Publications

4467

ABSTRACTCold seeps and hydrothermal vents deliver large amounts of methane and other gaseous alkanes into marine surface sediments. Consortia of archaea and partner bacteria thrive on the oxidation of these alkanes and its coupling to sulfate reduction. The inherently slow growth of the involved organisms and the lack of pure cultures have impeded the understanding of the molecular mechanisms of archaeal alkane degradation. Here, using hydrothermal sediments of the Guaymas Basin (Gulf of California) and ethane as substrate we cultured microbial consortia of a novel anaerobic ethane oxidizerCandidatusEthanoperedens thermophilum (GoM-Arc1 clade) and its partner bacteriumCandidatusDesulfofervidus auxilii previously known from methane-oxidizing consortia. The sulfate reduction activity of the culture doubled within one week, indicating a much faster growth than in any other alkane-oxidizing archaea described before. The dominance of a single archaeal phylotype in this culture allowed retrieving a closed genome ofCa. Ethanoperedens, a sister genus of the recently reported ethane oxidizerCandidatusArgoarchaeum. The metagenome-assembled genome ofCa. Ethanoperedens encoded for a complete methanogenesis pathway including a methyl-coenzyme M reductase (MCR) that is highly divergent from those of methanogens and methanotrophs. Combined substrate and metabolite analysis showed ethane as sole growth substrate and production of ethyl-coenzyme M as activation product. Stable isotope probing showed that the enzymatic mechanisms of ethane oxidation inCa. Ethanoperedens is fully reversible, thus its enzymatic machinery has potential for the biotechnological development of microbial ethane production from carbon dioxide.IMPORTANCEIn the seabed gaseous alkanes are oxidized by syntrophic microbial consortia that thereby reduce fluxes of these compounds into the water column. Because of the immense quantities of seabed alkane fluxes, these consortia are key catalysts of the global carbon cycle. Due to their obligate syntrophic lifestyle, the physiology of alkane-degrading archaea remains poorly understood. We have now cultivated a thermophilic, relatively fast-growing ethane oxidizer in partnership with a sulfate-reducing bacterium known to aid in methane oxidation, and have retrieved the first complete genome of a short-chain alkane-degrading archaeon. This will greatly enhance the understanding of non-methane alkane activation by non-canonical methyl-coenzyme M reductase enzymes, and provide insights into additional metabolic steps and the mechanisms underlying syntrophic partnerships. Ultimately, this knowledge could lead to the biotechnological development of alkanogenic microorganisms to support the carbon neutrality of industrial processes.EtymologyEthanoperedens. ethano, (new Latin): pertaining to ethane;peredens(Latin): consuming, devouring;thermophilum. (Greek): heat-loving. The name implies an organism capable of ethane oxidation at elevated temperatures.LocalityEnriched from hydrothermally heated, hydrocarbon-rich marine sediment of the Guaymas Basin at 2000 m water depth, Gulf of California, Mexico.DiagnosisAnaerobic, ethane-oxidizing archaeon, mostly coccoid, about 0.7 μm in diameter, forms large irregular cluster in large dual-species consortia with the sulfate-reducing partner bacterium ‘CandidatusDesulfofervidus auxilii’.

AbstractInferring the dispersal processes of vector-borne plant pathogens is a great challenge because the plausible epidemiological scenarios often involve complex spread patterns at multiple scales. The spatial genetic structure of ‘CandidatusPhytoplasma prunorum’, responsible for European stone fruit yellows disease, was investigated by the application of a combination of statistical approaches to genotype data of the pathogen sampled from cultivated and wild compartments in three FrenchPrunus-growing regions. This work revealed that the prevalence of the different genotypes is highly uneven both between regions and compartments. In addition, we identified a significant clustering of similar genotypes within a radius of 50 km or less, but not between nearby wild and cultivatedPrunus. We also provide evidence that infected plants are transferred between production areas, and that both species of theCacopsylla prunicomplex can spread the pathogen. Altogether, this work supports a main epidemiological scenario where ‘Ca. P. prunorum’ is endemic in — and generally acquired from — wildPrunusby its immature psyllid vectors. The latter then migrate to shelter plants that epidemiologically connect sites less than 50 km apart by later providing infectious mature psyllids to their “migration basins”. Such multi-scale studies could be useful for other pathosystems.

