Estrutura metabólica e genética de comunidades bacterianas em solo de cerrado sob diferentes manejos

O objetivo deste trabalho foi avaliar a estrutura metabólica e genética de comunidades bacterianas em Latossolo de cerrado sob vegetação nativa ou cultivado em sistema de rotação soja/milho sob preparo convencional e plantio direto. Foram utilizadas microplacas EcoPlate para determinar o perfil e a diversidade metabólica das comunidades bacterianas, e eletroforese em gel com gradiente desnaturante (DGGE) para avaliar a estrutura genética. O teste estatístico de Mantel foi utilizado para avaliar a relação entre a estrutura metabólica e a genética. A comunidade bacteriana sob vegetação nativa apresentou perfil metabólico diferente do encontrado em solos cultivados. No solo cultivado com soja sob preparo convencional, o padrão de utilização das fontes de carbono diferenciou-se dos demais tratamentos. Com base nos resultados de DGGE, a comunidade bacteriana sob vegetação nativa apresentou 35% de similaridade com as de áreas cultivadas. Foram formados grupos distintos de comunidades bacterianas do solo entre as áreas sob preparo convencional e plantio direto. Houve correlação significativa de 62% entre as matrizes geradas pelas microplacas EcoPlate e pela DGGE. Variações no perfil metabólico estão relacionadas às variações na estrutura genética das comunidades bacterianas do solo.

Qualidade e potencial nutracêutico do leite bovino em diferentes sistemas de produção e estações do ano

Resumo: O objetivo deste trabalho foi avaliar o efeito da interação entre sistemas produtivos e estações do ano sobre a qualidade química e microbiológica do leite bovino, além de propor um índice de potencial nutracêutico do perfil de ácidos graxos do leite. Três propriedades foram avaliadas mensalmente, durante as diferentes estações do ano, em quatro graus de especialização dos sistemas de produção: altamente especializado, especializado, semiespecializado e não especializado. Os sistemas de produção e as estações do ano interferem de forma conjunta no perfil de ácidos graxos e, de forma isolada, na qualidade química e microbiológica do leite. As maiores contagens de células somáticas e os menores conteúdos de proteína foram observados no verão, e o grau de especialização das unidades produtivas esteve indiretamente relacionado à contagem bacteriana total no leite. No inverno, sistemas não especializados produziram leite com o melhor índice nutracêutico, que apresentaram os maiores teores de ácidos graxos poli-insaturados, ácido rumênico (CLA, 18:2n7-c9,t11) e ácido t10,c12-octadecadienoico (CLA, 18:2n6-t10,c12).

Avaliação de protocolo para obtenção de mudas micropropagadas de bananeira cv. Prata-Anã (subgrupo AAB)

O trabalho teve como objetivo avaliar um sistema de micropropagação para a cultivar Prata-Anã, observando-se os principais fatores de eficiência e limitação no processo produtivo da muda. Os explantes foram estabelecidos em meio nutritivo MS, suplementado com 5mg/L de BAP (benzilaminopurina) e 30g/L de sacarose solidificado com 8g/L de ágar e pH ajustado em 5,7. A fase de multiplicação foi composta pelo mesmo meio de cultura e a de enraizamento constituída pela metade da concentração dos sais de MS e de sacarose, sem regulador de crescimento. Perdas por contaminação bacteriana foram maiores durante o estabelecimento in vitro e por fungos, nos dois últimos subcultivos. As maiores taxas de multiplicação ocorreram entre o 4º e o 5º subcultivos e, ao final do processo, observou-se maior proporção de brotos na classe entre 30 e 60mm. Com relação à eficiência da utilização da mão-de-obra no laboratório, observou-se que o processamento diário de frascos por operador foi baixo nas fases de estabelecimento, primeiro subcultivo e enraizamento, quando comparado com as fases de multiplicação exponencial dos explantes. Apesar de não terem sido constatadas perdas na fase de aclimatação, foi observada a ocorrência de 1% do total das plântulas com anomalias morfológicas.

