International Census of Marine MicrobesInternational Census of Marine Microbes

Explore the Explore the diversitydiversity, relative , relative abundanceabundance, , and environmental and environmental contextcontext of all of all

microbial life forms in the oceans microbial life forms in the oceans

Archaea Eukarya VirusesBacteria

International - Global Coverage

Competitive Tag Sequencing - 869 samples 660 completed~13.5 million tag sequences

Final Data set will exceed 18 million tag sequences

Microbial Population Structure of the World’s OceanMicrobial Population Structure of the World’s Ocean

Frisian Island SyltGuaymas Methane SeepsGulf of AqabaGlobal Protist SurveyHood Canal WashingtonHawaii Ocean Time-SeriesIOMM Cooperative RunGulf of MaineLaCAR Cooperative RunLost CityMount Hope BayHelgolandNew Zealand SedimentOcean Drilling ProjectEnglish ChannelSurreptitious Algal BacteriaStation M SedimentsSpongesSpatial Scaling DiversityHumboldt Marine EcosystemBlack Sea

Arctic Chukchi BeaufortAmazon-Guianas WaterLau Hydrothermal VentAnaerobic Protist ProjectAmundsen Sea AntarcticaAzorean Shallow VentsAzores Waters ProjectBlanes Microbial ObservatoryBaltic Sea ProperBlack Sea RedoxCensus Antarctic MarineCariaco BasinCaribbean Coral BacteriaDeep Subseafloor SedimentCoastal Microbial MatsCoastal New EnglandCoral Reef SedimentDeep Arctic OceanDeep Ocean FluxDeep Sea Eukarya

Phenotypic DiversityPhenotypic Diversity

Named species:

Bacteria and Archaea: 9,000

Protists: 200,000

Microbial creatures of untold diversity dominate every corner of our biosphere. Estimates of 10 - 100 X diversity of animals.

The number of different kinds of bacteria in the oceans could eclipse 5 to 10 million

Deep SequencingDeep Sequencing

BacteriaBacteria ArchaeaArchaeaTotal Unique V6 Tag SequencesTotal Unique V6 Tag Sequences 30,10830,108 5,9795,979Total OTUs at 3% DifferenceTotal OTUs at 3% Difference 18,53718,537 1,9311,931Chao1 Estimator of Richness at 3% DifferenceChao1 Estimator of Richness at 3% Difference 36,86936,869 2,7542,754ACE Estimator of Richness at 3% DifferenceACE Estimator of Richness at 3% Difference 37,03837,038 2,6782,678

Huber et al. 2007 Science

EvennessEvenness

ActinobacteriaAcidobacteria BacteroidetesChloroflexi

CyanobacteriaDeferrebacteres

Firmicutes

Gemmatimonadetes

NitrospiraLentisphaerae

Planctomycetes

Proteobacteria Verrucomicrobiae

112R 550 M -25.000°E, 50.400°N

115R 4,121 M -25.000°E, 50.400°N

FS312 Axial Sea Mount - Bag City Difuse Flow

FS312 Axial Sea Mount - Mkr 52 Difuse Flow

Soil-Kellogg-5 species

Soil-Kellogg-no plants

Marine vs. SoilEvenness

How many microbes can you find in a few How many microbes can you find in a few drops of seawater?drops of seawater?

~ 1,000,000 Bacteria~ 1,000,000 Bacteria

~ 1,000,000 Archaea~ 1,000,000 Archaea

~10-10,000 Protists~10-10,000 Protists

~10,000,000 Viruses~10,000,000 Viruses

AbundanceAbundance

10,000,000,000,000,000,000,000,000,00010,000,000,000,000,000,000,000,000,000 Microbial Cells in the OceanMicrobial Cells in the Ocean

Visualization Visualization http://vamps.mbl.edu

Human fecal

profile

Lake Water Combined Sewage overflow

Bacteroidetes Firmicutes

Detection of Anthropogenic Impacts

1001 1101 1201 1301 1401 1501 1601 1701 1801 1901 2001 2101

Human fecal

profile

Lake WaterCombined Sewage overflow

Firmicutes

Detection of Anthropogenic Impacts

• Low abundance taxa in rank-ordered, taxon abundance curves• Microbial abundance curves are “long-tail distributions”

