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:

PERSON(S) COMPLETING THIS FORM:

E-MAIL ADDRESS:

Francisco J Rivera-Figueroa

Frivera@suagm.edu

DATA SET IDENTIFIER : Canopy Trimming Experiment (CTE) Microbial EL-FAME Data

PROJECT TITLE : CTE - The effect of a natural disturbance in the microbial community's fatty acid profiles in the Luquillo Experimental Forest .

PROJECT DESCRIPTION : The long-term canopy trimming 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 soil and Leaf litter microbial community analysis: Microorganisms play an important role in the forest's restoration through their detritus dynamics. Our objective was to determine how the canopy openings and debris pulses affect the soil and leaf litter microbial community structure and composition in the forest before and after the canopy manipulation. We monitored the soil and leaf litter communities through the analysis of their cellular fatty acids also called ester linked fatty acid methyl ester (EL-FAME).

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.) Spatial and temporal distribution of population.

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 SET FILES (SUBSETS):

Data File No.

Data File Identifier

On-Line Filename

Starting Date

Periodicity of sample

End Period

1

Soil CTE-EL-FAME

CTE-SOIL_EL-FAME.txt

November 2002

4 month intervals (before and after canopy trimming)

June 17, 2006

2

Leaf Litter CTE-EL-FAME

 CTE-LEAF_LITTER_EL-FAME.txt

November 2, 2002

4 month intervals (before and after canopy trimming)

June 9, 2006

RESEARCH LOCATION: Block A: 30+ m West of western edge of Big Grid, on North and South side of Prieta stream, near Vogt old plots. Block B: 30+ m South of Big Grid, all plots along Oxcart Trail. Block C: 30+ m West of South East corner of Big Grid.

  INVESTIGATORS:

PRINCIPAL INVESTIGATORS

E-MAIL ADDRESS:

Sharon A. Cantrell Rodríguez

scantrel@suagm.edu


Other Researchers:

E-MAIL ADDRESS:

Francisco J. Rivera-Figueroa

Frivera@suagm.edu

D.J. Lodge

dlodge@fs.fed.us

Marirosa Molina

molina.marirosa@epa.gov


CONTACT PERSONS:

Phone Number
(Include area code):

E-MAIL ADDRESS:

Francisco J. Rivera-Figueroa

(787)743-7979 ext. 4170

Frivera@suagm.edu

Sharon A. Cantrell Rodríguez

(787)743-7979 ext. 4226

scantrel@suagm.edu

SOURCE OF FUNDING (SPONSOR): NSF LTER funding for materials, supplies, to make the CTE plots and tech time. Universidad Del Turabo for samples storage and processing and Environmental Protection Agency (EPA) in Athens Georgia for Gas Chromatography Analysis and scientist's time.

DATA SET ABSTRACT: The canopy trimming experiment at El Verde simulates some aspects (canopy openness and biomass redistribution) of hurricane disturbances. Soil samples and leaf litter were gathered from three replicate blocks, each with four treatment plots in Tabonuco Forest at in El Verde. Treatments (canopy trimming and debris addition) were applied in a 2 x 2 factorial design. Samples were obtained both before and after the canopy were trimmed and debris was applied in the appropriate treatments. Samples were collected every four months before and after treatments were applied. Molecular approaches such as EL-FAME are useful indicators of microbial community shifts in response to environmental change. In this experiment we analyzed microbial community composition and abundance in soil and leaf litter samples as reflected by EL-FAME profiles. All soil samples were cleaned by removing rocks and roots, and leaf litter samples were ground.

Fatty acid nomenclature: Fatty acids are named according to the conversion X:YωZ, where X represents the number of carbon atoms in the chain, followed by Y after the colon which represents the degree of the unsaturation. The symbol ω and Z represent the number of double bonds nearest to the carboxyl end. The prefixes a, i, cy and d refer to anteiso, iso, cyclopropyl branching and dicarboxylic fatty acid respectively; br indicates that the type of branching is unknown, while a number followed by Me indicates position of methyl group. Prefixes a and b indicate that the OH groups of an OH fatty acid are located at positions 2 and 3 respectively. Numbers preceded by w indicate the position of OH groups from the aliphatic end of the fatty acids (Kaur et al 2005).

