Progress 10/01/07 to 09/30/12
Outputs
OUTPUTS: At the highest level, the outputs of this research project were (1) extensive new understanding about soil microbial communities in grassland meadow soil, (2) the effect of predicted climate change on soil microbial communities, (3) the response of soil microbial communities under different climate regimes to the first fall rainfall (and associated carbon turnover), (4) the linkages between moss and microbial activity in soil and (5) a Ph.D.-trained researcher. Specifically, in the case of (5), the graduate is Dr. Karelyn Cruz, and female hispanic scientist (Pueto Rican) who is now an AAAS fellow in Washington DC. In addition to outputs(1) to (5), we conducted two linked studies on soil fungi (Dr. Anna Rosling) and soil mineral-organic interactions (Dr. Asmeret Berhe). The post doctoral training was key to professional development of two female scientists, one of whom (Asmeret Berhe), and African American, is now a faculty member at UC Merced. PARTICIPANTS: Karelyn Cruz - Ph.D. research project Anna Rosling - Post doctoral research project (independent salary funding) Blake Suttle - Post doctoral research project Asmeret Berhe - Post doctoral research project (independent salary funding) TARGET AUDIENCES: The broader scientific community (interested in climate change) Ecologists Soil biologists Climate change researchers Microbiologists PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
The research applied newly available methods for microbial characterization of soil to existing climate (rainfall) manipulation experimental plots in the Angelo Reserve in northern California. The details of the findings were reported in annual reports, and can be evaluated via the publications listed below. The effort in the past two years has been in finalizing manuscripts for publication.
Publications
- Rosling, A., Johansson, E., Suttle, K.B., van Hees, P.A.W., and Banfield J.F. (2007) Phosphorous availability influences the dissolution of apatite by soil fungi. Geobiology, 5, pp. 265-280
- Cruz-Martinez, K., Suttle, K.B., Brodie, E.L., Power, M.E., Andersen, G.L., and Banfield, J.F. (2009) Despite strong seasonal responses, soil microbial consortia are more resilient to long-term changes in rainfall than overlying grassland. ISME Journal, 1 - 7
- Cruz-Martinez, K., Rosling, A., Zhang, Y., Song, M., Andersen, G.L., Banfield, J.F. (2012) Effect of rainfall-induced soil geochemistry dynamics on grassland soil microbial communities. Appl. Environ. Microbiol. 78(21):7587. DOI: 10.1128/AEM.00203-12
- Berhe, A.A., Suttle, K.B., Burton, S.D., and Banfield, J.F. (2012) Contingency in the direction and mechanics of soil organic matter responses to increased rainfall. Plant and Soil 3581, 371 - 3383
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Progress 01/01/11 to 12/31/11
Outputs
OUTPUTS: Effect of rainfall-induced soil geochemistry dynamics on grassland soil microbial communities Here, we monitor changes in soil chemical and nutritional conditions during a natural wetting-drying episode to identify changes in soil microbial community structure. Soil samples were collected from a meadow in Northern California at four time points after the first two rainfall events of the rainy season. We used the 16S rRNA microarrays (PhyloChip) to track changes in bacterial and archaeal community composition. Microbial communities at time points one and three were significantly different than communities at time points two and four. Based on ordination analysis, available carbon, soil moisture, temperature, ammonium and pH explained most of the variation in community structure. A complementary approach using linear regression (LR) and generalized logical networks (GLN) was used to identify linear and non-linear associations among environmental variables and with the relative abundance of sub-families. Soil moisture, temperature and available carbon correlated with the relative abundance of many sub-families within the Actinobacteria, Acidobacteria, Proteobacteria, Bacteroidetes, Firmicutes, Cyanobacteria, Chloroflexi and Verrucomicrobia. Only the phylum Actinobacteria showed a lineage specific relationship to soil moisture but not carbon or nitrogen. The results indicate that use of high taxonomic rank in correlations with nutritional indicators might obscure divergent sub-family-level responses to environmental parameters. PARTICIPANTS: Karelyn Cruz-Martinez - Ph.D. student, graduate or UC Berkeley Anna Rosling (partner organization) Yang Zhang(partner organization) Mingzhou (Joe) Song(partner organization) Gary L. Andersen(partner organization) Jillian F. Banfield4 TARGET AUDIENCES: Nothing significant to report during this reporting period. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
n Mediterranean-type grassland ecosystems, the timing of rainfall events controls biogeochemical cycles as well as phenology and productivity of plants and animals. An important implication of this research is that there is short-term variation in microbial community composition driven in part by rainfall fluctuation that may not be evident in long-term studies with coarser time resolution. One paper from the past year is currently in review Effect of rainfall-induced soil geochemistry dynamics on grassland soil microbial communities. Cruz et al. Submitted to Applied and Environmental Microbiology
Publications
- No publications reported this period
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Progress 01/01/10 to 12/31/10
Outputs
OUTPUTS: The current project is proceeding with a suitably low level of activity, with most effort associated with data analysis and publication. This year, the main activity has been associated with a paper by Cruz Martinez, Rosling et al., as follows. In a Mediterranean grassland ecosystem the timing of rainfall events controls biogeochemical cycles as well as phenology and productivity of plants and animals. Here, we monitor changing geochemical conditions and microbial community structure during a natural soil moisture fluctuation to identify ecological strategies among bacteria and archaea. Soil samples were collected from a meadow in Northern California at four time points after the first two rainfall events of the winter rain season. Analysis of soil chemical parameters was performed to identify significant interaction among physical, chemical, and biological variables as well as significant changes in these over time. Using 16S rRNA microarrays (PhyloChip), we tracked changes in bacterial and archaeal community composition and the relative abundance of 400 identified sub-families. Soil moisture, available carbon, ammonium, pH, effective cation exchange capacity and soil temperature were identified as the main parameters driving the observed changes in community composition. The relative abundance of a majority of the sub-families was significantly correlated to carbon and nitrogen availability in the soil. We demonstrate how precipitation triggers natural cycles of soil geochemical processes and how these can be used to identify copiotrophic (r-selected) and oligotrophs (K-selected), ecological strategies among soil microorganisms. PARTICIPANTS: Nothing significant to report during this reporting period. TARGET AUDIENCES: Nothing significant to report during this reporting period. PROJECT MODIFICATIONS: Not relevant to this project.
