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Hao Yang - One of the best experts on this subject based on the ideXlab platform.
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a permian triassic boundary Microbialite deposit from the eastern yangtze platform jiangxi province south china geobiologic features ecosystem composition and redox conditions
Palaeogeography Palaeoclimatology Palaeoecology, 2017Co-Authors: Zhongqiang Chen, Yuheng Fang, Yu Pei, Hao Yang, James G OggAbstract:Abstract A Permian-Triassic (P-Tr) boundary Microbialite (PTB-Microbialite) deposit occurs near Xiushui on the southern margin of the eastern Yangtze Platform, South China. This 2-m-thick Microbialite overlies uppermost Permian bioclastic limestone with a 5-cm-thick oolite-like grainstone layer at the contact. This PTB-Microbialite consists of lower thrombolite (1.5-m thick) and an upper dendrolite (0.5-m thick). The thrombolite interval is characterized by a clotted texture of reddish sparitic patches embedded in a gray micritic matrix, whereas the dendrolite texture consists of brownish sparitic patches embedded within a yellow micritic matrix. Abundant calcified microbes occur in both the thrombolite and the dendrolite, including 1) columnar and clustered fabrics, which are especially rich in the thrombolite, assigned as products of Gakhumella or related microorganisms and 2) microspheroids, 40–60 μm in diameter, with different interior structures. These calcimicrobes are considered to have played an important role in constructing the Xiushui PTB-Microbialite. The demise of the Microbialite was likely due to a sea-level fall during the early Griesbachian (lowermost Triassic), which resulted in a lowering of the wave base thereby destroying the Microbialite frameworks and facilitating the deposition of winnowed skeletal grainstone. Metazoan community structures within the Microbialite changed sharply across the end-Permian extinction horizon, which is placed at a sharp negative shift in δ 13 C carb . Quantitative analyses show that the Xiushui Microbialite community is similar to that of Chongyang and Cili Microbialites. This is probably because all of these Microbialites grew along the margins of the Lower Yangtze region during the P-Tr transition. However, unlike other PTB-Microbialites, the Xiushui ecosystem contains fairly abundant metazoans, which are dominated by ostracods with minor occurrences of foraminifers, microgastropods and microconchids. Both the ostracod assemblage and the pyrite framboid analyses indicate an upper dysoxic zone to a well-oxygenated condition for the Xiushui Microbialite. This implies that some PTB-Microbialite ecosystems developed in conditions that were not always harsh; instead, some were hospitable for some metazoans to survive immediately after the end-Permian crisis. Considering that the redox conditions indicated by PTB-Microbialites are quite variable, we infer that oxygen levels probably were not the crucial factor affecting the growth of the PTB-Microbialites.
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microbial algal community changes during the latest permian ecological crisis evidence from lipid biomarkers at cili south china
Global and Planetary Change, 2013Co-Authors: Genming Luo, Hao Yang, Yongbiao Wang, Kliti Grice, Steve Kershaw, Thomas J Algeo, Xiaoyan Ruan, Chengling Jia, Shucheng XieAbstract:article i nfo Microbialites flourished globally immediately following the latest Permian mass extinction. In this study, lipid biomarker records were analyzed in the Cili section (Hunan Province, South China) in order to determine the types of microbes involved in Microbialite formation and their response to contemporaneous environmental changes. Various biomarkers were identified in the aliphatic and aromatic fractions using gas chromatography (GC) and GC-mass spectrometry (GC-MS). Low abundance of steranes in the Microbialite layer suggests that it did not contain large amounts of algae, in striking contrast to the abundant algal fossils and algal-derived steranes present in the underlying (pre-crisis) skeletal limestone. Although pristine/phytane (Pr/Ph) ratios increased in the Microbialite layer, covariation of Pr/Ph with the ratio of low- to high-molecular-weight n-alkanes (C20−/C20+) suggests that the former proxy was controlled by microbial (particularly cyanobacterial) inputs rather than by redox conditions. The Microbialite also yielded low ratios of hopanes to short-chain n-alkanes(HP/Lalk)andhighabundancesofC21n-alkylcyclohexane,indicatingthat,inadditiontocyanobacteria, anaerobic bacteria, archaea, and possibly acritarchs flourished in the aftermath of the marine extinction event. The upper part of the thinly bedded micritic limestone overlying the Microbialite exhibits a bimodal distribution of n-alkanes as well as increased abundances of extended tricyclic terpanes and steranes, suggesting a return of habitable shallow-marine conditions for eukaryotic algae several hundred thousand years after the latest Permian mass extinction. Increases in the dibenzofuran ratio (i.e., DBF/(DBF+DBT+F)) and in the coronene to phenanthrene ratio (Cor/P) in the skeletal limestone immediately below the Microbialite are evidence of enhanced soil erosion rates and wildfire intensity, marking the collapse of terrestrial ecosystems. The terrestrial crisisthus slightly preceded the marine biotic crisis inthe South China region, to which it may have been a major contributing factor.
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microbial algal community changes during the latest permian ecological crisis evidence from lipid biomarkers at cili south china
Grid and Pervasive Computing, 2013Co-Authors: Genming Luo, Hao Yang, Yongbiao Wang, Kliti Grice, Steve Kershaw, Thomas J Algeo, Xiaoyan Ruan, Chengling Jia, Shucheng XieAbstract:Abstract Microbialites flourished globally immediately following the latest Permian mass extinction. In this study, lipid biomarker records were analyzed in the Cili section (Hunan Province, South China) in order to determine the types of microbes involved in Microbialite formation and their response to contemporaneous environmental changes. Various biomarkers were identified in the aliphatic and aromatic fractions using gas chromatography (GC) and GC–mass spectrometry (GC–MS). Low abundance of steranes in the Microbialite layer suggests that it did not contain large amounts of algae, in striking contrast to the abundant algal fossils and algal-derived steranes present in the underlying (pre-crisis) skeletal limestone. Although pristine/phytane (Pr/Ph) ratios increased in the Microbialite layer, covariation of Pr/Ph with the ratio of low- to high-molecular-weight n-alkanes (C20 −/C20 +) suggests that the former proxy was controlled by microbial (particularly cyanobacterial) inputs rather than by redox conditions. The Microbialite also yielded low ratios of hopanes to short-chain n-alkanes (HP/Lalk) and high abundances of C21 n-alkylcyclohexane, indicating that, in addition to cyanobacteria, anaerobic bacteria, archaea, and possibly acritarchs flourished in the aftermath of the marine extinction event. The upper part of the thinly bedded micritic limestone overlying the Microbialite exhibits a bimodal distribution of n-alkanes as well as increased abundances of extended tricyclic terpanes and steranes, suggesting a return of habitable shallow-marine conditions for eukaryotic algae several hundred thousand years after the latest Permian mass extinction. Increases in the dibenzofuran ratio (i.e., DBF/(DBF + DBT + F)) and in the coronene to phenanthrene ratio (Cor/P) in the skeletal limestone immediately below the Microbialite are evidence of enhanced soil erosion rates and wildfire intensity, marking the collapse of terrestrial ecosystems. The terrestrial crisis thus slightly preceded the marine biotic crisis in the South China region, to which it may have been a major contributing factor.
