobacteria. C. aurantifolia and C. paradisi showed almost equal diversity, whereas C. reticulata Blanco had a higher proportion of Proteobacteria and Cyanobacteria in their leaves. To determine alpha diversity (AD), additional data was analyzed using statistical indices such as Shannon, Chao1, and Simpson. According to the inverse Simpson diversity index, the abundance of the microbial population in six different citrus samples was 0.48, 0.567, and 0.163, respectively. The metagenomics of microbiota in plant tissues was successfully recorded by NGS technology, which can help us learn more about the interactions between plants and microbes. This research is the first step toward a better understanding of 16SrRNA-based metagenomics from citrus in Pakistan using Illumina (Hi seq) Technology.
Collapse
Affiliation(s)
- Sehrish Mushtaq
- Faculty of Agricultural Sciences, Department of Plant Pathology, University of the Punjab, Quaid-e-Azam Campus, Lahore, Pakistan
| | - Muhammad Shafiq
- Faculty of Agricultural Sciences, Department of Horticulture Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore, Pakistan
| | - Tehseen Ashraf
- Department of Horticulture Sciences University of Sargodha, Sargodha, Pakistan
| | - Muhammad Saleem Haider
- Faculty of Agricultural Sciences, Department of Plant Pathology, University of the Punjab, Quaid-e-Azam Campus, Lahore, Pakistan
| | - Sagheer Atta
- Department of Plant Protection, Faculty of Agricultural Sciences, Ghazi University Dera Ghazhi Khan, Punjab, Pakistan
- Molecular Plant Pathology Laboratory, USDA-ARS, Beltsville, MD, United States of America
- * E-mail:
| | - Khalid S. Almaary
- Department of Botany and Microbiology, College of Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Mohammad Soliman Elshikh
- Department of Botany and Microbiology, College of Sciences, King Saud University, Riyadh, Saudi Arabia
| |
Collapse
|
5
|
Zhang L, Li Z, Bao M, Li T, Fang F, Zheng Y, Liu Y, Xu M, Chen J, Deng X, Zheng Z. A Novel Microviridae Phage (CLasMV1) From " Candidatus Liberibacter asiaticus". Front Microbiol 2021; 12:754245. [PMID: 34721359 PMCID: PMC8548822 DOI: 10.3389/fmicb.2021.754245] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 09/07/2021] [Indexed: 11/25/2022] Open
Abstract
“Candidatus Liberibacter asiaticus” (CLas) is an unculturable phloem-limited α-proteobacterium associated with citrus Huanglongbing (HLB; yellow shoot disease). HLB is currently threatening citrus production worldwide. Understanding the CLas biology is critical for HLB management. In this study, a novel single-stranded DNA (ssDNA) phage, CLasMV1, was identified in a CLas strain GDHZ11 from Guangdong Province of China through a metagenomic analysis. The CLasMV1 phage had a circular genome of 8,869 bp with eight open reading frames (ORFs). While six ORFs remain uncharacterized, ORF6 encoded a replication initiation protein (RIP), and ORF8 encoded a major capsid protein (MCP). Based on BLASTp search against GenBank database, amino acid sequences of both MCP and RIP shared similarities (coverage > 50% and identity > 25%) to those of phages in Microviridae, an ssDNA phage family. Phylogenetic analysis revealed that CLasMV1 MCP and RIP sequences were clustered with genes from CLas and “Ca. L. solanacearum” (CLso) genomes and formed a unique phylogenetic lineage, designated as a new subfamily Libervirinae, distinct to other members in Microviridae family. No complete integration form but partial sequence (∼1.9 kb) of CLasMV1 was found in the chromosome of strain GDHZ11. Read-mapping analyses on additional 15 HiSeq data sets of CLas strains showed that eight strains harbored complete CLasMV1 sequence with variations in single-nucleotide polymorphisms (SNPs) and small sequence insertions/deletions (In/Dels). PCR tests using CLasMV1-specific primer sets detected CLasMV1 in 577 out of 1,006 CLas strains (57%) from southern China. This is the first report of Microviridae phage associated with CLas, which expands our understanding of phage diversity in CLas and facilitates current research in HLB.
