The Tree of Life

Blog by Jonathan Eisen, Prof. at UC Davis. More info at: Lab Page , Profile , or Twitter. Go to fancy "dynamic" views here .

Storify/Tweet Notes from Noah Fierer's talk at UC Davis

By Jonathan Eisen .. 1/10/2013 10:48:00 PM

Email This BlogThis!Share to Twitter Share to Facebook

View the story "Noah Fierer talk at #UCDavis on biogeography of soil microbes" on Storify Noah Fierer talk at #UCDavis on biogeography of soil microbes Storified by Jonathan Eisen· Thu, Jan 10 2013 22:44:52 At #UCDavis tomorrow: Noah Fierer @NoahFierer on "Exploring Terra Incognita: the biogeography of soil microorganisms" http://shar.es/44O44Jonathan Eisen Reminder - today 4 PM #UCDavis Seminar by Noah Fierer #microbes #microbiomes #biogeography #evolution #soil http://wp.me/ph9ob-RvJonathan Eisen Awaiting talk at #UCDavis by @NoahFierer- starting in a few minutes "Exploring terra incognita - the biogeography of soil microorganisms"Jonathan Eisen Introduction for @NoahFierer talk at #ucdavis refers to him as a self described expert on cooties .. this has to be goodJonathan Eisen @phylogenomics @noahfierer Did you ever play the Cooties game? I did, now I'm an entomologist. Trapped.Jack C. Schultz For more on work of @noahfierer (whose talk at #UCDavis I am live tweeting) see http://www.colorado.edu/eeb/EEBprojects/FiererLab/Jonathan Eisen Now tweeting from @NoahFierer 's #UCDavis seminar "Exploring terra incognita: the biogeography of soil microorganisms" No eukaryotes tho :(Holly Bik Fierer at #UCDavis defends referring to plants and animals as "macrobes" as better than calling small things microbesJonathan Eisen Fierer at #UCDavis: 4000-2000 kg microbial biomass per hectare (from Fierer et al. 2009 Ecology letters)Jonathan Eisen Fierer at #UCDavis: vast majority of soil microbial diversity undescribed, quotes Donald Rumsfeld as "patron saint of microbial ecology"Jonathan Eisen Fierer at #UCDavis: example of Acidobacteria - up to 30% of bacteria in soil from this phylum yet only 5 described generalJonathan Eisen Fierer at #UCDavis: using microbes to test principles of biogeography/ecology; using biogeography to learn about poorly understood microbesJonathan Eisen Fierer at #UCDavis: in 2006 $10K = 400 bacteria IDd in each of 5 samples; 2012 $10K = > 10K bacteria IDd in each of 500 samplesJonathan Eisen Fierer at #UCDavis: reduction in sequencing cost / increase in capacity allows 1st time biogeography studies of microbes on large scaleJonathan Eisen Fierer: You can't do ecology with 5 samples (old methods) - now costs have dropped, we can sequence 100s of samples to look at ecologyHolly Bik Fierer at #UCDavis: dealing with this: "There is no biogeography of anything smaller than 1 millimeter" Bland Finlay Science 2005 vol 310Jonathan Eisen Fierer at #UCDavis: collected soil samples from diverse biomes (tundra, desert, prairie, forest) & asked what calls "19th century" eco ??sJonathan Eisen If the bacterial/archaeal people are doing 19th century ecology (as says @NoahFierer), then us eukaryote people are stuck in the dark ages..Holly Bik Fierer at #UCDavis discussing Lauber et al. 2009 http://www.ncbi.nlm.nih.gov/pubmed/19502440 - ~1000 sequences per sample x 80 + samplesJonathan Eisen Fierer at #UCDavis discussing this figure http://aem.asm.org/content/75/15/5111/F4.large.jpg from 2009 paper - where simple ordination did not distinguish samples wellJonathan Eisen Fierer at #UCDavis now discussing Figure B from http://aem.asm.org/content/75/15/5111/F4.large.jpg saying that soil pH shows strong association w/ microbe Beta diversityJonathan Eisen “@Dr_Bik: Fierer: You can't do ecology with 5 samples costs have dropped, we can