Shortened food chain length in a fished versus unfished coral reef.

Direct exploitation through fishing is driving dramatic declines of wildlife populations in ocean environments, particularly for predatory and large-bodied taxa. Despite wide recognition of this pattern and well-established consequences of such trophic downgrading on ecosystem function, there have been few empirical studies examining the effects of fishing on whole system trophic architecture. Understanding these kinds of structural impacts is especially important in coral reef ecosystems-often heavily fished and facing multiple stressors. Given the often high dietary flexibility and numerous functional redundancies in diverse ecosystems such as coral reefs, it is important to establish whether web architecture is strongly impacted by fishing pressure or whether it might be resilient, at least to moderate-intensity pressure. To examine this question, we used a combination of bulk and compound-specific stable isotope analyses measured across a range of predatory and low-trophic-level consumers between two coral reef ecosystems that differed with respect to fishing pressure but otherwise remained largely similar. We found that even in a high-diversity system with relatively modest fishing pressure, there were strong reductions in the trophic position (TP) of the three highest TP consumers examined in the fished system but no effects on the TP of lower-level consumers. We saw no evidence that this shortening of the affected food webs was being driven by changes in basal resource consumption, for example, through changes in the spatial location of foraging by consumers. Instead, this likely reflected internal changes in food web architecture, suggesting that even in diverse systems and with relatively modest pressure, human harvest causes significant compressions in food chain length. This observed shortening of these food webs may have many important emergent ecological consequences for the functioning of ecosystems impacted by fishing or hunting. Such important structural shifts may be widespread but unnoticed by traditional surveys. This insight may also be useful for applied ecosystem managers grappling with choices about the relative importance of protection for remote and pristine areas and the value of strict no-take areas to protect not just the raw constituents of systems affected by fishing and hunting but also the health and functionality of whole systems.

Bubble Stripping as a Tool To Reduce High Dissolved CO2 in Coastal Marine Ecosystems.

High dissolved CO2 concentrations in coastal ecosystems are a common occurrence due to a combination of large ecosystem metabolism, shallow water, and long residence times. Many important coastal species may have adapted to this natural variability over time, but eutrophication and ocean acidification may be perturbing the water chemistry beyond the bounds of tolerance for these organisms. We are currently limited in our ability to deal with the geochemical changes unfolding in our coastal ocean. This study helps to address this deficit of solutions by introducing bubble stripping as a novel geochemical engineering approach to reducing high CO2 in coastal marine ecosystems. We use a process-based model to find that air/sea gas exchange rates within a bubbled system are 1-2 orders of magnitude higher than within a nonbubbled system. By coupling bubbling-enhanced ventilation to a coastal ecosystem metabolism model, we demonstrate that strategically timed bubble plumes can mitigate exposure to high CO2 under present-day conditions and that exposure mitigation is enhanced in the more acidic conditions predicted by the end of the century. We argue that shallow water CO2 bubble stripping should be considered among the growing list of engineering approaches intended to increase coastal resilience in a changing ocean.

Positive and negative effects of a threatened parrotfish on reef ecosystems.

Species that are strong interactors play disproportionately important roles in the dynamics of natural ecosystems. It has been proposed that their presence is necessary for positively shaping the structure and functioning of ecosystems. We evaluated this hypothesis using the case of the world's largest parrotfish (Bolbometopon muricatum), a globally imperiled species. We used direct observation, animal tracking, and computer simulations to examine the diverse routes through which B. muricatum affects the diversity, dispersal, relative abundance, and survival of the corals that comprise the foundation of reef ecosystems. Our results suggest that this species can influence reef building corals in both positive and negative ways. Field observation and simulation outputs indicated that B. muricatum reduced the abundance of macroalgae that can outcompete corals, but they also feed directly on corals, decreasing coral abundance, diversity, and colony size. B. muricatum appeared to facilitate coral advancement by mechanically dispersing coral fragments and opening up bare space for coral settlement, but they also damaged adult corals and remobilized a large volume of potentially stressful carbonate sediment. The impacts this species has on reefs appears to be regulated in part by its abundance-the effects of B. muricatum were more intense in simulation scenarios populated with high densities of these fish. Observations conducted in regions with high and low predator (e.g., sharks) abundance generated results that are consistent with the hypothesis that these predators of B. muricatum may play a role in governing their abundance; thus, predation may modulate the intensity of the effects they have on reef dynamics. Overall our results illustrate that functionally unique and threatened species may not have universally positive impacts on ecosystems and that it may be necessary for environmental managers to consider the diverse effects of such species and the forces that mediate the strength of their influence.

