This Science Focus Area (SFA) aims to inform climate modeling and enable carbon management in terrestrial ecosystems. To achieve these aims, our program develops and uses community genomics approaches to discover widespread biological processes that control carbon storage and release in temperate biome soils. We are building on our model-community approach to discover traits that drive carbon cycling variation. Our proposed work follows a progression in system complexity that will lead in a later phase to application of validated, trait-based models in field studies. We use metagenomic, metatranscriptomic, stable-isotope probing, chemical profiling, and machine learning approaches to understand how model communities with substantial differences in carbon flow interact with environmental factors to control ecosystem carbon cycling under N deposition. This SFA merges DOE strengths in microbial genomics, computation, user-facility capabilities, and ecosystem science.
Our research objectives address BER grand challenges to discover widespread microbiological processes that influence ecosystem C cycling under altered environmental regimes (Grand Challenge 4.1) and to define the associated traits that ‘predict larger-scale ecosystem phenomena for an Earth system understanding’ (Grand Challenges 4.2 and 4.3).
The central concept of our proposed work is that microbial community variation creates a distribution of possible outcomes for every component of the C cycle in soil. Identifying the community features that create substantial variation in C cycling provides the foundational knowledge to define essential mechanisms (ecological traits) to improve modeling and management of soil C in natural ecosystems. Essential components of C-cycling subject to microbial modification include:
- Transformation of plant particulate organic matter (POM) at the soil surface & in the subsurface into dissolved organic carbon (DOC) stabilized by the soil matrix
- Transformation of plant DOC into other products stabilized by the soil matrix
- Transformation of microbial particulate organic matter (POM) or DOC into products stabilized by the soil matrix
- Destabilization and transformation of mineral-bound SOM or SOM within aggregates
- Modulation of plant primary production and spatial allocation of C to soil
The objectives below aim to characterize the breadth of community-driven variation that is possible for C-cycle components, exploit the observed distributions to discover the mechanistic processes (ecological traits) that drive the functional extremes, understand their relevance over climate gradients, and determine the consequences of interacting functional extremes over space and time.
Objective 1 – Predictive links between microbial traits and C flow.
In the prior phase of the SFA, we performed microcosm studies to discover microbial functional guilds driving DOC abundance in the early phase of decomposition of surface plant litter (pine, oak, and grass) in microcosms. Further work is needed to elevate the prior findings to the level of robust predictive links between traits and ecosystem phenomena. The next logical steps are to extend our findings to natural ecosystems and to determine the general mechanism that underpins control of DOC abundance by the functional guilds we identified. We will also expand the temporal and spatial scope by characterizing functional guilds controlling C fate during late stages of litter decomposition and C fate in subsurface soil. The tasks involve manipulative experiments with soil-core microcosms, 13C-labeled grass litter, and examination of traits in arid grassland and forest ecosystems.
Objective 2 – Interaction of microbial effect traits and environmental fluctuation.
In the prior phase, we found large (up to 7-fold) variation in community-driven C flow under constant environmental conditions in microcosms, but in nature, conditions fluctuate. This objective will assess whether environmental fluctuation is likely to amplify or dampen the variation in C flow caused by microbial functional guilds. These studies will provide foundational insights into potential impacts of changing climate on microbial-driven feedbacks. This objective will involve manipulative experiments with soil-core microcosms and 13C-labeled grass litter.
Objective 3 - Ecosystem-level consequences of microbial-driven variation in C flow.
This objective will quantify the ecosystem-level consequences of community-driven extremes in C flow. Do functional extremes in one component of C-cycling (e.g. surface litter decomposition) create cascading effects on other components (e.g. subsurface SOM formation) that modify the net behavior of the ecosystem? Or are functional extremes severely dampened by compensatory behavior in other C-cycle components? Answering such questions will provide foundational insights that inform management strategies and C-cycle process modeling. This objective will exploit two model microbial communities from the prior phase that cause divergent C-flow patterns with surface litter, mini-ecosystems (soil-cores with blue grama), stable isotope tracing, an accelerated 5-yr seasonal cycle, and data synthesis with an existing C-cycle process model (SOMIC 1.0).
