Biology subjects

Shaw, L. J.

Publications and source records attributed to Shaw, L. J..

6 recordsLinked to original sources

bioRxiv2025

Forest biogeochemical monitoring indicates altered microbial communities, macronutrient availability, CO2 emissions and litter chemistry in root zone soil of oak trees with Acute Decline symptoms

Acute and Chronic Oak Decline (AOD & COD) widely impact oak woodlands across Europe. AOD is known to cause rapid decline in tree health in a short span of 3-5 years. However, the interactions between such oak decline and soil biogeochemical dynamics are not fully understood. We selected three oak trees for each of the three treatments for biogeochemical monitoring: 1. No symptoms (Healthy), 2. AOD & 3. COD symptoms, in Writtle woodlands, Essex, UK. The selected trees were used for quarterly root zone soil sampling (cores to depth of 40 cm), and monthly surface soil (0-10 cm), leaf litter and GHG emissions sampling over a year (2022-23). Soil samples were characterised for their physico-chemical properties, total nutrient content & availability. Leaf litter samples were sorted into branches, leaves, seeds and flowers, weighed and their chemistry characterised. Soil microbial communities were characterised using phospholipid fatty acid analyses. Almost all the measured properties showed significant changes with season and depth, indicating a strong temporal and depth effect on forest soil biogeochemical dynamics. Notably macro-nutrient contents of leaf litter were greater in the summer period, which resulted in increased soil nutrient availability in autumn. This pattern was particularly exaggerated in AOD trees, which had greater nutrient content in litterfall in summer and greater nutrient availability in root zone soil in autumn than those of COD and Healthy trees. We found that AOD root zone soil have altered microbial communities, decreased CO2 emissions and increased macronutrient availability. Taken together, our study shows poor physiological nutrient management by diseased AOD trees revealed by greater nutrient concentration in AOD leaf litter indicating the lack of nutrient resorption and re-allocation before leaf senescence, and less active root zone soil under AOD trees, shown by reduced soil CO2 emissions and increased nutrient availability in oak root influenced zones. Hence, we conclude that the biogeochemical dynamics of AOD root zone soils are significantly different to that of healthy and COD trees, however controlled experiments are needed alongside these field observations to disentangle the causes from effects in understanding the relationship between soil health and oak decline. HighlightsO_LIWe monitored forest soil biogeochemical dynamics under oak trees of different health status C_LIO_LIAcute Oak Decline (AOD) trees had greater macronutrient availability in root zone soils C_LIO_LIAOD trees had greater nutrient content in litter added to the root zone soil C_LIO_LIAOD root zone soils had altered microbial community structure & reduced CO2 emissions C_LIO_LIWe conclude that AOD trees have poor physiological nutrient management and less active rhizosphere compared to healthy trees. C_LI

ecology↗

bioRxiv2025

The cause-effect conundrum of local-scale site and soil factors in acute oak decline (AOD)

Background and aimsAcute oak decline (AOD), a decline syndrome affecting mature oaks, involves bacterial pathogens which likely act as opportunists under host stress. Trees displaying symptoms (bleeding cankers) appear in localized clusters, not whole stands. This study investigates the potential involvement of local-scale factors, in interaction with large-scale environmental drivers, in influencing onset and progression of AOD. MethodsAOD-symptomatic (n=30) and asymptomatic trees (n=30) across three UK oak woodlands were assessed for tree characteristics, their surrounding context, and soil properties. ResultsTree health status was linked to significant differences in soil and tree properties across sites. Symptomatic trees exhibited greater loss of crown density, lower local stand (0-20 m) basal area and shallower depth to gleying. Significant differences in soil properties included lower concentrations of Olsen P, total N, and exchangeable Mg in symptomatic trees, alongside higher exchangeable Fe, especially at 40-50 cm depth. Depth to gleying and exchangeable Fe were identified as the most influential predictors of AOD. ConclusionsAOD symptomatic trees may experience seasonal soil water saturation closer to the surface compared to asymptomatic trees, resulting in a higher proportion of their roots being exposed to an anoxic, iron-reducing environment. This study is the first to report such an association between gleying depth, likely seasonal water saturation, and symptom status for AOD. It is unclear whether water balance and associated soil nutrient variations are predisposing factors or consequences of declining tree health, though the identified local-scale factors likely contribute to AOD. A feedback loop is conceptualised where declining tree health worsens soil conditions, creating a negative cycle that accelerates tree decline.

