1
|
Imminger S, Meier DV, Schintlmeister A, Legin A, Schnecker J, Richter A, Gillor O, Eichorst SA, Woebken D. Survival and rapid resuscitation permit limited productivity in desert microbial communities. Nat Commun 2024; 15:3056. [PMID: 38632260 DOI: 10.1038/s41467-024-46920-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 03/13/2024] [Indexed: 04/19/2024] Open
Abstract
Microbial activity in drylands tends to be confined to rare and short periods of rain. Rapid growth should be key to the maintenance of ecosystem processes in such narrow activity windows, if desiccation and rehydration cause widespread cell death due to osmotic stress. Here, simulating rain with 2H2O followed by single-cell NanoSIMS, we show that biocrust microbial communities in the Negev Desert are characterized by limited productivity, with median replication times of 6 to 19 days and restricted number of days allowing growth. Genome-resolved metatranscriptomics reveals that nearly all microbial populations resuscitate within minutes after simulated rain, independent of taxonomy, and invest their activity into repair and energy generation. Together, our data reveal a community that makes optimal use of short activity phases by fast and universal resuscitation enabling the maintenance of key ecosystem functions. We conclude that desert biocrust communities are highly adapted to surviving rapid changes in soil moisture and solute concentrations, resulting in high persistence that balances limited productivity.
Collapse
Affiliation(s)
- Stefanie Imminger
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
- University of Vienna, Doctoral School in Microbiology and Environmental Science, Vienna, Austria
| | - Dimitri V Meier
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
- Department of Ecological Microbiology, Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany
| | - Arno Schintlmeister
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
- Large-Instrument Facility for Environmental and Isotope Mass Spectrometry, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Anton Legin
- Faculty of Chemistry, Institute of Inorganic Chemistry, University of Vienna, Vienna, Austria
| | - Jörg Schnecker
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Andreas Richter
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Osnat Gillor
- Zuckerberg Institute for Water Research, Blaustein Institutes for Desert Research, Ben Gurion University of the Negev, Midreshet Ben Gurion, Israel
| | - Stephanie A Eichorst
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Dagmar Woebken
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria.
| |
Collapse
|
2
|
Nepel M, Mayer VE, Barrajon-Santos V, Woebken D. Bacterial diversity in arboreal ant nesting spaces is linked to colony developmental stage. Commun Biol 2023; 6:1217. [PMID: 38036598 PMCID: PMC10689775 DOI: 10.1038/s42003-023-05577-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 11/13/2023] [Indexed: 12/02/2023] Open
Abstract
The omnipresence of ants is commonly attributed to their eusocial organization and division of labor, however, bacteria in their nests may facilitate their success. Like many other arboreal ants living in plant-provided cavities, Azteca ants form dark-colored "patches" in their nesting space inside Cecropia host plants. These patches are inhabited by bacteria, fungi and nematodes and appear to be essential for ant colony development. Yet, detailed knowledge of the microbial community composition and its consistency throughout the life cycle of ant colonies was lacking. Amplicon sequencing of the microbial 16S rRNA genes in patches from established ant colonies reveals a highly diverse, ant species-specific bacterial community and little variation within an individual ant colony, with Burkholderiales, Rhizobiales and Chitinophagales being most abundant. In contrast, bacterial communities of early ant colony stages show low alpha diversity and no ant species-specific community composition. We suggest a substrate-caused bottleneck after vertical transmission of the bacterial patch community from mother to daughter colonies. The subsequent ecological succession is driven by environmental parameters and influenced by ant behavior. Our study provides key information for future investigations determining the functions of these bacteria, which is essential to understand the ubiquity of such patches among arboreal ants.
Collapse
Affiliation(s)
- Maximilian Nepel
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria.
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.