Albright MBN, LV Gallegos-Graves, K Feeser, JB Emerson, M Shakya, J Dunbar. 2022 Experimental evidence for the impact of soil virus additions on carbon cycling during surface plant litter decomposition. ISME Comm. https://www.nature.com/articles/s43705-022-00109-4
- Cotrufo MF, ML Haddix, J Dunbar, ME Kroeger, C Stewart. 2022. The role of plant litter, microbial and soil chemical diversity on the formation of particulate and mineral-associated organic matter. Soil Biol. Biochem. 168:108648.
Romero-Jiménez MJ, J Rudgers, AJumpponen, J Herrera, M Hutchinson, C Kuske, J Dunbar, D Knapp, G Kovács, A Porras-Alfaro. 2022. Darksidea phi sp. nov., a dark septate root-associated fungus in foundation grasses in North American Great Plains Mycologia. 114(2):254-269. doi: 10.1080/00275514.2022.2031780
- Albright MBN, S Louca, DE Winkler, KL. Feeser, S-J Haig, KL. Whiteson, JB Emerson, J Dunbar. 2021. Solutions in Microbiome Engineering: Prioritizing Barriers to Organism Establishment. ISME J. https://www.nature.com/articles/s41396-021-01088-5
- Campbell T, DEM Ulrich, J Toyoda, J Thompson, B Munsky, MBN Albright, VL Bailey, MM Tfaily, J Dunbar. 2021. Microbial communities influence soil DOC concentration by altering metabolite composition. Front. Microbiol. doi.org/10.3389/fmicb.2021.799014
- Ndinga-Muniania, C, RC Mueller, CR Kuske, A Porras-Alfaro. 2021. Seasonal Variation and Potential Roles of Dark Septate Fungi in an Arid Grassland. Mycologia. 113(6):1181-1198. doi: 10.1080/00275514.2021.1965852
- Hutchinson M. I., T. A. S. Bell, L. V. Gallegos-Graves, J. Dunbar, and M. Albright, 2021: Merging fungal and bacterial community profiles via an internal control. Microbial Ecology, https://doi.org/10.1007/s00248-020-01638-y
- Kroeger, ME, MR DeVan, J Thompson, R Johansen, LV Gallegos-Graves, D Lopez, A Runde, T Yoshida, B Munsky, S Sevanto, MBN Albright, J Dunbar. 2021. Microbial Community Composition Controls Carbon Flux Across Litter Types in Early Phase of Litter Decomposition. Environmental Microbiology. 23(11):6676-6693.
- Albright, M .B. N., L. Gallegos-Graves, and J. Dunbar, 2020: Biotic interactions are more important than propagule pressure in microbial community invasions. mBio. In review. https://doi.org/10.1128/mBio.02089-20
- Albright, M. B. N., A. Runde, D. Lopez, J. Gans, S. Sevanto, D. Woolf, and J. Dunbar, 2020: Initial microbial biomass abundance is a weak driver of variation in CO2 flux during plant litter decomposition. PLoS ONE 15(2): e0224641. https://doi.org/10.1371/journal.pone.0224641
- Albright, M., R. Johansen, J. Thompson, D. Lopez, L. Gallegos-Graves, M. E. Kroeger, A. Runde, R. Mueller, A. Washburne, B. Munsky, T Yoshida, and J. Dunbar, 2020: Soil bacterial and fungal richness forecast patterns of early pine litter decomposition. Frontiers in Microbiology. https://doi.org/10.3389/fmicb.2020.542220
- Albright, M., R. Johansen, J. Thompson, M. E. Kroeger, R. Johansen, D. E. M. Ulrich, L. Gallegos-Graves, B. Munsky, and J. Dunbar, 2020: Differences in substrate use linked to divergent carbon flow during litter decomposition. FEMS Microbiology Ecology, 96(8) https://doi.org/10.1093/femsec/fiaa135
- DOE-BER highlight: https://science.osti.gov/ber/Highlights/2020/BER-2020-08-b
- Albright, M. B. N., S. Louca, D. E. Winkler, K. L. Feeser, S.-J. Haig, K. L. Whiteson, J. B. Emerson, and J. Dunbar, 2021: Solutions in Microbiome Engineering: Prioritizing Barriers to Organism Establishment. ISME J. Submitted
