Kay D. Bidle

Accelerated dissolution of diatom silica by marine bacterial assemblages

Downward fluxes of biogenic silica and organic matter in the global ocean derive dominantly from the productivity of diatoms — phytoplankton with cell walls containing silica encased in an organic matrix,. As diatoms have an absolute requirement for silicon (as silicic acid), its supply into the photic zone — largely by silica dissolution and upwelling — controls diatom production (and consequently the biological uptake of atmospheric CO2 by the ocean) over vast oceanic areas. Current biogeochemical models assume silica dissolution to be controlled by temperature, zooplankton grazing and diatom aggregation,, but the role of bacteria has not been established. Yet bacteria utilize about half of the organic matter derived from oceanic primary production by varied strategies, including attack on dead and living diatoms by using hydrolytic enzymes,, and could adventitiously hasten silica dissolution by degrading the organic matrix which protects diatom frustules from dissolution,. Here we report the results of experiments in which natural assemblages of marine bacteria dramatically increased silica dissolution from two species of lysed marine diatoms compared to bacteria-free controls. Silica dissolution accompanied, and was caused by, bacterial colonization and hydrolytic attack. Bacteria-mediated silicon regeneration rates varied with diatom type and bacterial assemblage; observed rates could explain most of the reported upper-ocean silicon regeneration,. Bacteria-mediated silicon regeneration may thus critically control diatom productivity and the cycling and fate of silicon and carbon in the ocean.

The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the Functional Diversity of Eukaryotic Life in the Oceans through Transcriptome Sequencing.

Current sampling of genomic sequence data from eukaryotes is relatively poor, biased, and inadequate to address important questions about their biology, evolution, and ecology; this Community Page describes a resource of 700 transcriptomes from marine microbial eukaryotes to help understand their role in the worlds oceans.

Cell death in planktonic, photosynthetic microorganisms

Phytoplankton evolved in the Archaean oceans more than 2.8 billion years ago and are of crucial importance in regulating aquatic food webs, biogeochemical cycles and the Earths climate. Until recently, phytoplankton were considered immortal unless killed or eaten by predators. However, over the past decade, it has become clear that these organisms can either be infected by viruses or undergo programmed cell death (PCD) in response to environmental stress, resulting in mortality. Here, we discuss exogenous and endogenous mechanisms of phytoplankton death, specifically examining the experimental evidence for PCD in phytoplankton and exploring its evolutionary development and ecological impact. We consider phytoplankton PCD as an autocatalytic cell-suicide mechanism in which an endogenous biochemical pathway leads to cellular demise with apoptotic morphological changes. Phytoplankton have a core set of proteins that are orthologues of metazoan caspases. It seems that PCD in prokaryotic phytoplankton, and in independently evolving eukaryotic lineages, has deeply rooted origins that were appropriated and transferred to multicellular plants and animals in the past 700 million years of the Earths history.

Viral Glycosphingolipids Induce Lytic Infection and Cell Death in Marine Phytoplankton

The Death of Cocco Emiliania huxleyi is a coccolithophore, a class of unicellular phytoplankton that forms vast blooms mediating the oceanic carbon cycle through shedding of its calcium carbonate scales. E. huxleyi is routinely infected and killed by lytic viruses that can abruptly halt a bloom. Vardi et al. (p. 861) have found that in E. huxleyi strains that are sensitive or resistant to infection, a sphingolipid-based “arms race” appears to regulate cell fate during host-virus interactions. The lipid also serves as a biomarker for active infection that may help to quantify the role and activity of viruses and virus-mediated processes in the oceans. This information will help in assessing the biogeochemical impact of these plankton species. A specific virus encodes membrane components that broadcast cell death and population demise of its coccolithophore host. Marine viruses that infect phytoplankton are recognized as a major ecological and evolutionary driving force, shaping community structure and nutrient cycling in the marine environment. Little is known about the signal transduction pathways mediating viral infection. We show that viral glycosphingolipids regulate infection of Emiliania huxleyi, a cosmopolitan coccolithophore that plays a major role in the global carbon cycle. These sphingolipids derive from an unprecedented cluster of biosynthetic genes in Coccolithovirus genomes, are synthesized de novo during lytic infection, and are enriched in virion membranes. Purified glycosphingolipids induced biochemical hallmarks of programmed cell death in an uninfected host. These lipids were detected in coccolithophore populations in the North Atlantic, which highlights their potential as biomarkers for viral infection in the oceans.