- Doctoral School in Microbiology and Environmental Science, University of Vienna, Vienna, Austria.
| | - Veronika E Mayer
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria.
| | - Veronica Barrajon-Santos
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Doctoral School in Microbiology and Environmental Science, University of Vienna, Vienna, Austria
| | - Dagmar Woebken
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| |
Collapse
|
3
|
Schmidt H, Gorka S, Seki D, Schintlmeister A, Woebken D. Gold-FISH enables targeted NanoSIMS analysis of plant-associated bacteria. New Phytol 2023; 240:439-451. [PMID: 37381111 PMCID: PMC10962543 DOI: 10.1111/nph.19112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 06/14/2023] [Indexed: 06/30/2023]
Abstract
Bacteria colonize plant roots and engage in reciprocal interactions with their hosts. However, the contribution of individual taxa or groups of bacteria to plant nutrition and fitness is not well characterized due to a lack of in situ evidence of bacterial activity. To address this knowledge gap, we developed an analytical approach that combines the identification and localization of individual bacteria on root surfaces via gold-based in situ hybridization with correlative NanoSIMS imaging of incorporated stable isotopes, indicative of metabolic activity. We incubated Kosakonia strain DS-1-associated, gnotobiotically grown rice plants with 15 N-N2 gas to detect in situ N2 fixation activity. Bacterial cells along the rhizoplane showed heterogeneous patterns of 15 N enrichment, ranging from the natural isotope abundance levels up to 12.07 at% 15 N (average and median of 3.36 and 2.85 at% 15 N, respectively, n = 697 cells). The presented correlative optical and chemical imaging analysis is applicable to a broad range of studies investigating plant-microbe interactions. For example, it enables verification of the in situ metabolic activity of host-associated commercialized strains or plant growth-promoting bacteria, thereby disentangling their role in plant nutrition. Such data facilitate the design of plant-microbe combinations for improvement of crop management.
Collapse
Affiliation(s)
- Hannes Schmidt
- Centre for Microbiology and Environmental Systems ScienceUniversity of ViennaVienna1030Austria
| | - Stefan Gorka
- Centre for Microbiology and Environmental Systems ScienceUniversity of ViennaVienna1030Austria
- Doctoral School in Microbiology and Environmental ScienceUniversity of ViennaVienna1030Austria
| | - David Seki
- Centre for Microbiology and Environmental Systems ScienceUniversity of ViennaVienna1030Austria
| | - Arno Schintlmeister
- Centre for Microbiology and Environmental Systems ScienceUniversity of ViennaVienna1030Austria
- Large‐Instrument Facility for Environmental and Isotope Mass Spectrometry, Centre for Microbiology and Environmental Systems ScienceUniversity of ViennaVienna1030Austria
| | - Dagmar Woebken
- Centre for Microbiology and Environmental Systems ScienceUniversity of ViennaVienna1030Austria
| |
Collapse
|
4
|
Dietrich M, Montesinos-Navarro A, Gabriel R, Strasser F, Meier DV, Mayerhofer W, Gorka S, Wiesenbauer J, Martin V, Weidinger M, Richter A, Kaiser C, Woebken D. Both abundant and rare fungi colonizing Fagus sylvatica ectomycorrhizal root-tips shape associated bacterial communities. Commun Biol 2022; 5:1261. [DOI: 10.1038/s42003-022-04178-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 10/27/2022] [Indexed: 11/18/2022] Open
Abstract
AbstractEctomycorrhizal fungi live in close association with their host plants and form complex interactions with bacterial/archaeal communities in soil. We investigated whether abundant or rare ectomycorrhizal fungi on root-tips of young beech trees (Fagus sylvatica) shape bacterial/archaeal communities. We sequenced 16S rRNA genes and fungal internal transcribed spacer regions of individual root-tips and used ecological networks to detect the tendency of certain assemblies of fungal and bacterial/archaeal taxa to inhabit the same root-tip (i.e. modularity). Individual ectomycorrhizal root-tips hosted distinct fungal communities associated with unique bacterial/archaeal communities. The structure of the fungal-bacterial/archaeal association was determined by both, dominant and rare fungi. Integrating our data in a conceptual framework suggests that the effect of rare fungi on the bacterial/archaeal communities of ectomycorrhizal root-tips contributes to assemblages of bacteria/archaea on root-tips. This highlights the potential impact of complex fine-scale interactions between root-tip associated fungi and other soil microorganisms for the ectomycorrhizal symbiosis.
