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Simulations of the CMIP6 historical period 1850–2014, characterized by the emergence of anthropogenic climate drivers like greenhouse gases, are presented for different configurations of the NASA Goddard Institute for Space Studies (GISS) Earth System ModelE2.1. The GISS‐E2.1 ensembles are more sensitive to greenhouse gas forcing than their CMIP5 predecessors (GISS‐E2) but warm less during recent decades due to a forcing reduction that is attributed to greater longwave opacity in the GISS‐E2.1 pre‐industrial simulations. This results in an atmosphere less sensitive to increases in opacity from rising greenhouse gas concentrations, demonstrating the importance of the base climatology to forcing and forced climate trends. Most model versions match observed temperature trends since 1979 from the ocean to the stratosphere. The choice of ocean model is important to the transient climate response, as found previously in CMIP5 GISS‐E2: the model that more efficiently exports heat to the deep ocean shows a smaller rise in tropospheric temperature. Model sea level rise over the historical period is traced to excessive drawdown of aquifers to meet irrigation demand with a smaller contribution from thermal expansion. This shows how fully coupled models can provide indirect observational constraints upon forcing, in this case, constraining irrigation rates with observed sea level changes. The overall agreement of GISS‐E2.1 with observed trends is familiar from evaluation of its predecessors, as is the conclusion that these trends are almost entirely anthropogenic in origin. We thank two anonymous reviewers for their comments that substantially improved this article. Development of GISS‐E2.1 was supported by the NASA Modeling, Analysis, and Prediction (MAP) Program. CMIP6 simulations with GISS‐E2.1 were made possible by the NASA High‐End Computing (HEC) Program through the NASA Center for Climate Simulation (NCCS) at Goddard Space Flight Center. We thank Ellen Salmon and the NCCS staff for hosting and providing convenient access to the model output. Peer Reviewed "Article signat per 47 autors/es: Ron L. Miller, Gavin A. Schmidt, Larissa S. Nazarenko, Susanne E. Bauer, Maxwell Kelley, Reto Ruedy, Gary L. Russell , Andrew S. Ackerman, Igor Aleinov, Michael Bauer, Rainer Bleck, Vittorio Canuto, Grégory Cesana, Ye Cheng, Thomas L. Clune, Ben I. Cook, Carlos A. Cruz, Anthony D. Del Genio, Gregory S. Elsaesser, Greg Faluvegi, Nancy Y. Kiang, Daehyun Kim, Andrew A. Lacis , Anthony Leboissetie,r Allegra N. LeGrande, Ken K. Lo, John Marshall, Elaine E. Matthews, Sonali McDermid, Keren Mezuman, Lee T. Murray, Valdar Oinas, Clara Orbe, Carlos Pérez García‐Pando, Jan P. Perlwitz, Michael J. Puma, David Rind, Anastasia Romanou, Drew T. Shindell, Shan Sun, Nick Tausnev, Kostas Tsigaridis, George Tselioudis, Ensheng Weng, Jingbo Wu, Mao‐Sung Yao"

We present results from the NASA GISS ModelE2.1‐G‐CC Earth System Model with coupled climate‐carbon cycle simulations that were submitted to the sixth phase of the Coupled Model Intercomparison Project (CMIP6) Coupled Climate‐Carbon Cycle MIP (C4MIP). Atmospheric CO2 concentration and carbon budgets for the land and ocean in the historical simulations were generally consistent with observations. Low simulated atmospheric CO2 concentrations during 1850–1950 were due to excess uptake from prescribed land cover change, which erroneously replaced arid shrublands with higher biomass crops, and assumed high 2004 LAI values in vegetated lands throughout the historical simulation. At the end of the historical period, slightly higher simulated CO2 than observed resulted from the land being an insufficient net carbon sink, despite the net effect of CO2 fertilization and warming‐induced increases to leaf photosynthetic capacity. The global ocean carbon uptake agreed well with the observations with the largest discrepancies in the low latitudes. Future climate projection at 2091–2100 agreed with CMIP5 models in the northward shift, of temperate deciduous forest climate and expansion across Eurasia along 60°N latitude, and dramatic regional biome shifts from drying and warming in continental Europe. Carbon feedback parameters were largely similar to the CMIP5 model ensemble. For our model, the variation of land feedback parameters within the uncertainty arises from the fertilization feedback being less sensitive due to lack of increased vegetation growth, and the comparably more negative ocean carbon‐climate feedback is due to the large slowdown of the Atlantic overturning circulation.

