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Effect of Strategic Tillage in Soil Microbial Communities in Vertisols from Queensland, Australia Vivian Andrea Rincon Florez Bachelor in Microbiology

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Effect of Strategic Tillage in Soil Microbial Communities in Vertisols from Queensland, Australia Vivian Andrea Rincon Florez Bachelor in Microbiology Effect of strategic tillage in soil microbial communities in Vertisols from Queensland, Australia Vivian Andrea Rincon Florez Bachelor in Microbiology A thesis submitted for the degree of Doctor of Philosophy at The University of Queensland in 2016 School of Agriculture and Food Sciences 1 Abstract In the last decades, tendency amongst growers in Australia has been towards practising minimum disturbance for soil preparation and complete stubble retention. Consequently, farmers have reduced labour, energy and machinery costs, and improved soil quality and crop profitability. However, there is scepticism around such practices given the build-up of herbicide resistant weeds, stubble-borne diseases and nutrient stratification. To address these issues, occasional tillage (or strategic tillage, ST) has been applied to fields under long-term no-tillage (NT). ST aims to overcome constraints arisen by no-tillage and takes into account soil water content, tools for deployment and timing of application. Soil microbial communities play an important role in soil function and are often used as early indicators of soil disturbance due to their prompt response to environmental changes. I compared biological indicators of soil health including microbial biomass, microbial enzymatic activity, metabolic diversity, genetic structure; diversity of bacterial, archaeal and fungal communities, and abundances of nitrogen cycle genes to assess the impact of ST on long-term NT. I selected three sites under long-term NT: Biloela, Jimbour and Hermitage. For all sites, two soil depths were sampled, 0.0-0.1 m and 0.1-0.2 m. In Hermitage, ST was applied to soils under NT and conventional tillage (CT), in which stubble was retained. Soil samples were collected 3.5 and 13 months after ST operations. While it is clear that there would be immediate effects on soil biology, I chose these time points to allow a reasonable amount of time to evaluate whether microbial communities can restore and provide the ecosystem function needed for crop performance. I observed differences between NT and CT in enzymatic activity after 3.5 months, possibly attributed to physico-chemical properties and land management. However, one year after tillage deployment there were no changes in the biological indicators, microbial structure and diversity that were measured after ST. High throughput 16S rRNA gene amplicon sequencing targeting bacteria and archaea revealed 69 operational taxonomic units (OTU’s) at relative abundances higher than 1%. The most abundant phyla were Crenarchaeota (25%) and Acidobacteria (28.1%). Fungal communities profiled by internal transcribed region (ITS) amplicon high throughput sequencing showed no significant differences between treatments. The 2 most abundant phylum was Ascomycota (60%) with a relative abundance higher than 1%. Overall, the application of occasional tillage exerted minimal changes on the microbial communities in Hermitage. Edaphic properties of this Vertisol and environmental changes since ST application may have contributed to the results obtained. The impact of different tillage implements and frequencies on microbial indicators and community structure during fallow was evaluated in Jimbour and Biloela sites. Tillage was implemented in December 2012, January and March 2013 and included one, two or three passes of tillage. Compared to NT, ST did not impact significantly soil communities based on the wide range of biological indicators assessed. Changes were observed between soil depths and seems to be attributed to environmental factors. High resistance and/or resilience of Vertisols appears to be the major reason for these findings. Nevertheless, assessment of abundance of nitrogen cycle genes for the three sites showed a significant impact of ST management. In Hermitage and Jimbour, nitrogen fixers tended to be enriched after ST application probably due to organic residue incorporation, previously shown to influence the abundance of these organisms. In contrast, the abundance of nitrogen fixing communities tended to decrease on surface soils in Biloela. The decrease may be related to inorganic forms of N affecting the nitrogenase activity in diazotrophic communities. Ammonia oxidizing bacteria (AOB) had an increase in abundance after ST application in Hermitage for soils under NT. This increase was also observed after one-pass in March for surface soils in Biloela, one pass in December for subsoils and two passes in January for surface soils in Jimbour. Alternatively, AOB were supressed after one chisel pass in December subsoils and three passes on surface soils in Biloela. Tillage may increase the amount of ammonia in soils which may boost AOB communities. However, frequency and implement used for tillage can lower or enhance sources of mineral N after aggregate disruption. Nonetheless, ammonia oxidizing archaea (AOA) showed no significant changes for Hermitage, Biloela and Jimbour (after chisel use) after ST. However, two passes with offset-disc showed an increase in subsoils in Jimbour. The increase of AOA communities may be associated with low levels of fertilisers which can increment AOA abundance. 