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calcareous tubeworms as disaster forms after the end permian mass extinction in south china
PALAIOS, 2013Co-Authors: Yongbiao Wang, Hao Yang, Adam D Woods, Wei LiaoAbstract:Abundant calcareous tubeworms have been found in both shallow platform and deep basin deposits after the end-Permian mass extinction in the Cili area, South China. Tubeworms from the Microbialites deposited on the shallow platform appear to be cone-shaped tubes with diameters ranging from 0.5 to 1.8 mm (mean 1.1 mm), while those attached to Claraia, the most abundant bivalve fossil preserved in the deep basin deposits after the mass extinction, are planispiral tubes with smaller diameters (0.5–1.5 mm, mean 0.9 mm). The calcareous tubeworms are identified as Microconchida (Tentaculita) according to the typical laminated sheet texture of the tubeworms found on the shallow platform. The difference in morphology between the cone-shaped tubeworms found in the Microbialites and the planispiral tubeworms attached to Claraia in deeper water deposits may be related to differences in how fast the surrounding sediments were accumulating. Bacterially mediated precipitation of calcium carbonate led to rapid accumulation of the Microbialites that forced the tubeworms to grow upward so as to keep up with the rate of Microbialite growth and led to the cone-shaped tubes found there, whereas the slowly accumulating sediments surrounding the tubeworm-encrusted Claraia led to the development of the planispiral forms in basin deposits. Calcareous tubeworms found in the shallow platform and colonizing the shells of bivalve Claraia in basin deposits indicates calcareous tubeworms, as a significant disaster form, should have benefited from the opening of ecological space by the extinction of most marine invertebrates. Widespread oceanic anoxia has long been considered to be one of the extraordinary conditions after the end-Permian mass extinction. Tubeworm fossils flourishing in basin deposits within the short interval near the Permian-Triassic boundary implies that the deepwater environment immediately after the end-Permian mass extinction may not have been as anoxic as previously thought.
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composition and structure of Microbialite ecosystems following the end permian mass extinction in south china
Palaeogeography Palaeoclimatology Palaeoecology, 2011Co-Authors: Hao Yang, Zhongqiang Chen, Jinnan Tong, Yongbiao Wang, Haijun Song, Jing ChenAbstract:After the end-Permian mass extinction, Microbialites were widespread in the shallow marine environments in South China. Diverse Microbialites are characteristic of the Early Triassic carbonate sequences. Their stratigraphic range is rather short, just across the Permian–Triassic (P–Tr) boundary, and defined by conodonts N. meishanensis, H. changxingensis, and H. parvus Zones. Thus, the P–Tr Microbialites grew immediately after the first episode of the end-Permian mass extinction coinciding with the beginning of the conodont N. meishanensis Zone and ceased their growth at the beginning of the conodont I. staeschei Zone, which occurred just before the second episode of the end-Permian crisis at Meishan. They include three main types: stromatolites, thrombolites and dendrites in South China. The presence of abundant microbial remains of coccoid-type and Renalcis-like microbes strengthens the previous view that the P–Tr Microbialites are biogenic. Both cyanobacteria and other microbes have participated to construct the microbial ecosystems. The thrombolite communities are dominated by the Renalcis-like microbes and foraminifers and also contain ostracods, microgastropods, and microconchids. The stromatolite communities are dominated by coccoidal microbes with minor constituents of other undetermined microbes. Metazoans are rare. The dendrolite assemblage contains few identifiable microfossils. Most of Microbialite communities have a high-abundance, low-diversity community structure, characteristic of marine communities after the end-Permian mass extinction. Some metazoans of either opportunists or disaster forms dwelled in this special ecosystem. The Microbialite-builders formed the primary producer communities and constructed the lowest level ecosystem structure. The lower-level ecosystem proliferated due to the collapse of the higher level of ecosystem structure characterized by benthic shelly and predator communities in the end-Permian crisis.
Yongbiao Wang - One of the best experts on this subject based on the ideXlab platform.
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the evolution of Microbialite forms during the early triassic transgression a case study in chongyang of hubei province south china
Palaeogeography Palaeoclimatology Palaeoecology, 2018Co-Authors: Tan Wang, R V Burne, Aihua Yuan, Yongbiao WangAbstract:Abstract The widespread development of Microbialites in shallow areas of the Tethys Ocean at the start of the Early Triassic reflects the deterioration of marine ecosystems in the aftermath of the extinction that marked the demise of the majority of Palaeozoic marine faunas. Here we present a study of the evolving Microbialite forms and associated biotic assemblages of this pioneering Microbialite interval from exposures at Chongyang, Hubei Province, China. This research provides a perspective on the effects of eustatic transgression on marine ecosystems as water depths increased at the beginning of Mesozoic, through the study of the changing forms, microfacies and distribution of Microbialites. Microbialite forms evolved from stratiform stromatolites to a sequence of tabular thrombolites (with an intercalated layer of columnar stromatolites), followed by domical thrombolites that were overlain, in turn, by oolites. The stratiform stromatolites contain poorly preserved remains of calcified cyanobacteria, but microfossils with chambered structure can also be seen. Metazoan fossils increased from the base of the overlying tabular thrombolite, reflecting increasing biodiversity with deepening of seawater. The occurrence of columnar stromatolites within the tabular thrombolite may indicate a temporary sea-level shallowing. Foraminiferans and other metazoans are absent within the columnar stromatolites, but spherical cyanobacterial remains are extremely abundant. Well-preserved calcified cyanobacteria may reflect an absence of metazoan predation and/or carbonate supersaturation of seawater. As water deepened, domical thrombolites developed and the more complex seafloor relief created varied niches between and within the domes that harboured more ecologically diverse communities. During the process of transgression within the Microbialite interval, carbon isotopes exhibit a negative relationship with biodiversity, implying that upwelling of anoxic deep-ocean water, if associated with the negative excursion of carbon isotope values, did not inhibit the diversification of benthic organisms at least on shallow carbonate platforms in the period immediately after the end-Permian mass extinction.
