Bird’s Soil Biogeochemistry Research Group

Research Focus

Our research group is focused on belowground C and N cycling in terrestrial and estuarine ecosystems. Soils are critical controllers on the flow of matter and energy in the environment and are considered especially important in the Earth's response to climate change. Soils act as both a source of greenhouse gases to the atmosphere and as a sizable, stable sink for plant C and N inputs.

We investigate how soil microbial communities, plants, climate and mineralogy interact to control the turnover, loss or stabilization of soil C and N in boreal, temperate and tropical ecosystems.

Much of our work uses stable isotopic tracers (13C and 15N) to follow carbon and nitrogen among plants, soil microbes, and mineral surfaces to better understand how soils support ecological productivity, the production of food and fiber and environmental quality.


How will forested ecosystems respond to climate change?

One impact of climate change is more frequent and intense forest fires. Wildfires are a major ecosystem disturbance that alters the flow of C and N, especially through the addition of charcoal or pyrogenic organic matter (PyOM) to the air, soil and water. The forested site (shown above) last burned in 1980 and is host to a long-term study led by the Bird lab on the fate of pyrogenic organic matter in the environment. Soil samples from this site, located at the University of Michigan Biological Station in Pellston, MI, illustrate the distinct soil horizons present in this developing Spodosol. More information about this project is available on our research and publications pages.

Jeffrey A. Bird

Professor, Queens College - CUNY
Chair of the School of Earth and Environmental Sciences
PhD Faculty in Earth & Environmental Sciences and Ecology, Evolutionary Biology, and Behavior Programs, The CUNY Graduate Center
Queens College, City University of New York (CUNY)

PhD Soil Biogeochemistry, UC Davis
MS Plant and Soil Science, University of VT
BS Soil Science, Cornell

Office: Science Building D-216
Lab: Science Building E-223, E-225, D-104
Phone: 718-997-3332
Email: Jeffrey.Bird@qc.cuny.edu


Graduate Students

Annie Stoeth
Masters of Environmental Science, Yale University School of Forestry
Earth & Environmental Science PhD Program, The CUNY Graduate Center
Research focus: The role of anthropogenic waste in urban soil ecology, with an emphasis its interaction with soil fauna. I’m interested in how invertebrates and waste affect each other, and in examining questions of toxicity, incorporation, transport, and decomposition/bioremediation.

Elsa Rosario
Biology MA
Research Focus: How do cities impact soil fungal communities?


Research Staff

Jessenia Soriano
2017 - present

Kennly Weerasinghe
2017 - present

Adolfo Coyotl
2017 - present

Ashley Smith
2019 - present

Research Areas

  • Pyrogenic organic matter degradation and transport dynamics in forest soils
  • Wastewater C and N inputs into the Hudson River Estuary in NYC
  • How minerals and microbes interact to stabilize organic matter
  • What controls the magnitude and direction of soil priming
  • Microbial ecology of soil heterotrophs
  • Rhizosphere processes: How plant roots affect soil microbial activity
  • The effect of anthropogenic N additions on soil C turnover

Pyrogenic organic mater degradation and transport in forest soils

Pyrogenic organic matter (PyOM) or black carbon represents a substantial portion of the organic matter in many forest soils. PyOM is a heterogeneous group of materials that are the product of incomplete combustion of plant biomass. Until recently, PyOM in soil was thought to be relatively inert. Recent data from the Bird research group and others indicate that the turnover time for typical forest fire-produced PyOM materials is on the century scale and its turnover is biologically mediated. See Gibson et al. 2018; Santos et al., 2012.

We are involved in two on-going, long-term field studies examining the decomposition, loss and stabilization mechanisms governing PyOM in temperate forest soils. The first initiated in 2009 is located Lägeren, Switzerland is comparing the effects of elevated N deposition on PyOM dynamics (Swiss NFS funded, see Singh et al. 2014 and Maestrini et al. 2014). The second field study, initiated in 2011 is located at the University of Michigan Biological Station in Pellston, MI. It is examining the effects of charring temperature and wood source on PyOM structure and its dynamics in the soil (NSF funded). Recent papers by our group (papers by Gibson et al. 2018; Hatton et al. 2016) provide new insights on the important interactions between tree taxa and pyrolysis temperature on the chemical and physical structure of PyOM and its turnover rate in soil. A recent paper by Auclerc et al. 2019 provide new insights on how soil faunal communities are impacted by forest fires over the decadal scale.

