Characterisation of antagonistic Bacillus paralicheniformis (strain EAL) by LC-MS, antimicrobial peptide genes, and ISR determinants

Bacillus paralicheniformis SYN-191 isolated from ginger rhizosphere soil and its growth-promoting effects in ginger farming

BACKGROUND

The use of chemical fertilizers and pesticides and the farming without crop rotation may negatively impact the microbial community and the quality of the soils in ginger farm. It is important to improve soil properties to promote the healthy growth of ginger in ginger farm.

RESULTS

We isolated and identified the pathogenic Fusarium ramigenum from infected ginger roots. We then isolated a new Bacillus paralicheniformis strain SYN-191 from the rhizosphere soil around healthy ginger roots, and showed B. paralicheniformis SYN-91 could inhibit F. ramigenum growth, degrade proteins, dissolve silicate, and decompose cellulose. SYN-191 treatment significantly improved the agronomic traits of ginger seedlings in healthy soil and continuous cropping soil. Furthermore, SYN-191 treatment restructured the microbial microbiomes in rhizosphere soil, including reducing the number of harmful fungi, such as Fusarium, and increasing the beneficial bacterial populations such as Bacillus and Pseudomonas. Field experiments showed that SYN-191 application increased ginger yield by 26.47% (P < 0.01). Whole-genome sequencing of strain SYN-191 revealed the relevant genes for antibiotic synthesis, potassium dissolution, and cellulose decomposition.

CONCLUSIONS

A new plant-growth-promoting B. paralicheniformis SYN-191 was obtained. This strain could antagonize ginger root rot pathogenic fungus, improve agronomic traits and ginger yield in field, and improve the microbial community structure in the ginger rhizosphere soil. This study provides a valuable bacterial resource for overcoming obstacles in the continuous cropping of ginger.

Functional activity of endophytic bacteria G9H01 with high salt tolerance and anti-Magnaporthe oryzae that isolated from saline-alkali-tolerant rice

It holds significant practical importance to screen and investigate endophytic bacteria with salt-tolerant activity in rice for the development of relevant microbial agents. A total of 179 strains of endophytic bacteria were isolated from 24 samples of salt-tolerant rice seeds, with almost 95 % of these bacteria exhibiting tolerance to a salt content of 2 % (0.34 mol/L). Following the screening process, a bacterium named G9H01 was identified, which demonstrated a salt tolerance of up to 15 % (2.57 mol/L) and resistance to Magnaporthe oryzae, the causal agent of rice blast disease. Phylogenetic analysis confirmed G9H01 as a strain of Bacillus paralicheniformis. The complete genome of G9H01 was sequenced and assembled, revealing a considerable number of genes encoding proteins associated with salt tolerance. Further analysis indicated that G9H01 may alleviate salt stress in a high-salt environment through various mechanisms. These mechanisms include the utilization of proteins such as K+ transporters, antiporters, and Na+/H+ antiporters, which are involved in K+ absorption and Na+ excretion. G9H01 also demonstrated the ability to uptake and accumulate betaine, as well as secrete extracellular polysaccharides. Collectively, these findings suggest that Bacillus paralicheniformis G9H01 has potential as a biocontrol agent, capable of promoting rice growth under saline-alkali-tolerant conditions.

1H NMR-Based Metabolomics Profile of Green and Red Amaranthus Grown in Open Field versus Greenhouse Cultivation System

Traditionally, indigenous African leafy vegetables such as Amaranthus, blackjack, jute mallow, cleome monophyla, and spider plants have been conventionally and organically grown as weeds in open fields. However, the lack of land space due to the increase in population has resulted in unconventional, modern, and advanced agricultural farming. The introduction of a greenhouse has recently become the second most popular growing system alongside shade net and glasshouse to increase productivity and meet consumers' demand. Several studies on Amaranthus species have solely focused on physiological parameters and nutritional composition, leaving a huge gap on their metabolomic profile of the leaves which is crucial to comprehend when growing Amaranthus species in different cropping systems. Therefore, the study aimed to determine the influence of different cropping systems on the release of metabolites of two commonly consumed Amaranthus species in South Africa. H1 -Nuclear Magnetic Resonance (NMR) tool was used to profile the untargeted metabolites of green (Amaranthus graecizans L.) and red (Amaranthus cruentus L.) species. A total of 12 metabolites-trehalose, betaine, glutamine, choline, sucrose, caprate, adenosine, asparagine, carnitine, caffeine, aspartate, and alanine-were detected in green amaranth grown in open fields. Except for caffeine, aspartate, and caprate, which were found in the green amaranth grown in open fields, all the other metabolites were detected in the greenhouse grown once. Interestingly, allantoin, which serves as an allelochemical, was the sole distinct metabolite detected in greenhouse cultivated green amaranth. On the contrary, seven similar metabolites were quantified in red amaranth grown in both open fields and greenhouses, apart from caffeine, which was only detected in greenhouse-cultivated red amaranth.