sequence 100s of samples 4 ecology” SORT OF. Whoo R U? $$$Jack C. Schultz Fierer et al. refs http://aem.asm.org/content/75/15/5111/F3.large.jpg from 2009 paper that shows good relationship between soil pH and alpha diversityJonathan Eisen Fierer at #UCDavis: their soil data did not show any obvious relationship to latitude, mean annual temp, or other variables looked atJonathan Eisen Fierer at #UCDavis: their data showing relationship between pH and microbial diversity could have been due to some feature related to pHJonathan Eisen Fierer at #UCDavis: looked at soil microbes in one biome in arctic and still had correlation with pH and diversityJonathan Eisen Fiere at #UCDavis: refs. http://www.nature.com/ismej/journal/v4/n10/full/ismej201058a.html where even in controlled system (Rothamsted Research) pH & microbial diversity correlatedJonathan Eisen Does pH itself drive soil microbial assemblages, or aluminum toxicity (Al and pH closely linked)? We don't know yet says @NoahFiererHolly Bik At #UCDavis @NoahFierer: discussing PNAS 2012 Soil paper http://www.pnas.org/content/early/2012/12/05/1215210110.full.pdf - metagenomics of VERY different soil samplesJonathan Eisen At #UCDavis @NoahFierer: in soil metagenomic data only ~ 20% of reads could be annotated (i.e., function predicted)Jonathan Eisen At #UCDavis @NoahFierer: in soil metagenomic data there is a weak ++ correlation between 16S PD and functional diversityJonathan Eisen At #UCDavis @NoahFierer: desert soils VERY different from other soils in beta diversity of taxa & functionsJonathan Eisen At #UCDavis @NoahFierer: looked are which genes were driving the major differences beta. soils in deserts & other locationsJonathan Eisen At #UCDavis @NoahFierer quotes Willa Cather "elsewhere the sky is the roof of the world but here the earth was the floor of the sky"Jonathan Eisen . @NoahFierer heads to 19th century graveyards to sample native prairie grass habitats for soil microbes. One of least disturbed sites..Holly Bik At #UCDavis @NoahFierer refs paper that modelled distributions of Sasquatch http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2699.2009.02152.x/abstractJonathan Eisen At #UCDavis @NoahFierer discussing collaborative work w/ Josh Ladau from UCSF http://docpollard.com/jladau/index.html (who I collaborate w/ too)Jonathan Eisen At #UCDavis @NoahFierer says "Microbial ecology needs more Ecologists" (emphasizes the capital EJonathan Eisen At #UCDavis @NoahFierer: Ecology needs more microbial ecologyJonathan Eisen Pleas frm @NoahFierer: Microbial ecology needs more Ecologists--lots of data out there, not being fully used, & lots of reinvention of wheelHolly Bik At #UCDavis @NoahFierer: ecological restoration projects need to consider microbes as part of the storyJonathan Eisen “@phylogenomics: @NoahFierer: ecological restoration projects need to consider microbes as part of the story” or quit stupid reconstructionJack C. Schultz “@phylogenomics: At #UCDavis @NoahFierer says "Microbial ecology needs more Ecologists" (emphasizes the capital E” ) Brilliant!Jack C. Schultz @phylogenomics Lots of reasons reconstruction is purely subjective, starting with "which era do we reconstruct?". Not "science"Jack C. Schultz @phylogenomics For a different take (e.g., why is YOUR reconstruction THE reconstruction?) see http://www.amazon.com/Invasion-Biology-Oxford-Mark-Davis/dp/0199218765Jack C. Schultz Both true! - MTs: “@phylogenomics: At #UCDavis @NoahFierer: Ecology needs more MICROBIAL ecology” &"Microbial ecology needs more Ecologists"Gavin Collins @jackcschultz sure some restoration projects have issues but the "not science" accusation makes you sound sillyJonathan Eisen

