Naomi Levine

University of Southern California | USC · Department of Biological Sciences

The oceans sequester a vast amount of carbon thus playing a central role in the global carbon cycle. Assessing how carbon cycling will be impacted by climate change requires an improved understanding of microbial dynamics, which are responsible for most carbon transformations in the oceans. Current numerical models used for predicting future states...

Phytoplankton are photosynthetic marine microbes that affect food webs, nutrient cycles and climate regulation. Their roles are determined by correlated phytoplankton functional traits including cell size, chlorophyll content and cellular composition. Here, we explore patterns of evolution in interrelated trait values and correlations. Because both...

Microbial heterotrophs (‘picoheterotrophs’) drive global carbon cycling, but how to quantitatively organize their functional complexity remains unclear. Here, we generate a global-scale, mechanistic understanding of marine picoheterotrophic functional biogeography with a novel model-data synthesis. We build picoheterotrophic diversity into a trait-...

Microbial community dynamics on sinking particles control the amount of carbon that reaches the deep ocean and the length of time that carbon is stored, with potentially profound impacts on Earth’s climate. A mechanistic understanding of the controls on sinking particle distributions has been hindered by limited depth- and time-resolved sampling an...

Biogeochemical cycles constitute Earth’s life support system and distinguish our planet from others in this solar system. Microorganisms are the primary drivers of these cycles. Understanding the controls on marine microbial dynamics and how microbes will respond to environmental change is essential for building and assessing model-based forecasts...

Microbial community assembly is governed by complex interaction networks based on the secretion and exchange of metabolites. While the importance of trophic interactions (e.g. cross-feeding of metabolic byproducts) in structuring microbial communities is well-established, the roles of myriad natural products such as vitamins, siderophores, and anti...

Marine microbes like diatoms make up the base of marine food webs and drive global nutrient cycles. Despite their key roles in ecology, biogeochemistry, and biotechnology, we have limited empirical data on how forces other than adaptation may drive diatom diversification, especially in the absence of environmental change. One key feature of diatom...

Phytoplankton are responsible for half of all oxygen production and drive the ocean carbon cycle. Metabolic theory predicts that increasing global temperatures will cause phytoplankton to become more heterotrophic and smaller. Here, we uncover the metabolic trade-offs between cellular space, energy, and stress management driving phytoplankton therm...

Phytoplankton are responsible for half of all oxygen production and drive the ocean carbon cycle. Metabolic theory predicts that increasing global temperatures will cause phytoplankton to become more heterotrophic and smaller. Here we uncover the metabolic trade-offs between cellular space, energy, and stress management driving phytoplankton therma...

Heterotrophic microbes play an important role in the Earth System as key drivers of major biogeochemical cycles. Specifically, the consumption rate of organic matter is set by the interaction between diverse microbial communities and the chemical and physical environment in which they reside. Modeling these dynamics requires reducing the complexity...

Phytoplankton are photosynthetic marine microbes that affect food webs, nutrient cycles, and climate regulation. Their roles are determined by a correlated set of phytoplankton functional traits including cell size, chlorophyll content, and cellular composition. Here, we explore how interrelated trait values and correlations evolve. Because both ch...

Nitrification controls the oxidation state of bioavailable nitrogen. Distinct clades of chemoautotrophic microorganisms-predominantly ammonia-oxidizing ar-chaea (AOA) and nitrite-oxidizing bacteria (NOB)-regulate the two steps of nitrification in the ocean, but explanations for their observed relative abundances and nitrification rates remain incom...

Unicellular photosynthetic marine microbes, or phytoplankton, make up the base of marine food webs and drive global nutrient cycles. Despite their key roles in ecology and biogeochemistry, we have a limited understanding of how the basic features of their demographics along with dynamic environments affect trait evolution. A key feature of diatom e...

Nitrification controls the oxidation state of bioavailable nitrogen. Distinct clades of chemoautotrophic microorganisms – predominantly, ammonia-oxidizing archaea (AOA) and nitrite-oxidizing bacteria (NOB) – regulate the two steps of nitrification in the ocean, but explanations for their observed relative abundances and nitrification rates remain i...

