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Zhu QZ, Elvert M, Meador TB, Schröder JM, Doeana KD, Becker KW, Elling FJ, Lipp JS, Heuer VB, Zabel M, Hinrichs KU. Comprehensive molecular-isotopic characterization of archaeal lipids in the Black Sea water column and underlying sediments. GEOBIOLOGY 2024; 22:e12589. [PMID: 38465505 DOI: 10.1111/gbi.12589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 01/30/2024] [Accepted: 02/19/2024] [Indexed: 03/12/2024]
Abstract
The Black Sea is a permanently anoxic, marine basin serving as model system for the deposition of organic-rich sediments in a highly stratified ocean. In such systems, archaeal lipids are widely used as paleoceanographic and biogeochemical proxies; however, the diverse planktonic and benthic sources as well as their potentially distinct diagenetic fate may complicate their application. To track the flux of archaeal lipids and to constrain their sources and turnover, we quantitatively examined the distributions and stable carbon isotopic compositions (δ13 C) of intact polar lipids (IPLs) and core lipids (CLs) from the upper oxic water column into the underlying sediments, reaching deposits from the last glacial. The distribution of IPLs responded more sensitively to the geochemical zonation than the CLs, with the latter being governed by the deposition from the chemocline. The isotopic composition of archaeal lipids indicates CLs and IPLs in the deep anoxic water column have negligible influence on the sedimentary pool. Archaeol substitutes tetraether lipids as the most abundant IPL in the deep anoxic water column and the lacustrine methanic zone. Its elevated IPL/CL ratios and negative δ13 C values indicate active methane metabolism. Sedimentary CL- and IPL-crenarchaeol were exclusively derived from the water column, as indicated by non-variable δ13 C values that are identical to those in the chemocline and by the low BIT (branched isoprenoid tetraether index). By contrast, in situ production accounts on average for 22% of the sedimentary IPL-GDGT-0 (glycerol dibiphytanyl glycerol tetraether) based on isotopic mass balance using the fermentation product lactate as an endmember for the dissolved substrate pool. Despite the structural similarity, glycosidic crenarchaeol appears to be more recalcitrant in comparison to its non-cycloalkylated counterpart GDGT-0, as indicated by its consistently higher IPL/CL ratio in sediments. The higher TEX86 , CCaT, and GDGT-2/-3 values in glacial sediments could plausibly result from selective turnover of archaeal lipids and/or an archaeal ecology shift during the transition from the glacial lacustrine to the Holocene marine setting. Our in-depth molecular-isotopic examination of archaeal core and intact polar lipids provided new constraints on the sources and fate of archaeal lipids and their applicability in paleoceanographic and biogeochemical studies.
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Affiliation(s)
- Qing-Zeng Zhu
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Marcus Elvert
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Travis B Meador
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Biology Centre CAS, Soil and Water Research Infrastructure, České Budějovice, Czechia
- Faculty of Science, University of South Bohemia, České Budějovice, Czechia
| | - Jan M Schröder
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Katiana D Doeana
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Kevin W Becker
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Felix J Elling
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Julius S Lipp
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Verena B Heuer
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Matthias Zabel
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Kai-Uwe Hinrichs
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Faculty of Geosciences, University of Bremen, Bremen, Germany
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2
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Doytchinov VV, Peykov S, Dimov SG. Study of the Bacterial, Fungal, and Archaeal Communities Structures near the Bulgarian Antarctic Research Base "St. Kliment Ohridski" on Livingston Island, Antarctica. Life (Basel) 2024; 14:278. [PMID: 38398787 PMCID: PMC10890693 DOI: 10.3390/life14020278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 02/09/2024] [Accepted: 02/17/2024] [Indexed: 02/25/2024] Open
Abstract
As belonging to one of the most isolated continents on our planet, the microbial composition of different environments in Antarctica could hold a plethora of undiscovered species with the potential for biotechnological applications. This manuscript delineates our discoveries after an expedition to the Bulgarian Antarctic Base "St. Kliment Ohridski" situated on Livingston Island, Antarctica. Amplicon-based metagenomics targeting the 16S rRNA genes and ITS2 region were employed to assess the metagenomes of the bacterial, fungal, and archaeal communities across diverse sites within and proximal to the research station. The predominant bacterial assemblages identified included Oxyphotobacteria, Bacteroidia, Gammaprotobacteria, and Alphaprotobacteria. A substantial proportion of cyanobacteria reads were attributed to a singular uncultured taxon within the family Leptolyngbyaceae. The bacterial profile of a lagoon near the base exhibited indications of penguin activity, characterized by a higher abundance of Clostridia, similar to lithotelm samples from Hannah Pt. Although most fungal reads in the samples could not be identified at the species level, noteworthy genera, namely Betamyces and Tetracladium, were identified. Archaeal abundance was negligible, with prevalent groups including Woesearchaeales, Nitrosarchaeum, Candidatus Nitrosopumilus, and Marine Group II.
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Affiliation(s)
- Vesselin V Doytchinov
- Department of Genetics, Faculty of Biology, Sofia University "St. Kliment Ohridski", 1164 Sofia, Bulgaria
| | - Slavil Peykov
- Department of Genetics, Faculty of Biology, Sofia University "St. Kliment Ohridski", 1164 Sofia, Bulgaria
| | - Svetoslav G Dimov
- Department of Genetics, Faculty of Biology, Sofia University "St. Kliment Ohridski", 1164 Sofia, Bulgaria
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3
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Singh A, Varma A, Prasad R, Porwal S. Bioprospecting uncultivable microbial diversity in tannery effluent contaminated soil using shotgun sequencing and bio-reduction of chromium by indigenous chromate reductase genes. ENVIRONMENTAL RESEARCH 2022; 215:114338. [PMID: 36116499 DOI: 10.1016/j.envres.2022.114338] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 09/06/2022] [Accepted: 09/10/2022] [Indexed: 06/15/2023]
Abstract
The tannery industry generates a consequential threat to the environment by producing a large amount of potentially toxic metal-containing waste. Bioremediation has been a promising approach for treating potentially toxic metals, but the efficiency of remediation in microbes is one of the factors limiting their application in tanneries waste treatment. The motivation behind the present work was to explore the microbial diversity and chromate reductase genes present in the tannery effluent-contaminated soil using metagenomics approach. The use of shotgun sequencing enabled the identification of operational parameters that influence microbiome composition and their ability to reduce Chromium (Cr) concentration. The Cr concentration in Kanpur tannery effluent contaminated soil sample was 700 ppm which is many folds than the approved permissible limit by World Health Organisation (WHO) for Cr is 100 ppm. Metagenomic Deoxyribo Nucleic Acid (DNA) was extracted to explore taxonomic community structure, phylogenetic linkages, and functional profile. With a Guanine-Cytosine (GC) abundance of 54%, total of 45,163,604 high-quality filtered reads were obtained. Bacteria (83%), Archaebacteria (14%), and Viruses (3%) were discovered in the structural biodiversity. Bacteria were classified to phylum level, with Proteobacteria (52%) being the dominant population, followed by Bacteriodetes (15%), Chloroflexi (15%), Spirochaetes (7%), Thermotogae (5%), Actinobacteria (4%), and Firmicutes (1%). The OXR genes were cloned and checked for their efficiency to reduce Cr concentration. Insitu validation of OXR8 gene showed a reduction of Cr concentration from 700 ppm to 24 ppm in 72 h (96.51% reduction). The results of this study suggests that there is a huge reservoir of microbes and chromate reductase genes which are unexplored yet.
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Affiliation(s)
- Ayushi Singh
- Amity Institute of Microbial Technology, Amity University, Uttar Pradesh, Noida-201301, India
| | - Ajit Varma
- Amity Institute of Microbial Technology, Amity University, Uttar Pradesh, Noida-201301, India
| | - Ram Prasad
- Department of Botany, Mahatma Gandhi Central University, Motihari-845401, Bihar, India.
| | - Shalini Porwal
- Amity Institute of Microbial Technology, Amity University, Uttar Pradesh, Noida-201301, India.
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4
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Identification of a protein responsible for the synthesis of archaeal membrane-spanning GDGT lipids. Nat Commun 2022; 13:1545. [PMID: 35318330 PMCID: PMC8941075 DOI: 10.1038/s41467-022-29264-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 03/07/2022] [Indexed: 01/08/2023] Open
Abstract
Glycerol dibiphytanyl glycerol tetraethers (GDGTs) are archaeal monolayer membrane lipids that can provide a competitive advantage in extreme environments. Here, we identify a radical SAM protein, tetraether synthase (Tes), that participates in the synthesis of GDGTs. Attempts to generate a tes-deleted mutant in Sulfolobus acidocaldarius were unsuccessful, suggesting that the gene is essential in this organism. Heterologous expression of tes homologues leads to production of GDGT and structurally related lipids in the methanogen Methanococcus maripaludis (which otherwise does not synthesize GDGTs and lacks a tes homolog, but produces a putative GDGT precursor, archaeol). Tes homologues are encoded in the genomes of many archaea, as well as in some bacteria, in which they might be involved in the synthesis of bacterial branched glycerol dialkyl glycerol tetraethers.
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5
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Summons RE, Welander PV, Gold DA. Lipid biomarkers: molecular tools for illuminating the history of microbial life. Nat Rev Microbiol 2022; 20:174-185. [PMID: 34635851 DOI: 10.1038/s41579-021-00636-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/07/2021] [Indexed: 11/09/2022]
Abstract
Fossilized lipids preserved in sedimentary rocks offer singular insights into the Earth's palaeobiology. These 'biomarkers' encode information pertaining to the oxygenation of the atmosphere and oceans, transitions in ocean plankton, the greening of continents, mass extinctions and climate change. Historically, biomarker interpretations relied on inventories of lipids present in extant microorganisms and counterparts in natural environments. However, progress has been impeded because only a small fraction of the Earth's microorganisms can be cultured, many environmentally significant microorganisms from the past no longer exist and there are gaping holes in knowledge concerning lipid biosynthesis. The revolution in genomics and bioinformatics has provided new tools to expand our understanding of lipid biomarkers, their biosynthetic pathways and distributions in nature. In this Review, we explore how preserved organic molecules provide a unique perspective on the history of the Earth's microbial life. We discuss how advances in molecular biology have helped elucidate biomarker origins and afforded more robust interpretations of fossil lipids and how the rock record provides vital calibration points for molecular clocks. Such studies are open to further exploitation with the expansion of sequenced microbial genomes in accessible databases.
