Baross John A.

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John A.

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  • Article
    Diversity and distribution of subseafloor Thermococcales populations in diffuse hydrothermal vents at an active deep-sea volcano in the northeast Pacific Ocean
    (American Geophysical Union, 2006-12-20) Huber, Julie A. ; Butterfield, David A. ; Baross, John A.
    The presence, diversity, and distribution of a key group of subseafloor archaea, the Thermococcales, was examined in multiple diffuse flow hydrothermal vents at Axial Seamount, an active deep-sea volcano located in the northeast Pacific Ocean. A polymerase chain reaction (PCR) approach was used to determine if this group of subseafloor indicator organisms showed any phylogenetic distribution that may indicate distinct subseafloor communities at vents with different physical and chemical characteristics. Targeted primers for the Thermococcales 16S rRNA (small subunit ribosomal RNA) gene and intergenic transcribed spacer (ITS) region were designed and applied to organisms filtered in-situ directly from a variety of diffuse flow vents. Thermococcales were amplified from 9 of 11 samples examined, and it was determined that the ITS region is a better phylogenetic marker than the 16S rRNA in defining consistent groups of closely related sequences. Results show a relationship between environmental clone distribution and source vent chemistry. The most highly diluted vents with elevated iron and alkalinity contained a distinct group of Thermococcales as defined by the ITS region, suggesting separate subseafloor Thermococcales populations at diffuse vents within the Axial caldera.
  • Preprint
    Archaea and bacteria with surprising microdiversity show shifts in dominance over 1,000-year time scales in hydrothermal chimneys
    ( 2009-12-06) Brazelton, William J. ; Ludwig, Kristin A. ; Sogin, Mitchell L. ; Andreishcheva, Ekaterina N. ; Kelley, Deborah S. ; Shen, Chuan-Chou ; Edwards, R. Lawrence ; Baross, John A.
    The Lost City Hydrothermal Field, an ultramafic-hosted system located 15 km west of the Mid-Atlantic Ridge, has experienced at least 30,000 years of hydrothermal activity. Previous studies have shown that its carbonate chimneys form by mixing of ~90ºC, pH 9-11 hydrothermal fluids and cold seawater. Flow of methane and hydrogen-rich hydrothermal fluids in the porous interior chimney walls supports archaeal biofilm communities dominated by a single phylotype of Methanosarcinales. In this study, we have extensively sampled the carbonate-hosted archaeal and bacterial communities by obtaining sequences of >200,000 amplicons of the 16S rRNA V6 region and correlated the results with isotopic (230Th) ages of the chimneys over a 1200 year period. Rare sequences in young chimneys were often more abundant in older chimneys, indicating that members of the rare biosphere can become dominant members of the ecosystem when environmental conditions change. These results suggest that a long history of selection over many cycles of chimney growth has resulted in numerous closely related species at Lost City, each of which is pre-adapted to a particular set of re-occurring environmental conditions. Due to the unique characteristics of the Lost City Hydrothermal Field, these data offer an unprecedented opportunity to study the dynamics of a microbial ecosystem's rare biosphere over a thousand-year time scale.
  • Preprint
    Multiple scales of diversification within natural populations of archaea in hydrothermal chimney biofilms
    ( 2009-06-17) Brazelton, William J. ; Sogin, Mitchell L. ; Baross, John A.
    Corroborative data collected from 16S rRNA clone libraries, intergenic transcribed spacer (ITS) region clone libraries, and 16S rRNA hypervariable region tag pyrosequencing demonstrate microdiversity within single-species archaeal biofilms of the Lost City Hydrothermal Field. Both 16S rRNA clone libraries and pyrosequencing of the V6 hypervariable region show that Lost City Methanosarcinales (LCMS) biofilms are dominated by a single sequence, but the pyrosequencing dataset also reveals the presence of an additional 1654 rare sequences. Clone libraries constructed with DNA spanning the V6 hypervariable region and ITS show that multiple ITS sequences are associated with the same dominant V6 sequence. Furthermore, ITS variability differed among three chimney samples, and the sample with the highest ITS diversity also contained the highest V6 diversity as measured by clone libraries as well as tag pyrosequencing. These results indicate that the extensive microdiversity detected in V6 tag sequences is an underestimate of genetic diversity within the archaeal biofilms.
  • Article
    Evolutionary strategies of viruses, bacteria and archaea in hydrothermal vent ecosystems revealed through metagenomics
    (Public Library of Science, 2014-10-03) Anderson, Rika E. ; Sogin, Mitchell L. ; Baross, John A.
    The deep-sea hydrothermal vent habitat hosts a diverse community of archaea and bacteria that withstand extreme fluctuations in environmental conditions. Abundant viruses in these systems, a high proportion of which are lysogenic, must also withstand these environmental extremes. Here, we explore the evolutionary strategies of both microorganisms and viruses in hydrothermal systems through comparative analysis of a cellular and viral metagenome, collected by size fractionation of high temperature fluids from a diffuse flow hydrothermal vent. We detected a high enrichment of mobile elements and proviruses in the cellular fraction relative to microorganisms in other environments. We observed a relatively high abundance of genes related to energy metabolism as well as cofactors and vitamins in the viral fraction compared to the cellular fraction, which suggest encoding of auxiliary metabolic genes on viral genomes. Moreover, the observation of stronger purifying selection in the viral versus cellular gene pool suggests viral strategies that promote prolonged host integration. Our results demonstrate that there is great potential for hydrothermal vent viruses to integrate into hosts, facilitate horizontal gene transfer, and express or transfer genes that manipulate the hosts’ functional capabilities.
  • Preprint
    Biogeography and ecology of the rare and abundant microbial lineages in deep-sea hydrothermal vents
    ( 2014-11) Anderson, Rika E. ; Sogin, Mitchell L. ; Baross, John A.
    Environmental gradients generate countless ecological niches in deep-sea hydrothermal vent systems, which foster diverse microbial communities. The majority of distinct microbial lineages in these communities occur in very low abundance. However, the ecological role and distribution of rare and abundant lineages, particularly in deep, hot subsurface environments, remains unclear. Here, we use 16S rRNA tag sequencing to describe biogeographic patterning and microbial community structure of both rare and abundant archaea and bacteria in hydrothermal vent systems. We show that while rare archaeal lineages and almost all bacterial lineages displayed geographically restricted community structuring patterns, the abundant lineages of archaeal communities displayed a much more cosmopolitan distribution. Finally, analysis of one high-volume, high-temperature fluid sample representative of the deep hot biosphere described a unique microbial community that differed from microbial populations in diffuse flow fluid or sulfide samples, yet the rare thermophilic archaeal groups showed similarities to those that occur in sulfides. These results suggest that while most archaeal and bacterial lineages in vents are rare and display a highly regional distribution, a small percentage of lineages, particularly within the archaeal domain, are successful at widespread dispersal and colonization.