The organic sulfur compounds dimethylsulfoniopropionate (DMSP) and dimethyl sulfoxide (DMSO) play major roles in the marine microbial food web and have substantial climatic importance as sources and sinks of dimethyl sulfide (DMS). Seasonal shifts in the abundance and diversity of the phytoplankton and bacteria that cycle DMSP are likely to impact...

To swim up gradients of nutrients, E. coli senses nutrient concentrations within its periplasm. For small nutrient molecules, periplasmic concentrations typically match extracellular concentrations. However, this is not necessarily the case for saccharides, such as maltose, which are transported into the periplasm via a specific porin. Previous obs...

One-quarter of photosynthesis-derived carbon on Earth rapidly cycles through a set of short-lived seawater metabolites that are generated from the activities of marine phytoplankton, bacteria, grazers and viruses. Here we discuss the sources of microbial metabolites in the surface ocean, their roles in ecology and biogeochemistry, and approaches th...

Sinking particulate organic carbon out of the surface ocean sequesters carbon on decadal to millennial timescales. Predicting the particulate carbon flux is therefore critical for understanding both global carbon cycling and the future climate. Microbes play a crucial role in particulate organic carbon degradation, but the impact of depth-dependent...

Ecological interactions between marine bacteria and phytoplankton play a pivotal role in governing the ocean’s major biogeochemical cycles. Among these, members of the marine Roseobacter Group (MRG) can establish mutualistic relationships with phytoplankton that are, in part, maintained by exchanges of the organosulfur compound, dimethylsulfoniopro...

Trait-based approaches to phytoplankton ecology have gained traction in recent decades as phenotypic traits are incorporated into ecological and biogeochemical models. Here, we use high-throughput phenotyping to explore both intra- and interspecific constraints on trait combinations that are expressed in the cosmopolitan marine diatom genus Thalass...

To swim up gradients of nutrients, E. coli senses nutrient concentrations within its periplasm. For small nutrient molecules, periplasmic concentrations typically match extracellular concentrations. However, this is not necessarily the case for saccharides, such as maltose, which is transported into the periplasm via a specific porin. Previous obse...

High-throughput methods for phenotyping microalgae are in demand across a variety of research and commercial purposes. Many microalgae can be readily cultivated in multi-well plates for experimental studies which can reduce overall costs, while measuring traits from low volume samples can reduce handling. Here we develop a high-throughput quantitat...

Ocean phytoplankton play a critical role in the global carbon cycle, contributing ∼50% of global photosynthesis. As planktonic organisms, phytoplankton encounter significant environmental variability as they are advected throughout the ocean. How this variability impacts phytoplankton growth rates and population dynamics remains unclear. Here, we s...

Microbes form the base of food webs and drive biogeochemical cycling. Predicting the effects of microbial evolution on global elemental cycles remains a significant challenge due to the sheer number of interacting environmental and trait combinations. Here, we present an approach for integrating multivariate trait data into a predictive model of tr...

Marine bacterial diversity is immense and believed to be driven in part by trade-offs in metabolic strategies. Here we consider heterotrophs that rely on organic carbon as an energy source and present a molecular-level model of cell metabolism that explains the dichotomy between copiotrophs—which dominate in carbon-rich environments—and oligotrophs...

Primary productivity in the nutrient-poor subtropical ocean gyres depends on new nitrogen inputs from nitrogen fixers that convert inert dinitrogen gas into bioavailable forms. Temperature and iron (Fe) availability constrain marine nitrogen fixation, and both are changing due to anthropogenic ocean warming. We examined the physiological responses...

Tropical forests are an important part of global water and energy cycles, but the mechanisms that drive seasonality of their land-atmosphere exchanges have proven challenging to capture in models. Here, we (1) report the seasonality of fluxes of latent heat (LE), sensible heat (H), and outgoing short and longwave radiation at four diverse tropical...

