Microbial communities can be described by metabolic structure: A general framework and application to a seasonally variable, depth-stratified microbial community from the coastal west Antarctic peninsula

Bowman, J.S. & Ducklow, H.W.

PLoS ONE, 10(8), e0135868.

doi:10.1371/journal.pone.0135868, 2015.


Brief summary

In the journal PLoS ONE, BMSIS researcher Jeff Bowman, working in collaboration with Hugh Ducklow at the Lamont-Doherty Earth Observatory at Columbia University, describe a new method for inferring the function of a microbial community from its taxonomic composition. Microbial communities control almost every aspect of our lives, from individual health to the planetary biosphere. Determining what microbes are performing what ecosystem functions however, has been a challenge for microbial ecologists. While modern sequencing techniques make it easy to evaluate the taxonomic composition of a microbial community extending these methods to evaluate the complete genetic capacity of a microbial community is costly and time consuming. This makes the continual monitoring of microbial community function difficult. The new method, which the researchers titled PAPRICA (PAthway PRediction by phylogenetIC plAcement), improves on existing metabolic inference techniques. In an analysis of marine microbial communities from the West Antarctic Peninsula, an ecologically vulnerable region experiencing rapid climate change, the researchers show that predicted functions change across key ecological gradients, such as depth and season. PAPRICA and similar tools will allow microbial ecologists to monitor microbial community function at an unprecedented level of detail, and better understand the function of novel microbial communities.

Alkane hydroxylase genes in psychrophile genomes and the potential for cold active analysis

Bowman, J.S. & Deming, J.W.

BMC Genomics, 15, pp 1120.

doi:10.1186/1471-2164-15-1120, 2014.


Brief summary

Crude oil from natural and anthropogenic sources is degraded by bacteria through a process known as bioremediation. Because the rate of bacterial degradation is closely linked to temperature, with degradation proceeding more slowly at lower temperatures, there is concern about the ability of psychrophilic (cold-adapted) microbial communities–such as those in Arctic waters–to undertake bioremediation. To further explore this phenomenon, BMSIS researcher Jeff Bowman, working with Jody Deming at the University of Washington, evaluated the genomes of psychrophilic and mesophilic (not cold adapted) bacteria for genes likely to be involved in crude oil degradation. They identified a number of genes previously not recognized as crude oil degradation genes that are likely to play a role in this process. In some cases the psychrophilic putative crude oil degradation genes are substantially different from their mesophilic counterparts, suggesting enhancements for improved function at low temperature.

Geothermal heating enhances atmospheric asymmetries on synchronously rotating planets

Haqq-Misra, J. & Kopparapu, R.K.

Monthly Notices of the Royal Astronomical Society, 446, pp 428-438.

doi:10.1093/mnras/stu2052, 2014.

[arXiv] [Sciworthy]

Brief summary

Earth-like planets that orbit small, red stars (M-dwarfs) might be able to sustain liquid water on the surface and provide habitable conditions where life could develop. However, such planets orbit their parent star so closely that they are prone to fall into synchronous rotation so that the “sub-stellar point” of the planet always faces the star and is constantly heated, while the opposing “anti-stellar point” never receives starlight and is constantly cooled. These atmospheres can be at risk of collapsing into huge ice caps on the anti-stellar side, but the large-scale motions of the atmosphere can provide enough energy transport from the warm side to the cold side to keep the climate stable.

In this study we use a general circulation climate model (GCM) to find that geothermal heating from tidal interactions can act to amplify warming on the night side of a synchronously rotating planet due to changes in energy transport by large-scale atmospheric dynamics. We show that the patterns of circulation on these planets (which on Earth is known as the Hadley circulation) changes direction depending on the eastward or westward position from the sub-stellar point. We also demonstrate the presence of a cross-polar circulation that transports energy and mass from the sub-stellar to anti-stellar point across the northern and southern poles and also contributes to climate stability. Understanding the impact of physical processes on the dynamics of the atmosphere is critical to assessing the habitability of terrestrial planets orbiting low-mass stars.

Damping of glacial-interglacial cycles from anthropogenic forcing

Haqq-Misra, J.

Journal of Advances in Modeling Earth Systems, 6, 294-299.

doi:10.1002/2014MS000326, 2014.

[arXiv] [Sciworthy]

Brief summary

Geologic records over the past million years indicate a 100,000 year cycle in the extent of Earth’s surface covered by ice. These ice age cycles are a result of variations in Earth’s orbital geometry, but it is unclear how these variations will continue in the presence of significant human emissions. Here I develop a simple climate model to demonstrate the potential for human-induced climate change to damp out these variations in ice coverage, which suggests that human actions today could have long-lasting impacts into the future.

Extended summary

Long-term patterns in Earth’s climate show glacial cycles that correspond to variations in Earth’s orbital geometry and affect the overall amount of sunlight that the planet receives. Known as “Milankovitch cycles”, these variations are observed in geologic reconstructions of temperature and isotopes to show periodic changes every 23,000, 41,000 and 100,000 years. The first two of these correspond directly to changes in Earth’s tilt (i.e. obliquity) and wobble (i.e. precession), but the longer 100,000 year variations in orbit seem too weak in magnitude to drive the strong climate signals we observe.

One solution to this problem is that the climate system itself amplifies these small changes to create more noticeable periodic signals. These amplification mechanisms could be the large thermal intertia of the oceans, the vast energy required to move giant ice sheets, or long-term cycles in greenhouse gases such as carbon dioxide and methane. Any combination of mechanisms such as these could magnify small changes in sunlight from Milankovitch cycles and create the dominant 100,000 year cycle in ice coverage seen in the geologic record.

