Source: UNIVERSITY OF COLORADO submitted to NRP
COLLABORATIVE RESEARCH: HOW ARE ARCHAEL DIVERSITY, ABUNDANCE, AND FUNCTION REGULATED IN AGROECOSYSTEMS
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
COMPLETE
Funding Source
SPECIAL GRANT
Reporting Frequency
Annual
Accession No.
0215331
Grant No.
2008-34158-04713
Cumulative Award Amt.
$561,999.00
Proposal No.
2008-04346
Multistate No.
(N/A)
Project Start Date
Sep 1, 2008
Project End Date
Aug 31, 2013
Grant Year
2008
Program Code
[51.8A]- Microbial Biology (A): Microbial Observatories
Recipient Organization
UNIVERSITY OF COLORADO
(N/A)
BOULDER,CO 80309
Performing Department
REGENTS OF THE UNIVERSITY
Non Technical Summary
There are three domains of life: the bacteria, the archaea, and the eukarya. Of these three domains, the archaea are perhaps the least understood. Archaea are ubiquitous and abundant in soil with recent evidence suggesting that the relative abundance of archaea may be far higher in cultivated soils than in uncultivated soils. Despite their apparent abundance, we still know very little about the diversity of archaea. We know that soil archaeal communities are surprisingly diverse and that the composition of these communities is strongly influenced by changes in the soil environment, however we need a comprehensive series of studies exploring archaeal diversity and the spatiotemporal dyanmics in archaeal communities if we want to begin to address the current gap in our understanding of soil archaea. In addition to being abundant and diverse members of the soil microbial community, soil archaea may also have an important influence on belowground processess and the regulation of soil fertility. Recent studies sugest that archaea, not bacteria, may be the dominant nitrifiers in soil. If we are able to confirm this finding, it would suggest that microbiologists, by focusing on bacterial nitrifiers, have been studying the "wrong" (i.e. a minor) group of ammonia oxidizers for decades. This may have important ramifications for the study of ammonia oxidation in agroecosystems where archaea appear to be particularly abundant.
Animal Health Component
20%
Research Effort Categories
Basic
60%
Applied
20%
Developmental
20%
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
1020110110350%
2010110110350%
Knowledge Area
102 - Soil, Plant, Water, Nutrient Relationships; 201 - Plant Genome, Genetics, and Genetic Mechanisms;

Subject Of Investigation
0110 - Soil;

Field Of Science
1103 - Other microbiology;
Goals / Objectives
The archaea represent one of the three domains of life. Despite their relatively high abundance in cultivated soils, soil archaea have never been cultured and their role is not clear. Recent evidence suggests that at least some of the soil archaea are involved in ammonia oxidation and they may play a dominant role in this function, yet the ammonia oxidizing activity of these soil organisms is unknown. Likewise there is also some evidence that soil archaea may be far more abundant in cultivated soils than in uncultivated soil. However, this needs to be tested in a rigorous way in multiple locations. The specific effects of disturbance, succession, N fertilization, and cropping systems on the abundance and diversity of these soil organisms is not known. We will determine how agroecosystems influence the diversity, abundance, and function of archaea in soil. Specifically, the proposed work is focused on three objectives: 1) to determine the abundance and diversity of archaea in treatments that vary in disturbance, succession, and N fertilization regimes; 2) to determine archeal and bacterial abundance and diversity in response to changes in cropping systems and soil pH; and 3) to determine the ammonia oxidizing activity of soil archaea compare to that of ammonia oxidizing bacteria.
Project Methods
Soils from various experiments will be sampled once monthly during the growing season from field treatments that vary in N fertilization, succession, cropping systems, and disturbance. Three tiers of analyses will be performed on DNA extracted from the soil samples. In the first tier, quantitative PCR will be used to estimate the abundance of bacteria, archaea, and the archaeal ammonia monooxygenase gene. In the second tier, we will use a newly developed bar coded pyrosequencing technique in order to analyze the diversity and structure of archaeal communities in hundreds of samples in a given pyrosequencing run. In the third tier, we will use biochemical approaches to distinguish the activities of ammonia oxidizing archaea and bacteria. The analyses proposed for the first two tiers involve the development of new molecular methods and methods of DNA sequence analyses. We expect that these new methods will represent valuable contributions to numerous fields, including microbiology, molecular biology, and the applied agricultural sciences.