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microbial algal community changes during the latest permian ecological crisis evidence from lipid biomarkers at cili south china
Global and Planetary Change, 2013Co-Authors: Genming Luo, Hao Yang, Yongbiao Wang, Kliti Grice, Steve Kershaw, Thomas J Algeo, Xiaoyan Ruan, Chengling Jia, Shucheng XieAbstract:article i nfo Microbialites flourished globally immediately following the latest Permian mass extinction. In this study, lipid biomarker records were analyzed in the Cili section (Hunan Province, South China) in order to determine the types of microbes involved in Microbialite formation and their response to contemporaneous environmental changes. Various biomarkers were identified in the aliphatic and aromatic fractions using gas chromatography (GC) and GC-mass spectrometry (GC-MS). Low abundance of steranes in the Microbialite layer suggests that it did not contain large amounts of algae, in striking contrast to the abundant algal fossils and algal-derived steranes present in the underlying (pre-crisis) skeletal limestone. Although pristine/phytane (Pr/Ph) ratios increased in the Microbialite layer, covariation of Pr/Ph with the ratio of low- to high-molecular-weight n-alkanes (C20−/C20+) suggests that the former proxy was controlled by microbial (particularly cyanobacterial) inputs rather than by redox conditions. The Microbialite also yielded low ratios of hopanes to short-chain n-alkanes(HP/Lalk)andhighabundancesofC21n-alkylcyclohexane,indicatingthat,inadditiontocyanobacteria, anaerobic bacteria, archaea, and possibly acritarchs flourished in the aftermath of the marine extinction event. The upper part of the thinly bedded micritic limestone overlying the Microbialite exhibits a bimodal distribution of n-alkanes as well as increased abundances of extended tricyclic terpanes and steranes, suggesting a return of habitable shallow-marine conditions for eukaryotic algae several hundred thousand years after the latest Permian mass extinction. Increases in the dibenzofuran ratio (i.e., DBF/(DBF+DBT+F)) and in the coronene to phenanthrene ratio (Cor/P) in the skeletal limestone immediately below the Microbialite are evidence of enhanced soil erosion rates and wildfire intensity, marking the collapse of terrestrial ecosystems. The terrestrial crisisthus slightly preceded the marine biotic crisis inthe South China region, to which it may have been a major contributing factor.
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microbial algal community changes during the latest permian ecological crisis evidence from lipid biomarkers at cili south china
Grid and Pervasive Computing, 2013Co-Authors: Genming Luo, Hao Yang, Yongbiao Wang, Kliti Grice, Steve Kershaw, Thomas J Algeo, Xiaoyan Ruan, Chengling Jia, Shucheng XieAbstract:Abstract Microbialites flourished globally immediately following the latest Permian mass extinction. In this study, lipid biomarker records were analyzed in the Cili section (Hunan Province, South China) in order to determine the types of microbes involved in Microbialite formation and their response to contemporaneous environmental changes. Various biomarkers were identified in the aliphatic and aromatic fractions using gas chromatography (GC) and GC–mass spectrometry (GC–MS). Low abundance of steranes in the Microbialite layer suggests that it did not contain large amounts of algae, in striking contrast to the abundant algal fossils and algal-derived steranes present in the underlying (pre-crisis) skeletal limestone. Although pristine/phytane (Pr/Ph) ratios increased in the Microbialite layer, covariation of Pr/Ph with the ratio of low- to high-molecular-weight n-alkanes (C20 −/C20 +) suggests that the former proxy was controlled by microbial (particularly cyanobacterial) inputs rather than by redox conditions. The Microbialite also yielded low ratios of hopanes to short-chain n-alkanes (HP/Lalk) and high abundances of C21 n-alkylcyclohexane, indicating that, in addition to cyanobacteria, anaerobic bacteria, archaea, and possibly acritarchs flourished in the aftermath of the marine extinction event. The upper part of the thinly bedded micritic limestone overlying the Microbialite exhibits a bimodal distribution of n-alkanes as well as increased abundances of extended tricyclic terpanes and steranes, suggesting a return of habitable shallow-marine conditions for eukaryotic algae several hundred thousand years after the latest Permian mass extinction. Increases in the dibenzofuran ratio (i.e., DBF/(DBF + DBT + F)) and in the coronene to phenanthrene ratio (Cor/P) in the skeletal limestone immediately below the Microbialite are evidence of enhanced soil erosion rates and wildfire intensity, marking the collapse of terrestrial ecosystems. The terrestrial crisis thus slightly preceded the marine biotic crisis in the South China region, to which it may have been a major contributing factor.
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calcareous tubeworms as disaster forms after the end permian mass extinction in south china
PALAIOS, 2013Co-Authors: Yongbiao Wang, Hao Yang, Adam D Woods, Wei LiaoAbstract:Abundant calcareous tubeworms have been found in both shallow platform and deep basin deposits after the end-Permian mass extinction in the Cili area, South China. Tubeworms from the Microbialites deposited on the shallow platform appear to be cone-shaped tubes with diameters ranging from 0.5 to 1.8 mm (mean 1.1 mm), while those attached to Claraia, the most abundant bivalve fossil preserved in the deep basin deposits after the mass extinction, are planispiral tubes with smaller diameters (0.5–1.5 mm, mean 0.9 mm). The calcareous tubeworms are identified as Microconchida (Tentaculita) according to the typical laminated sheet texture of the tubeworms found on the shallow platform. The difference in morphology between the cone-shaped tubeworms found in the Microbialites and the planispiral tubeworms attached to Claraia in deeper water deposits may be related to differences in how fast the surrounding sediments were accumulating. Bacterially mediated precipitation of calcium carbonate led to rapid accumulation of the Microbialites that forced the tubeworms to grow upward so as to keep up with the rate of Microbialite growth and led to the cone-shaped tubes found there, whereas the slowly accumulating sediments surrounding the tubeworm-encrusted Claraia led to the development of the planispiral forms in basin deposits. Calcareous tubeworms found in the shallow platform and colonizing the shells of bivalve Claraia in basin deposits indicates calcareous tubeworms, as a significant disaster form, should have benefited from the opening of ecological space by the extinction of most marine invertebrates. Widespread oceanic anoxia has long been considered to be one of the extraordinary conditions after the end-Permian mass extinction. Tubeworm fossils flourishing in basin deposits within the short interval near the Permian-Triassic boundary implies that the deepwater environment immediately after the end-Permian mass extinction may not have been as anoxic as previously thought.
