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Gonzalez-Nayeck AC, Grim SL, Waldbauer J, Dick GJ, Pearson A. Isotopic Signatures of Carbon Transfer in a Proterozoic Analogue Microbial Mat. Appl Environ Microbiol 2023; 89:e0187022. [PMID: 37093010 PMCID: PMC10231192 DOI: 10.1128/aem.01870-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 03/24/2023] [Indexed: 04/25/2023] Open
Abstract
Modern microbial mats are potential analogues for Proterozoic ecosystems, yet only a few studies have characterized mats under low-oxygen conditions that are relevant to Proterozoic environments. Here, we use protein-stable isotope fingerprinting (P-SIF) to determine the protein carbon isotope (δ13C) values of autotrophic, heterotrophic, and mixotrophic organisms in a benthic microbial mat from the low-oxygen Middle Island Sinkhole, Lake Huron, USA (MIS). We also measure the δ13C values of the sugar moieties of exopolysaccharides (EPS) within the mat to explore the relationships between cyanobacterial exudates and heterotrophic anabolic carbon uptake. Our results show that Cyanobacteria (autotrophs) are 13C-depleted, relative to sulfate-reducing bacteria (heterotrophs), and 13C-enriched, relative to sulfur oxidizing bacteria (autotrophs or mixotrophs). We also find that the pentose moieties of EPS are systematically enriched in 13C, relative to the hexose moieties of EPS. We hypothesize that these isotopic patterns reflect cyanobacterial metabolic pathways, particularly phosphoketolase, that are relatively more active in low-oxygen mat environments, rather than oxygenated mat environments. This results in isotopically more heterogeneous C sources in low-oxygen mats. While this might partially explain the isotopic variability observed in Proterozoic mat facies, further work is necessary to systematically characterize the isotopic fractionations that are associated with the synthesis of cyanobacterial exudates. IMPORTANCE The δ13C compositions of heterotrophic microorganisms are dictated by the δ13C compositions of their organic carbon sources. In both modern and ancient photosynthetic microbial mats, photosynthetic exudates are the most likely source of organic carbon for heterotrophs. We measured the δ13C values of autotrophic, heterotrophic, and mixotrophic bacteria as well as the δ13C value of the most abundant photosynthetic exudate (exopolysaccharide) in a modern analogue for a Proterozoic environment. Given these data, future studies will be better equipped to estimate the most likely carbon source for heterotrophs in both modern environments as well as in Proterozoic environments preserved in the rock record.
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Affiliation(s)
- Ana C. Gonzalez-Nayeck
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, Massachusetts, USA
| | - Sharon L. Grim
- Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, Michigan, USA
| | - Jacob Waldbauer
- Department of the Geophysical Sciences, University of Chicago, Chicago, Illinois, USA
| | - Gregory J. Dick
- Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, Michigan, USA
| | - Ann Pearson
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, Massachusetts, USA
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Gonzalez-Nayeck AC, Mohr W, Tang T, Sattin S, Parenteau MN, Jahnke LL, Pearson A. Absence of canonical trophic levels in a microbial mat. GEOBIOLOGY 2022; 20:726-740. [PMID: 35831948 DOI: 10.1111/gbi.12511] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 06/16/2022] [Accepted: 06/26/2022] [Indexed: 06/15/2023]
Abstract
In modern ecosystems, the carbon stable isotope (δ13 C) ratios of consumers generally conform to the principle "you are what you eat, +1‰." However, this metric may not apply to microbial mat systems where diverse communities, using a variety of carbon substrates via multiple assimilation pathways, live in close physical association and phagocytosis is minimal or absent. To interpret the δ13 C record of the Proterozoic and early Paleozoic, when mat-based productivity likely was widespread, it is necessary to understand how a microbially driven producer-consumer structure affects the δ13 C compositions of biomass and preservable lipids. Protein Stable Isotope Fingerprinting (P-SIF) is a recently developed method that allows measurement of the δ13 C values of whole proteins, separated from environmental samples and identified taxonomically via proteomics. Here, we use P-SIF to determine the trophic relationships in a microbial mat sample from Chocolate Pots Hot Springs, Yellowstone National Park (YNP), USA. In this mat, proteins from heterotrophic bacteria are indistinguishable from cyanobacterial proteins, indicating that "you are what you eat, +1‰" is not applicable. To explain this finding, we hypothesize that sugar production and consumption dominate the net ecosystem metabolism, yielding a community in which producers and consumers share primary photosynthate as a common resource. This idea was validated by confirming that glucose moieties in exopolysaccharide were equal in δ13 C composition to both cyanobacterial and heterotrophic proteins, and by confirming that highly 13 C-depleted fatty acids (FAs) of Cyanobacteria dominate the lipid pool, consistent with flux-balance expectations for systems that overproduce primary photosynthate. Overall, the results confirm that the δ13 C composition of microbial biomass and lipids is tied to specific metabolites, rather than to autotrophy versus heterotrophy or to individual trophic levels. Therefore, we suggest that aerobic microbial heterotrophy is simply a case of "you are what you eat."