Progress 09/01/08 to 08/31/13

Outputs
Target Audience: Our primary objective was to describe the composition and diversity of soil archaeal communities across biomes, the climate and soil edaphic factors driving observed shifts in archaeal community structure, and the phylogeny of the dominant soil archaeal taxa. In addition, we examined how amending soils with nitrogen-based fertilizers influences the composition of both archaeal and bacterial communities, the functioning of these communities, and their phylogenetic structure. The completed work and the associated publications are likely to be of interest to researchers in a wide range of fields including soil ecology, microbial ecology, and soil biogeochemistry. More generally, the work will be useful to those individuals seeking to monitor soil health, promote soil fertility, and manage those ecosystem services provided by the microorganisms living in soil. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? This grant directly supported the training of three graduate students in my lab group, Kelly Ramirez, Gaddy Bergmann, and Christopher Gray. These students used a combination of molecular techniques and process-level measurements to explore nitrogen effects on microbial communities in both agricultural and non-agricultural sites. In addition, four undergraduate students gained valuable research experience by working on portions of the projects described above. How have the results been disseminated to communities of interest? Results have been published in 10 peer-reviewed publications, including high-profile scientific journals (e.g. Nature and Science). Project results have been presented at international scientific meetings (including meetings held by the International Society for Microbial Ecology, the Ecological Society of America, and the Soil Ecology Society) and numerous institutions worldwide. What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? To date, this funding has directly supported 10 publications published in peer-reviewed scientific journals (see citations below) – including papers published in Nature and Science. We have completed a large cross-site study of soil archaeal communities, a more detailed set of studies of how archaeal and bacterial communities shift across long-term experimental nitrogen gradients, and an integrated study of how changes in soil microbial communities associated with nitrogen fertilization influences soil carbon dynamics. Project results have been presented at international scientific meetings (including meetings held by the International Society for Microbial Ecology, the Ecological Society of America, and the Soil Ecology Society) and numerous institutions worldwide. Our key project findings are summarized below. 1) Soils across the globe are dominated by archaea within the crenarchaeotal 1.1b group. In particular, two phylotypes account for >75% of the >150,000 archaeal sequences recovered from >140 individual soils. This result is surprising as it suggest that, unlike bacteria, soil archaeal communities are dominated by just a few taxa and these taxa are not closely related to cultured archaeal isolates. 2) The relative abundance of soil archaea is highly variable across soils, ranging from >15% of the prokaryotic community to essentially undetectable. The relative abundance of archaea is not predictable from measured site or soil characteristics, highlighting that the ecological niches inhabited by archaea remain largely undetermined. However, we found that one dominant archaeal phylotype strongly co-occurs with bacterial methane oxidizers suggesting that this phylotype may be associated, directly or indirectly, with methane oxidation. 3) We examined shifts in the bacterial communities and the archaeal communities across two long-term nitrogen fertilization gradients. At both sites we observed consistent shifts in bacterial community composition with nitrogen, whether we used phylogenetic or taxonomic metrics of community composition. In contrast to the pronounced shifts in bacterial community composition and in direct contrast to the patterns often observed in plant communities, increases in N availability did not have consistent effects on the richness and diversity of soil bacterial communities. Archaeal communities (and archaeal:bacterial ratios) were largely unaffected by N fertilization, suggesting that the dominant archaeal populations in soil may not be ammonia oxidizers. 4) More recent work built on the archaeal and bacterial community analyses by using shotgun metagenomics and catabolic assays to examine the functional responses of the microbial communities across the nitrogen gradients. We demonstrated that nitrogen fertilization favors copiotrophic microbial taxa over more oligotrophic taxa, reducing the catabolic capabilities of the microbial communities and, perhaps, contributing to the widely-observed inhibition of microbial respiration rates with nitrogen additions. Moreover, we have demonstrated that additions of nitrogen fertilizer result in predictable shifts in the amounts and types of antibiotic-resistant genes found within soil bacterial communities.

