Determining the Ecological and Physiological Factors Contributing to the Competitive Success of Prochlorococcus in the Oligotrophic Ocean

Prochlorococcus is a genus of extremely successful marine cyanobacteria. This success is realized through its pervasive biogeographical range and presence in almost all open ocean environments where it usually it the dominant phytoplankton. Limited capabilities of culturing and genetic manipulation of this organism have resulted in assumptions about this success overwhelmingly based on field observations. These studies have assumed adaptations for resource uptake and utilization in nutrient limited environments to cause dominance of Prochlorococcus over other photosynthetic microbes. In an attempt to definitively explain this through laboratory culture, we developed a culturing system to assay questions of nutrient limitation effects upon Prochlorococcus and its competitive ability based on nitrogen limited populations within the North Pacific Subtropical Gyre. We determined that competition for nitrogen did explain the population dynamics of Prochlorococcus and another cyanobacterium, Synechococcus, and were able to recreate their observed abundances in nitrogen limited laboratory culture. Interestingly this outcome could only be achieved through the inclusion of a heterotrophic bacterium, which facilitated the success of Prochlorococcus through complex crossfeeding interactions. In an effort to further explore the important microbial interactions influencing this dominant cyanobacterium, we developed an additional culturing system to determine if rival phytoplankton (Synechococcus and picoeukaryotes), with whom Prochlorococcus competes for nutrients, could protect Prochlorococcus from oxidative stress from hydrogen peroxide. These rivals successfully protected Prochlorococcus from mortality when cocultured at ecologically relevant abundances. Lastly we determined the affect of seasonal change on Prochlorococcus ecotypes and potential relationships between high-light and low-light adapted ecotypes and between ecotypes and abundant microbial phyla that varied seasonally. Herein we speculate on the overall importance of microbial interactions based on nutrient transformation and environmental conditioning to the ecology and biogeography of Prochlorococcus

Selective and Differential Feeding on Marine Prokaryotes by Mucous Mesh Feeders

Microbial mortality impacts the structure of food webs, carbon flow, and the interactions that create dynamic patterns of abundance across gradients in space and time in diverse ecosystems. In the oceans, estimates of microbial mortality by viruses, protists, and small zooplankton do not account fully for observations of loss, suggesting the existence of underappreciated mortality sources. We examined how ubiquitous mucous mesh feeders (i.e. gelatinous zooplankton) could contribute to microbial mortality in the open ocean. We coupled capture of live animals by blue-water diving to sequence-based approaches to measure the enrichment and selectivity of feeding by two coexisting mucous grazer taxa (pteropods and salps) on numerically dominant marine prokaryotes. We show that mucous mesh grazers consume a variety of marine prokaryotes and select between coexisting lineages and similar cell sizes. We show that Prochlorococcus may evade filtration more than other cells and that planktonic archaea are consumed by macrozooplanktonic grazers. Discovery of these feeding relationships identifies a new source of mortality for Earth\u27s dominant marine microbes and alters our understanding of how top-down processes shape microbial community and function

Draft genomes of three closely related low light-adapted <i>Prochlorococcus</i>

OBJECTIVES: The marine cyanobacterium Prochlorococcus is a critical part of warm ocean ecosystems and a model for studying microbial evolution and ecology. To expand the representation of this organism's vast wild diversity in sequence collections, we performed a set of isolation efforts targeting low light-adapted Prochlorococcus. Three genomes resulting from this larger body of work are described here.DATA DESCRIPTION: We present draft-quality Prochlorococcus genomes from enrichment cultures P1344, P1361, and P1363, sampled in the North Pacific. The genomes were built from Illumina paired reads assembled de novo. Supporting datasets of raw reads, assessments, and sequences from co-enriched heterotrophic marine bacteria are also provided. These three genomes represent members of the low light-adapted LLIV Prochlorococcus clade that are closely related, with 99.9% average nucleotide identity between pairs, yet vary in gene content. Expanding the powerful toolkit of Prochlorococcus genomes, these sequences provide an opportunity to study fine-scale variation and microevolutionary processes.</p

Autotrophic Picoplankton: Their Presence and Significance In Marine and Freshwater Ecosystems

Invited lecture: Autotrophic Picoplankton Workshop, 52nd Congress of the Polish Botanical Society, Adam Mickiewicz University, Poznan, Poland, September 2001

