LUQ LTER DATA SETS DOCUMENTATION FORM
ON-LINE VERSION
A DATA SET is a series of observations collected by the same methodology. Each data set should have documentation sufficient for someone unfamiliar with the research to replicate the study. Data sets may be broken into subsets (data files) that are discrete in space and time, in that order. The documentation for a data set should include all spatial and temporal subdivisions of the data.
(Data, Abstract, Methods, Variables)
NOTES: This metadata is under revision by the LUQ IM to make it comply with the EML
- Add rows to tables or lines to paragraphs as you need them for entering your data.
- Contact emelendez@lternet.edu if you have any question.
- See online Guidelines (http://luq.lternet.edu/datamng/imdocs/division.html) to help you fill this form
- Get the description online of any of the highlighted item by locating your cursor on top of the item, holding the [Ctrl] key while left-clicking your mouse.
| PERSON(S) COMPLETING THIS FORM: | E-MAIL ADDRESS: |
| Sharon A. Cantrell | scantrel@suagm.edu |
DATA SET IDENTIFIER: Canopy Trimming Experiment (CTE) Litter Basket Microbial diversity DNA data
PROJECT TITLE: Canopy Trimming Experiment (CTE) (Leaf Litter Microbial Communities at different stages of decomposition with and without canopy opening and debris deposition)
PROJECT DESCRIPTION: This long-term experiment will increase the frequency of simulated hurricane effects above background levels to once every six years. The experiment will determine effects of repeated disturbance of the forest canopy and increased detrital inputs to the forest floor on germination, growth, survival, nutrient cycling, soil conditions, and trophic structure. Climate change models predict increased frequency and intensity of Caribbean hurricanes (Emmanuel 1987, Goldenberg et al. 2001), and our goal is to evaluate predictions regarding the effects of an increased rate of hurricane disturbance on tabonuco forest (Sanford et al. 1991). The experiment also is designed to decouple the effects of canopy disturbance (e.g. , light levels, temperature, moisture, etc. ) from those of increased detrital inputs on rates of detrital processing and resultant community and ecosystem processes. Manipulations and measurements of detrital processing, SOM, and soil properties associated with SOM will continue for at least three more funding periods (until 2024). In the short-term, we will use faunal manipulations nested within the canopy trimming experiment to measure the strength of interactions between autotrophic and detrital food webs in the context of hurricane-like disturbance. These results will be directed specifically at parameterizing the Trophic Interaction Model. This experiment also will provide a physical and intellectual focal point for the project participants. The Canopy Trimming Experiment has two parts: 1) a forest canopy manipulation with measurements of coupled changes in microclimate, structure, and biota and their associated impacts on ecosystem processes, and 2) specific manipulations of the biota that assess the importance of components of the food web.
CTE Litter Basket Microbial diversity DNA data: Leaf Litter Microbial Communities at different stages of decomposition with and without canopy opening and debris deposition. Hurricanes are common disturbances affecting forest ecosystems in the Caribbean. Our objective was to determine the relative abundance and diversity of microorganisms in leaf litter at different stages of decomposition, and the influence of canopy opening and debris addition or removal. The study was conducted in the tabonuco forest (subtropical moist) at El Yunque Rain Forest, Puerto Rico. Three blocks with four treatment plots were established. TRFLP profiles of the 16S rDNA digested with MnlI and fungal ITS digested with HaeIII showed that the microbial communities at 17, 31 and 55 weeks were highly divergent among treatments. Ratio of fungal to bacterial phylotypes increased for closed canopy with debris addition. Leaf mass loss was slowest in the treatment with canopy trimming and debris removal. Microbial community changes through time can be related to microclimate and the availability of labile compounds. Fungi appeared to control the succession of microorganisms in decomposing leaves.