Modern agricultural land cover and management are important as regional climate forcings. Previous work has shown that land cover change can significantly impact key climate variables, including turbulent fluxes, precipitation, and surface temperature. However, fewer studies have investigated how intensive crop management can impact background climate conditions, such as the strength of land–atmosphere coupling and evaporative regime. We conduct sensitivity experiments using a state-of-the-art climate model with modified vegetation characteristics to represent modern crop cover and management, using observed crop-specific leaf area indexes and calendars. We quantify changes in land–atmosphere interactions and climate over intensively cultivated regions situated at transitions between moisture- and energy-limited conditions. Results show that modern intensive agriculture has significant and geographically varying impacts on regional evaporative regimes and background climate conditions. Over the northern Great Plains, modern crop intensity increases the model simulated precipitation and soil moisture, weakening hydrologic coupling by increasing surface water availability and reducing moisture limits on evapotranspiration. In the U.S. Midwest, higher growing season evapotranspiration, coupled with winter and spring rainfall declines, reduces regional soil moisture, while crop albedo changes also reduce net surface radiation. This results overall in reduced dependency of regional surface temperature on latent heat fluxes. In central Asia, a combination of reduced net surface energy and enhanced pre–growing season precipitation amplify the energy-limited evaporative regime. These results highlight the need for improved representations of agriculture in global climate models to better account for regional climate impacts and interactions with other anthropogenic forcings.

Finding life on exoplanets from telescopic observations is an ultimate goal of exoplanet science. Life produces gases and other substances, such as pigments, which can have distinct spectral or photometric signatures. Whether or not life is found with future data must be expressed with probabilities, requiring a framework of biosignature assessment. We present a framework in which we advocate using biogeochemical "Exo-Earth System" models to simulate potential biosignatures in spectra or photometry. Given actual observations, simulations are used to find the Bayesian likelihoods of those data occurring for scenarios with and without life. The latter includes "false positives" where abiotic sources mimic biosignatures. Prior knowledge of factors influencing planetary inhabitation, including previous observations, is combined with the likelihoods to give the Bayesian posterior probability of life existing on a given exoplanet. Four components of observation and analysis are necessary. 1) Characterization of stellar (e.g., age and spectrum) and exoplanetary system properties, including "external" exoplanet parameters (e.g., mass and radius) to determine an exoplanet's suitability for life. 2) Characterization of "internal" exoplanet parameters (e.g., climate) to evaluate habitability. 3) Assessment of potential biosignatures within the environmental context (components 1-2) and any corroborating evidence. 4) Exclusion of false positives. The resulting posterior Bayesian probabilities of life's existence map to five confidence levels, ranging from "very likely" (90-100%) to "very unlikely" ($\le$10%) inhabited., Comment: Part of a NASA Nexus for Exoplanet System Science (NExSS) series of 5 papers. V.3 published as an Open Access paper in Astrobiology

The habitable fraction of a planet's surface is important for the detectability of surface biosignatures. The extent and distribution of habitable areas is influenced by external parameters that control the planet's climate, atmospheric circulation, and hydrological cycle. We explore these issues using the ROCKE-3D General Circulation Model, focusing on terrestrial water fluxes and thus the potential for the existence of complex life on land. Habitability is examined as a function of insolation and planet rotation for an Earth-like world with zero obliquity and eccentricity orbiting the Sun. We assess fractional habitability using an aridity index that measures the net supply of water to the land. Earth-like planets become ``superhabitable'' (a larger habitable surface area than Earth) as insolation and day-length increase because their climates become more equable, reminiscent of past warm periods on Earth when complex life was abundant and widespread. The most slowly rotating, most highly irradiated planets, though, occupy a hydrological regime unlike any on Earth, with extremely warm, humid conditions at high latitudes but little rain and subsurface water storage. Clouds increasingly obscure the surface as insolation increases, but visibility improves for modest increases in rotation period. Thus, moderately slowly rotating rocky planets with insolation near or somewhat greater than modern Earth's appear to be promising targets for surface characterization by a future direct imaging mission., 24 pages, 7 figures, 1 table; submitted to ApJ

Present-day Venus is an inhospitable place with surface temperatures approaching 750K and an atmosphere over 90 times as thick as present day Earth's. Billions of years ago the picture may have been very different. We have created a suite of 3D climate simulations using topographic data from the Magellan mission, solar spectral irradiance estimates for 2.9 and 0.715 billion years ago, present day Venus orbital parameters, an ocean volume consistent with current theory and measurements, and an atmospheric composition estimated for early Venus. Using these parameters we find that such a world could have had moderate temperatures if Venus had a rotation period slower than about 16 Earth days, despite an incident solar flux 46-70% higher than modern Earth receives. At its current rotation period of 243 days, Venus's climate could have remained habitable until at least 715 million years ago if it hosted a shallow primordial ocean. These results demonstrate the vital role that rotation and topography play in understanding the climatic history of exoplanetary Venus-like worlds being discovered in the present epoch., Comment: 13 pages, 4 Figures, submitted to Geophysical Research Letters

The potential habitability of known exoplanets is often categorized by a nominal equilibrium temperature assuming a Bond albedo of either 0.3, similar to Earth, or 0. As an indicator of habitability, this leaves much to be desired, because albedo on other planets can be very different, and because surface temperature exceeds equilibrium temperature due to the atmospheric greenhouse effect. We use an ensemble of 3-dimensional general circulation model simulations to show that for a range of habitable planets, much of the variability of Bond albedo, equilibrium temperature, and even surface temperature can be predicted with useful accuracy from incident stellar flux and stellar temperature, two known external parameters for every confirmed exoplanet., 45 pages including 8 figures, 5 tables; submitted to The Astrophysical Journal

