Publications

4477

‘Candidatus Phytoplasma prunorum’, the causal agent of European stone fruit yellows (ESFY), is one of the most important pathogens causing considerable economic losses in stone fruit orchards. This study evaluated trees infected and noninfected by phytoplasma ESFY of 16 apricot varieties grown in an orchard in Lednice (Czech Republic) between the years 2008-2014. Pomological traits, phenophases, pollen germination and seed viability were analysed as well as the presence of ‘Ca. P. prunorum’ in pollen, flower organs, fruit flesh, immature seeds and seedlings by nested PCR. One of the most detrimental impacts was the decreased fruit set of infected trees which occurred in 12 out of 16 studied varieties reaching an average fruit set decrease of 16.1%. Pollen germination rates also suffered, showing an average decrease by 11.78% in infected trees. In the analysis of some traits, overall significant differences were observed between the infected and noninfected trees. However, for all analysed traits in different varieties, both positive and negative influences of phytoplasma ESFY were observed. The presence of ‘Ca. P. prunorum’ in infected trees was confirmed in flower parts (only in peduncle in 70.2% of cases) and fruit parts (immature fruit flesh in 42.0% and milky kernels in 26.2% of cases), however, neither in seedlings nor in pollen.

Citrus production throughout the world is being severely threatened by Huanglongbing (HLB), which is a disease associated with the bacteria ‘Candidatus Liberibacter asiaticus’ (CLas), africanus, and americanus. This Resource Announcement provides amplicon-based next generation sequencing (NGS) datasets of the bacterial and fungal rRNA internal transcribed spacer (ITS) region from CLas-infected citrus budwood, leaves, and roots from five orchards located in different geographical regions in Florida (USA). To our knowledge, this is the first amplicon-based NGS study (i) that describes the fungal taxa associated with citrus and (ii) that provides comparative analyses of the bacterial and fungal taxa associated with budwood, leaves, and roots from the same citrus trees. This report also provides the sample metadata linked to these sequence datasets including HLB severity rating, tissue type, citrus rootstock, citrus scion, geographical region, and year trees were planted. When analyzed with other similar datasets, we anticipate that researchers will be able to obtain a greater understanding of the factors that shape the citrus microbiome as well as identify individual microorganisms or consortia of microorganisms that play a role in HLB suppression or exacerbation.

The bacterium ‘Candidatus Liberibacter solanacearum’ is a recent plant pathogen of several crops in Solanaceae and Apiaceae and is associated with economically important diseases. The bacterium is a carrot seed borne pathogen that can also be transmitted from potato mother tubers and by psyllid vectors. The psyllid Bactericera trigonica Hodkinson was described carrying CaLso associated with vegetative disorders in carrot and celery crops in Spain and its competence to transmit this phloem-limited bacterium among vegetables is currently being investigated. Here electrical penetration graphs showed that B. trigonica fed in the phloem of carrot and celery and probed the phloem in potato, but not in tomato plants. The bacterium was efficiently transmitted to carrot and celery plants when either single B. trigonica or groups of ten fed on these species. An inoculation access period of 24 hours was sufficient for a single B. trigonica to transmit the bacterium to carrot (67.8%), celery (21.1%) and eventually to potato and tomato (6.0%). Higher transmission rates were obtained with 10 individuals on celery (100%), carrot (80%), potato (10%) and tomato (10%). Bactericera trigonica laid eggs, and the hatched nymphs develop into adult on carrot and celery, but not on potato and tomato. CaLso was detected in 20% of the eggs laid by females carrying the bacterium. The results confirmed that B. trigonica is a vector of the bacterium to carrot and celery, and it is discussed the potential role of this psyllid in the transmission of the pathogen to potato and tomato plants.

