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Exoplanet Biosignatures Workshop-Without-Walls Review Papers - Discussion Forum

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19 Apr 2017

1. Exoplanet Biosignatures:  A Review of Remotely Detectable Signs of Life

  1. NExSS Manager

    Contact: Edward Schwieterman, edward.schwieterman *at*
    Summary: This paper provides an in-depth review of current understanding of potential exoplanet biosignatures including gaseous, surface, and temporal biosignatures. We focus particularly on advances made since the review by Des Marais et al. (2002).  This paper does not propose new biosignatures strategies, but reviews currently existing literature to provide a foundation for a path forward. We survey some biogenic spectral features that are well-known in the specialist literature but not yet robustly vetted in the context of exoplanet biosignatures.  We also briefly review advances in assessing biosignature plausibility, including novel methods of determining chemical disequilibrium and the minimum biomass required for a given atmospheric signature. 

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  2. Anthony D. Del Genio

    P. 6, last two lines: I feel that this statement is somewhat problematic. The "conservative" habitable zone limit is indeed conservative at the inner edge. It is not at the outer edge. As Wolf (2017) notes, he cannot make Trappist-1 f habitable even with 30 bars of CO2, even though it is well within the traditional conservative outer edge as depicted in Fig. 2.  He gives several reasons.  One is the assumption of saturated water vapor in the models that define the conservative outer edge, which has a lot to do with the depicted inner edge being a conservative estimate but which goes in the opposite direction at the outer edge. Another is the neglect of the increase in surface albedo as the outer edge is approached.  Quantitatively both of these are model-dependent.  But assuming saturation and fixed (< 1) albedo would seem to be overly optimistic, not conservative.  Zero relative humidity and surface albedo = 1 - THAT would truly be conservative for the outer edge. If I were designing observations of the TRAPPIST-1 system and could afford to observe 2 planets, after planet e I might take my chances on d (which admittedly Wolf finds to be uninhabitable but which may depend on what the clouds and convection do in a given model) before I spent time on f, whose shortcomings seem more difficult to avoid.

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  3. Edward Schwieterman

    Dear Tony, thank you for the helpful comment. You're right to note that the assumptions for calculating the outer edge of the HZ with 1D radiative-convective models are qualitatively different than those same assumptions applied to the inner edge. We'll make sure to modify the language to add this caveat. I'll also add a citation to Wolf (2017). This is all important for supporting the more general and consequential point that (at least Earth-like) biosignature searches are likely to be more successful when characterizing targets with conservative assumptions about planetary habitability. 

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  4. Tanai Cardona

    First of all, I want to thank you for this awesome reviews, they are really inspiring and exciting.

    I was kindly asked by Nancy to read and comment on section 5.1. So I will leave some comments and suggestions below. Thanks for your time, patience, and for providing this platform for others to get involved too!

    “Various lines of evidence support that anoxygenic photosynthesis preceded oxygenic, and theories on the origin of the RC Types and how oxygenic photosynthesis came to combine two photosystems are reviewed by Blankenship et al. (2007).”

    I just want to say that you should not take this as dogma… some of the lines of evidence that support the premise that anoxygenic photosynthesis preceded oxygenic photosynthesis are mostly speculation about the evolution of photochemical reaction centers or the evolution of cyanobacteria. Some of this speculation has lingered on from times when there were no sequences of reaction center proteins nor structures of reaction center proteins... not even sequenced genomes.

    I am not a geologist, but for what I understand, not even geochemical evidence for oxygen is clear or definitive on when biogenic oxygen appears for the first time. Another classic example: the hypothesis that cyanobacteira obtained photosynthesis via horizontal gene transfer from anoxygenic phototrophic bacteria is not supported by any data: in fact, such hypothesis can be rejected from basic structural comparisons of reaction center proteins.

    Of course, it is pointless at this stage to debate the evolution of photosynthesis. However, I think it is more correct to say in such an introductory statement that it is likely that some forms of photosynthesis evolved early during the evolutionary history of life on Earth, and that from this early origin a diversification of photosynthetic bacteria took place, some of these were anoxygenic, some of these may as well have been oxygenic. I think it is better to say that it is currently not understood at what moment in time the capacity to oxidize water appeared for the first time. "What comes first" is debatable and I don't think it is really useful as a guide to understand the evolution of photosynthesis.

    “The structure of this oxygen evolving complex (OEC), a four Mn cluster with Ca and Cl cofactors, was not characterized until crystallography work by Umena et al. (2011) (for which the presenter received a standing ovation), and there are no known primitive precursor molecules.”