The nearby exoplanet Proxima Centauri b will be a prime future target for characterization, despite questions about its retention of water. Climate models with static oceans suggest that an Earth-like Proxima b could harbor a small dayside region of surface liquid water at fairly warm temperatures despite its weak instellation. We present the first 3-dimensional climate simulations of Proxima b with a dynamic ocean. We find that an ocean-covered Proxima b could have a much broader area of surface liquid water but at much colder temperatures than previously suggested, due to ocean heat transport and depression of the freezing point by salinity. Elevated greenhouse gas concentrations do not necessarily produce more open ocean area because of possible dynamic regime transitions. For an evolutionary path leading to a highly saline present ocean, Proxima b could conceivably be an inhabited, mostly open ocean planet dominated by halophilic life. For an ocean planet in 3:2 spin-orbit resonance, a permanent tropical waterbelt exists for moderate eccentricity. Simulations of Proxima Centauri b may also be a model for the habitability of planets receiving similar instellation from slightly cooler or warmer stars, e.g., in the TRAPPIST-1, LHS 1140, GJ 273, and GJ 3293 systems., Comment: Submitted to Astrobiology; 38 pages, 12 figures, 5 tables

We present a large ensemble of simulations of an Earth-like world with increasing insolation and rotation rate. Unlike previous work utilizing idealized aquaplanet configurations we focus our simulations on modern Earth-like topography. The orbital period is the same as modern Earth, but with zero obliquity and eccentricity. The atmosphere is 1 bar N$_{2}$-dominated with CO$_{2}$=400 ppmv and CH$_{4}$=1 ppmv. The simulations include two types of oceans; one without ocean heat transport (OHT) between grid cells as has been commonly used in the exoplanet literature, while the other is a fully coupled dynamic bathtub type ocean. The dynamical regime transitions that occur as day length increases induce climate feedbacks producing cooler temperatures, first via the reduction of water vapor with increasing rotation period despite decreasing shortwave cooling by clouds, and then via decreasing water vapor and increasing shortwave cloud cooling, except at the highest insolations. Simulations without OHT are more sensitive to insolation changes for fast rotations while slower rotations are relatively insensitive to ocean choice. OHT runs with faster rotations tend to be similar with gyres transporting heat poleward making them warmer than those without OHT. For slower rotations OHT is directed equator-ward and no high latitude gyres are apparent. Uncertainties in cloud parameterization preclude a precise determination of habitability but do not affect robust aspects of exoplanet climate sensitivity. This is the first paper in a series that will investigate aspects of habitability in the simulations presented herein. The datasets from this study are opensource and publicly available., 27 pages ApJS accepted. Expanded Introduction and several additional figures

The rapid rate of discoveries of exoplanets has expanded the scope of the science possible for the remote detection of life beyond Earth. The Exoplanet Biosignatures Workshop Without Walls (EBWWW) held in 2016 engaged the international scientific community across diverse scientific disciplines, to assess the state of the science and technology in the search for life on exoplanets, and to identify paths for progress. The workshop activities resulted in five major review papers, which provide (1) an encyclopedic review of known and proposed biosignatures and models used to ascertain them (Schwieterman et al., 2018 in this issue); (2) an in-depth review of O2 as a biosignature, rigorously examining the nuances of false positives and false negatives for evidence of life (Meadows et al., 2018 in this issue); (3) a Bayesian framework to comprehensively organize current understanding to quantify confidence in biosignature assessments (Catling et al., 2018 in this issue); (4) an extension of that Bayesian framework in anticipation of increasing planetary data and novel concepts of biosignatures (Walker et al., 2018 in this issue); and (5) a review of the upcoming telescope capabilities to characterize exoplanets and their environment (Fujii et al., 2018 in this issue). Because of the immense content of these review papers, this summary provides a guide to their complementary scope and highlights salient features. Strong themes that emerged from the workshop were that biosignatures must be interpreted in the context of their environment, and that frameworks must be developed to link diverse forms of scientific understanding of that context to quantify the likelihood that a biosignature has been observed. Models are needed to explore the parameter space where measurements will be widespread but sparse in detail. Given the technological prospects for large ground-based telescopes and space-based observatories, the detection of atmospheric signatures of a few potentially habitable planets may come before 2030. Key Words: Exoplanets-Biosignatures-Remote observation-Spectral imaging-Bayesian analysis. Astrobiology 18, 619-626.

