Title: Tag-encoded pyrosequencing analysis of bacterial diversity in a single soil type as affected by management and land use Authors
|Sun, Yan - MEDICAL BIOFILM RESEARCH|
|Allen, Vivien - TEXAS TECH UNIVERSITY|
Submitted to: Soil Biology and Biochemistry
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: July 23, 2008
Publication Date: November 1, 2008
Citation: Acosta Martinez, V., Dowd, S.E., Sun, Y., Allen, V. 2008. Tag-encoded pyrosequencing analysis of bacterial diversity in a single soil type as affected by management and land use. Soil Biology and Biochemistry. 40(11):2762-2770. Interpretive Summary: The impacts of management and land uses on the soil bacterial diversity have not been well documented. Scientists from USDA-ARS, Texas Tech University and the Medical Biofilm Research Institute of Lubbock Texas have used a novel molecular biological method to describe the diversity of a soil under four typical systems of the Texas High Plains region: two non-disturbed grass systems such as pasture [P] and Conservation Reserve Program, and two agricultural systems such as a cotton -winter wheat-corn rotation [Ct-W-Cr] and the typical practice of the region, which is continuous monoculture cotton. This method showed to be sensitive to differences in the bacterial diversity of soil as affected by the management and land uses evaluated, and it involved less labor compared to traditional methods using cloning. Due to the higher number of sequences obtained with this method, the differences in bacterial diversity in soil were possible to be characterized at different levels. Differences were noted in terms of higher number of bacteria that were detected in soil under the Ct-W-Cr rotation (285 bacteria) compared to Ct-Ct (180 bacteria). There were also distinctions among the systems in terms of diversity indexes (from higher to lower diversity): Cotton-Wheat-Corn rotation > Pasture = CRP > Continuous Cotton. Distinct differences were also found in the phyla distribution among the systems. Decomposer bacterial species of the phylum Actinobacteria were more abundant under CRP (after >10 yrs) and P (after 3 yrs) while more invasive phyla like Bacteriodetes were predominant under agricultural systems (Ct-W-Cr and Ct-Ct). In addition, differences in the distribution of G+, G- and actinomycetes were identified among the systems studied. Generally, actinomecetes were more predominant in soil under CRP. These findings should be considered in selecting management practices to improve ecosystem services and soil functions because bacteria play a key role in decomposition processes, organic matter formation and soil structure.
Technical Abstract: The impacts of management and land uses on the soil bacterial diversity have not been well documented. Here we present the use of a novel bacterial tag encoded FLX amplicon pyrosequencing (bTEFAP) diversity method, which will promote studies in soil microbiomes. Using this modified FLX pyrosequencing approach we evaluated bacterial diversity of a soil (Fine, mixed, thermic Torrertic Paleustolls) with 38% clay and 34% sand (0-5 cm) under four systems. We evaluated two non-disturbed grass systems such as pasture (Bothriochloa bladhii (Retz) S.T. Blake) [P] and Conservation Reserve Program under a diverse mixture of grasses [CRP], and two agricultural systems such as a cotton (Gossypium hirsutum L.) -winter wheat (Triticum aestivum L.)-corn (Zea mays L.) rotation [Ct-W-Cr] and the typical practice of the region, which is continuous monoculture cotton. Differences due to the land use and management were observed in the soil microbial biomass C (CRP>P=Ct-W-Cr>Ct-Ct). Using 3 estimators of diversity, the maximum number of unique sequences operational taxonomic units (OTU; roughly corresponding to the species level) never exceeded 4,500 in these soils at the 3% dissimilarity level. The following trend was found using the most common estimators of bacterial diversity: Ct-W-Cr>P=CRP>Ct-Ct. Predominant phyla in this soil were Actinobacteria, Bacteriodetes and Fermicutes. Bacteroidetes were more predominant in soil under agricultural systems (Ct-W-Cr and Ct-Ct) compared to the same soil under non-disturbed grass systems (P and CRP). The opposite trend was found for the Actinobacteria, which were more predominant under non-disturbed grass systems (P and CRP). Higher G- bacteria and lower G+ bacteria were found under Ct-W-Cr rotation and highest abundance of actinomycetes under CRP. The bTEFAP technique proved to be a powerful method to characterize the bacterial diversity of the soil studied under different management and land use in terms not only on the presence or absence, but also in terms of distribution.