Genome evolution is not always shaped by a Darwinian-fashion of vertical inheritance from ancestral lineages. The historical gene content of a species contains many atypical gene sequences showing high similarity to those of distantly related taxa. This evolutionary phenomenon is referred to as lateral gene transfer (LGT). Lateral gene transfer permits the exchange of genetic material across lineages, completely ignoring any concept of taxonomic boundary. The rapid acquisition of foreign genes into bacterial genomes has greatly obscured the historical phylogeny of prokaryotes. In this thesis we calculate the rate of LGT on a Bacillaceae phylogeny, to determine the extent to which it controls species evolution. First, we examined the evolution of the phylogeny according to a simple model of maximum likelihood. We assume equal rates of gene insertion and deletion on the phylogeny and show high rates of evolution in the genomes of B. anthracis, B. cereus, and B. thuringiensis (Bc group), representative of adaptive evolution. We then improved the model to account for differential rates of gene insertion and deletion, thus offering a more realistic model of gene evolution. Again, we demonstrate that members of the Bc group are rapidly evolving, with the rate of gene insertion being significantly higher than the rated of gene deletion. Finally, we evaluate the sole effect of LGT on the phylogeny in a simple birth-death analysis with immigration. We show that LGT is the main vehicle of gene acquisition when the number of gene families substantially increases from external taxa to members of the Bc group. Collectively, our findings suggest that the Bacillaceae genome is rapidly expanding, and that laterally transferred genes may facilitate adaptive evolution and subsistence in a new niche. / Thesis / Master of Science (MSc)

The Malacothamnus alliance consists of three genera, Iliamna, Malacothamnus, and Phymosia. The genera are considered taxonomically complex since hybridization freely occurs, polyploidy levels vary, and there is a lack of distinct morphological characters to delineate taxa. Several taxonomic treatments have been prepared for each genus, but relationships within the genera and the relationship of the Malacothamnus alliance to others in the Malvaceae remains unknown. This multifaceted study aimed to (a) examine the monophyly of the Malacothamnus alliance and its position in the Malvaceae, (b) determine the relationships between genera in the alliance, (c) compare variation of nuclear and chloroplast genes in the alliance, (d) prepare revised taxonomic treatments for Iliamna and Malacothamnus, and (e) examine the probability of successful hybridization in Iliamna. The monophyly of the Malacothamnus alliance was not confirmed using DNA sequences of both nuclear and chloroplast regions. In Iliamna, little sequence variation was detected among taxa in the Rocky Mountains; however, the nuclear and chloroplast regions conflicted with regard to the relationships of the western and eastern taxa. An ancestral copy of the chloroplast genome is shared between the two eastern U.S. Iliamna species and Phymosia (Bahamas and Mexico). The nuclear ITS sequences indicated the western U.S. Iliamna species were more closely related to Phymosia and Malacothamnus than to other species in Iliamna. Neither data set provided sufficient variation to resolve relationships of species in Malacothamnus. Genetic variation and the feasibility of hybridization in Iliamna supported the results of the broader phylogenetic studies. Iliamna corei and I. remota are recently derived from I. rivularis. Hybrid offspring of I. corei and I. remota had higher viability and fecundity than did hybrids between crosses of either species and I. rivularis. The Virginia populations of I. corei and I. remota are more genetically similar than either is to Illinois populations of I. remota. However, the species are morphologically distinct and can easily be distinguished from others in the genus. Revised taxonomic treatments for Iliamna and Malacothamnus based on surveys of herbarium material are presented. Taxonomic revisions include the new combinations of Iliamna grandiflora subsp. grandiflora and I. grandiflora supsp. crandallii and the resurrection of Malacothamnus hallii and M. orbiculatus. / Ph. D.

