Publications

4502

AbstractThe Terrestrial Miscellaneous Euryarchaeota Group has been identified in various environments, and the single genome investigated thus far suggests that these archaea are anaerobic sulfite reducers. We assemble 35 new genomes from this group that, based on genome analysis, appear to possess aerobic and facultative anaerobic lifestyles and may oxidise rather than reduce sulfite. We propose naming this order (representing 16 genera) “Lutacidiplasmatales” due to their occurrence in various acidic environments and placement within the phylum Thermoplasmatota. Phylum-level analysis reveals that Thermoplasmatota evolution had been punctuated by several periods of high levels of novel gene family acquisition. Several essential metabolisms, such as aerobic respiration and acid tolerance, were likely acquired independently by divergent lineages through convergent evolution rather than inherited from a common ancestor. Ultimately, this study describes the terrestrially prevalent Lutacidiciplasmatales and highlights convergent evolution as an important driving force in the evolution of archaeal lineages.

It was shown that the SAP11 effector of different Candidatus Phytoplasma can destabilize some TEOSINE BRANCHES/CYCLOIDEA/PROLIFERATING CELL FACTORs (TCPs), resulting in plant phenotypes such as witches’ broom and crinkled leaves. Some SAP11 exclusively localize in the nucleus, while the others localize in the cytoplasm and the nucleus. The SAP11-like effector of Candidatus Phytoplasma mali strain PM19 (SAP11PM19) localizes in both compartments of plant cells. We show here that SAP11PM19 can destabilize TCPs in both the nucleus and the cytoplasm. However, expression of SAP11PM19 exclusively in the nucleus resulted in the disappearance of leaf phenotypes while still showing the witches’ broom phenotype. Moreover, we show that SAP11PM19 can not only destabilize TCPs but also relocalizes these proteins in the nucleus. Interestingly, three different transgenic Nicotiana species expressing SAP11PM19 show all the same witches’ broom phenotype but different leaf phenotypes. A possible mechanism of SAP11-TCP interaction is discussed.

El cultivo de papa representa en nuestro país una fuente de divisas y genera gran cantidad de empleos. Hasta la fecha no existe un estudio formal sobre la fluctuación poblacional de Bactericera cockerelli y Candidatus liberibacter. Este estudio se realizó con el propósito de determinar la dinámica poblacional de Bactericera cockerelli y la incidencia de Candidatus liberibacter en papa, el cual se llevó a cabo en los municipios Jinotega, La Concordia, San Rafael del Norte y Yalí, del departamento de Jinotega, en el periodo comprendido de febrero a septiembre del 2014.  El levantamiento de datos se desarrolló en 4 fincas de papa. En cada finca se ubicaron 30 trampas amarillas pegajosas y 30 estaciones para el muestreo visual. Los insectos Bactericera cockerelli encontrados, así como los síntomas de la enfermedad detectados en campo, se identificaron con ayuda de la guía temática utilizada por los especialistas fitosanitarios del Instituto de Protección y Sanidad Agropecuaria (IPSA). Se evaluó el número de insectos capturados en las trampas amarillas y el númede insectos observados, el número de plantas con síntomas de Candidatus liberibacter y la incidencia de daño en tubérculos en las fincas de papa. De acuerdo a los resultados obtenidos se demostró que las poblaciones de Bactericera cockerelli se presentaron en papa, desde marzo 14 hasta mayo 23, con el máximo pico poblacional abril 25, en el ciclo de primera y de junio 23 hasta septiembre 02, con el máximo pico poblacional en julio 22, en el ciclo de postrera; la incidencia de Candidatus liberibacter en papa fue mayor en el ciclo de primera que en postrera y la incidencia de Candidatus liberibacter en tubérculos fue mayor en la finca Buenos Aires con 72%, El Aguacate 1 presentó 32%, Las Piedras 23% y El Aguacate 2, 16%.

