In recent years there has been a desire to definitively catalogue the life on our planet. In light of the increasing extinction rates that are driven by human activities, it is unlikely that this will be achieved using traditional methods. Whilst most organisms which have a body size of more than 1cm have been described, the vast majority of animal life is smaller than this, collectively known as meiofauna, and is yet to be catalogued. Meiofaunal organisms present a range of problems for traditional taxonomy. Firstly they are microscopic, meaning that morphological features are often difficult to resolve. Secondly these creatures often exhibit cryptic diversity meaning that different species often look the same. Thirdly, it is often the case that the organisms are poorly described in the literature making it very difficult to confirm identification, assuming that someone has already described it. It is possible, however, to obtain DNA sequences from these organisms. DNA barcoding, the use of short sequences of DNA to identify individuals, is now commonly used in a wide range of applications. It has been proposed that a single target gene should be sufficient to describe all organisms this way. Barcodes can be acquired from individuals or from bulk extractions from environmental samples. In the latter case, many of the sequences obtained are novel and unlikely to ever have a type specimen associated with them. When this is the case, assessing the diversity of a sample becomes a computational exercise. However, as yet, there is no agreed standard method adopted for analyzing the barcodes produced. Indeed most methods currently employed lack objectivity. This thesis investigates the efficiency of a range of gene targets and analysis methods for DNA barcoding, with an emphasis on meiofaunal organisms (nematodes, tardigrades and thrips). DNA barcodes were generated for up to three genes for each specimen. Sequences for each gene were analysed using two programs, MOTU_define.pl and DOTUR. These programs use different methods to assign sequences to operational taxonomic units (OTU), which were then compared. An objective method for analysing sequences such as MOTU_define.pl, which relies on only the information contained in the sequences, was found to be most suitable for designating taxa. It does not attempt to apply evolutionary models to the data, and then infer taxa from the derived data. In addition to barcoding, some samples were pre-processed using video capture and editing (VCE). This creates a virtual slide of a specimen so that a sequence can be linked to a morphological identification. VCE proved to be an efficient method to preserve morphological data from specimens.

Hypolepis Bernh. é um gênero sub-cosmopolita com ca. 80 táxons, e com pouquíssimos estudos taxonômicos. O presente trabalho trata da revisão taxonômica das espécies ocorrentes na América do Sul, incluindo a Ilha de Cocos (Costa Rica). O mesmo se desenvolveu, principalmente, através do estudo morfológico dos tipos nomenclaturais e de exsicatas oriundas de herbários europeus, sul-americanos e de um neo-zeolandês. Algumas espécies também foram estudadas em campo. Para a América do Sul (incl. Cocos) são aqui reconhecidas 27 espécies, e um total de 31 táxons (espécies, subespécies e variedades). Destas, 11 representam novidades nomenclaturais: H. acantha Schwartsb., H. bogotensis var. glabra H. Karst. ex Schwartsb. & J. Prado, H. flexuosa var. zimmerae Schwartsb. & J. Prado, H. galapagensis Schwartsb. & J. Prado, H. Krameri Schwartsb. et al., H. Paulistana Schwartsb. & J. Prado, H. Pedropaloensis Schwartsb. & J. Prado, H. Rugosula subsp. poeppigiana (Mett.) Schwartsb. & J. Prado, H. Rugosula subsp. pradoana Schwartsb., H. Stolonifera var. nebularis Schwartsb., e H. Trinationalis Schwartsb. Grande parte dos táxons foram re-circunscritos, especialmente H. Flexuosa Sodiro var. flexuosa, H. Mitis Kunze ex Kuhn, H. Poeppigii (Kunze) R.A. Rodr., H. Repens (L.) C. Presl, H. Rigescens (Kunze ex Mart.) T. Moore, e H. Stolonifera Fée var. stolonifera. Foram reconhecidos oito padrões biogeográficos