Linking metabolic phenotypes to pathogenic traits among "Candidatus Liberibacter asiaticus" and its hosts

Study on the citrus greening disease: Current challenges and novel therapies

The unprecedented worldwide spread of the Citrus greening disorder, called Huanglongbing (HLB), has urged researchers for rapid interventions. HLB poses a considerable threat to global citriculture owing to its devastating impact on citrus species. This disease is caused by Candidatus Liberibacter species (CLs), primarily transferred through psyllid insects, such as Trioza erytreae and Diaphorina citri. It results in phloem malfunction, root decline, and altered plant source-sink relationships, leading to a deficient plant with minimal yield before it dies. Thus, many various techniques have been employed to eliminate HLB and control vector populations through the application of insecticides and antimicrobials. The latter have evidenced short-term efficiency. While nucleic acid-based analyses and symptom-based identification of the disease have been used for detection, they suffer from limitations such as false negatives, complex sample preparation, and high costs. To address these challenges, secreted protein-based biomarkers offer a promising solution for accurate, rapid, and cost-effective disease detection. This paper presents an overview of HLB symptoms in citrus plants, including leaf and fruit symptoms, as well as whole tree symptoms. The differentiation between HLB symptoms and those of nutrient deficiencies is discussed, emphasizing the importance of precise identification for effective disease management. The elusive nature of CLs and the challenges in culturing them in axenic cultures have hindered the understanding of their pathogenic mechanisms. However, genome sequencing has provided insights into CLs strains' metabolic traits and potential virulence factors. Efforts to identify potential host target genes for resistance are discussed, and a high-throughput antimicrobial testing method using Citrus hairy roots is introduced as a promising tool for rapid assessment of potential treatments. This review summarizes current challenges and novel therapies for HLB disease. It highlights the urgency of developing accurate and efficient detection methods and identifying the complex relations between CLs and their host plants. Transgenic citrus in conjunction with secreted protein-based biomarkers and innovative testing methodologies could revolutionize HLB management strategies toward achieving a sustainable citrus cultivation. It offers more reliable and practical solutions to combat this devastating disease and safeguard the global citriculture industry.

The genome-scale metabolic model for the purple non-sulfur bacterium Rhodopseudomonas palustris Bis A53 accurately predicts phenotypes under chemoheterotrophic, chemoautotrophic, photoheterotrophic, and photoautotrophic growth conditions

The purple non-sulfur bacterium Rhodopseudomonas palustris is recognized as a critical microorganism in the nitrogen and carbon cycle and one of the most common members in wastewater treatment communities. This bacterium is metabolically extremely versatile. It is capable of heterotrophic growth under aerobic and anaerobic conditions, but also able to grow photoautotrophically as well as mixotrophically. Therefore R. palustris can adapt to multiple environments and establish commensal relationships with other organisms, expressing various enzymes supporting degradation of amino acids, carbohydrates, nucleotides, and complex polymers. Moreover, R. palustris can degrade a wide range of pollutants under anaerobic conditions, e.g., aromatic compounds such as benzoate and caffeate, enabling it to thrive in chemically contaminated environments. However, many metabolic mechanisms employed by R. palustris to breakdown and assimilate different carbon and nitrogen sources under chemoheterotrophic or photoheterotrophic conditions remain unknown. Systems biology approaches, such as metabolic modeling, have been employed extensively to unravel complex mechanisms of metabolism. Previously, metabolic models have been reconstructed to study selected capabilities of R. palustris under limited experimental conditions. Here, we developed a comprehensive metabolic model (M-model) for R. palustris Bis A53 (iDT1294) consisting of 2,721 reactions, 2,123 metabolites, and comprising 1,294 genes. We validated the model using high-throughput phenotypic, physiological, and kinetic data, testing over 350 growth conditions. iDT1294 achieved a prediction accuracy of 90% for growth with various carbon and nitrogen sources and close to 80% for assimilation of aromatic compounds. Moreover, the M-model accurately predicts dynamic changes of growth and substrate consumption rates over time under nine chemoheterotrophic conditions and demonstrated high precision in predicting metabolic changes between photoheterotrophic and photoautotrophic conditions. This comprehensive M-model will help to elucidate metabolic processes associated with the assimilation of multiple carbon and nitrogen sources, anoxygenic photosynthesis, aromatic compound degradation, as well as production of molecular hydrogen and polyhydroxybutyrate.

