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Abstract
Archaeal membrane lipids are widely used for paleotemperature reconstructions, yet these molecular fossils also bear rich information about ecology and evolution of marine ammonia-oxidizing archaea (AOA). Here we identified thermal and nonthermal behaviors of archaeal glycerol dialkyl glycerol tetraethers (GDGTs) by comparing the GDGT-based temperature index (TEX86) to the ratio of GDGTs with two and three cyclopentane rings (GDGT-2/GDGT-3). Thermal-dependent biosynthesis should increase TEX86 and decrease GDGT-2/GDGT-3 when the ambient temperature increases. This presumed temperature-dependent (PTD) trend is observed in GDGTs derived from cultures of thermophilic and mesophilic AOA. The distribution of GDGTs in suspended particulate matter (SPM) and sediments collected from above the pycnocline-shallow water samples-also follows the PTD trend. These similar GDGT distributions between AOA cultures and shallow water environmental samples reflect shallow ecotypes of marine AOA. While there are currently no cultures of deep AOA clades, GDGTs derived from deep water SPM and marine sediment samples exhibit nonthermal behavior deviating from the PTD trend. The presence of deep AOA increases the GDGT-2/GDGT-3 ratio and distorts the temperature-controlled correlation between GDGT-2/GDGT-3 and TEX86. We then used Gaussian mixture models to statistically characterize these diagnostic patterns of modern AOA ecology from paleo-GDGT records to infer the evolution of marine AOA from the Mid-Mesozoic to the present. Long-term GDGT-2/GDGT-3 trends suggest a suppression of today's deep water marine AOA during the Mesozoic-early Cenozoic greenhouse climates. Our analysis provides invaluable insights into the evolutionary timeline and the expansion of AOA niches associated with major oceanographic and climate changes.
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Hedlund BP, Zhang C, Wang F, Rinke C, Martin WF. Editorial: Ecology, Metabolism and Evolution of Archaea-Perspectives From Proceedings of the International Workshop on Geo-Omics of Archaea. Front Microbiol 2022; 12:827229. [PMID: 35126338 PMCID: PMC8816317 DOI: 10.3389/fmicb.2021.827229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 12/21/2021] [Indexed: 11/13/2022] Open
Affiliation(s)
- Brian P. Hedlund
- School of Life Sciences, University of Nevada, Las Vegas, NV, United States
- Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, NV, United States
| | - Chuanlun Zhang
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Fengping Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- School of Oceanography, Shanghai JiaoTong University, Shanghai, China
| | - Christian Rinke
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
| | - William F. Martin
- Institute for Molecular Evolution, University of Dusseldorf Medical School, Düsseldorf, Germany
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Zhang C, Dang H, Azam F, Benner R, Legendre L, Passow U, Polimene L, Robinson C, Suttle CA, Jiao N. Evolving paradigms in biological carbon cycling in the ocean. Natl Sci Rev 2018. [DOI: 10.1093/nsr/nwy074] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
ABSTRACT
Carbon is a keystone element in global biogeochemical cycles. It plays a fundamental role in biotic and abiotic processes in the ocean, which intertwine to mediate the chemistry and redox status of carbon in the ocean and the atmosphere. The interactions between abiotic and biogenic carbon (e.g. CO2, CaCO3, organic matter) in the ocean are complex, and there is a half-century-old enigma about the existence of a huge reservoir of recalcitrant dissolved organic carbon (RDOC) that equates to the magnitude of the pool of atmospheric CO2. The concepts of the biological carbon pump (BCP) and the microbial loop (ML) shaped our understanding of the marine carbon cycle. The more recent concept of the microbial carbon pump (MCP), which is closely connected to those of the BCP and the ML, explicitly considers the significance of the ocean's RDOC reservoir and provides a mechanistic framework for the exploration of its formation and persistence. Understanding of the MCP has benefited from advanced ‘omics’ and novel research in biological oceanography and microbial biogeochemistry. The need to predict the ocean's response to climate change makes an integrative understanding of the BCP, ML and MCP a high priority. In this review, we summarize and discuss progress since the proposal of the MCP in 2010 and formulate research questions for the future.
