Lineages of Acidophilic Archaea Revealed by Community Genomic Analysis

Baker, Brett J.; Tyson, Gene W.; Webb, Richard I.; Flanagan, Judith; Hugenholtz, Philip; Allen, Eric E.; Banfield, Jillian F.

doi:10.1126/science.1132690

Cited by 213 publications

(179 citation statements)

References 22 publications

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“…We further detected a singleton crenarchaeal clone from Berrocal site 2 (BE2) related to an archaeal sequence from a subsurface acid-mine drainage system (99% similar to AY082452). We also recovered several euryarchaeal sequences from AG and OR stations that clustered with nanoarchaea (89% similarity to AY652726) reported from Iron Mountain, CA, USA (Baker et al, 2006). Baker et al argued that the discovery of their novel nanoarchaea was due to their metagenomic approach and cited the use of traditional primers covering a larger portion of the gene as the cause for failed amplification attempts in the past.…”

Section: Resultsmentioning

confidence: 95%

Microbial community structure across the tree of life in the extreme Río Tinto

et al. 2010

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Understanding biotic versus abiotic forces that shape community structure is a fundamental aim of microbial ecology. The acidic and heavy metal extreme Río Tinto (RT) in southwestern Spain provides a rare opportunity to conduct an ecosystem-wide biodiversity inventory at the level of all three domains of life, because diversity there is low and almost exclusively microbial. Despite improvements in high-throughput DNA sequencing, environmental biodiversity studies that use molecular metrics and consider entire ecosystems are rare. These studies can be prohibitively expensive if domains are considered separately, and differences in copy number of eukaryotic ribosomal RNA genes can bias estimates of relative abundances of phylotypes recovered. In this study we have overcome these barriers (1) by targeting all three domains in a single polymerase chain reaction amplification and (2) by using a replicated sampling design that allows for incidencebased methods to extract measures of richness and carry out downstream analyses that address community structuring effects. Our work showed that combined bacterial and archaeal richness is an order of magnitude higher than eukaryotic richness. We also found that eukaryotic richness was highest at the most extreme sites, whereas combined bacterial and archaeal richness was highest at less extreme sites. Quantitative community phylogenetics showed abiotic forces to be primarily responsible for shaping the RT community structure. Canonical correspondence analysis revealed co-occurrence of obligate symbionts and their putative hosts that may contribute to biotic forces shaping community structure and may further provide a possible mechanism for persistence of certain low-abundance bacteria encountered in the RT.

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Section: Resultsmentioning

confidence: 95%

Microbial community structure across the tree of life in the extreme Río Tinto

et al. 2010

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“…We were therefore surprised to discover Cas9 proteins encoded in genomes of the nanoarchaea ARMAN-1 (Candidatus Micrarchaeum acidiphilum ARMAN-1) and ARMAN-4 (Candidatus Parvarchaeum acidiphilum ARMAN-4) 12,13 in acid-mine drainage (AMD) metagenomic datasets (Extended Data Table 1 and Extended Data Fig. 1).…”

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confidence: 99%

“…Indeed, cryo-electron tomographic reconstructions often identified viral particles attached to ARMAN cells 12,14 . ARMAN-1 protospacers also derived from a putative transposon within the genome of ARMAN-2 (another nanoarchaeon 13 ) and a putative mobile element in the genomes of Thermoplasmatales archaea, including that of I-plasma 15 from the same ecosystem (Extended Data Fig. 5).…”

