Environmental conditions, biotic interactions, dispersal and history have been suggested to be important processes influencing the spatial distribution of organisms and thus to affect community assembly. Understanding how these processes influence community assembly is important, particularly because community diversity and composition are suggested to be relevant for ecosystem functioning. Moreover, bacteria are strongly contributing to nutrient and carbon cycle. Bacteria are highly abundant and ubiquitous, and thus it is relevant to study how they are assembled. This thesis aims to gain insight on the role of these processes on aquatic bacterial community assembly, diversity and functioning. The studies included in this thesis involve transplant and microcosm experiments performed in the lab as well as manipulation experiments and field surveys in a natural rock pool systems. Bacterial community composition was addressed by analysis of 16S rRNA gene and community functioning by measuring bacterial production, community respiration and the ability to use different carbon substrates. This thesis highlights that species sorting is a very important assembly mechanism for bacterial communities, but also finds that other processes such as dispersal and history contribute to the patterns observed. Dispersal caused rescuing effects compensating for losses of diversity; at the same time it increased the similarity between communities. Moreover, bacteria have shown a high level of functional plasticity when colonizing a new locality. Interestingly, past environmental conditions explained the structure of bacterial communities better than present-day environmental conditions. Disturbances and biotic interactions are also important in the assembly of communities. Disturbance caused temporary shifts in bacterial function and changes in composition, the magnitude of which depended on the intensity and the frequency of the disturbance. However, natural aquatic bacterial communities showed quite high resilience capacities. Competition can shift the proportion of generalists and specialists species whereas predation or trophic interactions have been found to decrease diversity and to modify the importance of stochasticity. Both caused alterations of community functioning. Finally, this thesis shows that the diversity-functioning relationship is context dependent. Further research should be directed to understanding the intensity and direction of changes in composition and how this affects the functionality of bacterial communities

Thesis advisor: Heather Craig Olins / Microbes play a critical role in the Earth’s ecosystems, and freshwater microbial communities are underappreciated players in biogeochemical cycles. Vernal pools are ecologically important habitats that are particularly sensitive to global warming. Microbial communities in vernal pools and other freshwater wetlands are both critical to supporting life on Earth as well as incredibly vulnerable to climate change. This thesis describes for the first time microbial community composition in freshwater wetlands in Newton, Massachusetts. Beta diversity analysis reveals that sites host distinct microbial communities, something not always seen at these spatial scales. Sediment samples from the Bare Pond vernal pool were dominated by Acidobacteria, Actinobacteria, Alphaproteobacteria, and Chloroflexi. Analysis of surface vs. subsurface sediment samples reveal taxonomic patterns that cross multiple sites. These findings are a first step towards better understanding ecologically important microbial activity in these local sites, and freshwater wetlands more broadly. / Thesis (BS) — Boston College, 2020. / Submitted to: Boston College. College of Arts and Sciences. / Discipline: Departmental Honors. / Discipline: Biology.

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Arctic ecosystems are amongst the most vulnerable on Earth to ongoing climate change. While the responses to these changes are well studied on land, less is known about how aquatic communities may respond to a warmer arctic. For stream invertebrate communities, predicting such responses requires basic understanding of how and why different taxonomic groups fluctuate throughout the year. However, few studies have assessed the community dynamics of stream macroinvertebrates across seasons in the Arctic. In this project, I asked how macroinvertebrate community structure changes between months and across seasons in a small Arctic stream in northern Sweden. I expected that community change over time would reflect changes in the supply of organic matter (e.g., leaf litter and algae) to dominant consumers. A total of five transects were sampled for macroinvertebrates each month from July to April using Surber sampling. I used descriptive and multivariate analyses to evaluate changes in community structure between months and seasons. Marked differences in community composition were found between the seasons with detritivores (shredders) dominating the autumn months possibly reflecting input of birch litter and high abundances of grazers during and post winter, possibly reflecting primary production early in spring. Expected climate change effects in the Arctic include warmer temperatures and increases in the terrestrial plant productivity. My results suggest that these shifts could cause changes in stream community composition, driven by increases in deciduous litter inputs that promote shredders and/or by increases in primary production during spring that favour grazers and collector-gatherers, which feed on algae.

