Publications

4372

GroE is a chaperonin folding system consisting of GroEL (Cpn60, a 60 kDa chaperonin), and the smaller co-chaperonin GroES (Cpn10). Many “client” proteins require GroE to fold properly, including several that are essential for cell viability. Unsurprisingly then, GroE is found in nearly all bacteria and eukaryotes. Mollicutes are the only microorganisms that lack GroE in almost all cases. Only two clades of Mollicutes have retained the ancestral GroE system, or perhaps reacquired one; these exceptions include the family Acholeplasmataceae (consisting of the genera Acholeplasma and Phytoplasma). The role of GroEL in these “exceptional” Mollicutes is a source of speculation, given how many non-canonical “moonlighting” roles have been ascribed to this protein. GroEL has been suggested to play a role in pathogenesis in plant and animal pathogenic Mollicutes, by binding to host cells and facilitating invasion. However, in one further layer of exception, the phytopathogenic taxon ‘Candidatus Phytoplasma pruni’ (ribosomal group 16SrIII), was reported to lack a GroE system. This study confirms the lack of a functional GroE system in 16SrIII by providing two new, high quality, non-fragmented genome assemblies, as well as a thorough survey of other 16SrIII genomes for genes encoding GroEL/GroES, including those that may not resemble phytoplasma groEL (ie. acquired by horizontal gene transfer, HGT). We discuss the implications of a clearly phytopathogenic, invasive group of Mollicutes that nevertheless lacks GroE, in light of the presumed role of GroEL for these microorganisms. We determined that three groups of genomes of 16SrIII contain short, non-functional groEL pseudogenes, while most of the reported genomes lack any semblance of a GroE system. Examination of the new assemblies allowed us to rule out HGT as a means of GroE acquisition.

Abstract The presence of fastidious phytopathogenic bacteria ‘Candidatus Arsenophonus phytopathogenicus’ and ‘Candidatus Phytoplasma solani’ challenges sugar beet cultivation in Austria. Reptalus quinquecostatus sensu Holzinger et al. 2023 is the principal vector of ‘Ca. P. solani’ to sugar beet in Serbia, while Pentastiridius leporinus is the primary vector of ‘Ca. A. phytopathogenicus’ in western Europe and can also transmit ‘Ca. P. solani’. This study investigates the epidemiology of the associated diseases in Austrian sugar beet fields. An extensive survey in 2024 at 33 locations revealed significant spatial and temporal variability in cixiid populations, with R. quinquecostatus emerging as the predominant species. Transmission trials and field surveys confirmed R. quinquecostatus as a vector of ‘Ca. A. phytopathogenicus’ and ‘Ca. P. solani’ 16SrXII-P driving a disease outbreak in Nikitsch. The predominance of R. quinquecostatus in nearly all monitored fields suggests its significant role in the pathogens' epidemiology on a broader scale in the Pannonian plain. Spatial and temporal variations in pathogen incidence in Austrian sugar beet mirror patterns in Serbia, driven by R. quinquecostatus. The co-occurrence of ‘Ca. A. phytopathogenicus’ and ‘Ca. P. solani’ 16SrXII-A and 16SrXII-P and their transmission by both R. quinquecostatus and P. leporinus complicate disease management efforts.

The genus Lactococcus was proposed by Schleifer et al. by separating Lactococcus lactis from the genus Streptococcus. Although the family Streptococcaceae consists of four genera, each genus contains a relatively small number of species, with the exception of the genus Streptococcus, which contains more than 100 species. The genera Lactococcus and Lactovum currently comprise 26 species and a single species, respectively. This study evaluated the taxonomy of the genus Lactococcus based on the 16S rRNA gene phylogeny, core-genome phylogeny and (conserved) pairwise average amino acid identity. These evaluations clearly indicated that the genus Lactococcus could be divided into two genus-level clusters, and we propose to reclassify this genus into two; the authentic Lactococcus, which includes the L. lactis group, and a novel genus for which the name Pseudolactococcus is proposed. Three lactic acid bacterial strains, RyT2T, OfM1T and OfM2, were isolated from the gut of termites in Okinawa, Japan. Based on the combination of genetic and phenotypic data, we conclude that these isolates represent two novel species of the genera Pseudolactococcus and Lactovum, respectively, for which we propose the names Pseudolactococcus yaeyamensis sp. nov. (RyT2T=JCM 36015T=DSM 118067T) and Lactovum odontotermitis sp. nov. (OfM1T=JCM 34431T=DSM 118066T, OfM2=JCM 34432), respectively.

