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Journal of Paleontology 89(5):695–729


kerogenous components; Schopf et al., 2005). All three techni- ques are nonintrusive and nondestructive—factors that permit their application to specimens archived in museum collections— and unlike optical photomicrographs, the three-dimensional digitized images provided by CLSM and three-dimensional spectroscopic imagery can be rotated and examined from multi- ple perspectives, a major advance over standard optical micro- scopy of particular relevance to studies of the taxonomy and taphonomy of minute fossil organisms.


Confocal laser scanning microscopy.—The history of the development of CLSM, and its principles and technical details are summarized in Claxton et al. (2005). By suppressing the image-blurring input of out-of-focus planes above and below the focal plane analyzed, CLSM provides a crisp image of a thin in-focus plane that cannot be provided by standard optical microscopy. The laser of such systems excites fluorescence in the material analyzed, for organic-walled kerogenous fossils emitted from the interlinked polycyclic aromatic hydrocarbons, “PAHs,” of which they are primarily composed (Schopf et al., 2005). This kerogen-derived fluorescence is then collected by the detector of the system in a wide spectral range at precisely defined depths of a rock-embedded fossil to produce its three- dimensional image at submicron lateral spatial resolution.


Raman spectroscopy.—Raman spectroscopyis ananalytical technique used widely in geochemistry for the identification and molecular-structural characterization of minerals (e.g., McMillan and Hofmeister, 1988; Williams et al., 1997) including graphite, the end-point of the geochemical alteration of kerogenous organics (e.g., Pasteris andWopenka, 1991;Wopenka and Pasteris, 1993; Jehlička et al., 2003). Raman can also be used to document the carbonaceous composition of geochemically less altered organic- walled fossils and the mineralogy of their enclosing matrices (Schopf et al., 2002, 2005, 2012; Schopf and Kudryavtsev, 2005, 2012; Chen et al., 2007). In analyses of permineralized carbonaceous matter, CLSM


and Raman are complementary, both being used to measure signals derived from properties of the kerogenous materials analyzed—for CLSM, laser-induced fluorescence derived chiefly from the electronic transitions of the interlinked PAHs that predominate in kerogen (Schopf et al, 2006); for Raman, vibrational transitions of such PAHs and their associated functional groups (Schopf et al., 2005)—with both being applicable to specimens analyzed at depths of up to 150µm within a fossil-containing thin section. Like CLSM, Raman is capable of providing both two- and three-dimensional images of the specimens analyzed (e.g., Schopf and Kudryavtsev, 2005, 2010, 2012; Schopf et al., 2002, 2005). UnlikeCLSM, however, Raman provides definitive molecular-structural data about the materials analyzed and for permineralized kerogen-walled fossils and associated carbonaceous matter provides a reliable index, the RIP, of its geochemical maturity (Schopf et al., 2005).


Fluorescence spectroscopy.—Unlike CLSM, which also relies on the fluorescence of the material analyzed, fluorescence spectroscopy analyzes narrow spectral ranges specificto particular luminophores. Prior to the current study, this techni- que had been applied to only one other fossiliferous deposit


(Schopf and Kudryavtsev, 2010; Cohen et al., 2011), primarily because fluorescing minerals are rarely associated with permi- neralized fossils. Apatite, however, prevalent in the Chulaktau cherts studied here, is an exception. Generally assumed to be nonfluorescing, apatite can be rendered laser-excitably fluor- escent by the presence of the rare earth element samarium+3 substituting for calcium in the Ca I and II sites of the apatite lattice (Gaft et al., 2005, p. 142, 143, 148). Such Sm+3- replacement at the highly symmetric Ca I site has been shown to occur under vacuum whereas that at the low-symmetry Ca II site occurs in the presence of air (Gaft et al., 1997a, 1997b), observations that applied to fossil-associated apatite may provide evidence of its environment of formation. Although additional studies are needed to confirm the


usefulness of such substitution to establish paleoenvironmental settings, it is likely that the cause of this effect is the presence or absence of oxygen. Air is 78% nitrogen, 21% oxygen, and <1% Ar, CO2, and other gases. The dominant component, triple-bondedN2, has a bond-energy of 226 kcal/mol, among the highest in nature. N2 is therefore essentially inert and was therefore originally named “azote” (meaning “without life”)by the French chemist Antoine Lavoisier, a property that explains its absence from common rock-forming minerals and its resulting accumulation in Earth’s atmosphere. In contrast, oxygen, the other principal component, is highly reactive and is soluble in apatite-depositing waters where it is present in variable concentrations that, as discussed below, are consistent with oxygen-related patterns of samarium-substitution.


Morphology, geochemistry, and permineralization of the Berkuta and Chulaktau microbiotas.—As is shown in Figure 3 for five organic-walled fossils permineralized in the Chulaktau cherts, optical microscopy, confocal laser scanning microscopy, and Raman and fluorescent spectroscopic imagery can be used to analyze the same individual specimen. Because of its confocal capability and high resolution—having a lateral spatial resolution of ~0.2 µm, some 50% greater than optical micro- scopy—CLSM is particularly useful for documenting the morphology and fine structure of three-dimensionally sinuous fossil filaments such as the specimen of Obruchevella parva shown in Figure 3.1 through 3.5. Similarly, the capability of such CLSM images to be rotated enables them to be studied from perspectives not permitted by optical microscopy, as shown in Figure 4.3 and 4.7 for cask-like to spheroidal vesicles of Berkutaphycus elongatus new gen. and sp. permineralized in cherts of the Berkuta Member of the Kyrshabakta Formation. As is typical of permineralized organic-walled fossils


(e.g., Schopf and Kudryavtsev, 2010; Schopf et al., 2010a, 2010b, 2012), comparison of the CLSM (black and white) and Raman-kerogen images (blue) in Figures 3 and 4 shows that much of the CLSM-detected fluorescence of the Chulaktau and Berkuta specimens is derived from the PAHs of their kerogenous cell walls and associated carbonaceous compo- nents. In addition, however, Raman imagery shows that apatite has permineralized the walls of various of the Chulaktau fossils and infilled their interiors, not only of the kerogen-walled trichomes of helically coiled Obruchevella parva (Fig. 3.4) and the cellular lumina of O. cf. meishucunensis (Fig. 3.9), but also of coccoidal sheath-enclosed cells of the colonial


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