LTER CORE AREAS: (Annotate all that apply) (See online list)
| Population Dynamics |
| Disturbance Patterns |
LEF LTER 1 RESEARCH TOPIC: Annotate all that apply (See online list)
| Recovery-Spat. Dist. |
We define a data file as a component of a data set. A data set can have only one data file or more. Basically, different data files have different data structures or format.
| Data File No. | Data File Identifier | On-Line Filename | Starting Date | Periodicity of sample | End Period |
1 |
CTE Litter Bacterial DNA | CTELitterTRFLP16SDNA.txt | July 5, 2006 | Every 1 - 3 months | July 13, 2006 |
| 2 | CTE Litter Fungal DNA | CTELitterTRFLPITSDNA.txt | July 5, 2005 | Every 1 - 3 months | July 13, 2006 |
RESEARCH LOCATION: 1) CTE A, B , C Plots:30+ m West of western edge of Big Grid, on North and South side of Prieta stream, near Vogt old plots; 30+ m South of Big Grid, all plots along Oxcart Trail;30+ m West of SE corner of Big Grid, respectively.
| PRINCIPAL INVESTIGATORS | E-MAIL ADDRESS |
S.A. Cantrell |
scantrel@suagm.edu |
| OTHER RESEARCHERS | E-MAIL ADDRESS |
| M. Ortiz | mortizciencias@yahoo.es |
| D.J. Lodge | dlodge@fs.fed.us djlodge@caribe.net |
| CONTACT PERSONS | Phone Number (Include area code) | E-MAIL ADDRESS |
| S.A. Cantrell | 787-743-7979 Ext. 4266 | scantrel@suagm.edu |
SOURCE OF FUNDING (SPONSOR): Grants DEB-0218039 and DEB-0620910 from the National Science Foundation to the Institute for Tropical Ecosystem Studies (ITES), University of Puerto Rico (UPR), and the International Institute for Tropical Forestry USDA Forest Service.
DATA SET ABSTRACT: Hurricanes are common disturbances in the Caribbean region that affect tree distribution, species diversity and biomass in forests. Little is known of how microbial communities in soil and litter are affected by natural or anthropogenic disturbances. The objective of our study was to determine the relative abundance and diversity of microorganisms in leaf litter at different stages of decomposition, and the effect of canopy opening and debris addition or removal.DATA SET METHODS: The study was located in subtropical moist forest (tabonuco forest type dominated by Dacryodes excelsa) at El Verde in the Caribbean National Forest, Puerto Rico. Three blocks with four treatment plots were established. Litter decomposition baskets were placed in five randomly selected subplots per plot. Plots received the following treatments: canopy trimmed and debris added, canopy trimmed and debris removed, not trimmed with debris added, and control. One basket per subplot was retrieved at 7, 14, 28, 40.5 and 53 weeks. Results: Leaf mass loss was slowest in the treatment with canopy trimming and debris removal. Canopy opening was associated with lower litter moisture, lower fungal connectivity between litter layers and slower mass loss after three months. Addition of green leaves increased moisture, and frequently accelerated mass loss of the senesced leaves below them at 17, 28 and 40.5, but not 53 weeks. After 28 weeks, mass loss showed a significant treatment interaction, and was concordant with fungal connectivity between litter cohorts. TRFLP profiles of the 16S rDNA digested with MnlI and fungal ITS digested with HaeIII shows that the microbial communities at 17, 28 and 53 weeks were highly divergent among treatments (Sorensen index of similarity). In comparisons of green versus senesced leaves within treatments, bacterial communities’ differed somewhat, fungal communities differed strongly, but mass loss did not differ. Conclusions: Microbial community changes through time can be related to microclimate and the availability of labile compounds. Fungi appeared to control the succession of microorganisms in decomposing leaves.
Open-mesh plastic baskets 35 x 25
cm were modified by cutting out the solid bottom and
replacing it with 2mm mesh woven nylon mesh. The experiment was set up between
July 1 and 10, 2005. The existing non-woody forest floor (FOFL) was carefully
transferred to the bottom of the basket, and a 1mm mesh plastic window screen
was placed over the forest floor layer. All baskets received 10 g air-dried
freshly fallen (senesced) leaves (FRFA) of Manilkara bidentata and Dacryodes excelsa in a near mono-layer covering
75%-85% of the forest floor cap screen, followed by an additional cap screen.