- Hamm P., R. C. Mueller, C. R. Kuske, and A. Porras-Alfaro, 2020: Keratinophilic fungi: specialized fungal communities in a desert ecosystem identified using cultured-based and Illumina sequencing approaches. Microbiological Research 239:126530. https://doi.org/10.1016/j.micres.2020.126530
- Kroeger, E. , M. R. DeVan, J. Thompson, R. Johansen, L. V. Gallegos-Graves, D. Lopez, A. Runde, T. Yoshida, B. Munsky, S. Sevanto, M. B. N. Albright, and J. Dunbar, 2021: Microbial Community Composition Controls Carbon Flux Across Litter Types in Early Phase of Litter Decomposition. Environmental Microbiology. Submitted
- Mueller, R. C., C. R. Kuske, and B. J. M. Bohannan, 2021: Variable thresholds in fungal and bacterial community response to experimental nitrogen deposition between two forest stands. Applied and Environmental Microbiology.
- Mueller R. C., L. V. Gallegos-Graves, S. C. Reed, J. Belnap, and C. R. Kuske, 2021: Temporal shifts in algal, but not bacterial, photoautotrophs associated with biological soil crusts in a dryland ecosystem. Plant and Soil. Submitted.
- Thompson, J., N. Lubbers, M. Kroeger, R. Johansen, R. Devan, J. Dunbar, and B. Munsky, 2021: Application of Bayesian networks to model microbial interactions with dissolved organic carbon. iScience. Submitted.
- Ulrich, D. E. M., S. Sevanto, S. Peterson, M. Ryan, and J. Dunbar, 2020: Effects of soil microbes on functional traits of loblolly pine (Pinus taeda) seedling families from contrasting climates. Frontiers in Plant Science, 10, 1643. https://doi.org/10.3389/fpls.2019.01643
- LA-UR-20-22843 Microbiome to Function: Next Generation Eco-Microbiology WorkshopReportAuthor(s):Dunbar, J, P. S. G Chain, M. B. N. Albright, J. Babilonia, M. Kroeger, E. Morales, P. Demosthenes, A. J. Robinson, R. E. McDonald, S. Iyer.
- Albright MBN, Mueller R, Gallegos-Graves LV, Belnap J, Reed S, Kuske CR. 2019. Interactions of microhabitat and time control dryland microbial community composition. Frontiers in Ecology and Evolution. https://doi.org/10.3389/fevo.2019.00367
- Challacombe, J. F., C. N. Hesse, L. M. Bramer, L. A. McCue, M. Lipton, S. Purvine, C. Nicora, L. Gallegos-Graves, A. Porras-Alfaro, and C. R. Kuske, 2019: Genomes and secretomes of Ascomycota fungi reveal diverse functions in plant biomass decomposition and pathogenesis. BMC Genomics, 20, 976. https://doi.org/10.1186/s12864-019-6358-x
- Deaver, N. R., C. Hesse, C. R. Kuske, and A. Porras-Alfaro, 2019: Presence and distribution of insect-associated and entomopathogenic fungi in temperate pine forest soil: An integrated approach. Fungal Biol., 123, 864-874. https://doi.org/10.1016/j.funbio.2019.09.006.
- Johansen, R., M. Albright, L. Gallegos-Graves, D. Lopez, A. Runde, T. Yoshida, and J. Dunbar, 2019: Tracking replicate divergence in microbial community composition and function in experimental microcosms. Microb. Ecol., 78, 1035-1039. https://doi.org/10.1007/s00248-019-01368-w
- Kuske, C. R., R. L. Sinsabaugh, L. Gallegos-Graves, M. B. N. Albright, R. C. Mueller, and J. Dunbar, 2019: Simple measurements in a complex system: Soil community responses to nitrogen amendment in a Pinus taeda forest. Ecosphere, 10, e02687. https://doi.org/10.1002/ecs2.2687
- Ndinga, M. C., R. C. Mueller, C. R. Kuske, and A. Porras-Alfaro, 2019: Seasonal variation and potential roles of dark septate fungi in an arid grasslands. Mycologia, in review.