Collapse
Affiliation(s)
- Ling Zhang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, China
| | - Ziyi Li
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, China
| | - Minli Bao
- China-United States Citrus Huanglongbing Joint Laboratory, National Navel Orange Engineering Research Center, Gannan Normal University, Ganzhou, China
| | - Tao Li
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, China
| | - Fang Fang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, China
| | - Yongqin Zheng
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, China
| | - Yaoxin Liu
- Horticulture Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Meirong Xu
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, China
| | - Jianchi Chen
- United States Department of Agriculture, San Joaquin Valley Agricultural Sciences Center, Agricultural Research Service, Parlier, CA, United States
| | - Xiaoling Deng
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, China
| | - Zheng Zheng
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, China
| |
Collapse
|
6
|
Huang J, Dai Z, Zheng Z, da Silvia PA, Kumagai L, Xiang Q, Chen J, Deng X. Bacteriomic Analyses of Asian Citrus Psyllid and Citrus Samples Infected With " Candidatus Liberibacter asiaticus" in Southern California and Huanglongbing Management Implications. Front Microbiol 2021; 12:683481. [PMID: 34276617 PMCID: PMC8283493 DOI: 10.3389/fmicb.2021.683481] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 05/17/2021] [Indexed: 11/13/2022] Open
Abstract
Citrus Huanglongbing (HLB; yellow shoot disease) is associated with an unculturable α-proteobacterium "Candidatus Liberibacter asiaticus" (CLas). HLB was found in southern California in 2012, and the current management strategy is based on suppression of the Asian citrus psyllid (Diaphorina citri) that transmits CLas and removal of confirmed CLas-positive trees. Little is known about Asian citrus psyllid-associated bacteria and citrus-associated bacteria in the HLB system. Such information is important in HLB management, particularly for accurate detection of CLas. Recent advancements in next-generation sequencing technology provide new opportunities to study HLB through genomic DNA sequence analyses (metagenomics). In this study, HLB-related bacteria in Asian citrus psyllid and citrus (represented by leaf midrib tissues) samples from southern California were analyzed. A metagenomic pipeline was developed to serve as a prototype for future bacteriomic research. This pipeline included steps of next-generation sequencing in Illumina platform, de novo assembly of Illumina reads, sequence classification using the Kaiju tool, acquisition of bacterial draft genome sequences, and taxonomic validation and diversity evaluation using average nucleotide identity. The identified bacteria in Asian citrus psyllids and citrus together included Bradyrhizobium, Buchnera, Burkholderia, "Candidatus Profftella armature," "Candidatus Carsonella ruddii," CLas, Mesorhizobium, Paraburkholderia, Pseudomonas, and Wolbachia. The whole genome of a CLas strain recently found in San Bernardino County was sequenced and classified into prophage typing group 1 (PTG-1), one of the five known CLas groups in California. Based on sequence similarity, Bradyrhizobium and Mesorhizobium were identified as possible source that could interfere with CLas detection using the 16S rRNA gene-based PCR commonly used for HLB diagnosis, particularly at low or zero CLas titer situation.
Collapse
Affiliation(s)
- Jiaquan Huang
- Laboratory of Citrus Huanglongbing Research, College of Plant Protection, South China Agricultural University, Guangzhou, China
- San Joaquin Valley Agricultural Sciences Center, Agricultural Research Service, United States Department of Agriculture, Parlier, CA, United States
| | - Zehan Dai
- Laboratory of Citrus Huanglongbing Research, College of Plant Protection, South China Agricultural University, Guangzhou, China
| | - Zheng Zheng
- Laboratory of Citrus Huanglongbing Research, College of Plant Protection, South China Agricultural University, Guangzhou, China
| | | | - Luci Kumagai
- Plant Pest Diagnostic Center, California Department of Food and Agriculture, Sacramento, CA, United States
| | - Qijun Xiang
- Jerry Dimitman Laboratory, Riverside, CA, United States
| | - Jianchi Chen
- San Joaquin Valley Agricultural Sciences Center, Agricultural Research Service, United States Department of Agriculture, Parlier, CA, United States
| | - Xiaoling Deng
- Laboratory of Citrus Huanglongbing Research, College of Plant Protection, South China Agricultural University, Guangzhou, China
| |
Collapse
|
7
|
Das AK, Chichghare SA, Sharma SK, Kumar JPT, Singh S, Baranwal VK, Kumar A, Nerkar S. Genetic diversity and population structure of 'Candidatus Liberibacter asiaticus' associated with citrus Huanglongbing in India based on the prophage types. World J Microbiol Biotechnol 2021; 37:95. [PMID: 33963452 DOI: 10.1007/s11274-021-03057-8] [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] [Received: 01/26/2021] [Accepted: 04/19/2021] [Indexed: 11/30/2022]
Abstract
Huanglongbing (HLB), also known as 'citrus greening', is an extremely destructive disease of citrus worldwide. HLB is associated with three species of the fastidious proteobacterium, Candidatus Liberibacter asiaticus (CaLas), Ca. L. africanus and Ca. L. americanus with CaLas being the most widely distributed around the world and the only species detected and described so far in India, one of the major global citrus fruit producers. Prophages are highly dynamic components in the bacterial genome and play an important role in intraspecies variations. Three types of prophages, Type 1, Type 2 and Type 3 have been identified and described in CaLas so far. In the present study, 441 CaLas isolates sampled across 18 Indian states were used for prophage typing. Based on detection of three prophage types by PCR, all the eight probable combinations of CaLas prophages were identified, including single Type 1 (26.5%), single Type 2 (18.8%), single Type 3 (1.4%), Type 1 + Type 2 (20.4%), Type 1 + Type 3 (12.5%), Type 2 + Type 3 (4.8%), Type 1 + Type 2 + Type 3 (11.3%) and None type (4.3%). Prophage types were confirmed by PCR amplicon sequencing and subsequent phylogenetic analysis. By discovery of all 3 prophages and based on genetic identity and genetic distance, CaLas populations from eighteen citrus growing states were separated into two major Prophage Typing Groups (PTGs): PTG1 and PTG2. The PTG1 comprised of CaLas from North-West India and PTG2 from rest of the country (North-East, Central and South India), and both major groups were further divided into two (PTG1-A, PTG1-B) and three (PTG2-A, PTG2-B and PTG2-C) subgroups respectively. The findings of CaLas population patterns provide evidence for independent origins of HLB-associated CaLas. CRISPR (clustered regularly interspaced short palindromic repeats) array was also detected in CaLas isolates. This is the first report evaluating the genetic variation of a large population of CaLas bacterium in India using the PCR markers from the prophage regions which would certainly assist the ongoing HLB management efforts in India.