Viral activation and recruitment of metacaspases in the unicellular coccolithophore, Emiliania huxleyi

Lytic viral infection and programmed cell death (PCD) are thought to represent two distinct death mechanisms in phytoplankton, unicellular photoautotrophs that drift with ocean currents. Here, we demonstrate an interaction between autocatalytic PCD and lytic viral infection in the cosmopolitan coccolithophorid, Emiliania huxleyi. Successful infection of E. huxleyi strain 374 with a lytic virus, EhV1, resulted in rapid internal degradation of cellular components, a dramatic reduction in the photosynthetic efficiency (Fv/Fm), and an up-regulation of metacaspase protein expression, concomitant with induction of caspase-like activity. Caspase activation was confirmed through in vitro cleavage in cell extracts of the fluorogenic peptide substrate, IETD-AFC, and direct, in vivo staining of cells with the fluorescently labeled irreversible caspase inhibitor, FITC-VAD-FMK. Direct addition of z-VAD-FMK to infected cultures abolished cellular caspase activity and protein expression and severely impaired viral production. The absence of metacaspase protein expression in resistant E. huxleyi strain 373 during EhV1 infection further demonstrated the critical role of these proteases in facilitating viral lysis. Together with the presence of caspase cleavage recognition sequences within virally encoded proteins, we provide experimental evidence that coccolithoviruses induce and actively recruit host metacaspases as part of their replication strategy. These findings reveal a critical role for metacaspases in the turnover of phytoplankton biomass upon infection with viruses and point to coevolution of host–virus interactions in the activation and maintenance of these enzymes in planktonic, unicellular protists.

Si and C interactions in the world ocean: Importance of ecological processes and implications for the role of diatoms in the biological pump

[1] Diatoms play a major role in carbon export from surface waters, but their role in the transport of carbon to the deep sea has been questioned by global analyses of sediment trap fluxes which suggest that organic carbon fluxes and transfer efficiencies through the mesopelagic are tightly correlated with CaCO 3 (Klaas and Archer, 2002; Francois et al., 2002). Here we explore the role of diatoms in the biological pump through a study of Si and C interactions from the molecular to the global scale. Recent findings on molecular interactions between Si and C are reviewed. The roles of bacteria, grazers and aggregation are explored and combined, to account for the extent of Si and C decoupling between surface waters and 1000 m, observed to be very homogeneous in different biogeochemical provinces of the ocean. It is suggested that the mesopelagic food web plays a crucial role in this homogeneity: Sites of high export are also sites where diatom C is being either remineralized or channeled toward the long-lived carbon pool most efficiently in the mesopelagic zone. The amount of carbon participating in the biological pump but not collected in sediment traps remains to be explored. It is also demonstrated that statistical analyses performed at global scales hide spatial variability in carrying coefficients, indicating a clear need to understand the mechanisms that control spatial and temporal variations in the relative importance of ballast minerals and other export mechanisms such as particle dynamics.

A Diatom Gene Regulating Nitric-Oxide Signaling and Susceptibility to Diatom-Derived Aldehydes

Diatoms are unicellular phytoplankton accounting for approximately 40% of global marine primary productivity [1], yet the molecular mechanisms underlying their ecological success are largely unexplored. We use a functional-genomics approach in the marine diatom Phaeodactylum tricornutum to characterize a novel protein belonging to the widely conserved YqeH subfamily [2] of GTP-binding proteins thought to play a role in ribosome biogenesis [3], sporulation [4], and nitric oxide (NO) generation [5]. Transgenic diatoms overexpressing this gene, designated PtNOA, displayed higher NO production, reduced growth, impaired photosynthetic efficiency, and a reduced ability to adhere to surfaces. A fused YFP-PtNOA protein was plastid localized, distinguishing it from a mitochondria-localized plant ortholog. PtNOA was upregulated in response to the diatom-derived unsaturated aldehyde 2E,4E/Z-decadienal (DD), a molecule previously shown to regulate intercellular signaling, stress surveillance [6], and defense against grazers [7]. Overexpressing cell lines were hypersensitive to sublethal levels of this aldehyde, manifested by altered expression of superoxide dismutase and metacaspases, key components of stress and death pathways [8, 9]. NOA-like sequences were found in diverse oceanic regions, suggesting that a novel NO-based system operates in diatoms and may be widespread in phytoplankton, providing a biological context for NO in the upper ocean [10].