- Thompson. J., R. Johansen, J. Dunbar, and B. Munsky, 2019: Machine learning regression models for analysis of microbiome data. PlosONE, 14(7), e0215502. https://doi.org/10.1371/journal.pone.0215502
- Ulrich, D. E. M., S. Sevanto, M. Ryan, M. B. N. Albright, R. B. Johansen, and J. Dunbar, 2019: Plant-microbe interactions before drought influence plant physiological responses to subsequent severe drought. Scientific Reports, 9(1), 249. doi:10.1038/s41598-018-36971-3
- Woolf, D., and J. Lehmann, 2019: Microbial models with minimal mineral protection can explain long-term soil organic carbon persistence. Sci. Reports, 9, 6522. doi:10.1038/s41598-019-43026-8
- Albright, M. B. N., B. Timalsina, J. Martiny, and J. Dunbar, 2018. Comparative genomics of nitrogen cycling pathways in bacteria and archaea. Microb. Ecol. doi:10.1007/s00248-018-1239-4 BER Highlight 9/24/2019 - https://science.osti.gov/ber/Highlights/2019/BER-2019-09-d
- Albright, M. B. N., R. Johansen, D. Lopez, V. Gallegos-Graves, B. Steven, C. R. Kuske, and J. Dunbar, 2018: Short-term transcriptional response of microbial communities to N-fertilization in a pine forest soil. Appl. Environ. Microbiol., 18, e00598-18. doi:10.1128/AEM.00598-18
- Koyama, A., B. Harlow, C. R. Kuske, J. Belnap, and R. D. Evans, 2018: Plant and microbial biomarkers suggest mechanisms of soil organic carbon accumulation in a Mojave Desert ecosystem under elevated CO2. Soil Biol. Biochem., 120, 48-57. doi:10.1016/j.soilbio.2018.01.033
- Steven, B., J. Belnap, and C. R. Kuske, 2018: Chronic physical disturbance substantially alters the response of biological soil crusts to a wetting pulse, as characterized by metatranscriptome sequencing. Front Microbiol., 9:2382. doi:10.3389/fmicb.2018.02382
- Torres-Cruz, T. J., C. Hesse, C. R. Kuske, and A. Porras-Alfaro, 2018: Presence and distribution of heavy metal tolerant fungi in surface soils of a temperate pine forest. Applied Soil Ecology, 131, 66-74. doi:10.1016/j.apsoil.2018.08.001
- Chung, Y. A., R. L. Sinsabaugh, C. R. Kuske, S. C. Reed, and J. A. Rudgers, 2017: Spatial variation in edaphic characteristics is a stronger control than nitrogen inputs in regulating soil microbial effects on a desert grass. J. Arid Environ., 142, 59-65. doi:10.1016/j.jaridenv.2017.03.005
- McHugh, T. A., E. M. Morrissey, R. C. Mueller, L. V. Gallegos-Graves, C. R. Kuske, and S. C. Reed, 2017: Bacterial, fungal, and plant communities exhibit no biomass or compositional response to two years of simulated nitrogen deposition in a semiarid grassland. Environ. Microbiol., 19, 1600-1611. doi:10.1111/1462-2920.13678
- Steven, B., C. Hesse, J. Soghigian, L. Gallegos-Graves, and J. Dunbar, 2017: Simulated rRNA/DNA ratios show potential to misclassify active populations as dormant. J. Appl. Environ. Microbiol., 83 e00696-17. doi:10.1128/AEM.00696-17