Headwaters are crucial linkages between upland ecosystems and navigable waterways, serving as important sources of water, sediment, energy, nutrients and invertebrate prey for downstream ecosystems. Surface coal mining in central Appalachia impacts headwaters by burying streams and introducing pollutants to remaining streams including excessive sediments, trace elements, and salinity. Benthic macroinvertebrates are widely used as indicators of biological conditions of streams and are frequently sampled using semi-quantitative methods that preclude calculations of areal densities. Studies of central Appalachian mining impacts in non-acidic streams often focus on biotic effects of salinity, but other types of pollution and habitat alteration can potentially affect benthic macroinvertebrate community (BMC) structure and perhaps related functions of headwater streams. Objectives were: 1) use quantitative sampling and enumeration to determine how density, richness, and composition of BMCs in non-acidic central Appalachian headwaters respond to elevated salinity caused by coal surface mining, and 2) determine if BMC structural differences among study streams may be attributed to habitat and water-quality effects in addition to elevated salinity. I analyzed BMC structure, specific conductance (SC, surrogate measure of salinity), and habitat-feature data collected from 15 streams, each visited multiple times during 2013-2014. BMC structure changed across seasonal samples. Total benthic macroinvertebrate densities did not appear to be impacted by SC during any months, but reduced densities of SC-sensitive taxa were offset by increased densities of SC-tolerant taxa in high-SC streams. Total richness also declined with increasing SC, whereas BMCs in high-SC streams were simplified and dominated by a few SC-tolerant taxa. Taxonomic replacement was detected in high-SC streams for groups of benthic macroinvertebrates that did not exhibit density or richness response, showing that taxonomic replacement could be a valuable tool for detecting BMC changes that are not evident from analyses using conventional metrics. Specific conductance, water-column selenium concentration, large-cobble-to-fines ratio of stream substrate, and relative bed stability were associated with changes in BMC structure. These results suggest multiple stressors are influencing BMCs in mining-influenced Appalachian streams. These findings can inform future management of headwater streams influenced by mining in central Appalachia. / Ph. D.

Thesis (MScAgric)--Stellenbosch University, 2013. / ENGLISH ABSTRACT: Cydia pomonella (codling moth), Thaumatotibia leucotreta (False codling moth), Thaumatotibia batrachopa (Macadamia nut borer), Grapholita molesta (Oriental fruit moth), Cryptophlebia peltastica (Litchi moth), Epichoristodes acerbella (Pear leafroller/Carnation worm) and Lozotaenia capensana (Apple leafroller) are the most economically important tortricids affecting various crops in South Africa. The correct identification of these species, especially of the larval stage, is of great importance in pest management. Using available literature, augmented by additional morphological studies, an interactive identification key (Lucid key) for larval and adult stages of the seven species was developed. The colour and markings of the head, characteristics of the prothoracic and anal shields, the position of the prespiracular setae (L-group) relative to the spiracle on the prothoracic segment, the position of the spiracle on the eighth abdominal segment and L-group on the ninth abdominal segment, as well as the presence or absence of the anal comb are key characteristics for larval identification. For adult identification, wing pattern and genitalia are the most important features. However, the use of genitalia for moth identification might be difficult for the lay user, as the dissection and mounting of these structures requires certain skills and specialized equipment. Thus, genitalia have not been included in the Lucid Key. Differences in the morphological characteristics of most pupae were so minute that this stage was also not included in the Lucid key. However, the pupae of E. acerbella and L. capensana are easily distinguished from those of the other species by the presence of acremaster. This study also included the first morphological description of the pupa of L. capensana, which can be distinguished from that of E. acerbella by various features of the cremaster, antennae, spiracle shape, number of setae on abdominal segments A5-7, the size of spines on A3-7, and the presence/absence of spines on A9. A previous study by Timm (2005) indicated that geographically isolated populations of T. leucotreta tend to be genetically distinct. This raised the question of whether speciation/subspeciation has occurred or is occurring. Male moth genitalia are thought to evolve rapidly and are often the only features that can reliably distinguish similar species. Hence, variation in the shape of the valvae of T. leucotreta was used to determine whether divergence has occurred between populations of T. leucotreta. Elliptical Fourier analysis was used to analyze the valvar variation in three different populations. Although some variation in valvar shape was detected among mean population values for certain traits, no clear pattern emerged. Principle component analysis also showed no distinct