Publications

4516

Abstract Phytoplasmas are wall-less parasitic bacteria living exclusively in plant phloem as consequence of transmission by sap-sucking insect vectors (Lee et al., 2000); they have been associated with several hundred plant diseases. 'Candidatus Phytoplasma phoenicium' (CaPphoe), subgroup 16SrIX-B, is the aetiological agent of almond witches'-broom (AlmWB), a severe disease affecting almond, peach and nectarine trees in Lebanon and Iran. The first epidemics of AlmWB occurred in almond trees in Lebanon in the early 1990s and in Iran in 1995. In Lebanon, the disease rapidly spread from coastal to high mountainous areas, killing almost 150,000 trees over a period of 15 years. CaPphoe was first added to the EPPO Alert List in 2001 and removed from the list in 2006. The more recent rapid spread of CaPphoe in peach and nectarine orchards and in other plant hosts, along with the identification of efficient insect vectors, increased the alarm about the risk it poses for stone fruit production in the Middle East and in all the countries of the Mediterranean basin. Thus it was re-inserted in the EPPO Alert List in 2015.

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.

Abstract Phytoplasmas are wall-less, phloem-limited unculturable bacteria that are naturally spread by sap-sucking insects. 'Candidatus Phytoplasma australiense', subgroup 16SrXII-B, is associated with a wide range of diseases in Australia and New Zealand. Important commercial crop hosts of 'Ca. Phytoplasma australiense' include grapevine, papaya and strawberry. This phytoplasma is associated with rapid death of its papaya and cabbage tree hosts. In New Zealand, the insect vectors have been confirmed to be the endemic Cixiid planthoppers, Zeoliarus atkinsoni and Z. oppositus, while in Australia no vector has yet been determined, although the leafhopper, Orosius argentatus, has been implicated. Long distance spread of the phytoplasma is possible through infected vegetative propagating material. 'Ca. Phytoplasma australiense' is on the A1 list of regulated organisms for Canada and Bahrain, and is listed as a quarantine pest for the USA.

Dysoxic marine waters (DMW, < 1 μM oxygen) are currently expanding in volume in the oceans, which has biogeochemical, ecological and societal consequences on a global scale. In these environments, distinct bacteria drive an active sulfur cycle, which has only recently been recognized for open‐ocean DMW. This review summarizes the current knowledge on these sulfur‐cycling bacteria. Critical bottlenecks and questions for future research are specifically addressed. Sulfate‐reducing bacteria (SRB) are core members of DMW. However, their roles are not entirely clear, and they remain largely uncultured. We found support for their remarkable diversity and taxonomic novelty by mining metagenome‐assembled genomes from the Black Sea as model ecosystem. We highlight recent insights into the metabolism of key sulfur‐oxidizing SUP05 and Sulfurimonas bacteria, and discuss the probable involvement of uncultivated SAR324 and BS‐GSO2 bacteria in sulfur oxidation. Uncultivated Marinimicrobia bacteria with a presumed organoheterotrophic metabolism are abundant in DMW. Like SRB, they may use specific molybdoenzymes to conserve energy from the oxidation, reduction or disproportionation of sulfur cycle intermediates such as S 0 and thiosulfate, produced from the oxidation of sulfide. We expect that tailored sampling methods and a renewed focus on cultivation will yield deeper insight into sulfur‐cycling bacteria in DMW.

Abstract Phytoplasmas are wall-less parasitic bacteria living exclusively in plant phloem as consequence of transmission by sap-sucking insect vectors (Lee et al., 2000); they have been associated with several hundred plant diseases. 'Candidatus Phytoplasma phoenicium' (CaPphoe), subgroup 16SrIX-B, is the aetiological agent of almond witches'-broom (AlmWB), a severe disease affecting almond, peach and nectarine trees in Lebanon and Iran. The first epidemics of AlmWB occurred in almond trees in Lebanon in the early 1990s and in Iran in 1995. In Lebanon, the disease rapidly spread from coastal to high mountainous areas, killing almost 150,000 trees over a period of 15 years. CaPphoe was first added to the EPPO Alert List in 2001 and removed from the list in 2006. The more recent rapid spread of CaPphoe in peach and nectarine orchards and in other plant hosts, along with the identification of efficient insect vectors, increased the alarm about the risk it poses for stone fruit production in the Middle East and in all the countries of the Mediterranean basin. Thus it was re-inserted in the EPPO Alert List in 2015.

‘Candidatus Liberibacter asiaticus’ (CLas), the causal agent of citrus huanglongbing (HLB), colonizes inside the phloem and is naturally transmitted by the Asian citrus psyllid (ACP). Here, we investigated spatiotemporal CLas colonization in different tissues after ACP transmission. Of the nine plants successfully infected via ACP transmission, CLas was detected in the roots of all trees at 75 days postremoval of ACPs (DPR) but in the mature leaf of only one tree; this finding is consistent with the model that CLas moves passively from source to sink tissues. At 75 and 365 DPR, CLas was detected in 11.1 and 43.1% of mature leaves not fed on by ACPs during transmission, respectively, unveiling active movement to the source tissue. The difference in colonization timing of sink and source tissues indicates that CLas is capable of both passive and active movement, with passive movement being dominant. At 225 DPR, leaves fed on by ACPs during the young stage showed the highest ratio of HLB symptomatic leaves and the highest CLas titer, followed by leaves that emerged after ACP removal and mature leaves not fed on by ACPs. Importantly, our data showed that ACPs were unable to transmit CLas via feeding on mature leaves. It is estimated that it takes 3 years at most for CLas to infect the whole tree. Overall, spatiotemporal detection of CLas in different tissues after ACP transmission helps visualize the infection process of CLas in planta and subsequent HLB symptom development and provides evidence showing that young leaves should be the focus of HLB management.