We introduce a Bayesian method for guiding future directions for detection of life on exoplanets. We describe empirical and theoretical work necessary to place constraints on the relevant likelihoods, including those emerging from better understanding stellar environment, planetary climate and geophysics, geochemical cycling, the universalities of physics and chemistry, the contingencies of evolutionary history, the properties of life as an emergent complex system, and the mechanisms driving the emergence of life. We provide examples for how the Bayesian formalism could guide future search strategies, including determining observations to prioritize or deciding between targeted searches or larger lower resolution surveys to generate ensemble statistics and address how a Bayesian methodology could constrain the prior probability of life with or without a positive detection. Key Words: Exoplanets—Biosignatures—Life detection—Bayesian analysis. Astrobiology 18, 779–824., Table of Contents 1. Introduction 2. Setting the Stage: What Is Life? What Is a Biosignature? 3. Detecting Unknown Biology on Unknown Worlds: A Bayesian Framework 3.1. Habitability in the Bayesian framework for biosignatures 4. P(data|abiotic) 4.1. Stellar environment 4.2. Climate and geophysics 4.2.1. Coupled tectonic–climate models 4.2.2. Community GCM projects for generating ensemble statistics for P(data|abiotic) and P(data|life) 4.3. Geochemical environment 4.3.1. Anticipating the unexpected: statistical approaches to characterizing atmospheres of non-Earth-like worlds 5. P(data|life) 5.1. Black-box approaches to living processes 5.1.1. Type classification of Seager et al. (2013a) 5.1.1.1. Energy capture (type I) 5.1.1.2. Biomass capture (type II) 5.1.1.3. Other uses (type III) 5.1.1.4. Products of modification of gases (type IV) 5.1.2. Alternatives for type classification 5.1.2.1. Type I, energy capture 5.1.2.2. Type II, biomass capture 5.1.2.3. Type III, “other uses” 5.1.2.4. Type IV 5.1.3. When is it appropriate to deconstruct a black box? 5.2. Life as improbable chemistry 5.3. Life as an evolutionary process 5.3.1. Life as a coevolution with its planet: Earth as an example 5.3.2. Calculating conditional probabilities in biological evolution from past biogeochemical states 5.4. Insights from universal biology 5.4.1. Network biosignatures 5.4.2. Universal scaling laws, applicable to other worlds? 6. P(life) 6.1. P(emerge): constraining the probability of the origins of life 6.2. Biological innovations and the conditional probabilities for living processes 7. A Bayesian Framework Example: Detecting Atmospheric Oxygen 8. Tuning Search Strategies Based on the Bayesian Framework 9. Conclusions Acknowledgments Author Disclosure Statement References Abbreviations Used

Life on Earth is molecular in nature, with its lifelike attributes- e.g., information processing and catalysis- emerging as a result of both the specific properties of those molecules and the interactions among them. If this is a general model for life, then life must require (i) a source of energy, with which to build and sustain molecular complexity and information processing; (ii) elemental raw materials, from which to construct molecules having specific properties and reactivity; (iii)a solvent that supports the synthesis of the full range of molecules required by life and properly mediates the full range of necessary interactions among those molecules; and (iv) physicochemical conditions in which life's molecules can be synthesized, are appropriately stable, and can interact as needed for lifelike function. For life on Earth, these general requirements, respectively, take the specific form: (i) light energy in visible-to-near-infrared wavelengths or chemical energy as provided by oxidation–reduction disequilibrium, (ii) the "biogenic "elements (carbon, hydrogen, oxygen, nitrogen, phosphorus, and sulfur) (iii)liquid water, and (iv) specific ranges in temperature, pH, salinity, pressure, and other environmental factors. Our knowledge of these factors relates to cellula rlife as we observe it now or can infer from the fossil or molecular records. Life's origin may be constrained by a more stringent set of requirements that are, as yet,not fully understood.

In the coming years and decades, advanced space- and ground-based observatories will allow an unprecedented opportunity to probe the atmospheres and surfaces of potentially habitable exoplanets for signatures of life. Life on Earth, through its gaseous products and reflectance and scattering properties, has left its fingerprint on the spectrum of our planet. Aided by the universality of the laws of physics and chemistry, we turn to Earth's biosphere, both in the present and through geologic time, for analog signatures that will aid in the search for life elsewhere. Considering the insights gained from modern and ancient Earth, and the broader array of hypothetical exoplanet possibilities, we have compiled a comprehensive overview of our current understanding of potential exoplanet biosignatures, including gaseous, surface, and temporal biosignatures. We additionally survey biogenic spectral features that are well known in the specialist literature but have not yet been robustly vetted in the context of exoplanet biosignatures. We briefly review advances in assessing biosignature plausibility, including novel methods for determining chemical disequilibrium from remotely obtainable data and assessment tools for determining the minimum biomass required to maintain short-lived biogenic gases as atmospheric signatures. We focus particularly on advances made since the seminal review by Des Marais et al. The purpose of this work is not to propose new biosignature strategies, a goal left to companion articles in this series, but to review the current literature, draw meaningful connections between seemingly disparate areas, and clear the way for a path forward. Key Words: Exoplanets—Biosignatures—Habitability markers—Photosynthesis—Planetary surfaces—Atmospheres—Spectroscopy—Cryptic biospheres—False positives. Astrobiology 18, 663–708., Table of Contents 1. Introduction 1.1. Requirements for life 1.2. Exoplanet biosignature definitions 1.3. Biosignature categories 2. Evaluating Planetary Habitability 3. Overview of Terrestrial Exoplanet Modeling Studies 3.1. Observations of earth 3.2. Spectral models 3.3. Photochemical studies of terrestrial atmospheres 3.4. Earth through time 4. Gaseous Biosignatures 4.1. Gaseous biosignature overview 4.2. Earth-like atmospheres 4.2.1. Oxygen (O2) 4.2.2. Ozone (O3) 4.2.3. Methane (CH4) 4.2.4. Nitrous oxide (N2O) 4.2.5. Sulfur gases (DMS, DMDS, CH3SH) and relation to detectable C2H6 4.2.6. Methyl chloride (CH3Cl) 4.2.7. Haze as a biosignature 4.2.8. Other gases 4.3. “False positives” for biotic O2/O3 and possible spectral discriminators 4.4. Biosignatures in other types of atmospheres 4.5. Effects of the host star spectrum on photochemistry 4.6. Impacts of flares and particle events on biosignature gases 5. Surface Biosignatures 5.1. Photosynthesis 5.1.1. Principles of photosynthesis 5.1.1.1. Relationship between band gap wavelength and reductant in the generation of biogenic gases and pigment color 5.1.1.2. Uniqueness of OP 5.1.2. Photosynthetic pigments and the color of phototrophs 5.1.2.1. Structure 5.1.2.2. Light absorption 5.1.3. The vegetation “red edge” 5.1.4. Speculation about photosynthesis and pigment signatures on exoplanets 5.2. Retinal pigments 5.3. Alternative surface biosignatures: nonphotosynthetic pigments and reflectance features 5.4. False positive surface biosignatures 5.5. Chiral and polarization biosignatures 5.6. Fluorescence and bioluminescence 6. Temporal Biosignatures 6.1. Oscillations of atmospheric gases 6.2. Oscillations in surface signatures 7. Assessing Biosignature Plausibility 7.1. Chemical disequilibrium 7.2. Biomass estimation 7.3. Applications of network theory to biosignatures 8. Cryptic Biospheres: “False Negatives” for Life? 9. Prospects for Detecting Exoplanet Biosignatures 10. Summary

