1
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Meyer NR, Morono Y, Dekas AE. Single-cell analysis reveals an active and heterotrophic microbiome in the Guaymas Basin deep subsurface with significant inorganic carbon fixation by heterotrophs. Appl Environ Microbiol 2024; 90:e0044624. [PMID: 38709099 PMCID: PMC11334695 DOI: 10.1128/aem.00446-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 04/04/2024] [Indexed: 05/07/2024] Open
Abstract
The marine subsurface is a long-term sink of atmospheric carbon dioxide with significant implications for climate on geologic timescales. Subsurface microbial cells can either enhance or reduce carbon sequestration in the subsurface, depending on their metabolic lifestyle. However, the activity of subsurface microbes is rarely measured. Here, we used nanoscale secondary ion mass spectrometry (nanoSIMS) to quantify anabolic activity in 3,203 individual cells from the thermally altered deep subsurface in the Guaymas Basin, Mexico (3-75 m below the seafloor, 0-14°C). We observed that a large majority of cells were active (83%-100%), although the rates of biomass generation were low, suggesting cellular maintenance rather than doubling. Mean single-cell activity decreased with increasing sediment depth and temperature and was most strongly correlated with porewater sulfate concentrations. Intracommunity heterogeneity in microbial activity decreased with increasing sediment depth and age. Using a dual-isotope labeling approach, we determined that all active cells analyzed were heterotrophic, deriving the majority of their cellular carbon from organic sources. However, we also detected inorganic carbon assimilation in these heterotrophic cells, likely via processes such as anaplerosis, and determined that inorganic carbon contributes at least 5% of the total biomass carbon in heterotrophs in this community. Our results demonstrate that the deep marine biosphere at Guaymas Basin is largely active and contributes to subsurface carbon cycling primarily by not only assimilating organic carbon but also fixing inorganic carbon. Heterotrophic assimilation of inorganic carbon may be a small yet significant and widespread underappreciated source of labile carbon in the global subsurface. IMPORTANCE The global subsurface is the largest reservoir of microbial life on the planet yet remains poorly characterized. The activity of life in this realm has implications for long-term elemental cycling, particularly of carbon, as well as how life survives in extreme environments. Here, we recovered cells from the deep subsurface of the Guaymas Basin and investigated the level and distribution of microbial activity, the physicochemical drivers of activity, and the relative significance of organic versus inorganic carbon to subsurface biomass. Using a sensitive single-cell assay, we found that the majority of cells are active, that activity is likely driven by the availability of energy, and that although heterotrophy is the dominant metabolism, both organic and inorganic carbon are used to generate biomass. Using a new approach, we quantified inorganic carbon assimilation by heterotrophs and highlighted the importance of this often-overlooked mode of carbon assimilation in the subsurface and beyond.
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Affiliation(s)
- Nicolette R. Meyer
- Department of Earth System Science, Stanford University, Stanford, California, USA
| | - Yuki Morono
- Kochi Institute for Core Sample Research, Institute for Extra-cutting-edge Science and Technology Avantgarde Research (X-STAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Nankoku, Kochi, Japan
| | - Anne E. Dekas
- Department of Earth System Science, Stanford University, Stanford, California, USA
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2
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Powell ME, McCoy SJ. Divide and conquer: Spatial and temporal resource partitioning structures benthic cyanobacterial mats. JOURNAL OF PHYCOLOGY 2024; 60:254-272. [PMID: 38467467 DOI: 10.1111/jpy.13443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 02/05/2024] [Accepted: 02/08/2024] [Indexed: 03/13/2024]
Abstract
Benthic cyanobacterial mats are increasing in abundance worldwide with the potential to degrade ecosystem structure and function. Understanding mat community dynamics is thus critical for predicting mat growth and proliferation and for mitigating any associated negative effects. Carbon, nitrogen, and sulfur cycling are the predominant forms of nutrient cycling discussed within the literature, while metabolic cooperation and viral interactions are understudied. Although many forms of nutrient cycling in mats have been assessed, the links between niche dynamics, microbial interactions, and nutrient cycling are not well described. Here, we present an updated review on how nutrient cycling and microbial community interactions in mats are structured by resource partitioning via spatial and temporal heterogeneity and succession. We assess community interactions and nutrient cycling at both intramat and metacommunity scales. Additionally, we present ideas and recommendations for research in this area, highlighting top-down control, boundary layers, and metabolic cooperation as important future directions.
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Affiliation(s)
- Maya E Powell
- Environment, Ecology and Energy Program, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Sophie J McCoy
- Environment, Ecology and Energy Program, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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3
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Sher AW, Aufrecht JA, Herrera D, Zimmerman AE, Kim YM, Munoz N, Trejo JB, Paurus VL, Cliff JB, Hu D, Chrisler WB, Tournay RJ, Gomez-Rivas E, Orr G, Ahkami AH, Doty SL. Dynamic nitrogen fixation in an aerobic endophyte of Populus. THE ISME JOURNAL 2024; 18:wrad012. [PMID: 38365250 PMCID: PMC10833079 DOI: 10.1093/ismejo/wrad012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 11/11/2023] [Accepted: 11/21/2023] [Indexed: 02/18/2024]
Abstract
Biological nitrogen fixation by microbial diazotrophs can contribute significantly to nitrogen availability in non-nodulating plant species. In this study of molecular mechanisms and gene expression relating to biological nitrogen fixation, the aerobic nitrogen-fixing endophyte Burkholderia vietnamiensis, strain WPB, isolated from Populus trichocarpa served as a model for endophyte-poplar interactions. Nitrogen-fixing activity was observed to be dynamic on nitrogen-free medium with a subset of colonies growing to form robust, raised globular like structures. Secondary ion mass spectrometry (NanoSIMS) confirmed that N-fixation was uneven within the population. A fluorescent transcriptional reporter (GFP) revealed that the nitrogenase subunit nifH is not uniformly expressed across genetically identical colonies of WPB and that only ~11% of the population was actively expressing the nifH gene. Higher nifH gene expression was observed in clustered cells through monitoring individual bacterial cells using single-molecule fluorescence in situ hybridization. Through 15N2 enrichment, we identified key nitrogenous metabolites and proteins synthesized by WPB and employed targeted metabolomics in active and inactive populations. We cocultivated WPB Pnif-GFP with poplar within a RhizoChip, a synthetic soil habitat, which enabled direct imaging of microbial nifH expression within root epidermal cells. We observed that nifH expression is localized to the root elongation zone where the strain forms a unique physical interaction with the root cells. This work employed comprehensive experimentation to identify novel mechanisms regulating both biological nitrogen fixation and beneficial plant-endophyte interactions.
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Affiliation(s)
- Andrew W Sher
- School of Environmental and Forest Sciences, College of the Environment, University of Washington, Seattle, WA, 98195-2100, United States
| | - Jayde A Aufrecht
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, United States
| | - Daisy Herrera
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, United States
| | - Amy E Zimmerman
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, United States
| | - Young-Mo Kim
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, United States
| | - Nathalie Munoz
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, United States
| | - Jesse B Trejo
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, United States
| | - Vanessa L Paurus
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, United States
| | - John B Cliff
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, United States
| | - Dehong Hu
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, United States
| | - William B Chrisler
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, United States
| | - Robert J Tournay
- School of Environmental and Forest Sciences, College of the Environment, University of Washington, Seattle, WA, 98195-2100, United States
| | - Emma Gomez-Rivas
- School of Environmental and Forest Sciences, College of the Environment, University of Washington, Seattle, WA, 98195-2100, United States
| | - Galya Orr
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, United States
| | - Amir H Ahkami
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, United States
| | - Sharon L Doty
- School of Environmental and Forest Sciences, College of the Environment, University of Washington, Seattle, WA, 98195-2100, United States
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4
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Meibom A, Plane F, Cheng T, Grandjean G, Haldimann O, Escrig S, Jensen L, Daraspe J, Mucciolo A, De Bellis D, Rädecker N, Martin-Olmos C, Genoud C, Comment A. Correlated cryo-SEM and CryoNanoSIMS imaging of biological tissue. BMC Biol 2023; 21:126. [PMID: 37280616 DOI: 10.1186/s12915-023-01623-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 05/10/2023] [Indexed: 06/08/2023] Open
Abstract
BACKGROUND The development of nanoscale secondary ion mass spectrometry (NanoSIMS) has revolutionized the study of biological tissues by enabling, e.g., the visualization and quantification of metabolic processes at subcellular length scales. However, the associated sample preparation methods all result in some degree of tissue morphology distortion and loss of soluble compounds. To overcome these limitations an entirely cryogenic sample preparation and imaging workflow is required. RESULTS Here, we report the development of a CryoNanoSIMS instrument that can perform isotope imaging of both positive and negative secondary ions from flat block-face surfaces of vitrified biological tissues with a mass- and image resolution comparable to that of a conventional NanoSIMS. This capability is illustrated with nitrogen isotope as well as trace element mapping of freshwater hydrozoan Green Hydra tissue following uptake of 15N-enriched ammonium. CONCLUSION With a cryo-workflow that includes vitrification by high pressure freezing, cryo-planing of the sample surface, and cryo-SEM imaging, the CryoNanoSIMS enables correlative ultrastructure and isotopic or elemental imaging of biological tissues in their most pristine post-mortem state. This opens new horizons in the study of fundamental processes at the tissue- and (sub)cellular level. TEASER CryoNanoSIMS: subcellular mapping of chemical and isotopic compositions of biological tissues in their most pristine post-mortem state.
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Affiliation(s)
- Anders Meibom
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, CH-1015, Switzerland.
- Center for Advanced Surface Analysis, Institute of Earth Sciences, University of Lausanne, Lausanne, CH-1015, Switzerland.
| | - Florent Plane
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, CH-1015, Switzerland
- Center for Advanced Surface Analysis, Institute of Earth Sciences, University of Lausanne, Lausanne, CH-1015, Switzerland
| | - Tian Cheng
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, CH-1015, Switzerland
| | - Gilles Grandjean
- Mechanical Workshop, School of Basic Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, CH-1015, Switzerland
| | - Olivier Haldimann
- Mechanical Workshop, School of Basic Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, CH-1015, Switzerland
| | - Stephane Escrig
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, CH-1015, Switzerland
| | - Louise Jensen
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, CH-1015, Switzerland
| | - Jean Daraspe
- Electron Microscopy Facility, University of Lausanne, Lausanne, CH-1015, Switzerland
| | - Antonio Mucciolo
- Electron Microscopy Facility, University of Lausanne, Lausanne, CH-1015, Switzerland
| | - Damien De Bellis
- Electron Microscopy Facility, University of Lausanne, Lausanne, CH-1015, Switzerland
| | - Nils Rädecker
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, CH-1015, Switzerland
| | - Cristina Martin-Olmos
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, CH-1015, Switzerland
- Center for Advanced Surface Analysis, Institute of Earth Sciences, University of Lausanne, Lausanne, CH-1015, Switzerland
| | - Christel Genoud
- Electron Microscopy Facility, University of Lausanne, Lausanne, CH-1015, Switzerland
| | - Arnaud Comment
- Institute of Physics, School of Basic Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, CH-1015, Switzerland
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5
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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] [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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6
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Millimeter-scale vertical partitioning of nitrogen cycling in hypersaline mats reveals prominence of genes encoding multi-heme and prismane proteins. THE ISME JOURNAL 2022; 16:1119-1129. [PMID: 34862473 PMCID: PMC8940962 DOI: 10.1038/s41396-021-01161-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 11/09/2021] [Accepted: 11/18/2021] [Indexed: 12/01/2022]
Abstract
Microbial mats are modern analogues of the first ecosystems on the Earth. As extant representatives of microbial communities where free oxygen may have first been available on a changing planet, they offer an ecosystem within which to study the evolution of biogeochemical cycles requiring and inhibited by oxygen. Here, we report the distribution of genes involved in nitrogen metabolism across a vertical oxygen gradient at 1 mm resolution in a microbial mat using quantitative PCR (qPCR), retro-transcribed qPCR (RT-qPCR) and metagenome sequencing. Vertical patterns in the presence and expression of nitrogen cycling genes, corresponding to oxygen requiring and non-oxygen requiring nitrogen metabolism, could be seen across gradients of dissolved oxygen and ammonium. Metagenome analysis revealed that genes annotated as hydroxylamine dehydrogenase (proper enzyme designation EC 1.7.2.6, hao) and hydroxylamine reductase (hcp) were the most abundant nitrogen metabolism genes in the mat. The recovered hao genes encode hydroxylamine dehydrogenase EC 1.7.2.6 (HAO) proteins lacking the tyrosine residue present in aerobic ammonia oxidizing bacteria (AOB). Phylogenetic analysis confirmed that those proteins were more closely related to ɛHao protein present in Campylobacterota lineages (previously known as Epsilonproteobacteria) rather than oxidative HAO of AOB. The presence of hao sequences related with ɛHao protein, as well as numerous hcp genes encoding a prismane protein, suggest the presence of a nitrogen cycling pathway previously described in Nautilia profundicola as ancestral to the most commonly studied present day nitrogen cycling pathways.
