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Ma C, Coffinet S, Lipp JS, Hinrichs KU, Zhang C. Marine Group II Euryarchaeota Contribute to the Archaeal Lipid Pool in Northwestern Pacific Ocean Surface Waters. Front Microbiol 2020; 11:1034. [PMID: 32582055 PMCID: PMC7291766 DOI: 10.3389/fmicb.2020.01034] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 04/27/2020] [Indexed: 12/17/2022] Open
Abstract
Planktonic archaea include predominantly Marine Group I Thaumarchaeota (MG I) and Marine Group II Euryarchaeota (MG II), which play important roles in the oceanic carbon cycle. MG I produce specific lipids called isoprenoid glycerol dibiphytanyl glycerol tetraethers (GDGTs), which are being used in the sea surface temperature proxy named TEX86. Although MG II may be the most abundant planktonic archaeal group in surface water, their lipid composition remains poorly characterized because of the lack of cultured representatives. Circumstantial evidence from previous studies of marine suspended particulate matter suggests that MG II may produce both GDGTs and archaeol-based lipids. In this study, integration of the 16S rRNA gene quantification and sequencing and lipid analysis demonstrated that MG II contributed significantly to the pool of archaeal tetraether lipids in samples collected from MG II-dominated surface waters of the Northwestern Pacific Ocean (NWPO). The archaeal lipid composition in MG II-dominated NWPO waters differed significantly from that of known MG I cultures, containing relatively more 2G-OH-, 2G- and 1G- GDGTs, especially in their acyclic form. Lipid composition in NWPO waters was also markedly different from MG I-dominated surface water samples collected in the East China Sea. GDGTs from MG II-dominated samples seemed to respond to temperature similarly to GDGTs from the MG I-dominated samples, which calls for further study using pure cultures to determine the exact impact of MG II on GDGT-based proxies.
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Affiliation(s)
- Cenling Ma
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, China
| | - Sarah Coffinet
- Organic Geochemistry Group, MARUM Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen, Bremen, Germany
| | - Julius S Lipp
- Organic Geochemistry Group, MARUM Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen, Bremen, Germany
| | - Kai-Uwe Hinrichs
- Organic Geochemistry Group, MARUM Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen, Bremen, Germany
| | - 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
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Meador TB, Bowles M, Lazar CS, Zhu C, Teske A, Hinrichs KU. The archaeal lipidome in estuarine sediment dominated by members of the Miscellaneous Crenarchaeotal Group. Environ Microbiol 2015; 17:2441-58. [PMID: 25403417 DOI: 10.1111/1462-2920.12716] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Accepted: 11/08/2014] [Indexed: 11/27/2022]
Abstract
The anoxic sediments of the White Oak River estuary comprise a distinctive sulfate-methane transition zone (SMTZ) and natural enrichment of the archaea affiliated with the Miscellaneous Crenarchaeotal Group (MCG). Archaeal biphytanes were generally depleted in (13) C, with δ(13) C values being less than -35‰, indicative of production by active sedimentary archaeal populations. Multivariate analysis of the downcore distributions of 63 lipid biomarkers identified three major groups of lipids that were enriched in the surface, SMTZ or subsurface depths. Intact polar lipids with phosphatidylglycerol headgroups and glycerol dibiphytanyl glycerol tetraethers containing one, two or three cyclopentane rings were enriched at the base of the SMTZ and likely represent the accumulated product of a small but active ANME-1 community. The recently identified butanetriol dibiphytanyl glycerol tetraethers (BDGT), which increased relatively to other lipids with depth, were correlated with the relative abundance of MCG in archaeal 16S rRNA clone libraries, and were (13) C depleted throughout the depth profile, suggesting BDGT lipids as putative biomarkers of an MCG community that may either be autotrophic or feeding on (13) C-depleted organic substrates transported by porewater.
