The diversity of microorganisms and the influence of their enzymatic activities in soil are critical to the maintenance of good soil health. Changes in these parameters may be the earliest predictors of soil quality changes, potentially indicating anthropogenic influences. The goal of this study was to investigate the soil microbial diversity and function of grasslands along an urbanization gradient. Soil samples were collected in the Potchefstroom municipal area, South Africa, at specific sites. Sampling sites were described as urban, suburban and rural - according to the V-I-S (Vegetation-Impervious surface-Soil) model of Ridd (1995). Soil samples were collected over a warmer, wet season (May) and a colder, dry season (August) over two years (2007 and 2008). Collected soil samples were characterised using certain physical and chemical parameters. Plant species composition and abundance were determined at each site, along with basic site data (soil compaction, percentage ground cover, percentage bare ground, percentage organic material present). The Shannon-Weaver diversity index was used to calculate biodiversity values for all the investigated sites regarding collected plant species composition. The microbial component of the soil was quantified and characterized using culture-dependent and culture-independent techniques. Culture-dependent techniques included the investigation of the aerobic heterotrophic bacteria and fungi. Organisms were plated out on different media, and the bacterial component was broadly grouped using morphology. Dominant organisms were identified by sequencing of PCR amplified 16S ribosomal DNA fragments. Shannon-Weaver index for bacterial diversity was determined for each of the sites. Denaturing gradient gel electrophoresis (DGGE) profiling of selected bacterial communities were also conducted. Microbial community function was determined using enzyme assays of five major groups of enzymes, namely (i) dehydrogenase; (ii) β-glucosidase; (iii) acid phosphatase, (iv) alkaline phosphatase and (v) urease. Plant species results were then brought into context with microbiological diversity and functionality results using multivariate statistics. Physical and chemical parameters of the collected soil samples revealed patterns present along the urbanization gradient. The pH values were mostly higher in the sub-urban and urban sites than in the rural sites. Electrical conductivity values were generally highest in the sub-urban sites. Plant species composition revealed trends along the urbanization gradient. Ordinations clearly grouped the plant species into rural, sub-urban and urban groups regarding plant species composition. Rural sites had the highest number of plant species. Shannon-Weaver values regarding the plant diversity supported the plant species composition data indicating higher plant diversity in the rural areas, followed by the sub-urban and the urban areas. Plant structural data indicated that forbs were most numerous in the rural sites, and less so in the urban sites. Higher average aerobic heterotrophic bacterial levels were present in the urban soil samples. The bacterial levels were lower in the sub-urban and rural soil samples. Subsequent identification of the dominant bacteria in the soil samples revealed organisms of the genus Bacillus dominated the aerobic heterotrophic bacterial communities in the soil samples. Bacillus species dominated the soil samples along the urbanization gradient. Shannon-Weaver indices based on culture-dependent methods indicated that urban sites had the highest biodiversity. These results could have been exaggerated, because of an overestimation of the number of bacterial morphotypes present in samples. Fungal levels were higher in the soil from samples collected at the rural samples sites. The culture-independent method (DGGE) was not optimized and inconclusive results were obtained. Enzyme assays revealed that potential dehydrogenase, β-glucosidase and urease activity followed a trend along the urbanization gradient, with urban samples registering the highest values and rural sites the lowest. Enzymes involved in carbohydrate catabolism (β-glucosidase and dehydrogenase) registered significantly higher potential activity in urban sites than the sub-urban and rural sites. The results could indicate that urban sites have the potential to lose carbon at higher rates than the rural sites. This aspect may need further investigation. Higher potential urease activity could indicate higher N-cycling in the urban soil environment. Ordination results for soil-, plant- and microbial diversity as well as microbial functionality indicated certain trends along the urbanization gradient. Plant