Faculté des sciences

Assessing the diversity and metabolism of oxalotrophic bacteria in tropical soils

Bravo, Daniel ; Junier, Pilar (Dir.)

Thèse de doctorat : Université de Neuchâtel, 2013.

Climate change is increasing as a consequence of elevated concentrations of CO2 in the atmosphere. Among the scientific strategies proposed to tackle the effect of elevated CO2, the biogeochemical oxalate-carbonate pathway (OCP) occurring in terrestrial habitats, appears to be important since it is considered as a potential carbon sink. This process occurs naturally in... Plus

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    Summary
    Climate change is increasing as a consequence of elevated concentrations of CO2 in the atmosphere. Among the scientific strategies proposed to tackle the effect of elevated CO2, the biogeochemical oxalate-carbonate pathway (OCP) occurring in terrestrial habitats, appears to be important since it is considered as a potential carbon sink. This process occurs naturally in Earth, with a particular importance in tropical forests. Previous studies were carried out in a subtropical forest to evaluate the precipitation and biomineralization of carbonate due to biologic (microbial oxalotrophy) activity. However, the knowledge about biodiversity and the metabolic rates of oxalate consumption, as well as the effect of microbial interactions over the OCP at several tropical soils was poorly described. Therefore, the aim of this thesis was to assess the diversity and metabolism of oxalotrophic bacteria related with the OCP in tropical habitats. This document represents the first detailed study about metabolism and diversity of oxalotrophic bacteria found in three tropical soils in Bolivia, Indian, and Cameroon, implicated in oxalate-carbonate transformations. At those sampling sites, oxalate producing trees (oxalogenic trees) were assessed by biotic and abiotic treats influencing the pathway occurring there. The manuscript is organized in seven chapters. The first two chapters deal with the development and application of analytical and molecular techniques, such as isothermal microcalorimetry (IMC) and BrdU labeling DNA - DGGE, to study metabolism and diversity of model and active environmental oxalotrophic bacteria. The relevance of active oxalotrophic bacteria is highlighted. For instance, the ecological role of relatives to Kribbella phylotypes and related actinobacteria within the oxalotrophic group found in Cameroon is discussed at the end of chapter three. Moreover, the following chapter deal with a collection of oxalotrophic bacteria isolated from soil samples recovered in field trips performed at Bolivia, India, and Cameroon, where oxalogenic trees were found. The chapter includes a complete characterization of ten oxalotrophs, with the interest to understand their capability to consume oxalate as sole carbon and energy source, as well as, their metabolic plasticity by the consumption of other carbon substrates. High oxalate consumption rates were observed for strains such as Variovorax soil C18, Lysobacter sp. A8, Agrobacterium sp. B23, and Streptomyces achromogenes A9. Chapter five describe the development of a new technique of isolation of autochthonous couples of bacteria and fungi from soil implied in oxalotrophy. The case of the fungus Trichoderma sp. and eight oxalotrophic bacteria obtained from soils samples influenced by oxalogenic trees in Cameroon is discussed. Furthermore, a global discussion including a comparison of abundance and vertical distribution of oxalotrophic bacteria through soil profiles influenced by oxalate-producer trees is part of the chapter six. Biotic and abiotic treats are correlated statistically to compare and understand the OCP systems occurring in India and Cameroon. The contribution to the knowledge in oxalotrophic diversity and metabolism relative to the oxalate-carbonate pathway occurring in tropical soils, as well as, the perspectives of this work in CO2 management are presented at the end of chapter six. In chapter seven is exposed a complete revision of the interactions between soil pH, fungi and bacteria as key actors at the geo-biological interface of the pathway, put it all in evidences through microcosms experiments.