Biology subjects

Tibbett, M.

Publications and source records attributed to Tibbett, M..

8 recordsLinked to original sources

bioRxiv2025

Furrow tillage reduces soil carbon loss and enhances microbial metabolism

With increasing global carbon loss from agricultural fields, agricultural practices should be monitored with proper regulatory measures. To address three problems of minimising carbon loss, optimising soil fertility and enhancing soil microbiota together, this study has developed a new innovative "Furrow tillage" approach that affords a balance between conventional and conservative tillage. Based on two years of trials in rice fields at multiple sites, this practice has justifications from agronomy, geochemistry, crop physiology, and molecular microbiology. Furrow tillage illustrated low carbon loss, similar to no-tillage, while retaining high nutrient bioavailability, similar to deep tillage. Microbial diversity, molecular responses and metabolic activities showed that furrow tillage induced microbial interactions while allowing a better entrapment of carbon dioxide in the soil. The study used CO2 flux, spatial distribution, total and available elemental analysis, plant ultra-structural observations, microbial metagenomics, high-throughput sequencing and molecular modelling to establish an optimal soil-crop quality, microbial maintenance and reduce carbon loss through furrow tillage practice.

ecology↗

bioRxiv2022

Fragment size and diversity of mulches affect their decomposition, nutrient dynamics, and soil microbiology

Plant-based mulch has been proposed as a sustainable way of maintaining soil fertility. However, the role of mulch diversity, quality, and size in decomposition dynamics, and their effect on crop yield are not fully explored. We investigated how mulch quality, proxied by the constituent plant species diversity, and residue size drive mulch decomposition, crop nutrition, and yield. A rhizotron experiment was set up with barley as a model crop, with the addition of mulch of two particle sizes (1.5 and 30 cm) and four different plant residue mixes (17, 12, 6, and 1 species) in a fully factorial design. Soil nutrient dynamics were measured at advanced decomposition stages, together with residue quality, arbuscular mycorrhizal fungal (AMF) root colonization, and crop yield. Residue mass loss was significantly affected by its chemical composition. Long residues retained significantly higher C and N content, than short residues. Crop yield was not affected by residue type or size. Residue size significantly affected barley growth rate, influencing seed protein content. Soil available K was significantly increased by residues with a higher initial C:N ratio. Short residues resulted in higher soil Zn. Residues of higher diversity resulted in higher AMF root colonization of the barley plants. Generally, long residue mulches maintain soil fertility for a longer period than short ones, without a deleterious effect on crop yield. Further investigation should evaluate the effect of continuous application of long residue mulches on soil fertility and microbial populations.

ecology↗

bioRxiv2021

Phosphorus uptake and toxicity is delimited by mycorrhizal symbiosis in P-sensitive Eucalyptus marginata but not in P-tolerant Acacia celastrifolia

Many plant species from regions with ancient, highly-weathered nutrient-depleted soils have specialised adaptations for acquiring P and are sensitive to excess P-supply. Mycorrhizal associations may regulate P-uptake at high external P-concentrations, potentially reducing P-toxicity. We predicted that excess P-application will negatively impact species from the nutrient-depleted jarrah forest of Western Australia and that mycorrhizal inoculation will reduce P-toxicity by regulating P-uptake. For seedlings of the N2-fixing legume Acacia celastrifolia and the tree species Eucalyptus marginata, we measured growth at P-concentrations of 0 to 90 mg kg-1 soil and in relation to inoculation with the arbuscular mycorrhizal fungus (AMF) Rhizophagus irregularis. Non-inoculated A. celastrifolia maintained leaf P-concentrations at <2 mg g-1 dry mass (DM) across the range of external P-concentrations. However, for non-inoculated E. marginata, as external P-concentrations increased leaf P also increased, reaching >9 mg g-1 DM at 30 mg P kg-1 soil. A. celastrifolia DM increased with increasing external P-concentrations, while E. marginata DM was maximal at 15 mg P kg-1 soil, declining at higher external P concentrations. Neither DM nor leaf P of A. celastrifolia were affected by inoculation with AMF. For E. marginata, even at 90 mg P kg-1 soil, inoculation with AMF resulted in leaf P remaining <1 mg g-1 DM, and DM being maintained. These data strengthen the evidence base that AMF may not only facilitate P-uptake at low external P-concentrations, but are also important for moderating P-uptake at elevated external P-concentrations and maintaining plant P concentrations within a relatively narrow concentration range.

