Distribution and Population Structure of the Invasive \u3ci\u3eNitellopsis obtusa\u3c/i\u3e (Desv. In Loisel.) J. Groves and Native Species of Characeae in the Northeast U.S.A.

Freshwater ecosystems are some of the most biologically diverse environments on Earth. Billions of humans rely on functioning freshwater ecosystems for drinking water and many other services. These ecosystems are increasingly threatened by human impacts including nutrient pollution, invasive species, and climate change. Here I contribute four research chapters that investigate freshwater diversity and ecosystem threats using the Characeae, a family of freshwater green macroalgae, as a study system. Characeae are a diverse and ancient group with more than 500 extant species and a fossil history spanning at least 250 million years. These algae are macrophytes in freshwater ecosystems, and serve important roles in stabilizing sediment, sequestering nutrients, and providing forage for fish and waterfowl. Although most Characeae are considered beneficial in freshwater ecosystems, one species, Nitellopsis obtusa (Desv. in Loisel.) J. Groves, has been identified as an invasive species in North America. In the first research chapter (Chapter 2) a systematic survey of 390 sites across New York state was conducted to discover new populations of Nitellopsis obtusa and confirm the known distribution of this invasive species. In the third chapter the survey was extended to include New England, for a total of 740 sites, from which species distribution models were constructed. These models demonstrated that water chemistry variables can predict Characeae habitat, and that species can be classified as specialist species, occurring in a narrow chemical niche, while others can be classified as generalist species that occur broadly across the region. Scenarios simulating increased nutrient pollution and future climate change were explored with some species predicted to increase in range and other species predicted to be extirpated from the region. Nitellopsis obtusa was found to be a hard water specialist, occurring at sites with elevated levels of calcium. Models found the niche of Nitellopsis obtusa similar to Chara contraria, a native species whose distribution can be used to identify sites that may be susceptible to Nitellopsis obtusa invasion. In the fourth chapter the fully sequenced and annotated organellar genomes of Nitellopsis obtusa are presented with an analysis of the genetic patterns of invasion. The chloroplast genome was more variable than the mitochondrial genome, and both genomes showed that samples in the invasive range were nearly identical, evidence of a single introduction event. Invasive samples clustered most closely but were not identical to samples from Western Europe, specifically France. Intra-individual polymorphism of the mitochondrial genome was detected and PacBio sequencing indicated that polymorphism likely arises from transfer of mitochondrial regions to the nuclear genome. In the fifth chapter a draft nuclear genome of Nitellopsis obtusa is presented and used to determine whether rapid adaptation in the invasive range gave rise to a more successful invasive genotype. The genome of Nitellopsis obtusa was estimated by kmer counting to be 2.5-5 Gb. A highly fragmented assembly of 2.3Gb was achieved. Double digest restriction site associated DNA sequencing (ddRAD) of individuals across the native and invasive range was unable to detect a signal of differentiation in putative adaptive genes, possibly due to cross-contamination during the pooling step of library construction. The results of these studies provide insights relevant for freshwater conservation and invasive species outreach and management

Ubiquity or Not Ubiquity: That is the Question

The nature of population structure in eukaryotic microbes has been the subject of intense debate, but until recently the tools to test these hypotheses were either problematic (e.g., allozymes that cannot detect all genetic changes) or beyond financial and technological limits of most laboratories (e.g., high throughput sequencing). In a recent issue of Molecular Ecology, Craig et al. (2019) use a genomic approach to investigate the population structure of a model alga, the chlorophyte Chlamydomonas reinhardtii (Figure 1). Using high throughput sequencing, read mapping, and variant calling, they detected strong signals of differentiation at a continental scale, while local patterns of admixture were complex. Population genomic techniques such as these have not been used extensively in studies of microbial eukaryotes and the fields of conservation genetics and evolution stand to benefit vastly from the adoption of these techniques to studies of diverse protist lineages