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Affiliation(s)
- Ana C Gonzalez-Nayeck
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, Massachusetts, USA
| | - Wiebke Mohr
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, Massachusetts, USA
- Max-Planck-Institute for Marine Microbiology, Bremen, Germany
| | - Tiantian Tang
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, Massachusetts, USA
- State Key Laboratory of Marine Environmental Science (Xiamen University), Xiamen, Fujian, China
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, China
| | - Sarah Sattin
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, Massachusetts, USA
| | | | - Linda L Jahnke
- NASA Ames Research Center, Moffett Field, California, USA
| | - Ann Pearson
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, Massachusetts, USA
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Abstract
Compound-specific isotope analysis encompasses a variety of methods for examining the naturally occurring isotope ratios of individual organic molecules. In marine environments, these methods have revealed heterogeneous sources and alteration processes that underlie the more commonly measured isotope ratios of bulk materials, as well as revealing signatures of marine metabolisms that may otherwise be impossible to isolate. Recently, compound-specific isotopic techniques have improved the reconstruction of metazoan diets and revealed a new potential of metazoan biomass as an archive of paleoecological information. Despite six decades of practice and a diversity of applications, the use of compound-specific isotopic techniques remains uncommon in marine studies. This review examines broad theoretical motivations behind compound-specific isotopic approaches, some applications to studies of marine carbon cycling and trophic relationships, and methodological limitations. In coming years, improvements in analytical efficiency and molecular or intramolecular specificity may transform compound-specific isotope analysis into a tool that can be applied more broadly and help to build global oceanographic data sets.
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Affiliation(s)
- Hilary G Close
- Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, Florida 33149, USA;
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4
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Kleiner M, Dong X, Hinzke T, Wippler J, Thorson E, Mayer B, Strous M. Metaproteomics method to determine carbon sources and assimilation pathways of species in microbial communities. Proc Natl Acad Sci U S A 2018; 115:E5576-E5584. [PMID: 29844191 PMCID: PMC6004456 DOI: 10.1073/pnas.1722325115] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Measurements of stable carbon isotope ratios (δ13C) are widely used in biology to address questions regarding food sources and metabolic pathways used by organisms. The analysis of these so-called stable isotope fingerprints (SIFs) for microbes involved in biogeochemical cycling and microbiota of plants and animals has led to major discoveries in environmental microbiology. Currently, obtaining SIFs for microbial communities is challenging as the available methods either only provide low taxonomic resolution, such as the use of lipid biomarkers, or are limited in throughput, such as nanoscale secondary ion MS imaging of single cells. Here we present "direct protein-SIF" and the Calis-p software package (https://sourceforge.net/projects/calis-p/), which enable high-throughput measurements of accurate δ13C values for individual species within a microbial community. We benchmark the method using 20 pure culture microorganisms and show that the method reproducibly provides SIF values consistent with gold-standard bulk measurements performed with an isotope ratio mass spectrometer. Using mock community samples, we demonstrate that SIF values can also be obtained for individual species within a microbial community. Finally, a case study of an obligate bacteria-animal symbiosis shows that direct protein-SIF confirms previous physiological hypotheses and can provide unexpected insights into the symbionts' metabolism. This confirms the usefulness of this approach to accurately determine δ13C values for different species in microbial community samples.