Impacts
This has been one of the few projects that has employed modern molecular soil microbiology methods to analyze community structure and analyze the data in the context of soil conditions and over a temporal series. Through choice of the sampling scheme, it has been possible to study the response of the soil microbiome to rainfall after the long dry summer period an to track the responses of specific taxa.
Publications
- Karelyn Cruz Martinez, Anna Rosling Yang Zhang Mingzhou (Joe) Song Gary L. Andersen Jillian F. Banfield (2011) Rainfall induced soil geochemistry dynamics reveals ecological strategies among soil microorganism. Molecular Ecology, in review.
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Progress 01/01/09 to 12/31/09
Outputs
OUTPUTS: The primary output of this project has been the PhD thesis of Dr. Karelyn Cruz, Microbiology Graduate Group, UC Berkeley. This AES funding supported a component of her salary and research costs. A number of publications as associated with this project, as listed below. PARTICIPANTS: Karelyn Cruz TARGET AUDIENCES: Soil scientists, landscape managers, researchers in climate change, and the public PROJECT MODIFICATIONS: Not relevant to this project.
Impacts
The primary focus of the research was to discover how water impacts microbial communities in northern Californian grasslands and to evaluate associated controls on soil physical and chemical properties. By combining geochemical, physical and microbiological surveys, the study evaluated the response of soil to early fall rainfall, considering both time and depth within the soil. The long term impact of the research is an improved understanding of soil microbial community dynamics. The work in the current grant period complements a longer term investigation in a a prior grant period in which samples were collected four times per year over four years (Cruz et al. ISME J). Thus, the current research provides a much higher resolution temporal view.
Publications
- (2010) Differences in soil microbial communities underneath bryophytes and grasses. Submitted to Applied and Environmental Microbiology.
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Progress 01/01/08 to 12/31/08
Outputs
OUTPUTS: For over six years, experimental plots on a meadow adjacent to the South Fork Eel in Mendocino County, California (39˚ 43' 45" N, 123˚ 38' 40" W, Angelo Coast Range Reserve, CA) were exposed to simulations of the two major climate predictions: the Hadley model, which calls for intensified winter rainy seasons and the Canadian model, which predicts extended rains into the spring and summer. We have expanded on an earlier study revealing profound changes in plant and invertebrate diversity in the grassland plots with added spring rainfall to evaluate how simulated climate change alters the structure of soil microbial communities to compare the above ground changes with changes in the soil. In the first phase of research, and working across two years, we used state-of-the-art, high-density 16S rRNA gene microarrays to analyze the responses of bacterial and archaeal taxa in a natural grassland to the predicted alternative precipitation regimes. The microarray enabled a remarkably comprehensive (approximately 9,000 distinct taxa) analysis of soil microbial community membership and comparisons between time points and treatments allowed us to test for treatment-specific effects. We have now completed this study (Cruz et al. 2009). Data defining the membership and abundances of microorganisms in plots that received the two treatments, plus the control plots, in combination with geochemical data, indicated that soil archaeal and bacterial responses are largely decoupled from changes in the production and composition of overlying organisms. Intriguingly, however, unusual weather events induce a short-lived response in microbial communities, but the perturbation is reset annually, implying unexpected resilience of soil consortia to climate changes of the magnitude tested. However, the findings do not to indicate that microbial communities are unperturbed by changes in physical and chemical conditions (just that the seasonal responses are not significantly altered by changes in rainfall amount and distribution). In fact, we see strong annual changes in community membership. Ongoing work is currently focusing on detailed analysis of these changes across all plots. The first two-year experiment focused on soil samples collected many weeks to months apart. A more recent phase of research initiated last year examines microbial community structure changes more in response to weather events over days to weeks timescales. Samples were taken at four time points over a 22-day period following the first rainfall after the long summer drought. Geochemical parameters indicate extreme spatial heterogeneity, some statistically significant differences in conditions with time, and high variation with soil depth. Microarray analysis of the microbial response in these experiments, as well as additional soil chemical data collection, has been the focus of recent research. These results, along with a soil-under-grass vs. soil-under-moss comparison, will be included in the Ph.D. thesis of Karelyn Cruz, expected completion date May, 2009. PARTICIPANTS: Individuals: Karelyn Cruz, Ph.D. student UC Berkeley Anna Rosling, previously at UC Berkeley, now in Sweden Blake Suttle, previously at UC Berkeley, now a faculty member in the UK Eoin Brodie, collaborator, LBNL Gary Andersen, collaborator, LBNL Partner organization: Univ. Minnesota Science and Techology: National Center for Earth Surface Dynamics, C. Paola, director. Angelo Coastal Reserve, Mary Power, director. TARGET AUDIENCES: The primary target audiences are the landscape / climate change, soil science, and microbial ecology groups. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