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Affiliation(s)
- Roger E Summons
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Paula V Welander
- Department of Earth System Science, Stanford University, Stanford, CA, USA
| | - David A Gold
- Department of Earth & Planetary Sciences, University of California Davis, Davis, CA, USA
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6
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Chen S, Tao J, Chen Y, Wang W, Fan L, Zhang C. Interactions Between Marine Group II Archaea and Phytoplankton Revealed by Population Correlations in the Northern Coast of South China Sea. Front Microbiol 2022; 12:785532. [PMID: 35145493 PMCID: PMC8821943 DOI: 10.3389/fmicb.2021.785532] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 12/14/2021] [Indexed: 11/30/2022] Open
Abstract
Marine Group II (MGII) archaea (Poseidoniales) are the most abundant surface marine planktonic archaea and are widely distributed in both coastal and pelagic waters. The factors affecting their distribution and activity are poorly understood. MGII archaea have the metabolic potential to utilize algae-derived organic matter and are frequently observed in high abundance during or following phytoplankton blooms, suggesting that they are key players of the marine food web. In this study, we studied interactions between MGII archaea and the diverse taxa of phytoplankton in the northern coast of South China Sea. Non-metric multidimensional scaling and cluster analyses demonstrated distinct MGII community patterns in the Pearl River plume (PRP) and the open regions of the northern South China Sea (ONSCS), with MGIIb dominating the former and MGIIa and MGIIb showing remarkable variations in the latter for the same sampling season. Nevertheless, positive correlations (Pearson correlation: R > 0.8 and P < 0.01) in absolute abundances of ribosomal RNA (rRNA)-derived complementary DNA and rRNA genes from network analyses were found between MGII archaea and phytoplankton (cyanobacteria, haptophytes, and stramenopiles in both PRP and ONSCS) among different particle size fractions, indicating their intrinsic relationships under changing environmental conditions. The results of this study may shed light on the multiple interactions between co-existing species in the micro-niches of different oceanic regions.
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Affiliation(s)
- Songze Chen
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Shenzhen, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Jianchang Tao
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Shenzhen, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Yufei Chen
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Shenzhen, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Wenxiu Wang
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Shenzhen, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Lu Fan
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Shenzhen, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Chuanlun Zhang
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Shenzhen, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Shanghai Sheshan National Geophysical Observatory, Shanghai, China
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7
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Blumberg KL, Ponsero AJ, Bomhoff M, Wood-Charlson EM, DeLong EF, Hurwitz BL. Ontology-Enriched Specifications Enabling Findable, Accessible, Interoperable, and Reusable Marine Metagenomic Datasets in Cyberinfrastructure Systems. Front Microbiol 2021; 12:765268. [PMID: 34956127 PMCID: PMC8692764 DOI: 10.3389/fmicb.2021.765268] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 11/16/2021] [Indexed: 11/13/2022] Open
Abstract
Marine microbial ecology requires the systematic comparison of biogeochemical and sequence data to analyze environmental influences on the distribution and variability of microbial communities. With ever-increasing quantities of metagenomic data, there is a growing need to make datasets Findable, Accessible, Interoperable, and Reusable (FAIR) across diverse ecosystems. FAIR data is essential to developing analytical frameworks that integrate microbiological, genomic, ecological, oceanographic, and computational methods. Although community standards defining the minimal metadata required to accompany sequence data exist, they haven’t been consistently used across projects, precluding interoperability. Moreover, these data are not machine-actionable or discoverable by cyberinfrastructure systems. By making ‘omic and physicochemical datasets FAIR to machine systems, we can enable sequence data discovery and reuse based on machine-readable descriptions of environments or physicochemical gradients. In this work, we developed a novel technical specification for dataset encapsulation for the FAIR reuse of marine metagenomic and physicochemical datasets within cyberinfrastructure systems. This includes using Frictionless Data Packages enriched with terminology from environmental and life-science ontologies to annotate measured variables, their units, and the measurement devices used. This approach was implemented in Planet Microbe, a cyberinfrastructure platform and marine metagenomic web-portal. Here, we discuss the data properties built into the specification to make global ocean datasets FAIR within the Planet Microbe portal. We additionally discuss the selection of, and contributions to marine-science ontologies used within the specification. Finally, we use the system to discover data by which to answer various biological questions about environments, physicochemical gradients, and microbial communities in meta-analyses. This work represents a future direction in marine metagenomic research by proposing a specification for FAIR dataset encapsulation that, if adopted within cyberinfrastructure systems, would automate the discovery, exchange, and re-use of data needed to answer broader reaching questions than originally intended.
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Affiliation(s)
- Kai L Blumberg
- Department of Biosystems Engineering, University of Arizona, Tucson, AZ, United States
| | - Alise J Ponsero
- Department of Biosystems Engineering, University of Arizona, Tucson, AZ, United States
| | - Matthew Bomhoff
- Department of Biosystems Engineering, University of Arizona, Tucson, AZ, United States
| | - Elisha M Wood-Charlson
- E.O. Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology Division, Berkeley, CA, United States
| | - Edward F DeLong
- Daniel K. Inouye Center for Microbial Oceanography, University of Hawai'i, Honolulu, HI, United States
| | - Bonnie L Hurwitz
- Department of Biosystems Engineering, University of Arizona, Tucson, AZ, United States.,BIO5 Institute, University of Arizona, Tucson, AZ, United States
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8
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Li F, Leu A, Poff K, Carlson LT, Ingalls AE, DeLong EF. Planktonic Archaeal Ether Lipid Origins in Surface Waters of the North Pacific Subtropical Gyre. Front Microbiol 2021; 12:610675. [PMID: 34589060 PMCID: PMC8473941 DOI: 10.3389/fmicb.2021.610675] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Accepted: 08/23/2021] [Indexed: 01/04/2023] Open
Abstract
Thaumarchaeota and Thermoplasmatota are the most abundant planktonic archaea in the sea. Thaumarchaeota contain tetraether lipids as their major membrane lipids, but the lipid composition of uncultured planktonic Thermoplasmatota representatives remains unknown. To address this knowledge gap, we quantified archaeal cells and ether lipids in open ocean depth profiles (0–200 m) of the North Pacific Subtropical Gyre. Planktonic archaeal community structure and ether lipid composition in the water column partitioned into two separate clusters: one above the deep chlorophyll maximum, the other within and below it. In surface waters, Thermoplasmatota densities ranged from 2.11 × 106 to 6.02 × 106 cells/L, while Thaumarchaeota were undetectable. As previously reported for Thaumarchaeota, potential homologs of archaeal tetraether ring synthases were present in planktonic Thermoplasmatota metagenomes. Despite the absence of Thaumarchaeota in surface waters, measurable amounts of intact polar ether lipids were found there. Based on cell abundance estimates, these surface water archaeal ether lipids contributed only 1.21 × 10–9 ng lipid/Thermoplasmatota cell, about three orders of magnitude less than that reported for Thaumarchaeota cells. While these data indicate that even if some tetraether and diether lipids may be derived from Thermoplasmatota, they would only comprise a small fraction of Thermoplasmatota total biomass. Therefore, while both MGI Thaumarchaeota and MGII/III Thermoplasmatota are potential biological sources of archaeal GDGTs, the Thaumarchaeota appear to be the major contributors of archaeal tetraether lipids in planktonic marine habitats. These results extend and confirm previous reports of planktonic archaeal lipid sources, and further emphasize the need for Thermoplasmatota cultivation, to better characterize the membrane lipid constituents of marine planktonic Thermoplasmatota, and more precisely define the sources and patterns of archaeal tetraether lipid distributions in marine plankton.
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Affiliation(s)
- Fuyan Li
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawai'i at Mânoa, Honolulu, HI, United States
| | - Andy Leu
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawai'i at Mânoa, Honolulu, HI, United States
| | - Kirsten Poff
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawai'i at Mânoa, Honolulu, HI, United States
| | - Laura T Carlson
- School of Oceanography, University of Washington, Seattle, WA, United States
| | - Anitra E Ingalls
- School of Oceanography, University of Washington, Seattle, WA, United States
| | - Edward F DeLong
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawai'i at Mânoa, Honolulu, HI, United States
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9
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DeLong EF. Exploring Marine Planktonic Archaea: Then and Now. Front Microbiol 2021; 11:616086. [PMID: 33519774 PMCID: PMC7838436 DOI: 10.3389/fmicb.2020.616086] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Accepted: 12/18/2020] [Indexed: 12/24/2022] Open
Abstract
In 1977, Woese and Fox leveraged molecular phylogenetic analyses of ribosomal RNAs and identified a new microbial domain of life on Earth, the Archaebacteria (now known as Archaea). At the time of their discovery, only one archaebacterial group, the strictly anaerobic methanogens, was known. But soon, other phenotypically unrelated microbial isolates were shown to belong to the Archaea, many originating from extreme habitats, including extreme halophiles, extreme thermophiles, and thermoacidophiles. Since most Archaea seemed to inhabit extreme or strictly anoxic habitats, it came as a surprise in 1992 when two new lineages of archaea were reported to be abundant in oxygen rich, temperate marine coastal waters and the deep ocean. Since that time, studies of marine planktonic archaea have revealed many more surprises, including their unexpected ubiquity, unusual symbiotic associations, unpredicted physiologies and biogeochemistry, and global abundance. In this Perspective, early work conducted on marine planktonic Archaea by my lab group and others is discussed in terms of the relevant historical context, some of the original research motivations, and surprises and discoveries encountered along the way.
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Affiliation(s)
- Edward F DeLong
- Daniel K. Inouye Center for Microbial Oceanography Research and Education, University of Hawai'i at Mănoa, Honolulu, HI, United States
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10
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Puigcorbé V, Ruiz-González C, Masqué P, Gasol JM. Sampling Device-Dependence of Prokaryotic Community Structure on Marine Particles: Higher Diversity Recovered by in situ Pumps Than by Oceanographic Bottles. Front Microbiol 2020; 11:1645. [PMID: 32760385 PMCID: PMC7373737 DOI: 10.3389/fmicb.2020.01645] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Accepted: 06/24/2020] [Indexed: 01/24/2023] Open
Abstract
Microbes associated with sinking marine particles play key roles in carbon sequestration in the ocean. The sampling of particle-attached microorganisms is often done with sediment traps or by filtration of water collected with oceanographic bottles, both involving a certain time lapse between collection and processing of samples that may result in changes in particle-attached microbial communities. Conversely, in situ water filtration through submersible pumps allows a faster storage of sampled particles, but it has rarely been used to study the associated microbial communities and has never been compared to other particle-sampling methods in terms of the recovery of particle microbial diversity. Here we compared the prokaryotic communities attached to small (1–53 μm) and large (>53 μm) particles collected from the mesopelagic zone (100–300 m) of two Antarctic polynyas using in situ pumps (ISP) and oceanographic bottles (BTL). Each sampling method retrieved largely different particle-attached communities, suggesting that they capture different kinds of particles. These device-driven differences were greater for large particles than for small particles. Overall, the ISP recovered 1.5- to 3-fold more particle-attached bacterial taxa than the BTL, and different taxonomic groups were preferentially recovered by each method. In particular, typical particle-attached groups such as Planctomycetes and Deltaproteobacteria recovered with ISP were nearly absent from BTL samples. Our results suggest that the method used to sample marine particles has a strong influence in our view of their associated microbial communities.
