Nicholas R. Record

Slow adaptation in the face of rapid warming leads to collapse of the Gulf of Maine cod fishery.

Several studies have documented fish populations changing in response to long-term warming. Over the past decade, sea surface temperatures in the Gulf of Maine increased faster than 99% of the global ocean. The warming, which was related to a northward shift in the Gulf Stream and to changes in the Atlantic Multidecadal Oscillation and Pacific Decadal Oscillation, led to reduced recruitment and increased mortality in the region’s Atlantic cod (Gadus morhua) stock. Failure to recognize the impact of warming on cod contributed to overfishing. Recovery of this fishery depends on sound management, but the size of the stock depends on future temperature conditions. The experience in the Gulf of Maine highlights the need to incorporate environmental factors into resource management. Warming waters prevented cod recovery in the North Atlantic. Double jeopardy In the best of worlds, exploited fish stocks are monitored so that harvest quotas protect the reproductive ability of the population. Climate change is likely to complicate this process substantially. Pershing et al. found that cod stocks declined continuously during intense warming in the North Atlantic. Fisheries quotas, even though they were responsibly set and followed by fishers, decreased the reproductive rate. Thus, managing fisheries in a warming world is going to be increasingly problematic. Science, this issue p. 809

The biogeography of marine plankton traits

Changes in marine plankton communities driven by environmental variability impact the marine food web and global biogeochemical cycles of carbon and other elements. To predict and assess these community shifts and their consequences, ecologists are increasingly investigating how the functional traits of plankton determine their relative fitness along environmental and biological gradients. Laboratory, field and modelling studies are adopting this trait-based approach to map the biogeography of plankton traits that underlies variations in plankton communities. Here, we review progress towards understanding the regulatory roles of several key plankton functional traits, including cell size, N2 -fixation and mixotrophy among phytoplankton, and body size, ontogeny and feeding behaviour for zooplankton. The trait biogeographical approach sheds light on what structures plankton communities in the current ocean, as well as under climate change scenarios, and also allows for finer resolution of community function because community trait composition determines the rates of significant processes, including carbon export. Although understanding of trait biogeography is growing, uncertainties remain that stem, in part, from the paucity of observations describing plankton functional traits. Thus, in addition to recommending widespread adoption of the trait-based approach, we advocate for enhanced collection, standardisation and dissemination of plankton functional trait data.

The Impact of Whaling on the Ocean Carbon Cycle: Why Bigger Was Better

Background Humans have reduced the abundance of many large marine vertebrates, including whales, large fish, and sharks, to only a small percentage of their pre-exploitation levels. Industrial fishing and whaling also tended to preferentially harvest the largest species and largest individuals within a population. We consider the consequences of removing these animals on the oceans ability to store carbon. Methodology/Principal Findings Because body size is critical to our arguments, our analysis focuses on populations of baleen whales. Using reconstructions of pre-whaling and modern abundances, we consider the impact of whaling on the amount of carbon stored in living whales and on the amount of carbon exported to the deep sea by sinking whale carcasses. Populations of large baleen whales now store 9.1×106 tons less carbon than before whaling. Some of the lost storage has been offset by increases in smaller competitors; however, due to the relative metabolic efficiency of larger organisms, a shift toward smaller animals could decrease the total community biomass by 30% or more. Because of their large size and few predators, whales and other large marine vertebrates can efficiently export carbon from the surface waters to the deep sea. We estimate that rebuilding whale populations would remove 1.6×105 tons of carbon each year through sinking whale carcasses. Conclusions/Significance Even though fish and whales are only a small portion of the oceans overall biomass, fishing and whaling have altered the oceans ability to store and sequester carbon. Although these changes are small relative to the total ocean carbon sink, rebuilding populations of fish and whales would be comparable to other carbon management schemes, including ocean iron fertilization.

Major role of nitrite-oxidizing bacteria in dark ocean carbon fixation

Dissolved inorganic carbon fixers revealed Most of the ocean is dark. Yet it is in this darkness, away from photosynthesizing sunlight, that most planetary carbon cycling occurs. Pachiadaki et al. show that nitrite-oxidizing bacteria in one phylum are the predominant fixers of dissolved inorganic carbon in the mesopelagic ocean. The authors sequenced thousands of single amplified genomes of marine prokaryotes. They identified more than 30 nitrite-oxidizing obligate chemoautotrophic bacteria that were unable to transport carbohydrate and that expressed nitrite oxidoreductase. This enzyme provides electrons to drive a reverse tricarboxylic acid cycle that fixes the carbon. Many of the genomes also suggest organisms that have the capacity to produce ammonium and other substrates, possibly to feed nitrite-producing metabolic partners. Science, this issue p. 1046 Obligate chemoautotrophic Nitrospinae bacteria make a major contribution to mesopelagic inorganic carbon fixation. Carbon fixation by chemoautotrophic microorganisms in the dark ocean has a major impact on global carbon cycling and ecological relationships in the ocean’s interior, but the relevant taxa and energy sources remain enigmatic. We show evidence that nitrite-oxidizing bacteria affiliated with the Nitrospinae phylum are important in dark ocean chemoautotrophy. Single-cell genomics and community metagenomics revealed that Nitrospinae are the most abundant and globally distributed nitrite-oxidizing bacteria in the ocean. Metaproteomics and metatranscriptomics analyses suggest that nitrite oxidation is the main pathway of energy production in Nitrospinae. Microautoradiography, linked with catalyzed reporter deposition fluorescence in situ hybridization, indicated that Nitrospinae fix 15 to 45% of inorganic carbon in the mesopelagic western North Atlantic. Nitrite oxidation may have a greater impact on the carbon cycle than previously assumed.

