Chapter 1 Isopentenoids and Geochemistry
Downloaded by UNIV OF COLORADO AURORA on December 14, 2014 | http://pubs.acs.org Publication Date: August 5, 1994 | doi: 10.1021/bk-1994-0562.ch001
Simon C . Brassell Biogeochemical Laboratories, Department of Geological Sciences, Indiana University, Bloomington, I N 47405-5101
Natural products survive beyond the demise of their source organism, although their fate depends on biological and geological factors, and their chemistry. Sediments accumulate organic debris from numerous sources, including diagnostic compounds whose structural specificity permits recognition and decipherment of their origins and degradation pathways. The complex compositions of sediments include components that either: (i) originate directly from organisms, (ii) are transformed by microbial activity, or (iii) are altered by geological processes, especially thermal effects accompanying burial. Compounds without biochemical precedent may derive from hitherto unknown or defunct biosynthetic pathways, or be geological transformation products. The geological record of isopentenoids reflects biochemical evolution. The diverse range, including steroids and hopenoids, in sediments billions of years old demonstrates the antiquity of their biosynthetic pathways and other occurrences coincide with the appearance of their putative source organisms. The evolution of Life on Earth can be explored in several distinct, yet inter-related ways. Historically, evolutionary changes in biota were primarily deduced from recognition of progressive changes in fossil morphology. Lineages inferred from such paleontological investigations could be further complemented by studies of the physiology of extant organisms viewed as descendants of fossilized ancestors. In combination these lines of evidence enabled reconstruction of detailed taxonomic relationships (/,2). In addition, biochemical evidence has been included in assessment of phylogeny, and, in general, has supported relationships based on morphology. Most recently such chemical studies have addressed the genetic affinities of organisms indicated by their R N A or D N A sequences (3,4), an approach that has also tended to substantiate established phylogenies. Attempts have now been made to extend the application of these techniques into the geological past by examination of ancient fossilized tissues (5, 6), but such efforts are fraught with complications and remain controversial. Exploration of the evolution of natural products requires knowledge of the occurrence of components within organisms and the evolutionary sequence of biological development
0097-6156/94/0562-0002$09.62/0 © 1994 American Chemical Society
In Isopentenoids and Other Natural Products; Nes, W.; ACS Symposium Series; American Chemical Society: Washington, DC, 1994.
1. BRASSELL
Isopentenoids and Geochemistry
3
Downloaded by UNIV OF COLORADO AURORA on December 14, 2014 | http://pubs.acs.org Publication Date: August 5, 1994 | doi: 10.1021/bk-1994-0562.ch001
The principal approach adopted seeks to derive phylogenetic relationships by combining the genetic composition of extant organisms with paleontological and geological evidence of their evolution (7). A n alternative approach involves investigation of the occurrences of natural products in the geological record. Specifically, it aims to identify the components present in rocks and petroleums of different ages and attempts to relate their occurrences with evolutionary changes in the organisms that constitute the biological sources of organic matter (5). It probably represents the most direct practical means to assess evolutionary changes in natural products over geological time, although it is beset with concerns centered on the survival of biosynthetic compounds. These issues form the focus of this paper. Geochemical Evidence Contained in Sedimentary Organic Matter Evaluation of the nature of geochemical evidence for the evolution of natural products first requires assessment of the various factors that determine limitations on the chemical nature and information content of sedimentary organic matter (9). These issues bear on a broader range of concerns, including: (i) How extensive and comprehensive is the rock record? (ii) What are the sources and sinks of organic matter in contemporary environments? (in) What conditions favor and influence the preservation of organic matter in the sedimentary record? (iv) To what extent is sedimentary organic matter representative of the range of its biological sources? (v) How does the onslaught of bacterial processes in surface sediments influence the composition of sedimentary organic matter? (vi) What structural and composition information survives and persists during sediment burial and thermal alteration? Answers to the above questions provide the necessary background information to determine whether evidence of evolutionary changes is preserved in the geological record of isopentenoids. Survival of the Rock Record. The preservation of the rock record and its constituent organic matter over geological time exerts a critical control on efforts to elucidate geochemical evidence for evolutionary changes in the biosynthesis of isopentenoids. Specifically, various geological processes, principally consisting of burial, metamorphism, uplift, weathering and erosion, effect the consolidation of sediments as sedimentary rocks, their subsequent transformation by heat and pressure, their deformation under stress by fracturing and folding, and their mechanical and chemical degradation and breakdown to particles that can be redeposited as sediments. A l l of these operations are part of the rock cycle which continuously shapes and changes the sediment record over geological time, encompassing both the formation of new deposits and the alteration, recycling and ultimate destruction of ancient sediments. As a direct result of the cumulative effects of these influences, the worldwide prevalence of sedimentary rocks within a given stratigraphic time unit tends to be inversely proportional to age. Thus, occurrences of the oldest rocks are more scant that those formed during more recent epochs and examination of the earliest record is hindered by the paucity of surviving strata from the most ancient eons. Gaps in the Geological Record. A second factor affecting the completeness of geochemical evidence for evolutionary processes is the fragmentary nature of the geological record. Sedimentary sequences inevitably contain gaps termed hiatuses which include periods of non-deposition, or non-continuous deposition, and episodes of erosion. A l l of these represent time intervals for which the rock record provides no
In Isopentenoids and Other Natural Products; Nes, W.; ACS Symposium Series; American Chemical Society: Washington, DC, 1994.