plant biology↗

bioRxiv2021

Meta-exoproteomics identifies active plant-microbe interactions operating in the rhizosphere

The advance of DNA sequencing technologies has drastically changed our perception of the complexity and structure of the plant microbiome and its role in augmenting plant health. By comparison, our ability to accurately identify the metabolically active fraction of soil microbiota and their specific functional role is relatively limited. Here, we combined our recently developed protein extraction method and an iterative bioinformatics pipeline to enable the capture and identification of extracellular proteins (meta-exoproteomics) expressed in the rhizosphere of Brassica spp. First, we validated our method in the laboratory by successfully identifying proteins related to the host plant (Brassica rapa) and a bacterial inoculant, Pseudomonas putida BIRD-1, revealing the latter expressed numerous rhizosphere specific proteins linked to the acquisition of plant-derived nutrients. Next, we analysed natural field-soil microbial communities associated with Brassica napus L (Oil Seed rape). By combining deep-sequencing metagenomics with meta-exoproteomics, a total of 1882 proteins were identified in bulk and rhizosphere samples. Importantly, meta-exoproteomics identified a clear shift (p<0.001) in the metabolically active fraction of the soil microbiota responding to the presence of B. napus roots that was not apparent in the composition of the total microbial community (metagenome). This metabolic shift was associated with the stimulation of rhizosphere-specialised bacteria, such as Gammaproteobacteria, Betaproteobacteria and Flavobacteriia and the upregulation of plant beneficial functions related to phosphorus and nitrogen mineralisation. By providing the first meta-proteomic level assessment of the active plant microbiome at the field-scale, this study demonstrates the importance of moving past a genomic assessment of the plant microbiome in order to determine ecologically important plant: microbe interactions driving plant growth.

microbiology↗

bioRxiv2021

Next generation restoration metrics: Using soil eDNA bacterial community data to measure trajectories towards rehabilitation targets

In post-mining rehabilitation, successful mine closure planning requires specific, measurable, achievable, relevant and time-bound (SMART) completion criteria, such as returning ecological communities to match a target level of similarity to reference sites. Soil microbiota are fundamentally linked to the restoration of degraded ecosystems, helping to underpin ecological functions and plant communities. High-throughput sequencing of soil eDNA to characterise these communities offers promise to help monitor and predict ecological progress towards reference states. Here we demonstrate a novel methodology for monitoring and evaluating ecological restoration using three long-term (> 25 year) case study post-mining rehabilitation soil eDNA-based bacterial community datasets. Specifically, we developed rehabilitation trajectory assessments based on similarity to reference data from restoration chronosequence datasets. Recognising that many alternative options for microbiota data processing have potential to influence these assessments, we comprehensively examined the influence of standard versus compositional data analyses, different ecological distance measures, sequence grouping approaches, eliminating rare taxa, and the potential for excessive spatial autocorrelation to impact on results. Our approach reduces the complexity of information that often overwhelms ecologically-relevant patterns in microbiota studies, and enables prediction of recovery time, with explicit inclusion of uncertainty in assessments. We offer a step change in the development of quantitative microbiota-based SMART metrics for measuring rehabilitation success. Our approach may also have wider applications where restorative processes facilitate the shift of microbiota towards reference states.

ecology↗

bioRxiv2021

Mixing crop residues induces a synergistic effect on microbial biomass and an additive effect on soil organic matter priming

