Research Approaches

The foundations of the LUQ program stem from eight decades of research on forest and stream composition, growth, and management by Forest Service scientists as well as 25 years of work on biogeochemical cycles supported by the Department of Energy and its predecessor the Atomic Energy Commission.  Results from these studies stimulated the formation of the LUQ and its focus on long-term measurements of forest and stream response to natural and anthropogenic disturbance.  These core measurements are complemented by hypothesis-driven experiments focused on improving our understanding of the cumulative effects of multiple disturbances across a steep gradient in climate. Products from the first 27 years of research in the Luquillo LTER include 790 peer-reviewed publications, 17 books and special features, 185 book chapters, and 85 dissertations and theses.

Below you will find a short summary of the research approaches LUQ uses to address ecosystem change in the Luquillo Experimental Forest (LEF).


The Luquillo Forest Dynamics Plot (LFDP) is located in tabonuco forest (200 – 600 m asl) in the northwest corner of the LEF. The LFDP covers 16 ha in which >110,000 woody plant stems ≥1.0 cm dbh have been studied over two and half decades (Thompson et al. 2002, Zimmerman et al. 2010). A large plot is needed to study species-rich communities where rare species are frequent, and to examine mechanisms promoting species diversity and coexistence (Condit 1995, Wills et al. 2006, Zimmerman et al. 2008). In the LFDP, we conduct spatially explicit censuses of trees, shrubs, seedlings (since 1999), and phenology/seed rain (since 1992) at time intervals relevant to their dynamics. Addition of dendrometers to the largest trees and annual measurements of coarse woody debris (CWD) in the plot allows us to estimate carbon storage in the plot as well. In 2010, we began monitoring soil moisture monthly (0-10 cm depth) in 320 m 1 m 2  plots. Intensive soil moisture measurements are made during dry periods (≥ 3 days without rainfall).  The abundance of key heterotrophs, including gastropods and phasmids, as well as lizards, frogs, and birds are measured at forty locations placed on a 60 x 60 m grid in the LFDP. 

The Bisley Experimental Watersheds (BEW) is located in tabonuco forest (200 – 600 m asl) in the northeast corner of the LEF. The BEW are two adjacent watersheds that total 13 ha. Forest composition and soil and plant nutrient content are monitored in 83 permanent 10 m diameter plots on a 40 x 40 m grid every 5 years. Throughfall, litterfall, and stream chemistry are measured weekly, along with coarse particulate export (Heartsill-Scalley et al. 2007, 2010, 2012), which is measured every two weeks.

Stream Monitoring is conducted in three streams of the BEW and in two streams in the El Verde Research Area, the Quebrada Sonadora and the Q. Prieta. Chemistry is measured weekly in these streams (since 1983), as well as in additional streams gauged by the USGS. In the Q. Prieta, we have monitored decapod shrimp weekly at 19 locations (pools) since 1988. Shrimp abundances are also measured twice yearly in two BEW streams. Algal abundance, ecosystem metabolism, chlorophyll a, and insect abundance are measured biannually in the Q. Prieta and one BEW stream. 

The Canopy Trimming Experiment (CTE) was established in the El Verde Research Area in 2002. Initially, this experiment was designed to separate the two principal effects of hurricanes, canopy opening and debris deposition (Shiels & González 2014). The CTE has helped us distinguish the effects of microclimate, detrital inputs, and different functional groups of decomposers in detrital processing and ecosystem resilience after hurricanes (Shiels & González 2014). Thereafter, through a series of repeated canopy  manipulations, the CTE will allow us to assess the effects of a projected increase in the frequency of intense hurricanes (Knutson et al. 2012) on forest composition, soil carbon storage, and nutrient dynamics (Sanford et al. 1991). The experiment originally included four treatments in each of three blocks. Each treatment cover a 30 x 30 m area and includes: 1) canopy trimmed, with trimmed biomass distributed on  the forest floor, changing microclimate, forest floor mass, and nutrient content, 2) canopy trimmed, with trimmed biomass removed changing microclimate, 3) canopy not trimmed, but canopy biomass from a trimmed plot distributed on the forest floor, changing forest floor mass and nutrient content, 4) untreated control. To simulate an increased frequency of intense hurricanes, treatments 1 and 4 (hurricane and control) are being repeated every 10 years for at least 50 years total. The first of the repeated disturbances, the second canopy trimming treatment, took place in late 2014.

