Publications

4870

AbstractNonulosonic acids (NulOs) are a family of acidic carbohydrates with a nine-carbon backbone, which include different related structures, such as sialic acids. They have mainly been studied for their relevance in animal cells and pathogenic bacteria. Recently, sialic acids have been discovered as an important compound in the extracellular matrix of virtually all microbial life and in “CandidatusAccumulibacter phosphatis”, a well-studied polyphosphate-accumulating organism, in particular. Here, bioaggregates highly enriched with these bacteria (approx. 95% based on proteomic data) were used to study the production of NulOs in an enrichment of this microorganism. Fluorescence lectin-binding analysis, enzymatic quantification, and mass spectrometry were used to analyze the different NulOs present, showing a wide distribution and variety of these carbohydrates, such as sialic acids and bacterial NulOs, in the bioaggregates. Phylogenetic analysis confirmed the potential of “Ca. Accumulibacter” to produce different types of NulOs. Proteomic analysis showed the ability of “Ca. Accumulibacter” to reutilize and reincorporate these carbohydrates. This investigation points out the importance of diverse NulOs in non-pathogenic bacteria, which are normally overlooked. Sialic acids and other NulOs should be further investigated for their role in the ecology of “Ca. Accumulibacter” in particular, and biofilms in general.Key Points•“Ca. Accumulibacter” has the potential to produce a range of nonulosonic acids.•Mass spectrometry and lectin binding can reveal the presence and location of nonulosonic acids.•The role of nonulosonic acid in non-pathogenic bacteria needs to be studied in detail.

Abstract Aster yellows (AY) group phytoplasmas affect plants by causing a general reduction in quantity and quality of yield. The most severely affected hosts are carrot, lettuce, onion, spinach and several ornamental crops, including aster, gladiolus, hydrangea, chrysanthemum and purple coneflower. Disease incidence may vary from year to year depending on the population trend of the vectors in the field. Infection rates varying from 20 to 30% were observed in lettuce and ranunculus fields in southern Italy (Marcone et al., 1995; Parrella et al., 2008). In Oklahoma, USA, according to Errampalli et al. (1991), AY group phytoplasma infections occurred in 80% of lettuce plants and 28% of carrots. In Ohio, disease incidence of 100% has been recorded in lettuce fields (Zhang et al., 2004). A major outbreak of AY disease occurred in 2000 in Texas that affected several vegetable crops. Among them, carrot was most severely damaged with infection rates that ranged from to 50 to near 100% (Lee et al., 2003). A severe AY disease of chrysanthemum which induced losses of 70 to 80% of the crop has been reported from China (Min et al., 2008) whereas losses of 90% were recorded in AY-affected aubergines in Bangladesh (Kelly et al., 2009). Infection rates of 60 and 99% were recorded in Hungary for AY-affected sugarbeet plants and India for AY-affected Jatropha curcas plants, respectively (Mumford et al., 2000; Kumar et al., 2010b). However, there are also several reports on sporadic occurrence and generally low incidence of AY group phytoplasmas in vegetable and ornamental crops (Smith et al., 1988; Vibio et al., 1995; Bertaccini et al., 1998). Cassava witches' broom, a disease affecting cassava in South East Asia (Vietnam, Thailand, Cambodia, Laos, China and the Philippines) is caused by 16SrI phytoplasma. The disease has resulted in significant reductions in cassava root starch content and up to 80% yield loss in parts of Vietnam (Anon., 2014).

Abstract RUS is of considerable economic importance, especially in areas where outbreaks occur. It has been described as a serious and widespread problem of raspberry in the former Soviet Union (see van der Meer (1987) for references). After the First World War, the disease became disastrous in raspberry areas in southern parts of The Netherlands, and many young plantations, started with healthy plant material, contained 60-90% infected plants in the second year after planting (see van der Meer (1987) for references). Small outbreaks and/or incidental occurrences of RUS disease have been reported from several other European countries (van der Meer, 1987).

Abstract Me.tha.no.tri.cha'les. N.L. fem. n. Methanothrix type genus of the order; suff. ‐ ales the ending to denote an order; N.L. fem. pl. n. Methanotrichales the order of Methanothrix . Cells are nonmotile, sheathed rods with flat ends. Gram‐stain negative. Lipids contain myo ‐inositol, ethanolamine, and galactose as the polar head groups. Species are oxygen‐tolerant anaerobe. However, growth and methanogenesis can only occur in strictly anaerobic and highly reducing conditions. Energy is obtained by splitting acetate into methane and CO 2 . When cocultured with electrogenic Geobacter spp., CO 2 is reduced to methane via direct interspecies electron transfer (DIET). Optimum growth pH range is 7.0–7.8. Mesophilic and thermophilic. Optimum growth temperatures are 34–37°C for mesophilic strains and 55–60°C for thermophilic strains. They occupy a wide range of anoxic habitats including anaerobic river mud, paddy field soil, hot springs, thermal lakes, thermophilic, and mesophilic anaerobic wastewater digesters treating domestic wastes; granular sludge, anaerobic fixed‐bed reactors, and other types of anaerobic systems. Genome sequences have been determined for strains of all three of the described species in the order, and the genome size ranges from 1.9 to 3.0 Mb. The order Methanotrichales consists of one family Methanotrichaceae . Although all three described species are currently classified in a single genus Methanothrix , phylogenomic analyses suggest that two species should be transferred to novel genera. DNA G + C content (mol%) : 51–61 (Genome). Type genus : Methanothrix Huser et al. 1982, VL10. Taxonomic and Nomenclature Notes According to the List of Prokaryotic names with Standing in Nomenclature (LPSN), the taxonomic status of the order Methanotrichales is: synonym (and no standing) (last update, February 2025) * . Correct name: Methanosarcinales LPSN classification: Archaea / Methanobacteriati / Methanobacteriota / Methanosarcinia / Methanosarcinales The order Methanotrichales can also be recovered in the Genome Taxonomy Database (GTDB) as o__Methanotrichales (version v220) ** . GTDB classification: d__Archaea / p__Halobacteriota / c__Methanosarcinia / o__Methanotrichales * Meier‐Kolthoff et al. ( 2022 ). Nucleic Acids Res , 50 , D801 – D807 ; DOI: 10.1093/nar/gkab902 ** Parks et al. ( 2022 ). Nucleic Acids Res , 50 , D785 – D794 ; DOI: 10.1093/nar/gkab776