Collapse
|
5
|
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 2022; 24:4962-4963. [PMID: 36254867 PMCID: PMC10117591 DOI: 10.1111/1462-2920.16213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/16/2022] [Indexed: 11/29/2022]
|
6
|
Falkenberg R, Fochler M, Sigl L, Bürstmayr H, Eichorst S, Michel S, Oburger E, Staudinger C, Steiner B, Woebken D. The breakthrough paradox. EMBO Rep 2022; 23:e54772. [PMID: 35620860 PMCID: PMC9253743 DOI: 10.15252/embr.202254772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 04/20/2022] [Accepted: 05/18/2022] [Indexed: 11/09/2022] Open
Affiliation(s)
- Ruth Falkenberg
- Research Platform Responsible Research and Innovation in Academic Practice University of Vienna Vienna Austria
| | - Maximilian Fochler
- Department of Science and Technology Studies University of Vienna Vienna Austria
| | - Lisa Sigl
- Research Platform Responsible Research and Innovation in Academic Practice University of Vienna Vienna Austria
| | - Hermann Bürstmayr
- Department of Agrobiotechnology University of Natural Resources and Life Sciences Tulln Austria
| | - Stephanie Eichorst
- Department of Microbiology and Ecosystem Science University of Vienna Vienna Austria
| | - Sebastian Michel
- Department of Agrobiotechnology University of Natural Resources and Life Sciences Tulln Austria
| | - Eva Oburger
- Institute of Soil Research University of Natural Resources and Life Sciences Vienna Austria
| | - Christiana Staudinger
- Institute of Soil Research University of Natural Resources and Life Sciences Vienna Austria
| | - Barbara Steiner
- Department of Agrobiotechnology University of Natural Resources and Life Sciences Tulln Austria
| | - Dagmar Woebken
- Department of Microbiology and Ecosystem Science University of Vienna Vienna Austria
| |
Collapse
|
7
|
Nepel M, Pfeifer J, Oberhauser FB, Richter A, Woebken D, Mayer VE. Nitrogen fixation by diverse diazotrophic communities can support population growth of arboreal ants. BMC Biol 2022; 20:135. [PMID: 35681192 PMCID: PMC9185989 DOI: 10.1186/s12915-022-01289-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 03/31/2022] [Indexed: 11/17/2022] Open
Abstract
Background Symbiotic ant-plant associations, in which ants live on plants, feed on plant-provided food, and protect host trees against threats, are ubiquitous across the tropics, with the Azteca-Cecropia associations being amongst the most widespread interactions in the Neotropics. Upon colonization of Cecropia’s hollow internodes, Azteca queens form small patches with plant parenchyma, which are then used as waste piles when the colony grows. Patches—found in many ant-plant mutualisms—are present throughout the colony life cycle and may supplement larval food. Despite their initial nitrogen (N)-poor substrate, patches in Cecropia accommodate fungi, nematodes, and bacteria. In this study, we investigated the atmospheric N2 fixation as an N source in patches of early and established ant colonies. Results Via 15N2 tracer assays, N2 fixation was frequently detected in all investigated patch types formed by three Azteca ant species. Quantified fixation rates were similar in early and established ant colonies and higher than in various tropical habitats. Based on amplicon sequencing, the identified microbial functional guild—the diazotrophs—harboring and transcribing the dinitrogenase reductase (nifH) gene was highly diverse and heterogeneous across Azteca colonies. The community composition differed between early and established ant colonies and partly between the ant species. Conclusions Our data show that N2 fixation can result in reasonable amounts of N in ant colonies, which might not only enable bacterial, fungal, and nematode growth in the patch ecosystems but according to our calculations can even support the growth of ant populations. The diverse and heterogeneous diazotrophic community implies a functional redundancy, which could provide the ant-plant-patch system with a higher resilience towards changing environmental conditions. Hence, we propose that N2 fixation represents a previously unknown potential to overcome N limitations in arboreal ant colonies. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01289-0.