Collapse
Affiliation(s)
- Ashis K Das
- Plant Pathology Lab, ICAR-Central Citrus Research Institute, Amravati Road, Nagpur, 440033, India.
| | - Subham A Chichghare
- Plant Pathology Lab, ICAR-Central Citrus Research Institute, Amravati Road, Nagpur, 440033, India
| | - Susheel K Sharma
- ICAR Research Complex for NEH Region, Manipur Centre, Imphal, 795004, India
| | - J Prasanth Tej Kumar
- Plant Pathology Lab, ICAR-Central Citrus Research Institute, Amravati Road, Nagpur, 440033, India
| | - Salvinder Singh
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, 785013, India
| | - Virendra K Baranwal
- Advanced Centre for Plant Virology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Ashok Kumar
- Plant Pathology Lab, ICAR-Central Citrus Research Institute, Amravati Road, Nagpur, 440033, India
| | - Sagar Nerkar
- Plant Pathology Lab, ICAR-Central Citrus Research Institute, Amravati Road, Nagpur, 440033, India
| |
Collapse
|
8
|
Huang CY, Araujo K, Sánchez JN, Kund G, Trumble J, Roper C, Godfrey KE, Jin H. A stable antimicrobial peptide with dual functions of treating and preventing citrus Huanglongbing. Proc Natl Acad Sci U S A 2021; 118:e2019628118. [PMID: 33526689 PMCID: PMC8017978 DOI: 10.1073/pnas.2019628118] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Citrus Huanglongbing (HLB), caused by a vector-transmitted phloem-limited bacterium Candidatus Liberibacter asiaticus (CLas), is the most devastating citrus disease worldwide. Currently, there are no effective strategies to prevent infection or to cure HLB-positive trees. Here, using comparative analysis between HLB-sensitive citrus cultivars and HLB-tolerant citrus hybrids and relatives, we identified a novel class of stable antimicrobial peptides (SAMPs). The SAMP from Microcitrusaustraliasica can rapidly kill Liberibacter crescens (Lcr), a culturable Liberibacter strain, and inhibit infections of CLas and CL. solanacearum in plants. In controlled greenhouse trials, SAMP not only effectively reduced CLas titer and disease symptoms in HLB-positive trees but also induced innate immunity to prevent and inhibit infections. Importantly, unlike antibiotics, SAMP is heat stable, making it better suited for field applications. Spray-applied SAMP was taken up by citrus leaves, stayed stable inside the plants for at least a week, and moved systemically through the vascular system where CLas is located. We further demonstrate that SAMP is most effective on α-proteobacteria and causes rapid cytosol leakage and cell lysis. The α-helix-2 domain of SAMP is sufficient to kill Lcr Future field trials will help determine the efficacy of SAMP in controlling HLB and the ideal mode of application.
Collapse
Affiliation(s)
- Chien-Yu Huang
- Department of Microbiology and Plant Pathology, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, CA 92521
| | - Karla Araujo
- Contained Research Facility, University of California, Davis, CA 95616
| | - Jonatan Niño Sánchez
- Department of Microbiology and Plant Pathology, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, CA 92521
| | - Gregory Kund
- Department of Entomology, University of California, Riverside, CA 92521
| | - John Trumble
- Department of Entomology, University of California, Riverside, CA 92521
| | - Caroline Roper
- Department of Microbiology and Plant Pathology, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, CA 92521
| | | | - Hailing Jin
- Department of Microbiology and Plant Pathology, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, CA 92521;
| |
Collapse
|
9
|
Brandenburg CA, Castro CA, Blacutt AA, Costa EA, Brinton KC, Corral DW, Drozd CL, Roper MC, Rolshausen PE, Maloney KN, Lockner JW. Synthesis of Deoxyradicinin, an Inhibitor of Xylella fastidiosa and Liberibacter crescens, a Culturable Surrogate for Candidatus Liberibacter asiaticus. JOURNAL OF NATURAL PRODUCTS 2020; 83:1810-1816. [PMID: 32510948 DOI: 10.1021/acs.jnatprod.9b01207] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Pierce's disease of grapevine and citrus huanglongbing are caused by the bacterial pathogens Xylella fastidiosa and Candidatus Liberibacter asiaticus (CLas), respectively. Both pathogens reside within the plant vascular system, occluding water and nutrient transport, leading to a decrease in productivity and fruit marketability and ultimately death of their hosts. Field observations of apparently healthy plants in disease-affected vineyards and groves led to the hypothesis that natural products from endophytes may inhibit these bacterial pathogens. Previously, we showed that the natural product radicinin from Cochliobolus sp. inhibits X. fastidiosa. Herein we describe a chemical synthesis of deoxyradicinin and establish it as an inhibitor of both X. fastidiosa and Liberibacter crescens, a culturable surrogate for CLas. The key to this three-step route is a zinc-mediated enolate C-acylation, which allows for direct introduction of the propenyl side chain without extraneous redox manipulations.
