Marine biodiversity and microbial diversity :

Marine biodiversity and microbial diversity :

a key for the functioning of marine ecosystems

Dr. Luis Felipe ArtigasCNRS UMR 8187 LOG - MREN ULCO

Wimereux, FRANCECoML South America and Caribbean

ICoMM - S.A.C.

What is biodiversity?What is biodiversity?

• CBD: The variability among living organisms from all sources, including inter alia, terrestrial, marine and other aquatic ecosystems and the ecological complexes of which they are part; this includes diversity within species, between species and of ecosystems

• “Normal language”: Biodiversity is essentially the richness of life on earth: the species that inhabit the earth, the genetic material they contain and the habitats in which they live. It takes thousands to millions of years of evolution to generate this richness.

Biodiversity and funtioning of marine ecosystems

Biodiversity and funtioning of marine ecosystems

One cannot pretend to understand the role of life in the functioning, stability and resilience of marine ecosystems without answering these three fundamental questions :

- what organisms are present and what is their respective abundance?- what are their roles in the functioning of marine ecosystems?- what are their metabolic and reproductive rates?

• Of the 30 multi-cellular Phyla, 13 are endemic of marine systems.

• The paradox is that only 15% of species described to date are marine species.

(Fred Grassle 2001)

55

J. Stachowicz, 2009

What do we mean by biodiversity?What do we mean by biodiversity?

Measurement of biodiversity must occur at several levels:

- The upper level represents the diversity within each species, here

cartooned by different DNA types within intertidal mussels.

- The middle level focuses on species diversity,

here illustrated as the set of macroinvertebrates of the rocky intertidal

zone.

- The lower level includes different habitat types within a region – in this

case, the rocky intertidal zone, seagrass beds, and kelp forests along

the California coast.

Measurement of biodiversityMeasurement of biodiversity

Palumbi et al., 2009

What are the goods provided by marine biodiversity?

• Food: fisheries (100 million tonnes per year), aquaculture (half the protein of the Philippines and Japan)

• Other products: enzymes, pharmaceuticals, anti-fouling, ornamental objects,…, genes

• Recreation, (eco)tourism (multi-billion € industries depend on ‘healthy’ marine systems)

• Physical protection: reefs, mangroves (vast areas in the tropics), salt marshes, dune- beach systems

• Land: carbonate platformsPr. Carlo Heip, 2006

Pr. Carlo Heip, 2006

Food chains vs. food websFood chains vs. food webs

J. Stachowicz, 2009

Biodiversity and food websBiodiversity and food webs

What are the services provided by marine biodiversity?

What are the services provided by marine biodiversity?

• System productivity• Remineralisation and nutrient recycling• Calcification, carbonate deposition• Waste management: oil degradation,

detoxification, • Stability and resilience of marine systems• Climate regulation

Pr. Carlo Heip, 2006

Biodiversity and funtioning of marine ecosystems

Biodiversity and funtioning of marine ecosystems

Links between pelagic biodiversity and marine ecosystem processes : 3 compartments, trophic flows (black arrows), list of traits likely to affect trophic flows, influences of those compartments on ecosystem services (grey arrows). DOM = Dissolved Organic Matter

Pelagic biodiversity and ecosystem processesPelagic biodiversity and ecosystem processes

Duffy & Stachowicz, MEPS, 2006

The « Biological pump »The « Biological pump »

Biological Pump Working Group Summary – Karl et al.http://www.msrc.sunysb.edu/octet/biological_pump.html

Services = Bacteria, Archaea, Viruses

Pr. Carlo Heip, 2006

Photo: N. Nichols

Services = phytoplankton

Pr. Carlo Heip, 2006

Emiliania

Services = phytoplankton

Pr. Carlo Heip, 2006

Number of microbial cells in the oceans is astronomical !!!100,000,000,000,000,000,000,000,000,000Microbial Cells in the Oceans

Archaea

animals & plants

Eukarya

Bacteria

~106 species. Who are they? What are they doing? Must we incorporate them in ecosystem models?

