Diversity of the bacterial community in the surface soil of a pear orchard based on 16S rRNA gene analysis

A cultivation-independent approach based on polymerase chain reaction (PCR)-amplified partial small subunit rRNA genes was used to characterize bacterial populations in the surface soil of a commercial pear orchard consisting of different pear cultivars during two consecutive growing seasons. Pyrus communis L. cvs Blanquilla, Conference, and Williams are among the most widely cultivated cultivars in Europe and account for the majority of pear production in Northeastern Spain. To assess the heterogeneity of the community structure in response to environmental variables and tree phenology, bacterial populations were examined using PCR-denaturing gradient gel electrophoresis (DGGE) followed by cluster analysis of the 16S ribosomal DNA profiles by means of the unweighted pair group method with arithmetic means. Similarity analysis of the band patterns failed to identify characteristic fingerprints associated with the pear cultivars. Both environmentally and biologically based principal-component analyses showed that the microbial communities changed significantly throughout the year depending on temperature and, to a lesser extent, on tree phenology and rainfall. Prominent DGGE bands were excised and sequenced to gain insight into the identities of the predominant bacterial populations. Most DGGE band sequences were related to bacterial phyla, such as Bacteroidetes, Cyanobacteria, Acidobacteria, Proteobacteria, Nitrospirae, and Gemmatimonadetes, previously associated with typical agronomic crop environments

Multifunctionality and Diversity in Bacterial Biofilms

Bacteria are highly diverse and drive a bulk of ecosystem processes. Analysis of relationships between diversity and single specific ecosystem processes neglects the possibility that different species perform multiple functions at the same time. The degradation of dissolved organic carbon (DOC) followed by respiration is a key bacterial function that is modulated by the availability of DOC and the capability to produce extracellular enzymes. In freshwater ecosystems, biofilms are metabolic hotspots and major sites of DOC degradation. We manipulated the diversity of biofilm forming communities which were fed with DOC differing in availability. We characterized community composition using molecular fingerprinting (T-RFLP) and measured functioning as oxygen consumption rates, the conversion of DOC in the medium, bacterial abundance and the activities of five specific enzymes. Based on assays of the extracellular enzyme activity, we calculated how the likelihood of sustaining multiple functions was affected by reduced diversity. Carbon source and biofilm age were strong drivers of community functioning, and we demonstrate how the likelihood of sustaining multifunctionality decreases with decreasing diversity

Diversitat bacteriana a les esponges marines

L’objectiu principal del projecte era aprofundir en el coneixement de les malalties de les esponges, centrant-nos en la diversitat bacteriana que acullen. Als estius 2008 i 2009 va haver episodis d’elevades temperatures de l’aigua de mar que van suposar importants mortalitats massives d’esponges a la Mediterrània. Contra tot pronòstic, els estius del projecte, el 2010 i el 2011, no van resultar especialment calorosos i no hi va haver episodis de mortalitat. És un fet molt positiu per les comunitats bentòniques però algun dels objectius específics de la meva proposta no es va poder dur a terme com havien estat platejats inicialment. Disposàvem de diferents mostres d’esponges malaltes de l’espècie Ircinia fasciculata, sanes i aigua circumdant recollides l’estiu 2009 i fixades per DNA, per això s’han pogut identificar i caracteritzar els canvis en la comunitat microbiològica de les esponges malaltes respecte de les sanes. Hem constatat que més que una infecció per un o pocs patògens puntuals, com havien proposat alguns autors, hi ha un canvi dràstic en la comunitat microbiològica associada a les esponges. Les esponges malaltes, on dominen els bacteris heterotròfics, presenten una major diversitat bacteriana que les sanes, on dominen els autòtrofs. Tot i que no es va poder realitzar un nou mostreig d’individus malalts, i algun objectiu específic no es va poder desenvolupar, vaig aprofitar l’estada en un centre de referència en estudis de la diversitat microbiana, per ampliar el coneixement general de les comunitats bacterianes associades a esponges. Es van realitzar nous estudis en què vam testar si totes les esponges (bacteriosponges i no) presenten simbionts reals o si les no-bacteriosponges presenten un enriquiment de les comunitats de l’aigua de mar però no una flora específica. El resultat és que totes les esponges presenten associacions molt específiques malgrat hi ha fortes diferències entre les comunitats microbianes associades a bacteriosponges i a no-bacteriosponges.

Infection prothétique de hanche à Listeria monocytogenes [Prosthetic hip infection due to Listeria monocytogenes: review of the literature and case report].

With the ageing of the population, articular prosthetic replacements are becoming more and more frequent. One of the most feared complications is prosthetic infection, mostly due to bacteria of the cutaneous flora. Listeria monocytogenes is rarely the cause. This paper describes the management of a hip prosthetic infection due to Listeria monocytogenes. The patient was cured with antimicrobial therapy and a two-stage exchange. This case report creates an opportunity to review the literature in the aim of determining the risk factors and the optimal care.

