Dry and wet periods drive rapid shifts in community assembly in an estuarine ecosystem.

The impacts of changing climate regimes on emergent processes controlling the assembly of ecological communities remain poorly understood. Human alterations to the water cycle in the western United States have resulted in greater interannual variability and more frequent and severe extremes in freshwater flow. The specific mechanisms through which such extremes and climate regime shifts may alter ecological communities have rarely been demonstrated, and baseline information on current impacts of environmental variation is widely lacking for many habitats and communities. Here, we used observations and experiments to show that interannual variation in winter salinity levels in San Francisco Bay controls the mechanisms determining sessile invertebrate community composition during the following summer. We found consistent community changes in response to decadal-scale dry and wet extremes during a 13-year period, producing strikingly different communities. Our results match theoretical predictions of major shifts in species composition in response to environmental forcing up to a threshold, beyond which we observed mass mortality and wholesale replacement of the former community. These results provide a window into potential future community changes, with environmental forcing altering communities by shifting the relative influences of the mechanisms controlling species distributions and abundances. We place these results in the context of historical and projected future environmental variation in the San Francisco Bay Estuary.

Evaluation of real-time fluorescence sensors and benchtop fluorescence for tracking and predicting sewage contamination in the Tijuana River Estuary at the US-Mexico border.

Cross-border flow of untreated sewage from Mexico into the USA via the Tijuana River is public health issue with negative consequences for coastal communities. Here we evaluate the potential application of fluorescence-based, submersible tryptophan-like (TRP) and humic-like (CDOM) fluorescence sensors for real-time tracking of wastewater pollution in an estuarine environment. Sonde fluorescence measurements were compared with benchtop fluorescence, fecal indicator bacteria (FIB) concentrations, and real-time specific conductivity measurements in the Tijuana River Estuary during dry and wet weather conditions, and with and without cross-border flow. TRP and CDOM fluorescence concentrations were low during times without cross-border flow and two-three orders of magnitude higher during storm events and after cross-border sewage flow events. Major deterioration in water quality, including hypoxic conditions, was observed after consistent, long-term cross-border sewage flow. Real-time TRP and CDOM fluorescence concentrations had a significant linear relationship with fecal indicator bacteria (FIB) concentrations during dry weather periods with cross-border flow (p < 0.001) but were poorly correlated during stormflow and during less polluted periods with no cross-border flow. TRP and CDOM fluorescence acquired on discrete samples using a benchtop fluorometer correlated significantly (p < 0.001) with FIB concentrations under all cross-border flow conditions. Based on relationships between benchtop TRP fluorescence and percent wastewater, the greatest amount of untreated wastewater in the estuary's surface layer during cross-border flow events was estimated at >80 % and occurred during neap tides, when concentrated, sewage-laden freshwater flowed over dense saline seawater due to stratification and lack of mixing in the estuary. These results are important because exposure to untreated sewage poses severe health risks for residents and visitors to adjacent coastal areas. While benchtop fluorescence was more effective for estimating the degree of wastewater pollution, submersible TRP and CDOM sensors provided a real-time alert of sewage contamination, which can be utilized in other sewage impacted estuarine environments.

Controls on spatial variation in porewater methane concentrations across United States tidal wetlands.

Tidal wetlands can be a substantial sink of greenhouse gases, which can be offset by variable methane (CH4) emissions under certain environmental conditions and anthropogenic interventions. Land managers and policymakers need maps of tidal wetland CH4 properties to make restoration decisions and inventory greenhouse gases. However, there is a mismatch in spatial scale between point-based sampling of porewater CH4 concentration and its predictors, and the coarser resolution mapping products used to upscale these data. We sampled porewater CH4 concentrations, salinity, sulfate (SO42-), ammonium (NH4+), and total Fe using a spatially stratified sampling at 27 tidal wetlands in the United States. We measured porewater CH4 concentrations across four orders of magnitude (0.05 to 852.9 µM). The relative contribution of spatial scale to variance in CH4 was highest between- and within-sites. Porewater CH4 concentration was best explained by SO42- concentration with segmented linear regression (p < 0.01, R2 = 0.54) indicating lesser sensitivity of CH4 to SO42- below 0.62 mM SO42-. Salinity was a significant proxy for CH4 concentration, because it was highly correlated with SO42- (p < 0.01, R2 = 0.909). However, salinity was less predictive of CH4 with segmented linear regression (p < 0.01, R2 = 0.319) relative to SO42-. Neither NH4+, total Fe, nor relative tidal elevation correlated significantly with porewater CH4; however, NH4+ was positively and significantly correlated with SO42- after detrending CH4 for its relationship with SO42- (p < 0.01, R2 = 0.194). Future sampling should focus on within- and between-site environmental gradients to accurately map CH4 variation. Mapping salinity at sub-watershed scales has some potential for mapping SO42-, and by proxy, constraining spatial variation in porewater CH4 concentrations. Additional work is needed to explain site-level deviations from the salinity-sulfate relationship and elucidate other predictors of methanogenesis. This work demonstrates a unique approach to remote team science and the potential to strengthen collaborative research networks.