Abstract‘Candidatus Phytoplasma meliae’ (subgroups 16SrXIII-G and XIII-C) has been reported in association to chinaberry yellowing disease in Argentina, Bolivia and Paraguay. In Argentina, this disease constitutes a major phytosanitary problem for chinaberry forestry production. To date, no genome information of this phytoplasma and others from 16SrXIII-group has been published, hindered its characterization at genomic level. Here we analyze the draft genome of ‘Candidatus Phytoplasma meliae’ strain ChTYXIII obtained from a chinaberry-infected plant using a metagenomics approach. The draft assembly consists of twenty-one contigs with a total length of 751.949 bp. The annotation contains 669 CDSs, 34tRNA and one set of rRNA operons. Metabolic pathways analysis indicated that the ChTYXIII contains the complete core genes for glycolysis and functional sec system for translocation of proteins. The phylogenetic relationships inferred 132 single copy genes (orthologues core) analysis revealed that ‘Ca. P. meliae’ constitutes a clade closely related to the ‘Ca. australiense’ and ‘Ca. P. solani’. Thirty-one putative effectors were identified, among which a homologue to SAP11 was found and others that have only been described in this pathogen. This work provides relevant genomic information for ‘Ca. P. meliae’ and constitutes the first genome described for the group 16SrXIII (MPV).

AbstractThe olive fruit fly, Bactrocera oleae, the most serious pest of olives, requires the endosymbiotic bacteria Candidatus Erwinia dacicola in order to complete its development in unripe green olives. Hence a better understanding of the symbiosis of Ca. E. dacicola and its insect host may lead to new strategies for reduction of B. oleae and thus minimize its economic impact on olive production. Studies of this symbiosis are hampered as the bacterium cannot be grown in vitro and the established B. oleae laboratory populations, raised on artificial diets, are devoid of this bacterium. Here, we sought to develop a method to transfer the bacteria from wild samples to laboratory populations. We tested several strategies. Cohabitation of flies from the field with the laboratory line did not result in a stable transfer of bacteria. We provided the bacteria directly to the egg and also in the food of the larvae but neither approach was successful. However, a robust method for transfer of Ca. E. dacicola from wild larvae or adults to uninfected flies by transplantation to females was established. Single female lines were set up and the bacteria were successfully transmitted for at least three generations. These results open up the possibilities to study the interaction between the symbiont and the host under controlled conditions, in view of both understanding the molecular underpinnings of an exciting, unique in nature symbiotic relationship, as well as developing novel, innovative control approaches.

Abstract Asgard archaea are widely distributed in anaerobic environments. Previous studies revealed the potential capability of Asgard archaea to utilize various organic substrates including proteins, carbohydrates, fatty acids, amino acids and hydrocarbons, suggesting that Asgard archaea play an important role in sediment carbon cycling. Here, we describe a previously unrecognized archaeal phylum, Hermodarchaeota, affiliated with the Asgard superphylum. The genomes of these archaea were recovered from metagenomes generated from mangrove sediments, and were found to encode alkyl/benzyl-succinate synthases and their activating enzymes that are similar to those identified in alkane-degrading sulfate-reducing bacteria. Hermodarchaeota also encode enzymes potentially involved in alkyl-coenzyme A and benzoyl-coenzyme A oxidation, the Wood–Ljungdahl pathway and nitrate reduction. These results indicate that members of this phylum have the potential to strictly anaerobically degrade alkanes and aromatic compounds, coupling the reduction of nitrate. By screening Sequence Read Archive, additional genes encoding 16S rRNA and alkyl/benzyl-succinate synthases analogous to those in Hermodarchaeota were identified in metagenomic datasets from a wide range of marine and freshwater sediments. These findings suggest that Asgard archaea capable of degrading alkanes and aromatics via formation of alkyl/benzyl-substituted succinates are ubiquitous in sediments.

Abstract Dichloromethane (DCM; CH2Cl2) is a toxic groundwater pollutant that also has a detrimental effect on atmospheric ozone levels. As a dense non-aqueous phase liquid, DCM migrates vertically through groundwater to low redox zones, yet information on anaerobic microbial DCM transformation remains scarce due to a lack of cultured organisms. We report here the characterisation of DCMF, the dominant organism in an anaerobic enrichment culture (DFE) capable of fermenting DCM to the environmentally benign product acetate. Stable carbon isotope experiments demonstrated that the organism assimilated carbon from DCM and bicarbonate via the Wood–Ljungdahl pathway. DCMF is the first anaerobic DCM-degrading population also shown to metabolise non-chlorinated substrates. It appears to be a methylotroph utilising the Wood–Ljungdahl pathway for metabolism of methyl groups from methanol, choline, and glycine betaine. The flux of these substrates from subsurface environments may either directly (DCM, methanol) or indirectly (choline, glycine betaine) affect the climate. Community profiling and cultivation of cohabiting taxa in culture DFE without DCMF suggest that DCMF is the sole organism in this culture responsible for substrate metabolism, while the cohabitants persist via necromass recycling. Genomic and physiological evidence support placement of DCMF in a novel genus within the Peptococcaceae family, ‘Candidatus Formimonas warabiya’.