    I was actually there when the standing ovation took place at the Photosynthesis Congress in China! It was a truly amazing, mind-blowing, and unforgettable experience that took everyone by surprise!

    I suggest to say: "The structure of this oxygen evolving complex, also known as the water oxidizing complex, a Mn4CaO5 cluster, was not resolved at atomic resolution until the crystallography work by…

    The Mn4CaO5 cluster had been studied and characterized for a very long time (decades) before the crystallographic work: for example, all the ligands to the cluster, the cubane configuration, details of the catalytic cycle, water binding, protonation states, all had been advanced to a very large extent well before the Umena structure. In fact, the Umena work would not have been possible without several less well-resolved structures that predated it.

    The chloride atoms are not really in the cluster and they mediate proton transfer rather than water oxidation itself.

    “Also, how the oxygens bind to the OEC to form O2 remains an active area of research”

    I suggest you say something like this: “Also, how the substrate waters bind to the OEC, and how the O-O bond is formed remains an active area of research”

    “The band gap for PS II is larger than for anoxygenic photosynthetic bacteria, because it must provide a more oxidizing potential to split water while at the same time, because of the highly-conserved structures of the RCs, the first acceptor molecule is still at a similar reducing potential as the same Type anoxygenic photosystem (Figure 8); the photon energy must be able to straddle both these oxidizing and reducing potentials. There is little room to change the oxidation potential of the primary donor pigment, but if it could be possible to tune the first acceptor to a less reducing potential, or even to simplify the entire electron transfer pathway, this could allow higher efficiencies, i.e. lower band gap energies for the same energy stored, and therefore longer wavelengths for photosynthetically active radiation”

    Another reason why the band gap for PSII is high is because of the incorporation of photoprotective mechanisms to avoid singlet oxygen and ROS that have to do with recombination pathways. This is discussed in detail by Rutherford et al., (2012). If I understand correctly, you could make the band gap smaller and still retain water oxidation, but at the expense of efficiency and enhanced damaged under variable environmental conditions.

    “Such environmental pressures inevitably lead to tuning of their their light harvesting pigments to optimize the capture of photons.”

    Delete extra “their”.

    “In the cyanobacterium Leptolyngbya sp. JSC-1, depletion of visible light and availability of near-infrared can trigger the production of the far-red chlorophyll f and reconstruction of the entire photosynthetic apparatus in response to changing light conditions (Gan et al., 2014; Ho et al., 2016)”

    It is not just Leptolyngbya, there is a significant diversity of cyanobacteria that have the capacity to make chlorophyll f and that show the far-red acclimation response described by Gan et al.

    Chlorophyll f synthesis was first demonstrated in a strain isolated from a stromatolite in Australia... known today as Halomicronema hongdechloris, the work of Prof. Min Chen. In Gan et al 2014., it was first shown that other cyanobacteria could also make chlorophyll f and they characterized for the first time the genetic and molecular mechanism for this adaptation to far-red light.

    “The major bacteriochlorophylls are a, b, c, d, e, and g and are found distributed in purple sulfur bacteria, purple non-sulfur bacteria, green sulfur bacteria, filamentous anoxygenic phototrophs, and heliobacteria”

    You forgot phototrophic Acidobacteria and phototrophic Gemmatimonadetes, they are unique clades different to all the above mentioned groups. I think you should also mention that chlorophyll a is also part of the core reaction center in those strains with homodimeric Type I reaction centers (green sulfurs, acidobacteria, heliobacteria), imporatant for charge separation.

    Perhaps you should use the phylum name: phototrophic Proteobacteria, Chlorobi, Chloroflexi, Acidobacteria, Firmicutes, and Gemmatimonadetes.

    “Chl f is an antenna pigment in some cyanobacteria induced by NIR light at longer wavelengths than the reaction center Chl a”

    No one has demonstrated yet that chlorophyll f is exclusively found in the antenna. It was speculated to be an antenna pigment only, but it has not been proven yet. Research here at Imperial suggests that chlorophyll f might also be bound in the core reaction center and might be important for charge separation, but this is unpublished. I think it should be enough to say that Chl f is incorporated into modified reaction centers in some cyanobacteria, induced by far-red light.

    Rutherford, A. W., Osyczka, A., & Rappaport, F. (2012). Back-reactions, short-circuits, leaks and other energy wasteful reactions in biological electron transfer: Redox tuning to survive life in o2. FEBS Lett, 586(5), 603-616. doi:10.1016/j.febslet.2011.12.039

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  5. Nancy Kiang

    Tanai -

    Thanks for the wordsmithing, and alerting us about those other clades!  Would you happen to have the references for these discoveries?

