Jaguc — A Software Package for Environmental Diversity Analyses

Nebel, Markus E.; Wild, Sebastian; Holzhauser, Michael; Hüttenberger, Lars; Reitzig, Raphael; Sperber, Matthias; Stoeck, Thorsten

doi:10.1142/s0219720011005781

Cited by 40 publications

(34 citation statements)

References 21 publications

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“…PCR products were purified from 1% agarose gels by using the Zymoclean Gel DNA Recovery Kit (Zymo Research) and cloned into the pCR4-TOPO TA cloning vector using the TOPO TA Cloning Kit (Invitrogen) for Sanger sequencing (one 96-well plate per sample). Sequences were clustered into OTUs at 97% similarity in QIIME (35), and taxonomy of OTU representatives was assigned using JAguc (36). We present unweighted data because these clone libraries may under-sample diversity.…”

Section: Methodsmentioning

confidence: 99%

Insights into foraminiferal influences on microfabrics of microbialites at Highborne Cay, Bahamas

Bernhard

Edgcomb

Visscher

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

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Microbialites, which are organosedimentary structures formed by microbial communities through binding and trapping and/or in situ precipitation, have a wide array of distinctive morphologies and long geologic record. The origin of morphological variability is hotly debated; elucidating the cause or causes of microfabric differences could provide insights into ecosystem functioning and biogeochemistry during much of Earth's history. Although rare today, morphologically distinct, co-occurring extant microbialites provide the opportunity to examine and compare microbial communities that may be responsible for establishing and modifying microbialite microfabrics. Highborne Cay, Bahamas, has extant laminated (i.e., stromatolites) and clotted (i.e., thrombolites) marine microbialites in close proximity, allowing focused questions about how community composition relates to physical attributes. Considerable knowledge exists about prokaryotic composition of microbialite mats (i.e., stromatolitic and thrombolitic mats), but little is known about their eukaryotic communities, especially regarding heterotrophic taxa. Thus, the heterotrophic eukaryotic communities of Highborne stromatolites and thrombolites were studied. Here, we show that diverse foraminiferal communities inhabit microbialite mat surfaces and subsurfaces; thecate foraminifera are relatively abundant in all microbialite types, especially thrombolitic mats; foraminifera stabilize grains in mats; and thecate reticulopod activities can impact stromatolitic mat lamination. Accordingly, and in light of foraminiferal impacts on modern microbialites, our results indicate that the microbialite fossil record may reflect the impact of the radiation of these protists.Neoproterozoic | geobiology | sedimentology | ooid

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Section: Methodsmentioning

confidence: 99%

Insights into foraminiferal influences on microfabrics of microbialites at Highborne Cay, Bahamas

Bernhard

Edgcomb

Visscher

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

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“…In summary, pyrosequencing flowgrams that had at least one flow with signal intensity between 0.5 and 0.7 or a cycle of four nucleotide flows (TACG) that failed to give a signal 40.5 before cycle number 400 (both indicative of noise) were discarded, and all reads were truncated at cycle number 600. Pyrosequencing noise was subsequently removed using PyroNoise (Quince et al, 2011) using the default settings, and PCR noise was removed using SeqNoise (ss ¼ 0.033 and cs ¼ 0.08) (Quince et al, 2011) after truncation at 400 bp to reduce noise further.These data were then subjected to sorting, clustering and BLAST analysis with Jaguc (Version 2.1; Nebel et al, 2011). Only reads starting at the forward primer and being longer than 200 bp were further analyzed.…”

Section: Methodsmentioning

confidence: 99%

“…Genotypes of non-target genes were removed before further analysis. Sequences were affiliated to genotypes, that is, operational taxonomic units (OTUs), based on similarity cutoff values of 77%, 80% and 80% for mxaF, mch and fae, respectively, which were determined using the average neighboring method (Nebel et al, 2011). Barcode identifiers were used to determine the relative frequency of a genotype in amplicons from a certain soil after clustering.…”

