Publications

4449

An anaerobic isolate, designated me31T, was isolated from pit mud in Yibin, Sichuan Province, PR China. Phylogenetic results based on 16S rRNA gene sequence showed that strain me31T belongs to the family Dysgonomonadaceae, and the most closely related isolated relatives were Seramator thermalis SYSU GA16112T (93.65%) and Proteiniphilum propionicum JNU-WLY501T (93.22%). The DNA G+C content was 44.26 mol%. The ANI and AAI values between strain me31T and the closely related strains were 69.25–71.18% and 69.59–71.15%, respectively. Cells of strain me31T were Gram-stain-negative, rod-shaped and non-motile. Growth of strain me31T was observed at 25–37 °C, pH 6.0–8.0 and a salt tolerance range of 0–1.0% (w/v). The predominant respiratory quinone was MK-9. The major fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and C17 : 0 2OH. The polar lipids of strain me31T were found to consist of phosphatidylethanolamine, three unidentified phospholipids, three unidentified phosphoglycolipids, one unidentified phosphoglycolipid, one unidentified lipid, two unidentified glycolipids and one aminophosphoglycolipid. According to the results of morphological, physiological, biochemical, chemotaxonomic, genotypic and phylogenetic analysis, strain me31T represents a novel species of a novel genus of the family Dysgonomonadaceae, for which the name Limibacterium fermenti gen. nov., sp. nov. is proposed. The type strain is me31T (=GDMCC 1.4237T=KCTC 25756T=WMCC 10035T).

A motile, rod-shaped and anaerobic strain WK13T was isolated from a secondary root canal infection of a human tooth. WK13T cells were Gram-stain-negative, catalase-positive and oxidase-negative. The major fatty acids (≥ 5.0%) were C16 : 0, C18 : 0, C16 : 1  ω7c, C18 : 1  ω9c and C18 : 2  ω6,9c. The DNA G+C content was 57.94 mol%. The major polar lipids were phosphatidylethanolamine, phosphatidylserine, diphosphatidylglycerol, phosphatidylcholine and lysophosphatidylcholine. There were no respiratory quinones detectable. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain WK13T belongs to the class Betaproteobacteria. WK13T showed a 93.6% and 93.5% 16S rRNA gene sequence similarity to the most closely related cultured species, Propionivibrio pelophilus strain DSM 12018T and Propionivibrio dicarboxylicus strain DSM 5885T, respectively. On the basis of physiological and biochemical data, the isolate is considered to represent a novel species of a new genus in the class Betaproteobacteria, for which we propose the name Dentiradicibacter hellwigii gen. nov., sp. nov. The type strain is WK13T (=DSM 112713T=NCTC 14938T).

Understanding the characteristics of microbes during long-term space missions is essential for safeguarding the health of astronauts and maintaining the functionality of spacecraft. In this study, a Gram-positive, aerobic, spore-forming, rod-shaped strain JL1B1071T was isolated from the surface of hardware on the China Space Station. This strain belongs to the genus Niallia, with its closest relative being Niallia circulans ATCC 4513T. The genome of JL1B1071T is 5 166 230 bp in size, with a G+C content of 35.6 mol%. The average nucleotide identity and digital DNA–DNA hybridization values between JL1B1071T and N. circulans ATCC 4513T are 83.3 and 27.5%, respectively, both below the recommended thresholds for species delineation. The major cellular fatty acids were anteiso-C15:0 and iso-C15:0. The major quinone was menaquinone-7 (MK-7). Notably, strain JL1B1071T demonstrates a unique ability to hydrolyse gelatin, suggesting that it can utilize gelatin as a substrate in nutrient-limited environments. Genomic analysis of JL1B1071T revealed two conserved signature indels in the GAF domain-containing protein and DNA ligase D protein, which are specific to the genus Niallia. Additionally, structural and functional differences in proteins BshB1 and SplA were identified, which may enhance biofilm formation, oxidative stress response and radiation damage repair, thereby aiding its survival in the space environment. Based on phenotypic, physiological and chemotaxonomic characteristics, as well as genome annotation, strain JL1B1071T was considered a novel species within the genus Niallia and is proposed to be named Niallia tiangongensis sp. nov. The type strain is JL1B1071T (=GDMCC 1.4642=KCTC 43715).