Aeromonas hydrophila lateral flagella gene transcriptional hierarchy

Aeromonas hydrophila AH-3 lateral flagella are not assembled when bacteria grow in liquid media; however, lateral flagellar genes are transcribed. Our results indicate that A. hydrophila lateral flagellar genes are transcribed at three levels (class I to III genes) and share some similarities with, but have many important differences from, genes of Vibrio parahaemolyticus. A. hydrophila lateral flagellum class I gene transcription is σ(70) dependent, which is consistent with the fact that lateral flagellum is constitutively transcribed, in contrast to the characteristics of V. parahaemolyticus. The fact that multiple genes are included in class I highlights that lateral flagellar genes are less hierarchically transcribed than polar flagellum genes. The A. hydrophila lafK-fliEJL gene cluster (where the subscript L distinguishes genes for lateral flagella from those for polar flagella) is exclusively from class I and is in V. parahaemolyticus class I and II. Furthermore, the A. hydrophila flgAMNL cluster is not transcribed from the σ(54)/LafK-dependent promoter and does not contain class II genes. Here, we propose a gene transcriptional hierarchy for the A. hydrophila lateral flagella.

Efeito de bactérias diazotróficas na produção de abacaxizeiro 'Cayenne Champac', sob irrigação, em dois níveis de adubação nitrogenada

Avaliou-se o efeito de bactérias diazotróficas na produção de abacaxizeiro cv. Cayenne Champac (Champaka), sob irrigação, em dois níveis de adubação nitrogenada. Os tratamentos constaram dos níveis de N de 180 kg ha-1 ano-1 e 300 kg ha-1 ano-1, nas parcelas e subparcelas de mudas micropropagadas inoculadas com bactéria relacionada a Burkholderia cepacia AB213, de bactéria Asaia bogorensis AB219 e controles sem inoculação bacteriana, utilizando-se de três repetições. A inoculação bacteriana foi realizada no laboratório (10(8) células planta-1) e a aclimatação das mudas, em casa de vegetação. Após 5 meses, as mudas foram transplantadas no campo, utilizando-se de 0,9 m entre as linhas e 0,3 m entre as plantas. A cultivar apresentou bom desempenho sob irrigação no solo arenoso de Pacajus, Estado do Ceará, quando adubado com o maior nível de N. Para cada quilograma do elemento fornecido, houve incremento de 124,3 kg ha-1 na massa fresca dos frutos com coroa, entre os níveis da adubação nitrogenada. Na dose maior de N, plantas inoculadas do AB219 produziram frutos maiores e massas frescas 19,4% e 17,3% superiores aos controles, respectivamente, para frutos sem e com coroa. O efeito do AB213 na produção foi menor (9,9%) no nível mais baixo de N. A evidência do efeito de bactérias diazotróficas na cultivar Cayenne Champac foi demonstrada.

Eficiência de argila silicatada no controle de Xanthomonas axonopodis pv. passiflorae, in vitro e em mudas de maracujazeiro-amarelo

A mancha bacteriana do maracujá, causada pela bactéria Xanthomonas axonopodis pv. passiflorae, ocorre em todas as regiões produtoras do País, sendo responsável por grandes perdas econômicas na cultura do maracujazeiro-amarelo. O presente trabalho teve como objetivos testar a eficiência de argila silicatada na inibição da bactéria X. axonopodis pv. passiflorae in vitro e no controle preventivo e curativo da mancha bacteriana em mudas de maracujazeiro-amarelo. A argila silicatada foi adicionada ao meio de cultura batata-dextrose-ágar fundente, nas concentrações de 0,0; 0,5; 1,0; 1,5 e 2,0%; vertido em placas de Petri. Após resfriamento do meio, repicou-se a suspensão bacteriana (10(7) UFC.mL-1) com uma alça, incubando-se as placas a 28 °C por três dias, quando se avaliou o crescimento bacteriano. Posteriormente, o produto, nas mesmas concentrações citadas, foi pulverizado em mudas de maracujá 'Afruvec' de forma preventiva ou curativa. A inoculação da bactéria foi realizada através de pulverização foliar da suspensão bacteriana (10(7) UFC.mL-1), 24 h antes ou após os tratamentos curativo e preventivo, respectivamente. A severidade da doença foi avaliada com auxílio de uma escala diagramática nas quatro primeiras folhas verdadeiras contadas de baixo para cima. Nas concentrações avaliadas, a argila silicatada inibiu a bactéria in vitro e os sintomas da mancha bacteriana no tratamento curativo, enquanto no tratamento preventivo, controle significativo foi obtido a partir de 1,0% de argila silicatada. Com base nestes resultados, a argila silicada pode ser recomendada, na concentração de 1,0-2,0%, para o controle da mancha bacteriana do maracujazeiro em pulverizações foliares.

