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.

Evaluation of the soil rhizosphere has been limited by the lack of robust assessments that can explore the vast complex structure and diversity of soil microbial communities. Our objective was to combine fatty acid methyl ester (FAME) and pyrosequencing techniques to evaluate soil microbial community structure and diversity. In addition, we evaluated biogeochemical functionality of the microbial communities via enzymatic activities of nutrient cycling. Samples were taken from a silt loam at 0–10 and 10–20 cm in an organic farm under lettuce (Lactuca sativa), potato (Solanum tuberosum), onion (Allium cepa L), broccoli (Brassica oleracea var. botrytis) and Tall fescue pasture grass (Festuca arundinacea). Several FAMEs (a15:0, i15:0, i15:1, i16:0, a17:0, i17:0, 10Me17:0, cy17:0, 16:1ω5c and 18:1ω9c) varied among the crop rhizospheres. FAME profiles of the soil microbial community under pasture showed a higher fungal:bacterial ratio compared to the soil under lettuce, potato, onion, and broccoli. Soil under potato showed higher sum of fungal FAME indicators compared to broccoli, onion and lettuce. Microbial biomass C and enzyme activities associated with pasture and potato were higher than the other rhizospheres. The lowest soil microbial biomass C and enzyme activities were found under onion. Pyrosequencing revealed significant differences regarding the maximum operational taxonomic units (OTU) at 3% dissimilarity level (roughly corresponding to the bacterial species level) at 0–10 cm (581.7–770.0) compared to 10–20 cm (563.3–727.7) soil depths. The lowest OTUs detected at 0–10 cm were under broccoli (581.7); whereas the lowest OTUs found at 10–20 cm were under potato (563.3). The predominant phyla (85%) in this soil at both depths were Bacteroidetes (i.e., Flavobacteria, Sphingobacteria), and Proteobacteria. Flavobacteriaceae and Xanthomonadaceae were predominant under broccoli. Rhizobiaceae, Hyphomicrobiaceae, and Acidobacteriaceae were more abundant under pasture compared to the cultivated soils under broccoli, potato, onion and lettuce. This study found significant differences in microbial community structure and diversity, and enzyme activities of nutrient cycling in this organic farming system under different rhizospheres, which can have implications in soil health and metabolic functioning, and the yield and nutritional value of each crop.

Manganese oxides, which may be biogenically produced in both pristine and contaminated environments, have a large affinity for many trace metals.