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Global warming, the most severe faunal mass extinction and the shift of biogeochemical cycles were observed in the ocean across the Permian-Triassic boundary about 252 million years ago, providing an analog to understanding the modern oceans. Along with the progressive global warming, the biogeochemical cycle was documented to show a shift from the decoupled processes of carbon, nitrogen and sulfur prior to the mass extinction to the coupled biogeochemical processes during faunal mass extinction. The coupled biogeochemical cycle was further observed to shift from the coupled C-N processes during the first episode of the faunal mass extinction to the coupled C-N-S processes during the second episode, diagnostic of the progressive development of more deteriorated marine environmental conditions and the more severe biotic crisis across the Permian-Triassic boundary. The biogeochemical cycles could thus be an indication to the progressive collapse of marine ecosystems triggered by the global warming in Earth history. In modern oceans, the coupled C-N cycle triggered by the global warming was observed in some regions. If these local C-N processes develop and expand to the global oceans, the coupled C-N-S processes might be brought into existence and the marine ecosystems are inevitable to suffer from complete collapse as observed at 252 million years ago. [ABSTRACT FROM AUTHOR]

Microbes not only show sensitive responses to environmental changes but also play important roles in geochemical and geophysical systems. It is well known that microbes have caused major changes in surface environments and biogeochemical cycles through Earth history. Microbial processes can also induce the synthesis of certain minerals under Earth-surface conditions that previously were believed to form only under high temperatures and pressures in the deep Earth. For example, microbes can promote the conversion of smectite to illite, synthesis of authigenic plagioclase, precipitation of dolomite, and biotransformation of geolipids. These effects of microbes are due to their large surface/volume ratios, enzyme production, and abundant functional groups. Microbial catalyzation of chemical reactions proceeds through reaction-specific enzymes, a decrease in Gibbs's free energy, and/or break through the dynamics reaction thresholds via their metabolisms and physiology. Microbes can lower the surface free energy of mineral nuclei via biophysical adsorption due to their large surface/volume ratios and abundant functional groups. The mineral precipitation and transformation processes induced by microbes are functionally equivalent to geological processes operating at high temperatures and pressures in the deep Earth, suggesting that microbial processes can serve as analogs to deep abiotic processes that are difficult to observe. [ABSTRACT FROM AUTHOR]

Geobiology is a new discipline on the crossing interface between earth science and life science, and aims to understand the interaction and co-evolution between organisms and environments. On the basis of the latest international achievements, the new data presented in the Beijing geobiology forum sponsored by Chinese Academy of Sciences in 2013, and the papers in this special issue, here we present an overview of the progress and perspectives on three important frontiers, including geobiology of the critical periods in Earth history, geomicrobes and their responses and feedbacks to global environmental changes, and geobiology in extreme environments. Knowledge is greatly improved about the close relationship of some significant biotic events such as origin, radiation, extinction, and recovery of organisms with the deep Earth processes and the resultant environmental processes among oceans, land, and atmosphere in the critical periods, although the specific dynamics of the co-evolution between ancient life and paleoenvironments is still largely unknown. A variety of geomicrobial functional groups were found to respond sensitively to paleoenvironmental changes, which enable the establishment of proxies for paleoenvironmental reconstruction, and to play active roles on the Earth environmental changes via elemental biogeochemical cycles and mineral bio-transformations, but to be deciphered are the mechanisms of these functional groups that change paleoenvironmental conditions. Microbes of potential geobiology significance were found and isolated from some extreme environments with their biological properties partly understood, but little is known about their geobiological functions to change Earth environments. The biotic processes to alter or modify the environments are thus proposed to be the very issue geobiology aims to decipher in the future. Geobiology will greatly extend the temporal and spatial scope of biotic research on Earth and beyond. It has great potential of application in the domains of resource exploration and global change. To achieve these aims needs coordinative multidisciplinary studies concerning geomicrobiology and related themes, database and modeling of biogeochemical cycles, typical geological environments, and coupling of biological, physical, and chemical processes. [ABSTRACT FROM AUTHOR]