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Affiliation(s)
- Viena Puigcorbé
- School of Science, Centre for Marine Ecosystems Research, Edith Cowan University, Joondalup, WA, Australia
| | - Clara Ruiz-González
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM-CSIC), Barcelona, Spain
| | - Pere Masqué
- School of Science, Centre for Marine Ecosystems Research, Edith Cowan University, Joondalup, WA, Australia.,Institut de Ciència i Tecnologia Ambientals (ICTA), Bellaterra, Spain.,Department of Physics, Autonomous University of Barcelona, Barcelona, Spain.,International Atomic Energy Agency, Monaco City, Monaco
| | - Josep M Gasol
- School of Science, Centre for Marine Ecosystems Research, Edith Cowan University, Joondalup, WA, Australia.,Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM-CSIC), Barcelona, Spain
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11
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Newman SA, Lincoln SA, O'Reilly S, Liu X, Shock EL, Kelemen PB, Summons RE. Lipid Biomarker Record of the Serpentinite-Hosted Ecosystem of the Samail Ophiolite, Oman and Implications for the Search for Biosignatures on Mars. ASTROBIOLOGY 2020; 20:830-845. [PMID: 32648829 DOI: 10.1089/ast.2019.2066] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Serpentinization is a weathering process in which ultramafic rocks react with water, generating a range of products, including serpentine and other minerals, in addition to H2 and low-molecular-weight hydrocarbons that are capable of sustaining microbial life. Lipid biomarker analyses of serpentinite-hosted ecosystems hold promise as tools for investigating microbial activity in ancient Earth environments and other terrestrial planets such as Mars because lipids have the potential for longer term preservation relative to DNA, proteins, and other more labile organic molecules. Here, we report the first lipid biomarker record of microbial activity in the mantle section of the Samail Ophiolite, in the Sultanate of Oman, a site undergoing active serpentinization. We detected isoprenoidal (archaeal) and branched (bacterial) glycerol dialkyl glycerol tetraether (GDGT) lipids, including those with 0-3 cyclopentane moieties, and crenarchaeol, an isoprenoidal GDGT containing four cyclopentane and one cyclohexane moieties, as well as monoether lipids and fatty acids indicative of sulfate-reducing bacteria. Comparison of our geochemical data and 16S rRNA data from the Samail Ophiolite with those from other serpentinite-hosted sites identifies the existence of a common core serpentinization microbiome. In light of these findings, we also discuss the preservation potential of serpentinite lipid biomarker assemblages on Earth and Mars. Continuing investigations of the Samail Ophiolite and other terrestrial analogues will enhance our understanding of microbial habitability and diversity in serpentinite-hosted environments on Earth and elsewhere in the Solar System.
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Affiliation(s)
- Sharon A Newman
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California
| | - Sara A Lincoln
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts
- Department of Geosciences, The Pennsylvania State University, University Park, Pennsylvania
| | - Shane O'Reilly
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts
- School of Earth Sciences, University College Dublin, Belfield, Ireland
| | - Xiaolei Liu
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts
- School of Geology and Geophysics, University of Oklahoma, Norman, Oklahoma
| | - Everett L Shock
- School of Earth and Space Exploration, Arizona State University, Tempe, Arizona
- School of Molecular Sciences, Arizona State University, Tempe, Arizona
- Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, Arizona
| | - Peter B Kelemen
- Lamont-Doherty Earth Observatory, Columbia University, Palisades, New York
| | - Roger E Summons
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts
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12
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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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13
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Besseling MA, Hopmans EC, Bale NJ, Schouten S, Damsté JSS, Villanueva L. The absence of intact polar lipid-derived GDGTs in marine waters dominated by Marine Group II: Implications for lipid biosynthesis in Archaea. Sci Rep 2020; 10:294. [PMID: 31941956 PMCID: PMC6962369 DOI: 10.1038/s41598-019-57035-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 12/19/2019] [Indexed: 11/09/2022] Open
Abstract
The marine pelagic archaeal community is dominated by three major groups, the marine group I (MGI) Thaumarchaeota, and the marine groups II and III (MGII and MGIII) Euryarchaeota. Studies of both MGI cultures and the environment have shown that the MGI core membrane lipids are predominantly composed of glycerol dibiphytanyl glycerol tetraether (GDGT) lipids and the diether lipid archaeol. However, there are no cultured representatives of MGII and III archaea and, therefore, both their membrane lipid composition and potential contribution to the marine archaeal lipid pool remain unknown. Here, we show that GDGTs present in suspended particulate matter of the (sub)surface waters of the North Atlantic Ocean and the coastal North Sea are derived from MGI archaea, and that MGII archaea do not significantly contribute to the pool of GDGTs and archaeol. This implies, in contrast to previous suggestions, that their lipids do not affect the widely used sea surface temperature proxy TEX86. These findings also indicate that MGII archaea are not able to produce any known archaeal lipids, implying that our understanding of the evolution of membrane lipid biosynthesis in Archaea is far from complete.
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Affiliation(s)
- Marc A Besseling
- NIOZ, Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, and Utrecht University., P.O. Box 59, NL-1790, AB Den Burg, The Netherlands.
| | - Ellen C Hopmans
- NIOZ, Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, and Utrecht University., P.O. Box 59, NL-1790, AB Den Burg, The Netherlands
| | - Nicole J Bale
- NIOZ, Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, and Utrecht University., P.O. Box 59, NL-1790, AB Den Burg, The Netherlands
| | - Stefan Schouten
- NIOZ, Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, and Utrecht University., P.O. Box 59, NL-1790, AB Den Burg, The Netherlands.,Utrecht University, Faculty of Geosciences, P.O. Box 80.021, 3508 TA, Utrecht, The Netherlands
| | - Jaap S Sinninghe Damsté
- NIOZ, Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, and Utrecht University., P.O. Box 59, NL-1790, AB Den Burg, The Netherlands.,Utrecht University, Faculty of Geosciences, P.O. Box 80.021, 3508 TA, Utrecht, The Netherlands
| | - Laura Villanueva
- NIOZ, Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, and Utrecht University., P.O. Box 59, NL-1790, AB Den Burg, The Netherlands
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14
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15
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GDGT cyclization proteins identify the dominant archaeal sources of tetraether lipids in the ocean. Proc Natl Acad Sci U S A 2019; 116:22505-22511. [PMID: 31591189 DOI: 10.1073/pnas.1909306116] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Glycerol dibiphytanyl glycerol tetraethers (GDGTs) are distinctive archaeal membrane-spanning lipids with up to eight cyclopentane rings and/or one cyclohexane ring. The number of rings added to the GDGT core structure can vary as a function of environmental conditions, such as changes in growth temperature. This physiological response enables cyclic GDGTs preserved in sediments to be employed as proxies for reconstructing past global and regional temperatures and to provide fundamental insights into ancient climate variability. Yet, confidence in GDGT-based paleotemperature proxies is hindered by uncertainty concerning the archaeal communities contributing to GDGT pools in modern environments and ambiguity in the environmental and physiological factors that affect GDGT cyclization in extant archaea. To properly constrain these uncertainties, a comprehensive understanding of GDGT biosynthesis is required. Here, we identify 2 GDGT ring synthases, GrsA and GrsB, essential for GDGT ring formation in Sulfolobus acidocaldarius Both proteins are radical S-adenosylmethionine proteins, indicating that GDGT cyclization occurs through a free radical mechanism. In addition, we demonstrate that GrsA introduces rings specifically at the C-7 position of the core GDGT lipid, while GrsB cyclizes at the C-3 position, suggesting that cyclization patterns are differentially controlled by 2 separate enzymes and potentially influenced by distinct environmental factors. Finally, phylogenetic analyses of the Grs proteins reveal that marine Thaumarchaeota, and not Euryarchaeota, are the dominant source of cyclized GDGTs in open ocean settings, addressing a major source of uncertainty in GDGT-based paleotemperature proxy applications.
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16
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Archaeal lipid biomarker constraints on the Paleocene-Eocene carbon isotope excursion. Nat Commun 2019; 10:4519. [PMID: 31586063 PMCID: PMC6778145 DOI: 10.1038/s41467-019-12553-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 09/17/2019] [Indexed: 11/12/2022] Open
Abstract
A negative carbon isotope excursion recorded in terrestrial and marine archives reflects massive carbon emissions into the exogenic carbon reservoir during the Paleocene-Eocene Thermal Maximum. Yet, discrepancies in carbon isotope excursion estimates from different sample types lead to substantial uncertainties in the source, scale, and timing of carbon emissions. Here we show that membrane lipids of marine planktonic archaea reliably record both the carbon isotope excursion and surface ocean warming during the Paleocene-Eocene Thermal Maximum. Novel records of the isotopic composition of crenarchaeol constrain the global carbon isotope excursion magnitude to −4.0 ± 0.4‰, consistent with emission of >3000 Pg C from methane hydrate dissociation or >4400 Pg C for scenarios involving emissions from geothermal heating or oxidation of sedimentary organic matter. A pre-onset excursion in the isotopic composition of crenarchaeol and ocean temperature highlights the susceptibility of the late Paleocene carbon cycle to perturbations and suggests that climate instability preceded the Paleocene-Eocene Thermal Maximum. The Paleocene-Eocene Thermal Maximum (c. 55 million years ago) was a period associated with massive carbon injection into the atmosphere, yet discrepancies in carbon isotope proxy records have led to substantial uncertainties in the source, scale, and timing of carbon emissions. Here, the authors propose that membrane lipids of marine planktonic archaea can reliably record the carbon isotope excursion and surface ocean warming, giving a new constraint for the source and size of the PETM carbon emissions.
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17
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Aalismail NA, Ngugi DK, Díaz-Rúa R, Alam I, Cusack M, Duarte CM. Functional metagenomic analysis of dust-associated microbiomes above the Red Sea. Sci Rep 2019; 9:13741. [PMID: 31551441 PMCID: PMC6760216 DOI: 10.1038/s41598-019-50194-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 09/06/2019] [Indexed: 02/08/2023] Open
Abstract
Atmospheric transport is a major vector for the long-range transport of microbial communities, maintaining connectivity among them and delivering functionally important microbes, such as pathogens. Though the taxonomic diversity of aeolian microorganisms is well characterized, the genomic functional traits underpinning their survival during atmospheric transport are poorly characterized. Here we use functional metagenomics of dust samples collected on the Global Dust Belt to initiate a Gene Catalogue of Aeolian Microbiome (GCAM) and explore microbial genetic traits enabling a successful aeolian lifestyle in Aeolian microbial communities. The GCAM reported here, derived from ten aeolian microbial metagenomes, includes a total of 2,370,956 non-redundant coding DNA sequences, corresponding to a yield of ~31 × 106 predicted genes per Tera base-pair of DNA sequenced for the aeolian samples sequenced. Two-thirds of the cataloged genes were assigned to bacteria, followed by eukaryotes (5.4%), archaea (1.1%), and viruses (0.69%). Genes encoding proteins involved in repairing UV-induced DNA damage and aerosolization of cells were ubiquitous across samples, and appear as fundamental requirements for the aeolian lifestyle, while genes coding for other important functions supporting the aeolian lifestyle (chemotaxis, aerotaxis, germination, thermal resistance, sporulation, and biofilm formation) varied among the communities sampled.
