Evaluation of thermogravimetric analysis as a rapid tool for the detection of rhizobacteria biostimulants used in precision agriculture

Publication history: Accepted - 31 October 2020; Published online - 17 January 2021Six-week-old root samples were evaluated using high resolution (maximum resolution [MaxRes]) thermogravimetric analyses (TGA) of the cell wall compositions of Gram-positive (Bacillus mucilaginosus, Bacillus amyloliquefaciens, and Bacillus subtilis) and Gram-negative (Burkholderia sp., Rahnella aquatilis strain H 2.6, and R. aquatilis strain RC 2.5) root colonizing plant growth promoting rhizobacteria (PGPR) commercial inoculant strains (biostimulants) applied to pot grown wheat plants. TGA discriminated the strains within the two types of rhizobacterial cohorts and thus provided a rapid non-molecular means for the detection of PGPR inoculant biostimulants within hours of root sampling. The latter was due to the greater degree of definition of TGA fingerprints of individual thermal weight loss events occurring over a degradation range, and heightened the corresponding peak temperature divergences within strains of either type of bacteria themselves for their unequivocal identification. Confirmation of biostimulant rhizobacteria identity in concomitant root samples was achieved through either cultural methods or direct tissue PCR molecular protocols within 5 days and 2 days of sampling, respectively. The results suggested that MaxRes TGA could serve as a rapid, inexpensive stand-alone tool or as combinatorial utility alongside pyrolysis gas chromatography mass spectra, and Fourier transform infrared analytics for the early detection of PGPR biostimulants in precision farmingWe thank EU-BIOFECTOR (Grant Agreement No. 312117) funded by the European Commission within the 7th Framework Programme, and the Department of Agriculture, Environment and Rural Affairs (DAERA), Northern Ireland, UK for their Evidence and Innovation grant (activity 48125) to carry out the study at the Agri-Food & Biosciences Institute laboratories (AFBINI.GOV.UK

Antimicrobial resistance to 14 antimicrobials in marine coastal waters around Northern Ireland: Use of the novel Relative Resistance Index as a marker of ecological status

Relatively little work has been published on the incidence of antibiotic resistance (ABR) in the marine microbiological environment, which is of importance to animal (fish, mammals, birds) health, zoonotic transmission, distribution of ABR bacteria with oceanic drift, and ultimately human health. A study was performed to determine the diversity of total ABR (intrinsic and acquired resistance) in marine bacteria in shallow coastal waters surrounding Northern Ireland through the use of a novel Relative Resistance Index (RRI) as a surrogate marker for ecological change, particularly in comparing marine water in commercial versus non-commercial sites. Total antibiotic resistance was observed to varying degrees in all marine water specimens and specific resistance levels were as follows, in order of diminishing antibacterial effectiveness: fluoroquinolones \u3e rifampicin \u3e polymyxin \u3e tetracycline \u3e sulphamethoxazole/trimethoprim \u3e third generation cephalosporin and streptomycin \u3e carbapenem \u3e macrolide \u3e clindamycin \u3e vancomycin \u3e fucidic acid \u3e penicillin. None of the sampling sites contained endogenous bacteria that were resistant to ciprofloxacin, while nearly all (19 of 20 sites; 95%) contained bacteria that were resistant to penicillin. Commercial sites had a higher mean RRI score of 6.57±3.58 than non-commercial sites (RRI = 4.08 ± 2.02), which was statistically significant (p = 0.037), indicating that bacteria isolated from seawater in commercial coastal harbors had a higher frequency of antibiotic resistance than non-commercial sources. This novel RRI marker may be useful in assessing ecological change in marine water environments. In conclusion, this study demonstrated that there can be a high level of total ABR (intrinsic and acquired) in bacterial populations in marine water environments, which are multi- and pan-resistant to up to 11 major classes of antibiotics simultaneously. Ecological studies are urgently needed to help define the fate of ABR marine bacteria in their natural environment and their ability to act as reservoirs and donors of ABR to pathogenic bacteria, many of which transiently inhabit the natural environment

Challenges and Opportunities for Management of Crop and Tree Diseases in Northern Ireland

Publication history: Accepted - 22 October 2020; Published online - 24 October 2020.Phytopathogens have beleaguered the island of Ireland since the 19th century great famine caused by the potato blight oomycete, Phytophthora infestans and in recent times by cohorts of serious bacterial wilt diseases such as Erwinia, Dickeya, Ralstonia, and fungal wilt diseases predominantly caused by saprophyte fungi (e.g. Fusarium oxysporum, Pythium, Rhizoctonia) have all shown their growing resistance to various conventional chemical control agents, and create enormous impact on sustainable agriculture, further exacerbated by global climate change pressures. The plant health outlook in Northern Ireland has further been tested by emergent Europe wide agro-forestry related diseases including the recent broad host insect vector-borne Xanthamonas bacterial phytopathogen Xylella fastidiosa that can affect a wide array of ornamental, arable crops and tree species alike. This mini-review focuses on potential alternative plant extracts and microbial sources as agents broadly known as biostimulants for not only their growth promotion via plant and soil nutrient management but also controlling phytopathogens in Northern Ireland. The multi-actor approach comprising stake holders, plant health policy makers, farmers, plant health advisors, researchers, knowledge transfer centres will be the key drivers for an effective data input and sustainable plant health. Integration of precision farming with latest information and communications technology (ICT), advanced automation for need based/site-specific use of biostimulants to combat biotic and abiotic stress, on-field plant pathogen remote sensors and their extended new tool applications for soil and phytosanitory inspections at port of entry points are some of the overarching comprehensive strategies planned for the future.The authors gratefully acknowledge the Department of Agriculture, Environment and Rural Affairs (DAERA), Northern Ireland for facilitating this literature review process through an Evidence and Innovation project 16/3/11, (activity 48125) and the European Commission funding via EU FP7-BIOFECTOR Grant (Agreement No. 312117), administered at Agri-Food & Biosciences Institute (AFBI), (www.afbini.gov.uk) to support plant health research

Microbiological assessments in a cut flower crop polytunnel field trial adopting soil covering and microbiocides for Fusarium wilt suppression

Publication history: Published online - 4 September 2020Cut flower Matthiola incana were raised by local commercial cultivators in a polytunnel. The field soil beds were either left uncovered as normal or covered with polythene sheets (except a hole for plant plug space). Average temperatures in the top 5 cm soil under cover dropped from 28 oC to 18 oC compared to its spiking up to 37 oC in uncovered counterparts. Microbiological analyses indicated that soil covering induced two log10 folds reduction of the wilt causal fungi Fusarium oxysporum and concomitantly increased one log10 fold wilt antagonistic natural soil inhabiting fungi populations. Standard dip/drench mixtures of commercial and local isolates microbiocides (bacteria) applied to M. incana plug roots improved plant health assessed by visible scores of the level of damage or wilt symptoms under soil covered treatments. Scanning electron microscopy, cultural and 16S rRNA PCR analyses revealed potent antifungal bacteria attached to the hyphal surfaces of F. oxysporum as ectosymbionts that may have implications for virulence regulation and host plants’ wilt disease control. Our microbiological data support the prospects of combining physiological and microbiological interventions upon covering the soil surface that offers the local horticulturists an evidence based sustainable means of Fusarium wilt control suppression in polytunnel crops.Department of Agriculture, Environment and Rural Affairs (DAERA) directed Evidence and Innovation project 16/3/11, and the support of a EU FP7–BIOFECTOR grant (JRR, CF, TM) for this stud