The biosphere interacts and co-evolves with natural environments. Much is known about the biosphere's response to ancient environmental perturbations, but less about the biosphere's influences on environmental change through earth history. Here, we discuss the roles of microbes in environmental changes during the critical Permian-Triassic (P-Tr) transition and present a perspective on future geomicrobiological investigations. Lipid biomarkers, stable isotopic compositions of carbon, nitrogen and sulfur, and mineralogical investigations have shown that a series of microbial functional groups might have flourished during the P-Tr transition, including those capable of sulfate reduction, anaerobic HS oxidation, methanogenesis, aerobic CH oxidation, denitrification, and nitrogen fixation. These microbes may have served to both enhance and degrade the habitability of the Earth-surface environment during this crisis. The integrated microbial roles have enabled the Earth's exosphere to be a self-regulating system. [ABSTRACT FROM AUTHOR]

Evaluating the pre-Jurassic marine source rocks in China has been difficult because these rocks are generally too high- or over-maturated for most traditional methods to work. As to the remaining parameter TOC (%), its lower limit for recognizing the carbonate source rocks in China has been in dispute. Nineteen Phanerozoic sections in the Middle-Upper Yangtze Platform and the Guizhou-Hunan-Guangxi Basin have been studied in search for a different approach to complementing the traditional evaluation method for these source rocks. We have applied a geobiological approach to tracing the organic carbon (OC) output and accumulation from the living stage (primary productivity) to the post-mortem deposited remains, and finally to the preserved burial organics. Four biological and geological parameters are employed to represent the OC of the three stages. A series of proxies of these parameters are discussed and integrated to establish a geobiological evaluation system independent of TOC and other traditional methods. Here we use the Guangyuan section in Sichuan as an example for the geobiological evaluation. Our results indicate that in the argillaceous rocks, the geobiological parameters show the qualified source rocks in accordance with high TOC values; but in the carbonates, the good source rocks delineated by the geobiological parameters have a wide range of TOC, from 0.03% to 1.59%, mostly <0.3%. We suggest that it is still premature to set TOC=0.3% or 0.5% as the lower limit for the pre-Jurassic carbonate source rocks in South China. [ABSTRACT FROM AUTHOR]

The temperature gradient along the altitude transect of Mt. Jianfengling provides a good opportunity to establish and evaluate the microbial lipid-based environmental proxies. The soils collected from 14 different altitudes of Mt. Jianfengling contain abundant microbial fatty acids and fatty alcohols, including iso/ anteiso fatty acids ( i/ aC- i/ aC), 10-Me-C fatty acid, iso/ anteiso fatty alcohols ( i/ aC- iC), 10-Me-C fatty alcohol and unsaturated fatty alcohols, which can indicate a strong microbial activity in the Jianfengling soils. The branched and unsaturated fatty alcohols can be only detected when saponification is performed, implying that these lipids are present as the constituents of bacterial wax esters in the soils. The ratio of aC/ iC fatty acids is positively correlated with altitude, suggesting that the decrease in temperature can induce the increase in the relative abundance of anteiso C fatty acid. In contrast, the ratio of aC/ iC fatty alcohols and of aC/ nC fatty alcohols both decrease with increased altitude or decreased temperature. Similarly, the ratio of nC/ nC fatty alcohols also decreases with decreased temperature, which is opposite to the previous observation that unsaturation of fatty acids in microorganism increases in response to decreased temperature. Besides, the average chain length (ACL) of long chain fatty alcohols (C-C) from leaf waxes and carbon preference index (CPI) of all n-fatty alcohols are also significantly correlated with altitude or mean annual temperature, demonstrating their potential for paleoclimate reconstruction. The correlation of microbial fatty acids and alcohols as well as ACL and CPI of plant wax-derived fatty alcohols with altitude may provide novel ways to reconstruct paleotemperature and paleoaltimetry. [ABSTRACT FROM AUTHOR]