Labels: Noah Fierer, seminars, UC Davis

0 comments:

About Me

View my complete profile

Subscribe To

Posts

Atom

Posts

Comments

Atom

Comments

Follow by Email

Google+ Followers

Twitter Updates

My Affiliations

Professor at UC Davis
UC Davis Dept. of Evolution and Ecology
UC Davis Genome Center
UC Davis Dept. of Medical Microbiology and Immunology
Adjunct Scientist DOE Joint Genome Institute
Chair of PLoS Biology Advisory Board
Fellow, American Academy of Microbiology
Member IOM Forum on Microbial Threats

More about me

About.me
CV

Google+ Badge

PLOS Biologue

Loading...

microBEnet blog

Loading...

Eisen Lab Blog

Loading...

Blog Archive

▼ 2013 (95)
- ► May 2013 (15)
- ► April 2013 (14)
- ► March 2013 (20)
- ► February 2013 (21)
- ▼ January 2013 (25)

► 2012 (388)
- ► December 2012 (22)
- ► November 2012 (23)
- ► October 2012 (11)
- ► September 2012 (26)
- ► August 2012 (39)
- ► July 2012 (32)
- ► June 2012 (25)
- ► May 2012 (27)
- ► April 2012 (28)
- ► March 2012 (39)
- ► February 2012 (46)
- ► January 2012 (70)

► 2011 (329)
- ► December 2011 (54)
- ► November 2011 (88)
- ► October 2011 (23)
- ► September 2011 (38)
- ► August 2011 (20)
- ► July 2011 (8)
- ► June 2011 (30)
- ► May 2011 (13)
- ► April 2011 (16)
- ► March 2011 (11)
- ► February 2011 (18)
- ► January 2011 (10)

► 2010 (139)
- ► December 2010 (2)
- ► November 2010 (8)
- ► October 2010 (8)
- ► September 2010 (13)
- ► August 2010 (20)
- ► July 2010 (11)
- ► June 2010 (9)
- ► May 2010 (4)
- ► April 2010 (12)
- ► March 2010 (17)
- ► February 2010 (16)
- ► January 2010 (19)

► 2009 (199)
- ► December 2009 (16)
- ► November 2009 (18)
- ► October 2009 (18)
- ► September 2009 (17)
- ► August 2009 (18)
- ► July 2009 (11)
- ► June 2009 (13)
- ► May 2009 (22)
- ► April 2009 (20)
- ► March 2009 (18)
- ► February 2009 (14)
- ► January 2009 (14)

► 2008 (247)
- ► December 2008 (10)
- ► November 2008 (20)
- ► October 2008 (29)
- ► September 2008 (31)
- ► August 2008 (19)
- ► July 2008 (17)
- ► June 2008 (36)
- ► May 2008 (20)
- ► April 2008 (23)
- ► March 2008 (10)
- ► February 2008 (20)
- ► January 2008 (12)

► 2007 (171)
- ► December 2007 (11)
- ► November 2007 (15)
- ► October 2007 (22)
- ► September 2007 (15)
- ► August 2007 (17)
- ► July 2007 (14)
- ► June 2007 (13)
- ► May 2007 (14)
- ► April 2007 (14)
- ► March 2007 (17)
- ► February 2007 (9)
- ► January 2007 (10)

► 2006 (67)
- ► December 2006 (13)
- ► November 2006 (9)
- ► October 2006 (11)
- ► September 2006 (10)
- ► August 2006 (10)
- ► July 2006 (5)
- ► June 2006 (9)

► 2005 (1)
- ► February 2005 (1)

Book Collections at Amazon

Microbiology for Kids
Evolution Textbooks
Field Guides to Microbes
Genome Evolution

Search This Blog

Loading...