Wastewater C and N inputs into the Hudson River Estuary in NYC

Every year, more than 27 billion gallons of combined, untreated sewage and polluted runoff are deposited in the local waterways in and around New York City. These events add large quantities of easily degradable C and N compounds to the Hudson River, its estuaries and the local wetland soils and sediments. The fate of this anthropogenic C and N is poorly understood, including the production of greenhouse gases and organic C accrual in these sediments. See our recent paper, Brigham et al. 2018 for more information.

In a joint research project with the O’Mullan lab (SEES, QC), Mr. Brigham has conducted several lab experiments and sampled throughout the Hudson River Estuary to address the fate of this pollution. Evidence from soil incubation experiments in combination with quantitative chemical analyses of untreated sewage and surface estuarine waters demonstrates that sewage discharge significantly increases the greenhouse gas efflux from the Hudson River Estuary. Increased greenhouse gas efflux we have measured are via two main mechanisms: (1) direct input of these gases into estuarine surface waters from urban wastewater treatment systems; and (2) indirect in-situ microbial production in response to labile C found in sewage discharge. See papers by Brigham et al. 2019 for more information on the GHG footprint of NYC on the HRE.

How minerals and microbes interact to stabilize organic matter

The physical and chemical mechanisms that stabilize organic matter in soils are critically important to enhance C storage in natural and managed terrestrial ecosystems. This soil mineral assemblage (at left) is from a 10-yr-long field study that compared aboveground plant litter (needles) versus belowground (fine roots) plant inputs to soil. The Bird lab uses physical and chemical extraction procedures to examine the partitioning and dynamics of soil C and N along the soil organic matter spectrum. In addition, we utilize 13C/15N and compound specific analyses to better understand how litter quality and mineralogy affect SOM stabilization processes. See Preis et al. 2017; Hatton et al. 2015; Mambelli et al., 2011).

Recent and ongoing projects are examining the fate of microbial bodies (and their EPS products) as precursors of stable SOM in temperate and tropical forest soils (Throckmorton et al. 2012, 2015) and related the stabilization mechanisms of PyOM in mineral soils.

What controls the magnitude and direction of soil priming

The phenomenon known as soil priming is the change in the rate of native soil C mineralization - either positive (enhanced) or negative (reduced) that is typically caused by an addition of organic matter or N to soil. Predicting the direction and magnitude of soil priming events has been a considerable challenge for soil scientists. However, the Bird lab has contributed to recent advances in this area that describe the important role of specific microbial groups (Bird et al. 2011), the organic matter pool that is being primed (Singh et al. 2012), the effect of organic input type (Gibson et al. 2018) and the strong influence of actively growing fine roots on soil priming (see review by Bird in Gärdenäs et al. 2011). One aspect of this topic we are hoping to contribute more to is the effect and mechanism behind negative priming of mineral-associated organic matter from PyOM additions to soil.

Aboveground versus belowground plant C & N inputs to soil

The Bird lab has previously demonstrated the relative stability of fine root C compared with aboveground needle C as soil organic matter in a Mediterranean forest soil (e.g., Bird & Torn, 2006, Mambelli et al. 2011, Hatton et al 2015, Pries et al. 2017). An important component of this research is better understanding the role of heterotrophic microbial communities in plant litter degradation and transformation. The role of the microbial communities is generally understood at the community level, but the quantitative utilization and succession pattern among microbial groups remains poorly quantified.

A recent paper by the Bird lab by Santos et al. 2016 (Biogeochemistry) demonstrated relatively rapid fine root C mineralization is a northern temperate forest soil. This paper illustrates that edaphic factors and a soil’s capacity to stabile decomposition products is a significant limitation to sequestering C, even from slowly decomposing fine roots.

