ePlatypus: an ecosystem for computational analysis of immunogenomics data.

Motivation: The maturation of systems immunology methodologies requires novel and transparent computational frameworks capable of integrating diverse data modalities in a reproducible manner.

Results: Here, we present the ePlatypus computational immunology ecosystem for immunogenomics data analysis, with a focus on adaptive immune repertoires and single-cell sequencing. ePlatypus is an open-source web-based platform and provides programming tutorials and an integrative database that helps elucidate signatures of B and T cell clonal selection.

Thermal acclimation of leaf respiration is consistent in tropical and subtropical populations of two mangrove species.

Populations from different climates often show unique growth responses to temperature, reflecting temperature adaptation. Yet, whether populations from different climates differ in physiological temperature acclimation remains unclear. Here, we test whether populations from differing thermal environments exhibit different growth responses to temperature and differences in temperature acclimation of leaf respiration.

Belize Blue Carbon: Establishing a national carbon stock estimate for mangrove ecosystems.

Mangrove ecosystems are among the most economically and ecologically valuable marine environments in the world. Mangroves are effective at long-term carbon storage within their sediments and are estimated to hold 12 billion metric tons of carbon worldwide. These ecosystems are therefore vitally important for carbon sequestration and, by extension, climate change mitigation.

Insectivorous birds reduce herbivory but do not increase mangrove growth across productivity zones.

Top-down effects of predators and bottom-up effects of resources are important drivers of community structure and function in a wide array of ecosystems. Fertilization experiments impose variation in resource availability that can mediate the strength of predator impacts, but the prevalence of such interactions across natural productivity gradients is less clear. We studied the joint impacts of top-down and bottom-up factors in a tropical mangrove forest system, leveraging fine-grained patchiness in resource availability and primary productivity on coastal cays of Belize.

Bird rookery nutrient over-enrichment as a potential accelerant of mangrove cay decline in Belize.

Coastal eutrophication is an issue of serious global concern and although nutrient subsidies can enhance primary productivity of coastal wetlands, they can be detrimental to their long-term maintenance. By supplying nutrients to coastal ecosystems at levels comparable to intensive agriculture practices, roosting colonial waterbirds provide a natural experimental design to examine the impacts of anthropogenic nutrient enrichment in these systems. We tested the hypothesis that long-term nutrient enrichment from bird guano deposition is linked to declines in island size, which may subsequently decrease the stability and resilience of mangrove cays in Belize.

Minimalistic peptidic scaffolds harbouring an artificial carbene-containing amino acid modulate reductase activity.

Inspired by the boom of new artificial metalloenzymes, we developed an Fmoc-protected histidinium salt (Hum) as N-heterocyclic carbene precursor. Hum was placed solid-phase peptide synthesis into short 7-mer peptides. Upon iridation, the metallo-peptidic construct displayed activity in catalytic hydrogenation that outperforms small molecule analogues and which is dependent on the peptide sequence, a typical feature of metalloenzymes.

Mangrove growth response to experimental warming is greatest near the range limit in northeast Florida.

Shrubs are invading into grasslands around the world, but we don't yet know how these shrubs will fare in a warmer future. In ecotonal coastal wetland ecosystems, woody mangroves are encroaching into herbaceous salt marshes owing to changes in temperature, precipitation, and sediment dynamics. Increasing mangrove biomass in wetlands often increases carbon storage, which is high in these productive ecosystems, but little is known about how mangrove growth will change in response to warming.

Salinity has little effect on photosynthetic and respiratory responses to seasonal temperature changes in black mangrove (Avicennia germinans) seedlings.

Temperature and salinity are important regulators of mangrove range limits and productivity, but the physiological responses of mangroves to the interactive effects of temperature and salinity remain uncertain. We tested the hypothesis that salinity alters photosynthetic responses to seasonal changes in temperature and vapor pressure deficit (D), as well as thermal acclimation _of leaf respiration in black mangrove (Avicennia germinans). To test this hypothesis, we grew seedlings of A.

Hurricanes overcome migration lag and shape intraspecific genetic variation beyond a poleward mangrove range limit.

Expansion of many tree species lags behind climate change projections. Extreme storms can rapidly overcome this lag, especially for coastal species, but how will storm-driven expansion shape intraspecific genetic variation? Do storms provide recruits only from the nearest sources, or from more distant sources? Answers to these questions have ecological and evolutionary implications, but empirical evidence is absent from the literature. In 2017, Hurricane Irma provided an opportunity to address this knowledge gap at the northern range limit of the neotropical black mangrove (Avicennia germinans) on the Atlantic coast of Florida, USA.

Mangroves give cause for conservation optimism, for now.

Friess et al. discuss the results of conservation efforts for mangrove forests in recent years.

Is the central-marginal hypothesis a general rule? Evidence from three distributions of an expanding mangrove species, Avicennia germinans (L.) L.

The central-marginal hypothesis (CMH) posits that range margins exhibit less genetic diversity and greater inter-population genetic differentiation compared to range cores. CMH predictions are based on long-held "abundant-centre" assumptions of a decline in ecological conditions and abundances towards range margins. Although much empirical research has confirmed CMH, exceptions remain almost as common.

Climate-driven regime shifts in a mangrove-salt marsh ecotone over the past 250 years.

Climate change is driving the tropicalization of temperate ecosystems by shifting the range edges of numerous species poleward. Over the past few decades, mangroves have rapidly displaced salt marshes near multiple poleward mangrove range limits, including in northeast Florida. It is uncertain whether such mangrove expansions are due to anthropogenic climate change or natural climate variability.

