Bacterial influence on the bloom dynamics of the Dinoflagellate Lingulodinium polyedrum

Algal blooms, particularly those dominated by dinoflagellates, are widespread in marine ecosystems and can have devastating ocean and human health impacts. The factors that lead to their demise are not well characterized but are thought to include a combination of physical, chemical, and biological factors. Previous studies have isolated bacteria that kill dinoflagellates in laboratory experiments, but little is known about the impact that such algicidal bacteria exert on natural blooms. In this dissertation, I investigated the possibility that algicidal bacteria can impact the population dynamics of the dinoflagellate Lingulodinium polyedrum, a species that causes large and long-lived blooms off the coast of Southern California. I used a combination of laboratory experiments and field sampling to try to link knowledge about model systems in controlled experiments with the complex world of natural blooms in the environment. Chapter one is a review of the current knowledge about the impact of algicidal bacteria in the sea. In chapter two, I report the isolation of algicidal bacteria that induced the formation of temporary cysts in L. polyedrum laboratory cultures as a probable defense mechanism against bacterial colonization. In chapter three, I report bacterial colonization intensities in various L. polyedrum cultures and in two natural blooms, suggesting a relationship between algal population dynamics and bacterial colonization intensity. In chapter four, I report a novel interaction of algicidal bacteria on L. polyedrum motility mediated by excreted putative proteases, and describe decreased motility at the end of an L. polyedrum bloom, suggesting algal cells were unhealthy before bloom decline. In chapter five, I report the novel cultivation of a globally widespread and abundant marine bacterium from the Roseobacter group that killed L. polyedrum cultures by attachment. Using species-specific DNA probes, I studied the colonization of this bacterium on L. polyedrum cells in a natural bloom and found increased colonization during the bloom decline phase, suggesting a direct effect of this algicidal bacterium on bloom dynamics

Metabolic Interactions Between Bacteria and Phytoplankton

The cycling of energy and elements in aquatic environments is controlled by the interaction of autotrophic and heterotrophic processes. In surface waters of lakes, rivers, and oceans, photosynthetic microalgae and cyanobacteria fix carbon dioxide into organic matter that is then metabolized by heterotrophic bacteria (and perhaps archaea). Nutrients are remineralized by heterotrophic processes and subsequently enable phototrophs to grow. The organisms that comprise these two major ecological guilds are numerous in both numbers and in their genetic diversity, leading to a vast array of physiological and chemical responses to their environment and to each other. Interactions between bacteria and phytoplankton range from obligate to facultative, as well as from mutualistic to parasitic, and can be mediated by cell-to-cell attachment or through the release of chemicals. The contributions to this Research Topic investigate direct or indirect interactions between bacteria and phytoplankton using chemical, physiological, and/or genetic approaches. Topics include nutrient and vitamin acquisition, algal pathogenesis, microbial community structure during algal blooms or in algal aquaculture ponds, cell-cell interactions, chemical exudation, signaling molecules, and nitrogen exchange. These studies span true symbiosis where the interaction is evolutionarily derived, as well as those of indirect interactions such as bacterial incorporation of phytoplankton-produced organic matter and man-made synthetic symbiosis/synthetic mutualism

Cultivation and Ecosystem Role of a Marine Roseobacter Clade-Affiliated Cluster Bacterium▿

Isolation and cultivation are a crucial step in elucidating the physiology, biogeochemistry, and ecosystem role of microorganisms. Many abundant marine bacteria, including the widespread Roseobacter clade-affiliated (RCA) cluster group, have not been cultured with traditional methods. Using novel techniques of cocultivation with algal cultures, we have accomplished successful isolation and propagation of a strain of the RCA cluster. Our experiments revealed that, in addition to growing on alga-excreted organic matter, additions of washed bacterial cells led to significant biomass decrease of dinoflagellate cultures as measured by in vivo fluorescence. Bacterial filtrate did not adversely affect the algal cultures, suggesting attachment-mediated activity. Using an RCA cluster-specific rRNA probe, we documented increasing attachment of these algicidal bacteria during a dinoflagellate bloom, with a maximum of 70% of the algal cells colonized just prior to bloom termination. Cross-correlation analyses between algal abundances and RCA bacterial colonization were statistically significant, in agreement with predator-prey models suggesting that RCA cluster bacteria caused algal bloom decline. Further investigation of molecular databases revealed that RCA cluster bacteria were numerically abundant during algal blooms sampled worldwide. Our findings suggest that the widespread RCA cluster bacteria may exert significant control over phytoplankton biomass and community structure in the oceans. We also suggest that coculture with phytoplankton may be a useful strategy to isolate and successfully grow previously uncultured but ecologically abundant marine heterotrophs

