The persistance of industrially derived polycyclic aromatic hydrocarbons in the subsurface may be significantly affected by the metabolism of soil bacteria. This study was conducted to determine the ability of indigenous soil bacteria to decrease the concentration of four polycyclic aromatic hydrocarbons (naphthalene, fluorene, anthracene, and pyrene) and to utilize the compounds as a substrate for growth. Soil cores from petroleum contaminated and non-contaminated sites contained 10⁵ - 10⁷ viable microorganisms per gram dry weight of soil. Gram negative rod-shaped bacteria predominated. Decreases in the concentration of the four polycyclic aromatic hydrocarbons were observed during incubation with bacterial isolates in aqueous suspension by the use of high performance liquid chromatography. Corresponding increases in bacterial numbers indicated utilization of the compounds as a carbon source. Soil samples from the contaminated sites contained greater numbers of bacteria utilizing anthracene and pyrene than soil samples from non-contaminated sites. Degradation rates of the four polycyclic aromatic hydrocarbons were related to the compound, its concentration, and the bacterium. Biodegradation of pyrene was positively correlated with the presence of oxygen. Pyrene was biodegraded by an Acinetobacter sp. under aerobic conditions but not under anaerobic or microaerophilic conditions. Studies with radiolabeled ¹⁴C-anthracene demonstrated utilization of the labeled carbon as a source of carbon by viable bacterial cells in aqueous suspension. Incorporation of ¹⁴C into cellular biomass however was not observed during incubation of ¹⁴C-anthracene in soil.

Declining infestations and the cyclic appearance of Phymatotrichum root rot of cotton from season to season led to the suggestion that antagonistic microorganisms were the cause of this phenomenon. This study was concerned primarily with Actinomycetes spp., fluorescent Pseudomonads, Trichoderma spp., and other fungi. There was a continuous fluctuation in the population of Actinomycetes spp. and fluorescent Pseudomonads on the surface of strands. Populations of these antagonistic organisms dropped as the viability of strands of P. omnivorum decline. Comparison of the rhizoplane microflora from infected and healthy roots showed no relationship between the populations of Actinomycetes spp. and fluorescent Pseudomonads and the resistance of healthy roots to invasion by P. omnivorum. Similarly, soil samples collected from areas with declining infestations and assayed for populations of Actinomycetes spp. and fluorescent Pseudomonads, revealed no differences in the populations of these antagonistic organisms. This indicates that the absence of the disease in areas with declining infestations is not due to the microorganisms investigated in this study. Higher mortality rates of strands of P. omnivorum occurred when strands were exposed to Actinomycetes spp. and fluorescent Pseudomonads or to their metabolites. The hyphal deformation observed on strands from the field could not be reproduced in vitro. The same antagonistic microorganisms sprayed on cotton roots containing strands failed to reduce strand viability.

A total of 200 Rhizobium meliloti isolates were sampled from alfalfa (Medicago sativa L.) nodules in five uninoculated fields throughout Arizona. Dominant strains (≥ 20% nodule occupancy at each site) were identified using plasmid profile analysis and intrinsic antibiotic resistance patterns. The major dominant strains and a commercial strain (102F77b) were evaluated for their N fixing effectiveness in a Leonard jar study. All strains were highly effective, and no significant differences were found (p ≥ 0.05) in shoot weight, root weight, nodule weight, acetylene reduction and total N content among the strain treatments. These effective dominant R. meliloti strains indigenous to Arizona soil probably contribute to the state's high alfalfa yield. Furthermore, indigenous strains AZTCYJ, AZSC, and AZY have potential as inoculants for arid lands due to their high effectiveness and unique resistances to extreme abiotic stresses present in arid land soils.

Actinomycetes are bacteria belonging to the order of Actinomyceteles and are / Thesis (M.Sc.)-University of KwaZulu-Natal, Pietermaritzburg, 2006.

Nitrous oxide (N2O) is a potent greenhouse gas mainly emitted from agriculture. In the biological process of denitrification, intermediates of the nitrogen cycle are reduced under oxygen limiting conditions thereby releasing N2O. Denitrification is influenced by various environmental factors and both bacteria and fungi are capable of denitrification. The ultimate aim of this thesis was to determine the significance of fungal and bacterial denitrification in arable soil and to investigate influences of soil pH and physical disturbance on potential denitrification rates and denitrifying communities. Long-term pH plots combined with a disturbance gradient have been utilised to investigate fungal and bacterial denitrification distinguished by application of selective inhibitors. Highest N2O production was measured from slightly acidic soil and soil with reduced disturbance. Fungi and bacteria contributed to N2O production with bacterial denitrification as dominant source. Fungal denitrification remained unaffected by soil pH and disturbance whereas bacterial denitrification was influenced by these factors. Bacterial denitrification was positively correlated with concentrations of fatty acids which suggested that these fatty acids were common to bacteria involved in N2O production in the soils investigated here. Bacterial community structure changed with soil pH and disturbance whereas fungal community structure was only influenced by disturbance. Bacterial denitrifier communities (nitrite reductases nirK and nirS) changed over the pH gradient but only the nirK community was affected by disturbance. This indicated that groups of bacterial denitrifiers follow different ecological strategies. Gene abundance of nirK and nirS was also correlated to concentrations of the fatty acids associated with denitrifying bacteria in the soils investigated here. In conclusion, fungal denitrification was significant in arable soil but remained unchanged by soil pH and disturbance. Therefore, fungal denitrification is important in agricultural ecosystems and should be considered when developing mitigation strategies for N2O production especially under conditions favourable for fungal denitrification.