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composition and structure of Microbialite ecosystems following the end permian mass extinction in south china
Palaeogeography Palaeoclimatology Palaeoecology, 2011Co-Authors: Hao Yang, Zhongqiang Chen, Jinnan Tong, Yongbiao Wang, Haijun Song, Jing ChenAbstract:After the end-Permian mass extinction, Microbialites were widespread in the shallow marine environments in South China. Diverse Microbialites are characteristic of the Early Triassic carbonate sequences. Their stratigraphic range is rather short, just across the Permian–Triassic (P–Tr) boundary, and defined by conodonts N. meishanensis, H. changxingensis, and H. parvus Zones. Thus, the P–Tr Microbialites grew immediately after the first episode of the end-Permian mass extinction coinciding with the beginning of the conodont N. meishanensis Zone and ceased their growth at the beginning of the conodont I. staeschei Zone, which occurred just before the second episode of the end-Permian crisis at Meishan. They include three main types: stromatolites, thrombolites and dendrites in South China. The presence of abundant microbial remains of coccoid-type and Renalcis-like microbes strengthens the previous view that the P–Tr Microbialites are biogenic. Both cyanobacteria and other microbes have participated to construct the microbial ecosystems. The thrombolite communities are dominated by the Renalcis-like microbes and foraminifers and also contain ostracods, microgastropods, and microconchids. The stromatolite communities are dominated by coccoidal microbes with minor constituents of other undetermined microbes. Metazoans are rare. The dendrolite assemblage contains few identifiable microfossils. Most of Microbialite communities have a high-abundance, low-diversity community structure, characteristic of marine communities after the end-Permian mass extinction. Some metazoans of either opportunists or disaster forms dwelled in this special ecosystem. The Microbialite-builders formed the primary producer communities and constructed the lowest level ecosystem structure. The lower-level ecosystem proliferated due to the collapse of the higher level of ecosystem structure characterized by benthic shelly and predator communities in the end-Permian crisis.
Darlene S. S. Lim - One of the best experts on this subject based on the ideXlab platform.
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Image_1_The Complete Genome and Physiological Analysis of the Eurythermal Firmicute Exiguobacterium chiriqhucha Strain RW2 Isolated From a Freshwater Microbialite, Widely Adaptable to Broad Thermal, pH, and Salinity Ranges.JPEG
2019Co-Authors: Richard Alle White, Sarah A. Soles, Greg Gavelis, Emma Gosseli, Greg F. Slate, Darlene S. S. Lim, Ia Leande, Curtis A. SuttleAbstract:Members of the genus Exiguobacterium are found in diverse environments from marine, freshwaters, permafrost to hot springs. Exiguobacterium can grow in a wide range of temperature, pH, salinity, and heavy-metal concentrations. We characterized Exiguobacterium chiriqhucha strain RW2 isolated from a permanently cold freshwater Microbialite in Pavilion Lake, British Columbia using metabolic assays, genomics, comparative genomics, phylogenetics, and fatty acid composition. Strain RW2 has the most extensive growth range for temperature (4–50°C) and pH (5–11) of known Exiguobacterium isolates. Strain RW2 genome predicts pathways for wide differential thermal, cold and osmotic stress using cold and heat shock cascades (e.g., csp and dnaK), choline and betaine uptake/biosynthesis (e.g., opu and proU), antiporters (e.g., arcD and nhaC Na+/K+), membrane fatty acid unsaturation and saturation. Here, we provide the first complete genome from Exiguobacterium chiriqhucha strain RW2, which was isolated from a freshwater Microbialite. Its genome consists of a single 3,019,018 bp circular chromosome encoding over 3,000 predicted proteins, with a GC% content of 52.1%, and no plasmids. In addition to growing at a wide range of temperatures and salinities, our findings indicate that RW2 is resistant to sulfisoxazole and has the genomic potential for detoxification of heavy metals (via mercuric reductases, arsenic resistance pumps, chromate transporters, and cadmium-cobalt-zinc resistance genes), which may contribute to the metabolic potential of Pavilion Lake Microbialites. Strain RW2 could also contribute to Microbialite formation, as it is a robust biofilm former and encodes genes involved in the deamination of amino acids to ammonia (i.e., L-asparaginase/urease), which could potentially boost carbonate precipitation by lowering the local pH and increasing alkalinity. We also used comparative genomic analysis to predict the pathway for orange pigmentation that is conserved across the entire Exiguobacterium genus, specifically, a C30 carotenoid biosynthesis pathway is predicted to yield diaponeurosporene-4-oic acid as its final product. Carotenoids have been found to protect against ultraviolet radiation by quenching reactive oxygen, releasing excessive light energy, radical scavenging, and sunscreening. Together these results provide further insight into the potential of Exiguobacterium to exploit a wide range of environmental conditions, its potential roles in ecosystems (e.g., Microbialites/microbial mats), and a blueprint model for diverse metabolic processes.