Publications

  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Forsberg, K.J., S. Patel, M.K. Gibson, C.L. Lauber, R. Knight, N. Fierer, G. Dantas. 2014. Bacterial phylogeny structures soil resistomes across habitats. Nature. 509:612-616.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Fierer, N., J. Ladau, J.C. Clemente, J. Leff, S.M. Owens, K.S. Pollard, R. Knight, J.A. Gilbert. R. L. McCulley. 2013. Reconstructing the microbial diversity and function of pre-agricultural tallgrass prairie soils in the United States. Science. 342: 621-624.
  • Type: Journal Articles Status: Published Year Published: 2012 Citation: Barber�n, A., S.T. Bates, E.O. Casamayor, N. Fierer. 2012. Using network analysis to explore co-occurrence patterns in soil microbial communities. ISME Journal. 6: 343-351.
  • Type: Journal Articles Status: Published Year Published: 2010 Citation: Ramirez, K.S., C.L. Lauber, R. Knight, M. A. Bradford, N. Fierer. 2010. Consistent effects of nitrogen fertilization on the phylogenetic composition of soil bacterial communities in contrasting systems. Ecology. 91: 3463-3470.
  • Type: Journal Articles Status: Published Year Published: 2010 Citation: Ramirez, K.S., J.M. Craine, N. Fierer. 2010. Nitrogen fertilization inhibits soil microbial respiration regardless of the form of nitrogen applied. Soil Biology & Biochemistry. 42: 2336-2338.
  • Type: Journal Articles Status: Published Year Published: 2012 Citation: Ramirez, K.S., J.M. Craine, N. Fierer. 2012. Consistent effects of nitrogen amendments on soil microbial communities and processes across biomes. Global Change Biology. 18: 1918-1927.
  • Type: Journal Articles Status: Published Year Published: 2012 Citation: Fierer, N., C.L. Lauber, K.S. Ramirez, J. Zaneveld, M.A. Bradford, R. Knight. 2012. Comparative metagenomic, phylogenetic, and physiological analyses of soil microbial communities across nitrogen gradients. ISME Journal. doi:10.1038/ismej.2011.159
  • Type: Journal Articles Status: Published Year Published: 2012 Citation: Gray, C.M., N. Fierer. 2012. Impacts of nitrogen fertilization on volatile organic compound emissions from decomposing plant litter. Global Change Biology. 18: 739-748
  • Type: Journal Articles Status: Published Year Published: 2011 Citation: Bates, S.T., D. Berg-Lyons, J.G. Caporaso, W.A. Walters, R. Knight, and N. Fierer. 2011. Examining the global distribution of dominant archaeal populations in soil. ISME Journal. 5: 908-917.
  • Type: Journal Articles Status: Published Year Published: 2011 Citation: Bergmann, G.T., S.T. Bates, K.G. Eilers, C.L. Lauber, J.G. Caporaso, W.A. Walters, R. Knight, N. Fierer. 2011. The under-recognized dominance of Verrucomicrobia in soil bacterial communities. Soil Biology & Biochemistry. 43: 1450-1455.