3-Hydroxy coumarin demonstrates anti-biofilm and anti-hyphal efficacy against Candida albicans via inhibition of cell-adhesion, morphogenesis, and virulent genes regulation

Candida albicans, a common fungus of human flora, can become an opportunistic pathogen and causes invasive candidiasis in immunocompromised individuals. Biofilm formation is the prime cause of antibiotic resistance during C. albicans infections and treating biofilm-forming cells is challenging due to their intractable and persistent nature. The study intends to explore the therapeutic potential of naturally produced compounds by competitive marine bacteria residing in marine biofilms against C. albicans biofilm. To this end, 3-hydroxy coumarin (3HC), a compound identified from the cell-free culture supernatant of the marine bacterium Brevundimonas abyssalis, was found to exhibit anti-biofilm and anti-hyphal activity against both reference and clinical isolates of C. albicans. The compound demonstrated significant inhibitory effects on biofilms and impaired the yeast-to-hyphal transition, wrinkle, and filament morphology at the minimal biofilm inhibitory concentration (MBIC) of 250 µg mL^-1. Intriguingly, quantitative PCR analysis of 3HC-treated C. albicans biofilm revealed significant downregulation of virulence genes (hst7, ume6, efg1, cph1, ras1, als1) associated with adhesion and morphogenesis. Moreover, 3HC displayed non-fungicidal and non-toxic characteristics against human erythrocytes and buccal cells. In conclusion, this study showed that marine biofilms are a hidden source of diverse therapeutic drugs, and 3HC could be a potent drug to treat C. albicans infections.

Exogenous inoculation of endophyte Penicillium sp. alleviated pineapple internal browning during storage

Pineapple is ranked sixth in terms of global fruit production and the most traded tropical fruit worldwide. Internal browning (IB), a physiological disorder of pineapple fruit after harvest, limits the export and industry development of pineapple. Evidence confirmed that endophyte played a pivotal role in plant disease. This study investigated the relationship between endophyte fungi community structure, population abundance in healthy and IB pineapple fruit; as well as the effect of endophyte Penicillium sp. inoculation on pineapple IB. Intended to explore a new effective measure for controlling IB and reducing postharvest losses in pineapple by an economical and environmentally friendly approach. We found the abundance of endophyte fungi in healthy pineapple fruit was different from that in IB fruit by high-throughput sequencing. The results emphasized that the endophyte Penicillium sp. inoculation dramatically alleviated pineapple IB intensity and severity, delayed crown withering and fruit yellowing, and maintained the exterior quality traits during the postharvest period at 20 °C. Penicillium sp. retarded H₂O₂ accumulation and increased the total phenols level in pineapple. Application of Penicillium sp. also maintained the higher antioxidant capacity by increasing antioxidant enzyme activity and ascorbic acids levels, regulated of the homeostasis of endogenous hormones, and increased the abundance of Penicillium sp. in the fruit. In summary, Penicillium sp. retarded the occurrence of IB and enhanced the storability of pineapple at postharvest, and this economical and environmentally friendly technology is convenient to spread in agriculture.

A Meta-Analysis Approach to Defining the Culturable Core of Plant Endophytic Bacterial Communities

Endophytic bacteria are key members of the plant microbiome, which phylogenetic diversity has been widely described through next-generation sequencing technologies in the last decades. On the other side, a synopsis of culturable plant endophytic bacteria is still lacking in the literature. However, culturability is necessary for biotechnology innovations related to sustainable agriculture, such as biofertilizer and biostimulant agents' development. In this review, 148 scientific papers were analyzed to establish a large data set of cultured endophytic bacteria, reported at the genus level, inhabiting different compartments of wild and farmed plants, sampled around the world from different soil types and isolated using various growth media. To the best of our knowledge, this work provides the first overview of the current repertoire of cultured plant endophytic bacteria. Results indicate the presence of a recurrent set of culturable bacterial genera regardless of factors known to influence the plant bacterial community composition and the growth media used for the bacterial isolation. Moreover, a wide variety of bacterial genera that are currently rarely isolated from the plant endosphere was identified, demonstrating that culturomics can catch previously uncultured bacteria from the plant microbiome, widening the panorama of strains exploitable to support plant holobiont health and production.