Collapse
Affiliation(s)
- Connor A Brandenburg
- Department of Chemistry, Point Loma Nazarene University, San Diego, California 92106, United States
| | - Claudia A Castro
- Department of Microbiology and Plant Pathology, University of California, Riverside, California 92521, United States
| | - Alex A Blacutt
- Department of Microbiology and Plant Pathology, University of California, Riverside, California 92521, United States
| | | | - Kyler C Brinton
- Department of Chemistry, Point Loma Nazarene University, San Diego, California 92106, United States
| | - Diana W Corral
- Department of Chemistry, Point Loma Nazarene University, San Diego, California 92106, United States
| | - Christopher L Drozd
- Department of Microbiology and Plant Pathology, University of California, Riverside, California 92521, United States
| | - M Caroline Roper
- Department of Microbiology and Plant Pathology, University of California, Riverside, California 92521, United States
| | - Philippe E Rolshausen
- Department of Botany and Plant Sciences, University of California, Riverside, California 92521, United States
| | - Katherine N Maloney
- Department of Chemistry, Point Loma Nazarene University, San Diego, California 92106, United States
| | - Jonathan W Lockner
- Department of Chemistry, Point Loma Nazarene University, San Diego, California 92106, United States
| |
Collapse
|
10
|
Thapa SP, De Francesco A, Trinh J, Gurung FB, Pang Z, Vidalakis G, Wang N, Ancona V, Ma W, Coaker G. Genome-wide analyses of Liberibacter species provides insights into evolution, phylogenetic relationships, and virulence factors. MOLECULAR PLANT PATHOLOGY 2020; 21:716-731. [PMID: 32108417 PMCID: PMC7170780 DOI: 10.1111/mpp.12925] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 01/27/2020] [Accepted: 01/28/2020] [Indexed: 05/04/2023]
Abstract
'Candidatus Liberibacter' species are insect-transmitted, phloem-limited α-Proteobacteria in the order of Rhizobiales. The citrus industry is facing significant challenges due to huanglongbing, associated with infection from 'Candidatus Liberibacter asiaticus' (Las). In order to gain greater insight into 'Ca. Liberibacter' biology and genetic diversity, we have performed genome sequencing and comparative analyses of diverse 'Ca. Liberibacter' species, including those that can infect citrus. Our phylogenetic analysis differentiates 'Ca. Liberibacter' species and Rhizobiales in separate clades and suggests stepwise evolution from a common ancestor splitting first into nonpathogenic Liberibacter crescens followed by diversification of pathogenic 'Ca. Liberibacter' species. Further analysis of Las genomes from different geographical locations revealed diversity among isolates from the United States. Our phylogenetic study also indicates multiple Las introduction events in California and spread of the pathogen from Florida to Texas. Texan Las isolates were closely related, while Florida and Asian isolates exhibited the most genetic variation. We have identified conserved Sec translocon (SEC)-dependent effectors likely involved in bacterial survival and virulence of Las and analysed their expression in their plant host (citrus) and insect vector (Diaphorina citri). Individual SEC-dependent effectors exhibited differential expression patterns between host and vector, indicating that Las uses its effector repertoire to differentially modulate diverse organisms. Collectively, this work provides insights into the evolution of 'Ca. Liberibacter' species, the introduction of Las in the United States and identifies promising Las targets for disease management.
Collapse
Affiliation(s)
- Shree P. Thapa
- Department of Plant PathologyUniversity of CaliforniaDavisCAUSA
| | - Agustina De Francesco
- Department of Microbiology and Plant PathologyUniversity of CaliforniaRiversideCAUSA
| | - Jessica Trinh
- Department of Microbiology and Plant PathologyUniversity of CaliforniaRiversideCAUSA
| | - Fatta B. Gurung
- Citrus CenterDepartment of Agriculture, Agribusiness and Environmental SciencesTexas A&M University‐KingsvilleWeslacoTXUSA
| | - Zhiqian Pang
- Citrus Research and Education CenterDepartment of Microbiology and Cell ScienceUniversity of FloridaLake AlfredFLUSA
| | - Georgios Vidalakis
- Department of Microbiology and Plant PathologyUniversity of CaliforniaRiversideCAUSA
| | - Nian Wang
- Citrus Research and Education CenterDepartment of Microbiology and Cell ScienceUniversity of FloridaLake AlfredFLUSA
| | - Veronica Ancona
- Citrus CenterDepartment of Agriculture, Agribusiness and Environmental SciencesTexas A&M University‐KingsvilleWeslacoTXUSA
| | - Wenbo Ma
- Department of Microbiology and Plant PathologyUniversity of CaliforniaRiversideCAUSA
| | - Gitta Coaker
- Department of Plant PathologyUniversity of CaliforniaDavisCAUSA
| |
Collapse
|
11
|
Blacutt A, Ginnan N, Dang T, Bodaghi S, Vidalakis G, Ruegger P, Peacock B, Viravathana P, Vieira FC, Drozd C, Jablonska B, Borneman J, McCollum G, Cordoza J, Meloch J, Berry V, Salazar LL, Maloney KN, Rolshausen PE, Roper MC. An In Vitro Pipeline for Screening and Selection of Citrus-Associated Microbiota with Potential Anti-" Candidatus Liberibacter asiaticus" Properties. Appl Environ Microbiol 2020; 86:e02883-19. [PMID: 32086307 PMCID: PMC7117939 DOI: 10.1128/aem.02883-19] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 02/11/2020] [Indexed: 12/13/2022] Open
Abstract
Huanglongbing (HLB) is a destructive citrus disease that is lethal to all commercial citrus plants, making it the most serious citrus disease and one of the most serious plant diseases. Because of the severity of HLB and the paucity of effective control measures, we structured this study to encompass the entirety of the citrus microbiome and the chemistries associated with that microbial community. We describe the spatial niche diversity of bacteria and fungi associated with citrus roots, stems, and leaves using traditional microbial culturing integrated with culture-independent methods. Using the culturable sector of the citrus microbiome, we created a microbial repository using a high-throughput bulk culturing and microbial identification pipeline. We integrated an in vitro agar diffusion inhibition bioassay into our culturing pipeline that queried the repository for antimicrobial activity against Liberibacter crescens, a culturable surrogate for the nonculturable "Candidatus Liberibacter asiaticus" bacterium associated with HLB. We identified microbes with robust inhibitory activity against L. crescens that include the fungi Cladosporium cladosporioides and Epicoccum nigrum and bacterial species of Pantoea, Bacillus, and Curtobacterium Purified bioactive natural products with anti-"Ca. Liberibacter asiaticus" activity were identified from the fungus C. cladosporioides Bioassay-guided fractionation of an organic extract of C. cladosporioides yielded the natural products cladosporols A, C, and D as the active agents against L. crescens This work serves as a foundation for unraveling the complex chemistries associated with the citrus microbiome to begin to understand the functional roles of members of the microbiome, with the long-term goal of developing anti-"Ca Liberibacter asiaticus" bioinoculants that thrive in the citrus holosystem.IMPORTANCE Globally, citrus is threatened by huanglongbing (HLB), and the lack of effective control measures is a major concern of farmers, markets, and consumers. There is compelling evidence that plant health is a function of the activities of the plant's associated microbiome. Using Liberibacter crescens, a culturable surrogate for the unculturable HLB-associated bacterium "Candidatus Liberibacter asiaticus," we tested the hypothesis that members of the citrus microbiome produce potential anti-"Ca Liberibacter asiaticus" natural products with potential anti-"Ca Liberibacter asiaticus" activity. A subset of isolates obtained from the microbiome inhibited L. crescens growth in an agar diffusion inhibition assay. Further fractionation experiments linked the inhibitory activity of the fungus Cladosporium cladosporioides to the fungus-produced natural products cladosporols A, C, and D, demonstrating dose-dependent antagonism to L. crescens.
