UniFrac is a β-diversity measure that uses phylogenetic information to compare environmental samples. UniFrac, coupled with standard multivariate statistical techniques including principal coordinates analysis (PCoA), identifies factors explaining differences among microbial communities. A recent simulation study concluded that UniFrac is unsuitable as a distance metric and should not be used for multivariate analysis (Schloss, 2008). We counter this argument by reassessing the data that led to this conclusion and by providing a mathematical proof showing that UniFrac is a distance metric. However, we confirm with actual sequence data that UniFrac values can be influenced by the number of sequences/sample, and recommend sequence jackknifing (that is, determining how often the cluster results are recovered using random subsets of the data) to avoid this issue.

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UniFrac: an effective distance metric for microbial community comparison

An expectation in soil ecology is that a microbial communities' fungal:bacterial dominance indicates both its response to environmental change and its impact on ecosystem function. We review a selection of the increasing body of literature on this subject and assess the relevance of its expectations by examining the methods used to determine, the impact of environmental factors on, and the expected ecosystem consequences of fungal:bacterial dominance. Considering methods, we observe that fungal:bacterial dominance is contingent on the actual measure used to estimate it. This has not been carefully considered; fungal:bacterial dominance of growth, biomass, and residue indicate different, and not directly relatable aspects, of the microbial community's influence on soil functioning. Considering relationships to environmental factors, we found that shifts in fungal:bacterial dominance were not always in line with the general expectation, in many instances even being opposite to them. This is likely because the traits expected to differentiate bacteria from fungi are often not distinct. Considering the impact of fungal:bacterial dominance on ecosystem function, we similarly found that expectations were not always upheld and this too could be due to trait overlap between these two groups. We explore many of the potential reasons why expectations related to fungal:bacterial dominance were not met, highlighting areas where future research, especially furthering a basic understanding of the ecology of bacteria and fungi, is needed. (C) 2010 Elsevier Ltd. All rights reserved. (Less)

Considering fungal:bacterial dominance in soils – Methods, controls, and ecosystem implications

Microbial processes have a central role in the global fluxes of the key biogenic greenhouse gases (carbon dioxide, methane and nitrous oxide) and are likely to respond rapidly to climate change. Whether changes in microbial processes lead to a net positive or negative feedback for greenhouse gas emissions is unclear. To improve the prediction of climate models, it is important to understand the mechanisms by which microorganisms regulate terrestrial greenhouse gas flux. This involves consideration of the complex interactions that occur between microorganisms and other biotic and abiotic factors. The potential to mitigate climate change by reducing greenhouse gas emissions through managing terrestrial microbial processes is a tantalizing prospect for the future.

Microorganisms and climate change: terrestrial feedbacks and mitigation options

Stimulation of terrestrial plant production by rising CO2 concentration is projected to reduce the airborne fraction of anthropogenic CO2 emissions. Coupled climate–carbon cycle models are sensitive to this negative feedback on atmospheric CO2, but model projections are uncertain because of the expectation that feedbacks through the nitrogen (N) cycle will reduce this so-called CO2 fertilization effect. We assessed whether N limitation caused a reduced stimulation of net primary productivity (NPP) by elevated atmospheric CO2 concentration over 11 y in a free-air CO2 enrichment (FACE) experiment in a deciduous Liquidambar styraciflua (sweetgum) forest stand in Tennessee. During the first 6 y of the experiment, NPP was significantly enhanced in forest plots exposed to 550 ppm CO2 compared with NPP in plots in current ambient CO2, and this was a consistent and sustained response. However, the enhancement of NPP under elevated CO2 declined from 24% in 2001–2003 to 9% in 2008. Global analyses that assume a sustained CO2 fertilization effect are no longer supported by this FACE experiment. N budget analysis supports the premise that N availability was limiting to tree growth and declining over time —an expected consequence of stand development, which was exacerbated by elevated CO2. Leaf- and stand-level observations provide mechanistic evidence that declining N availability constrained the tree response to elevated CO2; these observations are consistent with stand-level model projections. This FACE experiment provides strong rationale and process understanding for incorporating N limitation and N feedback effects in ecosystem and global models used in climate change assessments.

https://www.pnas.org/content/pnas/107/45/19368.full.pdf

CO2 enhancement of forest productivity constrained by limited nitrogen availability