Microorganisms exert fundamental controls on soil fertility and nutrient dynamics. Previously it has been impossible to survey the membership of soil microbial communities, preventing comparison of microbial responses to factors such as changing climate with those of plants and animals. This study examined climate changes impacts on all of these groups simultaneously. The effects of climate change on soils are uncertain, but are of great interest to the scientific community and public because of likely consequences for land use, agricultural productivity, and the natural environment. Here we show that microorganisms exhibit an unexpected degree of robustness in the face of changing climate. However, the combination of extreme weather events and altered precipitation patterns can push communities outside their window of adaptation. Ultimately, it may be the extreme events that are predicted to accompany global climate change that cause irreversible changes in soil biology. Our findings also show that, contrary to some public opinion, microorganisms are not 'canaries in the coalmine' for climate change effects.
Publications
- Cruz, K, Suttle, B., Brodie, E.L., Power, M., Andersen, G.L., and Banfield J.F. Soil microbial communities show higher resilience to effects of changing climate than overlying grassland, Nature ISME J. 2009.
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Progress 01/01/07 to 12/31/07
Outputs
OUTPUTS: For over six years, experimental plots on a meadow adjacent to the South Fork Eel in Mendocino County, California (39˚ 43' 45" N, 123˚ 38' 40" W, Angelo Coast Range Reserve, CA) have been exposed to simulations of the two major climate predictions: the Hadley model, which calls for intensified winter rainy seasons and the Canadian model, which predicts extended rains into the spring and summer. Results published recently reveal profound changes in plant and invertebrate diversity in the grassland plots with added spring rainfall but only weak changes with enhanced winter precipitation. The questions we answer in the current study are (i) does simulated climate change alter the structure of soil microbial communities, and (ii) are above ground changes paralleled by changes in subsurface consortia. We used state-of-the-art, high-density 16S rRNA gene microarrays to analyze the response of approximately 9,000 distinct bacterial and archaeal taxa in a natural grassland
to alternative precipitation regimes. Working across two consecutive years, we also compared patterns of microbial community response to responses of overlying grassland communities. Data defining the membership and abundances of microorganisms in plots that received the two treatments, plus the control plots, in combination with geochemical data, yielded two major advances: (1) soil archaeal and bacterial responses are largely decoupled from changes in the production and composition of overlying plants and (2) increases in the frequency and severity of extreme events may alter soil biology and function more than shifting baseline conditions. Given that experiments demonstrated that microbial community structure changes more in response to seasonal changes than treatments, we collected a new suite of samples to test short timescale responses. Samples were taken at four time points over a 22 day period following the first rainfall following the long summer drought. Results for
geochemical parameters on hand to date indicate extreme spatial heterogeneity, some statistically significant differences in conditions with time, and high variation with soil depth. Microarray experiments for these samples will be conducted in 2008.
PARTICIPANTS: Individuals: Karelyn Cruz, Ph.D. student UC Berkeley Anna Rosling, UC Berkeley Blake Suttle, UC Santa Cruz Eoin Brodie, collaborator, LBNL Gary Andersen, collaborator, LBNL Partner organization: Univ. Minnesota Science and Techology: National Center for Earth Surface Dynamics, C. Paola, director. Angelo Coastal Reserve, Mary Power, director.
TARGET AUDIENCES: The primary target audiences are the landscape / climate change and the soil science communities.
Impacts
Microorganisms exert fundamental controls on soil fertility and nutrient dynamics. Previously it has been impossible to survey the membership of soil microbial communities, preventing comparison of microbial responses to factors such as changing climate with those of plants and animals. This study examined climate changes impacts on all of these groups simultaneously. The effects of climate change on soils are uncertain, but are of great interest to the scientific community and public because of likely consequences for land use, agricultural productivity, and the natural environment. Here we show that microorganisms exhibit an unexpected degree of robustness in the face of changing climate. However, the combination of extreme weather events and altered precipitation patterns can push communities outside their window of adaptation. Ultimately, it may be the extreme events that are predicted to accompany global climate change that cause irreversible changes in soil
biology. Our findings also show that, contrary to some public opinion, microorganisms are not 'canaries in the coalmine' for climate change effects.
Publications
- No publications reported this period
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