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

Assessing the efficacy of antibiotic treatment for the creation of axenic earthworms

Earthworms are an integral part of soil ecosystems, especially for their role in soil functions such as organic matter (OM) decomposition and nutrient cycling. Earthworms and microorganisms are interdependent, and a considerable portion of the contribution earthworms make to influencing OM fate is through interactions with microorganisms. However, the importance of the earthworm-associated microbiome is not fully understood, because it is difficult to separate the direct influence of the earthworms from the indirect influence of their microbiome. Here, we evaluated an antibiotic-based procedure for producing axenic ecologically-contrasting earthworm species (E. fetida, L. terrestris, A. chlorotica) as the first step towards soil studies aimed at understanding the importance of the earthworm microbiome for host health and function. Individual earthworms were exposed to antibiotics: cycloheximide (150 g ml-1), ampicillin (100 g ml-1), ciprofloxacin (50 g ml-1), nalidixic acid (50 g ml-1), and gentamicin (50 g ml-1) either singly or in a cocktail via culture (96 h) in a semi-solid agar carrier. Compared to the non-antibiotic treated control, the cocktail (for all three species) and ciprofloxacin (for E. fetida and A. chlorotica) treatments significantly reduced (P<0.05) culturable microbial abundance on nutrient agar and potato dextrose agar. The microbial counts were reduced to below detection (<50 CFU individual-1) for E. fetida and A. chlorotica receiving the cocktail. Illumina 16S rDNA amplicon sequence analysis of culturable L. terrestris -associated bacteria showed that antibiotic treatment influenced community composition revealing putative sensitive (Comomonas, Kosakonia and Sphingobacterium) and insensitive (Aeromonas, Pseudochrobactrum) taxa. Overall, we report a rapid, with minimal earthworm-handling, process of creating axenic E. fetida and A. chlorotica individuals or L. terrestris with a suppressed microbiome as a tool to be used in future ecological studies of earthworm microbial interactions affecting host health and function.

ecology↗

bioRxiv2021

Legacy effect of constant and diurnally oscillating temperatures on soil respiration and microbial community structure

1.0Laboratory incubation studies evaluating the temperature sensitivity of soil respiration often use measurements of respiration taken at a constant incubation temperature from soil that has been pre-incubated at the same constant temperature. However, such constant temperature incubations do not represent the field situation where soils undergo diurnal temperature oscillations. We investigated the effects of constant and diurnally oscillating temperatures on soil respiration and soil microbial community composition. A grassland soil from the UK was either incubated at a constant temperature of 5 {degrees}C, 10 {degrees}C, or 15 {degrees}C, or diurnally oscillated between 5 {degrees}C and 15 {degrees}C. Soil CO2 flux was measured by temporarily moving incubated soils from each of the abovementioned treatments to 5 {degrees}C, 10 {degrees}C or 15 {degrees}C, such that soils incubated at each temperature had CO2 flux measured at every temperature. We hypothesised that, irrespective of measurement temperature, CO2 emitted from the 5 {degrees}C to 15 {degrees}C oscillating incubation would be most similar to the soil incubated at 10 {degrees}C. The results showed that both incubation and measurement temperatures influence soil respiration. Incubating soil at a temperature oscillating between 5 {degrees}C and 15 {degrees}C resulted in significantly greater CO2 flux than constant incubations at 10 {degrees}C or 5 {degrees}C, but was not significantly different to the 15 {degrees}C incubation. The greater CO2 flux from soils incubated at 15 {degrees}C, or oscillating between 5 {degrees}C and 15 {degrees}C, coincided with a depletion of dissolved organic carbon and a shift in the phospholipid fatty acid profile of the soil microbial community, consistent with the thermal adaptation of microbial communities to higher temperatures. However, diurnal temperature oscillation did not significantly alter Q10. Our results suggest that daily maximum temperatures are more important than daily minimum or daily average temperatures when considering the response of soil respiration to warming.

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↗