Significance Organic matter in the global ocean, soils, and sediments stores about five times more carbon than the atmosphere. Thus, the controls on the accumulation of organic matter are critical to global carbon cycling. However, we lack a quantitative understanding of these controls. This prevents meaningful descriptions of organic matter cyclin...

In the subtropical ocean, physical and biogeochemical patchiness exists across a range of spatial and temporal scales. As ocean surface temperatures rise, climate models suggest that the strength of basin-scale biological carbon pump may diminish due to increased stratification and depleted surface nutrients. However, global model predictions often...

News & Views Multi-omics and geochemical data reveal that dinoflagellates, abundant marine microorganisms, utilize numerous metabolic strategies to survive in diverse ocean environments.

Dimethylsulfoniopropionate (DMSP) is an important organic carbon and sulfur source in the surface ocean that fuels microbial activity and significantly impacts Earth’s climate. After three decades of research, the cellular role(s) of DMSP and environmental drivers of production remain enigmatic. Recent work suggests that cellular DMSP concentration...

Marine heterotrophic bacteria use a spectrum of nutrient uptake strategies, from that of copiotrophs—which dominate in nutrient-rich environments—to that of oligotrophs—which dominate in nutrient-poor environments. While copiotrophs possess numerous phosphotransferase systems (PTS), oligotrophs lack PTS and rely on ATP-binding cassette (ABC) transp...

Organic matter constitutes a key reservoir in global elemental cycles and the biological sequestration of carbon. However, our understanding of the dynamics of organic matter and its accumulation remains incomplete. Seemingly disparate hypotheses have been proposed to explain organic matter accumulation: the slow degradation of intrinsically recalc...

Microbes form the base of food webs and drive biogeochemical cycling. Predicting the effects of microbial evolution on global elemental cycles remains a significant challenge due to the sheer number of interacting environmental and trait combinations. Here we present an approach for modeling the interactive effects of de novo biological change and...

Marine microbes form the base of ocean food webs and drive ocean biogeochemical cycling. Yet little is known about the ability of microbial populations to adapt as they are advected through changing conditions. Here, we investigated the interplay between physical and biological timescales using a model of adaptation and an eddy-resolving ocean circ...

Remineralization of organic matter by heterotrophic organisms regulates the biological sequestration of carbon, thereby mediating atmospheric CO2. While surface nutrient supply impacts the elemental ratios of primary production, stoichiometric control by remineralization remains unclear. Here we develop a mechanistic description of remineralization...

The Ecosystem Demography model version 2.2 (ED-2.2) is a terrestrial biosphere model that simulates the biophysical, ecological, and biogeochemical dynamics of vertically and horizontally heterogeneous terrestrial ecosystems. In a companion paper (Longo et al., 2019a), we described how the model solves the energy, water, and carbon cycles, and veri...

Earth system models (ESMs) have been developed to represent the role of terrestrial ecosystems on the energy, water, and carbon cycles. However, many ESMs still lack representation of within-ecosystem heterogeneity and diversity. In this paper, we present the Ecosystem Demography model version 2.2 (ED-2.2). In ED-2.2, the biophysical and physiologi...

Ocean boundary current systems are key components of the climate system, are home to highly productive ecosystems, and have numerous societal impacts. Establishment of a global network of boundary current observing systems is a critical part of ongoing development of the Global Ocean Observing System. The characteristics of boundary current systems...

All known phototrophic metabolisms on Earth rely on one of three categories of energy-converting pigments: chlorophyll- a (rarely - d ), bacteriochlorophyll- a (rarely - b ), and retinal, which is the chromophore in rhodopsins. While the significance of chlorophylls in solar energy capture has been studied for decades, the contribution of retinal-b...

Remineralization of organic matter by heterotrophic organisms regulates the biological sequestration of carbon, thereby mediating atmospheric CO 2 . While surface nutrient supply impacts the elemental ratios of primary production, stoichiometric control by remineralization remains unclear. Here we develop a mechanistic description of remineralizati...

Sustained ocean time series are critical for characterizing marine ecosystem shifts in a time of accelerating, and at times unpredictable, changes. They represent the only means to distinguish between natural and anthropogenic forcings, and are the best tools to explore causal links and implications for human communities that depend on ocean resour...

