Linking microbial ecology to ecosystem process from mountain to reef to ocean

Transcription

1 Bacterial metabolism of dissolved organic matter Linking microbial ecology to ecosystem process from mountain to reef to ocean 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 Photo: Moorea Coral Reef LTER

2 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

3 Microbial Diversity: The Alien World Microbial Diversity dwarfs all of the known diversity of plants and animals

4 Microbial Diversity: The Alien World Just the Bacteria Most bacterial phyla are uncultured and known only from gene fragments sequenced from the environment Rappé and Giovannoni, Ann. Rev. Micro. 2003

5 Bacteria Regulate Ecosystems Earth s Carbon Pools: Atmospheric CO 2 = Terrestrial Plant Carbon = Aquatic Dissolved Organic Carbon Dissolved organic carbon is almost exclusively accessible to heterotrophic bacteria - Azam and Malfatti, Nature Reviews Microbiology 2007 Unproductive systems are dominated by bacterial biomass Bacterial Biomass Simon, et al Mar. Ecol. Prog. Ser. 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 Phytoplankton Biomass

6 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

7 Bacterioplankton and Dissolved Organic Matter: Linking microbes to ecosystems Complex dissolved organic matter pools Analytical chemistry Fluorescence spectroscopy Diverse microbial communities DNA amplicon/shotgun pyrosequencing Bacterial/Archaeal phylogenetics and metagenomics Dynamic ecosystem processes Ecosystem metabolism Microbial community energetics

8 Bacterioplankton and Dissolved Organic Matter: Linking microbes to ecosystems Complex dissolved organic matter pools Alpine Lakes Sierra Nevada Landscape cover and resource exports Coral Reefs Moorea/Tahiti Habitat heterogeneity and algal/coral exudates Diverse microbial communities Dynamic ecosystem processes Ecosystem Metabolism and Climate Patterns Phase shifts to algal dominance

9 Landscape microbial ecology Linking climate and landscape process with resource delivery to downstream ecosystems Land Cover Human Management Climate a Resource Quality/Quantity Microbial Community Structure & Metabolism Image courtesy USGS GAP land cover database Ecosystem Process and Trophic Structure Case Study: Alpine Lakes of the Sierra Nevada, California

10 Sierra Nevada Lakes 11,666 bodies of water above 2300 m >3000 larger than a typical pond (> 0.5 ha) Low Nutrient, Unproductive Ecosystems GIS analysis by Steve Sadro, UCSB unpublished Are bacteria the dominant plankton? Who are they? What do they eat? What is their role in the ecosystem? Emerald Lake, 2800m

11 Land Cover Climate a Resource Quality/Quantity Microbial Community Structure & Metabolism Ecosystem Process and Trophic Structure

12 Land Cover Resource Quality/Quantity John Melack Climate a Microbial Community Structure & Metabolism Ecosystem Process and Trophic Structure Steve Sadro Nelson, Sadro, Melack 2009 L&O and 2012 Ecosystems Mixed heirarchical regression modeling DIN:DON molar Dissolved Nitrogen Ratio Bacterioplankton (10 4 cells ml -1 ) Dissolved Organic Fluorescence (nm -1 ) Catchment Vegetation Cover

13 Land Cover Climate a Resource Quality/Quantity Microbial Community Structure & Metabolism Ecosystem Process and Trophic Structure Nelson 2008 ISME Journal NMS Ordination SNOWMELT ICE-OFF STRATIFIED OVERTURN ICE COVER Annual community phenology pattern repeated 2004, 2005, 2006 b Discharge Stratification Axis 1 54% Variance Best Correlate (r = 0.81): Snowmelt Discharge Axis 2 23% Variance Best Correlate (r = 0.73): Thermal Stability/Stratification Together: 75% Discriminant

14 Land Cover Climate a Resource Quality/Quantity Microbial Community Structure & Metabolism Ecosystem Process and Trophic Structure Nelson 2008 ISME Journal, Sadro et al 2011 L&O Microbial Succession (linked to snowmelt) Changing DOM Sources (snowmelt terrigenous inputs) Seasonal shifts in Ecosystem Metabolic Balance Depth (m) ICE COVER Autotrophic Day of Year phytoplankton DOM Fluorescence Index McKnight et al 2001 L&O terrestrial Heterotrophic Day of Year

15 Informing Sustainable Management of Coastal Ecosystems Land Cover Human Management Climate a Resource Quality/Quantity Microbial Community Structure & Metabolism Ecosystem Process and Trophic Structure ICE COVER Tourism, Development, Wastewater, Aquaculture, Fisheries, SWAC, OTEC, etc.

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17 Nelson, et al ISME Journal Spatial biogeochemical connectivity in nearshore tropical reef habitats Depleted DOC overlying the Reef Depleted bacterioplankton densities overlying the Reef BIG WAVES SMALL WAVES 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

18 High-resolution surveys

19 Dissolved Organic Carbon Bacterioplankton cells Nitrate Phosphate Hypothesis: Labile DOM derived from reef benthic producers facilitates remineralization of recalcitrant oceanic DOM Leichter et al. 2013, Oceanography

20 Bacterioplankton in the water column of reefs are different than those in the surrounding ocean Non-metric multidimensional scaling of ~40 bacterial community structure samples by 16S rrna T-RFLP Nelson, Alldredge, McCliment, Amaral-Zettler, and Carlson ISME Journal. Leichter et al. 2013, Oceanography

21 Phase shifts to algal dominance in Coral Reefs Overfishing Nutrient Pollution Images courtesy J. Smith

22 Maintenance of algal dominance by microbially-mediated feedbacks? 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) Boundary Layer Hypoxia Pathogen facilitation Smith et al Ecology Letters Rosenberg et al Oceanography

23 Effects of coral and algal exudates on bacterial growth and oxygen demand 8h Daylight Incubation Harvest DOM Exudate Sterile-filter (0.2 μm) Turbinaria Brown Macroalgae Ochrophyta Halimeda Green Macroalgae Chlorophyte Inoculate with reef water 48h Dark Incubation Track DOC, Oxygen, Cells Amansia Red Macroalgae Rhodophyte Porites Hermatypic Coral Cnidaria Photos a-c sourced from AlgaeBase: Guiry, M.D. & Guiry, G.M National University of Ireland, Galway; photo d sourced from MCR-LTER at 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 PLoS ONE

24 Effects of coral and algal exudates on bacterial community composition (16S rrna pyrosequencing) Community difference (Unifrac distance weighted by OTUs) Mostly uncultured open ocean clades Mostly uncultured Alphaproteobacteria Mostly cultured copiotrophs: Gammaproteobacteria & Flavobacteria Elevated in Ambient Waters & Controls Elevated in Coral Exudates Elevated in Algal Exudates 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 Brown Macroalgae Green Macroalgae Red Macroalgae Coral Control (Plankton) Ambient Reef Water Communities differ by exudate source Nelson, Goldberg, Kelly, Haas, Smith, Rohwer, Carlson ISME Journal

25 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

26 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