para os táxons: \"neotropical\", \"circum-caribenho\", \"circum-amazônico\", \"Monte Roraima\", \"andino\", \"ilhas\", \"sul-brasileiro\", e \"austral\". Altitudes mínimas e máximas parecem ser fortes fatores limitantes de distribuição. O tratamento taxonômico apresenta chaves de identificação, sinonímias, tipificações, descrição dos táxons, mapas de distribuição, ilustrações, material examinado, e comentários taxonômicos e/ou nomenclaturais. Em adição, são apresentadas breves discussões morfológicas, ecológicas, biogeográficas, de conceitos específicos e infra-específicos de alguns táxons, e de grupos informais de espécies; além de pranchas com secções anatômicas de quatro espécies. / Hypolepis Bernh. is a sub-cosmopolitan genus with ca. 80 taxa, and with few taxonomic studies. The present work deals with the taxonomic revision of the South American species, including the Cocos Island (Costa Rica). It has been based, mainly, on the morphological study of nomenclatural types and exsiccates from European, South American, and New Zealand herbaria. Some species were also studied in nature. For South America (incl. Cocos Island), 27 species are here recognized, and a total of 31 taxa (species, subspecies, and varieties). Among these, 11 represent nomenclatural novelties: H. acanthi Schwartsb., H. bogotensis var. glabra H. Karst. ex Schwartsb. & J. Prado, H. flexuosa var. zimmerae Schwartsb. & J. Prado, H. galapagensis Schwartsb. & J. Prado, H. Krameri Schwartsb. et al., H. Paulistana Schwartsb. & J. Prado, H. Pedropaloensis Schwartsb. & J. Prado, H. Rugosula subsp. poeppigiana (Mett.) Schwartsb. & J. Prado, H. Rugosula subsp. pradoana Schwartsb., H. Stolonifera var. nebularis Schwartsb., and H. Trinationalis Schwartsb. Most taxa were re-circunscribed, especially H. Flexuosa Sodiro var. flexuosa, H. Mitis Kunze ex Kuhn, H. Poeppigii (Kunze) R.A. Rodr., H. Repens (L.) C. Presl, H. Rigescens (Kunze ex Mart.) T. Moore, and H. Stolonifera Fée var. stolonifera. Eight bio-geographical patterns were recognized: \"Neotropical\", \"circum-Caribbean\", \"circum-Amazonian\", \"Mount Roraima\", \"Andean\", \"islanders\", \"southern Brazilian\", and \"Austral\". Minimum and maximum elevations seem to be strong limiting factors of distribution. The taxonomic treatment presents keys to taxa, synonymies, typifications, taxa description, distribution maps, illustrations, studied material, and taxonomic and/or nomenclatural comments. In addition, it is presented short discussions about morphology, ecology, bio-geography, specific/infra-specific concepts of some taxa, and informal groups of species; also, plates with anatomical sections of four species.

Bignonia, o quinto maior gênero da tribo Bignonieae (Bignoniaceae), é caracterizado por apresentar ramos com cunhas de floema em múltiplo de quatro, folhas 2-folioladas, gavinhas geralmente simples, flores com corola achatada e sem disco nectarífero, e sementes com alas opacas. A atual circunscrição é baseada num recente estudo filogenético que congregou 28 espécies anteriormente posicionadas em oito diferentes gêneros. Esta união tornou Bignonia um grupo complexo, com ampla variação morfológica, criando um grande desafio taxonômico. Assim, os objetivos foram revisar a taxonomia do gênero e reconstruir sua filogenia baseada em caracteres moleculares, incluindo sequenciamento em larga escala, para melhor compreender o grupo. Com o tratamento taxonômico apresentado aqui, são reconhecidas 30 espécies, duas das quais descritas como novas, uma reestabelecida e outra sinonimizada. Foram encontrados dez clados, todos suportados por sinapomorfias morfológicas, que são a base da classificação subgenérica proposta. Os resultados gerados aqui fornecerão subsídios para um futuro estudo evolutivo e biogeográfico / Bignonia, the fifth largest genus in the tribe Bignonieae (Bignoniaceae), is characterized by stems with phloem wedges in multiple of four, leaves 2-foliolated, tendrils usually simple, flowers with dorso-ventrally flattened corolla and absent nectariferous disk, and seed with opaque wings. The current circumscription is based on a