- Torres-Cruz, T. J., T. L. Billingsley Tobias, M. Almatruk, C. N. Hesse, C. R. Kuske, A. Desiro, G. M. N. Benucci, G. Bonito, J. E. Stajich, C. Dunlap, A. E. Arnold, and A. Porras-Alfaro, 2017: Bifiguratus adelaidae, gen. et sp. nov., a new member of Mucoromycotina in endophytic and soil-dwelling habitats. Mycologia, 109, 363-378. doi:10.1080/00275514.2017.1364958
- Yeager, C. M., L. Gallegos-Graves, J. Dunbar, C. N. Hesse, H. Daligault, and C. R. Kuske, 2017: Polysaccharide Degradation Capability of Actinomycetales Soil Isolates from a Semiarid Grassland of the Colorado Plateau. J. Appl. Environ. Microbiol., 83, e03020-16. doi:10.1128/AEM.03020-16
- Deshpande, V., Q. Wang, P. Greenfield, M. Charleston, A. Porras-Alfaro, C. R. Kuske, J. R. Cole, D. J. Midgley, and N. Tran-Dinh, 2016: Fungal identification using a Bayesian classifier and the Warcup training set of internal transcribed spacer sequences. Mycologia, 108, 1-5. doi:10.3852/14-293
- Hesse, C. N., T. J. Torres-Cruz, T. B. Tobias, M. Al-Matruk, A. Porras-Alfaro, and C. R. Kuske, 2016: Ribosomal RNA gene detection and targeted culture of novel nitrogen-responsive fungal taxa from temperate pine forest soil. Mycologia, 108, 1082-1090. doi:10.3852/16-086
- Maier, S., L. Muggia, C. R. Kuske, and M. Grube, 201:. Fungi and bacteria in biological soil crusts. Ecological Studies, 226.
- Mueller, R. C., L. Gallegos-Graves, and C. R. Kuske, 2016: A new fungal large subunit ribosomal RNA primer for high-throughput sequencing surveys. Fems Microbiology Ecology 92. doi:10.1093/femsec/fiv153
- Mueller, R. C., L. Gallegos-Graves, D. R. Zak, and C. R. Kuske, 2016: Assembly of active bacterial and fungal communities along a natural environmental gradient. Microbial Ecology, 71, 57-67. doi:10.1007/s00248-015-0655-y
- Porras-Alfaro, A., C. N. Muniania, P. Hamm, T. J. Torres-Cruz, and C. R. Kuske, 2016: "Fungal diversity, community structure and functional roles in desert soils." The Biology of Arid Soils, DeGruyter, 2016. 97-122.
- Reed, S. C., F. T. Maestre, R. Ochoa-Hueso, C. R. Kuske, M. Oliver, A. Darrouzet-Nardi, and B. Darby, et al., 2016. "Biocrusts in the context of global change." Biological Soil Crusts: An Organizing Principle in Drylands. Ecological Studies, 226, 451-476
- Sinsabaugh, R. L., B. L. Turner, J. M. Talbot, B. G. Waring, J. S. Powers, C. R. Kuske, D. L. Moorhead, and J. J. F. Shah, 2016: Stoichiometry of microbial carbon use efficiency in soils. Ecological Monographs, 86, 172-189. doi:10.1890/15-2110.1
- Steven, B., C. Hesse, L. Gallegos-Graves, J. Belnap, and C. R. Kuske, 2016: Fungal Diversity in Biological Soil Crusts of the Colorado Plateau, Proceedings of the 12th Biennial conference of Research on the Colorado Plateau. U.S. Geological Survey Scientific Investigations Report. 2015–5180.