Stable isotope labeling

The Bird laboratory produces and uses 13C and 15N enriched plant litters, soil microorganisms and soil organic matter for field and laboratory studies to better understand soil-plant-microbial interactions. Our stable isotope labeling plant chamber shown (right) has produced uniformly enriched material from perennial and annual species using enriched 13CO2 and inorganic 15N salts. Recently, the Bird lab completed a dual labeling (13C/15N) of Jack pine samplings (shown at right) for use in field and laboratory studies.

Undergraduate

  • GEOL 09: Environmental Issues
    The scientific background for some major environmental issues is introduced. These issues may include the availability and use of renewable and non-renewable resources; conservation, recycling, waste disposal, and pollution; and land use. Human impact on global environmental problems are examined from both scientific and social points of view.

  • ENSCI 100: Our Planet in the 21st Century
    Focuses on two major themes of increasing concern to society: global climate change and environment and human health. Theme I, Global Climate Change, introduces students to basic concepts in mathematics and physics and the implications of climate change to society. Theme II, Environment and Human Health, introduces students to the basic concepts in chemistry and biology used in the study of anthropogenic pollutants and naturally occurring poisons, and to policy changes aimed at reducing human exposure to pollutants in developed and developing countries.

  • ENSCI 200: Earth Systems Science
    A historical perspective of processes and interactions among the lithosphere, atmosphere, hydrosphere, and biosphere with humans as a force for change; knowledge of how the Earth system responds to changes in these forcings to mitigate the predicted effects for human civilization.

  • HMNS 225: Science and Technology in NYC
    Develop an understanding of scientific work and the tools employed by scientific researchers in two ways: 1) by engaging students in an examination of published scientific research, which will enable an examination of the questions asked and methodologies employed by researchers; and 2) by asking that students conduct, write up and present in poster form, a close examination of a scientific or technological problem of their choice.

  • GEOL 318: Soils in the Environment
    The processes and behavior of soils in natural and managed environments. This course will address the physical, chemical, and biological properties and processes of soils in the context of their roles in the environment. Topics include the function of soils in supporting plant growth, maintaining environmental quality, and their role in global biogeochemical cycling.

  • GEOL 370: Biogeochemistry
    Biogeochemistry processes of affecting Earth's environmental systems with emphasis on mechanisms for distribution and transport of elements and compounds in and between the atmosphere, biosphere, hydrosphere, and lithosphere.


Graduate Courses

  • GEOL 768: Soils, Wetlands, and Biodegradation

  • Graduate Seminar 799: Current Topics in Biogeochemistry

  • Graduate Seminar 799: Molecular Methods in Environmental Microbiology

Selected Publications

Brigham, B., J.A. Bird, A.R. Juhl, C.J. Zappa, A.D. Montero, G. O’Mullan. 2019. Anthropogenic inputs from a coastal megacity are linked to greenhouse gas concentrations in the surrounding estuary. Limnology & Oceanography; online/unassigned. doi: 10.1002/lno.11200

Auclerc A., J.M., LeMoine, P.J. Hatton, J.A. Bird, K.J. Nadelhoffer. 2019. Decadal post-fire succession of soil invertebrate communities is dependent on the soil surface properties in a Northern Temperate forest. Science of the Total Environment 647: 1058-1068. doi: 10.1016/j.scitotenv.2018.08.041

Gibson, C.D., P.J. Hatton, J.A. Bird, K.J. Nadelhoffer, C.P. Ward, R.E. Stark, T.R. Filley. 2018. Interacting controls of pyrolysis temperature and plant taxa on the degradability of PyOM in a fire-prone Northern Temperate forest soil. Soil Systems 2:48-65. (Feature article in Special Issue on SOM Dynamics) doi:10.3390/soilsystems2030048

Brigham, B., G. O’Mullan, J.A. Bird. 2018. Acetate additions stimulate CO2 and CH4 production from urban wetland soils. Soil Science Society of America Journal 82:1147-1159 doi: 10.2136/sssaj2018.01.0034