Studying this problem has proven to be challenging because of the long time scales involved. Most contemporary climate models are focused on patterns of climate on Earth today and in the near future of a few hundred years from now, but few modelers have focused their attention on the more distant future of climate. In this paper I develop a simple climate model that uses stochastic (i.e. randomly generated) forcing to achieve a state of resonance that displays a 100,000 year cycle in ice coverage. The model is an idealization of the more complicated Earth system and provides a tool for exploring the behavior of climate over these long time scales.

Calculations with this model show that the influence of human emissions into the atmosphere can affect the presence of the ice age cycles, either by damping the magnitude of changes or by ceasing the cycles altogether. The simplified calculations here cannot predict exactly when this should occur, but this study points toward the existence of a threshold beyond which ice age cycles may cease as a result of human emissions.

The future of Earth’s climate is becoming increasingly marked by the presence of human activity. Depending on the course of events over the next few hundred years, we may find that the damping or cessation of ice age cycles is yet another indicator of the dawning of the age of the anthropocene.

Habitable zones around main-sequence stars: Dependence on planetary mass

Kopparapu, R.K., Ramirez, R.M., SchottelKotte, J., Kasting, J.F., Domagal-Goldman, S. & Eymet, V.

Astrophysical Journal Letters, 787, L29.

doi:10.1088/2041-8205/787/2/L29, 2014.


Listen to the author interview! [mp3 download]

Brief summary

Estimates of habitable zones around other stars assume an Earth-mass planet with Earth-like atmospheres. But recent exoplanet discoveries are unveiling a wide range of rocky planets: mostly larger in mass/size than our Earth because our detection methods are sensitive to larger planets. So the question is: How different are the habitable zones for rocky planets that are not of Earth-size? Here we discuss this question, concluding that habitable zones are wider for larger mass planets than smaller ones.

Extended summary

Identifying habitable (and possibly inhabited) planets around other stars is one of the greatest long-term goals of current exoplanet surveys. If one is to find Earth-like exoplanets in the habitable zones (HZs), one needs to know at what distance they should be found from their parent star. Most of the HZ limits that we see in the exoplanet literature were based on a 1-D climate model initially developed by Jim Kasting at Penn State. Jim and his collaborators published a seminal paper in 1993 about Habitable Zones around main-sequence stars (stars that fuse hydrogen into helium in their core, like our sun). According to that paper, the inner edge of the HZ is at 0.95 AU, and the outer edge is at 1.67 AU. (AU stands for “astronomical unit”, and 1 AU equals the mean Earth-sun distance.)

For two decades, the Kasting et al. (1993) results were the prime source for HZ estimates. In 2013, I (along with other collaborators including Jim) published revised HZ estimates, updating Jim’s old climate model. At the time Jim published his paper, no exoplanet was discovered around any Main-sequence star. People were not sure if Earth-size/mass planets even existed. Two decades later several observational surveys detected several super-Earth sized planets, indicating that small planets do exist and, in fact, are probably more common than larger planets. With this in mind, we set to re-calculate HZs. We updated several things in the climate model, but the most important one was how strong water and carbon dioxide absorb infra-red (IR) radiation. As you may know, infra-red radiation is extremely important for the greenhouse budget of a planet. The stronger the absorption of IR, the greater the greenhouse effect on a planet.

We considered an Earth-mass planet around different kinds of stars, and derived HZ limits. To our surprise, we found that the inner edge of the HZ (i.e, how close to a star one can push a planet before all the water on the surface is evaporated) is at 0.99 AU! (and the outer edge was almost the same as Jim’s old result: 1.70 AU). Remember that, by definition, Earth is at 1 AU. So this implies that we are just a step away from being un-inhabitable. There is a caveat: Our 1-D model can not model clouds, and water clouds can cool a planet by increasing the planet’s albedo (how much sunlight is reflected to space). A higher albedo means more sunlight is reflected, potentially cooling the surface of a planet. So, our 0.99 AU inner edge is a pessimistic limit. And that is ok. We want to be conservative in our HZ estimates, so that we don’t over count the number of potentially habitable planets in our Galaxy.

After we published this paper, several researchers in the exoplanet community asked us what are the HZ limits for super-Earth mass planets? or sub-Earth mass planets? That is the paper I will explain briefly here. To perform this calculation, we assumed that the background Nitrogen pressure scales with the size (or mass) of a planet. Meaning larger mass planets have more N2 (they acquire more volatiles during the formation). For the inner edge of the HZ, We found that the amount of N2 in the atmosphere just delays when the planet loses the surface water into the atmosphere, but does not affect the domination of water vapor to the greenhouse effect. In essence, more N2 acts as a light-scattering gas, increasing the albedo, to an extent. But as the planet warms more and more (as we push it closer to the star to find the inner edge), water-vapor completely dominates the atmosphere, and any scattering of light by N2 becomes negligible.

What actually matters is the gravity of the planet. A lower mass planet has less gravity. So compared to a larger mass planet, it has more water-vapor at a given height (it is puffy). When there is more water-vapor in the atmosphere, it absorbs more IR radiation, increasing the greenhouse effect. Hence, one can not push a lower mass planet as close to a star as a higher-mass planet (because as the Star’s radiation increases, more heat is absorbed and the low mass planet reaches it’s inner edge sooner than a high-mass planet). The outer edge of the HZ does not change much at all due to competing effects of albedo and the greenhouse effect of carbon-dioxide atmosphere. That is why the width of the HZ for a low mass planet is small compared to a high-mass planet. And that is the essence of our paper.