Impact of land-use changes on the methanotrophic community structure

Methane (CH4) is one of the most potent greenhouse gases and its increasing concentration in the Earth’s atmosphere is linked to today’s global warming. The types of land and land-use have an impact on net CH4 fluxes, e.g. wetlands are generally net CH4 emitters while upland forest soils are a sink for CH4. This project aimed to elucidate the effect of afforestation and reforestation on net CH4 fluxes and to determine the control of the CH4-oxidising bacteria (methanotrophs) on net CH4 flux rate. This was investigated using a combination of molecular (T-RFLP, cloning/sequencing, microarray) and activity-specific (PLFA-SIP) approaches. Several sites were selected to analyse soil methanotrophs under shrubs regenerating after a fire compared to a native mature forest (in New Zealand), and under bog, grass, heath, pine and birch vegetation (in Scotland). Furthermore, a simple bottom-up approach was applied to seasonal measurements of local net CH4 fluxes in Scotland. These were upscaled to annual values in order to estimate the contribution to the national CH4 budget for each habitat investigated. The effect on CH4 mitigation of the conversion of different types of non-forested habitat to forests was then estimated. Afforestation/reforestation was always found to induce net CH4 oxidation at rates much faster than previously estimated. This preliminary analysis suggests that heathland conversion to birch forest was beneficial in term of CH4 sinks but it also induced large and permanent losses of soil C. However, bog afforestation with pine trees can potentially neutralise the national CH4 emissions from non-forested areas, while preserving soil C stocks. This project also revealed that changes in net CH4 flux due to land-use changes were closely related to shifts in the structure of the methanotrophic community. The relative abundance of members of the USCα cluster (high-affinity methanotrophs) was a strong predictor of net CH4 fluxes. Finally, the sole presence of trees suggested a niche-specific adaptation of the methanotrophs, which may have been correlated to some of the soil characteristics

Shifts in the microbial community structure explain the response of soil respiration to land-use change but not to climate warming

Soil stores more carbon (C) than plants and atmosphere combined and it is vulnerable to increased microbial respiration under projected global changes including land-use change and future climate scenarios (mainly elevated temperature). Land-use change is known to have a direct impact on soil organic C and soil respiration (Rs) but the mechanisms that drive these changes remain debatable. Similarly, recent studies and simulation models predict that Rs will respond positively to projected climate warming. However, there are significant uncertainties in the magnitude and mechanisms of this feedback response of Rs to global change. To identify the mechanisms of Rs response to land-use change and climate warming, we first investigated Rs from different land use types. Soil respiration was estimated seasonally from four different Scottish land uses: moorland, birch woodland, grassland and pine forest (n = 24). Our results demonstrated that despite a dramatic loss of total C and nitrogen (N) in the soils under birch trees, the Rs in the birch woodland was similar to that of the moorland and pine forest, with Rs in the grassland being significantly higher. The microbial community structure, estimated by Multiplex Terminal-Restriction Fragment Length Polymorphism (MT-RFLP) and 454 pyrosequencing, was significantly different under each land use type. A strong correlation of Rs with soil properties (pH, inorganic N, C:N ratio and moisture) and with microbial community structure was identified. To test the impact of elevated temperature on Rs and to identify potential microbial mechanisms, we performed laboratory incubation studies. Soils from different land uses were incubated at 7 °C (mean annual temperature (MAT) in Scotland) and 10 °C (MAT + 3 °C) with and without the presence of a labile (13C-glucose) and recalcitrant (13C-lignin) form of C to identify the active groups of microbes and to determine the role of substrate availability on feedback response. The warming treatment induced an increase in Rs rates in all soils. The magnitude of the Rs response to warming was modulated by the land use types, and the Rs was more prominent in soils with high C contents. The addition of glucose substantially increased both total and rate of Rs compared to no substrate- and lignin-amended soils, providing evidence of labile C depletion as a mechanism for the thermal response of Rs. The warming treatment did not impact the composition of the active or total microbial community as revealed by phospholipid fatty acid-stable isotope probing (PLFA-SIP), MT-RFLP and 454 pyrosequencing. Our results showed that the microbial metabolic activity was higher under warming treatment suggesting that a positive feedback of Rs to increased temperature is mediated by changes in substrate availability and microbial metabolic rates

Martins FE 2017 dataset

All data from the pape

Data from: Identifying environmental drivers of greenhouse gas emissions under warming and reduced rainfall in boreal-temperate forests