Serial post themes

fake science news (10)
freeing my father's publications (9)
open parkinsons (2)
story behind the paper (22)

Awards I Give Out

adaptationomics award (3)
bad omics word of the day (27)
Closed Access Award (2)
Genomics By Press Release Award (3)
open access pioneer award (7)
open science pioneer award (1)
Overselling genomics award (8)
overselling the microbiome award (12)
Quality Genomic Reporting Award (1)
Twisted tree of life award (16)
underselling genomics award (2)
Worst New Omics Word Award (18)

Pages

Home
My bio
My CV
Humor
Freeing My Father's Publications
Press and blog coverage
Story behind the paper series
Presentations
Publications
My doodles
My history in science
Posts on diversity (gender, etc) in science
Pubs as Table
My writings on #badomics words

Followers

Sciency Blogs I Like with Latest Items

A Man With A Ph.D.

Cutting edge capitalism that can change the world
Immortality Medicine

Stuart Schlossman interviews Brian Steingo, MD of Neurology on StuMSRadio — Blog Talk Radio – Video
LIVESTRONG Blog

Think thinksport on Don’t Fry Day
The Molecular Ecologist

What we’re reading: The trouble with novelty and the Norway spruce genome
Deep Sea News

Building Spanish Galleons 101
Egghead

Act now to avoid irreversible climate tipping point, scientists urge
Small Things Considered

A Whiff of Taxonomy – The Phylum Elusimicrobia
Rod Page's iPhylo

DOIs for specimens are here, but we're not quite there yet
Larry Moran's Sandwalk

How Do IDiots Define Evolution?
Byte Size Biology

Bats use blood to reshape tongue for feeding
it is NOT junk (Michael Eisen)

Apotheosis of cynicism and deceit from scholarly publishers
The Imaginary Journal of Poetic Economics

Two tough questions for Access Copyright
Antimicrobial Resistance

Intel ISEF Science Fair
Steven Salzberg' s Genomics, Evolution, and Pseudoscience

Poison for pain, the homeopathic way
Pedro Baltrao's Public Rambling

EBI-Sanger postdoctoral fellowship on Plasmodium kinase regulatory networks
Jenna Morgan's Jennomics

Busuknya Kebencian
Eukaryotic Ebullience

Wrap up of the #SMBEeuks meeting and QIIME workshop at UC Davis
Bethbeck's Blog

LAUNCH 2020 Summit: Genius
electric boogaloo

Seven things before the first sleep
RRResearch

Formatting figures for PLOS journals
Hyphal Tip

Basidiobolus! – genus of the month at ATCC
Blue Lab Coats

#Reviewdouchery
Neil Saunders' What You're Doing Is Rather Desperate

How to: remember that you once knew how to parse KEGG
Oliver Morton's Heliophage

Climate geoengineering for natural disasters
The Life of Science

The Life of Ernest Everett Jus
Adaptive Drift (Brian O'Meara)

Adaptive Information Filtering: Learning Drifting Concepts
Jonathan Eisen's Davis, CA Blog

#DavisCA lockdown update
T Ryan Gregory's Genomicron

Send This To Anyone Who Writes Or Reports On A Badaptationist Story
Cotch.Net

Lesser of The Lakes
Jonathan Badger's T. taxus

Carl Woese 1928-2012
The Loom (Carl Zimmer)

Moving Just A Click Away
Cryptogenomicon

Join Rob’s HMMER team
Jean-Claude Bradley's Useful Chemistry

Matthew McBride wins Nov 2012 ONS Challenge Award
McBlawg

The Making of PeerJ
The Rough Guide to Evolution

Visit of Randal Keynes part two
Mario's Entangled Bank

The mountains are calling and I must go now
John Logsdon's Sex, genes and evolution

