Archaea in Biogeochemical Cycles

Annual Review of Microbiology, Год журнала: 2013, Номер 67(1), С. 437 - 457

Опубликована: Июнь 29, 2013

Archaea constitute a considerable fraction of the microbial biomass on Earth. Like Bacteria they have evolved variety energy metabolisms using organic and/or inorganic electron donors and acceptors, many them are able to fix carbon from sources. thus play crucial roles in Earth's global geochemical cycles influence greenhouse gas emissions. Methanogenesis anaerobic methane oxidation important steps cycle; both performed exclusively by archaea. Oxidation ammonia nitrite is Thaumarchaeota. They represent only archaeal group that resides large numbers aerobic terrestrial marine environments Sulfur-dependent archaea confined mostly hot environments, but metal leaching acidophiles reduction sulfate anaerobic, nonthermophilic oxidizers potential impact environment. The number archaea, particular those dominating subsurface, remain be explored.

Язык: Английский

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PCR Biases Distort Bacterial and Archaeal Community Structure in Pyrosequencing Datasets

PLoS ONE, Год журнала: 2012, Номер 7(8), С. e43093 - e43093

Опубликована: Авг. 15, 2012

As 16S rRNA gene targeted massively parallel sequencing has become a common tool for microbial diversity investigations, numerous advances have been made to minimize the influence of and chimeric PCR artifacts through rigorous quality control measures. However, there little effort towards understanding effect multi-template biases on community structure. In this study, we used three bacterial archaeal mock communities consisting of, respectively, 33 24 sequences combined in different proportions compare influences (1) depth, (2) (sequencing errors artifacts), (3) PCR, interpretation structure pyrosequencing datasets. We also assessed each these variables α- β-diversity metrics that rely number OTUs alone (richness) those include both membership relative abundance detected (diversity). part redesigned primer sets target V3–V5 region gene, along with multiplexing barcodes, permit simultaneous products from two domains. conclude benefits deeper efforts extend beyond greater OTU detection result higher precision analyses by reducing variability between replicate libraries, despite presence more artifacts. Additionally, spurious resulting significant impact richness or shared-richness based metrics, whereas utilize (including OTUs) are minimally affected OTUs. greatest obstacle accurately evaluating estimated mean due associated reactions.

Язык: Английский

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Niche specialization of terrestrial archaeal ammonia oxidizers

Proceedings of the National Academy of Sciences, Год журнала: 2011, Номер 108(52), С. 21206 - 21211

Опубликована: Дек. 8, 2011

Soil pH is a major determinant of microbial ecosystem processes and potentially driver evolution, adaptation, diversity ammonia oxidizers, which control soil nitrification. Archaea are components communities contribute significantly to oxidation in some soils. To determine whether drives evolutionary adaptation community structure archaeal sequences amoA, key functional gene oxidation, were examined soils at global, regional, local scales. Globally distributed database clustered into 18 well-supported phylogenetic lineages that dominated specific ranges classified as acidic (pH <5), acido-neutral (5 ≤ <7), or alkalinophilic ≥ 7). patterns reproduced regional scales, amoA fragments amplified from DNA extracted 47 the United Kingdom 3.5-8.7), including pH-gradient formed by seven single site 4.5-7.5). High-throughput sequencing analysis identified an additional, previously undiscovered lineage revealed similar pH-associated distribution most evident for five abundant clusters. Archaeal abundance increased with pH, was only physicochemical characteristic measured influenced structure. These results suggest evolution based on adaptations niche specialization, resulting global have important consequences function nitrogen cycling.

Язык: Английский

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Bacterial community compositions of coking wastewater treatment plants in steel industry revealed by Illumina high-throughput sequencing

Bioresource Technology, Год журнала: 2014, Номер 179, С. 436 - 443

Опубликована: Дек. 20, 2014

Язык: Английский

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Biogeographic patterns in below-ground diversity in New York City's Central Park are similar to those observed globally

Proceedings of the Royal Society B Biological Sciences, Год журнала: 2014, Номер 281(1795), С. 20141988 - 20141988

Опубликована: Окт. 1, 2014

Soil biota play key roles in the functioning of terrestrial ecosystems, however, compared to our knowledge above-ground plant and animal diversity, biodiversity found soils remains largely uncharacterized. Here, we present an assessment soil biogeographic patterns across Central Park New York City that spanned all three domains life, demonstrating even urban, managed system harbours large amounts undescribed biodiversity. Despite high variability Park, below-ground diversity were predictable based on characteristics, with prokaryotic eukaryotic communities exhibiting overlapping patterns. Further, harboured nearly as many distinct microbial phylotypes types biomes globe (including arctic, tropical desert soils). This integrated cross-domain investigation highlights amount patterning novel uncharacterized at a single urban location matches observed natural ecosystems spanning multiple continents.

Язык: Английский

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