Bacterial metabolism of dissolved organic matter

Linking microbial ecolog y to ecosystem process from mountain to reef to ocean

Photo: Moorea Coral Reef LTER

Craig Nelson, Assistant Researcher Center for Microbial Oceanography: Research and Education (C-MORE)

Dept of Oceanography and UH Sea Grant University of Hawai‘i at Mānoa

Who I am, What I do, Where I’m going

• My areas of expertise and interest – Microbial community Metagenomics & Phylogenetics – Microbial biogeochemistry of Dissolved Organic Matter

• A few past projects and papers

– Alpine watershed microbial ecology/biogeochemistry – Coral reef biogeochemistry and microbial ecology

• A sampling of recent proposals • Projects I hope to pursue

Microbial Diversity: The Alien World

Microbial Diversity dwarfs all of the known diversity of plants and animals…

• Most bacterial phyla are uncultured and known only from gene fragments sequenced from the environment

Rappé and Giovannoni, Ann. Rev. Micro. 2003

Just the Bacteria

Microbial Diversity: The Alien World

Bacteria Regulate Ecosystems Ba

cter

ial B

iom

ass

Phytoplankton Biomass

Simon, et al. 1992 Mar. Ecol. Prog. Ser.

Unproductive systems are dominated by bacterial biomass

Earth’s Carbon Pools: Atmospheric CO2 = Terrestrial Plant Carbon = Aquatic Dissolved Organic Carbon “Dissolved organic carbon is almost exclusively accessible to heterotrophic bacteria” - Azam and Malfatti, Nature Reviews Microbiology 2007

– In almost any ecosystem, bacteria are responsible for a large fraction of aerobic respiration, all of the anaerobic respiration, and a large portion of the remineralization of organic nutrients.

• Cole, Ecosystems, 1999

What is a Metagenome? Whole community genomes from ~50 L of water Two Sizes of particles captured: 0.2um (free-living) and 5.0um (particle-attached) >600,000 DNA sequences each (~400 bp/read); matched against databases

DNA amplicon/shotgun pyrosequencing Bacterial/Archaeal phylogenetics and metagenomics

Analytical chemistry Fluorescence spectroscopy

Ecosystem metabolism Microbial community energetics

Bacterioplankton and Dissolved Organic Matter: Linking microbes to ecosystems

Complex dissolved organic matter pools

Diverse microbial communities

Dynamic ecosystem processes

Bacterioplankton and Dissolved Organic Matter: Linking microbes to ecosystems

Complex dissolved organic matter pools

Diverse microbial communities

Dynamic ecosystem processes

Landscape cover and resource exports

Habitat heterogeneity and algal/coral

exudates

Ecosystem Metabolism and Climate

Patterns

Phase shifts to algal

dominance

Alpine Lakes Sierra Nevada

Coral Reefs Moorea/Tahiti

Landscape microbial ecology

Land Cover

Climate

Resource Quality/Quantity

Microbial Community Structure & Metabolism

Ecosystem Process and Trophic Structure

a Human

Management

Case Study: Alpine Lakes of the Sierra Nevada, California

Image courtesy USGS GAP land cover database

Linking climate and landscape process with

resource delivery to downstream ecosystems

11,666 bodies of water above 2300 m >3000 larger than a typical “pond” (> 0.5 ha) Low Nutrient, Unproductive Ecosystems Are bacteria the dominant plankton? Who are they? What do they eat? What is their role in the ecosystem?