The mixture of freshly fallen leaves in Block A was 6 g Dacryodes excelsa and 4 g Manilkara bidentata. The mixture of freshly fallen
leaves in Blocks B and C was 4 g Dacryodes excelsa and 6 g Manilkara bidentata. The two treatments that received canopy
debris (canopy trimming plus debris, and no trimming plus debris) received 100
g fresh weight of green leaves (GL) trimmed from the understory in the
following proportions: 25 g Dacryodes excelsa, 33 g Sloanea berteriana, and 42 g Manilkara bidentata for all blocks. There wee three to four 100 g fresh weight subsamples of green
leaves per batch for determination of fresh weight to oven-dried weight ratios,
and initial nutrient concentrations of the green leaves. The green leaf layer
was followed by a cap screen to separate it from natural new litterfall (NL). There were five litter decomposition
subplots in each plot, and six litter decomposition baskets in each subplot.
However, the canopy trimming and debris removal treatment only had baskets in
four of the five litter decomposition subplots in blocks B and C. One
basket per subplot was picked at the following intervals: 7, 17, 28, 40.5, 53
and 80 weeks, but no microbial samples were taken at 80 weeks. At the 17 and 28
week harvests, an additional ‘cap’ screen was placed in the remaining baskets
to separate litterfall cohorts. Harvested baskets
were returned to the station, and 2 g of leaf litter per subplot basket were pooled
within plots for microbial analysis. . DNA was extracted from a 0.3 g of the
pooled sample using MoBio Ultra Clean Soil DNA
Isolation Kit. The 16S bacterial rDNA was amplified using primers 27F-FAM and 1525R, and
digested with MnlI. The fungal ITS region was amplified
using primers ITS1-FAM and ITS4, and digested with HaeIII. Samples were analyzed in
an ABI 3130 using GenScan 500 Liz Size Standard.
CROSS-REFERENCES (other data sets related to this one): LTERDBAS #145: Canopy Trimming Experiment (CTE) Litter decomposition and Connectivity basket data; LTERFBAS#160: Canopy Trimming Experiment (CTE) Microbial EL-FAME Data
STORAGE SITES(of data files): Universidad del Turabo
INVESTIGATOR'S ASSIGNED KEYWORDS:
LEF LTER OFFICIAL KEYWORDS (See table): EL VERDE, CTE blocks, SUBTROPICAL WET ECOSYSTEM, DISTURBANCE, DECOMPOSITION, HURRICANE, COMMUNITY COMPOSITION, SUCCESSION, FUNGI, MONERA
PUBLICATIONS:
May 21-25, 2007. American Society of Microbiology 107th General Meeting, Metro Toronto Convention Center, Toronto, Ontario, Canada.
Poster Presentation: Ortiz Hernández,
M. L., Lodge, D. J., Pérez Jiménez,
J. R., Cantrell, S. A. Leaf Litter Microbial Communities at different stages of
decomposition with and without canopy opening and debris deposition
September 19-23, 2006. All-Scientists Long-Term Ecological Research Meeting, Estes Park, Colorado. Poster Presentation: Cantrell, SA, García-Orta LM, Rivera-Figueroa F, Cruz C, González G, Zou X, Pett-Ridge J, Dubinsky E, Lodge DJ, Firestone M. 2006. “Microorganisms. Key players in ecosystem functions
September 19-23, 2006. All-Scientists Long-Term Ecological Research Meeting, Estes Park, Colorado. Poster Presentation: Zimmerman J, Shiels A, Bloch C, Cantrell S. Crowl T, Cruz C, Garcia L, González G, Klawinski P, Lebrón L, Lodge DJ, McDowell W, Melendez-Colom E, Prather C, Ramirez A, Reese E, Richardson B, Richardson M, Rivera F, Schowalter T, Sharpe J, Silver W, Brokaw N. 2006. “The Canopy Trimming Experiment at LUQRESTRICTED
DISSEMINATION: RESTRICTED ___ UNRESTRICTED _X_REASONS TO RESTRICT DATA IN THIS DATA SET BEYOND ITS TWO YEAR POLICY PERIOD*:
*WILL HAVE TO BE APPROVED BY AT LEAST ONE LUQ LTER PRINCIPAL INVESTIGATORS: N. Brokaw, J. ZIMMERMAN, A. LUGO
FILING:_X__ "File" copy only:Data Management will only file an electronic copy of the data file and its documentation
___ " Enter" data on-line:Data Management will be in charge of entering the data on computer files (Contact Eda C. Meléndez)
SITES DESCRIPTIONS:
1)CTE A, B , C Plots:30+ m West of western edge of Big Grid, on North and South
side of Prieta stream, near Vogt old plots; 30+ m
South of Big Grid, all plots along Oxcart Trail;30+ m West of SE corner of Big
Grid, respectively.
