Microbiota and Microsatellite genotypes of Pacific oysters stemming from three oyster bed in the Northern Wadden Sea

Background: Studies of oyster microbiomes have revealed that a limited number of microbes, including pathogens, can dominate microbial communities in host tissues such as gills and gut. Much of the bacterial diversity however remains underexplored and unexplained, although environmental conditions and host genetics have been implicated. We used 454 next generation 16S rRNA amplicon sequencing of individually tagged PCR reactions to explore the diversity of bacterial communities in gill tissue of the invasive Pacific oyster Crassostrea gigas stemming from genetically differentiated beds under ambient outdoor conditions and after a multifaceted disturbance treatment imposing stress on the host. Results: While the gill associated microbial communities in oysters were dominated by few abundant taxa (i.e. Sphingomonas, Mycoplasma) the distribution of rare bacterial groups correlated to relatedness between the hosts under ambient conditions. Exposing the host to disturbance broke apart this relationship by removing rare phylotypes thereby reducing overall microbial diversity. Shifts in the microbiome composition in response to stress did not result in a net increase in genera known to contain potentially pathogenic strains. Conclusion: The decrease in microbial diversity and the disassociation between population genetic structure of the hosts and their associated microbiome suggest that disturbance (i.e. stress) may play a significant role for the assembly of the natural microbiome. Such community shifts may in turn also feed back on the course of disease and the occurrence of mass mortality events in oyster populations.

Fungal microbiota from rain water and pathogenicity of Fusarium species isolated from atmospheric dust and rainfall dust

In order to determine the presence of Fusarium spp. in atmospheric dust and rainfall dust, samples were collected during September 2007, and July, August, and October 2008. The results reveal the prevalence of airborne Fusarium species coming from the atmosphere of the South East coast of Spain. Five different Fusarium species were isolated from the settling dust: Fusarium oxysporum, F. solani, F. equiseti, F. dimerum, and F. proliferatum. Moreover, rainwater samples were obtained during significant rainfall events in January and February 2009. Using the dilution-plate method, 12 fungal genera were identified from these rainwater samples. Specific analyses of the rainwater revealed the presence of three species of Fusarium: F. oxysporum, F. proliferatum and F. equiseti. A total of 57 isolates of Fusarium spp. obtained from both rainwater and atmospheric rainfall dust sampling were inoculated onto melon (Cucumis melo L.) cv. Piñonet and tomato (Lycopersicon esculentum Mill.) cv. San Pedro. These species were chosen because they are the main herbaceous crops in Almeria province. The results presented in this work indicate strongly that spores or propagules of Fusarium are able to cross the continental barrier carried by winds from the Sahara (Africa) to crop or coastal lands in Europe. Results show differences in the pathogenicity of the isolates tested. Both hosts showed root rot when inoculated with different species of Fusarium, although fresh weight measurements did not bring any information about the pathogenicity. The findings presented above are strong indications that long-distance transmission of Fusarium propagules may occur. Diseases caused by species of Fusarium are common in these areas. They were in the past, and are still today, a problem for greenhouses crops in Almería, and many species have been listed as pathogens on agricultural crops in this region. Saharan air masses dominate the Mediterranean regions. The evidence of long distance dispersal of Fusarium spp. by atmospheric dust and rainwater together with their proved pathogenicity must be taken into account in epidemiological studies.

Determinación de la capacidad parasitaria de la microbiota fúngica y de sus extractos acuosos en las semillas de cardo (Cynara cardunculus L.)