Influence of Light on Particulate Organic Matter Utilization by Attached and Free-Living Marine Bacteria

Light plays a central role on primary productivity of aquatic systems. Yet, its potential impact on the degradation of photosynthetically produced biomass is not well understood. We investigated the patterns of light-induced particle breakdown and bacterial assimilation of detrital C and N using 13C and 15N labeled freeze-thawed diatom cells incubated in laboratory microcosms with a marine microbial community freshly collected from the Pacific Ocean. Particles incubated in the dark resulted in increased bacterial counts and dissolved organic carbon concentrations compared to those incubated in the light. Light also influenced the attached and free-living microbial community structure as detected by 16S rRNA gene amplicon sequencing. For example, Sphingobacteriia were enriched on dark-incubated particles and taxa from the family Flavobacteriaceae and the genus Pseudoalteromonas were numerically enriched on particles in the light. Isotope incorporation analysis by phylogenetic microarray and NanoSIMS (a method called Chip-SIP) identified free-living and attached microbial taxa able to incorporate N and C from the particles. Some taxa, including members of the Flavobacteriaceae and Cryomorphaceae, exhibited increased isotope incorporation in the light, suggesting the use of photoheterotrophic metabolisms. In contrast, some members of Oceanospirillales and Rhodospirillales showed decreased isotope incorporation in the light, suggesting that their heterotrophic metabolism, particularly when occurring on particles, might increase at night or may be inhibited by sunlight. These results show that light influences particle degradation and C and N incorporation by attached bacteria, suggesting that the transfer between particulate and free-living phases are likely affected by external factors that change with the light regime, such as time of day, water column depth and season.Work performed by XM and PW was funded by the United States Department of Energy’s Office of Biological and Environmental Research Biofuels Science Focus Area Grant SCW1039, and work at LLNL was performed under the auspices of the United States Department of Energy at the Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344. LG-C was funded by the Marie Curie Actions–International Outgoing Fellowships (project 253970) and the United States National Science Foundation grant OCE1335269.Peer reviewe

Phylogenetic Patterns in the Microbial Response to Resource Availability: Amino Acid Incorporation in San Francisco Bay

<div><p>Aquatic microorganisms are typically identified as either oligotrophic or copiotrophic, representing trophic strategies adapted to low or high nutrient concentrations, respectively. Here, we sought to take steps towards identifying these and additional adaptations to nutrient availability with a quantitative analysis of microbial resource use in mixed communities. We incubated an estuarine microbial community with stable isotope labeled amino acids (AAs) at concentrations spanning three orders of magnitude, followed by taxon-specific quantitation of isotopic incorporation using NanoSIMS analysis of high-density microarrays. The resulting data revealed that trophic response to AA availability falls along a continuum between copiotrophy and oligotrophy, and high and low activity. To illustrate strategies along this continuum more simply, we statistically categorized microbial taxa among three trophic types, based on their incorporation responses to increasing resource concentration. The data indicated that taxa with copiotrophic-like resource use were not necessarily the most active, and taxa with oligotrophic-like resource use were not always the least active. Two of the trophic strategies were not randomly distributed throughout a 16S rDNA phylogeny, suggesting they are under selective pressure in this ecosystem and that a link exists between evolutionary relatedness and substrate affinity. The diversity of strategies to adapt to differences in resource availability highlights the need to expand our understanding of microbial interactions with organic matter in order to better predict microbial responses to a changing environment.</p></div

Pairwise comparisons of isotopic incorporation of ¹⁵N labeled AAs by 107 16S rRNA phylotypes from SF Bay at two concentrations (high, 5 micromolar and low, 50 nanomolar).

