The habitability of Earth is dependent upon the global recycling of elements essential for life, such as nitrogen, sulfur and carbon. Nutrient-cycling by micro-organisms is vital to these biogeochemical cycles because many key steps are mediated primarily, or exclusively, by microbial life. The dynamics of these cycles are highly complex, and environmental perturbations (such as changes in the oceanic oxygen concentration) can have unexpected or catastrophic effects; often causing abrupt switches between chemical states. Despite the importance of these environmental perturbations however, few theoretical models have addressed how they affect the dynamical behaviour of nutrient-cycling microbial ecosystems. In this work, we investigate the effect of environmental perturbations on microbially-mediated nutrient cycles and assess the likelihood of "sudden transitions" between chemical states of the ecosystem occurring in a variety of ecological contexts. To do this, we first use computational modelling of microbial nutrient-cycling, using a "box model" approach. We then move on to an experimental study using the microbial sulfur cycle as a model ecosystem, with freshwater pond sediment/water microcosms. These microcosms have the advantage of retaining many of the features of the real ecosystem (such as microbial diversity, spatial structure, and abiotic interactions) while allowing the controlled manipulation of environmental perturbations. We study these microcosms using a combination of chemical measurements and high-throughput sequencing of the microbial community. Finally, we return to the computational side, and attempt to reproduce chemical data from our experiments in a mathematical model containing realistic abiotic chemical interactions.

Early in 1962 the Forest Research Institute of the New Zealand Forest Service became aware that stands of second crop Pinus radiata (D. Don) on some areas of the Moutere Gravel formation were showing slow growth and had a chlorotic appearance (Fig. 1.1). The second crop followed clear felling of mature P. radiata trees and were aged from 0 to 15 years (stone and Will, 1965). It was felt that the apparent reduced growth of the second generation had much in common with similar productivity decline reported especially in European forestry literature. Stone and Will (1965) postulated that the immediate cause o£ the decline was a deficiency of nitrogen highlighted by the low levels of nitrogen in the leaves of the second crop trees, especially those growing on ridge sites. Numerous field trials have been laid out but many of the trials were poorly designed and consequently could not provide statistically sound results. However, some indication of nutrient deficiencies which occur on the Moutere Gravels were obtained. Even before these trials were laid down nutrient deficiencies had been highlighted by early attempts at farming. It was the partial failure of these crops that initially led to the planting of exotic pines, in the belief that these trees thrived on a limited supply of nutrients. The first crop of pines generally fulfilled expectations but nutrient deficiencies started to appear in extensive areas of the second crop. Accordingly, the Forest Research Institute made available three scholarships to study different aspects of the problem. Work was started on a study of the soil sequence across the Moutere Gravels to determine if there was a general decline in fertility of tho soil with the age of the soil and the environmental factors, such as climate which differs in the high inland areas and the low seaside areas of the Moutere Gravels, rather than a particular decline in fertility induced by the first crop of P. radiata. In another study the major weed species Ulex europaeus and Cytisus scoparius was studied to see if its value as a nitrogen fixer would outweigh its disadvantages as a silvicultural weed. Thirdly, a study of the microbial ecology of the soils was undertaken. Whyte (1966) reported that the second rotation trees started to increase their growth rate after approximately five years to a level paralleling the estimated growth rate of the first crop. It was postulated that the residues (needles, roots and branches) remaining after clear felling could cause an increase in microbial numbers and activity with a consequent immobilization of mineral nutrients which were not initially very plentiful. For this reason an area in Tasman Forest was selected in which mature trees and regeneration up to nine years old were found together to study microbial activity and numbers, energy dissipation and nitrogen dynamics to determine if immobilization of nutrients was causing the apparent declines.