Pattern and scale: evaluating generalities in crab distributions and marsh dynamics from small plots to a national scale.

The generality of ecological patterns depends inextricably on the scale at which they are examined. We investigated patterns of crab distribution and the relationship between crabs and vegetation in salt marshes at multiple scales. By using consistent monitoring protocols across 15 U.S. National Estuarine Research Reserves, we were able to synthesize patterns from the scale of quadrats to the entire marsh landscape to regional and national scales. Some generalities emerged across marshes from our overall models, and these are useful for informing broad coastal management policy. We found that crab burrow distribution within a marsh could be predicted by marsh elevation, distance to creek and soil compressibility. While these physical factors also affected marsh vegetation cover, we did not find a strong or consistent overall effect of crabs at a broad scale in our multivariate model, though regressions conducted separately for each site revealed that crab burrows were negatively correlated with vegetation cover at 4 out of 15 sites. This contrasts with recent smaller-scale studies and meta-analyses synthesizing such studies that detected strong negative effects of crabs on marshes, likely because we sampled across the entire marsh landscape, while targeted studies are typically limited to low-lying areas near creeks, where crab burrow densities are highest. Our results suggest that sea-level rise generally poses a bigger threat to marshes than crabs, but there will likely be interactions between these physical and biological factors. Beyond these generalities across marshes, we detected some regional differences in crab community composition, richness, and abundance. However, we found striking differences among sites within regions, and within sites, in terms of crab abundance and relationships to marsh integrity. Although generalities are broadly useful, our findings indicate that local managers cannot rely on data from other nearby systems, but rather need local information for developing salt marsh management strategies.

Ecosystem engineering in space and time.

The ecosystem engineering concept focuses on how organisms physically change the abiotic environment and how this feeds back to the biota. While the concept was formally introduced a little more than 10 years ago, the underpinning of the concept can be traced back to more than a century to the early work of Darwin. The formal application of the idea is yielding new insights into the role of species in ecosystems and many other areas of basic and applied ecology. Here we focus on how temporal, spatial and organizational scales usefully inform the roles played by ecosystem engineers and their incorporation into broader ecological contexts. Two particular, distinguishing features of ecosystem engineers are that they affect the physical space in which other species live and their direct effects can last longer than the lifetime of the organism--engineering can in essence outlive the engineer. Together, these factors identify critical considerations that need to be included in models, experimental and observational work. The ecosystem engineering concept holds particular promise in the area of ecological applications, where influence over abiotic variables and their consequent effects on biotic communities may facilitate ecological restoration and counterbalance anthropogenic influences.

Decoupling the response of an estuarine shrimp to architectural components of habitat structure.

In order to explore biotic attraction to structure, we examined how the amount and arrangement of artificial biotic stalks affected responses of a shrimp, Palaemon macrodactylus, absent other proximate factors such as predation or interspecific competition. In aquaria, we tested the effect of differing densities of both un-branched and branched stalks, where the amount of material in the branched stalk equaled four-times that of the un-branched. The results clearly showed that it was the amount of material, not how it was arranged, that elicited responses from shrimp. Also, although stalks were not purposefully designed to mimic structural elements found in nature, they did resemble biogenic structure such as hydroids, algae, or plants. In order to test shrimp attraction to a different, perhaps more unfamiliar habitat type, we examined responses to plastic "army men." These structural elements elicited similar attraction of shrimp, and, in general, shrimp response correlated well with the fractal dimension of both stalks and army men. Overall, these results indicate that attraction to physical structure, regardless of its nature, may be an important driver of high abundances often associated with complex habitats.