<p>Each data point represents the HCE (hybridization corrected enrichment) for a probe set (the slope of delta permil divided by fluorescence). Error bars indicate two standard errors of the slope calculation. The black line represents the linear regression and the blue the 1 to l line.</p

Bacterial response to spatial gradients of algal-derived nutrients in a porous microplate

Photosynthetic microalgae are responsible for 50% of the global atmospheric CO2 fixation into organic matter and hold potential as a renewable bioenergy source. Their metabolic interactions with the surrounding microbial community (the algal microbiome) play critical roles in carbon cycling, but due to methodological limitations, it has been challenging to examine how community development is influenced by spatial proximity to their algal host. Here we introduce a copolymer-based porous microplate to co-culture algae and bacteria, where metabolites are constantly exchanged between the microorganisms while maintaining physical separation. In the microplate, we found that the diatom Phaeodactylum tricornutum accumulated to cell abundances ~20 fold higher than under normal batch conditions due to constant replenishment of nutrients through the porous structure. We also demonstrate that algal-associated bacteria, both single isolates and complex communities, responded to inorganic nutrients away from their host as well as organic nutrients originating from the algae in a spatially predictable manner. These experimental findings coupled with a mathematical model suggest that host proximity and algal culture growth phase impact bacterial community development in a taxon-specific manner through organic and inorganic nutrient availability. Our novel system presents a useful tool to investigate universal metabolic interactions between microbes in aquatic ecosystems

Identification of Effector Metabolites Using Exometabolite Profiling of Diverse Microalgae.

Dissolved exometabolites mediate algal interactions in aquatic ecosystems, but microalgal exometabolomes remain understudied. We conducted an untargeted metabolomic analysis of nonpolar exometabolites exuded from four phylogenetically and ecologically diverse eukaryotic microalgal strains grown in the laboratory, freshwater Chlamydomonas reinhardtii, brackish Desmodesmus sp., marine Phaeodactylum tricornutum, and marine Microchloropsis salina, to identify released metabolites based on relative enrichment in the exometabolomes compared to cell pellet metabolomes. Exudates from the different taxa were distinct, but we did not observe clear phylogenetic patterns. We used feature-based molecular networking to explore the identities of these metabolites, revealing several distinct di- and tripeptides secreted by each of the algae, lumichrome, a compound that is known to be involved in plant growth and bacterial quorum sensing, and novel prostaglandin-like compounds. We further investigated the impacts of exogenous additions of eight compounds selected based on exometabolome enrichment on algal growth. Of these compounds, five (lumichrome, 5'-S-methyl-5'-thioadenosine, 17-phenyl trinor prostaglandin A2, dodecanedioic acid, and aleuritic acid) impacted growth in at least one of the algal cultures. Two of these compounds (dodecanedioic acid and aleuritic acid) produced contrasting results, increasing growth in some algae and decreasing growth in others. Together, our results reveal new groups of microalgal exometabolites, some of which could alter algal growth when provided exogenously, suggesting potential roles in allelopathy and algal interactions. IMPORTANCE Microalgae are responsible for nearly half of primary production on earth and play an important role in global biogeochemical cycling as well as in a range of industrial applications. Algal exometabolites are important mediators of algal-algal and algal-bacterial interactions that ultimately affect algal growth and physiology. In this study, we characterize exometabolomes across marine and freshwater algae to gain insights into the diverse metabolites they release into their environments ("exudates"). We observe that while phylogeny can play a role in exometabolome content, environmental conditions or habitat origin (freshwater versus marine) are also important. We also find that several of these compounds can influence algal growth (as measured by chlorophyll production) when provided exogenously, highlighting the importance of characterization of these novel compounds and their role in microalgal ecophysiology