Illuminating Protist Diversity in Pitcher Plants and Bromeliad Tanks

Many species of plants have evolved structures called phytotelmata that store water and trap detritus and prey. These structures house diverse communities of organisms, the inquiline microbiome, that aids breakdown of litter and prey. The invertebrate and bacterial food webs in these systems are well characterized, but less is known about microbial eukaryotic community dynamics. In this study we focus on microbes in the SAR clade (Stramenopila, Alveolata, Rhizaria) inhabiting phytotelmata. Using small subunit rDNA amplicon sequencing from repeated temporal and geographic samples of wild and cultivated plants across the Northeast U.S.A., we demonstrate that communities are variable within and between host plant type. Across habitats, communities from tropical bromeliads grown in a single room of a greenhouse were nearly as heterogeneous as wild pitcher plants spread across hundreds of kilometers. At the scale of pitcher plants in a single bog, analyses of samples from three time points suggest that seasonality is a major driver of protist community structure, with variable spring communities transitioning to more homogeneous communities that resemble the surrounding habitat. Our results indicate that protist communities in phytotelmata are variable, likely due to stochastic founder events and colonization/competition dynamics, leading to tremendous heterogeneity in inquiline microeukaryotic communities

Mapping localized surface plasmons within silver nanocubes using cathodoluminescence hyperspectral imaging

Localized surface plasmons within silver nanocubes less than 50 nm in size are investigated using high resolution cathodoluminescence hyperspectral imaging. Multivariate statistical analysis of the multidimensional luminescence dataset allows both the identification of distinct spectral features in the emission and the mapping of their spatial distribution. These results show a 490 nm peak emitted from the cube faces, with shorter wavelength luminescence coming from the vertices and edges; this provides direct experimental confirmation of theoretical predictions

Gene Expression Associated with Disease Resistance and Long-Term Growth in a Reef-Building Coral

Rampant coral disease, exacerbated by climate change and other anthropogenic stressors, threatens reefs worldwide, especially in the Caribbean. Physically isolated yet genetically connected reefs such as Flower Garden Banks National Marine Sanctuary (FGBNMS) may serve as potential refugia for degraded Caribbean reefs. However, little is known about the mechanisms and trade-offs of pathogen resistance in reef-building corals. Here, we measure pathogen resistance in Montastraea cavernosa from FGBNMS. We identified individual colonies that demonstrated resistance or susceptibility to Vibrio spp. in a controlled laboratory environment. Long-term growth patterns suggest no trade-off between disease resistance and calcification. Predictive (pre-exposure) gene expression highlights subtle differences between resistant and susceptible genets, encouraging future coral disease studies to investigate associations between resistance and replicative age and immune cell populations. Predictive gene expression associated with long-term growth underscores the role of transmembrane proteins involved in cell adhesion and cell-cell interactions, contributing to the growing body of knowledge surrounding genes that influence calcification in reef-building corals. Together these results demonstrate that coral genets from isolated sanctuaries such as FGBNMS can withstand pathogen challenges and potentially aid restoration efforts in degraded reefs. Furthermore, gene expression signatures associated with resistance and long-term growth help inform strategic assessment of coral health parameters

Crucial faith: the theology and ethics of H. Richard Niebuhr

The argument of this thesis is that H. Richard Niebuhr has produced a distinctive, indeed, unique theological crucis. Although Niebuhr never made this motif the explicit focus of his work, his writings, nonetheless, demonstrate a perennial reference to, and penetrating grasp of, the crucifixion and resurrection of Jesus Christ, as the defining events of the Christian gospel. After a short introduction to Niebuhr's life and work, and a brief discussion of that tradition which gives prominence to the theology of the cross (theologia crucis), an exposition and interpretation of Niebuhr's theologia crucis is carried out by means of six distinct, though interrelated perspectives: existential; evangelical; ethical; ecclesiological; ecumenical and eschatological. Despite his reluctance to present a full-blown dogmatics of systematics, I use these six perspectives to trace the contours of the coherent, yet largely, implicit theologia crucis that lied just below the surface of his corpus, so that my thesis may allow its form and content to crystallise more clearly in the mind's eye. Beginning with an existential exploration of Niebuhr's phenomenology of faith in terms of trust and loyalty, we are enabled to more fully apprehend the multi-faceted faithlessness of the social self-as exposed by the theologia crucis. In the next chapter, written from an evangelical perspective, we see how God in Christ has transformed the human situation by converting the various forms of faithlessness into that faithfulness which Niebuhr calls radical monotheism. Chapter three considers the ethical consequences of this faith-stance as depicted by Niebuhr in terms of response to the creative, governing and redemptive actions of God. Next, we analyse his ecclesiology, and see that this largely takes the form of a constructive critique in order to help clarify the mission of the ecclesia crucis

