The investigation presented in this thesis examined the microbial and functional diversity of the meltwater ponds Fresh, Orange and Salt Ponds on the McMurdo Ice Shelf, near Bratina Island, Antarctica. These sites were chosen because of the ecological importance and absence of detailed characterisations of their diversity and function as part of Antarctica?s largest wetland. Particular focus was on cyanobacterial diversity, nitrogen fixation and secondary metabolite production. Using 16S rRNA gene and morphological analysis a large diversity of cyanobacteria (more than 22 phylotypes) was identified with high phylogenetic similarities (up to 99% sequence identity) to cyanobacteria from mats in other regions of Antarctica. In addition biogeographical distributions were identified including potentially endemic and cosmopolitan cyanobacteria. High salinities were also connected to the change and reduction of diversity. Lipid marker analyses were performed targeting hydrocarbons, ether-linked hydrocarbons, methylated fatty acid esters (FAME), wax esters, hopanols and sterols. Lipid biomarker profiles were similar to typical cyanobacteria dominated mats with major input from microorganisms including oxygenic and anoxygenic phototrophs, obligate aerobic and anaerobic heterotrophs that conduct the metabolic processes of fermentation, sulphate reduction, sulphate and iron-oxidation, methanogeneses. Signature lipids indicative of Chloroflexus and archaea, as well as branched aliphatic alkanes with quaternary substituted carbon atoms (BAQCs), were identified for the first time in Fresh, Orange and Salt Ponds. Based on nifH gene analysis, the nitrogen fixing diversity characterised in Orange Pond consisted of cyanobacterial Nostoc sp. as well as firmicutes, beta-, gamma- and delta-proteobacteria. Acetylene reduction assays and nifH gene RNA transcript diversity identified Nostoc sp. as a main contributor of nitrogenase activity in these ponds. Furthermore, analytical methods were used to identify the cyanobacterial secondary metabolites microcystins, although the genetic basis for this production and the toxin producer could not been identified. However non-ribosomal peptide synthetases (NRPS) and polyketide synthases (PKS) genes were identified which could be the genetic basis for novel bioactives. The use of a multi-disciplinary approach synthesis and subsequent results significantly increased our understanding of the diversity and function of microbial mat communities in the unique meltwater ponds of the McMurdo Ice shelf, Antarctica.

Made available in DSpace on 2014-08-20T13:32:49Z (GMT). No. of bitstreams: 1 tese_erico_kunde.pdf: 287917 bytes, checksum: c139b1164d4ea5a2964a48d21cf91781 (MD5) Previous issue date: 2007-02-28 / Deep litter systems (DLS) have lower facility cost and less environmental impact than conventional swine production systems, but the animal thermal comfort may not be ideal, during warm seasons. This thesis studied the effect of the use of litters having different depths on indicators of environmental comfort, animal growth performance and physical, chemical and microbiological characteristics of the litter. Three treatments were compared: solid concrete floor (control); litter of rice husk with depth of 0.25 (L25) and 0.50 m (L50). The first liter was used in two lots and replaced by a second litter used in other two lots. The environmental conditions were determined by the relative humidity of the air (RH), atmospheric temperature (AT) and litter temperature at the center of the pen, both in the surface (TSF) and at half of the depth (THD). Feed intake, weight gain and feed conversion for the pigs raised on DLS were also estimated. Concentrations of thermophilic and mesophilic bacteria, fungi and actinomycetes were determined by the most probable number method. TSF was lowest in the control group (P < 0.05), but it did not differ between C25 and C50 (P > 0.05). TSF was higher for new than for used litters and for the first than for the second litters (P < 0.05). The highest levels of N, P and K found in the L25 indicate that its compost has greater agronomical values. The concentration of mesophilic bacteria was higher in L50 than in L25 (P < 0.05). Although no statistical comparison was performed for growth performance parameters, feed conversion was similar for pigs in the control and DLS groups, with an apparent advantage for L25. This thesis also studied the effect of the