Publications

4364

A hydrogenotrophic methanoarchaeon, designated strain FWC-SCC4T, was isolated from cold seep sediment of Four-Way Closure Ridge, offshore southwestern Taiwan. Strain FWC-SCC4Tutilizes H2/CO2 or formate, but not acetate, secondary alcohols, methylamines, methanol or ethanol for growth and methane production. Yeast extract is required for growth. The cell morphology is coccoid, with a diameter of 0.8–1.2 µm, and the cell envelope is composed of S-layer protein with Mr about 137.00 kDa. Cells possess multiple flagella and usually occur singly. Strain FWC-SCC4T grows at a temperature range of 20–40 °C (optimum 37 °C) and a pH range of 5.4–7.2 (optimum 7.0). The NaCl range for growth is 0–0.86 M (optimum 0.09 M). The result of phylogenetic analysis of 16S rRNA gene sequences indicates that the most closely related species are Methanoplanus limicola M3T and Methanoplanus endosymbiosus MC1T, with similarities of 95.95 and 95.63%, respectively. The G+C content of the genomic DNA is 40.3 mol%. The overall genome-relatedness indexes (OGRIs) and concatenated ribosomal protein (RBP) phylogenic analysis indicate that strain FWC-SCC4T is a novel lineage of Methanomicrobiaceae. In addition to strain FWC-SCC4T, the differences between Methanomicrobium antiquum MobHT and Methanomicrobium mobile BPT demonstrated by comparative analysis of genomic G+C content and phylogenetic analysis with non-type strain genomes are enough to support the establishment of a novel genus. In conclusion, strain FWC-SCC4T (BCRC AR10058T= NBRC 114595T) is proposed as the type strain of Methanochimaera problematica gen. nov., sp. nov., and Methanoeremita antiquus gen. nov., comb. nov. is proposed as the new name for Methanomicrobium antiquum MobHT (=DSM 21220T= NBRC 104160T).

ABSTRACTThe Coxiellaceae bacterial family, within the order Legionellales, is defined by a collection of poorly characterized obligate intracellular bacteria. The zoonotic pathogen and causative agent of human Q fever,Coxiella burnetii, represents the best characterized member of this family. Coxiellaceae establish replicative niches within diverse host cells and rely on their host for survival, making them challenging to isolate and cultivate within a laboratory setting. Here we describe a new genus within the Coxiellaceae family that has been previously shown to infect economically significant freshwater crayfish. Using culture-independent long-read metagenomics, we reconstructed the complete genome of this novel organism and demonstrate that the previously referred to as CandidatusCoxiella cheraxirepresents a novel genus within this family, herein denoted CandidatusParacoxiella cheracis. Interestingly, we demonstrate that CandidatusP. cheracisencodes for a complete, putatively functional Dot/Icm type 4 secretion system that likely mediates the intracellular success of this pathogen. In silico analysis defined a unique repertoire of Dot/Icm effector proteins and highlighted homologues of several importantC. burnetiieffectors including a homologue of CpeB that was demonstrated to be a Dot/Icm substrate inC. burnetii.IMPORTANCEUsing long-read sequencing technology we have uncovered the full genome sequence of CandidatusParacoxiellacheracis, a pathogen of economic importance in aquaculture. Analysis of this sequence has revealed new insight into this novel member of the Coxiellaceae family, demonstrating that it represents a new genus within this poorly characterized family of intracellular organisms. Importantly, the genome sequence reveals invaluable information that will support diagnostics and potentially both preventative and treatment strategies within crayfish breeding facilities. CandidatusP. cheracisalso represents a new member of Dot/Icm pathogens that rely on this system to establish an intracellular niche. CandidatusP. cheracispossesses a unique cohort of putative Dot/Icm substrates that constitute a collection of new eukaryotic cell biology manipulating effector proteins.

Abstract  The Gemmatimonadota phylum has been widely detected in diverse natural environments, yet their specific ecological roles in many habitats remain poorly investigated. Similarly, the Candidatus ARS69 phylum has been identified only in a few habitats, and literature on their metabolic functions is relatively scarce. In the present study, we investigated the ecological significance of phyla Ca. ARS69 and Gemmatimonadota in the Arctic glacier foreland (GF) ecosystems through genome-resolved metagenomics. We have reconstructed the first high-quality metagenome-assembled genome (MAG) belonging to Ca. ARS69 and 12 other MAGs belonging to phylum Gemmatimonadota from the three different Arctic GF samples. We further elucidated these two groups phylogenetic lineage and their metabolic function through phylogenomic and pangenomic analysis. The analysis showed that all the reconstructed MAGs potentially belonged to novel species. The MAGs belonged to Ca. ARS69 consist about 8296 gene clusters, of which only about 8% of single-copy core genes (n = 980) were shared among them. The study also revealed the potential ecological role of Ca. ARS69 is associated with carbon fixation, denitrification, sulfite oxidation, and reduction biochemical processes in the GF ecosystems. Similarly, the study demonstrates the widespread distribution of different classes of Gemmatimonadota across wide ranges of ecosystems and their metabolic functions, including in the polar region. Key points • Glacier foreland ecosystems act as a natural laboratory to study microbial community structure. • We have reconstructed 13 metagenome-assembled genomes from the soil samples. • All the reconstructed MAGs belonged to novel species with different metabolic processes. • Ca. ARS69 and Gemmatimonadota MAGs were found to participate in carbon fixation and denitrification processes.

ABSTRACTIn an era of trade globalization and climate change, crop pathogens and pests are a genuine threat to food security. The detailed characterization of emerging pathogen populations is a prerequisite for managing invasive species pathways and designing sustainable disease control strategies. Huanglongbing is the disease that causes the most damage to citrus, a crop that ranks #1 worldwide in terms of fruit production. Huanglongbing can be caused by three species of the phloem‐limited alpha‐proteobacterium, “Candidatus Liberibacter,” which are transmitted by psyllids. Two of these bacteria are of highest concern, “Ca. Liberibacter asiaticus” and “Ca. Liberibacter africanus,” and have distinct thermal optima. These pathogens are unculturable, which complicates their high‐throughput genetic characterization. In the present study, we used several genotyping techniques and an extensive sample collection to characterize Ca. Liberibacter populations associated with the emergence of huanglongbing in three French outermost regions of the European Union (Guadeloupe, Martinique and Réunion). The outbreaks were primarily caused by “Ca. Liberibacter asiaticus,” as “Ca. Liberibacter africanus” was only found at a single location in Réunion. We emphasize the low diversity and high genetic relatedness between samples from Guadeloupe and Martinique, which suggests the putative movement of the pathogen between the two islands and/or the independent introduction of closely related strains. These samples were markedly different from the samples from Réunion, where the higher genetic diversity revealed by tandem‐repeat markers suggests that the disease was probably overlooked for years before being officially identified in 2015. We show that “Ca. Liberibacter asiaticus” occurs from sea level to an altitude of 950 m above sea level and lacks spatial structure. This suggests the pathogen's medium‐ to long‐distance movement. We also suggest that backyard trees acted as relays for disease spread. We discuss the implications of population biology data for surveillance and management of this threatful disease.