Applying crop residues is a widely used strategy to increase soil organic matter (SOM) in arable soils because of its recorded effects on increasing microbial biomass and consequently necromass. However, fresh residue inputs could also "prime" the decomposition of native SOM, resulting in accelerated SOM depletion and greenhouse gas (GHG) emission. Increasing the botanical diversity of the crops grown in arable systems has been promoted to increase the delivery of multiple ecological functions, including increasing soil microbial biomass and SOM. Whether mixtures of fresh residues from different crops grown in polyculture contribute to soil carbon (C) pools to a greater extent than would be expected from applying individual residues (i.e., the mixture produces a non-additive synergistic effect) has not been systematically tested and is currently unknown. In this study, we used 13C isotope labelled cover crop residues (i.e., buckwheat, clover, radish, and sunflower) to track the fate of plant residue-derived C and C derived from the priming of SOM in treatments comprising a quaternary mixture of the residues and the average effect of the four individual residues one day after residue incorporation in a laboratory microcosm experiment. Our results indicate that, despite all treatments receiving the same amount of plant residue-derived C (1 mg-1 C g soil), the total microbial biomass in the treatment receiving the residue mixture was significantly greater, by 26% (3.69 {micro}g-1 C g), than the average microbial biomass observed in treatments receiving the four individual components of the mixture one day after applying crop residues. The greater microbial biomass C in the quaternary mixture, compared to average of the individual residue treatments, that can be attributed directly to the plant residue applied was also significantly greater, by 132% (3.61 {micro}g-1 C g). However, there was no evidence that the mixture resulted in any more priming of native SOM than average priming observed in the individual residue treatments. The soil microbial community structure, assessed using phospholipid fatty acid (PLFA) analysis, was significantly (P < 0.001) different in the soil receiving the residue mixture, compared to the average structures of the communities in soil receiving four individual residues. Differences in the biomass of fungi, general bacteria, and Gram-positive bacteria were responsible for the observed synergistic effect of crop residue mixtures on total microbial biomass and residue-derived microbial biomass, especially biomarkers 16:0, 18:2{omega}6 and 18:3{omega}3. Our study demonstrates that applying a mixture of crop residues increases soil microbial biomass to a greater extent than would be expected from applying individual residues and that this occurs either due to faster decomposition of the crop residues or greater carbon use efficiency (CUE), rather than priming the decomposition of native SOM. Therefore, growing crop polycultures (e.g., cover crop mixtures) and incorporating mixtures of the resulting crop residues into the soil could be an effective method to increase microbial biomass and ultimately C stocks in arable soils.

microbiology↗

bioRxiv2021

Cover crop residue diversity enhances microbial activity and biomass with additive effects on microbial structure

Cover crops have been widely used in agroecosystems to improve soil fertility and environmental sustainability. The decomposition of cover crop residues can have further effects on belowground communities and their activity, which is important for a series of soil functions (e.g., nutrient cycling and organic matter decomposition). We tested the effect of plant residues from a range of cover crop species on soil microbial activity and community assemblage. We predicted that cover crop residues would alter the soil microbial community and that a greater diversity of residues would enhance microbial decomposition. In an incubation study, we assessed the effect of crop residue diversity on microbial activity (soil respiration) and its consequent effects on microbial community composition (PLFA). We used either a biodiverse mixture of four cover crop residues (buckwheat, clover, sunflower and radish) or an equal mass of the residues of each of the individual species. The diverse mixture of cover crop residues had a significantly (P < 0.05) greater soil respiration rate, by 57.61 {micro}g C g-1 h-1, than the average of the four individual residues, but did not have a significantly different soil microbial biomass or microbial community structure. This finding could be attributed to a greater diversity of organic resources increasing the number biochemical niches, and hence activating dormant microbial communities to increase microbial activity without affecting microbial biomass or community composition. Greater respiration from similar microbial biomasses suggests that microbial activity might be more efficient after a more diverse substrate input. This study confirms the positive impact of cover crop residues on soil microbial biomass and activity and highlights that mixtures of cover crop residues may deliver enhanced soil functions beyond the sum of individual cover crop residues.

microbiology↗

bioRxiv2019

Novel mechanisms for phosphate acquisition in abundant rhizosphere-dwelling Bacteroidetes

Global food production is reliant on the application of finite phosphorus (P) fertilisers. Numerous negative consequences associated with intensive P fertilisation have resulted in a high demand to find alternative sustainable methods that will enhance crop P uptake. Bacteroidetes, primarily from the genus Flavobacterium, have recently been shown to be abundant members of the plant microbiome, but their general ecological role and potential to mobilise P in the rhizosphere remains very poorly characterised. Here, we sought to determine the P mobilisation potential of Flavobacterium strains isolated from the rhizosphere of oilseed rape (Brassica napus L.). We show that these Flavobacterium strains possess novel mechanisms for P mobilisation and subsequent acquisition. These include the constitutive and inducible expression of completely novel and phylogenetically distinct phosphatases, the phosphate starvation inducible expression of uncharacterised and hypothetical genes and gene clusters and, for the first time, the involvement of outer membrane SusCD transport complexes (usually associated with carbohydrate transport) in P acquisition. The genes encoding these unusual phosphate starvation inducible proteins were enriched in plant-associated Flavobacterium strains suggesting that this machinery represents niche-adaptive strategies for overcoming P scarcity in this genus. We propose that abundant rhizosphere-dwelling Flavobacterium spp. have evolved unique mechanisms for coping with Pi-stress which may provide novel solutions for future sustainable agricultural practices.

microbiology↗