Andrew E. Allen, Ph.D.

Professor of Microbial Oceanography and Ecology, Integrative Oceanography Division, University of California, San Diego (Scripps Institution of Oceanography)
Professor in the Microbial and Environmental Genomics Department, J. Craig Venter Institute
Andrew E. Allen’s website

PriME Project: Biological and Chemical Connections Within Phytoplankton Microbiomes

Microbial interactions within a microbiome are complex biological phenomena. They are more likely the rule, rather than exception, in governing natural microbial populations. In aquatic environments, multiple nutrients (e.g. iron, nitrogen, phosphorus, vitamin B12) can control the extent of primary productivity, including scenarios of co-limitation where often two nutrients are so scarce as to impact productivity simultaneously. It is also becoming evident that chemical activities of phytoplankton microbiomes can improve the fitness of the overall holobiont, and that these activities, including production of vitamins, metal-binding ligands, or conducting enzymatic reactions, are widespread in natural ecosystems and of biogeochemical importance. The emergence of these biological-chemical connections within a holobiont must be governed by changes in cellular stoichiometry, energetic costs, and the overriding influence of natural selection. Moreover, these complex holobiont systems then compete against each other ecologically within natural populations, creating a multi-tiered system of associations and competition. In work conducted here, the researchers will explore these emergent chemical and biological connections in a suite of up to four model phytoplankton systems, including ecologically dominant and emerging model taxa.

Andrew E. Allen is a joint professor of microbial oceanography and ecology in both the Integrative Oceanography Division at Scripps Institution of Oceanography, University of California, San Diego, and the J. Craig Venter Institute (JCVI). He received his Ph.D. in ecology from the University of Georgia in 2002. After several years as a postdoctoral scholar at Princeton University and at the École Normale Supérieure in Paris, France, he joined the faculty at JCVI 2007. In 2013 he assumed a faculty position at the Scripps Institution of Oceanography, University of California, San Diego.

Photosynthetic marine microbes account for around half of global photosynthesis annually and together viruses, bacteria and protists account for most of the biomass found in ocean ecosystems and are crucial components of coastal and pelagic ecosystems. Knowledge related to microbial diversity and function represents one of the great data gaps in marine observations.

Current projects in the Allen laboratory are concerned with development of new knowledge and new hypotheses related to gene function, biochemical pathways, ecophysiology and other genome-scale characteristics that typify and distinguish the major phytoplankton lineages. Various experimental approaches are concerned with characterization of cellular and genome-scale processes that facilitate adaptation to physiological stress and regulate nutrient biogeochemistry. Ongoing laboratory and oceanographic studies are aimed at investigation of biogeochemically relevant cellular features that influence the distribution and occurrence of major phytoplankton groups. Other current research interests in the Allen laboratory are related to eukaryotic phytoplankton interactions with bacteria and other microbes and associated cellular defense, resistance and interaction mechanisms. Together these studies seek to integrate physiological, bioinformatic, statistical, functional and comparative genomics strategies and data streams to elucidate the regulatory networks that regulate nutrient flux for the major lineages of marine eukaryotic phytoplankton.

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