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2015 Annual Science Report

Massachusetts Institute of Technology Reporting  |  JAN 2015 – DEC 2015

Executive Summary

Neoproterozoic Environments and Environmental Change
Members of the Johnston and Macdonald teams worked to further articulate the environmental changes associated with the late Proterozoic. These studies have taken two clear directions that are complementary, yet independent. First, and published in Nature, they presented the first reconstruction of ocean chemistry – as viewed through the iron speciation and trace metal proxy records – whereby true statistical tests are available (testing for bias, the symmetry of data distribution, etc). These results, which include contributions from team members Macdonald, Knoll and Sperling, illustrated the persistence of deep ocean anoxia well into the Paleozoic (Sperling et al 2015). In parallel, and along with NAI funded post-doc Ben Cowie, they built a custom fluorination line for extracting O2 from barite for high precision δ17O isotope analyses. These data place constraints on the collapse of the post Marinoan atmosphere and provide a timing constraint on the deposition of cap-carbonate sequences, and require that seawater sulfate be very low following the glaciation.

Other major achievements include the completion of a review of Neoproterozoic geochronology (Rooney et al., 2015) and long-format papers on the pre-Sturtian stratigraphy of the Yukon (Strauss et al., 2015), the pre-Sturtian stratigraphy of Death Valley (Smith et al., 2015), and Neoproterozoic stratigraphy of Mongolia (Bold et al., in press). Studies continue in: 1) Death Valley to unite the Neoproterozoic stratigraphy of SE Death Valley with that of the Panamint Mountains; 2) Newfoundland, to assess the degree to which the Gaskiers glaciation represents a regional ice advance or a global glaciation; 3) Peru to fully describe organic-rich Ediacaran successions that include the Shuram carbon isotope excursion; 4) Namibia and South Africa to extend descriptions of the Nama Group south where the Shuram excursion is expanded and better understand the relationship with the first appearance of calcifying metazoans; and 5) Mongolia to test the Bitter Springs Inertial Interchange True Polar Wander hypothesis.

Daniel Rothman has examined the major isotopic excursions of the Proterozoic, including the Paleoproterozoic Lomagundi-Jatuli excursion and the sequence of isotopic changes in the Neoproterozoic that terminate with the Shuram excursion. These events are interpreted as the dynamical consequence of a regime shift from a surface environment characterized by low O2 levels to one characterized by high O2 levels. A new theory concerning the physical protection of organic matter in marine sediments, one that focuses on better understanding of the conditions that lead to positive feedbacks in the burial of organic matter and the associated accumulation of O2, is being developed by Rothman and colleagues.

In a broad collaboration, including work with members of the Australian Center for Astrobiology, Martindale et al. (2015) published an account of the sedimentology, chemostratigraphy, and stromatolites of lower Paleoproterozoic carbonates, Turee Creek Group, Western Australia.

In a modern analog study, Sumner and colleagues examined microbial mats in a perennially anoxic region of Lake Fryxell, Antarctica and discovered that they create an O2-containing layer in the upper mat during summer, providing evidence for formation of benthic O2 oases (Sumner et al., 2015). Such oases, if they existed during Snowball Earth times, may have provided refugia for the ancestors of animals that appeared during the Ediacaran Period.

Early animals and the evolution of biological complexity during the Neoproterozoic
A new approach to evolutionary novelty and innovation has been developed by Erwin (Erwin 2015a-d) and colleagues. Some of this work is contained in two publications, in Geobiology and Current Biology. Sarah Tweedt completed work on Cambrian collections in Nanjing while Simon Darroch (largely funded through NMNH funds) continued his work on Ediacaran sections in southern Namibia. Ariel Chipman (Hebrew University) completed a project integrating knowledge of the developmental patterning of modern arthropods into the early history of arthropods.

Members of the Jacobs laboratory advanced understanding of the evolution of complexity associated with Neoproterozoic/ Cambrian evolution of complex life from a combined paleontological and developmental genetic perspective. Their recently published work integrates ontogenetic and developmental aspects of Neoproterozoic fossils with the genetic underpinnings of modern development that control the production of repeated features of the bilaterian bodyplan (Gold et al. 2015a). This ancestral state reconstruction approach to the iconic Ediacaran fossil, Dickinsonia provides objective means for informing past events with data only available in studies of living organisms.