Photosynthesis produces signs of life we can see from space: the absorbance spectrum of surface photosynthetic pigments and, with oxygenic photosynthesis, atmospheric oxygen. Since the first discovery of a planet in another solar system in 1989, there has been an explosion in the detection of exoplanets (over 1849 as of 7 November 2014) and we are getting ever closer to finding that Goldilocks planet that might harbour life. With telescope observations of these planets, oxygenic photosynthesis has been considered our most robust target ‘biosignature’ that would not appear on a lifeless planet. Since anoxygenic photosynthetic organisms do not produce unambiguously biogenic gases, there is interest in their pigments serving as spectral indicators of life. But will they look the same as on Earth, can we distinguish them from the abiotic, and what will dominate on another planet? Examples from Earth provide us with the potential to extrapolate some rules for photosynthesis to predict its signature on another planet, but there are yet things we must answer about life here to improve our confidence. In particular, given the combination of the available stellar spectrum and molecular constraints on photon energy use, can we predict the pigment spectral features that will dominate, which reductant will match, and what biogenic gases would result? We take clues from the diversity of anoxygenic photosynthetic metabolisms and three very recent examples of oxygenic photosynthesis utilizing other reaction centre (RC) chlorophylls in addition to chlorophyll a (Chl a).

Observations of climate change during the CMIP5 extended historical period (1850-2012) are compared to trends simulated by six versions of the NASA Goddard Institute for Space Studies ModelE2 Earth System Model. The six models are constructed from three versions of the ModelE2 atmospheric general circulation model, distinguished by their treatment of atmospheric composition and the aerosol indirect effect, combined with two ocean general circulation models, HYCOM and Russell. Forcings that perturb the model climate during the historical period are described. Five-member ensemble averages from each of the six versions of ModelE2 simulate trends of surface air temperature, atmospheric temperature, sea ice and ocean heat content that are in general agreement with observed trends, although simulated warming is slightly excessive within the past decade. Only simulations that include increasing concentrations of long-lived greenhouse gases match the warming observed during the twentieth century. Differences in twentieth-century warming among the six model versions can be attributed to differences in climate sensitivity, aerosol and ozone forcing, and heat uptake by the deep ocean. Coupled models with HYCOM export less heat to the deep ocean, associated with reduced surface warming in regions of deepwater formation, but greater warming elsewhere at high latitudes along with reduced sea ice. All ensembles show twentieth-century annular trends toward reduced surface pressure at southern high latitudes and a poleward shift of the midlatitude westerlies, consistent with observations.

We present a description of the ModelE2 version of the Goddard Institute for Space Studies (GISS) General Circulation Model (GCM) and the configurations used in the simulations performed for the Coupled Model Intercomparison Project Phase 5 (CMIP5). We use six variations related to the treatment of the atmospheric composition, the calculation of aerosol indirect effects, and ocean model component. Specifically, we test the difference between atmospheric models that have noninteractive composition, where radiatively important aerosols and ozone are prescribed from precomputed decadal averages, and interactive versions where atmospheric chemistry and aerosols are calculated given decadally varying emissions. The impact of the first aerosol indirect effect on clouds is either specified using a simple tuning, or parameterized using a cloud microphysics scheme. We also use two dynamic ocean components: the Russell and HYbrid Coordinate Ocean Model (HYCOM) which differ significantly in their basic formulations and grid. Results are presented for the climatological means over the satellite era (1980-2004) taken from transient simulations starting from the preindustrial (1850) driven by estimates of appropriate forcings over the 20th Century. Differences in base climate and variability related to the choice of ocean model are large, indicating an important structural uncertainty. The impact of interactive atmospheric composition on the climatology is relatively small except in regions such as the lower stratosphere, where ozone plays an important role, and the tropics, where aerosol changes affect the hydrological cycle and cloud cover. While key improvements over previous versions of the model are evident, these are not uniform across all metrics.

