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Kakouridis A, Yuan M, Nuccio EE, Hagen JA, Fossum CA, Moore ML, Estera-Molina KY, Nico PS, Weber PK, Pett-Ridge J, Firestone MK. Arbuscular mycorrhiza convey significant plant carbon to a diverse hyphosphere microbial food web and mineral-associated organic matter. New Phytol 2024; 242:1661-1675. [PMID: 38358052 DOI: 10.1111/nph.19560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Accepted: 12/04/2023] [Indexed: 02/16/2024]
Abstract
Arbuscular mycorrhizal fungi (AMF) transport substantial plant carbon (C) that serves as a substrate for soil organisms, a precursor of soil organic matter (SOM), and a driver of soil microbial dynamics. Using two-chamber microcosms where an air gap isolated AMF from roots, we 13CO2-labeled Avena barbata for 6 wk and measured the C Rhizophagus intraradices transferred to SOM and hyphosphere microorganisms. NanoSIMS imaging revealed hyphae and roots had similar 13C enrichment. SOM density fractionation, 13C NMR, and IRMS showed AMF transferred 0.77 mg C g-1 of soil (increasing total C by 2% relative to non-mycorrhizal controls); 33% was found in occluded or mineral-associated pools. In the AMF hyphosphere, there was no overall change in community diversity but 36 bacterial ASVs significantly changed in relative abundance. With stable isotope probing (SIP)-enabled shotgun sequencing, we found taxa from the Solibacterales, Sphingobacteriales, Myxococcales, and Nitrososphaerales (ammonium oxidizing archaea) were highly enriched in AMF-imported 13C (> 20 atom%). Mapping sequences from 13C-SIP metagenomes to total ASVs showed at least 92 bacteria and archaea were significantly 13C-enriched. Our results illustrate the quantitative and ecological impact of hyphal C transport on the formation of potentially protective SOM pools and microbial roles in the AMF hyphosphere soil food web.
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Affiliation(s)
- Anne Kakouridis
- University of California Berkeley, Berkeley, CA, 94720, USA
- Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Mengting Yuan
- University of California Berkeley, Berkeley, CA, 94720, USA
| | - Erin E Nuccio
- Lawrence Livermore National Laboratory, Livermore, 94550, CA, USA
| | - John A Hagen
- University of California Berkeley, Berkeley, CA, 94720, USA
| | | | - Madeline L Moore
- University of California Berkeley, Berkeley, CA, 94720, USA
- Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Katerina Y Estera-Molina
- University of California Berkeley, Berkeley, CA, 94720, USA
- Lawrence Livermore National Laboratory, Livermore, 94550, CA, USA
| | - Peter S Nico
- Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Peter K Weber
- Lawrence Livermore National Laboratory, Livermore, 94550, CA, USA
| | - Jennifer Pett-Ridge
- Lawrence Livermore National Laboratory, Livermore, 94550, CA, USA
- University of California Merced, Merced, 95343, CA, USA
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2
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Ricca JG, Mayali X, Qu J, Weber PK, Poirier G, Dufresne CP, Louda JW, Terentis AC. Endogenous Production and Vibrational Analysis of Heavy-Isotope-Labeled Peptides from Cyanobacteria. Chembiochem 2024; 25:e202400019. [PMID: 38311594 DOI: 10.1002/cbic.202400019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 01/31/2024] [Accepted: 02/01/2024] [Indexed: 02/06/2024]
Abstract
Stable isotope labeling is an extremely useful tool for characterizing the structure, tracing the metabolism, and imaging the distribution of natural products in living organisms using mass-sensitive measurement techniques. In this study, a cyanobacterium was cultured in 15 N/13 C-enriched media to endogenously produce labeled, bioactive oligopeptides. The extent of heavy isotope incorporation in these peptides was determined with LC-MS, while the overall extent of heavy isotope incorporation in whole cells was studied with nanoSIMS and AFM-IR. Up to 98 % heavy isotope incorporation was observed in labeled cells. Three of the most abundant peptides, microcystin-LR (MCLR), cyanopeptolin-A (CYPA), and aerucyclamide-A (ACAA), were isolated and further studied with Raman and FTIR spectroscopies and DFT calculations. This revealed several IR and Raman active vibrations associated with functional groups not common in ribosomal peptides, like diene, ester, thiazole, thiazoline, and oxazoline groups, which could be suitable for future vibrational imaging studies. More broadly, this study outlines a simple and relatively inexpensive method for producing heavy-labeled natural products. Manipulating the bacterial culture conditions by the addition of specific types and amounts of heavy-labeled nutrients provides an efficient means of producing heavy-labeled natural products for mass-sensitive imaging studies.
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Affiliation(s)
- John G Ricca
- Department of Chemistry and Biochemistry, Florida Atlantic University, 777 Glades Rd, 33431, Boca Raton, FL, USA
- Center for Environmental Studies, Florida Atlantic University, 3200 College Ave, 33314, Davie, FL, USA
| | - Xavier Mayali
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, 7000 East Avenue, 94550, Livermore, CA, USA
| | - Jing Qu
- Advanced Materials Characterization Lab, University of Delaware, 19716, Newark, DE, USA
| | - Peter K Weber
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, 7000 East Avenue, 94550, Livermore, CA, USA
| | - Gerald Poirier
- Advanced Materials Characterization Lab, University of Delaware, 19716, Newark, DE, USA
| | | | - J William Louda
- Department of Chemistry and Biochemistry, Florida Atlantic University, 777 Glades Rd, 33431, Boca Raton, FL, USA
| | - Andrew C Terentis
- Department of Chemistry and Biochemistry, Florida Atlantic University, 777 Glades Rd, 33431, Boca Raton, FL, USA
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3
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Qin W, Wei SP, Zheng Y, Choi E, Li X, Johnston J, Wan X, Abrahamson B, Flinkstrom Z, Wang B, Li H, Hou L, Tao Q, Chlouber WW, Sun X, Wells M, Ngo L, Hunt KA, Urakawa H, Tao X, Wang D, Yan X, Wang D, Pan C, Weber PK, Jiang J, Zhou J, Zhang Y, Stahl DA, Ward BB, Mayali X, Martens-Habbena W, Winkler MKH. Ammonia-oxidizing bacteria and archaea exhibit differential nitrogen source preferences. Nat Microbiol 2024; 9:524-536. [PMID: 38297167 DOI: 10.1038/s41564-023-01593-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 12/15/2023] [Indexed: 02/02/2024]
Abstract
Ammonia-oxidizing microorganisms (AOM) contribute to one of the largest nitrogen fluxes in the global nitrogen budget. Four distinct lineages of AOM: ammonia-oxidizing archaea (AOA), beta- and gamma-proteobacterial ammonia-oxidizing bacteria (β-AOB and γ-AOB) and complete ammonia oxidizers (comammox), are thought to compete for ammonia as their primary nitrogen substrate. In addition, many AOM species can utilize urea as an alternative energy and nitrogen source through hydrolysis to ammonia. How the coordination of ammonia and urea metabolism in AOM influences their ecology remains poorly understood. Here we use stable isotope tracing, kinetics and transcriptomics experiments to show that representatives of the AOM lineages employ distinct regulatory strategies for ammonia or urea utilization, thereby minimizing direct substrate competition. The tested AOA and comammox species preferentially used ammonia over urea, while β-AOB favoured urea utilization, repressed ammonia transport in the presence of urea and showed higher affinity for urea than for ammonia. Characterized γ-AOB co-utilized both substrates. These results reveal contrasting niche adaptation and coexistence patterns among the major AOM lineages.
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Affiliation(s)
- Wei Qin
- School of Biological Sciences, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA.
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA.
| | - Stephany P Wei
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
| | - Yue Zheng
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, China
| | - Eunkyung Choi
- Department of Microbiology and Cell Science, Fort Lauderdale Research and Education Center, University of Florida, Davie, FL, USA
| | - Xiangpeng Li
- School of Biological Sciences, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | | | - Xianhui Wan
- Department of Geosciences, Princeton University, Princeton, NJ, USA
| | - Britt Abrahamson
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
| | - Zachary Flinkstrom
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
| | - Baozhan Wang
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Hanyan Li
- School of Biological Sciences, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | - Lei Hou
- School of Biological Sciences, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, China
| | - Qing Tao
- School of Biological Sciences, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | - Wyatt W Chlouber
- School of Biological Sciences, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | - Xin Sun
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| | - Michael Wells
- School of Biological Sciences, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | - Long Ngo
- School of Biological Sciences, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | - Kristopher A Hunt
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
| | - Hidetoshi Urakawa
- Department of Ecology and Environmental Studies, Florida Gulf Coast University, Fort Myers, FL, USA
| | - Xuanyu Tao
- School of Biological Sciences, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | - Dongyu Wang
- School of Biological Sciences, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | - Xiaoyuan Yan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Dazhi Wang
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, China
| | - Chongle Pan
- School of Biological Sciences, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | - Peter K Weber
- Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Jiandong Jiang
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Jizhong Zhou
- School of Biological Sciences, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | - Yao Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, China
| | - David A Stahl
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
| | - Bess B Ward
- Department of Geosciences, Princeton University, Princeton, NJ, USA
| | - Xavier Mayali
- Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Willm Martens-Habbena
- Department of Microbiology and Cell Science, Fort Lauderdale Research and Education Center, University of Florida, Davie, FL, USA.
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4
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Dupuis S, Lingappa UF, Mayali X, Sindermann ES, Chastain JL, Weber PK, Stuart R, Merchant SS. Scarcity of fixed carbon transfer in a model microbial phototroph-heterotroph interaction. bioRxiv 2024:2024.01.26.577492. [PMID: 38328118 PMCID: PMC10849638 DOI: 10.1101/2024.01.26.577492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
While the green alga Chlamydomonas reinhardtii has long served as a reference organism, few studies have interrogated its role as a primary producer in microbial interactions. Here, we quantitatively investigated C. reinhardtii's capacity to support a heterotrophic microbe using the established coculture system with Mesorhizobium japonicum , a vitamin B 12 -producing α- proteobacterium. Using stable isotope probing and nanoscale secondary ion mass spectrometry (nanoSIMS), we tracked the flow of photosynthetic fixed carbon and consequent bacterial biomass synthesis under continuous and diel light with single-cell resolution. We found that more 13 C fixed by the alga was taken up by bacterial cells under continuous light, invalidating the hypothesis that the alga's fermentative degradation of starch reserves during the night would boost M. japonicum heterotrophy. 15 NH 4 assimilation rates and changes in cell size revealed that the carbon transferred was insufficient for balanced growth of M. japonicum cells, which instead underwent reductive division. However, despite this sign of starvation, M. japonicum still supported a B 12 -dependent C. reinhardtii mutant. Finally, we showed that bacterial proliferation could be supported solely by the algal lysis that occurred in coculture, highlighting the role of necromass in carbon cycling. Collectively, these results reveal the scarcity of fixed carbon in this microbial trophic relationship, demonstrate B 12 exchange even during bacterial starvation, and underscore the importance of quantitative approaches for assessing metabolic coupling in algal-bacterial interactions.
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5
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Caty SN, Alvarez-Buylla A, Vasek C, Tapia EE, Martin NA, McLaughlin T, Weber PK, Mayali X, Coloma LA, Morris MM, O'Connell LA. A toxic environment selects for specialist microbiome in poison frogs. bioRxiv 2024:2024.01.10.574901. [PMID: 38260330 PMCID: PMC10802471 DOI: 10.1101/2024.01.10.574901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Shifts in microbiome community composition can have large effects on host health. It is therefore important to understand how perturbations, like those caused by the introduction of exogenous chemicals, modulate microbiome community composition. In poison frogs within the family Dendrobatidae, the skin microbiome is exposed to the alkaloids that the frogs sequester from their diet and use for defense. Given the demonstrated antimicrobial effects of these poison frog alkaloids, these compounds may be structuring the skin microbial community. To test this, we first characterized microbial communities from chemically defended and closely related non-defended frogs from Ecuador. Then we conducted a laboratory experiment to monitor the effect of the alkaloid decahydroquinoline (DHQ) on the microbiome of a single frog species. In both the field and lab experiments, we found that alkaloid-exposed microbiomes are more species rich and phylogenetically diverse, with an increase in rare taxa. To better understand the strain-specific behavior in response to alkaloids, we cultured microbial strains from poison frog skin and found the majority of strains exhibited either enhanced growth or were not impacted by the addition of DHQ. Additionally, stable isotope tracing coupled to nanoSIMS suggests that some of these strains are able to metabolize DHQ. Taken together, these data suggest that poison frog chemical defenses open new niches for skin-associated microbes with specific adaptations, including the likely metabolism of alkaloids, that enable their survival in this toxic environment. This work helps expand our understanding of how exposure to exogenous compounds like alkaloids can impact host microbiomes.
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Affiliation(s)
| | | | - Cooper Vasek
- Department of Biology, Stanford University, Stanford CA, USA
| | - Elicio E Tapia
- Leibniz Institute for the Analysis of Biodiversity Change Martin-Luther-King-Platz 3 20146 Hamburg, Germany
| | - Nora A Martin
- Department of Biology, Stanford University, Stanford CA, USA
| | - Theresa McLaughlin
- Stanford University Mass Spectrometry, Stanford University, Stanford CA, USA
| | - Peter K Weber
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore CA, USA
| | - Xavier Mayali
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore CA, USA
| | - Luis A Coloma
- Centro Jambatu de Investigación y Conservación de Anfibios, Fundación Jambatu, San Rafael, Quito, Ecuador
| | - Megan M Morris
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore CA, USA
| | - Lauren A O'Connell
- Department of Biology, Stanford University, Stanford CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
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6
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Mayali X, Samo TJ, Kimbrel JA, Morris MM, Rolison K, Swink C, Ramon C, Kim YM, Munoz-Munoz N, Nicora C, Purvine S, Lipton M, Stuart RK, Weber PK. Single-cell isotope tracing reveals functional guilds of bacteria associated with the diatom Phaeodactylum tricornutum. Nat Commun 2023; 14:5642. [PMID: 37704622 PMCID: PMC10499878 DOI: 10.1038/s41467-023-41179-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 08/24/2023] [Indexed: 09/15/2023] Open
Abstract
Bacterial remineralization of algal organic matter fuels algal growth but is rarely quantified. Consequently, we cannot currently predict whether some bacterial taxa may provide more remineralized nutrients to algae than others. Here, we quantified bacterial incorporation of algal-derived complex dissolved organic carbon and nitrogen and algal incorporation of remineralized carbon and nitrogen in fifteen bacterial co-cultures growing with the diatom Phaeodactylum tricornutum at the single-cell level using isotope tracing and nanoSIMS. We found unexpected strain-to-strain and cell-to-cell variability in net carbon and nitrogen incorporation, including non-ubiquitous complex organic nitrogen utilization and remineralization. We used these data to identify three distinct functional guilds of metabolic interactions, which we termed macromolecule remineralizers, macromolecule users, and small-molecule users, the latter exhibiting efficient growth under low carbon availability. The functional guilds were not linked to phylogeny and could not be elucidated strictly from metabolic capacity as predicted by comparative genomics, highlighting the need for direct activity-based measurements in ecological studies of microbial metabolic interactions.