clustering of valvae shape among populations, providing no evidence for divergence in male genitalia and therefore no morphological evidence of incipient speciation. / AFRIKAANSE OPSOMMING: Cydia pomonella (Kodlingmot), Thaumatotibia leucotreta (Valskodlingmot), T. batrachopa (Makadamianeutboorder), Grapholita molesta (Oosterse vrugtemot), Cryptophlebia peltastica (Lietsjiemot), Epichoristodes acerbella (Peerbladroller/Angelierrusper) en Lozotaenia capensana (Appelbladroller) is die mees ekonomies belangrike tortrisiede van die vrugtebedryf in Suid-Afrika. Die juiste identifikasie van hierdie spesies, veral van hulle larwale stadium, is van groot belang by plaagbestuur. Deur gebruik te maak van beskikbare literatuur, aangevul deur bykomstige morfologiese studies, is ‗n interaktiewe uitkenningssleutel (―Lucid key‖) vir die larwale en volwasse stadia van die sewe spesies ontwikkel. Die kleur en tekening van die kop, kenmerke van die prothorakale en anale skild, die ligging van die prespirakulêre setae (L-groep) relatief tot die spiraculum op die prothorakale segment, die ligging van die spirakulum op die agste abdominale segment en L-groep op die negende abdominale segment, asook die aan- of afwesigheid van die anale kam is sleutel kenmerke vir larwale uitkenning. Vir die volwassenes is die vlerktekening en genitalia die mees belangrike kenmerke. Die gebruik van die genitalia vir motuitkenning kan egter vir die leek gebruiker moeilik wees omdat die disseksie en montering van hierdie strukture bepaalde vaardighede en gespesialiseerde toerusting vereis. Vir die rede is die genitalia nie in die Lucid-sleutel ingesluit nie. Verskille in die morfologiese kenmerke van meeste papies is klein en die stadium is gevolglik ook nie in die sleutel ingesluit nie. Die papies van E. acerbella en L. capensana kan egter maklik van die ander spesies onderskei word deur die aanwesigheid van ‗n cremaster. Hierdie studie sluit ook die eerste morfologiese beskrywing van die papie van L. capensana in, wat van dié van E. acerbella onderskei kan word deur gebruik te maak van kenmerke van die cremaster, antennae, spirakulêre vorm, aantal setae op abdominale segmente A5-7, die grootte van stekels op A3-7, en die aan- of afwesigheid van stekels op A9. ‗n Vroeëre studie (Timm 2005) het aangedui dat geografies geïsoleerde bevolkings van T. leucotreta neig om geneties verskillend te wees. Dit het die vraag laat ontstaan of spesiasie/subspesiasie moontlik plaasgevind het of steeds plaasvind. Manlike mot genitalië word geag om vinnig te ontwikkel en is dikwels die enigste kenmerke wat betroubaar tussen soortgelyke spesies kan onderskei. Dus is die variasie in die vorm van die valvae van T. leucotreta gebruik om te bepaal of divergensie wel tussen bevolkings van T. leucotreta plaasgevind het. Elliptiese Fourier ontleding is gebruik om die valvae se variasie by drie verskillende bevolkings te ontleed. Alhoewel enkele variasie in die vorm van die valvae bespeur is by die gemiddelde bevolkingswaardes vir bepaalde eienskappe, kon geen duidelike patroon bespeur word nie. Hoofkomponentontleding het ook geen duidelike groepering van valvae se vorm tussen bevolkings getoon nie, wat geen bewys lewer van divergensie in die manlike genitalia en dus geen morfologiese bewys van beginnende spesiasie.

Background: Taxonomic descriptions are traditionally composed in natural language and published in a format that cannot be directly used by computers. The Exploring Taxon Concepts (ETC) project has been developing a set of web-based software tools that convert morphological descriptions published in telegraphic style to character data that can be reused and repurposed. This paper introduces the first semi-automated pipeline, to our knowledge, that converts morphological descriptions into taxon-character matrices to support systematics and evolutionary biology research. We then demonstrate and evaluate the use of the ETC Input Creation - Text Capture - Matrix Generation pipeline to generate body part measurement matrices from a set of 188 spider morphological descriptions and report the findings. Results: From the given set of spider taxonomic publications, two versions of input (original and normalized) were generated and used by the ETC Text Capture and ETC Matrix Generation tools. The tools produced two corresponding spider body part measurement matrices, and the matrix from the normalized input was found to be much more similar to a gold standard matrix hand-curated by the scientist co-authors. Special conventions utilized in the original descriptions (e.g., the omission of measurement units) were attributed to the lower performance of using the original input. The results show that simple normalization of the description text greatly increased the quality of the machine-generated matrix and reduced edit effort. The machine-generated matrix also helped identify issues in the gold standard matrix. Conclusions: ETC Text Capture and ETC Matrix Generation are low-barrier and effective tools for extracting measurement values from spider taxonomic descriptions and are more effective when the descriptions are self-contained. Special conventions that make the description text less self contained challenge automated extraction of data from biodiversity descriptions and hinder the automated reuse of the published knowledge. The tools will be updated to support new requirements revealed in this case study.

