Terrence G. Gardner

Pyrosequencing Reveals Bacteria Carried in Different Wind-Eroded Sediments

Little is known about the microbial communities carried in wind-eroded sediments from various soil types and land management systems. The novel technique of pyrosequencing promises to expand our understanding of the microbial diversity of soils and eroded sediments because it can sequence 10 to 100 times more DNA fragments than previous techniques, providing enhanced exploration into what microbes are being lost from soil due to wind erosion. Our study evaluated the bacterial diversity of two types of wind-eroded sediments collected from three different organic-rich soils in Michigan using a portable field wind tunnel. The wind-eroded sediments evaluated were a coarse sized fraction with 66% of particles >106 μm (coarse eroded sediment) and a finer eroded sediment with 72% of particles <106 μm. Our findings suggested that (i) bacteria carried in the coarser sediment and fine dust were effective fingerprints of the source soil, although their distribution may vary depending on the soil characteristics because certain bacteria may be more protected in soil surfaces than others; (ii) coarser wind-eroded sediment showed higher bacterial diversity than fine dust in two of the three soils evaluated; and (iii) certain bacteria were more predominant in fine dust (, , and ) than coarse sediment ( and ), revealing different locations and niches of bacteria in soil, which, depending on wind erosion processes, can have important implications on the soil sustainability and functioning. Infrared spectroscopy showed that wind erosion preferentially removes particular kinds of C from the soil that are lost via fine dust. Our study shows that eroded sediments remove the active labile organic soil particulates containing key microorganisms involved in soil biogeochemical processes, which can have a negative impact on the quality and functioning of the source soil.

ITSxpress: Software to rapidly trim internally transcribed spacer sequences with quality scores for marker gene analysis

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.

Characterization of Microbes Carried in Dust

There is still a lack of understanding of how soil microbial community distribution is controlled by wind erosion. This information is of international concern as eroded sediments can potentially carry away the active labile organic soil particulates containing key microorganisms involved in soil biogeochemical processes, which can have a negative impact on the quality and functional potential of the soil. Pyrosequencing techniques promises to expand our understanding of the vast microbial diversity with respect to soils that experience high rates of wind erosion; because it is able to sequence 10-100 times more DNA fragments than previous techniques (traditional cloning). Our study evaluated the bacterial diversity on coarse and fine dust collected from three different silty soils in Michigan by using a portable field wind tunnel instrument. Our results indicated that Acidobacter was the predominant bacteria in these soils as well as the predominant bacteria carried via wind dispersion in coarse and fine dust from these soil sources. Soil 1, which had higher P levels than the other 2 soils, pH was basically 6 and it had higher organic matter (OM) content (47.3-55%), while showing this order of bacterial predominance: Acidobacter, Streptomyces, Levilinea, Patulibacter and Gemmatimonas. Although Streptomyces was the second most abundant bacteria in soil source 1, fine dust did not carry this species, and Levilinea was the second most predominant bacteria in this dust. Soil 2, which had lower P levels than soil 1 (within a range of 122-136 mg P kg-1), pH of about 5.5, and an intermediate OM content (42.9%) also showed the species predominance of Acidobacter followed by Patulibacter, Conexibacter, Rhizobium and Levilinea. Three of the 5 predominant bacteria in the soil source were also predominant in the fine dust except for Conexibacter and Rhizobium. Soil 3 had the lowest OM content (16.3-20.8%) of the 3 soils evaluated, and it had an average pH of 5.7, and P levels within a range of 123-153 P mg kg-1. This soil also showed a predominance of Acidobacter followed by Patulibacter, Rhizobium, Gemmatimonas, and Conexibacter. In addition to Acidobacter in fine dust, Conexibacter and Patulibacter were also carried. The coarse dust samples collected from these 3 soils demonstrated some differences in bacterial distribution compared to the fine dust, which may indicate that fine dust dispersion caused by wind erosion is the major carrier of soil predominant bacteria. The highest abundance of Acidobacter is explained by the acidic pH of these soils, and thus, it appears that they play an important ecological role in these soils functioning. Our findings suggested that bacteria carried in coarse or fine dust represent fingerprints of the soil source, but certain specific group of bacteria was more abundant in fine dust than coarse dust, revealing different niches in these soils. We are in the process of identifying the ecological role of the bacterial groups carried in these dust samples as they can have important implications on the soil sustainability and functioning. This research is focused on coupling the diversity of the soil microbial communities carried by wind erosion with biogeochemical functionality using enzymatic activities involved in nutrient cycling. This will allow us to identify keystone microbial species-assemblages associated with biogeochemical processes of the soil source.