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Affiliation(s)
- Travis B Meador
- MARUM Center for Marine Environmental Sciences, Department of Geosciences, University of Bremen, Bremen, Germany
| | - Marshall Bowles
- MARUM Center for Marine Environmental Sciences, Department of Geosciences, University of Bremen, Bremen, Germany
| | - Cassandre S Lazar
- MARUM Center for Marine Environmental Sciences, Department of Geosciences, University of Bremen, Bremen, Germany.,Department of Marine Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Chun Zhu
- MARUM Center for Marine Environmental Sciences, Department of Geosciences, University of Bremen, Bremen, Germany
| | - Andreas Teske
- Department of Marine Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kai-Uwe Hinrichs
- MARUM Center for Marine Environmental Sciences, Department of Geosciences, University of Bremen, Bremen, Germany
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Ghasimi DSM, Tao Y, de Kreuk M, Zandvoort MH, van Lier JB. Microbial population dynamics during long-term sludge adaptation of thermophilic and mesophilic sequencing batch digesters treating sewage fine sieved fraction at varying organic loading rates. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:171. [PMID: 26500697 PMCID: PMC4618146 DOI: 10.1186/s13068-015-0355-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 10/09/2015] [Indexed: 05/16/2023]
Abstract
BACKGROUND In this research, the feasibility of, and population dynamics in, one-step anaerobic sequencing batch reactor systems treating the fine sieved fraction (FSF) from raw municipal wastewater was studied under thermophilic (55 °C) and mesophilic (35 °C) conditions. FSF was sequestered from raw municipal wastewater, in the Netherlands, using a rotating belt filter (mesh size 350 micron). FSF is a heterogeneous substrate that mainly consists of fibres originating from toilet paper and thus contains a high cellulosic fraction (60-80 % of total solids content), regarded as an energy-rich material. RESULTS Results of the 656-day fed-batch operation clearly showed that thermophilic digestion was more stable, applying high organic loading rates (OLR) up to 22 kg COD/(m(3) day). In contrast, the mesophilic digester already failed applying an OLR of 5.5 kg COD/(m(3) day), indicated by a drop in pH and increase in volatile fatty acids (VFAs). The observed viscosity values of the mesophilic sludge were more than tenfold higher than the thermophilic sludge. 454-pyrosequencing of eight mesophilic and eight thermophilic biomass samples revealed that Bacteroides and aceticlastic methanogen Methanosaeta were the dominant genera in the mesophilic digester, whereas OP9 lineages, Clostridium and the hydrogenotrophic methanogen Methanothermobacter dominated the thermophilic one. CONCLUSIONS Our study suggests that applying thermophilic conditions for FSF digestion would result in a higher biogas production rate and/or a smaller required reactor volume, comparing to mesophilic conditions.
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Affiliation(s)
- Dara S. M. Ghasimi
- />Sanitary Engineering Section, Department of Water Management, Faculty of Civil Engineering and Geosciences, Delft University of Technology, Stevinweg 1, 2628 CN Delft, The Netherlands
| | - Yu Tao
- />Sanitary Engineering Section, Department of Water Management, Faculty of Civil Engineering and Geosciences, Delft University of Technology, Stevinweg 1, 2628 CN Delft, The Netherlands
- />Department of Chemical Engineering, Imperial College London, South Kensington Campus, London, SW7 2AZ the UK
| | - Merle de Kreuk
- />Sanitary Engineering Section, Department of Water Management, Faculty of Civil Engineering and Geosciences, Delft University of Technology, Stevinweg 1, 2628 CN Delft, The Netherlands
| | - Marcel H. Zandvoort
- />Waternet, Korte Ouderkerkerdijk 7, P.O. Box 94370, 1090 GJ Amsterdam, The Netherlands
| | - Jules B. van Lier
- />Sanitary Engineering Section, Department of Water Management, Faculty of Civil Engineering and Geosciences, Delft University of Technology, Stevinweg 1, 2628 CN Delft, The Netherlands
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Sinninghe Damsté JS, Rijpstra WIC, Hopmans EC, Foesel BU, Wüst PK, Overmann J, Tank M, Bryant DA, Dunfield PF, Houghton K, Stott MB. Ether- and ester-bound iso-diabolic acid and other lipids in members of acidobacteria subdivision 4. Appl Environ Microbiol 2014; 80:5207-18. [PMID: 24928878 PMCID: PMC4136120 DOI: 10.1128/aem.01066-14] [Citation(s) in RCA: 96] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2014] [Accepted: 06/04/2014] [Indexed: 11/20/2022] Open
Abstract
Recently, iso-diabolic acid (13,16-dimethyl octacosanedioic acid) has been identified as a major membrane-spanning lipid of subdivisions 1 and 3 of the Acidobacteria, a highly diverse phylum within the Bacteria. This finding pointed to the Acidobacteria as a potential source for the bacterial glycerol dialkyl glycerol tetraethers that occur ubiquitously in peat, soil, lakes, and hot springs. Here, we examined the lipid composition of seven phylogenetically divergent strains of subdivision 4 of the Acidobacteria, a bacterial group that is commonly encountered in soil. Acid hydrolysis of total cell material released iso-diabolic acid derivatives in substantial quantities (11 to 48% of all fatty acids). In contrast to subdivisions 1 and 3 of the Acidobacteria, 6 out of the 7 species of subdivision 4 (excepting "Candidatus Chloracidobacterium thermophilum") contained iso-diabolic acid ether bound to a glycerol in larger fractional abundance than iso-diabolic acid itself. This is in agreement with the analysis of intact polar lipids (IPLs) by high-performance liquid chromatography-mass spectrometry (HPLC-MS), which showed the dominance of mixed ether-ester glycerides. iso-Diabolic acid-containing IPLs were not identified, because these IPLs are not released with a Bligh-Dyer extraction, as observed before when studying lipid compositions of subdivisions 1 and 3 of the Acidobacteria. The presence of ether bonds in the membrane lipids does not seem to be an adaptation to temperature, because the five mesophilic isolates contained a larger amount of ether lipids than the thermophile "Ca. Chloracidobacterium thermophilum." Furthermore, experiments with Pyrinomonas methylaliphatogenes did not reveal a major influence of growth temperature over the 50 to 69°C range.
