Colonization by the gastric pathogen Helicobacter pylori has been shown to be intricately linked to the development of gastritis, ulcers, and gastric malignancy. Little is known about mechanisms employed by the bacterium that help it adapt to the hostile environment of the human stomach. In an effort to extend our knowledge of these mechanisms, we utilized spotted-DNA microarrays to characterize the response of H. pylori to low pH. Expression of approximately 7% of the bacterial genome was reproducibly altered by shift to low pH. Analysis of the differentially expressed genes led to the discovery that acid exposure leads to profound changes in motility of H. pylori, as a larger percentage of acid-exposed bacterial cells displayed motility and moved at significantly higher speeds. In contrast to previous publications, we found that expression of the bacterial virulence gene cagA was strongly repressed by acid exposure. Furthermore, this transcriptional repression was reflected at the level of protein accumulation in the H. pylori cell.

1. In a nitrogen (N)-limited river subject to Mediterranean summer drought hydrology, the colour of macroalgal proliferations changed with successional and seasonal changes in epiphyte assemblages. New growth of the dominant macroalga, Cladophora glomerata, was green, as were proliferations of Oedogonium, Mougeotia and Spirogyra, which did not become heavily colonized with diatoms. Green Cladophora turned yellow as Cladophora filaments became colonized by diatoms that were not N fixers, and turned rust-coloured as later-successional epiphyte assemblages became dominated by dense Epithemia turgida and E. sorex, which both contain N-fixing cyanobacterial endosymbionts. 2. The rate and composition of insect emergence from floating algal mats differed among proliferations of different colour. The rates of emergence (individuals day )1 500 cm )2 ) of nematoceran flies were three to 25 times greater from yellow or rusty-coloured Cladophora mats than from green Cladophora, Oedogonium or Mougeotia mats that had lower epiphyte densities. Biomass emergence from Cladophora mats that were rusty in colour was eight to 10 times greater than from yellow Cladophora mats, because larger nematocerans dominated in rusty mats (Chironominae versus Ceratopogonidae in yellow mats). 3. Proliferations of Epithemia-infested Cladophora occur at and above drainage areas of about 100 km 2 (channel widths of 25-30 m) in this river network, coinciding with the drainage area threshold where a step increase in concentration of total dissolved N is observed during summer. 4. In rivers under Mediterranean climate regimes, algal succession during the prolonged low flow season is less subject to stochastic interruption by spates than in rivers under more continental climates. Under these summer drought conditions, photogrammetric detection of colour changes in algal proliferations may help us track reach or basin-scale change in their ecological functions.

1. Nutrient spiralling provides a conceptual framework and a whole-system approach to investigate ecosystem responses to environmental changes. We use spiralling metrics to examine how the coupling of nitrogen and phosphorus uptake varies between streams dominated by either heterotrophic (i.e. bacteria-dominated) or autotrophic (algal-dominated) microbial communities. 2. Algae generally exhibit greater capacity to store nutrients than bacteria because of differences in cellular structures. These differences led us to hypothesise that the uptake of N and P in heterotrophic ecosystems should have reduced stoichiometric variation in response to changes in supply N : P compared to autotrophic ecosystems when assimilation dominates nutrient uptake. 3. To test this hypothesis, we used an array of serial nutrient additions in several streams in the South Fork Eel River watershed in Northern California. In one set of experiments, N and P were added alone and simultaneously in separate experiments to two small, heterotrophic streams to assess uptake rates and interactions between nutrient cycles. In a second set of experiments, N and P were added simultaneously at a range of N : P in one heterotrophic and one autotrophic stream to assess differences in uptake responses to changes in supply N : P. 4. Results of these experiments suggest two important conclusions. First, increased N supply significantly shortened P uptake lengths, while P addition had little impact on N uptake in both streams, indicating that uptake of non-limiting nutrients is tightly coupled to the availability of the limiting element. Second, changes in P uptake and uptake ratios (U N : U P ) with increased supply N : P supported our hypothesis that heterotrophic streams are more homeostatic in their responses to changes in nutrient supply than autotrophic streams, suggesting that physiological controls on nutrient use scale up to influence ecosystem-scale patterns in nutrient cycling.

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