Who are the microbes on your fruits and veggies?

Nice paper from Jonathan Leff and Noah Fierer in PLOS One: Bacterial Communities Associated with the Surfaces of Fresh Fruits and Vegetables

Abstract: Fresh fruits and vegetables can harbor large and diverse populations of bacteria. However, most of the work on produce-associated bacteria has focused on a relatively small number of pathogenic bacteria and, as a result, we know far less about the overall diversity and composition of those bacterial communities found on produce and how the structure of these communities varies across produce types. Moreover, we lack a comprehensive view of the potential effects of differing farming practices on the bacterial communities to which consumers are exposed. We addressed these knowledge gaps by assessing bacterial community structure on conventional and organic analogs of eleven store-bought produce types using a culture-independent approach, 16 S rRNA gene pyrosequencing. Our results demonstrated that the fruits and vegetables harbored diverse bacterial communities, and the communities on each produce type were significantly distinct from one another. However, certain produce types (i.e., sprouts, spinach, lettuce, tomatoes, peppers, and strawberries) tended to share more similar communities as they all had high relative abundances of taxa belonging to the family Enterobacteriaceae when compared to the other produce types (i.e., apples, peaches, grapes, and mushrooms) which were dominated by taxa belonging to the Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria phyla. Although potentially driven by factors other than farming practice, we also observed significant differences in community composition between conventional and organic analogs within produce types. These differences were often attributable to distinctions in the relative abundances of Enterobacteriaceae taxa, which were generally less abundant in organically-grown produce. Taken together, our results suggest that humans are exposed to substantially different bacteria depending on the types of fresh produce they consume with differences between conventionally and organically farmed varieties contributing to this variation.

Getting press attention.  Examples include:

Definitely worth a look.

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

//storify.com/phylogenomics/noah-fierer-talk-at-ucdavis-on-biogeography-of-soi.js?template=slideshow[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

Just say no (to prokaryotes) – a lesson in Google Drive autocorrect

So – I saw this tweet yesterday

//platform.twitter.com/widgets.js And since the author of the tweet is giving a talk at UC Davis tomorrow I decided to help him out.

From Norm Pace talk at UC Davis 2/24/2011