Marine microbes form the base of ocean food webs and drive ocean biogeochemical cycling. Yet little is known about how microbial populations will evolve due to global change-driven shifts in ocean dynamics. Understanding adaptive timescales is critical where long-term trends (e.g. warming) are coupled to shorter-term advection dynamics that move or...

The Ecosystem Demography Model version 2.2 (ED-2.2) is a terrestrial biosphere model that simulates the biophysical and biogeochemical cycles of dynamic ecosystems while considering the role of vertical structure of plant communities and the heterogeneity of such structures across the landscape. In a companion paper, we described in detail how the...

Earth System Models (ESMs) have been developed to represent the role of terrestrial ecosystems on the energy, water, and carbon cycles. However, many ESMs still lack representation of within-ecosystem heterogeneity and diversity. In this manuscript, we present the Ecosystem Demography Model version 2.2 (ED-2.2). In ED-2.2, the biophysical and physi...

Dimethylsulfoniopropionate (DMSP) is an important labile component of the marine dissolved organic matter pool that is produced by the majority of eukaryotic marine phytoplankton and by many prokaryotes. Despite decades of research, the contribution of different environmental drivers of DMSP production to regional and seasonal variability remains u...

Oceanic time series have been instrumental in providing an understanding of biological, physical, and chemical dynamics in the oceans and how these processes change over time. However, the extrapolation of these results to larger oceanographic regions requires an understanding and characterization of local versus regional drivers of variability. He...

The cyanobacterium Trichodesmium fixes as much as half of the nitrogen (N2) that supports tropical open-ocean biomes, but its growth is frequently limited by iron (Fe) availability1,2. How future ocean warming may interact with this globally widespread Fe limitation of Trichodesmium N2 fixation is unclear³. Here, we show that the optimum growth tem...

The impact of increases in drought frequency on the Amazon forest's composition, structure and functioning remain uncertain. We used a process‐ and individual‐based ecosystem model ( ED 2) to quantify the forest's vulnerability to increased drought recurrence. We generated meteorologically realistic, drier‐than‐observed rainfall scenarios for two A...

All known phototrophic metabolisms on Earth are based on one of three energy-converting pigments: chlorophyll- a , bacteriochlorophyll- a , and retinal, which is the chromophore in rhodopsins [1]. While the contribution of chlorophylls to global energy flows and marine carbon cycling has been studied for decades, the role of retinal-based phototrop...

Oceanic time-series have been instrumental in providing an understanding of biological, physical, and chemical dynamics in the oceans and how these processes change over time. However, the extrapolation of these results to larger oceanographic regions requires an understanding and characterization of local versus regional drivers of variability. He...

The nitrogen (N)-fixing cyanobacterium Trichodesmium is globally distributed in warm, oligotrophic oceans, where it contributes a substantial proportion of new N and fuels primary production. These photoautotrophs form macroscopic colonies that serve as relatively nutrient-rich substrates that are colonized by many other organisms. The nature of th...

Marine microbes are the engines that drive global biogeochemical cycling in the oceans. They produce and cycle a dissolved organic matter (DOM) reservoir that is roughly as big as the atmospheric carbon dioxide pool ( 1 ). Interactions between DOM and marine microbes may also play a key role in the evolving climate through changes in remineralizati...

To predict forest response to long-term climate change with high confidence requires that dynamic global vegetation models (DGVMs) be successfully tested against ecosystem response to short-term variations in environmental drivers, including regular seasonal patterns. Here, we used an integrated dataset from four forests in the Brasil flux network,...

Subtropical gyres contribute significantly to global ocean productivity. As the climate warms, the strength of these gyres as a biological carbon pump is predicted to diminish due to increased stratification and depleted surface nutrients. We present results suggesting that the impact of submesoscale physics on phytoplankton in the oligotrophic oce...

Significance Understanding how changes in climate will affect terrestrial ecosystems is particularly important in tropical forest regions, which store large amounts of carbon and exert important feedbacks onto regional and global climates. By combining multiple types of observations with a state-of-the-art terrestrial ecosystem model, we demonstrat...