recent phylogenetic study that congregated 28 species previously placed in eight different genera. This unification made Bignonia a complex group, with a wide morphological range, which created a big taxonomic challenge. In this manner, the objectives were to review the taxonomy of the genus and to reconstruct its phylogeny using molecular characters, including high throughput sequencing, to better understand this group. With the taxonomic treatment presented here, 30 species are recognized, two of these described as new, one reestablished and another synonymized. Ten clades were obtained, all supported by morphological characters, are the base for the subgeneric classification proposed. The results presented here will provide the base for future evolutionary and biogeographic study

Uma análise cladística baseada em parcimônia é utilizada para testar o monofiletismo do gênero Odontopeltis e suas relações com outras espécies de gêneros anteriormente relacionados. A matriz de dados compreende 15 terminais e 47 caracteres. A análise cladística com pesagem implícita de caracteres de concavidade igual a 2,012 resultou em uma árvore mais parcimoniosa com 99 passos (IC = 58; IR = 73). As seguintes sinapomorfias sustentam o clado Odontopeltis e são propostas como diagnoses para o gênero: (1) Formato do órgão de Tömösvary sub-oval; (2) borda do ozóporo simples; (3) dobras retrolaterais no acropódito; e (4) presença de um par de macro-cerdas delimitando o fim da região pré-femoral e o início da região femoral, no gonopódio. Para padronização das descrições de genitália, foi analisada toda a terminologia do gonopódio dos machos da família Chelodesmidae. O gonopódio dos machos é, então, formado por peças cujas homologias às peças das pernas é incerta: coxa, cânula, região pré-femoral, processo pré-femoral, região femoral e solenômero. Para o gênero Odontopeltis é proposta uma terminologia da genitália à parte, devido às modificações no gonopódio. O gênero é composto por 13 espécies, sendo oito espécies válidas e cinco insertis sedis, sendo elas: Odontopeltis conspersus, O. anchisteus, O. clarazianus, O. giganteus, O. sp. nov. 1, O. sp. nov. 2, O. sp. nov. 3 e O. sp. nov. 4, e as espécies insertis sedis são: O. próxima, O. gracilipes, O. decoloratus, O. borellii e O. balzanii. A tribo Macrocoxodesmini se mostrou parafilética e, portanto, foi desmembrada. A tribo Telonychopodini se manteve monofilética e o gênero Odontopeltis de fato não pertence a esta tribo. / A cladistic analysis based on parsimony is used to test the monophyly of the genus Odontopeltis and its relationship with related genera. The data matrix comprises 15 terminal taxa and 47 characters. The implied weighted analysis, with concavity 2,012, resulted in a 99 steps most parsimonious tree (CI = 58; RI = 73). The following sinapomorphies supports the clade Odontopeltis and are proposed as diagnosis characters for the genus: (1) Tömösvary organ sub-oval shaped; (2) ozopores edge simple; (3) retrolateral rims on acropodite; and (4) presence of macrobristles delimiting the end of the prefemoral region and the beginning of the femoral region, on the gonopods. To standardize the genitalia description, the terminology for the gonopods of the family Chelodesmidae was reviewed. Then, the male gonopods are composed by: coxae, cannula, prefemoral region, prefemoral process, femoral region and solenomere. There is no attempt to relate the homology of legs pieces with gonopod pieces. It\'s proposed a terminology for the gonopods of the genus Odontopeltis due to the modifications on the gonopods. The genus comprises 13 species, where eight are valid species and five are insertis sedis: Odontopeltis conspersus, O. anchisteus, O. clarazianus, O. giganteus, O. sp. nov. 1, O. sp. nov. 2, O. sp. nov. 3 and O. sp. nov. 4, and the insertis sedis species are: O. proxima, O. gracilipes, O. decoloratus, O. borellii and O. balzanii. The Macrocoxodesmini tribe showed as a paraphyletic group and, therefore, was dissolved. The Telonychopodini tribe is monophyletic and the genus Odontopeltis, indeed, do not belong to this tribe.