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Affiliation(s)
- Chuanlun Zhang
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Hongyue Dang
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Farooq Azam
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
| | - Ronald Benner
- Department of Biological Sciences and School of the Earth, Ocean and Environment, University of South Carolina, Columbia, SC 29208, USA
| | - Louis Legendre
- Sorbonne Université, Laboratoire d’Océanographie de Villefranche, LOV, 06230 Villefranche-sur-Mer, France
| | - Uta Passow
- Marine Science Institute, University of California Santa Barbara, CA 93106, USA
| | - Luca Polimene
- Plymouth Marine Laboratory, Prospect Place, The Hoe, Plymouth, PL1 3DH, UK
| | - Carol Robinson
- School of Environmental Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Curtis A Suttle
- Departments of Earth, Ocean and Atmospheric Sciences, Botany, and Microbiology and Immunology, and the Institute for the Oceans and Fisheries, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
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Wang JX, Xie W, Zhang YG, Meador TB, Zhang CL. Evaluating Production of Cyclopentyl Tetraethers by Marine Group II Euryarchaeota in the Pearl River Estuary and Coastal South China Sea: Potential Impact on the TEX 86 Paleothermometer. Front Microbiol 2017; 8:2077. [PMID: 29163386 PMCID: PMC5671491 DOI: 10.3389/fmicb.2017.02077] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 10/10/2017] [Indexed: 11/21/2022] Open
Abstract
TEX86 [TetraEther indeX of glycerol dialkyl glycerol tetraethers (GDGTs) with 86 carbon atoms] has been widely applied to reconstruct (paleo-) sea surface temperature. Marine Group I (MG-I) Thaumarchaeota were thought to be the primary source of GDGTs constituting the TEX86 formula; however, recent research has suggested that Marine Group II (MG-II) Euryarchaeota may also contribute significantly to the GDGT pool in the ocean. Little is known regarding the potential impact of MG-II Euryarchaeota-derived GDGTs on TEX86 values recorded in marine sediments. In this study, we assessed the relationship between distributions of GDGTs and MG-II Euryarchaeota and evaluated its potential effect on the TEX86 proxy. Lipid and DNA analyses were performed on suspended particulate matter and surface sediments collected along a salinity gradient from the lower Pearl River (river water) and its estuary (mixing water) to the coastal South China Sea (SCS, seawater). TEX86-derived temperatures from the water column and surface sediments were significantly correlated and both were lower than satellite-based temperatures. The ring index (RI) values in these environments were higher than predicted from the calculated TEX86-RI correlation, indicating that the GDGT pool in the water column of the PR estuary and coastal SCS comprises relatively more cyclopentane rings, which thereby altered TEX86 values. Furthermore, the abundance of MG-II Euryarchaeota 16S rRNA gene in the mixing water was two to three orders of magnitude higher than those observed in the river or seawater. Significant linear correlations were observed between the gene abundance ratio of MG-II Euryarchaeota to total archaea and the fractional abundance of GDGTs with cyclopentane rings. Collectively, these results suggest that MG-II Euryarchaeota likely produce a large proportion of GDGTs with 1–4 cyclopentane moieties, which may bias TEX86 values in the water column and sediments. As such, valid interpretation of TEX86 values in the sediment record, particularly in coastal oceans, should consider the contribution from MG-II Euryarchaeota.
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Affiliation(s)
- Jin-Xiang Wang
- MARUM-Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany.,Department of Marine Sciences, University of Georgia, Athens, GA, United States
| | - Wei Xie
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, China
| | - Yi Ge Zhang
- Department of Oceanography, Texas A&M University, College Station, TX, United States
| | - Travis B Meador
- MARUM-Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Chuanlun L Zhang
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, China.,Department of Ocean Science & Engineering, Southern University of Science and Technology, Shenzhen, China
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5
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Liu H, Zhang CL, Yang C, Chen S, Cao Z, Zhang Z, Tian J. Marine Group II Dominates Planktonic Archaea in Water Column of the Northeastern South China Sea. Front Microbiol 2017; 8:1098. [PMID: 28663746 PMCID: PMC5471323 DOI: 10.3389/fmicb.2017.01098] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 05/30/2017] [Indexed: 11/13/2022] Open
Abstract
Temperature, nutrients, and salinity are among the important factors constraining the distribution and abundance of microorganisms in the ocean. Marine Group II (MGII) belonging to Euryarchaeota commonly dominates the planktonic archaeal community in shallow water and Marine Group I (MGI, now is called Thaumarchaeota) in deeper water in global oceans. Results of quantitative PCR (qPCR) and 454 sequencing in our study, however, showed the dominance of MGII in planktonic archaea throughout the water column of the northeastern South China Sea (SCS) that is characterized by strong water mixing. The abundance of ammonia-oxidizing archaea (AOA) representing the main group of Thaumarchaeota in deeper water in the northeastern SCS was significantly lower than in other oceanic regions. Phylogenetic analysis showed that the top operational taxonomic units (OTUs) of the MGII occurring predominantly below 200 m depth may be unique in the northeastern SCS based on the observation that they are distantly related to known sequences (identity ranging from 90–94%). The abundance of MGII was also significantly correlated with total bacteria in the whole column, which may indicate that MGII and bacteria may have similar physiological or biochemical properties or responses to environmental variation. This study provides valuable information about the dominance of MGII over AOA in both shallow and deep water in the northeastern SCS and highlights the need for comprehensive studies integrating physical, chemical, and microbial oceanography.
