A cultura da cana-de-açúcar é a segunda maior cultura em valor de produção agrícola do país. Nos últimos anos ocorreu uma alteração no cenário canavieiro passando de colheita manual de cana queimada para mecanizada de cana crua. A colheita mecanizada da cana-de-açúcar acarreta muitos benefícios ambientais, porém o tráfego intenso de maquinários resulta na compactação do solo. Desse modo, buscamos avaliar como o efeito das alteração física do solo causado pelo tráfego de máquinas durante a colheita da cana interfere na composição das comunidades microbianas, especialmente as que participam das transformações do nitrogênio. As parcelas experimentais foram divididas em colheita manual (PDTR) e colheita mecanizada (PD). Todos os demais manejos e tratos culturais foram iguais, isolando a influência do impacto do maquinário durante a colheita. Para a avaliação da microbiota realizamos análise da estrutura da comunidade (DGGE ou T-RFLP) e análise de abundância (qPCR) de bactérias, fungos, arquéias, e do ciclo do nitrogênio envolvendo os genes marcadores para a nitrificação (amoA - AOA e AOB), fixação de nitrogênio (nifH) e desnitrificação (nirK, nirS, nosZ clado I e II). Observamos apenas a diferença dos parâmetros físicos na camada superficial por meio da resistência a penetração. A alteração no perfil da comunidade de bactérias e arquéias mostra que ambas são responsivas ao tratamento com tráfego do maquinário. Em relação aos microrganismos envolvidos nas transformações de nitrogênio, AOA foi altamente responsiva ao impacto do tráfego agrícola em ambos os tipos de textura, mas teve diferença na abundância apenas no solo arenoso. O gene nifH apresentou diferença na diversidade em solo argiloso e diferença de abundância em solo arenoso. E por fim, sugerimos que o gene nosZ em subsuperfície pode indicar uma possível campactação antes dos parâmetros físicos do solo. / In Brazil, sugarcane is the second most value of agricultural production. Lately, the harvest management in sugarcane fields has changed from manual harvesting methods with pre-harvest burns to mechanical harvests with green cane (unburnt harvest). The mechanized harvest brings many ambiental benefits. However, the intense traffic due to agricultural machines over the years is resulting in soil compaction. The purpose of this work was to evaluate how the physical effect of mechanized harvesting can interfere with the composition of soil microbial community, specially the microbial involved in the nitrogen cycle. Experimental plots were divided into manual harvest (PDTR) and mechanized harvest (PD). All aspects of crop management are the same, so we were able to study the impact of mechanical harvester traffic during the harvest in isolation. To evaluation of the microbiome we analyzed community structure (DGGE ou T-RFLP) along with their abundance (qPCR) for soil bacterial, fungal and archaeal, and microorganisms involved in the transformation of nitrogen that we used gene markers for nitrification (amoA - AOA and AOB), nitrogen fixation (nifH) and denitrification (nirK, nirS, nosZ clade I and II). We observed the difference between physical parameters only in topsoil by soil penetration resistance. Our results indicated structured community changes of bacterial and archaeal showed us that both are responsive to treatment of machinery traffic. Microorganisms involved in the nitrogen cycle, our results presented that AOA is highly responsive to the impact of agricultural traffic on both soil texture, but we observed the difference in abundance only in sandy soil. The nifH gene was different on community structure in clay soil and on abundance in sandy soil. Moreover, we suggest that nosZ gene could indicate a possible soil compaction before the physical parameters in a layer between 20 and 40 cm.

