Calibration of plant functional type parameters using the adJULES system

Land-surface models (LSMs) are crucial components of the Earth system models (ESMs) that are used to make coupled climate-carbon cycle projections for the 21st century. The Joint UK Land Environment Simulator (JULES) is the land-surface model used in the climate and weather forecast models of the UK Met Office. JULES is also extensively used offline as a land-surface impacts tool, forced with climatologies into the future. In this study, JULES is automatically differentiated with respect to JULES parameters using commercial software from FastOpt, resulting in an analytical gradient, or adjoint, of the model. Using this adjoint, the adJULES parameter estimation system has been developed to search for locally optimum parameters by calibrating against observations. This thesis describes adJULES in a data assimilation framework and demonstrates its ability to improve the model-data fit using eddy-covariance measurements of gross primary productivity (GPP) and latent heat (LE) fluxes. The adJULES system is extended to have the ability to calibrate over multiple sites simultaneously. This feature is used to define new optimised parameter values for the five plant functional types (PFTs) in JULES. The optimised PFT-specific parameters improve the performance of JULES at over 85% of the sites used in the study, at both the calibration and evaluation stages. The new improved parameters for JULES are presented along with the associated uncertainties for each parameter. The results of the calibrations are compared to structural changes and used in a cluster analysis in order to challenge the PFT definitions in JULES. This thesis concludes with simple sensitivity studies which assess how the calibration of JULES has affected the sensitivity of the model to CO2-induced climate change

Night-time decline in plant respiration is consistent with substrate depletion

Understanding the response of plant respiration to climate change is key to determining whether the global land carbon sink continues into the future or declines. Most global vegetation models use a classical growth-maintenance approach, which predicts that nocturnal plant respiration is controlled by temperature only. However, recently published observations of plant respiration show a decline through the night even at constant temperature, which these global models cannot reproduce. Here we assess the role of respiratory substrates in this observed decline by evaluating an alternative model of plant respiration, in which the rate of respiration at constant temperature is instead dependent on the size of available substrate pools. We find that the observed decline in nocturnal respiration is reproduced by a model with just two substrate pools, one fast and one slow. These results demonstrate a need to change the way that plant respiration is represented in global vegetation models, moving to models based on labile pools which represent only a fraction of total plant biomass. These models naturally represent plant acclimation via changing pool-sizes and may have a significant impact on the long-term predictions of the global land carbon sink

Lowering water table reduces carbon sink strength and carbon stocks in northern peatlands

Peatlands at high latitudes have accumulated \u3e400 Pg carbon (C) because saturated soil and cold temperatures suppress C decomposition. This substantial amount of C in Arctic and Boreal peatlands is potentially subject to increased decomposition if the water table (WT) decreases due to climate change, including permafrost thaw-related drying. Here, we optimize a version of the Organizing Carbon and Hydrology In Dynamic Ecosystems model (ORCHIDEE-PCH4) using site-specific observations to investigate changes in CO and CH fluxes as well as C stock responses to an experimentally manipulated decrease of WT at six northern peatlands. The unmanipulated control peatlands, with the WT (seasonal max up to 45 cm) below the surface, currently act as C sinks in most years (58 ± 34 g C m year ; including 6 ± 7 g C-CH m year emission). We found, however, that lowering the WT by 10 cm reduced the CO sink by 13 ± 15 g C m year and decreased CH emission by 4 ± 4 g CH m year , thus accumulating less C over 100 years (0.2 ± 0.2 kg C m ). Yet, the reduced emission of CH , which has a larger greenhouse warming potential, resulted in a net decrease in greenhouse gas balance by 310 ± 360 g CO m year . Peatlands with the initial WT close to the soil surface were more vulnerable to C loss: Non-permafrost peatlands lost \u3e2 kg C m over 100 years when WT is lowered by 50 cm, while permafrost peatlands temporally switched from C sinks to sources. These results highlight that reductions in C storage capacity in response to drying of northern peatlands are offset in part by reduced CH emissions, thus slightly reducing the positive carbon climate feedbacks of peatlands under a warmer and drier future climate scenario

Carbonyl sulfide : comparing a mechanistic representation of the vegetation uptake in a land surface model and the leaf relative uptake approach