Pathogenicity and Transcriptomic Analyses of Two "Candidatus Liberibacter asiaticus" Strains Harboring Different Types of Phages

"Candidatus Liberibacter asiaticus" is one of the putative causal agents of citrus Huanglongbing (HLB), a highly destructive disease threatening the global citrus industry. Several types of phages had been identified in "Ca. Liberibacter asiaticus" strains and found to affect the biology of "Ca. Liberibacter asiaticus." However, little is known about the influence of phages in "Ca. Liberibacter asiaticus" pathogenicity. In this study, two "Ca. Liberibacter asiaticus" strains, PYN and PGD, harboring different types of phages were collected and used for pathogenicity analysis in periwinkle (Catharanthus roseus). Strain PYN carries a type 1 phage (P-YN-1), and PGD harbors a type 2 phage (P-GD-2). Compared to strain PYN, strain PGD exhibited a faster reproduction rate and higher virulence in periwinkle: leaf symptoms appeared earlier, and there was a stronger inhibition in the growth of new flush. Estimation of phage copy numbers by type-specific PCR indicated that there are multiple copies of phage P-YN-1 in strain PYN, while strain PGD carries only a single copy of phage P-GD-2. Genome-wide gene expression profiling revealed the lytic activity of P-YN-1 phage, as evidenced by the unique expression of genes involved in lytic cycle, which may limit the propagation of strain PYN and lead to a delayed infection in periwinkle. However, the activation of genes involved in lysogenic conversion of phage P-GD-1 indicated it could reside within the "Ca. Liberibacter asiaticus" genome as a prophage form in strain PGD. Comparative transcriptome analysis showed that the significant differences in expression of virulence factor genes, including genes associated with pathogenic effectors, transcriptional factors, the Znu transport system, and the heme biosynthesis pathway, could be another major determinant of virulence variation between two "Ca. Liberibacter asiaticus" strains. This study expanded our knowledge of "Ca. Liberibacter asiaticus" pathogenicity and provided new insights into the differences in pathogenicity between "Ca. Liberibacter asiaticus" strains. IMPORTANCE Citrus Huanglongbing (HLB), also called citrus greening disease, is a highly destructive disease threatening citrus production worldwide. "Candidatus Liberibacter asiaticus" is one of the most common putative causal agents of HLB. Phages of "Ca. Liberibacter asiaticus" have recently been identified and found to affect "Ca. Liberibacter asiaticus" biology. Here, we found that "Ca. Liberibacter asiaticus" strains harboring different types of phages (type 1 or type 2) showed different levels of pathogenicity and multiplication patterns in the periwinkle plant (Catharanthus roseus). Transcriptome analysis revealed the possible lytic activity of type 1 phage in a "Ca. Liberibacter asiaticus" strain, which could limit the propagation of "Ca. Liberibacter asiaticus" and lead to the delayed infection in periwinkle. The heterogeneity in the transcriptome profiles, particularly the significant differences in expression of virulence factors genes, could be another major determinant of difference in virulence observed between the two "Ca. Liberibacter asiaticus" strains. These findings improved our understanding of "Ca. Liberibacter asiaticus"-phage interaction and provided insight into "Ca. Liberibacter asiaticus" pathogenicity.