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Affiliation(s)
- Haodong Liu
- State Key Laboratory of Marine Geology, Tongji UniversityShanghai, China
| | - Chuanlun L Zhang
- Department of Ocean Science and Engineering, Southern University of Science and TechnologyShenzhen, China
| | - Chunyan Yang
- State Key Laboratory of Marine Geology, Tongji UniversityShanghai, China.,CNOOC Gas and Power GroupBeijing, China
| | - Songze Chen
- State Key Laboratory of Marine Geology, Tongji UniversityShanghai, China
| | - Zhiwei Cao
- School of Life Sciences and Technology, Tongji UniversityShanghai, China
| | - Zhiwei Zhang
- Physical Oceanography Laboratory, Ocean University of ChinaQingdao, China
| | - Jiwei Tian
- Physical Oceanography Laboratory, Ocean University of ChinaQingdao, China
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Feyhl-Buska J, Chen Y, Jia C, Wang JX, Zhang CL, Boyd ES. Influence of Growth Phase, pH, and Temperature on the Abundance and Composition of Tetraether Lipids in the Thermoacidophile Picrophilus torridus. Front Microbiol 2016; 7:1323. [PMID: 27625636 PMCID: PMC5003844 DOI: 10.3389/fmicb.2016.01323] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 08/10/2016] [Indexed: 11/13/2022] Open
Abstract
The abundance and composition of glycerol dibiphytanyl glycerol tetraether (GDGT) and glycerol tribiphytanyl glycerol tetraether (GTGT) lipids were determined as a function of growth phase as a proxy for nutrient availability, the pH of growth medium, and incubation temperature in cultures of the thermoacidophile Picrophilus torridus. Regardless of the cultivation condition, the abundance of GDGTs and GTGTs was greater in the polar than core fraction, with a marked decrease in core GDGTs in cultures harvested during log phase growth. These data are consistent with previous suggestions indicating that core GDGTs are re-functionalized during polar lipid synthesis. Under all conditions examined, polar lipids were enriched in a GDGT with 2 cyclopentyl rings (GDGT-2), indicating GDGT-2 is the preferred lipid in this taxon. However, lag or stationary phase grown cells or cells subjected to pH or thermal stress were enriched in GDGTs with 4, 5, or 6 rings and depleted in GDGTs with 1, 2, 3, rings relative to log phase cells grown under optimal conditions. Variation in the composition of polar GDGT lipids in cells harvested during various growth phases tended to be greater than in cells cultivated over a pH range of 0.3–1.1 and a temperature range of 53–63°C. These results suggest that the growth phase, the pH of growth medium, and incubation temperature are all important factors that shape the composition of tetraether lipids in Picrophilus. The similarity in enrichment of GDGTs with more rings in cultures undergoing nutrient, pH, and thermal stress points to GDGT cyclization as a generalized physiological response to stress in this taxon.
