Publications

3805

AbstractCandidatusParvarchaeales, representing a DPANN archaeal group with limited metabolic potentials and reliance on hosts for their growth, were initially found in acid mine drainage (AMD). Due to the lack of representatives, however, their ecological roles and adaptation to extreme habitats such as AMD, as well as how they diverge across the lineage remain largely unexplored. By applying genome-resolved metagenomics, 28Parvarchaeales-associated metagenome-assembled genomes (MAGs) representing two orders and five genera were recovered. Among them, we identified three new genera and proposed the namesCandidatusJingweiarchaeum,CandidatusHaiyanarchaeum, andCandidatusRehaiarchaeum with the former two belonging to a new orderCandidatusJingweiarchaeales. Further analyses of metabolic potentials revealed substantial niche differentiation between Jingweiarchaeales and Parvarchaeales. Jingweiarchaeales may rely on fermentation, salvage pathways, partial glycolysis, and pentose phosphate pathway (PPP) for energy reservation, while the metabolic potentials of Parvarchaeales might be more versatile. Comparative genomic analyses suggested that Jingweiarchaeales are more favorable to habitats with higher temperatures andParvarchaealesare better adapted to acidic environments. We further revealed that the thermal adaptation of these lineages especially for Haiyanarchaeum might rely on innate genomic features such as the usage of specific amino acids, genome streamlining, and hyperthermal featured genes such asrgy. Notably, the acidic adaptation of Parvarchaeales was possibly driven by horizontal gene transfer (HGT). Reconstruction of ancestral states demonstrated that both may originate from thermal and neutral environments and later spread to mesothermal and acidic environments. These evolutionary processes may also be accompanied by adaptation toward oxygen-rich environments via HGT.ImportanceCandidatusParvarchaeales may represent a lineage uniquely distributed in extreme environments such as AMD and hot springs. However, little is known about the strategies and processes of how they adapted to these extreme environments. By the discovery of potential new order-level lineages - Jingweiarchaeales and in-depth comparative genomic analysis, we unveiled the functional differentiation of these lineages. Further, we show that the adaptation to high-temperature and acidic environments of these lineages was driven by different strategies, with the prior relying more on innate genomic characteristics and the latter more on the acquisition of genes associated with acid tolerance. Finally, by reconstruction of ancestral states of OGT andpI, we showed the potential evolutionary process of Parvarchaeales-related lineages with regard to the shift from a high-temperature environment of their common ancestors to low-temperature (potentially acidic) environments.

The International Code of Nomenclature of Prokaryotes (ICNP) recently underwent some major modifications regarding the higher taxonomic ranks. On the one hand, the phylum category was introduced into the ICNP, which rapidly led to the valid publication of more than forty names of phyla. On the other hand, a decision on the retroactivity of Rule 8 regarding the names of classes was made, which removed most of the nomenclatural uncertainty that had affected those names during the last decade. However, it turned out that a number of names at the ranks of class, order and family are either not validly published or are validly published but illegitimate, although these names occur in the literature and are based on the type genus of a phylum with a validly published name. A closer examination of the literature for these and similar cases indicates that the names are unavailable under the ICNP either because of minor formal errors in the original descriptions, because another name should have been adopted for the taxon when the name was proposed, because of taxonomic uncertainties that were settled in the meantime, or because the names were placed on the list of rejected names. The purpose of this article is to fill the gaps by providing the missing formal descriptions and to ensure that the resulting taxon names are attributed to the original authors who did the taxonomic work.

Comparing obligate endosymbionts with their free-living relatives is a powerful approach to investigate the evolution of symbioses, and it has led to the identification of several genomic traits consistently associated with the establishment of symbiosis. ‘Candidatus Nebulobacter yamunensis’ is an obligate bacterial endosymbiont of the ciliate Euplotes that seemingly depends on its host for survival. A subsequently characterized bacterial strain with an identical 16S rRNA gene sequence, named Fastidiosibacter lacustris , can instead be maintained in pure culture. We analysed the genomes of ‘Candidatus Nebulobacter’ and Fastidiosibacter seeking to identify key differences between their functional traits and genomic structure that might shed light on a recent transition to obligate endosymbiosis. Surprisingly, we found almost no such differences: the two genomes share a high level of sequence identity, the same overall structure, and largely overlapping sets of genes. The similarities between the genomes of the two strains are at odds with their different ecological niches, confirmed here with a parallel growth experiment. Although other pairs of closely related symbiotic/free-living bacteria have been compared in the past, ‘Candidatus Nebulobacter’ and Fastidiosibacter represent an extreme example proving that a small number of (unknown) factors might play a pivotal role in the earliest stages of obligate endosymbiosis establishment.