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Affiliation(s)
- Manuel Kleiner
- Department of Geoscience, University of Calgary, Calgary, AB, Canada T2N 1N4;
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695
| | - Xiaoli Dong
- Department of Geoscience, University of Calgary, Calgary, AB, Canada T2N 1N4
| | - Tjorven Hinzke
- Department of Geoscience, University of Calgary, Calgary, AB, Canada T2N 1N4
- Department of Pharmaceutical Biotechnology, Institute of Pharmacy, University of Greifswald, 17489 Greifswald, Germany
- Institute of Marine Biotechnology, 17489 Greifswald, Germany
| | - Juliane Wippler
- Symbiosis Department, Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
| | - Erin Thorson
- Department of Geoscience, University of Calgary, Calgary, AB, Canada T2N 1N4
| | - Bernhard Mayer
- Department of Geoscience, University of Calgary, Calgary, AB, Canada T2N 1N4
| | - Marc Strous
- Department of Geoscience, University of Calgary, Calgary, AB, Canada T2N 1N4;
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Zhao Y, Nelson DM, Clegg BF, An CB, Hu FS. Isotopic analysis on nanogram quantities of carbon from dissolved insect cuticle: a method for paleoenvironmental inferences. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2017; 31:1825-1834. [PMID: 28833668 DOI: 10.1002/rcm.7965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 08/10/2017] [Accepted: 08/15/2017] [Indexed: 06/07/2023]
Abstract
RATIONALE Carbon isotope (δ13 C ) data from arthropod cuticles provide invaluable information on past and present biogeochemical processes. However, such analyses typically require large sample sizes that may mask important variation in δ13 C values within or among species. METHODS We have evaluated a spooling-wire microcombustion (SWiM) device and isotope ratio mass spectrometry (IRMS) to measure the δ13 C values of carbon dissolved from the cuticle of chitinous aquatic zooplankton. The effects of temperature, pH, and reaction time on the δ13 C values of acid-dissolved bulk cuticle and purified chitin fractions obtained from a single species of chironomid from four commercial suppliers were assessed. These results were compared with baseline δ13 C values obtained on solid cuticle using conventional EA (elemental analyzer)/IRMS. RESULTS The results indicate differential, time-dependent dissolution of chitin, lipid and protein fractions of cuticle concomitant with slow depolymerization and deacetylation of chitin. Isotopic offsets between dissolved bulk head capsules and a purified chitin fraction suggest the contributions of other isotopically lighter components of the bulk head capsules to bulk chitin extracts. The SWiM/IRMS δ13 C results obtained on dissolved cuticle using a treatment of 4 N HCl at 25 °C for 24 h produced generally stable δ13 C values, large sample/blank CO2 yields and a positive correlation with conventional EA/IRMS results on unprocessed cuticle. CONCLUSIONS The SWiM/IRMS system offers a reliable method to determine δ13 C values on nanogram quantities of carbon from dissolved insect cuticle, thus reducing sample size requirements and providing new opportunities to use δ13 C variation among/within species for reconstructing paleo-biogeochemical processes.
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Affiliation(s)
- Yongtao Zhao
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- College of Earth and Environmental Sciences, MOE Key Laboratory of Western China's Environmental Systems, Lanzhou University, Lanzhou, 730000, China
| | - David M Nelson
- Appalachian Laboratory, University of Maryland Center for Environmental Science, Frostburg, MD, 21532, USA
| | - Benjamin F Clegg
- School of Integrative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Cheng-Bang An
- College of Earth and Environmental Sciences, MOE Key Laboratory of Western China's Environmental Systems, Lanzhou University, Lanzhou, 730000, China
| | - Feng Sheng Hu
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Geology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Program in Ecology, Evolution, and Conservation Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
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Tang T, Mohr W, Sattin SR, Rogers DR, Girguis PR, Pearson A. Geochemically distinct carbon isotope distributions in Allochromatium vinosum DSM 180 T grown photoautotrophically and photoheterotrophically. GEOBIOLOGY 2017; 15:324-339. [PMID: 28042698 DOI: 10.1111/gbi.12221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 11/07/2016] [Indexed: 06/06/2023]
Abstract
Anoxygenic, photosynthetic bacteria are common at redox boundaries. They are of interest in microbial ecology and geosciences through their role in linking the carbon, sulfur, and iron cycles, yet much remains unknown about how their flexible carbon metabolism-permitting either autotrophic or heterotrophic growth-is recorded in the bulk sedimentary and lipid biomarker records. Here, we investigated patterns of carbon isotope fractionation in a model photosynthetic sulfur-oxidizing bacterium, Allochromatium vinosum DSM180T . In one treatment, A. vinosum was grown with CO2 as the sole carbon source, while in a second treatment, it was grown on acetate. Different intracellular isotope patterns were observed for fatty acids, phytol, individual amino acids, intact proteins, and total RNA between the two experiments. Photoautotrophic CO2 fixation yielded typical isotopic ordering for the lipid biomarkers: δ13 C values of phytol > n-alkyl lipids. In contrast, growth on acetate greatly suppressed intracellular isotopic heterogeneity across all molecular classes, except for a marked 13 C-depletion in phytol. This caused isotopic "inversion" in the lipids (δ13 C values of phytol < n-alkyl lipids). The finding suggests that inverse δ13 C patterns of n-alkanes and pristane/phytane in the geologic record may be at least in part a signal for photoheterotrophy. In both experimental scenarios, the relative isotope distributions could be predicted from an isotope flux-balance model, demonstrating that microbial carbon metabolisms can be interrogated by combining compound-specific stable isotope analysis with metabolic modeling. Isotopic differences among molecular classes may be a means of fingerprinting microbial carbon metabolism, both in the modern environment and the geologic record.
