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This investigation has for its aim the confirmation of the correlation between soil moisture and the microflora of soils, and a lesser relation between the soil temperature and the microflora. The soils used in this study are typical clay soils of Denton County, Texas. The samples were taken from virgin pasture lands and analyses made monthly or semimonthly. The wide seasonal variation of temperature and rainfall afford a good opportunity for this study.

Thesis (M. Tech.(Biomedical Technology)) - Central University of technology, Free State, 2011 / The existence of geophagia from as early as 460 BC up to now, makes it relevant to investigate all aspects related to geophagia. Geophagia is a direct route for potential transmission of pathogens to the human host, through the ingestion of soil. Soil-borne diseases in humans are causing growing concern as sewage disposal, which involve sewage sludge and waste water drainage from these plants, is on the increase. It is estimated that approximately seven million tons of sewage sludge is produced annually and that 54% of this sewage sludge is introduced into soil. Data on enteric infection in humans caused by contamination from soil is limited and need further investigation. The aim of the study was, therefore, to collect information on the microbiological presence in geophagic soil in the Qwa-Qwa district. Objectives included the collecting of information regarding various sampling sites in the Qwa-Qwa district and also soil samples sold by vendors, investigation of the prevalence of known human pathogenic bacteria and fungi in geophagic soil, investigating the culturability of Salmonella enteritidis in geophagic soil in comparison with the viability of these organisms in soil for long periods of time, investigating potential antimicrobial activity of geophagic soil, as some of the geophagists are convinced that the geophagic soils have medicinal properties, and to determine the microbial diversity of geophagic soils, which can not be accomplished by conventional microbial culturing methods.

Thesis (PhD(Agric))--Stellenbosch University, 2009. / ENGLISH ABSTRACT: The global movement in agriculture is towards more environmentally friendly, sustainable production practices, since the role of soil microbial functions in ensuring crop production and soil fertility has become more evident in agricultural systems. Furthermore, with the impeding phase-out of methyl bromide, apple replant disease (ARD) is becoming an increasingly important problem and biological management practises are needed. Since microbial activity is generally carbon-limited in agricultural soil, it is widely accepted that management practices providing a range of organic compounds on a regular basis will tend to maintain an active and diverse microbial population. It was hypothesised that the application of various biological amendments can affect soil microbial numbers and function, thereby having a positive effect on fruit tree growth and yield. The effect of continued applications of organic material, various microbial inoculants and biostimulants on tree performance were evaluated in conventional management systems. Field trials were established in a conventional pear orchard, potential apple replant disease sites, as well as an optimally managed, high density apple orchard under controlled fertigation. The use of compost, compost extracts, a Bacillus inoculant and humates were investigated intensively. Furthermore, to improve our understanding of soil biological systems a combination of simple, practical methods were used to evaluate the effect of biological amendments on soil microbial properties and effects were related to tree performance. Regular application of compost extract in combination with compost showed the most significant effect in improving tree performance in commercial pome fruit orchards under various conditions. In the pear orchard, cumulative yield over the first two seasons was improved by more than 50% compared to controls, while in the fertigated orchard yield was improved by 22%. Biological amendments also showed improved growth in orchards suffering from stunted growth symptoms typical of ARD. However, in severe ARD cases methyl bromide fumigation showed the most consistent effects. Other