Abstract Background: ‘Ca. Aenigmarchaeota’ represents an evolutionary branch within the DPANN superphylum. However, their ecological roles and potential host-symbiont interactions are poorly understood.Results: Here, we analyze eight metagenomic-assembled genomes from hot spring habitats and reveal their functional potentials. Although they have limited metabolic capacities, they harbor substantial carbohydrate metabolizing abilities. Further investigation suggests that horizontal gene transfer might be the main driver that endows these abilities to ‘Ca. Aenigmarchaeota’, including enzymes involved in glycolysis. Additionally, members from the TACK superphylum and Euryarchaeota contribute substantially to the niche expansion of ‘Ca. Aenigmarchaeota’, especially genes related to carbohydrate metabolism and stress responses. Based on co-occurrence network analysis, we conjecture that ‘Ca. Aenigmarchaeota’ may be symbionts associated with TACK archaea and Euryarchaeota, though host-specificity might be wide and variable across different ‘Ca. Aenigmarchaeota’ genomes. Conclusion: This study provides significant insights into possible host-symbiont interactions and ecological roles of ‘Ca. Aenigmarchaeota’.

The Asian citrus psyllid (ACP), Diaphorina citri Kuwayama (Hemiptera: Liviidae), is an important transmission vector of the citrus greening disease Candidatus Liberibacter asiaticus (CLas). The D. citri midgut exhibits an important tissue barrier against CLas infection. However, the molecular mechanism of the midgut response to CLas infection has not been comprehensively elucidated. In this study, we identified 778 differentially expressed genes (DEGs) in the midgut upon CLas infection, by comparative transcriptome analyses, including 499 upregulated DEGs and 279 downregulated DEGs. Functional annotation analysis showed that these DEGs were associated with ubiquitination, the immune response, the ribosome, endocytosis, the cytoskeleton and insecticide resistance. KEGG enrichment analysis revealed that most of the DEGs were primarily involved in endocytosis and the ribosome. A total of fourteen DEG functions were further validated by reverse transcription quantitative PCR (RT-qPCR). This study will contribute to our understanding of the molecular interaction between CLas and D. citri.

AbstractHuanglongbing (HLB) is a serious disease of Citrus sp. worldwide. In Africa and the Mascarene Islands, a similar disease is known as African citrus greening (ACG) and is associated with the bacterium Candidatus Liberibacter africanus (Laf). In recent years, Candidatus Liberibacter asiaticus (Las) associated with the severe HLB has been reported in Ethiopia. Thus, we aimed to identify the Liberibacter species affecting citrus, the associated vectors in Eastern Africa and their ecological distribution. We assessed the presence of generic Liberibacter in symptomatic leaf samples by quantitative PCR. Subsequently, we sequenced the 50 S ribosomal protein L10 (rplJ) gene region in samples positive for Liberibacters and identified the species by comparison with public sequence data using phylogenetic reconstruction and genetic distances. We detected generic Liberibacter in 26%, 21% and 66% of plants tested from Uganda, Ethiopia and Kenya, respectively. The rplJ sequences revealed the most prevalent Liberibacters in Uganda and Ethiopia were LafCl (22%) and Las (17%), respectively. We detected Las in Kenya for the first time from three sites in the coastal region. Finally, we modelled the potential habitat suitability of Las in Eastern Africa using MaxEnt. The projection showed large areas of suitability for the pathogen in the three countries surveyed. Moreover, the potential distribution in Eastern Africa covered important citrus-producing parts of Ethiopia, Kenya, Uganda and Tanzania, and included regions where the disease has not been reported. These findings will guide in the development of an integrated pest management strategy to ACG/HLB management in Africa.

