Nathan Basiliko

The importance of plant genotype and contemporary evolution for terrestrial ecosystem processes

Plant genetic variation and evolutionary dynamics are predicted to impact ecosystem processes but these effects are poorly understood. Here we test the hypothesis that plant genotype and contemporary evolution influence the flux of energy and nutrients through soil, which then feedback to affect seedling performance in subsequent generations. We conducted a multiyear field evolution experiment using the native biennial plant Oenothera biennis. This experiment was coupled with experimental assays to address our hypothesis and quantify the relative importance of evolutionary and ecological factors on multiple ecosystem processes. Plant genotype, contemporary evolution, spatial variation, and herbivory affected ecosystem processes (e.g., leaf decay, soil respiration, seedling performance, N cycling), but their relative importance varied between specific ecosystem variables. Insect herbivory and evolution also contributed to a feedback that affected seedling biomass of O. biennis in the next generation. Our results show that heritable variation among plant genotypes can be an important factor affecting local ecosystem processes, and while effects of contemporary evolution were detectable and sometimes strong, they were often contingent on other ecological, factors.

A Novel Isolate And Widespread Abundance Of The Candidate Alphaproteobacterial Order (Ellin 329), In Southern Appalachian Peatlands

Peatlands of all latitudes play an integral role in global climate change by serving as a carbon sink and a primary source of atmospheric methane; however, the microbial ecology of mid-latitude peatlands is vastly understudied. Herein, next generation Illumina amplicon sequencing of small subunit rRNA genes was utilized to elucidate the microbial communities in three southern Appalachian peatlands. In contrast to northern peatlands, Proteobacteria dominated over Acidobacteria in all three sites. An average of 11 bacterial phyla was detected at relative abundance values >1%, with three candidate divisions (OP3, WS3 and NC10) represented, indicating high phylogenetic diversity. Physiological traits of isolates within the candidate alphaproteobacterial order, Ellin 329, obtained here and in previous studies indicate that bacteria of this order may be involved in hydrolysis of poly-, di- and monosaccharides. Community analyses indicate that Ellin 329 is the third most abundant order and is most abundant near the surface layers where plant litter decomposition should be primarily occurring. In sum, members of Ellin 329 likely play important roles in organic matter decomposition, in southern Appalachian peatlands and should be investigated further in other peatlands and ecosystem types.

Profiling undergraduate soil science education in Canada: Status and projected trends

Abstract: Global declines in postsecondary enrollment in soil science programs over the last several decades have been mainly attributed to an overemphasis on the connection with agronomy and production agriculture but recent enrollment increases in the USA suggest change is afoot. To determine if similar trends are occurring in Canada, we inventoried undergraduate soil science course offerings at postsecondary institutions and conducted a survey to assess the status and projected trends in soil science education. We found that 64% of universities and 37% of colleges offer undergraduate soil science courses as part of degrees or diplomas in which knowledge of soil science is important (e.g., agriculture and resource management). In Canada, there are 149 undergraduate soil science courses taught in universities and 58 at colleges. On average, there are 3.2 courses taught at each university and 1.9 at each college that offer soil science courses. Soil science programs at the University of British Columbia, University of Saskatchewan, and University of Manitoba offer between eight and nine soil science courses and represent 17.4% of the national total. Enrollments in all courses across the country are projected to be steady with some anticipated growth, trends that are consistent with those reported in the USA and the Netherlands.

Bringing guest scientists to the university biology classroom via the web

This commentary describes an initiative to bring national and international guest scientists to undergraduate and introductory graduate classrooms via web videoconferencing to facilitate interesting and effective research-informed teaching. Interactions center around both journal articles authored by the guests that are in line with weekly course lecture topics and on learning about the nature of academia in other parts of the world. Some particularly interesting perspectives from guests have come about by connecting with a journal editor-in-chief, a textbook author and with a scientist who shared a recently rejected manuscript and peer reviews. Beyond allowing students a unique behind-the-scenes look into how research questions are asked and answered, this initiative helps overcome the limited nature of a single instructors research area to better complement the comprehensive scope of university courses.

A role for methanogens and methane in the regulation of GLP-1

The gastrointestinal (GI) microbiome has emerged as a potential regulator of metabolism. However, the precise mechanisms of how microorganisms may influence physiology remain largely unknown. Interestingly, GI microorganisms, including methanogens, are localized within the same regions as the glucagon‐like peptide‐1 (GLP‐1) secreting L cells. GLP‐1 plays key roles appetite and glucose regulation. Furthermore, both methane and GLP‐1 levels are altered in obese humans with metabolic disease. We predict that high‐fat diet‐induced obesity alters the abundance of GI methanogens and that methane may play a role in the GLP‐1 secretory response from the L cell.

Blended pulp mill, forest humus and mine residual material Technosols for mine reclamation: A growth-chamber study to explore the role of physiochemical properties of substrates and microbial inoculation on plant growth

A growth chamber trial was conducted to investigate the effects of blends of pulp and paper mill residuals and forest humus on soil properties, microbial communities and germination rate and biomass production of annual ryegrass (Lolium multiflorum) in both acid-producing and neutral to mildly alkaline mine tailings in a mine reclamation context. The organic residual amendments improved the nutritional status of the tailings substrates, and increased pH in acid-generating tailings, leading to higher germination rates and improved plant growth. A trace addition (<0.02% of sludge by dry weight) of natural forest floor material as a microbial inoculum to the sludge could increase plant biomass up to four-fold. The effects of sludge application on bioavailability of metals were variable, with the concentration of soluble copper (Cu) and nickel (Ni) increasing in some of the substrates following organic amendments. Addition of paper mill residuals to mine tailings modified the microbial communities observed in the oligotrophic tailings with the majority of DNA sequences in the sludge amended substrates being found to be closely related to heterotrophic bacterial species rather than the chemolithotrophic communities that dominate tailings environments.

Approaches to R education in Canadian universities.

Introduction: R language is a powerful tool used in a wide array of research disciplines and owes a large amount of its success to its open source and adaptable nature. The popularity of R has grown rapidly over the past two decades and the number of users and packages is increasing at a near exponential rate. This rapid growth has prompted a number of formal and informal online and text resources, the volume of which is beginning to present challenges to novices learning R. Students are often first exposed to R in upper division undergraduate classes or during their graduate studies. The way R is presented likely has consequences for the fundamental understanding of the program and language itself; user comprehension of R may be better if learning the language itself followed by conducting analyses, compared to someone who is learning another subject (e.g. statistics) using R for the first time. Consequently, an understanding of the approaches to R education is critical. Methods: To establish how students are exposed to R, we used a survey to evaluate the current use in Canadian university courses, including the context in which R is presented and the types of uses of R in the classroom. Additionally, we looked at the reasons professors either do or don’t use/teach R. Results: We found that R is used in a broad range of course disciplines beyond statistics (e.g. ecology) and just over one half of Canadian universities have at least one course that uses R. Discussion and Conclusions: Developing programming-literate students is of utmost importance and our hope is that this benchmark study will influence how post-secondary educators, as well as other programmers, approach R, specifically when developing educational and supplemental content in online, text, and package-specific formats aiding in student’s comprehension of the R language.