The discipline of "Bio-Organic Geochemistry" is a cross research field between biogeochemistry and traditional organic geochemistry, which focuses on geochemical processes related to the biosynthesis of organic molecules (particularly lipids) by (micro) organisms, organic matter production by primary producers, degradation of organic matter by microbial processes recorded by retainable lipid biomarkers, and organic proxies for studies of paleo-climate, paleo-environments, paleoecology and Earth evolution. This field aims to go beyond the traditional petroleum-oriented Organic Geochemistry by integrating with biogeochemical concepts concerned mostly with biomolecules from cellular material such as DNA and lipids. A formal Chinese organization in Bio-Organic Geochemistry was established in 2012 when the first conference was held in Guangzhou. This organization has witnessed rapid growth over the past six years with focused research addressing organic proxies in paleoclimate and paleoenvironmental applications, with particular rapid development in glycerol dialkyl glycerol tetraethers-derived proxies. Most progresses in China so far are made following or paralleling the international trend in biogeochemical studies. Things have begun to change with China's ambitious initiatives in several bio-geo programs such as the Ocean Deep Drilling Program of China, the Microbial Hydrosphere Program, the Deep Carbon Observatory, and the Microbiome Program. Looking forward in the 21st Century, the growing Chinese research community in Bio-Organic Geochemistry faces grand opportunities and challenges as Chinese scientists propel themselves toward global research frontiers. [ABSTRACT FROM AUTHOR]

Geomicrobiology is a sub-discipline of geobiology and emphasizes the interaction between microorganisms and their environment on Earth. There is a need to explicitly emphasize the biogeochemical processes performed by microorganisms associated with Earth’s tectonic activities, especially under the framework of the modern theory of plate tectonics. Tectonomicrobiology aims to create a better synergy between microbial and active tectonic processes. This explicit synergy should also foster better communications between solid Earth scientists and life scientists in terms of holistic Earth system dynamics at both tectonic and micro-scales. [ABSTRACT FROM AUTHOR]

The recently proposed global and local calibrations for the mean annual air temperature (MAT) reconstruction on the basis of 5- and 6-methyl brGDGTs have rarely been applied to the Chinese LPS yet, leaving the applicability of these calibrations unclear. Here, we used the improved chromatography method to analyze 198 loess-paleosol samples from the Weinan section in the southern CLP for the past 350 kyr. The 6-methyl brGDGTs comprise a major proportion of total brGDGTs, pointing to alkaline conditions for most soil samples from the Weinan LPS. The decoupled profile variation of MBT′ and MBT′ suggests their response to different enviromental factors, possibly soil pH (or soil moisture) and temperature, respectively. This discrimination further corraborates that temperature and monsoonal precipitation were not in phase during the last four deglaciations on the CLP. Temperature estimates for the six calibrations tested show similar trends but remarkably differ in amplitudes. The soil moisture appears to affect the global MBT′/CBT calibration, the global MAT calibration (a calibration based on the multiple linear regression) and the Chinese local SSM (Stepwise Selection Method) calibration, resulting in a significant underestimation of late Holocene temperature. In contrast, the dry climate has no effect on the global MBT′ calibration. Of the six calibrations, only the Chinese local SSM calibration and global MAT calibration produce temperature variation amplitude over the past 350 ka that is consistent with other independent proxy data. The recently proposed local calibrations based on 5- and 6-methyl brGDGTs for North China yield the amplitude of temperature changes that is much larger than the results determined by other approaches. All the six calibrations have their own weakness in the MAT reconstruction, due partly to the inconsistency between the brGDGT distribution in the Weinan LPS and the modern soils used to establish these calibrations. [ABSTRACT FROM AUTHOR]