Genome size (GS) is a fundamental trait influencing cellular, developmental and ecological parameters, and varies c. 2400- fold in angiosperms. This astonishing range has the potential to influence a plant's nutrient demands, since nucleic acids are amongst the most phosphate and nitrogen demanding cellular biomolecules, and hence its ability to grow and compete in environments where macronutrients are limited. Angiosperm GS are strongly skewed towards small genomes, despite the prevalence of polyploidy in the ancestry of most if not all angiosperm lineages. This thesis examines the hypothesis that large genome sizes are costly to build and maintain and that angiosperm species with large GS are constrained by nitrogen and phosphate limitation. It untangles the interactions between GS, polyploidy and competition in plant communities, and examines how herbivory and GS play a role in plant productivity, measured as above-ground biomass. The hypothesis that large GS are costly was approached by analysing: 1) plant communities growing under different macronutrient conditions at the Park Grass Experiment (Rothamsted, UK); 2) plant communities under different conditions of macronutrient limitation and insect, mollusc, and rabbit herbivory at Nash's Field in Silwood Park (UK); and, 3) Ellenberg's indicator values which represent the realised niche of a species in terms light, water, and soil fertility. Support for the hypothesis was found in all experiments. The range of analyses show that angiosperm plants with large genomes (e.g. 1C-value > 5 pg) are indeed under greater macronutrient limitation in comparison to plants with small genomes, and that it is polyploid plants with large GS which are the most competitive when macronutrient resources are plentiful. In terms of herbivory, the key finding is a highly significant negative association between GS and rabbit herbivory. A species' realised niche for soil fertility was found to show a positive association with its GS. Overall the thesis shows that angiosperm GS plays a central role in plant community composition and responses to macronutrient conditions, and potentially on higher ecosystem processes through associations at different trophic levels.

The intestinal tract microbiota – microbial community of the gut – is an important field in microbiology not only because of its critical role in the host development, but also increasingly large number of diseases are associated with certain state of the gut microbiota. The community structure and function of the gut microbiota is relatively well studied in humans and related higher vertebrates, but is severely understudied in fish. This is especially true for the coral reef fishes, who constitute the most diverse assemblage of vertebrates spread over a very local scale, and are essential for the resilience of the reefs. In order to bridge this gap in knowledge, this dissertation studied the community structure, interactions and functions of the gut microbial community from the surgeonfishes in the Red Sea – with special focus on the surgeonfish enteric symbiont Epulopiscium spp. Initially, I studied the composition of the gut microbiota of nine surgeonfish and three nonsurgeonfish species from the Red Sea using 454 pyrosequencing. Upon discovering the high abundance of Epulopiscium spp. in herbivorous surgeonfishes, I then proceeded to identify their phylogenetic diversity, distribution, as well as deducing their coevolutionary relationship with the host. Because Epulopiscium spp. undergo substantial changes in the cell size (grow up to ~600μm) and the DNA concentration (from 85 to over 250pg per cell) throughout their diel lifecycle, I also studied the temporal changes in their expression pattern using RNA-seq. Overall, this dissertation shed light on the complex structure, interaction and function of an important family of coral reef fish from the Red Sea through range of molecular techniques.

As the world continues to experience substantial rates of habitat loss, habitat restoration has become of prime interest to ecologists worldwide. Restoration has shown to be successful in recovering targeted components of certain ecosystems but it is important to achieve a holistic understanding of the resulting ecological impacts it has on communities. To address this, four oyster reefs and three living shorelines were restored during the summer of 2017. These sites, along with four dead oyster reefs, four living oyster reefs, and three undisturbed (control) living shorelines, were sampled before restoration and regularly post-restoration for one year using lift nets. Macroinvertebrates were collected and enumerated in the lab. Diversity indices, community composition, and similarity percentages were then calculated and compared across treatments, time, and treatment-by-time. Live reefs displayed significantly higher species richness and Shannon diversity than restored and dead reefs. Simpson diversity did not differ between live and restored oyster reefs but both were significantly higher than dead reefs. Though not statistically detectable, species richness and Shannon diversity on restored reefs were relatively similar to dead reefs before restoration but became increasingly similar to live reefs over the course of the study. Additionally, analyses revealed significantly different community compositions between live reefs and restored reefs, as well as between live and dead reefs. Living shorelines showed no significant differences in diversity indices but did experience similar seasonal fluctuations in diversity across treatments. Just as with oyster reefs, restored and control living shorelines harbored significantly different communities across time. The findings of this study emphasize the need for dedication to thorough monitoring and multi-metric evaluation of success in restoration efforts. This study and future research will equip resource managers with ways to quantify the effects of restoration that will consider several important ecosystem components.

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