Les sols pollués par des métaux lourds sont colonisés par des communautés de microorganismes qui ont développé différentes adaptations leur permettant de résister à ces contaminants. Afin d'analyser au niveau moléculaire la diversité de ces adaptations, une approche expérimentale innovante basée sur l'étude du méta transcriptome eucaryote des sols a été utilisée pour comparer les fonctions exprimées au sein d'une communauté de microorganismes eucaryotes colonisant un sol contaminé, anciennement contaminé et non contaminé par des métaux lourds. Les banques d’ADNc eucaryotes construites à partir des ARNm extraits directement de ces sols ont été criblées par séquençage aléatoire de leurs inserts et par complémentation fonctionnelle de mutants de levures sensibles au cadmium.Cette étude a permis d’identifier de nouveaux gènes et de nouveaux mécanismes impliqués dans la résistance au cadmium ainsi qu’un nombre important de nouvelles protéines hypothétiques. Ceci démontre l’intérêt appliqué de cette approche pour la recherche de nouveaux bio catalyseurs et molécules bio actives.En parallèle, la diversité microbienne eucaryote a été révélée et comparée entre les sols par le clonage-séquençage du gène codant la petite sous-unité ribosomique 18S. Cette étude a mis en évidence une diversité inattendue de microorganismes eucaryotes dans ces sols et une analyse phylogénétique a permis de découvrir un nouveau clade de protistes (Rhizaria,Cercozoa). / Heavy metal-polluted soils are colonised by microbial communities which have developed different adaptations that allow them to resist to these pollutants. The objectives of this study were to reveal at the molecular level the diversity of these adaptations. To this aim,we implemented an innovative approach based upon the analysis of soil eukaryotic metatranscriptome to compare resistance mechanisms expressed by eukaryotic microorganisms living in heavy metal contaminated and control non contaminated or formerly-contaminated soils. Eukaryotic cDNA libraries were prepared using mRNA directly extracted from these soils and screened by either systematic sequencing of their inserts or functional complementation of yeast mutants sensitive to cadmium. This study allowed us to characterise novel genes and mechanisms implicated in Cd resistance as well as numerousnovel hypothetical proteins. This study also demonstrates the potential of this experimental approach to look for novel biocatalysts as well as novel bio-active molecules.In addition, eukaryotic molecular diversity was studied by the cloning-sequencing of the gene encoding the 18S ribosomal RNA. This study revealed an unexpected diversity of eukaryotic diversity in the studied soils and allowed us to discover a novel clade of protists(Rhizaria, Cercozoa).

Bombyliidae é uma das maiores famílias de Diptera com mais de 4822 espécies descritas ao redor do mundo, divididas em 16 subfamílias e 18 tribos. A tribo Exoprosopini dividem-se em 11 gêneros, dos quais Exoprosopa e Ligyra tem distribuição cosmopolita. O gênero Ligyra Newman s.l. objeto deste estudo, possui 109 espécies, das quais 20 têm sido descritas no Novo Mundo. Uma revisão taxonômica das espécies neárticas e neotropicais de Ligyra é feita no presente estudo, incluindo redescrições e registros fotográficos das mesmas. Após a revisão taxonômica, quatro espécies foram sinonimizadas (L. fenestella syn. nov. e L. maracaensis syn. nov. são consideradas sinônimos júnior de Gen. nov. harpyia; L. guerinii syn. nov. foi considerado sinônimo júnior de Gen. nov. latreilli; L. klugii syn. nov. foi considerado sinônimo júnior de Gen. nov. proserpina e a subespécie Ligyra cerberus trifigurata foi considerada sinônimo júnior de Gen. nov. cerberus). Uma chave para identificação destas espécies, baseada em caracteres morfológicos diagnósticos, de fácil observação, também é apresentada. Além da revisão taxonômica uma análise cladística de Ligyra no Novo Mundo foi feita a fim de testar se essas espécies, que atualmente estão incluídas no gênero, pertencem, de fato, a este grupo ou se precisam ser realocadas em algum outro gênero de Exoprosopini ou ainda em um novo gênero. Para tal, neste estudo foi utilizada uma matriz de caracteres morfológicos disponível em literatura, que já vem sendo utilizada para inferir a filogenia dos Exoprosopini. A análise cladística contou com 92 táxons terminais e 207 caracteres morfológicos obtendo-se como resultado, após análise com algoritmos de novas tecnologias a partir do software TNT, 12 árvores mais parcimoniosas cujo consenso estrito possui L=3089, CI: 15 e RI: 49. Os resultados apontam que Ligyra s.l. forma um grupo monofilético composto pelos gêneros: Ligyra s. str. (spp. Australianas), Euligyra (spp. Afrotropicais) e Gênero novo (spp. do Novo Mundo). As espécies de Ligyra s.l. no Novo Mundo foram realocadas em um gênero novo suportado por uma sinapomorfia e quatro homoplasias. / Bombyliidae is one of the largest families of Diptera with more than 4800 species, known worldwide, divided in 16 subfamilies and 18 tribes. The tribe Exoprosopini is divided into 11 genera, of which Exoprosopa Macquart and Ligyra Newman has cosmopolitan distribution. The genus Ligyra s.l., main