The roles of productivity and ecosystem size in determining food chain length in tropical terrestrial ecosystems.

Many different drivers, including productivity, ecosystem size, and disturbance, have been considered to explain natural variation in the length of food chains. Much remains unknown about the role of these various drivers in determining food chain length, and particularly about the mechanisms by which they may operate in terrestrial ecosystems, which have quite different ecological constraints than aquatic environments, where most food chain length studies have been thus far conducted. In this study, we tested the relative importance of ecosystem size and productivity in influencing food chain length in a terrestrial setting. We determined that (1) there is no effect of ecosystem size or productive space on food chain length; (2) rather, food chain length increases strongly and linearly with productivity; and (3) the observed changes in food chain length are likely achieved through a combination of changes in predator size, predator behavior, and consumer diversity along gradients in productivity. These results lend new insight into the mechanisms by which productivity can drive changes in food chain length, point to potential for systematic differences in the drivers of food web structure between terrestrial and aquatic systems, and challenge us to consider how ecological context may control the drivers that shape food chain length.

Plants cause ecosystem nutrient depletion via the interruption of bird-derived spatial subsidies.

Plant introductions and subsequent community shifts are known to affect nutrient cycling, but most such studies have focused on nutrient enrichment effects. The nature of plant-driven nutrient depletions and the mechanisms by which these might occur are relatively poorly understood. In this study we demonstrate that the proliferation of the commonly introduced coconut palm, Cocos nucifera, interrupts the flow of allochthonous marine subsidies to terrestrial ecosystems via an indirect effect: impact on birds. Birds avoid nesting or roosting in C. nucifera, thus reducing the critical nutrient inputs they bring from the marine environment. These decreases in marine subsidies then lead to reductions in available soil nutrients, decreases in leaf nutrient quality, diminished leaf palatability, and reduced herbivory. This nutrient depletion pathway contrasts the more typical patterns of nutrient enrichment that follow plant species introductions. Research on the effects of spatial subsidy disruptions on ecosystems has not yet examined interruptions driven by changes within the recipient community, such as plant community shifts. The ubiquity of coconut palm introductions across the tropics and subtropics makes these observations particularly noteworthy. Equally important, the case of C. nucifera provides a strong demonstration of how plant community changes can dramatically impact the supply of allochthonous nutrients and thereby reshape energy flow in ecosystems.

Zinc stimulation of coastal productivity in low carbon dioxide environments.

Zinc (Zn) is a key micronutrient used by phytoplankton for carbon (C) acquisition, yet there have been few observations of its influence on natural oceanic phytoplankton populations. In this study, we observed Zn limitation of growth in the natural phytoplankton community of Terra Nova Bay, Antarctica, due to low (~220 µatm) pCO2 conditions, in addition to primary iron (Fe) limitation. Shipboard incubation experiments amended with Zn and Fe resulted in significantly higher chlorophyll a content and dissolved inorganic carbon drawdown compared to Fe addition alone. Zn and Fe response proteins detected in incubation and environmental biomass provided independent verification of algal co-stress for these micronutrients. These observations of Zn limitation under low pCO2 conditions demonstrate Zn can influence coastal primary productivity. Yet, as surface ocean pCO2 rises with continued anthropogenic emissions, the occurrence of Zn/C co-limitation will become rarer, impacting the biogeochemical cycling of Zn and other trace metal micronutrients.

Assessing the effects of large mobile predators on ecosystem connectivity.

Large predators are often highly mobile and can traverse and use multiple habitats. We know surprisingly little about how predator mobility determines important processes of ecosystem connectivity. Here we used a variety of data sources drawn from Palmyra Atoll, a remote tropical marine ecosystem where large predators remain in high abundance, to investigate how these animals foster connectivity. Our results indicate that three of Palmyra's most abundant large predators (e.g., two reef sharks and one snapper) use resources from different habitats creating important linkages across ecosystems. Observations of cross-system foraging such as this have important implications for the understanding of ecosystem functioning, the management of large-predator populations, and the design of conservation measures intended to protect whole ecosystems. In the face of widespread declines of large, mobile predators, it is important that resource managers, policy makers, and ecologists work to understand how these predators create connectivity and to determine the impact that their depletions may be having on the integrity of these linkages.