species composition and structure data indicated that urbanization has a definite effect on the plant communities in the urban ecosystem. Results regarding aerobic heterotrophic bacteria populations and potential enzyme activity of the dehydrogenase, β-glucosidase (both active in the carbon cycle) and urease (active in the nitrogen cycle) illustrated clear trends along the urbanization gradient. In conclusion, results indicated that urbanization has an effect on plant species composition, and the population and function of aerobic heterotrophic bacteria and the fungal population. Furthermore, this study demonstrated the potential of using microbial diversity and activity as tools to investigate carbon utilization and storage along an urban-rural gradient. / MSc (Environmental Sciences), North-West University, Potchefstroom Campus, 2011

Biofumigation is an important crop protection practice that uses a plant’s natural defence mechanisms to control agricultural crop pathogens and diseases. Glucosinolates are volatile compounds found in most Brassica species and when hydrolysed, it forms a range of natural toxins including isothiocyanates that act as biofumigants. Research suggests that biofumigation is a good alternative to chemical fumigants as it is effective in controlling plant pests but with lower health and environmental risks. Several studies have confirmed the effectiveness of the breakdown products, especially isothiocyanates, as fungicidal, bactericidal and nematicidal products against a series of plant pests. However, very little information is available on the effects of glucosinolates and its breakdown products on non-target and beneficial soil organisms. Negative effects on beneficial soil organisms can have serious negative impacts on soil quality especially when essential ecosystem functions such as nutrient cycling and soil bioturbation are affected. Three biofumigants, broccoli, mustard and oilseed radish, and two chemical fumigants, metham sodium and cadusafos, were investigated for possible effects on non-target and essential soil organisms such as earthworms and the soil microbial community. Sublethal endpoints, including growth and reproductive success of the earthworms, were monitored. The genotoxicity of the biologically active compounds found in the fumigants, towards earthworms, was evaluated by means of the comet assay. The DNA damage was quantified by tail intensity parameters. Furthermore, the changes in the soil microbial community function and structure were evaluated by means of community level physiological profiling (CLPP) and phospholipid fatty acid (PLFA) analyses respectively. All exposures were done in artificial soil prepared according to the OECD standard guidelines. In the biofumigant treated soils, results varied and different effects were observed on the non-target soil organisms. Broccoli reduced cocoon production and the number of hatchlings while mustard induced more DNA strand breaks in earthworm cells compared to the control. All the biofumigants stimulated microbial growth but broccoli and oilseed radish changed the microbial functional diversity. Mustard had no lasting effect on the functional diversity but altered the microbial community structure. The chemical fumigants had a marked negative impact on the survival, growth, reproduction and the genotoxicity of the earthworms with metham sodium causing greater harm than cadusafos. The effects on the microbial community varied. Both chemicals had an inhibitory effect on the microbial growth in terms of the viable biomass determined by PLFA and the average well colour development in the Biolog™ Ecoplates. No lasting effects were observed in the community structure. Overall, cadusafos had a more pronounced effect on the microbial community functional diversity than metham sodium. Results indicated that each bioindicator species illustrates effects at their own level of organisation / MSc (Environmental Sciences), North-West University, Potchefstroom Campus, 2015

