Publications

4493

Abstract Here, an established approach to the generation of well-formed arbitrary Latinate names at a scale has been adopted and adapted to name tens of thousands of new, but unnamed taxa within GTDB Release r214.1. New Latinate Candidatus names have been created and assigned to two new archaeal and twelve new bacterial phyla; six new archaeal and 48 new bacterial classes; 13 new archaeal and 158 new bacterial orders; 60 new archaeal and 597 new bacterial families; 271 new archaeal and 3,869 new bacterial genera; and 1,097 new archaeal and 18,126 new bacterial species. New Candidatus names for bacterial phyla include Ca. Afuciota, Ca.Axiviota, Ca. Bobupiota, Ca. Fitepiota, Ca. Hubebiota, Ca.Ibociota, Ca. Inuciota, Ca. Luxamiota, Ca. Megaciota, Ca.Nasexiota, Ca. Oviciota, Ca. Ucifiota, and Ca. Uvuciota, while new names for archaeal phyla include Ca. Acigarchota and Ca.Omefarchota. These efforts show that the creation of arbitrary names for prokaryotic taxa remains sustainable, despite the relentless progress of discovery.

The apple orchards in Niğde, Turkiye were surveyed for ‘Candidatus Phytoplasma mali’ associated with apple proliferation disease, and the suspicious samples were tested by PCR-RFLP methods. A comprehensive study was conducted which included sampling from a total of 19 orchards from four different districts. The samples were collected according to the major symptoms of phytoplasma disease which were foliar reddening, witches’ brooms, leaf rosettes, yellowing, longer peduncles and development of undersized fruits. It was determined that six out of 62 plant samples were infected with pyhtoplasma. Also, two out of six infected samples were determined as infected by ‘Ca. P. mali’ and unexpectedly four out of six infected samples were determined as infected by ‘Ca. P. prunorum’ associated with European Stone Fruit Yellows disease. Even if the incidence of the disease (9.7%) was low, the characterized phytoplasmas were considered as a significant potential threat for these locations. Key words: PCR-RFLP Survey, Niğde, Apple proliferation, European stone fruit yellows

ABSTRACT “ Candidatus Liberibacter asiaticus” (CLas), the causal agent of citrus Huanglongbing (HLB), is able to multiply to a high abundance in citrus fruit pith. However, little is known about the biological processes and phytochemical substances that are vital for CLas colonization and growth in fruit pith. In this study, CLas-infected fruit pith of three citrus cultivars (“Shatangju” mandarin, “Guanxi” pomelo, and “Shatian” pomelo) exhibiting different tolerance to CLas were collected and used for dual RNA-Seq and untargeted metabolome analysis. Comparative transcriptome analysis found that the activation of the CLas noncyclic TCA pathway and pathogenic-related effectors could contribute to the colonization and growth of CLas in fruit pith. The pre-established Type 2 prophage in the CLas genome and the induction of its CRISPR/ cas system could enhance the phage resistance of CLas and, in turn, facilitate CLas population growth in fruit pith. CLas infection caused the accumulation of amino acids that were correlated with tolerance to CLas. The accumulation of most sugars and organic acids in CLas-infected fruit pith, which could be due to the phloem blockage caused by CLas infection, was thought to be beneficial for CLas growth in localized phloem tissue. The higher levels of flavonoids and terpenoids in the fruit pith of CLas-tolerant cultivars, particularly those known for their antimicrobial properties, could hinder the growth of CLas. This study advances our understanding of CLas multiplication in fruit pith and offers novel insight into metabolites that could be responsible for tolerance to CLas or essential to CLas population growth. IMPORTANCE Citrus Huanglongbing (HLB, also called citrus greening disease) is a highly destructive disease currently threatening citrus production worldwide. HLB is caused by an unculturable bacterial pathogen, “ Candidatus Liberibacter asiaticus” (CLas). However, the mechanism of CLas colonization and growth in citrus hosts is poorly understood. In this study, we utilized the fruit pith tissue, which was able to maintain the CLas at a high abundance, as the materials for dual RNA-Seq and untargeted metabolome analysis, aiming to reveal the biological processes and phytochemical substances that are vital for CLas colonization and growth. We provided a genome-wide CLas transcriptome landscape in the fruit pith of three citrus cultivars with different tolerance and identified the important genes/pathways that contribute to CLas colonization and growth in the fruit pith. Metabolome profiling identified the key metabolites, which were mainly affected by CLas infection and influenced the population dynamic of CLas in fruit pith.