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7
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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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8
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Naafs BDA, Bianchini G, Monteiro FM, Sánchez-Baracaldo P. The occurrence of 2-methylhopanoids in modern bacteria and the geological record. GEOBIOLOGY 2022; 20:41-59. [PMID: 34291867 DOI: 10.1111/gbi.12465] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 07/10/2021] [Indexed: 06/13/2023]
Abstract
The 2-methylhopanes (2-MeHops) are molecular fossils of 2-methylbacteriohopanepolyols (2-MeBHPs) and among the oldest biomarkers on Earth. However, these biomarkers' specific sources are currently unexplained, including whether they reflect an expansion of marine cyanobacteria. Here, we study the occurrence of 2-MeBHPs and the genes involved in their synthesis in modern bacteria and explore the occurrence of 2-MeHops in the geological record. We find that the gene responsible for 2-MeBHP synthesis (hpnP) is widespread in cyano- and ⍺-proteobacteria, but absent or very limited in other classes/phyla of bacteria. This result is consistent with the dominance of 2-MeBHP in cyano- and ⍺-proteobacterial cultures. The review of their geological occurrence indicates that 2-MeHops are found from the Paleoproterozoic onwards, although some Precambrian samples might be biased by drilling contamination. During the Phanerozoic, high 2-MeHops' relative abundances (index >15%) are associated with climatic and biogeochemical perturbations such as the Permo/Triassic boundary and the Oceanic Anoxic Events. We analyzed the modern habitat of all hpnP-containing bacteria and find that the only one species coming from an undisputed open marine habitat is an ⍺-proteobacterium acting upon the marine nitrogen cycle. Although organisms can change their habitat in response to environmental stress and evolutionary pressure, we speculate that the high sedimentary 2-MeHops' occurrence observed during the Phanerozoic reflect ⍺-proteobacteria expansion and marine N-cycle perturbations in response to climatic and environmental change.
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Affiliation(s)
- B D A Naafs
- Organic Geochemistry Unit, School of Chemistry and School of Earth Sciences, University of Bristol, Bristol, UK
| | - G Bianchini
- School of Geographical Sciences, University of Bristol, Bristol, UK
| | - F M Monteiro
- School of Geographical Sciences, University of Bristol, Bristol, UK
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9
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Methods for Studying Bacterial–Fungal Interactions in the Microenvironments of Soil. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11199182] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Due to their small size, microorganisms directly experience only a tiny portion of the environmental heterogeneity manifested in the soil. The microscale variations in soil properties constrain the distribution of fungi and bacteria, and the extent to which they can interact with each other, thereby directly influencing their behavior and ecological roles. Thus, to obtain a realistic understanding of bacterial–fungal interactions, the spatiotemporal complexity of their microenvironments must be accounted for. The objective of this review is to further raise awareness of this important aspect and to discuss an overview of possible methodologies, some of easier applicability than others, that can be implemented in the experimental design in this field of research. The experimental design can be rationalized in three different scales, namely reconstructing the physicochemical complexity of the soil matrix, identifying and locating fungi and bacteria to depict their physical interactions, and, lastly, analyzing their molecular environment to describe their activity. In the long term, only relevant experimental data at the cell-to-cell level can provide the base for any solid theory or model that may serve for accurate functional prediction at the ecosystem level. The way to this level of application is still long, but we should all start small.
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10
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Calabrese F, Stryhanyuk H, Moraru C, Schlömann M, Wick LY, Richnow HH, Musat F, Musat N. Metabolic history and metabolic fitness as drivers of anabolic heterogeneity in isogenic microbial populations. Environ Microbiol 2021; 23:6764-6776. [PMID: 34472201 DOI: 10.1111/1462-2920.15756] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 08/30/2021] [Accepted: 08/30/2021] [Indexed: 11/26/2022]
Abstract
Microbial populations often display different degrees of heterogeneity in their substrate assimilation, that is, anabolic heterogeneity. It has been shown that nutrient limitations are a relevant trigger for this behaviour. Here we explore the dynamics of anabolic heterogeneity under nutrient replete conditions. We applied time-resolved stable isotope probing and nanoscale secondary ion mass spectrometry to quantify substrate assimilation by individual cells of Pseudomonas putida, P. stutzeri and Thauera aromatica. Acetate and benzoate at different concentrations were used as substrates. Anabolic heterogeneity was quantified by the cumulative differentiation tendency index. We observed two major, opposing trends of anabolic heterogeneity over time. Most often, microbial populations started as highly heterogeneous, with heterogeneity decreasing by various degrees over time. The second, less frequently observed trend, saw microbial populations starting at low or very low heterogeneity, and remaining largely stable over time. We explain these trends as an interplay of metabolic history (e.g. former growth substrate or other nutrient limitations) and metabolic fitness (i.e. the fine-tuning of metabolic pathways to process a defined growth substrate). Our results offer a new viewpoint on the intra-population functional diversification often encountered in the environment, and suggests that some microbial populations may be intrinsically heterogeneous.
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Affiliation(s)
- Federica Calabrese
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Hryhoriy Stryhanyuk
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Cristina Moraru
- Institute for Chemistry and Biology of Marine Environment, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Michael Schlömann
- Department of Environmental Microbiology, Institute of Biosciences, TU-Bergakademie Freiberg, Germany
| | - Lukas Y Wick
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Hans H Richnow
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Florin Musat
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Niculina Musat
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
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11
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Yester JW, Liu H, Gyngard F, Ammanamanchi N, Little KC, Thomas D, Sullivan MLG, Lal S, Steinhauser ML, Kühn B. Use of stable isotope-tagged thymidine and multi-isotope imaging mass spectrometry (MIMS) for quantification of human cardiomyocyte division. Nat Protoc 2021; 16:1995-2022. [PMID: 33627842 PMCID: PMC8221415 DOI: 10.1038/s41596-020-00477-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 11/30/2020] [Indexed: 12/26/2022]
Abstract
Quantification of cellular proliferation in humans is important for understanding biology and responses to injury and disease. However, existing methods require administration of tracers that cannot be ethically administered in humans. We present a protocol for the direct quantification of cellular proliferation in human hearts. The protocol involves administration of non-radioactive, non-toxic stable isotope 15Nitrogen-enriched thymidine (15N-thymidine), which is incorporated into DNA during S-phase, in infants with tetralogy of Fallot, a common form of congenital heart disease. Infants with tetralogy of Fallot undergo surgical repair, which requires the removal of pieces of myocardium that would otherwise be discarded. This protocol allows for the quantification of cardiomyocyte proliferation in this discarded tissue. We quantitatively analyzed the incorporation of 15N-thymidine with multi-isotope imaging spectrometry (MIMS) at a sub-nuclear resolution, which we combined with correlative confocal microscopy to quantify formation of binucleated cardiomyocytes and cardiomyocytes with polyploid nuclei. The entire protocol spans 3-8 months, which is dependent on the timing of surgical repair, and 3-4.5 researcher days. This protocol could be adapted to study cellular proliferation in a variety of human tissues.
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Affiliation(s)
- Jessie W Yester
- Division of Cardiology, Pediatric Institute for Heart Regeneration and Therapeutics (I-HRT), UPMC Children's Hospital of Pittsburgh and Department of Pediatrics, Pittsburgh, PA, USA
| | - Honghai Liu
- Division of Cardiology, Pediatric Institute for Heart Regeneration and Therapeutics (I-HRT), UPMC Children's Hospital of Pittsburgh and Department of Pediatrics, Pittsburgh, PA, USA
| | - Frank Gyngard
- Center for NanoImaging, Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Cambridge, MA, USA
| | - Niyatie Ammanamanchi
- Division of Cardiology, Pediatric Institute for Heart Regeneration and Therapeutics (I-HRT), UPMC Children's Hospital of Pittsburgh and Department of Pediatrics, Pittsburgh, PA, USA
| | - Kathryn C Little
- Clinical Research Support Services (CRSS), UPMC Children's Hospital of Pittsburgh and Department of Pediatrics, Pittsburgh, PA, USA
- UPMC Shadyside Hospital, Pittsburgh, PA, USA
| | - Dawn Thomas
- Clinical Research Support Services (CRSS), UPMC Children's Hospital of Pittsburgh and Department of Pediatrics, Pittsburgh, PA, USA
| | - Mara L G Sullivan
- Center for Biologic Imaging, University of Pittsburgh School of Medicine, Department of Cell Biology, Pittsburgh, PA, USA
| | - Sean Lal
- Division of Cardiology, Pediatric Institute for Heart Regeneration and Therapeutics (I-HRT), UPMC Children's Hospital of Pittsburgh and Department of Pediatrics, Pittsburgh, PA, USA
- Center for NanoImaging, Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Cambridge, MA, USA
- School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales, Australia
- Division of Cardiology, Royal Prince Alfred Hospital, Sydney, New South Wales, Australia
| | - Matthew L Steinhauser
- Center for NanoImaging, Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Cambridge, MA, USA.
- UPMC Heart and Vascular Institute, UPMC Presbyterian, Pittsburgh, PA, USA.
- Aging Institute, University of Pittsburgh, Bridgeside Point 1, Pittsburgh, PA, USA.
| | - Bernhard Kühn
- Division of Cardiology, Pediatric Institute for Heart Regeneration and Therapeutics (I-HRT), UPMC Children's Hospital of Pittsburgh and Department of Pediatrics, Pittsburgh, PA, USA.