Infection is one of the factors that may contribute to non-healing of chronic wounds; the presence of antibiotic resistant bacteria serves to exacerbate the problem due to limited treatment options. Bacteria utilise several mechanisms to survive exposure to antibiotics, including synthesis of deactivating enzymes, target modification or substitution, changes to membrane permeability, upregulation of efflux pumps and the formation of a biofilm. Quorum sensing is a density-dependent mechanism of bacterial cell to cell communication that can be instrumental in co-ordinating biofilm initiation. Hyperbaric oxygen therapy (HBOT) is an option offered to some patients with chronic wounds, including diabetic foot ulcers. Evidence suggests that HBOT can reduce the incidence of major amputation in these patients. As well as the direct toxicity of increased tissue oxygenation on anaerobic bacteria HBOT may also increase levels of reactive oxygen and nitrogen species in the wound environment. This study aimed to investigate the effects of hyperoxia and oxidative damage on three specific mechanisms of antibiotic resistance: the activity of penicillinase, an antibiotic deactivating enzyme synthesised by bacteria; the activity of quorum sensing signalling molecules (AHLs); and biofilms and their associated bacteria. It also analysed the population dynamics of, primarily, bacteria in diabetic foot ulcers during HBOT, by the use of molecular analysis tools such as PCRDGGE. The presence of fungal species was investigated in wounds prior to HBOT and in two wounds at two points during HBOT. This study found that hydrogen peroxide, hypochlorous acid and peroxynitrite reduced the activity of penicillinase in vitro. Hypochlorous acid reduced the activity of a range of AHLs in vitro but not in vivo. Oxygen concentration did not have any impact on biofilm mass, nor did it significantly affect the ability of an oxidant-generating enzyme to reduce live bacterial cells within a biofilm. The population dynamics of bacterial species identified in all the wounds were complex and did not undergo identifiable changes during HBOT. Fungal species were identified in all wounds prior to HBOT, though different profiles were observed in the two wounds investigated during HBOT. These results suggest that oxidants could play a role in the attenuation of antibiotic resistance in chronic wound bacteria. It is unclear whether HBOT alters the population dynamics of non-healing wound microflora

Thesis (PhD)--Stellenbosch University, 2012. / ENGLISH ABSTRACT: see item for full text / AFRIKAANSE OPSOMMING: sien item vir volteks

The rehabilitation of degraded soils, such as those associated with post-mining sites, requires knowledge of the soil ecosystem and its physical, chemical, and biological composition in order for rehabilitation efforts to fulfil the long-term goal of reconstructing a stable ecosystem for rehabilitated mine soil. This study addresses the need for appropriate assessment criteria to determine the progress of rehabilitation and subsequently the success of management practices. Significant contributions made by this investigation included the establishment of minimum and maximum values for microbial community measurements from two case studies of rehabilitated coal discard sites. Furthermore, it was shown that there was no relationship between changes in microbial community function and structure and the rehabilitation age of the sites. Following this, the considerable impact of management practices on microbial communities was illustrated. The first part of the study investigated the temporal changes in microbial community function and structure in a chronosequence of rehabilitated coal discard sites aged 1 to 11 years. The most important observation made during the investigation of the microbial communities in the different aged soil covers of the rehabilitated coal discard sites, was that there was no relationship between rehabilitation age and microbial activity or abundance of certain microbial groups. What was responsible for a clear differentiation between sites and a shift in microbial community attributes was the management practices applied. A comparison of two chronosequences of rehabilitated coal discard sites was achieved by an application of the 'space-for-time' hypothesis. Sites of different ages and at separate locations ('space') were identified to obtain a chronosequence of ages ('time'). The two chronosequences included sites aged 1 to 11 years (chronosequence A) and 6 to 17 years (chronosequence B), respectively. Sites in the same chronosequence were managed identically, while there was a distinct difference in management practices applied to each chronosequence. The long-term effect of the different management regimes on the soil microbial community function and structure was investigated. Again, there was no relationship between rehabilitation age and microbial community measurements. Fluctuations of selected microbial properties occurred in both chronosequences and similar temporal trends existed over the rehabilitation periods. However, the less intensively managed chronosequence (8) seemed more stable (less fluctuation occurred) over the rehabilitation period than the more intensively managed chronosequence (A). It was therefore concluded that the microbial communities in the less managed sites maintained their functional and structural integrity within bounds in the absence of management inputs or disturbance. While there was similarity in the trends over time for individual microbial community measurements, the seemingly more stable conditions in chronosequence 6 are important in terms of the goal of rehabilitation. / Thesis (Ph.D. (Environmental Science)--North-West University, Potchefstroom Campus, 2007