The UlaG protein familly defines novel structural and functional motifs grafted on an ancient RNase fold

Background: Bacterial populations are highly successful at colonizing new habitats and adapting to changing environmental conditions, partly due to their capacity to evolve novel virulence and metabolic pathways in response to stress conditions and to shuffle them by horizontal gene transfer (HGT). A common theme in the evolution of new functions consists of gene duplication followed by functional divergence. UlaG, a unique manganese-dependent metallo-b-lactamase (MBL) enzyme involved in L-ascorbate metabolism by commensal and symbiotic enterobacteria, provides a model for the study of the emergence of new catalytic activities from the modification of an ancient fold. Furthermore, UlaG is the founding member of the so-called UlaG-like (UlaGL) protein family, a recently established and poorly characterized family comprising divalent (and perhaps trivalent)metal-binding MBLs that catalyze transformations on phosphorylated sugars and nucleotides. Results: Here we combined protein structure-guided and sequence-only molecular phylogenetic analyses to dissect the molecular evolution of UlaG and to study its phylogenomic distribution, its relatedness with present-day UlaGL protein sequences and functional conservation. Phylogenetic analyses indicate that UlaGL sequences are present in Bacteria and Archaea, with bona fide orthologs found mainly in mammalian and plant-associated Gramnegative and Gram-positive bacteria. The incongruence between the UlaGL tree and known species trees indicates exchange by HGT and suggests that the UlaGL-encoding genes provided a growth advantage under changing conditions. Our search for more distantly related protein sequences aided by structural homology has uncovered that UlaGL sequences have a common evolutionary origin with present-day RNA processing and metabolizing MBL enzymes widespread in Bacteria, Archaea, and Eukarya. This observation suggests an ancient origin for the UlaGL family within the broader trunk of the MBL superfamily by duplication, neofunctionalization and fixation. Conclusions: Our results suggest that the forerunner of UlaG was present as an RNA metabolizing enzyme in the last common ancestor, and that the modern descendants of that ancestral gene have a wide phylogenetic distribution and functional roles. We propose that the UlaGL family evolved new metabolic roles among bacterial and possibly archeal phyla in the setting of a close association with metazoans, such as in the mammalian gastrointestinal tract or in animal and plant pathogens, as well as in environmental settings. Accordingly, the major evolutionary forces shaping the UlaGL family include vertical inheritance and lineage-specific duplication and acquisition of novel metabolic functions, followed by HGT and numerous lineage-specific gene loss events.

Similar and Divergent Effects of ppGpp and DksA Deficiencies on Transcription in Escherichia coli.

The concerted action of ppGpp and DksA in transcription has been widely documented. In disparity with this model, phenotypic studies showed that ppGpp and DksA might also have independent and opposing roles in gene expression in Escherichia coli. In this study we used a transcriptomic approach to compare the global transcriptional patterns of gene expression in strains deficient in ppGpp (ppGpp0) and/or DksA ( dksA). Approximately 6 and 7% of all genes were significantly affected by more than twofold in ppGpp- and DksAdeficient strains, respectively, increasing to 13% of all genes in the ppGpp0 dksA strain. Although the data indicate that most of the affected genes were copositively or conegatively regulated by ppGpp and DksA, some genes that were independently and/or differentially regulated by the two factors were found. The large functional group of chemotaxis and flagellum synthesis genes were notably differentially affected, with all genes being upregulated in the DksA-deficient strain but 60% of them being downregulated in the ppGpp-deficient strain. Revealingly, mutations in the antipausing Gre factors suppress the upregulation observed in the DksA-deficient strain, emphasizing the importance of the secondary channel of the RNA polymerase for regulation and fine-tuning of gene expression in E. coli.