- McGowan Institute of Regenerative Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
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12
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Deng X, Saito J, Kaksonen A, Okamoto A. Enhancement of cell growth by uncoupling extracellular electron uptake and oxidative stress production in sediment sulfate-reducing bacteria. ENVIRONMENT INTERNATIONAL 2020; 144:106006. [PMID: 32795748 DOI: 10.1016/j.envint.2020.106006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 06/25/2020] [Accepted: 07/20/2020] [Indexed: 06/11/2023]
Abstract
Microbial extracellular electron uptake (EEU) from solid electron donors has critical implications for microbial energy acquisition in energy-limited environments as well as electrochemical microbial technologies. Although EEU supplies sufficient energy to support cellular growth, additional soluble electron donors are required for most microbes to grow on electrode surfaces. Here, we demonstrated that the minimization of exogenous and endogenous oxidative stress greatly enhanced the growth rate of the sediment EEU-capable sulfate-reducing bacterium Desulfovibrio ferrophilus IS5 on an electrode without the addition of a soluble electron donor. Single-cell activity analysis by nanoscale secondary ion mass spectrometry showed that the metabolic activity of IS5 cells on the electrode was significantly enhanced following incubation in an H-type reactor, which was configured to reduce the exposure of cells to the potential oxidative stress source of the Pt counter electrode (CE). Additionally, the highest metabolic activity was observed at an electrode potential of -0.4 V (versus the standard hydrogen electrode), where electron uptake rate was not at peak. Compared to a single-chamber reactor, incubation in an H-type reactor at -0.4 V shortened the cell doubling time by 50-fold, which resulted in sufficient anabolism for cell replication (15N/Ntotal > 50%). The production of strongly oxidizing species at the CE was confirmed by X-ray photoelectron spectroscopy and inductively coupled plasma mass spectrometry analyses. Transcriptome analysis revealed overexpression of antioxidative genes in cells incubated at a potential with higher current production. These results suggested that higher levels of endogenous oxidative species were produced by a more reduced electron-transport chain from trace amounts of oxygen in the reactor, thereby lowering cell activity. In conclusion, EEU may enable sediment microbes to undergo enhanced cell growth and to find niches on minerals under anaerobic energy-limited conditions, where oxidative stress is much less likely to be present.
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Affiliation(s)
- Xiao Deng
- International Center for Materials Nanoarchitectonics, National Institute for Materials Science, 1-1 Namiki, Tsukuba 305-0044, Japan; Center for Sensor and Actuator Material, National Institute for Materials Science, 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan; School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku 113-8656, Japan; CSIRO Land and Water, 147 Underwood Avenue, Floreat, WA 6014, Australia
| | - Junki Saito
- International Center for Materials Nanoarchitectonics, National Institute for Materials Science, 1-1 Namiki, Tsukuba 305-0044, Japan; School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku 113-8656, Japan
| | - Anna Kaksonen
- CSIRO Land and Water, 147 Underwood Avenue, Floreat, WA 6014, Australia; School of Biomedical Sciences, University of Western Australia, 35 Stirling Highway, Nedlands, WA 6009, Australia
| | - Akihiro Okamoto
- International Center for Materials Nanoarchitectonics, National Institute for Materials Science, 1-1 Namiki, Tsukuba 305-0044, Japan; Center for Sensor and Actuator Material, National Institute for Materials Science, 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan; Graduate School of Chemical Sciences and Engineering, Hokkaido University, North 13 West 8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan.
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13
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Newsome L, Lopez Adams R, Downie HF, Moore KL, Lloyd JR. NanoSIMS imaging of extracellular electron transport processes during microbial iron(III) reduction. FEMS Microbiol Ecol 2019; 94:5033680. [PMID: 29878195 PMCID: PMC6041951 DOI: 10.1093/femsec/fiy104] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 06/05/2018] [Indexed: 01/25/2023] Open
Abstract
Microbial iron(III) reduction can have a profound effect on the fate of contaminants in natural and engineered environments. Different mechanisms of extracellular electron transport are used by Geobacter and Shewanella spp. to reduce insoluble Fe(III) minerals. Here we prepared a thin film of iron(III)-(oxyhydr)oxide doped with arsenic, and allowed the mineral coating to be colonised by Geobacter sulfurreducens or Shewanella ANA3 labelled with 13C from organic electron donors. This preserved the spatial relationship between metabolically active Fe(III)-reducing bacteria and the iron(III)-(oxyhydr)oxide that they were respiring. NanoSIMS imaging showed cells of G. sulfurreducens were co-located with the iron(III)-(oxyhydr)oxide surface and were significantly more 13C-enriched compared to cells located away from the mineral, consistent with Geobacter species requiring direct contact with an extracellular electron acceptor to support growth. There was no such intimate relationship between 13C-enriched S. ANA3 and the iron(III)-(oxyhydr)oxide surface, consistent with Shewanella species being able to reduce Fe(III) indirectly using a secreted endogenous mediator. Some differences were observed in the amount of As relative to Fe in the local environment of G. sulfurreducens compared to the bulk mineral, highlighting the usefulness of this type of analysis for probing interactions between microbial cells and Fe-trace metal distributions in biogeochemical experiments.
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Affiliation(s)
- Laura Newsome
- Williamson Research Centre, School of Earth and Environmental Sciences, University of Manchester, Manchester, M13 9PL, UK
| | - Rebeca Lopez Adams
- Williamson Research Centre, School of Earth and Environmental Sciences, University of Manchester, Manchester, M13 9PL, UK
| | - Helen F Downie
- Williamson Research Centre, School of Earth and Environmental Sciences, University of Manchester, Manchester, M13 9PL, UK
| | - Katie L Moore
- School of Materials, University of Manchester, Manchester, M13 9PL, UK.,Photon Science Institute, University of Manchester, Manchester, M13 9PL, UK
| | - Jonathan R Lloyd
- Williamson Research Centre, School of Earth and Environmental Sciences, University of Manchester, Manchester, M13 9PL, UK
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14
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Giardina M, Cheong S, Marjo CE, Clode PL, Guagliardo P, Pickford R, Pernice M, Seymour JR, Raina JB. Quantifying Inorganic Nitrogen Assimilation by Synechococcus Using Bulk and Single-Cell Mass Spectrometry: A Comparative Study. Front Microbiol 2018; 9:2847. [PMID: 30538685 PMCID: PMC6277480 DOI: 10.3389/fmicb.2018.02847] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Accepted: 11/05/2018] [Indexed: 12/03/2022] Open
Abstract
Microorganisms drive most of the major biogeochemical cycles in the ocean, but the rates at which individual species assimilate and transform key elements is generally poorly quantified. One of these important elements is nitrogen, with its availability limiting primary production across a large proportion of the ocean. Nitrogen uptake by marine microbes is typically quantified using bulk-scale approaches, such as Elemental Analyzer-Isotope Ratio Mass Spectrometry (EA-IRMS), which averages uptake over entire communities, masking microbial heterogeneity. However, more recent techniques, such as secondary ion mass spectrometry (SIMS), allow for elucidation of assimilation rates at the scale at which they occur: the single-cell level. Here, we combine and compare the application of bulk (EA-IRMS) and single-cell approaches (NanoSIMS and Time-of-Flight-SIMS) for quantifying the assimilation of inorganic nitrogen by the ubiquitous marine primary producer Synechococcus. We aimed to contrast the advantages and disadvantages of these techniques and showcase their complementarity. Our results show that the average assimilation of 15N by Synechococcus differed based on the technique used: values derived from EA-IRMS were consistently higher than those derived from SIMS, likely due to a combination of previously reported systematic depletion as well as differences in sample preparation. However, single-cell approaches offered additional layers of information, whereby NanoSIMS allowed for the quantification of the metabolic heterogeneity among individual cells and ToF-SIMS enabled identification of nitrogen assimilation into peptides. We suggest that this coupling of stable isotope-based approaches has great potential to elucidate the metabolic capacity and heterogeneity of microbial cells in natural environments.
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Affiliation(s)
- Marco Giardina
- Climate Change Cluster, University of Technology Sydney, Sydney, NSW, Australia
| | - Soshan Cheong
- Mark Wainwright Analytical Centre, University of New South Wales, Kensington, NSW, Australia
| | - Christopher E. Marjo
- Mark Wainwright Analytical Centre, University of New South Wales, Kensington, NSW, Australia
| | - Peta L. Clode
- Centre for Microscopy Characterisation and Analysis, The University of Western Australia, Perth, WA, Australia
- UWA School of Biological Sciences, The University of Western Australia, Perth, WA, Australia
- UWA Oceans Institute, The University of Western Australia, Perth, WA, Australia
| | - Paul Guagliardo
- Centre for Microscopy Characterisation and Analysis, The University of Western Australia, Perth, WA, Australia
| | - Russell Pickford
- Bioanalytical Mass Spectrometry Facility, University of New South Wales, Sydney, NSW, Australia
| | - Mathieu Pernice
- Climate Change Cluster, University of Technology Sydney, Sydney, NSW, Australia
| | - Justin R. Seymour
- Climate Change Cluster, University of Technology Sydney, Sydney, NSW, Australia
| | - Jean-Baptiste Raina
- Climate Change Cluster, University of Technology Sydney, Sydney, NSW, Australia
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15
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Stryhanyuk H, Calabrese F, Kümmel S, Musat F, Richnow HH, Musat N. Calculation of Single Cell Assimilation Rates From SIP-NanoSIMS-Derived Isotope Ratios: A Comprehensive Approach. Front Microbiol 2018; 9:2342. [PMID: 30337916 PMCID: PMC6178922 DOI: 10.3389/fmicb.2018.02342] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 09/12/2018] [Indexed: 11/18/2022] Open
Abstract
The nanoSIMS-based chemical microscopy has been introduced in biology over a decade ago. The spatial distribution of elements and isotopes analyzed by nanoSIMS can be used to reconstruct images of biological samples with a resolution down to tens of nanometers, and can be also interpreted quantitatively. Currently, a unified approach for calculation of single cell assimilation rates from nanoSIMS-derived changes in isotope ratios is missing. Here we present a comprehensive concept of assimilation rate calculation with a rigorous mathematical model based on quantitative evaluation of nanoSIMS-derived isotope ratios. We provide a detailed description of data acquisition and treatment, including the selection and accumulation of nanoSIMS scans, defining regions of interest and extraction of isotope ratios. Next, we present alternative methods to determine the cellular volume and the density of the element under scrutiny. Finally, to compensate for alterations of original isotopic ratios, our model considers corrections for sample preparation methods (e.g., air dry, chemical fixation, permeabilization, hybridization), and when known, for the stable isotope fractionation associated with utilization of defined growth substrates. As proof of concept we implemented this protocol to quantify the assimilation of 13C-labeled glucose by single cells of Pseudomonas putida. In addition, we provide a calculation template where all protocol-derived formulas are directly available to facilitate routine assimilation rate calculations by nanoSIMS users.
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Affiliation(s)
- Hryhoriy Stryhanyuk
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Federica Calabrese
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Steffen Kümmel
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Florin Musat
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Hans H Richnow
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Niculina Musat
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
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16
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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] [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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17
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Cui L, Yang K, Li HZ, Zhang H, Su JQ, Paraskevaidi M, Martin FL, Ren B, Zhu YG. Functional Single-Cell Approach to Probing Nitrogen-Fixing Bacteria in Soil Communities by Resonance Raman Spectroscopy with 15N 2 Labeling. Anal Chem 2018; 90:5082-5089. [PMID: 29557648 DOI: 10.1021/acs.analchem.7b05080] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Nitrogen (N) fixation is the conversion of inert nitrogen gas (N2) to bioavailable N essential for all forms of life. N2-fixing microorganisms (diazotrophs), which play a key role in global N cycling, remain largely obscure because a large majority are uncultured. Direct probing of active diazotrophs in the environment is still a major challenge. Herein, a novel culture-independent single-cell approach combining resonance Raman (RR) spectroscopy with 15N2 stable isotope probing (SIP) was developed to discern N2-fixing bacteria in a complex soil community. Strong RR signals of cytochrome c (Cyt c, frequently present in diverse N2-fixing bacteria), along with a marked 15N2-induced Cyt c band shift, generated a highly distinguishable biomarker for N2 fixation. 15N2-induced shift was consistent well with 15N abundance in cell determined by isotope ratio mass spectroscopy. By applying this biomarker and Raman imaging, N2-fixing bacteria in both artificial and complex soil communities were discerned and imaged at the single-cell level. The linear band shift of Cyt c versus 15N2 percentage allowed quantification of N2 fixation extent of diverse soil bacteria. This single-cell approach will advance the exploration of hitherto uncultured diazotrophs in diverse ecosystems.