addition of inoculums, in a pilot scale, on litters similar to those used in DLS, on the parameters mentioned above. The experimental units were boxes having area equal to 1 m2., on which litter of rice husk was added at the depths of 0.25 (L25) and 0.50 m (L50). On a daily basis, 6.4 l of swine dejects were added to the boxes, which consisted of three treatments: control without inoculums (T1); inoculation of 250 g of Bacillus cereus var. tyoii with 8,4 x 107 UFC/g (T2); and inoculation of 250 g of EnziLimp with 8,4 x 107 UFC/g (T3). Concentration of mesophilic and thermophilic bacteria, fungi and actinomycetes were determined and the chemical characteristics of the litter were evaluated. The addition of inoculums allowed higher concentration of thermophilic bacteria than in the control group (P < 0.05), so it would not be recommended for DLS. There was a higher concentration of thermophilic bacteria and fungi in the first lot of L50 (P < 0.05). Increased N level had a negative association with the concentration of all the thermophilic microbial populations (P < 0.05). Therefore, L25 can be recommended as a feasible option for DLS because it is associated with reduced concentration of thermophilic microbial populations in the litter, which leads to better thermal comfort for the pigs, without negative effects for growth performance, also generating compost having high agronomical value. / Em comparação com sistemas convencionais de criação de suínos, o sistema de produção sobre cama (SPC) utiliza edificações de menor custo e menor impacto ambiental, mas pode prejudicar o conforto térmico dos animais, em climas quentes. Esta tese estudou os efeitos das camas usadas para SPC, com diferentes profundidades, sobre indicadores de condicionamento ambiental da edificação, desempenho de crescimento dos animais, e características físicas, químicas e microbiológicas das camas. Três tratamentos foram comparados: piso de concreto (controle) e camas de casca de arroz com profundidade de 0.50 (C50) e 0.25 m (C25). A primeira cama foi usada em duas repetições e substituída por uma segunda cama usada em outras duas. A condição ambiental foi determinada através da umidade relativa do ar (UR) e das temperaturas atmosférica (TA) e no centro da baia, tanto na superfície (TCS), como na metade da profundidade (TCI). Também foram estimados o consumo de alimento, o ganho de peso e a conversão alimentar dos animais. Através de NMP, determinaram-se as concentrações de bactérias, fungos e actinomicetos, mesófilos e termófilos. A TCS foi mais baixa para o controle (P < 0,05), mas sem diferença entre C25 e C50 (P > 0,05). A TCS foi maior nas camas novas do que nas usadas e para as primeiras do que nas segundas camas (P < 0,05). Os maiores teores de N, P e K presentes na C25 indicaram que o composto produzido nesta profundidade possui melhor valor agronômico. A concentração de bactérias termófilas foi maior na C50 do que na C25 (P < 0,05). Ainda que não tenham sido feitas comparações estatísticas, a conversão alimentar foi similar para os animais no grupo controle e no SPC, com aparente benefício na C25. Esta tese também estudou o efeito da adição de inóculos, em escala piloto, sobre camas similares as usadas no SPC, sobre os parâmetros mencionados acima, em experimento realizado em uma granja comercial. As unidades experimentais foram caixas com 1 m2 de área, nas quais foi adicionada cama de casca de arroz, em profundidades de 0,25 (C25) e 0,50 m (C50). Diariamente, foram adicionados 6,4 l de dejetos por caixa, formando três tratamentos: controle sem inoculo (T1); inoculação de 250 g de Bacillus cereus var. tyoii com 8,4 x 107 UFC/g (T2); e inoculação de 250 g de EnziLimp com 8,4 x 107 UFC/g (T3). Foram determinadas as concentrações de bactérias, fungos e actinomicetos, mesófilos e termófilos e analisadas as características químicas das camas. A adição dos inóculos propiciou uma maior concentração de bactérias termófilas (P < 0,05), em relação ao controle, não sendo recomendável para animais em crescimento e terminação. Houve maior concentração de bactérias e fungos termófilos na primeira repetição da C50 (P < 0,05). A elevação do teor de N influenciou negativamente todas as concentrações microbianas termófilas (P < 0,05). Em conclusão, a C25 é uma opção viável para SPC, por apresentar um maior valor agronômico e possibilitar uma melhor conversão alimentar dos animais quando comparada com a C50.

No description available.