We describe the implementation of a biochemical model of isoprene emission that depends on the electron requirement for isoprene synthesis into the Farquhar–Ball–Berry leaf model of photosynthesis and stomatal conductance that is embedded within a global chemistry-climate simulation framework. The isoprene production is calculated as a function of electron transport-limited photosynthesis, intercellular and atmospheric carbon dioxide concentration, and canopy temperature. The vegetation biophysics module computes the photosynthetic uptake of carbon dioxide coupled with the transpiration of water vapor and the isoprene emission rate at the 30 min physical integration time step of the global chemistry-climate model. In the model, the rate of carbon assimilation provides the dominant control on isoprene emission variability over canopy temperature. A control simulation representative of the present-day climatic state that uses 8 plant functional types (PFTs), prescribed phenology and generic PFT-specific isoprene emission potentials (fraction of electrons available for isoprene synthesis) reproduces 50% of the variability across different ecosystems and seasons in a global database of 28 measured campaign-average fluxes. Compared to time-varying isoprene flux measurements at 9 select sites, the model authentically captures the observed variability in the 30 min average diurnal cycle (R2 = 64–96%) and simulates the flux magnitude to within a factor of 2. The control run yields a global isoprene source strength of 451 TgC yr−1 that increases by 30% in the artificial absence of plant water stress and by 55% for potential natural vegetation.

We present a regularization technique based on the minimum description length (MDL) principle for the linear manifold clustering. We suggest an inexact minimum description length method based on describing the data structure as linear manifold clusters. We examine the behavior of the proposed method and compare it performance against simulated clustering results of various dimensionality and structure. Finally, we empirically evaluate the proposed technique on a climate data.

The cyanobacterium Acaryochloris marina uses chlorophyll d to carry out oxygenic photosynthesis in environments depleted in visible and enhanced in lower-energy, far-red light. However, the extent to which low photon energies limit the efficiency of oxygenic photochemistry in A. marina is not known. Here, we report the first direct measurements of the energy-storage efficiency of the photosynthetic light reactions in A. marina whole cells, and find it is comparable to or higher than that in typical, chlorophyll a-utilizing oxygenic species. This finding indicates that oxygenic photosynthesis is not fundamentally limited at the photon energies employed by A. marina, and therefore is potentially viable in even longer-wavelength light environments.

In a previous paper, we developed an analytical clumped two-stream model (ACTS) of canopy radiative transfer from an analytical geometric-optical and radiative transfer (GORT) scheme ( Ni-Meister et al., 2010 ). The ACTS model accounts for clumping of foliage and the influence of trunks in vegetation canopies for modeling of photosynthesis, radiative fluxes and surface albedo in dynamic global vegetation models (DGVMs), and particularly for the Ent Dynamic Global Terrestrial Ecosystem Model (DGTEM). This study evaluates the gap probability and transmittance estimates from the ACTS model by comparing the modeled results with ground-based data, as well as with the original full GORT model and a layered Beer's law scheme. The ground data used in this study include vertical profile measurements of incident photosynthetically active radiation (PAR) in (1) mixed deciduous forests in Morgan-Monroe State Forest, IN, USA, (2) coniferous forests in central Canada, (3) mixed deciduous forests in Harvard Forest, MA, and (4) ground lidar measurements of the canopy gap fraction in woodland in Australia. The model comparisons with these measurements demonstrate that the ACTS model achieves better or similar performance compared to the full GORT and the layered Beer's law schemes with regard to agreements with field measurements and computational cost. The ACTS model has excellent accuracy and flexibility to model the canopy gap probability and transmittance for various forest scenarios. Also, it has advantages relative to the currently widely used two-stream scheme through better radiation estimation for photosynthesis by accounting for the impact of both vertical and horizontal structure heterogeneity of complex vegetation on radiative transfer. Currently the ACTS is being implemented in Ent and will be further tested for how it improves surface energy balance and carbon flux estimates.