The Lure of the Obscure? Guest Post by Frank Stahl
PZ Myers' Pharyngula

The great renovation
Jason Rosenhouse's EvolutionBlog

ScienceBlogs Migration
Tara Smith's Aetiology

Tenured and promoted!
Microbial Population Biology

Final proposal details
Attila Csordas' Pimm - Partial immortalization

Test
Skeptic Wonder

Free ImageJ Macro -- for citing images
TreeTapper-Dev

TreeTapper down Dec. 26-28
Aaron Darling's The Secret Microbe

Google knol to die? PLoS currents?
Superbug

If you came here from Bittman's Opinionator at the New York Times...
Anna's Bones

Be Right Back.
Chris Patil's Ouroboros

Pathobiology of Aging & Age-related Diseases: a new open-access journal
Artful Amoeba

Video of New Hydrothermal Rift Discovered in Galapagos
Context and variation

Hey! I miss you!
Bora Zivkovic's A Blog Around The Clock

New URL for this blog
Dechronization (by the TreeThinkers)
Not Exactly Rocket Science

Greetings WIRED UK readers
Karl Mogel's The Inoculated Mind

Whither now, my blog?
Unicorns of the Hydrocalypse

That's What She Said, Episode 1
Bill Hooker's Open Reading Frame

give your brain a workout
John Dennehy's The Evilutionary Biologist

RIP George Williams (May 12, 1926 - September 8, 2010)
Fresno, Evolving

What would YOU tell the wealthy nations to do to halt biodiversity loss?
The SciFri Blog

Double the solar power efficiency, double the fun
Olivia Judson's Wild Side

So Long, and Thanks
Evolutionary Novelties (Todd Oakley)

Mnemonic 2010
semaphoront

Texas school board approval
Henry Gee's The End Of The Pier Show

Cromer Is So Bracing 2010 – First Circular
Pam Ronald's Tomorrow's Table

Tomorrow's Table moves to Science Blogs
Deepak Singh's business|bytes|genes|molecules

Open Science meet Open Source
Nodalpoint

no idea
Kay's Suicyte Notes

The perils of having foreign co-authors… (just kidding)
RPM's Evolgen

This is a Good-bye Post
Microbeworld: Discover Unseen Life on Earth

Show 25 Show All

My blog about Davis, CA

Loading...

Labels

evolution microbiology Open Access genomics UCDavis metagenomics meetings #OccupyUCDavis humor human microbiome UC Davis science SPAM open science plos bacteria bad omics word of the day phylogeny education story behind the paper draft blog post cleanup plos one microbes microbial diversity phylogenomics Davis occupyucdavis politics symbioses Worst New Omics Word Award Nature microbenet phylogenetics rRNA Twisted tree of life award scifoo microbiome bioinformatics science and art archaea tree of life women in science funding overselling the microbiome award Scientific Publishing plos biology conference spam fake science news jobs research blogging science humor twitter JGI meeting TedMed ecology freeing my father's publications nobel prize science blogging Overselling genomics award evolution education Darwin Field Guide to the Microbes GEBA Marco Island AGBT Meeting 2008 Mars New York Times University of California arsenic open access pioneer award synthetic biology Lake Arrowhead germophobia google scholar guardians of microbial diversity marketing peer review probiotics #opengate Sarah Palin antibiotics systematics #PLOS One Adaptationism academic freedom asm2012 brain doping historical open access open evolution open metagenomics Genomics By Press Release Award adaptationomics award Tetrahymena open microbial diversity Vaccines

Translate

Copyright

This work is licensed under a Creative Commons Attribution 3.0 United States License.

Disclosures

Some disclosures that might be relevant to what I write about:
1. I am involved with the Public Library of Science in multiple ways, and my brother was a co-founder. I receive no money from them (although in theory I can get compensated for expenses).
2. My wife worked for Mendel Biotechnology many years ago and we still own a small amount of their stock.
3. I make some money from sales of my Evolution textbook.

Powered by Blogger.

Storify/Tweet Notes from Noah Fierer's talk at UC Davis

0 comments:

Post a Comment