Microalgae-bacteria consortium for wastewater treatment and biomass production

The diversity of microalgae and bacteria allows them to form a complementary consortium for efficient wastewater treatment and nutrient recovery. This review highlights the potential of wastewater-derived microalgal biomass as a renewable feedstock for producing animal feed, biofertilisers, biofuel, and many valuable biochemicals. Data corroborated from this review shows that microalgae and bacteria can thrive in many environments. Microalgae are especially effective at utilising nutrients from the water as they grow. This review also consolidates the current understanding of microalgae characteristics and their interactions with bacteria in a consortium system. Recent studies on the performance of only microalgae and microalgae-bacteria wastewater treatment are compared and discussed to establish a research roadmap for practical implementation of the consortium systems for various wastewaters (domestic, industrial, agro-industrial, and landfill leachate wastewater). In comparison to the pure microalgae system, the consortium system has a higher removal efficiency of up to 15% and shorter treatment time. Additionally, this review addresses a variety of possibilities for biomass application after wastewater treatment.

Identification and Characterization of Potato Zebra Chip Resistance Among Wild Solanum Species

Potato zebra chip (ZC) disease, associated with the uncultured phloem-limited bacterium, Candidatus Liberibacter solanacearum (CLso), is transmitted by the potato psyllid Bactericera cockerelli. Potato ZC disease poses a significant threat to potato production worldwide. Current management practices mainly rely on the control of the psyllid to limit the spread of CLso. The present study investigated new sources of ZC resistance among wild Solanum species. A taxonomically diverse collection of tuber-bearing Solanum species was screened; one ZC-resistant accession and three ZC-tolerant accessions were identified among the 52 screened accessions. Further characterization of the resistant accession showed that the resistance was primarily associated with antibiosis effects due to differences in leaf trichome density and morphology of the wild accession, which could limit the psyllid feeding and oviposition. This germplasm offers a good resource for further understanding ZC and psyllid resistance mechanisms, contributing to potato breeding efforts to develop ZC resistance cultivars. Alternatively, it could be used as a potential trap crop to manage psyllid and control ZC disease.

A reverse-ecology framework to uncover the potential metabolic interplay among 'Candidatus Liberibacter' species, Citrus hosts and psyllid vector

'Candidatus Liberibacter' species have developed a dependency on essential nutrients and metabolites from the host cell, as a result of substantial genome reduction. Still, it is difficult to state which nutrients they acquire and whether or not they are metabolically reliant. We used a reverse-ecology model to investigate the potential metabolic interactions of 'Ca Liberibacter' species, Citrus, and the psyllid Diaphorina citri in the huanglongbing disease pyramid. Our findings show that hosts (citrus and psyllid) tend to support the nutritional needs of 'Ca. Liberibacter' species, implying that the pathogen's metabolism has become tightly linked to hosts, which may reflect in the parasite lifestyle of this important genus.

A synthetic 'essentialome' for axenic culturing of 'Candidatus Liberibacter asiaticus'

OBJECTIVE

'Candidatus Liberibacter asiaticus' (CLas) is associated with the devastating citrus 'greening' disease. All attempts to achieve axenic growth and complete Koch's postulates with CLas have failed to date, at best yielding complex cocultures with very low CLas titers detectable only by PCR. Reductive genome evolution has rendered all pathogenic 'Ca. Liberibacter' spp. deficient in multiple key biosynthetic, metabolic and structural pathways that are highly unlikely to be rescued in vitro by media supplementation alone. By contrast, Liberibacter crescens (Lcr) is axenically cultured and its genome is both syntenic and highly similar to CLas. Our objective is to achieve replicative axenic growth of CLas via addition of missing culturability-related Lcr genes.

RESULTS

Bioinformatic analyses identified 405 unique ORFs in Lcr but missing (or truncated) in all 24 sequenced CLas strains. Site-directed mutagenesis confirmed and extended published EZ-Tn5 mutagenesis data, allowing elimination of 310 of these 405 genes as nonessential, leaving 95 experimentally validated Lcr genes as essential for CLas growth in axenic culture. Experimental conditions for conjugation of large GFP-expressing plasmids from Escherichia coli to Lcr were successfully established for the first time, providing a practical method for transfer of large groups of 'essential' Lcr genes to CLas.