Gibson, C.D., P.J. Hatton, J.A. Bird, K.J. Nadelhoffer, T.R. Filley. 2018. Tree taxa and pyrolysis temperature interact to control pyrogenic organic matter induced native soil organic carbon priming. Soil Biology & Biochemistry 119:174-183. doi: 10.1016/j.soilbio.2018.01.022

Pries, C. H., J.A. Bird, C. Castanha, P.J. Hatton, M.S. Torn. 2017. Long term decomposition: The influence of litter type and soil horizon on retention of plant carbon and nitrogen in soils. Biogeochemistry Letters 34:5-16. doi: 10.1007/s10533-017-0345-6

Wang, R. C.D. Gibson, T.D. Berry, Y. Jiang, J.A. Bird, T.R. Filley. 2017. Photooxidation of pyrogenic organic matter (PyOM) reduces the reactive, labile C pool and the apparent soil oxidative microbial enzyme response. Geoderma 293:10-18. doi: 10.1016/j.geoderma.2017.01.011

Hatton, P.J., S. Chatterjee, T.R. Filley, K. Dastmalchi, A.F. Plante, S. Abiven, X. Ga, C.A. Masiello, S.W. Leavitt, K.J. Nadelhoffer, R.E. Stark, J.A. Bird. 2016. Tree taxa and pyrolysis temperature interact to control the efficacy of pyrogenic organic matter formation. Biogeochemistry 130: 103-116. doi: 10.1007/s10533-016-0245-1

Santos, F., K.J. Nadelhoffer, J.A. Bird. 2016. Rapid fine root C and N mineralization in a northern temperate forest soil. Biogeochemistry 128:187-200. doi: 10.1007/s10533-016-0202-z

Gibson, C., T.D. Berry, R. Wang, J.A. Spencer, C.T. Johnston, Y. Jiang, J.A. Bird, T.R. Filley. 2016. Weathering of pyrogenic organic matter induces fungal oxidative enzyme response in single culture inoculation experiments. Organic Geochemistry 92:32-41. doi:10.1016/j.orggeochem.2015.12.003

Crumsey, J.M., Y. Capowiez, M.M. Goodsitt, S. Larson, J.M. Le Moine, J.A. Bird, G.W. Kling, K.J. Nadelhoffer. 2015. Exotic earthworm community composition interacts with soil texture to affect redistribution and retention of litter-derived C and N in northern temperate forest soils. Biogeochemistry 126:379-395. doi: 10.1007/s10533-015-0164-6

Hatton, P.J., C. Castanha, M.S. Torn, J.A. Bird. 2015. Litter type control on soil C and N stabilization dynamics in a temperate forest. Global Change Biology 21:1358–1367. doi: 10.1111/gcb.12786

Throckmorton, H., J.A. Bird, N. Monte, T. Doane, M.K. Firestone, W.R. Horwath. 2015. The soil matrix increases microbial C stabilization in temperate and tropical forest soils. Biogeochemistry 122:35–45. doi: 10.1007/s10533-014-0027-6

Maestrini, B., S. Abiven, N. Singh, J.A. Bird, M.S. Torn, M.W.I. Schmidt. 2014. Carbon losses from pyrolysed and original wood in a forest soil under natural and increased N deposition. Biogeosciences 11: 5199–5213. doi: 10.5194/bg-11-5199-2014

Santos, F., M.P. Fraser, J.A. Bird. 2014. Atmospheric black carbon deposition and characterization of biomass burning tracers in a northern temperate forest. Atmospheric Environment 95:383-390. doi: 10.1016/j.atmosenv.2014.06.038

Singh, N., S. Abiven, B. Maestrini, J.A. Bird, M.S. Torn, M.W.I Schmidt. 2014. Transformation and stabilization of pyrogenic organic matter in a temperate forest field experiment. Global Change Biology 20:1629–1642. doi: 10.1111/gcb.12459

Throckmorton, H., J.A. Bird, L. Dane, M.K. Firestone, W.R. Horwath. 2012. The source of microbial C has little impact on soil organic matter stabilization in forest ecosystems. Ecology Letters 15: 1257–1265 doi: 10.1111/j1461-0248. 2012.01848.x

