Publications

4980

Abstract Elm yellows develops in sporadic epidemics after introduction of 'Ca. Phytoplasma ulmi' to areas where vectors are abundant.

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.We tried to determine the epidemiology and species of human dirofilariasis observed at two tertiary care hospitals in Kerala. We searched the hospital database to identify cases of dirofilariosis from January 2005 to March 2020. Along with human isolates, one dog Dirofilaria isolate was also subjected to PCR and sequencing of pan filarial primers cytochrome oxidase subunits 1 and 12S rDNA. We documented 78 cases of human dirofilariosis. The orbit, eyelid, and conjunctiva were the most commonly affected sites. Molecular characterization identified one dog and five human isolates as Candidatus Dirofilaria Hongkongensis. A rare case of subconjunctival infestation by B. malayi was also documented. Human dirofilariosis is a public health problem in the state of Kerala in India, and it is mostly caused by Candidatus Dirofilaria Hongkongensis. We propose that all diroifilaria isolates are subjected to sequencing for identification.

Abstract Phytoplasmas are cell-wall-less plant pathogenic bacteria of the class Mollicutes, which inhabit the phloem sieve tubes of plants and have been associated with several hundred diseases affecting economically important crops. Over the past few decades 'Candidatus Phytoplasma solani', belonging to the 16SrXII-A ribosomal subgroup, has been found to cause a range of plant diseases in different agro-ecosystems in many countries in Europe and the eastern Mediterranean area and a number of others all over the world. It is thought likely that it has always been present, at least in its European range, but has only been noticed in recent years. Diseases caused include bois noir in grapevines, stolbur in tomatoes, potatoes and other wild and cultivated plants, maize redness, lavender decline, and yellowing, reddening, decline, dwarfism, leaf malformation and degeneration diseases of other plants. 'Ca. P. solani' is usually transmitted from plant to plant by the polyphagous insect vector Hyalesthes obsoletus (Cixiidae) which, although it can complete its life cycle on only a small number of plant species, feeds on a much wider range. Recent studies have demonstrated the presence of additional insect vectors of this phytoplasma in Europe, such as Reptalus panzeri in Serbia, possibly R. quinquecostatus in Serbia and France, and Anaceratagallia ribauti in Austria. This scenario highlights the extreme complexity of the ecology of both 'Ca. Phytoplasma solani' and its insect vectors, underlying the difficulty in studying the epidemiology of diseases associated with this pathogen and in developing efficient control strategies. 'Ca. Phytoplasma solani' is also transmitted by parasitic plants and by grafting and vegetative propagation of infected host plants; it can be spread when host plants are transported by people. In the European Union it is listed as a harmful organism necessitating restrictions on the import of plants in the family Solanaceae.

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’.

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 Sponges underpin the productivity of coral reefs, yet few of their microbial symbionts have been functionally characterised. Here we present an analysis of ~1200 metagenome-assembled genomes (MAGs) spanning seven sponge species and 25 microbial phyla. Compared to MAGs derived from reef seawater, sponge-associated MAGs were enriched in glycosyl hydrolases targeting components of sponge tissue, coral mucus and macroalgae, revealing a critical role for sponge symbionts in cycling reef organic matter. Further, visualisation of the distribution of these genes amongst symbiont taxa uncovered functional guilds for reef organic matter degradation. Genes for the utilisation of sialic acids and glycosaminoglycans present in sponge tissue were found in specific microbial lineages that also encoded genes for attachment to sponge-derived fibronectins and cadherins, suggesting these lineages can utilise specific structural elements of sponge tissue. Further, genes encoding CRISPR and restriction-modification systems used in defence against mobile genetic elements were enriched in sponge symbionts, along with eukaryote-like gene motifs thought to be involved in maintaining host association. Finally, we provide evidence that many of these sponge-enriched genes are laterally transferred between microbial taxa, suggesting they confer a selective advantage within the sponge niche and therefore play a critical role in host ecology and evolution.

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).