Barbara J. Benson

Web-Based Phylogenetic Assignment Tool for Analysis of Terminal Restriction Fragment Length Polymorphism Profiles of Microbial Communities

ABSTRACT Culture-independent DNA fingerprints are commonly used to assess the diversity of a microbial community. However, relating species composition to community profiles produced by community fingerprint methods is not straightforward. Terminal restriction fragment length polymorphism (T-RFLP) is a community fingerprint method in which phylogenetic assignments may be inferred from the terminal restriction fragment (T-RF) sizes through the use of web-based resources that predict T-RF sizes for known bacteria. The process quickly becomes computationally intensive due to the need to analyze profiles produced by multiple restriction digests and the complexity of profiles generated by natural microbial communities. A web-based tool is described here that rapidly generates phylogenetic assignments from submitted community T-RFLP profiles based on a database of fragments produced by known 16S rRNA gene sequences. Users have the option of submitting a customized database generated from unpublished sequences or from a gene other than the 16S rRNA gene. This phylogenetic assignment tool allows users to employ T-RFLP to simultaneously analyze microbial community diversity and species composition. An analysis of the variability of bacterial species composition throughout the water column in a humic lake was carried out to demonstrate the functionality of the phylogenetic assignment tool. This method was validated by comparing the results generated by this program with results from a 16S rRNA gene clone library.

Effects of sensor spatial resolution on landscape structure parameters

We examined the effects of increasing grain size from 20 m to 1100 m on landscape parameters characterizing spatial structure in the northern Wisconsin lake district. We examined whether structural parameters remain relatively constant over this range and whether aggregation algorithms permit extrapolation within this range. Images from three different satellite sensors were employed in this study: (1) the SPOT multispectral high resolution visible (HRV), (2) the Landsat Thematic Mapper (TM), and (3) the NOAA Advanced Very High Resolution Radiometer (AVHRR). Each scene was classified as patches of water in a matrix of land. Spatial structure was quantified using several landscape parameters: percent water, number of lakes (patches), average lake area and perimeter, fractal dimension, and three measures of texture (homogeneity, contrast, and entropy). Results indicate that most measures were sensitive to changes in grain size. As grain size increased from 20 m using HRV image data to 1100 m (AVHRR), the percent water and the number of lakes decreased while the average lake area, perimeter, the fractal dimension, and contrast increased. The other two texture measures were relatively invariant with grain size. Although examination of texture at various angles of adjacency was performed to investigate features which vary systematically with angle, the angle did not have an important effect on the texture parameter values. An aggregation algorithm was used to simulate additional grain sizes. Grain was increased successively by a factor of two from 20 m (the HRV image) to 1280 m. We then calculated landscape parameter values at each grain size. Extrapolated values closely approximated the actual sensor values. Because the grain size has an important effect on most landscape parameters, the choice of satellite sensor must be appropriate for the research question asked. Interpolation between the grain sizes of different satellite sensors is possible with an approach involving aggregation of pixels.

Understanding Regional Change: A Comparison of Two Lake Districts

ABSTRACT We compared long-term change in two lake districts, one in a forested rural setting and the other in an urbanizing agricultural region, using lakes as sentinel ecosystems. Human population growth and land-use change are important drivers of ecosystem change in both regions. Biotic changes such as habitat loss, species invasions, and poorer fishing were prevalent in the rural region, and lake hydrology and biogeochemistry responded to climate trends and landscape position. Similar biotic changes occurred in the urbanizing agricultural region, where human-caused changes in hydrology and biogeochemistry had conspicuous effects. Feedbacks among ecosystem dynamics, human uses, economics, social dynamics, and policy and practice are fundamental to understanding change in these lake districts. Sustained support for interdisciplinary collaboration is essential to build understanding of regional change.

