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In an effort to better portray changing health conditions in Chesapeake Bay and support restoration efforts, a Bay Health Index (BHI) was developed to assess the ecological effects of nutrient and sediment loading on 15 regions of the estuary. Three water quality and three biological measures were combined to formulate the BHI. Water quality measures of chlorophyll-a, dissolved oxygen, and Secchi depth were averaged to create the Water Quality Index (WQI), and biological measures of the phytoplankton and benthic indices of biotic integrity (P-IBI and B-IBI, respectively) and the area of submerged aquatic vegetation (SAV) were averaged to create the Biotic Index (BI). The WQI and BI were subsequently averaged to give a BHI value representing ecological conditions over the growing season (i.e., March-October). Lower chlorophyll-a concentrations, higher dissolved oxygen concentrations, deeper Secchi depths, higher phytoplankton and benthic indices relative to ecological health-based thresholds, and more extensive SAV area relative to restoration goal areas, characterized the least-impaired regions. The WQI, P-IBI and BHI were significantly correlated with (1) regional river flow (r=-0.64, -0.57 and -0.49, respectively; p0.01), (2) nitrogen (N), phosphorus (P) and sediment loads (all positively correlated with flow), and (3) the sum of developed and agricultural land use (highest annual r(2)=0.86, 0.71 and 0.68, respectively) in most reporting regions, indicating that the BHI is strongly regulated by nutrient and sediment loads from these land uses. The BHI uses ecological health-based thresholds that give an accurate representation of the health conditions in Chesapeake Bay and was the basis for an annual, publicly released environmental report card that debuted in 2007.

An updated assessment of nutrient related impacts in US estuaries was completed in 2007. This assessment evaluates three components for each estuary: the influencing factors (e.g. land use, nutrient loads), the overall eutrophic condition (e.g. chlorophyll a, presence of nuisance/toxic algae and macroalgae, extent of dissolved oxygen problems, loss of submerged aquatic vegetation), and future outlook. Eutrophication is a widespread problem with 65% of assessed systems showing moderate to high level problems. The most impacted region was the mid-Atlantic. The majority of estuaries assessed, with the exception of North Atlantic systems (Cape Cod north to Maine), are highly influenced by human related activities that contribute to land-based nutrient loads. Conditions were predicted to worsen in 65% and to improve in 19% of the assessed estuaries in the future. Analysis of the extent of change from the early 1990s to the early 2000s, for those systems for which sufficient data were available, shows that conditions mostly remained the same (32 of 58 systems) though changes were observed in several smaller systems; 13 systems improved and 13 systems worsened. Chlorophyll a and HAB impacts have increased in the mid-Atlantic region, the only region with data adequate for comparison. These symptoms are more prevalent in systems with longer residence times, such as coastal lagoons. The successful restoration of seagrass in Tampa Bay is encouraging though future management to sustain the recovery will be difficult given expected population increases. This national assessment illustrates the need for coordinated and integrated action that balances management action, efficient monitoring to assess the effectiveness of the management, focused research, and a communication campaign aimed at engaging the broader community.

The abundance and productivity of benthic microalgae in coral reef sediments are poorly known compared with other, more conspicuous (e.g. coral zooxanthellae, macroalgae) primary producers of coral reef habitats. A survey of the distribution, biomass, and productivity of benthic microalgae on a platform reef flat and in a cross-shelf transect in the southern Great Barrier Reef indicated that benthic microalgae are ubiquitous, abundant (up to 995.0 mg chlorophyll (chl) a m−2), and productive (up to 110 mg O2 m−2 h−1) components of the reef ecosystem. Concentrations of benthic microalgae, expressed as chlorophyll a per surface area, were approximately 100-fold greater than the integrated water column concentrations of microalgae throughout the region. Benthic microalgal biomass was greater on the shallow water platform reef than in the deeper waters of the cross-shelf transect. In both areas the benthic microalgal communities had a similar composition, dominated by pennate diatoms, dinoflagellates, and cyanobacteria. Benthic microalgal populations were potentially nutrient-limited, based on responses to nitrogen and phosphorus enrichments in short-term (7-day) microcosm experiments. Benthic microalgal productivity, measured by O2 evolution, indicated productive communities responsive to light and nutrient availability. The benthic microalgal concentrations observed (92–995 mg chl a m−2) were high relative to other reports, particularly compared with temperate regions. This abundance of productive plants in both reef and shelf sediments in the southern Great Barrier Reef suggests that benthic microalgae are key components of coral reef ecosystems.

Direct comparisons between photosynthetic O2 evolution rate and electron transport rate (ETR) were made in situ over 24 h using the benthic macroalga Ulva lactuca (Chlorophyta), growing and measured at a depth of 1.8 m, where the midday irradiance rose to 400–600 μmol photons m−2 s−1. O2 exchange was measured with a 5-chamber data-logging apparatus and ETR with a submersible pulse amplitude modulated (PAM) fluorometer (Diving-PAM). Steady-state quantum yield ((Fm′−Ft)/Fm′) decreased from 0.7 during the morning to 0.45 at midday, followed by some recovery in the late afternoon. At low to medium irradiances (0–300 μmol photons m−2 s−1), there was a significant correlation between O2 evolution and ETR, but at higher irradiances, ETR continued to increase steadily, while O2 evolution tended towards an asymptote. However at high irradiance levels (600–1200 μmol photons m−2 s−1) ETR was significantly lowered. Two methods of measuring ETR, based on either diel ambient light levels and fluorescence yields or rapid light curves, gave similar results at low to moderate irradiance levels. Nutrient enrichment (increases in [NO3 −], [NH4 +] and [HPO4 2-] of 5- to 15-fold over ambient concentrations) resulted in an increase, within hours, in photosynthetic rates measured by both ETR and O2 evolution techniques. At low irradiances, approximately 6.5 to 8.2 electrons passed through PS II during the evolution of one molecule of O2, i.e., up to twice the theoretical minimum number of four. However, in nutrient-enriched treatments this ratio dropped to 5.1. The results indicate that PAM fluorescence can be used as a good indication of the photosynthetic rate only at low to medium irradiances.

Nitrogen loading to aquatic ecosystems from sewage is recognised worldwide as a growing problem. The use of nitrogen stable isotopes as a means of discerning sewage nitrogen in the environment has been used annually by the Ecosystem Health Monitoring Program in Moreton Bay (Australia) since 1997 when the technique was first developed. This ("sewage plume mapping") technique, which measures the delta(15)N isotopic signature of the red macroalga Catenella nipae after incubation in situ, has demonstrated a large reduction in the magnitude and spatial extent of sewage nitrogen within Moreton Bay over the past 5 years. This observed reduction coincides with considerable upgrades to the nitrogen removal efficacy at several sewage treatment plants within the region. This paper describes the observed changes and evaluates whether they can be attributed to the treatment upgrades.