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Affiliation(s)
- Xavier Mayali
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA.
| | - Ty J Samo
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Jeff A Kimbrel
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Megan M Morris
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Kristina Rolison
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Courtney Swink
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Christina Ramon
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Young-Mo Kim
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Nathalie Munoz-Munoz
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Carrie Nicora
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Sam Purvine
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Mary Lipton
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Rhona K Stuart
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Peter K Weber
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
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7
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Trubl G, Stedman KM, Bywaters KF, Matula EE, Sommers P, Roux S, Merino N, Yin J, Kaelber JT, Avila-Herrera A, Johnson PA, Johnson JC, Borges S, Weber PK, Pett-Ridge J, Boston PJ. Astrovirology: how viruses enhance our understanding of life in the Universe. Int J Astrobiol 2023; 22:247-271. [PMID: 38046673 PMCID: PMC10691837 DOI: 10.1017/s1473550423000058] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Viruses are the most numerically abundant biological entities on Earth. As ubiquitous replicators of molecular information and agents of community change, viruses have potent effects on the life on Earth, and may play a critical role in human spaceflight, for life-detection missions to other planetary bodies and planetary protection. However, major knowledge gaps constrain our understanding of the Earth's virosphere: (1) the role viruses play in biogeochemical cycles, (2) the origin(s) of viruses and (3) the involvement of viruses in the evolution, distribution and persistence of life. As viruses are the only replicators that span all known types of nucleic acids, an expanded experimental and theoretical toolbox built for Earth's viruses will be pivotal for detecting and understanding life on Earth and beyond. Only by filling in these knowledge and technical gaps we will obtain an inclusive assessment of how to distinguish and detect life on other planetary surfaces. Meanwhile, space exploration requires life-support systems for the needs of humans, plants and their microbial inhabitants. Viral effects on microbes and plants are essential for Earth's biosphere and human health, but virus-host interactions in spaceflight are poorly understood. Viral relationships with their hosts respond to environmental changes in complex ways which are difficult to predict by extrapolating from Earth-based proxies. These relationships should be studied in space to fully understand how spaceflight will modulate viral impacts on human health and life-support systems, including microbiomes. In this review, we address key questions that must be examined to incorporate viruses into Earth system models, life-support systems and life detection. Tackling these questions will benefit our efforts to develop planetary protection protocols and further our understanding of viruses in astrobiology.
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Affiliation(s)
- Gareth Trubl
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Kenneth M. Stedman
- Center for Life in Extreme Environments, Department of Biology, Portland State University, Portland, OR, USA
| | | | | | | | - Simon Roux
- DOE Joint Genome Institute, Berkeley, CA, USA
| | - Nancy Merino
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - John Yin
- Chemical and Biological Engineering, Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA
| | - Jason T. Kaelber
- Institute for Quantitative Biomedicine, Rutgers, the State University of New Jersey, Piscataway, NJ, USA
| | - Aram Avila-Herrera
- Computing Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Peter Anto Johnson
- Faculty of Medicine & Dentistry, University of Alberta, Edmonton, AB, Canada
| | | | | | - Peter K. Weber
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
- Life & Environmental Sciences Department, University of California Merced, Merced, CA, USA
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8
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Yee DP, Samo TJ, Abbriano RM, Shimasaki B, Vernet M, Mayali X, Weber PK, Mitchell BG, Hildebrand M, Decelle J, Tresguerres M. The V-type ATPase enhances photosynthesis in marine phytoplankton and further links phagocytosis to symbiogenesis. Curr Biol 2023; 33:2541-2547.e5. [PMID: 37263270 PMCID: PMC10326425 DOI: 10.1016/j.cub.2023.05.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 03/20/2023] [Accepted: 05/09/2023] [Indexed: 06/03/2023]
Abstract
Diatoms, dinoflagellates, and coccolithophores are dominant groups of marine eukaryotic phytoplankton that are collectively responsible for the majority of primary production in the ocean.1 These phytoplankton contain additional intracellular membranes around their chloroplasts, which are derived from ancestral engulfment of red microalgae by unicellular heterotrophic eukaryotes that led to secondary and tertiary endosymbiosis.2 However, the selectable evolutionary advantage of these membranes and the physiological significance for extant phytoplankton remain poorly understood. Since intracellular digestive vacuoles are ubiquitously acidified by V-type H+-ATPase (VHA),3 proton pumps were proposed to acidify the microenvironment around secondary chloroplasts to promote the dehydration of dissolved inorganic carbon (DIC) into CO2, thus enhancing photosynthesis.4,5 We report that VHA is localized around the chloroplasts of centric diatoms and that VHA significantly contributes to their photosynthesis across a wide range of oceanic irradiances. Similar results in a pennate diatom, dinoflagellate, and coccolithophore, but not green or red microalgae, imply the co-option of phagocytic VHA activity into a carbon-concentrating mechanism (CCM) is common to secondary endosymbiotic phytoplankton. Furthermore, analogous mechanisms in extant photosymbiotic marine invertebrates6,7,8 provide functional evidence for an adaptive advantage throughout the transition from endosymbiosis to symbiogenesis. Based on the contribution of diatoms to ocean biogeochemical cycles, VHA-mediated enhancement of photosynthesis contributes at least 3.5 Gtons of fixed carbon per year (or 7% of primary production in the ocean), providing an example of a symbiosis-derived evolutionary innovation with global environmental implications.
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Affiliation(s)
- Daniel P Yee
- Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Cell and Plant Physiology Laboratory, University of Grenoble Alpes, CNRS, CEA, INRAE, and IRIG, 17 Avenue des Martyrs, Grenoble 38054, Auvergne-Rhone-Alpes, France.
| | - Ty J Samo
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA 94550, USA
| | - Raffaela M Abbriano
- Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Bethany Shimasaki
- Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Maria Vernet
- Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Xavier Mayali
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA 94550, USA
| | - Peter K Weber
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA 94550, USA
| | - B Greg Mitchell
- Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Mark Hildebrand
- Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Johan Decelle
- Cell and Plant Physiology Laboratory, University of Grenoble Alpes, CNRS, CEA, INRAE, and IRIG, 17 Avenue des Martyrs, Grenoble 38054, Auvergne-Rhone-Alpes, France
| | - Martin Tresguerres
- Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
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9
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Palmer M, Covington JK, Zhou EM, Thomas SC, Habib N, Seymour CO, Lai D, Johnston J, Hashimi A, Jiao JY, Muok AR, Liu L, Xian WD, Zhi XY, Li MM, Silva LP, Bowen BP, Louie K, Briegel A, Pett-Ridge J, Weber PK, Tocheva EI, Woyke T, Northen TR, Mayali X, Li WJ, Hedlund BP. Thermophilic Dehalococcoidia with unusual traits shed light on an unexpected past. ISME J 2023:10.1038/s41396-023-01405-0. [PMID: 37041326 DOI: 10.1038/s41396-023-01405-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 03/22/2023] [Accepted: 03/27/2023] [Indexed: 04/13/2023]
Abstract
Although the phylum Chloroflexota is ubiquitous, its biology and evolution are poorly understood due to limited cultivability. Here, we isolated two motile, thermophilic bacteria from hot spring sediments belonging to the genus Tepidiforma and class Dehalococcoidia within the phylum Chloroflexota. A combination of cryo-electron tomography, exometabolomics, and cultivation experiments using stable isotopes of carbon revealed three unusual traits: flagellar motility, a peptidoglycan-containing cell envelope, and heterotrophic activity on aromatics and plant-associated compounds. Outside of this genus, flagellar motility has not been observed in Chloroflexota, and peptidoglycan-containing cell envelopes have not been described in Dehalococcoidia. Although these traits are unusual among cultivated Chloroflexota and Dehalococcoidia, ancestral character state reconstructions showed flagellar motility and peptidoglycan-containing cell envelopes were ancestral within the Dehalococcoidia, and subsequently lost prior to a major adaptive radiation of Dehalococcoidia into marine environments. However, despite the predominantly vertical evolutionary histories of flagellar motility and peptidoglycan biosynthesis, the evolution of enzymes for degradation of aromatics and plant-associated compounds was predominantly horizontal and complex. Together, the presence of these unusual traits in Dehalococcoidia and their evolutionary histories raise new questions about the timing and selective forces driving their successful niche expansion into global oceans.
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Affiliation(s)
- Marike Palmer
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA.
| | - Jonathan K Covington
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA
| | - En-Min Zhou
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, 510275, Guangzhou, People's Republic of China
- Key Laboratory of Microbial Diversity in Southwest China of Ministry of Education, Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, 650091, Kunming, People's Republic of China
| | - Scott C Thomas
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, NY, 10010, USA
| | - Neeli Habib
- Key Laboratory of Microbial Diversity in Southwest China of Ministry of Education, Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, 650091, Kunming, People's Republic of China
- Department of Microbiology, Shaheed Benazir Bhutto Women University, Peshawar, Khyber Pakhtunkhwa (KPK), Pakistan
| | - Cale O Seymour
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA
| | - Dengxun Lai
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA
| | - Juliet Johnston
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Ameena Hashimi
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, BC, Canada
| | - Jian-Yu Jiao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, 510275, Guangzhou, People's Republic of China
| | - Alise R Muok
- Institute of Biology, Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
| | - Lan Liu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, 510275, Guangzhou, People's Republic of China
| | - Wen-Dong Xian
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, 510275, Guangzhou, People's Republic of China
| | - Xiao-Yang Zhi
- Key Laboratory of Microbial Diversity in Southwest China of Ministry of Education, Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, 650091, Kunming, People's Republic of China
| | - Meng-Meng Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, 510275, Guangzhou, People's Republic of China
| | - Leslie P Silva
- The Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Benjamin P Bowen
- The Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Katherine Louie
- The Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Ariane Briegel
- Institute of Biology, Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
- Life and Environmental Sciences, University of California Merced, Merced, CA, 95343, USA
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Peter K Weber
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Elitza I Tocheva
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, BC, Canada
| | - Tanja Woyke
- The Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Life and Environmental Sciences, University of California Merced, Merced, CA, 95343, USA
| | - Trent R Northen
- The Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Xavier Mayali
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, 510275, Guangzhou, People's Republic of China
| | - Brian P Hedlund
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA.
- Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA.
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10
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Parada AE, Mayali X, Weber PK, Wollard J, Santoro AE, Fuhrman JA, Pett-Ridge J, Dekas AE. Constraining the composition and quantity of organic matter used by abundant marine Thaumarchaeota. Environ Microbiol 2023; 25:689-704. [PMID: 36478085 DOI: 10.1111/1462-2920.16299] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 11/27/2022] [Indexed: 12/12/2022]
Abstract
Marine Group I (MGI) Thaumarchaeota were originally described as chemoautotrophic nitrifiers, but molecular and isotopic evidence suggests heterotrophic and/or mixotrophic capabilities. Here, we investigated the quantity and composition of organic matter assimilated by individual, uncultured MGI cells from the Pacific Ocean to constrain their potential for mixotrophy and heterotrophy. We observed that most MGI cells did not assimilate carbon from any organic substrate provided (glucose, pyruvate, oxaloacetate, protein, urea, and amino acids). The minority of MGI cells that did assimilate it did so exclusively from nitrogenous substrates (urea, 15% of MGI and amino acids, 36% of MGI), and only as an auxiliary carbon source (<20% of that subset's total cellular carbon was derived from those substrates). At the population level, MGI assimilation of organic carbon comprised just 0.5%-11% of total biomass carbon. We observed extensive assimilation of inorganic carbon and urea- and amino acid-derived nitrogen (equal to that from ammonium), consistent with metagenomic and metatranscriptomic analyses performed here and previously showing a widespread potential for MGI to perform autotrophy and transport and degrade organic nitrogen. Our results constrain the quantity and composition of organic matter used by MGI and suggest they use it primarily to meet nitrogen demands for anabolism and nitrification.
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Affiliation(s)
- Alma E Parada
- Department of Earth System Science, Stanford University, Stanford, California, USA
| | - Xavier Mayali
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
| | - Peter K Weber
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
| | - Jessica Wollard
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
| | - Alyson E Santoro
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, California, USA
| | - Jed A Fuhrman
- Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
| | - Anne E Dekas
- Department of Earth System Science, Stanford University, Stanford, California, USA
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
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11
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Harding KJ, Turk-Kubo KA, Mak EWK, Weber PK, Mayali X, Zehr JP. Cell-specific measurements show nitrogen fixation by particle-attached putative non-cyanobacterial diazotrophs in the North Pacific Subtropical Gyre. Nat Commun 2022; 13:6979. [PMID: 36379938 PMCID: PMC9666432 DOI: 10.1038/s41467-022-34585-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 10/31/2022] [Indexed: 11/16/2022] Open
Abstract
Biological nitrogen fixation is a major important source of nitrogen for low-nutrient surface oceanic waters. Nitrogen-fixing (diazotrophic) cyanobacteria are believed to be the primary contributors to this process, but the contribution of non-cyanobacterial diazotrophic organisms in oxygenated surface water, while hypothesized to be important, has yet to be demonstrated. In this study, we used simultaneous 15N-dinitrogen and 13C-bicarbonate incubations combined with nanoscale secondary ion mass spectrometry analysis to screen tens of thousands of mostly particle-associated, cell-like regions of interest collected from the North Pacific Subtropical Gyre. These dual isotope incubations allow us to distinguish between non-cyanobacterial and cyanobacterial nitrogen-fixing microorganisms and to measure putative cell-specific nitrogen fixation rates. With this approach, we detect nitrogen fixation by putative non-cyanobacterial diazotrophs in the oxygenated surface ocean, which are associated with organic-rich particles (<210 µm size fraction) at two out of seven locations sampled. When present, up to 4.1% of the analyzed particles contain at least one active putative non-cyanobacterial diazotroph. The putative non-cyanobacterial diazotroph nitrogen fixation rates (0.76 ± 1.60 fmol N cell-1 d-1) suggest that these organisms are capable of fixing dinitrogen in oxygenated surface water, at least when attached to particles, and may contribute to oceanic nitrogen fixation.
