The Tree of Life

Blog of Jonathan A. Eisen, Professor at U.C. Davis.

Pages

Home
STEM Diversity
Microbiomania and "Overselling the Microbiome"
Story Behind the Paper
Freeing My Father's Publications
Lab Page
microBEnet
Twitter

Thursday, January 10, 2013

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

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

at January 10, 2013

Email This BlogThis!Share to Twitter Share to Facebook Share to Pinterest

Labels: Noah Fierer, seminars, UC Davis

No comments:

About Me

Jonathan Eisen

View my complete profile

Some T-shirts

Microbe quotes
by Jonathan Eisen

Subscribe To

Posts

Atom

Posts

Comments

Atom

Comments

More About Me

My lab page
Talks and Presentations
Publications
Press Coverage
LinkedIn
microBEnet
My Ted Talk
Me on Twitter

microBEnet

Loading...

Eisen Lab Blog

Loading...

Most recent post

Pumpkin Carving as a model for Genome Assembly

So - we have this pumpkin carving contest every year in the UC Davis Genome Center. And people from my lab have done some excellent pumpkin...

Search This Blog

Google+ Badge

Subscribe To

Posts

Atom

Posts

Comments

Atom

Comments

Blog Archive

► 2018 (17)
- ► November (1)
- ► October (3)
- ► September (1)
- ► May (1)
- ► April (2)
- ► March (6)
- ► February (2)
- ► January (1)

► 2017 (54)
- ► December (11)
- ► November (6)
- ► October (7)
- ► September (2)
- ► August (5)
- ► July (5)
- ► June (5)
- ► May (3)
- ► April (1)
- ► March (4)
- ► February (3)
- ► January (2)

► 2016 (52)
- ► October (6)
- ► September (6)
- ► August (1)
- ► July (7)
- ► May (3)
- ► April (8)
- ► March (9)
- ► February (4)
- ► January (8)

► 2015 (108)
- ► December (14)
- ► November (12)
- ► October (9)
- ► September (4)
- ► August (3)
- ► July (9)
- ► June (8)
- ► May (10)
- ► April (4)
- ► March (14)
- ► February (8)
- ► January (13)

► 2014 (180)
- ► December (9)
- ► November (9)
- ► October (15)
- ► September (17)
- ► August (17)
- ► July (5)
- ► June (6)
- ► May (20)
- ► April (13)
- ► March (17)
- ► February (24)
- ► January (28)

▼ 2013 (201)
- ► December (8)
- ► November (9)
- ► October (16)
- ► September (14)
- ► August (17)
- ► July (16)
- ► June (14)
- ► May (22)
- ► April (14)
- ► March (20)
- ► February (26)
- ▼ January (25)

► 2012 (408)
- ► December (22)
- ► November (23)
- ► October (11)
- ► September (26)
- ► August (41)
- ► July (33)
- ► June (26)
- ► May (28)
- ► April (34)
- ► March (43)
- ► February (46)
- ► January (75)

► 2011 (389)
- ► December (62)
- ► November (119)
- ► October (38)
- ► September (39)
- ► August (20)
- ► July (8)
- ► June (32)
- ► May (14)
- ► April (17)
- ► March (11)
- ► February (19)
- ► January (10)

► 2010 (151)
- ► December (2)
- ► November (8)
- ► October (8)
- ► September (13)
- ► August (21)
- ► July (16)
- ► June (10)
- ► May (5)
- ► April (13)
- ► March (18)
- ► February (16)
- ► January (21)

► 2009 (228)
- ► December (17)
- ► November (21)
- ► October (21)
- ► September (21)
- ► August (20)
- ► July (11)
- ► June (14)
- ► May (29)
- ► April (23)
- ► March (18)
- ► February (19)
- ► January (14)

► 2008 (280)
- ► December (11)
- ► November (23)
- ► October (32)
- ► September (36)
- ► August (19)
- ► July (22)
- ► June (40)
- ► May (25)
- ► April (27)
- ► March (11)
- ► February (21)
- ► January (13)

► 2007 (178)
- ► December (11)
- ► November (16)
- ► October (22)
- ► September (15)
- ► August (17)
- ► July (14)
- ► June (15)
- ► May (15)
- ► April (14)
- ► March (17)
- ► February (12)
- ► January (10)

► 2006 (76)
- ► December (16)
- ► November (12)
- ► October (11)
- ► September (11)
- ► August (12)
- ► July (5)
- ► June (9)

► 2005 (1)
- ► February (1)

Social Icons

Pages

Home
STEM Diversity
Microbiomania and "Overselling the Microbiome"
Story Behind the Paper
Press
Humor
My Bio
#badomics words
Publications
Presentations
Disclosures

Pages

Thursday, January 10, 2013

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

No comments:

Post a Comment