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Affiliation(s)
- T Tang
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA, USA
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - W Mohr
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA, USA
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - S R Sattin
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA, USA
| | - D R Rogers
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Department of Chemistry, Stonehill College, Easton, MA, USA
| | - P R Girguis
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - A Pearson
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA, USA
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7
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Barhate CL, Regalado EL, Contrella ND, Lee J, Jo J, Makarov AA, Armstrong DW, Welch CJ. Ultrafast Chiral Chromatography as the Second Dimension in Two-Dimensional Liquid Chromatography Experiments. Anal Chem 2017; 89:3545-3553. [PMID: 28192943 DOI: 10.1021/acs.analchem.6b04834] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Chromatographic separation and analysis of complex mixtures of closely related species is one of the most challenging tasks in modern pharmaceutical analysis. In recent years, two-dimensional liquid chromatography (2D-LC) has become a valuable tool for improving peak capacity and selectivity. However, the relatively slow speed of chiral separations has limited the use of chiral stationary phases (CSPs) as the second dimension in 2D-LC, especially in the comprehensive mode. Realizing that the recent revolution in the field of ultrafast enantioselective chromatography could now provide significantly faster separations, we herein report an investigation into the use of ultrafast chiral chromatography as a second dimension for 2D chromatographic separations. In this study, excellent selectivity, peak shape, and repeatability were achieved by combining achiral and chiral narrow-bore columns (2.1 mm × 100 mm and 2.1 mm × 150 mm, sub-2 and 3 μm) in the first dimension with 4.6 mm × 30 mm and 4.6 mm × 50 mm columns packed with highly efficient chiral selectors (sub-2 μm fully porous and 2.7 μm fused-core particles) in the second dimension, together with the use of 0.1% phosphoric acid/acetonitrile eluents in both dimensions. Multiple achiral × chiral and chiral × chiral 2D-LC examples (single and multiple heart-cutting, high-resolution sampling, and comprehensive) using ultrafast chiral chromatography in the second dimension are successfully applied to the separation and analysis of complex mixtures of closely related pharmaceuticals and synthetic intermediates, including chiral and achiral drugs and metabolites, constitutional isomers, stereoisomers, and organohalogenated species.
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Affiliation(s)
- Chandan L Barhate
- Department of Chemistry, University of Texas at Arlington , Arlington, Texas 76019, United States
| | | | | | - Joon Lee
- Agilent Technologies, Incorporated , Wilmington, Delaware 19808, United States
| | | | | | - Daniel W Armstrong
- Department of Chemistry, University of Texas at Arlington , Arlington, Texas 76019, United States
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van Roij L, Sluijs A, Laks JJ, Reichart G. Stable carbon isotope analyses of nanogram quantities of particulate organic carbon (pollen) with laser ablation nano combustion gas chromatography/isotope ratio mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2017; 31:47-58. [PMID: 27766694 PMCID: PMC5132107 DOI: 10.1002/rcm.7769] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 10/17/2016] [Accepted: 10/17/2016] [Indexed: 05/26/2023]
Abstract
RATIONALE Analyses of stable carbon isotope ratios (δ13 C values) of organic and inorganic matter remains have been instrumental for much of our understanding of present and past environmental and biological processes. Until recently, the analytical window of such analyses has been limited to samples containing at least several μg of carbon. METHODS Here we present a setup combining laser ablation, nano combustion gas chromatography and isotope ratio mass spectrometry (LA/nC/GC/IRMS). A deep UV (193 nm) laser is used for optimal fragmentation of organic matter with minimum fractionation effects and an exceptionally small ablation chamber and combustion oven are used to reduce the minimum sample mass requirement compared with previous studies. RESULTS Analyses of the international IAEA CH-7 polyethylene standard show optimal accuracy, and precision better than 0.5‰, when measuring at least 42 ng C. Application to untreated modern Eucalyptus globulus (C3 plant) and Zea mays (C4 plant) pollen grains shows a ~ 16‰ offset between these species. Within each single Z. mays pollen grain, replicate analyses show almost identical δ13 C values. CONCLUSIONS Isotopic offsets between individual pollen grains exceed analytical uncertainties, therefore probably reflecting interspecimen variability of ~0.5-0.9‰. These promising results set the stage for investigating both δ13 C values and natural carbon isotopic variability between single specimens of a single population of all kinds of organic particles yielding tens of nanograms of carbon. © 2016 The Authors. Rapid Communications in Mass Spectrometry Published by John Wiley & Sons Ltd.