Sierra Nevada Lakes

GIS analysis by Steve Sadro, UCSB unpublished

Emerald Lake, 2800m

Land Cover

Climate

Resource Quality/Quantity

Microbial Community Structure & Metabolism

Ecosystem Process and Trophic Structure

a

Land Cover

Climate

Resource Quality/Quantity

Microbial Community Structure & Metabolism

Ecosystem Process and Trophic Structure

a

Nelson, Sadro, Melack 2009 L&O and 2012 Ecosystems

Diss

olve

d O

rgan

ic

Fluo

resc

ence

(nm

-1)

Bact

erio

plan

kton

(1

04 cel

ls m

L-1)

DIN

:DO

N m

olar

Di

ssol

ved

Nitr

ogen

Rat

io

Catchment Vegetation Cover

Mixed heirarchical regression modeling

Steve Sadro

John Melack

Land Cover

Climate

Resource Quality/Quantity

Microbial Community Structure & Metabolism

Ecosystem Process and Trophic Structure

a

Annual community phenology pattern repeated 2004, 2005, 2006

2004 2005 2006 b.

ICE COVER

SNOWMELT ICE-OFF STRATIFIED OVERTURN

NMS Ordination

Axis 1 – 54% Variance Best Correlate (r = 0.81): Snowmelt Discharge Axis 2 – 23% Variance Best Correlate (r = 0.73): Thermal Stability/Stratification

Nelson 2008 ISME Journal

Together: 75% Discriminant

Stra

tific

atio

n Discharge

Land Cover

Climate

Resource Quality/Quantity

Microbial Community Structure & Metabolism

Ecosystem Process and Trophic Structure

a

Nelson 2008 ISME Journal, Sadro et al 2011 L&O

Day of Year

Dept

h (m

)

2005

2009

1 3 5 7 9 1 3 5 7 9

phytoplankton

DOM

Flu

ores

cenc

e In

dex

McK

nigh

t et a

l 200

1 L&

O

Day of Year

terrestrial

Autotrophic Heterotrophic

Microbial Succession (linked to snowmelt) Changing DOM Sources (snowmelt terrigenous inputs) Seasonal shifts in Ecosystem Metabolic Balance

ICE COVER

2004 2005 2006

Informing Sustainable Management of Coastal Ecosystems

Land Cover

Climate

Resource Quality/Quantity

Microbial Community Structure & Metabolism

Ecosystem Process and Trophic Structure

a Human

Management

Tourism, Development, Wastewater, Aquaculture, Fisheries, SWAC, OTEC, etc.

ICE COVER

2004 2005 2006

Mo’orea, French Polynesia Site of Coral Reef Long Term Ecological Research Program Five years of Spatial Surveying among Offshore, Forereef, Backreef and Bay Habitats

Depleted DOC overlying the Reef Depleted bacterioplankton densities overlying the Reef

Spatial biogeochemical connectivity in nearshore tropical reef habitats

Nelson, et al. 2011 ISME Journal

BIG WAVES SMALL WAVES

High-resolution surveys 2010-11

Bacterioplankton cells Dissolved Organic Carbon

Nitrate Phosphate

Hypothesis: Labile DOM derived from reef benthic producers facilitates remineralization of recalcitrant oceanic DOM

Leichter et al. 2013, Oceanography

Bacterioplankton in the water column of reefs are different than those in the surrounding ocean

Nelson, Alldredge, McCliment, Amaral-Zettler, and Carlson. 2011. ISME Journal. Leichter et al. 2013, Oceanography

Non-metric multidimensional scaling of ~40 bacterial community structure samples by 16S rRNA T-RFLP

Phase shifts to algal dominance in Coral Reefs

Overfishing Nutrient Pollution

Images courtesy J. Smith

Hypothesis: Algal dissolved organic matter (DOM) exudates foster bacterial growth and oxygen removal, selecting for copiotrophic organisms and potential pathogens

15-30% of production as DOM – rich in saccharides (labile)

Smith et al. 2006 Ecology Letters

Boundary Layer

Hypoxia

Rosenberg et al. 2007 Oceanography

Pathogen facilitation

Maintenance of algal dominance by microbially-mediated feedbacks?

