Niall P. McNamara

Effects of acute gamma irradiation on chemical, physical and biological properties of soils

The use of gamma (γ-) irradiation as a method for soil sterilisation for laboratory experiments has been recommended over other sterilisation techniques. We reviewed literature dating back over 50 years to investigate the chemical and biological effects on γ-irradiated soils and to determine its practicality for sterilising soils which will subsequently be used for experimental purposes. Typically, γ-irradiation at 10 kGy will eliminate actinomycetes, fungi and invertebrates in most soils. The majority of soil bacteria are eliminated by 20 kGy, however, a dose higher than 70 kGy may be required to kill certain radio-resistant bacteria. We recommend prior to experimentation that the radiosensitivity of soils are determined so as to ensure the desired chemical and biological effects are achieved. γ-Irradiation may not be an appropriate method for all experiments as it can influence soil chemical properties, in particular soil nitrate and ammonium levels. Where chemical stability is required we recommend sterilising soils air-dry rather than moist.

Long-term consequences of grazing and burning on northern peatland carbon dynamics

A bstractUsing a 50-year-old field experiment, we investigated the effects of the long-term land management practices of repeated burning and grazing on peatland vegetation and carbon dynamics (C). Plant community composition, C stocks in soils and vegetation, and C fluxes of CO2, CH4 and DOC, were measured over an 18-month period. We found that both burning and grazing reduced aboveground C stocks, and that burning reduced C stocks in the surface peat. Both burning and grazing strongly affected vegetation community composition, causing an increase in graminoids and a decrease in ericoid subshrubs and bryophytes relative to unburned and ungrazed controls; this effect was especially pronounced in burned treatments. Soil microbial properties were unaffected by grazing and showed minor responses to burning, in that the C:N ratio of the microbial biomass increased in burned relative to unburned treatments. Increases in the gross ecosystem CO2 fluxes of respiration and photosynthesis were observed in burned and grazed treatments relative to controls. Here, the greatest effects were seen in the burning treatment, where the mean increase in gross fluxes over the experimental period was greater than 40%. Increases in gross CO2 fluxes were greatest during the summer months, suggesting an interactive effect of land use and climate on ecosystem C cycling. Collectively, our results indicate that long-term management of peatland has marked effects on ecosystem C dynamics and CO2 flux, which are primarily related to changes in vegetation community structure.

Revealing the uncultivated majority: combining DNA stable-isotope probing, multiple displacement amplification and metagenomic analyses of uncultivated Methylocystis in acidic peatlands

Peatlands represent an enormous carbon reservoir and have a potential impact on the global climate because of the active methanogenesis and methanotrophy in these soils. Uncultivated methanotrophs from seven European peatlands were studied using a combination of molecular methods. Screening for methanotroph diversity using a particulate methane monooxygenase-based diagnostic gene array revealed that Methylocystis-related species were dominant in six of the seven peatlands studied. The abundance and methane oxidation activity of Methylocystis spp. were further confirmed by DNA stable-isotope probing analysis of a sample taken from the Moor House peatland (England). After ultracentrifugation, (13)C-labelled DNA, containing genomic DNA of these Methylocystis spp., was separated from (12)C DNA and subjected to multiple displacement amplification (MDA) to generate sufficient DNA for the preparation of a fosmid metagenomic library. Potential bias of MDA was detected by fingerprint analysis of 16S rRNA using denaturing gradient gel electrophoresis for low-template amplification (0.01 ng template). Sufficient template (1-5 ng) was used in MDA to circumvent this bias and chimeric artefacts were minimized by using an enzymatic treatment of MDA-generated DNA with S1 nuclease and DNA polymerase I. Screening of the metagenomic library revealed one fosmid containing methanol dehydrogenase and two fosmids containing 16S rRNA genes from these Methylocystis-related species as well as one fosmid containing a 16S rRNA gene related to that of Methylocella/Methylocapsa. Sequencing of the 14 kb methanol dehydrogenase-containing fosmid allowed the assembly of a gene cluster encoding polypeptides involved in bacterial methanol utilization (mxaFJGIRSAC). This combination of DNA stable-isotope probing, MDA and metagenomics provided access to genomic information of a relatively large DNA fragment of these thus far uncultivated, predominant and active methanotrophs in peatland soil.

Vegetation affects the relative abundances of dominant soil bacterial taxa and soil respiration rates in an upland grassland soil.

Plant-derived organic matter inputs are thought to be a key driver of soil bacterial community composition and associated soil processes. We sought to investigate the role of acid grassland vegetation on soil bacterial community structure by assessing bacterial diversity in combination with other soil variables in temporally and spatially distinct samples taken from a field-based plant removal experiment. Removal of aboveground vegetation resulted in reproducible differences in soil properties, soil respiration and bacterial diversity. Vegetated soils had significantly increased carbon and nitrogen concentrations and exhibited higher rates of respiration. Molecular analyses revealed that the soils were broadly dominated by Alphaproteobacterial and Acidobacterial lineages, with increased abundances of Alphaproteobacteria in vegetated soils and more Acidobacteria in bare soils. This field-based study contributes to a growing body of evidence documenting the effect of soil nutrient status on the relative abundances of dominant soil bacterial taxa, with Proteobacterial taxa dominating over Acidobacteria in soils exhibiting higher rates of C turnover. Furthermore, we highlight the role of aboveground vegetation in mediating this effect by demonstrating that plant removal can alter the relative abundances of dominant soil taxa with concomitant changes in soil CO2-C efflux.

