Oligotyping reveals stronger relationship of organic soil bacterial community structure with N-amendments and soil chemistry in comparison to that of mineral soil at Harvard Forest, MA, USA

Abstract

The impact of chronic nitrogen amendments on bacterial communities was evaluated at Harvard Forest, Petersham, MA, USA. Thirty soil samples (3 treatments × 2 soil horizons × 5 subplots) were collected in 2009 from untreated (control), low nitrogen-amended (LN; 50 kg NH4NO3 ha-1 yr-1) and high nitrogen-amended (HN; 150 kg NH4NO3 ha-1 yr-1) plots. PCR-amplified partial 16S rRNA gene sequences made from soil DNA were subjected to pyrosequencing (Turlapati et al., 2013) and analyses using oligotyping. The parameters M (the minimum count of the most abundant unique sequence in an oligotype) and s (the minimum number of samples in which an oligotype is expected to be present) had to be optimized for forest soils because of high diversity and the presence of rare organisms. Comparative analyses of the pyrosequencing data by oligotyping and operational taxonomic unit clustering tools indicated that the former yields more refined units of taxonomy with sequence similarity of ≥99.5%. Sequences affiliated with four new phyla and 73 genera were identified in the present study as compared to 27 genera reported earlier from the same data (Turlapati et al., 2013). Significant rearrangements in the bacterial community structure were observed with N-amendments revealing the presence of additional genera in N-amended plots with the absence of some that were present in the control plots. Permutational MANOVA analyses indicated significant variation associated with soil horizon and N treatment for a majority of the phyla. In most cases soil horizon partitioned more variation relative to treatment and treatment effects were more evident for the organic (Org) horizon. Mantel test results for Org soil showed significant positive correlations between bacterial communities and most soil parameters including NH4 and NO3. In mineral soil, correlations were seen only with pH, NH4, and NO3. Regardless of the pipeline used, a major hindrance for such a study remains to be the lack of reference databases for forest soils.

Ecological dynamics and co-occurrence among marine phytoplankton, bacteria and myoviruses shows microdiversity matters

“…Often these finely resolved taxa display distinct ecological dynamics, suggesting they are functionally different in ecologically relevant ways (Eren et al, 2013Tikhonov et al, 2015). These single-base pair differences are obscured by standard 16S rRNA sequence clustering techniques (for example, Reveillaud et al, 2014;Newton et al, 2015;Turlapati et al, 2015). Here we examine the extent of significant sequence variations within sequence clusters to help understand the extent to which clusters appear to be made up of a single genetic entity, that is, 'clone-line', which is a consequence of the evolutionary and ecological forces that dictate the success of taxa.…”

Impact of Land Use on Microbial Communities in the Great Bend Prairie Aquifer

“…Soils contain diverse microbial communities that can be affected by changes to the soil environment ). Tilling and compaction of soil changes soil structure, which in turn affects soil aerobic and anaerobic zones that result from oxygen availability and water percolation ability (Turlapati et al 2015;Keiluweit et al 2017). Coupled nitrificationdenitrification, specifically, has been shown to occur in the oxic and anoxic zonation of aggregates larger than 0.5 cm and increased NH4 + availability, with denitrification taking over as the dominant N-process in aggregate sizes above 1.5 cm (Kremen et al 2005;Hoffmann et al 2007;Ayoubi et al 2011).…”

“…Coupled nitrificationdenitrification, specifically, has been shown to occur in the oxic and anoxic zonation of aggregates larger than 0.5 cm and increased NH4 + availability, with denitrification taking over as the dominant N-process in aggregate sizes above 1.5 cm (Kremen et al 2005;Hoffmann et al 2007;Ayoubi et al 2011). Addition of fertilizers affects soil water pH and soil nutrient availability, which are key factors in microbial community composition (Bru et al 2011;Turlapati et al 2015). In fact, the abundance of archaea involved in nitrification can increase with decreasing soil pH; the abundance of bacteria involved in nitrification, however, tends to increase with increasing pH (Nicol et al 2008).…”

Hotspots of Sequence Variability in Gut Microbial Genes Encoding Pro-Inflammatory Factors Revealed by Oligotyping

“…The use of this entropy-based decomposition makes it possible to resolve closely related variants that differ by as little as one nucleotide at the amplified region (Eren et al, 2016). Oligotyping has been used to investigate ecological questions in diverse environments including the oral microbiota, gut microbiota, raw sewage, and soil (Mark Welch et al, 2014; Fisher et al, 2015; Turlapati et al, 2015; Vineis et al, 2016).…”