Geographical positional system (GPS) Coordinates for each location:
location |
latitude |
longitude |
| El Verde | 18.3 | 65.8 |
The following table displays the x and y coordinates in Puerto Rico Planar Coordinates:
| BlockPlot | X | Y |
| A1 | 217379 | 54625 |
| A2 | 217437 | 54631 |
| A3 | 217423 | 54720 |
| A4 | 217460 | 54684 |
| B1 | 217824 | 54356 |
| B2 | 217875 | 54344 |
| B3 | 217913 | 54278 |
| B4 | 217970 | 54217 |
| C1 | 217878 | 54476 |
| C2 | 217933 | 54476 |
| C3 | 217998 | 54480 |
| C4 | 218094 | 54544 |
| File Name or # above (all in which the variable appears) | 1,2 |
1,2 | 1,2 | 1, 2 |
| AbbreviationAbbreviation(as it appears on the data file) | Block |
Plot |
Litter_Layer_Cohort | Weeks_decomposition |
| NAME OF VARIABLE | Block identifier |
Plot Identifier |
Litter Cohort | number of weeks decomposing in field |
| DEFINITION OF VARIABLE | Name given to a grouping of 4-like plots in one of three locations |
Name given to a 20m X 20m plot of a Block. No missing data |
Litter layer name | |
| UNIT | weeks | |||
| PRECISION | 0.5 | |||
| RANGE OR LIST OF VALUES | A = West of western edge of Big Grid plot |
1,..., 4 |
FOFL= Forest Floor, FRFA = Fresh fallen, GL = Green Leaf, NL = New Litter | |
| DATA TYPE | alphabetic |
integer |
alphabetic | decimal |
| MISSING DATA CODES | No missing data | No missing data |
VARIABLES (ATTRIBUTES):
| File Name or # above (all in which the variable appears) | 1,2 | 1,2 | 1,2 | 1,2 | 1,2 | 1,2 |
| Abbreviation (as it appears on the data file) | Date_Initial | Date_Final | Sample Peak | Size | Height | Area |
| NAME OF VARIABLE | Date Initial | Date Final | Sample Peak | Size | Height | Area |
| DEFINITION OF VARIABLE | Date the pre-weighed leaf cohorts were placed in field. No data is missing. | Date the baskets were harvested. No missing data. | Sequential number assigned to peaks according to their appearance/size. No missing data. | Number of base pairs in DNA fragment. No missing data. | Fluorescence units datetime. | Area below the peak |
| UNIT | ||||||
| PRECISION | ||||||
| RANGE OR LIST OF VALUES | ||||||
| DATA TYPE | datetime | datetime | integer | decimal | integer | decimal |
| MISSING DATA CODES |
COMPUTATIONAL METHODS:
| Variable Name | Formula |
FOR DATA MANAGER USE ONLY
DATE OF LAST REVIEW: May 29, 2009
DATE OF LAST ENTRY:
STAGE OF DATA SET MANAGEMENT (dates):
RECEIVED: March 27, 2009
ENTERED:
May 29, 2009
FILED ON-LINE:
May 29, 2009
REVIEWED BY RESEARCHER:
FILING MEDIA:
NAME OF DOCUMENTATION FILE: LTERDBAS
RECORD #: 159
DOCUMENT TYPE: binary
PRIORITY TO BE ENTERED: N/A
Rev. date of this form: 28 July 200/ 15 July 2001/June 9, 2003/March 16, 2004/12 April 2005/ 8 November 2005/ 16 January 2006