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confidence: 99%

New CRISPR–Cas systems from uncultivated microbes

Burstein

Harrington

Strutt

et al. 2016

Nature

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CRISPR-Cas systems provide microbes with adaptive immunity by employing short sequences, termed spacers, that guide Cas proteins to cleave foreign DNA 1,2 . Class 2 CRISPR-Cas systems are streamlined versions in which a single Cas protein bound to RNA recognizes and cleaves targeted sequences 3,4 . The programmable nature of these minimal systems has enabled their repurposing as a versatile technology that is broadly revolutionizing biological and clinical research 5 . However, current CRISPR-Cas technologies are based solely on systems from isolated bacteria, leaving untapped the vast majority of enzymes from organisms that have not been cultured. Metagenomics, the sequencing of DNA extracted from natural microbial communities, provides access to the genetic material of a huge array of uncultivated organisms 6,7 . Here, using genome-resolved metagenomics, we identified novel CRISPR-Cas systems, including the first reported Cas9 in the archaeal domain of life. This divergent Cas9 protein was found in littlestudied nanoarchaea as part of an active CRISPR-Cas system. In bacteria, we discovered two

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“…General archaea primers failed to amplify an archaeal 16S rRNA gene signal. By contrary, primers deduced Ecological niches of acidophilic microorganisms S Ziegler et al from the archaeal probe ARCH915 combined with a universal primer and specific primers for the recently discovered ARMAN-enabled PCR product formation (Supplementary Table S2) (Baker et al, 2006). Sequence analysis revealed the presence of clones most closely related to the ARMAN species described by Baker et al (2006) as well as clones belonging to the Thermoplasmatales.…”

Section: Microorganisms In the Biofilmmentioning

confidence: 99%

“…Furthermore, novel archaea, called ARMAN (Archaeal Richmond Mine Acidophilic Nanoorganism) were recently discovered by shotgun sequencing of specimens that were sampled at the Iron Mountain Superfund Site in California. They belong to deeply branching lineages that were not found previously owing to mismatches of the hitherto believed universal archaea primer sets (Baker et al, 2006). Using metagenomic and proteomic data, it was assumed that these novel archaea are aerobic chemoheterotrophs.…”

Section: Introductionmentioning

confidence: 99%

Oxygen-dependent niche formation of a pyrite-dependent acidophilic consortium built by archaea and bacteria

et al. 2013

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Biofilms can provide a number of different ecological niches for microorganisms. Here, a multispecies biofilm was studied in which pyrite-oxidizing microbes are the primary producers. Its stability allowed not only detailed fluorescence in situ hybridization (FISH)-based characterization of the microbial population in different areas of the biofilm but also to integrate these results with oxygen and pH microsensor measurements conducted before. The O 2 concentration declined rapidly from the outside to the inside of the biofilm. Hence, part of the population lives under microoxic or anoxic conditions. Leptospirillum ferrooxidans strains dominate the microbial population but are only located in the oxic periphery of the snottite structure. Interestingly, archaea were identified only in the anoxic parts of the biofilm. The archaeal community consists mainly of so far uncultured Thermoplasmatales as well as novel ARMAN (Archaeal Richmond Mine Acidophilic Nanoorganism) species. Inductively coupled plasma analysis and X-ray absorption near edge structure spectra provide further insight in the biofilm characteristics but revealed no other major factors than oxygen affecting the distribution of bacteria and archaea. In addition to catalyzed reporter deposition FISH and oxygen microsensor measurements, microautoradiographic FISH was used to identify areas in which active CO 2 fixation takes place. Leptospirilla as well as acidithiobacilli were identified as primary producers. Fixation of gaseous CO 2 seems to proceed only in the outer rim of the snottite. Archaea inhabiting the snottite core do not seem to contribute to the primary production. This work gives insight in the ecological niches of acidophilic microorganisms and their role in a consortium. The data provided the basis for the enrichment of uncultured archaea.

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Lineages of Acidophilic Archaea Revealed by Community Genomic Analysis

Cited by 213 publications

References 22 publications

Microbial community structure across the tree of life in the extreme Río Tinto

Microbial community structure across the tree of life in the extreme Río Tinto

New CRISPR–Cas systems from uncultivated microbes

Oxygen-dependent niche formation of a pyrite-dependent acidophilic consortium built by archaea and bacteria

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