El presente estudio evalúa el efecto que 6 diferentes géneros hongos aislados a partir de semillas de 54 diferentes cultivares de cardo y sus extractos acuosos tienen sobre la germinación y nascencia de las semillas. Se han realizado pruebas de patogenicidad con dos aislados de cada uno de los seis géneros de mayor frecuencia del inventario (Aspergillus, Penicillium, Fusarium, Rhizopus, Cladosporium y Alternaria), así como de los extractos producidos tras 3, 7 y 11 días de incubación de los micetos. Los resultados de las inoculaciones con los micetos muestran efectos negativos sobre los porcentajes de germinación, con reducciones en la germinación que fueron máximas tras las inoculaciones con Rhizopus stolonifer (29% de disminución) y Fusarium verticillioides (23%). Los porcentajes de emergencia disminuyen tras duplicar la concentración del inóculo, aumentando además drásticamente el número de plántulas dañadas sobre el total de las emergidas. En el significativo caso de la inoculación con Cladosporium la duplicación del inóculo disminuyó la germinación hasta en un 31% respecto al testigo. Las plántulas emergidas tras las inoculaciones con los extractos obtenidos a partir de cultivos líquidos de los hongos ensayados presentaban los mismos síntomas de atrofias y daños sobre raíz y coleóptilo que los descritos para cada hongo. Los extractos acuosos de los géneros estudiados disminuyen también la germinación. Los resultados nos muestran la diferente capacidad parasitaria de cada una de las especies estudiadas apreciándose además diferencias según los diferentes periodos de agitación de los hongos y permiten asegurar que la producción de toxinas está regulada por el hongo, y que no aumenta linealmente con el crecimiento miceliar.

Microbiota fúngica asociada a la fumagina del madroño (Arbutus unedo L.) parasitado por pulgones (Hemiptera, Aphidoidea) en la Comunidad de Madrid.

Se ha realizado un estudio sobre la microbiota fúngica asociada a la fumagina del madroño, determinándose las especies de pulgones recogidas sobre madroños muestreados en la Comunidad de Madrid (España). Las especies de pulgones del madroño encontradas en los muestreos han sido dos: Aphis arbuti Ferrari y Wahlgreniella nervata (Gillette). La especie más frecuente ha sido W. nervata cuya presencia se observó en el 80% de las muestras, mientras que A. arbuti estuvo presente en el 35% de ellas. Parecen ser especies bastante específicas del madroño, de las que no se habían recogido citas en la Comunidad de Madrid. Los análisis microbiológicos realizados sobre las hojas de madroño muestran que no existen diferencias apreciables entre las que visualmente tienen negrilla y pulgones de aquellas que están aparentemente normales. La microbiota fúngica total de las ramillas es muy semejante a la de las hojas. Sobresalen entre los géneros y/o especies Alternaria, Aspergillus, Niger, Aureobasidium, Cladosporium y Fusarium. Este último género representado por dos especies (F. dinerum y F. solari) no ha incrementado considerablemente su presencia cuando se ha utilizado un medio específico para el análisis.

Evaluación de la patogeneicidad de la microbiota fúngica asociada a cinco variedades autóctonas españolas de judión (Phaseolus coccineus L.)

Se caracterizó la micoflora presente en las semillas de 5 cultivares de judión (Phaseolus coccineus L.) procedentes de una explotación dedicada a la agricultura ecológica de Oteruelo del Valle (Parque natural de Rascafría, Madrid) y de 5 variedades incluidas en el Catálogo Común de variedades Comerciales de la Unión Europea. Se analizaron un total de 3200 semillas de todos los lotes cosechadas en la campaña 2005-2006. Para ello se colocaron 5 semillas de cada muestra en placas de Petri con medio agar de patata glucosado (PDA) y 6 semillas por muestra en cámara húmeda, realizándose 20 repeticiones en cada caso, analizándose de esta manera al menos 220 semillas por muestra. Para conocer la presencia del género Fusarium se realizaron análisis específicos con todas las muestras, utilizando para ello medio selectivo para Fusarium realizándose lecturas periódicas y anotando el número de especies presentes en cada semilla. Se identificaron un total de 11 especies fúngicas diferentes. la presencia de los diferentes géneros varió entre los cultivares estudiados, siendo mucho menor, aunque no ausente en las semillas comerciales. Entre la microbiota fúngica aislada cabe destacar, por su potencial patogeneicidd o por su capacidad para la producción de micotoxinas o metabolitos secundarios, especies de los géneros Aspergillus, Alternaria o Rhizoctonia. En una segunda parte del estudio se evaluó el efecto que dichos hongos tienen sobre la germinación y nascencia de las semillas, realizándose pruebas de patogeneicidad sobre un total de 200 semillas de Phaseolus vulgaris variedad Calgary. Las inoculaciones se realizaron con cada uno de los dos aislados de los seis géneros de mayor importancia cuantitativa del inventario(Aspergillus, Penicillium Ulocladium, Rhizopus, Cladosporium y Alternaria) Los resultados de las inoculaciones muestran efectos negativos sobre los porcentajes de germinación en todos los tratamientos estudiados y muestran la diferente capacidad parasitaria de cada una de las especies estudiadas sobre Phaseolus vulgaris.

