Browsing by Author "Reid, Tessa E."

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    Agricultural intensification reduces selection of putative plant growth-promoting rhizobacteria in wheat
    (Oxford University Press (OUP), 2024-01-01) Reid, Tessa E.; Kavamura, Vanessa N.; Torres-Ballesteros, Adriana; Smith, Monique E.; Abadie, Maïder; Pawlett, Mark; Clark, Ian M.; Harris, Jim A.; Mauchline, Tim H.
    The complex evolutionary history of wheat has shaped its associated root microbial community. However, consideration of impacts from agricultural intensification has been limited. This study investigated how endogenous (genome polyploidization) and exogenous (introduction of chemical fertilizers) factors have shaped beneficial rhizobacterial selection. We combined culture-independent and -dependent methods to analyze rhizobacterial community composition and its associated functions at the root–soil interface from a range of ancestral and modern wheat genotypes, grown with and without the addition of chemical fertilizer. In controlled pot experiments, fertilization and soil compartment (rhizosphere, rhizoplane) were the dominant factors shaping rhizobacterial community composition, whereas the expansion of the wheat genome from diploid to allopolyploid caused the next greatest variation. Rhizoplane-derived culturable bacterial collections tested for plant growth-promoting (PGP) traits revealed that fertilization reduced the abundance of putative plant growth-promoting rhizobacteria in allopolyploid wheats but not in wild wheat progenitors. Taxonomic classification of these isolates showed that these differences were largely driven by reduced selection of beneficial root bacteria representative of the Bacteroidota phylum in allopolyploid wheats. Furthermore, the complexity of supported beneficial bacterial populations in hexaploid wheats was greatly reduced in comparison to diploid wild wheats. We therefore propose that the selection of root-associated bacterial genera with PGP functions may be impaired by crop domestication in a fertilizer-dependent manner, a potentially crucial finding to direct future plant breeding programs to improve crop production systems in a changing environment.
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    Has plant domestication decoupled beneficial Plant-microbe interactions in wheat?
    (Cranfield University, 2021-11) Reid, Tessa E.; Mauchline, Tim H.; Harris, Jim A.; Pawlett, Mark; Clark, Ian M.; Nessner-Kavamura, Vanessa
    Domestication of plant species has substantially contributed to human civilization, but also caused a strong decrease in the genetic diversity of modern crop cultivars by selecting for high-yielding dwarf crops which are reliant on unsustainable levels of inorganic fertilizer. This transition from natural to agricultural systems has played an important role in the development of agriculture over the last 10,000 years but may have affected the ability of plants to establish beneficial associations with rhizosphere microbes. Plant growth-promoting rhizobacteria (PGPR) are essential for plant health and fitness and play an important role in the sustainable intensification of agriculture. This thesis assesses the impacts of domestication on beneficial plant-microbial interactions in wheat with a view to developing robust microbial inocula for enhanced crop growth. Culture dependent and independent approaches were used to explore the influence of widely used nitrogen-phosphate-potassium (NPK) fertilizer on the abundance of wheat rhizobacterial genera with plant growth-promoting traits. Putative plant growth-promoting rhizobacteria (PGPR) were reduced in fertilized wheat plants. Approximately 1,500 bacterial isolates were amassed from the rhizosphere and rhizoplane of Cadenza wheat plants grown in low nutrient soil either supplemented with or without fertilizer in pot greenhouse experiments, representing an inherently more controlled design than many literature field studies. PGPR were taxonomically identified by Sanger sequencing of the 16S rRNA gene and functionally characterized using single colony functional bioassays (nitrogen, phosphate, potassium, iron, and zinc solubilization) and subsequently identified in high throughput 16S rRNA gene amplicon sequence derived culture-independent community datasets, which revealed a significantly lower abundance of nutrient-solubilizing rhizobacteria in fertilized plants. The same methods were applied to rhizoplane samples from 19 ancestral and domesticated wheat genotypes grown in the same conditions which resulted in isolation of approximately 15,000 bacterial isolates. Notably, there was a significantly lower abundance of PGPR isolated from unplanted control pots (bulk soil) compared to plants and no difference between fertilization conditions. Moreover, differences in the abundance of PGPR under contrasting fertilization conditions were more pronounced in domesticated wheat, which we hypothesize is due to a loss of plant-microbe signalling pathways as the wheat genome underwent expansion. Key genera differentially more abundant in non-fertilized wheats included members of the phylum Cyanobacteria (Nostoc) and Proteobacteria (Bradyrhizobium, Pseudomonas) compared to fertilized wheats which were richer in Actinobacteria (Arthrobacter, Catenulispora, Leifsonia, and Streptomyces). Introduction of the Reduced height (Rht) genes during the Green Revolution has been hypothesized to reduce PGPR selection due to their influence on the plant hormone gibberellin (GA). 16S rRNA gene amplicon sequencing revealed a markedly different rhizosphere microbiome in severe Cadenza wheat Rht dwarf mutants which became more pronounced with mineral fertilizer addition. There was a higher differential abundance in Acidobacteria, Chloroflexi and Gemmatimonadetes, phyla more commonly associated with bulk soil, in Rht mutant cultivars compared with a higher differential abundance of Bacteroidetes, Firmicutes and Proteobacteria, phyla more commonly associated with plant growth promotion, in wildtype Cadenza wheat. The research presented in this thesis contributes to our understanding of the impact domestication has had on plant-microbe interactions in the presence and absence of agriculturally important but potentially environmentally deleterious chemicals, as well as presenting a method for functional characterization of microbiomes. This knowledge will benefit the development of more targeted ecologically benign biofertilization strategies.
