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LabMtg042310

Math-Worm
by

Danielle Winget

on 1 May 2010

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Transcript of LabMtg042310

Viruses around the world 3 things we always say Deep Mines Naica Kidd Creek Saanich Inlet Viral Abundance Viral Concentrates Deep 454 pyrosequencing of PCR amplicons

The Samples:
GOB (3)
Saanich (2)
Arctic (1) Richness
The primer sets:
AVS - algal viruses - ~700bp
g23 - myoviruses - 400-700bp
Podo - podoviruses - 1.2kb
16S - V3 region - ~100bp
18S - euks - ~210bp




GOB1a
Lab meeting
April 23, 2010
Danielle Winget Ubiquitous
Viruses Timmins, ON Kidd Creek Naica, Mexico 7850 ft below ground:
2 Boreholes: 2 to 5 x 10 VLPs/mL
1 to 1.6 x 10 bacteria/mL
Service Water: 4.5 x 10 VLPs/mL
5.1 x 10 bacteria/mL 9000 ft below ground:
3 Boreholes: 7 to 10 x 10 VLPs/mL
1 to 22 x 10 bacteria/mL
Service Water: 4.3 x 10 VLPs/mL
1.1 x 10 bacteria/mL Crystal Cave
1.5mL Queen's Eye
1.5mL Hell Pipe
1.5mL Lake
0.5mL Virus - 1.6 x 10 /mL
Bacteria - 4.7 x 10 /mL Virus - 1.5 x 10 /mL
Bacteria - 2.9 x 10 /mL Virus - 1.7 x 10 /mL
Bacteria - 1.6 x 10 /mL Virus - 1.6 x 10 /mL
Bacteria - 7.4 x 10 /mL
Viruses in deep sub-surface environments
10,000 to 10,000,000 per mL
Contaminants or indigenous?

Likely contaminants - Kidd Creek Level 9000 & Los Cristales
Possibly indigenous - Queen's Eye & Hell Pipe
Variations in
Viral Assemblages Average Concentration Efficiency - 20%
Why so low?
Range 1-99% Correlations
Entire data set - Viral abundance in concentrates (+)
Month
Conc. eff. >50% - 11 data points
Month
Conc. eff. <10% - 47 data points
Viral abundance in concentrates (+) Viral Continued problems

Perseverance
Can amplify
AVS, g23, Podo, ssDNA
Avg. Length - 222bp

Avg. % GC - 50%
85% sequences with primer "good"
15% chimeric
GOB1a breakdown

Primer Total no. seq % chimeric
Podo 1,181 22
AVS 7,035 24
g23 23,196 40
Prok 44,885 27
Euk 86,844 0.5 4 4 7 5 6 7 7 7 8 6 6 5 6 6 6 7 205,982 reads

Range: 32 - 1098bp

Range: 15 - 71%

(GOB1)


(2,121) (31)
(189) (22)
(30,025) (0.7)
(40,216) (0.07)
(7,817) (2) GOB1 GOB1a GOB1a
Sequences & chimeras


Rarefaction


Rare biosphere



Shearing
Hot spots chimerism

How many to plateau?
Differences between f & r

AVS - 79% singletons
Podo - 88 %
g23 - 12%
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