Microbiota asociada a la enfermedad de la punta negra del trigo duro. Efectos del riego, el abonado nitrogenado y la variedad cultivada en la incidencia de la enfermedad

La enfermedad fúngica de la punta negra del trigo se caracteriza por provocar en las semillas afectadas un oscurecimiento de la zona del embrión que en ocasiones puede extenderse hacia la hendidura central dejando el grano completamente ennegrecido. Su incidencia en el cultivo de trigo es extremadamente variable y depende en gran medida de las condiciones ambientales, así pues, condiciones de alta humedad pueden incrementar a punta negra. Su presencia en el trigo duro repercute en el rendimiento semolero. Además la pasta elaborada a partir de semilla enferma presenta manchas negras y adquiere color y olor desagradable. Esta enfermedad es poco conocida a nivel europeo, sin embargo existen numerosos estudios para conocer su etiología y los factores que afectan a su aparición en países como Nueva Zelanda, Australia, Estados Unidos o Canadá. El presente trabajo pretende dar a conocer esta patología en España, determinando la influencia del riego, el abonado nitrogenado y la variedad cultivada en la incidencia de la enfermedad. Para ello se ha contado con un diseño experimental basado en 10 cultivares sembrados en parcelas con dos tratamientos de riego y dos de abonado nitrogenado. El análisis de las semillas infectadas en cámara húmeda y medios de cultivo PDA y K reveló 12 géneros fúngicos diferentes, de los cuales Alternaria alternata y Fusarium proliferatum estaban presentes en todas las muestras. El estudio del riego y abonado nitrogenado mostró diferencias significativas en la incidencia de punta negra pero fueron los 10 cultivares incluidos en el ensayo los que mayor importancia cobraron desde el punto de vista de la aparición de la enfermedad. El genotipo resultó determinante a la hora de establecer los niveles de afectación ya que las muestras encuadradas botánicamente como Triticum turgidum subsp. Turgidum convar. Turgidum presentaron una mayor susceptibilidad. las prueas de patogenicidd con los tres principales hongos asociados a la punta negra dieron resultados negativos para la germinación-nascencia de las plántulas de trigo duro inoculadas.

Respiratory microbiota resistance and resilience to pulmonary exacerbation and subsequent antimicrobial intervention

This study was supported by the UK Natural Environment Research Council (NE/H019456/1) to CJvdG, by the Wellcome Trust (WT 098051) to AWW and JP for sequencing costs, and by The Anna Trust (KB2008) to KDB. AWW and The Rowett Institute of Nutrition and Health, University of Aberdeen, receive core funding support from the Scottish Government Rural and Environmental Science and Analysis Service (RESAS). We thank Paul Scott, Richard Rance and the Wellcome Trust Sanger Institute’s sequencing team for generating 16S rRNA gene sequence data.

Special issue : The Human Intestinal Microbiota

Peer reviewed

Individual-specific changes in the human gut microbiota after challenge with enterotoxigenic Escherichia coli and subsequent ciprofloxacin treatment

IA, JNP, and MP were partly supported by the NIH, grants R01-AI-100947 to MP, and R21-GM-107683 to Matthias Chung, subcontract to MP. JNP was partly supported by an NSF graduate fellowship number DGE750616. IA, JNP, BRL, OCS and MP were supported in part by the Bill and Melinda Gates Foundation, award number 42917 to OCS. JP and AWW received core funding support from The Wellcome Trust (grant number 098051). AWW, and the Rowett Institute of Nutrition and Health, University of Aberdeen, receive core funding support from the Scottish Government Rural and Environmental Science and Analysis Service (RESAS).

