Stefanie Moorthi

Defining DNA-Based Operational Taxonomic Units for Microbial-Eukaryote Ecology

ABSTRACT DNA sequence information has increasingly been used in ecological research on microbial eukaryotes. Sequence-based approaches have included studies of the total diversity of selected ecosystems, studies of the autecology of ecologically relevant species, and identification and enumeration of species of interest for human health. It is still uncommon, however, to delineate protistan species based on their genetic signatures. The reluctance to assign species-level designations based on DNA sequences is in part a consequence of the limited amount of sequence information presently available for many free-living microbial eukaryotes and in part a consequence of the problematic nature of and debate surrounding the microbial species concept. Despite the difficulties inherent in assigning species names to DNA sequences, there is a growing need to attach meaning to the burgeoning amount of sequence information entering the literature, and there is a growing desire to apply this information in ecological studies. We describe a computer-based tool that assigns DNA sequences from environmental databases to operational taxonomic units at approximately species-level distinctions. This approach provides a practical method for ecological studies of microbial eukaryotes (primarily protists) by enabling semiautomated analysis of large numbers of samples spanning great taxonomic breadth. Derivation of the algorithm was based on an analysis of complete small-subunit (18S) rRNA gene sequences and partial gene sequences obtained from the GenBank database for morphologically described protistan species. The program was tested using environmental 18S rRNA data sets for two oceanic ecosystems. A total of 388 operational taxonomic units were observed for 2,207 sequences obtained from samples collected in the western North Atlantic and eastern North Pacific oceans.

Chapter 1 - Hutchinson Reversed, or Why There Need to Be So Many Species

Summary There is compelling evidence for dispersal limitation among microscopic organisms, including phyto- and zooplankton, especially from studies addressing spatial patterns in taxon richness. This evidence is not in conflict with the widely accepted importance of strong local interactions in the plankton. However, the simultaneous importance of dispersal limitation and strong local interactions can only be understood when taking high temporal turnover rates into account. Current observational and experimental evidence suggests that biodiversity–ecosystem functioning (B–EF) relationships do not differ systematically from those known from higher organisms. Plankton communities are not saturated by default. Although the pelagial has little spatial structure, it is rich in environmental dimensionality when considering the dimensionality in time and chemical and physical properties, resulting in complex biotic interactions. We propose a conceptual model explaining B–EF effects in plankton, which contrasts environmental dimensionality with trait dimensionality of the community. This model, which is applicable to ecological communities in general, predicts that positive B–EF relationships depend on sufficient environmental dimensionality. We show how this model can be applied to understand B–EF relationships along gradients of productivity and stoichiometry. Our major conclusions are that local community dynamics of plankton communities may be better understood when putting them into a wider spatial context, that is, considering regional species pools. Moreover, the framework of environmental and trait dimensionality can be used to make concise predictions for the occurrence and strength of B–EF relationships.

Phylogenetic affiliations of mesopelagic acantharia and acantharian-like environmental 18S rRNA genes off the southern California coast.

Incomplete knowledge of acantharian life cycles has hampered their study and limited our understanding of their role in the vertical flux of carbon and strontium. Molecular tools can help identify enigmatic life stages and offer insights into aspects of acantharian biology and evolution. We inferred the phylogenetic position of acantharian sequences from shallow water, as well as acantharian-like clone sequences from 500 and 880 m in the San Pedro Channel, California. The analyses included validated acantharian and polycystine sequences from public databases with environmental clone sequences related to acantharia and used Bayesian inference methods. Our analysis demonstrated strong support for two branches of unidentified organisms that are closely related to, but possibly distinct from the Acantharea. We also found evidence of acantharian sequences from mesopelagic environments branching within the chaunacanthid clade, although the morphology of these organisms is presently unknown. HRP-conjugated probes were developed to target Acantharea and phylotypes from Unidentified Clade 1 using Catalyzed Reporter Deposition Fluorescence In Situ Hybridization (CARD-FISH) on samples collected at 500 m. Our CARD-FISH experiments targeting phylotypes from an unidentified clade offer preliminary glimpses into the morphology of these protists, while a morphology for the aphotic acantharian lineages remains unknown at this time.

Human Assisted Robotic Team Campaigns for Aquatic Monitoring

Large-scale environmental sensing, e.g., understanding microbial processes in an aquatic ecosystem, requires coordination across a multidisciplinary team of experts working closely with a robotic sensing and sampling system. We describe a human-robot team that conducted an aquatic sampling campaign in Lake Fulmor, San Jacinto Mountains Reserve, California during three consecutive site visits (May 9–11, June 19–22, and August 28–31, 2006). The goal of the campaign was to study the behavior of phytoplankton in the lake and their relationship to the underlying physical, chemical, and biological parameters. Phytoplankton form the largest source of oxygen and the foundation of the food web in most aquatic ecosystems. The reported campaign consisted of three system deployments spanning four months. The robotic system consisted of two subsystems—NAMOS (networked aquatic microbial observing systems) comprised of a robotic boat and static buoys, and NIMS-RD (rapidly deployable networked infomechanical systems) comprised of an infrastructure-supported tethered robotic system capable of high-resolution sampling in a two-dimensional cross section (vertical plane) of the lake. The multidisciplinary human team consisted of 25 investigators from robotics, computer science, engineering, biology, and statistics.We describe the lake profiling campaign requirements, the robotic systems assisted by a human team to perform high fidelity sampling, and the sensing devices used during the campaign to observe several environmental parameters. We discuss measures taken to ensure system robustness and quality of the collected data. Finally, we present an analysis of the data collected by iteratively adapting our experiment design to the observations in the sampled environment. We conclude with the plans for future deployments.

Prey diversity effects on ecosystem functioning depend on consumer identity and prey composition

Consumer diversity effects on ecosystem functioning are highly context dependent and are determined by consumer specialization and other consumer and prey specific traits such as growth and grazing rates. Despite complex reciprocal interactions between consumers and their prey, few experimental studies have focused on prey diversity effects on consumer dynamics and trophic transfer. In microbial microcosms, we investigated effects of algal prey diversity (one, two and four species) on the production, evenness and grazing rates of 4 ciliate consumers, differing in grazing preferences and rates. Prey diversity increased prey biovolume in the absence of consumers and had opposing effects on different consumers, depending on their specialization and their preferred prey. Consumers profited from prey mixtures compared to monocultures of non-preferred prey, but responded negatively if preferred prey species were offered together with other species. Prey diversity increased consumer evenness by preventing dominance of specific consumers, demonstrating that the loss of prey species may have cascading effects resulting in reduced consumer diversity. Our study emphasizes that not only the degree of specialization but also the selectivity for certain prey species within the dietary niche may alter the consequences of changing prey diversity in a food web context.