Similar and Divergent Effects of ppGpp and DksA Deficiencies on Transcription in Escherichia coli.

The concerted action of ppGpp and DksA in transcription has been widely documented. In disparity with this model, phenotypic studies showed that ppGpp and DksA might also have independent and opposing roles in gene expression in Escherichia coli. In this study we used a transcriptomic approach to compare the global transcriptional patterns of gene expression in strains deficient in ppGpp (ppGpp0) and/or DksA ( dksA). Approximately 6 and 7% of all genes were significantly affected by more than twofold in ppGpp- and DksAdeficient strains, respectively, increasing to 13% of all genes in the ppGpp0 dksA strain. Although the data indicate that most of the affected genes were copositively or conegatively regulated by ppGpp and DksA, some genes that were independently and/or differentially regulated by the two factors were found. The large functional group of chemotaxis and flagellum synthesis genes were notably differentially affected, with all genes being upregulated in the DksA-deficient strain but 60% of them being downregulated in the ppGpp-deficient strain. Revealingly, mutations in the antipausing Gre factors suppress the upregulation observed in the DksA-deficient strain, emphasizing the importance of the secondary channel of the RNA polymerase for regulation and fine-tuning of gene expression in E. coli.

Allelic diversity and population structure in Vibrio cholerae O139 Bengal based on nucleotide sequence analysis

Comparative analysis of gene fragments of six housekeeping loci, distributed around the two chromosomes of Vibrio cholerae, has been carried out for a collection of 29 V. cholerae O139 Bengal strains isolated from India during the first epidemic period (1992 to 1993). A toxigenic O1 ElTor strain from the seventh pandemic and an environmental non-O1/non-O139 strain were also included in this study. All loci studied were polymorphic, with a small number of polymorphic sites in the sequenced fragments. The genetic diversity determined for our O139 population is concordant with a previous multilocus enzyme electrophoresis study in which we analyzed the same V. cholerae O139 strains. In both studies we have found a higher genetic diversity than reported previously in other molecular studies. The results of the present work showed that O139 strains clustered in several lineages of the dendrogram generated from the matrix of allelic mismatches between the different genotypes, a finding which does not support the hypothesis previously reported that the O139 serogroup is a unique clone. The statistical analysis performed in the V. cholerae O139 isolates suggested a clonal population structure. Moreover, the application of the Sawyer's test and split decomposition to detect intragenic recombination in the sequenced gene fragments did not indicate the existence of recombination in our O139 population.

Draft genome sequence of Aeromonas molluscorum strain 848TT, isolated from bivalve molluscs

We report here the draft genome sequence of Aeromonas molluscorum 848T, the type strain of this Aeromonas species, which was isolated from wedge shells (Donax trunculus) obtained from a retail market in Barcelona, Spain, in 1997.

Genome sequence of Plesiomonas shigelloides strain 302-73 (serotype O1)

Plesiomonas shigelloides, the only species of the genus, is an emergent pathogenic bacterium associated with human diarrheal and extraintestinal disease. We present the whole-genome sequence analysis of the representative strain for the O1 serotype (strain 302-73), providing a tool for studying bacterial outbreaks, virulence factors, and accurate diagnostic methods.