Bacterial diversity within the human subgingival crevice

Molecular, sequence-based environmental surveys of microorganisms have revealed a large degree of previously uncharacterized diversity. However, nearly all studies of the human endogenous bacterial flora have relied on cultivation and biochemical characterization of the resident organisms. We used molecular methods to characterize the breadth of bacterial diversity within the human subgingival crevice by comparing 264 small subunit rDNA sequences from 21 clone libraries created with products amplified directly from subgingival plaque, with sequences obtained from bacteria that were cultivated from the same specimen, as well as with sequences available in public databases. The majority (52.5%) of the directly amplified 16S rRNA sequences were <99% identical to sequences within public databases. In contrast, only 21.4% of the sequences recovered from cultivated bacteria showed this degree of variability. The 16S rDNA sequences recovered by direct amplification were also more deeply divergent; 13.5% of the amplified sequences were more than 5% nonidentical to any known sequence, a level of dissimilarity that is often found between members of different genera. None of the cultivated sequences exhibited this degree of sequence dissimilarity. Finally, direct amplification of 16S rDNA yielded a more diverse view of the subgingival bacterial flora than did cultivation. Our data suggest that a significant proportion of the resident human bacterial flora remain poorly characterized, even within this well studied and familiar microbial environment.

Análise da microbiota intestinal em adultos com hábitos alimentares distintos e de associações com a inflamação e resistência à insulina

Introdução: A microbiota intestinal possui grande diversidade de bactérias, predominantemente dos filos Bacteroidetes e Firmicutes, com múltiplas funções. A alimentação pode alterar sua composição e função. Alto teor de gordura saturada altera a permeabilidade intestinal, eleva os lipopolissacarídeos e predispõe à inflamação subclínica crônica. Dieta rica em fibras, como a vegetariana, induz elevação de ácidos graxos de cadeia curta e benefícios metabólicos. Objetivos: Para analisar a composição da microbiota intestinal de adventistas com diferentes hábitos alimentares e associá-los à inflamação subclínica e resistência à insulina, esta tese incluiu: 1) revisão dos mecanismos que associam a alimentação à microbiota intestinal e ao risco cardiometabólico; 2) verificação da composição da microbiota intestinal segundo diferentes hábitos alimentares e de associações com biomarcadores de doenças cardiometabólicas; 3) avaliação da associação entre a abundância de Akkermansia muciniphila e o metabolismo da glicose; 4) análise da presença de enterótipos e de associações com características clínicas. Métodos: Este estudo transversal incluiu 295 adventistas estratificados segundo hábitos alimentares (vegetariano estrito, ovo-lacto-vegetariano e onívoro). Foram avaliadas associações com dados clínicos, bioquímicos e inflamatórios. O perfil da microbiota foi obtido por sequenciamento do gene 16S rRNA (Illumina® Miseq). Resultados: 1) Há evidências de que as relações entre dieta, inflamação, resistência à insulina e risco cardiometabólico são em parte mediadas pela composição da microbiota intestinal. 2) Vegetarianos apresentaram melhor perfil clínico quando comparados aos onívoros. Confirmou-se maior abundância de Firmicutes e Bacteroidetes, que não diferiram segundo a adiposidade corporal. Entretanto, vegetarianos estritos apresentaram mais Bacteroidetes, menos Firmicutes e maior abundância do gênero Prevotella quando comparados aos outros dois grupos de hábitos alimentares. Entre os ovo-lactovegetarianos verificou-se maior proporção de Firmicutes especialmente do gênero Faecalibacterium. Nos onívoros, houve super-representação do filo Proteobacteria (Succinivibrio e Halomonas) comparados aos vegetarianos. 3) Indivíduos normoglicêmicos apresentaram maior abundância de Akkermansia muciniphila que aqueles com glicemia alterada. A abundância desta bactéria correlacionou-se inversamente à glicemia e hemoglobina glicosilada. 4) Foram identificados três enterótipos (Bacteroides, Prevotella e Ruminococcaceae), similares àqueles previamente descritos. As concentrações de LDL-C foram menores no enterótipo 2, no qual houve maior frequência de vegetarianos estritos. Discussão: 1) Conhecimentos sobre participação da microbiota na fisiopatologia de doenças poderão reverter em estratégias para manipulá-la para promover saúde. 2) Apoia-se a hipótese de que hábitos alimentares se associam favorável ou desfavoravelmente a características metabólicas e inflamatórias do hospedeiro via alterações na composição da microbiota intestinal. Sugerimos que a exposição a alimentos de origem animal possa impactar negativamente nas proporções de comunidades bacterianas. 3) Sugerimos que a abundância da Akkermansia muciniphila possa participar do metabolismo da glicose. 4) Reforçamos que a existência de três enterótipos não deva ser específica de certas populações/continentes. Apesar de desconhecido o significado biológico destes agrupamentos, as correlações com o perfil lipídico podem sugerir sua utilidade na avaliação do risco cardiometabólico. Conclusões: Nossos achados fortalecem a ideia de que a composição da microbiota intestinal se altera mediante diferentes hábitos alimentares, que, por sua vez, estão associados a alterações nos perfis metabólicos e inflamatórios. Estudos prospectivos deverão investigar o potencial da dieta na prevenção de distúrbios cardiometabólicos mediados pela microbiota.