Collapse
Affiliation(s)
- Maximilian Nepel
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria. .,Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.
| | - Josephine Pfeifer
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Felix B Oberhauser
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria.,Centre for the Advanced Study of Collective Behaviour, University of Konstanz, Konstanz, Germany
| | - Andreas Richter
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Dagmar Woebken
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.
| | - Veronika E Mayer
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| |
Collapse
|
8
|
Nepel M, Angel R, Borer ET, Frey B, MacDougall AS, McCulley RL, Risch AC, Schütz M, Seabloom EW, Woebken D. Global Grassland Diazotrophic Communities Are Structured by Combined Abiotic, Biotic, and Spatial Distance Factors but Resilient to Fertilization. Front Microbiol 2022; 13:821030. [PMID: 35418962 PMCID: PMC8996192 DOI: 10.3389/fmicb.2022.821030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 02/21/2022] [Indexed: 11/25/2022] Open
Abstract
Grassland ecosystems cover around 37% of the ice-free land surface on Earth and have critical socioeconomic importance globally. As in many terrestrial ecosystems, biological dinitrogen (N2) fixation represents an essential natural source of nitrogen (N). The ability to fix atmospheric N2 is limited to diazotrophs, a diverse guild of bacteria and archaea. To elucidate the abiotic (climatic, edaphic), biotic (vegetation), and spatial factors that govern diazotrophic community composition in global grassland soils, amplicon sequencing of the dinitrogenase reductase gene—nifH—was performed on samples from a replicated standardized nutrient [N, phosphorus (P)] addition experiment in 23 grassland sites spanning four continents. Sites harbored distinct and diverse diazotrophic communities, with most of reads assigned to diazotrophic taxa within the Alphaproteobacteria (e.g., Rhizobiales), Cyanobacteria (e.g., Nostocales), and Deltaproteobacteria (e.g., Desulforomonadales) groups. Likely because of the wide range of climatic and edaphic conditions and spatial distance among sampling sites, only a few of the taxa were present at all sites. The best model describing the variation among soil diazotrophic communities at the OTU level combined climate seasonality (temperature in the wettest quarter and precipitation in the warmest quarter) with edaphic (C:N ratio, soil texture) and vegetation factors (various perennial plant covers). Additionally, spatial variables (geographic distance) correlated with diazotrophic community variation, suggesting an interplay of environmental variables and spatial distance. The diazotrophic communities appeared to be resilient to elevated nutrient levels, as 2–4 years of chronic N and P additions had little effect on the community composition. However, it remains to be seen, whether changes in the community composition occur after exposure to long-term, chronic fertilization regimes.
Collapse
Affiliation(s)
- Maximilian Nepel
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.,Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Roey Angel
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Elizabeth T Borer
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN, United States
| | - Beat Frey
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | | | - Rebecca L McCulley
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, United States
| | - Anita C Risch
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Martin Schütz
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Eric W Seabloom
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN, United States
| | - Dagmar Woebken
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| |
Collapse
|
9
|
Mayerhofer W, Schintlmeister A, Dietrich M, Gorka S, Wiesenbauer J, Martin V, Gabriel R, Reipert S, Weidinger M, Clode P, Wagner M, Woebken D, Richter A, Kaiser C. Recently photoassimilated carbon and fungus-delivered nitrogen are spatially correlated in the ectomycorrhizal tissue of Fagus sylvatica. New Phytol 2021; 232:2457-2474. [PMID: 34196001 PMCID: PMC9291818 DOI: 10.1111/nph.17591] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 06/01/2021] [Indexed: 05/04/2023]
Abstract
Ectomycorrhizal plants trade plant-assimilated carbon for soil nutrients with their fungal partners. The underlying mechanisms, however, are not fully understood. Here we investigate the exchange of carbon for nitrogen in the ectomycorrhizal symbiosis of Fagus sylvatica across different spatial scales from the root system to the cellular level. We provided 15 N-labelled nitrogen to mycorrhizal hyphae associated with one half of the root system of young beech trees, while exposing plants to a 13 CO2 atmosphere. We analysed the short-term distribution of 13 C and 15 N in the root system with isotope-ratio mass spectrometry, and at the cellular scale within a mycorrhizal root tip with nanoscale secondary ion mass spectrometry (NanoSIMS). At the root system scale, plants did not allocate more 13 C to root parts that received more 15 N. Nanoscale secondary ion mass spectrometry imaging, however, revealed a highly heterogenous, and spatially significantly correlated distribution of 13 C and 15 N at the cellular scale. Our results indicate that, on a coarse scale, plants do not allocate a larger proportion of photoassimilated C to root parts associated with N-delivering ectomycorrhizal fungi. Within the ectomycorrhizal tissue, however, recently plant-assimilated C and fungus-delivered N were spatially strongly coupled. Here, NanoSIMS visualisation provides an initial insight into the regulation of ectomycorrhizal C and N exchange at the microscale.