Efforts to understand the evolution of complex sensory features and neural organization are continuing with work on Aurelia, the moon jellyfish. With this system it is possible to study the evolution of complex sensory systems with multiple sense organs that operate in different modalities. Recently published results (Nakanishi et al. 2015) integrate expression data obtained through in situ hybridization studies with RNA sequencing based expression assays. This approach supports the operation of a combinatorial code in development differentiating and specifying sensory organ type. This class of regulatory phenomena appears important in permitting the evolution of complex neural and sensory systems. Augmenting this approach Gold et al. 2015 published new work on the tentacles of Aurelia. Tentacles are complexly innervated sensory/motor systems; morphologically and operationally distinct tentacle types occur in different stages of the Aurelia life history. Pursuit of flow-modeling studies of the Ediacaran fauna continues with colleague Marco Ghisalberti in Perth.

Peterson and colleagues finalized a major review on microRNAs (miRNAs) that appeared in December 2015 in the Annual Review of Genetics. Their study evaluated every single reported microRNA sequence in five animal taxa (human, chicken, zebrafish, Drosophila and C. elegans) in addition to building and sequencing libraries to describe the near-complete repertoire of a fifth taxon, the nudibranch Melibe leonine. They also evaluated every reported miRNA family in miRBase and devised a new nomenclature system for vertebrate miRNA genes that takes into account both phylogenetic relatedness and genomic synteny. Further, they reconstructed the evolutionary history of the entire human microRNAom and detailed the evolutionary pressures on vertebrate miRNA sequences for both the mature gene product and the opposing arm (or star). Only about 16% of the reported miRNA sequences in miRBase (the on-line repository for miRNA sequences) are the products of miRNA genes.

A new miRNA database that is focused on the manual curation of miRNA genes (called MirGeneDB.org) has been constructed. Genomes (the gastrotrich Mesodasys laticaudatus, the polychaete annelid Trilobodrylus axi, and the gnathostomulid Gnathostomula paradoxa) were sequenced to pursue the hypothesis that reductions in body plan complexity (e.g., the invasion of the meiofaunal realm) is accompanied by a reduction in the animal’s miRNA repertoire. This work is currently in progress, and will accompany the work already conducted on rotifers, flatworms, and another species of gastrotrich.

Remarkable fossil discoveries and taphonomic processes
Bosak collaborated with Dr. Dan Lahr, a biologist at University of Sao Paulo, on the evolution of silicifying testate amoebae (Lahr et al., 2015) and with Dr. David McNeil at the Geological Survey of Canada on the preservation of agglutinated foraminifera (McNeil et al., 2014). Kelsey Moore, an undergraduate working with Dr. Sara Pruss at Smith College, has found new assemblages of agglutinated fossils in the Cryogenian cap carbonates of Mongolia and Zambia and new localities of the Rasthof Formation, Namibia and assemblages of coiled Obruchevella in cap carbonates from Arctic Alaska.

Cohen and Macdonald (2015) published a major review of Neoproterozoic fossils including a detailed compilation of all known Proterozoic eukaryotic fossils, analyzed in the context of stratigraphic, geochemical, and evolutionary datasets. This work promises to become the new gold standard for our understanding of the Proterozoic eukaryotic fossil record and the biases that affect this record and will set the stage for new research on eukaryotic evolution and the fossil record. New ornamented fossil forms described by Cohen and co-workers document the rise of macroalgae in the Neoproterozoic (Cohen et al., 2015).

Giulio Mariotti, a postdoctoral scholar in the Bosak laboratory, established an experimental system to study the biogeochemical properties of, and microbial growth on, sandy sediments in the presence of bedforms and oscillatory flow. They identified interactions between oscillatory flow and cm-scale microbial aggregates that produce elongated trails on the surface of a sediment bed. Such trails abound in late Ediacaran and early Paleozoic sandstones and siltstones and are often attributed to early animals. An article describing these results is currently under review (Mariotti et al., 2015).

Sharon Newman, a PhD student in the Bosak lab, studies how cyanobacteria become fossilized in siliciclastic environments. She found that thin filamentous cyanobacteria trapped suspended sediment within days when in the presence of moderate to high suspended sediment loads and agitation which did not mobilize sand grains, but mobilized clay. Localized precipitation of minerals around cyanobacterial filaments occurred over longer timescales (>1 month), and was facilitated by high silica concentrations (0.1-0.4 mM). These experiments better constrain physical and chemical conditions that preserved microbial mats, textures and fossils in sandy and silty environments during the Ediacaran, with more general implications for the preservation of organic matter in sandstones, siltstones and shales.