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Affiliation(s)
- Katie J Harding
- Department of Ocean Sciences, University of California, Santa Cruz, CA, USA
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Kendra A Turk-Kubo
- Department of Ocean Sciences, University of California, Santa Cruz, CA, USA
| | | | - Peter K Weber
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Xavier Mayali
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA.
| | - Jonathan P Zehr
- Department of Ocean Sciences, University of California, Santa Cruz, CA, USA.
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12
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Kakouridis A, Hagen JA, Kan MP, Mambelli S, Feldman LJ, Herman DJ, Weber PK, Pett‐Ridge J, Firestone MK. Routes to roots: direct evidence of water transport by arbuscular mycorrhizal fungi to host plants. New Phytol 2022; 236:210-221. [PMID: 35633108 PMCID: PMC9543596 DOI: 10.1111/nph.18281] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 05/16/2022] [Indexed: 05/19/2023]
Abstract
Arbuscular mycorrhizal fungi (AMF) can help mitigate plant responses to water stress, but it is unclear whether AMF do so by indirect mechanisms, direct water transport to roots, or a combination of the two. Here, we investigated if and how the AMF Rhizophagus intraradices transported water to the host plant Avena barbata, wild oat. We used two-compartment microcosms, isotopically labeled water, and a fluorescent dye to directly track and quantify water transport by AMF across an air gap to host plants. Plants grown with AMF that had access to a physically separated compartment containing 18 O-labeled water transpired almost twice as much as plants with AMF excluded from that compartment. Using an isotopic mixing model, we estimated that water transported by AMF across the air gap accounted for 34.6% of the water transpired by host plants. In addition, a fluorescent dye indicated that hyphae were able to transport some water via an extracytoplasmic pathway. Our study provides direct evidence that AMF can act as extensions of the root system along the soil-plant-air continuum of water movement, with plant transpiration driving water flow along hyphae outside of the hyphal cell membrane.
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Affiliation(s)
- Anne Kakouridis
- University of California BerkeleyBerkeleyCA94720USA
- Lawrence Berkeley National LaboratoryBerkeleyCA94720USA
| | | | - Megan P. Kan
- University of California BerkeleyBerkeleyCA94720USA
- Lawrence Livermore National LaboratoryLivermoreCA94550USA
| | - Stefania Mambelli
- University of California BerkeleyBerkeleyCA94720USA
- Center for Stable Isotope BiogeochemistryBerkeleyCA94720USA
| | | | - Donald J. Herman
- University of California BerkeleyBerkeleyCA94720USA
- Lawrence Berkeley National LaboratoryBerkeleyCA94720USA
| | - Peter K. Weber
- Lawrence Livermore National LaboratoryLivermoreCA94550USA
| | - Jennifer Pett‐Ridge
- Lawrence Livermore National LaboratoryLivermoreCA94550USA
- University of California MercedMercedCA95344USA
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13
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Hui C, Schmollinger S, Strenkert D, Holbrook K, Montgomery HR, Chen S, Nelson HM, Weber PK, Merchant SS. Simple steps to enable reproducibility: culture conditions affecting Chlamydomonas growth and elemental composition. Plant J 2022; 111:995-1014. [PMID: 35699388 DOI: 10.1111/tpj.15867] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 06/01/2022] [Accepted: 06/03/2022] [Indexed: 05/26/2023]
Abstract
Even subtle modifications in growth conditions elicit acclimation responses affecting the molecular and elemental makeup of organisms, both in the laboratory and in natural habitats. We systematically explored the effect of temperature, pH, nutrient availability, culture density, and access to CO2 and O2 in laboratory-grown algal cultures on growth rate, the ionome, and the ability to accumulate Fe. We found algal cells accumulate Fe in alkaline conditions, even more so when excess Fe is present, coinciding with a reduced growth rate. Using a combination of Fe-specific dyes, X-ray fluorescence microscopy, and NanoSIMS, we show that the alkaline-accumulated Fe was intracellularly sequestered into acidocalcisomes, which are localized towards the periphery of the cells. At high photon flux densities, Zn and Ca specifically over-accumulate, while Zn alone accumulates at low temperatures. The impact of aeration was probed by reducing shaking speeds and changing vessel fill levels; the former increased the Cu quota of cultures, the latter resulted in a reduction in P, Ca, and Mn at low fill levels. Trace element quotas were also affected in the stationary phase, where specifically Fe, Cu, and Zn accumulate. Cu accumulation here depends inversely on the Fe concentration of the medium. Individual laboratory strains accumulate Ca, P, and Cu to different levels. All together, we identified a set of specific changes to growth rate, elemental composition, and the capacity to store Fe in response to subtle differences in culturing conditions of Chlamydomonas, affecting experimental reproducibility. Accordingly, we recommend that these variables be recorded and reported as associated metadata.
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Affiliation(s)
- Colleen Hui
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA
- Chemical Sciences Division, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, 94720, USA
| | - Stefan Schmollinger
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, 94720, USA
| | - Daniela Strenkert
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, 94720, USA
| | - Kristen Holbrook
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA
| | - Hayden R Montgomery
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA
| | - Si Chen
- Advanced Photon Source, Argonne National Laboratory, Argonne, IL, 60439, USA
| | - Hosea M Nelson
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA
| | - Peter K Weber
- Lawrence Livermore National Laboratory, Physical and Life Science Directorate, Livermore, CA, 94550, USA
| | - Sabeeha S Merchant
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
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14
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Chaffin JD, Westrick JA, Furr E, Birbeck JA, Reitz LA, Stanislawczyk K, Li W, Weber PK, Bridgeman TB, Davis TW, Mayali X. Quantification of microcystin production and biodegradation rates in the western basin of Lake Erie. Limnol Oceanogr 2022; 67:1470-1483. [PMID: 36248197 PMCID: PMC9543754 DOI: 10.1002/lno.12096] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 04/08/2022] [Accepted: 04/16/2022] [Indexed: 06/15/2023]
Abstract
Cyanobacterial biomass forecasts currently cannot predict the concentrations of microcystin, one of the most ubiquitous cyanotoxins that threaten human and wildlife health globally. Mechanistic insights into how microcystin production and biodegradation by heterotrophic bacteria change spatially and throughout the bloom season can aid in toxin concentration forecasts. We quantified microcystin production and biodegradation during two growth seasons in two western Lake Erie sites with different physicochemical properties commonly plagued by summer Microcystis blooms. Microcystin production rates were greater with elevated nutrients than under ambient conditions and were highest nearshore during the initial phases of the bloom, and production rates were lower in later bloom phases. We examined biodegradation rates of the most common and toxic microcystin by adding extracellular stable isotope-labeled microcystin-LR (1 μg L-1), which remained stable in the abiotic treatment (without bacteria) with minimal adsorption onto sediment, but strongly decreased in all unaltered biotic treatments, suggesting biodegradation. Greatest biodegradation rates (highest of -8.76 d-1, equivalent to the removal of 99.98% in 18 h) were observed during peak bloom conditions, while lower rates were observed with lower cyanobacteria biomass. Cell-specific nitrogen incorporation from microcystin-LR by nanoscale imaging mass spectrometry showed that a small percentage of the heterotrophic bacterial community actively degraded microcystin-LR. Microcystin production and biodegradation rates, combined with the microcystin incorporation by single cells, suggest that microcystin predictive models could be improved by incorporating toxin production and biodegradation rates, which are influenced by cyanobacterial bloom stage (early vs. late bloom), nutrient availability, and bacterial community composition.
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Affiliation(s)
- Justin D. Chaffin
- F.T. Stone Laboratory and Ohio Sea GrantThe Ohio State UniversityPut‐In‐BayOhioUSA
| | - Judy A. Westrick
- Lumigen Instrument CenterWayne State UniversityDetroitMichiganUSA
| | - Elliot Furr
- Department of Biological SciencesBowling Green State UniversityBowling GreenOhioUSA
| | | | - Laura A. Reitz
- Department of Biological SciencesBowling Green State UniversityBowling GreenOhioUSA
- Present address:
Department of Earth and Environmental SciencesUniversity of MichiganAnn ArborMichiganUSA
| | - Keara Stanislawczyk
- F.T. Stone Laboratory and Ohio Sea GrantThe Ohio State UniversityPut‐In‐BayOhioUSA
| | - Wei Li
- Physical and Life Sciences DirectorateLawrence Livermore National LaboratoryLivermoreCaliforniaUSA
| | - Peter K. Weber
- Physical and Life Sciences DirectorateLawrence Livermore National LaboratoryLivermoreCaliforniaUSA
| | | | - Timothy W. Davis
- Department of Biological SciencesBowling Green State UniversityBowling GreenOhioUSA
| | - Xavier Mayali
- Physical and Life Sciences DirectorateLawrence Livermore National LaboratoryLivermoreCaliforniaUSA
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15
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Buessecker S, Palmer M, Lai D, Dimapilis J, Mayali X, Mosier D, Jiao JY, Colman DR, Keller LM, St John E, Miranda M, Gonzalez C, Gonzalez L, Sam C, Villa C, Zhuo M, Bodman N, Robles F, Boyd ES, Cox AD, St Clair B, Hua ZS, Li WJ, Reysenbach AL, Stott MB, Weber PK, Pett-Ridge J, Dekas AE, Hedlund BP, Dodsworth JA. An essential role for tungsten in the ecology and evolution of a previously uncultivated lineage of anaerobic, thermophilic Archaea. Nat Commun 2022; 13:3773. [PMID: 35773279 PMCID: PMC9246946 DOI: 10.1038/s41467-022-31452-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 06/17/2022] [Indexed: 11/19/2022] Open
Abstract
Trace metals have been an important ingredient for life throughout Earth's history. Here, we describe the genome-guided cultivation of a member of the elusive archaeal lineage Caldarchaeales (syn. Aigarchaeota), Wolframiiraptor gerlachensis, and its growth dependence on tungsten. A metagenome-assembled genome (MAG) of W. gerlachensis encodes putative tungsten membrane transport systems, as well as pathways for anaerobic oxidation of sugars probably mediated by tungsten-dependent ferredoxin oxidoreductases that are expressed during growth. Catalyzed reporter deposition-fluorescence in-situ hybridization (CARD-FISH) and nanoscale secondary ion mass spectrometry (nanoSIMS) show that W. gerlachensis preferentially assimilates xylose. Phylogenetic analyses of 78 high-quality Wolframiiraptoraceae MAGs from terrestrial and marine hydrothermal systems suggest that tungsten-associated enzymes were present in the last common ancestor of extant Wolframiiraptoraceae. Our observations imply a crucial role for tungsten-dependent metabolism in the origin and evolution of this lineage, and hint at a relic metabolic dependence on this trace metal in early anaerobic thermophiles.
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Affiliation(s)
- Steffen Buessecker
- Department of Earth System Science, Stanford University, Stanford, CA, USA.
| | - Marike Palmer
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, USA.
| | - Dengxun Lai
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, USA
| | - Joshua Dimapilis
- Department of Biology, California State University, San Bernardino, CA, USA
| | - Xavier Mayali
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Damon Mosier
- Department of Biology, California State University, San Bernardino, CA, USA
- Department of Geoscience, University of Calgary, Calgary, AB, Canada
| | - Jian-Yu Jiao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, PR China
| | - Daniel R Colman
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Lisa M Keller
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Emily St John
- Department of Biology, Portland State University, Portland, OR, USA
| | - Michelle Miranda
- Department of Biology, California State University, San Bernardino, CA, USA
| | - Cristina Gonzalez
- Department of Biology, California State University, San Bernardino, CA, USA
| | - Lizett Gonzalez
- Department of Biology, California State University, San Bernardino, CA, USA
| | - Christian Sam
- Department of Biology, California State University, San Bernardino, CA, USA
| | - Christopher Villa
- Department of Biology, California State University, San Bernardino, CA, USA
| | - Madeline Zhuo
- Department of Biology, California State University, San Bernardino, CA, USA
| | - Nicholas Bodman
- Department of Biology, California State University, San Bernardino, CA, USA
| | - Fernando Robles
- Department of Biology, California State University, San Bernardino, CA, USA
| | - Eric S Boyd
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Alysia D Cox
- Department of Chemistry and Geochemistry, Montana Technological University, Butte, MT, USA
| | - Brian St Clair
- Department of Chemistry and Geochemistry, Montana Technological University, Butte, MT, USA
| | - Zheng-Shuang Hua
- Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, PR China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, PR China
- College of Fisheries, Henan Normal University, Xinxiang, PR China
| | | | - Matthew B Stott
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Peter K Weber
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
- Life & Environmental Sciences Department, University of Merced, Merced, CA, USA
| | - Anne E Dekas
- Department of Earth System Science, Stanford University, Stanford, CA, USA
| | - Brian P Hedlund
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, USA
| | - Jeremy A Dodsworth
- Department of Biology, California State University, San Bernardino, CA, USA.
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16
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See CR, Keller AB, Hobbie SE, Kennedy PG, Weber PK, Pett-Ridge J. Hyphae move matter and microbes to mineral microsites: Integrating the hyphosphere into conceptual models of soil organic matter stabilization. Glob Chang Biol 2022; 28:2527-2540. [PMID: 34989058 DOI: 10.1111/gcb.16073] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 12/03/2021] [Accepted: 12/03/2021] [Indexed: 06/14/2023]
Abstract
Associations between soil minerals and microbially derived organic matter (often referred to as mineral-associated organic matter or MAOM) form a large pool of slowly cycling carbon (C). The rhizosphere, soil immediately adjacent to roots, is thought to control the spatial extent of MAOM formation because it is the dominant entry point of new C inputs to soil. However, emphasis on the rhizosphere implicitly assumes that microbial redistribution of C into bulk (non-rhizosphere) soils is minimal. We question this assumption, arguing that because of extensive fungal exploration and rapid hyphal turnover, fungal redistribution of soil C from the rhizosphere to bulk soil minerals is common, and encourages MAOM formation. First, we summarize published estimates of fungal hyphal length density and turnover rates and demonstrate that fungal C inputs are high throughout the rhizosphere-bulk soil continuum. Second, because colonization of hyphal surfaces is a common dispersal mechanism for soil bacteria, we argue that hyphal exploration allows for the non-random colonization of mineral surfaces by hyphae-associated taxa. Third, these bacterial communities and their fungal hosts determine the chemical form of organic matter deposited on colonized mineral surfaces. Collectively, our analysis demonstrates that omission of the hyphosphere from conceptual models of soil C flow overlooks key mechanisms for MAOM formation in bulk soils. Moving forward, there is a clear need for spatially explicit, quantitative research characterizing the environmental drivers of hyphal exploration and hyphosphere community composition across systems, as these are important controls over the rate and organic chemistry of C deposited on minerals.