Collapse
Affiliation(s)
- Werner Mayerhofer
- Centre for Microbiology and Environmental Systems ScienceUniversity of ViennaViennaA‐1030Austria
| | - Arno Schintlmeister
- Centre for Microbiology and Environmental Systems ScienceUniversity of ViennaViennaA‐1030Austria
- Large‐Instrument Facility for Environmental and Isotope Mass SpectrometryUniversity of ViennaViennaA‐1030Austria
| | - Marlies Dietrich
- Centre for Microbiology and Environmental Systems ScienceUniversity of ViennaViennaA‐1030Austria
| | - Stefan Gorka
- Centre for Microbiology and Environmental Systems ScienceUniversity of ViennaViennaA‐1030Austria
| | - Julia Wiesenbauer
- Centre for Microbiology and Environmental Systems ScienceUniversity of ViennaViennaA‐1030Austria
| | - Victoria Martin
- Centre for Microbiology and Environmental Systems ScienceUniversity of ViennaViennaA‐1030Austria
| | - Raphael Gabriel
- Centre for Microbiology and Environmental Systems ScienceUniversity of ViennaViennaA‐1030Austria
| | - Siegfried Reipert
- Core Facility Cell Imaging and Ultrastructure ResearchUniversity of ViennaViennaA‐1030Austria
| | - Marieluise Weidinger
- Core Facility Cell Imaging and Ultrastructure ResearchUniversity of ViennaViennaA‐1030Austria
| | - Peta Clode
- Centre for Microscopy, Characterisation & AnalysisUniversity of Western AustraliaPerthWA6009Australia
| | - Michael Wagner
- Centre for Microbiology and Environmental Systems ScienceUniversity of ViennaViennaA‐1030Austria
- Large‐Instrument Facility for Environmental and Isotope Mass SpectrometryUniversity of ViennaViennaA‐1030Austria
- Department of Chemistry and BioscienceAalborg UniversityAalborgDK‐9220Denmark
| | - Dagmar Woebken
- Centre for Microbiology and Environmental Systems ScienceUniversity of ViennaViennaA‐1030Austria
| | - Andreas Richter
- Centre for Microbiology and Environmental Systems ScienceUniversity of ViennaViennaA‐1030Austria
| | - Christina Kaiser
- Centre for Microbiology and Environmental Systems ScienceUniversity of ViennaViennaA‐1030Austria
| |
Collapse
|
10
|
Mayerhofer W, Schintlmeister A, Dietrich M, Gorka S, Wiesenbauer J, Martin V, Gabriel R, Reipert S, Weidinger M, Clode P, Wagner M, Woebken D, Richter A, Kaiser C. Recently photoassimilated carbon and fungus-delivered nitrogen are spatially correlated in the ectomycorrhizal tissue of Fagus sylvatica. New Phytol 2021; 232:2457-2474. [PMID: 34196001 DOI: 10.5281/zenodo.5035482] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 06/01/2021] [Indexed: 05/21/2023]
Abstract
Ectomycorrhizal plants trade plant-assimilated carbon for soil nutrients with their fungal partners. The underlying mechanisms, however, are not fully understood. Here we investigate the exchange of carbon for nitrogen in the ectomycorrhizal symbiosis of Fagus sylvatica across different spatial scales from the root system to the cellular level. We provided 15 N-labelled nitrogen to mycorrhizal hyphae associated with one half of the root system of young beech trees, while exposing plants to a 13 CO2 atmosphere. We analysed the short-term distribution of 13 C and 15 N in the root system with isotope-ratio mass spectrometry, and at the cellular scale within a mycorrhizal root tip with nanoscale secondary ion mass spectrometry (NanoSIMS). At the root system scale, plants did not allocate more 13 C to root parts that received more 15 N. Nanoscale secondary ion mass spectrometry imaging, however, revealed a highly heterogenous, and spatially significantly correlated distribution of 13 C and 15 N at the cellular scale. Our results indicate that, on a coarse scale, plants do not allocate a larger proportion of photoassimilated C to root parts associated with N-delivering ectomycorrhizal fungi. Within the ectomycorrhizal tissue, however, recently plant-assimilated C and fungus-delivered N were spatially strongly coupled. Here, NanoSIMS visualisation provides an initial insight into the regulation of ectomycorrhizal C and N exchange at the microscale.
