David W. Hopkins

Field and pulping performances of transgenic trees with altered lignification

The agronomic and pulping performance of transgenic trees with altered lignin has been evaluated in duplicated, long-term field trials. Poplars expressing cinnamyl alcohol dehydrogenase (CAD) or caffeate/5-hydroxy-ferulate O-methyltransferase (COMT) antisense transgenes were grown for four years at two sites, in France and England. The trees remained healthy throughout the trial. Growth indicators and interactions with insects were normal. No changes in soil microbial communities were detected beneath the transgenic trees. The expected modifications to lignin were maintained in the transgenics over four years, at both sites. Kraft pulping of tree trunks showed that the reduced-CAD lines had improved characteristics, allowing easier delignification, using smaller amounts of chemicals, while yielding more high-quality pulp. This work highlights the potential of engineering wood quality for more environmentally benign papermaking without interfering with tree growth or fitness.

Biological Diversity and Function in Soils.

Although soil provides physical support for plants and contributes to a variety of important environmental functions, many questions about the ecological significance of its biological diversity, and how ecosystem function is affected, have never been asked. Recent technical developments, as well as new experimental and modelling approaches, have led to a renaissance in soil biodiversity research. The key areas are reflected in this new volume, which brings together many leading contributions on the role and importance of soil biota.

Temperature sensitivity of soil respiration rates enhanced by microbial community response

Soils store about four times as much carbon as plant biomass, and soil microbial respiration releases about 60 petagrams of carbon per year to the atmosphere as carbon dioxide. Short-term experiments have shown that soil microbial respiration increases exponentially with temperature. This information has been incorporated into soil carbon and Earth-system models, which suggest that warming-induced increases in carbon dioxide release from soils represent an important positive feedback loop that could influence twenty-first-century climate change. The magnitude of this feedback remains uncertain, however, not least because the response of soil microbial communities to changing temperatures has the potential to either decrease or increase warming-induced carbon losses substantially. Here we collect soils from different ecosystems along a climate gradient from the Arctic to the Amazon and investigate how microbial community-level responses control the temperature sensitivity of soil respiration. We find that the microbial community-level response more often enhances than reduces the mid- to long-term (90 days) temperature sensitivity of respiration. Furthermore, the strongest enhancing responses were observed in soils with high carbon-to-nitrogen ratios and in soils from cold climatic regions. After 90 days, microbial community responses increased the temperature sensitivity of respiration in high-latitude soils by a factor of 1.4 compared to the instantaneous temperature response. This suggests that the substantial carbon stores in Arctic and boreal soils could be more vulnerable to climate warming than currently predicted.

β-Glucosidase activity in pasture soils

β-Glucosidase is involved in the degradation of cellulose in soils and has potential for monitoring biological soil quality. We assayed β-glucosidase activity in 29 permanent grassland soils from England and Wales with contrasting physico-chemical and biological properties (clay content 22–68%; total carbon 29–80 mg g−1; microbial carbon 412–3412 μg g−1). Substrate induced β-glucosidase activity ranged between 1.12 and 6.12 μmol para-nitrophenol g−1 soil h−1 and was positively correlated with concentrations of clay, total carbon and microbial carbon. This suggests that substrate-induced β-glucosidase activity is an integrative measure of physico-chemical and biological soil properties and may have applications in monitoring biological soil quality.

Soil microbial respiration in arctic soil does not acclimate to temperature

Warming-induced release of CO2 from the large carbon (C) stores in arctic soils could accelerate climate change. However, declines in the response of soil respiration to warming in long-term experiments suggest that microbial activity acclimates to temperature, greatly reducing the potential for enhanced C losses. As reduced respiration rates with time could be equally caused by substrate depletion, evidence for thermal acclimation remains controversial. To overcome this problem, we carried out a cooling experiment with soils from arctic Sweden. If acclimation causes the reduction in soil respiration observed after experimental warming, then it should subsequently lead to an increase in respiration rates after cooling. We demonstrate that thermal acclimation did not occur following cooling. Rather, during the 90 days after cooling, a further reduction in the soil respiration rate was observed, which was only reversed by extended re-exposure to warmer temperatures. We conclude that over the time scale of a few weeks to months, warming-induced changes in the microbial community in arctic soils will amplify the instantaneous increase in the rates of CO2 production and thus enhance C losses potentially accelerating the rate of 21st century climate change.

