Lineages of acidophilic archaea revealed by community genomic analysis

Department of Earth and Planetary Sciences, University of California, Berkeley, CA 94720, USA.
Science (Impact Factor: 31.48). 12/2006; 314(5807):1933-5. DOI: 10.1126/science.1132690
Source: PubMed

ABSTRACT Novel, low-abundance microbial species can be easily overlooked in standard polymerase chain reaction (PCR)-based surveys. We used community genomic data obtained without PCR or cultivation to reconstruct DNA fragments bearing unusual 16S ribosomal RNA (rRNA) and protein-coding genes from organisms belonging to novel archaeal lineages. The organisms are minor components of all biofilms growing in pH 0.5 to 1.5 solutions within the Richmond Mine, California. Probes specific for 16S rRNA showed that the fraction less than 0.45 micrometers in diameter is dominated by these organisms. Transmission electron microscope images revealed that the cells are pleomorphic with unusual folded membrane protrusions and have apparent volumes of <0.006 cubic micrometer.

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    Current Biology 02/2015; DOI:10.1016/j.cub.2015.01.014 · 9.92 Impact Factor
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    ABSTRACT: Analysis of whole-community sequence data is unveiling the diversity and function of specific microbial groups within uncultured phyla and across entire microbial ecosystems Brett J. Baker and Gregory J. Dick " Somewhere, something incredible is waiting to be known. " —Carl Sagan Much like astronomy, the microbial sciences are confronted with staggering unknowns and are reliant on tools and technology to probe the fron-tiers of knowledge. The fırst realizations of just how extraordinarily diverse and unexplored mi-croorganisms are came after analyzing microbial ribosomal RNA (rRNA) gene sequences directly from environmental samples. Norm Pace of the University of Colorado, Boulder, and his collab-orators 20 years ago helped to uncover the array of microorganisms from hot springs and compa-rable environments. However, the novel microorganisms that they revealed are not restricted to extreme environ-ments. In fact, we need to look no farther than the dirt outside our homes and workplaces, the lakes and streams that provide us with water to drink, and the surfaces on and within our bodies. Pace's approach, applied to many environments, led many other microbiologists to realize that many phyla in the natural world are waiting to be dis-covered. Indeed, these ongoing efforts to learn more about microorganisms from so many dif-ferent environments continue to alter our views of the tree of life (Fig. 1 and 2). Advances in DNA sequencing techniques made it possible to move from analyzing rRNA genes to entire genomes. Although this approach, called metagenomics, is based on random shot-gun DNA sequencing of microbial communities and has proved powerful for interrogating micro-bial communities, it does not provide informa-tion about which genes are being expressed at any specifıc moment. However, whole-community transcriptomics and proteomics are helping to address questions about gene expression. Here we highlight how such whole-community omic analyses provide unique perspectives of micro-bial diversity and discuss the importance of using de novo assembly to analyze this type of data. Understanding Microbial Communities in the Wild Nearly a decade ago, Jill Banfıeld of the University of California, Berkeley, and her collaborators applied random shotgun DNA sequencing to microbial biofılms from extremely acidic waters in the Iron Mountain mine in California, assem-bling genomes for the most abundant of those microbes. Although they relied on Sanger se-quencing, whose yields are modest compared to other DNA-sequencing techniques that are now available, their efforts showed that genome se-quences could be reconstructed directly from en-vironmental samples, bypassing cultivation while SUMMARY
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    ABSTRACT: L’étude des communautés procaryotes est une part importante de l’écologie microbienne. Dans un contexte de changement climatique global, comprendre comment se structurent les communautés est nécessaire pour estimer comment les communautés sont impactées et comment les mécanismes de résilience peuvent se mettre en place. Les processus qui structurent les communautés sont de deux natures : stochastique par des événements aléatoires de dispersion, de naissance et de mort ; et déterministe par la sélection de l’habitat et les interactions entre les micro-organismes. La puissance des technologies de séquençage et du traitement informatique permet actuellement d’enrichir les connaissances sur les processus qui structurent les communautés microbiennes. Nous avons, dans le cadre du projet MIGRAMD, réalisé une étude comparative de douze sites provenant de drainage minier acide (DMA) de trois régions du monde : le sud-est de la France, le sud-ouest de la péninsule ibérique et la Bolivie. Avec un séquençage profond des gènes de l’ARNr 16S des douze sites et la mesure de paramètres physico-chimiques, nous avons montré l’importance du filtre de l’habitat sur la structuration des communautés procaryotes dont une majorité sont spécifique de cet environnement. Les relations entre les organismes sont importantes au sein des communautés, mais leur étude est compliquée surtout avec des organismes réfractaires à la culture. Les approches récentes d’études de réseaux de coocurrence peuvent nous renseigner sur ces relations. Nous avons mis en place une telle étude qui suggère des relations privilégiées entre certains micro-organismes. Une grande partie de la richesse archaea des DMA n’est pas caractérisée et elle est grandement influencée par les particularités environnementales de chaque site. Enfin nous avons étudié la diversité des transporteurs membranaires d’arsenic ArsB et Acr3 et observé des patrons d’échanges de populations entre les communautés des DMA
    11/2014, Degree: Docteur en Microbiologie, Supervisor: Beatrice Lauga, Robert Duran

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