Collapse
Affiliation(s)
- Werner Mayerhofer
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, A-1030, Austria
| | - Arno Schintlmeister
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, A-1030, Austria
- Large-Instrument Facility for Environmental and Isotope Mass Spectrometry, University of Vienna, Vienna, A-1030, Austria
| | - Marlies Dietrich
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, A-1030, Austria
| | - Stefan Gorka
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, A-1030, Austria
| | - Julia Wiesenbauer
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, A-1030, Austria
| | - Victoria Martin
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, A-1030, Austria
| | - Raphael Gabriel
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, A-1030, Austria
| | - Siegfried Reipert
- Core Facility Cell Imaging and Ultrastructure Research, University of Vienna, Vienna, A-1030, Austria
| | - Marieluise Weidinger
- Core Facility Cell Imaging and Ultrastructure Research, University of Vienna, Vienna, A-1030, Austria
| | - Peta Clode
- Centre for Microscopy, Characterisation & Analysis, University of Western Australia, Perth, WA, 6009, Australia
| | - Michael Wagner
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, A-1030, Austria
- Large-Instrument Facility for Environmental and Isotope Mass Spectrometry, University of Vienna, Vienna, A-1030, Austria
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, DK-9220, Denmark
| | - Dagmar Woebken
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, A-1030, Austria
| | - Andreas Richter
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, A-1030, Austria
| | - Christina Kaiser
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, A-1030, Austria
| |
Collapse
|
11
|
Meier DV, Greve AJ, Chennu A, van Erk MR, Muthukrishnan T, Abed RMM, Woebken D, de Beer D. Limitation of Microbial Processes at Saturation-Level Salinities in a Microbial Mat Covering a Coastal Salt Flat. Appl Environ Microbiol 2021; 87:e0069821. [PMID: 34160273 PMCID: PMC8357274 DOI: 10.1128/aem.00698-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 06/16/2021] [Indexed: 12/18/2022] Open
Abstract
Hypersaline microbial mats are dense microbial ecosystems capable of performing complete element cycling and are considered analogs of early Earth and hypothetical extraterrestrial ecosystems. We studied the functionality and limits of key biogeochemical processes, such as photosynthesis, aerobic respiration, and sulfur cycling, in salt crust-covered microbial mats from a tidal flat at the coast of Oman. We measured light, oxygen, and sulfide microprofiles as well as sulfate reduction rates at salt saturation and in flood conditions and determined fine-scale stratification of pigments, biomass, and microbial taxa in the resident microbial community. The salt crust did not protect the mats against irradiation or evaporation. Although some oxygen production was measurable at salinities of ≤30% (wt/vol) in situ, at saturation-level salinity (40%), oxygenic photosynthesis was completely inhibited and only resumed 2 days after reducing the porewater salinity to 12%. Aerobic respiration and active sulfur cycling occurred at low rates under salt saturation and increased strongly upon salinity reduction. Apart from high relative abundances of Chloroflexi, photoheterotrophic Alphaproteobacteria, Bacteroidetes, and Archaea, the mat contained a distinct layer harboring filamentous Cyanobacteria, which is unusual for such high salinities. Our results show that the diverse microbial community inhabiting this salt flat mat ultimately depends on periodic salt dilution to be self-sustaining and is rather adapted to merely survive salt saturation than to thrive under the salt crust. IMPORTANCE Due to their abilities to survive intense radiation and low water availability, hypersaline microbial mats are often suggested to be analogs of potential extraterrestrial life. However, even the limitations imposed on microbial processes by saturation-level salinity found on Earth have rarely been studied in situ. While abundance and diversity of microbial life in salt-saturated environments are well documented, most of our knowledge on process limitations stems from culture-based studies, few in situ studies, and theoretical calculations. In particular, oxygenic photosynthesis has barely been explored beyond 5 M NaCl (28% wt/vol). By applying a variety of biogeochemical and molecular methods, we show that despite abundance of photoautotrophic microorganisms, oxygenic photosynthesis is inhibited in salt-crust-covered microbial mats at saturation salinities, while rates of other energy generation processes are decreased several-fold. Hence, the complete element cycling required for self-sustaining microbial communities only occurs at lower salt concentrations.
