How will expanding taxonomic and functional molecular characterization of complex soil microbial assemblages advance our understanding of microbial ecology?

Background/Question/Methods

Application of the existing theoretical frameworks of macro-organismal community ecology to complex microbial communities promises to provide a structure and clarity to otherwise huge and overwhelmingly complex sets of data.   For many years, analysis of naturally-occurring microbial communities was limited by inability to identify prokaryotes and associate functional roles with populations.  Rapid expansion of technology for analysis of community metagenomes now enables microbial ecologists to more comprehensively and realistically describe microbial communities.  Two case studies using molecular characterization demonstrate the potentials and the pitfalls of soil microbial community analysis:  one based on 16S RNA and the other on functional genes and transcripts.

Results/Conclusions

In the first study, trajectories of subsurface bacterial assemblages receiving carbon augmentation were followed using data from high density microarray analyses.  Ordination analyses and rank abundance distributions showed that independent of the amount or type of carbon source supplied, community composition converged over a period of about 300 days.   In a second analysis, the first rainfall following a long dry period in a semi-arid ecosystem provided a large, abrupt change in the water potential that was potentially a severe physiological stress and/or a defined stimulus for the reawakening of soil microbial communities rendered inactive by low-water conditions. We followed the responses of indigenous communities of ammonia-oxidizing bacteria, ammonia-oxidizing archaea, and nitrite-oxidizing bacteria to water addition to soils from two California annual grasslands following a typically-dry Mediterranean summer. We quantified the abundance of transcripts for ammonia monooxygenases (amoA) and bacterial nitrite oxidoreductase (nxrA) in soil from 15 minutes to 72 hours after water addition. The response patterns for these three groups of nitrifiers were significantly different and were consistent in the two soils. Induction of bacterial amoA transcripts was detectable within one hour of wet-up and continued until the rate of ammonia oxidation was greater than the resupply of ammonium, suggesting that transcription can serve as a control point for ammonia oxidation in soil.  High-density microarray analysis of 16S rRNA from the wet-up soils suggested that nitrite-oxidizing Nitrobacter spp.respond in tandem with ammonia-oxidizing bacteria while nitrite-oxidizing Nitrospina and Nitrospira may not. Ammonia-oxidizing archaea appear to have a distinct temporal niche, responding after bacterial ammonia-oxidizers but maintaining activity for a longer period. Despite months of desiccation-induced inactivation, we found that transcriptional response occurs very rapidly for all three groups of soil nitrifiers.