Glycerol dialkyl glycerol tetraethers (GDGTs) in lake sediments are useful biomarkers for the continental paleoclimatic reconstruction. However, the environmental controls on the distribution of these compounds, in particular the 6-methyl isomers of bacterial branched GDGTs (bGDGTs), in the lakes with contrasting pH, are still unknown, hindering their application for paleo-reconstructions. Here, we investigated the environmental impacts on the distribution of GDGTs in 17 alkaline lakes and 1 acid lake in China. It was found that the dissolved oxygen content in water column may have an impact on the distribution of archaeal isoprenoid GDGTs (iGDGTs) by causing the change in archaeal communities. The ratio of GDGT-0/crenarchaeol increases with decreasing oxygen content, indicating that the relative abundance of anaerobic methanogenic archaea or Miscellaneous Crenarchaeotic Group (MCG) vs. aerobic Thaumarchaeota is controlled by the oxygen content dissolved in water of these lakes. Thaumarchaeota are likely to contribute only a small proportion of iGDGTs in the relatively oxygen-depleted lakes, and thus TEX is not suitable for the reconstruction of the surface temperature of these lakes. The abundance ratio of iGDGTs to bGDGTs ( R) appears to show no relationship with water pH in all the lakes, but exhibits a significant positive correlation with the water depth of the acid Lake Qinghai in Tengchong. As expected, the methylation degree of bGDGTs (MBT′) was found to correlate with both mean annual air temperature (MAT) and water pH, and the cyclization degree of bGDGTs (CBT) correlates only with water pH in these lakes. However, the MBT′, an index to measure the methylation degree of 5-methyl bGDGTs, exhibits no relationship with MAT, whereas MBT′, the methylation degree of 6-methyl bGDGTs, was found to correlate significantly with MAT. This is opposite to the situation observed in the global soils, pointing to a different adaptation of bGDGT-producing bacteria to environmental variables or different microbial sources of bGDGTs in these lakes. The relative abundance of 6- vs. 5-methyl bGDGTs is controlled by pH in these lakes, similar to that observed in worldwide soils. Hence, the isomer ratio (IR) of 6-methyl bGDGTs or CBT′ can be used as a proxy for water pH, although they might be influenced by other environmental factors including temperature in the lakes with a narrow range of pH. [ABSTRACT FROM AUTHOR]

Molybdenum (Mo) proxies, including bulk concentration and isotopic composition, have been increasingly used to reconstruct ancient ocean redox states. This study systematically reviews Mo cycles and their accompanying isotopic fractionations in modern ocean as well as their application in paleo-ocean redox reconstruction. Our review indicates that Mo enrichment in sediments mainly records the adsorption of Fe-Mn oxides/hydroxides and chemical bonding of HS. Thus, Mo enrichment in anoxic sediments generally reflects the presence of HS in the water column or pore waters. In addition to the effect of euxinia, sedimentary Mo enrichment is related to the size of the oceanic Mo reservoir. Given these primary mechanisms for oceanic Mo cycling, Mo abundance data and Mo/TOC ratios acquired from euxinic sediments in geological times show that fluctuations of the oceanic Mo reservoir are well correlated with oxygenation of the atmosphere and oceans and suggest that oxygenation occurred in phases. Mo proxies suggest that Mo isotopes in strongly euxinic sediments reflect the contemporaneous Mo isotopic composition of seawater, but other processes such as iron-manganese (Fe-Mn) adsorption and weak euxinia can result in different fractionations. Diagenesis may complicate Mo enrichment and its isotopic fractionation in sediments. With appropriate constraints on the Mo isotopic composition of seawater and various outputs, a Mo isotope mass-balance model can quantitatively reconstruct global redox conditions over geological history. In summary, Mo proxies can be effectively used to reconstruct oceanic redox conditions on various timescales due to their sensitivity to both local and global marine redox conditions. However, given the complexity of geochemical processes, particularly the effects of diagenesis, further work is required to apply Mo proxies to ancient oceans. [ABSTRACT FROM AUTHOR]

Early oceans (>520 Ma) were characterized by widespread water-column anoxia, stratification, and limited oxidant availability, which are comparable to the chemical characteristics of modern marine sedimentary pore-waters in productive continental margins. Based on this similarity and our current understanding of the formation mechanism of early Earth ocean chemistry, we propose an idealized chemical zonation model for early oceans that includes the following redox zones (from shallow nearshore to deep offshore regions): oxic, nitrogenous (NO-NO-enriched), manganous-ferruginous (Mn or Fe-enriched), sulfidic (HS-enriched), methanic (CH-enriched), and ferruginous (Fe-enriched). These zones were dynamically maintained by a combination of processes including surface-water oxygenation by atmospheric free oxygen, nitrate reduction beneath the chemocline, nearshore manganese-iron reduction, sulfate reduction, methanogenesis, and hydrothermal Fe inputs from the deep ocean. Our modified 'euxinic wedge' model expands on previous versions of this model, providing a more complete theoretical framework for the chemical zonation of early Earth oceans that helps to explain observations of unusual Mo-S-C isotope patterns. This model may provide a useful foundation for future studies of ocean chemistry evolution and elemental biogeochemical cycles in early Earth history. [ABSTRACT FROM AUTHOR]