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Affiliation(s)
- Craig R See
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona, USA
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, Minnesota, USA
| | - Adrienne B Keller
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, Minnesota, USA
| | - Sarah E Hobbie
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, Minnesota, USA
| | - Peter G Kennedy
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, Minnesota, USA
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, Minnesota, USA
| | - Peter K Weber
- Physical and Life Science Directorate, Lawrence Livermore National Lab, Livermore, California, USA
| | - Jennifer Pett-Ridge
- Physical and Life Science Directorate, Lawrence Livermore National Lab, Livermore, California, USA
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17
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Wang D, Poyneer LA, Chen D, Mark Ammons S, Morrison KD, Lee J, Ly SS, Laurence TA, Weber PK. Wavefront shaping with a Hadamard basis for scattering soil imaging. Appl Opt 2022; 61:F47-F54. [PMID: 35333225 DOI: 10.1364/ao.442957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 12/17/2021] [Indexed: 06/14/2023]
Abstract
Soil is a scattering medium that inhibits imaging of plant-microbial-mineral interactions that are essential to plant health and soil carbon sequestration. However, optical imaging in the complex medium of soil has been stymied by the seemingly intractable problems of scattering and contrast. Here, we develop a wavefront shaping method based on adaptive stochastic parallel gradient descent optimization with a Hadamard basis to focus light through soil mineral samples. Our approach allows a sparse representation of the wavefront with reduced dimensionality for the optimization. We further divide the used Hadamard basis set into subsets and optimize a certain subset at once. Simulation and experimental optimization results demonstrate our method has an approximately seven times higher convergence rate and overall better performance compared to that with optimizing all pixels at once. The proposed method can benefit other high-dimensional optimization problems in adaptive optics and wavefront shaping.
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18
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Lee J, Hestrin R, Nuccio EE, Morrison KD, Ramon CE, Samo TJ, Pett-Ridge J, Ly SS, Laurence TA, Weber PK. Label-Free Multiphoton Imaging of Microbes in Root, Mineral, and Soil Matrices with Time-Gated Coherent Raman and Fluorescence Lifetime Imaging. Environ Sci Technol 2022; 56:1994-2008. [PMID: 35029104 DOI: 10.1021/acs.est.1c05818] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Imaging biogeochemical interactions in complex microbial systems─such as those at the soil-root interface─is crucial to studies of climate, agriculture, and environmental health but complicated by the three-dimensional (3D) juxtaposition of materials with a wide range of optical properties. We developed a label-free multiphoton nonlinear imaging approach to provide contrast and chemical information for soil microorganisms in roots and minerals with epi-illumination by simultaneously imaging two-photon excitation fluorescence (TPEF), coherent anti-Stokes Raman scattering (CARS), second-harmonic generation (SHG), and sum-frequency mixing (SFM). We used fluorescence lifetime imaging (FLIM) and time gating to correct CARS for the autofluorescence background native to soil particles and fungal hyphae (TG-CARS) using time-correlated single-photon counting (TCSPC). We combined TPEF, TG-CARS, and FLIM to maximize image contrast for live fungi and bacteria in roots and soil matrices without fluorescence labeling. Using this instrument, we imaged symbiotic arbuscular mycorrhizal fungi (AMF) structures within unstained plant roots in 3D to 60 μm depth. High-quality imaging was possible at up to 30 μm depth in a clay particle matrix and at 15 μm in complex soil preparation. TG-CARS allowed us to identify previously unknown lipid droplets in the symbiotic fungus, Serendipita bescii. We also visualized unstained putative bacteria associated with the roots of Brachypodium distachyon in a soil microcosm. Our results show that this multimodal approach holds significant promise for rhizosphere and soil science research.
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Affiliation(s)
- Janghyuk Lee
- Materials Science Division, Physical & Life Sciences, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Rachel Hestrin
- Nuclear and Chemical Sciences Division, Physical & Life Sciences, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Erin E Nuccio
- Nuclear and Chemical Sciences Division, Physical & Life Sciences, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Keith D Morrison
- Nuclear and Chemical Sciences Division, Physical & Life Sciences, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Christina E Ramon
- Nuclear and Chemical Sciences Division, Physical & Life Sciences, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Ty J Samo
- Nuclear and Chemical Sciences Division, Physical & Life Sciences, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Jennifer Pett-Ridge
- Nuclear and Chemical Sciences Division, Physical & Life Sciences, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
- Life and Environmental Sciences Department, University of California Merced, Merced, California 95343, United States
| | - Sonny S Ly
- Materials Science Division, Physical & Life Sciences, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Ted A Laurence
- Materials Science Division, Physical & Life Sciences, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Peter K Weber
- Nuclear and Chemical Sciences Division, Physical & Life Sciences, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
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19
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Abstract
High-resolution imaging with secondary ion mass spectrometry (nanoSIMS) has become a standard method in systems biology and environmental biogeochemistry and is broadly used to decipher ecophysiological traits of environmental microorganisms, metabolic processes in plant and animal tissues, and cross-kingdom symbioses. When combined with stable isotope-labeling-an approach we refer to as nanoSIP-nanoSIMS imaging offers a distinctive means to quantify net assimilation rates and stoichiometry of individual cell-sized particles in both low- and high-complexity environments. While the majority of nanoSIP studies in environmental and microbial biology have focused on nitrogen and carbon metabolism (using 15N and 13C tracers), multiple advances have pushed the capabilities of this approach in the past decade. The development of a high-brightness oxygen ion source has enabled high-resolution metal analyses that are easier to perform, allowing quantification of metal distribution in cells and environmental particles. New preparation methods, tools for automated data extraction from large data sets, and analytical approaches that push the limits of sensitivity and spatial resolution have allowed for more robust characterization of populations ranging from marine archaea to fungi and viruses. NanoSIMS studies continue to be enhanced by correlation with orthogonal imaging and 'omics approaches; when linked to molecular visualization methods, such as in situ hybridization and antibody labeling, these techniques enable in situ function to be linked to microbial identity and gene expression. Here we present an updated description of the primary materials, methods, and calculations used for nanoSIP, with an emphasis on recent advances in nanoSIMS applications, key methodological steps, and potential pitfalls.
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Affiliation(s)
- Jennifer Pett-Ridge
- Lawrence Livermore National Lab, Physical and Life Science Directorate, Livermore, CA, USA.
| | - Peter K Weber
- Lawrence Livermore National Lab, Physical and Life Science Directorate, Livermore, CA, USA.
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20
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Nuccio EE, Nguyen NH, Nunes da Rocha U, Mayali X, Bougoure J, Weber PK, Brodie E, Firestone M, Pett-Ridge J. Community RNA-Seq: multi-kingdom responses to living versus decaying roots in soil. ISME Commun 2021; 1:72. [PMID: 36765158 PMCID: PMC9723751 DOI: 10.1038/s43705-021-00059-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 09/14/2021] [Accepted: 09/23/2021] [Indexed: 12/25/2022]
Abstract
Roots are a primary source of organic carbon input in most soils. The consumption of living and detrital root inputs involves multi-trophic processes and multiple kingdoms of microbial life, but typical microbial ecology studies focus on only one or two major lineages. We used Illumina shotgun RNA sequencing to conduct PCR-independent SSU rRNA community analysis ("community RNA-Seq") and simultaneously assess the bacteria, archaea, fungi, and microfauna surrounding both living and decomposing roots of the annual grass, Avena fatua. Plants were grown in 13CO2-labeled microcosms amended with 15N-root litter to identify the preferences of rhizosphere organisms for root exudates (13C) versus decaying root biomass (15N) using NanoSIMS microarray imaging (Chip-SIP). When litter was available, rhizosphere and bulk soil had significantly more Amoebozoa, which are potentially important yet often overlooked top-down drivers of detritusphere community dynamics and nutrient cycling. Bulk soil containing litter was depleted in Actinobacteria but had significantly more Bacteroidetes and Proteobacteria. While Actinobacteria were abundant in the rhizosphere, Chip-SIP showed Actinobacteria preferentially incorporated litter relative to root exudates, indicating this group's more prominent role in detritus elemental cycling in the rhizosphere. Our results emphasize that decomposition is a multi-trophic process involving complex interactions, and our methodology can be used to track the trajectory of carbon through multi-kingdom soil food webs.
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Affiliation(s)
- Erin E Nuccio
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA.
| | - Nhu H Nguyen
- Department of Tropical Plant and Soil Sciences, University of Hawai'i at Mānoa, Honolulu, HI, USA
| | - Ulisses Nunes da Rocha
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Xavier Mayali
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Jeremy Bougoure
- Centre for Microscopy, Characterisation & Analysis, The University of Western Australia, Perth, Australia
| | - Peter K Weber
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Eoin Brodie
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, USA
| | - Mary Firestone
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, USA
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA.
- Life and Environmental Sciences Department, University of California Merced, Merced, CA, USA.
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21
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Trubl G, Kimbrel JA, Liquet-Gonzalez J, Nuccio EE, Weber PK, Pett-Ridge J, Jansson JK, Waldrop MP, Blazewicz SJ. Active virus-host interactions at sub-freezing temperatures in Arctic peat soil. Microbiome 2021; 9:208. [PMID: 34663463 PMCID: PMC8522061 DOI: 10.1186/s40168-021-01154-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 08/19/2021] [Indexed: 05/02/2023]
Abstract
BACKGROUND Winter carbon loss in northern ecosystems is estimated to be greater than the average growing season carbon uptake and is primarily driven by microbial decomposers. Viruses modulate microbial carbon cycling via induced mortality and metabolic controls, but it is unknown whether viruses are active under winter conditions (anoxic and sub-freezing temperatures). RESULTS We used stable isotope probing (SIP) targeted metagenomics to reveal the genomic potential of active soil microbial populations under simulated winter conditions, with an emphasis on viruses and virus-host dynamics. Arctic peat soils from the Bonanza Creek Long-Term Ecological Research site in Alaska were incubated under sub-freezing anoxic conditions with H218O or natural abundance water for 184 and 370 days. We sequenced 23 SIP-metagenomes and measured carbon dioxide (CO2) efflux throughout the experiment. We identified 46 bacterial populations (spanning 9 phyla) and 243 viral populations that actively took up 18O in soil and respired CO2 throughout the incubation. Active bacterial populations represented only a small portion of the detected microbial community and were capable of fermentation and organic matter degradation. In contrast, active viral populations represented a large portion of the detected viral community and one third were linked to active bacterial populations. We identified 86 auxiliary metabolic genes and other environmentally relevant genes. The majority of these genes were carried by active viral populations and had diverse functions such as carbon utilization and scavenging that could provide their host with a fitness advantage for utilizing much-needed carbon sources or acquiring essential nutrients. CONCLUSIONS Overall, there was a stark difference in the identity and function of the active bacterial and viral community compared to the unlabeled community that would have been overlooked with a non-targeted standard metagenomic analysis. Our results illustrate that substantial active virus-host interactions occur in sub-freezing anoxic conditions and highlight viruses as a major community-structuring agent that likely modulates carbon loss in peat soils during winter, which may be pivotal for understanding the future fate of arctic soils' vast carbon stocks. Video abstract.
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Affiliation(s)
- Gareth Trubl
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA.
| | - Jeffrey A Kimbrel
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Jose Liquet-Gonzalez
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Erin E Nuccio
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Peter K Weber
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
- Department of Life and Environmental Sciences, University of California, Merced, CA, 95343, USA
| | - Janet K Jansson
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Mark P Waldrop
- U.S. Geological Survey, Geology, Minerals, Energy, and Geophysics Science Center, Menlo Park, CA, USA
| | - Steven J Blazewicz
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA.
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22
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Hestrin R, Weber PK, Pett-Ridge J, Lehmann J. Plants and mycorrhizal symbionts acquire substantial soil nitrogen from gaseous ammonia transport. New Phytol 2021; 231:1746-1757. [PMID: 34077566 DOI: 10.1111/nph.17527] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 05/20/2021] [Indexed: 06/12/2023]
Abstract
Nitrogen (N) is an essential nutrient that limits plant growth in many ecosystems. Here we investigate an overlooked component of the terrestrial N cycle - subsurface ammonia (NH3 ) gas transport and its contribution to plant and mycorrhizal N acquisition. We used controlled mesocosms, soil incubations, stable isotopes, and imaging to investigate edaphic drivers of NH3 gas efflux, track lateral subsurface N transport originating from 15 NH3 gas or 15 N-enriched organic matter, and assess plant and mycorrhizal N assimilation from this gaseous transport pathway. NH3 is released from soil organic matter, travels belowground, and contributes to root and fungal N content. Abiotic soil properties (pH and texture) influence the quantity of NH3 available for subsurface transport. Mutualisms with arbuscular mycorrhizal (AM) fungi can substantially increase plant NH3 -N uptake. The grass Brachypodium distachyon acquired 6-9% of total plant N from organic matter-N that traveled as a gas belowground. Colonization by the AM fungus Rhizophagus irregularis was associated with a two-fold increase in total plant N acquisition from subsurface NH3 gas. NH3 gas transport and uptake pathways may be fundamentally different from those of more commonly studied soil N species and warrant further research.