The Throughfall Exclusion Experiment (TEE) will be used to determine the impact of multiple short-term droughts on soil biogeochemistry as well as on microbes, seedlings, and litter organisms. Small (3 x 3 m) clear plastic structures significantly reduce soil moisture without causing significant changes in other environmental conditions (e.g., temperature or light; Wood & Silver 2012, Bouskill et al. 2013). Replicate shelters will be placed in ridge, slope, and valley positions, and paired with untreated controls. Roofs are removed weekly to deposit collected litterfall on the soil surface. Throughfall amount and chemistry will be measured according to Wood & Silver 2012 allowing us to determine both water and nutrient removal as a result of simulated drought. We will use volumetric moisture and temperature sensors, a Hydrosense CS620 for gravimetric moisture (Campbell Scientific, Logan, UT), and soil psychrometers (Wescor PST-55, Logan, UT) to convert soil moisture measurements to soil water potential. Soil O sensors (Apogee Instruments, Logan UT) will be installed in a subset of plots in each topographic position. Each shelter will be divided into quadrats to minimize any sampling effects across different measurements (i.e. seedlings, sensors, soil, litter organisms). Results of the TEE will be incorporated into models to investigate potential long-term effects and will help us evaluate feasibility of future large scale throughfall exclusions, which are logistically challenging in forested ecosystems (Meir et al. in press). 
The Stream Drought Experiment (SDE) will be developed in two 150-m long stretches of tributaries of the Q. Prieta (Fig. 9). Our long-term data provide a basis for the selection of these two study reaches: the  Prieta has been studied for over 25 years (Schaefer et al. 2000). We will construct a dam and weir to divert 50% of stream flow (excepting high flow events) to below the de-watered reach between June-Aug (predicted by downscaled climate models to show the largest increase in drought) over three consecutive years during this funding cycle and three additional years in the future. An un-manipulated arm of the stream with similar slope, width (1-3 m), biota, and chemistry will serve as a reference reach. We will add riparian leaf litter to the stream in pulses during the drought treatment to simulate increased leaf drop. We will use Randomized Intervention Analysis (RIA, Carpenter et al. 1989), a design well suited to the analysis of un-replicated whole-ecosystem manipulations.  RIA requires a manipulated system and a reference system.  As required for RIA, all measurements will be conducted concurrently in both streams to create a time-series for each characteristic. Similar to other whole-stream manipulations using RIA (Wallace et al. 1997), we will collect 2 years of pre-manipulation data (2016-17) before the beginning of the reduced-flow manipulation, resulting in one year of post treatment data (2018) for the current proposal, to be continue to complete at least 6 years of post treatment data. A future manipulation (LUQ VI) will include litter inputs and canopy opening in both tributaries of the Q. Prieta. Mapped trees in the 1 ha area will allow estimation of litter inputs during experimental studies (Uriarte et al. in press).


The Long-Term Elevation Plots measure emergent ecosystem properties every six years in three series of plots placed at 50 m intervals along the gradient. In one of these series (Sonadora transect) we compare upland forest types to adjacent palm forest. We also monitor climate, rainfall chemistry, diameter increment, and litterfall. Soil properties and plant species composition have been measured in these plots; we have also conducted decomposition experiments as part of previous LTER research (Silver et al. 1999, McGroddy & Silver 2000, Dubinsky et al 2010). The infrastructure for the LTE, where we will continue long-term monitoring of community changes, was established for vegetation in LUQ III (Barone et al. 2008) in three watersheds (Mameyes, Icacos, and Sonadora).


Our approaches to synthesis include working groups focused on specific research agendas, implementation of new analytical approaches to existing data, and simulation modeling within our own site and across sites.  A simulation model describing community responses to disturbance (SORTIE-PR; Uriarte et al. 2009), as well as analyses using a metacommunity framework (Barone et al. 2008), have provided information to understand biotic structure over space and time.  Using long-term demographic data sets from the LFDP and other secondary forests and newly gathered physiological data from one of the best-studied tropical forests in the world, we will improve and expand the parameterization of the Ecosystem Demography model (version 2.1, hereafter ED2; Moorcroft et al. 2001, Medvigy et al. 2009). 


Barone, J. A., J. Thomlinson, P. A. Cordero, and J. K. Zimmerman. 2008. Metacommunity structure of tropical forest along an elevation gradient in Puerto Rico. Journal of Tropical Ecology

Bouskill, N. J., H. C. Lim, S. Borglin, R. Salve, T. E. Wood, W. L. Silver, and E. L. Brodie. 2013. Pre- exposure to drought increases the resistance of tropical forest soil bacterial communities to extended drought. The ISME Journal 7:384-394.

Carpenter, S. R., T. M. Frost, D. Heisey, and T. K. Kratz. 1989. Randomized intervention analysis and the interpretation of whole-ecosystem experiments. Ecology 70:1142–1152

Condit, R. 1995. Research in large, long-term tropical forest plots. Trends in Ecology & Evolution 10:18-22.

Dubinsky, E. A., W. L. Silver, and M. K. Firestone. 2010. Microbial ecology drives coupled iron – carbon biogeochemistry in tropical forest ecosystems. Ecology 91:2604-2612.

Heartsill-Scalley, T., F. N. Scatena, C. Estrada, W. H. McDowell, and A. E. Lugo. 2007. Disturbance and long-term patterns of rainfall and throughfall nutrient fluxes in a subtropical wet forest in Puerto Rico. Journal of Hydrology 333:472-485.