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Affiliation(s)
- Nojood A Aalismail
- Red Sea Research Centre (RSRC) and Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955, Saudi Arabia.
| | - David K Ngugi
- Department of Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Culture, Inhoffenstrasse 7B, B38124, Braunschweig, Germany
| | - Rubén Díaz-Rúa
- Red Sea Research Centre (RSRC) and Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955, Saudi Arabia
| | - Intikhab Alam
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Michael Cusack
- Red Sea Research Centre (RSRC) and Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955, Saudi Arabia
| | - Carlos M Duarte
- Red Sea Research Centre (RSRC) and Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955, Saudi Arabia
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18
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Pereira O, Hochart C, Auguet JC, Debroas D, Galand PE. Genomic ecology of Marine Group II, the most common marine planktonic Archaea across the surface ocean. Microbiologyopen 2019; 8:e00852. [PMID: 31264806 PMCID: PMC6741140 DOI: 10.1002/mbo3.852] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 04/08/2019] [Accepted: 04/08/2019] [Indexed: 01/22/2023] Open
Abstract
Planktonic Archaea have been detected in all the world's oceans and are found from surface waters to the deep sea. The two most common Archaea phyla are Thaumarchaeota and Euryarchaeota. Euryarchaeota are generally more common in surface waters, but very little is known about their ecology and their potential metabolisms. In this study, we explore the genomic ecology of the Marine Group II (MGII), the main marine planktonic Euryarchaeota, and test if it is composed of different ecologically relevant units. We re‐analyzed Tara Oceans metagenomes from the photic layer and the deep ocean by annotating sequences against a custom MGII database and by mapping gene co‐occurrences. Our data provide a global view of the distribution of Euryarchaeota, and more specifically of MGII subgroups, and reveal their association to a number of gene‐coding sequences. In particular, we show that MGII proteorhodopsins were detected in both the surface and the deep chlorophyll maximum layer and that different clusters of these light harvesting proteins were present. Our approach helped describing the set of genes found together with specific MGII subgroups. We could thus define genomic environments that could theoretically describe ecologically meaningful units and the ecological niche that they occupy.
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Affiliation(s)
- Olivier Pereira
- Sorbonne Université, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques (LECOB), Observatoire Océanologique de Banyuls, Banyuls sur Mer, France
| | - Corentin Hochart
- Laboratoire Microorganismes: Génome et Environnement, UMR 6023, CNRS - Université Blaise Pascal, Aubière, France
| | - Jean Christophe Auguet
- Marine Biodiversity, Exploitation and Conservation (MARBEC), Université de Montpellier, CNRS, IFREMER, Montpellier, France
| | - Didier Debroas
- Laboratoire Microorganismes: Génome et Environnement, UMR 6023, CNRS - Université Blaise Pascal, Aubière, France
| | - Pierre E Galand
- Sorbonne Université, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques (LECOB), Observatoire Océanologique de Banyuls, Banyuls sur Mer, France
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19
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Sollai M, Villanueva L, Hopmans EC, Keil RG, Sinninghe Damsté JS. Archaeal Sources of Intact Membrane Lipid Biomarkers in the Oxygen Deficient Zone of the Eastern Tropical South Pacific. Front Microbiol 2019; 10:765. [PMID: 31031734 PMCID: PMC6470261 DOI: 10.3389/fmicb.2019.00765] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 03/26/2019] [Indexed: 11/13/2022] Open
Abstract
Archaea are ubiquitous in the modern ocean where they are involved in the carbon and nitrogen biogeochemical cycles. However, the majority of Archaea remain uncultured. Archaeal specific membrane intact polar lipids (IPLs) are biomarkers of the presence and abundance of living cells. They comprise archaeol and glycerol dibiphytanyl glycerol tetraethers (GDGTs) attached to various polar headgroups. However, little is known of the IPLs of uncultured marine Archaea, complicating their use as biomarkers. Here, we analyzed suspended particulate matter (SPM) obtained in high depth resolution from a coastal and open ocean site in the eastern tropical South Pacific (ETSP) oxygen deficient zone (ODZ) with the aim of determining possible biological sources of archaeal IPL by comparing their composition by Ultra High Pressure Liquid Chromatography coupled to high resolution mass spectrometry with the archaeal diversity by 16S rRNA gene amplicon sequencing and their abundance by quantitative PCR. Thaumarchaeotal Marine Group I (MGI) closely related to Ca. Nitrosopelagicus and Nitrosopumilus dominated the oxic surface and upper ODZ water together with Marine Euryarchaeota Group II (MGII). High relative abundance of hexose phosphohexose- (HPH) crenarchaeol, the specific biomarker for living Thaumarchaeota, and HPH-GDGT-0, dihexose- (DH) GDGT-3 and -4 were detected in these water masses. Within the ODZ, DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaea) of the Woesearchaeota DHVE-6 group and Marine Euryarchaeota Group III (MGIII) were present together with a higher proportion of archaeol-based IPLs, which were likely made by MGIII, since DPANN archaea are supposedly unable to synthesize their own IPLs and possibly have a symbiotic or parasitic partnership with MGIII. Finally, in deep suboxic/oxic waters a different MGI population occurred with HPH-GDGT-1, -2 and DH-GDGT-0 and -crenarchaeol, indicating that here MGI synthesize membranes with IPLs in a different relative abundance which could be attributed to the different detected population or to an environmental adaptation. Our study sheds light on the complex archaeal community of one of the most prominent ODZs and on the IPL biomarkers they potentially synthesize.
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Affiliation(s)
- Martina Sollai
- Royal Netherlands Institute for Sea Research (NIOZ), Department of Marine Microbiology and Biogeochemistry, Utrecht University, Den Burg, Netherlands
| | - Laura Villanueva
- Royal Netherlands Institute for Sea Research (NIOZ), Department of Marine Microbiology and Biogeochemistry, Utrecht University, Den Burg, Netherlands
| | - Ellen C Hopmans
- Royal Netherlands Institute for Sea Research (NIOZ), Department of Marine Microbiology and Biogeochemistry, Utrecht University, Den Burg, Netherlands
| | - Richard G Keil
- School of Oceanography, University of Washington, Seattle, WA, United States
| | - Jaap S Sinninghe Damsté
- Royal Netherlands Institute for Sea Research (NIOZ), Department of Marine Microbiology and Biogeochemistry, Utrecht University, Den Burg, Netherlands.,Faculty of Geosciences, Utrecht University, Utrecht, Netherlands
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20
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Wemheuer F, von Hoyningen-Huene AJE, Pohlner M, Degenhardt J, Engelen B, Daniel R, Wemheuer B. Primary Production in the Water Column as Major Structuring Element of the Biogeographical Distribution and Function of Archaea in Deep-Sea Sediments of the Central Pacific Ocean. ARCHAEA (VANCOUVER, B.C.) 2019; 2019:3717239. [PMID: 31015799 PMCID: PMC6421829 DOI: 10.1155/2019/3717239] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 12/04/2018] [Accepted: 01/08/2019] [Indexed: 01/08/2023]
Abstract
Information on environmental conditions shaping archaeal communities thriving at the seafloor of the central Pacific Ocean is limited. The present study was conducted to investigate the diversity, composition, and function of both entire and potentially active archaeal communities within Pacific deep-sea sediments. For this purpose, sediment samples were taken along the 180° meridian of the central Pacific Ocean. Community composition and diversity were assessed by Illumina tag sequencing targeting archaeal 16S rRNA genes and transcripts. Archaeal communities were dominated by Candidatus Nitrosopumilus (Thaumarchaeota) and other members of the Nitrosopumilaceae (Thaumarchaeota), but higher relative abundances of the Marine Group II (Euryarchaeota) were observed in the active compared to the entire archaeal community. The composition of the entire and the active archaeal communities was strongly linked to primary production (chlorophyll content), explaining more than 40% of the variance. Furthermore, we found a strong correlation of the entire archaeal community composition to latitude and silicic acid content, while the active community was significantly correlated with primary production and ferric oxide content. We predicted functional profiles from 16S rRNA data to assess archaeal community functions. Latitude was significantly correlated with functional profiles of the entire community, whereas those of the active community were significantly correlated with nitrate and chlorophyll content. The results of the present study provide first insights into benthic archaeal communities in the Pacific Ocean and environmental conditions shaping their diversity, distribution, and function. Additionally, they might serve as a template for further studies investigating archaea colonizing deep-sea sediments.
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Affiliation(s)
- Franziska Wemheuer
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
- Applied Marine and Estuarine Ecology, Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
| | | | - Marion Pohlner
- Paleomicrobiology Group, Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Julius Degenhardt
- Paleomicrobiology Group, Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Bert Engelen
- Paleomicrobiology Group, Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Rolf Daniel
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
| | - Bernd Wemheuer
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
- Centre for Marine Bio-Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
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21
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Abstract
Archaea are ubiquitous and abundant members of the marine plankton. Once thought of as rare organisms found in exotic extremes of temperature, pressure, or salinity, archaea are now known in nearly every marine environment. Though frequently referred to collectively, the planktonic archaea actually comprise four major phylogenetic groups, each with its own distinct physiology and ecology. Only one group-the marine Thaumarchaeota-has cultivated representatives, making marine archaea an attractive focus point for the latest developments in cultivation-independent molecular methods. Here, we review the ecology, physiology, and biogeochemical impact of the four archaeal groups using recent insights from cultures and large-scale environmental sequencing studies. We highlight key gaps in our knowledge about the ecological roles of marine archaea in carbon flow and food web interactions. We emphasize the incredible uncultivated diversity within each of the four groups, suggesting there is much more to be done.