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Affiliation(s)
- Rachel Hestrin
- Soil and Crop Sciences, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
- Lawrence Livermore National Laboratory, Physical and Life Science Directorate, Livermore, CA, 94550, USA
| | - Peter K Weber
- Lawrence Livermore National Laboratory, Physical and Life Science Directorate, Livermore, CA, 94550, USA
| | - Jennifer Pett-Ridge
- Lawrence Livermore National Laboratory, Physical and Life Science Directorate, Livermore, CA, 94550, USA
| | - Johannes Lehmann
- Soil and Crop Sciences, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
- Cornell Atkinson Center for Sustainability, Cornell University, Ithaca, NY, 14853, USA
- Institute for Advanced Study, TU München, Garching, 85748, Germany
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23
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Stuart RK, Pederson ERA, Weyman PD, Weber PK, Rassmussen U, Dupont CL. Bidirectional C and N transfer and a potential role for sulfur in an epiphytic diazotrophic mutualism. ISME J 2020; 14:3068-3078. [PMID: 32814866 PMCID: PMC7784912 DOI: 10.1038/s41396-020-00738-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 06/09/2020] [Accepted: 08/05/2020] [Indexed: 01/23/2023]
Abstract
In nitrogen-limited boreal forests, associations between feathermoss and diazotrophic cyanobacteria control nitrogen inputs and thus carbon cycling, but little is known about the molecular regulators required for initiation and maintenance of these associations. Specifically, a benefit to the cyanobacteria is not known, challenging whether the association is a nutritional mutualism. Targeted mutagenesis of the cyanobacterial alkane sulfonate monooxygenase results in an inability to colonize feathermosses by the cyanobacterium Nostoc punctiforme, suggesting a role for organic sulfur in communication or nutrition. Isotope probing paired with high-resolution imaging mass spectrometry (NanoSIMS) demonstrated bidirectional elemental transfer between partners, with carbon and sulfur both being transferred to the cyanobacteria, and nitrogen transferred to the moss. These results support the hypothesis that moss and cyanobacteria enter a mutualistic exosymbiosis with substantial bidirectional material exchange of carbon and nitrogen and potential signaling through sulfur compounds.
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Affiliation(s)
- Rhona K Stuart
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA.
| | - Eric R A Pederson
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 106 91, Stockholm, Sweden
| | - Philip D Weyman
- J. Craig Venter Institute, La Jolla, CA, 92037, USA
- Zymergen Inc., Emeryville, CA, USA
| | - Peter K Weber
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA
| | - Ulla Rassmussen
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 106 91, Stockholm, Sweden
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24
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Jovanovic SV, Weber PK, Pidduck AJ, Gaffney AM, Girard P, Pointurier F, Hedberg M, Simons AJ, Stebelkov V, Kell T, Knight K, Parsons-Davis T, Kristo M, Williams RW, Treinen KC, Montgomery NJ, King J, Wickenden A, Knight D, Fauré AL, Hubert A, Albert N, Vincent MC, Wallenius M, Elantyev IA, Zhizhin KD, Schwantes JM, Marsden O, Taylor F. Uncovering uranium isotopic heterogeneity of fuel pellets from the fifth collaborative materials exercise of The Nuclear Forensics International Technical Working Group. J Radioanal Nucl Chem 2020. [DOI: 10.1007/s10967-020-07470-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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25
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Gross A, Lin Y, Weber PK, Pett‐Ridge J, Silver WL. The role of soil redox conditions in microbial phosphorus cycling in humid tropical forests. Ecology 2019; 101:e02928. [DOI: 10.1002/ecy.2928] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 07/16/2019] [Accepted: 09/25/2019] [Indexed: 11/10/2022]
Affiliation(s)
- Avner Gross
- Department of Environmental Science, Policy, & Management University of California Berkeley Berkeley California 94720 USA
- Department of Geography and Environmental Development Ben Gurion University of the Negev Beer Sheva Israel
| | - Yang Lin
- Department of Environmental Science, Policy, & Management University of California Berkeley Berkeley California 94720 USA
| | - Peter K. Weber
- Lawrence Livermore National Laboratory Physical and Life Science Directorate Livermore California 94550 USA
| | - Jennifer Pett‐Ridge
- Lawrence Livermore National Laboratory Physical and Life Science Directorate Livermore California 94550 USA
| | - Whendee L. Silver
- Department of Environmental Science, Policy, & Management University of California Berkeley Berkeley California 94720 USA
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26
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Dekas AE, Parada AE, Mayali X, Fuhrman JA, Wollard J, Weber PK, Pett-Ridge J. Characterizing Chemoautotrophy and Heterotrophy in Marine Archaea and Bacteria With Single-Cell Multi-isotope NanoSIP. Front Microbiol 2019; 10:2682. [PMID: 31920997 PMCID: PMC6927911 DOI: 10.3389/fmicb.2019.02682] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 11/05/2019] [Indexed: 11/28/2022] Open
Abstract
Characterizing and quantifying in situ metabolisms remains both a central goal and challenge for environmental microbiology. Here, we used a single-cell, multi-isotope approach to investigate the anabolic activity of marine microorganisms, with an emphasis on natural populations of Thaumarchaeota. After incubating coastal Pacific Ocean water with 13C-bicarbonate and 15N-amino acids, we used nanoscale secondary ion mass spectrometry (nanoSIMS) to isotopically screen 1,501 individual cells, and 16S rRNA amplicon sequencing to assess community composition. We established isotopic enrichment thresholds for activity and metabolic classification, and with these determined the percentage of anabolically active cells, the distribution of activity across the whole community, and the metabolic lifestyle—chemoautotrophic or heterotrophic—of each cell. Most cells (>90%) were anabolically active during the incubation, and 4–17% were chemoautotrophic. When we inhibited bacteria with antibiotics, the fraction of chemoautotrophic cells detected via nanoSIMS increased, suggesting archaea dominated chemoautotrophy. With fluorescence in situ hybridization coupled to nanoSIMS (FISH-nanoSIMS), we confirmed that most Thaumarchaeota were living chemoautotrophically, while bacteria were not. FISH-nanoSIMS analysis of cells incubated with dual-labeled (13C,15N-) amino acids revealed that most Thaumarchaeota cells assimilated amino-acid-derived nitrogen but not carbon, while bacteria assimilated both. This indicates that some Thaumarchaeota do not assimilate intact amino acids, suggesting intra-phylum heterogeneity in organic carbon utilization, and potentially their use of amino acids for nitrification. Together, our results demonstrate the utility of multi-isotope nanoSIMS analysis for high-throughput metabolic screening, and shed light on the activity and metabolism of uncultured marine archaea and bacteria.
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Affiliation(s)
- Anne E Dekas
- Department of Earth System Science, Stanford University, Stanford, CA, United States.,Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Alma E Parada
- Department of Earth System Science, Stanford University, Stanford, CA, United States.,Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States
| | - Xavier Mayali
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Jed A Fuhrman
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States
| | - Jessica Wollard
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Peter K Weber
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States
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27
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Tsednee M, Castruita M, Salomé PA, Sharma A, Lewis BE, Schmollinger SR, Strenkert D, Holbrook K, Otegui MS, Khatua K, Das S, Datta A, Chen S, Ramon C, Ralle M, Weber PK, Stemmler TL, Pett-Ridge J, Hoffman BM, Merchant SS. Manganese co-localizes with calcium and phosphorus in Chlamydomonas acidocalcisomes and is mobilized in manganese-deficient conditions. J Biol Chem 2019; 294:17626-17641. [PMID: 31527081 DOI: 10.1074/jbc.ra119.009130] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 09/09/2019] [Indexed: 12/27/2022] Open
Abstract
Exposing cells to excess metal concentrations well beyond the cellular quota is a powerful tool for understanding the molecular mechanisms of metal homeostasis. Such improved understanding may enable bioengineering of organisms with improved nutrition and bioremediation capacity. We report here that Chlamydomonas reinhardtii can accumulate manganese (Mn) in proportion to extracellular supply, up to 30-fold greater than its typical quota and with remarkable tolerance. As visualized by X-ray fluorescence microscopy and nanoscale secondary ion MS (nanoSIMS), Mn largely co-localizes with phosphorus (P) and calcium (Ca), consistent with the Mn-accumulating site being an acidic vacuole, known as the acidocalcisome. Vacuolar Mn stores are accessible reserves that can be mobilized in Mn-deficient conditions to support algal growth. We noted that Mn accumulation depends on cellular polyphosphate (polyP) content, indicated by 1) a consistent failure of C. reinhardtii vtc1 mutant strains, which are deficient in polyphosphate synthesis, to accumulate Mn and 2) a drastic reduction of the Mn storage capacity in P-deficient cells. Rather surprisingly, X-ray absorption spectroscopy, EPR, and electron nuclear double resonance revealed that only little Mn2+ is stably complexed with polyP, indicating that polyP is not the final Mn ligand. We propose that polyPs are a critical component of Mn accumulation in Chlamydomonas by driving Mn relocation from the cytosol to acidocalcisomes. Within these structures, polyP may, in turn, escort vacuolar Mn to a number of storage ligands, including phosphate and phytate, and other, yet unidentified, compounds.
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Affiliation(s)
| | - Madeli Castruita
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095
| | - Patrice A Salomé
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095.,Institute for Genomics and Proteomics, UCLA, Los Angeles, California 90095
| | - Ajay Sharma
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208
| | - Brianne E Lewis
- Department of Pharmaceutical Sciences, Wayne State University, Detroit, Michigan 48201
| | - Stefan R Schmollinger
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095.,Institute for Genomics and Proteomics, UCLA, Los Angeles, California 90095
| | - Daniela Strenkert
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095.,Institute for Genomics and Proteomics, UCLA, Los Angeles, California 90095
| | - Kristen Holbrook
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095
| | - Marisa S Otegui
- Departments of Botany and Genetics, University of Wisconsin, Madison, Wisconsin 53706
| | - Kaustav Khatua
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
| | - Sayani Das
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
| | - Ankona Datta
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
| | - Si Chen
- Advanced Photon Source, Argonne National Laboratory, Lemont, Illinois 60439
| | - Christina Ramon
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550
| | - Martina Ralle
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, Oregon 97239
| | - Peter K Weber
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550
| | - Timothy L Stemmler
- Department of Pharmaceutical Sciences, Wayne State University, Detroit, Michigan 48201
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550
| | - Brian M Hoffman
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208
| | - Sabeeha S Merchant
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095 .,Institute for Genomics and Proteomics, UCLA, Los Angeles, California 90095
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Kips R, Weber PK, Kristo MJ, Jacobsen B, Ramon EC. Microscale Isotopic Variation in Uranium Fuel Pellets with Implications for Nuclear Forensics. Anal Chem 2019; 91:11598-11605. [DOI: 10.1021/acs.analchem.9b01737] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ruth Kips
- Lawrence Livermore National Laboratory, Mailstop L-235, P.O. Box 808, Livermore, California 94550, United States
| | - Peter K. Weber
- Lawrence Livermore National Laboratory, Mailstop L-235, P.O. Box 808, Livermore, California 94550, United States
| | - Michael J. Kristo
- Lawrence Livermore National Laboratory, Mailstop L-235, P.O. Box 808, Livermore, California 94550, United States
| | - Benjamin Jacobsen
- Lawrence Livermore National Laboratory, Mailstop L-235, P.O. Box 808, Livermore, California 94550, United States
| | - Erick C. Ramon
- Lawrence Livermore National Laboratory, Mailstop L-235, P.O. Box 808, Livermore, California 94550, United States
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29
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Gómez-Consarnau L, Needham DM, Weber PK, Fuhrman JA, Mayali X. Influence of Light on Particulate Organic Matter Utilization by Attached and Free-Living Marine Bacteria. Front Microbiol 2019; 10:1204. [PMID: 31214143 PMCID: PMC6558058 DOI: 10.3389/fmicb.2019.01204] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 05/13/2019] [Indexed: 11/13/2022] Open
Abstract
Light plays a central role on primary productivity of aquatic systems. Yet, its potential impact on the degradation of photosynthetically produced biomass is not well understood. We investigated the patterns of light-induced particle breakdown and bacterial assimilation of detrital C and N using 13C and 15N labeled freeze-thawed diatom cells incubated in laboratory microcosms with a marine microbial community freshly collected from the Pacific Ocean. Particles incubated in the dark resulted in increased bacterial counts and dissolved organic carbon concentrations compared to those incubated in the light. Light also influenced the attached and free-living microbial community structure as detected by 16S rRNA gene amplicon sequencing. For example, Sphingobacteriia were enriched on dark-incubated particles and taxa from the family Flavobacteriaceae and the genus Pseudoalteromonas were numerically enriched on particles in the light. Isotope incorporation analysis by phylogenetic microarray and NanoSIMS (a method called Chip-SIP) identified free-living and attached microbial taxa able to incorporate N and C from the particles. Some taxa, including members of the Flavobacteriaceae and Cryomorphaceae, exhibited increased isotope incorporation in the light, suggesting the use of photoheterotrophic metabolisms. In contrast, some members of Oceanospirillales and Rhodospirillales showed decreased isotope incorporation in the light, suggesting that their heterotrophic metabolism, particularly when occurring on particles, might increase at night or may be inhibited by sunlight. These results show that light influences particle degradation and C and N incorporation by attached bacteria, suggesting that the transfer between particulate and free-living phases are likely affected by external factors that change with the light regime, such as time of day, water column depth and season.
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Affiliation(s)
- Laura Gómez-Consarnau
- Departamento de Oceanografía Biológica, Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), Ensenada, Mexico.,Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States
| | - David M Needham
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States
| | - Peter K Weber
- Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Jed A Fuhrman
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States
| | - Xavier Mayali
- Lawrence Livermore National Laboratory, Livermore, CA, United States
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30
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Kraft ML, Yeager AN, Weber PK, Joshua J. Direct Imaging of the Cholesterol and Sphingolipid Abundance at the Site of Influenza Virus Assembly with High‐Resolution SIMS. FASEB J 2019. [DOI: 10.1096/fasebj.2019.33.1_supplement.797.5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Mary L Kraft
- Chemical & Biomolecular EngrUniversity of Illinois, Urbana‐ChampaignUrbanaIL
| | - Ashley N Yeager
- Chemical & Biomolecular EngrUniversity of Illinois, Urbana‐ChampaignUrbanaIL
| | - Peter K Weber
- Glenn T. Seaborg InstituteLawrence Livermore National LaboratLivermoreCA
| | - Joshua Joshua
- Laboratory of Cellular and Molecular BiophysicsNational Institute of Child Health and Human DevelopmentBethesdaMD
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31
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Samo TJ, Kimbrel JA, Nilson DJ, Pett-Ridge J, Weber PK, Mayali X. Attachment between heterotrophic bacteria and microalgae influences symbiotic microscale interactions. Environ Microbiol 2018; 20:4385-4400. [PMID: 30022580 DOI: 10.1111/1462-2920.14357] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 05/15/2018] [Accepted: 07/08/2018] [Indexed: 01/25/2023]
Abstract
The surface and surroundings of microalgal cells (phycosphere) are critical interaction zones but have been difficult to functionally interrogate due to methodological limitations. We examined effects of phycosphere-associated bacteria for two biofuel-relevant microalgal species (Phaeodactylum tricornutum and Nannochloropsis salina) using stable isotope tracing and high spatial resolution mass spectrometry imaging (NanoSIMS) to quantify elemental exchanges at the single-cell level. Each algal species responded differently to bacterial attachment. In P. tricornutum, a high percentage of cells had attached bacteria (92%-98%, up to eight bacteria per alga) and fixed 64% more carbon with attached bacteria compared to axenic cells. In contrast, N. salina cells were less commonly associated with bacteria (42%-63%), harboured fewer bacteria per alga, and fixed 10% more carbon without attached bacteria compared to axenic cells. An uncultivated bacterium related to Haliscomenobacter sp. was identified as an effective mutualist; it increased carbon fixation when attached to P. tricornutum and incorporated 71% more algal-fixed carbon relative to other bacteria. Our results illustrate how phylogenetic identity and physical location of bacteria and algae facilitate diverse metabolic responses. Phycosphere-mediated, mutualistic chemical exchanges between autotrophs and heterotrophs may be a fruitful means to increase microalgal productivity for applied engineering efforts.
