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Community-level physiological profiling analyses show potential to identify the copiotrophic bacteria present in soil
Salvador Lladó1, Petr Baldrian1
1Laboratory of Environmental Microbiology, Institute of Microbiology of the CAS, Prague, Czech Republic.
Plos One
|February 8, 2017
Summary
Community-level physiological profiling (CLPP) can identify fast-growing bacteria in soil. This method, combined with sequencing, reveals that copiotrophic bacteria, like Gammaproteobacteria, are rare in forest soil despite their rapid growth on simple sugars.
Area of Science:
- Environmental microbiology
- Soil science
- Bacterial community analysis
Background:
- Community-level physiological profiling (CLPP) is widely used to assess bacterial metabolic potential.
- CLPP has limitations in characterizing entire microbial communities, especially in nutrient-poor environments like forest soil.
Purpose of the Study:
- To evaluate CLPP combined with high-throughput sequencing and qPCR for identifying the copiotrophic fraction of soil bacterial communities.
- To characterize the substrate utilization patterns and dominant taxa within the fast-growing bacterial community in coniferous forest soil and litter.
Main Methods:
- Analysis of litter and soil samples from a Czech Republic coniferous forest using BIOLOG GN2 plates.
- Application of CLPP in conjunction with high-throughput sequencing and quantitative PCR (qPCR).
- Comparison of bacterial communities in CLPP wells versus original soil and litter samples.
Main Results:
- Monosaccharides and amino acids were utilized more rapidly than other carbon substrates.
- Bacterial biodiversity decreased significantly in CLPP wells compared to the original samples.
- Communities in CLPP wells were enriched in Gammaproteobacteria and Pseudomonas, indicating these copiotrophic taxa are rare in situ.
- Abundant taxa in original samples were seldom detected as fast-growing under CLPP conditions.
Conclusions:
- CLPP is effective for detecting copiotrophic bacteria in soil environments.
- Bacterial growth and substrate utilization are highly substrate-specific.
- Copiotrophic bacteria, favored by high nutrient availability, appear to be a minor component of typical forest soil and litter bacterial communities.