Turbinaria Brown Macroalgae

Ochrophyta

Halimeda Green Macroalgae

Chlorophyte

Amansia Red Macroalgae

Rhodophyte

Porites Hermatypic Coral

Cnidaria

8h Daylight Incubation Harvest DOM Exudate Sterile-filter (0.2 μm)

Inoculate with reef water 48h Dark Incubation

Track DOC, Oxygen, Cells

Effects of coral and algal exudates on bacterial growth

and oxygen demand

Photos a-c sourced from AlgaeBase: Guiry, M.D. & Guiry, G.M. 2011. http://www.algaebase.org, National University of Ireland, Galway; photo d sourced from MCR-LTER at http://mcr.lternet.edu/education with respective copyrights: a) Eric Coppejans( eric.coppejans@ugent.be); b) John Huisman (j.huisman@murdoch.edu.au); c) Heroen Verbruggen (heroen.verbruggen@gmail.com); d) Matthew Meier , MCRLTER.

Haas, Nelson, Kelly, Carlson, Rohwer, Leichter, Wyatt, Smith. 2011. PLoS ONE

Chloroflexi_SAR202

Deltaproteobacteria_SAR324

Deferribacteres_SAR406

Actinobacteria_Acidimicrobiales

Alphaproteobacteria_Rhodospirillaceae

Alphaproteobacteria_SAR116

Alphaproteobacteria_SAR11

Cyanobacteria_Synechococcus

Gammaproteobacteria_Oleiphilaceae

Betaproteobacteria_Methylophilaceae

Planctomycetes_Planctomycetaceae

Planctomycetes_OM190

Deltaproteobacteria_Bacteriovoraceae

Alphaproteobacteria_Erythrobacteraceae

Alphaproteobacteria_Kordiimonadaceae

Alphaproteobacteria_Hyphomonadaceae

Alphaproteobacteria_Sneathiellaceae

Alphaproteobacteria_Rhodobacteraceae

Flavobacteria_Flavobacteriaceae

Flavobacteria_Cryomorphaceae

Gammaproteobacteria_OMG

Gammaproteobacteria_Alteromonadaceae

Gammaproteobacteria_Oceanospirillaceae

Gammaproteobacteria_Pseudoalteromonadaceae

Gammaproteobacteria_Vibrionaceae

0.4 0.3 0.2 0.1

Community difference

(Unifrac distance weighted by

OTUs)

Elevated in Ambient Waters

& Controls

Elevated in Coral

Exudates

Elevated in Algal

Exudates

Mostly cultured copiotrophs: Gammaproteobacteria & Flavobacteria

Mostly uncultured Alphaproteobacteria

Mostly uncultured open ocean clades

Effects of coral and algal exudates on bacterial community composition (16S rRNA pyrosequencing)

Nelson, Goldberg, Kelly, Haas, Smith, Rohwer, Carlson. 2013. ISME Journal

Bro

wn

M

acro

alga

e G

reen

M

acro

alga

e R

ed

Mac

roal

gae

Cor

al

Con

trol

(P

lank

ton)

Am

bien

t R

eef W

ater

Communities differ by exudate source

Some Recent Proposals • Microbial Source Tracking (State of California Water Resources Board):

– Assessment of Bacterial Water Quality in the Lahontan Region: A study to provide data on bacterial indicator concentrations and sources of bacteria in surface waters

• Aquaculture and Microbes (NSF Small Business STTR/SBIR):

– KRuMBS: The Kyphosid Ruminant Microbial Biodigestor of Seaweeds: The alimentary microbiome of an herbivorous reef fish as a transformer of algal feedstocks

• Reef Ecosystem Biodiversity (NOAA):

– CREBON: The US Pacific Demonstration Coral Reef Ecosystem Biodiversity Observation Network

• Coral Microbial Ecology (NSF Biological Oceanography):

– Coral Microbiome Resilience to Macroalgal Exudates and Thermal Stressors

Projects I hope to pursue

• Groundwater discharge and microbes in Hawai‘i

• Microbial communities and metagenomes as source tracking and ecosystem assessment tools

• Coral Reef Ecosystem Microbiomes: diversity and biogeochemical relevance