Publications

3806

Objective: The objective of this study was to investigate the group/subgroup of phytoplasma agent in peppers showing phytoplasma symptoms. Material and Methods: In this study, plants collected from Iğdır province in 2020 were analyzed using direct and nested PCR tests, and BLASTn, iphyClassifier, Mega 7, and pDRAW32 programs were used. Results: In the tests performed, approximately 1.2 kb of DNA fragments specific to phytoplasma were obtained. The 16S rRNA nucleotide sequence (1254 bp in length) (OM663745) revealed that it was showed more than 99.44% nucleotide similarity to other ‘Ca. P. trifolii’ members. The tentative RFLP and phylogenetic analyzes performed proved the ‘Ca. P. trifolii’ the infection from the Clover proliferation group (16SrVI) group and subgroup A in symptomatic pepper plants. Conclusion: The presence of ‘Ca. P. trifolii’ in naturally infected peppers in Iğdır province of Turkey was detected using PCR-RFLP and cladistic analysis.

The black-eared opossum (Didelphis aurita) is a South American synanthropic marsupial. The presence of opossums in domestic spaces is relevant in the One-Health context since they are hosts of pathogens and ectoparasites that may affect the health of domestic animals and humans. In this study, we aim to determine the occurrence of hemoplasmas and selected tick-borne pathogens in free-ranging black-eared opossums, along with their molecular characterization, hematological and biochemical evaluation and factors associated with infection, in the municipality of Viçosa, State of Minas Gerais, southeastern Brazil. Thirty black-eared opossums were trapped between March 2021 and June 2022. Ectoparasites were collected. Hematological and biochemical analyses were performed. DNA from EDTA-blood samples were analyzed by PCR and qPCR assays. By molecular analyses, ‘Candidatus Mycoplasma haemoalbiventris’ was the most prevalent hemoparasite (73.3%), followed by Hepatozoon sp. (22.2%). Significant differences were observed in the number of platelets, and in the concentration of protein and globulins in the animals infected by ‘Ca. M. haemoalbiventris’ when compared with the negative group. This is the first report of ‘Ca. M. haemoalbiventris’ infection in D. aurita.

CLas inhibits callose deposition in the sieve pores and the accumulation of reactive oxygen species to favor its cell-to-cell movement.

Citrus Huanglongbing (HLB) is the most devastating citrus disease in the world. Candidatus Liberibacter asiaticus (Las) is the prevalent HLB pathogen, which is yet to be cultivated. A recent study demonstrates that Las does not contain pathogenicity factors that are directly responsible for HLB symptoms. Instead, Las triggers systemic and chronic immune responses, representing a pathogen-triggered immune disease. Importantly, overproduction of reactive oxygen species (ROS) causes systemic cell death of phloem tissues, thus causing HLB symptoms. Because Las resides in the phloem tissues, it is expected that phloem cell might recognize outer membrane proteins, outer membrane vesicle (OMV) proteins and extracellular proteins of Las to contribute to the immune responses. Because Las has not been cultivated, we used Liberibacter crescens (Lcr) as a surrogate to identify proteins in the OM fraction, OMV proteins and extracellular proteins by liquid chromatography with tandem mass spectrometry (LC–MS/MS). We observed OMVs of Lcr under scanning electron microscope, representing the first experimental evidence that Liberibacter can deliver proteins to the extracellular compartment. In addition, we also further analyzed LC–MS/MS data using bioinformatic tools. Our study provides valuable information regarding the biology of Ca. Liberibacter species and identifies many putative proteins that may interact with host proteins in the phloem tissues.

AbstractThe understanding and manipulation of microbial communities toward the conversion of lignocellulose and plastics are topics of interest in microbial ecology and biotechnology. In this study, the polymer-degrading capability of a minimal lignocellulolytic microbial consortium (MELMC) was explored by genome-resolved metagenomics. The MELMC was mostly composed (>90%) of three bacterial members (Pseudomonas protegens; Pristimantibacillus lignocellulolyticus gen. nov., sp. nov; and Ochrobactrum gambitense sp. nov) recognized by their high-quality metagenome-assembled genomes (MAGs). Functional annotation of these MAGs revealed that Pr. lignocellulolyticus could be involved in cellulose and xylan deconstruction, whereas Ps. protegens could catabolize lignin-derived chemical compounds. The capacity of the MELMC to transform synthetic plastics was assessed by two strategies: (i) annotation of MAGs against databases containing plastic-transforming enzymes; and (ii) predicting enzymatic activity based on chemical structural similarities between lignin- and plastics-derived chemical compounds, using Simplified Molecular-Input Line-Entry System and Tanimoto coefficients. Enzymes involved in the depolymerization of polyurethane and polybutylene adipate terephthalate were found to be encoded by Ps. protegens, which could catabolize phthalates and terephthalic acid. The axenic culture of Ps. protegens grew on polyhydroxyalkanoate (PHA) nanoparticles and might be a suitable species for the industrial production of PHAs in the context of lignin and plastic upcycling.