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Affiliation(s)
- Alyson E Santoro
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, California 93106, USA;
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22
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Sollai M, Villanueva L, Hopmans EC, Reichart G, Sinninghe Damsté JS. A combined lipidomic and 16S rRNA gene amplicon sequencing approach reveals archaeal sources of intact polar lipids in the stratified Black Sea water column. GEOBIOLOGY 2019; 17:91-109. [PMID: 30281902 PMCID: PMC6586073 DOI: 10.1111/gbi.12316] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 08/02/2018] [Accepted: 08/21/2018] [Indexed: 05/25/2023]
Abstract
Archaea are important players in marine biogeochemical cycles, and their membrane lipids are useful biomarkers in environmental and geobiological studies. However, many archaeal groups remain uncultured and their lipid composition unknown. Here, we aim to expand the knowledge on archaeal lipid biomarkers and determine the potential sources of those lipids in the water column of the euxinic Black Sea. The archaeal community was evaluated by 16S rRNA gene amplicon sequencing and by quantitative PCR. The archaeal intact polar lipids (IPLs) were investigated by ultra-high-pressure liquid chromatography coupled to high-resolution mass spectrometry. Our study revealed both a complex archaeal community and large changes with water depth in the IPL assemblages. In the oxic/upper suboxic waters (<105 m), the archaeal community was dominated by marine group (MG) I Thaumarchaeota, coinciding with a higher relative abundance of hexose phosphohexose crenarchaeol, a known marker for Thaumarchaeota. In the suboxic waters (80-110 m), MGI Nitrosopumilus sp. dominated and produced predominantly monohexose glycerol dibiphytanyl glycerol tetraethers (GDGTs) and hydroxy-GDGTs. Two clades of MGII Euryarchaeota were present in the oxic and upper suboxic zones in much lower abundances, preventing the detection of their specific IPLs. In the deep sulfidic waters (>110 m), archaea belonging to the DPANN Woesearchaeota, Bathyarchaeota, and ANME-1b clades dominated. Correlation analyses suggest that the IPLs GDGT-0, GDGT-1, and GDGT-2 with two phosphatidylglycerol (PG) head groups and archaeol with a PG, phosphatidylethanolamine, and phosphatidylserine head groups were produced by ANME-1b archaea. Bathyarchaeota represented 55% of the archaea in the deeper part of the euxinic zone and likely produces archaeol with phospho-dihexose and hexose-glucuronic acid head groups.
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Affiliation(s)
- Martina Sollai
- Departments of Marine Microbiology and Biogeochemistry and Ocean SystemsNIOZ Royal Netherlands Institute for Sea Researchand Utrecht UniversityDen BurgThe Netherlands
| | - Laura Villanueva
- Departments of Marine Microbiology and Biogeochemistry and Ocean SystemsNIOZ Royal Netherlands Institute for Sea Researchand Utrecht UniversityDen BurgThe Netherlands
| | - Ellen C. Hopmans
- Departments of Marine Microbiology and Biogeochemistry and Ocean SystemsNIOZ Royal Netherlands Institute for Sea Researchand Utrecht UniversityDen BurgThe Netherlands
| | - Gert‐Jan Reichart
- Departments of Marine Microbiology and Biogeochemistry and Ocean SystemsNIOZ Royal Netherlands Institute for Sea Researchand Utrecht UniversityDen BurgThe Netherlands
- Department of Earth SciencesFaculty of GeosciencesUniversity of UtrechtUtrechtThe Netherlands
| | - Jaap S. Sinninghe Damsté
- Departments of Marine Microbiology and Biogeochemistry and Ocean SystemsNIOZ Royal Netherlands Institute for Sea Researchand Utrecht UniversityDen BurgThe Netherlands
- Department of Earth SciencesFaculty of GeosciencesUniversity of UtrechtUtrechtThe Netherlands
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23
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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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24
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Environmental factors shaping the archaeal community structure and ether lipid distribution in a subtropic river and estuary, China. Appl Microbiol Biotechnol 2017; 102:461-474. [PMID: 29103169 DOI: 10.1007/s00253-017-8595-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 10/11/2017] [Accepted: 10/12/2017] [Indexed: 10/18/2022]
Abstract
Archaea are widespread and abundant in aquatic and terrestrial habitats and play fundamental roles in global biogeochemical cycles. Archaeal lipids, such as isoprenoid glycerol diakyl glycerol tetraethers (iGDGTs), are important biomarkers tracing changes in archaeal community structure and biogeochemical processes in nature. However, the linkage between the archaeal populations and the GDGT distribution in the natural environment is poorly examined, which hindered the application and interpretation of GDGT-based climate or environmental proxies. We addressed this question by investigating changes in archaeal lipid composition and community structure in the context of environmental variables along the subtropical Jiulong River Watershed (JRW) and Jiulong River Estuary (JRE) in southern China. The results showed that both the archaeal cells and the polar GDGTs (P-GDGTs) in the JRW and JRE were mostly autochthonous rather than exogenous input from surrounding soils. We further found that only five (Methanobacteriales, Ca. Bathyarchaeota, Marine Benthic Groups A (MBGA), Marine Benthic Groups B (MBGB), and Marine Benthic Groups D (MBGD)) out of sixteen lineages showed significant impacts on the composition of P-GDGTs, suggesting the significant contribution of those archaea to the changes of P-GDGT compositions. Salinity and total phosphorus (TP) showed significant impact on the distribution of both genetic and P-GDGTs compositions of archaea; whereas, sand and silt contents only had significant impact on the P-GDGTs. MBGD archaea, which occur widely in marine sediments, showed positive correlations with P-TEX86 in the JRW and JRE, suggesting that uncultivated MBGD might also contribute to the variations in TEX86 signals in marine sediments. This study provided insight into the sources of P-GDGTs and the factors controlling their distributions in river-dominated continental margins, which has relevance to applications of GDGT-based proxies in paleoclimate studies.
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25
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Xia X, Guo W, Liu H. Basin Scale Variation on the Composition and Diversity of Archaea in the Pacific Ocean. Front Microbiol 2017; 8:2057. [PMID: 29109713 PMCID: PMC5660102 DOI: 10.3389/fmicb.2017.02057] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 10/06/2017] [Indexed: 01/09/2023] Open
Abstract
The Archaea are a widely distributed group of prokaryotes that inhabit and thrive in many different environments. In the sea, they play key roles in various global biogeochemical processes. Here, in order to investigate the vertical profiles of archaeal community across a large geographic distance, the compositions of archaeal communities in seven seawater columns in the Pacific Ocean were investigated using high throughput 454 pyrosequencing of the 16S rRNA gene. The surface archaeal communities showed lower diversity and greater variability than those in the deeper layers. Two of the major archaeal phyla that displayed different depth preferences were Thaumarchaeota and Euryarchaeota. The majority of Thaumarchaeota belonged to Marine Group I (MGI), which had high relative abundance in deep water. In contrast, Euryarchaeota, which mainly consisted of Marine Group II (MGII) and III (MGIII), were dominant in the surface layer. Compared with MGI and MGII, MGIII were less abundant in seawater and generally absent from the surface water of the subarctic Pacific. In addition, niche separation in the MGI, MGII, and MGIII subgroups was also observed. For example, MGI.C and MGII.A (the major subgroups of MGI and MGII, respectively) displayed a strong negative correlation with each other. The highest level of archaeal diversity was found in the core of an oxygen minimum zone (OMZ) located off Costa Rica, which resulted from the co-occurrence of both anaerobic and aerobic archaea. For example, methanotrophic archaea ANME-2, methanogenic archaea and several sediment origin archaea, such as Marine Benthic Group A (MBGA) and Bathyarchaeota, were all detected at relatively high abundance in the OMZ. Together, our findings indicate that vertical heterogeneities along water columns and latitudinal differentiation in the surface waters are ubiquitous features of archaeal communities in the Pacific Ocean, and the OMZ off Costa Rica is an archaeal biodiversity hot-spot.
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Affiliation(s)
| | | | - Hongbin Liu
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong, Hong Kong
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26
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Cleary DFR, Polónia ARM. Bacterial and archaeal communities inhabiting mussels, sediment and water in Indonesian anchialine lakes. Antonie Van Leeuwenhoek 2017; 111:237-257. [PMID: 29027059 DOI: 10.1007/s10482-017-0944-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 09/13/2017] [Indexed: 11/24/2022]
Abstract
Anchialine lakes are a globally rare and unique ecosystem consisting of saline lakes surrounded by land and isolated from the surrounding marine environment. These lakes host a unique flora and fauna including numerous endemic species. Relatively few studies have, however, studied the prokaryote communities present in these lakes and compared them with the surrounding 'open water' marine environment. In the present study, we used a 16S rRNA gene barcoded pyrosequencing approach to examine prokaryote (Bacteria and Archaea) composition in three distinct biotopes (sediment, water and the mussel Brachidontes sp.) inhabiting four habitats, namely, three marine lakes and the surrounding marine environment of Berau, Indonesia. Biotope and habitat proved significant predictors of variation in bacterial and archaeal composition and higher taxon abundance. Most bacterial sequences belonged to OTUs assigned to the Proteobacteria. Compared to sediment and water, mussels had relatively high abundances of the classes Mollicutes and Epsilonproteobacteria. Most archaeal sequences, in turn, belonged to OTUs assigned to the Crenarchaeota with the relative abundance of crenarchaeotes highest in mussel samples. For both Bacteria and Archaea, the main variation in composition was between water samples on the one hand and sediment and mussel samples on the other. Sediment and mussels also shared much more OTUs than either shared with water. Abundant bacterial OTUs in mussels were related to organisms previously obtained from corals, oysters and the deepsea mussel Bathymodiolus manusensis. Abundant archaeal OTUs in mussels, in contrast, were closely related to organisms previously obtained from sediment.
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Affiliation(s)
- D F R Cleary
- CESAM and Department of Biology, Universidade de Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal.
| | - A R M Polónia
- CESAM and Department of Biology, Universidade de Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
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27
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Han D, Nam SI, Kim JH, Stein R, Niessen F, Joe YJ, Park YH, Hur HG. Inference on Paleoclimate Change Using Microbial Habitat Preference in Arctic Holocene Sediments. Sci Rep 2017; 7:9652. [PMID: 28851886 PMCID: PMC5575242 DOI: 10.1038/s41598-017-08757-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 07/19/2017] [Indexed: 12/11/2022] Open
Abstract
The present study combines data of microbial assemblages with high-resolution paleoceanographic records from Core GC1 recovered in the Chukchi Sea. For the first time, we have demonstrated that microbial habitat preferences are closely linked to Holocene paleoclimate records, and found geological, geochemical, and microbiological evidence for the inference of the sulphate-methane transition zone (SMTZ) in the Chukchi Sea. In Core GC1, the layer of maximum crenarchaeol concentration was localized surrounding the SMTZ. The vertically distributed predominant populations of Gammaproteobacteria and Marine Group II Euryarchaeota (MG-II) were consistent with patterns of the known global SMTZs. MG-II was the most prominent archaeal group, even within the layer of elevated concentrations of crenarchaeol, an archaeal lipid biomarker most commonly used for Marine Group I Thaumarchaeota (MG-I). The distribution of MG-I and MG-II in Core GC1, as opposed to the potential contribution of MG-I to the marine tetraether lipid pool, suggests that the application of glycerol dibiphytanyl glycerol tetraethers (GDGT)-based proxies needs to be carefully considered in the subsurface sediments owing to the many unknowns of crenarchaeol. In conclusion, microbiological profiles integrated with geological records seem to be useful for tracking microbial habitat preference, which reflect climate-triggered changes from the paleodepositional environment.