Eucalyptus species account for almost 80% of the forests planted in Brazil, which makes silviculture an activity of great importance in the national and international scenario. Despite its adaptability, Eucalyptus is subject to damages caused by climate change, especially the water deficit. Most plants have survival strategies in water deficit situations. Association with mycorrhizal fungi (FM) is one of them, since they increase water and nutrients uptake by the roots. Thus, the main objective of this study was to evaluate the colonization of mycorrhizal fungi in six Eucalyptus species with different levels of drought tolerance: E. brassiana, E. camaldulensis, E. citriodora, E. cloeziana, E. grandis and E. urophylla. Two trials were carried out, one in the field and another in a greenhouse. In the greenhouse, the substrate of the pots were submitted to different levels of water retention, 50, 75 and 100% of the field capacity, for three months. In the field, soil and roots were sampled at two different periods: after the dry period and after the rainy season. The soil samples and fine roots collected from the two experiments were submitted to microbiological and molecular analyses. AMF root colonization was evaluated. The ITS genes were analyzed by quantitative PCR (qPCR) and the fungal community structure by restriction fragment polymorphism (T-RFLP). Among the eucalypt species studied, E. urophylla presented higher colonization in both trials. Soil microbial activity was strongly affected by soil moisture. The fungal community structure did not differ clearly among the treatments. Age of plants and soil moisture seemed to affect the plant species more than levels of water stress tolerance. / As espécies de eucalipto respondem por quase 80% das florestas plantadas no Brasil, o que faz da silvicultura uma atividade de grande importância no cenário nacional e internacional. Apesar de sua adaptabilidade, o eucalipto está sujeito a danos que as alterações climáticas podem causar, especialmente o déficit hídrico. A maioria das plantas possui estratégias de sobrevivência em situações de déficit hídrico. A associação com fungos micorrízicos arbusculares (FMA) é uma delas, pois aumenta a absorção de água e nutrientes pelas raízes. Assim, o objetivo principal deste trabalho foi avaliar a colonização de fungos micorrízicos em seis espécies de Eucalyptus com diferentes níveis de tolerância à seca: E. brassiana, E. camaldulensis, E. citriodora, E. cloeziana, E. grandis e E. urophylla. Dois ensaios foram realizados: um no campo e outro em casa de vegetação. Em casa de vegetação, os vasos foram submetidos a diferentes níveis de água: 50, 75 e 100% da capacidade de campo, por três meses. No campo, as amostras foram coletadas em dois períodos diferentes: após o período seco e após a estação chuvosa. As amostras de solo e raízes finas coletadas nos dois experimentos foram submetidas à análise microbiológica e molecular. A colonização da raiz por FMA foi avaliada. Os genes ITS foram analisados por PCR quantitativo (qPCR) e a estrutura da comunidade fúngica por polimorfismo de fragmentos de restrição (T-RFLP). Dentre as espécies estudadas, E. urophylla apresentou maior colonização em ambos os ensaios. A atividade microbiana do solo foi fortemente afetada pela umidade do solo. A estrutura da comunidade fúngica não se diferenciou claramente entre os tratamentos. A idade das plantas e a umidade do solo parecem ter maior efeito no desempenho das espécies de eucalipto do que seu nível de tolerância ao estresse hídrico.

Bibliography: leaves 116-127.

"September 2001" Includes bibliographical references (leaves 206-230)