Can biochar reduce soil greenhouse gas emissions from a Miscanthus bioenergy crop

Energy production from bioenergy crops may significantly reduce greenhouse gas (GHG) emissions through substitution of fossil fuels. Biochar amendment to soil may further decrease the net climate forcing of bioenergy crop production, however, this has not yet been assessed under field conditions. Significant suppression of soil nitrous oxide (N2O) and carbon dioxide (CO2) emissions following biochar amendment has been demonstrated in short‐term laboratory incubations by a number of authors, yet evidence from long‐term field trials has been contradictory. This study investigated whether biochar amendment could suppress soil GHG emissions under field and controlled conditions in a Miscanthus × Giganteus crop and whether suppression would be sustained during the first 2 years following amendment. In the field, biochar amendment suppressed soil CO2 emissions by 33% and annual net soil CO2 equivalent (eq.) emissions (CO2, N2O and methane, CH4) by 37% over 2 years. In the laboratory, under controlled temperature and equalised gravimetric water content, biochar amendment suppressed soil CO2 emissions by 53% and net soil CO2 eq. emissions by 55%. Soil N2O emissions were not significantly suppressed with biochar amendment, although they were generally low. Soil CH4 fluxes were below minimum detectable limits in both experiments. These findings demonstrate that biochar amendment has the potential to suppress net soil CO2 eq. emissions in bioenergy crop systems for up to 2 years after addition, primarily through reduced CO2 emissions. Suppression of soil CO2 emissions may be due to a combined effect of reduced enzymatic activity, the increased carbon‐use efficiency from the co‐location of soil microbes, soil organic matter and nutrients and the precipitation of CO2 onto the biochar surface. We conclude that hardwood biochar has the potential to improve the GHG balance of bioenergy crops through reductions in net soil CO2 eq. emissions.

Microbial community composition explains soil respiration responses to changing carbon inputs along an Andes-to-Amazon elevation gradient

1. The Andes are predicted to warm by 3–5 °C this century with the potential to alter the processes regulating carbon (C) cycling in these tropical forest soils. This rapid warming is expected to stimulate soil microbial respiration and change plant species distributions, thereby affecting the quantity and quality of C inputs to the soil and influencing the quantity of soil-derived CO2 released to the atmosphere. 2. We studied tropical lowland, premontane and montane forest soils taken from along a 3200-m elevation gradient located in south-east Andean Peru. We determined how soil microbial communities and abiotic soil properties differed with elevation. We then examined how these differences in microbial composition and soil abiotic properties affected soil C-cycling processes, by amending soils with C substrates varying in complexity and measuring soil heterotrophic respiration (RH). 3. Our results show that there were consistent patterns of change in soil biotic and abiotic properties with elevation. Microbial biomass and the abundance of fungi relative to bacteria increased significantly with elevation, and these differences in microbial community composition were strongly correlated with greater soil C content and C:N (nitrogen) ratios. We also found that RH increased with added C substrate quality and quantity and was positively related to microbial biomass and fungal abundance. 4. Statistical modelling revealed that RH responses to changing C inputs were best predicted by soil pH and microbial community composition, with the abundance of fungi relative to bacteria, and abundance of gram-positive relative to gram-negative bacteria explaining much of the model variance. 5. Synthesis. Our results show that the relative abundance of microbial functional groups is an important determinant of RH responses to changing C inputs along an extensive tropical elevation gradient in Andean Peru. Although we do not make an experimental test of the effects of climate change on soil, these results challenge the assumption that different soil microbial communities will be ‘functionally equivalent’ as climate change progresses, and they emphasize the need for better ecological metrics of soil microbial communities to help predict C cycle responses to climate change in tropical biomes.

Environmental distribution and abundance of the facultative methanotroph Methylocella

Methylocella spp. are facultative methanotrophs, which are able to grow not only on methane but also on multicarbon substrates such as acetate, pyruvate or malate. Methylocella spp. were previously thought to be restricted to acidic soils such as peatlands, in which they may have a key role in methane oxidation. There is little information on the abundance and distribution of Methylocella spp. in the environment. New primers were designed, and a real-time quantitative PCR method was developed and validated targeting Methylocella mmoX (encoding the α-subunit of the soluble methane monooxygenase) that allowed the quantification of Methylocella spp. in environmental samples. We also developed and validated specific PCR assays, which target 16S rRNA genes of known Methylocella spp. These were used to investigate the distribution of Methylocella spp. in a variety of environmental samples. It was revealed that Methylocella species are widely distributed in nature and not restricted to acidic environments.