Extreme events, trends, and variability in Northern Hemisphere lake-ice phenology (1855-2005)

Often extreme events, more than changes in mean conditions, have the greatest impact on the environment and human well-being. Here we examine changes in the occurrence of extremes in the timing of the annual formation and disappearance of lake ice in the Northern Hemisphere. Both changes in the mean condition and in variability around the mean condition can alter the probability of extreme events. Using long-term ice phenology data covering two periods 1855–6 to 2004–5 and 1905–6 to 2004–5 for a total of 75 lakes, we examined patterns in long-term trends and variability in the context of understanding the occurrence of extreme events. We also examined patterns in trends for a 30-year subset (1975–6 to 2004–5) of the 100-year data set. Trends for ice variables in the recent 30-year period were steeper than those in the 100- and 150-year periods, and trends in the 150-year period were steeper than in the 100-year period. Ranges of rates of change (days per decade) among time periods based on linear regression were 0.3−1.6 later for freeze, 0.5−1.9 earlier for breakup, and 0.7−4.3 shorter for duration. Mostly, standard deviation did not change, or it decreased in the 150-year and 100-year periods. During the recent 50-year period, standard deviation calculated in 10-year windows increased for all ice measures. For the 150-year and 100-year periods changes in the mean ice dates rather than changes in variability most strongly influenced the significant increases in the frequency of extreme lake ice events associated with warmer conditions and decreases in the frequency of extreme events associated with cooler conditions.

Evolution of a multisite network information system: the LTER information management paradigm.

urban watershed, coastal estuary, eastern deciduous forest, tropical rain forest, tallgrass prairie—these are just a few of the ecosystems represented in the 24 sites of the Long-Term Ecological Research (LTER) Network (Franklin et al. 1990). By combining information from the diverse ecosystems represented in the LTER network, participants have a unique opportunity for large-scale investigations of complex phenomena like climate change, biodiversity, soil dynamics, and environmental policy. In 1996, to facilitate data exchange and synthesis from its multiple sites, LTER launched the LTER Network Information System (NIS), based on an independent site and central office organizational infrastructure. Other organizational partnerships provide examples of earlier efforts also focused on communications and data sharing: the Worm Community System, the Flora of North America Project (FNAP), and the Organization of Biological Field Stations (OBFS). The Worm Community System was developed—before Internet connectivity became available—as a collaborative software environment through which its 1400 widely dispersed researchers could share information on the genetics, behavior, and biology of the soil nematode species Caenorhabditis elegans. Insight into the complexity of a network structure was gained through attention to the design and analysis of both the system’s structure and usability (Star and Ruhleder 1996). The FNAP system, in contrast, was developed with Internet technology. The FNAP, with a goal of identifying and cataloging all plant species, uses online technology to create

Perspectives on next‐generation technology for environmental sensor networks

Sensor networks promise to transform and expand environmental science. However, many technological difficulties must be overcome to achieve this potential. Partnerships of ecologists with computer scientists and engineers are critical in meeting these challenges. Technological issues include promoting innovation in new sensor design, incorporating power optimization schemes, integrating appropriate communication protocols, streamlining data management and access, using innovative graphic and statistical analyses, and enabling both scientists and the public to access the results. Multidisciplinary partnerships are making major contributions to technological advances, and we showcase examples of this exciting new technology, as well as new approaches for training researchers to make effective use of emerging tools.

Temporal and Spatial Variability as Neglected Ecosystem Properties: Lessons Learned From 12 North American Ecosystems

Evaluating and monitoring the “health” of large-scale systems will require new and innovative approaches. One such approach is to look for ecological signals in the structure of ecological variability observed in space and time. Such variability is sometimes considered something to minimize by clever sampling design, but may in itself contain interesting ecological information (Kratz et al. 1991). In fact, much of ecology can be considered an attempt to understand the patterns of spatial and temporal variability that occur in nature and the processes that lead to these patterns. Despite widespread interest in patterns of variation there have been relatively few attempts to describe comprehensively the temporal and spatial variation exhibited by ecological parameters. As a result, we have no general laws that allow us to predict die relative magnitude of temporal and spatial variability of different types of parameters across the full diversity of ecological systems. Even within single ecosystems, understanding of the interplay between temporal and spatial variability is lacking. For example, Lewis (1978) noted that despite a large literature, the relation between temporal and spatial variability in plankton distribution within a lake is not well understood. Matthews (1990) makes a similar point regarding fish communities in streams.