Downloaded by UNIV OF COLORADO AURORA on December 14, 2014 | http://pubs.acs.org Publication Date: August 5, 1994 | doi: 10.1021/bk-1994-0562.ch001
4
ISOPENTENOIDS AND OTHER NATURAL PRODUCTS
vestige of any events that took place during these specific periods. Such hiatuses are found in virtually all sedimentary deposits, though their prevalence varies. Despite such constraints, efforts to derive a comprehensive history of changes occurring through geological time are still feasible if constructed in a piecemeal fashion from the combination of records collated from series of fragmentary sedimentary sequences. One encouraging consideration is that the entire documentation of evolution based on paleontology relies on interpretation of fossil remains preserved in sediments, despite the incomplete nature of individual stratigraphic sections and other limitations, such as the scarcity of evidence for earliest life forms (70). In principle, however, it should be possible to explore chemical evidence of evolutionary changes in parallel with the morphological fossil record, although the conditions that favor preservation of organic materials differ from those that lead to the survival of morphological remains, primarily skeletal material and other hard body parts. Hence, an important aspect of the exploration of organic records is the need to identify depositional settings and associated environmental conditions, and lithologic variations that are conducive to the preservation of organic debris. M i n e r a l , Fossil and Chemical Composition of Sediments. Sediments are primarily composed of a mineral matrix variously constituted by combinations of clastic detritus (e.g. sand, silt and clay particles containing silicate minerals), chemical precipitates (e.g. carbonates, gypsum), biogenic skeletal debris that may be composed of calcareous (e.g. coccolithophorids, foraminifera), and siliceous (e.g. diatoms, silicoflagellates, radiolaria) materials, augmented by primary (e.g. phosphorites, barite) and secondary minerals (e.g. pyrite). Co-occurring with this material are biogenic particles that are principally composed of organic matter (e.g. dinoflagellate cysts, fecal pellets). Open marine sediments tend to accumulate detritus from pelagic sources that are typically a combination of biogenic and clastic components originating from the overlying water column coupled with advected material. Hence, it is to be expected that sediments should contain organic compounds in markedly lower abundance than living cells because of the dilution effects inherent in the process of sediment formation and the lability of organic matter, when compared to carbonate and silicate minerals, which arises from its biological degradation. M a j o r Biological Processes within the Geochemical Carbon Cycle. The principal process effecting carbon fixation is the photosynthetic uptake of CO2 by phytoplankton and terrestrial vegetation. A diverse range and biological specific series of enzymatic reactions then serve to build, modify and transform the initial biosynthetic building blocks into the wide variety or organic compounds found within the biosphere. Subsequently, this transient reservoir of carbon in biota is extensively degraded by further biological, physical and chemical processes so that the vast majority of primary production is recycled and does not enter the sedimentary domain. Thus, the annual flow of carbon from the atmosphere or hydrosphere through the biosphere to the lithosphere (ca. 2 x 1014 gCa-i; 77) represents a comparatively minor proportion of that contained in living systems. Sedimentary Accumulation of Carbon. The amount of carbon accumulated in sediments (ca. 6 x IO1 gC; 77) greatly exceeds the present day inventory of carbon in the biosphere (ca. 5 x lO * gC; 77). Inevitably the comparative size of these carbon reservoirs reflects the longevity of geological time whereby even the small flux of carbon that escapes remineralization and recycling to become incorporated in sediments ultimately amounts to the largest accumulation of carbon on earth. The sequestering of carbon through geological time, however, has not been constant; there are specific periods in the past that are associated with enhanced organic carbon accumulation in petroleum source rocks or coals (72). Thus, the sedimentary reservoir of carbon has 7
2
In Isopentenoids and Other Natural Products; Nes, W.; ACS Symposium Series; American Chemical Society: Washington, DC, 1994.
Downloaded by UNIV OF COLORADO AURORA on December 14, 2014 | http://pubs.acs.org Publication Date: August 5, 1994 | doi: 10.1021/bk-1994-0562.ch001
1. BRASSELL
Isopentenoids and Geochemistry
5
fluctuated over time driven, in part, by evolutionary developments. For example, the diversification of pteridophytes and gymnosperms in the Carboniferous (ca. 360-290 Ma) appears to precede a major era of coal formation (72). The precise causes of developments or perturbations in carbon production and burial are the subject of much active research, not least because of their direct links with global carbon climate. In particular, global carbon budgets are potentially induced by events, such as increases in the frequency or magnitude of volcanic eruptions or the steadfast growth in anthropogenic combustion of fossil fuels, that cause changes in atmospheric CO2 levels and may lead to global warming. Efforts to evaluate ancient records prompts an exploration of the factors that influence the sources of organic matter and their alteration during and after deposition (9). Toward this objective, studies of contemporary depositional settings can provide evidence of the principal influences on the production and preservation of organic matter in the rock record. Most importantly, a detailed perspective of contemporary processes permits consideration of the varied controls that determine the survival of both total organic matter and specific organic compounds like isopentenoids. The Abundance and Nature of Sedimentary Organic Matter. T h e proportion of organic carbon in sediments tends to be small, typically totaling