Flux balance analysis of the ammonia-oxidizing bacterium Nitrosomonas europaea ATCC19718 unravels specific metabolic activities while degrading toxic compounds

The ammonia-oxidizing bacterium Nitrosomonas europaea has been widely recognized as an important player in the nitrogen cycle as well as one of the most abundant members in microbial communities for the treatment of industrial or sewage wastewater. Its natural metabolic versatility and extraordinary ability to degrade environmental pollutants (e.g., aromatic hydrocarbons such as benzene and toluene) enable it to thrive under various harsh environmental conditions. Constraint-based metabolic models constructed from genome sequences enable quantitative insight into the central and specialized metabolism within a target organism. These genome-scale models have been utilized to understand, optimize, and design new strategies for improved bioprocesses. Reduced modeling approaches have been used to elucidate Nitrosomonas europaea metabolism at a pathway level. However, genome-scale knowledge about the simultaneous oxidation of ammonia and pollutant metabolism of N. europaea remains limited. Here, we describe the reconstruction, manual curation, and validation of the genome-scale metabolic model for N. europaea, iGC535. This reconstruction is the most accurate metabolic model for a nitrifying organism to date, reaching an average prediction accuracy of over 90% under several growth conditions. The manually curated model can predict phenotypes under chemolithotrophic and chemolithoorganotrophic conditions while oxidating methane and wastewater pollutants. Calculated flux distributions under different trophic conditions show that several key pathways are affected by the type of carbon source available, including central carbon metabolism and energy production.

Nitrosomonas europaea catalyzes the first step of the nitrification process (ammonia to nitrite). It has been recognized as one of the most important members of microbial communities of wastewater treatment processes. Genome-scale models are powerful tools in process optimization since they can predict the organism’s behavior under different growth conditions. The final genome-scale model of N. europaea ATCC19718, iGC535, can predict growth and oxygen uptake rates with 90.52% accuracy under chemolithotrophic and chemolitoorganotrophic conditions. Moreover, iGC535 can predict the simultaneous oxidation of ammonia and wastewater pollutants, such as benzene, toluene, phenol and, chlorobenzene. iGC535 represents the most comprehensive knowledge-base for a nitrifying organism available to date. The genome-scale model reconstructed in this work brings us closer to understanding N. europaea’s role in a community with other nitrifying bacteria.

Cultural Management of Huanglongbing: Current Status and Ongoing Research

Huanglongbing (HLB), formerly known as greening, is a bacterial disease restricted to some Asian and African regions until two decades ago. Nowadays, associated bacteria and their vectors have spread to almost all citrus-producing regions, and it is currently considered the most devastating citrus disease. HLB management can be approached in terms of prevention, limiting or avoiding pathogen and associated vectors to reach an area, or in terms of control, trying to reduce the impact of the disease by adopting different cultural strategies depending on infestation/infection levels. In both cases, control of psyllid populations is currently the best way to stop HLB spread. Best cultural actions (CHMAs, TPS system) to attain this goal and, thus, able to limit HLB spread, and ongoing research in this regard is summarized in this review.

Growth of 'Candidatus Liberibacter asiaticus' in Commercial Grapefruit Juice-Based Media Formulations Reveals Common Cell Density-Dependent Transient Behaviors

The phloem-restricted, insect-transmitted bacterium 'Candidatus Liberibacter asiaticus' (CLas) is associated with huanglongbing (HLB), the most devastating disease of citrus worldwide. The inability to culture CLas impairs the understanding of its virulence mechanisms and the development of effective management strategies to control this incurable disease. Previously, our research group used commercial grapefruit juice (GJ) to prolong the viability of CLas in vitro. In the present study, GJ was amended with a wide range of compounds and incubated under different conditions to optimize CLas growth. Remarkably, results showed that CLas growth ratios were inversely proportional to the initial inoculum concentration. This correlation is probably regulated by a cell density-dependent mechanism, because diluting samples between subcultures allowed CLas to resume growth. Moreover, strategies to reduce the cell density of CLas, such as subculturing at short intervals and incubating samples under flow conditions, allowed this bacterium to multiply and reach maximum growth as early as 3 days after inoculation, although no sustained exponential growth was observed under any tested condition. Unfortunately, cultures were only transient, because CLas lost viability over time; nevertheless, we obtained populations of about 10⁵ genome equivalents/ml repeatedly. Finally, we established an ex vivo system to grow CLas within periwinkle calli that could be used to propagate bacterial inoculum in the lab. In this study we determined the influence of a comprehensive set of conditions and compounds on CLas growth in culture. We hope our results will help guide future efforts toward the long-sought goal of culturing CLas axenically.