biological amendments which showed positive effects on yield were application of Bacillus inoculants (Biostart®) in combination with a labile C source and a low dosage humate product, as well as a combination of compost and humates. It was clear that a combination of labile organic matter and a diverse group of microorganisms showed most promise. Although for some specific treatments increased microbial numbers and activity may have resulted in improved tree performance, in general, changes in culture-based plate counts, soil enzyme activity and carbon utilisation profiles could not be used as an indicator of yield. It was suggested that improved synchronisation of nutrient release and plant uptake, as well as microbial phytohormone production, may play an important role in improving tree performance with application of biological amendments. More research is needed on the exact mechanisms through which compost extracts improve yield and studies on root growth proliferation, as well as effects in the rhizosphere are recommended. / AFRIKAANSE OPSOMMING: Binne lanbouverband is daar tans wêreldwyd die neiging om die uitwerking van produksie-praktykte op die omgewing in ag te neem en sodoende meer verantwoordelik op te tree. Omdat die belangrike rol wat grondmikro-organisme funksionering in volhoubare verbouingspraktyke speel nou deeglik besef word, word meer volhoubare bestuurspraktyke bepleit. Hiermee saam, noodsaak aspekte soos die uitfasering van metielbromied vir die beheer van appelhervestigingsiekte, dat biologiese bestuurspraktyke meer aandag geniet. Daar word geredelik aanvaar dat gereelde toediening en aanvulling van organiese materiaal ‘n aktiewe, diverse mikrobe populasie in die grond tot gevolg sal hê. Die hipotese is gestel dat die toediening van ‘n verskeidenheid biologiese produkte grondmikrobe getalle en werking gunstig kan beïnvloed. Dit kan moontlik weer aanleiding gee tot positiewe reaskies wat die groei en drag van vrugtebome betref. In hierdie studie is die uitwerking van voortgesette toedienings van organiese materiaal, mikrobiese inokulante, asook biostimulante, op die prestasievermoë van vrugtebome ondersoek. Veldproewe is uitgelê in ‘n konvensionele peerboord, verskeie boorde met moontlike appelhervestigingsiekte probleme, asook ‘n hoëdigtheidsaanplanting appelboord onder optimale bestuur. ‘n Deeglike ondersoek is gedoen met betrekking tot die gebruik van kompos, komposekstrak, Bacillus-inokulante en humate. Eenvoudige, praktiese metodes is aangewend om vas te stel hoe biologiese toevoegings grondmikrobe eienskappe beïnvloed en of dit verband hou met veranderinge in boomprestasie. Die studie het aangetoon dat die gereelde toediening van komposekstrak saammet kompos, betekenisvolle verbetering in boomprestasie van kernvrugboorde teweeg bring onder verskeie omstandighede. Die kumulatiewe opbrengs van ‘n peerboord is oor twee seisoene met meer as 50% verhoog teenoor die kontrole. In ‘n optimaal bestuurde appelboord onder sproeibemesting, is opbrengs met 22% verhoog in vergelyking met die kontrole. Biologiese toevoegings het ook groei verbeter in boorde waar appelhervestigingsiekte bome se groei vertraag het. In die geval van ernstige appelhervestigingsimptome het metielbromied egter steeds die mees konstante positiewe uitwerking gehad. Ander biologiese toevoegings wat ‘n gunstige uitwerking op opbrengs getoon het, was ‘n kombinasie van Bacillus inokulante, ‘n lae dosis humaat en ‘n aktiewe koolstofbron, asook kompos in kombinasie met humate. Dit is duidelik dat ‘n kombinasie van ‘n maklik afbreekbare koolstofbron (soos kompos) tesame met ‘n diverse groep mikroorganismes mees belowend is vir gebruik in biologiese verbouingssisteme. Resultate toon dat veranderings in aantal organismes gemeet deur plaattellings, die aktiwiteit van grondensieme, en verbruikspotensiaal van verskillende koolstofbronne, nie as ‘n aanduiding van boomprestasie gebruik kan word nie. Daar is voorgestel dat verbeterde sinkronisasie van voedingselementvrystelling en plantopname, sowel as produksie van plantgroeihormone deur mikrobe, moontlik ‘n rol speel by boomreaksies op biologiese toevoegings. Meer navorsing wat verband hou met die meganisme waardeur komposekstrak opbrengs verbeter, is nodig. Verder word studies op fynwortelontwikkeling sowel as aspekte van die wortelrisosfeer aanbeveel.

