Current Projects

UKRI/BBSRC-NSF/BIO: The evolutionary transition of host-microbe interactions from commensal symbionts to blood parasites. (NSF IOS2422697)

Apicomplexans include the deadliest eukaryotic pathogens on the planet and have long been assumed to be a parasitic group of organisms that only live within host cells.  The story has become more complex, however, with lineages of ‘exceptions’ discovered that challenge the interpretation of a single ancient development of parasitism. One such group is the Nephromycidae, which live inside their host without invading cells and have been shown to be related to the important blood parasites such as the causative agent of malaria. Despite their lifestyle, Nephromyces still features the typical apicomplexan cellular invasion machinery—the apical complex. Nephromyces, therefore, provides an opportunity to understand the ancestral state that served as a platform for the development of major blood pathogens of humans and animals. The research will use a combination of cutting-edge microscopy and genomics to compare the invasion machinery between related virulent pathogens and mutualistic members of Apicomplexa to identify critical elements of pathogen cell invasion.

PurSUiT: Untangling a clade of inter-dependent apicomplexans and their bacterial endosymbionts. (NSF DEB2231583)

Symbiosis has repeatedly given rise to evolutionary innovation across the tree of life. Apicomplexans, including the causative agent of malaria, are the deadliest eukaryotic parasites on the planet. However, in one lineage of apicomplexans, taking on bacterial endosymbionts has not only enabled an escape from a parasitic lifestyle, but caused a massive radiation of species. This project aims to both characterize the diversity of these species and understand the interactions between host and symbiont that turned a parasite into harmless inhabitant. This work will benefit society by advancing understanding of the diversity and contribution of eukaryotes to metabolic function of the planet’s biota, with results that will be disseminated through peer-reviewed literature, and presentations for scientific and lay audiences. The research will also be communicated through a workshop for professional scientific journalists, focusing on molecular advances and our current understanding of Earth’s biodiversity.
The aims of this PurSUiT proposal will work in concert to untangle the various biological entities that make up the Nephromyces community, across six species of tunicates. Next generation DNA sequencing will be used to determine the diversity of the community, then employ single cell isolation techniques to capture, image and describe individual Nephromyces species and their bacterial endosymbionts. Using fluorescent in situ hybridization labels, the different life stages of each species will be collected and photo-documented for the full life history. At least 10 Nephromyces species from each of the six tunicate species will be formally named, as well as their bacterial endosymbionts to the extent possible under the evolving prokaryotic Code of Nomenclature. From existing genomic data, cutting edge techniques will be employed to determine whether genes have been laterally transferred from endosymbiont to host.

Completed Projects

Comparative genomics of a unique mutualistic apicomplexan (NIH Grant AI124092)

Apicomplexa is a group of unicellular organisms that has been long been considered an exclusively parasitic clade. There are many ecologically and medically important apicomplexans, including the causative agent of malaria. However, recent evidence has revealed one group of mutualistic apicomplexans: the marine symbiont genus, Nephromyces. Nephromyces are unusual apicomplexans in many ways. First, members of this genus are found exclusively inside one family of sea squirts, where they colonize a large, ductless organ, the renal sac. Within this organ, Nephromyces surround urate and calcium oxalate deposits. Second, unusually for apicomplexans, Nephromyces cells contain intracellular bacteria. This mutualistic apicomplexan offers a singular opportunity to address the important question about apicomplexan biology. With a long-term goal of completely characterizing this system, here we propose to focus on comparing the Nephromyces genome to its closest relative, the parasitic genus, Cardiosporidium. Members of Cardiosporidium parasitize a broad range of sea squirts yet, like Nephromyces, also contain endosymbiotic bacteria. The genomes of the bacteria inhabiting both Nephromyces and Cardiosporidium will also be sequenced. Data generation will have an emphasis on the hypothesis that the bacterial symbionts may provide key metabolic functions in the evolution of this mutualism. The genome sequences from these organisms will provide a stepping-stone for cytological, microscopy and functional genomic research. Understanding the genomic signatures of lifestyle transitions in Apicomplexa will have significant impact on determining which, as yet under appreciated, genomic features are correlated with virulence and parasitism.