Opening up the black box of marine phototroph-heterotroph interactions

Although marine microorganisms drive the major biogeochemical cycles in marine ecosystems, there is a dearth of information on interactions between phototrophic and heterotrophic organisms co-occurring in oceanic waters. The aim of this project was to study these interactions using Synechococcus sp. as the model phototroph – a cosmopolitan and highly abundant member of the picophytoplankton. Heterotrophic bacteria most-frequently present in non-axenic Synechococcus sp. cultures, were identified by PCR screening using primers targeting the 16S rRNA gene. Members of the Nitratireductor, Rhodobacteraceae, Muricauda and Phyllobacteriacae genera were present in more than half of all the cultures tested (Chapter 3). Using a member of the Rhodobacteraceae as the model heterotroph, specific metabolites present in axenic cultures and co-cultures were analysed (Chapter 4). Much lower concentrations of these specific metabolites were present in the milieu of Synechococcus – Roseobacter co-cultures compared to axenic Synechococcus cultures as discovered by LC-MS. Natural product database searches suggest that these may be a group of novel compounds. A Synechococcus sp. WH7803 null mutant in the gene encoding a type III polyketide synthase was constructed (Chapter 5). A targeted exometabolomic analysis showed a decreased production of the metabolites identified above in the mutant strain compared to the wild type. Growth was considerably affected in the T3 PKS mutant and T3 PKS mutant culture supernatants had a stronger negative growth effect on a range of picocyanobacteria and green algal species than the wild type extract. Further research is required to establish the precise biological function of the observed molecules, their biosynthetic pathway and their function in the natural environment. Improving our understanding of interactions between environmentally important microorganisms not only helps us to learn more about how biogeochemical cycles in the ocean function, but can also provide new natural products for use in the pharmaceutical industry

Autotrophic Picoplankton: Their Presence and Significance in Marine and Freshwater Ecosystems

Invited lecture: Autotrophic Picoplankton Workshop, 52nd Congress of the Polish Botanical Society, Adam Mickiewicz University, Poznan, Poland, September 2001

The need to account for cell biology in characterizing predatory mixotrophs in aquatic environments

Photosynthesis in eukaryotes first arose through phagocytotic processes wherein an engulfed cyanobacterium was not digested, but instead became a permanent organelle. Other photosynthetic lineages then arose when eukaryotic cells engulfed other already photosynthetic eukaryotic cells. Some of the resulting lineages subsequently lost their ability for phagocytosis, while many others maintained the ability to do both processes. These mixotrophic taxa have more complicated ecological roles, in that they are both primary producers and consumers that can shift more towards producing the organic matter that forms the base of aquatic food chains, or towards respiring and releasing CO2. We still have much to learn about which taxa are predatory mixotrophs as well as about the physiological consequences of this lifestyle, in part, because much of the diversity of unicellular eukaryotes in aquatic ecosystems remains uncultured. Here, we discuss existing methods for studying predatory mixotrophs, their individual biases, and how single-cell approaches can enhance knowledge of these important taxa. The question remains what the gold standard should be for assigning a mixotrophic status to ill-characterized or uncultured taxa—a status that dictates how organisms are incorporated into carbon cycle models and how their ecosystem roles may shift in future lakes and oceans

Dependence of the Cyanobacterium Prochlorococcus on Hydrogen Peroxide Scavenging Microbes for Growth at the Ocean's Surface

The phytoplankton community in the oligotrophic open ocean is numerically dominated by the cyanobacterium Prochlorococcus, accounting for approximately half of all photosynthesis. In the illuminated euphotic zone where Prochlorococcus grows, reactive oxygen species are continuously generated via photochemical reactions with dissolved organic matter. However, Prochlorococcus genomes lack catalase and additional protective mechanisms common in other aerobes, and this genus is highly susceptible to oxidative damage from hydrogen peroxide (HOOH). In this study we showed that the extant microbial community plays a vital, previously unrecognized role in cross-protecting Prochlorococcus from oxidative damage in the surface mixed layer of the oligotrophic ocean. Microbes are the primary HOOH sink in marine systems, and in the absence of the microbial community, surface waters in the Atlantic and Pacific Ocean accumulated HOOH to concentrations that were lethal for Prochlorococcus cultures. In laboratory experiments with the marine heterotroph Alteromonas sp., serving as a proxy for the natural community of HOOH-degrading microbes, bacterial depletion of HOOH from the extracellular milieu prevented oxidative damage to the cell envelope and photosystems of co-cultured Prochlorococcus, and facilitated the growth of Prochlorococcus at ecologically-relevant cell concentrations. Curiously, the more recently evolved lineages of Prochlorococcus that exploit the surface mixed layer niche were also the most sensitive to HOOH. The genomic streamlining of these evolved lineages during adaptation to the high-light exposed upper euphotic zone thus appears to be coincident with an acquired dependency on the extant HOOH-consuming community. These results underscore the importance of (indirect) biotic interactions in establishing niche boundaries, and highlight the impacts that community-level responses to stress may have in the ecological and evolutionary outcomes for co-existing species

Physiological characterization of \u3ci\u3eProchlorococcus\u3c/i\u3e under abiotic stressors temperature and hydrogen peroxide