Chatterjee, S., F. Santos, S. Abiven, B. Itin, R. Stark, J.A. Bird. 2012. Elucidating the chemical structure of pyrogenic organic matter by combining magnetic resonance, mid-infrared spectroscopy and mass spectrometry. Organic Geochemistry 51:35–44. doi: 10.1016/j.orggeochem.2012.07.006

Santos, F., M.S. Torn., J.A. Bird. 2012. Biological degradation of pyrogenic organic matter in temperate forest soils. Soil Biology & Biochemistry 51:115-124. doi: 10.1016/j.soilbio.2012.04.005

Yarnes, C., F. Santos, N. Singh, S. Abiven, M.W.I. Schmidt, J.A. Bird. 2011. Stable isotopic analysis of pyrogenic organic matter in soils by LC-IRMS of benzene polycarboxylic acids. Rapid Communications in Mass Spectrometry 25:3723–3731. doi: 10.1002/rcm.5272

Mambelli, S., J.A. Bird, G. Gleixner, T.E. Dawson, M.S. Torn. 2011. Relative contribution of needle and fine root pine litter to the molecular composition of soil organic matter after in situ degradation. Organic Geochemistry 42:1099-1108. doi: 10.1016/j.orggeochem.2011.06.008

Bird, J.A., D. Herman, M.K. Firestone. 2011. Rhizosphere priming of soil organic matter by bacterial groups in a grassland soil. Soil Biology & Biochemistry Special Section 43:718-725. doi: 10.1016/jsoilbio.2010.08.010

Gärdenäs, A.I. G.I. Ågren, J.A. Bird, M. Clarholm, S. Hallin, P. Ineson, T. Kätterer, H. Knicker, S.I. Nilsson, T. Näsholm, S. Ogle, K. Paustian, T. Persson, J. Stendahl. 2011. Knowledge gaps in soil C and N interactions - From molecular to global scale. Soil Biology & Biochemistry Special Section 43:702-717. doi: 10.1016/jsoilbio.2010.04.006

Gärdenäs, A.I. G.I. Ågren, J.A. Bird, M. Clarholm, S. Hallin, P. Ineson, T. Kätterer, H. Knicker, S.I. Nilsson, T. Näsholm, S. Ogle, K. Paustian, T. Persson, J. Stendahl. 2011. Knowledge gaps in soil C and N interactions - From molecular to global scale. Soil Biology & Biochemistry Special Section 43:702-717. doi: 10.1016/jsoilbio.2010.04.006

Fan, T.W.-M., J.A. Bird, E L. Brodie, A.N. Lane. 2009. 13C-Isotopomer-based metabolomics of microbial groups isolated from two forest soils. Metabolomics 5 :108–122. doi: 10.1007/s11306-0080150-2

Gärdenäs, A.I. G.I. Ågren, J.A. Bird, M. Clarholm, S. Hallin, P. Ineson, T. Kätterer, H. Knicker, S.I. Nilsson, T. Näsholm, S. Ogle, K. Paustian, T. Persson, J. Stendahl. 2011. Knowledge gaps in soil C and N interactions - From molecular to global scale. Soil Biology & Biochemistry Special Section 43:702-717. doi: 10.1016/jsoilbio.2010.04.006

Bird, J.A., M. Kleber, M.S. Torn. 2008. 13C and 15N stabilization dynamics in soil organic matter fractions during needle and fine root decomposition. Organic Geochemistry 39:465–477.

Gärdenäs, A.I. G.I. Ågren, J.A. Bird, M. Clarholm, S. Hallin, P. Ineson, T. Kätterer, H. Knicker, S.I. Nilsson, T. Näsholm, S. Ogle, K. Paustian, T. Persson, J. Stendahl. 2011. Knowledge gaps in soil C and N interactions - From molecular to global scale. Soil Biology & Biochemistry Special Section 43:702-717. doi: 10.1016/jsoilbio.2010.04.006

Bird, J.A. and M.S. Torn. 2006. Fine roots versus needles: A comparison of 13C and 15N dynamics in a ponderosa pine forest soil. Biogeochemistry 79:361-382.