Understanding temporal biological phenomena is a challenging task that can be approached using network analysis. Here, we explored whether network reconstruction can be used to better understand the temporal dynamics of bois noir, which is associated with ‘Candidatus Phytoplasma solani’, and is one of the most widespread phytoplasma diseases of grapevine in Europe. We proposed a methodology that explores the temporal network dynamics at the community level, i.e., densely connected subnetworks. The methodology offers both insights into the functional dynamics via enrichment analysis at the community level, and analyses of the community dissipation, as a measure that accounts for community degradation. We validated this methodology with cases on experimental temporal expression data of uninfected grapevines and grapevines infected with ‘Ca. P. solani’. These data confirm some known gene communities involved in this infection. They also reveal several new gene communities and their potential regulatory networks that have not been linked to ‘Ca. P. solani’ to date. To confirm the capabilities of the proposed method, selected predictions were empirically evaluated.

Background: ‘Candidatus Liberibacter asiaticus’ (CLas) is a major causal agent of citrus greening disease. The disease primarily involves an asymptomatic, often latent infection of CLas. However, there is no effective technique to distinguish latent-infected trees from healthy ones. This study describes the development of a new detection method for latent CLas infection using cuttings. Methods: Root tissues regenerated from cuttings using symptomatic and asymptomatic citrus trees were prepared for real-time a polymerase chain reaction (PCR) test which was used to investigate latent CLas. When some of the regenerated roots were negative for CLas in the first real-time PCR assay, a subsequent cultivation in soils was performed using the CLas-negative cuttings. CLas development during cultivation was evaluated by a second real-time PCR assay using soil-grown roots from seedlings. Results: Previously, CLas had not been detected from leaves of the latent-infected trees in our greenhouse by real-time PCR. In this study, however, CLas was detected at a moderate frequency from the root tissues of cuttings derived from the latent-infected trees, by the same PCR test. For cuttings with regenerated roots that tested negative for CLas by real-time PCR, CLas was frequently detected from roots grown in nursery soil with autoclaving, after cultivation for a month or more. Conclusions: Latent infection with CLas was detectable by real-time PCR using root tissues regenerated by cuttings and roots grown in nursery soil with autoclaving. These results suggest that the new method of investigation would provide great opportunities for early detection of CLas in asymptomatic citrus trees from field surveys, and would accelerate the eradication practice of citrus greening.

Bois noir is the most widespread phytoplasma grapevine disease in Europe. It is associated with ‘Candidatus Phytoplasma solani’, but molecular interactions between the causal pathogen and its host plant are not well understood. In this work, we combined the analysis of high-throughput RNA-Seq and sRNA-Seq data with interaction network analysis for finding new cross-talks among pathways involved in infection of grapevine cv. Zweigelt with ‘Ca. P. solani’ in early and late growing seasons. While the early growing season was very dynamic at the transcriptional level in asymptomatic grapevines, the regulation at the level of small RNAs was more pronounced later in the season when symptoms developed in infected grapevines. Most differentially expressed small RNAs were associated with biotic stress. Our study also exposes the less-studied role of hormones in disease development and shows that hormonal balance was already perturbed before symptoms development in infected grapevines. Analysis at the level of communities of genes and mRNA-microRNA interaction networks revealed several new genes (e.g., expansins and cryptdin) that have not been associated with phytoplasma pathogenicity previously. These novel actors may present a new reference framework for research and diagnostics of phytoplasma diseases of grapevine.

Abstract The reference strain of 'Ca. Phytoplasma trifolii' is the causative agent of clover proliferation (CP) disease of alsike clover (Trifolium hybridum). The CP disease was first reported in Canada in the early 1960s when the aetiological agent was mistakenly presumed to be a yellows-type virus (Chiykowski, 1965). Subsequent investigations revealed that the disease was associated with infection by a mycoplasma-like organism (Chen and Hiruki, 1975; Hiruki and Chen, 1984), now termed phytoplasma, strain CPR (Hiruki and Wang, 2004). Later, phytoplasmas of the same lineage (subgroup 16SrVI-A) were found in the USA, Mexico, and many countries in Europe and Asia, causing diseases in diverse leguminous and vegetable crops, responsible for significant yield losses and quality reductions. Phytoplasmas of the same lineage also caused disease in elm trees in the USA. Phytoplasmas of closely-related lineages (various subgroups of group 16SrVI) also have wide distributions around the world.

In this study, we present a combined computational and experimental methodology that allows a rapid and efficient identification of the ncSecPs from bacteria, in particular the unculturable bacteria like CLas. Meanwhile, the study determined that a number of CLas ncSecPs suppressed HR-based cell death, and thus indicated a novel role for the bacterial ncSecPs in extracellular milieu.