Abstract Legumes Lessertia diffusa and Calobota sericea, indigenous to South Africa, are commonly used as fodder crops with potential for sustainable livestock pasture production. Rhizobia were isolated from their root nodules grown in their respective soils from the Succulent Karoo biome (SKB) in South Africa, identified and characterized using a polyphasic approach. Sequence analysis of the 16S rRNA gene confirmed all isolates as Mesorhizobium members, which were categorized into two distinct lineages using five housekeeping protein-coding genes. Lineage I included 14 strains from both legumes, while Lineage II comprised a single isolate from C. sericea. Differences in phenotypic traits were observed between the lineages and corroborated by average nucleotide identity analyses. While all strains nodulated their original hosts, strains from C. sericea failed to effectively nodulate L. diffusa and vice versa. Phylogenetic analyses of nitrogen fixation (nifH) and nodulation (nodA, nodC) loci grouped all strains in a single clade, suggesting that unique symbiotic loci determine nodulation of these legumes. We designated Lineage I and II as Mesorhizobium salmacidum sp. nov. (Ld1326Ts; GCA_037179605.1Ts) and Mesorhizobium argentiipisi sp. nov. (Cs1330R2N1Ts; GCA_037179585.1Ts), using genome sequences as nomenclatural types according to the Nomenclatural Code for Prokaryotes using Sequence Data, thus avoiding complications with South Africa's biodiversity regulations. Identifying effective microsymbionts of L. diffusa and C. sericea is essential for conservation of Succulent Karoo Biome, where indigenous invasive species like Vachellia karroo and non-native Australian acacia species are present. Furthermore, targeted management practices using effective symbionts of the studied legumes can sustain the biome's socio-economic contribution through fodder provision.

The occurrence of ‘Candidatus Liberibacter’ spp. and ‘Ca. Phytoplasma’ spp. associated with blotchy mottle symptoms poses challenges to huanglongbing (HLB) diagnosis using molecular techniques. The ability to detect multiple targets simultaneously and specifically is a key aspect met by quantitative PCR (qPCR). A set of primers and hydrolysis probes useful in either single or multiplex reactions for the detection and quantification of HLB-associated bacteria were developed. Sequences from conserved genes of the ribosomal proteins for Liberibacter and phytoplasma circumvent the lack of specificity and cross-reactivity problems related to 16Sr DNA gene amplification, allowing precise and specific detection of HLB-associated bacteria in citrus and in the Liberibacter vector, Diaphorina citri. The triplex reaction exhibited high quality and precision as a robust tool for quantifying ‘Ca. L. asiaticus’ (CLas), ‘Ca. L. americanus’ (CLam), and 16Sr IX phytoplasma. Triplex qPCR showed consistent results and comparable sensitivity to the ribonuclease reductase test, although quantification cycle (Cq) values were higher when compared with 16SrDNA qPCR. Detection tests using field samples indicate that the qPCR triplex can identify HLB-associated bacteria in samples with varying levels of symptoms, ranging from typical to asymptomatic. Assessment of field samples from growers indicated more than 78.6% had Cq lower than 35.0, below the cutoff established for qPCR reactions used in this work. qPCR triplex is a safe, specific, and sufficiently sensitive technique for detecting CLas, CLam, and 16Sr IX phytoplasma simultaneously, in both citrus and D. citri samples. Its application is of importance in assisting growers in making decisions for HLB management.

ABSTRACT Biogas reactors operating at elevated ammonia levels are commonly susceptible to process disturbances, further augmented at thermophilic temperatures. The major cause is assumed to be linked to inhibition followed by an imbalance between different functional microbial groups, centred around the last two steps of the anaerobic digestion, involving acetogens, syntrophic acetate oxidisers (SAOB) and methanogens. Acetogens are key contributors to reactor efficiency, acting as the crucial link between the hydrolysis and fermentation steps and the final methanogenesis step. Their major product is acetate, at high ammonia levels further converted by SAOB and hydrogenotrophic methanogens to biogas. Even though these functionally different processes are well recognised, less is known about the responsible organism at elevated temperature and ammonia conditions. The main aim of this study was to garner insights into the penultimate stages in three thermophilic reactors (52°C) operated under high ammonia levels (FAN 0.7–1.0 g/L; TAN 3.6–4.4 g/L). The primary objective was to identify potential acetogens and SAOBs. Metagenomic data from the three reactors were analysed for the reductive acetyl‐CoA pathway (Wood–Ljungdahl Pathway) and glycine synthase reductase pathway. The results revealed a lack of true acetogens but uncovered three potential SAOB candidates that harbour the WLP, ‘ Candidatus Thermodarwinisyntropha acetovorans’, ‘ Candidatus Thermosyntrophaceticus schinkii’, ‘ Candidatus Thermotepidanaerobacter aceticum’, and a potential lipid‐degrader ‘ Candidatus Thermosyntrophomonas ammoiaca’.

Abstract In 2022, EFSA was mandated by the European Commission's Directorate‐General for Health and Food Safety (M‐2022‐00070) to provide technical assistance on the list of Union quarantine pests qualifying as priority pests, as specified in Article 6(2) of Regulation (EU) 2016/2031 on protective measures against plant pests. As part of Task C, EFSA conducted comprehensive expert knowledge elicitations for candidate priority pests on the lag period, rate of expansion and impact on production (yield and quality losses) and the environment. This report provides the rationale for the dataset on the three Candidatus Liberibacter species associated with citrus greening disease, delivered to the European Commission's Joint Research Centre, to feed into the Impact Indicator for Priority Pest (I2P2) model and complete the pest prioritisation ranking exercise.