Moenkhausia cotinho Eigenmann é atualmente uma espécie considerada amplamente distribuída nos rios da bacia amazônica do rio Orinoco e nas Guianas. A espécie apresenta variações morfológicas ao longo de sua distribuição, principalmente com relação à linha lateral (linha lateral completa vs. incompleta) como já relatado por outros autores. Visando compreender os limites taxonômicos de M. cotinho foram examinados 1570 espécimes de M. cotinho e de outras espécies morfologicamente similares depositados em coleções ictiológicas do Brasil (INPA; MPEG; MZSUP; UNIR; ZUEC) e norte americanas (ANSP, CAS, FMNH, INHS, MCZ; ROM), foram analisados dados de morfologia externa, dados morfométricos e merísticos. Moenkhausia cotinho difere do congêneres por apresentar mancha escura na base da nadadeira caudal (vs. ausência de mancha escura na base da nadadeira caudal), três escamas abaixo (vs. duas ou mais que três escamas) e cinco escamas acima da linha lateral (vs. mais de 5 escamas). Todos os espécimes possuem linha latera completa, dentes do pré-maxilar e do dentário com dentes com cinco cúspides, exceto por poucos exemplares das drenagens do Mazaruni e Potaro com linha lateral incompleta e com dentes do pré-maxilar e dentário com sete cúspides, essas duas condições foram observadas independentemente uma da outra. Na ausência de informações adicionais que possam indicar o reconhecimento de espécies distintas, identificamos tentativamente todos os espécimes da Guiana como M. cotinho. Além de M. cotinho, duas novas espécies foram reconhecidas: Moenkhausia sp 1 ocorre nas drenagens do rio Beni, Guaporé, Madeira e Madre de Dios, e Moenkhausia sp 2 ocorre no baixo rio Madeira, baixo Tapajós e rio Trombetas. M. cotinho é ainda amplamente distribuída nas drenagens em rios da bacia Amazônica. As novas espécies são diagnosticadas principalmente com base no padrão de colorido e no comprimento relativo de nadadeiras peitorais e dentição. Hemigrammus newboldi Fernández-Yépez, sugerido previamente como sinônimo de M. cotinho, aqui foi considerado como uma espécie válida, baseando no padrão de colorido, linha lateral incompleta, comprimento relativo de nadadeira peitoral e dentição. H. newboldi apresenta uma distribuição periférica na amazônia occidental / Moenkhausia cotinho Eigenmann is currently considered a widely distributed species in the Amazon and Orinoco river basins and in the rivers of the Guyana. The species presents morphological variation throughout its distribution range, and previous authors have specifically reported variation in the number of perforated scales in the lateral line (lateral line complete vs. incomplete). In order to understand the taxonomic limits of M. cotinho, 1570 specimens of M. cotinho and other species similar morphologically, from Brazilian (INPA; MPEG; MZSUP; UNIR; ZUEC) and North American ichthyological collections (ANSP, CAS, FMNH, INHS, MCZ; and ROM) were analyzed based on data from external morphology, morphometric and meristic data. Moenkhausia cotinho differs from its congeners in the presence of a dark spot on the caudal peduncle (vs. dark spot absent), three rows of scales below (vs. two or more than three) and five scales above the lateral line (vs. more than five). All specimens possess a complete lateral line, pre-maxilary and dentary teeth with five cups. Many specimens from drainages of Cuyuni, Mazaruni and Potaro have an incomplete lateral line,pre-maxilary anddentary teeth with seven cusps, with those two features varying independently from each other. In the absence of additional information that could indicate the recognition of distinct species, we tentatively identified all specimens from the Guyana as M. cotinho. In addition to M. cotinho, two new species were recognized: Moenkhausia sp. 1 from the Rio Beni, Rio Guaporé, Rio Madeira and Rio Madre de Dios drainages, and Moenkhausia sp. 2 from Rio Madeira, lower Rio Tapajós and lower Rio Trombetas. M. cotinho is still widely distributed in rivers of the Amazon and Orinoco basin. The new species are diagnosed on the basis of differences in color pattern, relative length of the pectoral fin, and number of teeth on the dentary. Hemmigrammus newbodi Fernandez-Yépez, previously suggested to be a synonym of M. cotinho, is herein considered a valid species based on differences in color pattern, by having an incomplete lateral, and a relatively long pectoral fin. This species presents a peripheral distribution in rivers of the upper Amazon and Orinoco basins. The synonymy of Knodus albolineatus Holly with M. cotinho is herein corroborated

Este trabalho é dividido em uma revisão taxonômica do gênero Pseudophallus Herald 1940 e em um estudo osteológico de P. brasiliensis. Pseudophallus foi descrito a partir de duas espécies distribuídas nas drenagens costeiras do Oceano Pacífico no continente americano (P. starskii e P. elcapitanensis) e posteriormente foi incluída uma espécie das drenagens costeiras do Oceano Atlântico, P. mindii, com ocorrência registrada até recentemente entre o estado de São Paulo, Brasil até Belize na América Central, incluindo as ilhas do Caribe. Em 1974 foi descrita uma nova espécie, P. brasiliensis, com base em exemplares coletados no Rio Tocantins com contagens merísticas mais baixas do que os exemplares da América Central e do resto do território brasileiro. Além disso, os exemplares brasileiros apresentavam uma variação clinal decrescente em sentido Sul-Norte nas contagens merísticas. Em 1982 esta espécie foi sinonimizada com P. mindii pelo fato de outros exemplares coletados em localidades distintas apresentarem valores merísticos próximos aos