This study develops a simple but physically based canopy radiative transfer scheme for photosynthesis, radiative fluxes and surface albedo estimates in dynamic global vegetation models (DGVMs), and particularly for the Ent Dynamic Global Terrestrial Ecosystem Model (Ent DGTEM). The Ent DGTEM can represent vegetation in mixed as opposed to homogeneous canopies. With active growth and competition, it must predict radiative transfer for dynamically changing vegetation structure, and requires computational speed for coupling with atmospheric general circulation models (GCMs). The canopy radiative transfer scheme accounts for both vertical and horizontal heterogeneity of plant canopies by combining the simple two-stream scheme with a well-described actual vertical foliage profile, an analytically derived foliage clumping factor from geometric optical theory, and, for needleleaf trees, an empirical needle-to-shoot-clumping factor. In addition, the model accounts for the effect of trunks, which is significant in bare canopies. This model provides better radiation estimates (light profiles, albedo) than the two-stream scheme currently being used in most GCMs to describe light interactions with vegetation canopies. This scheme has the same computational cost as the current typical scheme being used in GCMs, but promises to provide better canopy radiative transfer estimates for DGVMs, particularly those that model heterogeneous vegetation canopies.

A full description of the ModelE version of the Goddard Institute for Space Studies (GISS) atmospheric general circulation model (GCM) and results are presented for present-day climate simulations (ca. 1979). This version is a complete rewrite of previous models incorporating numerous improvements in basic physics, the stratospheric circulation, and forcing fields. Notable changes include the following: the model top is now above the stratopause, the number of vertical layers has increased, a new cloud microphysical scheme is used, vegetation biophysics now incorporates a sensitivity to humidity, atmospheric turbulence is calculated over the whole column, and new land snow and lake schemes are introduced. The performance of the model using three configurations with different horizontal and vertical resolutions is compared to quality-controlled in situ data, remotely sensed and reanalysis products. Overall, significant improvements over previous models are seen, particularly in upper-atmosphere temperatures and winds, cloud heights, precipitation, and sea level pressure. Data–model comparisons continue, however, to highlight persistent problems in the marine stratocumulus regions.

Savannas and open grasslands often co-exist in semi-arid regions. Questions that remain unanswered and are of interest to biometeorologists include: how do these contrasting landscapes affect the exchanges of energy on seasonal and annual time scales; and, do biophysical constraints imposed by water supply and water demand affect whether the land is occupied by open grasslands or savanna? To address these questions, and others, we examine how a number of abiotic, biotic and edaphic factors modulate water and energy flux densities over an oak–grass savanna and an annual grassland that coexist in the same climate but on soils with different hydraulic properties. The net radiation balance was greater over the oak woodland than the grassland, despite the fact that both canopies received similar sums of incoming short and long wave radiation. The lower albedo and lower radiative surface temperature of the transpiring woodland caused it to intercept and retain more long and shortwave energy over the course of the year, and particularly during the summer dry period. The partitioning of available energy into sensible and latent heat exchanged over the two canopies differed markedly. The annual sum of sensible heat exchange over the woodland was 40% greater than that over the grassland (2.05 GJ m −2 per year versus 1.46 GJ m −2 per year). With regards to evaporation, the oak woodland evaporated about 380 mm of water per year and the grassland evaporated about 300 mm per year. Differences in available energy, canopy roughness, the timing of physiological functioning, water holding capacity of the soil and rooting depth of the vegetation explained the observed differences in sensible and latent heat exchange of the contrasting vegetation surfaces. The response of canopy evaporation to diminishing soil moisture was quantified by comparing normalized evaporation rates (in terms of equilibrium evaporation) with soil water potential and volumetric water content measurements. When soil moisture was ample normalized values of latent heat flux density were greater for the grassland (1.1–1.2) than for the oak savanna (0.7–0.8) and independent of moisture content. Normalized rates of evaporation over the grassland declined as volumetric water content dropped below 0.15 m 3 m −3 , which corresponded with a soil water potential of −1.5 MPa. The grassland senesced and quit transpiring when the volumetric water content of the soil dropped below −2.0 MPa. The oak trees, on the other hand, were able to transpire, albeit at low rates, under very dry soil conditions (soil water potentials below −4.0 MPa). The trees were able to endure such low water potentials and maintain basal levels of metabolism because ecological forcings kept the tree density and leaf area index of the woodland low, physiological factors forced the stomata to close progressively and the trees were able to tap deeper water sources (below 0.6 m) than the grasses.

Resolving Orbital and Climate Keys of Earth and Extraterrestrial Environments with Dynamics (ROCKE-3D) is a 3-Dimensional General Circulation Model (GCM) developed at the NASA Goddard Institute for Space Studies for the modeling of atmospheres of Solar System and exoplanetary terrestrial planets. Its parent model, known as ModelE2 (Schmidt et al. 2014), is used to simulate modern and 21st Century Earth and near-term paleo-Earth climates. ROCKE-3D is an ongoing effort to expand the capabilities of ModelE2 to handle a broader range of atmospheric conditions including higher and lower atmospheric pressures, more diverse chemistries and compositions, larger and smaller planet radii and gravity, different rotation rates (slowly rotating to more rapidly rotating than modern Earth, including synchronous rotation), diverse ocean and land distributions and topographies, and potential basic biosphere functions. The first aim of ROCKE-3D is to model planetary atmospheres on terrestrial worlds within the Solar System such as paleo-Earth, modern and paleo-Mars, paleo-Venus, and Saturn's moon Titan. By validating the model for a broad range of temperatures, pressures, and atmospheric constituents we can then expand its capabilities further to those exoplanetary rocky worlds that have been discovered in the past and those to be discovered in the future. We discuss the current and near-future capabilities of ROCKE-3D as a community model for studying planetary and exoplanetary atmospheres.