Most marine biodiversity is microbialMost marine biodiversity is microbial

Size Biomass Primary SecondaryProduction Production

___________________________________________________

Prokaryotes <3µm 82% 91%Protists <0.3mm 18% 9%Zooplankton < 3 cm 0.3% 93%Swimmers <3m 0.07% 7%Megafauna > 3m 0.01% 0.5%____________________________________________________Millions Tons Carbon 145,000 50,000 7,400

Relative abundance and productivity of Marine Life

Diversity Seed bank

BIODIVERSITY

Determining Marine Microbial Diversity

Pedrós-Alió, 2006

Microbial Diversity

Heterotrophicbacteria

Dinoflagellate

Synechococcus

Prochlorococcus

Prokaryotic diversity : heterotrophic bacteria Prokaryotic diversity : heterotrophic bacteria

• One of the most successful organisms on earth, Pelagibacter ubique (SAR 11) , which may account for 20 % of the prokaryotic cells in the ocean, was only discovered in 2001.

Prochlorococcus

Synechococcus

Prochlorococcus and Synecho- coccus may be responsible for up to two thirds of the CO2 fixation in the oceans and thus for one third of the total primary biomass production on Earth. Prochlorococcus was discovered in 1988

Prokaryotic diversity : autotrophic cyanobacteria

Prokaryotic diversity : autotrophic cyanobacteria

Pr. Carlo Heip, 2006

Chemoautotrophic bacteria oxidize reduced substrates and are able to couple the energy produced to the synthesis of carbohydrate.

• Iron bacteria (oxidize Fe2+)

• Sulfur bacteria (oxidize H2 S)

• Nitrifying bacteria (oxidize NH4+)

• Purple sulfur bacteria use H2 S and produce elemental S.

• Cyanobacteria are an exception because they can perform oxygenic photosynthesis.

Photoautotrophic bacteria use sunlight as energy to synthesize carbohydrate

Prokaryotic Diversity

Heterotrophic bacteria mineralize (decompose, respire) organic matter into inorganic C and nutrients.

Use a variety of electron acceptors :Reduction of O2

Reduction of NO3-

Reduction of Mn4+ to Mn2+

Reduction of Fe3+ to Fe2+

Reduction of SO42- to H2 S

Reduction of CO2 to CH4

Redox potential

Heterotrophic bacterial productivity = rate of C assimilation from organic matter sources.

Prokaryotic Diversity

Pico-eukaryotic diversityPico-eukaryotic diversity

• Large diversity of new eukaryotes discovered by new techniques• Cells smaller than 3 μm • Primary producers• Grazers of picophytoplankton

Bolidomonas

Ostreococcus = the smallest autotrophic Eukarya

Picofagus

Pr. Carlo Heip, 2006

Protozoa and viruses major predators on bacteria

Image from Suzuki lab Image from Noble lab

Marine Microbial Diversity

Microbial networksunlight

Sinking

N, P, Fe

ZooplanktonPhytoplankton

Bact eria

Fish

DissolvedOrganic Mat t er

Virus

Prot ozoa

Pat hogensSewage

CO2

CO2

Photosynthet ic bact eria

Modified from: Azam, F. 1998. Science 280: 694-696

sunlightPollutants

Exotic microbes Pathogens Pollutants Sewage

Zooplankton Fish

aggregation

Photosynthetic bacteria

N, P, Si, Fe

Phytoplankton

Need to revise models to incorporate microbial diversity and ecosystem functions

Azam, F. 1998 Science 280:694-696

Microscale complexity

Corals are microbial landscapes

100s of species associated with healthy corals – ecosystem roles are unknown Rohwer, Azam & Knowlton. 2002.

Hydrothermal Vents: discovered 1979are based on microbial chemotrophy

Pr. Carlo Heip, 2006

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 EukaryaBacteria

http://icomm.mbl.edu

ICoMM’s Tag Sequencing StrategyICoMM’s Tag Sequencing Strategy

• Sequence many V6 regions• Each “tag”is a proxy for a

microbe • Query each tag against a

reference data base• Identify taxonomic source of

each V6-Tag to infer community composition.