Progress 09/01/08 to 08/31/09

Outputs
OUTPUTS: To date, this funding has supported the education of one Ph.D. student (Kelly Ramirez) and has partially supported the education of one postdoctoral researcher (Dr. Christian Lauber). With their efforts and the efforts of my collaborator on this project (Dr. Rob Knight), this funding has yielded the following outputs: 1) Development of a high-throughput pyrosequencing method to survey soil archaeal communities. More specifically, we have developed a barcoded pyrosequencing method and a primer test that will allow us to conduct sequence-based surveys of both bacterial and archaeal communities simultaneously. This technique not only allows us to survey communities from individual samples in greater details (obtaining many of thousands of sequences per sample), we can also analyze >100 samples in a given pyrosequencing run. This technique has already been described in the publications listed below. 2) Development of a bioinformatics pipeline that allows us to handle high-throughput pyrosequencing data from soil archaeal surveys. This pipeline will allow researchers to, for the first time, analyze soil archaeal communities in a streamlined and comprehensive manner. The software will be freely available to the public within three months. 3) We have completed a comprehensive spatial and temporal sampling of experimental plots at the Cedar Creek Ecosystem Science Reserve in Minnesota, the Kellogg Biological Station in Michigan, and the Nelson Environmental Studies Area in eastern Kansas. The collected soils from these plots have already been analyzed and the results presented at talks given at universities within the U.S. (Northern Arizona Univ., Rutgers Univ. , Duke Univ.) and at international meetings (annual meetings of the Soil Ecology Society and the Ecological Society of America). In addition, the results from these projects (explained in more detail below) have been integrated into my general microbiology course (150 students enrolled) to illustrate fundamental principles in soil microbiology. 4) Current work is expanding on the results from the projects described above to further explore the phylogenetic, physiological, and ecological characteristics of soil archaea. We expect to continue disseminating research findings via meeting presentations and peer-reviewed publications. PARTICIPANTS: Dr. Christian Lauber: Postdoctoral researcher directly working on this project. Kelly Ramirez: Ph.D. student exploring nitrogen effects on soil archaeal communities. Dr. Rob Knight: collaborator on all aspects of the methods development associated with the proposed work. Spencer Debenport, Kaitlyn Hoyt, Garrett Cropsey: undergraduate student working on various aspects of this project. TARGET AUDIENCES: Nothing significant to report during this reporting period. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

Impacts
With our development of the high-throughput pyrosequencing method and the associated bioinformatics pipeline described above, we have conducted the first comprehensive survey of soil archaeal and bacterial communities across a wide range of soil types. We have found that archaeal 16S rRNA gene copies are, on average, 5% of bacterial 16S rRNA gene copies and this ratio is highly variable. The ratio of archaeal:bacterial gene copies is unaffected by soil nitrogen levels or fertilization treatments, suggesting that the size of soil archaeal population sizes is not strongly influenced by nitrogen availability. However, archaea seem to be most abundant in arid soils and temperate forest soils, suggesting that they have predictable ecological attributes. In addition, we find that archaeal communities in soil are highly diverse, with most soils having a relatively large abundance of novel (or poorly described) crenarchaeotal taxa. Our sampling of the long-term nitrogen addition experiments in Minnesota, Michigan, and Kansas have shown that both soil bacterial and archaeal communities respond in a predictable manner to increased nitrogen availability. In particular, we see relative increases in gamma-Proteobacteria, Bacteroidetes, alpha-Proteobacteria, and specific crenarcheotal groups with increased nitrogen inputs. Our current hypothesis is that these shifts in bacterial and archaeal communities are largely driven by the fertilization effects on plant productivity (i.e. increased C availability to the microbial communities). We are currently testing this hypothesis with more controlled laboratory experiments.

Publications

  • Fierer, N., M.S. Strickland, D. Liptzin, M.A. Bradford, C.C. Cleveland. 2009. Global patterns in belowground communities. Ecology Letters.
  • Lauber, C.L., R. Knight, M. Hamady, N. Fierer. 2009. Soil pH as a predictor of soil bacterial community structure at the continental scale: a pyrosequencing-based assessment. Applied & Environmental Microbiology.75:5111-5120.
  • Jones, R.T., M.S. Robeson, C.L.. Lauber, M. Hamady, R. Knight, N. Fierer. 2009. A comprehensive survey of soil acidobacterial diversity using pyrosequencing and clone library analyses. Int. Soc. for Microbial Ecology Journal. 3:442-453.