Genome-Scale Metabolic Modeling Enables In-Depth Understanding of Big Data

Genome-scale metabolic models (GEMs) enable the mathematical simulation of the metabolism of archaea, bacteria, and eukaryotic organisms. GEMs quantitatively define a relationship between genotype and phenotype by contextualizing different types of Big Data (e.g., genomics, metabolomics, and transcriptomics). In this review, we analyze the available Big Data useful for metabolic modeling and compile the available GEM reconstruction tools that integrate Big Data. We also discuss recent applications in industry and research that include predicting phenotypes, elucidating metabolic pathways, producing industry-relevant chemicals, identifying drug targets, and generating knowledge to better understand host-associated diseases. In addition to the up-to-date review of GEMs currently available, we assessed a plethora of tools for developing new GEMs that include macromolecular expression and dynamic resolution. Finally, we provide a perspective in emerging areas, such as annotation, data managing, and machine learning, in which GEMs will play a key role in the further utilization of Big Data.

Molecular signatures between citrus and Candidatus Liberibacter asiaticus

Citrus Huanglongbing (HLB), also known as citrus greening, is one of the most devastating citrus diseases worldwide. Candidatus Liberibacter asiaticus (CLas) is the most prevalent strain associated with HLB, which is yet to be cultured in vitro. None of the commercial citrus cultivars are resistant to HLB. The pathosystem of Ca. Liberibacter is complex and remains a mystery. In this review, we focus on the recent progress in genomic research on the pathogen, the interaction of host and CLas, and the influence of CLas infection on the transcripts, proteins, and metabolism of the host. We have also focused on the identification of candidate genes for CLas pathogenicity or the improvements of HLB tolerance in citrus. In the end, we propose potentially promising areas for mechanistic studies of CLas pathogenicity, defense regulators, and genetic improvement for HLB tolerance/resistance in the future.

Metabolomic Analysis Provides New Insight Into Tolerance of Huanglongbing in Citrus

There have been efforts to develop citrus cultivars that are tolerant of Huanglongbing (HLB), a catastrophic phloem-limited disease. Previous studies demonstrated that continuous plant growth with phloem regeneration is one of the major characteristics of HLB tolerance. In this study, the metabolic mechanisms of HLB tolerance in citrus were elucidated using a multiple pathway-targeted metabolomic approach. Comparative analysis of healthy and infected HLB-tolerant and HLB-sensitive mandarin cultivars (Citrus reticulata) revealed differentially expressed metabolic responses among different groups. Pathway enrichment analysis indicated aspartate and glutamate metabolism, purine metabolism, and biosynthesis of plant hormones were upregulated in the tolerant group, except salicylic acid signaling. Catabolic pathways linked to energy-yielding metabolism were also upregulated in the tolerant group. These metabolisms and pathways were interconnected with each other, unveiling a pivotal metabolic network associated with HLB tolerance. In the network, auxins and cytokinins, the plant hormones responsible for plant growth and phloem regeneration, were accumulated. In addition, purine metabolites serving as energy carriers and nitrogen sources of plants were increased. Only salicylic acid-related metabolites for plant defense responses were decreased in the tolerant group. Our findings may evidence the strategy of HLB-tolerant cultivars that sustain plant growth and phloem formation rather than displaying direct plant defense to overcome the disease.