Cyanobacteria of the genus Prochlorococcus are the smallest and most abundant phytoplankters in the ocean. Temperature is a major influence on Prochlorococcus abundance and distribution in the ocean, but the physiological basis for this relationship is not well understood. In other microbes, lipid and fatty acid composition have been shown to be influenced by temperature, and temperature has also been proposed as a relevant factor for setting the elemental allocation in marine phytoplankton. In this study, we found that percentage of fatty acids unsaturation was negatively related with temperature in some Prochlorococcus strains, but this was not universal. Temperature had a significant linear positive effect on nitrogen and carbon cell quotas across all strains. As temperature increased 10˚C, nitrogen and carbon quotas rose by 40.0% and 34.6%, respectively. Individual strains displayed negative relationships between growth rate and phosphorus quota. Studies in other photosynthetic organisms suggested that HOOH and temperature extremes act together as stressors. Importantly, it also has been shown that Prochlorococcus is highly susceptible to hydrogen peroxide (HOOH) and co-occurring heterotrophs such as Alteromonas sp. facilitate the growth of Prochlorococcus at the ocean surface by scavenging HOOH. To address the potential synergistic effects of temperature and HOOH on Prochlorococcus, we monitored the growth of environmental-relevant concentrations of cold-adapted (MED4) and warm-adapted (MIT9312) Prochlorococcus strains with different initial concentrations of HOOH under a range of temperatures. While not impacting the temperature optima for growth, higher concentrations of HOOH severely diminished the permissive temperature range for growth of both Prochlorococcus strains. At the permissive temperatures, the growth rates of both Prochlorococcus strains decreased as a function of HOOH, and temperature extremes increased susceptibility of photosystem II to HOOH-mediated damage. While these effects were manifest in both strains, they were more pronounced in the warm-adapted strain. Heterotrophic bacteria, serving as a proxy for the natural community, increased the Prochlorococcus growth rate under these temperatures and increased the growth temperature range (MED4), and this was attributed in part to their ability to remove HOOH from the medium

Picoplancton de l'Océan Atlantique Nord-Ouest : diversité et structure des communautés eucaryotes

Le picoplancton inclut des organismes dont la taille varie entre 0.2 et 3 μm, comprenant des cyanobactéries, ainsi qu’une grande diversité d’eucaryotes dont l’écologie et la diversité sont peu connues. Ces deux composantes assurent une part importante de la fixation du carbone dans les océans en contribuant de manière significative à la biomasse et à la production primaire. L’objectif de cette thèse a été d’appréhender l’importance relative des espèces picoeucaryotiques autotrophes et hétérotrophes. L’étude a porté sur des échantillons de surface et du maximum de chlorophylle sub-surface prélevés dans le golfe du Maine (Juillet 2010) et le plateau Néo-Écossais (Avril et Octobre 2009). La combinaison de plusieurs techniques moléculaires (banques de clones, pyroséquençage), de plusieurs approches (gène structural 18S ARNr, gène fonctionnel psbA codant pour la proteine D1 du photosystème II), ainsi que la comparaison de l’ADNr vs ARNr ont été appliqués. Il apparait que les picoeucaryotes forment une communauté dynamique avec des assemblages distincts, entre les communautés issues des efflorescences printanières vs conditions automnales, ainsi qu’entre régions proches des côtes vs au large. Les différences de distribution, de composition taxonomique et de structure sont associées à des changements hydrographiques, où la température (qui influence fortement la stratification) semble jouer un rôle majeur. L’étude de la composition taxonomique des picoeucaryotes autotrophes souligne la diversité des haptophytes et l’abondance relative des Mamiellophyceae (Chlorophyta). La diversité au sein des flagellés hétérotrophes montre une variabilité dans le temps pour certains taxons (Choanoflagellates, MAST-1, -4, -7) alors que d’autres persistent. La comparaison ADNr/ARNr a permis d’obtenir une vision d’ensemble sur l’état des communautés et clarifie les potentialités de ces approches.Picoplankton includes planktonic microbes ranging from 0.2 to 3 μm in diameter. Among photosynthetic groups are cyanobacteria, and microbial eukaryotes whose ecology and diversity are poorly known. These picophytoplankton contribute significantly to oceanic carbon fixation and primary production. The objective of this thesis was to investigate the relative importance of autotrophic plankton along with heterotrophic picoeukaryotes. The study focused on samples of surface and subsurface chlorophyll maximum collected in the Gulf of Maine (July 2010) and the Scotian Shelf (April and October 2009). The combination of molecular techniques clone libraries and pyrosequencing, targeting 18S rRNA genes and transcripts as well as the functional gene psbA, which codes for a protein D1 of photosystem II were used. It was apparent that the picoeukaryotes are dynamic communities with distinct assemblages during the spring blooms compared to late summer - autumn conditions, and between regions near shore vs offshore. Differences in distribution, species composition and community structure were associated with hydrographic changes, where the temperature, which strongly influences the stratification, seemed to play a major role. Overall the study revealed the diversity of haptophytes and the high relative abundance of Mamiellophyceae (Chlorophyta). Heterotrophic flagellates varied over time for some taxa (Choanoflagellates, MAST-1, -4, -7) while others persisted. Comparisons between rRNA genes rRNA provided a new perspection on the status of communities and highlighted the potential of using both approachesto describe the state of the ecosystem