dos exemplares coletados no Rio Tocantins, indicando que esses valores mais baixos eram resultado de variação intraespecífica ao longo da distribuição de P. mindii. A fim de investigar a variação intraespecífica em P. mindii foi proposta uma revisão taxonômica de P. mindii que acabou se desdobrando em uma revisão do gênero Pseudophallus. Foram analisados caracteres morfométricos e merísticos de 443 exemplares de todas as espécies de Pseudophallus, provenientes de todas suas distribuições nas drenagens do Atlântico e do Pacífico e incluindo material-tipo. Cinco espécies puderam ser reconhecidas: P. elcapitanensis e P. starksii nas drenagens costeiras do Oceano Pacífico, P. mindii e P. brasiliensis nas drenagens do Oceano Atlântico, revalidando P. brasiliensis, e uma espécie nova endêmica do Lago Izabal na Guatemala. Estas espécies são redefinidas e redescritas, com algumas considerações taxonômicas e biogeográficas. Na segunda parte deste trabalho, abordou-se de forma exploratória a osteologia de P. brasiliensis com intuito de se familiarizar com o esqueleto de Syngnathidae e abordar questões nomenclaturais de sua anatomia. A família Syngnathidae é representada por diferentes espécies de peixes cachimbo, cavalos marinhos e dragões marinhos, com um grande conjunto de características que tornam esse grupo facilmente identificável como o corpo coberto por anéis ósseos, maxilase dêntulas, ausência de nadadeiras pélvicas e ossos intermusculares, abertura opercular reduzida a um poro na membrana opercular e principalmente pelo fato dos machos carregarem os ovos fecundados em uma bolsa incubadora. Embora seja um grupo tão peculiar e distinto morfologicamente, estudos osteológicos são raros e focados principalmente nos cavalos marinhos (gênero Hippocampus) e não existem trabalhos filogenéticos com base em caracteres morfológicos. Neste estudo foi possível levantar informações acerca da osteologia de P. brasiliensis que permitiram comparar e discutir questões da morfologia deste grupo que foram debatidas ao longo dos anos em diferentes trabalhos disponíveis na literatura, como a questão da existência do metapterigóide, composição dos arcos branquiais e da cintura peitoral. A osteologia de P. brasiliensis foi estudada levando em consideração essas questões a fim de se criar uma base para futuros estudos anatômicos e filogenéticos do grupo / This work is divided in a taxonomic review of the genus Pseudophallus Herald 1940 and an osteological study of P. brasiliensis. Pseudophallus was described based on two species occurring on the coastal drainages of the Pacific Ocean in the new world (P. starskii and P. elcapitanensis) and later, an additional species from the coastal drainages of the Atlantic Ocean, P. mindii, with a distribution ranging until recently from the Brazilian state of São Paulo, to Belize in Central America, including the Caribbean islands. In 1974 a new species, P. brasiliensis, was described based on specimens collected in the Tocantins River with lower meristic counts than the Central American specimens and the ones from the rest of the Brazilian territory. Besides that, the Brazilian specimens presented a decreasing clinal variation in a South-to-North direction in some meristic counts. In 1982 this species was synonymized with P. mindii due to the fact that specimens collected in other localities presented meristic counts similar to those collected in the Tocantins River, indicating that these lower counts were due to an intraspecific variation along the distribution of P. mindii. In order to investigate this intraspecific variation in P. mindii, a taxonomic review was proposed which became a taxonomic review of the genus Pseudophallus. In total 443 specimens, including type material, of all the species of Pseudophallus from along their entire distribution on the Atlantic and Pacific drainages had their meristic and morphometric characters studied. Five species are recognized: P. elcapitanensis and P. starksii from the Pacific drainages, P. mindii and P. brasiliensis from the Atlantic drainages, revalidating P. brasiliensis, and a new species endemic of the Lake Izabal, in Guatemala. Those species were redefined and redescribed herein, with some comments on their taxonomy and biogeography. On the second part of this study, an exploratory study on the osteology of P. brasiliensis was conducted, with the purpose of getting familiar with the osteology of the Syngnathidae and to address nomenclatural questions of their anatomy. The Syngnathidae are represented by different species of pipefishes, seahorses and seadragons, with a great array of characteristics that make this group easily recognizable such as the body armor, edentulous jaws, absence of pelvic fins and intermuscular bones, gill opening reduced to a pore on the opercular membrane and mainly by the fact that the males carry the eggs in a breeding pouch. Although this group is so peculiar and morphologically distinct, osteological studies are rare and focused mainly on the seahorses (genus Hippocampus) and there are no phylogenetic studies based on morphological characters. In this study, it was possible to gather information about the osteology of P. brasiliensis that allowed comparing and discussing morphological questions that are being debated along the years in different studies available on the literature, such as the existence of the metapterygoid, and branchial arch and pectoral girdle arrangement. The osteology of P. brasiliensis was conducted taking in consideration these questions in order to create a basis for future anatomical and phylogenetical studies in this group.