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Affiliation(s)
- Ty J Samo
- Lawrence Livermore National Laboratory, Nuclear and Chemical, Sciences Division, 7000 East Avenue, Livermore, California
| | - Jeffrey A Kimbrel
- Lawrence Livermore National Laboratory, Bioscience and Biotechnology Division, 7000 East Avenue, Livermore, California
| | - Daniel J Nilson
- Lawrence Livermore National Laboratory, Nuclear and Chemical, Sciences Division, 7000 East Avenue, Livermore, California
| | - Jennifer Pett-Ridge
- Lawrence Livermore National Laboratory, Nuclear and Chemical, Sciences Division, 7000 East Avenue, Livermore, California
| | - Peter K Weber
- Lawrence Livermore National Laboratory, Nuclear and Chemical, Sciences Division, 7000 East Avenue, Livermore, California
| | - Xavier Mayali
- Lawrence Livermore National Laboratory, Nuclear and Chemical, Sciences Division, 7000 East Avenue, Livermore, California
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32
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Lee JZ, Everroad RC, Karaoz U, Detweiler AM, Pett-Ridge J, Weber PK, Prufert-Bebout L, Bebout BM. Metagenomics reveals niche partitioning within the phototrophic zone of a microbial mat. PLoS One 2018; 13:e0202792. [PMID: 30204767 PMCID: PMC6133358 DOI: 10.1371/journal.pone.0202792] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2018] [Accepted: 08/09/2018] [Indexed: 11/19/2022] Open
Abstract
Hypersaline photosynthetic microbial mats are stratified microbial communities known for their taxonomic and metabolic diversity and strong light-driven day-night environmental gradients. In this study of the upper photosynthetic zone of hypersaline microbial mats of Elkhorn Slough, California (USA), we show how metagenome sequencing can be used to meaningfully assess microbial ecology and genetic partitioning in these complex microbial systems. Mapping of metagenome reads to the dominant Cyanobacteria observed in the system, Coleofasciculus (Microcoleus) chthonoplastes, was used to examine strain variants within these metagenomes. Highly conserved gene subsystems indicated a core genome for the species, and a number of variant genes and subsystems suggested strain level differentiation, especially for nutrient utilization and stress response. Metagenome sequence coverage binning was used to assess ecosystem partitioning of remaining microbes to both reconstruct the model organisms in silico and identify their ecosystem functions as well as to identify novel clades and propose their role in the biogeochemical cycling of mats. Functional gene annotation of these bins (primarily of Proteobacteria, Bacteroidetes, and Cyanobacteria) recapitulated the known biogeochemical functions in microbial mats using a genetic basis, and revealed significant diversity in the Bacteroidetes, presumably in heterotrophic cycling. This analysis also revealed evidence of putative phototrophs within the Gemmatimonadetes and Gammaproteobacteria residing in microbial mats. This study shows that metagenomic analysis can produce insights into the systems biology of microbial ecosystems from a genetic perspective and to suggest further studies of novel microbes.
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Affiliation(s)
- Jackson Z. Lee
- Exobiology Branch, NASA Ames Research Center, Moffett Field, CA, United States of America
- Bay Area Environmental Research Institute, Petaluma, CA, United States of America
- * E-mail:
| | - R. Craig Everroad
- Exobiology Branch, NASA Ames Research Center, Moffett Field, CA, United States of America
| | - Ulas Karaoz
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, United States of America
| | - Angela M. Detweiler
- Exobiology Branch, NASA Ames Research Center, Moffett Field, CA, United States of America
- Bay Area Environmental Research Institute, Petaluma, CA, United States of America
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States of America
| | - Peter K. Weber
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States of America
| | - Leslie Prufert-Bebout
- Exobiology Branch, NASA Ames Research Center, Moffett Field, CA, United States of America
| | - Brad M. Bebout
- Exobiology Branch, NASA Ames Research Center, Moffett Field, CA, United States of America
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33
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Mayali X, Weber PK. Quantitative isotope incorporation reveals substrate partitioning in a coastal microbial community. FEMS Microbiol Ecol 2018; 94:4944225. [PMID: 29562328 DOI: 10.1093/femsec/fiy047] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Accepted: 03/17/2018] [Indexed: 11/13/2022] Open
Abstract
To quantitatively link microbial identity with biogeochemical function, we carried out 14 simultaneous stable isotope probing experiments with organic and inorganic C and N substrates to measure the isotope incorporation by over one hundred co-occurring eukaryotic and prokaryotic populations in a coastal community. We found that nitrate was the most commonly incorporated substrate, and that light-driven carbon fixation was carried out by some bacterial taxa from the Flavobacteriales and OM60 (NOR5) clade, in addition to photoautotrophic phytoplankton. We found that organisms that incorporated starch, maltose, glucose, lactose and bicarbonate were phylogenetically clustered, suggesting that specific bacterial lineages specialized in the incorporation of these substrates. The data further revealed that coastal microorganisms spanned a range of resource utilization strategies from generalists to specialists and demonstrated a high level of substrate partitioning, with two thirds of taxa exhibiting unique substrate incorporation patterns and the remaining third shared by no more than three OTUs each. Specialists exhibited more extreme incorporation levels (high or low), whereas generalists displayed more intermediate activity levels. These results shed valuable insights into the bottom-up ecological strategies enabling the persistence of high microbial diversity in aquatic ecosystems.
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Affiliation(s)
- Xavier Mayali
- Nuclear and Chemical Science Division, Lawrence Livermore National Laboratory, 7000 East Ave, Livermore CA 94550 USA
| | - Peter K Weber
- Nuclear and Chemical Science Division, Lawrence Livermore National Laboratory, 7000 East Ave, Livermore CA 94550 USA
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34
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Yeager AN, Weber PK, Kraft ML. Cholesterol is enriched in the sphingolipid patches on the substrate near nonpolarized MDCK cells, but not in the sphingolipid domains in their plasma membranes. Biochim Biophys Acta Biomembr 2018; 1860:2004-2011. [PMID: 29684331 DOI: 10.1016/j.bbamem.2018.04.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2018] [Revised: 03/15/2018] [Accepted: 04/16/2018] [Indexed: 10/17/2022]
Abstract
Information about the distributions of cholesterol and sphingolipids within the plasma membranes of mammalian cells provides insight into the roles of these molecules in membrane function. In this report, high-resolution secondary ion mass spectrometry was used to image the distributions of metabolically incorporated rare isotope-labeled sphingolipids and cholesterol on the surfaces of nonpolarized epithelial cells. Sphingolipid domains that were not enriched with cholesterol were detected in the plasma membranes of subconfluent Madin-Darby canine kidney cells. Surprisingly, cholesterol-enriched sphingolipid patches were observed on the substrate adjacent to these cells. Based on the shapes of these cholesterol-enriched sphingolipid patches on the substrate and their proximity to cellular projections, we hypothesize that they are deposits of membranous particles released by the cell.
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Affiliation(s)
- Ashley N Yeager
- Department of Chemical and Biomolecular Engineering, University of Illinois, Urbana, IL 61801, United States
| | - Peter K Weber
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94551, United States
| | - Mary L Kraft
- Department of Chemical and Biomolecular Engineering, University of Illinois, Urbana, IL 61801, United States.
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35
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Ackerman CM, Weber PK, Xiao T, Thai B, Kuo TJ, Zhang E, Pett-Ridge J, Chang CJ. Multimodal LA-ICP-MS and nanoSIMS imaging enables copper mapping within photoreceptor megamitochondria in a zebrafish model of Menkes disease. Metallomics 2018; 10:474-485. [PMID: 29507920 DOI: 10.1039/c7mt00349h] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Copper is essential for eukaryotic life, and animals must acquire this nutrient through the diet and distribute it to cells and organelles for proper function of biological targets. Indeed, mutations in the central copper exporter ATP7A contribute to a spectrum of diseases, including Menkes disease, with symptoms ranging from neurodegeneration to lax connective tissue. As such, a better understanding of the fundamental impacts of ATP7A mutations on in vivo copper distributions is of relevance to those affected by these diseases. Here we combine metal imaging and optical imaging techniques at a variety of spatial resolutions to identify tissues and structures with altered copper levels in the Calamitygw71 zebrafish model of Menkes disease. Rapid profiling of tissue slices with LA-ICP-MS identified reduced copper levels in the brain, neuroretina, and liver of Menkes fish compared to control specimens. High resolution nanoSIMS imaging of the neuroretina, combined with electron and confocal microscopies, identified the megamitochondria of photoreceptors as loci of copper accumulation in wildtype fish, with lower levels of megamitochondrial copper observed in Calamitygw71 zebrafish. Interestingly, this localized copper decrease does not result in impaired photoreceptor development or altered megamitochondrial morphology, suggesting the prioritization of copper at sufficient levels for maintaining essential mitochondrial functions. Together, these data establish the Calamitygw71 zebrafish as an optically transparent in vivo model for the study of neural copper misregulation, illuminate a role for the ATP7A copper exporter in trafficking copper to the neuroretina, and highlight the utility of combining multiple imaging techniques for studying metals in whole organism settings with spatial resolution.
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Affiliation(s)
- Cheri M Ackerman
- Department of Chemistry, University of California, Berkeley, California, USA.
| | - Peter K Weber
- Nuclear and Chemical Sciences Division, Lawrence Livermore National Laboratory, Livermore, California, USA.
| | - Tong Xiao
- Department of Chemistry, University of California, Berkeley, California, USA. and Howard Hughes Medical Institute, University of California, Berkeley, California, USA
| | - Bao Thai
- Department of Chemistry, University of California, Berkeley, California, USA.
| | - Tiffani J Kuo
- Department of Chemistry, University of California, Berkeley, California, USA.
| | - Emily Zhang
- Department of Chemistry, University of California, Berkeley, California, USA.
| | - Jennifer Pett-Ridge
- Nuclear and Chemical Sciences Division, Lawrence Livermore National Laboratory, Livermore, California, USA.
| | - Christopher J Chang
- Department of Chemistry, University of California, Berkeley, California, USA. and Howard Hughes Medical Institute, University of California, Berkeley, California, USA and Department of Molecular and Cellular Biology, University of California, Berkeley, California, USA and Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
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36
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Gates SD, Condit RC, Moussatche N, Stewart BJ, Malkin AJ, Weber PK. High Initial Sputter Rate Found for Vaccinia Virions Using Isotopic Labeling, NanoSIMS, and AFM. Anal Chem 2018; 90:1613-1620. [PMID: 29295620 DOI: 10.1021/acs.analchem.7b02786] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
High-lateral-resolution secondary ion mass spectrometry (SIMS) has the potential to provide functional and depth resolved information from small biological structures, such as viral particles (virions) and phage, but sputter rate and sensitivity are not characterized at shallow depths relevant to these structures. Here we combine stable isotope labeling of the DNA of vaccinia virions with correlated SIMS imaging depth profiling and atomic force microscopy (AFM) to develop a nonlinear, nonequilibrium sputter rate model for the virions and validate the model on the basis of reconstructing the location of the DNA within individual virions. Our experiments with a Cs+ beam show an unexpectedly high initial sputter rate (∼100 um2·nm·pA-1·s-1) with a rapid decline to an asymptotic rate of 0.7 um2·nm·pA-1·s-1 at an approximate depth of 70 nm. Correlated experiments were also conducted with glutaraldehyde-fixed virions, as well as O- and Ga+ beams, yielding similar results. Based on our Cs+ sputter rate model, the labeled DNA in the virion was between 50 and 90 nm depth in the virion core, consistent with expectations, supporting our conclusions. Virion densification was found to be a secondary effect. Accurate isotopic ratios were obtained from the initiation of sputtering, suggesting that isotopic tracers could be successfully used for smaller virions and phage.
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Affiliation(s)
| | - Richard C Condit
- Department of Molecular Genetics and Microbiology, University of Florida , Gainesville, Florida 32610, United States
| | - Nissin Moussatche
- Department of Molecular Genetics and Microbiology, University of Florida , Gainesville, Florida 32610, United States
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37
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D'haeseleer P, Lee JZ, Prufert-Bebout L, Burow LC, Detweiler AM, Weber PK, Karaoz U, Brodie EL, Glavina Del Rio T, Tringe SG, Bebout BM, Pett-Ridge J. Metagenomic analysis of intertidal hypersaline microbial mats from Elkhorn Slough, California, grown with and without molybdate. Stand Genomic Sci 2017; 12:67. [PMID: 29167704 PMCID: PMC5688640 DOI: 10.1186/s40793-017-0279-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 10/25/2017] [Indexed: 11/10/2022] Open
Abstract
Cyanobacterial mats are laminated microbial ecosystems which occur in highly diverse environments and which may provide a possible model for early life on Earth. Their ability to produce hydrogen also makes them of interest from a biotechnological and bioenergy perspective. Samples of an intertidal microbial mat from the Elkhorn Slough estuary in Monterey Bay, California, were transplanted to a greenhouse at NASA Ames Research Center to study a 24-h diel cycle, in the presence or absence of molybdate (which inhibits biohydrogen consumption by sulfate reducers). Here, we present metagenomic analyses of four samples that will be used as references for future metatranscriptomic analyses of this diel time series.