subject of this study, has 109 species, of which 20 were described to the New World. A taxonomic review of the Nearctic and Neotropical species of Ligyra is implemented in this study, including redescription and photographic records of them. After the taxonomic review, four species were synonymized (L. fenestella syn. nov.and L. maracaensis syn. nov. are considered junior synonym of Gen. nov. harpyia; L. guerinii syn. nov. is considered junior synonym of Gen. nov. latreilli; L. klugii syn. nov .is considered junior synonym of Gen. nov. proserpina and the subspecies Ligyra Cerberus trifigurata is considered junior synonym of Gen. nov. cerberus). An identification key for these species, based on morphological diagnostic characters, easily seen, is also presented. Besides the taxonomic revision a cladistics analysis of the New Worlds Ligyra is implemented in order to test whether these species, which are currently included in the genus, belong, in fact, to this group or if they need to be relocated at some other genus of Exoprosopini or even to a new genus. For this purpose, we used a matrix of morphological characters available in the literature, which is already being used to infer the phylogeny of Exoprosopini. The cladistic analysis included 92 terminal taxa and 207 morphological characters. After analysis with algorithms of new technologies from the software TNT, 12 more parsimonious trees, whose strict consensus has L = 3089, CI 15 and RI: 49, are obtained. The results show that Ligyra s.l. constitutes a monophyletic group composed by the following genera: Ligyra s. str. (Australian spp.), Euligyra (Afrotropical spp.) and New Genus (New World spp.). The species of Ligyra s.l. in the New World are relocated into a new genus, which monophyly is supported by one synapomorphy and four homoplasies.

Entre os múltiplos grupos que compõem as Seções Spissipes e Melanoconion do subgênero Melanoconion de Culex, Atratus e Educator apresentam espécies que estão envolvidas na transmissão de arbovírus ao ser humano e animais em ambientes rurais e silvestres. Porém, esses grupos exibem grande dificuldade na identificação das espécies, seja devido à grande semelhança morfológica entre seus representantes ou à falta de chaves de identificação atualizadas. Diante disso, objetivou-se realizar a revisão taxonômica das espécies pertencentes aos Grupos Atratus e Educator da Seção Melanoconion de Culex (Melanoconion). Para isso, foi realizado o estudo morfológico detalhado das diversas fases de desenvolvimento dos espécimes de interesse, verificada a existência de espécies a serem nomeadas e/ou espécies válidas colocadas na sinonímia de outras. Como resultado do estudo morfológico das espécies do Grupo Atratus, foram redefinidas oito espécies. Destas, duas foram validadas, pois estavam na sinonímia de outras e seis espécies desconhecidas da ciência foram descritas e serão formalmente nomeadas. Para o Grupo Educator, oito espécies foram descritas, sendo uma removida da sinonímia e três espécies desconhecidas da ciência foram descritas e serão formalmente nomeadas. Chaves de identificação ilustradas, com caracteres usados para o reconhecimento das espécies, foram elaboradas para todas as formas de desenvolvimento das espécies de ambos os grupos. Foram construídos mapas de distribuição geográfica das espécies, foram atualizados dados bionômicos, elaboradas ilustrações e pranchas fotográficas para comparação de estruturas morfológicas externas das formas imaturas, adultos e genitália masculina. / Among the multiple groups that compose the Spissipes and Melanoconion Sections of the subgenus Melanoconion of Culex, the Atratus and Educator Groups present species that are involved in the transmission of arboviruses to man and animals in rural and wild environments. However, these groups present great difficulty in identifying the species, either because of the great morphological similarity between their representatives or the lack of updated identification keys. The aim of this study was to carry out a taxonomic review of the species belonging to the Atratus and Educator Groups of the Melanoconion Section of Culex (Melanoconion). Therefore, a detailed morphological study of the several stages of development of the specimens of interest was carried out, verifying the existence of species to be named and/or valid species placed in the synonymy of others. As a result of the morphological study of the Atratus Group species, eight species were redefined. Of these, two were resurrected from the synonymy of others and six species unknown to science were described and will be formally named. For the Educator Group, eight species have been described, one being removed from the synonymy and three species unknown to science have been described and will be formally named. Illustrated identification keys, with characters used for species recognition, have been created for all forms of development of species in both Groups. Geographic distribution maps of the species were created, illustrations and photographic plates for comparison of external morphological structures of the immatures forms, adults and male genitalia were provided, and bionomic data were updated.