Fungi are key components in forest ecosystems, being involved in decomposition of plant biomass and the cycling of nutrients in forest soils. Despite their importance little is understood about the influence forest management practices, such as long-term prescribed burning and forest conversion are having on soil fungal communities. Part of the work described in this thesis investigated the effects of long-term repeated prescribed burning on the total soil fungal community, the diversity of mycelial communities of ectomycorrhizal fungi and the influence of biennial prescribed burning on the cellulolytic soil fungal community using stable isotope probing techniques. The influence of long-term repeated prescribed burning on soil fungal communities was investigated through a series of studies conducted at Peachester State Forest, Queensland, Australia. This site has been the centre of a long-term repeated prescribed burning experiment, established since 1972, consisting of plots subjected to biennial, quadrennial or no burning. Denaturing gradient gel electrophoresis (DGGE) was used to show that long-term prescribed burning significantly altered the total fungal community structure in the top 10 cm of soil, when compared with unburned plots. Hyphal ingrowth bags, used to target ectomycorrhizal (ECM) mycelia in soil, along with DGGE analysis, indicated that profiles of the soil fungal community from 2 yr burn plots significantly differed from those of the 4 yr burn and unburned plots. Following analysis of clone assemblages from the different burn regimes, results indicated that this difference reflected an altered ECM fungal community composition. 13C stable isotope probing (SIP), following the incubation of soil with 13C labelled cellulose, and DGGE analysis was found to significantly alter the active fungal community in the upper 10cm of soil at Peachester State Forest. Fewer active fungi in the 2 yr burn plots were found to have incorporated 13C compared to the unburned plots, strongly suggesting that the activities of cellulolytic fungi were negatively affected by the 2 yr burning treatment. The thesis also incorporated work that assessed the effect of forest conversion from native eucalypt to Pinus elliottii plantation on the soil fungal community at Beerburrum State Forest, Queensland, Australia. ITS and 18S RNA and DNA were used, along with terminal restriction fragment length polymorphism (T-RFLP) and DGGE analysis, indicating that total and active fungal communities differed significantly between the native eucalypt forest and first rotation P. elliottii plantation. This suggested that the conversion from native eucalypt forest to P. elliotti plantation significantly altered the soil fungal community at the Beerburrum site. / Doctor of Philosophy (PhD)

Soils research at the University of Western Sydney, Hawkesbury Campus, was undertaken to investigate bacterial communities and soil salinity in an applied study. Microbial ecology was used to inform an understanding of conditions in soil irrigated with treated effluent. Several hypotheses were investigated examining changes in ecological organization conducted under laboratory and field conditions. Results indicated that relative abundance distributions for candidate forms of the bacteria community associated with higher and lower salinity, as defined using canonical correlation analysis, were reproducible between laboratory incubation experiments and field samples. The investigation is the first to apply the ecological parameter of richness and abundance to a study of microbial communities and their environment in order to determine soil conditions for sites irrigated with treated effluent. The thesis tests the theory and application of applying quantitative ecology to microbial community analysis. / Doctor of Philosophy (PhD)

"September 2001" / Includes bibliographical references (leaves 206-230) / xviii, 230 leaves : ill., plates ; 30 cm. / Title page, contents and abstract only. The complete thesis in print form is available from the University Library. / Thesis (Ph.D.)--University of Adelaide, Dept. of Agronomy and Farming Systems, 2002

An experimental and numerical modeling investigation was conducted to study interactions between microbial dynamics and transport processes in variably saturated porous media. These interactions are important in a variety of applied problems such as water and wastewater treatment, bioremediation, and oil-field recovery operations. These processes and interactions also have great ecological significance, with global scale implications for carbon cycling in the environment and the related issue of climate change. Experiments were conducted under variably saturated flow conditions in columns and 2D light-transmission chambers packed with translucent quartz sand. A bioluminescent Pseudomonas fluorescens bacterium was utilized in the experiments and bioluminescence was used as a non-destructive measure of bacterial density and distribution. In the column experiments, pressure heads increased (became less negative) at all measured depths, but significant changes in apparent volumetric water contents were only observed in the upper 5 cm of the columns. Permeability was reduced by a factor of 40 within one week during growth on glucose. In the chamber experiments, aqueous-phase saturations decreased by 7-9% in the region of primary colonization and the capillary fringe dropped by 5 cm during the 6-day experiment. The colonized region expanded laterally by 15 cm and upward against the flow by about 7-8 cm. The desaturation phenomenon resulted in increased lateral spreading of solutes around the colonized region. A numerical model was developed and used to help interpret the experimental data. Water flow was modeled using the single-phase Richards equation. Solute and bacterial transport, cell growth, substrate consumption, and gas diffusion were modeled using advection-dispersion-reaction equations. Observed changes in saturations and pressure heads were reproduced approximately using fluid-media scaling to represent an apparent surface-tension lowering effect, which was assumed to be due to sorption of cells and/or biosurfactants at gas-liquid interfaces. Microbial dynamics, and substrate and oxygen consumption were represented using first-order reversible kinetics for cell attachment/detachment, and dual Monod-type kinetics for cell growth and substrate and oxygen consumption. Reasonably good matches were obtained between the observed and simulated results. / Graduation date: 2003