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Table_2_The Complete Genome and Physiological Analysis of the Eurythermal Firmicute Exiguobacterium chiriqhucha Strain RW2 Isolated From a Freshwater Microbialite, Widely Adaptable to Broad Thermal, pH, and Salinity Ranges.xlsx
2019Co-Authors: Richard Alle White, Sarah A. Soles, Greg Gavelis, Emma Gosseli, Greg F. Slate, Darlene S. S. Lim, Ia Leande, Curtis A. SuttleAbstract:Members of the genus Exiguobacterium are found in diverse environments from marine, freshwaters, permafrost to hot springs. Exiguobacterium can grow in a wide range of temperature, pH, salinity, and heavy-metal concentrations. We characterized Exiguobacterium chiriqhucha strain RW2 isolated from a permanently cold freshwater Microbialite in Pavilion Lake, British Columbia using metabolic assays, genomics, comparative genomics, phylogenetics, and fatty acid composition. Strain RW2 has the most extensive growth range for temperature (4–50°C) and pH (5–11) of known Exiguobacterium isolates. Strain RW2 genome predicts pathways for wide differential thermal, cold and osmotic stress using cold and heat shock cascades (e.g., csp and dnaK), choline and betaine uptake/biosynthesis (e.g., opu and proU), antiporters (e.g., arcD and nhaC Na+/K+), membrane fatty acid unsaturation and saturation. Here, we provide the first complete genome from Exiguobacterium chiriqhucha strain RW2, which was isolated from a freshwater Microbialite. Its genome consists of a single 3,019,018 bp circular chromosome encoding over 3,000 predicted proteins, with a GC% content of 52.1%, and no plasmids. In addition to growing at a wide range of temperatures and salinities, our findings indicate that RW2 is resistant to sulfisoxazole and has the genomic potential for detoxification of heavy metals (via mercuric reductases, arsenic resistance pumps, chromate transporters, and cadmium-cobalt-zinc resistance genes), which may contribute to the metabolic potential of Pavilion Lake Microbialites. Strain RW2 could also contribute to Microbialite formation, as it is a robust biofilm former and encodes genes involved in the deamination of amino acids to ammonia (i.e., L-asparaginase/urease), which could potentially boost carbonate precipitation by lowering the local pH and increasing alkalinity. We also used comparative genomic analysis to predict the pathway for orange pigmentation that is conserved across the entire Exiguobacterium genus, specifically, a C30 carotenoid biosynthesis pathway is predicted to yield diaponeurosporene-4-oic acid as its final product. Carotenoids have been found to protect against ultraviolet radiation by quenching reactive oxygen, releasing excessive light energy, radical scavenging, and sunscreening. Together these results provide further insight into the potential of Exiguobacterium to exploit a wide range of environmental conditions, its potential roles in ecosystems (e.g., Microbialites/microbial mats), and a blueprint model for diverse metabolic processes.
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The Complete Genome and Physiological Analysis of the Eurythermal Firmicute Exiguobacterium chiriqhucha Strain RW2 Isolated From a Freshwater Microbialite, Widely Adaptable to Broad Thermal, pH, and Salinity Ranges
Frontiers Media S.A., 2019Co-Authors: Richard Alle White, Sarah A. Soles, Greg Gavelis, Emma Gosseli, Greg F. Slate, Darlene S. S. Lim, Ia Leande, Curtis A. SuttleAbstract:Members of the genus Exiguobacterium are found in diverse environments from marine, freshwaters, permafrost to hot springs. Exiguobacterium can grow in a wide range of temperature, pH, salinity, and heavy-metal concentrations. We characterized Exiguobacterium chiriqhucha strain RW2 isolated from a permanently cold freshwater Microbialite in Pavilion Lake, British Columbia using metabolic assays, genomics, comparative genomics, phylogenetics, and fatty acid composition. Strain RW2 has the most extensive growth range for temperature (4–50°C) and pH (5–11) of known Exiguobacterium isolates. Strain RW2 genome predicts pathways for wide differential thermal, cold and osmotic stress using cold and heat shock cascades (e.g., csp and dnaK), choline and betaine uptake/biosynthesis (e.g., opu and proU), antiporters (e.g., arcD and nhaC Na+/K+), membrane fatty acid unsaturation and saturation. Here, we provide the first complete genome from Exiguobacterium chiriqhucha strain RW2, which was isolated from a freshwater Microbialite. Its genome consists of a single 3,019,018 bp circular chromosome encoding over 3,000 predicted proteins, with a GC% content of 52.1%, and no plasmids. In addition to growing at a wide range of temperatures and salinities, our findings indicate that RW2 is resistant to sulfisoxazole and has the genomic potential for detoxification of heavy metals (via mercuric reductases, arsenic resistance pumps, chromate transporters, and cadmium-cobalt-zinc resistance genes), which may contribute to the metabolic potential of Pavilion Lake Microbialites. Strain RW2 could also contribute to Microbialite formation, as it is a robust biofilm former and encodes genes involved in the deamination of amino acids to ammonia (i.e., L-asparaginase/urease), which could potentially boost carbonate precipitation by lowering the local pH and increasing alkalinity. We also used comparative genomic analysis to predict the pathway for orange pigmentation that is conserved across the entire Exiguobacterium genus, specifically, a C30 carotenoid biosynthesis pathway is predicted to yield diaponeurosporene-4-oic acid as its final product. Carotenoids have been found to protect against ultraviolet radiation by quenching reactive oxygen, releasing excessive light energy, radical scavenging, and sunscreening. Together these results provide further insight into the potential of Exiguobacterium to exploit a wide range of environmental conditions, its potential roles in ecosystems (e.g., Microbialites/microbial mats), and a blueprint model for diverse metabolic processes
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Spatial Distribution and Preservation of Carbon Isotope Biosignatures in Freshwater Microbialite Carbonate