Bringing the SAR clade into a modern genomic context (NSF award #1541510)

The bulk of eukaryotic diversity is microbial and, when compared to plants, animals and fungi, much of this microbial diversity has been undersampled from the standpoint of morphological, phylogenetic and genomic data. This skew in data not only has consequences for our understanding of the biodiversity of eukaryotic life on Earth, but also how we interpret cellular and evolutionary biology in the broadest sense. One of the most diverse major clades of eukaryotes that has recently emerged from phylogenomic analyses united the Stramenopila, Alveolata and Rhizaria into the ‘SAR’ group. Initially this clade was controversial because it forced a re-evaluation of the evolution of several characters, most notably the spread of photosynthesis across eukaryotes. However, additional data have robustly supported SAR as an independent clade. Among the diverse lineages within SAR, genomic-scale data are rare and concentrated in only a few areas, Apicomplexa (e.g. malarial parasites), omycetes (e.g. parasite ‘water molds’) and diatoms (e.g. ecologically important phytoplankton). Despite their global ecological importance, fewer than 50% of all SAR clades, and only one third of non-photosynthetic SAR clades, are represented by even a single genome in public databases. This work will add at least 250 novel genomic-scale datasets (transcriptomes, draft genomes, single-cell amplified genomes), focused primarily on capturing diversity within SAR.

Red Algal Adelphoparasites (NSF award #1257472)

Red algal parasites are ideal model organisms for investigating the origins of a parasitic life-style for two important reasons. First, most red algal parasites share an immediate common ancestor with an extant free-living red algal species, which is almost always their host, earning them the title adelphoparasites (adelphose is the Greek term for “kin”). Because of this sister-species relationship between parasite and host, a single pair of organisms can provide direct comparative data on the cellular and genomic changes occurring early in the evolution of a parasite, as well as information on host/parasite co-evolutionary dynamics. Second, hundreds of independently evolved red algal parasites have been described, all with varying degrees of divergence and relationship with their hosts, providing an enormous amount of comparative data with which to test mechanistic hypotheses. Red algal parasites have an unusual infection mechanism, whereby the unit of infection is the DNA-containing organelles of the parasite, rather than the entire organism. Because of this strange life history, this system further lends itself to understanding the principles behind such evolutionarily and medically relevant issues as the co-existence of two genomes in a cell (as in many endosymbioses) and the break down of self recognition factors, which are important in autoimmune diseases and the spread of cancer. Therefore, establishing red algal parasites as a model system for genomic study will produce broad-reaching data for years to come.

How does parasitism evolve at the lineage level?

Oomycetes are water moulds, rusts and plant pathogens that were once regarded as true fungi, but are now recognized to be members of the stramenopiles (also called heterokonts): a diverse lineage including both photosynthetic and non-photosynthetic members. In molecular phylogenies, a pattern of increasing virulence is apparent across the evolution of oomycetes. Early diverging members of the lineage are free-living saprobic decomposers, whereas species that diverge in the middle of the tree are mostly facultative pathogens. What the group is best known for, organisms like Phytophthora spp. that caused the Irish potato famine and Sudden Oak Death today, and obligate parasites that have evolved most recently. In collaboration with Dr. Craig Bailey (UNC Wilmington), we are investigating how parasitism evolved in the oomycete lineage, using a comparative genomic approach.

The Bermuda Seaweed Project (NSF award #1120652)

In collaboration with Dr. Craig Schneider (Trinity College), the Lane lab is also involved in The Bermuda Seaweed Project, located in Bermuda. The islands of Bermuda are ideally located for marine biodiversity assessment studies, because the isolated archipelago is at the interface of tropical and warm temperate biogeographic zones. Despite its distant location from North America and its tropical summer temperatures, Bermuda’s small size at present supports only ca. 450 species of red, brown and green seaweeds, and endemism among these groups is reportedly less than 3%. The small size of the total flora make it possible to completely assess this archipelago’s algal diversity over a short time period; a project that would be near impossible for larger-sized, and more diversely populated, islands in the Caribbean. Additionally, based on work done by the Drs. Lane and Schneider over the last decade, a significant number of Bermuda’s algal species have already been shown to have misapplied misapplied binomials, based on European heterospecifics. Molecular assessment of all Bermuda species will both continue to uncover numerous cryptic species and identify cases of misnamed taxa, thereby increasing the level of endemisms in these islands and the accuracy of biodiversity assessments.

The Rhode Island Seaweed Project

During the 2012-2013 we will be additionally assessing the marine flora of Rhode Island as part of a joint RI STAC grant with Dr. Brian Wysor at Roger Williams University.