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Affiliation(s)
- Li Cui
- Key Lab of Urban Environment and Health, Institute of Urban Environment , Chinese Academy of Sciences , Xiamen 361021 , China
| | - Kai Yang
- Key Lab of Urban Environment and Health, Institute of Urban Environment , Chinese Academy of Sciences , Xiamen 361021 , China.,University of Chinese Academy of Sciences , 19A Yuquan Road , Beijing 100049 , China
| | - Hong-Zhe Li
- Key Lab of Urban Environment and Health, Institute of Urban Environment , Chinese Academy of Sciences , Xiamen 361021 , China.,University of Chinese Academy of Sciences , 19A Yuquan Road , Beijing 100049 , China
| | - Han Zhang
- Key Lab of Urban Environment and Health, Institute of Urban Environment , Chinese Academy of Sciences , Xiamen 361021 , China
| | - Jian-Qiang Su
- Key Lab of Urban Environment and Health, Institute of Urban Environment , Chinese Academy of Sciences , Xiamen 361021 , China
| | - Maria Paraskevaidi
- School of Pharmacy and Biomedical Sciences , University of Central Lancashire , Preston PR1 2HE , U.K
| | - Francis L Martin
- School of Pharmacy and Biomedical Sciences , University of Central Lancashire , Preston PR1 2HE , U.K
| | - Bin Ren
- Department of Chemistry , Xiamen University , Xiamen 361005 , China
| | - Yong-Guan Zhu
- Key Lab of Urban Environment and Health, Institute of Urban Environment , Chinese Academy of Sciences , Xiamen 361021 , China.,State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences , Chinese Academy of Sciences , Beijing 100085 , China
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18
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Angel R, Panhölzl C, Gabriel R, Herbold C, Wanek W, Richter A, Eichorst SA, Woebken D. Application of stable-isotope labelling techniques for the detection of active diazotrophs. Environ Microbiol 2018; 20:44-61. [PMID: 29027346 PMCID: PMC5814836 DOI: 10.1111/1462-2920.13954] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 09/16/2017] [Accepted: 10/02/2017] [Indexed: 12/02/2022]
Abstract
Investigating active participants in the fixation of dinitrogen gas is vital as N is often a limiting factor for primary production. Biological nitrogen fixation is performed by a diverse guild of bacteria and archaea (diazotrophs), which can be free-living or symbionts. Free-living diazotrophs are widely distributed in the environment, yet our knowledge about their identity and ecophysiology is still limited. A major challenge in investigating this guild is inferring activity from genetic data as this process is highly regulated. To address this challenge, we evaluated and improved several 15 N-based methods for detecting N2 fixation activity (with a focus on soil samples) and studying active diazotrophs. We compared the acetylene reduction assay and the 15 N2 tracer method and demonstrated that the latter is more sensitive in samples with low activity. Additionally, tracing 15 N into microbial RNA provides much higher sensitivity compared to bulk soil analysis. Active soil diazotrophs were identified with a 15 N-RNA-SIP approach optimized for environmental samples and benchmarked to 15 N-DNA-SIP. Lastly, we investigated the feasibility of using SIP-Raman microspectroscopy for detecting 15 N-labelled cells. Taken together, these tools allow identifying and investigating active free-living diazotrophs in a highly sensitive manner in diverse environments, from bulk to the single-cell level.
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Affiliation(s)
- Roey Angel
- Division of Microbial Ecology, Department of Microbiology and Ecosystem ScienceResearch network “Chemistry meets Microbiology,” University of ViennaVienna 1090Austria
| | - Christopher Panhölzl
- Division of Microbial Ecology, Department of Microbiology and Ecosystem ScienceResearch network “Chemistry meets Microbiology,” University of ViennaVienna 1090Austria
| | - Raphael Gabriel
- Division of Microbial Ecology, Department of Microbiology and Ecosystem ScienceResearch network “Chemistry meets Microbiology,” University of ViennaVienna 1090Austria
- Present address:
Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Emeryville, CA, USA;Institute for Genetics, Technische Universität Braunschweig, Braunschweig, Germany
| | - Craig Herbold
- Division of Microbial Ecology, Department of Microbiology and Ecosystem ScienceResearch network “Chemistry meets Microbiology,” University of ViennaVienna 1090Austria
| | - Wolfgang Wanek
- Division of Terrestrial Ecosystem Research, Department of Microbiology and Ecosystem ScienceResearch network “Chemistry meets Microbiology,” University of ViennaVienna 1090Austria
| | - Andreas Richter
- Division of Terrestrial Ecosystem Research, Department of Microbiology and Ecosystem ScienceResearch network “Chemistry meets Microbiology,” University of ViennaVienna 1090Austria
| | - Stephanie A. Eichorst
- Division of Microbial Ecology, Department of Microbiology and Ecosystem ScienceResearch network “Chemistry meets Microbiology,” University of ViennaVienna 1090Austria
| | - Dagmar Woebken
- Division of Microbial Ecology, Department of Microbiology and Ecosystem ScienceResearch network “Chemistry meets Microbiology,” University of ViennaVienna 1090Austria
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19
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Pasulka AL, Thamatrakoln K, Kopf SH, Guan Y, Poulos B, Moradian A, Sweredoski MJ, Hess S, Sullivan MB, Bidle KD, Orphan VJ. Interrogating marine virus-host interactions and elemental transfer with BONCAT and nanoSIMS-based methods. Environ Microbiol 2017; 20:671-692. [DOI: 10.1111/1462-2920.13996] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 11/10/2017] [Accepted: 11/12/2017] [Indexed: 11/29/2022]
Affiliation(s)
- Alexis L. Pasulka
- Division of Geological and Planetary Sciences; California Institute of Technology; CA USA
| | | | - Sebastian H. Kopf
- Department of Geological Sciences, University of Colorado Boulder; CO USA
| | - Yunbin Guan
- Division of Geological and Planetary Sciences; California Institute of Technology; CA USA
| | - Bonnie Poulos
- Department of Ecology and Evolutionary Biology, University of Arizona; AZ USA
| | - Annie Moradian
- Proteome Exploration Laboratory, California Institute of Technology; CA USA
| | | | - Sonja Hess
- Proteome Exploration Laboratory, California Institute of Technology; CA USA
| | | | - Kay D. Bidle
- Department of Marine and Coastal Studies; Rutgers University; NJ USA
| | - Victoria J. Orphan
- Division of Geological and Planetary Sciences; California Institute of Technology; CA USA
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20
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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] [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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21
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Hubas C, Boeuf D, Jesus B, Thiney N, Bozec Y, Jeanthon C. A Nanoscale Study of Carbon and Nitrogen Fluxes in Mats of Purple Sulfur Bacteria: Implications for Carbon Cycling at the Surface of Coastal Sediments. Front Microbiol 2017; 8:1995. [PMID: 29114241 PMCID: PMC5660696 DOI: 10.3389/fmicb.2017.01995] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 09/28/2017] [Indexed: 11/25/2022] Open
Abstract
Mass blooms of purple sulfur bacteria growing seasonally on green stranded macroalgae have a major impact on the microbial composition and functionality of intertidal mats. To explore the active anoxygenic phototrophic community in purple bacterial mats from the Roscoff Aber Bay (Brittany, France), we conducted a combined approach including molecular and high-resolution secondary ion mass spectrometry (NanoSIMS) analyses. To investigate the dynamics of carbon and nitrogen assimilation activities, NanoSIMS was coupled with a stable isotope probing (SIP) experiment and a compound specific isotope analysis (CSIA) of fatty acid methyl ester (FAME). Sediment samples were incubated with 13C- and/or 15N-labeled acetate, pyruvate, bicarbonate and ammonium. NanoSIMS analysis of 13C - and 15N -incubated samples showed elevated incorporations of 13C - and 15N in the light and of 13C -acetate in the dark into dense populations of spherical cells that unambiguously dominated the mats. These results confirmed CSIA data that ranked vaccenic acid, an unambiguous marker of purple sulfur bacteria, as the most strongly enriched in the light after 13C -acetate amendment and indicated that acetate uptake, the most active in the mat, was not light-dependent. Analysis of DNA- and cDNA-derived pufM gene sequences revealed that Thiohalocapsa-related clones dominated both libraries and were the most photosynthetically active members of the mat samples. This study provides novel insights into the contribution of purple sulfur bacteria to the carbon cycle during their seasonal developments at the sediment surface in the intertidal zone.
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Affiliation(s)
- Cédric Hubas
- Muséum National d'Histoire Naturelle, UMR BOREA, MNHN-CNRS-UCN-UPMC-IRD-UA, Station de Biologie Marine de Concarneau, Concarneau, France
| | - Dominique Boeuf
- CNRS, Station Biologique de Roscoff, Adaptation et Diversité en Milieu Marin, Roscoff, France.,Sorbonne Universités, UPMC Univ Paris 06, UMR 7144, Station Biologique de Roscoff, Adaptation et Diversité en Milieu Marin, Roscoff, France
| | - Bruno Jesus
- EA2160, Laboratoire Mer Molécules Santé, Université de Nantes, Nantes, France.,BioISI - Biosystems & Integrative Sciences Institute, Campo Grande University of Lisbon, Faculty of Sciences, Lisbon, Portugal
| | - Najet Thiney
- Muséum National d'Histoire Naturelle, UMR BOREA, MNHN-CNRS-UCN-UPMC-IRD-UA, Bâtiment Arthropodes, Paris, France
| | - Yann Bozec
- CNRS, Station Biologique de Roscoff, Adaptation et Diversité en Milieu Marin, Roscoff, France.,Sorbonne Universités, UPMC Univ Paris 06, UMR 7144, Station Biologique de Roscoff, Adaptation et Diversité en Milieu Marin, Roscoff, France
| | - Christian Jeanthon
- CNRS, Station Biologique de Roscoff, Adaptation et Diversité en Milieu Marin, Roscoff, France.,Sorbonne Universités, UPMC Univ Paris 06, UMR 7144, Station Biologique de Roscoff, Adaptation et Diversité en Milieu Marin, Roscoff, France
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22
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Abstract
Secondary ion mass spectrometry (SIMS) has become an increasingly utilized tool in biologically relevant studies. Of these, high lateral resolution methodologies using the NanoSIMS 50/50L have been especially powerful within many biological fields over the past decade. Here, the authors provide a review of this technology, sample preparation and analysis considerations, examples of recent biological studies, data analyses, and current outlooks. Specifically, the authors offer an overview of SIMS and development of the NanoSIMS. The authors describe the major experimental factors that should be considered prior to NanoSIMS analysis and then provide information on best practices for data analysis and image generation, which includes an in-depth discussion of appropriate colormaps. Additionally, the authors provide an open-source method for data representation that allows simultaneous visualization of secondary electron and ion information within a single image. Finally, the authors present a perspective on the future of this technology and where they think it will have the greatest impact in near future.
