Publications

4483

Cyanobacterial taxonomy is facing a period of rapid changes thanks to the ease of 16S rRNA gene sequencing and established workflows for description of new taxa. Since the last comprehensive review of the cyanobacterial system in 2014 until 2021, at least 273 species in 140 genera were newly described. These taxa were mainly placed into previously defined orders and families although several new families were proposed. However, the classification of most taxa still relied on hierarchical relationships inherited from the classical morphological taxonomy. Similarly, the obviously polyphyletic orders such as Synechococcales and Oscillatoriales were left unchanged. In this study, the rising number of genomic sequences of cyanobacteria and well‐described reference strains allowed us to reconstruct a robust phylogenomic tree for taxonomic purposes. A less robust but better sampled 16S rRNA gene phylogeny was mapped to the phylogenomic backbone. Based on both these phylogenies, a polyphasic classification throughout the whole phylum of Cyanobacteria was created, with ten new orders and fifteen new families. The proposed system of cyanobacterial orders and families relied on a phylogenomic tree but still employed phenotypic apomorphies where possible to make it useful for professionals in the field. It was, however, confirmed that morphological convergence of phylogenetically distant taxa was a frequent phenomenon in cyanobacteria. Moreover, the limited phylogenetic informativeness of the 16S rRNA gene, resulting in ambiguous phylogenies above the genus level, emphasized the integration of genomic data as a prerequisite for the conclusive taxonomic placement of a vast number of cyanobacterial genera in the future.

AbstractCandidatus Neoehrlichia mikurensis (CNM) and Hepatozoon spp. are important vector-borne parasites of humans and animals. CNM is a relatively recently discovered pathogen of humans. Hepatozoon are parasites of reptiles, amphibians and mammals, commonly found in rodents and carnivores worldwide. The present study aimed to determine the prevalence of CNM and Hepatozoon spp. in three species of Microtus and to assess the occurrence of vertical transmission in naturally-infected voles. Molecular techniques were used to detect pathogen DNA in blood and tissue samples of captured voles and their offspring. The prevalence of CNM in the vole community ranged 24–47% depending on Microtus species. The DNA of CNM was detected in 21% of pups from three litters of six infected Microtus dams (two Microtus arvalis and one M. oeconomus) and in 3/45 embryos (6.6%) from two litters of eight CNM-infected pregnant females. We detected Hepatozoon infection in 14% of M. arvalis and 9% of M. oeconomus voles. Hepatozoon sp. DNA was detected in 48.7% of pups from seven litters (6 M. arvalis and 1 M. oeconomus) and in two embryos (14.3%) obtained from one M. arvalis litter. The high prevalence of CNM infections in the Microtus spp. community may be a result of a relatively high rate of vertical transmission among naturally infected voles. Vertical transmission was also demonstrated for Hepatozoon sp. in M. arvalis and M. oeconomus. Our study underlines the significance of alternative routes of transmission of important vector-borne pathogens.

Huanglongbing (HLB) is associated with Candidatus Liberibacter asiaticus (CLas). It is a destructive disease of citrus. The objective of this study was to determine the genetic diversity of 90 strains of CLas infecting eight citrus species trees from the Central Pacific in Mexico. Genetic diversity among CLas was estimated by fourteen variable numbers of tandem repeat (VNTRs) loci. Three loci were polymorphic, SSR00 and SSR077 amplified four alleles each, while the locus SSR-A amplified two alleles, and the other loci only one allele per locus, resulting in a total of 21 alleles. Dendrogram analysis showed two clusters. No clear genetic structure was found in relation to geographical origin or host. The cluster I was mostly constituted by the majority of CLas strains (82%), but the cluster II comprised twelve strains of CLas collected in Tecoman location, State of Colima, and were obtained from different citrus hosts species. The frequency of 17 haplotypes among strains of CLas from the states of Nayarit, Jalisco, Colima and Michoacán was analyzed; in Colima 14 haplotypes were determinated, while in Michoacan all strains were identified in one haplotype. These results indicate a large genetic diversity among the strains of CLas present in the Central Pacific region in Mexico.

In Mexico, Huanglongbing HLB has become endemic in all Mexican lime producing areas. This disease is transmitted by the insect Diaphorina citri (Hemiptera: Liviidae). The objective of the study was to evaluate different plant extracts and biorational products for the control of D. citri in mexican lime. Two evaluations were made under field conditions; the first one included five treatments, with previous sampling and at 8, 20 and 27 days after the application of the treatments. In the second, eight treatments were evaluated, with prior sampling and at 6, 21 and 27 days. The response variable was the number of D. citri. A completely randomized experimental design with ten repetitions was used. A test of normality and homogeneity of variances was applied to the data, and they were processed through an analysis of variance and separation of means using Tukey (p≤ 0.05). The sweet clover extract (6.0 mL L-1) at 20 days decreased the population density by 59.2%, and Pyrifluquinazon (0.58 mL L-1) at 6 days the decrease was 31.3%. All the extracts showed to be a sustainable alternative for the management of D. citri.

Abstract The Genome Taxonomy Database (GTDB) is a taxonomic framework that defines prokaryotic taxa as monophyletic groups in concatenated protein reference trees according to systematic criteria. This has resulted in a substantial number of changes to existing classifications (https://gtdb.ecogenomic.org). In the case of union of taxa, GTDB names were applied based on the priority of publication. The division of taxa or change in rank led to the formation of new Latin names above the rank of genus that were only made publicly available via the GTDB website without associated published taxonomic descriptions. This has sometimes led to confusion in the literature and databases. A number of the provisional GTDB names were later published in other studies, while many still lack authorships. To reduce further confusion, here we propose names and descriptions for 329 GTDB-defined prokaryotic taxa, 223 of which are suitable for validation under the International Code of Nomenclature of Prokaryotes (ICNP) and 49 under the Code of Nomenclature of Prokaryotes described from Sequence Data (SeqCode). For the latter, we designated 23 genomes as type material. An additional 57 taxa that do not currently satisfy the validation criteria of either code are proposed as Candidatus.

In Europe and the Mediterranean region, ‘Candidatus Liberibacter solanacearum’ (Lso) is associated with emerging diseases of Apiaceae crops, mainly carrot. Emergency measures for import of carrot seed were set, requiring seed to be heat-treated at 50°C or tested as Lso-negative by PCR. The germination response to heat treatment was assessed for 24 carrot cultivar and hybrid seed lots. Ten parsley, five fennel, and two celery seed lots were also analysed. Of these 41 seed lots, 21 were Lso-infected. Water heat treatment significantly decreased germinability compared to dry heat treatment, indicating that dry heat treatment is a cheaper and less detrimental procedure. However, the dry heat treatment significantly decreased seed germination compared to untreated controls in four of 24 seed lots of carrot, four of ten parsley seed lots, three of five fennel seed lots, and one of two celery seed lots. For parsley, the heat treatment reduced germinability to a lesser extent in Lso-infected than Lso-free seed lots. These data show that heat treatment can affect the germination of Apiaceae seeds to varying degrees, depending on species or variety, the type of heat treatment, and the sanitary status of the seeds.