Diversity, functioning and stability in microbial communities

  • Federica Colombo

Western Sydney University thesis: Doctoral thesis

Abstract

Biodiversity loss is among the major drivers of ecosystem change. Understanding the consequences of loss of biodiversity on the functioning of the ecosystems is of paramount importance in order to assess the sustainability of a system. Ecosystem stability is a measure of sustainability and it is defined as the degree of resistance and resilience of a system to perturbations. Microbes are the most abundant organisms on Earth and they are responsible for many ecologically important ecosystem processes. Despite this, the knowledge of the role of their diversity in ecosystem functioning and functional stability is still incomplete. This research investigated the relationship between bacterial diversity and functioning (BEF) and stability in soil ecosystems in order to better understand the consequences of decline in microbial diversity on ecosystem sustainability. Firstly, the soil microbial community was experimentally manipulated using the dilution-to-extinction approach in a soil extract medium microcosms experiment to analyse the consequences of microbial diversity loss on general and specific functions and their stability to a heat disturbance. Community respiration and the utilisation of compounds of different complexity (i.e. glucose and lignin) were used as functional parameters. Terminal restriction fragment length polymorphism (T-RLFP) analysis revealed that a reduction in richness of 77% led to a significative decrease in respiration rates in aggregate function (i. e. community respiration) and specific functions, but did not affect general functions. A positive linear correlation was found between bacterial richness and community respiration and lignin-induced respiration, but it was not possible to identify a clear relationship with the utilisation of glucose. Bacterial communities with lower diversity showed lower functional stability to heat disturbance. These results indicate that both general and specific functions depend on bacterial diversity and a loss of diversity in soil systems has the potential to affect their functional stability. The BEF under environmental conditions was then investigated in agricultural and forest ecosystems by means of field studies. Finally, I investigated the functional stability of forest soils with naturally different levels of bacterial diversity following a transient heat disturbance in a soil microcosm experiment. Microbial processes involved in nutrients cycling were analysed by means of potential enzyme activity, basal respiration and substrate-induced respiration. The diversity and composition of bacterial communities were investigated by means of Illumina MiSeq sequencing of the 16S rRNA gene. The relationship between bacterial diversity components (i. e. diversity, richness, composition) and soil processes and functional stability was investigated by means of stepwise multiple regressions examining the explanatory power of microbial community variables and environmental properties. In the agricultural system investigated, the combination of different perennial grasses with crop, under different nitrogen regimes did not produce sharp differences in bacterial communities variables and no correlation between microbial communities and soil functioning was found. The main predictors of soil processes were abiotic factors, suggesting that the soil environment had a stronger influence on the functional properties than the biotic component in these soils. In a forest plantation experiment, the application of irrigation and fertilisation influenced bacterial community composition and diversity. The functioning of forest soils was predicted by bacterial richness and abundance, and by edaphic factors. Bacterial richness and abundance, and soil functions involved in nutrient cycling were linked by significant linear relationship. Changes in microbial diversity had functional consequences for soil processes, showing that even a moderate loss (circa 20%) in biodiversity can have important effects on ecosystem functioning. The functional stability of forest soils was estimated by evaluating resistance and resilience to heat disturbance of soil respiration and potential enzymes activity. The stepwise multiple regressions. The resistance and resilience of all functions analysed were predicted by bacterial diversity components, demonstrating that bacterial communities are important drivers of soil functional stability in the forest ecosystem analysed. The results of this work highlight that declining microbial diversity has direct consequences for functioning and functional stability to disturbance of soil ecosystems. These findings suggest that the functional redundancy (i. e. when several species in a system carry out the same function) of microbial communities may be not as prevalent as generally thought, and hence preserving the microbiota might be as important as preserving the diversity of higher organisms, to ensure the sustainability of the ecosystems. This work also suggests that disruptive land management practices, such as agricultural ones, can influence the BEF in soil ecosystems through habitat homogenisation and modification of biogeochemical cycles.
Date of Award2015
Original languageEnglish

Keywords

  • biodiversity
  • soil microbiology
  • soil ecology
  • ecosystem health
  • microbial ecology
  • microbial diversity
  • stability

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