Biological and chemical properties of arable soils affected by long-term organic and inorganic fertilizer applications

Abstract Using soils from field plots in four different arable crop experiments that have received combinations of manure, lime and inorganic N, P and K for up to 20 years, the effects of these fertilizers on soil chemical properties and estimates of soil microbial community size and activity were studied. The soil pH was increased or unaffected by the addition of organic manure plus inorganic fertilizers applied in conjunction with lime, but decreased in the absence of liming. The soil C and N contents were greater for all fertilized treatments compared to the control, yet in all cases the soil samples from fertilized plots had smaller C:N ratios than soil from the unfertilized plots. The soil concentrations of all the other inorganic nutrients measured were greater following fertilizer applications compared with the unfertilized plots, and this effect was most marked for P and K in soils from plots that had received the largest amounts of these nutrients as fertilizers. Both biomass C determined by chloroform fumigation and glucose-induced respiration tended to increase as a result of manure and inorganic fertilizer applications, although soils which received the largest additions of inorganic fertilizers in the absence of lime contained less biomass C than those to which lime had been added. Dehydrogenase activity was lower in soils that had received the largest amounts of fertilizers, and was further decreased in the absence of lime. This suggests that dehydrogenase activity was highly sensitive to the inhibitory effects associated with large fertilizer additions. Potential denitrification and anaerobic respiration determined in one soil were increased by fertilizer application but, as with both the microbial biomass and dehydrogenase activity, there were significant reductions in both N2O and CO2 production in soils which received the largest additions of inorganic fertilizers in the absence of lime. In contrast, the size of the denitrifying component of the soil microbial community, as indicated by denitrifying enzyme activity, was unaffected by the absence of lime at the largest rate of inorganic fertilizer applications. The results indicated differences in the composition or function of microbial communities in the soils in response to long-term organic and inorganic fertilization, especially when the soils were not limited.

Acquisition and assimilation of nitrogen as peptide-bound and D-enantiomers of amino acids by wheat.

Nitrogen is a key regulator of primary productivity in many terrestrial ecosystems. Historically, only inorganic N (NH4 + and NO3 -) and L-amino acids have been considered to be important to the N nutrition of terrestrial plants. However, amino acids are also present in soil as small peptides and in D-enantiomeric form. We compared the uptake and assimilation of N as free amino acid and short homopeptide in both L- and D-enantiomeric forms. Sterile roots of wheat (Triticum aestivum L.) plants were exposed to solutions containing either 14C-labelled L-alanine, D-alanine, L-trialanine or D-trialanine at a concentration likely to be found in soil solution (10 µM). Over 5 h, plants took up L-alanine, D-alanine and L-trialanine at rates of 0.9±0.3, 0.3±0.06 and 0.3±0.04 µmol g−1 root DW h−1, respectively. The rate of N uptake as L-trialanine was the same as that as L-alanine. Plants lost ca.60% of amino acid C taken up in respiration, regardless of the enantiomeric form, but more (ca.80%) of the L-trialanine C than amino acid C was respired. When supplied in solutions of mixed N form, N uptake as D-alanine was ca.5-fold faster than as NO3 -, but slower than as L-alanine, L-trialanine and NH4 +. Plants showed a limited capacity to take up D-trialanine (0.04±0.03 µmol g−1 root DW h−1), but did not appear to be able to metabolise it. We conclude that wheat is able to utilise L-peptide and D-amino acid N at rates comparable to those of N forms of acknowledged importance, namely L-amino acids and inorganic N. This is true even when solutes are supplied at realistic soil concentrations and when other forms of N are available. We suggest that it may be necessary to reconsider which forms of soil N are important in the terrestrial N cycle.

Decomposition in soil of tobacco plants with genetic modifications to lignin biosynthesis