The 1- O-monoalkyl glycerol ethers (MAGEs) were initially viewed as the biomarkers for sulfate-reducing bacteria (SRB) mediating anaerobic oxidation of methane in the marine environments. However, limited information is known about their distribution in terrestrial and other aquatic settings including soils, fresh water lakes, and cave sediments, which may obscure our understanding of their biological sources. Here we found that MAGEs were ubiquitous but differed obviously in distributional pattern among those environments. The surface soils are dominated generally by iC-MAGE, followed by nC-MAGE whereas the lake sediments show the opposite, resulting in significantly higher iC/ nC ratios in soils than in lake sediments. The cave deposits are characterized by considerably higher proportions of branched MAGEs than the former two environments. The logarithm of iC/ aC ratio shows a significant negative correlation with soil pH, likely reflecting an adaptation of microbial cell membrane to change in the ambient proton concentration. The MAGE profiles in cultured bacteria cannot fully explain the MAGE distribution in all the samples analyzed. Therefore, MAGEs in soil, lake sediments, and cave deposits likely have additional biological source(s) other than SRB and cultured MAGE-producing bacteria. The difference in MAGE pattern among environments is likely to be attributed to change in microbial communities. [ABSTRACT FROM AUTHOR]

Following the Ediacaran metazoan radiation, the 'Cambrian Explosion' set up the major framework of todays' animal phyla as well as modern marine ecosystem. Here, we present a preliminary investigation on the temporal and spatial (from shallow to deep waters) variations of the early Cambrian ocean chemistry in South China through analyzing a Fe-S-C systematic dataset integrated from literature. Our investigation indicates that the early Cambrian deep ocean in South China was still anoxic and Fe-enriched (i.e., ferruginous) although its surface was oxic, and in between a metastable euxinic (anoxic and sulfidic) water zone may have dynamically developed in anoxic shelf waters with an increasing weathering sulfate supply. Furthermore, accompanying marine transgression and regression cycles in the early Cambrian, such a 'sandwich' structure in ocean redox chemistry demonstrates five evolutional stages, which can be well correlated to the spatiotemporal patterns of fossil records in South China. The good correlation between metazoan fossil occurrences and water chemistry in South China suggests that early animals possibly possessed ability to inhabit anoxic but generally not euxinic environments as free HS was fatal to most eukaryotes. This view can well explain why those small shell fauna and sponges disappeared from shelf to slope areas where sulfidic Ni-Mo-rich shales were widely deposited. Thus, we conclude that the spatiotemporal variations of ocean chemistry and its biological effects probably played a key role in the phased animal radiations and 'extinctions' in the early Cambrian. [ABSTRACT FROM AUTHOR]

The distributions of microbial tetraether lipids, i.e. glycerol dialkyl glycerol tetraethers (GDGTs), were investigated in a variety of Chinese soils featured by a wide range of pH values in different climate zones. The bacterial branched GDGTs and archaeal isoprenoid GDGTs were found to be widely distributed in Chinese soils and their relative abundance was controlled primarily by soil pH. The bacterial bGDGTs usually dominate over archaeal iGDGTs in abundance when the soil pH is below 8.0. However, archaeal iGDGTs become dominant and the abundance of halophilic archaea characterized by GDGT V without cyclopentyl ring increases dramatically in the alkaline soil with pH greater than 8.0. The relative abundance of archaeal iGDGTs to bacterial bGDGTs was defined here as RAI index. The RAI index decreases with elevated soil pH and a linear correlation is found between them, indicating that the relative abundance of archaeal iGDGTs to bacterial bGDGTs increases with increased pH. The RAI index thus could be a novel proxy of the pH values of paleosol. The terrestrial input index, BIT (Branched and Isoprenoid Tetraethers Index), decreases with increased soil pH, suggesting that soil pH should be taken into consideration when the terrestrial contribution to marine sediments is estimated by BIT index. Moreover, the TEX86 index cannot be used to reconstruct sea surface temperature in the sediments featured by a large terrestrial input. [ABSTRACT FROM AUTHOR]