Abstract Mycoplasma haemofelis (Mhf), Candidatus Mycoplasma haemominutum (CMhm), and Candidatus Mycoplasma turicensis (CMt) are the major feline hemotropic Mycoplasma (FHM) species identified in cats worldwide. Data concerning FHM in Egypt is limited; therefore, the current study aimed to gain further insights into disease epidemiology by investigating FHM molecular prevalence, risk factors, and hemogram abnormalities in 246 Egyptian cats (shelter-housed and client-owned) during 2022–2024. Additionally, 16 S rRNA gene-based maximum-likelihood (ML) phylogenetic analysis was performed for all CMt-positive samples for the first time in Egypt. FHM was detected in 16.3% (n = 40) of cats and typed as CMhm, Mhf, and CMt in 15.4% (n = 38), 3.6% (n = 9), and 2.4% (n = 6) of cats, respectively. Single CMhm and Mhf infections were detected in 12.6% (n = 31) and 0.8% (n = 2) of cats, respectively. Dual (Mhf and CMhm) and triple (Mhf, CMhm, and CMt) infections were found in 0.4% (n = 1) and 2.4% (n = 6) of cats, respectively. CMhm was significantly associated with single infections rather than coinfections compared to other FHM species. Male sex and anemia were identified as predictors of FHM PCR positivity. FHM-infected cats had significantly lower hematocrit %, RBC counts, and hemoglobin concentrations than non-infected ones. Egyptian CMt sequences showed 97.6–100% nucleotide identity with each other. Egyptian and reference CMt strains represented nine nucleotide sequence types clustered into three well-supported clades on the ML tree without clear geographic distinction. The data generated in this study, conducted in Egypt, is crucial for enhancing our understanding of disease epidemiology and implementing effective preventive measures.

ABSTRACT Candidatus Altiarchaea are widespread across aquatic subsurface ecosystems and possess a highly conserved core genome, yet adaptations of this core genome to different biotic and abiotic factors based on gene expression remain unknown. Here, we investigated the metatranscriptome of two Ca. Altiarchaeum populations that thrive in two substantially different subsurface ecosystems. In Crystal Geyser, a high‐CO 2 groundwater system in the USA, Ca. Altiarchaeum crystalense co‐occurs with the symbiont Ca. Huberiarchaeum crystalense, while in the Muehlbacher sulfidic spring in Germany, an artesian spring high in sulfide concentration, Ca. A . hamiconexum is heavily infected with viruses. We here mapped metatranscriptome reads against their genomes to analyse the in situ expression profile of their core genomes. Out of 537 shared gene clusters, 331 were functionally annotated and 130 differed significantly in expression between the two sites. Main differences were related to genes involved in cell defence like CRISPR‐Cas, virus defence, replication, transcription and energy and carbon metabolism. Our results demonstrate that altiarchaeal populations in the subsurface are likely adapted to their environment while influenced by other biological entities that tamper with their core metabolism. We consequently posit that viruses and symbiotic interactions can be major energy sinks for organisms in the deep biosphere.

A Gram-stain-negative, non-motile, rod-shaped and imazamox-resistant bacterium, designated as H34T, was isolated from soil obtained from a farmland. Strain H34T grew at pH 6.0–9.0 (optimum, 7.0), temperature 15–40 °C (optimum, 30 °C) and salinity of 0–3.0% NaCl (optimum 0.5% NaCl, w/v). Phylogenetic analysis of the 16S rRNA gene and genome sequences showed that strain H34T was affiliated to the family Chitinophagaceae but formed a distinct phyletic branch. The values of 16S rRNA gene sequence similarity, average nt identity (ANI), digital DNA–DNA hybridization (dDDH) and average aa identity (AAI) between strain H34T and closely related type strains of the genera Flavisolibacter, Paraflavisolibacter, Paracnuella, Flaviaesturariibacter and Cnuella were 90.9–92.6%, 68.4–72.1%, 18.7–20.5% and 60.5–65.9%, respectively. The genome size was 7.01 Mb with a G+C content of 56.5 mol%. The major fatty acids (≥10%) were iso-C15 : 0, iso-C15 : 1 G and C16 : 1  ω5c. The only isoprenoid quinone was menaquinone-7. The major polar lipids were phosphatidylethanolamine, one unidentified aminophospholipid, one unidentified aminophosphoglycolipid, two unidentified phospholipids, three unidentified aminolipids and four unidentified lipids. The distinct phylogenetic relationships; low values of 16S rRNA gene sequence similarity, AAI, ANI and dDDH; and the differences in phenotypic and genotypic characteristics support that strain H34T represents a novel species in a novel genus in the family Chitinophagaceae, for which the name Huijunlia imazamoxiresistens gen. nov., sp. nov. is proposed (type strain H34T=MCCC 1K09117T=KCTC 102287T).