AbstractNatural microbial communities are phylogenetically and metabolically diverse. In addition to underexplored organismal groups1, this diversity encompasses a rich discovery potential for ecologically and biotechnologically relevant enzymes and biochemical compounds2,3. However, studying this diversity to identify genomic pathways for the synthesis of such compounds4and assigning them to their respective hosts remains challenging. The biosynthetic potential of microorganisms in the open ocean remains largely uncharted owing to limitations in the analysis of genome-resolved data at the global scale. Here we investigated the diversity and novelty of biosynthetic gene clusters in the ocean by integrating around 10,000 microbial genomes from cultivated and single cells with more than 25,000 newly reconstructed draft genomes from more than 1,000 seawater samples. These efforts revealed approximately 40,000 putative mostly new biosynthetic gene clusters, several of which were found in previously unsuspected phylogenetic groups. Among these groups, we identified a lineage rich in biosynthetic gene clusters (‘CandidatusEudoremicrobiaceae’) that belongs to an uncultivated bacterial phylum and includes some of the most biosynthetically diverse microorganisms in this environment. From these, we characterized the phospeptin and pythonamide pathways, revealing cases of unusual bioactive compound structure and enzymology, respectively. Together, this research demonstrates how microbiomics-driven strategies can enable the investigation of previously undescribed enzymes and natural products in underexplored microbial groups and environments.

Summary The recently proposed order Candidatus Thermoprofundales, currently containing only one family‐level lineage Marine Benthic Group‐D (MBG‐D), is distributed in global subsurface ecosystems and ecologically important, but its diversity, evolution and metabolism remain largely unknown. Here we described two novel family‐level specialized lineages in Ca . Thermoprofundales, JdFR‐43 and HyVt, which are restricted to specific biotopes (primarily in marine hydrothermal vents and occasionally in oil reservoirs and hot springs) in contrast to the cosmopolitan lineage MBG‐D. The comparative genomics revealed that the specialized lineages have streamlined genomes, higher GC contents, enriched genes associated with nucleotide biosynthesis, ribosome biogenesis and DNA repair and additional thermostable aminopeptidases, enabling them to adapt to high‐temperature habitats such as marine hydrothermal vents, deep subsurface oil reservoirs and hot springs. On the contrary, the unique metabolic traits of the cosmopolitan MBG‐D, motility, glycolysis, butanoate metabolism, secondary metabolites production and additional genes for specific peptides and carbohydrates degradation potentially enhance its response to environmental change. Substrate preference is found for most MAGs across all lineages with the ability to utilize both polysaccharides (chitin and starch) and proteinaceous substances, whereas JdFR‐43 members from oil reservoirs can only utilize proteins. These results expand the diversity of C a . Thermoprofundales significantly and further improve our understandings of the adaptations of C a . Thermoprofundales to various environments.

Abstract Background In addition to Mycoplasma haemocanis and Candidatus Mycoplasma haematoparvum, a few hemoplasma species that mainly infect other livestock have been detected in dogs. ‘Candidatus Mycoplasma haemobos’ (Ca. M. haemobos) has been found in a variety of animals in China. The present study was aimed to investigate the occurrence of ‘Ca. M. haemobos’ infections in dogs and ticks collected from the Henan province, China. Results Overall, 55 dog blood samples and 378 ticks on skins were collected from anemic and healthy dogs, and these samples were subjected to PCR, sequence analysis, and identification. The results showed that Haemaphysalis longicornis (266) and Rhipicephalus (Boophilus) microplus (112) were the only two parasitic ticks on dogs. Molecular detection revealed that 163 M. haemocanis, 88 ‘Ca. M. haemobos’ and 32 Anaplasma platys positive amplicons could be amplified from dogs, H. longicornis and R. (B.) microplus. In addition, co-infections (M. haemocanis + A. platys and ‘Ca. M. haemobos’+ A. platys) could be also detected. Conclusions To the best of our knowledge, this is the first molecular evidence of ‘Ca. M. haemobos’ natural infection in dogs and tick species identified as H. longicornis and R. (B.) microplus from China.

AbstractCandidatus Branchiomonas cysticola is an intracellular, gram-negative Betaproteobacteria causing epitheliocystis in Atlantic Salmon (Salmo salar L.). The bacterium has not been genetically characterized at the intraspecific level despite its high prevalence among salmon suffering from gill disease in Norwegian aquaculture. DNA from gill samples of Atlantic salmon PCR positive for Cand. B. cysticola and displaying pathological signs of gill disease, was, therefore, extracted and subject to next-generation sequencing (mNGS). Partial sequences of four housekeeping (HK) genes (aceE, lepA, rplB, rpoC) were ultimately identified from the sequenced material. Assays for real-time RT-PCR and fluorescence in-situ hybridization, targeting the newly acquired genes, were simultaneously applied with existing assays targeting the previously characterized 16S rRNA gene. Agreement in both expression and specificity between these putative HK genes and the 16S gene was observed in all instances, indicating that the partial sequences of these HK genes originate from Cand. B. cysticola. The knowledge generated from the present study constitutes a major prerequisite for the future design of novel genotyping schemes for this bacterium.