Take-all, caused by the soilborne fungus, Gaeumannomyces graminis var. tritici (Ggt), is an important root disease of wheat that can be reduced by take-all decline (TAD) in successive wheat crops, due to general and/or specific suppression. A study of 112 New Zealand wheat soils in 2003 had shown that Ggt DNA concentrations (analysed using real-time PCR) increased with successive years of wheat crops (1-3 y) and generally reflected take-all severity in subsequent crops. However, some wheat soils with high Ggt DNA concentrations had low take-all, suggesting presence of TAD. This study investigated 26 such soils for presence of TAD and possible suppressive mechanisms, and characterised the microorganisms from wheat roots and rhizosphere using polymerase chain reaction (PCR) and denaturing gradient gel electrophoresis (DGGE). A preliminary pot trial of 29 soils (including three from ryegrass fields) amended with 12.5% w/w Ggt inoculum, screened their suppressiveness against take-all in a growth chamber. Results indicated that the inoculum level was too high to detect the differences between soils and that the environmental conditions used were unsuitable. Comparison between the Ggt DNA concentrations of the same soils collected in 2003 and in 2004 (collected for the pot trial), showed that most soils cropped with 2, 3 and 4 y of successive wheat had reduced Ggt DNA concentrations (by 195-2911 pg g-1 soil), and their disease incidences revealed 11 of the 29 test soils with potential take-all suppressiveness. Further pot trials improved the protocols, such that they were able to differentiate the magnitudes of suppressiveness among the soils. The first of the subsequent trials, using 4% w/w Ggt inoculum level, controlled conditions at 16°C, 80% RH with alternate 12 h light/dark conditions, and watering the plants twice weekly to field capacity (FC), screened 13 soils for their suppressiveness against take-all. The 13 soils consisted of 11 from the preliminary trial, one wheat soil that had been cropped with 9 y of wheat (considered likely to be suppressive), and a conducive ryegrass soil. The results revealed that 10 of these soils were suppressive to take-all. However, in only four of them were the effects related to high levels of microbial/biological involvement in the suppression, which were assessed in an experiment that first sterilised the soils. In a repeat trial using five of the soils H1, H3, M2, P7 (previously cropped with 3, 3, 4 and 9 y successive wheat, respectively) and H15 (previously cropped with 5 y of ryegrass), three of them (H1, H3 and M2) had reduced Ggt DNA concentrations (>1000 pg g-1 soil reductions), and were confirmed to be suppressive to take-all. A pot trial, in which 1% of each soil was transferred into a γ-irradiated base soil amended with 0.1% Ggt inoculum, indicated that soils H1 and H3 (3 y wheat) were specific in their suppressiveness, and M2 (4 y wheat) was general in its suppressiveness. The microbial communities within the rhizosphere and roots of plants grown in the soils, which demonstrated conduciveness, specific or general suppressiveness to take-all, were characterised using PCR-DGGE, and identities of the distinguishing microorganisms (which differentiated the soils) identified by sequence analysis. Results showed similar clusters of microorganisms associated with conducive and suppressive soils, both for specific and general suppression. Further excision, re-amplification, cloning and sequencing of the distinguishing bands showed that some actinomycetes (Streptomyces bingchengensis, Terrabacter sp. and Nocardioides sp.), ascomycetes (Fusarium lateritium and Microdochium bolleyi) and an unidentified fungus, were associated with the suppressive soils (specific and general). Others, such as the proteobacteria (Pseudomonas putida and P. fluorescens), an actinomycete (Nocardioides oleivorans), ascomycete (Gibberella zeae), and basidiomycete (Penicillium allii), were unique in the specific suppressiveness. This indicated commonality of some microorganisms in the take-all suppressive soils, with a selected distinguishing group responsible for specific suppressiveness. General suppressiveness was considered to be due to no specific microorganisms, as seen in soil M2. An attempt to induce TAD by growing successive wheat crops in pots of Ggt-infested soils was unsuccessful with no TAD effects shown, possibly due to variable Ggt DNA concentrations in the soils and addition of nutrients during the experiment. Increasing numbers of Pseudomonas fluorescens CFU in the rhizosphere of plants, during successive wheat crops was independent of the Ggt DNA concentrations and disease incidence, suggesting that increases in P. fluorescens numbers were associated with wheat monoculture. This study has demonstrated that TAD in New Zealand was due to both specific and general suppressiveness, and has identified the distinguishing microorganisms associated with the suppression. Since most of these distinguishing microorganisms are known to show antagonistic activities against Ggt or other soilborne pathogens, they are likely to act as antagonists of Ggt in the field. Future work should focus on validating their effects either individually, or interactively, on Ggt in plate and pot assays and under field conditions.

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.