Abstract BACKGROUND Rickettsia spp. are human pathogens that cause a number of diseases and are transmitted by arthropods, including ixodid ticks. Estonia contributes a region, where the distribution area of two exophilic tick species of known medical importance, Ixodes persulcatus and I. ricinus, overlap. The presence of the nidicolous rodent-associated I. trianguliceps has recently been shown for Estonia. Although there is no Estonian data available on human disease caused by tick-borne Rickettsia spp., the presence of three Rickettsia species in non-nidicolous ticks, albiet at very dissimilar rates, was also previously reported. The aim of this studywas to screen, identify and characterize Rickettsia species in nidicolous and non-nidicolous ticks attached to rodents. RESULTS Nymphs and larvae of I. ricinus ( n = 1004), I . persulcatus ( n = 75) and I. trianguliceps ( n = 117) attached to rodents and shrews caught in different parts of Estonia were studied for the presence of Rickettsia spp. by nested PCR. Ticks were removed from 314 small animals of 5 species (bank voles Myodes glareolus , yellow necked mice Apodemus flavicollis , striped field mice A. agrarius, pine voles M. subterranius and common shrews S. araneus) . Rickettsial DNA was detected in 8,7% (103/1186) studied ticks. In addition to R. helvetica, previously found in questing ticks, this study reports the first identification of the recently described I. trianguliceps- associated Candidatus R. uralica in west of the Ural.

Zebra chip (ZC) disease of potato (Solanum tuberosum) is associated with infection by ‘Candidatus Liberibacter solanacearum’ (Lso). Two haplotypes of Lso—A and B—occur in the United States. Lso haplotype B is more virulent than haplotype A, causing greater disease incidence in tubers, more severe symptoms, and greater loss in tuber yield. This study assessed whether tubers from infected plants generate new infected plants the following year. The effects of both Lso haplotypes A and B on tuber resprout were examined on five potato cultivars. When compared with noninfected tubers, overall plant emergence rate from Lso A- or B-infected tubers was lower, plants emerged slower, and plants generated lower daughter tuber yields in weight and quantity. Plants generally emerged poorly from Lso B-infected tubers and produced lower daughter tuber yields than Lso A-infected tubers. Regardless of Lso treatment, all daughter tubers were asymptomatic, and only 0.3% tested positive for Lso in experiments conducted over 2 years. This suggests that plants generated from Lso A- and Lso B-infected seed potatoes with severe ZC symptoms are likely not a significant source of Lso in potato fields.

Abstract The potato/tomato psyllid Bactericera cockerelli (Šulc) transmits ‘Candidatus Liberibacter solanacearum’ (Lso) (also known as ‘Candidatus Liberibacter psyllaurous’), the bacterium associated with zebra chip disease (ZC) in potato. When disease incidence is high, ZC causes large economic losses through reductions in potato yield and tuber quality. No commercial potato variety has been found totally resistant to the pathogen. We evaluated host acceptance behaviors using no-choice assays on three breeding clones derived from Solanum chacoense Bitter with putative tolerance to Lso and/or ZC as part of an effort to determine whether the disease tolerance observed in those breeding clones was related to effects on psyllid settling behavior. We also counted the number of eggs laid and nymphs hatched on the different genotypes to observe any differences in reproduction. The potato variety ‘Russet Burbank’ was used as a susceptible control. Probing frequency and female walking duration were greater on Russet Burbank than the other genotypes. Oviposition did not differ among genotypes. However, female psyllids on two of the Lso-tolerant genotypes displayed reduced fertility 18–24 d after confinement with a male, relative to females on Russet Burbank. These results suggest that although the germplasms display minor abiotic activity on psyllid fertility, tolerance to Lso may be more strongly linked with plant tolerance to the pathogen rather than effects on host acceptance behaviors.