A Thesis, submitted to the Faculty of Science, University of the Witwatersrand, in fulfilment of the requirements for the degree of Doctor of Philosophy. Johannesburg, 2013 / A novel holistic approach was used to study the mycotrophic nature of commercial sugarcane varieties grown in KwaZulu-Natal, South Africa. All five varieties were mycotrophic, but N12 had the highest overall mycorrhization and was selected for a pot study to assess the growth response of sugarcane to inoculation with indigenous arbuscular mycorrhizal (AM) fungi and microflora. The pot study suggested that sugarcane will respond positively to inoculation with AM fungi, but the effects are most clear in the early phase of growth and less obvious in later elongation phases. This observation, taken together with the ability of sugarcane to grow well in sterile soil without microflora additions suggests that the plant may be facultatively mycotrophic. A multivariate analysis determined the nutrient relationships between soil and corresponding leaf nutrient levels on 72 sugarcane field plants, categorised according to either high or low percentage colonisation. Highly colonised plants were found to have more positive nutrient correlations compared to lower percentage colonised plants. AM fungi were identified from spore morphology and associated mycorrhizal bacteria (AMB) were identified by 16s rDNA analysis. Partial molecular identification was conducted using a universal eukaryotic forward NS31 primer and general fungal AM1 primers confirming the spores to be of AM fungi origin. A nested PCR was performed, using the universal fungal primers, NS5 and ITS4, followed by primer combinations to target sequences of specific Glomalean groups. Only partial molecular identification was conducted, as RFLPs were not successfully optimised. DNA from the Acaulospora gerdemannii/Acaulospora trappei group, Glomus occultum/Glomus brasilianum group, Glomus mosseae/Glomus intraradices group, Glomus etunicatum/ Glomus clariodeum group and Acaulosporaceae sensu stricto were detected, indicating AM fungi diversity. Bacteria, Brevibacillus reuszeri isolated from Scutellospora nigra, Bacillus megaterium and Stenotrophomonas maltophilia isolated from Glomus geosporum, Paenibacillus chitinolyticus and Bacillus cereus isolated from Acaulospora mellea and Gigaspora margarita spores respectively, were tested for biocontrol capability against pathogenic nematodes of Paratrichodorus, Meloidogyne and Pratylenchus genera. Meloidogyne was the least susceptible to associated mycorrhizal bacteria biocontrol and Paratrichodorus the most susceptible. These studies have contributed to understanding the role of AM in sugarcane agriculture in South Africa. Keywords: arbuscular mycorrhiza, sugarcane varieties, multivariate analysis, nutrient relationships, associated mycorrhizal bacteria, biocontrol, nematodes

Este trabalho teve por objetivo avaliar a biodegradação do glifosato em amostras de solos, quantificando o grupo de microrganismos mais ativos durante este período, além de determinar um método de extração e análise para este herbicida. Foram utilizadas amostras de dois tipos de solos, um da Fazenda Experimental da ESALQ-USP, classificado como podzólico vermelho-amarelo (PV), e outro da Estação Experimental do IAPAR/PR, classificado como latossolo vermelho (LV), ambos com e sem histórico de aplicação de glifosato. O trabalho foi realizado no Laboratório de Ecotoxicologia do Centro de Energia Nuclear na Agricultura, da Universidade de São Paulo, utilizando o glifosato em sua fórmula técnica, na dosagem para condições de campo (2,16 mg i.a./kg de solo). A biodegradação do glifosato foi avaliada monitorando a evolução do CO2 pelos microrganismos durante um período de 32 dias. Foram também quantificados durante o período, os resíduos de glifosato e do seu metabólito ácido aminometil fosfônico (AMPA) através de extração seguida de análise por cromatografia liquida de alta eficiência (CLAE). Além disso, foi avaliada a atividade microbiana e o número de microrganismos presentes durante o período. Os resultados mostraram que o glifosato foi degradado pelos microrganismos do solo durante o período avaliado, com a formação do metabólito AMPA. O glifosato favoreceu um aumento na atividade microbiana das amostras dos solos que receberam aplicação do herbicida. Em relação ao número de microrganismos, os fungos e actinomicetos tiveram um aumento em população com a presença do glifosato, enquanto que as bactéria permaneceram em número constante durante o período de incubação. Os resíduos de glifosato e AMPA, extraídos com NH4OH e KH2PO4 e analisados por CLAE, foram detectados nas amostras avaliadas, mostrando que o método de extração utilizado foi eficiente, com recuperação acima de 70%, para estes dois compostos. / The aim of this work was to evaluate the biodegradation of glyphosate in soil samples, quantifying the group of more active microorganisms during this period, and also to establish an extraction and analysis methods for this herbicide. Two soils types were analysed, one from the ESALQ Experimental Station (USP), classified as typic hapludult (PV), and another from the IAPAR Experimental Station, classified as typic hapludox, with and without report of glyphosate application, in total of 4 samples. The work was carried out using the technical glyphosate in the doses for field conditions (2,16 mg a.i./kg of soil). The assessment of degradation was made using the CO2 evolution during a period of 32 days. The residues of glyphosate and metabolite aminomethyl phosphonic acid (AMPA) were quantified during the same period, through extraction and analysis by high-pressure liquid chromatography (HPLC). The soil microbial activity and the enumeration of microorganisms were evaluated during the same period. The results showed that glyphosate was degraded by the soil microorganisms, with the formation of the metabolite AMPA. The application of glyphosate provided an increase in the microbial activity of the soil samples. In relation to enumeration of fungi and actinomycetes had an increase in the population with the glyphosate application, while the number of bacteria remained constant through the whole experiment. The HPLC analyse of glyphosate and AMPA residues, extracted with NH4OH and KH2PO4, resulted in a recovery above 70% showing that the extraction method used was efficient for these two compounds.