The Genome of "Candidatus Liberibacter asiaticus" Is Highly Transcribed When Infecting the Gut of Diaphorina citri

The Asian citrus psyllid, Diaphorina citri, is the vector of the bacterium "Candidatus Liberibacter asiaticus" (Las), associated with the devastating, worldwide citrus disease huanglongbing. In order to explore the molecular interactions of this bacterium with D. citri during the vector acquisition process, cDNA libraries were sequenced on an Illumina platform, obtained from the gut of adult psyllids confined in healthy (H) and in Las-infected young shoots (Las) for different periods of times (I = 1/2 days, II = 3/4 days, and III = 5/6 days). In each sampling time, three biological replicates were collected, containing 100 guts each, totaling 18 libraries depleted in ribosomal RNA. Reads were quality-filtered and mapped against the Chinese JXGC Las strain and the Floridian strain UF506 for the analysis of the activity of Las genome and SC1, SC2, and type 3 (P-JXGC-3) prophages of the studied Las strain. Gene activity was considered only if reads of at least two replicates for each acquisition access period mapped against the selected genomes, which resulted in coverages of 44.4, 79.9, and 94.5% of the JXGC predicted coding sequences in Las I, Las II, and Las III, respectively. These genes indicate an active metabolism and increased expression according to the feeding time in the following functional categories: energy production, amino acid metabolism, signal translation, cell wall, and replication and repair of genetic material. Pilins were among the most highly expressed genes regardless of the acquisition time, while only a few genes from cluster I of flagella were not expressed. Furthermore, the prophage region had a greater coverage of reads for SC1 and P-JXGC-3 prophages and low coverage in SC2 and no indication of activity for the lysis cycle. This research presents the first descriptive analysis of Las transcriptome in the initial steps of the D. citri gut colonization, where 95% of Las genes were active.

Engineering of citrus to obtain huanglongbing resistance

Huanglongbing (HLB) disease is threatening the sustainability of citriculture in affected regions because of its rapid spread and the severity of the symptoms it induces. Herein, we summarise the main research findings that can be exploited to develop HLB-resistant cultivars. A major bottleneck has been the lack of a system for the ex vivo cultivation of HLB-associated bacteria (CLs) in true plant hosts, which precludes the evaluation of target genes/metabolites in reliable plant/pathogen/vector environments. With regard to HLB vectors, several biotechnologies which have been proven in laboratory settings to be effective for insect control are presented. Finally, new genotypes that are resistant to CLs or their insect vectors are described, and the most relevant strategies for fighting HLB are highlighted.

Establishment of a Cuscuta campestris-mediated enrichment system for genomic and transcriptomic analyses of 'Candidatus Liberibacter asiaticus'

‘Candidatus Liberibacter asiaticus’ (CLas) is a phloem‐limited non‐culturable α‐proteobacterium associated with citrus Huanglongbing, a highly destructive disease threatening global citrus industry. Research on CLas is challenging due to the current inability to culture CLas in vitro and the low CLas titre in citrus plant. Here, we develop a CLas enrichment system using the holoparasitic dodder plant (Cuscuta campestris) as an amenable host to acquire and enrich CLas from CLas‐infected citrus shoots maintained hydroponically. Forty‐eight out of fifty‐five (87%) dodder plants successfully parasitized CLas‐infected citrus shoots with detectable CLas by PCR. Among 48 dodders cultures, 30 showed two‐ to 419‐fold CLas titre increase as compared to the corresponding citrus hosts. The CLas population rapidly increased and reached the highest level in dodder tendrils at 15 days after parasitizing citrus shoot. Genome sequencing and assembly derived from CLas‐enriched dodder DNA samples generated a higher resolution than those obtained for CLas from citrus hosts. No genomic variation was detected in CLas after transmission from citrus to dodder during short‐term parasitism. Dual RNA‐Seq experiments showed similar CLas gene expression profiles in dodder and citrus samples, yet dodder samples generated a higher resolution of CLas transcriptome data. The ability of dodder to support CLas multiplication to high levels, as well as its advantage in CLas genomic and transcriptomic analyses, make it an optimal model for further studies on CLas–host interaction.