The ongoing searches for exoplanetary systems have revealed a wealth of planets with diverse physical properties. Planets even smaller than the Earth have already been detected, and the efforts of future missions are placed on the discovery, and perhaps characterization, of small rocky exoplanets within the habitable zone of their stars. Clearly what we know about our planet will be our guideline for the characterization of such planets. But the Earth has been inhabited for at least 3.8 Ga, and its appearance has changed with time. Here, we have studied the Earth during the Archean eon, 3.0 Ga ago. At that time one of the more widespread life forms on the planet were purple bacteria. These bacteria are photosynthetic microorganisms and can inhabit both aquatic and terrestrial environments. Here, we used a radiative transfer model to simulate the visible and near-IR radiation reflected by our planet, taking into account several scenarios regarding the possible distribution of purple bacteria over continents and oceans. We find that purple bacteria have a reflectance spectrum which has a strong reflectivity increase, similar to the red edge of leafy plants, although shifted redwards. This feature produces a detectable signal in the disk-averaged spectra of our planet, depending on cloud amount and on purple bacteria concentration/distribution. We conclude that by using multi-color photometric observations, it is possible to distinguish between an Archean Earth in which purple bacteria inhabit vast extensions of the planet, and a present-day Earth with continents covered by deserts, vegetation or microbial mats., 26 pages, 10 figures, accepted for publication in ApJ

Acaryochloris marina is the only species known to utilize chlorophyll (Chl) d as a principal photopigment. The peak absorption wavelength of Chl d is redshifted approx. 40 nm in vivo relative to Chl a, enabling this cyanobacterium to perform oxygenic phototrophy in niche environments enhanced in far-red light. We present measurements of the in vivo energy-storage (E-S) efficiency of photosynthesis in A. marina, obtained using pulsed photoacoustics (PA) over a 90-nm range of excitation wavelengths in the red and far-red. Together with modeling results, these measurements provide the first direct observation of the trap energies of PSI and PSII, and also the photosystem-specific contributions to the total E-S efficiency. We find the maximum observed efficiency in A. marina (40+/-1% at 735 nm) is higher than in the Chl a cyanobacterium Synechococcus leopoliensis (35+/-1% at 690 nm). The efficiency at peak absorption wavelength is also higher in A. marina (36+/-1% at 710 nm vs. 31+/-1% at 670 nm). In both species, the trap efficiencies are approx. 40% (PSI) and approx. 30% (PSII). The PSI trap in A. marina is found to lie at 740+/-5 nm, in agreement with the value inferred from spectroscopic methods. The best fit of the model to the PA data identifies the PSII trap at 723+/-3 nm, supporting the view that the primary electron-donor is Chl d, probably at the accessory (ChlD1) site. A decrease in efficiency beyond the trap wavelength, consistent with uphill energy transfer, is clearly observed and fit by the model. These results demonstrate that the E-S efficiency in A. marina is not thermodynamically limited, suggesting that oxygenic photosynthesis is viable in even redder light environments.

We investigate the issue of "dangerous human-made interference with climate" using simulations with GISS modelE driven by measured or estimated forcings for 1880-2003 and extended to 2100 for IPCC greenhouse gas scenarios as well as the 'alternative' scenario of Hansen and Sato. Identification of 'dangerous' effects is partly subjective, but we find evidence that added global warming of more than 1 degree C above the level in 2000 has effects that may be highly disruptive. The alternative scenario, with peak added forcing ~1.5 W/m2 in 2100, keeps further global warming under 1 degree C if climate sensitivity is \~3 degrees C or less for doubled CO2. We discuss three specific sub-global topics: Arctic climate change, tropical storm intensification, and ice sheet stability. Growth of non-CO2 forcings has slowed in recent years, but CO2 emissions are now surging well above the alternative scenario. Prompt actions to slow CO2 emissions and decrease non-CO2 forcings are needed to achieve the low forcing of the alternative scenario., Comment: 21 pages; 10 figures; to be submitted to Atmospheric Chemistry and Physics

Why do plants reflect in the green and have a 'red edge' in the red, and should extrasolar photosynthesis be the same? We provide: 1) a brief review of how photosynthesis works; 2) an overview of the diversity of photosynthetic organisms, their light harvesting systems, and environmental ranges; 3) a synthesis of photosynthetic surface spectral signatures; 4) evolutionary rationales for photosynthetic surface reflectance spectra with regard to utilization of photon energy and the planetary light environment. Given the surface incident photon flux density spectrum and resonance transfer in light harvesting, we propose some rules with regard to where photosynthetic pigments will peak in absorbance: a) the wavelength of peak incident photon flux; b) the longest available wavelength for core antenna or reaction center pigments; and c) the shortest wavelengths within an atmospheric window for accessory pigments. That plants absorb less green light may not be an inefficient legacy of evolutionary history, but may actually satisfy the above criteria., 69 pages, 7 figures, forthcoming in Astrobiology March 2007