Provides massively parallel ability to count different kinds of microbes in a community but it is NOT A PHYLOGENETIC TOOL!

International - Global Coverage

Keck Tag Sequencing Project: 52 projects, 852 datasets, ~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 WashingtonIOMM Cooperative RunGulf of MaineLaCAR Cooperative RunLost CityHelgolandNew Zealand SedimentEnglish ChannelSurreptitious Algal BacteriaStation M SedimentsSpongesSpatial Scaling DiversityHumboldt Marine EcosystemDeep Subseafloor SedimentActive But RareBlack 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 BacteriaCoastal Microbial MatsCoastal New EnglandCoral Reef SedimentDeep Arctic OceanDeep Ocean FluxDeep Sea EukaryaAtlantic Ocean Transect

VisualizationVisualization

https://vamps.mbl.edu

• 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 AbundancePopulations

Taxon-rank distribution curve for microbial communities

Low AbundancePopulations

The Rare Biosphere

Biodiversity changesBiodiversity changes

• Changes in biodiversity have been observed for macro-organisms = goods

• Changes in micro-organisms? = services

Pr. Carlo Heip, 2006

Changing services: surface pH will decrease with increased CO2

Changing services: surface pH will decrease with increased CO2

Wallace in SOLAS programme plan 2001Pr. Carlo Heip, 2006

Pr. Carlo Heip, 2006

A global network of researchersengaged in an international collaborative

initiative to assess and explain the diversity, distribution, and abundance

of marine life in the oceans – past, present, and future – and to identify the current

limits to knowledge (what isknown, unknown and unknowable)

The First Census: 2000-2010

The Census of Marine Life: Making ocean life count

Census of Marine LifeCensus of Marine Life

Exploration and DiscoveryExploration and Discovery

A comb jelly from the high Arctic waters of the Canada Basin. Photo: Kevin Raskoff, Monterey Peninsula College.

A deepwater shrimp species from French Frigate Shoals in the Northwestern Hawaiian Islands. Photo: Susan Middleton © 2006, courtesy U.S. NOAA, PIFSC, Northwestern Hawaiian Islands Marine National Monument.

Some new species discoveries…

This species is the first record of a hydrothermal vent zoanthid, an order of invertebrates related to corals. Photo: Charles Fisher, Penn State University.

Much more than ExplorationMuch more than Exploration

CoML has discovered more than 5,300 potential new, marine animals since 2003. Of these, 110 have gone through the rigorous scientific review process for formal description as a new species.

Collectively, CoML is discovering new species at a much faster rate than the capacity to describe them. To aid in the effort, Census researchers are developing & supporting efficient but still cautious authentication of species by DNA barcoding and cybertaxonomy.

While the discovery of new species is always exciting…

the greater contribution to our understanding of marine life is what CoML scientists are learning about the diversity and distribution of marine life in the global oceans.

Census findings support…Census findings support…

• Sustainable Fisheries

• Identification of Marine Protected Areas (e.g. biodiversity hotspots)

• Management of Habitat Loss and Pollution

• Environmental Assessments

• Identification & tracking of Invasive Species and Endangered Species

• Understanding of Global Climate Change Impacts, including Ocean Acidification

• Preservation of Biodiversity and Ecosystem Services

Photo: NASA

Grand Challenge Questions

CoML ComponentsCoML Components

Oceans PastWhat did live in the

oceans?

History of Marine Animal

Populations (HMAP)

Oceans PresentWhat does live in the

oceans?

Ocean Realm Field Projects

Oceans FutureWhat will live in the

oceans?

