The geomicrobiology of iron, cobalt, nickel and manganese in lateritic tropical soils from the Santa Elena Peninsula, Costa Rica

  • Agustín Solano Arguedas

Student thesis: Phd


There is an increasing interest in the biogeochemistry of metals, like cobalt, fuelled by the growing need for batteries and other high technology products. Bioprocessing of Co has been proposed to improve its recovery from Ni-rich laterites, but the natural biogeochemistry of Co and other metals associated such as Fe, Ni and Mn in laterites is still relatively unexplored. In Costa Rica, the Santa Elena Peninsula is closely associated with the Santa Elena Ophiolite, and the tropical climate alongside the lack of anthropogenic alteration for nearly 50 years, make this a unique area to study natural biogeochemical processes in a laterite/serpentine context. This thesis therefore aimed to understand the biogeochemical cycling of Fe, Co, Ni and Mn in the lateritic soils of the Santa Elena Peninsula. The geochemical composition, mineralogy and microbial structure (prokaryotic and fungal) of these soils were described for the first time, considering a landscape approach. Three types of lateritic soils were identified based on the geochemistry, geography and microbial composition: mountain soils, inner ophiolite lowland soils and north lowland soils. Each type of soil was studied using fluctuating redox microcosm experiments to emulate a complete anaerobic-aerobic cycle. With glucose biostimulation, bioweathering and biomineralisation of Fe/Mg minerals were more intense in the mountain soils and mediated by microbial Fe redox cycling, while methanogenesis was enhanced in the lowland soils, highlighting the potential importance of these lateritic systems for carbon fluxes. For a better understanding of the natural conditions underpinning those biogeochemical cycles, the fluctuating redox microcosm experiments were extended by using samples from both dry and wet seasons and using cellulose as an electron donor analogous to the natural plant matter found in the soils. Under anoxic conditions mobilisation of Co, Ni and Mn was enhanced by microbial cellulose degradation and linked to microbial Fe(III) reduction and bioweathering of Fe-oxides. However, when oxic conditions were imposed, Co, Ni and Mn solubilisation increased, likely associated with the bioweathering of Mg minerals including hydrous silicates or clays but still linked to cellulose degradation. Organisms affiliated with the Firmicutes played a key role in these processes, likely degrading cellulose into smaller molecules bioavailable for other microbial processes such as Fe redox cycling (or metal chelation). Other microorganisms found that could be directly or indirectly associated with the cycling of Co, Ni and Mn included Fe(III) and Mn(IV) reducing bacteria, methanogens and fungi. Seasonal precipitation was key to induce redox processes in the serpentine soils by facilitating the development of anoxic conditions, and the impact depended on the soil geographical/geochemical origin. Despite the unique environment of the Santa Elena Peninsula, some of the results of this thesis supported previous observations in laterites and serpentine areas worldwide, evidencing the potential of the Santa Elena Peninsula as a model location to understand natural biogeochemical cycles in tropical serpentine ecosystems; but with outcomes that can also be extrapolated to other sites, landscapes and ecological contexts.
Date of Award31 Dec 2019
Original languageEnglish
Awarding Institution
  • The University of Manchester
SupervisorClare Robinson (Supervisor) & Jonathan Lloyd (Supervisor)


  • Serpentine ecosystem
  • Climate Change
  • Landscape ecology
  • Seasonal precipitation
  • Methanogenesis
  • Biomineralisation
  • Serpentine soil
  • Biogeochemical cycling
  • Santa Elena Ophiolite
  • Laterite
  • Bioweathering

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