Collapse
Affiliation(s)
- Dimitri V. Meier
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | | | - Arjun Chennu
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- Leibniz Centre for Tropical Marine Research, Bremen, Germany
| | | | | | - Raeid M. M. Abed
- Biology Department, College of Science, Sultan Qaboos University, Muscat, Sultanate of Oman
| | - Dagmar Woebken
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Dirk de Beer
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| |
Collapse
|
12
|
Meier DV, Imminger S, Gillor O, Woebken D. Distribution of Mixotrophy and Desiccation Survival Mechanisms across Microbial Genomes in an Arid Biological Soil Crust Community. mSystems 2021; 6:e00786-20. [PMID: 33436509 PMCID: PMC7901476 DOI: 10.1128/msystems.00786-20] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 12/08/2020] [Indexed: 02/06/2023] Open
Abstract
Desert surface soils devoid of plant cover are populated by a variety of microorganisms, many with yet unresolved physiologies and lifestyles. Nevertheless, a common feature vital for these microorganisms inhabiting arid soils is their ability to survive long drought periods and reactivate rapidly in rare incidents of rain. Chemolithotrophic processes such as oxidation of atmospheric hydrogen and carbon monoxide are suggested to be a widespread energy source to support dormancy and resuscitation in desert soil microorganisms. Here, we assessed the distribution of chemolithotrophic, phototrophic, and desiccation-related metabolic potential among microbial populations in arid biological soil crusts (BSCs) from the Negev Desert, Israel, via population-resolved metagenomic analysis. While the potential to utilize light and atmospheric hydrogen as additional energy sources was widespread, carbon monoxide oxidation was less common than expected. The ability to utilize continuously available energy sources might decrease the dependency of mixotrophic populations on organic storage compounds and carbon provided by the BSC-founding cyanobacteria. Several populations from five different phyla besides the cyanobacteria encoded CO2 fixation potential, indicating further potential independence from photoautotrophs. However, we also found population genomes with a strictly heterotrophic genetic repertoire. The highly abundant Rubrobacteraceae (Actinobacteriota) genomes showed particular specialization for this extreme habitat, different from their closest cultured relatives. Besides the ability to use light and hydrogen as energy sources, they encoded extensive O2 stress protection and unique DNA repair potential. The uncovered differences in metabolic potential between individual, co-occurring microbial populations enable predictions of their ecological niches and generation of hypotheses on the dynamics and interactions among them.IMPORTANCE This study represents a comprehensive community-wide genome-centered metagenome analysis of biological soil crust (BSC) communities in arid environments, providing insights into the distribution of genes encoding different energy generation mechanisms, as well as survival strategies, among populations in an arid soil ecosystem. It reveals the metabolic potential of several uncultured and previously unsequenced microbial genera, families, and orders, as well as differences in the metabolic potential between the most abundant BSC populations and their cultured relatives, highlighting once more the danger of inferring function on the basis of taxonomy. Assigning functional potential to individual populations allows for the generation of hypotheses on trophic interactions and activity patterns in arid soil microbial communities and represents the basis for future resuscitation and activity studies of the system, e.g., involving metatranscriptomics.