<p>Afforestation, the conversion of historically treeless areas into forests, is a rapidly spreading land-use change with the potential to sequester carbon. Afforested plantations typically feature fast growing exotic tree species that give landowners rapid returns. The efficient growth of plantations compared to less intensively managed forests also can provide greater timber yields in a smaller area. This increased efficiency in turn could require fewer acres to meet global forest product demands and could also reduce the need to log intact primary forests. Reduced primary forest harvest and high primary productivity make afforestation a highly efficient carbon sequestration tool.</p><p> However, the rapid growth and planting disturbance due to afforestation can have deleterious effects on soils and hydrology that undermine its benefits in some locations. The effects on hydrology include depletion of groundwater and reduced or complete elimination of surface water flow. Additionally, groundwater use can lead to increased concentrations of salts and trace metals in soil that could be deleterious for future plant productivity. Plantations have also been shown to acidify surface soils and stream water and to reduce soil carbon and nitrogen.</p><p> Despite the known effects of afforestation on soils, there has been little research on the mechanisms controlling these effects. For instance, there have been few studies on the effects of afforestation on soil microbes which mediate most biogeochemical processes. There is also little knowledge on what controls the effects of afforestation on soil carbon and nitrogen, vital indexes of soil quality, across regions with high levels of afforestation. The overarching goal of this dissertation is to examine the effects of afforestation on soils, microbes, and biogeochemical processes across local, regional and global scales. Understanding the mechanisms by which afforestation alters soils and biogeochemical cycling and how these mechanisms change across different scales will aid in evaluating the true costs and benefits of afforestation. These results will be useful in determining if the benefits of afforestation will continue to outweigh its costs in the long-term.</p><p> The goal of Chapter 1 is to evaluate how afforestation across the globe affects mineral soil quality, including pH, sodium, exchangeable cations, organic carbon, and nitrogen, and to examine the magnitude of these changes in regions where afforestation rates are high. To control for different initial soil conditions across the globe, I examined paired sites of afforested plantations and controls. Controls included land-use types that are frequently afforested, such as grasslands, shrublands, and pastures. I also examined potential mechanisms to reduce the impacts of afforestation on soils and to maintain long-term productivity. Across diverse plantation types (153 sites) to a depth of 30cm of mineral soil, I observed significant decreases in nutrient cations (Ca, K, Mg), increases in sodium (Na), or both with afforestation. For the global dataset, afforestation reduced soil concentrations of the macronutrient Ca by 29% on average compared with native controls (p<0.05). Afforestation by Pinus alone decreased soil K by 23% (p<0.05). Overall, plantations of all genera also led to an average 71% increase of soil Na (p<0.05). Average pH decreased 0.3 units (p<0.05) with afforestation. Afforestation caused a 6.7% and 15% (p<0.05) decrease in soil C and N content respectively, though the effect was driven principally by Pinus plantations (15% and 20% decrease, p<0.05). Carbon to nitrogen ratios in soils under plantations were 5.7-11.6% higher (p<0.05). The major implication of these results are that in several regions with high rates of afforestation, cumulative losses of C, N, Ca, and Mg are likely in the range of tens of millions of metric tons. The decreases indicate that trees take up considerable amounts of nutrients from soils; harvesting this biomass repeatedly could impair long-term soil fertility and productivity in some locations. Based on this study and a review of other literature, I suggest that proper site preparation and sustainable harvest practices, such as avoiding the removal or burning of harvest residue, could minimize the impact of afforestation on soils. These sustainable practices could in turn slow erosion, organic matter loss, and soil compaction from harvesting equipment, maintaining soil fertility to the greatest extent possible. </p><p> Soil microbes are highly diverse and control most soil biogeochemical reactions. Given the observed changes in Chapter 1, in Chapters 2 and 3 I