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Affiliation(s)
| | | | | | - Luke C Burow
- NASA Ames Research Center, Moffett Field, CA USA.,Stanford University, Stanford, CA USA
| | - Angela M Detweiler
- NASA Ames Research Center, Moffett Field, CA USA.,Bay Area Environmental Research Institute, Petaluma, CA USA
| | - Peter K Weber
- Lawrence Livermore National Laboratory, Livermore, CA USA
| | - Ulas Karaoz
- Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Eoin L Brodie
- Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Tijana Glavina Del Rio
- Lawrence Berkeley National Laboratory, Berkeley, CA USA.,Department of Energy Joint Genome Institute, Walnut Creek, CA USA
| | - Susannah G Tringe
- Lawrence Berkeley National Laboratory, Berkeley, CA USA.,Department of Energy Joint Genome Institute, Walnut Creek, CA USA
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38
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Bryson S, Li Z, Chavez F, Weber PK, Pett-Ridge J, Hettich RL, Pan C, Mayali X, Mueller RS. Phylogenetically conserved resource partitioning in the coastal microbial loop. ISME J 2017; 11:2781-2792. [PMID: 28800138 PMCID: PMC5702734 DOI: 10.1038/ismej.2017.128] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 05/18/2017] [Accepted: 06/01/2017] [Indexed: 11/09/2022]
Abstract
Resource availability influences marine microbial community structure, suggesting that population-specific resource partitioning defines discrete niches. Identifying how resources are partitioned among populations, thereby characterizing functional guilds within the communities, remains a challenge for microbial ecologists. We used proteomic stable isotope probing (SIP) and NanoSIMS analysis of phylogenetic microarrays (Chip-SIP) along with 16S rRNA gene amplicon and metagenomic sequencing to characterize the assimilation of six 13C-labeled common metabolic substrates and changes in the microbial community structure within surface water collected from Monterey Bay, CA. Both sequencing approaches indicated distinct substrate-specific community shifts. However, observed changes in relative abundance for individual populations did not correlate well with directly measured substrate assimilation. The complementary SIP techniques identified assimilation of all six substrates by diverse taxa, but also revealed differential assimilation of substrates into protein and ribonucleotide biomass between taxa. Substrate assimilation trends indicated significantly conserved resource partitioning among populations within the Flavobacteriia, Alphaproteobacteria and Gammaproteobacteria classes, suggesting that functional guilds within marine microbial communities are phylogenetically cohesive. However, populations within these classes exhibited heterogeneity in biosynthetic activity, which distinguished high-activity copiotrophs from low-activity oligotrophs. These results indicate distinct growth responses between populations that is not apparent by genome sequencing alone.
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Affiliation(s)
- Samuel Bryson
- Department of Microbiology, Oregon State University, Corvallis, OR, USA
| | - Zhou Li
- Graduate School of Genome Science and Technology, The University of Tennessee, Knoxville, TN, USA.,Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | | | - Peter K Weber
- Lawrence Livermore National Laboratory, Livermore, CA, USA
| | | | - Robert L Hettich
- Graduate School of Genome Science and Technology, The University of Tennessee, Knoxville, TN, USA.,Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Chongle Pan
- Graduate School of Genome Science and Technology, The University of Tennessee, Knoxville, TN, USA.,Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Xavier Mayali
- Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Ryan S Mueller
- Department of Microbiology, Oregon State University, Corvallis, OR, USA
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39
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Stuart RK, Mayali X, Thelen MP, Pett-Ridge J, Weber PK. Measuring Cyanobacterial Metabolism in Biofilms with NanoSIMS Isotope Imaging and Scanning Electron Microscopy (SEM). Bio Protoc 2017; 7:e2263. [PMID: 34541249 DOI: 10.21769/bioprotoc.2263] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 03/26/2017] [Accepted: 03/31/2017] [Indexed: 11/02/2022] Open
Abstract
To advance the understanding of microbial interactions, it is becoming increasingly important to resolve the individual metabolic contributions of microorganisms in complex communities. Organisms from biofilms can be especially difficult to separate, image and analyze, and methods to address these limitations are needed. High resolution imaging secondary ion mass spectrometry (NanoSIMS) generates single cell isotopic composition measurements, and can be used to quantify incorporation and exchange of an isotopically labeled substrate among individual organisms. Here, incorporation of cyanobacterial extracellular organic matter (EOM) by members of a cyanobacterial mixed species biofilm is used as a model to illustrate this method. Incorporation of stable isotope labeled (15N and 13C) EOM by two groups, cyanobacteria and associated heterotrophic microbes, are quantified. Methods for generating, preparing, and analyzing samples for quantifying uptake of stable isotope-labeled EOM in the biofilm are described.
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Affiliation(s)
- Rhona K Stuart
- Physical and Life Sciences Division, Lawrence Livermore National Laboratory, Livermore, USA
| | - Xavier Mayali
- Physical and Life Sciences Division, Lawrence Livermore National Laboratory, Livermore, USA
| | - Michael P Thelen
- Physical and Life Sciences Division, Lawrence Livermore National Laboratory, Livermore, USA
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Division, Lawrence Livermore National Laboratory, Livermore, USA
| | - Peter K Weber
- Physical and Life Sciences Division, Lawrence Livermore National Laboratory, Livermore, USA
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40
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Kraft ML, Yeager AN, Weber PK, Zimmerberg J. Probing the lipid composition at the site of influenza virus assembly and budding with high‐resolution SIMS. FASEB J 2017. [DOI: 10.1096/fasebj.31.1_supplement.629.20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Mary L. Kraft
- Department of Chemical & Biomolecular EngrUniversity of Illinois at Urbana‐ChampaignUrbanaIL
| | - Ashley N. Yeager
- Department of Chemical & Biomolecular EngrUniversity of Illinois at Urbana‐ChampaignUrbanaIL
| | - Peter K. Weber
- Glenn T. Seaborg Institute, Lawrence Livermore National LaboratoryLivermoreCA
| | - Joshua Zimmerberg
- Program in Physical BiologyNational Institute of Child Health and Human Development, National Institutes of HealthBethesdaMD
- Program in Physical BiologyEunice Kennedy Shriver National Institute of Child Health and Human DevelopmentBethesdaMD
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41
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Arandia-Gorostidi N, Weber PK, Alonso-Sáez L, Morán XAG, Mayali X. Elevated temperature increases carbon and nitrogen fluxes between phytoplankton and heterotrophic bacteria through physical attachment. ISME J 2016; 11:641-650. [PMID: 27922602 DOI: 10.1038/ismej.2016.156] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 09/21/2016] [Accepted: 10/05/2016] [Indexed: 11/09/2022]
Abstract
Quantifying the contribution of marine microorganisms to carbon and nitrogen cycles and their response to predicted ocean warming is one of the main challenges of microbial oceanography. Here we present a single-cell NanoSIMS isotope analysis to quantify C and N uptake by free-living and attached phytoplankton and heterotrophic bacteria, and their response to short-term experimental warming of 4 °C. Elevated temperature increased total C fixation by over 50%, a small but significant fraction of which was transferred to heterotrophs within 12 h. Cell-to-cell attachment doubled the secondary C uptake by heterotrophic bacteria and increased secondary N incorporation by autotrophs by 68%. Warming also increased the abundance of phytoplankton with attached heterotrophs by 80%, and promoted C transfer from phytoplankton to bacteria by 17% and N transfer from bacteria to phytoplankton by 50%. Our results indicate that phytoplankton-bacteria attachment provides an ecological advantage for nutrient incorporation, suggesting a mutualistic relationship that appears to be enhanced by temperature increases.
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Affiliation(s)
- Nestor Arandia-Gorostidi
- Centro Oceanográfico de Gijón/Xixón, Instituto Español de Oceanografía, Centro Oceanográfico de Gijón/Xixón, Gijón/Xixón, Asturias, Spain
| | - Peter K Weber
- Nuclear and Chemical Sciences Division, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Laura Alonso-Sáez
- Centro Oceanográfico de Gijón/Xixón, Instituto Español de Oceanografía, Centro Oceanográfico de Gijón/Xixón, Gijón/Xixón, Asturias, Spain.,AZTI, Sukarrieta, Bizkaia, Spain
| | - Xosé Anxelu G Morán
- Centro Oceanográfico de Gijón/Xixón, Instituto Español de Oceanografía, Centro Oceanográfico de Gijón/Xixón, Gijón/Xixón, Asturias, Spain.,Red Sea Research Center, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Xavier Mayali
- Nuclear and Chemical Sciences Division, Lawrence Livermore National Laboratory, Livermore, CA, USA.,Oregon State University, Microbiology Department, Corvallis, OR, USA
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de-Bashan LE, Mayali X, Bebout BM, Weber PK, Detweiler AM, Hernandez JP, Prufert-Bebout L, Bashan Y. Establishment of stable synthetic mutualism without co-evolution between microalgae and bacteria demonstrated by mutual transfer of metabolites (NanoSIMS isotopic imaging) and persistent physical association (Fluorescent in situ hybridization). ALGAL RES 2016. [DOI: 10.1016/j.algal.2016.02.019] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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43
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Mayali X, Stewart B, Mabery S, Weber PK. Temporal succession in carbon incorporation from macromolecules by particle-attached bacteria in marine microcosms. Environ Microbiol Rep 2016; 8:68-75. [PMID: 26525158 DOI: 10.1111/1758-2229.12352] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Revised: 09/25/2015] [Accepted: 10/27/2015] [Indexed: 05/26/2023]
Abstract
We investigated bacterial carbon assimilation from stable isotope-labelled macromolecular substrates (proteins; lipids; and two types of polysaccharides, starch and cellobiose) while attached to killed diatom detrital particles during laboratory microcosms incubated for 17 days. Using Chip-SIP (secondary ion mass spectrometry analysis of RNA microarrays), we identified generalist operational taxonomic units (OTUs) from the Gammaproteobacteria, belonging to the genera Colwellia, Glaciecola, Pseudoalteromonas and Rheinheimera, and from the Bacteroidetes, genera Owenweeksia and Maribacter, that incorporated the four tested substrates throughout the incubation period. Many of these OTUs exhibited the highest isotope incorporation relative to the others, indicating that they were likely the most active. Additional OTUs from the Gammaproteobacteria, Bacteroidetes and Alphaproteobacteria exhibited generally (but not always) lower activity and did not incorporate all tested substrates at all times, showing species succession in organic carbon incorporation. We also found evidence to suggest that both generalist and specialist OTUs changed their relative substrate incorporation over time, presumably in response to changing substrate availability as the particles aged. This pattern was demonstrated by temporal succession from relatively higher starch incorporation early in the incubations, eventually switching to higher cellobiose incorporation after 2 weeks.
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Affiliation(s)
- Xavier Mayali
- Physical and Life Science Directorate, Lawrence Livermore National Laboratory, 7000 East Ave, Livermore, CA, 94550, USA
| | - Benjamin Stewart
- Physical and Life Science Directorate, Lawrence Livermore National Laboratory, 7000 East Ave, Livermore, CA, 94550, USA
| | - Shalini Mabery
- Physical and Life Science Directorate, Lawrence Livermore National Laboratory, 7000 East Ave, Livermore, CA, 94550, USA
| | - Peter K Weber
- Physical and Life Science Directorate, Lawrence Livermore National Laboratory, 7000 East Ave, Livermore, CA, 94550, USA
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44
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Wilson RL, Frisz JF, Klitzing HA, Zimmerberg J, Weber PK, Kraft ML. Hemagglutinin clusters in the plasma membrane are not enriched with cholesterol and sphingolipids. Biophys J 2016; 108:1652-1659. [PMID: 25863057 DOI: 10.1016/j.bpj.2015.02.026] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Revised: 02/11/2015] [Accepted: 02/18/2015] [Indexed: 01/28/2023] Open
Abstract
The clusters of the influenza envelope protein, hemagglutinin, within the plasma membrane are hypothesized to be enriched with cholesterol and sphingolipids. Here, we directly tested this hypothesis by using high-resolution secondary ion mass spectrometry to image the distributions of antibody-labeled hemagglutinin and isotope-labeled cholesterol and sphingolipids in the plasma membranes of fibroblast cells that stably express hemagglutinin. We found that the hemagglutinin clusters were neither enriched with cholesterol nor colocalized with sphingolipid domains. Thus, hemagglutinin clustering and localization in the plasma membrane is not controlled by cohesive interactions between hemagglutinin and liquid-ordered domains enriched with cholesterol and sphingolipids, or from specific binding interactions between hemagglutinin, cholesterol, and/or the majority of sphingolipid species in the plasma membrane.
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Affiliation(s)
- Robert L Wilson
- Department of Chemistry, University of Illinois, Urbana, Illinois
| | - Jessica F Frisz
- Department of Chemistry, University of Illinois, Urbana, Illinois
| | - Haley A Klitzing
- Department of Chemistry, University of Illinois, Urbana, Illinois
| | - Joshua Zimmerberg
- Section on Cellular and Membrane Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
| | - Peter K Weber
- Glenn T. Seaborg Institute, Lawrence Livermore National Laboratory, Livermore, California
| | - Mary L Kraft
- Department of Chemistry, University of Illinois, Urbana, Illinois; Department of Chemical and Biomolecular Engineering, University of Illinois, Urbana, Illnois.
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45
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Sturrock AM, Wikert JD, Heyne T, Mesick C, Hubbard AE, Hinkelman TM, Weber PK, Whitman GE, Glessner JJ, Johnson RC. Reconstructing the Migratory Behavior and Long-Term Survivorship of Juvenile Chinook Salmon under Contrasting Hydrologic Regimes. PLoS One 2015; 10:e0122380. [PMID: 25992556 PMCID: PMC4439044 DOI: 10.1371/journal.pone.0122380] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 01/31/2015] [Indexed: 11/21/2022] Open
Abstract
The loss of genetic and life history diversity has been documented across many taxonomic groups, and is considered a leading cause of increased extinction risk. Juvenile salmon leave their natal rivers at different sizes, ages and times of the year, and it is thought that this life history variation contributes to their population sustainability, and is thus central to many recovery efforts. However, in order to preserve and restore diversity in life history traits, it is necessary to first understand how environmental factors affect their expression and success. We used otolith 87Sr/86Sr in adult Chinook salmon (Oncorhynchus tshawytcha) returning to the Stanislaus River in the California Central Valley (USA) to reconstruct the sizes at which they outmigrated as juveniles in a wetter (2000) and drier (2003) year. We compared rotary screw trap-derived estimates of outmigrant timing, abundance and size with those reconstructed in the adults from the same cohort. This allowed us to estimate the relative survival and contribution of migratory phenotypes (fry, parr, smolts) to the adult spawning population under different flow regimes. Juvenile abundance and outmigration behavior varied with hydroclimatic regime, while downstream survival appeared to be driven by size- and time-selective mortality. Although fry survival is generally assumed to be negligible in this system, >20% of the adult spawners from outmigration year 2000 had outmigrated as fry. In both years, all three phenotypes contributed to the spawning population, however their relative proportions differed, reflecting greater fry contributions in the wetter year (23% vs. 10%) and greater smolt contributions in the drier year (13% vs. 44%). These data demonstrate that the expression and success of migratory phenotypes vary with hydrologic regime, emphasizing the importance of maintaining diversity in a changing climate.