    Chl f in the cyanobacteria reaction centers?!?  Yes, where exactly the Chl f is physically is not known, and it has been assumed it was only an antenna pigment.   Please publish that soon!

    I think by the time these missions are up, the understanding of oxygenic photosynthesis will have changed...

    Thanks for the Rutherford et al. (2012) reference -- excellent one to cite.

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  6. Tanai Cardona

    Hi Nancy,

    The reference for the discovery of phototrophic Acidobacteria is (Bryant et al., 2007) and the characterization of the reaction center of Acidobacteria was published in (Tsukatani et al., 2012). Phototrophic Gemmatimonadetes was first reported here (Zeng et al., 2014), but see also (Huang et al., 2016)

    Bryant, D. A., Costas, A. M. G., Maresca, J. A., Chew, A. G. M., Klatt, C. G., Bateson, M. M., . . . Ward, D. M. (2007). Candidatus chloracidobacterium thermophilum: An aerobic phototrophic acidobacterium. Science, 317(5837), 523-526. doi:10.1126/science.1143236

    Huang, Y., Zeng, Y., Lu, H., Feng, H., Zeng, Y., & Koblizek, M. (2016). Novel acsf gene primers revealed a diverse phototrophic bacterial population, including gemmatimonadetes, in lake taihu (china). Appl Environ Microbiol, 82(18), 5587-5594. doi:10.1128/AEM.01063-16

    Tsukatani, Y., Romberger, S. P., Golbeck, J. H., & Bryant, D. A. (2012). Isolation and characterization of homodimeric type-i reaction center complex from candidatus chloracidobacterium thermophilum, an aerobic chlorophototroph. J Biol Chem, 287(8), 5720-5732. doi:DOI 10.1074/jbc.M111.323329

    Zeng, Y. H., Feng, F. Y., Medova, H., Dean, J., & Koblizek, M. (2014). Functional type 2 photosynthetic reaction centers found in the rare bacterial phylum gemmatimonadetes. Proc Natl Acad Sci U S A, 111(21), 7795-7800. doi:DOI 10.1073/pnas.1400295111

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  7. Nancy Kiang

    Tanai - Thanks so much for these references!  Will put them in!

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  8. Stephen Kane

    I apologize for the late comment (hey, it's still June 9th where I am ...), but I do feel I need to point out a critical piece missing from the review of HZ boundaries. It is often assumed that we can determine precise HZ boundaries based on the stellar properties. However, the fundamental parameter of the intrinsic stellar luminosity is notoriously difficult to determine, particularly for late-type stars where stellar radii are poorly understood. The result of this is large uncertainties on stellar parameters that are rarely translated into uncertainties in the location of the HZ boundaries. I performed an analysis of this effect in Kane, 2014, ApJ, 782, 111 and found the effect to be quite severe for relatively distant (Kepler) stars. Even so, it demonstrates the critical aspect of stellar characterization for the nearest stars since HZ boundaries will be used as a target selection tool for deciding where to use extremely precious WFIRST/LUVOIR/HabEx time.

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  9. Edward Schwieterman

    Dear Tanai, thank you for taking time to provide helpful comments about photosynthesis here and for the other papers in the NExSS series!

    Nancy et al., I would suggest that we maintain our structure in the topics addressed between the relevant NExSS papers when incorporating the forum comments (for all papers). EB1 is concerned with providing an overview of remotely detectable signatures (of which surface signatures are just one part), so observable edge wavelengths, and the relation of reflectance signatures to pigments and reaction centers should go here. (And we should certainly moderate any text that appears to be taking a position on open questions.) EB2 is more focused on oxygen as a biosignature specifically, so nuanced points about the evolution of water oxidation on the way to oxygenic photosynthesis should go there if we include them.  I think EB4 is the more appropriate venue for more speculative ventures about the likelihood of oxygenic photosynthesis and how this might affect statistical searches/estimations for the distribution of life in the universe. 

    It also sounds like it might be fruitful to have a separate effort later that digs into some of the topics raised more deeply, since we want to keep the focus on observable signatures here. 

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  10. Edward Schwieterman

    Hi Stephen, thanks for your comment. How potential uncertainties in stellar parameters affect the inferred HZ limits and therefore target selection is an important topic, and we'll be sure to include this caveat in the submitted version of the manuscript. (Though we likely won't be too detailed, as this is a small part of the paper). 

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