Anne C.S. McIntosh

Database design for ecologists: Composing core entities with observations

Abstract The ecoinformatics community recognizes that ecological synthesis across studies, space, and time will require new informatics tools and infrastructure. Recent advances have been encouraging, but many problems still face ecologists who manage their own datasets, prepare data for archiving, and search data stores for synthetic research. In this paper, we describe how work by the Canopy Database Project (CDP) might enable use of database technology by field ecologists: increasing the quality of database design, improving data validation, and providing structural and semantic metadata — all of which might improve the quality of data archives and thereby help drive ecological synthesis. The CDP has experimented with conceptual components for database design, templates, to address information technology issues facing ecologists. Templates represent forest structures and observational measurements on these structures. Using our software, researchers select templates to represent their study’s data and can generate normalized relational databases. Information hidden in those databases is used by ancillary tools, including data intake forms and simple data validation, data visualization, and metadata export. The primary question we address in this paper is, which templates are the right templates. We argue for defining simple templates (with relatively few attributes) that describe the domains major entities, and for coupling those with focused and flexible observation templates. We present a conceptual model for the observation data type, and show how we have implemented the model as an observation entity in the DataBank database designer and generator. We show how our visualization tool CanopyView exploits metadata made explicit by DataBank to help scientists with analysis and synthesis. We conclude by presenting future plans for tools to conduct statistical calculations common to forest ecology and to enhance data mining with DataBank databases. DataBank could be extended to another domain by replacing our forest–ecology-specific templates with those for the new domain. This work extends the basic computer science idea of abstract data types and user-defined types to ecology-specific database design tools for individual users, and applies to ecoinformatics the software engineering innovations of domain-specific languages, software patterns, components, refactoring, and end-user programming.

Use of Unmanned Aerial Vehicles for Monitoring Recovery of Forest Vegetation on Petroleum Well Sites

Photogrammetric point clouds (PPCs) provide a source of three-dimensional (3-D) remote sensing data that is well-suited to use over small areas that are within the scope of observation by unmanned aerial vehicles (UAVs). We compared PPC-based structural metrics to traditional ground surveys conducted by field personnel in order to assess the capacity of PPC data to contribute to vegetation-reclamation surveys. We found good statistical agreement between key structural vegetation parameters, such as mean and maximum vegetation height, with PPC metrics successfully predicting most height and tree-diameter metrics using multivariate linear regression. However, PPC metrics were not as useful for estimating ground-measured vegetation cover. We believe that part of the issue lies in the mismatch between PPC- and ground-based measurement approaches, including subjective judgement on behalf of ground crews: a topic that requires more investigation. Our work highlights the emerging value of UAV-based PPCs to complement, and in some cases supplement, traditional ground-based sources of measured vegetation structure.

Extraction and Analysis of Microbial Phospholipid Fatty Acids in Soils.

Phospholipid fatty acids (PLFAs) are key components of microbial cell membranes. The analysis of PLFAs extracted from soils can provide information about the overall structure of terrestrial microbial communities. PLFA profiling has been extensively used in a range of ecosystems as a biological index of overall soil quality, and as a quantitative indicator of soil response to land management and other environmental stressors. The standard method presented here outlines four key steps: 1. lipid extraction from soil samples with a single-phase chloroform mixture, 2. fractionation using solid phase extraction columns to isolate phospholipids from other extracted lipids, 3. methanolysis of phospholipids to produce fatty acid methyl esters (FAMEs), and 4. FAME analysis by capillary gas chromatography using a flame ionization detector (GC-FID). Two standards are used, including 1,2-dinonadecanoyl-sn-glycero-3-phosphocholine (PC(19:0/19:0)) to assess the overall recovery of the extraction method, and methyl decanoate (MeC10:0) as an internal standard (ISTD) for the GC analysis.