Bignonia, o quinto maior gênero da tribo Bignonieae (Bignoniaceae), é caracterizado por apresentar ramos com cunhas de floema em múltiplo de quatro, folhas 2-folioladas, gavinhas geralmente simples, flores com corola achatada e sem disco nectarífero, e sementes com alas opacas. A atual circunscrição é baseada num recente estudo filogenético que congregou 28 espécies anteriormente posicionadas em oito diferentes gêneros. Esta união tornou Bignonia um grupo complexo, com ampla variação morfológica, criando um grande desafio taxonômico. Assim, os objetivos foram revisar a taxonomia do gênero e reconstruir sua filogenia baseada em caracteres moleculares, incluindo sequenciamento em larga escala, para melhor compreender o grupo. Com o tratamento taxonômico apresentado aqui, são reconhecidas 30 espécies, duas das quais descritas como novas, uma reestabelecida e outra sinonimizada. Foram encontrados dez clados, todos suportados por sinapomorfias morfológicas, que são a base da classificação subgenérica proposta. Os resultados gerados aqui fornecerão subsídios para um futuro estudo evolutivo e biogeográfico / Bignonia, the fifth largest genus in the tribe Bignonieae (Bignoniaceae), is characterized by stems with phloem wedges in multiple of four, leaves 2-foliolated, tendrils usually simple, flowers with dorso-ventrally flattened corolla and absent nectariferous disk, and seed with opaque wings. The current circumscription is based on a recent phylogenetic study that congregated 28 species previously placed in eight different genera. This unification made Bignonia a complex group, with a wide morphological range, which created a big taxonomic challenge. In this manner, the objectives were to review the taxonomy of the genus and to reconstruct its phylogeny using molecular characters, including high throughput sequencing, to better understand this group. With the taxonomic treatment presented here, 30 species are recognized, two of these described as new, one reestablished and another synonymized. Ten clades were obtained, all supported by morphological characters, are the base for the subgeneric classification proposed. The results presented here will provide the base for future evolutionary and biogeographic study

In spite of the great economic importance of north American Scolytidae, many taxonomic descriptions remain inadequate for the identification of species, and existing keys have been made obsolete by the recent description of new species. To bring these keys up to date and make them useful to students and practical foresters, detailed studies of the morphological structure of the various species are necessary. The purpose of the present investigation has been to clarify and revise existing keys and to describe briefly the species of Scolytidae occurring in the Logan Canyon area of Utah. The following keys and descriptions will be of value to students, foresters, and taxonomists in identifying the species of Scolytidae occurring in northern Utah. Information secured in this investigation also contributes toward the geographic and host distributional knowledge of the Scolytidae in Utah.