Bacterial adhesion efficiency on implant abutments: a comparative study

The attachment of Escherichia coli ATCC 25922 and Staphylococcus aureus ATCC 28213 onto six different materials used to manufacture dental implant abutments was quantitatively determined after 2 and 24 h of contact between the materials and the bacterial cultures. The materials were topographically characterized and their wettability determined, with both parameters subsequently related to bacterial adhesion. Atomic force microscopy, interferometry, and contact angle measurement were used to characterize the materials" surfaces. The results showed that neither roughness nor nano-roughness greatly influenced bacterial attachment whereas wettability strongly correlated with adhesion. After 2 h the degree of E. coli attachment markedly differed depending on the material whereas similar differences were not observed for S. aureus, which yielded consistently higher counts of adhered cells. Nevertheless, after 24 h the adhesion of the two species to the different test materials no longer significantly differed, although on all surfaces the numbers of finally adhered E. coli were higher than those of S. aureus

Melanization and pathogenicity in Tenebrio molitor and Pacifastacus leniusculus by Aeromonas hydrophila.

Aeromonas hydrophila is the most common Aeromonas species causing infections in human and other animals such as amphibians, reptiles, fish and crustaceans. Pathogenesis of Aeromonas species have been reported to be associated with virulence factors such as lipopolysaccharides (LPS), bacterial toxins, bacterial secretion systems, flagella, and other surface molecules. Several mutant strains of A. hydrophila AH-3 were initially used to study their virulence in two animal species, Pacifastacus leniusculus (crayfish) and Tenebrio molitor larvae (mealworm). The AH-3 strains used in this study have mutations in genes involving the synthesis of flagella, LPS structures, secretion systems, and some other factors, which have been reported to be involved in A. hydrophila pathogenicity. Our study shows that the LPS (O-antigen and external core) is the most determinant A. hydrophila AH-3 virulence factor in both animals. Furthermore, we studied the immune responses of these hosts to infection of virulent or non-virulent strains of A. hydrophila AH-3. The AH-3 wild type (WT) containing the complete LPS core is highly virulent and this bacterium strongly stimulated the prophenoloxidase activating system resulting in melanization in both crayfish and mealworm. In contrast, the ΔwaaE mutant which has LPS without O-antigen and external core was non-virulent and lost ability to stimulate this system and melanization in these two animals. The high phenoloxidase activity found in WT infected crayfish appears to result from a low expression of pacifastin, a prophenoloxidase activating enzyme inhibitor, and this gene expression was not changed in the ΔwaaE mutant infected animal and consequently phenoloxidase activity was not altered as compared to non-infected animals. Therefore we show that the virulence factors of A. hydrophila are the same regardless whether an insect or a crustacean is infected and the O-antigen and external core is essential for activation of the proPO system and as virulence factors for this bacterium.

Dual role of LldR in regulation of the lldPRD operon, involved in l-Lactate metabolism in Escherichia coli.

The lldPRD operon of Escherichia coli, involved in L-lactate metabolism, is induced by growth in this compound. We experimentally identified that this system is transcribed from a single promoter with an initiation site located 110 nucleotides upstream of the ATG start codon. On the basis of computational data, it had been proposed that LldR and its homologue PdhR act as regulators of the lldPRD operon. Nevertheless, no experimental data on the function of these regulators have been reported so far. Here we show that induction of an lldP-lacZ fusion by L-lactate is lost in an lldR mutant, indicating the role of LldR in this induction. Expression analysis of this construct in a pdhR mutant ruled out the participation of PdhR in the control of lldPRD. Gel shift experiments showed that LldR binds to two operator sites, O1 (positions 105 to 89) and O2 (positions 22 to 38), with O1 being filled at a lower concentration of LldR. L-Lactate induced a conformational change in LldR that did not modify its DNA binding activity. Mutations in O1 and O2 enhanced the basal transcriptional level. However, only mutations in O1 abolished induction by L-lactate. Mutants with a change in helical phasing between O1 and O2 behaved like O2 mutants. These results were consistent with the hypothesis that LldR has a dual role, acting as a repressor or an activator of lldPRD. We propose that in the absence of L-lactate, LldR binds to both O1 and O2, probably leading to DNA looping and the repression of transcription. Binding of L-lactate to LldR promotes a conformational change that may disrupt the DNA loop, allowing the formation of the transcription open complex.