Dataset Information

Rainfall-induced carbon dioxide pulses result from sequential resuscitation of phylogenetically clustered microbial groups.

ABSTRACT: The pulse of carbon dioxide (CO(2)) resulting from the first rainfall after the dry summer in Mediterranean ecosystems is so large that it is well documented at the landscape scale, with the CO(2) released in a few days comparable in magnitude to the annual net carbon exchange of many terrestrial ecosystems. Although the origin of this CO(2) is debated, we show that the pulse of CO(2) is produced by a three-step resuscitation of the indigenous microbial community. Specific phylogenetic groups of microorganisms activate and contribute to the CO(2) pulse at different times after a simulation of the first rainfall following the severe summer drought. Differential resuscitation was evident within 1 h of wet-up, with three primary response strategies apparent according to patterns of relative ribosomal quantity. Most bacteria could be classified as rapid responders (within 1 h of wet-up), intermediate responders (between 3 and 24 h after wet-up), or delayed responders (24-72 h after wet-up). Relative ribosomal quantities of rapid responders were as high in the prewet dry soils as at any other time, suggesting that specific groups of organisms may be poised to respond to the wet-up event, in that they preserve their capacity to synthesize proteins rapidly. Microbial response patterns displayed phylogenetic clustering and were primarily conserved at the subphylum level, suggesting that resuscitation strategies after wet-up of dry soil may be a phylogenetically conserved ecological trait.

SUBMITTER: Placella SA

PROVIDER: S-EPMC3390866 | biostudies-other | 2012 Jul

REPOSITORIES: biostudies-other

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Rainfall-induced carbon dioxide pulses result from sequential resuscitation of phylogenetically clustered microbial groups.

Placella Sarah A SA Brodie Eoin L EL Firestone Mary K MK

Proceedings of the National Academy of Sciences of the United States of America 20120619 27

The pulse of carbon dioxide (CO(2)) resulting from the first rainfall after the dry summer in Mediterranean ecosystems is so large that it is well documented at the landscape scale, with the CO(2) released in a few days comparable in magnitude to the annual net carbon exchange of many terrestrial ecosystems. Although the origin of this CO(2) is debated, we show that the pulse of CO(2) is produced by a three-step resuscitation of the indigenous microbial community. Specific phylogenetic groups of ...[more]

PMID: 22715291

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Project description:Microbial traits related to ecological responses and functions could provide a common currency facilitating synthesis and prediction; however, such traits are difficult to measure directly for all taxa in environmental samples. Past efforts to estimate trait values based on phylogenetic relationships have not always distinguished between traits with high and low phylogenetic conservatism, limiting reliability, especially in poorly known environments, such as soil. Using updated reference trees and phylogenetic relationships, we estimated two phylogenetically conserved traits hypothesized to be ecologically important from DNA sequences of the 16S rRNA gene from soil bacterial and archaeal communities. We sampled these communities from an environmental change experiment in California grassland applying factorial addition of late-season precipitation and soil nutrients to multiple soil types for 3 years prior to sampling. Estimated traits were rRNA gene copy number, which contributes to how rapidly a microbe can respond to an increase in resources and may be related to its maximum growth rate, and genome size, which suggests the breadth of environmental and substrate conditions in which a microbe can thrive. Nutrient addition increased community-weighted mean estimated rRNA gene copy number and marginally increased estimated genome size, whereas precipitation addition decreased these community means for both estimated traits. The effects of both treatments on both traits were associated with soil properties, such as ammonium, available phosphorus, and pH. Estimated trait responses within several phyla were opposite to the community mean response, indicating that microbial responses, although largely consistent among soil types, were not uniform across the tree of life. Our results show that phylogenetic estimation of microbial traits can provide insight into how microbial ecological strategies interact with environmental changes. The method could easily be applied to any of the thousands of existing 16S rRNA sequence data sets and offers potential to improve our understanding of how microbial communities mediate ecosystem function responses to global changes.

Project description:BackgroundWe present here the PhIGs database, a phylogenomic resource for sequenced genomes. Although many methods exist for clustering gene families, very few attempt to create truly orthologous clusters sharing descent from a single ancestral gene across a range of evolutionary depths. Although these non-phylogenetic gene family clusters have been used broadly for gene annotation, errors are known to be introduced by the artifactual association of slowly evolving paralogs and lack of annotation for those more rapidly evolving. A full phylogenetic framework is necessary for accurate inference of function and for many studies that address pattern and mechanism of the evolution of the genome. The automated generation of evolutionary gene clusters, creation of gene trees, determination of orthology and paralogy relationships, and the correlation of this information with gene annotations, expression information, and genomic context is an important resource to the scientific community.DiscussionThe PhIGs database currently contains 23 completely sequenced genomes of fungi and metazoans, containing 409,653 genes that have been grouped into 42,645 gene clusters. Each gene cluster is built such that the gene sequence distances are consistent with the known organismal relationships and in so doing, maximizing the likelihood for the clusters to represent truly orthologous genes. The PhIGs website contains tools that allow the study of genes within their phylogenetic framework through keyword searches on annotations, such as GO and InterPro assignments, and sequence similarity searches by BLAST and HMM. In addition to displaying the evolutionary relationships of the genes in each cluster, the website also allows users to view the relative physical positions of homologous genes in specified sets of genomes.SummaryAccurate analyses of genes and genomes can only be done within their full phylogenetic context. The PhIGs database and corresponding website http://phigs.org address this problem for the scientific community. Our goal is to expand the content as more genomes are sequenced and use this framework to incorporate more analyses.

Dataset Information

Rainfall-induced carbon dioxide pulses result from sequential resuscitation of phylogenetically clustered microbial groups.

Publications

Rainfall-induced carbon dioxide pulses result from sequential resuscitation of phylogenetically clustered microbial groups.

Similar Datasets

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