Researchers agree that climate change factors such as rising atmospheric [CO2] and warming will likely interact to modify ecosystem properties and processes. However, the response of the microbial communities that regulate ecosystem processes is less predictable. We measured the direct and interactive effects of climatic change on soil fungal and bacterial communities (abundance and composition) in a multifactor climate change experiment that exposed a constructed old-field ecosystem to different atmospheric CO2 concentration (ambient, +300 ppm), temperature (ambient, +3 degrees C), and precipitation (wet and dry) might interact to alter soil bacterial and fungal abundance and community structure in an old-field ecosystem. We found that (i) fungal abundance increased in warmed treatments; (ii) bacterial abundance increased in warmed plots with elevated atmospheric [CO2] but decreased in warmed plots under ambient atmospheric [CO2]; (iii) the phylogenetic distribution of bacterial and fungal clones and their relative abundance varied among treatments, as indicated by changes in 16S rRNA and 28S rRNA genes; (iv) changes in precipitation altered the relative abundance of Proteobacteria and Acidobacteria, where Acidobacteria decreased with a concomitant increase in the Proteobacteria in wet relative to dry treatments; and (v) changes in precipitation altered fungal community composition, primarily through lineage specific changes within a recently discovered group known as soil clone group I. Taken together, our results indicate that climate change drivers and their interactions may cause changes in bacterial and fungal overall abundance; however, changes in precipitation tended to have a much greater effect on the community composition. These results illustrate the potential for complex community changes in terrestrial ecosystems under climate change scenarios that alter multiple factors simultaneously.

Soil microbial community responses to multiple experimental climate change drivers

Increased vegetative growth and soil carbon (C) storage under elevated carbon dioxide concentration ([CO 2 ]) has been demonstrated in a number of experiments. However, the ability of ecosystems, either above- or belowground, to maintain increased C storage relies on the response of soil processes, such as those that control nitrogen (N) mineralization, to climatic change. These soil processes are mediated by microbial communities whose activity and structure may also respond to increasing atmospheric [CO 2 ]. We took advantage of a long-term (ca 10 y) CO 2 enrichment experiment in a sweetgum plantation located in the southeastern United States to test the hypothesis that observed increases in root production in elevated relative to ambient CO 2 plots would alter microbial community structure, increase microbial activity, and increase soil nutrient cycling. We found that elevated [CO 2 ] had no detectable effect on microbial community structure using 16S rRNA gene clone libraries, on microbial activity measured with extracellular enzyme activity, or on potential soil N mineralization and nitrification rates. These results support findings at other forested Free Air [CO 2 ] Enrichment (FACE) sites.

Assessment of 10 years of CO2 fumigation on soil microbial communities and function in a sweetgum plantation

Development and validation of a citrate synthase directed quantitative PCR marker for soil bacterial communities

Molecular innovations in microbial ecology are allowing scientists to correlate microbial community characteristics to a variety of ecosystem functions. However, to date the majority of soil microbial ecology studies target phylogenetic rRNA markers, while a smaller number target functional markers linked to soil processes. We validated a new primer set targeting citrate synthase (gtlA), a central enzyme in the citric acid cycle linked to aerobic respiration. Primers for a 225 bp fragment suitable for qPCR were tested for specificity and assay performance verified on multiple soils. Clone libraries of the PCR-amplified gtlA gene exhibited high diversity and recovered most major groups identified in a previous 16S rRNA gene study. Comparisons among bacterial communities based on gtlA sequencing using UniFrac revealed differences among the experimental soils studied. Conditions for gtlA qPCR were optimized and calibration curves were highly linear (R2 > 0.99) over six orders of magnitude (4.56 10^5 to 4.56 10^11 copies), with high amplification efficiencies (>1.7). We examined the performance of the gtlA qPCR across a variety of soils and ecosystems, spanning forests, old fields and agricultural areas. We were able to amplify gtlA genes in all tested soils, and detected differences in gtlA abundance within and among environments.more » These results indicate that a fully developed gtlA-targeted qPCR approach may have potential to link microbial community characteristics with changes in soil respiration.« less

Emily E. Austin

Papers

Soil microbial community responses to multiple experimental climate change drivers

Assessment of 10 years of CO2 fumigation on soil microbial communities and function in a sweetgum plantation

Development and validation of a citrate synthase directed quantitative PCR marker for soil bacterial communities

Development and validation of a citrate synthase directed quantitative PCR marker for soil bacterial communities