Plum Island Ecosystems LTER Database

Acceptance and utilization of LTER data requires that:

(1) The Principal Investigator be sent a notice stating reasons for acquiring any data and a description of the publication intentions.
(2) The Principal Investigator of the data set be sent a copy of the report or manuscript prior to submission and be adequately cited in any resultant publications.
(3) A copy of any resultant publications should be sent to:

Principal Investigator
Ecosystems Center
Marine Biological Laboratory
7 MBL St.
Woods Hole, MA 02543

Dataset URLs:METADATA: HTML, Rich Text, XML(EML compliant)
DATA: Comma Delimited, Excel file with Metadata and data
Dataset ID:PIE-Microbes-Genomics.05
Dataset Title:Descriptive data file for information regarding microbial genetic research in the environs of Plum Island Sound watersheds, PIE LTER, Massachusetts.
Investigator 1: 
First Name:Anne
Last Name:Giblin
Address line 1:Ecosystems Center
Address line 2:MBL
Address line 3:7 MBLSt
City:Woods Hole
State:MA
Zip Code:02543
Country:USA
Investigator 2: 
First Name:John
Last Name:Hobbie
Address line 1:Ecosystems Center
Address line 2:MBL
Address line 3:7 MBLSt
City:Woods Hole
State:MA
Zip Code:02543
Country:USA
Investigator 3: 
First Name:Byron
Last Name:Crump
Address line 1:University of Maryland Center for Environmental Science
Address line 2:Horn Point Laboratory
Address line 3:5745 Lovers lane
City:Cambridge
State:MD
Zip Code:21613
Country:USA
Investigator 4: 
First Name:Jennifer
Last Name:Bowen
Address line 1:Department of Marine and Environmental Science
Address line 2:Northeastern University
Address line 3:430 Nahant Road
City:Nahant
State:MA
Zip Code:01908
Country:USA
Associate Investigators:Jane Tucker, Hap Garritt
Keywords:PIE LTER, population dynamics, Parker River, Plum Island Sound, Ipswich River, watershed, microbes, genome, diversity, community, phylogenetic tree, sequence, accession number, bacterioplankton, ammonia oxidizers, nitogenase, Archaea, sulfate reducers, Vibrionaceae, chitin, salinity, marsh
Abstract:This is a descriptive, tabular dataset of publications related to microbial or genomic research conducted within PIE. Assession numbers for genetic sequences generated from PIE samples are provided where available, followed by a very brief description of analysis type and study objectives. Sampling locations within PIE, sampling dates, and habitat type (sea water, fresh water, sediment, marsh) are also given. Environmental data are included in some publications and are listed here (if brief) or availability is described. Links to sequence databases are given below in Methods.
Contact: Plum Island Ecosystems LTER Information Manager
The Ecosystems Center
Marine Biological Lab
7 MBL St
Woods Hole, MA 02543
Phone (508) 289 7485
Email: pie_im@mbl.edu
Online URL: http://pie-lter.ecosystems.mbl.edu
DATA FILE INFORMATION:
Data File URL http://ecosystems.mbl.edu/PIE/data-archive/MIC/data/PIE-Microbe-Genomics.csv
Data File Name PIE-Microbe-Genomics
Beginning Date 1/1/2002
End Date 7/26/2021
Number of Data Records 32
Other Files to Reference
Availability Status Type 1
Quality Control Information
Maintenance Description On going studies
Log of Changes: Version 01: March 6, 2012, updated data and metadata. Used MarcrosExportEML_HTML (working)pie_excel2007.xlsm 2/28/2012 8:18 PM for QA/QC to EML 2.1.0
Version 02: April 20, 2018, data and metadata created to comply with importation to Drupal and LTER PASTA. Used MarcrosExportEML_HTML (working)pie_excel2007_Jan2018.xlsm 1/30/2018 2:24 PM for QA/QC to EML 2.1.0
Version 03: August 13, 2019, edited URL made shorter, data and metadata updates to comply with importation to DEIMS7 and LTER Data Portal. Used MarcrosExportEML_HTML (working)pie_excel2007_Jun2019.xlsm 6/7/19 12:58 PM for QA/QC to EML 2.1.0
Version 04: August 26, 2019, data and metadata updates to comply with importation to DEIMS7 and LTER Data Portal. Used MarcrosExportEML_HTML (working)pie_excel2007_Jun2019.xlsm 6/7/19 12:58 PM for QA/QC to EML 2.1.0
Version 05:July 29, 2021, Data and metadata updates. Used MarcrosExportEML_HTML (working)pie_excel2007_Jul2021.xlsm 7/26/2021 9:04 AM for QA/QC to EML 2.1.0.
 
RESEARCH LOCATION: MON-PIE-Site Site 2
Geographic Description PIE LTER research site including watersheds and estuary, Essex County, MA  
Location Bounding Box    
West Bounding Coordinate -71.22  
East Bounding Coordinate -70.75  
North Bounding Coordinate 42.83  
South Bounding Coordinate 42.5  
OR if single point location    
Latitude    
Longitude    
Elevation    
     
     
 
TAXONOMIC COVERAGE:
Taxonomic Protocols genetic sequencing
Organisms studied Bacteria; Archaea; Eukarya
 
Methods:Microbial genomic sequence data are available by conducting searches using accession numbers associated with the sequence of interest.
Examples of of searches are:
Entrez search, easily search by single accession number; returns sequence and publication information. Link: http://www.ncbi.nlm.nih.gov/sites/gquery
Batch Entrez, Batch search a series of accession numbers after creating a Fasta-formatted text file; returns links to GenBank, Fasta, Graphics, Population Set and Related Sequences for each accession number. Link: http://ncbi.nlm.nih.gov/sites/batchentrez

Batch Entrez Fasta-formatted text file should be a single column list of accession numbers with a ".1" added like a file extension. File should have no header line. Go to http://ncbi.nlm.nih.gov/sites/batchentrez, follow the web site directions for using Batch Entrez
Fasta-formatted text file example:
AY836800.1
AY836801.1
AY836802.1
AY836803.1
etc..

To access MG-RAST annotation and raw sequences, the user will need to navigate to this page:
http://www.mg-rast.org/mgmain.html?mgpage=search
and enter the project id listed in the PIE-Microbe-Genomics tab (e.g. mgp84173) into the text box at the upper left of the page adjacent to the "search" button.  
The search will return a list of the samples associated with the project and a link to download the annotation, fasta files, and associated metadata.
 
Data can also be accessed through the API according to the instructions here
http://api-ui.mg-rast.org/api.html
 
Also available, courtesy of Joe Vineis, is a small git repository that includes some simple instructions for handling the API for beginners:
https://github.com/jvineis/mg_rast_processing


Data Table

Variable Name Variable Description Units Measurement Scale Code Information Number Type DateTime Format Missing Value Code Missing Value Code Explanation
Bacterial Genome Citation Publications associated with bacterial genome research in PlE LTER   nominal       NA NA=data not available
Accession Numbers Description of accession numbers published in corresponding BacterialGenomeCitation   nominal       NA NA=data not available
Study Type Type of genomic study   nominal       NA NA=data not available
Location at PIE Geographic location where samples were collected for sequencing   nominal       NA NA=data not available
Habitat Type Habitat from which samples were collected for sequencing   nominal       NA NA=data not available
Environ Parameters Brief description of "environmental conditions" pertinent to samples collected for sequencing   nominal       NA NA=data not available
NotesKeywords Notes and keywords from associated Bacterial Genome Citation   nominal       NA NA=data not available