Exploring the Diversity of Microeukaryotic Communities in New England Tide Pools

Though historically understudied, due in large part to most species being uncultivable, microbial eukaryotes (i.e. protists) are abundant and widespread across diverse habitats. Recent advances in molecular techniques, including metabarcoding, allow for the characterization of poorly known protist lineages. This study surveys the diversity of SAR (Stramenopila, Alveolata, and Rhizaria), a major eukaryotic clade that is estimated to represent about half of all eukaryotic diversity. SAR lineages use varied metabolic strategies like mixotrophy in dinoflagellates (Alveolata), parasitism in apicomplexans (Alveolata) and labyrinthulids (Stramenopila), and life cycle stages that include encystment and attachment (e.g. in ciliates, Alveolata) to survive in highly dynamic habitats. Using metabarcoding primers designed specifically to target a portion of the 18S small subunit ribosomal RNA (SSU-rRNA) gene of SAR lineages, we compare protist community composition from tide pools in Acadia National Park, Maine, USA. We characterize over 500 lineages, here operational taxonomic units (OTUs), many of which are found abundant in the tide pool environment. We also find that communities vary by month sampled and exhibit patterns by size (i.e. macro-, micro-, and nano-sized). Taken together, these data allow us to further catalog protist diversity in extreme environments (e.g. those subject to extreme fluctuations in temperature and salinity during tidal cycles). Such data are critical in the explorations of biodiversity patterns among microorganisms on our rapidly changing planet

Testate Amoebae (Arcellinida, Amoebozoa) Community Diversity in New England Bogs and Fens Assessed through Lineage-Specific Amplicon Sequencing

Testate amoebae (order Arcellinida) are abundant in freshwater ecosystems, including low pH bogs and fens. Within these environments, Arcellinida are considered top predators in microbial food webs and their tests are useful bioindicators of paleoclimatic changes and anthropogenic pollutants. Accurate species identifications and characterizations of diversity are important for studies of paleoclimate, microbial ecology, and environmental change; however, morphological species definitions mask cryptic diversity, which is a common phenomenon among microbial eukaryotes. Lineage-specific primers recently designed to target Arcellinida for amplicon sequencing successfully captured a poorly-described yet diverse fraction of the microbial eukaryotic community. Here, we leveraged the application of these newly-designed primers to survey the diversity of Arcellinida in four low-pH New England bogs and fens, investigating variation among bogs (2018) and then across seasons and habitats within two bogs (2019). Three OTUs represented 66% of Arcellinida reads obtained across all habitats surveyed. 103 additional OTUs were present in lower abundance with some OTUs detected in only one sampling location, suggesting habitat specificity. By establishing a baseline for Arcellinida diversity, we provide a foundation to monitor key taxa in habitats that are predicted to change with increasing anthropogenic pressure and rapid climate change

First draft genome assembly of Coleochaete orbicularis

Comparative genomics of the embryophytes (land plants) provide basis to understand their divergence and adaptation to the terrestrial environment. The focus of the genome sequencing has been on the understanding of the patterns of genetic development and adaptation, particularly of the crop and some model species. Rapidly increased transcriptome sequencing effort and availability of the ample genetic marker data have allowed comparisons of early embryophytes and tracheophytes (vascular plants). The key to understand the deepest nodes requires the availability of the genomes and high-quality gene models from the early lineages of the streptophytes to understand the genomic synteny, gene duplication and losses as well as the diverged genes across the streptophytes, and in particular embryophytes. We present the first genome assembly of Coleochaete orbicularis and compare it also with the recently released genome of Chara braunii, another freshwater green alga.Peer reviewe

Assessment of COVID-19 in primary care: the identification of symptoms, signs, characteristics, comorbidities and clinical signs in adults which may indicate a higher risk of progression to severe disease

No abstract available