A comparison of dequalinium chloride vaginal tablets (Fluomizin®) and clindamycin vaginal cream in the treatment of bacterial vaginosis: a single-blind, randomized clinical trial of efficacy and safety.

AIMS: To investigate if vaginal application of dequalinium chloride (DQC, Fluomizin®) is as effective as vaginal clindamycin (CLM) in the treatment of bacterial vaginosis (BV). METHODS: This was a multinational, multicenter, single-blind, randomized trial in 15 centers, including 321 women. They were randomized to either vaginal DQC tablets or vaginal CLM cream. Follow-up visits were 1 week and 1 month after treatment. Clinical cure based on Amsel's criteria was the primary outcome. Secondary outcomes were rate of treatment failures and recurrences, incidence of post-treatment vulvovaginal candidosis (VVC), lactobacillary grade (LBG), total symptom score (TSC), and safety. RESULTS: Cure rates with DQC (C1: 81.5%, C2: 79.5%) were as high as with CLM (C1: 78.4%, C2: 77.6%). Thus, the treatment with DQC had equal efficacy as CLM cream. A trend to less common post-treatment VVC in the DQC-treated women was observed (DQC: 2.5%, CLM: 7.7%; p = 0.06). Both treatments were well tolerated with no serious adverse events occurring. CONCLUSION: Vaginal DQC has been shown to be equally effective as CLM cream, to be well tolerated with no systemic safety concerns, and is therefore a valid alternative therapy for women with BV [ClinicalTrials.gov, Med380104, NCT01125410].

Use of the frc gene as a molecular marker to characterize oxalate-oxidizing bacterial abundance and diversity structure in soil.

Oxalate catabolism, which can have both medical and environmental implications, is performed by phylogenetically diverse bacteria. The formyl-CoA-transferase gene was chosen as a molecular marker of the oxalotrophic function. Degenerated primers were deduced from an alignment of frc gene sequences available in databases. The specificity of primers was tested on a variety of frc-containing and frc-lacking bacteria. The frc-primers were then used to develop PCR-DGGE and real-time SybrGreen PCR assays in soils containing various amounts of oxalate. Some PCR products from pure cultures and from soil samples were cloned and sequenced. Data were used to generate a phylogenetic tree showing that environmental PCR products belonged to the target physiological group. The extent of diversity visualised on DGGE pattern was higher for soil samples containing carbonate resulting from oxalate catabolism. Moreover, the amount of frc gene copies in the investigated soils was detected in the range of 1.64x10(7) to 1.75x10(8)/g of dry soil under oxalogenic tree (representing 0.5 to 1.2% of total 16S rRNA gene copies), whereas the number of frc gene copies in the reference soil was 6.4x10(6) (or 0.2% of 16S rRNA gene copies). This indicates that oxalotrophic bacteria are numerous and widespread in soils and that a relationship exists between the presence of the oxalogenic trees Milicia excelsa and Afzelia africana and the relative abundance of oxalotrophic guilds in the total bacterial communities. This is obviously related to the accomplishment of the oxalate-carbonate pathway, which explains the alkalinization and calcium carbonate accumulation occurring below these trees in an otherwise acidic soil. The molecular tools developed in this study will allow in-depth understanding of the functional implication of these bacteria on carbonate accumulation as a way of atmospheric CO(2) sequestration.

Transposase and cointegrase: specialized transposition proteins of the bacterial insertion sequence IS21 and related elements.

The bacterial insertion sequence IS21 shares with many insertion sequences a two-step, reactive junction transposition pathway, for which a model is presented in this review: a reactive junction with abutted inverted repeats is first formed and subsequently integrated into the target DNA. The reactive junction occurs in IS21-IS21 tandems and IS21 minicircles. In addition, IS21 shows a unique specialization of transposition functions. By alternative translation initiation, the transposase gene codes for two products: the transposase, capable of promoting both steps of the reactive junction pathway, and the cointegrase, which only promotes the integration of reactive junctions but with higher efficiency. This review also includes a survey of the IS21 family and speculates on the possibility that other members present a similar transpositional specialization.

