Pyrosequencing and mid-infrared spectroscopy reveal distinct aggregate stratification of soil bacterial communities and organic matter composition

Marko Davinic, Lisa M. Fultz, Veronica Acosta-Martinez, Francisco J. Calderón, Stephen B. Cox, Scot E. Dowd, Vivien G. Allen, John C. Zak, Jennifer Moore-Kucera

Research output: Contribution to journalArticlepeer-review

188 Scopus citations


This study integrated physical, chemical, and molecular techniques to assess relationships between soil bacterial community structures and the quantity and quality of soil organic carbon (SOC) at the soil microenvironment scale (e.g., within different aggregate size-fractions). To accomplish this goal, soil samples (0-5cm) were collected from the Texas High Plains region under a variety of dryland and irrigated cropping systems. The soil was separated into macroaggregates, microaggregates, and silt+clay fractions that were analyzed for (1) bacterial diversity via pyrosequencing of the 16s rRNA gene and (2) SOC quantity and quality using a combustion method and mid-infrared diffuse reflectance spectroscopy (mid-IR), respectively. Results from pyrosequencing showed that each soil microenvironment supported a distinct bacterial community. Similarly, mid-IR data revealed distinct spectral features indicating that these fractions were also distinguished by organic and mineral composition. Macroaggregates showed relatively high abundance of Actinobacteria (excluding order Rubrobacteriales) and α-Proteobacteria and contained the most SOC. Microaggregates showed high relative abundance of Rubrobacteriales and the least amount of SOC. Predominance within the soil microenvironment and correlations along the mid-IR spectra were different between members of the order Rubrobacteriales compared with all other members of the Actinobacteria phyla, suggesting they have different ecological niches. Mid-IR results revealed microaggregates had greater absorbance in the 1370-1450cm -1 region for phenolic and alkyl groups (possibly recalcitrant C). Silt+clay fractions were distinguished by Gemmatimonadetes and OP10 phyla, which positively correlated with spectral absorption in the1250-1150cm -1 range (indicating both degradable and recalcitrant C forms). In contrast to general diversity index measurements, distributions of the more rare bacterial phyla (phyla representing <6% of the identified population) were more important for differentiating between communities in soil microenvironments. To our knowledge, this is the first study to investigate soil bacterial communities among soil aggregates using pyrosequenging and to associate these communities to specific soil C chemistries as indicated by mid-IR absorbance.

Original languageEnglish
Pages (from-to)63-72
Number of pages10
JournalSoil Biology and Biochemistry
StatePublished - Mar 2012


  • Aggregate-size fractions
  • Mid-IR spectroscopy
  • Pyrosequencing
  • Soil bacterial communities
  • UniFrac


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