Organic matter (OM) plays a major role in both terrestrial and oceanic biogeochemical cycles. The amount of carbon stored in these systems is far greater than that of carbon dioxide (CO2 ) in the atmosphere, and annual fluxes of CO2 from these pools to the atmosphere exceed those from fossil fuel combustion. Understanding the processes that determi...

Accurately predicting the response of Amazonia to climate change is important for predicting climate change across the globe. Changes in multiple climatic factors simultaneously result in complex non-linear ecosystem responses, which are difficult to predict using vegetation models. Using leaf- and canopy-scale observations, this study evaluated th...

There is considerable interest in understanding the fate of the Amazon over the coming century in the face of climate change, rising atmospheric CO2 levels, on-going land transformation, and changing fire regimes within the region. In this analysis, we explore the fate of Amazonian ecosystems under the combined impact of these four environmental fo...

This work investigates how the integrated land use of northern South America has affected the present day regional patterns of hydrology. A model of the terrestrial ecosystems (ecosystem demography model 2: ED2) is combined with an atmospheric model (Brazilian Regional Atmospheric Modeling System: BRAMS). Two realizations of the structure and compo...

Environmental contextMicroscopic marine organisms have the potential to influence the global climate through the production of a trace gas, dimethylsulfide, which contributes to cloud formation. Using 3 years of observations, we investigated the environmental drivers behind the production and degradation of dimethylsulfide and its precursor dimethy...

Accurately predicting the response of Amazonia to climate change is important for predicting changes across the globe. However, changes in multiple climatic factors simultaneously may result in complex non-linear responses, which are difficult to predict using vegetation models. Using leaf and canopy scale observations, this study evaluated the cap...

This study analyzes the inter-annual variability (IAV) of simulations of 21 different land surface model formulations, driven by meteorological conditions measured at 8 flux towers, located in rain forest, forest-savanna ecotone and pasture sites in Amazonia, and one in savanna site in Southeastern Brazil. Annual totals of net ecosystem exchange (N...

This work investigates how landuse changes over northern South America, driven by human interventions, have affected the regional patterns of hydrology. Comparisons are made to scenarios where no human disturbance of the regional vegetation is assumed. A numerical model of the terrestrial biosphere (Ecosystem Demography Model 2 – ED2) is combined w...

A physical model of the terrestrial biosphere (Ecosystem Demography Model) is combined with an atmospheric model (Brazilian Regional Atmospheric Modeling System) to investigate how land conversion in the Amazon and Northern South America have changed the hydrology of the region. Two numerical realizations of the structure and composition of terrest...

Considerable uncertainty surrounds the fate of Amazon rainforests in response to climate change. Here, carbon (C) flux predictions of five terrestrial biosphere models (Community Land Model version 3.5 (CLM3.5), Ecosystem Demography model version 2.1 (ED2), Integrated BIosphere Simulator version 2.6.4 (IBIS), Joint UK Land Environment Simulator ver...

A mosaic of protected areas, including indigenous lands, sustainable-use production forests and reserves and strictly protected forests is the cornerstone of conservation in the Amazon, with almost 50 per cent of the region now protected. However, recent research indicates that isolation from direct deforestation or degradation may not be sufficien...

Export Date: 25 July 2013, Source: Scopus, Article in Press

Dimethylsulfide (DMS) is a climatically relevant trace gas produced and cycled by the surface ocean food web. Mechanisms driving intraannual variability in DMS production and dimethylsulfoniopropionate (DMSP) degradation in open-ocean, oligotrophic regions were investigated during a 10-month time-series at the Bermuda Atlantic Time-series Study sit...

The impact of drought-induced disturbances and deforestation on the Amazonian ecosystems has been substantial and is predicted to increase due to future land-use and climate changes. The resulting fate of the Amazon forests and the carbon stored within them has important implications for both the future climate of the region and the global climate...