Community analysis based on fatty acids: Fatty acid biomarkers could represent a group of particular microorganisms present in soil and leaf litter. Fatty acids used in literature as biomarkers are: Branched chain fatty acids (br 17:0, br 18:0, i17:0, a17:0, i16:0, i16:1, 10Me16:0, 10Me17:0), iso and anteiso isomers of 15:0 for gram positive bacteria; Cyclopropane fatty acids (cy17:0, cy19:0, 16:1w9, 16:1w7c, 16:1w5, 18:1w7,19:1) for gram-negative bacteria; 18:2w6 for fungi; 10Me16:0, 10Me17 : 0 and 10Me18 : 0 for Actinomycetes; cy17:0 and 10Me16:0 for Sulphate reducing bacteria; 16:1w8, 18:1w8 for Methanogens (Modified from Zelles, 1999; Kaur et al 2005).

DATA SET METHODS:   A PVC core (5cm diameter) was used to collect 0-10cm soil samples from five sub plots in each treatment plot. The five sub plot samples were clean (rocks, wood and invertebrates debris and roots) and pooled. Approximately 20 g of leaf litter samples were gathered close to where the soil cores were taken, then pooled and ground. All samples were kept at -4 °C after being pre-processed then moved to a -70 °C for longer storage.   Lipids were extracted directly from soil and leaf litter using the EL-FAME method described by Schutter and Dick (2000). The lipid extraction procedure used a mild alkaline methylation, which in theory, remove the cellular ester linked fatty acid and not free fatty acids. After extracting the fatty acids by this method, they were cleaned with an amilopropyl (NH2) column to remove any humic substances. Fatty acid samples were kept frozen at -20 °C in darkness until their analysis in gas chromatograph.

REFERENCES :

Schutter ME, Dick RP. 2000. Comparison of fatty acid methyl ester (FAME) methods for characterizing microbial communities. Soil Scientists of America Journal 64:1659-1668

Kaur A, Chaudhary A, Kaur A, Choudhary R, Kaushik R. 2005. Phospholipid fatty acid- A bioindicator of environmental monitoring and assessment in soil ecosystem. Current Science. 89:1103-1112.

CROSS-REFERENCES (other data sets related to this one): LTERDB159: Canopy Trimming Experiment (CTE) Litter Basket Microbial diversity DNA data

SAMPLE LOCATION :

CTE plots:

Block

Treatment

Plot

A

Control

1

A

Trim + removal

2

A

Trim +debris

3

A

No cut +debris

4

B

Control

1

B

Trim +debris

2

B

No cut +debris

3

B

Trim + removal

4

C

No cut +debris

1

C

Trim +debris

2

C

Trim + removal

3

C

Control

4

STORAGE SITES (of data files): Universidad del Turabo, School of Science and Technology, Cantrell's Lab.

INVESTIGATOR'S ASSIGNED KEYWORDS: EL-FAME analysis, Microbial communities

LEF LTER OFFICIAL KEYWORDS (See table): CTE blocks, SUBTROPICAL, TABONUCO, COMMUNITY COMPOSITION, DISTURBANCE, SOILS, MONERA, FUNGI

PUBLICATIONS : Rivera Figueroa, F.J.. 2008. Dissertation: "Efecto de un disturbio natural en el perfil de ácidos grasos de comunidades microbianas en el bosque experimental de Luquillo en Puerto Rico". Universidad del Turabo. 123 p.