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Affiliation(s)
- Jayme Feyhl-Buska
- Department of Microbiology and Immunology, Montana State University Bozeman, MT, USA
| | - Yufei Chen
- State Key Laboratory of Marine Geology, Tongji University Shanghai, China
| | - Chengling Jia
- State Key Laboratory of Marine Geology, Tongji University Shanghai, China
| | - Jin-Xiang Wang
- State Key Laboratory of Marine Geology, Tongji University Shanghai, China
| | - Chuanlun L Zhang
- State Key Laboratory of Marine Geology, Tongji University Shanghai, China
| | - Eric S Boyd
- Department of Microbiology and Immunology, Montana State UniversityBozeman, MT, USA; NASA Astrobiology InstituteMountain View, CA, USA
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Zhu C, Wakeham SG, Elling FJ, Basse A, Mollenhauer G, Versteegh GJM, Könneke M, Hinrichs KU. Stratification of archaeal membrane lipids in the ocean and implications for adaptation and chemotaxonomy of planktonic archaea. Environ Microbiol 2016; 18:4324-4336. [DOI: 10.1111/1462-2920.13289] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 03/03/2016] [Indexed: 11/27/2022]
Affiliation(s)
- Chun Zhu
- MARUM Center for Marine Environmental Sciences and Department of Geosciences; University of Bremen; D-28359 Bremen Germany
- School of Earth and Ocean Sciences; Cardiff University; Cardiff CF10 3AT UK
| | - Stuart G. Wakeham
- Skidaway Institute of Oceanography; 10 Ocean Science Circle Savannah GA 31411 USA
| | - Felix J. Elling
- MARUM Center for Marine Environmental Sciences and Department of Geosciences; University of Bremen; D-28359 Bremen Germany
| | - Andreas Basse
- MARUM Center for Marine Environmental Sciences and Department of Geosciences; University of Bremen; D-28359 Bremen Germany
- Alfred-Wegener-Institute for Polar and Marine Research (AWI); Bremerhaven Germany
| | - Gesine Mollenhauer
- MARUM Center for Marine Environmental Sciences and Department of Geosciences; University of Bremen; D-28359 Bremen Germany
- Alfred-Wegener-Institute for Polar and Marine Research (AWI); Bremerhaven Germany
| | - Gerard J. M. Versteegh
- MARUM Center for Marine Environmental Sciences and Department of Geosciences; University of Bremen; D-28359 Bremen Germany
| | - Martin Könneke
- MARUM Center for Marine Environmental Sciences and Department of Geosciences; University of Bremen; D-28359 Bremen Germany
| | - Kai-Uwe Hinrichs
- MARUM Center for Marine Environmental Sciences and Department of Geosciences; University of Bremen; D-28359 Bremen Germany
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8
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A TEX₈₆ surface sediment database and extended Bayesian calibration. Sci Data 2015; 2:150029. [PMID: 26110065 PMCID: PMC4477698 DOI: 10.1038/sdata.2015.29] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 05/18/2015] [Indexed: 11/30/2022] Open
Abstract
Quantitative estimates of past temperature changes are a cornerstone of paleoclimatology. For a number of marine sediment-based proxies, the accuracy and precision of past temperature reconstructions depends on a spatial calibration of modern surface sediment measurements to overlying water temperatures. Here, we present a database of 1095 surface sediment measurements of TEX86, a temperature proxy based on the relative cyclization of marine archaeal glycerol dialkyl glycerol tetraether (GDGT) lipids. The dataset is archived in a machine-readable format with geospatial information, fractional abundances of lipids (if available), and metadata. We use this new database to update surface and subsurface temperature calibration models for TEX86 and demonstrate the applicability of the TEX86 proxy to past temperature prediction. The TEX86 database confirms that surface sediment GDGT distribution has a strong relationship to temperature, which accounts for over 70% of the variance in the data. Future efforts, made possible by the data presented here, will seek to identify variables with secondary relationships to GDGT distributions, such as archaeal community composition.
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Xie W, Zhang CL, Wang J, Chen Y, Zhu Y, de la Torre JR, Dong H, Hartnett HE, Hedlund BP, Klotz MG. Distribution of ether lipids and composition of the archaeal community in terrestrial geothermal springs: impact of environmental variables. Environ Microbiol 2014; 17:1600-14. [PMID: 25142282 DOI: 10.1111/1462-2920.12595] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Accepted: 08/08/2014] [Indexed: 11/26/2022]
Abstract
Archaea can respond to changes in the environment by altering the composition of their membrane lipids, for example, by modification of the abundance and composition of glycerol dialkyl glycerol tetraethers (GDGTs). Here, we investigated the abundance and proportions of polar GDGTs (P-GDGTs) and core GDGTs (C-GDGTs) sampled in different seasons from Tengchong hot springs (Yunnan, China), which encompassed a pH range of 2.5-10.1 and a temperature range of 43.7-93.6°C. The phylogenetic composition of the archaeal community (reanalysed from published work) divided the Archaea in spring sediment samples into three major groups that corresponded with spring pH: acidic, circumneutral and alkaline. Cluster analysis showed correlation between spring pH and the composition of P- and C-GDGTs and archaeal 16S rRNA genes, indicating an intimate link between resident Archaea and the distribution of P- and C-GDGTs in Tengchong hot springs. The distribution of GDGTs in Tengchong springs was also significantly affected by temperature; however, the relationship was weaker than with pH. Analysis of published datasets including samples from Tibet, Yellowstone and the US Great Basin hot springs revealed a similar relationship between pH and GDGT content. Specifically, low pH springs had higher concentrations of GDGTs with high numbers of cyclopentyl rings than neutral and alkaline springs, which is consistent with the predominance of high cyclopentyl ring-characterized Sulfolobales and Thermoplasmatales present in some of the low pH springs. Our study suggests that the resident Archaea in these hot springs are acclimated if not adapted to low pH by their genetic capacity to effect the packing density of their membranes by increasing cyclopentyl rings in GDGTs at the rank of community.
