Marine Microbial Ecology Group

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Our lab focuses on mechanisms and controls of microbial population dynamics. Our research has an emphasis on carbon cycling in marine ecosystems – processes which regulate carbon fixation and energy transfer to higher trophic levels. These processes are critical to sustainability of oceanic food webs, global climate and human health.

Much of our work has focused on growth and grazing mortality rates of microbial photoautotrophs, including picophytoeukaryotes (cells < 2 microm in diameter). This research highlights the need to understand interactions between unicellular algae, heterotrophic microbes and the protists that consume them in order to more fully comprehend and model carbon cycling. See YouTube video on genomic approaches to this work.

We are pursuing three interlinked research areas in order to develop a mechanistic understanding of microbial contributions to global carbon cycling: molecular underpinnings of physiological growth controls; microbe-microbe interactions, including competition processes/trophic linkages (food web dynamics); and quantitative, mechanistically-based models of functional diversity, primary production and trophic transfer in marine environments – or, at the moment, working to provide data that can improve such models. Fundamental to these studies is the recognition that:

  1. microbes cannot be treated as bulk communities because their individual adaptive strategies and real time behavior are critical to food web dynamics, and
  2. microbes must be studied at habitat scales relevant to their adaptive strategies to determine how their metabolism influences larger-scale ecosystem dynamics.

This type of research is essential to the development of mechanistic models of ocean biogeochemistry and efforts to conserve marine ecosystems.

Specific Research Directions:

Neither top-down (e.g. grazing mortality) nor bottom-up (e.g. nutrient stress) approaches provide the necessary basis for understanding population dynamics and biotic transport of carbon in marine systems. Detailed identification and characterization of specific forces acting on important microbial populations as well as the interaction between these forces will allow better understanding of ecosystem dynamics. This requires going beyond measurements of community based properties (e.g. bulk bacterial activity) or even population specific rates. Instead, we must develop a mechanistic view of autotroph/heterotroph as well as heterotroph/heterotroph interactions.

We are addressing mechanisms and controls of trophic transfer using a multi-faceted approach employing molecular and biochemical techniques, genomics, proteomics andin situ studies. We also use flow cytometry quite extensively, and have in house both a standard clinical instrument (EPICS XL, Coulter Corp., ACCURI, BD) as well as a high speed cell sorter (InFlux, BD) which we use for discrimination and separation of natural microbial populations. Most recently we have used this instrument to sort natural populations at sea and sequence their genomes – an approach we term Targeted Metagenomics – because we don’t go through the process of culturing, nor do we deal with the bulk community. Four major research objectives are being combined to aid development of high resolution, population specific field approaches:

Population dynamics of phytoplankton

To thoroughly understand food webs, it is essential to study the tiniest of marine primary producers. These picoeukaryotes also shed light on the evolution of higher plants.

Microbial predators

Tremendous diversity of marine protists has been revealed based on environmental SSU rDNA gene sequencing. Many of these are novel, not yet cultured, and have unknown functional roles.

Microbe-algae interactions

Although we know that bacteria attach to algae (even to picophytoplankton), the relationship between these organisms has not yet been characterized despite its potential influence on population dynamics and biogeochemical cycles.

Targeted metagenomics

There are still many uncultured marine protists – including within the pico-size fraction. An approach developed in the lab that has generated new discoveries on their evolution and ecology has been sequence partial genomes from cells taken directly from the environment.

Worden lab in the news

Worden lab research and people in the news, interviews, and commentaries

Join the Worden lab

Undergraduates who are excited about conducting research are welcome to work with the Worden lab group. Please contact Dr. Worden by email to see if there are positions and projects available.

Resources - Worden lab

Genomic resources, getting started with picophytoplankton, DNA extraction protocols, and genome browser


Former lab members


Upper-ocean systems
Acoustical ocean ecology
Acoustic instruments
Acoustic fingerprinting
Acoustic community ecology
Acoustics in the news
Marine biogeochemistry
Ocean carbon export
Technology development
Coastal carbon cycling and ocean acidification
Carbon cycle feedbacks
Western boundary current carbon cycling
Lab news
Biological oceanography
Global modes of sea surface temperature
Nitrate supply estimates in upwelling systems
Chemical sensors
Chemical data
Land/Ocean Biogeochemical Observatory in Elkhorn Slough
Listing of floats
SOCCOM float visualization
Periodic table of elements in the ocean
Biogeochemical-Argo Report
Profiling float
Marine microbes
Population dynamics of phytoplankton
Microbial predators
Microbe-algae interactions
Targeted metagenomics
In the news
Upcoming events and lab news
Past talks and presentations
Join the lab
Interdisciplinary field experiments
Ecogenomic Sensing
Genomic sensors
Field experiments
Harmful algal blooms (HABs)
Water quality
Environmental Sample Processor (ESP)
ESP Web Portal
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Ocean observing system
Midwater research
Midwater ecology
Deep-sea squids and octopuses
Food web dynamics
Midwater time series
Respiration studies
Zooplankton biodiversity
Seafloor processes
Revealing the secrets of Sur Ridge
Exploring Sur Ridge’s coral gardens
Life at Sur Ridge
Mapping Sur Ridge
Biology and ecology
Effects of humans
Ocean acidification, warming, deoxygenation
Lost shipping container study
Effects of upwelling
Faunal patterns
Previous research
Technology development
High-CO2 / low-pH ocean
Benthic respirometer system
Climate change in extreme environments
Station M: A long-term observatory on the abyssal seafloor
Station M long-term time series
Monitoring instrumentation suite
Sargasso Sea research
Antarctic research
Geological changes
Arctic Shelf Edge
Continental Margins and Canyon Dynamics
Coordinated Canyon Experiment
CCE instruments
CCE repeat mapping data
Monterey Canyon: A Grand Canyon beneath the waves
Submarine volcanoes
Mid-ocean ridges
Magmatic processes
Volcanic processes
Explosive eruptions
Hydrothermal systems
Back arc spreading ridges
Near-ridge seamounts
Continental margin seamounts
Non-hot-spot linear chains
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Margin processes
Hydrates and seeps
California borderland
Hot spot research
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Magmatic processes
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Automated chemical sensors
Methane in the seafloor
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Seafloor biology research
Volcanoes and seamounts
Hydrothermal vents
Methane in the seafloor
Submarine canyons
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Ocean acidification
Physical oceanography and climate change
Ocean circulation and algal blooms
Ocean cycles and climate change
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Molecular ecology
Molecular systematics
SIMZ Project
Bone-eating worms
Gene flow and dispersal
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Ocean chemistry of greenhouse gases
Emerging science of a high CO2/low pH ocean
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