Background: Alfalfa, Medicago sativa L. is the most important and widely grown leguminous fodder crop in temperate and tropical regions of the world. The production of alfalfa crop is limited by several biotic stresses, among which witches’ broom disease (AWB) was reported to cause significant economic losses. Methods: The phytoplasma infected alfalfa plants were collected from a central research farm, ICAR-IGFRI, Jhansi, U.P. Qualitative parameters such as crude protein content, acid detergent fibre and neutral detergent fibre were estimated in diseased and healthy plants. Phytoplasma universal primer (P1/P7) and nested primer (R16mF2/R16mR1) were used for the molecular characterization of AWB infected plants and phytoplasma infected, Parthenium hysterophorus. Result: The incidence of AWB disease ranged from 8-10%. The quantitative analysis of disease plants showed reduced plant height (-35%), fresh weight (-46.89%) and dry weight (-50.08%) compared to healthy plants. The diseased plant recorded low crude protein content (-21.38%) and higher dry matter content (+0.68%), acid detergent fibre (+33.72%) and neutral detergent fibre (+13.06%). The association of phytoplasma in diseased alfalfa and parthenium samples was confirmed by using P1/P7 and R16mF2/R16mR1 primer pair and Blastn analysis shared 99.6-100% similarity with ‘Candidatus Phytoplasma australasia’ belongs to the 16Sr group II-D.

AbstractSymbiotic microbes from the genus ‘Candidatus Megaira’ (Rickettsiales) are known to be common associates of algae and ciliates. However genomic resources for these bacteria are scarce, limiting our understanding of their diversity and biology. We therefore utilized SRA and metagenomic assemblies to explore the diversity of this genus. We successfully extracted four draft ‘Ca. Megaira’ genomes including one complete scaffold for a ‘Ca. Megaira’ and identified an additional 14 draft genomes from uncategorised environmental Metagenome-Assembled Genomes. We use this information to resolve the phylogeny for the hyper-diverse ‘Ca. Megaira’, with hosts broadly spanning ciliates, micro- and macro-algae, and find that the current single genus designation ‘Ca. Megaira’ significantly underestimates their diversity. We also evaluate the metabolic potential and diversity of ‘Ca. Megaira’ from this new genomic data and find no clear evidence of nutritional symbiosis. In contrast, we hypothesize a potential for defensive symbiosis in ‘Ca. Megaira’. Intriguingly, one symbiont genome revealed a proliferation of ORFs with ankyrin, tetratricopeptide and Leucine rich repeats like those observed in the genus Wolbachia where they are considered important for host-symbiont protein-protein interactions. Onward research should investigate the phenotypic interactions between ‘Ca. Megaira’ and their various potential hosts, including the economically important Nemacystus decipiens, and target acquisition of genomic information to reflect the diversity of this massively variable group.Data SummaryGenomes assembled in this project have been deposited in bioproject PRJNA867165Impact statementBacteria that live inside larger organisms commonly form symbiotic relationships that impact the host’s biology in fundamental ways, such as improving defences against natural enemies or altering host reproduction. Certain groups like ciliates and algae are known to host symbiotic bacteria commonly, but our knowledge of their symbiont’s evolution and function is limited. One such bacteria is ‘Candidatus Megaira’, a Rickettsiales that was first identified in ciliates, then later in algae. To improve the available data for this common but understudied group, we searched the genomes of potential hosts on online databases for Rickettsiales and assembled their genomes. We found 4 ‘Ca. Megaira’ this way and then used these to find a further 14 genomes in environmental metagenomic data. Overall, we increased the number of known ‘Ca. Megaira’ draft genomes from 2 to 20. These new genomes show us that ‘Ca. Megaira’ is far more diverse than previously thought and that it is potentially involved in defensive symbioses. In addition, one genome shows striking resemblance to well characterized symbiont, Wolbachia, in encoding many proteins predicted to interact directly with host proteins. The genomes we have identified and examined here provide baseline resources for future work investigating the real-world interactions between the hyper diverse ‘Ca. Megaira’ and its various potential hosts, like the economically important Nemacystus decipiens.

Thousands of new bacterial and archaeal species and higher-level taxa are discovered each year through the analysis of genomes and metagenomes. The Genome Taxonomy Database (GTDB) provides hierarchical sequence-based descriptions and classifications for new and as-yet-unnamed taxa. However, bacterial nomenclature, as currently configured, cannot keep up with the need for new well-formed names. Instead, microbiologists have been forced to use hard-to-remember alphanumeric placeholder labels. Here, we exploit an approach to the generation of well-formed arbitrary Latinate names at a scale sufficient to name tens of thousands of unnamed taxa within GTDB. These newly created names represent an important resource for the microbiology community, facilitating communication between bioinformaticians, microbiologists and taxonomists, while populating the emerging landscape of microbial taxonomic and functional discovery with accessible and memorable linguistic labels.