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Affiliation(s)
- Wei Xie
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, 200092, China; Department of Marine Sciences, University of Georgia, Athens, GA, 30602, USA
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10
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Wu W, Zhang CL, Wang H, He L, Li W, Dong H. Impacts of temperature and pH on the distribution of archaeal lipids in Yunnan hot springs, China. Front Microbiol 2013; 4:312. [PMID: 24194734 PMCID: PMC3812992 DOI: 10.3389/fmicb.2013.00312] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Accepted: 09/28/2013] [Indexed: 11/13/2022] Open
Abstract
In culture experiments and many low temperature environments, the distribution of isoprenoid glycerol dialkyl glycerol tetraethers (GDGTs) commonly shows a strong correlation with temperature; however, this is often not the case in hot springs. We studied 26 hot springs in Yunnan, China, in order to determine whether temperature or other factors control the distribution of GDGTs in these environments. The hot springs ranged in temperature from 39.0 to 94.0°C, and in pH from 2.35 to 9.11. Water chemistry including nitrogen-, sulfur-, and iron species was also determined. Lipids from the samples were analyzed using liquid chromatography-mass spectrometry (LC-MS). Distributions of GDGTs in these hot springs were examined using cluster analysis, which resulted in two major groups. Group 1 was characterized by the lack of dominance of any individual GDGTs, while Group 2 was defined by the dominance of GDGT-0 or thaumarchaeol. Temperature was the main control on GDGT distribution in Group 1, whereas pH played an important role in the distribution of GDGTs in Group 2. However, no correlations were found between the distribution of GDGTs and any of the nitrogen-, sulfur-, or iron species. Results of this study indicate the dominance of temperature or pH control on archaeal lipid distribution, which can be better evaluated in the context of lipid classification.
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Affiliation(s)
- Weiyan Wu
- State Key Laboratory of Marine Geology, Tongji University Shanghai, China
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11
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Boyd ES, Hamilton TL, Wang J, He L, Zhang CL. The role of tetraether lipid composition in the adaptation of thermophilic archaea to acidity. Front Microbiol 2013; 4:62. [PMID: 23565112 PMCID: PMC3615187 DOI: 10.3389/fmicb.2013.00062] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2013] [Accepted: 03/04/2013] [Indexed: 01/10/2023] Open
Abstract
Diether and tetraether lipids are fundamental components of the archaeal cell membrane. Archaea adjust the degree of tetraether lipid cyclization in order to maintain functional membranes and cellular homeostasis when confronted with pH and/or thermal stress. Thus, the ability to adjust tetraether lipid composition likely represents a critical phenotypic trait that enabled archaeal diversification into environments characterized by extremes in pH and/or temperature. Here we assess the relationship between geochemical variation, core- and polar-isoprenoid glycerol dibiphytanyl glycerol tetraether (C-iGDGT and P-iGDGT, respectively) lipid composition, and archaeal 16S rRNA gene diversity and abundance in 27 geothermal springs in Yellowstone National Park, Wyoming. The composition and abundance of C-iGDGT and P-iGDGT lipids recovered from geothermal ecosystems were distinct from surrounding soils, indicating that they are synthesized endogenously. With the exception of GDGT-0 (no cyclopentyl rings), the abundances of individual C-iGDGT and P-iGDGT lipids were significantly correlated. The abundance of a number of individual tetraether lipids varied positively with the relative abundance of individual 16S rRNA gene sequences, most notably crenarchaeol in both the core and polar GDGT fraction and sequences closely affiliated with Candidatus Nitrosocaldus yellowstonii. This finding supports the proposal that crenarchaeol is a biomarker for nitrifying archaea. Variation in the degree of cyclization of C- and P-iGDGT lipids recovered from geothermal mats and sediments could best be explained by variation in spring pH, with lipids from acidic environments tending to have, on average, more internal cyclic rings than those from higher pH ecosystems. Likewise, variation in the phylogenetic composition of archaeal 16S rRNA genes could best be explained by spring pH. In turn, the phylogenetic similarity of archaeal 16S rRNA genes was significantly correlated with the similarity in the composition of C- and P-iGDGT lipids. Taken together, these data suggest that the ability to adjust the composition of GDGT lipid membranes played a central role in the diversification of archaea into or out of environments characterized by extremes of low pH and high temperature.