Collapse
Affiliation(s)
- Alex Blacutt
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, California, USA
| | - Nichole Ginnan
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, California, USA
| | - Tyler Dang
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, California, USA
| | - Sohrab Bodaghi
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, California, USA
| | - Georgios Vidalakis
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, California, USA
| | - Paul Ruegger
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, California, USA
| | - Beth Peacock
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, California, USA
| | - Polrit Viravathana
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, California, USA
| | - Flavia Campos Vieira
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, California, USA
| | - Christopher Drozd
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, California, USA
| | - Barbara Jablonska
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, California, USA
| | - James Borneman
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, California, USA
| | - Greg McCollum
- U.S. Department of Agriculture, Agricultural Research Service, Fort Pierce, Florida, USA
| | | | | | - Victoria Berry
- Point Loma Nazarene University, San Diego, California, USA
| | | | | | - Philippe E Rolshausen
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, California, USA
| | - M Caroline Roper
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, California, USA
| |
Collapse
|
12
|
Functional and Comparative Genomic Analysis of Integrated Prophage-Like Sequences in " Candidatus Liberibacter asiaticus". mSphere 2019; 4:4/6/e00409-19. [PMID: 31722990 PMCID: PMC6854039 DOI: 10.1128/msphere.00409-19] [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] [Indexed: 11/20/2022] Open
Abstract
Huanglongbing (HLB) disease is threatening citrus production worldwide. The causative agent is “Candidatus Liberibacter asiaticus.” Prior work using mapping-based approaches identified prophage-like sequences in some “Ca. Liberibacter asiaticus” genomes but not all. Here, we utilized a de novo approach that expands the number of prophage-like elements found in “Ca. Liberibacter asiaticus” from 16 to 33 and identified at least one prophage-like sequence in all “Ca. Liberibacter asiaticus” strains. Furthermore, we identified a prophage-like sequence type that is a remnant of an integrated prophage—expanding the number of prophage types in “Ca. Liberibacter asiaticus” from 3 to 4. Overall, the findings will help researchers investigate the role of prophage in the ecology, evolution, and pathogenicity of “Ca. Liberibacter asiaticus.” Huanglongbing disease (HLB; yellow shoot disease) is a severe worldwide infectious disease for citrus family plants. The pathogen “Candidatus Liberibacter asiaticus” is an alphaproteobacterium of the Rhizobiaceae family that has been identified as the causative agent of HLB. The virulence of “Ca. Liberibacter asiaticus” has been attributed, in part, to prophage-carried genes. Prophage and prophage-like elements have been identified in 12 of the 15 available “Ca. Liberibacter asiaticus” genomes and are classified into three prophage types. Here, we reexamined all 15 “Ca. Liberibacter asiaticus” genomes using a de novo prediction approach and expanded the number of prophage-like elements from 16 to 33. Further, we found that all of the “Ca. Liberibacter asiaticus” genomes contained at least one prophage-like sequence. Comparative analysis revealed a prevalent, albeit previously unknown, prophage-like sequence type that is a remnant of an integrated prophage. Notably, this remnant prophage is found in the Ishi-1 “Ca. Liberibacter asiaticus” strain that had previously been reported as lacking prophages. Our findings provide both a resource for data and new insights into the evolutionary relationship between phage and “Ca. Liberibacter asiaticus” pathogenicity. IMPORTANCE Huanglongbing (HLB) disease is threatening citrus production worldwide. The causative agent is “Candidatus Liberibacter asiaticus.” Prior work using mapping-based approaches identified prophage-like sequences in some “Ca. Liberibacter asiaticus” genomes but not all. Here, we utilized a de novo approach that expands the number of prophage-like elements found in “Ca. Liberibacter asiaticus” from 16 to 33 and identified at least one prophage-like sequence in all “Ca. Liberibacter asiaticus” strains. Furthermore, we identified a prophage-like sequence type that is a remnant of an integrated prophage—expanding the number of prophage types in “Ca. Liberibacter asiaticus” from 3 to 4. Overall, the findings will help researchers investigate the role of prophage in the ecology, evolution, and pathogenicity of “Ca. Liberibacter asiaticus.”