The potential importance of deep soil moisture reserves for maintaining evergreen canopies across the seasonally wet Amazon has been recognized for some time, but only until recently has the modeling community explored how to incorporate moisture reserves into land surface models (LSMs) that couple to the atmosphere. Mechanisms employed by models f...

The studies of the interaction between vegetation and climate change in the Amazon Basin indicate that up to half of region's forests may be displaced by savanna vegetation by the end of the century. Additional analyses suggest that complex interactions between land use, fire-frequency, and episodic drought are driving an even more rapid process of...

The Amazonian rainforests play a vital role in global water, energy and carbon cycling. The sensitivity of this system to natural and anthropogenic disturbances therefore has important implications for the global climate. Some global models have predicted large-scale forest dieback and the savannization of Amazonia over the next century [Meehl et a...

Given business as usual land-use practices, it is estimated that by 2050 roughly half of the Amazon's pre-anthropogenic closed-canopy forest stands would remain. Of this, eight of the Amazon's twelve major hydrologic basins would lose more than half of their forest cover to deforestation. With the availability of these land-use projections, we may...

A key outstanding challenge in earth system science is a quantitative understanding of how ecological processes will influence the response of terrestrial ecosystems to anthropogenic climate change. Using specific examples drawn from both tropical and temperate ecosystems, this talk interrogates how measurements, analyses, and models that incorpora...

A common approach for estimating the oceanic uptake of anthropogenic carbon dioxide (C anthro) depends on the linear approximation of oceanic dissolved inorganic carbon (DIC) from a suite of physical and biological ocean parameters. The extended multiple linear regression (eMLR) method assumes that baseline correlations and the resulting residual f...

The North Atlantic Ocean accounts for about 25% of the global oceanic anthropogenic carbon sink. This basin experiences significant interannual variability primarily driven by the North Atlantic Oscillation (NAO). A suite of biogeochemical model simulations is used to analyze the impact of interannual variability on the uptake and storage of contem...

The Amazonian rainforests play a vital role in global water, energy and carbon cycling. The sensitivity of this system to natural and anthropogenic disturbances therefore has important implications for the global climate. Field observations suggest that there has been a net increase in biomass in old growth Amazonian forests over the past two decad...

The Amazon rainforest is amongst the largest contiguous tropical rainforest, contributing significantly to the Earth's water, energy, and carbon cycle. Over the past 40 years, about 20% of the original area has been converted to croplands and pastures directly impacting the total carbon stored in the forest. However, deforestation may also cause im...

Repeat observations along the meridional Atlantic section A16 from Iceland to 56S show substantial changes in the total dissolved inorganic carbon (DIC) concentrations in the ocean between occupations from 1989 through 2005. The changes correspond to the expected increase in DIC driven by the uptake of anthropogenic CO2 from the atmosphere, but the...

Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution February 2010 Anthropogenic activity is rapidly changing the global climate through the emission of carbon dioxide. Ocean carbon and sulfur cycles have the potential to...

The isotopic composition of dissolved oxygen in the mesopelagic ocean is a unique tracer of respiration and transport. New delta 18O of O2 data from the tropical South Atlantic oxygen minimum zone are presented and compared to global delta 18O data. The delta 18O variability in oxygen poor waters is attributed to differences in physical and biogeoc...

Once ventilated to the atmosphere, the oxidation products of biologically produced DMS are non sea salt sulfate and methane sulfonate aerosols which potentially exert considerable control on the global climate via alterations in radiative properties, acid-base chemistry, halogen cycles, and aerosol iron availability. The most significant obstacle t...

Dissolved inorganic carbon (DIC) in the upper ocean is increasing over time due to the invasion of anthropogenic CO2 from the atmosphere. The CLIVAR/CO2 Repeat Hydrography Program is attempting to quantifying these trends by reoccupying on approximately decadal time-scales ocean sections that were first sampled during the WOCE/JGOFS era in the late...

Author Posting. © American Geophysical Union, 2008. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research 113 (2008): C03019, doi:10.1029/2007JC004153. Estimates of temporal trends in oceanic anthropogenic carbon dioxi...