Nick Ostle

Export of dissolved organic carbon from peatlands under elevated carbon dioxide levels

Peatlands represent a vast store of global carbon. Observations of rapidly rising dissolved organic carbon concentrations in rivers draining peatlands have created concerns that those stores are beginning to destabilize. Three main factors have been put forward as potential causal mechanisms, but it appears that two alternatives—warming and increased river discharge—cannot offer satisfactory explanations. Here we show that the third proposed mechanism, namely shifting trends in the proportion of annual rainfall arriving in summer, is similarly unable to account for the trend. Instead we infer that a previously unrecognized mechanism—carbon dioxide mediated stimulation of primary productivity—is responsible. Under elevated carbon dioxide levels, the proportion of dissolved organic carbon derived from recently assimilated carbon dioxide was ten times higher than that of the control cases. Concentrations of dissolved organic carbon appear far more sensitive to environmental drivers that affect net primary productivity than those affecting decomposition alone.

Microbial contributions to climate change through carbon cycle feedbacks

There is considerable interest in understanding the biological mechanisms that regulate carbon exchanges between the land and atmosphere, and how these exchanges respond to climate change. An understanding of soil microbial ecology is central to our ability to assess terrestrial carbon cycle–climate feedbacks, but the complexity of the soil microbial community and the many ways that it can be affected by climate and other global changes hampers our ability to draw firm conclusions on this topic. In this paper, we argue that to understand the potential negative and positive contributions of soil microbes to land–atmosphere carbon exchange and global warming requires explicit consideration of both direct and indirect impacts of climate change on microorganisms. Moreover, we argue that this requires consideration of complex interactions and feedbacks that occur between microbes, plants and their physical environment in the context of climate change, and the influence of other global changes which have the capacity to amplify climate-driven effects on soil microbes. Overall, we emphasize the urgent need for greater understanding of how soil microbial ecology contributes to land–atmosphere carbon exchange in the context of climate change, and identify some challenges for the future. In particular, we highlight the need for a multifactor experimental approach to understand how soil microbes and their activities respond to climate change and consequences for carbon cycle feedbacks.

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.

Active root-inhabiting microbes identified by rapid incorporation of plant-derived carbon into RNA

Plant roots harbor a large diversity of microorganisms that have an essential role in ecosystem functioning. To better understand the level of intimacy of root-inhabiting microbes such as arbuscular mycorrhizal fungi and bacteria, we provided 13CO2 to plants at atmospheric concentration during a 5-h pulse. We expected microbes dependent on a carbon flux from their host plant to become rapidly labeled. We showed that a wide variety of microbes occurred in roots, mostly previously unknown. Strikingly, the greatest part of this unsuspected diversity corresponded to active primary consumers. We found 17 bacterial phylotypes co-occurring within roots of a single plant, including five potentially new phylotypes. Fourteen phylotypes were heavily labeled with the 13C. Eight were phylogenetically close to Burkholderiales, which encompass known symbionts; the others were potentially new bacterial root symbionts. By analyzing unlabeled and 13C-enriched RNAs, we demonstrated differential activity in C consumption among these root-inhabiting microbes. Arbuscular mycorrhizal fungal RNAs were heavily labeled, confirming the high carbon flux from the plant to the fungal compartment, but some of the fungi present appeared to be much more active than others. The results presented here reveal the possibility of uncharacterized root symbioses.

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.

The use of fluorogenic substrates for measuring enzyme activity in peatlands

The fluorogenic model substrates, methylumbelliferyl [MUF]-β-D-glucoside, MUF-phosphate and MUF-sulphate, were used to investigate the activities of β-glucosidase, phosphatase and sulphatase, respectively, in Welsh peatland soils. The method was used to investigate depth dependent variations in enzyme activity in a riparian wetland, and flush channel wetland. The highest activities were found at depths of less than 10 cm, thus confirming other studies which suggest this upper depth to be the site of greatest microbial activity. The most serious limitation to the technique was found to be the (fluorescence) quenching effects of the phenolic materials that dominate peatland dissolved organic carbon. The problem necessitates the adoption of a time consuming quench correction procedure with every sample. Fluorogenic substrates have led to a greater understanding of the role of enzymes in other aquatic systems. It seems likely that they will prove of equal value in elucidating their role in nutrient cycling and the biogeochemistry of peatlands.