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23
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Description of new genera and species of marine cyanobacteria from the Portuguese Atlantic coast. Mol Phylogenet Evol 2017; 111:18-34. [DOI: 10.1016/j.ympev.2017.03.006] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 01/18/2017] [Accepted: 03/04/2017] [Indexed: 01/21/2023]
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24
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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: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [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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25
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Klawonn I, Nahar N, Walve J, Andersson B, Olofsson M, Svedén JB, Littmann S, Whitehouse MJ, Kuypers MMM, Ploug H. Cell-specific nitrogen- and carbon-fixation of cyanobacteria in a temperate marine system (Baltic Sea). Environ Microbiol 2016; 18:4596-4609. [PMID: 27696654 DOI: 10.1111/1462-2920.13557] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 08/16/2016] [Accepted: 09/27/2016] [Indexed: 11/27/2022]
Abstract
We analysed N2 - and carbon (C) fixation in individual cells of Baltic Sea cyanobacteria by combining stable isotope incubations with secondary ion mass spectrometry (SIMS). Specific growth rates based on N2 - and C-fixation were higher for cells of Dolichospermum spp. than for Aphanizomenon sp. and Nodularia spumigena. The cyanobacterial biomass, however, was dominated by Aphanizomenon sp., which contributed most to total N2 -fixation in surface waters of the Northern Baltic Proper. N2 -fixation by Pseudanabaena sp. and colonial picocyanobacteria was not detectable. N2 -fixation by Aphanizomenon sp., Dolichospermum spp. and N. spumigena populations summed up to total N2 -fixation, thus these genera appeared as sole diazotrophs within the Baltic Sea's euphotic zone, while their mean contribution to total C-fixation was 21%. Intriguingly, cell-specific N2 -fixation was eightfold higher at a coastal station compared to an offshore station, revealing coastal zones as habitats with substantial N2 -fixation. At the coastal station, the cell-specific C- to N2 -fixation ratio was below the cellular C:N ratio, i.e. N2 was assimilated in excess to C-fixation, whereas the C- to N2 -fixation ratio exceeded the C:N ratio in offshore sampled diazotrophs. Our findings highlight SIMS as a powerful tool not only for qualitative but also for quantitative N2 -fixation assays in aquatic environments.
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Affiliation(s)
- I Klawonn
- Department of Ecology, Environment and Plant Sciences Stockholm University, Stockholm, Sweden
| | - N Nahar
- Department of Biology and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
| | - J Walve
- Department of Ecology, Environment and Plant Sciences Stockholm University, Stockholm, Sweden
| | - B Andersson
- Department of Biology and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
| | - M Olofsson
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
| | - J B Svedén
- Department of Ecology, Environment and Plant Sciences Stockholm University, Stockholm, Sweden
| | - S Littmann
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | | | - M M M Kuypers
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - H Ploug
- Department of Ecology, Environment and Plant Sciences Stockholm University, Stockholm, Sweden.,Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
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26
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Everroad RC, Stuart RK, Bebout BM, Detweiler AM, Lee JZ, Woebken D, Prufert-Bebout L, Pett-Ridge J. Permanent draft genome of strain ESFC-1: ecological genomics of a newly discovered lineage of filamentous diazotrophic cyanobacteria. Stand Genomic Sci 2016; 11:53. [PMID: 27559430 PMCID: PMC4995827 DOI: 10.1186/s40793-016-0174-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 08/15/2016] [Indexed: 11/10/2022] Open
Abstract
The nonheterocystous filamentous cyanobacterium, strain ESFC-1, is a recently described member of the order Oscillatoriales within the Cyanobacteria. ESFC-1 has been shown to be a major diazotroph in the intertidal microbial mat system at Elkhorn Slough, CA, USA. Based on phylogenetic analyses of the 16S RNA gene, ESFC-1 appears to belong to a unique, genus-level divergence; the draft genome sequence of this strain has now been determined. Here we report features of this genome as they relate to the ecological functions and capabilities of strain ESFC-1. The 5,632,035 bp genome sequence encodes 4914 protein-coding genes and 92 RNA genes. One striking feature of this cyanobacterium is the apparent lack of either uptake or bi-directional hydrogenases typically expected within a diazotroph. Additionally, a large genomic island is found that contains numerous low GC-content genes and genes related to extracellular polysaccharide production and cell wall synthesis and maintenance.
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Affiliation(s)
- R. Craig Everroad
- Exobiology Branch, NASA Ames Research Center, Moffett Field, CA USA
- Bay Area Environmental Research Institute, Petaluma, CA USA
| | - Rhona K. Stuart
- 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
| | - Angela M. Detweiler
- Exobiology Branch, NASA Ames Research Center, Moffett Field, CA USA
- Bay Area Environmental Research Institute, Petaluma, CA USA
| | - Jackson Z. Lee
- Exobiology Branch, NASA Ames Research Center, Moffett Field, CA USA
- Bay Area Environmental Research Institute, Petaluma, CA USA
| | - Dagmar Woebken
- Exobiology Branch, NASA Ames Research Center, Moffett Field, CA USA
- Current address: Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network “Chemistry meets Microbiology”, University of Vienna, Vienna, Austria
| | | | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA USA
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27
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NanoSIMS chemical imaging combined with correlative microscopy for biological sample analysis. Curr Opin Biotechnol 2016; 41:130-135. [PMID: 27506876 DOI: 10.1016/j.copbio.2016.06.006] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 06/17/2016] [Accepted: 06/23/2016] [Indexed: 12/18/2022]
Abstract
Nano-scale Secondary Ion Mass Spectrometry (NanoSIMS) is one of the most powerful in situ elemental and isotopic analysis techniques available to biologists. The combination of stable isotope probing with NanoSIMS (nanoSIP) has opened up new avenues for biological studies over the past decade. However, due to limitations inherent with any analytical methodology, additional information from correlative techniques is usually required to address real biological questions. Here we review recent developments in correlative analysis applied to complex biological systems: first, high-resolution tracking of molecules (e.g. peptides, lipids) by correlation with electron microscopy and atomic force microscopy; second, identification of a specific microbial taxon with fluorescence in situ hybridization and quantification of its metabolic capacities; and, third, molecular specific imaging with new probes.
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28
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Musat N, Musat F, Weber PK, Pett-Ridge J. Tracking microbial interactions with NanoSIMS. Curr Opin Biotechnol 2016; 41:114-121. [PMID: 27419912 DOI: 10.1016/j.copbio.2016.06.007] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Revised: 06/09/2016] [Accepted: 06/23/2016] [Indexed: 12/29/2022]
Abstract
The combination of stable isotope probing (SIP), NanoSIMS imaging and microbe identification via fluorescence in situ hybridization (FISH) is often used to link identity to function at the cellular level in microbial communities. Many opportunities remain for nanoSIP to identify metabolic interactions and nutrient fluxes within syntrophic associations and obligate symbioses where exchanges can be extremely rapid. However, additional data, such as genomic potential, gene expression or other imaging modalities are often critical to deciphering the mechanisms underlying specific interactions, and researchers must keep sample preparation artefacts in mind. Here we focus on recent applications of nanoSIP, particularly where used to track exchanges of isotopically labelled molecules between organisms. We highlight metabolic interactions within syntrophic consortia, carbon/nitrogen fluxes between phototrophs and their heterotrophic partners, and symbiont-host nutrient sharing.
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Affiliation(s)
- Niculina Musat
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany.
| | - Florin Musat
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Peter Kilian Weber
- Physical and Life Science Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Jennifer Pett-Ridge
- Physical and Life Science Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
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29
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Abstract
UNLABELLED Although it is becoming clear that many microbial primary producers can also play a role as organic consumers, we know very little about the metabolic regulation of photoautotroph organic matter consumption. Cyanobacteria in phototrophic biofilms can reuse extracellular organic carbon, but the metabolic drivers of extracellular processes are surprisingly complex. We investigated the metabolic foundations of organic matter reuse by comparing exoproteome composition and incorporation of (13)C-labeled and (15)N-labeled cyanobacterial extracellular organic matter (EOM) in a unicyanobacterial biofilm incubated using different light regimes. In the light and the dark, cyanobacterial direct organic C assimilation accounted for 32% and 43%, respectively, of all organic C assimilation in the community. Under photosynthesis conditions, we measured increased excretion of extracellular polymeric substances (EPS) and proteins involved in micronutrient transport, suggesting that requirements for micronutrients may drive EOM assimilation during daylight hours. This interpretation was supported by photosynthesis inhibition experiments, in which cyanobacteria incorporated N-rich EOM-derived material. In contrast, under dark, C-starved conditions, cyanobacteria incorporated C-rich EOM-derived organic matter, decreased excretion of EPS, and showed an increased abundance of degradative exoproteins, demonstrating the use of the extracellular domain for C storage. Sequence-structure modeling of one of these exoproteins predicted a specific hydrolytic activity that was subsequently detected, confirming increased EOM degradation in the dark. Associated heterotrophic bacteria increased in abundance and upregulated transport proteins under dark relative to light conditions. Taken together, our results indicate that biofilm cyanobacteria are successful competitors for organic C and N and that cyanobacterial nutrient and energy requirements control the use of EOM. IMPORTANCE Cyanobacteria are globally distributed primary producers, and the fate of their fixed C influences microbial biogeochemical cycling. This fate is complicated by cyanobacterial degradation and assimilation of organic matter, but because cyanobacteria are assumed to be poor competitors for organic matter consumption, regulation of this process is not well tested. In mats and biofilms, this is especially relevant because cyanobacteria produce an extensive organic extracellular matrix, providing the community with a rich source of nutrients. Light is a well-known regulator of cyanobacterial metabolism, so we characterized the effects of light availability on the incorporation of organic matter. Using stable isotope tracing at the single-cell level, we quantified photoautotroph assimilation under different metabolic conditions and integrated the results with proteomics to elucidate metabolic status. We found that cyanobacteria effectively compete for organic matter in the light and the dark and that nutrient requirements and community interactions contribute to cycling of extracellular organic matter.
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30
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Renslow RS, Lindemann SR, Cole JK, Zhu Z, Anderton CR. Quantifying element incorporation in multispecies biofilms using nanoscale secondary ion mass spectrometry image analysis. Biointerphases 2016; 11:02A322. [PMID: 26872582 PMCID: PMC5848783 DOI: 10.1116/1.4941764] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 01/26/2016] [Accepted: 01/28/2016] [Indexed: 11/17/2022] Open
Abstract
Elucidating nutrient exchange in microbial communities is an important step in understanding the relationships between microbial systems and global biogeochemical cycles, but these communities are complex and the interspecies interactions that occur within them are not well understood. Phototrophic consortia are useful and relevant experimental systems to investigate such interactions as they are not only prevalent in the environment, but some are cultivable in vitro and amenable to controlled scientific experimentation. Nanoscale secondary ion mass spectrometry (NanoSIMS) is a powerful, high spatial resolution tool capable of visualizing the metabolic activities of single cells within a biofilm, but quantitative analysis of the resulting data has typically been a manual process, resulting in a task that is both laborious and susceptible to human error. Here, the authors describe the creation and application of a semiautomated image-processing pipeline that can analyze NanoSIMS-generated data, applied to phototrophic biofilms as an example. The tool employs an image analysis process, which includes both elemental and morphological segmentation, producing a final segmented image that allows for discrimination between autotrophic and heterotrophic biomass, the detection of individual cyanobacterial filaments and heterotrophic cells, the quantification of isotopic incorporation of individual heterotrophic cells, and calculation of relevant population statistics. The authors demonstrate the functionality of the tool by using it to analyze the uptake of (15)N provided as either nitrate or ammonium through the unicyanobacterial consortium UCC-O and imaged via NanoSIMS. The authors found that the degree of (15)N incorporation by individual cells was highly variable when labeled with (15)NH4 (+), but much more even when biofilms were labeled with (15)NO3 (-). In the (15)NH4 (+)-amended biofilms, the heterotrophic distribution of (15)N incorporation was highly skewed, with a large population showing moderate (15)N incorporation and a small number of organisms displaying very high (15)N uptake. The results showed that analysis of NanoSIMS data can be performed in a way that allows for quantitation of the elemental uptake of individual cells, a technique necessary for advancing research into the metabolic networks that exist within biofilms with statistical analyses that are supported by automated, user-friendly processes.