<p>A study of the microbial diversity in sediments of the Great Berg River estuary is carried out using modern molecular phylogenetic methods. The aim of this study was to determine the effect of (pollution by) the effluents of the fish industry on the composition of the microbial community in the sediments. The diversity in microbial groups of sediment samples that received wastewater from the local fishing industry was investigated by a PCR-DGGE (polymerase chain reaction-denaturing gradient gel electrophoresis) approach and compared to an unaffected site.</p>

This dissertation comprises three parts and is presented in two chapters. Chapter 1 concerns Arthrobacter, a bacterium with an intriguing growth cycle. Whereas most bacteria exist as either a rod or coccus, this bacterium shares the rod/coccus lifestyle. It therefore seemed important to examine the growth regulatory pathways from the rod and coccus. The committed step, that catalyzed by aspartate transcarbamoylase (ATCase), in the pyrimidine biosynthetic pathway was chosen. The ATCase in Arthrobacter is like the well known Pseudomonas enzyme except that it has an active dihydroorotase (DHOase) associated. Included in Chapter 1 is the description of a microorganism, Burkholderia cepacia, whose ATCase has characteristics that are at once reminiscent of bacteria, mammals, and fungi. It differs in size or aggregation based on environmental conditions. In addition, it has an active DHOase associated with the ATCase, like Arthrobacter. B. cepacia is important both medically and for bioremediation. Since B. cepacia is resistant to most antibiotics, its unique ATCase is a prime target for inhibition. Whereas the first chapter deals with the de novo pathway to making pyrimidines, which is found mainly in the lag and log phase, Chapter 2 addresses the salvage pathway, which comes more into play during the stationary phase. This section focuses on the isolation, identification, and grouping of a number of natural soil bacteria from various soil locations. These organisms are important agriculturally, medically, and industrially. Addition of these soil isolates to poor soils has been found to improve the soil. In a previous study by D.A. Beck, the salvage schemes for a number of laboratory strains of microorganisms were determined. Nine separate classes of salvage were designated by determining the salvage enzymes present. In this study emphasis has been placed on soil bacteria, which had not previously been analyzed. A number of species of soil bacteria were identified using the MIDI. The salvage enzymes were then determined for these organisms and a comparison of these isolates to the previous study was performed in order to group the new organisms into 19 salvage schemes, that is 10 more than in the previous study.

The inclusion of lime in burials is observed in historical and archaeological records, in contemporary mass graves and forensic cases. Clearly there are controversies within the literature and there is a general misconception of the effects of lime on decomposition. Recent casework in Belgium and the UK involving the search for human remains buried with lime, have demonstrated the need for a more detailed understanding of the effect of different types of lime on cadaver decomposition and its micro-environment. Field and laboratory experiments using pigs as human body analogues were undertaken to obtain a better understanding of the taphonomic processes that govern lime burials. The changes observed in the experiments were related back to archaeological parallels in which white residues have been found. The combined results of these studies demonstrate that despite conflicting evidence in the literature, hydrated lime and quicklime both delay the initial stages of the decay process but do not arrest it completely. The end result is ultimately the same: skeletonisation. Furthermore this study stresses the importance of the specific microenvironment in taphonomic research and highlights the need for chemical analysis of white residues when encountered in a burial. Not all white powder is lime. White residue could be identified as calcium carbonate, building material, body decomposition products, minerals or degraded lead. This study has implications for the investigation of clandestine burials and for a better understanding of archaeological plaster burials. Knowledge of the effects of lime on decomposition processes also have bearing on practices involving the disposal of animal carcasses and potentially the management of mass graves and mass disasters by humanitarian organisation and DVI teams.