- Hesse, C. N., R. Mueller, M. Vuyisich, L. V. Gallegos-Graves, C. Gleasner, D. R. Zak, and C. R. Kuske, 2015: Forest floor community metatranscriptomes identify fungal and bacterial responses to N deposition in two maple forests. Frontiers Microbiol., 6:337. doi:10.3389/fmicb.2015.00337
- Kuske, C. R., C. N. Hesse, J. F. Challacombe, D. Cullen, J. R. Herr, R. C. Mueller, A. Tsang, and R. Vilgalys, 2015: Prospects and challenges for fungal metatranscriptomics of complex communities. Fungal Ecol., 14, 133-137. doi:10.1016/j.funeco.2014.12.005
- Maier, S., L. Muggia, C. R. Kuske, and M. Grube, 2015: "Fungi and bacteria in biological soil crusts." In: Biological Soil Crusts: Structure, Function and Management, 3rd edition. Ed. J Belnap
- Mueller, R. C., J. Belnap, and C. R. Kuske, 2015: Soil bacterial and fungal community responses to nitrogen addition across soil depth and microhabitat in an arid shrubland. Front. Microbiol., 6, 891. doi:10.3389/fmicb.2015.00891
- Sinsabaugh, R. L., J. Belnap, J. Rudgers, C. R. Kuske, N. Martinez, and D. Sandquist, 2015: Soil microbial responses to nitrogen addition in arid ecosystems. Front. Microbiol., 6:819. doi:10.3389/fmicb.2015.00819
- Steven, B., C. R. Kuske, L. V. Gallegos-Graves, S. C. Reed, and J. Belnap, 2015: Climate change and physical disturbance manipulations result in distinct biological soil crust communities. Appl. Environ. Microbiol., 81, 7448-7459. doi:10.1128/AEM.01443-15
- Berthrong, S., C. M. Yeager, L. Gallegos-Graves, B. Steven, S. Eichorst, R. B. Jackson, and C. R, Kuske, 2014: Nitrogen fertilization has a stronger effect on soil N-fixing bacterial communities than elevated atmospheric CO2. Appl. Environ. Microbiol., 80, 3103-3112. doi:10.1128/AEM.04034-13
- Dunbar, J., L. V. Gallegos-Graves, B. Steven, R. Mueller, C. Hesse, D. R. Zak, and C. R. Kuske, 2014: Surface soil fungal and bacterial communities in aspen stands and resilient to eleven years of elevated CO2 and O3. Soil Biol. Biochem., 76, 227-234. doi:10.1016/j.soilbio.2014.05.027
- Lipson, D. A., C. R. Kuske, L. V. Gallegos-Graves, and W. C. Oechel, 2014: Elevated atmospheric CO2 stimulates soil fungal diversity through increased fine root production in a semiarid shrubland ecosystem. Glob. Change. Biol., 20, 2555–2565. doi:10.1111/gcb.12609
- Mueller, R. C., M. Moya-Balasch, and C. R. Kuske, 2014: Contrasting soil fungal community responses to experimental nitrogen addition using the large subunit rRNA taxonomic marker and cellobiohydrolase I functional marker. Molec. Ecol., 23, 4406-4417. doi:10.1111/mec.12858
- Porras-Alfaro, A., K-L. Liu, C. R. Kuske, and G. Xie, 2014: From genus to phylum: large subunit and internal transcribed spacer rRNA operon regions show similar classification accuracies influenced by database composition. Appl. Environ. Microbiol., 80, 829-840. doi:10.1128/AEM.02894-13
- Sinsabaugh, R. L., J. Belnap, S. G. Findlay, J. J. Follstad Shah, B. H. Hill, K. A. Kuehn, C. R. Kuske, M. Litvak, N. G. Martinez, D. L. Moorhead, and D. D. Warnock, 2014: Extracellular enzyme kinetics scale with resource availability. Biogeochem., 121, 287-304. doi:10.1007/s10533-014-0030-y
- Steven, B., L. V. Gallegos-Graves, C. Yeager, J. Belnap, and C. R. Kuske, 2014: Common and distinguishing features of the bacterial and fungal communities in biological soil crusts and shrub root zone soils. Soil Biol. Biochem., 69, 302-312. doi:10.1016/j.soilbio.2013.11.008
- Cole. J. R., Q. Wang, J. A. Fish, B. Chai, D. McGarrell, Y. Sun, C. T. Brown, A. Porras-Alfaro, C. R. Kuske, and J. M. Tiedje, 2013: Ribosomal database project: data and tools for high throughput rRNA analysis. Nucl. Acids Res., 42, D633-D642. doi:10.1093/nar/gkt1244
- Lindahl, B. D., and C. R. Kuske, 2013: Metagenomics for study of fungal ecology. Chapter 13. In: The Ecological Genomics of Fungi. Ed. Francis Martin. Wiley-Blackwell. 400 pg. ISBN: 978-1-119-94610-6.