Abstract Psyllids are major vectors of plant diseases, including Candidatus Liberibacter solanacearum (CLso), the bacterial agent associated with “zebra chip” disease in potatoes and “carrot yellows” disease in carrot. Despite their agricultural significance, there is limited knowledge on the genome structure and genetic diversity of psyllids. In this study, we provide chromosome-level genome assemblies for three psyllid species known to transmit CLso: Dyspersa apicalis (carrot psyllid), Dyspersa pallida, and Trioza urticae (nettle psyllid). As D. apicalis is recognized as the primary vector of CLso by carrot growers in Northern Europe, we also resequenced populations of this species from Finland, Norway, and Austria. Genome assemblies were constructed using PacBio HiFi and Hi–C sequencing data, yielding genome sizes of 594.01 Mbp for D. apicalis; 587.80 Mbp for D. pallida; and 655.58 Mbp for T. urticae. Over 90% of sequences anchored into 13 pseudo-chromosomes per species. D. apicalis and D. pallida assemblies exhibited high completeness, capturing over 92% of conserved Hemiptera single-copy orthologs. Furthermore, we identified sequences of the primary psyllid symbiont, Candidatus Carsonella ruddii, in all three species. Gene annotations were produced for each assembly: 17,932 unique protein-coding genes were predicted for D. apicalis; 18,292 for D. pallida; and 16,007 for T. urticae. We observed significant expansions in gene families, particularly those linked to potential insecticide detoxification, within the Dyspersa lineage. Resequencing also revealed the existence of multiple subpopulations of D. apicalis across Europe. These high-quality genome resources will support future research on genome evolution, insect–plant–pest interactions, and disease management strategies.

ABSTRACT Huanglongbing (HLB) is a bacterial disease that affects citrus trees and is considered the most severe citrus disease in the world. The three HLB-associated ‘Ca.Liberibacter’ species harbor prophage regions which have been described to play critical roles in their evolution and biology. In this study, we assembled and characterized the accessory genome of the first circularde novo‘CandidatusLiberibacter asiaticus’ (CLas) assembly (V1R1) from Réunion, one of the sparse areas worldwide hosting CLas and ‘Ca.Liberibacter africanus’ (CLaf). This 1,272 Mb-long whole-genome harbored 1,129 coding sequences and two complete prophages, including a 37,934 bp-long Type 1 prophage, frequently present in CLas genomes, and a 40,501 bp-long undescribed CLas prophage designated as P-V1R1-5. Comparative genomic approaches suggested that P-V1R1-5 have all the genetic elements to produce new viral particles and revealed that it likely belongs to a new CLas Type 5 prophage. While being reported for the first time in a CLas strain, P-V1R1-5-like prophages were previously identified in CLaf genomes, making it the first evidence of shared prophage-like sequence among HLB-associated ‘Ca, Liberibacter’ species. Using PCR amplifications targeting P-V1R1-5, we also showed that 85.7% of the tested CLas strains from Réunion and all tested CLaf strains from Madagascar and Réunion harbored a Type 5-like prophage. The identification of CLas Type 5-like prophages not only expanded our knowledge of CLas genomic diversity in Réunion, but also provided new insights into the role of horizontally transferred elements in the evolution of the sympatric HLB-associated bacteria. IMPORTANCE Huanglongbing (HLB) is the most severe citrus disease worldwide. The disease is associated with three ‘CandidatusLiberibacter’ species harboring prophage regions that have been described to play critical roles in their biology. In this study, we assembled and characterized the accessory genome of the first circularde novo‘Ca.Liberibacter asiaticus’ (CLas) assembly from Réunion, one of the very few areas in the world where both of CLas and ‘Ca.Liberibacter africanus’ (CLaf) coexist. Comparative genomic approaches demonstrated that this genome harbored two complete prophages, including a new CLas Type 5 prophage that was previously identified in CLaf but was reported for the first time in a CLas strain. This first evidence of shared prophage-like sequences among HLB-associated species expands our knowledge of CLas genomic diversity, but also provides new insights into the role of the accessory genome in the evolution of these bacteria.