<p>Microorganisms mediate many biogeochemical processes critical to the functioning of ecosystems, which places them as an intermediate between environmental change and the resulting ecosystem response. Yet, we have an incomplete understanding of these relationships, how to predict them, and when they are influential. Understanding these dynamics will inform ecological principles developed for macroorganisms and aid expectations for microbial responses to new gradients. To address this research goal, I used two studies of environmental gradients and a literature synthesis.</p><p>With the gradient studies, I assessed microbial community composition in stream biofilms across a gradient of alkaline mine drainage. I used multivariate approaches to examine changes in the non-eukaryote microbial community composition of taxa (chapter 2) and functional genes (chapter 3). I found that stream biofilms at sites receiving alkaline mine drainage had distinct community composition and also differed in the composition of functional gene groups compared with unmined reference sites. Compositional shifts were not dominated by groups that could benefit from mining associated increases of terminal electron acceptors; two-thirds of responsive taxa and functional gene groups were negatively associated with mining. The majority of subsidies and stressors (nitrate, sulfate, conductivity) had no consistent relationships with taxa or gene abundances. However, methane metabolism genes were less abundant at mined sites and there was a strong, positive correlation between selenate reductase gene abundance and mining-associated selenium. These results highlighted the potential for indirect factors to also play an important role in explaining compositional shifts.</p><p>In the fourth chapter, I synthesized studies that use environmental perturbations to explore microbial community structure and microbial process connections. I examined nine journals (2009–13) and found that many qualifying papers (112 of 148) documented structure and process responses, but few (38 of 112 papers) reported statistically testing for a link. Of these tested links, 75% were significant. No particular approach for characterizing structure or processes was more likely to produce significant links. Process responses were detected earlier on average than responses in structure. Together, the findings suggested that few publications report statistically testing structure-process links; but when tested, links often occurred yet shared few commonalities in linked processes or structures and the techniques used for measuring them. </p><p>Although the research community has made progress, much work remains to ensure that the vast and growing wealth of microbial informatics data is translated into useful ecological information. In part, this challenge can be approached through using hypotheses to guide analyses, but also by being open to opportunities for hypothesis generation. The results from my dissertation work advise that it is important to carefully interpret shifts in community composition in relation to abiotic characteristics and recommend considering ecological, thermodynamic, and kinetic principles to understand the properties governing community responses to environmental perturbation.</p> / Dissertation

Les activités anthropiques génèrent une contamination à de faibles doses des boues de station d'épuration par des micropolluants organiques persistants tels que les hydrocarbures aromatiques polycycliques (HAP), les polychlorobiphényles et le nonylphénol. Cette étude porte sur la détermination de l'influence des microorganismes au cours de la méthanisation sur le devenir de ces trois familles de micropolluants. Un protocole spécifique a été mis au point pour extraire des microorganismes de leur écosystème d'origine tout en conservant la singularité structurelle et fonctionnelle des communautés. Trois communautés, au passif de pollution différent, ont ainsi été soumises à la même pression de sélection (substrat et disponibilité en micropolluant) dans des bioréacteurs continus de méthanisation. Ces trois écosystèmes se sont alors distingués parfaitement via les caractéristiques de leurs communautés et la réalisation de fonctions diverses de digestion. Or, la dégradation des micropolluants a convergé