Determination of bacterial quantity by sonication in vacum-assisted closure (VAC) foams used for treatment of chronic wounds

Background: Negative pressure wound treatment is increasingly used through a Vacuum-Assisted Closure (VAC) device in complex wound situations. For this purpose, sterile polyurethane (PU) and polyvinyl alcohol (PVA) foam dressings are fitted to the wound size and covered with an adhesive drape to create an airtight seal. Little information exists about the type and quantity of microorganisms within the foams. Therefore, we investigated VAC foams after removal from the wound using a validated method (sonication) to detect the bacterial bioburden in the foam consisting as microbial biofilms.Methods: We prospectively included VAC foams (PU and PVA, KCI, Rümlamg, Switzerland) without antibacterial additions (e.g. silver), which were removed from wounds in patients with chronic ulcers from January 2007 through December 2008. Excluded were patients with acute wound infection, necrotizing fasciitis, underlying osteomyelitis or implant. Removed foams from regular changes of dressing were aseptically placed in a container with 100 ml sterile Ringer's solution. Within 4 hours after removal, foams were sonicated for 5 min at 40 kHz (as described in NEJM 2007;357:654). The resulting sonication fluid was cultured at 37°C on aerobic blood agar plates for 5 days. Microbes were quantified as No. of colony-forming units (CFU)/ml sonication fluid and identified to the species level.Results: A total of 68 foams (38 PU and 30 PVA) from 55 patients were included in the study (median age 71 years; range 33-88 years, 57% were man). Foams were removed from the following anatomic sites: sacrum (n=29), ischium (n=18), heel (n=13), calves (n=6) and ankle (n=2). The median duration of being in place was 3 days (range, 1-8 days). In all 68 foams, bacteria were found in large quantities (median 105 CFU/ml, range 102-7 CFU/ml sonication fluid. No differences were found between PU and PVA foams. One type of organisms was found in 11 (16%), two in 17 (24%) and 3 or more in 40 (60%) foams. Gram-negative rods (Escherichia coli, Proteus mirabilis, Klebsiella pneumoniae, Acinetobacter baumanii, Pseudomonas aeruginosa) were isolated in 70%, followed by Staphylococcus aureus (20%), koagulase-negative staphylococci, streptococci (8%), and enterococci (2%).Conclusion: With sonication, a high density of bacteria present in VAC foams was demonstrated after a median of 3 days. Future studies are needed to investigate whether antimicrobial-impregnated foams can reduce the bacterial load in foams and potentially improve wound healing.

A Flora do Distrito de Aveiro : Paeoniaceae a Linaceae

O presente estudo teve como principal objectivo contribuir para o conhecimento da diversidade florística do Distrito de Aveiro, com base nos dados do Herbário da Universidade de Aveiro e revisão bibliográfica. Como é natural, este catálogo florístico não inclui todos os espécimes que se encontram depositados no herbário, mas sim uma percentagem significativa dos mesmos. Catalogou-se cerca de 178 taxa, distribuídos por 18 famílias e 86 géneros, inseridos nas famílias Paeoniaceae a Linaceae, segundo a Nova Flora de Portugal (FRANCO, 1971). Realizou-se uma análise fitogeográfica, considerando os espectros taxonómicos, biológico e corológico, incluindo também uma análise fenológica de floração e frutificação e do estatuto de conservação das plantas, relacionando-os com factores abióticos como geologia, hidrografia e bioclimatologia, factores que parecem influenciar a diversidade florística da região.

Iowa's Water - Ambient Monitoring Program: Bacterial Monitoring of Iowa's Beaches, January 2001

The Iowa Department of Natural Resources has produced an 4 page article about how to assess Iowa's streams and rivers. How to use ambient monitoring of streams and river in Iowa.

Flora de Cabo Verde

O Projecto Flora de Cabo Verde é uma iniciativa conjunta do Instituto de Investigação Científica Tropical (IICT) e do Instituto Nacional de Investigação e Desenvolvimento Agrário (INIDA) de Cabo Verde, iniciado em 1990. O objectivo do projecto é a publicação, em português e em forma de Flora, de fascículos contendo, cada um, o estudo de uma família de plantas vasculares ocorrendo no Arquipélago de Cabo Verde, tanto as nativas, em que se incluem as endémicas, como as exóticas naturalizadas. A obra é dirigida por uma Comissão Editorial constituída por dois elementos do IICT, dois do INIDA e um do Instituto Botânico de Coimbra. O estudo das diversas famílias é feito de acordo com o sistema de classificação de Cronquist, de utilização comum na região oeste-africana. O tratamento taxonómico é o mais uniforme possível. Todos os taxa são introduzidos em chaves dicotómicas para permitir uma rápida distinção com recurso a características facilmente observáveis e descritos morfologicamente. Para cada espécie ou taxon infra-específico é citada a bibliografia respectiva respeitante à área geográfica, assim como as sinonímias igualmente respeitantes à área. É referida a sua distribuição em Cabo Verde com uma ou duas citações de materiais por ilha e a distribuição mundial. São ainda feitas referências à ecologia, utilizações e nomes vulgares nas diversas ilhas. A obra é iconografada com estampas relativas a todos os géneros com espécies nativas ou naturalizadas. A base do estudo é constituída pelos materiais depositados nos diversos herbários que reconhecidamente possuem plantas colectadas na região, com particular ênfase nos Herbários do Instituto de Investigação Científica Tropical (LISC), do Instituto Nacional de Investigação e Desenvolvimento Agrário, de Cabo Verde (CECV), do Instituto Botânico da Universidade de Coimbra (COI), do Instituto Botânico da Universidade de Lisboa (LISU), do Muséum National d’Histoire Naturelle, de Paris (P) e do Botanical Garden and Museum, de Oslo (O). Quando finalizada, a Flora de Cabo Verde irá abranger mais de 700 taxa pertencentes a diversas famílias de Pteridófitos, a 97 famílias de Dicotiledóneas e a 18 famílias de Monocotiledóneas. Até à data foram publicadas 88 famílias, incluindo 232 géneros e 417 taxa. Este projecto, ao ter por finalidade o conhecimento da diversidade vegetal nas ilhas do Arquipélago, constituirá um suporte básico para outros tipos de estudos como sejam a caracterização da vegetação, a avaliação de impactos ambientais, o planeamento de políticas ambientais e agrárias ou conservação da biodiversidade.