examined how microbial functional genes and biogeochemical pools responded to the altered chemical inputs accompanying afforestation. I examined paired native grasslands and adjacent Eucalyptus plantations (previously grasslands) in Uruguay, a region that lacked forests before European settlement. Along with measurements of soil carbon, nitrogen, and bacterial diversity, I analyzed functional genes using the GeoChip 2.0 microarray that simultaneously quantified several thousand genes involved in soil carbon and nitrogen cycling. Plantations and grasslands differed significantly in functional gene profiles, bacterial diversity, and biogeochemical pool sizes. Afforestation decreased both bacterial diversity and richness compared to grasslands, though diversity remained relatively high. Most grassland functional gene profiles were similar, but plantation profiles generally differed from grasslands due to differences in functional gene abundance across many microbial groups. Eucalypts decreased ammonification and N-fixation functional genes by 11% and 7.9% (p<0.01) which correlated with decreased microbial biomass N and more NH4+ in plantation soils. Chitinase, an important carbon polymer degrading enzyme, decreased in functional gene abundance 7.8% in plantations compared to grasslands (p=0.017), and C polymer degrading genes decreased by 1.5% overall (p<0.05), which likely contributed to 54% (p<0.05) more C in undecomposed extractable soil pools and 27% less microbial C (p<0.01) in plantation soils. In general, afforestation altered the abundance of many microbial functional genes corresponding with changes in soil biogeochemistry. These changes were driven by shifts in the whole community functional gene profile, not just one or two constituent microbial taxa. Such changes in microbial functional genes correspond with altered C and N storage and have implications for long-term productivity in these soils.</p><p> The area studied in Chapters 2 and 3 lies near the middle of a precipitation gradient that stretches across the Rio de la Plata grasslands. In Chapter 4 I studied if the effects of afforestation on soil C and N from Chapters 2 and 3 varied with different precipitation levels. The effect of afforestation on soil C has been shown to depend on mean annual precipitation (MAP), with drier sites gaining C and wetter sites losing C with afforestation. This precipitation dependence of soil C changes with afforestation may be controlled by changes in soil nitrogen (N) cycling. In particular, loss of N due to leaching after afforestation could lead to soil C losses. However, the link between C and N changes due to afforestation has primarily been suggested by models and to my knowledge has never been explicitly tested across a precipitation gradient. The goal of this study was to test how precipitation affects changes in labile and bulk pools of soil C and N across a precipitation gradient, which will provide novel insight into the linkage between land-use change, different pools of soil C and N, and precipitation. I conducted this study across a gradient of precipitation in the Rio de la Plata grasslands of Argentina and Uruguay which ranged from 600mm to 1500mm of precipitation per year. The sites were all former grasslands that had been planted with Eucalyptus. I found that changes in bulk soil C and N were related to MAP with drier sites gaining and wetter sites losing C and N (R2=0.59, p=0.003), which supports the idea that N losses are strongly linked to C losses with afforestation. C and N in microbial biomass and extractable pools followed similar patterns to bulk soil C and N. Interestingly, losses of C and N decreased as the plantations aged, suggesting that longer rotation times for plantations could reduce potential soil carbon and nitrogen losses. These results indicate that afforestation is still be a valuable tool for carbon sequestration, but calculations of the benefits of afforestation must take into account site factors such as age and precipitation to accurately calculate total sequestration benefit and ensure continued high productivity and carbon sequestration.</p><p> In conclusion, afforestation could be an effective tool for carbon sequestration. However, its benefits need to be carefully weighed against its costs for soil such as reduced microbial diversity, decreased soil microbial functional capacity, losses of soil organic matter, and nutrient depletion. Careful management and consideration of afforestation is needed to ensure the greatest benefits with the least long-term damage to soils.</p> / Dissertation

published_or_final_version / Biological Sciences / Doctoral / Doctor of Philosophy