Spatial and Temporal Examination of Bivalve Communities in Several Estuaries of Southern California and Northern Baja California, MX.

A combination of historical bivalve surveys spanning 30-50 years and contemporary sampling were used to document the changes in bivalve community structure over time at four southern California and one northern Baja California estuaries. While there are limitations to the interpretation of historic data, we observed generally similar trends of reduced total bivalve species richness, losses of relatively large and/or deeper-dwelling natives, and gains of relatively small, surface dwelling introduced species across the southern California estuaries, despite fairly distinct bivalve communities. A nearly 50-year absence of bivalves from two wetlands surveyed in a Baja California estuary continued. A combination of site history and current characteristics (e.g., location, depth) likely contributes to maintenance of distinct communities, and both episodic and gradual environmental changes likely contribute to within-estuary temporal shifts (or absences). We highlight future research needed to determine mechanisms underlying patterns so that we can better predict responses of bivalve communities to future scenarios, including climate change and restoration.

Characterizing anti-HIV monoclonal antibodies and immune sera by defining the mechanism of neutralization.

Understanding the nature of neutralization may provide information for crafting improvements in HIV vaccines. Using JR-FL as a prototype primary pseudovirus, we first investigated anti-HIV monoclonal antibodies (mAbs) in several neutralization formats designed to elucidate the timing of neutralization. MAb b12 was most effective before receptor binding, 2G12 neutralized effectively even after CD4 binding, and X5 and a V3 loop mAb (LE311) were inactive in a standard format but were induced by sCD4. Consistent with this latter finding, native PAGE indicated that X5 and V3 mAb binding to Envelope trimers was dependent on sCD4 binding. In contrast, 2F5 and 4E10 were active even post-CD4/CCR5 engagement. We next analyzed the neutralization mechanism of a panel of HIV+ donor plasmas of various potencies. All mediated high levels of post-CD4 neutralization that was not associated with activity in the standard format. None, however, neutralized effectively in the post-CD4/CCR5 format, suggesting that 2F5/4E10-like Abs were absent or at low concentrations. Finally, we analyzed a non-neutralizing plasma spiked with mAbs b12, 2G12 or 2F5, which resulted in increases in neutralization titers consistent with the activities of the mAbs. We conclude that these methods, together with other mapping approaches, may provide a better understanding of neutralization that could be useful in vaccine research.

Utilization of invasive tamarisk by salt marsh consumers.

Plant invasions of coastal wetlands are rapidly changing the structure and function of these systems globally. Alteration of litter dynamics represents one of the fundamental impacts of an invasive plant on salt marsh ecosystems. Tamarisk species (Tamarix spp.), which extensively invade terrestrial and riparian habitats, have been demonstrated to enter food webs in these ecosystems. However, the trophic impacts of the relatively new invasion of tamarisk into marine ecosystem have not been assessed. We evaluated the trophic consequences of invasion by tamarisk for detrital food chains in the Tijuana River National Estuarine Research Reserve salt marsh using litter dynamics techniques and stable isotope enrichment experiments. The observations of a short residence time for tamarisk combined with relatively low C:N values indicate that tamarisk is a relatively available and labile food source. With an isotopic (15N) enrichment of tamarisk, we demonstrated that numerous macroinvertebrate taxonomic and trophic groups, both within and on the sediment, utilized 15N derived from labeled tamarisk detritus. Infaunal invertebrate species that took up no or limited 15N from labeled tamarisk (A. californica, enchytraeid oligochaetes, coleoptera larvae) occurred in lower abundance in the tamarisk-invaded environment. In contrast, species that utilized significant 15N from the labeled tamarisk, such as psychodid insects, an exotic amphipod, and an oniscid isopod, either did not change or occurred in higher abundance. Our research supports the hypothesis that invasive species can alter the trophic structure of an environment through addition of detritus and can also potentially impact higher trophic levels by shifting dominance within the invertebrate community to species not widely consumed.

Using ecosystem engineers to restore ecological systems.

Ecosystem engineers affect other organisms by creating, modifying, maintaining or destroying habitats. Despite widespread recognition of these often important effects, the ecosystem engineering concept has yet to be widely used in ecological applications. Here, we present a conceptual framework that shows how consideration of ecosystem engineers can be used to assess the likelihood of restoration of a system to a desired state, the type of changes necessary for successful restoration and how restoration efforts can be most effectively partitioned between direct human intervention and natural ecosystem engineers.