Publications

4472

The members of the genusFrankiaare, with a few exceptions, a group of nitrogen-fixing symbiotic actinobacteria that nodulate mostly woody dicotyledonous plants belonging to three orders, eight families and 23 genera of pioneer dicots. These bacteria have been characterized phylogenetically and grouped into four molecular clusters. One of the clusters, cluster 1 contains strains that induce nodules onAlnusspp. (Betulaceae),Myricaspp.,Morellaspp. andComptoniaspp. (Myricaceae) that have global distributions. Some of these strains produce not only hyphae and vesicles, as other cluster 1 strains do, but also numerous sporangia in their host symbiotic tissues, hence their phenotype being described as spore-positive (Sp+). While Sp+ strains have resisted repeated attempts at cultivation, their genomes have recently been characterized and found to be different from those of all described species, being markedly smaller than their phylogenetic neighbours. We thus hereby propose to create a 'CandidatusFrankia alpina' species for some strains present in nodules ofAlnus alnobetulaandA. incanathat grow in alpine environments at high altitudes or in subarctic environments at high latitudes.

Abstract Background Huanglongbing (HLB) is a major botanical pandemic of citrus crops caused by Candidatus Liberibacter asiaticus (Clas). It is important to understand the different mechanisms involved in interaction of pathogen with plants to develop novel management strategy against HLB. However, until now there has been no control strategy to manage this disease in vitro and on large scale in citrus grove. We found that, indigenous endophyte Bacillus subtilis L1-21, a patented strain isolated from healthy citrus tree, may have the potential to reduce the impact of pathogen through restructuring of core endophytes. Results A novel half-leaf method was developed to test the efficacy of B. subtilis L1-21 against Clas. Concentration of B. subtilis L1-21 at 104 cfu ml− 1 resulted in a 1000-fold reduction in Clas copy densities per gram of leaf midrib (107 to 104) by 4 d after treatment. With endophytes, where HLB incidence was reduced to < 3% and Clas copy density was reduced from 109 to 104 pathogen g− 1 of diseased leaf midrib. We found that 16 of 93 tree samples became Clas-free and functional pathways and pathogen resistance genes were regulated in diseased citrus trees after treatment. Conclusions This is the first large-scale study using an indigenous endophyte and shows its potential utility in sustainable disease management through strengthening the citrus microbiome.

Abstract Background: Ehrlichia is a genus of Rickettsiales bacteria closely related to human/animal disease and it plays an important role in public health. Naturally they are hosted by mammals such as canines, bovines, wild rodents and vectored by ticks. Results: In this study, we collected 121 rodent samples including 67 Niviventer fulvescens, 27 Rattus tanezumi, 24 Chiromyscus sp., 2 Rattus nitidus and 1 Leopoldamys edwardsi from Hainan province, which consists of the second largest island in China. The presence and genetic diversity of Ehrlichia was evaluated and characterized by amplifying and sequencing the 16S rRNA, groEL and gltA genes. An Ehrlichia species was detected in 5 of the 67 Niviventer fulvescens samples (7.46%). The 16S rRNA, groEL and gltA genes show highest 99.20%, 89.87% and 83.86% identity to known Ehrlichia sequences. In the phylogenetic trees they form a distinct cluster from any other species. Conclusions: We propose that this species present a putative novel Ehrlichia species nominated as ‘Candidatus Ehrlichia hainanensis’. Its pathogenicity to human is still to be further researched and molecular surveillance in local populations is needed.

Abstract Me.tha.no.tri.cha.ce'ae. N.L. fem. n. Methanothrix type genus of the family; suff. – aceae ending to denote a family; N.L. fem. pl. n. Methanotrichaceae the Methanothrix family. Sheathed, rod‐shaped cells with flat ends, usually 0.8–1.3 μm wide by 2.0–6.0 μm long. Nonmotile. Gram‐stain‐negative. Oxygen‐tolerant anaerobe. Slow‐growing organotrophic, splitting acetate into methane and CO 2 for energy generation. Some strains split formate into hydrogen and CO 2 without generating methane. CO 2 can be reduced into methane when cocultured with electrogenic Geobacter spp. via direct interspecies electron transfer (DIET). Lipids contain myo ‐inositol, ethanolamine, and galactose as the polar head groups. Genome sequences have been determined for all described species. Habitats : Widely distributed in anaerobic river mud, paddy field soil, hot springs, thermal lakes, thermophilic and mesophilic anaerobic wastewater digestors treating domestic wastes, granular sludge, anaerobic fixed‐bed reactors, and other types of anaerobic systems. DNA G + C content (mol%) : 51–61 (Genome). Type genus : Methanothrix Huser et al. 1982, VL10. Taxonomic and Nomenclature Notes According to the List of Prokaryotic names with Standing in Nomenclature (LPSN), the taxonomic status of the family Methanotrichaceae is: correct name (last update, February 2025) * . LPSN classification: Archaea / Methanobacteriati / Methanobacteriota / Methanosarcinia / Methanosarcinales / Methanotrichaceae The family Methanotrichaceae can also be recovered in the Genome Taxonomy Database (GTDB) as f__Methanotrichaceae (version v220) ** . GTDB classification: d__Archaea / p__Halobacteriota / c__Methanosarcinia / o__Methanotrichales / f__Methanotrichaceae * Meier‐Kolthoff et al. ( 2022 ). Nucleic Acids Res , 50 , D801 – D807 ; DOI: 10.1093/nar/gkab902 ** Parks et al. ( 2022 ). Nucleic Acids Res , 50 , D785 – D794 ; DOI: 10.1093/nar/gkab776