DISSEMINATION : UNRESTRICTED

RESTRICTED                          UNRESTRICTED X

REASONS TO RESTRICT DATA IN THIS DATA SET BEYOND ITS TWO YEAR POLICY PERIOD*:

*WILL HAVE TO BE APPROVED BY LTER PRINCIPAL INVESTIGATORS: N. BROKAW, 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. Melendez)

SITES DESCRIPTIONS: Block A: Elevation (340-360); aspect SW-facing; Location 30+ m West of western edge of Big Grid, on North and South side of Prieta stream, near Vogt old plots. Block B: Elevation (450-485); aspect W-SW facing; Location 30+ m South of Big Grid, all plots along Oxcart Trail. Block C: Elevation (435-480 m); aspect West-facing; Location 30+ m West of SE corner of Big Grid.

Geographical positional system (GPS) Coordinates for each location:

location

latitude

longitude

El Verde-CTE Blocks

+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

VARIABLES (ATTRIBUTES):    

File Name or # above (all in which the variable appears)

all

all

all

all

Abbreviation Abbreviation

(as it appears on the data file)

YEAR

BLOCK

TRT

DATE

NAME OF VARIABLE

Year

Block

Treatment

 

DEFINITION OF

VARIABLE

Name given to samples from the pre treatment and post treatment period. No data are missing in the data file.

Name given to a grouping of  4-similar plots in one of three locations. No data are missing in the data file.

Name given to treatment applied on each plot of a Block. No data are missing in the data file.

Sampling date (in mm/dd/yyyy) . No data are missing in the data file.

UNIT

     

 

PRECISION

       

RANGE OR LIST OF VALUES

Pre-Trt = data from pre-treatment period, Post-Trt = data from post-treatment period

A = West of western edge of Big Grid plot, B = South of Big Grid,
C =West of South East of Big Grid corner

Not  = Control, T+R = Trim + removal, T + D = Trim + debris, NOT + D = No cut + debris

 

DATA TYPE

alphabetic

alphabetic

alphabetic

datetime

MISSING

DATA CODES

       

VARIABLES (ATTRIBUTES):

File Name or # above (all in which the variable appears)

all

all

Abbreviation Abbreviation

(as it appears on the data file)

EL-FAME

CONC.

NAME OF VARIABLE

Ester-linked fatty acid methyl esters

Concentration

DEFINITION OF

VARIABLE

Ester-linked fatty acid methyl esters present. Each fatty acid could represent a group of microorganisms in the community.

Amount of each fatty acid in the substrate

UNIT

 

micro molesPerGram

PRECISION

   

RANGE OR LIST OF VALUES

11:00, 2OH - 10:0, 12:00, 13:00, 2OH - 12:0, 3OH - 12:0, br 14:0, 14:00, i15:0, a15:0, 15:00, br16:0, 2OH - 14:0, 3OH - 14:0, i16:0, 16:1w7c, 16:1w7t, 16:1w5, 16:00, 10Me 16:0, br 17:0, i17:0, a17:0, 17:1w7c, cy17:0, 17:00, br 18:0, 2OH - 16:0, br18:0, 18:3w6, 18:2w6, 18:1w9, 18:1w7, 18:1w5, 18:00, 10Me 18:0, br 19:0, i19:0, cy19:0, 19:00, br 20:0, 20:5w3, 20:3w6, 20:3w3, 20:00, 2 OH- cy19:0, 22:01, 22:00, 24:00

  

DATA TYPE

alphanumeric

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 : June 17, 2006

STAGE OF DATA SET MANAGEMENT (dates) :

RECEIVED: May 28, 2008
ENTERED: May 29, 2008
FILED ON-LINE: May 29, 2008
REVIEWED BY RESEARCHER:

FILING MEDIA :

NAME OF DOCUMENTATION FILE : lterdb160.htm, CTE_EL_FAME_Francisco.htm
NAME OF ON - LINE CATALOG : LTERDBAS
RECORD # :   160
DOCUMENT TYPE : binary
PRIORITY TO BE ENTERED : N/A



Rev. date of this form: 28 July 2001 / July 15, 2001 / June 9, 2003 / March 16, 2004 / 12 April 2005 / November 8, 2005