2019Co-Authors: Mark A. Belan, Allyson L. Brady, Darlene S. S. Lim, Sang-tae Kim, Greg F. SlaterAbstract:Understanding formation mechanisms of modern Microbialites enables interpretation of biosignatures associated with fossilized stromatolites. Photosynthetic influences on carbonate precipitation are one proposed mechanism. Photosynthetic isotope biosignatures (13C) associated with freshwater Microbialites in Pavilion Lake, British Columbia were widespread through the lake but less prevalent with increasing depth. Importantly, they were variably detectable on the exterior surface of individual Microbialites. At depths ≤18 m, Microbialite surface carbonates, associated with either nodular microbial communities or surface biofilms, had δ13Ccarb values up to +3.7‰ that were 13C-enriched above the predicted range of δ13Ccarb values for equilibrium precipitation from bulk ambient lake water dissolved inorganic carbon (DIC) (predicted mean δ13Ccarb = −0.2 ± 1.3‰). Vertical profiles of exterior, non-nodular biofilm present on Microbialites collected from depths of 21 m and below showed instances of 13C-enrichment near the apex, consistent with hypothesized maximum light exposure. With increased distance from the apex toward the structure base, δ13Ccarb values typically decreased into the predicted range of equilibrium δ13C values. Surface biosignatures persisted internally for distances of 0.5 to 2 cm below the exterior of the structures, beyond which they fell within the predicted isotopic equilibrium range. This shift in δ13Ccarb values may be due to secondary carbonate precipitation masking of the 13C-enriched signature. The contribution of secondary carbonate precipitation was estimated to be 14–59% of total carbonate mass if derived from heterotroph-influenced or bulk lake DIC, respectively. Growth rate estimates suggested these accretion processes can mask photosynthetic signatures in 20–400 years
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reconstruction of limnology and Microbialite formation conditions from carbonate clumped isotope thermometry
Geobiology, 2015Co-Authors: Victoria A Petryshyn, Allyson L. Brady, Darlene S. S. Lim, B L Laval, Gregory F Slater, Aradhna K TripatiAbstract:Quantitative tools for deciphering the environment of Microbialite formation are relatively limited. For example, the oxygen isotope carbonate-water geothermometer requires assumptions about the isotopic composition of the water of formation. We explored the utility of using ‘clumped’ isotope thermometry as a tool to study the temperatures of Microbialite formation. We studied Microbialites recovered from water depths of 10–55 m in Pavilion Lake, and 10–25 m in Kelly Lake, spanning the thermocline in both lakes. We determined the temperature of carbonate growth and the 18 O/ 16 O ratio of the waters that Microbialites grew in. Results were then compared to current limnological data from the lakes to reconstruct the history of Microbialite formation. Modern Microbialites collected at shallow depths (11.7 m) in both lakes yield clumped isotope-based temperatures of formation that are within error of summer water temperatures, suggesting that clumped isotope analyses may be used to reconstruct past climates and to probe the environments in which Microbialites formed. The deepest Microbialites (21.7–55 m) were recovered from below the present-day thermoclines in both lakes and yield radioisotope ages indicating they primarily formed earlier in the Holocene. During this time, pollen data and our reconstructed water 18 O/ 16 O ratios indicate a period of aridity, with lower lake levels. At present, there is a close association between both photosynthetic and heterotrophic communities, and carbonate precipitation/Microbialite formation, with biosignatures of photosynthetic influences on carbonate detected in Microbialites from the photic zone and above the thermocline (i.e., depths of generally <20 m). Given the deeper Microbialites are receiving <1% of photosynthetically active radiation (PAR), it is likely these Microbialites primarily formed when lower lake levels resulted in Microbialites being located higher in the photic zone, in warm surface waters.
Curtis A. Suttle - One of the best experts on this subject based on the ideXlab platform.
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Image_1_The Complete Genome and Physiological Analysis of the Eurythermal Firmicute Exiguobacterium chiriqhucha Strain RW2 Isolated From a Freshwater Microbialite, Widely Adaptable to Broad Thermal, pH, and Salinity Ranges.JPEG
2019Co-Authors: Richard Alle White, Sarah A. Soles, Greg Gavelis, Emma Gosseli, Greg F. Slate, Darlene S. S. Lim, Ia Leande, Curtis A. SuttleAbstract:Members of the genus Exiguobacterium are found in diverse environments from marine, freshwaters, permafrost to hot springs. Exiguobacterium can grow in a wide range of temperature, pH, salinity, and heavy-metal concentrations. We characterized Exiguobacterium chiriqhucha strain RW2 isolated from a permanently cold freshwater Microbialite in Pavilion Lake, British Columbia using metabolic assays, genomics, comparative genomics, phylogenetics, and fatty acid composition. Strain RW2 has the most extensive growth range for temperature (4–50°C) and pH (5–11) of known Exiguobacterium isolates. Strain RW2 genome predicts pathways for wide differential thermal, cold and osmotic stress using cold and heat shock cascades (e.g., csp and dnaK), choline and betaine uptake/biosynthesis (e.g., opu and proU), antiporters (e.g., arcD and nhaC Na+/K+), membrane fatty acid unsaturation and saturation. Here, we provide the first complete genome from Exiguobacterium chiriqhucha strain RW2, which was isolated from a freshwater Microbialite. Its genome consists of a single 3,019,018 bp circular chromosome encoding over 3,000 predicted proteins, with a GC% content of 52.1%, and no plasmids. In addition to growing at a wide range of temperatures and salinities, our findings indicate that RW2 is resistant to sulfisoxazole and has the genomic potential for detoxification of heavy metals (via mercuric reductases, arsenic resistance pumps, chromate transporters, and cadmium-cobalt-zinc resistance genes), which may contribute to the metabolic potential of Pavilion Lake Microbialites. Strain RW2 could also contribute to Microbialite formation, as it is a robust biofilm former and encodes genes involved in the deamination of amino acids to ammonia (i.e., L-asparaginase/urease), which could potentially boost carbonate precipitation by lowering the local pH and increasing alkalinity. We also used comparative genomic analysis to predict the pathway for orange pigmentation that is conserved across the entire Exiguobacterium genus, specifically, a C30 carotenoid biosynthesis pathway is predicted to yield diaponeurosporene-4-oic acid as its final product. Carotenoids have been found to protect against ultraviolet radiation by quenching reactive oxygen, releasing excessive light energy, radical scavenging, and sunscreening. Together these results provide further insight into the potential of Exiguobacterium to exploit a wide range of environmental conditions, its potential roles in ecosystems (e.g., Microbialites/microbial mats), and a blueprint model for diverse metabolic processes.