Heartsill-Scalley, T., F. N. Scatena, A. E. Lugo, S. Moya, and C. Estrada. 2010. Changes in structure, composition, and nutrients during 15 yr of hurricane-induced succession in a subtropical wet forest in Puerto Rico. Biotropica 42:455-463.

Heartsill-Scalley, T., F. N. Scatena, S. Moya, and A. E. Lugo. 2012. Long-term dynamics of organic matter and elements exported as coarse particulates from two Caribbean montane watersheds. Journal of Tropical Ecology 28:127-139.

Knutson, T. R., J. L. McBride, J. Chan, K. Emanuel, G. Holland, C. Landsea, I. Held, J. P. Kossin, A. K. Srivastava, and M. Sugi. 2010. Tropical cyclones and climate change. Nature Geoscience 3:157- 163.

McGroddy, M. E., and W. L. Silver. 2000. Variations in belowground carbon storage and soil CO2 flux rates along a wet tropical climate gradient. Biotropica 32:614-624.

Medvigy, D., S. C. Wofsy, J. W. Munger, D. Y. Hollinger, and P. R. Moorcroft. 2009. Mechanistic scaling of ecosystem function and dynamics in space and time: the Ecosystem Demography model version 2. Journal of Geophysical Research - Biogeosciences (2005-2015) 114.

Moorcroft, P. R., G. C. Hurtt, and S. W. Pacala. 2001. A method for scaling vegetation dynamics: the ecosystem demography model (ED). Ecological Monographs 71:557-586.

Sanford, R. L., Jr., W. J. Parton, D. S. Ojima, and D. J. Lodge. 1991. Hurricane effects on soil organic matter dynamics and forest production in the Luquillo Experimental Forest, Puerto Rico: results of simulation modeling. Biotropica 23:364-372.

Schaefer, D. A., W. H. McDowell, F. N. Scatena, and C. E. Asbury. 2000. Effects of hurricane disturbance on stream water concentrations and fluxes in eight tropical forest watersheds of the Luquillo Experimental Forest, Puerto Rico. Journal of Tropical Ecology 16:189-207.

Shiels, A. B., and G. González. 2014. Understanding the key mechanisms of tropical forest responses to canopy loss and biomass deposition from experimental hurricane effects. Forest Ecology and Management 332:1-10.

Silver, W. L., A. Lugo, and M. Keller. 1999. Soil oxygen availability and biogeochemistry along rainfall and topographic gradients in upland wet tropical forest soils. Biogeochemistry 44:301-328.

Thompson, J., N. V. L. Brokaw, J. K. Zimmerman, R. B. Waide, E. Everham, D. J. Lodge, C. M. Taylor, D. Garcia-Montiel, and M. Fluet. 2002. Land use history, environment, and tree composition in a tropical forest. Ecological Applications 12:1344-1363.

Uriarte, M., C. D. Canham, J. Thompson, J. K. Zimmerman, S. F. Murphy, A. M. Sabat, N. Fetcher, and B. L. Haines. 2009. Natural disturbance and human land use as determinants of tropical forest dynamics: results from a forest simulator. Ecological Monographs 79:423-443.

Wallace, J. B., S. L. Eggert, J. L. Meyer, J. L., and J. R. Webster. 1997. Multiple trophic levels of a forest stream linked to terrestrial litter inputs. Science 277:102-104.

Wills, C., K. E. Harms, R. Condit, D. King, J. Thompson, F. He, G. M. Muller, P. Ashton, E. Losos, L. S. Comita, S. P. Hubbell, J. LaFrankie, S. Bunyavejchewin, H. S. Dattaraja, S. J. Davies, S. Esufali, D. Foster, S. Gunatilleke, C. A. S. Hall, A. Itoh, R. John, S. Kiratiprayoon, S. L. d. Lao, M. Massa, C. Nath, M. N. S. Noor, A. R. Kassim, R. Sukumar, H. S. Suresh, I. Sun, S. Tan, T. Yamakura, and J. K. Zimmerman. 2006. Nonrandom processes maintain diversity in tropical forests. Science 311:527-531.

Wood, T. E., and W. L. Silver. 2012. Strong spatial variability in trace gas dynamics following experimental drought in a humid tropical forest. Global Biogeochemical Cycles 26:GB3005.

Zimmerman, J. K., J. Thompson, and N. V. L. Brokaw. 2008. Large tropical forest dynamics plots: laboratories for testing ecological theory. Pages 98-117 in W. Carson and S. Schnitzer, editors. Tropical Forest Community Ecology. Blackwell Publications Oxford, Blackwell, Oxford.

      Zimmerman, J. K., L. S. Comita, M. Uriarte, N. V. L. Brokaw, and J. Thompson. 2010. Patch dynamics and community metastability of a tropical forest: compound effects of natural disturbance 
and human land use. Landscape Ecology 25:1099-1111.