The tropical rainforest has interested ecologists for hundreds of years because of its vast species diversity. The distribution and establishment of trees is related to soil properties and rootassociated microorganisms. The coexistence of hyper-diverse plant communities in tropical rainforests has resulted in associations being formed with belowground communities, mycorrhizas (particularly arbuscular mycorrhizal (AM), ectomycorrhizas (ECM)) and root associated bacterial communities. The rapid deforestation in Southeast Asia is causing the loss of the dominant and important tree species belonging to the family Dipterocarpaceae. It is important to understand whether different host species in the same environment maintain mycorrhizal and bacterial diversity, especially mycorrhizas with a restricted host range. In this study, I examine the ecology of mycorrhizas and bacteria associated with Dipterocarpaceae and also the plant community as a whole. The aim of this project is to understand the effect of host properties (e.g. species, size), soil factors (e.g. nutrient concentrations) and spatial factors on mycorrhizal fungi and bacterial diversity and community structure. The research took place in two Centre for Tropical Forest Science (CTFS) plots in Malaysia: Pasoh Forest Reserve (in Negeri Sembilan) and Danum Valley Conservation Area (in Sabah). Molecular protocols and a modern technique, Next Generation Sequencing (NGS), were adopted to quantify mycorrhizal and bacterial loads in tropical plants. ITS1 and ITS2 regions were used for ECM, 18S rRNA were used for AM, and 16S rRNA were used for bacteria. Mycorrhizas and bacteria present in the roots of Dipterocarpaceae from 60 individual plants belonged to 25 species within 6 genera were traced and sampled in 2015. To my knowledge, this study is the first attempt to study root-associated bacteria across multiple species within a single family, Dipterocarpaceae. Dipterocarpaceae's species was found to significantly influence root bacteria. Analyses showed that mycorrhizal communities are similar on the host, unlike the null model. Dipterocarpaceae was previously believed to solely host ECM, but this study disproves this. This study shows that Dipterocarpaceae can have dual colonization, as it iv can also associate with AM fungi. One soil core of 10 cm × 10 cm × 7.5 cm were collect randomly in three subplot and further divided at 2.5 cm each slice into 75 individual 'microcubes' of 2 cm × 2 cm × 2.5 cm depths enumerates a total of 192 fine root samples. Multivariate analysis revealed that AM fungi tend to associate with non-dipterocarp (as well as unidentified families) while ECM fungi tend to associate with dipterocarps. Data was also collected on host attributes, plant size, and root density. Dipterocarpaceae size does not influence the distribution of mycorrhizal or bacterial communities. The root density reduces as depth increases. Therefore, root density does have a significant influence on mycorrhizal community structure. The diversity of ECM and AM fungal communities within cubes decreased significantly with depth (p < 0.001), whereas the mycorrhizal communities did not change across horizontal distances within cubes. To investigate whether there is a relationship between belowground communities and soil properties, soil macro and micro nutrients were examined and a multivariate analysis was performed. The results showed that communities of belowground (mycorrhizal and bacterial) species correlate with soil parameters. Spatial scale also had an effect on community assembly, independent of environmental variation. These results demonstrate that mycorrhizal fungal communities can vary substantially over very fine spatial scales, and that the distribution of roots from different species do not reflect their proximity aboveground. This study clearly demonstrates the widespread presence of mycorrhizal fungi and root associated bacteria in tropical rainforest plants.

No description available.

Thesis (Ph.D.)--University of Missouri-Columbia, 2006. / The entire dissertation/thesis text is included in the research.pdf file; the official abstract appears in the short.pdf file (which also appears in the research.pdf); a non-technical general description, or public abstract, appears in the public.pdf file. Title from title screen of research.pdf file viewed on (February 27, 2007) Vita. Includes bibliographical references.