The internally transcribed spacer (ITS) region between the small subunit ribosomal RNA gene and large subunit ribosomal RNA gene is a widely used phylogenetic marker for fungi and other taxa. The eukaryotic ITS contains the conserved 5.8S rRNA and is divided into the ITS1 and ITS2 hypervariable regions. These regions are variable in length and are amplified using primers complementary to the conserved regions of their flanking genes. Previous work has shown that removing the conserved regions results in more accurate taxonomic classification. An existing software program, ITSx, is capable of trimming FASTA sequences by matching hidden Markov model profiles to the ends of the conserved genes using the software suite HMMER. ITSxpress was developed to extend this technique from marker gene studies using Operational Taxonomic Units (OTU’s) to studies using exact sequence variants; a method used by the software packages Dada2, Deblur, QIIME 2, and Unoise. The sequence variant approach uses the quality scores of each read to identify sequences that are statistically likely to represent real sequences. ITSxpress enables this by processing FASTQ rather than FASTA files. The software also speeds up the trimming of reads by a factor of 14-23 times on a 4-core computer by temporarily clustering highly similar sequences that are common in amplicon data and utilizing optimized parameters for Hmmsearch. ITSxpress is available as a QIIME 2 plugin and a stand-alone application installable from the Python package index, Bioconda, and Github.
Recent efforts have attempted to establish emission estimates for greenhouse gas (GHGs) from agricultural soils in the United States. This research project was conducted to assess the influence of cropping system management on non-COj GHG emissions from an eastern Com Belt Alfisol. Corn (Zea mays L.) and soybean [Glydne max (L.) Merr.) rotation plots were established, as were plots in continuous management of native grasses or sorghum-sudangrass [Sorghum bicolor (L.) Moench nothossp. drummondii (Steud.) de Wet ex Davidse]. Greenhouse gas fluxes were monitored throughout each growing season from 2004 through 2007. Fluxes of N,0 were significantly correlatedwith soil temperature [P < 0.001), and thus a temperature (J^IQ) correction was made (3.48 for NjO). Nitrous oxide emissions from corn were lowest from the precision tillage treatment (2.4 kg N ha-' yr" '), significandy lower than the conventional tillage (4.9 kg N ha" yr" ) or cover crop corn treatments (5.0 kg N ha~ yr~ ). Corn-soybean and biomass-based cropping systems resulted in significantly greater NjO emissions than native grasses. There was a positive correlation between the N fertilization rate and N-f) emissions when comparing all treatments in this study. These soils were typically a sink for atmospheric CH^ for these cropping systems, and thus NjO is the primary non-COj GHGs of concern. When evaluating the entire cropping system, native grasses resulted in the lowest NjO emissions, while a corn-soybean rotation planted with precision tillage resulted in NjO emissions similar to bare soil and were significandy lower than emissions from the other cropping systems assessed.Abbreviations: GHG, greenhouse gas.
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