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Affiliation(s)
- Eric S Boyd
- Department of Chemistry and Biochemistry, Montana State University Bozeman, MT, USA
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Thaumarchaeotal signature gene distribution in sediments of the northern South China Sea: an indicator of the metabolic intersection of the marine carbon, nitrogen, and phosphorus cycles? Appl Environ Microbiol 2013; 79:2137-47. [PMID: 23335759 DOI: 10.1128/aem.03204-12] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Thaumarchaeota are abundant and active in marine waters, where they contribute to aerobic ammonia oxidation and light-independent carbon fixation. The ecological function of thaumarchaeota in marine sediments, however, has rarely been investigated, even though marine sediments constitute the majority of the Earth's surface. Thaumarchaeota in the upper layer of sediments may contribute significantly to the reservoir of nitrogen oxides in ocean waters and thus to productivity, including the assimilation of carbon. We tested this hypothesis in the northern South China Sea (nSCS), a section of a large oligotrophic marginal sea with limited influx of nutrients, including nitrogen, by investigating the diversity, abundance, community structure, and spatial distribution of thaumarchaeotal signatures in surface sediments. Quantitative real-time PCR using primers designed to detect 16S rRNA and amoA genes in sediment community DNA revealed a significantly higher abundance of pertinent thaumarchaeotal than betaproteobacterial genes. This finding correlates with high levels of hcd genes, a signature of thaumarchaeotal autotrophic carbon fixation. Thaumarchaeol, a signature lipid biomarker for thaumarchaeota, constituted the majority of archaeal lipids in marine sediments. Sediment temperature and organic P and silt contents were identified as key environmental factors shaping the community structure and distribution of the monitored thaumarchaeotal amoA genes. When the pore water PO4(3-) concentration was controlled for via partial-correlation analysis, thaumarchaeotal amoA gene abundance significantly correlated with the sediment pore water NO2(-) concentration, suggesting that the amoA-bearing thaumarchaeota contribute to nitrite production. Statistical analyses also suggest that thaumarchaeotal metabolism could serve as a pivotal intersection of the carbon, nitrogen, and phosphorus cycles in marine sediments.
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Abstract
The majority of marine dissolved organic carbon (DOC) is resistant to biological degradation and thus can remain in the water column for thousands of years, constituting carbon sequestration in the ocean. To date the origin of such recalcitrant DOC (RDOC) is unclear. A recently proposed conceptual framework, the microbial carbon pump (MCP), emphasizes the microbial transformation of organic carbon from labile to recalcitrant states. The MCP is concerned with both microbial uptakes and outputs of DOC compounds, covering a wide range from gene to ecosystem levels. In this minireview, the ATP binding cassette (ABC) transporter is used as an example for the microbial processing of DOC at the genetic level. The compositions of the ABC transporter genes of the two major marine bacterial clades Roseobacter and SAR11 demonstrate that they have distinct patterns in DOC utilization: Roseobacter strains have the advantage of taking up carbohydrate DOC, while SAR11 bacteria prefer nitrogen-containing DOC. At the ecosystem level, bacterially derived RDOC based on d-amino acid biomarkers is reported to be responsible for about a quarter of the total marine RDOC pool. Under future global warming scenarios, partitioning of primary production into DOC could be enhanced, and thus the MCP could play an even more important role in carbon sequestration by the ocean. Joint efforts to study the MCP from multiple disciplines are required to obtain a better understanding of ocean carbon cycle and its coupling with global change.
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