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Affiliation(s)
- Ryan S Renslow
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, Washington 99354
| | - Stephen R Lindemann
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, Washington 99354
| | - Jessica K Cole
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, Washington 99354
| | - Zihua Zhu
- Environmental Molecular Sciences Laboratory, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, Washington 99354
| | - Christopher R Anderton
- Environmental Molecular Sciences Laboratory, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, Washington 99354
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31
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Marchant HK, Mohr W, Kuypers MM. Recent advances in marine N-cycle studies using 15N labeling methods. Curr Opin Biotechnol 2016; 41:53-59. [PMID: 27218834 DOI: 10.1016/j.copbio.2016.04.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 03/01/2016] [Accepted: 04/18/2016] [Indexed: 01/01/2023]
Abstract
15N enriched compounds such as ammonium and nitrate, as well as 15-15N2 gas are invaluable tools in marine N-cycle research. 15N stable isotope approaches allow researchers to delve into the often complex world of N-transformations and trace microbially mediated processes such as nitrification, denitrification, anammox and N-fixation. While 15N stable isotope approaches are well established, experimental approaches which take advantage of them are constantly evolving. Here we summarize recent advances in methodology, including in the direct application of 15N stable isotopes themselves, improved experimental design and the use of 15N stable isotopes in single cell studies. Furthermore, we discuss how these advances have led to new insights into marine N-cycling, particularly in the fields of nitrification and N-fixation.
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Affiliation(s)
| | - Wiebke Mohr
- Max Planck Institute for Marine Microbiology, Bremen, Germany
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32
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Bravakos P, Kotoulas G, Skaraki K, Pantazidou A, Economou-Amilli A. A polyphasic taxonomic approach in isolated strains of Cyanobacteria from thermal springs of Greece. Mol Phylogenet Evol 2016; 98:147-60. [DOI: 10.1016/j.ympev.2016.02.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 02/08/2016] [Accepted: 02/12/2016] [Indexed: 01/11/2023]
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33
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Proetto MT, Anderton CR, Hu D, Szymanski CJ, Zhu Z, Patterson JP, Kammeyer JK, Nilewski LG, Rush AM, Bell NC, Evans JE, Orr G, Howell SB, Gianneschi NC. Cellular Delivery of Nanoparticles Revealed with Combined Optical and Isotopic Nanoscopy. ACS NANO 2016; 10:4046-54. [PMID: 27022832 PMCID: PMC8459375 DOI: 10.1021/acsnano.5b06477] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Direct polymerization of an oxaliplatin analogue was used to reproducibly generate amphiphiles in one pot, which consistently and spontaneously self-assemble into well-defined nanoparticles (NPs). Despite inefficient drug leakage in cell-free assays, the NPs were observed to be as cytotoxic as free oxaliplatin in cell culture experiments. We investigated this phenomenon by super-resolution fluorescence structured illumination microscopy (SIM) and nanoscale secondary ion mass spectrometry (NanoSIMS). In combination, these techniques revealed NPs are taken up via endocytic pathways before intracellular release of their cytotoxic cargo. As with other drug-carrying nanomaterials, these systems have potential as cellular delivery vehicles. However, high-resolution methods to track nanocarriers and their cargo at the micro- and nanoscale have been underutilized in general, limiting our understanding of their interactions with cells and tissues. We contend this type of combined optical and isotopic imaging strategy represents a powerful and potentially generalizable methodology for cellular tracking of nanocarriers and their cargo.
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Affiliation(s)
- Maria T. Proetto
- Department of Chemistry & Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Christopher R. Anderton
- Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Dehong Hu
- Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Craig J. Szymanski
- Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Zihua Zhu
- Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Joseph P. Patterson
- Department of Chemistry & Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Jacquelin K. Kammeyer
- Department of Chemistry & Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Lizanne G. Nilewski
- Department of Chemistry & Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Anthony M. Rush
- Department of Chemistry & Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Nia C. Bell
- Department of Chemistry & Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - James E. Evans
- Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Galya Orr
- Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Stephen B. Howell
- Moores Cancer Center, University of California, San Diego, La Jolla, California 92093, United States
| | - Nathan C. Gianneschi
- Department of Chemistry & Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
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34
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Cyanobacterial reuse of extracellular organic carbon in microbial mats. ISME JOURNAL 2015; 10:1240-51. [PMID: 26495994 PMCID: PMC5029224 DOI: 10.1038/ismej.2015.180] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Revised: 08/21/2015] [Accepted: 09/02/2015] [Indexed: 11/09/2022]
Abstract
Cyanobacterial organic matter excretion is crucial to carbon cycling in many microbial communities, but the nature and bioavailability of this C depend on unknown physiological functions. Cyanobacteria-dominated hypersaline laminated mats are a useful model ecosystem for the study of C flow in complex communities, as they use photosynthesis to sustain a more or less closed system. Although such mats have a large C reservoir in the extracellular polymeric substances (EPSs), the production and degradation of organic carbon is not well defined. To identify extracellular processes in cyanobacterial mats, we examined mats collected from Elkhorn Slough (ES) at Monterey Bay, California, for glycosyl and protein composition of the EPS. We found a prevalence of simple glucose polysaccharides containing either α or β (1,4) linkages, indicating distinct sources of glucose with differing enzymatic accessibility. Using proteomics, we identified cyanobacterial extracellular enzymes, and also detected activities that indicate a capacity for EPS degradation. In a less complex system, we characterized the EPS of a cyanobacterial isolate from ES, ESFC-1, and found the extracellular composition of biofilms produced by this unicyanobacterial culture were similar to that of natural mats. By tracing isotopically labeled EPS into single cells of ESFC-1, we demonstrated rapid incorporation of extracellular-derived carbon. Taken together, these results indicate cyanobacteria reuse excess organic carbon, constituting a dynamic pool of extracellular resources in these mats.
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35
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Eichorst SA, Strasser F, Woyke T, Schintlmeister A, Wagner M, Woebken D. Advancements in the application of NanoSIMS and Raman microspectroscopy to investigate the activity of microbial cells in soils. FEMS Microbiol Ecol 2015; 91:fiv106. [PMID: 26324854 PMCID: PMC4629873 DOI: 10.1093/femsec/fiv106] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 06/04/2015] [Accepted: 08/24/2015] [Indexed: 11/15/2022] Open
Abstract
The combined approach of incubating environmental samples with stable isotope-labeled substrates followed by single-cell analyses through high-resolution secondary ion mass spectrometry (NanoSIMS) or Raman microspectroscopy provides insights into the in situ function of microorganisms. This approach has found limited application in soils presumably due to the dispersal of microbial cells in a large background of particles. We developed a pipeline for the efficient preparation of cell extracts from soils for subsequent single-cell methods by combining cell detachment with separation of cells and soil particles followed by cell concentration. The procedure was evaluated by examining its influence on cell recoveries and microbial community composition across two soils. This approach generated a cell fraction with considerably reduced soil particle load and of sufficient small size to allow single-cell analysis by NanoSIMS, as shown when detecting active N2-fixing and cellulose-responsive microorganisms via (15)N2 and (13)C-UL-cellulose incubations, respectively. The same procedure was also applicable for Raman microspectroscopic analyses of soil microorganisms, assessed via microcosm incubations with a (13)C-labeled carbon source and deuterium oxide (D2O, a general activity marker). The described sample preparation procedure enables single-cell analysis of soil microorganisms using NanoSIMS and Raman microspectroscopy, but should also facilitate single-cell sorting and sequencing.
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Affiliation(s)
- Stephanie A Eichorst
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research network 'Chemistry meets Microbiology', University of Vienna, Vienna 1090 Austria
| | - Florian Strasser
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research network 'Chemistry meets Microbiology', University of Vienna, Vienna 1090 Austria
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Arno Schintlmeister
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research network 'Chemistry meets Microbiology', University of Vienna, Vienna 1090 Austria Large-Instrument Facility for Advanced Isotope Research, University of Vienna, Vienna 1090 Austria
| | - Michael Wagner
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research network 'Chemistry meets Microbiology', University of Vienna, Vienna 1090 Austria Large-Instrument Facility for Advanced Isotope Research, University of Vienna, Vienna 1090 Austria
| | - Dagmar Woebken
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research network 'Chemistry meets Microbiology', University of Vienna, Vienna 1090 Austria
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36
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Gao D, Huang X, Tao Y. A critical review of NanoSIMS in analysis of microbial metabolic activities at single-cell level. Crit Rev Biotechnol 2015; 36:884-90. [DOI: 10.3109/07388551.2015.1057550] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Dawen Gao
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, P.R. China
| | - Xiaoli Huang
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, P.R. China
| | - Yu Tao
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, P.R. China
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37
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Zimmermann M, Escrig S, Hübschmann T, Kirf MK, Brand A, Inglis RF, Musat N, Müller S, Meibom A, Ackermann M, Schreiber F. Phenotypic heterogeneity in metabolic traits among single cells of a rare bacterial species in its natural environment quantified with a combination of flow cell sorting and NanoSIMS. Front Microbiol 2015; 6:243. [PMID: 25932020 PMCID: PMC4399338 DOI: 10.3389/fmicb.2015.00243] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 03/12/2015] [Indexed: 11/24/2022] Open
Abstract
Populations of genetically identical microorganisms residing in the same environment can display marked variability in their phenotypic traits; this phenomenon is termed phenotypic heterogeneity. The relevance of such heterogeneity in natural habitats is unknown, because phenotypic characterization of a sufficient number of single cells of the same species in complex microbial communities is technically difficult. We report a procedure that allows to measure phenotypic heterogeneity in bacterial populations from natural environments, and use it to analyze N2 and CO2 fixation of single cells of the green sulfur bacterium Chlorobium phaeobacteroides from the meromictic lake Lago di Cadagno. We incubated lake water with 15N2 and 13CO2 under in situ conditions with and without NH4+. Subsequently, we used flow cell sorting with auto-fluorescence gating based on a pure culture isolate to concentrate C. phaeobacteroides from its natural abundance of 0.2% to now 26.5% of total bacteria. C. phaeobacteroides cells were identified using catalyzed-reporter deposition fluorescence in situ hybridization (CARD-FISH) targeting the 16S rRNA in the sorted population with a species-specific probe. In a last step, we used nanometer-scale secondary ion mass spectrometry to measure the incorporation 15N and 13C stable isotopes in more than 252 cells. We found that C. phaeobacteroides fixes N2 in the absence of NH4+, but not in the presence of NH4+ as has previously been suggested. N2 and CO2 fixation were heterogeneous among cells and positively correlated indicating that N2 and CO2 fixation activity interact and positively facilitate each other in individual cells. However, because CARD-FISH identification cannot detect genetic variability among cells of the same species, we cannot exclude genetic variability as a source for phenotypic heterogeneity in this natural population. Our study demonstrates the technical feasibility of measuring phenotypic heterogeneity in a rare bacterial species in its natural habitat, thus opening the door to study the occurrence and relevance of phenotypic heterogeneity in nature.