Collapse
|
13
|
Dominguez-Mirazo M, Jin R, Weitz JS. Functional and Comparative Genomic Analysis of Integrated Prophage-Like Sequences in " Candidatus Liberibacter asiaticus". mSphere 2019; 4. [PMID: 31722990 DOI: 10.1101/661967] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/21/2023] Open
Abstract
Huanglongbing disease (HLB; yellow shoot disease) is a severe worldwide infectious disease for citrus family plants. The pathogen "Candidatus Liberibacter asiaticus" is an alphaproteobacterium of the Rhizobiaceae family that has been identified as the causative agent of HLB. The virulence of "Ca. Liberibacter asiaticus" has been attributed, in part, to prophage-carried genes. Prophage and prophage-like elements have been identified in 12 of the 15 available "Ca. Liberibacter asiaticus" genomes and are classified into three prophage types. Here, we reexamined all 15 "Ca. Liberibacter asiaticus" genomes using a de novo prediction approach and expanded the number of prophage-like elements from 16 to 33. Further, we found that all of the "Ca. Liberibacter asiaticus" genomes contained at least one prophage-like sequence. Comparative analysis revealed a prevalent, albeit previously unknown, prophage-like sequence type that is a remnant of an integrated prophage. Notably, this remnant prophage is found in the Ishi-1 "Ca. Liberibacter asiaticus" strain that had previously been reported as lacking prophages. Our findings provide both a resource for data and new insights into the evolutionary relationship between phage and "Ca. Liberibacter asiaticus" pathogenicity.IMPORTANCE Huanglongbing (HLB) disease is threatening citrus production worldwide. The causative agent is "Candidatus Liberibacter asiaticus." Prior work using mapping-based approaches identified prophage-like sequences in some "Ca. Liberibacter asiaticus" genomes but not all. Here, we utilized a de novo approach that expands the number of prophage-like elements found in "Ca. Liberibacter asiaticus" from 16 to 33 and identified at least one prophage-like sequence in all "Ca. Liberibacter asiaticus" strains. Furthermore, we identified a prophage-like sequence type that is a remnant of an integrated prophage-expanding the number of prophage types in "Ca. Liberibacter asiaticus" from 3 to 4. Overall, the findings will help researchers investigate the role of prophage in the ecology, evolution, and pathogenicity of "Ca. Liberibacter asiaticus."
Collapse
Affiliation(s)
- Marian Dominguez-Mirazo
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
- Interdisciplinary Graduate Program in Quantitative Biosciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Rong Jin
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Joshua S Weitz
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia, USA
| |
Collapse
|
14
|
Lessons from One Fastidious Bacterium to Another: What Can We Learn about Liberibacter Species from Xylella fastidiosa. INSECTS 2019; 10:insects10090300. [PMID: 31527458 PMCID: PMC6780969 DOI: 10.3390/insects10090300] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 09/11/2019] [Accepted: 09/12/2019] [Indexed: 02/06/2023]
Abstract
Huanglongbing is causing economic devastation to the citrus industry in Florida, and threatens the industry everywhere the bacterial pathogens in the Candidatus Liberibacter genus and their insect vectors are found. Bacteria in the genus cannot be cultured and no durable strategy is available for growers to control plant infection or pathogen transmission. However, scientists and grape growers were once in a comparable situation after the emergence of Pierce’s disease, which is caused by Xylella fastidiosa and spread by its hemipteran insect vector. Proactive quarantine and vector control measures coupled with interdisciplinary data-driven science established control of this devastating disease and pushed the frontiers of knowledge in the plant pathology and vector biology fields. Our review highlights the successful strategies used to understand and control X. fastidiosa and their potential applicability to the liberibacters associated with citrus greening, with a focus on the interactions between bacterial pathogen and insect vector. By placing the study of Candidatus Liberibacter spp. within the current and historical context of another fastidious emergent plant pathogen, future basic and applied research to develop control strategies can be prioritized.
Collapse
|
15
|
Merfa MV, Pérez-López E, Naranjo E, Jain M, Gabriel DW, De La Fuente L. Progress and Obstacles in Culturing ' Candidatus Liberibacter asiaticus', the Bacterium Associated with Huanglongbing. PHYTOPATHOLOGY 2019; 109:1092-1101. [PMID: 30998129 DOI: 10.1094/phyto-02-19-0051-rvw] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In recent decades, 'Candidatus Liberibacter spp.' have emerged as a versatile group of psyllid-vectored plant pathogens and endophytes capable of infecting a wide range of economically important plant hosts. The most notable example is 'Candidatus Liberibacter asiaticus' (CLas) associated with Huanglongbing (HLB) in several major citrus-producing areas of the world. CLas is a phloem-limited α-proteobacterium that is primarily vectored and transmitted among citrus species by the Asian citrus psyllid (ACP) Diaphorina citri. HLB was first detected in North America in Florida (USA) in 2005, following introduction of the ACP to the State in 1998. HLB rapidly spread to all citrus growing regions of Florida within three years, with severe economic consequences to growers and considerable expense to taxpayers of the state and nation. Inability to establish CLas in culture (except transiently) remains a significant scientific challenge toward effective HLB management. Lack of axenic cultures has restricted functional genomic analyses, transfer of CLas to either insect or plant hosts for fulfillment of Koch's postulates, characterization of host-pathogen interactions and effective screening of antibacterial compounds. In the last decade, substantial progress has been made toward CLas culturing: (i) three reports of transient CLas cultures were published, (ii) a new species of Liberibacter was identified and axenically cultured from diseased mountain papaya (Liberibacter crescens strain BT-1), (iii) psyllid hemolymph and citrus phloem sap were biochemically characterized, (iv) CLas phages were identified and lytic genes possibly affecting CLas growth were described, and (v) genomic sequences of 15 CLas strains were made available. In addition, development of L. crescens as a surrogate host for functional analyses of CLas genes, has provided valuable insights into CLas pathogenesis and its physiological dependence on the host cell. In this review we summarize the conclusions from these important studies.