Mangrove microclimates alter seedling dynamics at the range edge.

Recent climate warming has led to asynchronous species migrations, with major consequences for ecosystems worldwide. In woody communities, localized microclimates have the potential to create feedback mechanisms that can alter the rate of species range shifts attributed to macroclimate drivers alone. Mangrove encroachment into saltmarsh in many areas is driven by a reduction in freeze events, and this encroachment can further modify local climate, but the subsequent impacts on mangrove seedling dynamics are unknown.

Indirect effects of ecosystem engineering combine with consumer behaviour to determine the spatial distribution of herbivory.

Ecosystem engineers alter environments by creating, modifying or destroying habitats. The indirect impacts of ecosystem engineering on trophic interactions should depend on the combination of the spatial distribution of engineered structures and the foraging behaviour of consumers that use these structures as refuges. In this study, we assessed the indirect effects of ecosystem engineering by a wood-boring beetle in a neotropical mangrove forest system.

Review of the ecosystem service implications of mangrove encroachment into salt marshes.

Salt marsh and mangrove have been recognized as being among the most valuable ecosystem types globally in terms of their supply of ecosystem services and support for human livelihoods. These coastal ecosystems are also susceptible to the impacts of climate change and rising sea levels, with evidence of global shifts in the distribution of mangroves, including encroachment into salt marshes. The encroachment of woody mangrove shrubs and trees into herbaceous salt marshes may represent a substantial change in ecosystem structure, although resulting impacts on ecosystem functions and service provisions are largely unknown.

Mangrove dieback during fluctuating sea levels.

Recent evidence indicates that climate change and intensification of the El Niño Southern Oscillation (ENSO) has increased variation in sea level. Although widespread impacts on intertidal ecosystems are anticipated to arise from the sea level seesaw associated with climate change, none have yet been demonstrated. Intertidal ecosystems, including mangrove forests are among those ecosystems that are highly vulnerable to sea level rise, but they may also be vulnerable to sea level variability and extreme low sea level events.

Chronic warming stimulates growth of marsh grasses more than mangroves in a coastal wetland ecotone.

Increasing temperatures and a reduction in the frequency and severity of freezing events have been linked to species distribution shifts. Across the globe, mangrove ranges are expanding toward higher latitudes, likely due to diminishing frequency of freezing events associated with climate change. Continued warming will alter coastal wetland plant dynamics both above- and belowground, potentially altering plant capacity to keep up with sea level rise.

Precocious reproduction increases at the leading edge of a mangrove range expansion.

Climate change-driven shifts in species ranges are ongoing and expected to increase. However, life-history traits may interact with climate to influence species ranges, potentially accelerating or slowing range shifts in response to climate change. Tropical mangroves have expanded their ranges poleward in the last three decades.

Nutrient enrichment intensifies hurricane impact in scrub mangrove ecosystems in the Indian River Lagoon, Florida, USA.

Mangroves are an ecological assemblage of trees and shrubs adapted to grow in intertidal environments along tropical, subtropical, and warm temperate coasts. Despite repeated demonstrations of their ecologic and economic value, multiple stressors including nutrient over-enrichment threaten these and other coastal wetlands globally. These ecosystems will be further stressed if tropical storm intensity and frequency increase in response to global climate changes.

Environmental tolerances of rare and common mangroves along light and salinity gradients.

Although mangroves possess a variety of morphological and physiological adaptations for life in a stressful habitat, interspecific differences in survival and growth under different environmental conditions can shape their local and geographic distributions. Soil salinity and light are known to affect mangrove performance, often in an interactive fashion. It has also been hypothesized that mangroves are intrinsically shade intolerant due to the high physiological cost of coping with saline flooded soils.

Variable nutrient stoichiometry (carbon:nitrogen:phosphorus) across trophic levels determines community and ecosystem properties in an oligotrophic mangrove system.

Our study investigated the carbon:nitrogen:phosphorus (C:N:P) stoichiometry of mangrove island of the Mesoamerican Barrier Reef (Twin Cays, Belize). The C:N:P of abiotic and biotic components of this oligotrophic ecosystem was measured and served to build networks of nutrient flows for three distinct mangrove forest zones (tall seaward fringing forest, inland dwarf forests and a transitional zone). Between forest zones, the stoichiometry of primary producers, heterotrophs and abiotic components did not change significantly, but there was a significant difference in C:N:P, and C, N, and P biomass, between the functional groups mangrove trees, other primary producers, heterotrophs, and abiotic components.

Trophic behaviour of juvenile reef fishes inhabiting interlinked mangrove-seagrass habitats in offshore mangrove islets.

Stable isotope (δ(13)C and δ(15)N) and gut content analyses were used to investigate size-related feeding habits of four reef fishes (the beaugregory Stegastes leucostictus, the french grunt Haemulon flavolineatum, the schoolmaster snapper Lutjanus apodus and the yellowtail snapper Ocyurus chrysurus) inhabiting an offshore (non-estuarine) mangrove islet off Belize, Central America. Comparisons of isotopic niche space and Schoener diet similarity index suggested a low to moderate degree of niche overlap between fish size groups. The δ(13)C gradient between mangrove and seagrass prey as well as results of Bayesian mixing models revealed that sampled fishes relied mostly on seagrass prey items.

Integrating physiological threshold experiments with climate modeling to project mangrove species' range expansion.

Predictions of climate-related shifts in species ranges have largely been based on correlative models. Due to limitations of these models, there is a need for more integration of experimental approaches when studying impacts of climate change on species distributions. Here, we used controlled experiments to identify physiological thresholds that control poleward range limits of three species of mangroves found in North America.