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Table_2_The Complete Genome and Physiological Analysis of the Eurythermal Firmicute Exiguobacterium chiriqhucha Strain RW2 Isolated From a Freshwater Microbialite, Widely Adaptable to Broad Thermal, pH, and Salinity Ranges.xlsx
2019Co-Authors: Richard Alle White, Sarah A. Soles, Greg Gavelis, Emma Gosseli, Greg F. Slate, Darlene S. S. Lim, Ia Leande, Curtis A. SuttleAbstract:Members of the genus Exiguobacterium are found in diverse environments from marine, freshwaters, permafrost to hot springs. Exiguobacterium can grow in a wide range of temperature, pH, salinity, and heavy-metal concentrations. We characterized Exiguobacterium chiriqhucha strain RW2 isolated from a permanently cold freshwater Microbialite in Pavilion Lake, British Columbia using metabolic assays, genomics, comparative genomics, phylogenetics, and fatty acid composition. Strain RW2 has the most extensive growth range for temperature (4–50°C) and pH (5–11) of known Exiguobacterium isolates. Strain RW2 genome predicts pathways for wide differential thermal, cold and osmotic stress using cold and heat shock cascades (e.g., csp and dnaK), choline and betaine uptake/biosynthesis (e.g., opu and proU), antiporters (e.g., arcD and nhaC Na+/K+), membrane fatty acid unsaturation and saturation. Here, we provide the first complete genome from Exiguobacterium chiriqhucha strain RW2, which was isolated from a freshwater Microbialite. Its genome consists of a single 3,019,018 bp circular chromosome encoding over 3,000 predicted proteins, with a GC% content of 52.1%, and no plasmids. In addition to growing at a wide range of temperatures and salinities, our findings indicate that RW2 is resistant to sulfisoxazole and has the genomic potential for detoxification of heavy metals (via mercuric reductases, arsenic resistance pumps, chromate transporters, and cadmium-cobalt-zinc resistance genes), which may contribute to the metabolic potential of Pavilion Lake Microbialites. Strain RW2 could also contribute to Microbialite formation, as it is a robust biofilm former and encodes genes involved in the deamination of amino acids to ammonia (i.e., L-asparaginase/urease), which could potentially boost carbonate precipitation by lowering the local pH and increasing alkalinity. We also used comparative genomic analysis to predict the pathway for orange pigmentation that is conserved across the entire Exiguobacterium genus, specifically, a C30 carotenoid biosynthesis pathway is predicted to yield diaponeurosporene-4-oic acid as its final product. Carotenoids have been found to protect against ultraviolet radiation by quenching reactive oxygen, releasing excessive light energy, radical scavenging, and sunscreening. Together these results provide further insight into the potential of Exiguobacterium to exploit a wide range of environmental conditions, its potential roles in ecosystems (e.g., Microbialites/microbial mats), and a blueprint model for diverse metabolic processes.
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The Complete Genome and Physiological Analysis of the Eurythermal Firmicute Exiguobacterium chiriqhucha Strain RW2 Isolated From a Freshwater Microbialite, Widely Adaptable to Broad Thermal, pH, and Salinity Ranges
Frontiers Media S.A., 2019Co-Authors: Richard Alle White, Sarah A. Soles, Greg Gavelis, Emma Gosseli, Greg F. Slate, Darlene S. S. Lim, Ia Leande, Curtis A. SuttleAbstract:Members of the genus Exiguobacterium are found in diverse environments from marine, freshwaters, permafrost to hot springs. Exiguobacterium can grow in a wide range of temperature, pH, salinity, and heavy-metal concentrations. We characterized Exiguobacterium chiriqhucha strain RW2 isolated from a permanently cold freshwater Microbialite in Pavilion Lake, British Columbia using metabolic assays, genomics, comparative genomics, phylogenetics, and fatty acid composition. Strain RW2 has the most extensive growth range for temperature (4–50°C) and pH (5–11) of known Exiguobacterium isolates. Strain RW2 genome predicts pathways for wide differential thermal, cold and osmotic stress using cold and heat shock cascades (e.g., csp and dnaK), choline and betaine uptake/biosynthesis (e.g., opu and proU), antiporters (e.g., arcD and nhaC Na+/K+), membrane fatty acid unsaturation and saturation. Here, we provide the first complete genome from Exiguobacterium chiriqhucha strain RW2, which was isolated from a freshwater Microbialite. Its genome consists of a single 3,019,018 bp circular chromosome encoding over 3,000 predicted proteins, with a GC% content of 52.1%, and no plasmids. In addition to growing at a wide range of temperatures and salinities, our findings indicate that RW2 is resistant to sulfisoxazole and has the genomic potential for detoxification of heavy metals (via mercuric reductases, arsenic resistance pumps, chromate transporters, and cadmium-cobalt-zinc resistance genes), which may contribute to the metabolic potential of Pavilion Lake Microbialites. Strain RW2 could also contribute to Microbialite formation, as it is a robust biofilm former and encodes genes involved in the deamination of amino acids to ammonia (i.e., L-asparaginase/urease), which could potentially boost carbonate precipitation by lowering the local pH and increasing alkalinity. We also used comparative genomic analysis to predict the pathway for orange pigmentation that is conserved across the entire Exiguobacterium genus, specifically, a C30 carotenoid biosynthesis pathway is predicted to yield diaponeurosporene-4-oic acid as its final product. Carotenoids have been found to protect against ultraviolet radiation by quenching reactive oxygen, releasing excessive light energy, radical scavenging, and sunscreening. Together these results provide further insight into the potential of Exiguobacterium to exploit a wide range of environmental conditions, its potential roles in ecosystems (e.g., Microbialites/microbial mats), and a blueprint model for diverse metabolic processes
R V Burne - One of the best experts on this subject based on the ideXlab platform.
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Microbialite development through the ediacaran cambrian transition in china distribution characteristics and paleoceanographic implications
Global and Planetary Change, 2021Co-Authors: Jiating Deng, Stephen Kershaw, R V Burne, Qiaolin Gong, Hao Tang, Binsong Zheng, Sichong Luo, Zhimin Jin, Xiucheng TanAbstract:Abstract Widespread development of Microbialites harbors a series of clues about microbial activity, environmental condition, and aquatic chemistry. The Ediacaran-Cambrian transition draws extensive attention on the co-evolution of complex life and Earth's environment but the associated microorganism development has been largely ignored. In this study, we present a high-resolution database with respect to the spatial and temporal distributions of Microbialites in China through the terminal Ediacaran to the early Cambrian Period and describe morphological and petrological characteristics of stromatolites and thrombolites in detail to shed light on the evolutionary process of microbial carbonates. Microbialite development experienced two thriving intervals during the Ediacaran-Cambrian transition: latest Ediacaran to early Fortunian, and Cambrian Age 3 to middle Age 4. The columnar and domical stromatolites show no marked morphological changes in the Ediacaran-Cambrian transition, but stratiform stromatolites exhibit a notable decline in Cambrian time, likely caused by increasing bioturbation in the Cambrian shelf environments. Meanwhile, thrombolites evolved to form large and complicated structures in the early Cambrian featured by meter-level mound morphology and columnar-branching microbial forms (fan-like/dendritic structures), likely indicating an improved environmental adaptation (e.g., photosynthesis efficiency and hydrodynamic conditions). Another remarkable change in Microbialites is the emergence of large numbers of calcified microbial microfossils preserved within the laminated/clotted mesostructures in Cambrian facies, compared with the Ediacaran forms that lack such unique structural features. For the main control over the Cambrian microbial calcification event, this study stresses again the essential role of seawater chemistry (Mg/Ca molar ratios and Ca2+ concentrations) in the formation and preservation of calcified microorganisms based on previous insights and elaborate characteristics of their occurrence and microstructures in China. The transition of the Neoproterozoic “aragonite-dolomite sea” to the Cambrian “calcite sea” (likely widely distributed in Age 3) may have promoted to the generation of an original calcite mineralogy in microbial fossils, which has a stronger ability to resist diagenetic dissolution and substitution (e.g., phosphatization and silicification) than that of the aragonite precursor.
