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

Authors: DAVINIC, MARKO - Texas Tech University; FULTZ, LISA - Texas Tech University; Acosta-Martinez, Veronica; Calderon, Francisco; COX, STEPHEN - Research & Testing Laboratory; DOWD, SCOT - Research & Testing Laboratory; ALLEN, VIVIEN - Texas Tech University; ZAK, JOHN - Texas Tech University; MOORE-KUCERA, JENNIFER - Texas Tech University

Submitted to: Soil Biology and Biochemistry
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/17/2011
Publication Date: 3/1/2012
Citation: Davinic, M., Fultz, L.J., Acosta Martinez, V., Calderon, F.J., Cox, S.R., Dowd, S., Allen, V., Zak, J., Moore-Kucera, J. 2012. Pyrosequencing and mid-infrared spectroscopy techniques reveal distinct aggregate stratification of soil bacterial communities and organic matter composition. Soil Biology and Biochemistry. 46:63-72.

Interpretive Summary: Scientists from Texas Tech University in Lubbock TX and USDA-ARS in Lubbock TX and Akron CO evaluated the relationship between soil microbial diversity and the chemical composition of soil organic matter (SOM) within soil aggregates. The research is important because little is known on how SOM differences within soil aggregates can provide an environment for soil microbes key to decomposition processes and supply of nutrients to crops. Soil samples (0-5cm) were collected from the Texas High Plains region under dryland and irrigated cropping systems. Then, the soil was separated into different aggregate classes that were analyzed for: (1) bacterial composition using a nucleic acid technique named pyrosequencing, and (2) SOM quantity and quality using a combustion method and infrared spectroscopy. Results show that distinct bacterial communities are present within the different soil aggregates. Similarly, spectroscopy data revealed distinct spectra for each soil aggregate which indicates that soil aggregates differ in their organic and mineral composition, which may have implications for their resistance to decomposition and their role in carbon accumulation in soils. Combining the nucleic acid and spectroscopy techniques allowed for the first time to establish linkages between the soil bacterial groups associated to different soil aggregates and their relationship to specific soil C chemistries.

Technical Abstract: 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 a-Proteobacteria and contained the most SOC. Microaggregates showed high relative abundance of Rubrobacteriales and the least amount of SOC. Predominance within 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 1370-1450 cm-1 region for phenolic and alkyl groups (possibly recalcitrant C). Silt+clay fractions were distinguished by Gemmatimonadetes and OP10 phyla, which positively correlate with spectral absorption in the1250-1150 cm-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.