A imensa diversidade de micro-organismos no solo leva a uma inevitável riqueza de interações entre espécies. Neste intuito, esse projeto é inovador na identificação dos cogumelos da Mata Atlântica, e na descrição da comunidade bacteriana associada às suas micosferas. Usando corpos de frutificação dos fungos (cogumelos) como indicadores para sistemas ricos em nutrientes, as amostras foram coletadas para investigar as interações entre os fungos (maioria do domínio Basidiomycota) e as bactérias presentes no solo em volta das micélios fúngicos (ambiente micosférico). As análises foram feitas com técnicas independentes de cultivo (análise PCR-DGGE, sequenciamento Sanger de fragmentos de ITS/18S e pirosequenciamento de tags da região V4 de 16S DNAr). As famílias fúngicas Marasmiaceae e Lepiotaceae, do domínio Basidiomycota foram as mais abundantes entre os cogumelos amostrados (13 e 5 cogumelos, respectivamente), e estavam presentes entre todas as três parcelas de estudo. As demais amostras foram alocadas dentro das famílias Marasmiaceae, Lepiotaceae, Inocybaceae, Lachnocladiaceae, Bolbitiaceae, Entolomataceae, Hygrophoraceae, Hymenogastraceae, Mycenaceae e Strophariaceae, além de dois do domínio Ascomycota. Baseado na análise de DGGE, é bastante claro que existe uma grande diferença na comunidade bacteriana (de toda a comunidade bacteriana, de ?- proteobacteria e de ?-proteobacteria) entre os solos associados ou não com os corpos de frutificação. Os dados de pirosequenciamento indicaram que dentro dos tratamentos as amostras se agruparam baseado nas famílias fúngicas ou no substrato onde os cocumeglos ocorrem (solo ou serrapilheira), sendo clara em algumas micosferas as alterações na ocorrência de grupos microbianos. O grupo de UTOs mais induzidas na região da micosfera foi composto dos grupos Burkholderia, Acidobacteria Gp1, Comamonadaceae, Sphingobacteriaceae, Burkholderiaceae, Chitinophagaceae), Schlesneria, Acidobacteria Gp3 e Spartobacteria gênero incertae sedis. Isto indica que existe um processo de seleção para bactérias específicas dependendo das diversas variáveis e fatores ambientais presentes no microhabitat micosfera. / The immense microbial diversity in the soil leads to inevitable richness in inter-species interactions. For this reason, this is a novel project that focuses on identifying mushrooms and the associated bacterial community with their mycospheres in the Brazilian Atlantic Rainforest. Using fungal fruiting bodies (mushrooms) as indicators of nutrient-rich systems, samples were taken to investigate the interactions between fungi (mostly of the domain Basidiomycota) and bacteria present in the soil surrounding fungal mycelia (mycosphere environment). The analyses were conducted using culture-independent techniques, where isolating DNA of bacteria and/or mushrooms attempts to provide information on microbial functionality. These culture-independent analyses (PCR-DGGE, Sanger sequencing of ITS/18S fragments, and pyrosequencing of tags from the V4 region of 16S rDNA) generated extensive data on the bacterial diversity selected for in the presence of fungal structures in the soil. The fungal families Maramiaceae and Lepiotaceae, of the domain Basidiomycota were the most abundant among the mushrooms sampled (13 and 5 mushrooms, respectively) and were present in all of the three sampling sites. The rest of the mushrooms were found to be within the families Marasmiaceae, Lepiotaceae, Inocybaceae, Lachnocladiaceae, Bolbitiaceae, Entolomataceae, Hygrophoraceae, Hymenogastraceae, Mycenaceae, and Strophariaceae, in addition to two of the domain Ascomycota. Based on DGGE analysis, it is clear that there is a great difference in the bacterial community (entire bacterial community, of ?- proteobacteria and of ?-proteobacteria) between all fungal fruiting body-associated and non-associated soils. The pyrosequencing data indicated that within each treatment group, the samples did not separate according to fungal families or substrate where the mushrooms were found (in the soil or amoung the leaf litter). However, some mycospheres exhibited clearly altered bacterial communities. The group of OTUs most induced in the mycosphere region consisted of Burkholderia, Acidobacteria Gp1, Comamonadaceae, Sphingobacteriaceae, Burkholderiaceae, Chitinophagaceae), Schlesneria, Acidobacteria Gp3, and Spartobacteria genus incertae sedis. This indicates that there is a selection process for specific bacteria depending on a wide range of variable and environmental factors acting in the mycosphere microhabitat.