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the evolution of Microbialite forms during the early triassic transgression a case study in chongyang of hubei province south china
Palaeogeography Palaeoclimatology Palaeoecology, 2018Co-Authors: Tan Wang, R V Burne, Aihua Yuan, Yongbiao WangAbstract:Abstract The widespread development of Microbialites in shallow areas of the Tethys Ocean at the start of the Early Triassic reflects the deterioration of marine ecosystems in the aftermath of the extinction that marked the demise of the majority of Palaeozoic marine faunas. Here we present a study of the evolving Microbialite forms and associated biotic assemblages of this pioneering Microbialite interval from exposures at Chongyang, Hubei Province, China. This research provides a perspective on the effects of eustatic transgression on marine ecosystems as water depths increased at the beginning of Mesozoic, through the study of the changing forms, microfacies and distribution of Microbialites. Microbialite forms evolved from stratiform stromatolites to a sequence of tabular thrombolites (with an intercalated layer of columnar stromatolites), followed by domical thrombolites that were overlain, in turn, by oolites. The stratiform stromatolites contain poorly preserved remains of calcified cyanobacteria, but microfossils with chambered structure can also be seen. Metazoan fossils increased from the base of the overlying tabular thrombolite, reflecting increasing biodiversity with deepening of seawater. The occurrence of columnar stromatolites within the tabular thrombolite may indicate a temporary sea-level shallowing. Foraminiferans and other metazoans are absent within the columnar stromatolites, but spherical cyanobacterial remains are extremely abundant. Well-preserved calcified cyanobacteria may reflect an absence of metazoan predation and/or carbonate supersaturation of seawater. As water deepened, domical thrombolites developed and the more complex seafloor relief created varied niches between and within the domes that harboured more ecologically diverse communities. During the process of transgression within the Microbialite interval, carbon isotopes exhibit a negative relationship with biodiversity, implying that upwelling of anoxic deep-ocean water, if associated with the negative excursion of carbon isotope values, did not inhibit the diversification of benthic organisms at least on shallow carbonate platforms in the period immediately after the end-Permian mass extinction.
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modern lacustrine Microbialites towards a synthesis of aqueous and carbonate geochemistry and mineralogy
Earth-Science Reviews, 2016Co-Authors: Gregory E. Webb, R V Burne, Anderson A P Chagas, Gordon SouthamAbstract:Abstract Lacustrine Microbialites record evidence of their depositional environments in their morphology, mineralogy and geochemistry. This synthesis reviews geochemical data both for Microbialites and lake water for 21 modern lacustrine Microbialite occurrences younger than 15,000 years. Although these data are limited, several trends and associations are identified that provide useful criteria to aid interpretation of the environmental settings of ancient analogues. These Microbialites are either thrombolites or thrombolitic stromatolites. They form in diverse settings, including karst, volcanic, coastal and inland (athalassic) lakes. Surveyed lakes are mostly closed basins subject to evaporative processes. Lakes vary from stratified to totally mixed examples. The major hydrochemical types include Na-Cl, Ca-SO4, Ca-HCO3 and Soda Lakes. The salinity and alkalinity of the lakes correlates, as expected, with the mode of mineralization, which in turn is reflected in the microstructure of the Microbialites. A correlation between the δ13Ccarbonate and the Ca2 +/alkalinity ratio (Ca/Alk) is observed. Generally, lakes with Ca/Alk > 1 are subject to carbonate precipitation driven by either uptake of CO2 that results in a broad range of positive and negative δ13Ccarbonate, or mineralization mediated by sulphate reducing-bacteria in saline to hypersaline environments that results in negative δ13Ccarbonate. Ca/Alk 39) are associated with hydromagnesite. Dolomite, high-Mg calcite (HMC) and monohydrocalcite are associated with the total aqueous concentration of Mg (cMg), occurring only in lakes with cMg > 75 meq/L. Evaporites (e.g., gypsum) are related to high lake water salinities. The absolute concentration of aqueous Si, commonly associated with dissolution of diatom tests, influences precipitation of crystalline and/or amorphous silicates/silica to form Microbialites with Si concentrations above 0.54 mmol/L, either as amorphous phases or as minerals such as stevensite and kerolite. Combined, the trends observed in this survey demonstrate that modern lacustrine Microbialites can preserve information symptomatic of the environments in which they formed. However, in a limited number of examples this is not the case, as subsequent diagenesis may alter the original mineralogy to a point where the geochemical evidence conserved from the depositional environment is lost. Additionally, some geochemical information may be the product of isolated microenvironments within living biofilms, and thus not necessarily directly related to the chemistry of ambient lake water. Further misleading conclusions would result if the hydrochemistry at the time of study had changed from those prevailing when the Microbialites were mineralized. Thus, all the correlations developed in this work represent hypotheses to be tested rather than interpretations to be accepted. This compilation demonstrates how Microbialites respond to different lacustrine hydrochemical environments, and is intended to provide a guide for future field studies and laboratory simulations. This review also highlights the general scarcity of trace-element data for lake waters and Microbialites. However, some recent studies suggest that lacustrine Microbialites may fractionate rare earth elements (REE) during uptake from water whereas marine Microbialites appear to record the REE distribution from seawater without modification. This possible difference in REE behaviour could have implications for the interpretation of palaeoenvironmental proxies.