Se identificaron nuevos haplotipos de Diaphorina citri también conocido como el psílido asiático de los cítricos, denominados DcitACC-1, DcitACC-2 y DcitACC-3. Los estudios se basaron en la amplificación de ADN del gen COI mitocondrial y se utilizaron individuos de diferentes zonas citrícolas del país, en algunas zonas productoras del país no se han realizado muestreos con anterioridad, específicamente en los municipios de Acatlán de Pérez, Oaxaca, Misantla y Tantoyuca, Veracruz y Huejutla, Hidalgo, por lo que se procedió a colectar insectos adultos sin distinción de género. El número de individuos de cada sitio colectado dependió de la disponibilidad de insectos en el lugar. Se obtuvieron en total 60 individuos colectados. La amplificación del ADN se realizó con los iniciadores específicos DCITRI COI-L y DCITRI COI-R, el producto de la reacción PCR se secuenció en el Instituto Potosino de Investigación Científica y Tecnológica, AC (IPICYT). Las secuencias obtenidas se compararon con las reportadas en el Genebank y se determinó que existe una línea matriz que corresponde a los haplotipos Dcit-01 y Dcit-04 con número de identificación FJ190300 y FJ190306 (Boykin, 2007). Se obtuvieron 22 secuencias que se analizaron con los programas Oligo analizer y Clustal Omega y se identificaron 11 secuencias iguales a los haplotipos Dcit-01 y Dcit-04. Los resultados mostraron 13 secuencias con diferencias en tres nucleótidos específicos: 61, 253 y 636, mismos que son reportados en este trabajo como nuevos haplotipos.

El objetivo de este trabajo fue identificar en el genoma de Candidatus Liberibacter asiaticus (CLas), proteínas de membrana externa con potencial para el desarrollo y optimización de un método de detección inmunoenzimático. El estudio se realizó durante 2019 y se utilizó el servidor web Predict Protein, así como las bases de datos HhPred/HhSearch y Pfam. Se detectaron 52 proteínas de membrana externa en el genoma completo de CLas, de las cuales, 11 no habían sido caracterizadas previamente. Los análisis predictivos realizados en la proteína B8Y674 generaron ocho posibles epítopos y cuatro de ellos evaluados experimentalmente en células B, mostraron porcentajes de identidad entre 80 a 90%. Se detectó a CLas mediante PCR-punto final a partir del ADN extraído de limón mexicano con síntomas de Huanglongbing utilizando iniciadores diseñados sobre la secuencia del gen Omp que codifica para la proteína B8Y674 y se registró 95% de identidad entre las secuencias generadas y secuencias de CLas previamente reportadas. Los resultados obtenidos nos permiten inferir que la proteína B8Y674 es un candidato potencial para ser utilizada en la detección inmunoenzimática de CLas.

Citrus greening, also known as Huanglongbing (HLB), is caused by the unculturable bacterium Candidatus Liberibacter spp. (e.g., CLas), and has caused a devastating decline in citrus production in many areas of the world. As of yet, there are no definitive treatments for controlling the disease. Antimicrobial peptides (AMPs) that have the potential to block secretion-dependent effector proteins at the outer-membrane domains were screened in silico. Predictions of drug-receptor interactions were built using multiple in silico techniques, including molecular docking analysis, molecular dynamics, molecular mechanics generalized Born surface area analysis, and principal component analysis. The efflux pump TolC of the Type 1 secretion system interacted with natural bacteriocin plantaricin JLA-9, blocking the β barrel. The trajectory-based principal component analysis revealed the possible binding mechanism of the peptides. Furthermore, in vitro assays using two closely related culturable surrogates of CLas (Liberibacter crescens and Rhizobium spp.) showed that Plantaricin JLA-9 and two other screened AMPs inhibited bacterial growth and caused mortality. The findings contribute to designing effective therapies to manage plant diseases associated with Candidatus Liberibacter spp.

“Candidatus Liberibacter asiaticus” (CLas) is a phloem-restricted α-proteobacterium that is associated with citrus huanglongbing (HLB), which is the most destructive disease that affects all varieties of citrus. Although midrib is usually used as a material for CLas detection, we recently found that the bacterium was enriched in fruits, especially in the fruit pith. However, no study has revealed the molecular basis of these two parts in responding to CLas infection. Therefore, we performed transcriptome and UHPLC–MS-based targeted and untargeted metabolomics analyses in order to organize the essential genes and metabolites that are involved. Transcriptome and metabolome characterized 4834 differentially expressed genes (DEGs) and 383 differentially accumulated metabolites (DAMs) between the two materials, wherein 179 DEGs and 44 DAMs were affected by HLB in both of the tissues, involving the pathways of phenylpropanoid biosynthesis, phytohormone signaling transduction, starch and sucrose metabolism, and photosynthesis. Notably, we discovered that the gene expression that is related to beta-glucosidase and endoglucanase was up-regulated in fruits. In addition, defense-related gene expression and metabolite accumulation were significantly down-regulated in infected fruits. Taken together, the decreased amount of jasmonic acid, coupled with the reduced accumulation of phenylpropanoid and the increased proliferation of indole-3-acetic acid, salicylic acid, and abscisic acid, compared to leaf midribs, may contribute largely to the enrichment of CLas in fruit piths, resulting in disorders of photosynthesis and starch and sucrose metabolism.