Microbial activity and enzymic decomposition processes following peatland water table drawdown

Microbial activity and enzymic decomposition processes were followed during a field-based experimental lowering of the water table in a Welsh peatland. Respiration was not significantly affected by the treatment. However, the enzymes sulphatase, β-glucosidase and phosphatase were stimulated by between 31 and 67% upon water table drawdown. A further enzyme, phenol oxidase, was not significantly affected. The observation of elevated enzyme activities without an associated increase in microbial respiratory activity suggests that drought conditions influence peatland mineralisation rates through a direct stimulation of existing enzymes, rather than through a generalised stimulation of microbial metabolism (with associated de-novo enzyme synthesis). Hydrochemical data suggest that the stimulation may have been caused by a reduction in the inhibitory action of iron and phenolics in the peat pore waters. Overall, the findings support the recent hypothesis that drier conditions associated with climate change could stimulate mineralisation within wetlands. ei]R Merckx

Carbon assimilation and turnover in grassland vegetation using anin situ13CO2 pulse labelling system

A mobile laboratory was developed to administer a controlled flow of (13)C labelled CO(2) at ambient concentrations ( approximately 350 ppm) in the field. The stable isotope delivery (SID) system consists of an isotope-mixing unit with flow control to a series of 12 independent labelling chambers. In-line CPU controlled infrared gas analysers allow automated measurement of chamber CO(2) concentrations and gas flow management. A preliminary experiment was established on an upland pasture located at the NERC Soil Biodiversity experimental site, Sourhope, UK, in August 1999. The objective of this investigation was to determine the magnitude of pulse-derived C incorporation into a typical upland plant community. To achieve this, the SID system was deployed to pulse-label vegetation with CO(2) enriched with (13)C (50 atom %) at ambient concentrations ( approximately 350 ppm) on two consecutive days in August 1999. Samples of headspace CO(2), shoot and root were taken on four occasions over a period of 28 days after (13)C labelling. These materials were then prepared for (13)C/(12)C ratio determination by continuous-flow/combustion/isotope ratio mass spectrometry (CF-C-IRMS). Results showed that pulse derived CO(2)-C was assimilated at a rate of 128 +/- 32 microg g shoot-C hour(-1). Dynamic samplings showed that pulse-derived (13)C concentrations in the labelled plant tissues declined by 77.4 +/- 6% after 48 hours. The rapid decline in (13)C concentrations in plant matter was the result of C loss from the plant in the form of respired CO(2) and root exudates, and dilution by subsequent unlabelled C assimilates. This novel system offers considerable potential for in situ tracer investigations.

Active microbial RNA turnover in a grassland soil estimated using a 13CO2 spike

Rhizosphere microbes are critical to the initial transfer and transformation of root carbon inputs to the soil but our understanding of the activity of these organisms remains constrained by their limited culturability. In this study we combined isotopic 13C tracer and molecular approaches to measure the incorporation of recently assimilated plant C into soil microbial RNA and DNA pools as a means to determine the turnover of the ‘active’ rhizosphere community. This required the development of a method for the extraction, purification and preparation of small-sample soil DNA and RNA (<5 μg C) for isotope analysis. Soil, plant and respired CO2 samples were collected from a 13CO2 pulse-chase experiment at intervals for 20 days post-labelling. The peak of 13C release in soil/root respired CO2 came between 5 and 48 h after 13CO2 pulse-labelling and was followed by a secondary peak of soil heterotroph 13C respiration after 136 h. Results showed that both soil DNA and RNA rapidly incorporated recent photosynthate with greatest 13C found in the ‘active’ microbial RNA fraction reflecting higher rates of microbial RNA turnover. The dilution rate of the pulse derived 13C in RNA-C was used to estimate a microbial RNA turnover of approximately 20% day−1 with a 15–20 day residence time for photosynthate derived 13C in the RNA pool. The findings of this work confirm the rapid transfer of photosynthate C inputs through soil microorganisms to the atmosphere as CO2 and the potential of the biomolecular-isotope tracer approach in soil C research.

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.