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Affiliation(s)
- Matthias Zimmermann
- Department of Environmental Systems Sciences, ETH Zurich - Swiss Federal Institute of Technology Zurich, Switzerland ; Molecular Microbial Ecology Group, Department of Environmental Microbiology, Eawag - Swiss Federal Institute of Aquatic Science and Technology Zurich, Switzerland
| | - Stéphane Escrig
- Department of Environmental Microbiology, Helmholtz-Centre for Environmental Research, Leipzig Germany
| | - Thomas Hübschmann
- Department of Environmental Microbiology, Helmholtz-Centre for Environmental Research, Leipzig Germany
| | - Mathias K Kirf
- Department of Environmental Systems Sciences, ETH Zurich - Swiss Federal Institute of Technology Zurich, Switzerland ; Department of Surface Waters, Eawag - Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum Switzerland
| | - Andreas Brand
- Department of Environmental Systems Sciences, ETH Zurich - Swiss Federal Institute of Technology Zurich, Switzerland ; Department of Surface Waters, Eawag - Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum Switzerland
| | - R Fredrik Inglis
- Department of Environmental Systems Sciences, ETH Zurich - Swiss Federal Institute of Technology Zurich, Switzerland ; Molecular Microbial Ecology Group, Department of Environmental Microbiology, Eawag - Swiss Federal Institute of Aquatic Science and Technology Zurich, Switzerland
| | - Niculina Musat
- Department of Isotope Biogeochemistry, Helmholtz-Centre for Environmental Research, Leipzig Germany
| | - Susann Müller
- Department of Environmental Systems Sciences, ETH Zurich - Swiss Federal Institute of Technology Zurich, Switzerland
| | - Anders Meibom
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne Lausanne, Switzerland ; Center for Advanced Surface Analysis, Institute of Earth Sciences, University of Lausanne, Lausanne Switzerland
| | - Martin Ackermann
- Department of Environmental Systems Sciences, ETH Zurich - Swiss Federal Institute of Technology Zurich, Switzerland ; Molecular Microbial Ecology Group, Department of Environmental Microbiology, Eawag - Swiss Federal Institute of Aquatic Science and Technology Zurich, Switzerland
| | - Frank Schreiber
- Department of Environmental Systems Sciences, ETH Zurich - Swiss Federal Institute of Technology Zurich, Switzerland ; Molecular Microbial Ecology Group, Department of Environmental Microbiology, Eawag - Swiss Federal Institute of Aquatic Science and Technology Zurich, Switzerland
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38
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Kopf SH, McGlynn SE, Green-Saxena A, Guan Y, Newman DK, Orphan VJ. Heavy water and (15) N labelling with NanoSIMS analysis reveals growth rate-dependent metabolic heterogeneity in chemostats. Environ Microbiol 2015; 17:2542-56. [PMID: 25655651 DOI: 10.1111/1462-2920.12752] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Revised: 12/11/2014] [Accepted: 12/12/2014] [Indexed: 11/30/2022]
Abstract
To measure single-cell microbial activity and substrate utilization patterns in environmental systems, we employ a new technique using stable isotope labelling of microbial populations with heavy water (a passive tracer) and (15) N ammonium in combination with multi-isotope imaging mass spectrometry. We demonstrate simultaneous NanoSIMS analysis of hydrogen, carbon and nitrogen at high spatial and mass resolution, and report calibration data linking single-cell isotopic compositions to the corresponding bulk isotopic equivalents for Pseudomonas aeruginosa and Staphylococcus aureus. Our results show that heavy water is capable of quantifying in situ single-cell microbial activities ranging from generational time scales of minutes to years, with only light isotopic incorporation (∼0.1 atom % (2) H). Applying this approach to study the rates of fatty acid biosynthesis by single cells of S. aureus growing at different rates in chemostat culture (∼6 h, 1 day and 2 week generation times), we observe the greatest anabolic activity diversity in the slowest growing populations. By using heavy water to constrain cellular growth activity, we can further infer the relative contributions of ammonium versus amino acid assimilation to the cellular nitrogen pool. The approach described here can be applied to disentangle individual cell activities even in nutritionally complex environments.
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Affiliation(s)
- Sebastian H Kopf
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA.,Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.,Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA, USA
| | - Shawn E McGlynn
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
| | - Abigail Green-Saxena
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Yunbin Guan
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA.,Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA, USA
| | - Dianne K Newman
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA.,Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.,Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA, USA
| | - Victoria J Orphan
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
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39
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Kaiser C, Kilburn MR, Clode PL, Fuchslueger L, Koranda M, Cliff JB, Solaiman ZM, Murphy DV. Exploring the transfer of recent plant photosynthates to soil microbes: mycorrhizal pathway vs direct root exudation. THE NEW PHYTOLOGIST 2015; 205:1537-1551. [PMID: 25382456 PMCID: PMC4357392 DOI: 10.1111/nph.13138] [Citation(s) in RCA: 170] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Accepted: 09/23/2014] [Indexed: 05/19/2023]
Abstract
Plants rapidly release photoassimilated carbon (C) to the soil via direct root exudation and associated mycorrhizal fungi, with both pathways promoting plant nutrient availability. This study aimed to explore these pathways from the root's vascular bundle to soil microbial communities. Using nanoscale secondary ion mass spectrometry (NanoSIMS) imaging and (13) C-phospho- and neutral lipid fatty acids, we traced in-situ flows of recently photoassimilated C of (13) CO2 -exposed wheat (Triticum aestivum) through arbuscular mycorrhiza (AM) into root- and hyphae-associated soil microbial communities. Intraradical hyphae of AM fungi were significantly (13) C-enriched compared to other root-cortex areas after 8 h of labelling. Immature fine root areas close to the root tip, where AM features were absent, showed signs of passive C loss and co-location of photoassimilates with nitrogen taken up from the soil solution. A significant and exclusively fresh proportion of (13) C-photosynthates was delivered through the AM pathway and was utilised by different microbial groups compared to C directly released by roots. Our results indicate that a major release of recent photosynthates into soil leave plant roots via AM intraradical hyphae already upstream of passive root exudations. AM fungi may act as a rapid hub for translocating fresh plant C to soil microbes.
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Affiliation(s)
- Christina Kaiser
- Soil Biology and Molecular Ecology Group, School of Earth and Environment, Institute of Agriculture, The University of Western AustraliaCrawley, WA, 6009, Australia
- Department of Microbiology and Ecosystem Science, Division of Terrestrial Ecosystem Research, Faculty of Life Sciences, University of ViennaAlthanstrasse 14, Vienna, A-1090, Austria
| | - Matt R Kilburn
- Centre for Microscopy, Characterisation and Analysis, The University of Western AustraliaCrawley, WA, 6009, Australia
| | - Peta L Clode
- Centre for Microscopy, Characterisation and Analysis, The University of Western AustraliaCrawley, WA, 6009, Australia
| | - Lucia Fuchslueger
- Department of Microbiology and Ecosystem Science, Division of Terrestrial Ecosystem Research, Faculty of Life Sciences, University of ViennaAlthanstrasse 14, Vienna, A-1090, Austria
| | - Marianne Koranda
- Department of Microbiology and Ecosystem Science, Division of Terrestrial Ecosystem Research, Faculty of Life Sciences, University of ViennaAlthanstrasse 14, Vienna, A-1090, Austria
| | - John B Cliff
- Centre for Microscopy, Characterisation and Analysis, The University of Western AustraliaCrawley, WA, 6009, Australia
| | - Zakaria M Solaiman
- Soil Biology and Molecular Ecology Group, School of Earth and Environment, Institute of Agriculture, The University of Western AustraliaCrawley, WA, 6009, Australia
| | - Daniel V Murphy
- Soil Biology and Molecular Ecology Group, School of Earth and Environment, Institute of Agriculture, The University of Western AustraliaCrawley, WA, 6009, Australia
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40
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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. THE ISME JOURNAL 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] [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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41
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Abstract
The biodiversity of phytoplankton is a core measurement of the state and activity of marine ecosystems. In the context of historical approaches, we review recent major advances in the technologies that have enabled deeper characterization of the biodiversity of phytoplankton. In particular, high-throughput sequencing of single loci/genes, genomes, and communities (metagenomics) has revealed exceptional phylogenetic and genomic diversity whose breadth is not fully constrained. Other molecular tools-such as fingerprinting, quantitative polymerase chain reaction, and fluorescence in situ hybridization-have provided additional insight into the dynamics of this diversity in the context of environmental variability. Techniques for characterizing the functional diversity of community structure through targeted or untargeted approaches based on RNA or protein have also greatly advanced. A wide range of techniques is now available for characterizing phytoplankton communities, and these tools will continue to advance through ongoing improvements in both technology and data interpretation.
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Affiliation(s)
- Zackary I Johnson
- Marine Laboratory (Nicholas School of the Environment) and Department of Biology, Duke University, Beaufort, North Carolina 28516;
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42
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Carrell AA, Frank AC. Pinus flexilis and Picea engelmannii share a simple and consistent needle endophyte microbiota with a potential role in nitrogen fixation. Front Microbiol 2014; 5:333. [PMID: 25071746 PMCID: PMC4082182 DOI: 10.3389/fmicb.2014.00333] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Accepted: 06/16/2014] [Indexed: 02/01/2023] Open
Abstract
Conifers predominantly occur on soils or in climates that are suboptimal for plant growth. This is generally attributed to symbioses with mycorrhizal fungi and to conifer adaptations, but recent experiments suggest that aboveground endophytic bacteria in conifers fix nitrogen (N) and affect host shoot tissue growth. Because most bacteria cannot be grown in the laboratory very little is known about conifer–endophyte associations in the wild. Pinus flexilis (limber pine) and Picea engelmannii (Engelmann spruce) growing in a subalpine, nutrient-limited environment are potential candidates for hosting endophytes with roles in N2 fixation and abiotic stress tolerance. We used 16S rRNA pyrosequencing to ask whether these conifers host a core of bacterial species that are consistently associated with conifer individuals and therefore potential mutualists. We found that while overall the endophyte communities clustered according to host species, both conifers were consistently dominated by the same phylotype, which made up 19–53% and 14–39% of the sequences in P. flexilis and P. engelmannii, respectively. This phylotype is related to Gluconacetobacter diazotrophicus and other N2 fixing acetic acid bacterial endophytes. The pattern observed for the P. flexilis and P. engelmannii needle microbiota—a small number of major species that are consistently associated with the host across individuals and species—is unprecedented for an endophyte community, and suggests a specialized beneficial endophyte function. One possibility is endophytic N fixation, which could help explain how conifers can grow in severely nitrogen-limited soil, and why some forest ecosystems accumulate more N than can be accounted for by known nitrogen input pathways.