Os manguezais compõem um bioma de transição entre o ambiente marinho e terrestre característico de regiões tropicais e subtropicais. Dentro deste ambiente, a diversidade microbiana desempenha um importante papel na ciclagem de nutrientes. No entanto, a diversidade de fungos em manguezais é pouco estudada, bem como o estabelecimento de relações ecológicas entre esses organismos e o ambiente. Neste intuito, o presente trabalho teve como objetivo comparar a diversidade fúngica no sedimento de dois manguezais localizados na cidade de Bertioga [um contaminado com petróleo (OilMgv), e um manguezal próximo (AntMgv)]. As análises se basearam em metodologias independentes de cultivo, como a técnica de PCR-DGGE baseada na região ITS (internal transcribed sequence), que mostrou padrões complexos e uma grande abundância de bandas, sendo que dentro dos perfis obtidos é possível observar grupos selecionados para cada manguezal e para cada região dentro de um mesmo manguezal. A construção e análise de bibliotecas de clones também desta região mostraram a dominância de fungos afiliados aos filos Basidiomycota e Ascomycota, com destaque para a ocorrência dos gêneros Epicoccum, Nigrospora e Cladosporium. Uma análise mais ampla, por meio de pirosequenciamento permitiu uma melhor visualização destas comunidades e corroborou os dados anteriores, comprovando a ocorrência de grupos fúngicos distintos nos manguezais estudados (sequenciamento baseado em amplicons da região ITS), e permitindo a observação de outros grupos eucarióticos nos manguezais avaliados (análise de metagenômica). Em resumo, os dados apresentados constituem a primeira descrição robusta destas comunidades que desempenham funções essenciais à manutenção e ao funcionamento do ambiente estudado. / Mangroves ecosystems make up a transition biome between land and marine environments, particular occurring in tropical and subtropical regions. Within this environment, the microbial diversity plays an important role in nutrient cycling. However, the diversity of fungi in mangrove is still poorly studied, as well as the establishment of ecological relationships between these organisms and the environment. In this sense, this study aimed to compare the fungal diversity in the sediment of two mangroves located in the city of Bertioga [an oil-spilled mangrove (OilMgv) and a nearby unaffected mangrove (AntMgv)]. Analyzes were based on culture-independent methods, such as PCR-DGGE based on the ITS region (internal transcribed sequence), which showed complex patterns and an abundance of bands, allowing the observations of groups selected for each mangrove and each region inside the same mangrove. The construction and analysis of clone libraries showed the dominance of fungi affiliated with the phyla Ascomycota and Basidiomycota, with a remark for the occurrence of the genera Epicoccum, Nigrospora e Cladosporium. A more robust approach, performed by pyrosequencing, allowed better visualization of these communities, corroborating the previous results, reinforcing the differential occurrence of fungi groups in assessed mangroves (based on sequencing of the ITS region amplicons), and allowing the observation of other eukaryotic groups in these areas (metagenômica analysis). In summary, the present data provide the first robust description of these communities that perform essential roles for the functioning and maintenance of the studied environment.