Collapse
Affiliation(s)
- Marcus V Merfa
- 1 Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849, U.S.A
| | - Edel Pérez-López
- 1 Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849, U.S.A
| | - Eber Naranjo
- 1 Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849, U.S.A
| | - Mukesh Jain
- 2 Department of Plant Pathology, University of Florida, Gainesville, FL 32611, U.S.A
| | - Dean W Gabriel
- 2 Department of Plant Pathology, University of Florida, Gainesville, FL 32611, U.S.A
| | - Leonardo De La Fuente
- 1 Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849, U.S.A
| |
Collapse
|
16
|
Dai Z, Wu F, Zheng Z, Yokomi R, Kumagai L, Cai W, Rascoe J, Polek M, Chen J, Deng X. Prophage Diversity of 'Candidatus Liberibacter asiaticus' Strains in California. PHYTOPATHOLOGY 2019; 109:551-559. [PMID: 30303769 DOI: 10.1094/phyto-06-18-0185-r] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Huanglongbing (HLB) is a highly destructive citrus disease and is associated with a nonculturable bacterium, 'Candidatus Liberibacter asiaticus'. 'Ca. L. asiaticus' in the United States was first found in Florida in 2005 and is now endemic there. In California, 'Ca. L. asiaticus' was first detected in Hacienda Heights in Los Angeles County in 2012 and has now been detected in multiple urban locations in southern California. Knowledge of 'Ca. L. asiaticus' strain diversity in California is important for HLB management. In this study, genomic diversity among 10 'Ca. L. asiaticus' strains from six California locations were analyzed using a next-generation sequencing (NGS) (Illumina MiSeq and HiSeq) approach. Draft genome sequences of 'Ca. L. asiaticus' strains were assembled. Sequences of the 16S ribosomal RNA gene and nrdB confirmed 'Ca. L. asiaticus' identity. Prophages were detected in all 'Ca. L. asiaticus' strains. The California 'Ca. L. asiaticus' strains formed four prophage typing groups (PTGs): PTG1, with type 1 prophage only (strains from Anaheim, San Gabriel, and Riverside); PTG2, with type 2 prophage only (strains from Hacienda Heights); PTG1-3, with both type 1 and 3 prophages (a strain from Cerritos); and PTG1-2, with both type 1 and type 2 prophages (a strain from La Habra). Analyses of the terL sequence showed that all California 'Ca. L. asiaticus' strains were not introduced from Florida but likely from locations in Asia. Miniature inverted-repeat transposable elements were found in all 'Ca. L. asiaticus' strains, yet, a jumping-out event was detected in the 'Ca. L. asiaticus' strain from Cerritos. Altogether, this study demonstrated that the NGS approach focusing on prophage variation was sensitive and effective in revealing diversity of 'Ca. L. asiaticus' strains in California.
Collapse
Affiliation(s)
- Z Dai
- 1 Department of Plant Pathology, South China Agricultural University, Guangzhou, Guangdong, China
| | - F Wu
- 1 Department of Plant Pathology, South China Agricultural University, Guangzhou, Guangdong, China
| | - Z Zheng
- 1 Department of Plant Pathology, South China Agricultural University, Guangzhou, Guangdong, China
| | - R Yokomi
- 2 United States Department of Agriculture (USDA)-Agricultural Research Service, San Joaquín Valley Agricultural Sciences Center, Parlier, CA, U.S.A
| | - L Kumagai
- 3 Plant Pest Diagnostic Center, California Department of Food and Agriculture, Sacramento, U.S.A
| | - W Cai
- 4 USDA Animal and Plant Health Inspection Service-Plant Protection and Quarantine, Beltsville, MD, U.S.A.; and
| | - J Rascoe
- 3 Plant Pest Diagnostic Center, California Department of Food and Agriculture, Sacramento, U.S.A
| | - M Polek
- 5 National Clonal Germplasm Repository for Citrus and Dates, Riverside, CA, U.S.A
| | - J Chen
- 2 United States Department of Agriculture (USDA)-Agricultural Research Service, San Joaquín Valley Agricultural Sciences Center, Parlier, CA, U.S.A
| | - X Deng
- 1 Department of Plant Pathology, South China Agricultural University, Guangzhou, Guangdong, China
| |
Collapse
|
17
|
Zheng Z, Chen J, Deng X. Historical Perspectives, Management, and Current Research of Citrus HLB in Guangdong Province of China, Where the Disease has been Endemic for Over a Hundred Years. PHYTOPATHOLOGY 2018; 108:1224-1236. [PMID: 30156499 DOI: 10.1094/phyto-07-18-0255-ia] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Citrus huanglongbing (HLB) is a highly destructive disease currently threatening citrus production worldwide. In China, the disease is exclusively associated with 'Candidatus Liberibacter asiaticus', a nonculturable proteobacterium. HLB was observed in Guangdong of China over a hundred years ago. Researchers and citrus growers have been battling with the disease through vigorous research and have exercised various control practices. Much of the early work was not well known outside China. This review is intended to fill in gaps of historical information by reviewing selected literature records. Along the way, the HLB system within southern China was evaluated. Emphases were on comparison of symptomatology, evolution of etiology, control practices, and impacts of using next-generation sequencing technology for 'Ca. L. asiaticus' research and detection.
