Publications

4504

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.

AbstractBACKGROUNDHuanglongbing (HLB) is the primary and most destructive disease affecting citrus, caused by a pathogen transmitted by an insect vector, Diaphorina citri. There are no curative methods for the disease, and rapid and accurate methods are needed for early detection in the field, even before symptoms appear. These will facilitate the faster removal of infected trees, preventing the spread of the bacteria through commercial citrus orchards.RESULTSIt was possible to determine ranges of hyperspectral bands that demonstrated significant differences in relative reflectance between treatments consisting of healthy and infected plants from the first days of evaluation, when plants infected with ‘Candidatus Liberibacter asiaticus’ (CLas) were still in the asymptomatic stage of the disease. From the Week 2 of evaluation [58 days after infection (DAI) of plants] until the last week, spectral differences were detected in the red edge region (660–750 nm). From the Week 6 onwards (86 DAI), spectral differences between healthy and symptomatic plants were observed in bands close to the visible region (520–680 nm).CONCLUSIONSpectral differences were detected in the leaves of C. sinensis infected by CLas before the appearance of symptoms, making it feasible to use the hyperspectral sensor to monitor the disease. Our results indicate the need for future studies to validate the use of hyperspectral sensors for managing and detecting HLB in commercial citrus orchards, contributing to the integrated management of the disease. © 2024 Society of Chemical Industry.

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.

AbstractBACKGROUNDThe brown marmorated stink bug Halyomorpha halys has become an invasive insect pest of many crops. A promising control strategy to manage the proliferation of H. halys is based on the suppression of its obligate and vertically transmitted uncultivated symbiotic bacterium Candidatus Pantoea carbekii through surface‐sterilization of H. halys eggs. Indeed, the application of antimicrobial formulations on the eggs of H. halys could cause mortality of endosymbiont and consequently of newly emerged nymphs.In this study, a microbial live/dead assay was applied directly on H. halys eggs to evaluate Ca. P. carbekii loss of viability after treatments with seven commercial formulations including fungicides (copper hydroxide, sulphur, sweet orange essential oil) and plant biostimulants (flavonoids and chestnut tannin extract) compared with two disinfectants for civil and industrial use (sodium hypochlorite/hydrated sodium/tetraborate decahydrate and peracetic acid/hydrogen peroxide). Impact of mode of application was also evaluated, as surface treatment of egg masses was performed through spraying and dipping in laboratory conditions. Antimicrobial activity data were finally complemented with observations of egg hatching and vitality of the nymphs.RESULTSThe optimization of live/dead staining is useful for evaluating Ca. P. carbekii mortality directly on eggs, providing a rapid and reliable culture‐independent approach. Sodium hypochlorite, copper, sulphur, tannins and sweet orange essential oil showed an antimicrobial effect against Ca. P. carbekii and a H. halys egg hatching reduction and nymph's vitality.CONCLUSIONSThe antimicrobial and insecticidal effects of these commercial products should be further studied to assess their in‐field efficiency as well as the impact of these substances on non‐target organisms. The approach followed in this study could be considered a robust pipeline of analyses to evaluate the effectiveness of antimicrobial eco‐friendly compounds in symbiotic control of H. halys. © 2024 Society of Chemical Industry.

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’.