dans ces 3 systèmes, démontrant l'absence de lien direct entre méthanogenèse et dégradation de ces molécules et une absence de spécialisation des communautés pour cette dégradation. En outre, il a été observé que la répartition des micropolluants au sein de la boue est influencée par les voies métaboliques des communautés. Plus le degré de digestion est avancé, plus les micropolluants sont abondants dans le compartiment aqueux et sorbés à la matière dissoute et colloïdale. Des fonctions, spécifiques de la dégradation des micropolluants, ont été étudiées (i) en suivant l'assimilation de phénanthrène marqué au 13C en culture batch, source principale de carbone, ce qui n'a pas permis d'observer sa minéralisation et (ii) en recherchant la présence de gènes fonctionnels ce qui n'a pas permis la détection des fonctions ciblée. Des activités œstrogéniques, androgéniques, dioxin-like et HAP-like, l'activité HAP-like est la plus exprimée dans les réacteurs à l'équilibre. Le degré de digestion, via une modification de la répartition des HAP, explique l'augmentation de l'activité HAP-like dans le compartiment aqueux des boues les plus digérées (et sa diminution dans le compartiment particulaire). L'activité HAP-like n'est pas entièrement expliquée par le dosage des HAP, ce qui suggère la présence d'intermédiaires métaboliques ayant une activité biologique et dont la nature différerait suivant le métabolisme exprimé par les communautés microbiennes. / Due to anthropogenic activity the sludge of wastewater treatment plants are contaminated by organic micropollutants like polycyclic aromatic hydrocarbons (PAH), polychlorinated biphenyls and nonylphenol. This study focuses on the influence of microbial communities on the fate of these three micropollutant families during the anaerobic digestion process. A specific protocol was developed to extract microorganisms from their native ecosystem while maintaining their structural and functional singularity. Three communities, with different pollution history, were thus extracted and subjected to the same selection pressure (availability of substrate and micropollutant) in continuous anaerobic digesters. These three ecosystems can be perfectly identified through the characteristics of their microbial communities and their global metabolism. However, our results show also that the degradation of micropollutant converged in these 3 systems, demonstrating no direct link between methanogenesis and micropollutant degradation and no specialization of the microbial communities toward this degradation. In addition, the distribution of micropollutants in sludge is influenced by the metabolic pathways of those communities. The more the digestion is advanced, the greater the micropollutants are abundant in the aqueous compartment and adsorbed to the dissolved and colloidal matter. Specific functions for micropollutant degradation were studied (i) by following the 13C-labeled phenanthrene assimilation as main carbon source, which did not allow observing its mineralization and (ii) by exploring the presence of functional genes, which did not allow the detection of the targeted functions. Among the estrogenic, androgenic, dioxin-like and PAH-like activities, PAH-like activity is more expressed in all reactors at the steady state. The different degrees of digestion, through a change in PAH distribution, explain the increase in PAH-like activity in the aqueous compartment of the most digested sludge (and its decrease in the particulate compartment). PAH-like activity is not fully explained by PAH quantification, suggesting the presence of by-products with biological activity and which could be different depending on the metabolic pathway of the microbial communities.

Through complex metabolic interactions aquatic microbial life is essential as a driver of ecosystem functions and hence a prerequisite for sustaining plant and animal life in the sea and on Earth. Despite its ecological importance, infor­mation on the complexity of microbial functions and how these are related to environmental conditions is limited. Due to climate change and eutrophication, marine areas facing oxygen depletion are increasing and predicted to continue to do so in the future. Vertically steep oxygen gradients are particularly pronoun­ced in the Baltic Sea. In this thesis, therefore, the ecosystem functions of micro­bial communities were investigated, using metagenomics, to understand how they were distributed along the steep oxygen gradient at the Landsort Deep, the deepest point of the Baltic Sea. Furthermore, microbial communities from the Lands­ort Deep transect were compared to microbial communities of other marine environments to establish