Host–virus dynamics and subcellular controls of cell fate in a natural coccolithophore population

Marine viruses are major evolutionary and biogeochemical drivers in marine microbial foodwebs. However, an in-depth understanding of the cellular mechanisms and the signal transduction pathways mediating host–virus interactions during natural bloom dynamics has remained elusive. We used field-based mesocosms to examine the “arms race” between natural populations of the coccolithophore Emiliania huxleyi and its double-stranded DNA-containing coccolithoviruses (EhVs). Specifically, we examined the dynamics of EhV infection and its regulation of cell fate over the course of bloom development and demise using a diverse suite of molecular tools and in situ fluorescent staining to target different levels of subcellular resolution. We demonstrate the concomitant induction of reactive oxygen species, caspase-specific activity, metacaspase expression, and programmed cell death in response to the accumulation of virus-derived glycosphingolipids upon infection of natural E. huxleyi populations. These subcellular responses to viral infection simultaneously resulted in the enhanced production of transparent exopolymer particles, which can facilitate aggregation and stimulate carbon flux. Our results not only corroborate the critical role for glycosphingolipids and programmed cell death in regulating E. huxleyi–EhV interactions, but also elucidate promising molecular biomarkers and lipid-based proxies for phytoplankton host–virus interactions in natural systems.

Fossil genes and microbes in the oldest ice on Earth

Although the vast majority of ice that formed on the Antarctic continent over the past 34 million years has been lost to the oceans, pockets of ancient ice persist in the Dry Valleys of the Transantarctic Mountains. Here we report on the potential metabolic activity of microbes and the state of community DNA in ice derived from Mullins and upper Beacon Valleys. The minimum age of the former is 100 ka, whereas that of the latter is ≈8 Ma, making it the oldest known ice on Earth. In both samples, radiolabeled substrates were incorporated into macromolecules, and microbes grew in nutrient-enriched meltwaters, but metabolic activity and cell viability were critically compromised with age. Although a 16S rDNA-based community reconstruction suggested relatively low bacterial sequence diversity in both ice samples, metagenomic analyses of community DNA revealed many diverse orthologs to extant metabolic genes. Analyses of five ice samples, spanning the last 8 million years in this region, demonstrated an exponential decline in the average community DNA size with a half-life of ≈1.1 million years, thereby constraining the geological preservation of microbes in icy environments and the possible exchange of genetic material to the oceans.

The Molecular Ecophysiology of Programmed Cell Death in Marine Phytoplankton

Planktonic, prokaryotic, and eukaryotic photoautotrophs (phytoplankton) share a diverse and ancient evolutionary history, during which time they have played key roles in regulating marine food webs, biogeochemical cycles, and Earths climate. Because phytoplankton represent the basis of marine ecosystems, the manner in which they die critically determines the flow and fate of photosynthetically fixed organic matter (and associated elements), ultimately constraining upper-ocean biogeochemistry. Programmed cell death (PCD) and associated pathway genes, which are triggered by a variety of nutrient stressors and are employed by parasitic viruses, play an integral role in determining the cell fate of diverse photoautotrophs in the modern ocean. Indeed, these multifaceted death pathways continue to shape the success and evolutionary trajectory of diverse phytoplankton lineages at sea. Research over the past two decades has employed physiological, biochemical, and genetic techniques to provide a novel, comprehensive, mechanistic understanding of the factors controlling this key process. Here, I discuss the current understanding of the genetics, activation, and regulation of PCD pathways in marine model systems; how PCD evolved in unicellular photoautotrophs; how it mechanistically interfaces with viral infection pathways; how stress signals are sensed and transduced into cellular responses; and how novel molecular and biochemical tools are revealing the impact of PCD genes on the fate of natural phytoplankton assemblages.