Extreme longevity in proteinaceous deep-sea corals.

Deep-sea corals are found on hard substrates on seamounts and continental margins worldwide at depths of 300 to approximately 3,000 m. Deep-sea coral communities are hotspots of deep ocean biomass and biodiversity, providing critical habitat for fish and invertebrates. Newly applied radiocarbon age dates from the deep water proteinaceous corals Gerardia sp. and Leiopathes sp. show that radial growth rates are as low as 4 to 35 mum year(-1) and that individual colony longevities are on the order of thousands of years. The longest-lived Gerardia sp. and Leiopathes sp. specimens were 2,742 years and 4,265 years, respectively. The management and conservation of deep-sea coral communities is challenged by their commercial harvest for the jewelry trade and damage caused by deep-water fishing practices. In light of their unusual longevity, a better understanding of deep-sea coral ecology and their interrelationships with associated benthic communities is needed to inform coherent international conservation strategies for these important deep-sea habitat-forming species.

Autonomous submersible multiport water sampler.

Oceanography and limnology projects often require the collection of water samples for chemical analysis. Manual water sample collection is labor-intensive and often difficult, especially in remote locations or during nighttime hours. Here we describe a compact and inexpensive autonomous submersible multiport water sampler (AutoSampler) that is largely fabricated with off-the-shelf parts making it easier to build and maintain. The system can collect up to 12 discrete samples at user controllable times or intervals and is operated using open source Arduino hardware and software that can be user modified to meet deployment requirements. While the underwater pressure housing presented here is custom built from readily available materials, there are many commercially available pressure case options that can be used as a substitute. The electronic mounting plates and battery pack are designed so that they can easily be adapted to fit into other pressure case housings. Samples can be collected into bags or syringes and sample volume is set by adjusting how long the peristaltic pump is actuated. This AutoSampler allows research that would otherwise be too labor-intensive or logistically difficult to conduct, especially in remote locations.

Automated multiport flow-through water pumping and sampling system.

Flow-through systems are often used in aquarium and aquaculture facilities, laboratories, and aboard research vessels and other mobile systems to collect, analyze, and monitor water properties as they vary across time and location. These systems most often intake water from a single source and deliver it to a suite of flow-through sensors after which waste water either exits the system or is recirculated back to the source. Here we describe a system that is designed to take water from multiple sources via a multiport valve manifold and deliver it to a common sample stream, facilitating analysis by a single suite of flow-through and probe type sensors. Build cost depends on the manifold design and the number of valves, but generally under $9000. The inclusion of a Free Surface Interface Cup (FSIC) allows probe type sensors or sample "sippers" that require unpressurized conditions to be utilized down-stream of the pumping system and manifold. With the exception of the multiport sampling manifold, all components of this system are available off-the-shelf, simplifying construction, service, and maintenance. The operating system code is open source and based on the Arduino platform, enabling users to customize the code to better fit their requirements.

Autonomous underwater pumping system.

We present an inexpensive autonomous underwater pumping system that is lightweight, compact, independent, and versatile, making it easy to deploy in a multitude of settings. This system can be used to pump water into discrete and flow-through sensor systems. With the exception of the custom built pressure case housing, this system can be fabricated with off-the-shelf parts, making it easier to maintain. This system uses open source Arduino software code for easier customization and operations. The electronics and battery pack used to power this system can be adapted to fit into commercially available pressure case housings.

Author Correction: Coral carbon isotope sensitivity to growth rate and water depth with paleo-sea level implications.

The original version of the Source Data associated with this Article included an error, in which the 'Fiji AB d13C-Suess' data point and the 'TNI2 d13C-Suess Effect' data point for the year '1950.5' where incorrectly omitted from the Figure 3 tab. The missing values are '-0.24' and '-0.64', respectively. The HTML has been updated to include a corrected version of Source Data.

Coral carbon isotope sensitivity to growth rate and water depth with paleo-sea level implications.

