Ecologists are trying to determine how much of the carbon stored in permafrost may be released as temperatures warm and permafrost thaws.

The field of microbial ecology has grown tremendously with the advent of novel molecular techniques, allowing the study of uncultured microbes in the environment, and producing a paradigm shift: now, rather than using bacteria cultures for evaluating cell-specific questions, researchers use RNA and DNA techniques to examine more broad-based ecological and evolutionary constructs such as biogeography and the long-debated biological species concept. Recent work has begun to relate bacteria functional genes to ecosystem processes and functioning, thereby enabling a better understanding of the interactive role of bacteria in different and often-changing environments. The field continues to mature and will most likely make substantial contributions in the future with additional efforts that include metagenomics and genomics. Here we review progress in the application of molecular techniques to study microbial communities in freshwater environments.

Microscopic, unicellular, free-living green algae are found in desert microbiotic crusts worldwide. Although morphologically simple, green algae in desert crusts have recently been found to be extraordinarily diverse, with membership spanning five green algal classes and encompassing many taxa new to science. This overview explores this remarkable diversity and its potential to lead to new perspectives on the diversity and evolution of green plants. Molecular systematic and physiological data gathered from desert taxa demonstrate that these algae are long-term members of desert communities, not transient visitors from aquatic habitats. Variations in desiccation tolerance and photophysiology among these algae include diverse evolutionary innovations that developed under selective pressures in the desert. Combined with the single embryophyte lineage to which more familiar terrestrial green plants belong, multiple desert green algal lineages provide independent evolutionary units that may enhance understanding of the evolution and ecology of eukaryotic photosynthetic life on land.

A diverse array of fire-adapted plant communities once covered the eastern United States. European settlement greatly altered fire regimes, often increasing fire occurrence (e.g., in northern hardwoods) or substantially decreasing it (e.g., in tallgrass prairies). Notwithstanding these changes, fire suppression policies, beginning around the 1920s, greatly reduced fire throughout the East, with profound ecological consequences. Fire-maintained open lands converted to closed-canopy forests. As a result of shading, shade-tolerant, fire-sensitive plants began to replace heliophytic (sun-loving), fire-tolerant plants. A positive feedback cycle—which we term “mesophication”—ensued, whereby microenvironmental conditions (cool, damp, and shaded conditions; less flammable fuel beds) continually improve for shade-tolerant mesophytic species and deteriorate for shade-intolerant, fire-adapted species. Plant communities are undergoing rapid compositional and structural changes, some with no ecological antecedent. Stand-level species richness is declining, and will decline further, as numerous fire-adapted plants are replaced by a limited set of shade-tolerant, fire-sensitive species. As this process continues, the effort and cost required to restore fire-adapted ecosystems escalate rapidly.

The emerging discipline of urban ecology is shifting focus from ecological processes embedded within cities to integrative studies of large urban areas as biophysical-social complexes. Yet this discipline lacks a theory. Results from the Baltimore Ecosystem Study, part of the Long Term Ecological Research Network, expose new assumptions and test existing assumptions about urban ecosystems. The findings suggest a broader range of structural and functional relationships than is often assumed for urban ecological systems. We address the relationships between social status and awareness of environmental problems, and between race and environmental hazard. We present patterns of species diversity, riparian function, and stream nitrate loading. In addition, we probe the suitability of land-use models, the diversity of soils, and the potential for urban carbon sequestration. Finally, we illustrate lags between social patterns and vegetation, the biogeochemistry of lawns, ecosystem nutrient retention, and social-biophysical feedbacks. These results suggest a framework for a theory of urban ecosystems.

Worldwide, humans have access to a greater range of food plants than does any other species. Examination of phylogenetic patterns in plants consumed by animals has recently uncovered important ecological processes. The same techniques, however, have not been applied to our own species. Here we show that although humans tend to eat more species in certain families (e.g., Rosaceae) and fewer in others (e.g., Orchidaceae), the proportion of edible species in most families is similar to random expectations. Phylogenetic patterning in angiosperm edibility is also weak. We argue that the remarkable breadth of the human diet is the result of humans' huge geographic range, diverse food-collection methods, and ability to process normally inedible items. Humans are thus generalist feeders in the broadest sense. Cross-cultural analyses of diversity in the plant diet of humans could represent a fascinating new field of research linking ecology, anthropology, history, and sociology.

Bibliometric indices based on publishing output, and citation records used to measure scientific quality, are increasingly being employed to supplement and even replace traditional alternatives, such as the peer-review system. In this article we question whether peer review can predict bibliometric indices for individual researchers. We compared the ratings of scientific quality obtained using a peer-review system with the most popular bibliometric scores (h-, m-, and g-indices; total citations; and mean number of citations per publication) for 163 botanists and zoologists. Although the peer-review ratings were correlated with the bibliometric measures, they explained less than 40 percent of the variation in the scores. Most of this unexplained variation is presumably due to limitations of both the peer-review system and bibliometric scores. We propose a synergy between peer-review and bibliometric scores that can improve the assessment of scientific quality, especially by benchmarking peer-review decisions against bibliometric thresholds.

Coral reefs, one of the most biologically diverse and important ecosystems on Earth, are experiencing unprecedented and increasing ecological decline, yet the fish faunas of such reefs and other tropical shoreline habitats remain poorly known in many areas. Rotenone, a natural substance traditionally used by subsistence fishers, is a uniquely efficient tool for sampling reef and other shore fishes for marine research. Unfortunately, such sampling is perceived as being highly destructive, and increasing prohibitions against using rotenone in many countries will soon cripple essential research on reef-fish biodiversity worldwide. In this article we dispel common misconceptions about the environmental effects of small-scale rotenone sampling in marine research.