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Affiliation(s)
- Jaap S Sinninghe Damsté
- NIOZ-Royal Netherlands Institute for Sea Research, Department of Marine Organic Biogeochemistry, Den Burg, the Netherlands
| | - W Irene C Rijpstra
- NIOZ-Royal Netherlands Institute for Sea Research, Department of Marine Organic Biogeochemistry, Den Burg, the Netherlands
| | - Ellen C Hopmans
- NIOZ-Royal Netherlands Institute for Sea Research, Department of Marine Organic Biogeochemistry, Den Burg, the Netherlands
| | - Bärbel U Foesel
- Department of Microbial Ecology and Diversity Research, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Pia K Wüst
- Department of Microbial Ecology and Diversity Research, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Jörg Overmann
- Department of Microbial Ecology and Diversity Research, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Marcus Tank
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Donald A Bryant
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Peter F Dunfield
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Karen Houghton
- GNS Science, Extremophile Research Group, Taupo, New Zealand
| | - Matthew B Stott
- GNS Science, Extremophile Research Group, Taupo, New Zealand
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Hedlund BP, Paraiso JJ, Williams AJ, Huang Q, Wei Y, Dijkstra P, Hungate BA, Dong H, Zhang CL. Wide distribution of autochthonous branched glycerol dialkyl glycerol tetraethers (bGDGTs) in U.S. Great Basin hot springs. Front Microbiol 2013; 4:222. [PMID: 23964271 PMCID: PMC3737515 DOI: 10.3389/fmicb.2013.00222] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Accepted: 07/21/2013] [Indexed: 11/18/2022] Open
Abstract
Branched glycerol dialkyl glycerol tetraethers (bGDGTs) are membrane-spanning lipids that likely stabilize membranes of some bacteria. Although bGDGTs have been reported previously in certain geothermal environments, it has been suggested that they may derive from surrounding soils since bGDGTs are known to be produced by soil bacteria. To test the hypothesis that bGDGTs can be produced by thermophiles in geothermal environments, we examined the distribution and abundance of bGDGTs, along with extensive geochemical data, in 40 sediment and mat samples collected from geothermal systems in the U.S. Great Basin (temperature: 31–95°C; pH: 6.8–10.7). bGDGTs were found in 38 out of 40 samples at concentrations up to 824 ng/g sample dry mass and comprised up to 99.5% of total GDGTs (branched plus isoprenoidal). The wide distribution of bGDGTs in hot springs, strong correlation between core and polar lipid abundances, distinctness of bGDGT profiles compared to nearby soils, and higher concentration of bGDGTs in hot springs compared to nearby soils provided evidence of in situ production, particularly for the minimally methylated bGDGTs I, Ib, and Ic. Polar bGDGTs were found almost exclusively in samples ≤70°C and the absolute abundance of polar bGDGTs correlated negatively with properties of chemically reduced, high temperature spring sources (temperature, H2S/HS−) and positively with properties of oxygenated, low temperature sites (O2, NO−3). Two-way cluster analysis and nonmetric multidimensional scaling based on relative abundance of polar bGDGTs supported these relationships and showed a negative relationship between the degree of methylation and temperature, suggesting a higher abundance for minimally methylated bGDGTs at high temperature. This study presents evidence of the widespread production of bGDGTs in mats and sediments of natural geothermal springs in the U.S. Great Basin, especially in oxygenated, low-temperature sites (≤70°C).
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Affiliation(s)
- Brian P Hedlund
- School of Life Sciences, University of Nevada, Las Vegas Las Vegas, NV, USA
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