Future of Marine Animal

Populations (FMAP)

Ocean Biogeographic Information System (OBIS)Web-based provider of global geo-referenced information on marine species

Ocean Realms

Ocean Realm ProjectsOcean Realm Projects

Human Edges• NaGISA - Natural Geography In Shore Areas• CReefs - Coral Reef Ecosystems• GOMA - Gulf of Maine Area Census (Regional Ecosystem)• POST - Pacific Ocean Shelf Tracking

Central Waters• TOPP - Tagging of Pacific Pelagics (Top Predators)• CMarZ - Census of Marine Zooplankton• MAR-ECO - Mid-Atlantic Ridge Ecosystems

Hidden Boundaries• CoMargE - Continental Margins Ecosystems• CeDAMar - Census of Diversity of Abyssal Marine Life• CenSeam - Census of Seamounts• ChEss - Chemosynthetic Ecosystems (Vents)

Ice Oceans• ArcOD - Arctic Ocean Diversity• CAML - Census of Antarctic Marine Life

Microscopic Ocean• ICOMM - International Census of Marine Microbes

Global CollaborationGlobal Collaboration

Arabian Sea(Oman, 2007)

Stars indicate National or Regional Activity Headquarters

80 countries

Over 2000 scientists

Data Infrastructure & IntegrationData Infrastructure & IntegrationTo become a national, regional and international infrastructure for information and biogeographic data on marine species and

their distribution and abundance.

OBIS will…• Contribute data to WoRMS (World Register of Marine Species) which will be visible through the Encyclopedia of Life (EoL)• Build system to provide support synthesis activities of all other Census projects• Provide products based on scientific and societal relevance: education, conservation, global algal blooms, fisheries, biogeography

OBIS: www.iobis.orgOBIS: www.iobis.org

Currently in OBIS (Jan. 2009):

16.7 million records of 104,000 species from 501 databases

2007: 13.6 million records2006: 10 million records2005: 5 million records

Filling in the data gaps – Southern Hemisphere, deeper waters, taxonomic groups

< 100 meters< 100 meters

100-1000 meters100-1000 meters

1000-3000 meters1000-3000 meters

> 3000 meters> 3000 meters

How to Record 10,000,000 Marine Life Forms?How to Record 10,000,000 Marine Life Forms?

TricorderTricorderAny resemblanceAny resemblancepurely coincidental.purely coincidental.

BarcoderBarcoder??

May, 2004, Smithsonian

TechnologyTechnologyTo review the CoML Research Plan and make recommendations about

technologies that could be applied to CoML projects & advise on project technology needs.

To identify and bring to the attention of the international community of fisheries scientists, marine biologists and others, the potential benefits of emerging

technologies in the detection of marine life.

To explore the relative merits of different technologies and identify those that deserve further research based on their potential for making significant

contributions to the detection of marine life.

Synthesis:

• Cross-project synthesis of technology used by CoML, documenting technologies used by CoML projects, particularly in terms of technologies that CoML has advanced.

• Workshop on ocean biology observatories to contribute to the Global Ocean Observing System (GOOS)

ConclusionsConclusions

• Marine biodiversity is still poorly known• Less than 1 % of the ocean is explored• Perhaps less than 10 % of macroscopic

species is described• Microbial diversity is vast with largely

unknown functionality• Ergo: exploration

Pr. Carlo Heip, 2006

ConclusionsConclusions

• Marine biodiversity is changing• Oceanic and coastal food webs change

as top predators disappear• Changes in distribution over the North

Atlantic Ocean have been documented• Fisheries and climate change are the

most important causes globally• Many local impacts: eutrophication,

pollution, invading species, habitat destruction, are changing coastal communities

• Ergo: observationPr. Carlo Heip, 2006

ConclusionsConclusions

• What are the consequences?• Are marine species going extinct?• Is system functioning affected by

biodiversity changes?• Productivity• Element cycling• Food webs

• Ergo: experiments, concepts and theories

Pr. Carlo Heip, 2006

ConclusionsConclusions

• Why should we care?• What is valued by people?• Is marine biodiversity part of the human

socio-economic and psychological ‘environment’?

• Ethics, perception of nature, sense of discovery and stewardship?

• Ergo: Communication, outreach

Pr. Carlo Heip, 2006

Thank you for your attention!

Merci pour votre attention!

Muchas gracias por su atención!