Este trabalho trata da revisão taxonômica das espécies de Morion do Continente Americano (M. arida, M. boliviensis, M. brasiliensis, M. cordata, M. costigera, M. cycloma, M. lafertii, M. monilicornis e M. simplex), sendo que apenas uma não ocorre na região Neotropical (M. monilicornis). Foi realizado um estudo morfológico detalhado de todas as espécies, visando encontrar novos caracteres diagnósticos para testar a hipótese taxonômica vigente e para facilitar a identificação das espécies. Não foram identificadas espécies novas e as nove spécies mostraram-se válidas. A análise de novas estruturas, além de revelar características antes não estudadas (como braquipteria em M. brasiliensis) deu mais robustez à hipótese existente. Também foram confeccionados mapas de distribuição geográfica de todas as espécies, o que revelou que algumas apresentam distribuição bastante restrita (principalmente as espécies braquípteras), enquanto outras têm uma distribuição bastante ampla. Uma chave dicotômica para a identificação das espécies foi preparada, visando facilitar a identificação das mesmas. / This study is a taxonomic revision of the New World Morion, which has nine valid species (M. arida, M. boliviensis, M. brasiliensis, M. cordata, M. costigera, M. ycloma, M. lafertii, M. monilicornis and M. simplex), of which, only one of them is not recorded in the Neotropical region (M. monilicornis). A detailed morphological study was done aiming for finding out new diagnostic characteristics in order to test the current taxonomic hypothesis and to make specific identification easier. These nine species were analyzed and remained valid; no new one was found. The analysis of new structures made it possible to find some characters never studied before (e.g., M. brasiliensis brachyptery) and strengthened the previous hypothesis. The maps representing the geographic distribution of all species revealed that some of them have a limited area of occurrence (mainly the flightless species), although others are widespread. A dichotomic identification key was also done to facilitate species identification.

Atividades humanas podem causar degradação e impedir que serviços ambientais cheguem á sociedade. Evitá-la demanda constante monitoramento, que pode ser realizado com indicadores ambientais. Buscamos selecionar indicadores da exploração de petróleo nas comunidades microbianas de riachos da Amazônia, Mata Atlântica, Cerrado e Caatinga. Avaliamos as diversidades taxonômica (Sequenciamento 16S) e funcional (GeoChip 5.0M) e comparamos os resultados de amostras de água, sedimento, biofilme e solo das margens de riachos influenciados por campos de petróleo com áreas de referência. Todas as estações apresentaram alta riqueza, baixa similaridade taxonômica e alta similaridade funcional. Impactos da atividade de exploração de petróleo foram relacionados ao uso do solo e não à contaminação por hidrocarbonetos, já que as estações não tinham histórico de vazamentos. Os indicadores identificados não foram atreldos a grupos taxonômicos ou atividades metabólicas específicas, sendo mais promissora a utilização de um conceito baseado em sequencias genéticas indicadoras. / Human activities can cause degradation and prevent environmental services from reaching society. Avoid it demand constant monitoring, which can be carried out with environmental indicators. We sought to select indicators of oil exploration in the microbial communities of streams in the Amazon, Atlantic Forest, Cerrado and Caatinga morphoclimatic domains. We evaluated taxonomic (16S Sequencing) and functional (GeoChip 5.0M) diversity and compared the results from water, sediment, biofilm and soil (from the margins of streams) samples influenced by oil fields with reference areas. All of them presented high richness, low taxonomic similarity and high functional similarity. Impacts of the oil exploration activity are related to the use of soil and not to hydrocarbon contamination, since the sampling stations we choose are historically not affected by oil spills. The indicators we identified are not related to taxonomic groups or specific metabolic activities, and the use of a concept based on indicator sequences is more promising.