Gully hotspot contribution to landscape methane (CH4) and carbon dioxide (CO2) fluxes in a northern peatland

Peatlands are long term carbon catchments that sink atmospheric carbon dioxide (CO(2)) and source methane (CH(4)). In the uplands of the United Kingdom ombrotrophic blanket peatlands commonly exist within Calluna vulgaris (L.) dominated moorland ecosystems. These landscapes contain a range of topographical features that influence local hydrology, climate and plant community composition. In this study we examined the variation in ecosystem CO(2) respiration and net CH(4) fluxes from typical plant-soil systems in dendritic drainage gullies and adjacent blanket peat during the growing season. Typically, Eriophorum spp., Sphagnum spp. and mixed grasses occupied gullies while C. vulgaris dominated in adjacent blanket peat. Gross CO(2) respiration was highest in the areas of Eriophorum spp. (650+/-140 mg CO(2) m(-2) h(-1)) compared to those with Sphagnum spp. (338+/-49 mg CO(2) m(-2) h(-1)), mixed grasses (342+/-91 mg CO(2) m(-2) h(-1)) and C. vulgaris (174+/-63 mg CO(2) m(-2) h(-1)). Measurements of the net CH(4) flux showed higher fluxes from the Eriophorum spp (2.2+/-0.6 mg CH(4) m(-2) h(-1)) locations compared to the Sphagnum spp. (0.6+/-0.4 mg CH(4) m(-2) h(-1)), mixed grasses (0.1+/-0.1 mg CH(4) m(-2) h(-1)) and a negligible flux detected from C. vulgaris (0.0+/-0.0 mg CH(4) m(-2) h(-1)) locations. A GIS approach was applied to calculate the contribution of gullies to landscape scale greenhouse gas fluxes. Findings from the Moor House National Nature Reserve in the UK showed that although gullies occupied only 9.3% of the total land surface, gullies accounted for 95.8% and 21.6% of the peatland net CH(4) and CO(2) respiratory fluxes, respectively. The implication of these findings is that the relative contribution of characteristic gully systems need to be considered in estimates of landscape scale peatland greenhouse gas fluxes.

Effects of land-use on the activity and diversity of methane oxidizing bacteria in forest soils

Abstract Methane is an important greenhouse gas and CH 4 oxidation in soil represents a significant sink for this gas. High capacity CH 4 oxidation potentials and molecular profiles of CH 4 oxidizing bacteria in soil were compared for five land-use treatments at a fully replicated experimental site within the Gisburn Forest Experiment, to assess the effects of land-use on both the potential activity of CH 4 oxidizing bacteria and their diversity. Forestry land-use was found to have a highly significant effect on CH 4 oxidation potentials. Highest CH 4 oxidation potentials were found in soils collected under stands of oak, in grassland plots, and in one soil under Norway spruce. A negative relationship between soil water nitrate concentration and CH 4 oxidation capacity was evident across the experimental site, with the high nitrate soils under stands of alder exhibiting little or no capacity for CH 4 oxidation even at optimal temperature and water content. Molecular profiles indicated that a diverse range of bacteria with the potential to oxidize CH 4 were present in all soils, however no clear correlation with CH 4 oxidation potential was identified.

Environmental costs and benefits of growing Miscanthus for bioenergy in the UK

Planting the perennial biomass crop Miscanthus in the UK could offset 2–13 Mt oil eq. yr−1, contributing up to 10% of current energy use. Policymakers need assurance that upscaling Miscanthus production can be performed sustainably without negatively impacting essential food production or the wider environment. This study reviews a large body of Miscanthus relevant literature into concise summary statements. Perennial Miscanthus has energy output/input ratios 10 times higher (47.3 ± 2.2) than annual crops used for energy (4.7 ± 0.2 to 5.5 ± 0.2), and the total carbon cost of energy production (1.12 g CO2‐C eq. MJ−1) is 20–30 times lower than fossil fuels. Planting on former arable land generally increases soil organic carbon (SOC) with Miscanthus sequestering 0.7–2.2 Mg C4‐C ha−1 yr−1. Cultivation on grassland can cause a disturbance loss of SOC which is likely to be recovered during the lifetime of the crop and is potentially mitigated by fossil fuel offset. N2O emissions can be five times lower under unfertilized Miscanthus than annual crops and up to 100 times lower than intensive pasture. Nitrogen fertilizer is generally unnecessary except in low fertility soils. Herbicide is essential during the establishment years after which natural weed suppression by shading is sufficient. Pesticides are unnecessary. Water‐use efficiency is high (e.g. 5.5–9.2 g aerial DM (kg H2O)−1, but high biomass productivity means increased water demand compared to cereal crops. The perennial nature and belowground biomass improves soil structure, increases water‐holding capacity (up by 100–150 mm), and reduces run‐off and erosion. Overwinter ripening increases landscape structural resources for wildlife. Reduced management intensity promotes earthworm diversity and abundance although poor litter palatability may reduce individual biomass. Chemical leaching into field boundaries is lower than comparable agriculture, improving soil and water habitat quality.