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Affiliation(s)
- Linda van Roij
- Department of Earth Sciences, Faculty of GeosciencesUtrecht UniversityHeidelberglaan 2, 3584 CS UtrechtThe Netherlands
| | - Appy Sluijs
- Department of Earth Sciences, Faculty of GeosciencesUtrecht UniversityHeidelberglaan 2, 3584 CS UtrechtThe Netherlands
| | - Jelmer J. Laks
- Department of Earth Sciences, Faculty of GeosciencesUtrecht UniversityHeidelberglaan 2, 3584 CS UtrechtThe Netherlands
| | - Gert‐Jan Reichart
- Department of Earth Sciences, Faculty of GeosciencesUtrecht UniversityHeidelberglaan 2, 3584 CS UtrechtThe Netherlands
- Royal Netherlands Institute for Sea Research (NIOZ)Landsdiep 4, 1797 SZ ‘t Horntje (Texel)The Netherlands
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Marlow JJ, Skennerton CT, Li Z, Chourey K, Hettich RL, Pan C, Orphan VJ. Proteomic Stable Isotope Probing Reveals Biosynthesis Dynamics of Slow Growing Methane Based Microbial Communities. Front Microbiol 2016; 7:563. [PMID: 27199908 PMCID: PMC4850331 DOI: 10.3389/fmicb.2016.00563] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2016] [Accepted: 04/04/2016] [Indexed: 01/02/2023] Open
Abstract
Marine methane seep habitats represent an important control on the global flux of methane. Nucleotide-based meta-omics studies outline community-wide metabolic potential, but expression patterns of environmentally relevant proteins are poorly characterized. Proteomic stable isotope probing (proteomic SIP) provides additional information by characterizing phylogenetically specific, functionally relevant activity in mixed microbial communities, offering enhanced detection through system-wide product integration. Here we applied proteomic SIP to 15NH4+ and CH4 amended seep sediment microcosms in an attempt to track protein synthesis of slow-growing, low-energy microbial systems. Across all samples, 3495 unique proteins were identified, 11% of which were 15N-labeled. Consistent with the dominant anaerobic oxidation of methane (AOM) activity commonly observed in anoxic seep sediments, proteins associated with sulfate reduction and reverse methanogenesis—including the ANME-2 associated methylenetetrahydromethanopterin reductase (Mer)—were all observed to be actively synthesized (15N-enriched). Conversely, proteins affiliated with putative aerobic sulfur-oxidizing epsilon- and gammaproteobacteria showed a marked decrease over time in our anoxic sediment incubations. The abundance and phylogenetic range of 15N-enriched methyl-coenzyme M reductase (Mcr) orthologs, many of which exhibited novel post-translational modifications, suggests that seep sediments provide niches for multiple organisms performing analogous metabolisms. In addition, 26 proteins of unknown function were consistently detected and actively expressed under conditions supporting AOM, suggesting that they play important roles in methane seep ecosystems. Stable isotope probing in environmental proteomics experiments provides a mechanism to determine protein durability and evaluate lineage-specific responses in complex microbial communities placed under environmentally relevant conditions. Our work here demonstrates the active synthesis of a metabolically specific minority of enzymes, revealing the surprising longevity of most proteins over the course of an extended incubation experiment in an established, slow-growing, methane-impacted environmental system.
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Affiliation(s)
- Jeffrey J Marlow
- Division of Geological and Planetary Sciences, California Institute of Technology Pasadena, CA, USA
| | - Connor T Skennerton
- Division of Geological and Planetary Sciences, California Institute of Technology Pasadena, CA, USA
| | - Zhou Li
- Chemical Sciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA
| | - Karuna Chourey
- Chemical Sciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA
| | - Robert L Hettich
- Chemical Sciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA
| | - Chongle Pan
- Chemical Sciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA
| | - Victoria J Orphan
- Division of Geological and Planetary Sciences, California Institute of Technology Pasadena, CA, USA
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