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Affiliation(s)
- Anna M. Sturrock
- Institute of Marine Sciences, University of California Santa Cruz, Santa Cruz, California, United States of America
- * E-mail:
| | - J. D. Wikert
- US Fish and Wildlife Service, Lodi, California, United States of America
| | - Timothy Heyne
- Tuolumne River Restoration Center, California Department of Fish and Wildlife, La Grange, California, United States of America
| | - Carl Mesick
- US Fish and Wildlife Service, Lodi, California, United States of America
| | - Alan E. Hubbard
- School of Public Health, Division of Biostatistics, University of California, Berkeley, California, United States of America
| | | | - Peter K. Weber
- Glenn T. Seaborg Institute, Lawrence Livermore National Laboratory, Livermore, California, United States of America
| | - George E. Whitman
- Department of Animal Sciences, University of California Davis, Davis, California, United States of America
| | - Justin J. Glessner
- UC Davis Interdisciplinary Center for Plasma Mass Spectrometry, Department of Geology, University of California Davis, Davis, California, United States of America
| | - Rachel C. Johnson
- Department of Animal Sciences, University of California Davis, Davis, California, United States of America
- National Marine Fisheries Service, Southwest Fisheries Science Center, Santa Cruz, California, United States of America
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46
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Woebken D, Burow LC, Behnam F, Mayali X, Schintlmeister A, Fleming ED, Prufert-Bebout L, Singer SW, Cortés AL, Hoehler TM, Pett-Ridge J, Spormann AM, Wagner M, Weber PK, Bebout BM. Revisiting N₂ fixation in Guerrero Negro intertidal microbial mats with a functional single-cell approach. ISME J 2015; 9:485-96. [PMID: 25303712 PMCID: PMC4303640 DOI: 10.1038/ismej.2014.144] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2014] [Revised: 06/15/2014] [Accepted: 06/29/2014] [Indexed: 11/09/2022]
Abstract
Photosynthetic microbial mats are complex, stratified ecosystems in which high rates of primary production create a demand for nitrogen, met partially by N₂ fixation. Dinitrogenase reductase (nifH) genes and transcripts from Cyanobacteria and heterotrophic bacteria (for example, Deltaproteobacteria) were detected in these mats, yet their contribution to N2 fixation is poorly understood. We used a combined approach of manipulation experiments with inhibitors, nifH sequencing and single-cell isotope analysis to investigate the active diazotrophic community in intertidal microbial mats at Laguna Ojo de Liebre near Guerrero Negro, Mexico. Acetylene reduction assays with specific metabolic inhibitors suggested that both sulfate reducers and members of the Cyanobacteria contributed to N₂ fixation, whereas (15)N₂ tracer experiments at the bulk level only supported a contribution of Cyanobacteria. Cyanobacterial and nifH Cluster III (including deltaproteobacterial sulfate reducers) sequences dominated the nifH gene pool, whereas the nifH transcript pool was dominated by sequences related to Lyngbya spp. Single-cell isotope analysis of (15)N₂-incubated mat samples via high-resolution secondary ion mass spectrometry (NanoSIMS) revealed that Cyanobacteria were enriched in (15)N, with the highest enrichment being detected in Lyngbya spp. filaments (on average 4.4 at% (15)N), whereas the Deltaproteobacteria (identified by CARD-FISH) were not significantly enriched. We investigated the potential dilution effect from CARD-FISH on the isotopic composition and concluded that the dilution bias was not substantial enough to influence our conclusions. Our combined data provide evidence that members of the Cyanobacteria, especially Lyngbya spp., actively contributed to N₂ fixation in the intertidal mats, whereas support for significant N₂ fixation activity of the targeted deltaproteobacterial sulfate reducers could not be found.
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Affiliation(s)
- Dagmar Woebken
- Departments of Chemical Engineering, and of Civil and Environmental Engineering, Stanford University, Stanford, CA, USA
- Exobiology Branch, NASA Ames Research Center, Moffett Field, CA, USA
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Luke C Burow
- Departments of Chemical Engineering, and of Civil and Environmental Engineering, Stanford University, Stanford, CA, USA
- Exobiology Branch, NASA Ames Research Center, Moffett Field, CA, USA
| | - Faris Behnam
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Xavier Mayali
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Arno Schintlmeister
- Large-Instrument Facility for Advanced Isotope Research, University of Vienna, Vienna, Austria
| | - Erich D Fleming
- Exobiology Branch, NASA Ames Research Center, Moffett Field, CA, USA
| | | | - Steven W Singer
- Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Alejandro López Cortés
- Laboratory of Geomicrobiology and Biotechnology, Northwestern Center for Biological Research (CIBNOR), La Paz, Mexico
| | - Tori M Hoehler
- Exobiology Branch, NASA Ames Research Center, Moffett Field, CA, USA
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Alfred M Spormann
- Departments of Chemical Engineering, and of Civil and Environmental Engineering, Stanford University, Stanford, CA, USA
| | - Michael Wagner
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
- Large-Instrument Facility for Advanced Isotope Research, University of Vienna, Vienna, Austria
| | - Peter K Weber
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Brad M Bebout
- Exobiology Branch, NASA Ames Research Center, Moffett Field, CA, USA
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Kraft ML, Frisz JF, Klitzing HA, Wilson RL, Yeager A, Lizunov V, Zimmerberg JJ, Weber PK. Investigating the Mechanisms of Non-Random Sphingolipid Organization in the Plasma Membranes of Fibroblast Cells. Biophys J 2015. [DOI: 10.1016/j.bpj.2014.11.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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48
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Hong-Hermesdorf A, Miethke M, Gallaher SD, Kropat J, Dodani SC, Chan J, Barupala D, Domaille DW, Shirasaki DI, Loo JA, Weber PK, Pett-Ridge J, Stemmler TL, Chang CJ, Merchant SS. Subcellular metal imaging identifies dynamic sites of Cu accumulation in Chlamydomonas. Nat Chem Biol 2014; 10:1034-42. [PMID: 25344811 PMCID: PMC4232477 DOI: 10.1038/nchembio.1662] [Citation(s) in RCA: 111] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Accepted: 09/05/2014] [Indexed: 12/03/2022]
Abstract
We identified a Cu accumulating structure with a dynamic role in intracellular Cu homeostasis. During Zn limitation, Chlamydomonas reinhardtii hyperaccumulated Cu, dependent on the nutritional Cu sensor CRR1, but was functionally Cu-deficient. Visualization of intracellular Cu revealed major Cu accumulation sites coincident with electron-dense structures that stained positive for low pH and polyphosphate, suggesting that they are lysosome-related organelles. NanoSIMS showed colocalization of Ca and Cu, and X-ray absorption spectroscopy (XAS) was consistent with Cu+ accumulation in an ordered structure. Zn resupply restored Cu homeostasis concomitant with reduced abundance of these structures. Cu isotope labeling demonstrated that sequestered Cu+ became bio-available for the synthesis of plastocyanin, and transcriptome profiling indicated that mobilized Cu became visible to CRR1. Cu trafficking to intracellular accumulation sites may be a strategy for preventing protein mis-metallation during Zn deficiency and enabling efficient cuproprotein (re)-metallation upon Zn resupply.
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Affiliation(s)
- Anne Hong-Hermesdorf
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, California, USA
| | - Marcus Miethke
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, California, USA
| | - Sean D Gallaher
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, California, USA
| | - Janette Kropat
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, California, USA
| | - Sheel C Dodani
- 1] Department of Chemistry, University of California-Berkeley, Berkeley, California, USA. [2] Howard Hughes Medical Institute, University of California-Berkeley, Berkeley, California, USA
| | - Jefferson Chan
- 1] Department of Chemistry, University of California-Berkeley, Berkeley, California, USA. [2] Howard Hughes Medical Institute, University of California-Berkeley, Berkeley, California, USA
| | - Dulmini Barupala
- Department of Pharmaceutical Sciences, Wayne State University, Detroit, Michigan, USA
| | - Dylan W Domaille
- 1] Department of Chemistry, University of California-Berkeley, Berkeley, California, USA. [2] Howard Hughes Medical Institute, University of California-Berkeley, Berkeley, California, USA
| | - Dyna I Shirasaki
- Department of Biological Chemistry, University of California-Los Angeles, Los Angeles, California, USA
| | - Joseph A Loo
- 1] Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, California, USA. [2] Department of Biological Chemistry, University of California-Los Angeles, Los Angeles, California, USA. [3] Institute for Genomics and Proteomics, University of California-Los Angeles, Los Angeles, USA
| | - Peter K Weber
- Chemical Sciences Division, Lawrence Livermore National Laboratory, Livermore, USA
| | - Jennifer Pett-Ridge
- Chemical Sciences Division, Lawrence Livermore National Laboratory, Livermore, USA
| | - Timothy L Stemmler
- Department of Pharmaceutical Sciences, Wayne State University, Detroit, Michigan, USA
| | - Christopher J Chang
- 1] Department of Chemistry, University of California-Berkeley, Berkeley, California, USA. [2] Howard Hughes Medical Institute, University of California-Berkeley, Berkeley, California, USA
| | - Sabeeha S Merchant
- 1] Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, California, USA. [2] Institute for Genomics and Proteomics, University of California-Los Angeles, Los Angeles, USA
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Burow LC, Woebken D, Marshall IPG, Singer SW, Pett-Ridge J, Prufert-Bebout L, Spormann AM, Bebout BM, Weber PK, Hoehler TM. Identification of Desulfobacterales as primary hydrogenotrophs in a complex microbial mat community. Geobiology 2014; 12:221-230. [PMID: 24730641 DOI: 10.1111/gbi.12080] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Accepted: 01/22/2014] [Indexed: 06/03/2023]
Abstract
Hypersaline microbial mats have been shown to produce significant quantities of H2 under dark, anoxic conditions via cyanobacterial fermentation. This flux of a widely accessible microbial substrate has potential to significantly influence the ecology of the mat, and any consumption will affect the net efflux of H2 that might otherwise be captured as a resource. Here, we focus on H2 consumption in a microbial mat from Elkhorn Slough, California, USA, for which H2 production has been previously characterized. Active biologic H2 consumption in this mat is indicated by a significant time-dependent decrease in added H2 compared with a killed control. Inhibition of sulfate reduction, as indicated by a decrease in hydrogen sulfide production relative to controls, resulted in a significant increase in H2 efflux, suggesting that sulfate-reducing bacteria (SRB) are important hydrogenotrophs. Low methane efflux under these same conditions indicated that methanogens are likely not important hydrogenotrophs. Analyses of genes and transcripts that encode for rRNA or dissimilatory sulfite reductase, using both PCR-dependent and PCR-independent metatranscriptomic sequencing methods, demonstrated that Desulfobacterales are the dominant, active SRB in the upper, H2-producing layer of the mat (0-2 mm). This hypothesis was further supported by the identification of transcripts encoding hydrogenases derived from Desulfobacterales capable of H2 oxidation. Analysis of molecular data provided no evidence for the activity of hydrogenotrophic methanogens. The combined biogeochemical and molecular data strongly indicate that SRB belonging to the Desulfobacterales are the quantitatively important hydrogenotrophs in the Elkhorn Slough mat.
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Affiliation(s)
- L C Burow
- Departments of Chemical, Civil and Environmental Engineering, Stanford University, Stanford, CA, USA; Exobiology Branch, NASA Ames Research Center, Moffett Field, CA, USA
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50
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Mayali X, Weber PK, Mabery S, Pett-Ridge J. Phylogenetic patterns in the microbial response to resource availability: amino acid incorporation in San Francisco Bay. PLoS One 2014; 9:e95842. [PMID: 24752604 PMCID: PMC3994146 DOI: 10.1371/journal.pone.0095842] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 03/30/2014] [Indexed: 12/03/2022] Open
Abstract
Aquatic microorganisms are typically identified as either oligotrophic or copiotrophic, representing trophic strategies adapted to low or high nutrient concentrations, respectively. Here, we sought to take steps towards identifying these and additional adaptations to nutrient availability with a quantitative analysis of microbial resource use in mixed communities. We incubated an estuarine microbial community with stable isotope labeled amino acids (AAs) at concentrations spanning three orders of magnitude, followed by taxon-specific quantitation of isotopic incorporation using NanoSIMS analysis of high-density microarrays. The resulting data revealed that trophic response to AA availability falls along a continuum between copiotrophy and oligotrophy, and high and low activity. To illustrate strategies along this continuum more simply, we statistically categorized microbial taxa among three trophic types, based on their incorporation responses to increasing resource concentration. The data indicated that taxa with copiotrophic-like resource use were not necessarily the most active, and taxa with oligotrophic-like resource use were not always the least active. Two of the trophic strategies were not randomly distributed throughout a 16S rDNA phylogeny, suggesting they are under selective pressure in this ecosystem and that a link exists between evolutionary relatedness and substrate affinity. The diversity of strategies to adapt to differences in resource availability highlights the need to expand our understanding of microbial interactions with organic matter in order to better predict microbial responses to a changing environment.
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Affiliation(s)
- Xavier Mayali
- Physical and Life Science Directorate, Lawrence Livermore National Laboratory, Livermore California, United States of America
- * E-mail:
| | - Peter K. Weber
- Physical and Life Science Directorate, Lawrence Livermore National Laboratory, Livermore California, United States of America
| | - Shalini Mabery
- Physical and Life Science Directorate, Lawrence Livermore National Laboratory, Livermore California, United States of America
| | - Jennifer Pett-Ridge
- Physical and Life Science Directorate, Lawrence Livermore National Laboratory, Livermore California, United States of America
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