Protozoan Parasites of Bivalve Molluscs: Literature Follows Culture

Bivalve molluscs are key components of the estuarine environments as contributors to the trophic chain, and as filter –feeders, for maintaining ecosystem integrity. Further, clams, oysters, and scallops are commercially exploited around the world both as traditional local shellfisheries, and as intensive or semi–intensive farming systems. During the past decades, populations of those species deemed of environmental or commercial interest have been subject to close monitoring given the realization that these can suffer significant decline, sometimes irreversible, due to overharvesting, environmental pollution, or disease. Protozoans of the genera Perkinsus, Haplosporidium, Marteilia, and Bonamia are currently recognized as major threats for natural and farmed bivalve populations. Since their identification, however, the variable publication rates of research studies addressing these parasitic diseases do not always appear to reflect their highly significant environmental and economic impact. Here we analyzed the peer– reviewed literature since the initial description of these parasites with the goal of identifying potential milestone discoveries or achievements that may have driven the intensity of the research in subsequent years, and significantly increased publication rates. Our analysis revealed that after initial description of the parasite as the etiological agent of a given disease, there is a time lag before a maximal number of yearly publications are reached. This has already taken place for most of them and has been followed by a decrease in publication rates over the last decade (20– to 30– year lifetime in the literature). Autocorrelation analyses, however, suggested that advances in parasite purification and culture methodologies positively drive publication rates, most likely because they usually lead to novel molecular tools and resources, promoting mechanistic studies. Understanding these trends should help researchers in prioritizing research efforts for these and other protozoan parasites, together with their development as model systems for further basic and translational research in parasitic diseases.

First principles of copepod development help explain global marine diversity patterns

A major goal of modern ecology is to understand macroecological patterns based on their mechanistic underpinnings. The metabolic theory of ecology predicts a monotonic increase of biodiversity with temperature based on the principles of metabolism. For marine copepods, observations have shown that while biodiversity does increase with temperature, the theory’s prediction overestimates the slope of this relationship by a factor of two. By relaxing the theory’s assumption that size is invariant with respect to temperature, and by incorporating a mechanistic description of copepod development into the theory, we provide an adjusted prediction that agrees with the observed relationship. The addition of development into the theory adds the potential to refine the prediction for a wider range of taxa, to account for discrepancies between prediction and observations, and to describe a wider variety of temperature–richness relationships.

Response to Comments on “Slow adaptation in the face of rapid warming leads to collapse of the Gulf of Maine cod fishery”

Palmer et al. and Swain et al. suggest that our “extra mortality” time series is spurious. In response, we show that including temperature-dependent mortality improves abundance estimates and that warming waters reduce growth rates in Gulf of Maine cod. Far from being spurious, temperature effects on this stock are clear, and continuing to ignore them puts the stock in jeopardy.

The power and pitfalls of Dirichlet-multinomial mixture models for ecological count data

The Dirichlet-multinomial mixture model (DMM) and its extensions provide powerful new tools for interpreting the ecological dynamics underlying taxon abundance data. However, like many complex models, how effectively they capture the many features of empirical data is not well understood. In this work, we expand the DMM to an infinite mixture model (iDMM) and use posterior predictive distributions (PPDs) to explore the performance in three case studies, including two amplicon metagenomic time series. We avoid concentrating on fluctuations within individual taxa and instead focus on consortial-level dynamics, using straight-forward methods for visualizing this perspective. In each study, the iDMM appears to perform well in organizing the data as a framework for biological interpretation. Using the PPDs, we also observe several exceptions where the data appear to significantly depart from the model in ways that give useful ecological insight. We summarize the conclusions as a set of considerations for field researchers: problems with samples and taxa; relevant scales of ecological fluctuation; additional niches as outgroups; and possible violations of niche neutrality.

Quantifying Tradeoffs for Marine Viruses

The effects of viruses on marine microbial communities are myriad. The high biodiversity of viruses and their complex interactions with diverse hosts makes it a challenge to link modeling work with experimental work. In various trophic groups, trait-based approaches have helped to simplify this complexity, as traits describe organism properties in terms of taxon-transcending units, allowing for easier identification of generic, underlying principles. By predicting large-scale biogeography of different plankton functional types based on key sets of traits and their associated tradeoffs, these approaches have made major contributions to our understanding of global biogeochemistry and ecology. This review addresses the question of how a trait-based approach can make contributions toward understanding marine virus ecology. We review and synthesize current knowledge on virus traits with a focus on quantifying the associated tradeoffs. We use three case studies--virulence, host range, and cost of resistance--to illustrate how quantification of tradeoffs can help to explain observed patterns, generate hypotheses, and improve our theoretical understanding of virus ecology. Using a nutrient-susceptible-infected-virus model as a framework, we discuss tradeoffs as a link between model building (theory) and experimental design (practice). Finally, we address how insights from virus ecology can contribute back to the trait-based ecology community.

Coastal amplification of supply and transport (CAST): a new hypothesis about the persistence of Calanus finmarchicus in the Gulf of Maine

hypothesis about the persistence of Calanus finmarchicus in the Gulf of Maine Rubao Ji*, Zhixuan Feng, Benjamin T. Jones, Cameron Thompson, Changsheng Chen, Nicholas R. Record, and Jeffrey A. Runge Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA School of Marine Sciences, University of Maine and Gulf of Maine Research Institute, Portland, ME, USA School for Marine Science and Technology, University of Massachusetts Dartmouth, Dartmouth, MA, USA Bigelow Laboratory for Ocean Sciences, 60 Bigelow Dr, East Boothbay, ME 04544, USA