3 I conclude that the use of ST in no-till soils had minimal effect in the short-tem for Vertisols in Queensland. Despite slight changes observed in the biological indicators evaluated, more studies using different types of soils and different combination of crops would provide deeper insights into a broader picture of the microbial responses to ST. Thus, I provide evidence to suggest that ST can be considered a suitable approach. For Vertisols, it is suggested to use one pass during the fallow period applying a superficial tillage using disc or chisel. This study did not address long-term effects of ST and not all aspects of functional diversity of soil microbial communities. Future studies also follow up on the effect on N cycling, identified in the present study, on microbial communities, soil health and crop performance. 4 Declaration by author This thesis is composed of my original work, and contains no material previously published or written by another person except where due reference has been made in the text. I have clearly stated the contribution by others to jointly-authored works that I have included in my thesis. I have clearly stated the contribution of others to my thesis as a whole, including statistical assistance, survey design, data analysis, significant technical procedures, professional editorial advice, and any other original research work used or reported in my thesis. The content of my thesis is the result of work I have carried out since the commencement of my research higher degree candidature and does not include a substantial part of work that has been submitted to qualify for the award of any other degree or diploma in any university or other tertiary institution. I have clearly stated which parts of my thesis, if any, have been submitted to qualify for another award. I acknowledge that an electronic copy of my thesis must be lodged with the University Library and, subject to the policy and procedures of The University of Queensland, the thesis be made available for research and study in accordance with the Copyright Act 1968 unless a period of embargo has been approved by the Dean of the Graduate School. I acknowledge that copyright of all material contained in my thesis resides with the copyright holder(s) of that material. Where appropriate I have obtained copyright permission from the copyright holder to reproduce material in this thesis. 5 Publications during candidature Book chapters Liu H, Mirzaee H. Rincon-Florez V, Moyle R, Spohn Marie, Carvalhais L, Schenk P (2016). Emerging culture-independent tools to enhance our understanding for soil microbial ecology. Microbial Biomass – A New Paradigm in Terrestrial Biogeochemistry, 1-17. Rincon-Florez VA; Carvalhais, LC; Dang, Y; Schenk, P (2015) Soil microbial communities under tillage systems in Australia. Plant, Soil and Microbes Volume 1: Interactions and Implications in Crop Science 93-102. Peer-reviewed-papers Rincon-Florez VA, Ng C, Dang Y, Schenk, P, Carvalhais LC (2016). Short-term impact of an occasional tillage on microbial communities in a Vertisol after 43 years of no-tillage or conventional tillage. European Journal of soil Biology.74, 32-38 Liu H, Carvalhais LC, Rincon-Florez VA, Crawford MH, Dang Y, Dennis P, Schenk P (2016). One-time strategic tillage does not cause major impacts on soil microbial properties in a no-till Calcisol. Soil and Tillage research 158: 91-99. (Publication included in the appendix) Citations: 4 Rincon-Florez VA, Crawford MH, Dang YP, Schenk PM, Carvalhais LC (2015) Occasional tillage has no effect on soil microbial biomass, activity and composition in Vertisols under long-term no-till. Biology and fertility of soils 52: 191-202. Citations: 3 Crawford MH, Rincon-Florez V, Balzer A, Dang Y, Carvalhais LC, Liu H, Schenk P (2014) Changes in the soil quality attributes of continuous no-till farming systems following a strategic tillage. Soil Research 53, 263-273. (Publication included in the appendix) Citations: 10 6 Rincon-Florez VA, Carvalhais, LC, Schenk PM (2013) Culture-independent molecular tools for soil and rhizosphere microbiology. Diversity 5, 581-612. Citations: 19 Conference abstracts and presentations VA Rincon-Florez, LC Carvalhais, YP Dang, H Liu, MH Crawford, MJ Bell, PM Schenk (2015). Impact of strategic tillage in nitrogen cycle genes (amoA and nifH) in no-till systems from Queensland, Australia. Ecology of soil microorganisms. Prague 29–3 December. (Poster) VA Rincon-Florez; LC Carvalhais, YP Dang; MH Crawford, A Balzer, M Bell, H Liu, C Ng, PG, Dennis, PM Schenk (2015) Strategic tillage caused minimal impact on soil microbial communities in a Vertisol under 44 years of no-tillage and conventional tillage managements in Queensland, Australia. 20th International soil tillage research organization conference. Nanjing 14-18 September. (Oral presentation). VA Rincon-Florez, LC Carvalhais, H Liu, YP Dang, MH Crawford, A Balzer, M Bell, D Ram, PM Schenk (2014). Strategic tillage did not affect soil microbial bioindicators in long-term no-till farming systems in Vertisols from Queensland, Australia.
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