Concept of the Rare BiosphereConcept of the Rare Biosphere

• The tail is much greater than previously known• Diversity eclipses all prior estimates of

•Bacterial, Archaeal and Eukaryl diversity• Never-before-seen populations

High Abundance Populations

Taxon-rank distribution curve for microbial communities

Low Abundance Populations

The Rare Biosphere

Explaining the Rare BiosphereExplaining the Rare Biosphere

• Biogeography• Dispersal from yet to be discovered endemic

sites

Human

Sponge

Mouse

Rio TintoDeep subsurface

Sulfides/Basalts

Cariaco

Salt Marsh

Lau Seamount

Salt Pond

English Channel

Amunsen

Palmer LTER

Global Distribution of Abundant Tags

Explaining the Rare BiosphereExplaining the Rare Biosphere

• Biogeography• Dispersal from yet to be discovered endemic sites• Keystone species• Always rare - possibly slow growing or dormant• Persistently rare but capable of becoming

abundant

“Seed” organisms

Genomic novelty• Analogous to heterozygosity in animals or plants• Products of historical ecological change?• Responders to environmental shifts

May serve as sentinel for global change

Limits to KnowledgeLimits to KnowledgeOperational issues for the Rare Biosphere:

•Definition of microbial diversity - key data - •Start and length of the long tail •Existence of viral, archaeal and eukaryl Rare Biosphere •Tools necessary to define limits of the rare biosphere•Criteria for targeting studies of rare biosphere members

Questions about the Rare Biosphere and how can we seek answers?

•Is the Rare Biosphere globally distributed? or does the Rare biosphere reflect dispersal from endemic sites?

•Does membership in the Rare Biosphere shift across different spatial/temporal scales? •What mechanisms determine membership in the Rare Biosphere? •Why is there a rare biosphere? •Do microbes in the rare biosphere compete for niche space? •Is the rare biosphere a nearly unlimited source of genetic information that can

transfer between microbial populations?•How important are reservoirs in protecting microbial diversity?•Do rare organisms have a selective advantage? •Are there specific mechanisms that allow low-abundance populations

to become dominant in response to environmental shifts?•How does the rare biosphere shape the environment past, present and future?•How might rare organisms impact human health and well being?•Can the rare biosphere serve as a sentinel for global change?•Do rare microbes play a key role in preserving biodiversity?

AcknowledgementsAcknowledgementsICoMM 454 participants:Paula AguiarRobert AndersenFelipe ArtigasStefan BertilssonChristina BienholdHenk BolhuisWilliam BrazeltonDavid CaronD. ChandramohanAndrei ChistoserdovMarco CoolenMark DennettSteve D’HondtSlava EpsteinKatrina EdwardsRima FranklinEric GaidosVictor Ariel GallardoGunnar GerdtsJack GilbertKoji HamasakiJulie HuberDavid Karl

David KirchmanConnie LovejoyEls MaasAna MartinsAlison MurrayJan PawlowskiMartin PolzThomas PommierAnton PostJames ProsserAlban RametteMichael RappeAnna-Louise ReysenbachGabrielle RocapJuliette Rooney-VargaJames StaleyThorsten StoeckShinichi SunagawaAndreas TeskeMichael WagnerGordon WebsterPatricia Yager

ICoMM Scientific Organizing Committee:Mitchell SoginJan de LeeuwDavid PattersonLucas StalGerhard HerndlStefan Schouten

ICoMM Secretariat:Linda Amaral-Zettler

ICoMM IT Specialist:Phillip NealAnne ThessenICoMM Scientific Advisory Council:John Baross (Chair)Robert AndersenFelipe ArtigasAntje BoetiusD. ChandramohanKazuhiro KogureCarlos Pedros-AlioFrancisco Rodriguez-Valera