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Shaw, L. J.

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

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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

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

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

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