Section: Methodsmentioning

confidence: 99%

Methanol oxidation by temperate soils and environmental determinants of associated methylotrophs

et al. 2012

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The role of soil methylotrophs in methanol exchange with the atmosphere has been widely overlooked. Methanol can be derived from plant polymers and be consumed by soil microbial communities. In the current study, methanol-utilizing methylotrophs of 14 aerated soils were examined to resolve their comparative diversities and capacities to utilize ambient concentrations of methanol. Abundances of cultivable methylotrophs ranged from 10 6 -10 8 g soilDW. Methanol dissimilation was measured based on conversion of supplemented 14 C-methanol, and occurred at concentrations down to 0.002 lmol methanol g soilDW À 1. Tested soils exhibited specific affinities to methanol (a 0 s ¼ 0.01 d À 1 ) that were similar to those of other environments suggesting that methylotrophs with similar affinities were present. Two deep-branching alphaproteobacterial genotypes of mch responded to the addition of ambient concentrations of methanol (p0.6 lmol methanol g soilDW) in one of these soils. Methylotroph community structures were assessed by amplicon pyrosequencing of genes of mono carbon metabolism (mxaF, mch and fae). Alphaproteobacteria-affiliated genotypes were predominant in all investigated soils, and the occurrence of novel genotypes indicated a hitherto unveiled diversity of methylotrophs. Correlations between vegetation type, soil pH and methylotroph community structure suggested that plant-methylotroph interactions were determinative for soil methylotrophs.

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“…narG and nosZ sequences shorter than 350 bp, and nirK as well as nirS sequences shorter than 300 bp were likewise excluded from further analyses. Amplicon sequences were sorted according to their barcodes and primers, and combined subsets of sequences for each structural gene (that is, containing sequences from both cryoturbated and unturbated peat soils) were clustered (that is, assigned to operational taxonomic units (OTUs)) at specieslevel threshold distances of 33% (narG (Palmer et al, 2009)), 17% (nirK (PS Depkat-Jakob, HL Drake, MA Horn, personal communication)), 18% (nirS (PS Depkat-Jakob, HL Drake, MA Horn, personal communication)) or 20% (nosZ (Palmer et al, 2009)) based on DNA sequences using the JAguc2 pipeline (http://wwwagak.informatik.uni-kl.de/research/JAguc/; Nebel et al, 2011;Supplementary Figure S1). In brief, JAguc2 generates a pairwise sequence alignment before calculation of a distance matrix and clustering with the average similarity method.…”

Section: Sequence Filtering and Analysismentioning

confidence: 99%

Contrasting denitrifier communities relate to contrasting N2O emission patterns from acidic peat soils in arctic tundra

2011

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Cryoturbated peat circles (that is, bare surface soil mixed by frost action; pH 3-4) in the Russian discontinuous permafrost tundra are nitrate-rich 'hotspots' of nitrous oxide (N 2 O) emissions in arctic ecosystems, whereas adjacent unturbated peat areas are not. N 2 O was produced and subsequently consumed at pH 4 in unsupplemented anoxic microcosms with cryoturbated but not in those with unturbated peat soil. Nitrate, nitrite and acetylene stimulated net N 2 O production of both soils in anoxic microcosms, indicating denitrification as the source of N 2 O. Up to 500 and 10 lM nitrate stimulated denitrification in cryoturbated and unturbated peat soils, respectively. Apparent maximal reaction velocities of nitrite-dependent denitrification were 28 and 18 nmol N 2 O g DW À1 h À1 , for cryoturbated and unturbated peat soils, respectively. Barcoded amplicon pyrosequencing of narG, nirK/nirS and nosZ (encoding nitrate, nitrite and N 2 O reductases, respectively) yielded E49 000 quality-filtered sequences with an average sequence length of 444 bp. Up to 19 species-level operational taxonomic units were detected per soil and gene, many of which were distantly related to cultured denitrifiers or environmental sequences. Denitrification-associated gene diversity in cryoturbated and in unturbated peat soils differed. Quantitative PCR (inhibition-corrected per DNA extract) revealed higher copy numbers of narG in cryoturbated than in unturbated peat soil. Copy numbers of nirS were up to 1000 Â higher than those of nirK in both soils, and nirS nirK À1 copy number ratios in cryoturbated and unturbated peat soils differed. The collective data indicate that the contrasting N 2 O emission patterns of cryoturbated and unturbated peat soils are associated with contrasting denitrifier communities.

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Jaguc — A Software Package for Environmental Diversity Analyses

Cited by 40 publications

References 21 publications

Insights into foraminiferal influences on microfabrics of microbialites at Highborne Cay, Bahamas

Insights into foraminiferal influences on microfabrics of microbialites at Highborne Cay, Bahamas

Methanol oxidation by temperate soils and environmental determinants of associated methylotrophs

Contrasting denitrifier communities relate to contrasting N2O emission patterns from acidic peat soils in arctic tundra

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