Collapse
Affiliation(s)
- Zheng Zheng
- First and third authors: Laboratory of Citrus Huanglongbing Research, Department of Plant Pathology, South China Agricultural University, Guangzhou, China; and second author: San Joaquin Valley Agricultural Sciences Center, United States Department of Agriculture-Agricultural Research Service, Parlier, CA
| | - Jianchi Chen
- First and third authors: Laboratory of Citrus Huanglongbing Research, Department of Plant Pathology, South China Agricultural University, Guangzhou, China; and second author: San Joaquin Valley Agricultural Sciences Center, United States Department of Agriculture-Agricultural Research Service, Parlier, CA
| | - Xiaoling Deng
- First and third authors: Laboratory of Citrus Huanglongbing Research, Department of Plant Pathology, South China Agricultural University, Guangzhou, China; and second author: San Joaquin Valley Agricultural Sciences Center, United States Department of Agriculture-Agricultural Research Service, Parlier, CA
| |
Collapse
|
18
|
Sudhan D, Puttamuk T, Vuttipongchaikij S, Chuawong P. Cloning, overexpression, and purification of a gene of unknown function of prophage loci from ‘ Candidatus Liberibacter asiaticus,’ the destructive bacterial pathogen of huanglongbing disease in citrus plants. Protein Expr Purif 2018; 150:72-80. [DOI: 10.1016/j.pep.2018.05.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 05/19/2018] [Accepted: 05/19/2018] [Indexed: 10/16/2022]
|
19
|
Zheng Z, Bao M, Wu F, Van Horn C, Chen J, Deng X. A Type 3 Prophage of 'Candidatus Liberibacter asiaticus' Carrying a Restriction-Modification System. PHYTOPATHOLOGY 2018; 108:454-461. [PMID: 29192841 DOI: 10.1094/phyto-08-17-0282-r] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Prophages, the lysogenic form of bacterial phages, are important genetic entities of 'Candidatus Liberibacter asiaticus' (CLas), a nonculturable α-proteobacterium associated with citrus Huanglongbing. Two CLas prophages have been described, SC1 (NC_019549.1, Type 1) and SC2 (NC_019550.1, Type 2), which involve the lytic cycle and the lysogenic cycle, respectively. To explore the prophage repertoire, 523 CLas DNA samples extracted from leaf petioles of CLas-infected citrus were collected from southern China and surveyed for Type 1 and Type 2 prophages by specific PCR. Eighteen samples were found lacking both prophages. One sample, JXGC, sequenced using Illumina HiSeq, generated >100 million short sequence reads (150 bp per read). Read mapping to known prophage sequences showed a sequence coverage of 46% to SC1 and 50% to SC2. BLAST search using SC1 and SC2 as queries identified three contigs from the JXGC de novo assembly that form a circular P-JXGC-3 (31,449 bp), designated as a new Type 3 prophage. Chromosomal integration of P-JXGC-3 was detected to occur within a helicase gene, resulting in a duplication of this gene. P-JXGC-3 had 36 open reading frames (ORFs), 10 of which were not found in Type 1 or Type 2 prophages, including four genes that encoded a restriction-modification (R-M) system (hsdR, hsdS, hsdM1, and hsdM2). Typed by prophage-specific PCR, the CLas strains in southern China contained all combinations of the three prophage types with the exception of a Type 2-Type 3 combination, suggesting active ongoing prophage-phage interactions. Based on gene annotation, P-JXGC-3 is not capable of reproduction via the lytic cycle. The R-M system was speculated to play a role against Type 1 prophage-phage invasion.
Collapse
Affiliation(s)
- Zheng Zheng
- First, second, third, and sixth author: Department of Plant Pathology, South China Agricultural University, Guangzhou, Guangdong, China; and first, fourth, and fifth authors: San Joaquín Valley Agricultural Sciences Center, Parlier, CA
| | - Minli Bao
- First, second, third, and sixth author: Department of Plant Pathology, South China Agricultural University, Guangzhou, Guangdong, China; and first, fourth, and fifth authors: San Joaquín Valley Agricultural Sciences Center, Parlier, CA
| | - Fengnian Wu
- First, second, third, and sixth author: Department of Plant Pathology, South China Agricultural University, Guangzhou, Guangdong, China; and first, fourth, and fifth authors: San Joaquín Valley Agricultural Sciences Center, Parlier, CA
| | - Christopher Van Horn
- First, second, third, and sixth author: Department of Plant Pathology, South China Agricultural University, Guangzhou, Guangdong, China; and first, fourth, and fifth authors: San Joaquín Valley Agricultural Sciences Center, Parlier, CA
| | - Jianchi Chen
- First, second, third, and sixth author: Department of Plant Pathology, South China Agricultural University, Guangzhou, Guangdong, China; and first, fourth, and fifth authors: San Joaquín Valley Agricultural Sciences Center, Parlier, CA
| | - Xiaoling Deng
- First, second, third, and sixth author: Department of Plant Pathology, South China Agricultural University, Guangzhou, Guangdong, China; and first, fourth, and fifth authors: San Joaquín Valley Agricultural Sciences Center, Parlier, CA
| |
Collapse
|