Persistence of coherence of ice-off dates for inland lakes across the Laurentian Great Lakes region

lee phenologies, dates of ice-on and ice-off on lakes and rivers, provide information on climate change and variability. These long-term records indicate that lakes and rivers are sensitive to climatic change and variability. A symposium on ice phenologies o f lakes as a climate indicator was held at the 271h Congress of the Intemational Association of Theoretical and Applied Limnology in Dublin and published in the Verhandlungen (MAGNUSON et al. 2000b ). lee records have been especially useful because they can be long, over 150 years in length, and occur broadly around the Northem Hemisphere. In some areas, such as Finland (Kuustsro & ELO 2000), Sweden (WEYHENMEYER et al. 2004), and the Great Lakes region of North America (MAGNUSON et al. 2005a, b), lakes with records o f moderate length are common enough so that spatial pattems in dynamics can be analyzed. In some cases, records are sufficient to examine global, or at least intercontinental, trends (MAGNUSON et al. 2000a) and dynamics (LIVINGSTONE 2000, MAGNUSON et al. 2004). Our purpose here is to examine the spatial pattems o f temporal coherence or synchrony in time series o f ice-off dates between lakes in the Laurentian Great Lakes region. In particular, we (l) compare the coherence within and between four states and one province bordering the Great Lakes, (2) describe the persistence and decline of coherence between lakes with increasing latitudinal and longitudinal distances between them, and (3) suggest explanations for the observed pattem of coherence at multiple spatial scales. Coherence, as quantified here, is the shared variance between two time series. Discussions of coherent dynamics between lakes are reviewed in MAGNUSON & KRATZ (2000) and MAGNUSON et al. (2005b).

Response of lake ice breakup in the Northern Hemisphere to the 1976 interdecadal shift in the North Pacific

Lake ice phenology is a useful indicator of climatic warming (ROBERTSON et al. 1992, WYNNE & LILLESAND 1993, AssEL & RoBERTSON 1995). ScHINDLER et al. (1990) examined a set of parameters for a lake in western Ontario, Canada over the period 1969 through 1988 and foun d evidence of climatic warming. The duration of the ice-free season decreased primarily owing to earlier ice-out dates; ice-on dates did not have a significant trend. An analysis o f iceout dates of 20 Wisconsin lakes in the north-central United States over the same period al! showed a trend toward earlier ice-out (ANDERSON et al. 1996). Here we examine 205 lakes across the northern hemisphere to determine whether the trend toward earlier ice-out from 1969-1988 was a global phenomenon.

Conceptual Challenges and Practical Issues in Building The Global Lake Ecological Observatory Network

Freshwater lakes provide a number of important ecosystem services such as supply of drinking water, support of biotic diversity, transportation of commercial goods, and opportunity for recreation. Wireless sensor networks allow continuous, fine-grained, in situ measurements of key variables such as water temperature, dissolved gases, pH, conductivity, and chlorophyll. Instrumenting lakes with sensors capable of sampling environmental variables is becoming a standard practice. Furthermore, many limnologists around the world are interested in getting access to and performing research on data collected from lakes around the globe to provide local, regional and even global understanding of lake ecosystems. To that end, a number of limnologists, information technology experts, and engineers have joined forces to create a new, grassroots, international network, the Global Lake Ecological Observatory Network. One of our goals is to build a global scalable, persistent network of lake ecology observatories. However, implementing and designing technology that meets requirements of a large-scale distributed observing systems such as GLEON has, thus far, been challenging and instructive. In this paper, we describe several key conceptual challenges in building GLEON network. We also describe several practical issues and lessons learned during operation of a typical GLEON site.