Screening of sunflower associated bacteria as biocontrol agents for plant growth promotion

Deleterious effects of artificially applied chemicals have highlighted the significance of biocontrol agents as suitable substitute for sustainable agriculture. In present study, three endophytic bacterial strains SV7, SV10 and LV19 showed extensive range of antifungal as well as plant growth promoting activities signifying potential to accomplish the requirement. Phylogenetic analysis revealed 100% similarity of three strains with taxon Firmicute. However, there was division among these isolates on basis of subgroups as SV7 belonged to Exiguobacterium auranticum, SV10 belonged to Paenibacillus sp. and LV19 was best fit in subgroup Priestia koreensis. All strains showed antifungal activity against Fusarium oxysporum on three different media (PDA, NA, LA) with maximum activity (53%) of LV19 strain on NA and least activity (13%) on PDA medium as recorded by zones of inhibition. In growth promotion experiments, combination of LV19 with Fusarium significantly suppressed chances of Fusarium wilt which is commonly caused by Fusarium oxysporum in sunflower plants. Diverse growth parameters (seed germination percentage, lengths and fresh weights of root and shoot) were significantly increased from 34 to 909% over pathogen infected plants only which was further proved by their root colonization analysis. Based on most efficient growth promotion by LV19 strain, expression of five plant defense related genes (SOD, PAL, NPR1, PR5, Chitinase) was evaluated revealing enhanced expression by 1.7-270-folds in consortium of LV19 and Fusarium. Thus, current study provided a scientific justification that bacterial strains in specific LV19 (Priestia koreensis) could be further developed as biocontrol agent with potential of plant growth promotion.

Update of the list of QPS-recommended biological agents intentionally added to food or feed as notified to EFSA 14: suitability of taxonomic units notified to EFSA until March 2021

The qualified presumption of safety (QPS) approach was developed to provide a regularly updated generic pre-evaluation of the safety of biological agents, intended for addition to food or feed, to support the work of EFSA's Scientific Panels. The QPS approach is based on an assessment of published data for each agent, with respect to its taxonomic identity, the body of relevant knowledge, safety concerns and occurrence of antimicrobial resistance. Safety concerns identified for a taxonomic unit (TU) are, where possible, confirmed at the species/strain or product level and reflected by 'qualifications'. In the period covered by this statement, no new information was found that would change the status of previously recommended QPS TUs. Schizochytrium limacinum, which is a synonym for Aurantiochytrium limacinum, was added to the QPS list. Of the 78 microorganisms notified to EFSA between October 2020 and March 2021, 71 were excluded; 16 filamentous fungi, 1 Dyella spp., 1 Enterococcus faecium, 7 Escherichia coli, 1 Streptomyces spp., 1 Schizochytrium spp. and 44 TUs that had been previously evaluated. Seven TUs were evaluated: Corynebacterium stationis and Kodamaea ohmeri were re-assessed because an update was requested for the current mandate. Anoxybacillus caldiproteolyticus, Bacillus paralicheniformis, Enterobacter hormaechei, Eremothecium ashbyi and Lactococcus garvieae were assessed for the first time. The following TUs were not recommended for QPS status: A. caldiproteolyticus due to the lack of a body of knowledge in relation to its use in the food or feed chain, E. hormaechei, L. garvieae and K. ohmeri due to their pathogenic potential, E. ashbyi and C. stationis due to a lack of body of knowledge on their occurrence in the food and feed chain and to their pathogenic potential. B. paralicheniformis was recommended for the QPS status with the qualification 'absence of toxigenic activity' and 'absence of genetic information to synthesize bacitracin'.

Antagonistic Effects of Delia antiqua (Diptera: Anthomyiidae)-Associated Bacteria Against Four Phytopathogens

Recent studies have revealed multiple roles of insect-associated microbes such as lignin degradation, entomopathogen inhibition, and antibiotic production. These functions improve insect host fitness, and provide a novel source of discovering beneficial microbes for industrial and agricultural production. Previously published research found that in the symbiosis formed by the dipteran pest Delia antiqua (Meigen) (Diptera: Anthomyiidae) and its associated bacteria, the bacteria showed effective inhibition of one fungal entomopathogen, Beauveria bassiana. The antifungal activity of those associated bacteria indicates their potential to be used as biocontrol agents for fungal phytopathogens. In this study, we first isolated and identified bacteria associated with D. antiqua using a culture-dependent method. Second, we tested the antifungal activity of these bacteria against four phytopathogens including Fusarium moniliforme, Botryosphaeria dothidea, and two Fusarium oxysporum strains using the dual-culture method. In total, 74 species belonging to 30 genera, 23 families, eight classes, and four phyla were isolated and identified. Among those bacteria, Ochrobactrum anthropi, Morganella morganii, Arthrobacter sp. 3, and Acinetobacter guillouiae showed significant volatile inhibition activity against F. moniliforme, B. dothidea, and both F. oxysporum, respectively. Moreover, bacteria including Rhodococcus equi, Leucobacter aridicollis, Paenibacillus sp. 3, and Lampropedia sp. showed significant contact inhibition activity against F. moniliforme, B. dothidea, and both F. oxysporum. Our work provides a new source for discovering biocontrol agents against phytopathogens.