The Tree of Life

Blog of Jonathan A. Eisen ( @phylogenomics ), Professor at U.C. Davis.

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

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Labels: Noah Fierer, seminars, UC Davis

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