Abstract Genetic modification of the amount, conformation and composition of lignin in plant materials is being explored both to understand better the process of lignin biosynthesis and with a view to enhancing forage digestibility or paper pulping properties. We have investigated the interaction between the effects of genetic modifications to lignin biosynthesis and the activity of decomposer organisms to provide information in relation to understanding the wider ecological effects of specific genetic modifications to crop plants and because the plants with modified lignin biosynthesis may be useful models in decomposition studies. The decomposition of material from the stems of four lines of tobacco (Nicotiana tabacum L.) plants, three of which had genetic modifications to lignin biosynthesis, were followed during a 77 day incubation in four different soils under laboratory conditions. The tobacco plants were either unmodified (wild-type) or had antisense or partial sense transgenes for one of three crucial enzymes [cinnamyl alcohol dehydrogenase (CAD), caffeic acid O-methyltransferase (COMT) or cinnamoyl CoA-reductase (CCR)] for lignin biosynthesis. Solid-state 13C nuclear magnetic resonance spectroscopy indicated that stem material from the unmodified plants, reduced CAD and reduced COMT plants all had similar amount of lignins, whereas stem material from the reduced CCR plants contained less lignin. Material from all of the modified plants decomposed more rapidly than material from the wild-type plants. Depending on the soil, between 11.7 and 16.3% of the C added in the plant material was lost as CO2 during a 77 day incubation from reduced CCR plants compared with between 6.1 and 9.2% for the reduced COMT plants, between 3.6 and 7.9% for the reduced CAD plants and between 3.1 and 5.9% for the wild-type plants. The increased decomposition rate of reduced CAD and reduced COMT plants compared with material from the wild-type plants was attributed primarily to differences in the degree of protection from microbial attack afforded to the polysaccharides and other relatively labile plant components by the lignin. In the reduced CAD and the reduced COMT plants, the composition and conformation but not the concentration of the lignin was altered compared to the wild-type plants. The greater rate of decomposition of reduced CCR plants compared with the wild-type plants was most likely the result of the smaller lignin content of these plants.

Carbon transformations during decomposition of different components of plant leaves in soil.

Abstract We investigated the effect of lime addition to an upland organic soil on the decomposition of Lolium perenne leaves and isolated fractions of L. perenne leaves in a laboratory experiment lasting 75 d. The L. perenne plants were grown in a 13 CO 2 -enriched environment and some leaf material was pretreated with ethanol and detergent in order to remove some cell contents and soluble material. The ethanol- and detergent-treated leaves had less alkyl-C, as seen by solid-state 13 C nuclear magnetic spectroscopy (NMR), and a greater proportion of cellulose and hemicellulose than the untreated leaves. Solid-state 13 C NMR spectroscopy and scanning electron microscopy (SEM) were used to follow aspects of the C transformations during decomposition. C mineralization was estimated from total CO 2 production. The size and activity of the microbial community was greater in limed than in soils without lime, and microbial respiration was less in both soils amended with ethanol- and detergent-treated leaves compared to soils amended with untreated leaves. In both limed and unlimed soils, amendment with untreated leaves led to additional CO 2 production within 7 d of addition, whereas amendment with treated leaves led to a smaller increase in CO 2 production. The flush of CO 2 production was attributed to decomposition of the more accessible and soluble plant components that, in the ethanol- and detergent-treated leaves, had been removed during the ethanol and detergent treatment. The 13 C NMR spectra recorded for plant material separated from soil 1 d after addition of ethanol- and detergent-treated leaves had larger alkyl-C (30 ppm) signals compared with spectra from untreated leaves. This was interpreted as representing an accumulation of residues from decomposition of plant structural components.

Biochar in bioenergy cropping systems: impacts on soil faunal communities and linked ecosystem processes

Biochar amendment of soil and bioenergy cropping are two eco‐engineering strategies at the forefront of attempts to offset anthropogenic carbon dioxide (CO2) emissions. Both utilize the ability of plants to assimilate atmospheric CO2, and are thus intrinsically linked with soil processes. Research to date has shown that biochar and bioenergy cropping change both aboveground and belowground carbon cycling and soil fertility. Little is known, however, about the form and function of soil food webs in these altered ecosystems, or of the consequences of biodiversity changes at higher trophic levels for soil carbon sequestration. Hitherto studies on this topic have been chiefly observational, and often report contrasting results, thus adding little mechanistic understanding of biochar and bioenergy cropping impacts on soil organisms and linked ecosystem processes. This means it is difficult to predict, or control for, changes in biotic carbon cycling arising from biochar and bioenergy cropping. In this study we explore the potential mechanisms by which soil communities might be affected by biochar, particularly in soils which support bioenergy cropping. We outline the abiotic (soil quality‐mediated) and biotic (plant‐ and microbe‐mediated) shifts in the soil environment, and implications for the abundance, diversity, and composition of soil faunal communities. We offer recommendations for promoting biologically diverse, fertile soil via biochar use in bioenergy crop systems, accompanied by specific future research priorities.