The Yale group of Briggs, Tarhan, McMahon, Anderson, Saupe and their colleagues focused on Neoproterozoic life with an emphasis on factors influencing fossil preservation. A combination of field and experimental approaches has been used to study preservation of Ediacara-type fossils and to test the prevailing ‘death-mask’ hypothesis that considers iron sulfides to have been a primary agent. Results indicate that ferruginization was a late-stage process and not consistent with this model suggesting an important role for early silicification. Further, experimental results show that microbial mats are prone to silicification and that their presence in association with invertebrate carcasses inhibits decay and enhances the preservation of soft-bodied organisms.

An investigation of factors controlling the preservation of eukaryotic microfossils in Proterozoic rocks is also underway. A collaboration with Nick Tosca (Oxford), on some 400 samples of carbonate rocks from sequences between the Cryogenian snowball Earth ice ages in Mongolia and Namibia, indicates that clay mineral contact impacts preservation. Experimental data indicate that certain clays inhibit the growth of decay bacteria such as Pseudoaltermonas.

New fossil assemblages from grey shales and cherts have been discovered from this same interval — a significant development because very few fossils have been described from rocks between the two Snowball Earth ice ages. A parallel investigation of how clay minerals impact the preservation of Burgess Shale type (carbonaceous) fossils from classic Cambrian localities is underway to test the hypothesis that the factors responsible for their preservation are similar to those that favor the occurrence of Proterozoic organic-walled microfossils. The preponderance of exceptional preservations in the Cambrian and subsequent early Paleozoic may be explained in part by a delay in intense mixing of marine shelf sediments by bioturbators, which did not develop until the Devonian. This slow onset of thorough mixing may also have contributed to the late rise of sulfate in the oceans and a mid-Paleozoic drop in oxygen levels.

Knoll and colleagues completed research on well-preserved microfossils from ca. 1500 million year old rocks in Russia (Sergeev et al., 2015). The Kaltasy microfossil assemblage highlights the importance of environment, as well as age, in determining the distributions of remains that record the early diversification of marine eukaryotes.

Knoll and Kotrc completed long-term research on the evolution of diatoms, among Earth’s most abundant primary producers. Morphospace analysis corroborates the hypothesis that diatoms achieved most of their present day structural variety early in their evolutionary history.

Ancient gene families and HGT
Fournier et al. (2015) have identified a subset of genes that appear to have been horizontally transferred from very ancient lineages that diverged earlier than the ancestor of the 3 known Domains of life.

Biosignatures
A number of discrete investigations have focused on identification and understanding of biosignatures for both microbial communities and animals.

Lipid biomarkers of Archaea, known as GDGTs, are have been the subject of studies at both MIT and Harvard. Sarah Hurley conducted experiments that showed the distribution of GDGTs depends on growth rate. These results offered both a re-interpretation of GDGT-based paleothermometry (TEX86 index) and also pointed to potential future use of GDGTs as tracers for the rates of marine productivity in the past; a paper is in review (Hurley et al., 2015). At MIT Xiaolei Liu has identified a novel GDGT in the water column of the meromictic Fayetteville Green Lake, a Neoproterozoic analog environment. Summons collaborated with numerous colleagues to document lipid and isotopic biosignatures in cultured bacteria (Baesman et al., 2015; Escobedo-Hinojosa et al., 2015), microbial communities from extreme environments (Schubotz et al. 2015).

In studies of Neoproterozoic molecular fossils, Love and Summons (2015) refuted criticism of the ‘sponge biomarker’ hypothesis, French et al. (2015) evaluated the distributions of biomarkers for anoxygenic photosynthesis from the Precambrian through Cenozoic while Bender et al. (2015) used chemical synthesis to determine the structure of a novel fossil sterane reported, so far, only in Ediacaran-Early Cambrian rocks. In efforts to apply our biosignature work on recent timescales we studied the fecal sterols of great apes and determined that they were distinct from the fecal sterols of Neandethals and modern humans (Sistiaga et al., 2015).

Pearson’s team has collaborated with Dianne Newman’s group (Caltech) to prepare a review paper documenting the recent case studies for understanding the distribution and role of hopanoid biosynthesis in Bacteria (Newman et al., 2015). Members of the Pearson team also address the 15N isotope proxy for understanding the early Earth nitrogen cycle. N-isotope analyses were conducted on a variety of ancient sediment cores and crude oils comprise data on bulk samples and purified porphyrins. These data provide detailed insights into the response of the marine N-cycle to the Aptian OAE 1a, demonstrating that anoxia became widespread, leading to intense denitrification widespread ammonia assimilation.