Understory Plant Community Composition Is Associated with Fine-Scale Above- and Below-Ground Resource Heterogeneity in Mature Lodgepole Pine (Pinus contorta) Forests

Understory plant communities play critical ecological roles in forest ecosystems. Both above- and below-ground ecosystem properties and processes influence these communities but relatively little is known about such effects at fine (i.e., one to several meters within-stand) scales, particularly for forests in which the canopy is dominated by a single species. An improved understanding of these effects is critical for understanding how understory biodiversity is regulated in such forests and for anticipating impacts of changing disturbance regimes. Our primary objective was to examine the patterns of fine-scale variation in understory plant communities and their relationships to above- and below-ground resource and environmental heterogeneity within mature lodgepole pine forests. We assessed composition and diversity of understory vegetation in relation to heterogeneity of both the above-ground (canopy tree density, canopy and tall shrub basal area and cover, downed wood biomass, litter cover) and below-ground (soil nutrient availability, decomposition, forest floor thickness, pH, and phospholipid fatty acids (PLFAs) and multiple carbon-source substrate-induced respiration (MSIR) of the forest floor microbial community) environment. There was notable variation in fine-scale plant community composition; cluster and indicator species analyses of the 24 most commonly occurring understory species distinguished four assemblages, one for which a pioneer forb species had the highest cover levels, and three others that were characterized by different bryophyte species having the highest cover. Constrained ordination (distance-based redundancy analysis) showed that two above-ground (mean tree diameter, litter cover) and eight below-ground (forest floor pH, plant available boron, microbial community composition and function as indicated by MSIR and PLFAs) properties were associated with variation in understory plant community composition. These results provide novel insights into the important ecological associations between understory plant community composition and heterogeneity in ecosystem properties and processes within forests dominated by a single canopy species.

Ecology of understory and below-ground communities in lodgepole pine forests under changing disturbance regimes

As climate changes and disturbance regimes shift, there is a need to better understand and anticipate potential impacts of both natural and anthropogenic disturbance agents on forest ecosystems. Lodgepole pine forests in western Canada are experiencing an unprecedented mountain pine beetle (MPB) outbreak, and the ecosystem-level effects of ongoing expansion of MPB into novel habitats east of the Canadian Rockies are unknown. Another way ecosystems are being disturbed is through management practices that are attempting to enhance timber production by using introduced species in plantations; lodgepole pine has been introduced around the world as an important timber species, but its invasive potential in some areas, such as Sweden, remains unclear. To better understand the ecological impacts of disturbance in lodgepole pine ecosystems I investigated: i) fine-scale patterns in understory plant and microbial communities in mature lodgepole pine forests; ii) effects of simulated MPB attack and salvage harvest on aboveand below-ground dynamics of these forests; iii) potential for pine regeneration after MPB attack in newly invaded stands; and iv) effects of the introduction of lodgepole pine to Sweden on forest floor properties and processes. In mature undisturbed lodgepole pine forests I identified four fine-scale plant communities, primarily influenced by below-ground factors; four structural microbial communities, primarily influenced by the understory composition; and four functional microbial communities that were not strongly associated with any environmental factors measured in my study. I found short-term resistance to ecosystem change after simulated MPB attack, compared with more immediate ecosystem changes in response to salvage harvest. Regeneration of lodgepole pine seedlings appears unlikely to occur in the short term after MPB attack without active silvicultural intervention. In northern Sweden, introduced lodgepole pine had minor ecosystem-level effects compared with the native pine; the impacts of species introductions are likely functions of both regional influences and ecological differences between the introduced and native species. Overall, my thesis provides novel insights into the ecology of lodgepole pine forests in the face of changing disturbance regimes and forest management practices, demonstrating the important ecological roles that both aboveand below-ground properties and processes play in these forested ecosystems.

Severity of impacts of an introduced species corresponds with regional eco-evolutionary experience

Invasive plant impacts vary widely across introduced ranges. We tested the hypothesis that differences in the eco-evolutionary experience of native communities with the invader correspond with the impacts of invasive species on native vegetation, with impacts increasing with ecological novelty. We compared plant species richness and composition beneath Pinus contorta to that in adjacent vegetation and other P. contorta stands across a network of sites in its native (Canada and USA) and nonnative (Argentina, Chile, Finland, New Zealand, Scotland, Sweden) ranges. At sites in North America and Europe, within the natural distribution of the genus Pinus, P. contorta was not associated with decreases in diversity. In the Southern Hemisphere, where there are no native Pinaceae, plant communities beneath P. contorta were less diverse than in other regions and compared to uninvaded native vegetation. Effects on native vegetation were particularly pronounced where P. contorta was a more novel life form and exhibited higher growth rates. Our results support the hypothesis that the eco-evolutionary experience of the native vegetation, and thus the novelty of the invader, determines the magnitude of invader impacts on native communities. Understanding the eco-evolutionary context of invasions will help to better understand and predict where invasion impacts will be greatest and to prioritize invasive species management.