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    Inorganic chemical fertilizer application reduces putative plant growth-promoting rhizobacteria in wheat
    (Frontiers Media, 2021-03-11) Reid, Tessa E.; Kavamura, Vanessa N.; Abadie, Maïder; Torres-Ballesteros, Adriana; Pawlett, Mark; Clark, Ian M.; Harris, Jim A.; Mauchline, Tim H.
    The profound negative effect of inorganic chemical fertilizer application on rhizobacterial diversity has been well documented using 16S rRNA gene amplicon sequencing and predictive metagenomics. We aimed to measure the function and relative abundance of readily culturable putative plant growth-promoting rhizobacterial (PGPR) isolates from wheat root soil samples under contrasting inorganic fertilization regimes. We hypothesized that putative PGPR abundance will be reduced in fertilized relative to unfertilized samples. Triticum aestivum cv. Cadenza seeds were sown in a nutrient depleted agricultural soil in pots treated with and without Osmocote® fertilizer containing nitrogen-phosphorous-potassium (NPK). Rhizosphere and rhizoplane samples were collected at flowering stage (10 weeks) and analyzed by culture-independent (CI) amplicon sequence variant (ASV) analysis of rhizobacterial DNA as well as culture-dependent (CD) techniques. Rhizosphere and rhizoplane derived microbiota culture collections were tested for plant growth-promoting traits using functional bioassays. In general, fertilizer addition decreased the proportion of nutrient-solubilizing bacteria (nitrate, phosphate, potassium, iron, and zinc) isolated from rhizocompartments in wheat whereas salt tolerant bacteria were not affected. A “PGPR” database was created from isolate 16S rRNA gene sequences against which total amplified 16S rRNA soil DNA was searched, identifying 1.52% of total community ASVs as culturable PGPR isolates. Bioassays identified a higher proportion of PGPR in non-fertilized samples [rhizosphere (49%) and rhizoplane (91%)] compared to fertilized samples [rhizosphere (21%) and rhizoplane (19%)] which constituted approximately 1.95 and 1.25% in non-fertilized and fertilized total community DNA, respectively. The analyses of 16S rRNA genes and deduced functional profiles provide an in-depth understanding of the responses of bacterial communities to fertilizer; our study suggests that rhizobacteria that potentially benefit plants by mobilizing insoluble nutrients in soil are reduced by chemical fertilizer addition. This knowledge will benefit the development of more targeted biofertilization strategies.
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    Unlocking the agro-physiological potential of wheat rhizoplane fungi under low P conditions using a niche-conserved consortium approach
    (Oxford University Press (OUP), 2025-05-01) Benbrik, Brahim; Reid, Tessa E.; Nkir, Dounia; Chaouki, Hicham; Aallam, Yassine; Clark, Ian M.; Mauchline, Tim H.; Harris, Jim A.; Pawlett, Mark; Barakat, Abdellatif; Rchiad, Zineb; Bargaz, Adnane
    Plant growth-promoting fungi (PGPF) hold promise for enhancing crop yield. This study delves into the fungal diversity of the wheat rhizoplane across seven Moroccan agricultural regions, employing a niche-conserved strategy to construct fungal consortia (FC) exhibiting higher phosphorus (P) acquisition and plant growth promotion. This study combined culture-independent and culture-dependent methods exploring taxonomic and functional diversity in the rhizoplane of wheat plants obtained from 28 zones. Twenty fungal species from eight genera were isolated and confirmed through internal transcribed spacer (ITS) Sanger sequencing. P solubilization (PS) capacity was assessed for individual species, with Talaromyces sp. (F11) and Rhizopus arrhizus CMRC 585 (F12) exhibiting notable PS rates, potentially due to production of organic acids such as gluconic acid. PGPF traits and antagonism activities were considered when constructing 28 niche-conserved FC (using isolates from the same zone), seven intra-region FC (different zones within a region), and one inter-region FC. Under low P conditions, in planta inoculation with niche-conserved FC (notably FC14 and FC17) enhanced growth, physiological parameters, and P uptake of wheat, in both vegetative and reproductive stages. FC14 and FC17, composed of potent fungi such as F11 and F12, demonstrated superior plant growth benefits compared with intra- and inter-region constructed FC. Our study underscores the efficacy of the niche-conserved strategy in designing synthetic fungal community from isolates within the same niche, proving significant agro-physiological potential to enhance P uptake and plant growth of wheat.