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Affiliation(s)
- Alyssa A Carrell
- Life and Environmental Sciences and Sierra Nevada Research Institute, School of Natural Sciences, University of California, Merced Merced, CA, USA
| | - Anna C Frank
- Life and Environmental Sciences and Sierra Nevada Research Institute, School of Natural Sciences, University of California, Merced Merced, CA, USA
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43
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Musat N, Stryhanyuk H, Bombach P, Adrian L, Audinot JN, Richnow HH. The effect of FISH and CARD-FISH on the isotopic composition of 13C- and 15N-labeled Pseudomonas putida cells measured by nanoSIMS. Syst Appl Microbiol 2014; 37:267-76. [DOI: 10.1016/j.syapm.2014.02.002] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Revised: 02/17/2014] [Accepted: 02/18/2014] [Indexed: 11/26/2022]
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44
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Lee JZ, Burow LC, Woebken D, Everroad RC, Kubo MD, Spormann AM, Weber PK, Pett-Ridge J, Bebout BM, Hoehler TM. Fermentation couples Chloroflexi and sulfate-reducing bacteria to Cyanobacteria in hypersaline microbial mats. Front Microbiol 2014; 5:61. [PMID: 24616716 PMCID: PMC3935151 DOI: 10.3389/fmicb.2014.00061] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Accepted: 01/30/2014] [Indexed: 11/17/2022] Open
Abstract
Past studies of hydrogen cycling in hypersaline microbial mats have shown an active nighttime cycle, with production largely from Cyanobacteria and consumption from sulfate-reducing bacteria (SRB). However, the mechanisms and magnitude of hydrogen cycling have not been extensively studied. Two mats types near Guerrero Negro, Mexico-permanently submerged Microcoleus microbial mat (GN-S), and intertidal Lyngbya microbial mat (GN-I)-were used in microcosm diel manipulation experiments with 3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU), molybdate, ammonium addition, and physical disruption to understand the processes responsible for hydrogen cycling between mat microbes. Across microcosms, H2 production occurred under dark anoxic conditions with simultaneous production of a suite of organic acids. H2 production was not significantly affected by inhibition of nitrogen fixation, but rather appears to result from constitutive fermentation of photosynthetic storage products by oxygenic phototrophs. Comparison to accumulated glycogen and to CO2 flux indicated that, in the GN-I mat, fermentation released almost all of the carbon fixed via photosynthesis during the preceding day, primarily as organic acids. Across mats, although oxygenic and anoxygenic phototrophs were detected, cyanobacterial [NiFe]-hydrogenase transcripts predominated. Molybdate inhibition experiments indicated that SRBs from a wide distribution of DsrA phylotypes were responsible for H2 consumption. Incubation with (13)C-acetate and NanoSIMS (secondary ion mass-spectrometry) indicated higher uptake in both Chloroflexi and SRBs relative to other filamentous bacteria. These manipulations and diel incubations confirm that Cyanobacteria were the main fermenters in Guerrero Negro mats and that the net flux of nighttime fermentation byproducts (not only hydrogen) was largely regulated by the interplay between Cyanobacteria, SRBs, and Chloroflexi.
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Affiliation(s)
- Jackson Z. Lee
- Exobiology Branch, NASA Ames Research CenterMoffett Field, CA, USA
- Bay Area Environmental Research InstituteSonoma, CA, USA
| | - Luke C. Burow
- Exobiology Branch, NASA Ames Research CenterMoffett Field, CA, USA
- Departments of Civil and Environmental Engineering, and Chemical Engineering, Stanford UniversityStanford, CA, USA
| | - Dagmar Woebken
- Exobiology Branch, NASA Ames Research CenterMoffett Field, CA, USA
- Departments of Civil and Environmental Engineering, and Chemical Engineering, Stanford UniversityStanford, CA, USA
| | | | - Mike D. Kubo
- Exobiology Branch, NASA Ames Research CenterMoffett Field, CA, USA
- The SETI InstituteMountain View, CA, USA
| | - Alfred M. Spormann
- Departments of Civil and Environmental Engineering, and Chemical Engineering, Stanford UniversityStanford, CA, USA
| | - Peter K. Weber
- Lawrence Livermore National Lab, Chemical Sciences DivisionLivermore, CA, USA
| | - Jennifer Pett-Ridge
- Lawrence Livermore National Lab, Chemical Sciences DivisionLivermore, CA, USA
| | - Brad M. Bebout
- Exobiology Branch, NASA Ames Research CenterMoffett Field, CA, USA
| | - Tori M. Hoehler
- Exobiology Branch, NASA Ames Research CenterMoffett Field, CA, USA
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45
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Chew YV, Holmes AJ, Cliff JB. Visualization of metabolic properties of bacterial cells using nanoscale secondary ion mass spectrometry (NanoSIMS). Methods Mol Biol 2014; 1096:133-146. [PMID: 24515366 DOI: 10.1007/978-1-62703-712-9_11] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
NanoSIMS combines high-resolution imaging and mass spectrometry with simultaneous collection of up to seven different masses, providing an invaluable technique for determining the isotopic and elemental composition in microscopic target samples. It has been used in varying fields, from studying the elemental composition of mineral samples to tracking cell uptake of isotope-labelled substrates. In combination with in situ hybridization techniques, NanoSIMS offers a powerful method of linking metabolic capacity to phylogenetic identity in cell samples. Here, we describe methods and considerations for microbial sample preparation, visualization, and analysis using NanoSIMS.
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Affiliation(s)
- Yi Vee Chew
- School of Molecular Bioscience, University of Sydney, Sydney, NSW, Australia
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46
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Carpenter KJ, Weber PK, Davisson ML, Pett-Ridge J, Haverty MI, Keeling PJ. Correlated SEM, FIB-SEM, TEM, and NanoSIMS imaging of microbes from the hindgut of a lower termite: methods for in situ functional and ecological studies of uncultivable microbes. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2013; 19:1490-501. [PMID: 24119340 DOI: 10.1017/s1431927613013482] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The hindguts of lower termites harbor highly diverse, endemic communities of symbiotic protists, bacteria, and archaea essential to the termite's ability to digest wood. Despite over a century of experimental studies, ecological roles of many of these microbes are unknown, partly because almost none can be cultivated. Many of the protists associate with bacterial symbionts, but hypotheses for their respective roles in nutrient exchange are based on genomes of only two such bacteria. To show how the ecological roles of protists and nutrient transfer with symbiotic bacteria can be elucidated by direct imaging, we combined stable isotope labeling (13C-cellulose) of live termites with analysis of fixed hindgut microbes using correlated scanning electron microscopy, focused ion beam-scanning electron microscopy (FIB-SEM), transmission electron microscopy, and high resolution imaging mass spectrometry (NanoSIMS). We developed methods to prepare whole labeled cells on solid substrates, whole labeled cells milled with a FIB-SEM instrument to reveal cell interiors, and ultramicrotome sections of labeled cells for NanoSIMS imaging of 13C enrichment in protists and associated bacteria. Our results show these methods have the potential to provide direct evidence for nutrient flow and suggest the oxymonad protist Oxymonas dimorpha phagocytoses and enzymatically degrades ingested wood fragments, and may transfer carbon derived from this to its surface bacterial symbionts.
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Affiliation(s)
- Kevin J Carpenter
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, P.O. Box 808, L-231, Livermore, CA 94551, USA
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47
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Everroad RC, Woebken D, Singer SW, Burow LC, Kyrpides N, Woyke T, Goodwin L, Detweiler A, Prufert-Bebout L, Pett-Ridge J. Draft Genome Sequence of an Oscillatorian Cyanobacterium, Strain ESFC-1. GENOME ANNOUNCEMENTS 2013; 1:e00527-13. [PMID: 23908279 PMCID: PMC3731833 DOI: 10.1128/genomea.00527-13] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Accepted: 06/24/2013] [Indexed: 11/20/2022]
Abstract
The nonheterocystous filamentous cyanobacterium strain ESFC-1 has recently been isolated from a marine microbial mat system, where it was identified as belonging to a recently discovered lineage of active nitrogen-fixing microorganisms. Here, we report the draft genome sequence of this isolate. The assembly consists of 3 scaffolds and contains 5,632,035 bp with a GC content of 46.5%.
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Affiliation(s)
- R. Craig Everroad
- Exobiology Branch, NASA Ames Research Center, Moffett Field, California, USA
| | - Dagmar Woebken
- Exobiology Branch, NASA Ames Research Center, Moffett Field, California, USA
- Departments of Chemical Engineering and Civil and Environmental Engineering, Stanford University, Stanford, California, USA
| | - Steven W. Singer
- Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Luke C. Burow
- Exobiology Branch, NASA Ames Research Center, Moffett Field, California, USA
- Departments of Chemical Engineering and Civil and Environmental Engineering, Stanford University, Stanford, California, USA
| | - Nikos Kyrpides
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Lynne Goodwin
- Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - Angela Detweiler
- Exobiology Branch, NASA Ames Research Center, Moffett Field, California, USA
| | | | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
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48
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Anoxic carbon flux in photosynthetic microbial mats as revealed by metatranscriptomics. ISME JOURNAL 2012; 7:817-29. [PMID: 23190731 PMCID: PMC3603402 DOI: 10.1038/ismej.2012.150] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Photosynthetic microbial mats possess extraordinary phylogenetic and functional diversity that makes linking specific pathways with individual microbial populations a daunting task. Close metabolic and spatial relationships between Cyanobacteria and Chloroflexi have previously been observed in diverse microbial mats. Here, we report that an expressed metabolic pathway for the anoxic catabolism of photosynthate involving Cyanobacteria and Chloroflexi in microbial mats can be reconstructed through metatranscriptomic sequencing of mats collected at Elkhorn Slough, Monterey Bay, CA, USA. In this reconstruction, Microcoleus spp., the most abundant cyanobacterial group in the mats, ferment photosynthate to organic acids, CO2 and H2 through multiple pathways, and an uncultivated lineage of the Chloroflexi take up these organic acids to store carbon as polyhydroxyalkanoates. The metabolic reconstruction is consistent with metabolite measurements and single cell microbial imaging with fluorescence in situ hybridization and NanoSIMS.
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49
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Abstract
We determined a significant fraction of the genome sequence of a representative of Thiovulum, the uncultivated genus of colorless sulfur Epsilonproteobacteria, by analyzing the genome sequences of four individual cells collected from phototrophic mats from Elkhorn Slough, California. These cells were isolated utilizing a microfluidic laser-tweezing system, and their genomes were amplified by multiple-displacement amplification prior to sequencing. Thiovulum is a gradient bacterium found at oxic-anoxic marine interfaces and noted for its distinctive morphology and rapid swimming motility. The genomic sequences of the four individual cells were assembled into a composite genome consisting of 221 contigs covering 2.083 Mb including 2,162 genes. This single-cell genome represents a genomic view of the physiological capabilities of isolated Thiovulum cells. Thiovulum is the second-fastest bacterium ever observed, swimming at 615 μm/s, and this genome shows that this rapid swimming motility is a result of a standard flagellar machinery that has been extensively characterized in other bacteria. This suggests that standard flagella are capable of propelling bacterial cells at speeds much faster than typically thought. Analysis of the genome suggests that naturally occurring Thiovulum populations are more diverse than previously recognized and that studies performed in the past probably address a wide range of unrecognized genotypic and phenotypic diversities of Thiovulum. The genome presented in this article provides a basis for future isolation-independent studies of Thiovulum, where single-cell and metagenomic tools can be used to differentiate between different Thiovulum genotypes.
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