Phanerozoic Mass Extinctions
Daniel Rothman compiled a database of 30 mass extinction events, each characterized by the size of the carbon isotopic excursion and the time scale over which it extends. Each shift is interpreted as a transfer of carbon from organic matter to CO2, expressed as a relative increase in the size of the oceanic reservoir of dissolved inorganic carbon (DIC). One major finding is the existence of a characteristic rate of increase in the DIC pool. Above this characteristic rate, the carbon-cycle event is catastrophic, resulting in mass extinction. At or below this rate, the change in the carbon cycle can be severe but the effect on marine animal life appears minimal. Consideration of the geochemical expression of these carbon-cycle changes shows that the characteristic rate bounds quasistatic change. Events slower than the characteristic rate represent changes consistent with maintenance of a steady state, while faster events instead represent dynamic change. Because a great many events play out at the boundary between the two domains, these results suggest that the carbon cycle is generally in a state of marginal stability in which reactive reservoirs of marine organic carbon slowly accumulate. When one or more of these reservoirs reach a critical size, they are rapidly remineralized, yielding an isotopic “event”. The fastest of these events are associated with Earth-system instability and mass extinction.

In an unrelated project, we disproved prior reports that fullerenes (e.g C60) are present in sediments deposited at the end-Permian and end-Cretaceous mass extinction horizons. Accordingly, fullerenes are not makers for either mass extinctions or bolide impacts.

Missions to Mars
Recent results from the Curiosity rover (Grotzinger et al., 2015) show that the landforms of northern Gale crater on Mars expose thick sequences of sedimentary rocks. Based on rover images these outcrops are interpreted as evidence for past fluvial, deltaic, and lacustrine environments. Degradation of the crater wall and rim most likely supplied these sediments, which advanced inward from the wall, infilling both the crater and an internal lake basin by at least 75 m. This intracrater lake system likely existed intermittently for thousands to millions of years implying a relatively wet climate that supplied moisture to the crater rim, and transported sediment in streams and down into the lake basin. The deposits in Gale crater were then exhumed, likely by wind-driven erosion, creating Aeolis Mons (Mt. Sharp). Curiosity is presently ascending the lower slopes of Mt. Sharp as it continues its exploration of Gale Crater.

NAI team member Andrew Knoll continued to work as part of the science team for the MER mission to Mars. Exploration continues along the clay-rich lip of Endeavor crater. Publications in 2015 include a synthesis of recent research in the Endeavour region and an analysis of Mn-bearing surface features exposed along Murray Ridge.

Mars Analog Studies
Milliken and his team (Kaplan and Milliken, 2015; Kaplan et al., 2015) continue to focus on how remote sensing, and reflectance spectroscopy in particular, can be used as a rapid, non-destructive technique for organic detection and quantification in geologic materials. Over the past year they examined a variety of clay-organic mixtures, including both ancient (Proterozoic) rocks and synthetic mixtures. The goals are to understand detection limits of organics in sedimentary rocks and carbonaceous chondrite meteorites using reflectance spectroscopy and to assess whether or not current spectral models can also be used to rapidly quantify organic matter in these settings. In addition to terrestrial drill core and meteorite applications, this work will provide an important foundation for detecting and quantifying organic compounds on asteroid surfaces during the upcoming Hayabusa2 and OSIRIS-REx missions, both of which will investigate and sample C-type asteroids. Current results indicate that confounding effects of low-albedo and water content can be mitigated with certain spectral models, and detection limits of organics in very dark materials using reflectance spectroscopy may be on the order of 0.5 wt.% or better for a wide range of clay and organic-bearing samples.

Spectral and mineralogical results from field work in Rio Tinto, Spain have been finalized and compared to spectral (CRISM) data of Mars. They demonstrated that portions of the Rio Tinto system may be appropriate mineralogical analogs for certain locations on Mars. Intriguingly, these clay and sulfate-bearing assemblages on Mars hold promise for preservation of organic compounds despite their association with potentially low pH and oxidizing conditions, as is the case for deposits in Rio Tinto.

Education and Public Outreach
EPO activities included an abundance of media interviews, particularly those concerning the Mars Science Laboratory mission, participation of the Cambridge Science Festival and planning assistance for the Virtual Field Trips to K/T Boundary sections. MIT team member Benjamin Kotrc worked with partners at Science Club for Girls, a Cambridge, MA-based organization providing free out-of-school-time programs to “foster excitement, confidence and literacy in STEM for girls from underrepresented communities”, to develop a middle-school-age astrobiology curriculum. The 8-week curriculum, leveraging many existing astrobiology education resources, including many from NASA, was implemented in a program in Lawrence, MA in spring 2015. With Ben’s departure during 2015, Christy Grettenberger, who is now based at UC Davis, has taken over the EPO leadership for the MIT team.