Hemoglobin enhances the biological activity of synthetic and natural bacterial (endotoxic) virulence factors: a general principle.

Although hemoglobin (Hb) is mainly present in the cytoplasm of erythrocytes (red blood cells), lower concentrations of pure, cell-free Hb are released permanently into the circulation due to an inherent intravascular hemolytic disruption of erythrocytes. Previously it was shown that the interaction of Hb with bacterial endotoxins (lipopolysaccharides, LPS) results in a significant increase of the biological activity of LPS. There is clear evidence that the enhancement of the biological activity of LPS by Hb is connected with a disaggregation of LPS. From these findings one questions whether the property to enhance the biological activity of endotoxin, in most cases proven by the ability to increase the cytokine (tumor-necrosis-factor-alpha, interleukins) production in human mononuclear cells, is restricted to bacterial endotoxin or is a more general principle in nature. To elucidate this question, we investigated the interaction of various synthetic and natural virulence (pathogenicity) factors with hemoglobin of human or sheep origin. In addition to enterobacterial R-type LPS a synthetic bacterial lipopeptide and synthetic phospholipid-like structures mimicking the lipid A portion of LPS were analysed. Furthermore, we also tested endotoxically inactive LPS and lipid A compounds such as those from Chlamydia trachomatis. We found that the observations made for endotoxically active form of LPS can be generalized for the other synthetic and natural virulence factors: In every case, the cytokine-production induced by them is increased by the addition of Hb. This biological property of Hb is connected with its physical property to convert the aggregate structures of the virulence factors into one with cubic symmetry, accompanied with a considerable reduction of the size and number of the original aggregates.

Flora de cabo Verde: Plantas Vasculares – 55. Rhamnaceae

Árvores, arbustos, subarbustos ou lianas, raramente ervas, glabros ou com pêlos simples. Folhas alternas, raramente opostas, simples, geralmente pecioladas; limbo inteiro, dentado, serrado ou trenado, peninérveo ou com 3-5 nervuras desde a base; estípulas em regra presentes, algumas vezes espinescentes, f caducas. Inflorescências axilares, mais raramente terminais, com as flores em cimeiras, racemos ou fascículos, por vezes, unifloras. Flores brancas, esverdeadas ou amareladas, actinomórficas, periginicas ou epigínicas, bissexuadas raramente unissexuadas. Receptáculo de cónico a obcónico. Sépalas (4) 5, valvadas. Pétalas (4) 5, por vezes nulas, com frequência unguiculadas, muitas vezes cuculadas cobrindo parcial ou totalmente os estames, alternadas com as sépalas e geralmente menores que estas. Disco nectarífero em regra presente e bem desenvolvido, geralmente soldado ao hipanto, intrastaminal, livre ou unido ao ovario, muito variável na forma. Estames (4) 5, epipétalos; filetes livres, soldados à base das pétalas; anteras (1) 2-tecas, introrsas, longitudinalmente deiscentes. Ovário sincárpico, séssil, livre e súpero ou imerso no disco e ínfero ou semi-ínfero, (1) 2-3 (5)-locular; lóculos 1-ovulados com placentacão basilar; óvulos erectos, anatrópicos; estilete 2-4lobado ou 2-3-fido. Fruto urna drupa, cápsula septicida ou esquizocarpo, por vezes alado. Sementes em regra com albúmen pouco abundante, por vezes nulo; embrião grande, direito. Familia com cerca de 55 géneros e 900 espécies, distribuidas pelas regiões tropicais e subtropicais de África, América, Ásia e Austrália.