1.Atmospheric concentrations of carbon dioxide (CO2), methane (CH4) and nitrous oxide (N2O) are predicted to increase as a consequence of fossil fuel emissions and the impact on biosphere-atmosphere interactions. Forest ecosystems in general, and forest soils in particular, can be sinks or sources for CO2, CH4, and N2O. Environmental studies traditionally target soil temperature and moisture as the main predictors of soil greenhouse gas (GHG) flux from different ecosystems; however, these emissions are primarily biologically driven. Thus, little is known about the degree of regulation by soil biotic vs. abiotic factors on GHG emissions, particularly under predicted increase in global temperatures, and changes in intensity and frequency of precipitation events. 2.Here we measured net CO2, CH4 and N2O fluxes after 5 years of experimental warming (+3.4°C), and 2 years of ≈45% summer rainfall reduction, in two forest sites in a boreal-temperate ecotone under different habitat conditions (closed or open canopy) in Minnesota, USA. We evaluated the importance of microbial gene abundance and climo-edaphic factors (soil texture, canopy, seasonality, climate and soil physicochemical properties) driving GHG emissions. 3.We found that changes in CO2 fluxes were predominantly determined abiotically by temperature and moisture, after accounting for bacterial abundance. Methane fluxes on the other hand, were determined both abiotically, by gas diffusivity (via soil texture) and microbially, by methanotroph pmoA gene abundance, whereas, N2O emissions showed only a strong biotic regulation via ammonia-oxidizing bacteria amoA gene abundance. Warming did not significantly alter CO2 and CH4 fluxes after 5 years of manipulation, while N2O emissions were greater with warming under open canopy. 4.Our findings provide evidence that soil GHG emissions result from multiple direct and indirect interactions of microbial and abiotic drivers. Overall, this study highlights the need to include both microbial and climo-edaphic properties in predictive models in order to provide improved mechanistic understanding for the development of future mitigation strategies

Evidence of Microbial Regulation of Biogeochemical Cycles from a Study on Methane Flux and Land Use Change

Microbes play an essential role in ecosystem functions, including carrying out biogeochemical cycles, but are currently considered a black box in predictive models and all global biodiversity debates. This is due to (i) perceived temporal and spatial variations in microbial communities and (ii) lack of ecological theory explaining how microbes regulate ecosystem functions. Providing evidence of the microbial regulation of biogeochemical cycles is key for predicting ecosystem functions, including greenhouse gas fluxes, under current and future climate scenarios. Using functional measures, stable-isotope probing, and molecular methods, we show that microbial (community diversity and function) response to land use change is stable over time. We investigated the change in net methane flux and associated microbial communities due to afforestation of bog, grassland, and moorland. Afforestation resulted in the stable and consistent enhancement in sink of atmospheric methane at all sites. This change in function was linked to a niche-specific separation of microbial communities (methanotrophs). The results suggest that ecological theories developed for macroecology may explain the microbial regulation of the methane cycle. Our findings provide support for the explicit consideration of microbial data in ecosystem/climate models to improve predictions of biogeochemical cycles

Response of methanotrophic communities to afforestation and reforestation in New Zealand

Methanotrophs use methane (CH4) as a carbon source. They are particularly active in temperate forest soils. However, the rate of change of CH4 oxidation in soil with afforestation or reforestation is poorly understood. Here, soil CH4 oxidation was examined in New Zealand volcanic soils under regenerating native forests following burning, and in a mature native forest. Results were compared with data for pasture to pine land-use change at nearby sites. We show that following soil disturbance, as little as 47 years may be needed for development of a stable methanotrophic community similar to that in the undisturbed native forest soil. Corresponding soil CH4-oxidation rates in the regenerating forest soil have the potential to reach those of the mature forest, but climo-edaphic fators appear limiting. The observed changes in CH4-oxidation rate were directly linked to a prior shift in methanotrophic communities, which suggests microbial control of the terrestrial CH4 flux and identifies the need to account for this response to afforestation and reforestation in global prediction of CH4 emission

The fate of carbon in a mature forest under carbon dioxide enrichment

Atmospheric carbon dioxide enrichment (eCO2) can enhance plant carbon uptake and growth1–5, thereby providing an important negative feedback to climate change by slowing the rate of increase of the atmospheric CO2 concentration6. Although evidence gathered from young aggrading forests has generally indicated a strong CO2 fertilization effect on biomass growth3–5, it is unclear whether mature forests respond to eCO2 in a similar way. In mature trees and forest stands7–10, photosynthetic uptake has been found to increase under eCO2 without any apparent accompanying growth response, leaving the fate of additional carbon fixed under eCO2 unclear4,5,7–11. Here using data from the first ecosystem-scale Free-Air CO2 Enrichment (FACE) experiment in a mature forest, we constructed a comprehensive ecosystem carbon budget to track the fate of carbon as the forest responded to four years of eCO2 exposure. We show that, although the eCO2 treatment of +150 parts per million (+38 per cent) above ambient levels induced a 12 per cent (+247 grams of carbon per square metre per year) increase in carbon uptake through gross primary production, this additional carbon uptake did not lead to increased carbon sequestration at the ecosystem level. Instead, the majority of the extra carbon was emitted back into the atmosphere via several respiratory fluxes, with increased soil respiration alone accounting for half of the total uptake surplus. Our results call into question the predominant thinking that the capacity of forests to act as carbon sinks will be generally enhanced under eCO2, and challenge the efficacy of climate mitigation strategies that rely on ubiquitous CO2 fertilization as a driver of increased carbon sinks in global forests