Open AccessJournal Article
Ammonia-oxidizing archaea and bacteria are structured by geography
Yevgeniy Marusenko,Scott T. Bates,Ian Anderson,Shannon L. Johnson,Tanya Soule,Ferran Garcia-Pichel +5 more
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In this paper, the authors used clone libraries and quantitative PCR targeting the amoA gene, which codes for the ammonia monooxygenase enzyme, universally present in ammonia-oxidizing microbes.Abstract:
IntroductionBiological soil crusts (BSCs) can dominate surface cover in dry lands worldwide, playing an integral role in arid land biogeochemistry, particularly in N fertilization through fixation and cycling. Nitrification is a characteristic and universal N transformation in BSCs that becomes important for the export of N beyond the microscopic bounds of the crust itself. The contribution of ammonia-oxidizing bacteria (AOB) in BSCs has been shown, but the role and extent of the recently discovered ammonia-oxidizing archaea (AOA) have not.MethodsWe sampled various types of crusts in four desert regions across the western United States and characterized the composition and size of ammonia-oxidizing communities using clone libraries and quantitative PCR targeting the amoA gene, which codes for the ammonia monooxygenase enzyme, universally present in ammonia-oxidizing microbes.ResultsAll archaeal amoA sequences retrieved from BSCs belonged to the Thaumarchaeota (Nitrososphaera associated Group I.1b). Sequences from the Sonoran Desert, Colorado Plateau, and Great Basin were indistinguishable from each other but distinct from those of the Chihuahuan Desert. Based on amoA gene abundances, archaeal and bacterial ammonia oxidizers were ubiquitous in our survey, but the ratios of archaeal to bacterial ammonia oxidizers shifted from bacterially dominated in northern, cooler deserts to archaeally dominated in southern, warmer deserts.ConclusionsArchaea are shown to be potentially important biogeochemical agents of biological soil crust N cycling. Conditions associated with different types of BSCs and biogeographical factors reveal a niche differentiation between AOA and AOB, possibly driven by temperature.read more
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Erratum to The chemical and functional characterization of soil N and its biotic components
Paolo Nannipieri,Paul Eldor +1 more
TL;DR: In this article, the authors describe and discuss the concepts that have been employed to interpret N mineralization-immobilization in soil, and how N turnover is related to the characteristics of organic N and the biota conducting the transformations.
Journal ArticleDOI
Photoautotrophic organisms control microbial abundance, diversity, and physiology in different types of biological soil crusts.
Stephanie Maier,Alexandra Tamm,Dianming Wu,Dianming Wu,Jennifer Caesar,Martin Grube,Bettina Weber +6 more
TL;DR: This study suggests that the photoautotrophic organisms facilitate specific microbial communities, which themselves strongly influence the overall physiological properties of biocrusts and hence local to global nutrient cycles.
Book ChapterDOI
Patterns and Controls on Nitrogen Cycling of Biological Soil Crusts
TL;DR: A large number of studies across a wide range of biomes clearly confirm that not only the presence of biocrusts but biocust community composition strongly influences N-fixation activity, with N fixation increasing with level of development as discussed by the authors.
Journal ArticleDOI
Differences in thallus chemistry are related to species-specific effects of biocrust-forming lichens on soil nutrients and microbial communities
Manuel Delgado-Baquerizo,Manuel Delgado-Baquerizo,Antonio Gallardo,Felisa Covelo,Ana Prado-Comesaña,Victoria Ochoa,Fernando T. Maestre +6 more
TL;DR: The results support the idea that, as found with vascular plants, biocrust-forming lichens have species-specific effects on soil microbial communities and C, N and P cycling.
Journal ArticleDOI
Microbial nursery production of high-quality biological soil crust biomass for restoration of degraded dryland soils
TL;DR: The results constitute an advance in the quest to actively restore biological soil covers by providing a means to obtain high-quality inoculum within a reasonable time (a few months), thereby allowing land managers to recover essential, but damaged, ecosystem services in a sustainable, self-perpetuating way as provided by biocrust communities.
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MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods
Koichiro Tamura,Daniel S. Peterson,Nicholas Peterson,Glen Stecher,Masatoshi Nei,Sudhir Kumar +5 more
TL;DR: The newest addition in MEGA5 is a collection of maximum likelihood (ML) analyses for inferring evolutionary trees, selecting best-fit substitution models, inferring ancestral states and sequences, and estimating evolutionary rates site-by-site.
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Past: paleontological statistical software package for education and data analysis
TL;DR: PAST (PAleontological STatistics) as discussed by the authors is a simple-to-use software package for executing a range of standard numerical analysis and operations used in quantitative paleontology.
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MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform
TL;DR: A simplified scoring system is proposed that performs well for reducing CPU time and increasing the accuracy of alignments even for sequences having large insertions or extensions as well as distantly related sequences of similar length.
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Canonical Correspondence Analysis: A New Eigenvector Technique for Multivariate Direct Gradient Analysis
TL;DR: In this article, a new multivariate analysis technique, called canonical correspondence analysis (CCA), was developed to relate community composition to known variation in the environment, where ordination axes are chosen in the light of known environmental variables by imposing the extra restriction that the axes be linear combinations of environmental variables.
Journal ArticleDOI
Environmental Genome Shotgun Sequencing of the Sargasso Sea
J. Craig Venter,Karin A. Remington,John F. Heidelberg,Aaron L. Halpern,Doug Rusch,Jonathan A. Eisen,Dongying Wu,Ian T. Paulsen,Karen E. Nelson,William C. Nelson,Derrick E. Fouts,Samuel Levy,Anthony H. Knap,Michael W. Lomas,Kenneth H. Nealson,Owen White,Jeremy Peterson,Jeff Hoffman,Rachel Parsons,Holly Baden-Tillson,Cynthia Pfannkoch,Yu-Hui Rogers,Hamilton O. Smith +22 more
TL;DR: Over 1.2 million previously unknown genes represented in these samples, including more than 782 new rhodopsin-like photoreceptors are identified, suggesting substantial oceanic microbial diversity.