Pseudomonads, particularly the fluorescent pseudomonads, are common rhizosphere bacteria accounting for a significant portion of the culturable rhizosphere bacteria. The presence and diversity of Pseudomonas spp. in the rhizosphere is important because of their ability to influence plant and soil health. Diversity is generated as the result of mutation, the rearrangement of genes within the genome and the acquisition of genes by horizontal transfer systems, e.g. plasmids, bacteriophages, transposons or integrons. The purpose of this study was to examine the phenotypic and genotypic diversity of a subset of pseudomonads (N=133) isolated from the rhizosphere and root-interior of four cultivars of field-grown canola. Pseudomonads were analyzed according to their 16S rRNA and cpn60 gene sequences and selected phenotypic properties (fatty acid methyl ester (FAME) profiles, antibiotic resistance, extracellular enzyme production and carbon substrate utilization). On the basis of 16S rRNA and cpn60 gene sequences, two major clusters were observed, the Pseudomonas fluorescens complex and the P. putida complex. Phylogenetic analysis of the partial gene sequences suggested that the phylogeny of root-associated pseudomonads had no effect on their associations with different cultivars or root zones (i.e. rhizosphere and root interior). Principal component analysis (PCA) of their phenotypic properties revealed little variation among the pseudomonads associated with different canola cultivars. Importantly, while little difference was observed in isolates from different cultivars significant phenotypic variation was observed in isolates from different root zones. Cluster analysis of their phenotypic properties exhibited little correlation with their phylogenetic relationships. In the majority of situations, the isolates grouped into a phylogenetic cluster had less than 75-80% similarity among their phenotypic traits despite a close evolutionary relationship as determined by 16S rRNA and cpn60 gene sequencing. The results indicated that the genotype of the rhizosphere pseudomonads was not accurately reflected in their phenotype. Analysis of the mobile genetic elements (MGEs) associated with a randomly selected subset of the pseudomonad isolates (N=66) revealed that 58% (N=38) contained plasmids, 50% (N=33) contained inducible prophages, 24% (N=16) contained integrons and 23% (N=15) contained transposons. Examination of the MGEs associated with a subset of rhizosphere pseudomonads revealed that MGEs were present in the isolates independent of the degree of similarity between their phenotypic and phylogenetic relationships. Therefore, mutation and genomic rearrangement appear to be the major influences in the observed incongruence between the phylogenetic and the phenotypic relationships of the bacteria examined.

Pseudomonads, particularly the fluorescent pseudomonads, are common rhizosphere bacteria accounting for a significant portion of the culturable rhizosphere bacteria. The presence and diversity of Pseudomonas spp. in the rhizosphere is important because of their ability to influence plant and soil health. Diversity is generated as the result of mutation, the rearrangement of genes within the genome and the acquisition of genes by horizontal transfer systems, e.g. plasmids, bacteriophages, transposons or integrons. The purpose of this study was to examine the phenotypic and genotypic diversity of a subset of pseudomonads (N=133) isolated from the rhizosphere and root-interior of four cultivars of field-grown canola. Pseudomonads were analyzed according to their 16S rRNA and cpn60 gene sequences and selected phenotypic properties (fatty acid methyl ester (FAME) profiles, antibiotic resistance, extracellular enzyme production and carbon substrate utilization). On the basis of 16S rRNA and cpn60 gene sequences, two major clusters were observed, the Pseudomonas fluorescens complex and the P. putida complex. Phylogenetic analysis of the partial gene sequences suggested that the phylogeny of root-associated pseudomonads had no effect on their associations with different cultivars or root zones (i.e. rhizosphere and root interior). Principal component analysis (PCA) of their phenotypic properties revealed little variation among the pseudomonads associated with different canola cultivars. Importantly, while little difference was observed in isolates from different cultivars significant phenotypic variation was observed in isolates from different root zones. Cluster analysis of their phenotypic properties exhibited little correlation with their phylogenetic relationships. In the majority of situations, the isolates grouped into a phylogenetic cluster had less than 75-80% similarity among their phenotypic traits despite a close evolutionary relationship as determined by 16S rRNA and cpn60 gene sequencing. The results indicated that the genotype of the rhizosphere pseudomonads was not accurately reflected in their phenotype. Analysis of the mobile genetic elements (MGEs) associated with a randomly selected subset of the pseudomonad isolates (N=66) revealed that 58% (N=38) contained plasmids, 50% (N=33) contained inducible prophages, 24% (N=16) contained integrons and 23% (N=15) contained transposons. Examination of the MGEs associated with a subset of rhizosphere pseudomonads revealed that MGEs were present in the isolates independent of the degree of similarity between their phenotypic and phylogenetic relationships. Therefore, mutation and genomic rearrangement appear to be the major influences in the observed incongruence between the phylogenetic and the phenotypic relationships of the bacteria examined.