Land surface modellers need measurable proxies to constrain the quantity of carbon dioxide (CO2) assimilated by continental plants through photosynthesis, known as gross primary production (GPP). Carbonyl sulfide (COS), which is taken up by leaves through their stomates and then hydrolysed by photosynthetic enzymes, is a candidate GPP proxy. A former study with the ORCHIDEE land surface model used a fixed ratio of COS uptake to CO2 uptake normalised to respective ambient concentrations for each vegetation type (leaf relative uptake, LRU) to compute vegetation COS fluxes from GPP. The LRU approach is known to have limited accuracy since the LRU ratio changes with variables such as photosynthetically active radiation (PAR): while CO2 uptake slows under low light, COS uptake is not light limited. However, the LRU approach has been popular for COS-GPP proxy studies because of its ease of application and apparent low contribution to uncertainty for regional-scale applications. In this study we refined the COS-GPP relationship and implemented in ORCHIDEE a mechanistic model that describes COS uptake by continental vegetation. We compared the simulated COS fluxes against measured hourly COS fluxes at two sites and studied the model behaviour and links with environmental drivers. We performed simulations at a global scale, and we estimated the global COS uptake by vegetation to be -756 Gg S yr(-1) , in the middle range of former studies (-490 to -1335 Gg S yr(-1)). Based on monthly mean fluxes simulated by the mechanistic approach in ORCHIDEE, we derived new LRU values for the different vegetation types, ranging between 0.92 and 1.72, close to recently published averages for observed values of 1.21 for C-4 and 1.68 for C-3 plants. We transported the COS using the monthly vegetation COS fluxes derived from both the mechanistic and the LRU approaches, and we evaluated the simulated COS concentrations at NOAA sites. Although the mechanistic approach was more appropriate when comparing to high-temporal-resolution COS flux measurements, both approaches gave similar results when transporting with monthly COS fluxes and evaluating COS concentrations at stations. In our study, uncertainties between these two approaches are of secondary importance compared to the uncertainties in the COS global budget, which are currently a limiting factor to the potential of COS concentrations to constrain GPP simulated by land surface models on the global scale.Peer reviewe

Eukaryote culturomics of the gut reveals new species.

The repertoire of microeukaryotes in the human gut has been poorly explored, mainly in individuals living in northern hemisphere countries. We further explored this repertoire using PCR-sequencing and culture in seven individuals living in four tropical countries. A total of 41 microeukaryotes including 38 different fungal species and three protists were detected. Four fungal species, Davidiella tassiana, Davidiella sp., Corticiaceae sp., and Penicillium sp., were uniquely detected by culture; 27 fungal species were uniquely detected using PCR-sequencing and Candida albicans, Candida glabrata, Trichosporon asahii, Clavispora lusitaniae, Debaryomyces hansenii, Malassezia restricta, and Malassezia sp. were detected using both molecular and culture methods. Fourteen microeukaryotes were shared by the seven individuals, whereas 27 species were found in only one individual, including 11 species in Amazonia, nine species in Polynesia, five species in India, and two species in Senegal. These data support a worldwide distribution of Malassezia sp., Trichosporon sp., and Candida sp. in the gut mycobiome. Here, 13 fungal species and two protists, Stentor roeseli and Vorticella campanula, were observed for first time in the human gut. This study revealed a previously unsuspected diversity in the repertoire of human gut microeukaryotes, suggesting spots for further exploring this repertoire

Gut microeukaryotes during anorexia nervosa: a case report.

International audienceBACKGROUND: Few studies have focused on eukaryote community in the human gut. Here, the diversity of microeukaryotes in the gut microbiota of an anorexic patient was investigated using molecular and culture approaches. CASE PRESENTATION: A 21-year-old Caucasian woman was admitted in an intensive care unit for severe malnutrition in anorexia nervosa. One stool specimen was collected from the anorexic patient, culture and polymerase chain reaction-based explorations yielded a restricted diversity of fungi but four microeukaryotes Tetratrichomonas sp., Aspergillus ruber Penicillium solitum and Cladosporium bruhnei previously undescribed in the human gut. CONCLUSIONS: Establishing microeukaryote repertoire in gut microbiota contributes to the understanding of its role in human health

Plant and fungal diversity in gut microbiota as revealed by molecular and culture investigations.

BACKGROUND: Few studies describing eukaryotic communities in the human gut microbiota have been published. The objective of this study was to investigate comprehensively the repertoire of plant and fungal species in the gut microbiota of an obese patient. METHODOLOGY/PRINCIPAL FINDINGS: A stool specimen was collected from a 27-year-old Caucasian woman with a body mass index of 48.9 who was living in Marseille, France. Plant and fungal species were identified using a PCR-based method incorporating 25 primer pairs specific for each eukaryotic phylum and universal eukaryotic primers targeting 18S rRNA, internal transcribed spacer (ITS) and a chloroplast gene. The PCR products amplified using these primers were cloned and sequenced. Three different culture media were used to isolate fungi, and these cultured fungi were further identified by ITS sequencing. A total of 37 eukaryotic species were identified, including a Diatoms (Blastocystis sp.) species, 18 plant species from the Streptophyta phylum and 18 fungal species from the Ascomycota, Basidiomycota and Chytridiocomycota phyla. Cultures yielded 16 fungal species, while PCR-sequencing identified 7 fungal species. Of these 7 species of fungi, 5 were also identified by culture. Twenty-one eukaryotic species were discovered for the first time in human gut microbiota, including 8 fungi (Aspergillus flavipes, Beauveria bassiana, Isaria farinosa, Penicillium brevicompactum, Penicillium dipodomyicola, Penicillium camemberti, Climacocystis sp. and Malassezia restricta). Many fungal species apparently originated from food, as did 11 plant species. However, four plant species (Atractylodes japonica, Fibraurea tinctoria, Angelica anomala, Mitella nuda) are used as medicinal plants. CONCLUSIONS/SIGNIFICANCE: Investigating the eukaryotic components of gut microbiota may help us to understand their role in human health

Using soil moisture and land surface temperature Earth Observations to optimize land surface model performance

International audienc