DOI: 10.6073/pasta/96aab0f4e254d3f181eb51d6abbf4e2d
title: Stream biofilm bacterial community composition

description: The Baltimore Ecosystem Study stream biofilm bacterial community composition was obtained from 8 long-term sampling network sites in and near the Gwynns Falls watershed to examine how bacterial communities differ along an urban-rural gradient. Sampling was conducted at the same time as stream chemistry sampling on 18 June 2014 and 21 Oct 2014. Note: biofilm samples were taken about 50 meters east from the Carroll Park monitoring station, just under the I95 highway overpass, due to high water depth, high water flow, and lack of rock substrates for sampling.
      
      
          This dataset presents the number of sequences matching the taxonomic classifications in a reference database of 16S rRNA genes. See the full metadata record for detailed methods.
      
      
          Column, Codes and Abbreviations
      
          A,	taxlevel - taxonomic classification level; 1=kingdom, 2=phylum, 3=class, 4=order, 5=family, 6=genus.
      
          B,	rankID - pedigree of the taxon lineage. For example, 0.1.1.1 and 0.1.1.2 are two taxa in the same phylum (0.1.1) but different classes.
      
          C,	taxon - name of the taxon; unclassified=sequence with a 97% match in the reference database could not be found.
      
          D,	daughterlevels - number of children lineages within a taxon. For example, a phylum with 24 daughterlevels has 24 distinct classes identified in the samples.
      
          E,	total - total number of sequences.
      
          F,	POBR1 - Pond Branch forested reference site - Forested reference - 18-Jun-2014
      
          G,	BARN1 - Baisman Run at Ivy Hill Road - Suburban unsewered - 18-Jun-2014
      
          H,	GFGL1 - Gwynns Falls at Glyndon - Suburban headwaters - 18-Jun-2014
      
          I,	GFGB1 - Gwynns Falls at Gwynnbrook Avenue (Delight) - Suburban - 18-Jun-2014
      
          J,	GFVN1 -  Gwynns Falls at Villa Nova - Suburban/urban boundary - 18-Jun-2014
      
          K,	DRKR1 - Dead Run at Krome Avenue - Urban - 18-Jun-2014
      
          L,	GFCP1 - Gwynns Falls at Carroll Park - Urban - 18-Jun-2014
      
          M,	GRGF1 - Gwynns Run at Gwynns Falls - Urban - 18-Jun-2014
      
          N,	POBR2 - Pond Branch forested reference site - Forested reference - 21-Oct-2014
      
          O,	BARN2 - Baisman Run at Ivy Hill Road - Suburban unsewered - 21-Oct-2014
      
          P,	GFGL2 - Gwynns Falls at Glyndon - Suburban headwaters - 21-Oct-2014
      
          Q,	GFGB2 - Gwynns Falls at Gwynnbrook Avenue (Delight) - Suburban - 21-Oct-2014
      
          R,	GFVN2 - Gwynns Falls at Villa Nova - Suburban/urban boundary - 21-Oct-2014
      
          S,	DRKR2 - Dead Run at Krome Avenue - Urban - 21-Oct-2014
      
          T,	GFCP2 - Gwynns Falls at Carroll Park - Urban - 21-Oct-2014
      
          U,	GRGF2 - Gwynns Run at Gwynns Falls - Urban - 21-Oct-2014
      
      
      
          Methods:
      
          At each sampling location, 5 rocks (size 2-10 inches long) were collected and scrubbed to obtain a biofilm slurry. Subsamples of the slurry were frozen at -80 degrees C until further processing. In the lab, DNA extraction was performed using the MoBio Powersoil DNA extraction kit and PCR amplification of partial bacterial 16S rRNA genes was performed using primers 515F and 806R to amplify the V4 hypervariable region of bacterial and archaeal 16S rRNA genes. Amplicons were sequenced in a 2x250 base pair paired-end format using the Illumina MiSeq platform. Sequencing of amplicons was performed by DNA Services Facility at the University of Illinois at Chicago (Chicago, IL). 
      
      
      
          See the full metadata record for the following information:
      
      
          Section 1: Sampling Network
      
          Section 2: Sample Collection and Processing
      
          Section 3: Sequence Analysis 
      
      
          Summary of Section 1: Sampling Network
      
          1.1. Long-term stream monitoring sites along the Gwynns Falls and Oregon Ridge watersheds, excluding McDonogh.
      
      
          Summary of Section 2: Sample Collection and Processing
      
          2.1. Collection of Stream Biofilms
      
          2.2. DNA Extraction and Sequencing
      
      
          Summary of Section 3: Sequence Analysis
      
          3.1. mothur
      
          3.2. Taxonomic Classification
      
          3.3. MiSeq Pipeline