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Affiliation(s)
- Dukki Han
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology, Gwangju, 61005, Republic of Korea
| | - Seung-Il Nam
- Korea Polar Research Institute, Incheon, 21990, Republic of Korea.
| | - Ji-Hoon Kim
- Petroleum and Marine Research Division, Korea Institute of Geosciences and Mineral Resources, 124 Gwahang-no Yuseong-gu, Daejeon, 34131, Republic of Korea
| | - Ruediger Stein
- Alfred Wegener Institute (AWI) Helmholtz Centre for Polar and Marine Research, Am Alten Hafen 26, Bremerhaven, 27568, Germany.,Department of Geosciences (FB5), Klagenfurter Str. 4, University of Bremen, 28359, Bremen, Germany
| | - Frank Niessen
- Alfred Wegener Institute (AWI) Helmholtz Centre for Polar and Marine Research, Am Alten Hafen 26, Bremerhaven, 27568, Germany
| | - Young Jin Joe
- Korea Polar Research Institute, Incheon, 21990, Republic of Korea
| | - Yu-Hyeon Park
- Division of Earth Environmental System, Pusan National University, Busan, 609-735, Republic of Korea
| | - Hor-Gil Hur
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology, Gwangju, 61005, Republic of Korea.
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28
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Li F, Zheng F, Wang Y, Liu W, Zhang CL. Thermoplasmatales and Methanogens: Potential Association with the Crenarchaeol Production in Chinese Soils. Front Microbiol 2017; 8:1200. [PMID: 28717356 PMCID: PMC5494375 DOI: 10.3389/fmicb.2017.01200] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 06/12/2017] [Indexed: 11/13/2022] Open
Abstract
Crenarchaeol is a unique isoprenoid glycerol dibiphytanyl glycerol tetraether (iGDGT) lipid, which is only identified in cultures of ammonia-oxidizing Thaumarchaeota. However, the taxonomic origins of crenarchaeol have been debated recently. The archaeal populations, other than Thaumarchaeota, may have associations with the production of crenarchaeol in ecosystems characterized by non-thaumarchaeotal microorganisms. To this end, we investigated 47 surface soils from upland and wetland soils and rice fields and another three surface sediments from river banks. The goal was to examine the archaeal community compositions in comparison with patterns of iGDGTs in four fractional forms (intact polar-, core-, monoglycosidic- and diglycosidic-lipid fractions) along gradients of environments. The DistLM analysis identified that Group I.1b Thaumarchaeota were mainly responsible for changes in crenarchaeol in the overall soil samples; however, Thermoplasmatales may also contribute to it. This is further supported by the comparison of crenarchaeol between samples characterized by methanogens, Thermoplasmatales or Group I.1b Thaumarchaeota, which suggests that the former two may contribute to the crenarchaeol pool. Last, when samples containing enhanced abundance of Thermoplasmatales and methanogens were considered, crenarchaeol was observed to correlate positively with Thermoplasmatales and archaeol, respectively. Collectively, our data suggest that the crenarchaeol production is mainly derived from Thaumarchaeota and partly associated with uncultured representatives of Thermoplasmatales and archaeol-producing methanogens in soil environments that may be in favor of their growth. Our finding supports the notion that Thaumarchaeota may not be the sole source of crenarchaeol in the natural environment, which may have implication for the evolution of lipid synthesis among different types of archaea.
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Affiliation(s)
- Fuyan Li
- Department of Ocean Science and Engineering, Southern University of Science and TechnologyShenzhen, China.,College of Life Sciences, Wuhan UniversityWuhan, China.,Division of Geological and Planetary Sciences, California Institute of Technology, PasadenaCA, United States.,State Key Laboratory of Marine Geology, Tongji UniversityShanghai, China
| | - Fengfeng Zheng
- State Key Laboratory of Marine Geology, Tongji UniversityShanghai, China
| | - Yongli Wang
- Key Laboratory of Petroleum Resources Research, Institute of Geology and Geophysics, Chinese Academy of SciencesLanzhou, China
| | - Weiguo Liu
- State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of SciencesXi'an, China.,School of Human Settlement and Civil Engineering, Xi'an Jiaotong UniversityXi'an, China
| | - Chuanlun L Zhang
- Department of Ocean Science and Engineering, Southern University of Science and TechnologyShenzhen, China
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29
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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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30
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Elling FJ, Könneke M, Nicol GW, Stieglmeier M, Bayer B, Spieck E, de la Torre JR, Becker KW, Thomm M, Prosser JI, Herndl GJ, Schleper C, Hinrichs KU. Chemotaxonomic characterisation of the thaumarchaeal lipidome. Environ Microbiol 2017; 19:2681-2700. [PMID: 28419726 DOI: 10.1111/1462-2920.13759] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 04/05/2017] [Accepted: 04/07/2017] [Indexed: 11/28/2022]
Abstract
Thaumarchaeota are globally distributed and abundant microorganisms occurring in diverse habitats and thus represent a major source of archaeal lipids. The scope of lipids as taxonomic markers in microbial ecological studies is limited by the scarcity of comparative data on the membrane lipid composition of cultivated representatives, including the phylum Thaumarchaeota. Here, we comprehensively describe the core and intact polar lipid (IPL) inventory of ten ammonia-oxidising thaumarchaeal cultures representing all four characterized phylogenetic clades. IPLs of these thaumarchaeal strains are generally similar and consist of membrane-spanning, glycerol dibiphytanyl glycerol tetraethers with monoglycosyl, diglycosyl, phosphohexose and hexose-phosphohexose headgroups. However, the relative abundances of these IPLs and their core lipid compositions differ systematically between the phylogenetic subgroups, indicating high potential for chemotaxonomic distinction of thaumarchaeal clades. Comparative lipidomic analyses of 19 euryarchaeal and crenarchaeal strains suggested that the lipid methoxy archaeol is synthesized exclusively by Thaumarchaeota and may thus represent a diagnostic lipid biomarker for this phylum. The unprecedented diversity of the thaumarchaeal lipidome with 118 different lipids suggests that membrane lipid composition and adaptation mechanisms in Thaumarchaeota are more complex than previously thought and include unique lipids with as yet unresolved properties.
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Affiliation(s)
- Felix J Elling
- Organic Geochemistry Group, MARUM - Center for Marine Environmental Sciences & Department of Geosciences, University of Bremen, Bremen, 28359, Germany
| | - Martin Könneke
- Organic Geochemistry Group, MARUM - Center for Marine Environmental Sciences & Department of Geosciences, University of Bremen, Bremen, 28359, Germany.,Marine Archaea Group, MARUM - Center for Marine Environmental Sciences & Department of Geosciences, University of Bremen, Bremen, 28359, Germany
| | - Graeme W Nicol
- Environmental Microbial Genomics, Laboratoire Ampère, École Centrale de Lyon, Université de Lyon, 69134, Ecully, France
| | | | - Barbara Bayer
- Limnology and Bio-Oceanography, Center of Ecology, University of Vienna, Vienna, 1090, Austria
| | - Eva Spieck
- Biocenter Klein Flottbek, Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, 22609, Germany
| | - José R de la Torre
- Department of Biology, San Francisco State University, San Francisco, CA, USA
| | - Kevin W Becker
- Organic Geochemistry Group, MARUM - Center for Marine Environmental Sciences & Department of Geosciences, University of Bremen, Bremen, 28359, Germany
| | - Michael Thomm
- Lehrstuhl für Mikrobiologie und Archaeenzentrum, Universität Regensburg, Regensburg, 93053, Germany
| | - James I Prosser
- Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, Aberdeen, AB24 3UU, UK
| | - Gerhard J Herndl
- Limnology and Bio-Oceanography, Center of Ecology, University of Vienna, Vienna, 1090, Austria.,Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Utrecht University, 1790 AB Den Burg, Texel, The Netherlands
| | | | - Kai-Uwe Hinrichs
- Organic Geochemistry Group, MARUM - Center for Marine Environmental Sciences & Department of Geosciences, University of Bremen, Bremen, 28359, Germany
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31
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Philosof A, Yutin N, Flores-Uribe J, Sharon I, Koonin EV, Béjà O. Novel Abundant Oceanic Viruses of Uncultured Marine Group II Euryarchaeota. Curr Biol 2017; 27:1362-1368. [PMID: 28457865 PMCID: PMC5434244 DOI: 10.1016/j.cub.2017.03.052] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2017] [Revised: 03/09/2017] [Accepted: 03/21/2017] [Indexed: 12/16/2022]
Abstract
Marine group II Euryarchaeota (MG-II) are among the most abundant microbes in oceanic surface waters [1, 2, 3, 4]. So far, however, representatives of MG-II have not been cultivated, and no viruses infecting these organisms have been described. Here, we present complete genomes for three distinct groups of viruses assembled from metagenomic sequence datasets highly enriched for MG-II. These novel viruses, which we denote magroviruses, possess double-stranded DNA genomes of 65 to 100 kilobases in size that encode a structural module characteristic of head-tailed viruses and, unusually for archaeal and bacterial viruses, a nearly complete replication apparatus of apparent archaeal origin. The newly identified magroviruses are widespread and abundant and therefore are likely to be major ecological agents. A novel viral group, magroviruses, likely infects marine group II archaea Magroviruses are highly abundant in oceanic surface waters worldwide Magroviruses have linear, double-stranded DNA genomes of about 100 kilobases Magroviruses encode a near complete replication apparatus of apparent archaeal origin
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Affiliation(s)
- Alon Philosof
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa 32000, Israel.
| | - Natalya Yutin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - José Flores-Uribe
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa 32000, Israel
| | - Itai Sharon
- Migal Galilee Research Institute, Kiryat Shmona 11016, Israel; Tel Hai College, Upper Galilee 12210, Israel
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Oded Béjà
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa 32000, Israel.