O nitrogênio é o quinto elemento mais abundante em nosso sistema solar, é essencial para a síntese de ácidos nucleicos e proteínas, os dois polímeros mais importantes da vida. Apesar da importância do nitrogênio e sua abundância na atmosfera, o N2 é praticamente inerte; assim, as formas de nitrogênio inorgânico fixados mais comuns são os íons nitrato e amônio que muitas vezes limitam a produtividade primária nos ecossistemas marinhos e terrestres. Uma biosfera ativa requer a incorporação do nitrogênio em moléculas biológicas por meio da fixação de nitrogênio, um processo no qual os domínios em procarióticos Bacteria e Archaea reduzem gás nitrogênio em amônia. Porém, a maioria dos organismos não pode fixar nitrogênio, mas sim obtê-lo na forma de nitrogênio orgânico a partir do ambiente, ou a partir da redução do nitrato. O amônio é retornado para o ambiente quando os organismos morrem e isto depende da presença do oxigênio nestes locais. Na presença do oxigênio, o amônio é oxidado em nitrato, numa via conhecida como nitrificação. Na ausência de oxigênio, o nitrato é utilizado por muitos microrganismos como um receptor de elétrons, como na redução dissimilatória de nitrato a amônia (DNRA), acoplada à oxidação anaeróbica de carbono orgânico; o nitrato pode ser convertido em gás dinitrogênio pela desnitrificação, ou ainda uma via alternativa pode transformar o nitrogênio fixado em N2, realizada por um grupo de bactérias conhecido como planctomycetes, onde a oxidação do amônio é acoplada a redução de nitrato, no processo chamado anammox. Neste trabalho de tese foi realizada a avaliação do ciclo do nitrogênio, buscando entendimento de três vias de transformação deste elemento. Neste sentido, estas vias foram avaliadas quanto as suas taxas de ocorrência, com uso incubações do sedimento de manguezais e nitrogênio marcado, como também por meio da identificação de genes funcionais envolvidos nestes três processos, por meio de pirosequenciamento. O grupo Planctomycetes ainda pode ser estudado utilizando a hibridização com sonda fluorescente in situ FISH. Os resultados indicam a presença marcante de genes identificados como parte da via desnitrificação, assim como as taxas de incubação observadas para esta via foram muito expressivas quando comparadas com as taxas obtidas para o processo anammox e DNRA. Os resultados obtidos com as análises metagenômicas e com a técnica FISH sustentam os resultados obtidos com as incubações. Pode-se observar que a filogenia sugere a tendência do agrupamento com organismos planctomycetes não descritos como responsáveis pelo processo anammox. Por meio da técnica FISH pode-se confirmar a detecção destas bactérias e visualizar sua menor presença nos manguezais amostrados, quando comparadas às bactérias totais encontradas nestas amostras. / Nitrogen is the fifth most abundant element in our solar system, essential for the synthesis of nucleic acids and proteins, one of the most important polymers of life. Despite the importance of nitrogen and its overwhelming abundance in the atmosphere, N2 is practically inert, so the most commom forms of inorganic nitrogen fixed are nitrate and ammonium ions, which often limit primary productivity in marine and terrestrial ecosystems. An active biosphere requires the incorporation of nitrogen in biological molecules through nitrogen fixation, a process in which domains Archaea and Bacteria reduce nitrogen gas into ammonia. The most organisms can\'t fix nitrogen, but they can get it in inorganic nitrogen form from the environment or from the reduction of nitrate. The ammonia is returned to environment when organisms die and it depends on the presence of oxygen at these sites. In the presence of oxygen, ammonia is oxidized to nitrate, in a way known as nitrification, and in the absence of oxygen, the nitrate being used by many microbes as an electron acceptor, such as dissimilatory nitrate reduction to ammonia (DNRA), coupled to anaerobic oxidation of organic carbon. The nitrate can be converted to dinitrogen gas by denitrification, or an alternative route can turn fixed nitrogen in N2, performed by a bacteria group known as Planctomycetes, where oxidation is coupled to the ammonium nitrate reduction, in a process called anammox. In this work, with mangrove sediments from Bertioga city, State of São Paulo, the evaluation of these three pathways of nitrogen transformation was performed as their rates of occurrence, with incubations with labeled nitrogen, as well as through the identification of functional genes involved in these three cases, by pyrosequencing. The group Planctomycetes can also be studied using the hybridization probe FISH fluorescence in situ. The results show the strong presence of genes identified as part of the denitrification pathway, as well as the rates observed for incubation of this pathway were very significant when compared with the rates obtained for the process anammox and DNRA. The results obtained from the metagenomic analyze and the FISH technique support the results obtained with incubations. It can be observed that the trend suggests the phylogeny of the organisms group with Planctomycetes not described as responsible for anammox process. Through the FISH technique, it was possible to confirm the detection of these bacteria and view its reduced presence in mangrove sampled compared to total bacteria found in these samples.