- Steven, B., L. V. Gallegos-Graves, J. Belnap, and C. R. Kuske, 2013: Dryland soil bacterial communities display spatial biogeographic patterns associated with soil depth and soil parent material. FEMS Microbiol Ecol., 86, 101-113. doi:10.1111/1574-6941.12143
- Steven, B., M. Lionard, C. R. Kuske, and W. F. Vincent, 2013: High bacterial diversity of biological soil crusts in water tracks over permafrost in the high Arctic polar desert. PLoS ONE 8, 271489. doi:10.1371/journal.pone.0071489
- Weber, C. F., R. Vilgalys, and C. R. Kuske, 2013: Changes in fungal community composition in response to elevated atmospheric CO2 and nitrogen fertilization vary with soil horizon. Front. Microbiol., 4, 78. doi:10.3389/fmicb.2013.00078
- Bates, S. T., S. Ahrendt, H. Bik, T. Bruns, J. G. Caparaso, J. Cole, M. Dwan, N. Fierer, D. Gu, S. Houston, R. Knight, J. Leff, C. Lewis, D. McDonald, H. Nilsson, A. Porras-Alfaro, V. Robert, C. Schoch, J. Scott, L. Taylor, L. Wegener-Parfrey, and J. E. Stajich, 2013: Meeting report: Fungal ITS workshop (October 2012). Standards in Genomic Sciences. 8, 118-123. doi:10.4056/sigs.3737409
- Berendzen, J., W. J. Bruno, J. D. Cohn, N. W. Hengartner, C. R. Kuske, B. H. McMahon, M. A. Wolinsky, and G. Xie, 2012: Rapid phylogenetic and functional classification of short genomic fragments with signature peptides. BMC Research Notes, 5, 460. doi:10.1186/1756-0500-5-460
- Challacombe, J. F., and C. R, Kuske, 2012: Mobile genetic elements in the bacterial phylum Acidobacteria. Mobile Genetic Elements, 2, 179-183. doi:10.4161/mge.21943
- Dunbar, J., S. A. Eichorst, L. Gallegos-Graves, S. Silva, G. Xie, N. Hengartner, B. A. Hungate, R. B. Jackson, D. R. Zak, R. Vilgalys, R. D. Evans, C. W. Schadt, J. P. Megonigal, and C. R. Kuske, 2012: Common bacterial responses in six ecosystems exposed to ten years of elevated atmospheric carbon dioxide. Environ. Microbiol., 14, 1145-1158. doi:10.1111/j.1462-2920.2011.02695.x
- Eichorst, S. A., and C. R. Kuske, 2012: Identification of cellulose-responsive bacterial and fungal communities in geographically and edaphically different soils by using stable isotope probing. Appl. Environ. Microbiol., 78, 2316-2327. doi:10.1128/AEM.07313-11
- Gans, J. D., J. Dunbar, S. A. Eichorst, L. V. Gallegos-Graves, M. Wolinsky, and C. R. Kuske, 2012: A robust primer design platform applied to detection of Acidobacteria Group 1 in soil. Nucleic Acids Res., 40, e96. doi:10.1093/nar/gks238
- Johnson, S. L., C. R. Kuske, T. D. Carney, D. C. Housman, L. V. Gallegos-Graves, and J. Belnap, 2012: Increased temperature and altered summer precipitation have differential effects on biological soil crusts in a dryland ecosystem. Glob. Change Biol., 18, 2583-2593. doi:10.1111/j.1365-2486.2012.02709.x
- Kuske, C. R., C. M. Yeager, S. Johnson, L. O. Ticknor, and J. Belnap, 2012: Response and resilience of soil biocrust bacterial communities to chronic physical disturbance in arid shrublands. The ISME Journal, 6, 886-897. doi:10.1038/ismej.2011.153
- Liu, K-L., A. Porras-Alfaro, C. R. Kuske, S. A. Eichorst, and G. Xie, 2012: Accurate, rapid taxonomic classification of fungal large subunit rRNA genes. Appl. Environ. Microbiol., 78, 1523-1533. doi:10.1128/AEM.06826-11