AbstractAmmonia oxidizing archaea (AOA) of the phylum Thaumarchaeota are widespread in moderate environments but their occurrence and activity has also been demonstrated in hot springs. Here we present the first cultivated thermophilic representative with a sequenced genome, which allows to search for adaptive strategies and for traits that shape the evolution of Thaumarchaeota.CandidatusNitrosocaldus cavascurensis has been cultivated from a hot spring in Ischia, Italy. It grows optimally at 68°C under chemolithoautotrophic conditions on ammonia or urea converting ammonia stoichiometrically into nitrite with a generation time of approximately 25h. Phylogenetic analyses based on ribosomal proteins place the organism as a sister group to all known mesophilic AOA. The 1.58 Mb genome ofCa.N. cavascurensis harbors an amoAXCB gene cluster encoding ammonia monooxygenase, genes for a 3-hydroxypropionate/4-hydroxybutyrate pathway for autotrophic carbon fixation, but also genes that indicate potential alternative energy metabolisms. Although a bona fide gene for nitrite reductase is missing, the organism is sensitive to NO-scavenging, underlining the importance of this compound for AOA metabolism.Ca.N. cavascurensis is distinct from all other AOA in its gene repertoire for replication, cell division and repair. Its genome has an impressive array of mobile genetic elements and other recently acquired gene sets, including conjugative systems, a provirus, transposons and cell appendages. Some of these elements indicate recent exchange with the environment, whereas others seem to have been domesticated and might convey crucial metabolic traits.

Secondary metabolites, which are small-molecule organic compounds produced by living organisms, provide or inspire drugs for many different diseases. These natural products have evolved over millions of years to provide a survival benefit to the producing organism and often display potent biological activity with important therapeutic applications. For instance, defensive compounds in the environment may be cytotoxic to eukaryotic cells, a property exploitable for cancer treatment. Here, we describe the genome of an uncultured symbiotic bacterium that makes such a cytotoxic metabolite. This symbiont is losing genes that do not endow a selective advantage in a hospitable host environment. Secondary metabolism genes, however, are repeated multiple times in the genome, directly demonstrating their selective advantage. This finding shows the strength of selective forces in symbiotic relationships and suggests that uncultured bacteria in such relationships should be targeted for drug discovery efforts.

AbstractAmmonia-oxidizing archaea (AOA) within the phylumThaumarchaeaare the only known aerobic ammonia oxidizers in geothermal environments. Although molecular data indicate the presence of phylogenetically diverse AOA from theNitrosocaldusclade, group 1.1b and group 1.1aThaumarchaeain terrestrial high-temperature habitats, only one enrichment culture of an AOA thriving above 50 °C has been reported and functionally analyzed. In this study, we physiologically and genomically characterized a novelThaumarchaeonfrom the deep-branchingNitrosocaldaceaefamily of which we have obtained a high (∼85 %) enrichment from biofilm of an Icelandic hot spring (73 °C). This AOA, which we provisionally refer to as “CandidatusNitrosocaldus islandicus”, is an obligately thermophilic, aerobic chemolithoautotrophic ammonia oxidizer, which stoichiometrically converts ammonia to nitrite at temperatures between 50 °C and 70 °C.Ca.N. islandicus encodes the expected repertoire of enzymes proposed to be required for archaeal ammonia oxidation, but unexpectedly lacks anirKgene and also possesses no identifiable other enzyme for nitric oxide (NO) generation. Nevertheless, ammonia oxidation by this AOA appears to be NO-dependent asCa.N. islandicus is, like all other tested AOA, inhibited by the addition of an NO scavenger. Furthermore, comparative genomics revealed thatCa.N. islandicus has the potential for aromatic amino acid fermentation as its genome encodes an indolepyruvate oxidoreductase(iorAB)as well as a type 3b hydrogenase, which are not present in any other sequenced AOA. A further surprising genomic feature of this thermophilic ammonia oxidizer is the absence of DNA polymerase D genes - one of the predominant replicative DNA polymerases in all other ammonia-oxidizingThaumarchaea.Collectively, our findings suggest that metabolic versatility and DNA replication might differ substantially between obligately thermophilic and other AOA.