Although reef coral skeletal carbon isotopes (δ13C) are routinely measured, interpretation remains controversial. Here we show results of a consistent inverse relationship between coral δ13C and skeletal extension rate over the last several centuries in Porites corals at Fiji, Tonga, Rarotonga and American Samoa in the southwest Pacific. Beginning in the 1950s, this relationship breaks down as the atmospheric 13C Suess effect shifts skeletal δ13C > 1.0‰ lower. We also compiled coral δ13C from a global array of sites and find that mean coral δ13C decreases by -1.4‰ for every 5 m increase in water depth (R = 0.68, p < 0.01). This highlights the fundamental sensitivity of coral δ13C to endosymbiotic photosynthesis. Collectively, these results suggest that photosynthetic rate largely determines mean coral δ13C while changes in extension rate and metabolic effects over time modulate skeletal δ13C around this mean value. The newly quantified coral δ13C-water depth relationship may be an effective tool for improving the precision of paleo-sea level reconstruction using corals.

Living coral tissue slows skeletal dissolution related to ocean acidification.

Climate change is causing major changes to marine ecosystems globally, with ocean acidification of particular concern for coral reefs. Using a 200 d in situ carbon dioxide enrichment study on Heron Island, Australia, we simulated future ocean acidification conditions, and found reduced pH led to a drastic decline in net calcification of living corals to no net growth, and accelerated disintegration of dead corals. Net calcification declined more severely than in previous studies due to exposure to the natural community of bioeroding organisms in this in situ study and to a longer experimental duration. Our data suggest that reef flat corals reach net dissolution at an aragonite saturation state (ΩAR) of 2.3 (95% confidence interval: 1.8-2.8) with 100% living coral cover and at ΩAR > 3.5 with 30% living coral cover. This model suggests that areas of the reef with relatively low coral mortality, where living coral cover is high, are likely to be resistant to carbon dioxide-induced reef dissolution.

Recent history of persistent organic pollutants (PAHs, PCBs, PBDEs) in sediments from a large tropical lake.

210Pb-dated sediment cores and surface sediments from Lake Chapala (LC), Mexico, were analyzed to assess the temporal trends in concentrations and fluxes of persistent organic pollutants (POPs: PAHs, PCBs and PBDEs). Total sediment concentrations of PAHs (95-1,482 ng g-1), PCBs (9-27 ng g-1) and PBDEs (0.2-2.5 ng g-1) were indicative of moderate to intense contamination. The POP concentrations have progressively increased since the 1990s. The light molecular weight PAHs, and the prevalence of PCB congeners with low-chlorination levels (e.g., di- to tri-CB) and low-to medium-brominated (tri- to penta-BDE) PBDEs in most sections of the sediment profiles, suggested that these POPs have most likely reached these sediments by long-range atmospheric transport from distant sources; although the significant presence of heavier PAH, PCB and PBDE congeners in the topmost sediments, indicate that other nearby and local sources (soil erosion from the catchment, urban and industrial wastewaters discharges, as well as navigation) might have also contributed to the recent input of POPs to LC. Taking into account the relevance of LC as regional freshwater supply and commercial fishing ground, the potential risk posed by the organic contaminated sediments to the biota and human population should not be underestimated.

Acetoclastic Methanosaeta are dominant methanogens in organic-rich Antarctic marine sediments.

Despite accounting for the majority of sedimentary methane, the physiology and relative abundance of subsurface methanogens remain poorly understood. We combined intact polar lipid and metagenome techniques to better constrain the presence and functions of methanogens within the highly reducing, organic-rich sediments of Antarctica's Adélie Basin. The assembly of metagenomic sequence data identified phylogenic and functional marker genes of methanogens and generated the first Methanosaeta sp. genome from a deep subsurface sedimentary environment. Based on structural and isotopic measurements, glycerol dialkyl glycerol tetraethers with diglycosyl phosphatidylglycerol head groups were classified as biomarkers for active methanogens. The stable carbon isotope (δ13C) values of these biomarkers and the Methanosaeta partial genome suggest that these organisms are acetoclastic methanogens and represent a relatively small (0.2%) but active population. Metagenomic and lipid analyses suggest that Thaumarchaeota and heterotrophic bacteria co-exist with Methanosaeta and together contribute to increasing concentrations and δ13C values of dissolved inorganic carbon with depth. This study presents the first functional insights of deep subsurface Methanosaeta organisms and highlights their role in methane production and overall carbon cycling within sedimentary environments.

Examining the utility of coral Ba/Ca as a proxy for river discharge and hydroclimate variability at Coiba Island, Gulf of Chirquí, Panamá.