- Steven, B., L. V. Gallegos-Graves, C. M. Yeager, J. Belnap, R. D. Evans, and C. R. Kuske, 2012: Dryland biological soil crust cyanobacteria show unexpected decreases in abundance under long-term elevated CO2. Environ. Microbiol., 14, 3247-3258. doi:10.1111/1462-2920.12011
- Steven, B., L. Gallegos-Graves, S. R. Starkenburg, P. S. Chain, and C. R. Kuske, 2012: Targeted and shotgun metagenomic approaches provide different descriptions of dryland soil microbial communities in a manipulated field study. Environ. Microbiol. Rep., 4, 248-256. doi:10.1111/j.1758-2229.2012.00328.x
- Weber, C. F., and C. R. Kuske, 2012: Comparative assessment of fungal cellobiohydrolase I richness and composition in cDNA generated using oligo(dT) primers or random hexamers. J. Microbiol. Meth., 88, 224-228. doi:10.1016/j.mimet.2011.11.016
- Weber C. F., M. M. Balasch, Z. Gossage, A. Porras-Alfaro, and C. R. Kuske, 2012: Soil fungal cellobiohydrolase I (cbhI) composition and expression in a loblolly pine plantation under elevated atmospheric CO2 and nitrogen fertilization. Appl. Environ. Microbiol., 78, 3950-3957. doi:10.1128/AEM.08018-11
- Yeager, C. M., C. R. Kuske, T. D. Carney, S. L. Johnson, L. O. Ticknor, and J. Belnap, 2012: Response of biological soil crust diazotrophs to season, altered summer precipitation and year-round increased temperature in field plots of the Colorado Plateau, USA. Front Microbiol., 3, 358. doi:10.3389/fmicb.2012.00358
- Microbiome profiling - Internal control spike-in for bacterial and fungal profiling
- Hutchinson, M. I., T. A. S. Bell, L. V. Gallegos-Graves, J. Dunbar, and M. Albright, 2021: Merging fungal and bacterial community profiles via an internal control. Microbial Ecology, https://doi.org/10.1007/s00248-020-01638-y
- Plasmid vector with internal control is available upon request.
- Machine learning for microbiome - "RFINN (Random Forest, Indicator Species, Neural Network)" software to identify robust features predicting community function
- Thompson, J., R. Johansen, J. Dunbar, and B. Munsky, 2019: Machine learning regression models for analysis of microbiome data. PlosONE, 14(7), e0215502. https://doi.org/10.1371/journal.pone.0215502
- Codes are available for direct download at https://github.com/MunskyGroup/thompson_etal_plos_one_2019
Marie Kroeger, Research Manager, SFA Lead PI
Sanna Sevanto, Technical co-PI
La Verne Gallegos-Graves (chief technician)
Emily Boak (postdoc, microbial ecology)
James Brunner (CNLS Postdoctoral Fellow, mathematics)
Samuel Hafer (post-baccalaureate student, molecular biology)
Olivia Schwartz (post-baccalaureate student, metaproteomics)
Trevor Glaros (B-Tek group leader/staff scientist, metaproteomics)
Ethan McBride (staff scientist, metaproteomics)
Phillip Mach (staff scientist, metabolomics)
Abigale Mikolitis (post-baccalaureate student, metaproteomics)
External Collaborators (2021):
- Johannes Lehmann, Cornell University
- Rachelle LaCroix (PhD student)
- Daniel Buckley, Cornell University
- Cassandra Wattenburger (PhD student)
- Vanessa Bailey, Pacific Northwest National Laboratory