Applied Environmental Microbiology Core

1
Applied Environmental Microbiology Core

• Current
• and
• Future Work

2
Strain/Species Sequencing

• DP4 in progress
• Other DvH?
• Other SRBs?

3
MICs

• Stressors to date O2, NO3, NO2, pH (5.5, 10),
  NaCl, KCl, Cr, Heat Cold shock
• DvH other stresses?
• DvH mutants repeat with previous stresses? DP4?
• DvH stress with Cr, U reduction?
• SO aerobic and anaerobic nearly complete for all
  previous DvH stresses
• Gm with stresses used for DvH?

4
Phenotype Microarrays

• On Biofiles (9)
• DvH WT (6), JW707, JW3011, JW3047, JW7019
• So WT, 1422, 1607, 3629
• To be uploaded to Biofiles (8)
• DvH additonal WT and JW707, JW3012
• So 2847, 2438, 769, 843, 2366
• In the que (to be done DvH9, So19)
• DvH DP4, StahlFRC, DvHAM88, DvHAM66, DvHAM65,
  DvHAM64, DvHAM63, DvHAM62, DvHAM61
• So GH1, GH3, DSP10_ArchA, DSP10_Crp, DSP10_fur,
  DSP10_EtrA, _Crp, DSP10_EtrA, _fur, DSP10_EtrA,
  MR1-LB, DSP10, 859, 1355, 1963, 1538, 3904, 1578,
  1393, 0300
• Gm???

5
Biomass Production Refinements

• Switch to turbidostat or chemostat production
  (need 4 more bioreactors)
• Replicate protocol each starter culture is 10
  frozen stock to 3 starter cultures, starter
  cultures C1 and V1, C2 and V2, C3 and V3.
• Pooling protocol?
• Transcriptomics - all triplicates
• Phenomics - all triplicates
• Proteomics and Metabolomics T0 all C and V
  replicates pooled, after T1 C and V replicates
  pooled.
• Wish List?

6
DvH Biomass Production

• Expt Date Stressor Vol (L) Notations
• 47 4/7/2005 Cr 0.55 mM 12.0
• 48 5/26/2005 nitrate 6500 ppm 12.0
• 49 6/24/2005 strep-tagged mutants 3.0 Expt 51
  repeated for Expt 49
• 50 7/8/2005 Metabolite study 3.0
• 51 7/11/2005 strep-tagged mutants 3.0
• 52 7/21/2005 NaCl 250 mM 12.0 Cancelled incubator
  turned off
• 53 7/28/2005 NaCl 250 mM 12.0
• 54 7/28/2005 DvH cells 12.0
• 55 7/28/2005 DvH cells 12.0
• 8/4/2005 JW0707 Fur mutant 12.0
• 8/25/2005 Cr 0.55 mM 2 time points for all (need
  analysis on transcriptome)
• 9/1/2005 Fur/limited iron 1 5 time point?
  transcriptome only
• 9/6/2005 Chemostat NO3 stress, 2 time point for
  all??
• 9/8/2005 SO or GM with NaCl or NO3 or NO2 5
  time point transcriptome
• 9/15/2005 SO or GM with NaCl or NO3 or NO2 5 time
  point transcriptome
• 9/22/2005 Fur/limited iron 2 5 time point?
  Transcriptome only
• 9/29/2005 SO or GM with NaCl or NO3 or NO2 5
  time point transcriptome

7
Dual Phase Cultures

• In Progress
• Chemostat comparison to batch in progress
• Resolve RNA isolation/labeling/hybridization
• Stressors H2, NaCl, KCl, NO3, NO2, O2, pH????

8
Soil Columns?????

• Bioaugmentation (DvH) and stress induction (NO3,
  low pH) with Cr or U?
• Stress (NO3, low pH) from FRC sediment and
  lactate biostimulation?
• Others?
• Measurements Transcriptomics? Proteomics?

9
Field Studies

• Complete paper on FRC (M. Keller)
• Submit collaborative Polyphasic paper on FRC (M.
  Fields)
• Upload field data from FRC (Fields Hazen)
• Upload data from Hanford 100 H field tests
  (Hazen)
• Send Stahl group ground water from Hanford for
  enrichment and isolation? (Hazen)
• Complete metagenome analysis of FRC groundwater,
  additional sites (J. Zhou)
• Metagenome analysis of sediment of FRC ()
• Compare metagenome to Diversa results and
  additional sampling for groundwater and sediment?
• Diversa sampling of Hanford 100 H?
• Lake DePue sampling?
• FACs interegation of Hanford, FRC, Lake DePue?