whether the environment at this site resulted in a characteristic community. To reveal what microbial community functions and taxa were active in the anoxic sediment a metatranscriptomic approach was used. Results showed a marked effect of the coupled environmental parameters dissolved oxygen, salinity and temperature on distribution of taxa and par­ti­cularly community functions. Microbial communities showed functional capa­cities consistent with a copiotrophic life-style dependent on organic ma­terial sinking through the water column. The eutrophic condition with high organic load was further reflected in the metatranscriptome of the anoxic sedi­ment com­munity, which indicated active carbon mineralisation through ana­erobic hetero­trophic-autotrophic community synergism. New putative linkages between nitro­gen and- sulphur metabolisms were identified at anoxic depths. Further­more, viable Cyanobacteria in the anoxic sediment was evident from the tran­script analyses as another reflection of marine snow. High abundance and expres­­sion of integron integrases were identified as a charac­teristic feature of the Lands­ort Deep communities, and may provide these communities with a mech­an­ism for short-term-adaptation to environmental change. In summary, this thesis clearly documents what impact eutrophication and oxygen depletion have on microbial community functions. Furthermore, it specifically advances the mechanistic insight into microbial processes in anoxic deep-water sediment at both genomic and transcriptional level. Given the predicted progress of oxygen depletion in marine and brackish environments, this work advances information necessary to estimate effects on marine and in particular brackish ecosystem functions where anoxic conditions prevail. / Mikroorganismer är essentiella för fungerande ekosystemfunktioner i akvatiska miljöer och därmed en förutsättning för övrigt växt- och djurliv på vår planet. Trots deras ekologiska nyckelroll är kunskapen om mikroorganismernas funk­tion och komplexitet samt hur dessa är relaterade till miljön begränsad. På grund av eutrofiering och klimatförändringar har marina områden som lider av syrebrist ökat och en ytterligare utbredning av marina och bräckta områden med syrebrist är predicerad i framtiden. Stora områden av Östersjön kännetecknas av vertikala syregradienter med syresatt ytvatten och anoxiskt bottenvatten. I denna avhandling undersöktes därför med metagenomik hur mikrobiella ekosystems funktioner var utbredda längs den vertikala syregradienten i Östersjöns djupaste del, Landsortsdjupet. Dessutom jämfördes de mikrobiella samhällena från Lands­­­ortsdjupet med mikrobiella samhällen från andra marina miljöer för att utröna om den karakteristiska miljön i Landsortsdjupet återspeglade de mikro­biella samhällen som lever där. För att undersöka vilka mikroorganismer samt vilka mikrobiella ekosystemfunktioner som var aktiva i det anoxiska sedimentet i Lands­ortsdjupet användes metatranskriptomik. Resultaten visade en stark kor­re­lation mellan miljöparametrarna syrehalt, salinitet och temperatur och för­del­ningen av mikrobiell taxa och i synnerhet mikrobiell funktion längs Lands­orts­djupets transekt. De mikrobiella samhällena uppvisade en funktionell kapa­citet förenlig med en livsstrategi beroende av organiskt material som sjunker genom vattenkolonnen som en konsekvens av eutrofiering. Eutrofa förhållanden med hög halt av organiskt material var även återspeglad i metatranskriptomet från det anoxiska sedimentet, som indikerade aktiv mineralisering av organiskt kol genom anaerob heterotrof-autotrof synergism. Nya möjliga kopplingar mellan kväve- och svavelmetabolism identifierades i det anoxiska vattnet. Vidare visade resultat från metatranskriptom-analys att livsdugliga cyanobakterier var abun­danta i det mörka och anoxiska sedimentet, vilket även detta kan vara en konse­kvens av sjunkande organiskt material. Hög abundans och hög transkribering av integrongener kunde identifieras som ett karakteristiskt kännetecken hos de mikro­biella samhällena i Landsortsdjupet vilket skulle kunna förse dem med en me­kanism för anpassning till miljöförändringar. Sammanfattningsvis dokumen­terar denna avhandling tydligt vilken påverkan eutrofiering och syrebrist har på mikrobiella funktioner. Dessutom för den specifikt kunskapen om mikrobiella processer i anoxiska djupvattensediment framåt på både genom- och transkrip­tions­nivå. Mot bakgrund av en predicerad ökning av syrebristen i marina mil­jöer, bidrar denna avhandling med information som är viktig för att kunna förutse vilka effekter anoxiska förhållanden kan komma att få på ekosystemfunktioner i marina miljöer och i brackvattenmiljöer i synnerhet.