Interactions of maize bushy stunt phytoplasma with the leafhopper vector, Dalbulus maidis (Delong and Wolcott) (Hemiptera: Cicadellidae) and associated microbiota

Phytoplasmas are bacteria with a persistent propagative transmission by insect vectors that generates direct and indirect interactions among them. In order to understand these interactions for maize bushy stunt phytoplasma (MBSP) and the leafhopper vector Dalbulus maidis (Hemiptera: Cicadellidae), two research lines were addressed. The first one aimed to determine the indirect effects of maize infection by MBSP on some biological and behavioral parameters of the vector, whereas a second line investigated direct interactions of the phytoplasma with D. maidis during its movement through the vector body following acquisition from plants, and associated microbiota. Indirect effects were investigated in choice experiments in which alighting and oviposition preferences by D. maidis were compared on healthy vs. MBSP-infected plants with variable incubation time (diseased plants with early and advanced symptoms, or still asymptomatic). Likewise, indirect effect of MBSP on the D. maidis biology was determined in two life table experiments in which the vector was reared on healthy vs. MBSP-infected plants expressing advanced disease symptoms or still asymptomatic. Choice experiments showed that alighting and oviposition preferences of D. maidis on MBSP-infected plants compared to healthy plants depend on the pathogen incubation period in the plant. The leafhopper preferred MBSP-infected plants over healthy ones during the asymptomatic phase of the disease, but rejected infected plants with advanced symptoms. The vector was able to acquire MBSP from asymptomatic infected plants shortly (3 days) after inoculation, but transmission efficiency increased when acquisition occurred at later stages of the pathogen incubation period (≥14 days) in the source plants and the test plants showed disease symptoms faster. These results suggest that MBSP modulates D. maidis preference for asymptomatic infected plants in the early stages of the crop, allowing rapid spread of this pathogen. Maize infection by the phytoplasma had a neutral effect on most life table parameters of D. maidis; a lower net reproductivity rate (Ro) was observed in the cohort reared on MBSP-infected plants with advanced symptoms, which was compensated to some extent by a higher sexual ratio. MBSP acquisition by all vector nymphal stadia was confirmed by PCR, and the pathogen as detected in both male and female reproductive organs. Concerning direct MBSP-vector interactions, transmission electron microscopy analyses showed phytoplasma-like cells in the midgut lumen, microvilli and epithelial cells, suggesting that MBSP enters the epithelium midgut through the microvilli wall. Within the epithelial cells, mitochondria and bacteria-like cells (possibly endosymbionts) were observed together with masses of phythoplasma-like cells. In the hemocoel, phytoplasma-like cells grouped into a matrix were also observed in association with bacteria-like cells similar to those observed in the midgut epithelium. Similar associations were found in the salivary gland. Interestingly, in-situ hybridization (FISH) technique revealed a variation in diversity and abundance of the microbiota in intestine and salivary glands of D. maidis adults over time after MBSP acquisition from plants. Sulcia sp., Cardinium sp. and eubacteria increased their abundance over time, whereas Rickettsia sp. decreased. The frequent association of the vector microbiota with the phytoplasma in some tissues of D. maidis suggests that endosymbiotic bacteria may play some role in MBSP-vector interactions.