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32
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Gomez-Saez GV, Pop Ristova P, Sievert SM, Elvert M, Hinrichs KU, Bühring SI. Relative Importance of Chemoautotrophy for Primary Production in a Light Exposed Marine Shallow Hydrothermal System. Front Microbiol 2017; 8:702. [PMID: 28484442 PMCID: PMC5399606 DOI: 10.3389/fmicb.2017.00702] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 04/05/2017] [Indexed: 01/09/2023] Open
Abstract
The unique geochemistry of marine shallow-water hydrothermal systems promotes the establishment of diverse microbial communities with a range of metabolic pathways. In contrast to deep-sea vents, shallow-water vents not only support chemosynthesis, but also phototrophic primary production due to the availability of light. However, comprehensive studies targeting the predominant biogeochemical processes are rare, and consequently a holistic understanding of the functioning of these ecosystems is currently lacking. To this end, we combined stable isotope probing of lipid biomarkers with an analysis of the bacterial communities to investigate if chemoautotrophy, in parallel to photoautotrophy, plays an important role in autotrophic carbon fixation and to identify the key players. The study was carried out at a marine shallow-water hydrothermal system located at 5 m water depth off Dominica Island (Lesser Antilles), characterized by up to 55°C warm hydrothermal fluids that contain high amounts of dissolved Fe2+. Analysis of the bacterial diversity revealed Anaerolineae of the Chloroflexi as the most abundant bacterial class. Furthermore, the presence of key players involved in iron cycling generally known from deep-sea hydrothermal vents (e.g., Zetaproteobacteria and Geothermobacter), supported the importance of iron-driven redox processes in this hydrothermal system. Uptake of 13C-bicarbonate into bacterial fatty acids under light and dark conditions revealed active photo- and chemoautotrophic communities, with chemoautotrophy accounting for up to 65% of the observed autotrophic carbon fixation. Relatively increased 13C-incorporation in the dark allowed the classification of aiC15:0, C15:0, and iC16:0 as potential lipid biomarkers for bacterial chemoautotrophy in this ecosystem. Highest total 13C-incorporation into fatty acids took place at the sediment surface, but chemosynthesis was found to be active down to 8 cm sediment depth. In conclusion, this study highlights the relative importance of chemoautotrophy compared to photoautotrophy in a shallow-water hydrothermal system, emphasizing chemosynthesis as a prominent process for biomass production in marine coastal environments influenced by hydrothermalism.
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Affiliation(s)
- Gonzalo V Gomez-Saez
- Hydrothermal Geomicrobiology Group, MARUM - Center for Marine Environmental Sciences, University of BremenBremen, Germany
| | - Petra Pop Ristova
- Hydrothermal Geomicrobiology Group, MARUM - Center for Marine Environmental Sciences, University of BremenBremen, Germany
| | - Stefan M Sievert
- Biology Department, Woods Hole Oceanographic Institution, Woods HoleMA, USA
| | - Marcus Elvert
- Organic Geochemistry Group, MARUM - Center for Marine Environmental Sciences and Department of Geosciences, University of BremenBremen, Germany
| | - Kai-Uwe Hinrichs
- Organic Geochemistry Group, MARUM - Center for Marine Environmental Sciences and Department of Geosciences, University of BremenBremen, Germany
| | - Solveig I Bühring
- Hydrothermal Geomicrobiology Group, MARUM - Center for Marine Environmental Sciences, University of BremenBremen, Germany
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33
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Rush D, Sinninghe Damsté JS. Lipids as paleomarkers to constrain the marine nitrogen cycle. Environ Microbiol 2017; 19:2119-2132. [PMID: 28142226 PMCID: PMC5516240 DOI: 10.1111/1462-2920.13682] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 01/24/2017] [Accepted: 01/25/2017] [Indexed: 11/30/2022]
Abstract
Global climate is, in part, regulated by the effect of microbial processes on biogeochemical cycling. The nitrogen cycle, in particular, is driven by microorganisms responsible for the fixation and loss of nitrogen, and the reduction‐oxidation transformations of bio‐available nitrogen. Within marine systems, nitrogen availability is often the limiting factor in the growth of autotrophic organisms, intrinsically linking the nitrogen and carbon cycles. In order to elucidate the state of these cycles in the past, and help envisage present and future variability, it is essential to understand the specific microbial processes responsible for transforming bio‐available nitrogen species. As most microorganisms are soft‐bodied and seldom leave behind physical fossils in the sedimentary record, recalcitrant lipid biomarkers are used to unravel microbial processes in the geological past. This review emphasises the recent advances in marine nitrogen cycle lipid biomarkers, underlines the missing links still needed to fully elucidate past shifts in this biogeochemically‐important cycle, and provides examples of biomarker applications in the geological past.
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Affiliation(s)
- Darci Rush
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, and Utrecht University, Den Burg, P.O. Box 59 1790 AB, The Netherlands.,School of Civil Engineering and Geosciences, Newcastle University, Newcastle-upon-Tyne, NE1 7RU, United Kingdom
| | - Jaap S Sinninghe Damsté
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, and Utrecht University, Den Burg, P.O. Box 59 1790 AB, The Netherlands.,Department of Earth Sciences, Faculty of Geosciences, Utrecht University, TA Utrecht, P.O. Box 80.121, 3508, The Netherlands
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Unusual Butane- and Pentanetriol-Based Tetraether Lipids in Methanomassiliicoccus luminyensis, a Representative of the Seventh Order of Methanogens. Appl Environ Microbiol 2016; 82:4505-4516. [PMID: 27208108 DOI: 10.1128/aem.00772-16] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 05/10/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED A new clade of archaea has recently been proposed to constitute the seventh methanogenic order, the Methanomassiliicoccales, which is related to the Thermoplasmatales and the uncultivated archaeal clades deep-sea hydrothermal vent Euryarchaeota group 2 and marine group II Euryarchaeota but only distantly related to other methanogens. In this study, we investigated the membrane lipid composition of Methanomassiliicoccus luminyensis, the sole cultured representative of this seventh order. The lipid inventory of M. luminyensis comprises a unique assemblage of novel lipids as well as lipids otherwise typical for thermophilic, methanogenic, or halophilic archaea. For instance, glycerol sesterpanyl-phytanyl diether core lipids found mainly in halophilic archaea were detected, and so were compounds bearing either heptose or methoxylated glycosidic head groups, neither of which have been reported so far for other archaea. The absence of quinones or methanophenazines is consistent with a biochemistry of methanogenesis different from that of the methanophenazine-containing methylotrophic methanogens. The most distinctive characteristic of the membrane lipid composition of M. luminyensis, however, is the presence of tetraether lipids in which one glycerol backbone is replaced by either butane- or pentanetriol, i.e., lipids recently discovered in marine sediments. Butanetriol dibiphytanyl glycerol tetraether (BDGT) constitutes the most abundant core lipid type (>50% relative abundance) in M. luminyensis We have thus identified a source for these unusual orphan lipids. The complementary analysis of diverse marine sediment samples showed that BDGTs are widespread in anoxic layers, suggesting an environmental significance of Methanomassiliicoccales and/or related BDGT producers beyond gastrointestinal tracts. IMPORTANCE Cellular membranes of members of all three domains of life, Archaea, Bacteria, and Eukarya, are largely formed by lipids in which glycerol serves as backbone for the hydrophobic alkyl chains. Recently, however, archaeal tetraether lipids with either butanetriol or pentanetriol as a backbone were identified in marine sediments and attributed to uncultured sediment-dwelling archaea. Here we show that the butanetriol-based dibiphytanyl tetraethers constitute the major lipids in Methanomassiliicoccus luminyensis, currently the only isolate of the novel seventh order of methanogens. Given the absence of these lipids in a large set of archaeal isolates, these compounds may be diagnostic for the Methanomassiliicoccales and/or closely related archaea.
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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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36
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Li M, Baker BJ, Anantharaman K, Jain S, Breier JA, Dick GJ. Genomic and transcriptomic evidence for scavenging of diverse organic compounds by widespread deep-sea archaea. Nat Commun 2015; 6:8933. [PMID: 26573375 PMCID: PMC4660358 DOI: 10.1038/ncomms9933] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 10/14/2015] [Indexed: 12/31/2022] Open
Abstract
Microbial activity is one of the most important processes to mediate the flux of organic carbon from the ocean surface to the seafloor. However, little is known about the microorganisms that underpin this key step of the global carbon cycle in the deep oceans. Here we present genomic and transcriptomic evidence that five ubiquitous archaeal groups actively use proteins, carbohydrates, fatty acids and lipids as sources of carbon and energy at depths ranging from 800 to 4,950 m in hydrothermal vent plumes and pelagic background seawater across three different ocean basins. Genome-enabled metabolic reconstructions and gene expression patterns show that these marine archaea are motile heterotrophs with extensive mechanisms for scavenging organic matter. Our results shed light on the ecological and physiological properties of ubiquitous marine archaea and highlight their versatile metabolic strategies in deep oceans that might play a critical role in global carbon cycling.
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Affiliation(s)
- Meng Li
- Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, Michigan 48109, USA.,Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
| | - Brett J Baker
- Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, Michigan 48109, USA.,Department of Marine Science, University of Texas Austin, Marine Science Institute, 750 Channel View Drive, Port Aransas, Texas 78373, USA
| | - Karthik Anantharaman
- Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Sunit Jain
- Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - John A Breier
- Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, USA.,University of Texas Rio Grande Valley, Brownsville, Texas 78520, USA
| | - Gregory J Dick
- Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, Michigan 48109, USA.,Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109, USA.,Center of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, USA
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Zhang CL, Xie W, Martin-Cuadrado AB, Rodriguez-Valera F. Marine Group II Archaea, potentially important players in the global ocean carbon cycle. Front Microbiol 2015; 6:1108. [PMID: 26528260 PMCID: PMC4602124 DOI: 10.3389/fmicb.2015.01108] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 09/25/2015] [Indexed: 11/26/2022] Open
Abstract
Marine Group (MG) I (currently known as Thaumarchaeota) and MG II Archaea were first reported over two decades ago. While significant progress has been made on MG I microbiology and ecology, the progress on MG II has been noticeably slower. The common understanding is that while MG I mainly function as chemolithoautotrophs and occur predominantly in the deep ocean, MG II reside mostly in the photic zone and live heterotrophically. Studies to date have shown that MG II are abundant in the marine aquatic environment and display great seasonal and spatial variation and phylogenetic diversity. They also show unique patterns of organic carbon degradation and their energy requirements may be augmented by light in the photic zone. However, no pure culture of MG II has been obtained and thus their precise ecological role remains elusive.
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Affiliation(s)
- Chuanlun L Zhang
- State Key Laboratory of Marine Geology, Tongji University Shanghai, China
| | - Wei Xie
- State Key Laboratory of Marine Geology, Tongji University Shanghai, China
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38
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Open Questions on the Origin of Eukaryotes. Trends Ecol Evol 2015; 30:697-708. [PMID: 26455774 DOI: 10.1016/j.tree.2015.09.005] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 09/03/2015] [Accepted: 09/04/2015] [Indexed: 12/21/2022]
Abstract
Despite recent progress, the origin of the eukaryotic cell remains enigmatic. It is now known that the last eukaryotic common ancestor was complex and that endosymbiosis played a crucial role in eukaryogenesis at least via the acquisition of the alphaproteobacterial ancestor of mitochondria. However, the nature of the mitochondrial host is controversial, although the recent discovery of an archaeal lineage phylogenetically close to eukaryotes reinforces models proposing archaea-derived hosts. We argue that, in addition to improved phylogenomic analyses with more comprehensive taxon sampling to pinpoint the closest prokaryotic relatives of eukaryotes, determining plausible mechanisms and selective forces at the origin of key eukaryotic features, such as the nucleus or the bacterial-like eukaryotic membrane system, is essential to constrain existing models.
