Excessive use and lack of appropriate disposal technology for industrial xenobiotics have resulted in the contamination of ecosystems globally impacting the self-regulating capacity of the biosphere. This often results in irreversible alterations of ecosystem's structure and function, but the outcomes of these events on soil microbial communities (and their functional capabilities) are poorly understood. Assessing the impact of xenobiotics on soil microbial communities is of paramount importance as they play a vital role in ecosystem services and maintain soil health, which are key requirements for sustainable land use in terms of food security and environmental sustainability. Bacteria are the most abundant and diverse soil micro-flora and play a key role in the biogeochemical cycles of important elements including carbon (C), nitrogen (N), and phosphorus (P) and sulphur (S). The current work aimed to unravel the two-way interactions between xenobiotics and soil microbial communities; i.e., how soil microbial communities modulate xenobiotic persistence through biodegradation and what impacts xenobiotic have on soil microbial community's structure and functions, with particular focus on widely used pesticides (chlorpyrifos and imidacloprid) and industrial solvents (trichloroethene). In Chapter 2, characterisation of active methanotrophs involved in trichloroethene (TCE) degradation under different methane (CH4) concentrations was evaluated. Methane (CH4) enriched methanotrophic consortia from three Australian soils (Sydney University, Victoria Park and Botany Industrial Park) were examined for their effectiveness in TCE (50M) degradation at 1%, 10% and 33% CH4 concentration at 20oC. Only the methanotrophic consortium from Sydney University (SU) soil was able to co-metabolically degrade TCE. The (SU) methanotrophic growth and TCE degradation was accelerated under high CH4 concentration degrading up to 30% (within 2 days) and 20% (within 5 days) TCE under 33% and 10% CH4, respectively. No degradation of TCE was observed at 1% CH4 concentration or in the absence of CH4 suggesting the dependence on relatively high CH4 availability for TCE degradation. pmoA-based stable isotope probing (SIP), terminal restriction fragment length polymorphism (T-RFLP), clone library construction and sequencing of TCE degrading SU methanotroph consortium revealed the dominance of novel uncultivable Type I methanotrophs (distantly related to Methylovulum-88%) belonging to TRF-53 in TCE degradation. In Chapter 3, the effects of the pesticides chlorpyrifos (CP) and imidacloprid (IC) on soil microbial processes (e.g. biodegradation and respiration) and community structure were evaluated. Two soil treatments (from five sugarcane farms), one with no history of pesticide application (non-treated; 1H, 2H, 3H, 4H and 5H) and the other with ~20 years pesticide application (pesticide-treated; 1R, 2R, 3R, 4R and 5R), were used in this study. MicroRespTM, q-PCR and T-RFLP analyses were combined to explore the relationship between pesticide degradation and soil microbial communities in soils spiked (3 times) with 10 mg/kg of CP or IC, under lab conditions. The results showed that the half-lives of CP decreased with application frequency and were 23-47, 8-20 and 3-17 days following the first, second and third application, respectively (for soils from five sugarcane farms). In particular, the soils from 4R, 4H and 5R showed enhanced CP degradation even when not exposed to CP for last 13 years due to legacy effect of the pesticide. Parallel analyses of IC degradation (10 mg/kg) showed high persistence of this pesticide in soil where repeated application increased half-lives from 30-60 days for the first treatment to 45-65 days for second treatment. The application of both pesticides (CP and IC) reduced soil respiration (basal and substrate-induced) between 7-76% with the lowest respiration found in 5R and highest in 1R after the pesticides treatment, indicating that application of pesticides had an adverse impact on soil functional activity. The molecular analyses showed that both CP and IC significantly altered the soil bacterial community structure and reduced diversity, evenness and richness. In Chapter 4, sequential soil and liquid culture enrichments enabled the isolation of six bacterial CP degraders with sequence homologies to Xanthomonas sp. (3), Pseudomonas sp. (1), Rhizobium sp. (1) and Lysobacter sp. (1). The efficacy of the isolated strains: Xanthomonas sp. 4R3-M1, Pseudomonas sp. 4H1-M3 and Rhizobium sp. 4H1-M1 were further investigated for biodegradation of CP and its primary metabolic product, TCP (3,5,6-trichloro-2-pyridinol). The results indicated that all three bacterial strains utilised CP (10 mg/l) and TCP (as CP degradation product) in mineral salt media (MSM) as a sole source of C and N. Bacterial strains Xanthomonas sp. 4R3-M1 and Pseudomonas sp. 4H1-M3 could also degrade 10 mg/l TCP as a sole C- and N-source, when provided externally. Thus, these bacterial strains promise to be effective in practical application of bioremediation of both CP and TCP. In Chapter 5, using next-generation sequencing, the structure and potential functions of bacterial communities in pesticide-treated and non-treated reference sites was compared at finer levels. Across all soils, the functional beta diversity was correlated with taxonomic diversity indicating possible linkages between the structure and functioning of soil microbial communities. The pesticide-treated sites had higher relative abundance of Proteobacteria and Bacteroidetes, with Archaea exhibiting the opposite pattern. Metagenomic analysis revealed increases in the relative abundance of genes associated with key specialised functions (iron acquisition and metabolism, motility, cell signalling, stress response) at pesticide-treated sites. The results suggested impacts of long-term pesticide application on soil microbial community composition and potential functions. Despite, a CP legacy effect, no marked difference was observed in abundance of genes related to P-metabolism between pesticide-treated and non-treated sites. Overall, the results supported taxonomic and functional adaptations in the soil microbial communities following pesticide treatment. Overall, this study provides the novel insights into the interaction between xenobiotics and soil microbial communities both at structural (diversity, community structure) and functional (degradation) levels and should be considered in developing new bioremediation technologies and agronomic practices such as number and frequency of pesticide applications.
| Date of Award | 2016 |
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| Original language | English |
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