Gärdenäs, A.I. G.I. Ågren, J.A. Bird, M. Clarholm, S. Hallin, P. Ineson, T. Kätterer, H. Knicker, S.I. Nilsson, T. Näsholm, S. Ogle, K. Paustian, T. Persson, J. Stendahl. 2011. Knowledge gaps in soil C and N interactions - From molecular to global scale. Soil Biology & Biochemistry Special Section 43:702-717. doi: 10.1016/jsoilbio.2010.04.006

Bird, J.A., C. van Kessel, W.R. Horwath. 2003. Stabilization of 13C-carbon and immobilization of 15N-nitrogen from rice straw in humic fractions. Soil Sci. Soc. Am. J. 67:806-815.

Gärdenäs, A.I. G.I. Ågren, J.A. Bird, M. Clarholm, S. Hallin, P. Ineson, T. Kätterer, H. Knicker, S.I. Nilsson, T. Näsholm, S. Ogle, K. Paustian, T. Persson, J. Stendahl. 2011. Knowledge gaps in soil C and N interactions - From molecular to global scale. Soil Biology & Biochemistry Special Section 43:702-717. doi: 10.1016/jsoilbio.2010.04.006

Torn, M.S., S. Davis, J.A. Bird, M.R. Shaw, M. Conrad. 2003. Automated analyses of 13C/12C ratios in CO2 and dissolved inorganic carbon for ecological and environmental applications. Rapid Communications in Mass Spectrometry 17:2575-2582.

Gärdenäs, A.I. G.I. Ågren, J.A. Bird, M. Clarholm, S. Hallin, P. Ineson, T. Kätterer, H. Knicker, S.I. Nilsson, T. Näsholm, S. Ogle, K. Paustian, T. Persson, J. Stendahl. 2011. Knowledge gaps in soil C and N interactions - From molecular to global scale. Soil Biology & Biochemistry Special Section 43:702-717. doi: 10.1016/jsoilbio.2010.04.006 Bird, J.A., C. van Kessel, W.R. Horwath. 2002. Nitrogen dynamics in humic fractions under alternative straw management in temperate rice. Soil Sci. Soc. Am. J. 66:478-488.

Gärdenäs, A.I. G.I. Ågren, J.A. Bird, M. Clarholm, S. Hallin, P. Ineson, T. Kätterer, H. Knicker, S.I. Nilsson, T. Näsholm, S. Ogle, K. Paustian, T. Persson, J. Stendahl. 2011. Knowledge gaps in soil C and N interactions - From molecular to global scale. Soil Biology & Biochemistry Special Section 43:702-717. doi: 10.1016/jsoilbio.2010.04.006 Bird, J.A., G.S. Pettygrove, J.M. Eadie. 2000. The impact of waterfowl foraging on the decomposition of rice straw: mutual benefits for rice growers and waterfowl. J. Appl. Ecol. 37:728-741.

News

Brian Brigham (PhD from CUNY EES Program in 2019) recently had a major paper accepted from his dissertation work in the journal, Limnology & Oceanography - it is entitled Anthropogenic inputs from a coastal megacity are linked to greenhouse gas concentrations in the surrounding estuary. His multifaceted data set demonstrated that CH4 and CO2 surface concentrations are explained in part by enterococci concentrations, a widely used wastewater biological indicator, explicitly linking wastewater inputs to GHG surface concentrations in the Hudson River Estuary.


Opportunities

Undergraduate Research Assistant Positions
Undergraduate students interested in working part-time or on independent research in the Bird lab are encouraged to apply. Students should have completed 1 year of college-level chemistry and biology. Please send Professor Bird an email indicating your interest to Jeffrey.Bird@qc.cuny.edu

Graduate Students/Postdoctoral Research
Potential graduate students (MA or PhD) are encouraged to contact Dr. Bird by email at Jeffrey.Bird@qc.cuny.edu. Please include a CV and a brief statement of research interests.


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