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Tierney JE, Ummenhofer CC, deMenocal PB. Past and future rainfall in the Horn of Africa. SCIENCE ADVANCES 2015; 1:e1500682. [PMID: 26601306 PMCID: PMC4646820 DOI: 10.1126/sciadv.1500682] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 07/20/2015] [Indexed: 05/04/2023]
Abstract
The recent decline in Horn of Africa rainfall during the March-May "long rains" season has fomented drought and famine, threatening food security in an already vulnerable region. Some attribute this decline to anthropogenic forcing, whereas others maintain that it is a feature of internal climate variability. We show that the rate of drying in the Horn of Africa during the 20th century is unusual in the context of the last 2000 years, is synchronous with recent global and regional warming, and therefore may have an anthropogenic component. In contrast to 20th century drying, climate models predict that the Horn of Africa will become wetter as global temperatures rise. The projected increase in rainfall mainly occurs during the September-November "short rains" season, in response to large-scale weakening of the Walker circulation. Most of the models overestimate short rains precipitation while underestimating long rains precipitation, causing the Walker circulation response to unrealistically dominate the annual mean. Our results highlight the need for accurate simulation of the seasonal cycle and an improved understanding of the dynamics of the long rains season to predict future rainfall in the Horn of Africa.
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Affiliation(s)
- Jessica E. Tierney
- Department of Geosciences, The University of Arizona, Tucson, AZ 85721, USA
- Woods Hole Oceanographic Institution, Woods Hole, MA 02540, USA
- Corresponding author. E-mail:
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40
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Confounding effects of oxygen and temperature on the TEX86 signature of marine Thaumarchaeota. Proc Natl Acad Sci U S A 2015; 112:10979-84. [PMID: 26283385 DOI: 10.1073/pnas.1501568112] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Marine ammonia-oxidizing archaea (AOA) are among the most abundant of marine microorganisms, spanning nearly the entire water column of diverse oceanic provinces. Historical patterns of abundance are preserved in sediments in the form of their distinctive glycerol dibiphytanyl glycerol tetraether (GDGT) membrane lipids. The correlation between the composition of GDGTs in surface sediment and the overlying annual average sea surface temperature forms the basis for a paleotemperature proxy (TEX86) that is used to reconstruct surface ocean temperature as far back as the Middle Jurassic. However, mounting evidence suggests that factors other than temperature could also play an important role in determining GDGT distributions. We here use a study set of four marine AOA isolates to demonstrate that these closely related strains generate different TEX86-temperature relationships and that oxygen (O2) concentration is at least as important as temperature in controlling TEX86 values in culture. All of the four strains characterized showed a unique membrane compositional response to temperature, with TEX86-inferred temperatures varying as much as 12 °C from the incubation temperatures. In addition, both linear and nonlinear TEX86-temperature relationships were characteristic of individual strains. Increasing relative abundance of GDGT-2 and GDGT-3 with increasing O2 limitation, at the expense of GDGT-1, led to significant elevations in TEX86-derived temperature. Although the adaptive significance of GDGT compositional changes in response to both temperature and O2 is unclear, this observation necessitates a reassessment of archaeal lipid-based paleotemperature proxies, particularly in records that span low-oxygen events or underlie oxygen minimum zones.
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41
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Guo J, Wang Q, Wang X, Wang F, Yao J, Zhu H. Horizontal gene transfer in an acid mine drainage microbial community. BMC Genomics 2015; 16:496. [PMID: 26141154 PMCID: PMC4490635 DOI: 10.1186/s12864-015-1720-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Accepted: 06/25/2015] [Indexed: 01/17/2023] Open
Abstract
Background Horizontal gene transfer (HGT) has been widely identified in complete prokaryotic genomes. However, the roles of HGT among members of a microbial community and in evolution remain largely unknown. With the emergence of metagenomics, it is nontrivial to investigate such horizontal flow of genetic materials among members in a microbial community from the natural environment. Because of the lack of suitable methods for metagenomics gene transfer detection, microorganisms from a low-complexity community acid mine drainage (AMD) with near-complete genomes were used to detect possible gene transfer events and suggest the biological significance. Results Using the annotation of coding regions by the current tools, a phylogenetic approach, and an approximately unbiased test, we found that HGTs in AMD organisms are not rare, and we predicted 119 putative transferred genes. Among them, 14 HGT events were determined to be transfer events among the AMD members. Further analysis of the 14 transferred genes revealed that the HGT events affected the functional evolution of archaea or bacteria in AMD, and it probably shaped the community structure, such as the dominance of G-plasma in archaea in AMD through HGT. Conclusions Our study provides a novel insight into HGT events among microorganisms in natural communities. The interconnectedness between HGT and community evolution is essential to understand microbial community formation and development. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1720-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jiangtao Guo
- State Key Laboratory for Turbulence and Complex Systems and Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, 100871, China. .,Center for Quantitative Biology, Peking University, Beijing, 100871, China.
| | - Qi Wang
- State Key Laboratory for Turbulence and Complex Systems and Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, 100871, China. .,Center for Quantitative Biology, Peking University, Beijing, 100871, China.
| | - Xiaoqi Wang
- State Key Laboratory for Turbulence and Complex Systems and Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, 100871, China. .,Center for Quantitative Biology, Peking University, Beijing, 100871, China.
| | - Fumeng Wang
- State Key Laboratory for Turbulence and Complex Systems and Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, 100871, China. .,Center for Quantitative Biology, Peking University, Beijing, 100871, China.
| | - Jinxian Yao
- School of Life Sciences, Peking University, Beijing, 100871, China.
| | - Huaiqiu Zhu
- State Key Laboratory for Turbulence and Complex Systems and Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, 100871, China. .,Center for Quantitative Biology, Peking University, Beijing, 100871, China.
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42
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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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43
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López-García P, Zivanovic Y, Deschamps P, Moreira D. Bacterial gene import and mesophilic adaptation in archaea. Nat Rev Microbiol 2015; 13:447-56. [PMID: 26075362 DOI: 10.1038/nrmicro3485] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
It is widely believed that the archaeal ancestor was hyperthermophilic, but during archaeal evolution, several lineages - including haloarchaea and their sister methanogens, the Thaumarchaeota, and the uncultured Marine Group II and Marine Group III Euryarchaeota (MGII/III) - independently adapted to lower temperatures. Recent phylogenomic studies suggest that the ancestors of these lineages were recipients of massive horizontal gene transfer from bacteria. Many of the acquired genes, which are often involved in metabolism and cell envelope biogenesis, were convergently acquired by distant mesophilic archaea. In this Opinion article, we explore the intriguing hypothesis that the import of these bacterial genes was crucial for the adaptation of archaea to mesophilic lifestyles.
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Affiliation(s)
- Purificación López-García
- Unité d'Ecologie, Systématique et Evolution, Centre National de la Recherche Scientifique UMR 8079, Université Paris-Sud, 91405 Orsay, France
| | - Yvan Zivanovic
- Institut de Génétique et Microbiologie, Centre National de la Recherche Scientifique UMR 8621, Université Paris-Sud, 91405 Orsay, France
| | - Philippe Deschamps
- Unité d'Ecologie, Systématique et Evolution, Centre National de la Recherche Scientifique UMR 8079, Université Paris-Sud, 91405 Orsay, France
| | - David Moreira
- Unité d'Ecologie, Systématique et Evolution, Centre National de la Recherche Scientifique UMR 8079, Université Paris-Sud, 91405 Orsay, France
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Fontanez KM, Eppley JM, Samo TJ, Karl DM, DeLong EF. Microbial community structure and function on sinking particles in the North Pacific Subtropical Gyre. Front Microbiol 2015; 6:469. [PMID: 26042105 PMCID: PMC4436931 DOI: 10.3389/fmicb.2015.00469] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 04/29/2015] [Indexed: 01/20/2023] Open
Abstract
Sinking particles mediate the transport of carbon and energy to the deep-sea, yet the specific microbes associated with sedimenting particles in the ocean's interior remain largely uncharacterized. In this study, we used particle interceptor traps (PITs) to assess the nature of particle-associated microbial communities collected at a variety of depths in the North Pacific Subtropical Gyre. Comparative metagenomics was used to assess differences in microbial taxa and functional gene repertoires in PITs containing a preservative (poisoned traps) compared to preservative-free traps where growth was allowed to continue in situ (live traps). Live trap microbial communities shared taxonomic and functional similarities with bacteria previously reported to be enriched in dissolved organic matter (DOM) microcosms (e.g., Alteromonas and Methylophaga), in addition to other particle and eukaryote-associated bacteria (e.g., Flavobacteriales and Pseudoalteromonas). Poisoned trap microbial assemblages were enriched in Vibrio and Campylobacterales likely associated with eukaryotic surfaces and intestinal tracts as symbionts, pathogens, or saprophytes. The functional gene content of microbial assemblages in poisoned traps included a variety of genes involved in virulence, anaerobic metabolism, attachment to chitinaceaous surfaces, and chitin degradation. The presence of chitinaceaous surfaces was also accompanied by the co-existence of bacteria which encoded the capacity to attach to, transport and metabolize chitin and its derivatives. Distinctly different microbial assemblages predominated in live traps, which were largely represented by copiotrophs and eukaryote-associated bacterial communities. Predominant sediment trap-assocaited eukaryotic phyla included Dinoflagellata, Metazoa (mostly copepods), Protalveolata, Retaria, and Stramenopiles. These data indicate the central role of eukaryotic taxa in structuring sinking particle microbial assemblages, as well as the rapid responses of indigenous microbial species in the degradation of marine particulate organic matter (POM) in situ in the ocean's interior.
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Affiliation(s)
- Kristina M Fontanez
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology Cambridge, MA, USA
| | - John M Eppley
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology Cambridge, MA, USA ; Department of Oceanography, School of Ocean and Earth Science and Technology, University of Hawaii Honolulu, HI, USA ; Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawaii Honolulu, HI, USA
| | - Ty J Samo
- Department of Oceanography, School of Ocean and Earth Science and Technology, University of Hawaii Honolulu, HI, USA ; Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawaii Honolulu, HI, USA ; Lawrence Livermore National Laboratory, Nuclear and Chemical Sciences Division Livermore, CA, USA
| | - David M Karl
- Department of Oceanography, School of Ocean and Earth Science and Technology, University of Hawaii Honolulu, HI, USA ; Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawaii Honolulu, HI, USA
| | - Edward F DeLong
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology Cambridge, MA, USA ; Department of Oceanography, School of Ocean and Earth Science and Technology, University of Hawaii Honolulu, HI, USA ; Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawaii Honolulu, HI, USA
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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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46
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Are Marine Group II Euryarchaeota significant contributors to tetraether lipids in the ocean? Proc Natl Acad Sci U S A 2014; 111:E4285. [PMID: 25239232 DOI: 10.1073/pnas.1416176111] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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47
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Reply to Schouten et al.: Marine Group II planktonic Euryarchaeota are significant contributors to tetraether lipids in the ocean. Proc Natl Acad Sci U S A 2014; 111:E4286. [PMID: 25239231 DOI: 10.1073/pnas.1416736111] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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