L’anthropisation est la principale source de perturbations dans les grottes, et dans la grotte de Lascaux cela a entrainé la prolifération de microorganismes et des altérations de paroi menaçant sa conservation. L’objectif de cette thèse était de mieux comprendre l’écologie des microorganismes colonisant la grotte de Lascaux, en identifiant sa communauté microbienne à différentes échelles spatio-temporelles, de caractériser les facteurs qui structurent cette communauté et d’en étudier la dynamique fonctionnelle en utilisant le séquençage à haut débit d’acides nucléiques, une nouvelle approche à Lascaux. Une comparaison à l’échelle régionale de différentes grottes de Dordogne, plus ou moins anthropisées a été réalisée, puis à une échelle locale avec l’étude de salles de Lascaux, le Passage pour évaluer le rôle des substrats minéraux, et l’Abside qui présente deux types d’altérations (taches noires et zones sombres). Nos résultats montrent que les grottes anthropisées (dont Lascaux) ont des communautés microbiennes particulières. Le substrat minéral structure davantage la communauté du Passage que la présence de taches. Dans l’Abside, bien que les zones sombres soient visuellement différentes des taches noires, les communautés microbiennes présentent des similarités fortes, et notamment le rôle des interactions entre les collemboles, les champignons noirs et des bactéries. Enfin, les profils métatranscriptomiques diffèrent en fonction des salles et de la présence de taches. Ce projet a permis de caractériser l’écologie de la communauté microbienne de Lascaux et permet de mieux comprendre le fonctionnement microbien de la grotte / Anthropisation is the main source of disturbance in the caves, and in the cave of Lascaux it has led to the proliferation of microorganisms and alterations of the wall threatening its conservation.The objective of this thesis was to better understand the ecology of microorganisms colonizing the cave of Lascaux, by identifying its microbial community at different spatio-temporal scales, to characterize the factors that structure this community and to study its functional dynamics in using high throughput sequencing of nucleic acids, a new approach to Lascaux.A regional comparison of different Dordogne caves, more or less anthropised was carried out, then at a local scale with the study of Lascaux rooms, the Passage to evaluate the role of mineral substrates, and the Apse which presents two types of alterations (black spots and dark areas).Our results show that anthropogenic caves (including Lascaux) have particular microbial communities. The mineral substrate structures the Passage community more than the presence of spots. In the Apse, although dark areas are visually different from black spots, microbial communities show strong similarities, including the role of interactions between collembolans, black fungi, and bacteria. Finally, the metatranscriptomic profiles differ according to the rooms and the presence of spots.This project has made it possible to characterize the ecology of the Lascaux microbial community and to better understand the microbial functioning of the cave

A utilização de técnicas moleculares têm facilitado o estudo de comunidades bacterianas complexas no ambiente. O presente trabalho teve como objetivo utilizar a técnica DGGE para avaliação dos efeitos do aumento da temperatura, causado pela queima de um canavial, na estrutura da comunidade bacteriana de solo, com ênfase ao grupo dos actinomicetos. Foram coletadas amostras de solo em diferentes profundidades, antes e depois da queima, e dados físico-químicos e climáticos associados. O DNA da comunidade bacteriana foi amplificado utilizando conjunto de primers específicos para o Domínio Bacteria e para o grupo de actinomicetos, e os produtos de amplificação analisados por DGGE. Resultados obtidos para as populações de actinomicetos não foram conclusivos. Apesar da variação dos parâmetros físico-químicos do solo provocadas pela queima, os padrões de bandas obtidos com os primers para o Domínio Bacteria, apresentaram-se uniformes. Sendo assim, nas condições de estudo deste trabalho, os resultados obtidos não revelaram alterações na estrutura da comunidade bacteriana do solo de canavial depois da queima. / The utilization of molecular techniques has facilitated the study of complex bacterial communities in the environment. The present study aimed at using DGGE technique to evaluate the effect of temperature variation, caused by sugar-cane plantation burn, in the soil bacterial community structure emphasizing the actinomycete group. Soil samples from different depths, were collected before and after the bum, as well as physical-chemical and climatic associated data. The bacterial community DNA was amplified using a specific primer set and the amplification products analyzed by DGGE. The results obtained for the actinomycete populations were not conclusive. Despite the variation of the soil parameters caused by the burn, the band patterns obtained used in this study were uniform. Therefore, under the conditions used in this study, the results obtained did not show any alteration in the structure of soil bacterial community associated with sugar-cane plantation after the burn.