Panamá's extreme hydroclimate seasonality is driven by Intertropical Convergence Zone rainfall and resulting runoff. River discharge (Q) carries terrestrially-derived barium to coastal waters that can be recorded in coral. We present a Ba/Ca record (1996-1917) generated from a Porites coral colony in the Gulf of Chiriquí near Coiba Island (Panamá) to understand regional hydroclimate. Here coral Ba/Ca is correlated to instrumental Q (R=0.67, p<0.001), producing a seasonally-resolved Reduced Major Axis regression of Ba/Ca (µmol/mol)=Q (m3/s)×0.006±0.001 (µmol/mol)(m3/s)-1+4.579±0.151. Our results support work in the neighboring Gulf of Panamá that determined seawater Ba/Ca, controlled by Q, is correlated to coral Ba/Ca (LaVigne et al., 2016). Additionally, the Coiba coral Ba/Ca records at least 5 El Niño events and identified 22 of the 37 wet seasons with below average precipitation. These data corroborate the Q proxy and provide insight into the use of coral Ba/Ca as an El Niño and drought indicator.

Coral skeletal delta(15)N reveals isotopic traces of an agricultural revolution.

This study introduces a new method of tracing the history of nutrient loading in coastal oceans via delta(15)N analysis of organic nitrogen preserved in the skeleton of the massive Porites coral. Four coral cores were collected in Bali, Indonesia, from reefs exposed to high levels of fertilizers in agricultural run-off, from lagoonal corals impacted by sewage, and from a reef located 30 km offshore. Skeletal delta(15)N in the agriculturally exposed coral declined from 10.7+/-0.4 per thousand in 1970-1971, when synthetic fertilizers (-0.8 per thousand+/-0.2 per thousand) were introduced to Bali, to a depleted "anthropogenic" baseline of 3.5 per thousand+/-0.4% in the mid-1990s. delta(15)N values were negatively correlated with rainfall, suggesting that marine delta(15)N lowers during flood-bourn influxes of waste fertilizers. Reef cores exposed to untreated sewage in terrestrial discharge were enriched (7.8 and 7.3+/-0.4 per thousand), while the offshore core reflected background oceanic signals (6.2+/-0.4 per thousand). delta(15)N, N concentration, and C:N systematics indicate that the N isotopic composition of skeletal organic matter was generally well preserved over 30 years. We suggest that skeletal organic delta(15)N can serve as a recorder of past nitrogen sources. In Bali, this tracer suggests that the intensification of Western style agricultural practices since 1970 are contributing to the degradation of coastal coral reefs.

Conservation management options and actions: putative decline of coral cover at Palmyra Atoll, Northern Line Islands, as a case study.

Localised loss of live coral cover at Palmyra Atoll (central Pacific Ocean) has been attributed to increased temperature and/or sedimentation arising from alterations made to the lagoon system. It has been hypothesised that a causeway spanning the lagoon hinders water circulation, resulting in warmer and/or more turbid water flowing towards a site of high coral cover and diversity (Coral Gardens). Analyses of a multi-site and multi-year data set revealed no differences in mean temperature or turbidity values on either side of the causeway and provided no evidence of significantly warmer or more turbid water at Coral Gardens. We conclude that the putative decline in live coral cover cannot be attributed to the presence of the causeway and that proposed management actions involving modification to the causeway cannot achieve the conservation outcomes suggested of them.

Long-range atmospheric transport of persistent organic pollutants to remote lacustrine environments.

Concentrations, temporal trends and fluxes of persistent organic pollutants (POPs: PAHs, PCBs and PBDEs) were determined in soil and (210)Pb-dated sediment cores from remote lacustrine environments (El Tule and Santa Elena lakes) in rural areas of Central Mexico. In both areas, the concentrations of target analytes in soil and sediment samples were comparable and indicative of slightly contaminated environments. The prevalence of low-molecular-weight PAHs in soils suggested their mainly atmospheric origin, in contrast to the aquatic sediments where runoff contribution was also significant. Increasing contamination trends of PCBs and PBDEs were evident, showing maximum fluxes of 4.8 ± 2.1 and 0.3 ± 0.1 ng cm(-2) a(-1) for PCBs and PBDEs, respectively. The predominance of lower-brominated PBDEs and lower-chlorinated PCBs in soils and sediments indicated that their presence is mostly due to long-range atmospheric transport.