Ciliates are unicellular eukaryotes, regularly involved in symbiotic associations. Symbionts may colonize the inside of their cells as well as their surface as ectosymbionts. Here, we report on a new ciliate species, designated asZoothamnium mariellasp. nov. (Peritrichia, Sessilida), discovered in the northern Adriatic Sea (Mediterranean Sea) in 2021. We found this ciliate species to be monospecifically associated with a new genus of ectosymbiotic bacteria, here proposed asCandidatusFusimicrobium zoothamnicola gen. nov., sp. nov. To formally describe the new ciliate species, we investigated its morphology and sequenced its 18S rRNA gene. To demonstrate its association with a single species of bacterial ectosymbiont, we performed 16S rRNA gene sequencing, fluorescencein situhybridization, and scanning electron microscopy. Additionally, we explored the two partners’ cultivation requirements and ecology.Z. mariellasp. nov. was characterized by a colony length of up to 1 mm. A consistent number of either seven or eight long branches alternated on the stalk in close distance to each other. The colony developed three different types of zooids: microzooids (“trophic stage”), macrozooids (“telotroch stage”), and terminal zooids (“dividing stage”). Viewed from inside the cell, the microzooids’ oral ciliature ran in 1 ¼ turns in a clockwise direction around the peristomial disc before entering the infundibulum, where it performed another ¾ turn. Phylogenetic analyses assignedZ. mariellasp. nov. to clade II of the family Zoothamnidae. The ectosymbiont formed a monophyletic clade within theGammaproteobacteriaalong with two other ectosymbionts of peritrichous ciliates and a free-living vent bacterium. It colonized the entire surface of its ciliate host, except for the most basal stalk of large colonies, and exhibited a single, spindle-shaped morphotype. Furthermore, the two partners together appear to be generalists of temperate, oxic, marine shallow-water environments and were collectively cultivable in steady flow-through systems.

Abstract The Candidate Phyla Radiation (CPR) encompasses widespread uncultivated bacteria with reduced genomes and limited metabolic capacities. Most CPR bacteria lack the minimal set of enzymes required for peptidoglycan (PG) synthesis, leaving it unclear how these bacteria produce this essential envelope component. In this study, we analysed the distribution of d ‐amino acid racemases that produce the universal PG components d ‐glutamate ( d ‐Glu) or d ‐alanine ( d ‐Ala). We also examined moonlighting enzymes that synthesize d ‐Glu or d ‐Ala. Unlike other phyla in the domain Bacteria, CPR bacteria do not exhibit these moonlighting activities and have, at most, one gene encoding either a Glu or Ala racemase. One of these ‘orphan’ racemases is a predicted Glu racemase (MurI CPR ) from the CPR bacterium Candidatus Saccharimonas aalborgenesis . The expression of MurI CPR restores the growth of a Salmonella d ‐Glu auxotroph lacking its endogenous racemase and results in the substitution of l ‐Ala by serine as the first residue in a fraction of the PG stem peptides. In vitro, MurI CPR exclusively racemizes Glu as a substrate. Therefore, Ca. Saccharimonas aalborgensis may couple Glu racemization to serine and d ‐Glu incorporation into the stem peptide. Our findings provide the first insights into the synthesis of PG by an uncultivated environmental bacterium and illustrate how to experimentally test enzymatic activities from CPR bacteria related to PG metabolism.

Huanglongbing (HLB) is a disease caused by the phloem- limited Candidatus Liberibacter asiaticus (CLas) that affects the citrus industry worldwide. To date, only indirect strategies have been implemented to eradicate HLB. Included among these is the population control of the psyllid vector (Diaphorina citri), which usually provides inconsistent results. Even though strategies for direct CLas suppression seem a priori more promising, only a handful of reports have been focused on a confrontation of the pathogen. Recent developments in polymer chemistry have allowed the design of polycationic self-assembled block copolymers with outstanding antibacterial capabilities. Here, we report the use of polymeric nano-sized bactericide particles (PNB) to control CLas directly in the phloem vasculature. The field experiments were performed in Rioverde, San Luis Potosí, and is one of the most important citrusproducing regions in Mexico. An average 52% reduction in the bacterial population was produced when PNB was injected directly into the trunk of 20 infected trees, although, in some cases, reduction levels reached 97%. These results position PNB as a novel and promising nanotechnological tool for citrus crop protection against CLas and other related pathogens.