Collapse
Affiliation(s)
- Dimitri V Meier
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Stefanie Imminger
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Osnat Gillor
- Zuckerberg Institute for Water Research, Blaustein Institutes for Desert Research, Ben Gurion University of the Negev, Sde Boker, Israel
| | - Dagmar Woebken
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| |
Collapse
|
13
|
Giguere AT, Eichorst SA, Meier DV, Herbold CW, Richter A, Greening C, Woebken D. Acidobacteria are active and abundant members of diverse atmospheric H 2-oxidizing communities detected in temperate soils. ISME J 2020; 15:363-376. [PMID: 33024291 PMCID: PMC8027828 DOI: 10.1038/s41396-020-00750-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 07/30/2020] [Accepted: 08/12/2020] [Indexed: 12/24/2022]
Abstract
Significant rates of atmospheric dihydrogen (H2) consumption have been observed in temperate soils due to the activity of high-affinity enzymes, such as the group 1h [NiFe]-hydrogenase. We designed broadly inclusive primers targeting the large subunit gene (hhyL) of group 1h [NiFe]-hydrogenases for long-read sequencing to explore its taxonomic distribution across soils. This approach revealed a diverse collection of microorganisms harboring hhyL, including previously unknown groups and taxonomically not assignable sequences. Acidobacterial group 1h [NiFe]-hydrogenase genes were abundant and expressed in temperate soils. To support the participation of acidobacteria in H2 consumption, we studied two representative mesophilic soil acidobacteria, which expressed group 1h [NiFe]-hydrogenases and consumed atmospheric H2 during carbon starvation. This is the first time mesophilic acidobacteria, which are abundant in ubiquitous temperate soils, have been shown to oxidize H2 down to below atmospheric concentrations. As this physiology allows bacteria to survive periods of carbon starvation, it could explain the success of soil acidobacteria. With our long-read sequencing approach of group 1h [NiFe]-hydrogenase genes, we show that the ability to oxidize atmospheric levels of H2 is more widely distributed among soil bacteria than previously recognized and could represent a common mechanism enabling bacteria to persist during periods of carbon deprivation.
Collapse
Affiliation(s)
- Andrew T Giguere
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.,Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Stephanie A Eichorst
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.
| | - Dimitri V Meier
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Craig W Herbold
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Andreas Richter
- Division of Terrestrial Ecosystem Research, Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Chris Greening
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia.,School of Biological Sciences, Monash University, Clayton, VIC, 3800, Australia
| | - Dagmar Woebken
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| |
Collapse
|
14
|
Abstract
Microbial life is surprisingly abundant and diverse in global desert ecosystems. In these environments, microorganisms endure a multitude of physicochemical stresses, including low water potential, carbon and nitrogen starvation, and extreme temperatures. In this review, we summarize our current understanding of the energetic mechanisms and trophic dynamics that underpin microbial function in desert ecosystems. Accumulating evidence suggests that dormancy is a common strategy that facilitates microbial survival in response to water and carbon limitation. Whereas photoautotrophs are restricted to specific niches in extreme deserts, metabolically versatile heterotrophs persist even in the hyper-arid topsoils of the Atacama Desert and Antarctica. At least three distinct strategies appear to allow such microorganisms to conserve energy in these oligotrophic environments: degradation of organic energy reserves, rhodopsin- and bacteriochlorophyll-dependent light harvesting, and oxidation of the atmospheric trace gases hydrogen and carbon monoxide. In turn, these principles are relevant for understanding the composition, functionality, and resilience of desert ecosystems, as well as predicting responses to the growing problem of desertification.
Collapse
Affiliation(s)
- Pok Man Leung
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia
- Department of Microbiology, Biomedicine Discovery Institute, Clayton, Victoria, Australia
| | - Sean K Bay
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia
- Department of Microbiology, Biomedicine Discovery Institute, Clayton, Victoria, Australia
| | - Dimitri V Meier
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Eleonora Chiri
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia
- Department of Microbiology, Biomedicine Discovery Institute, Clayton, Victoria, Australia
| | - Don A Cowan
- Centre for Microbial Ecology and Genomics, University of Pretoria, Hatfield, Pretoria, South Africa
| | - Osnat Gillor
- Zuckerberg Institute for Water Research, Blaustein Institutes for Desert Research, Ben Gurion University of the Negev, Sde Boker, Israel
| | - Dagmar Woebken
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Chris Greening
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia
- Department of Microbiology, Biomedicine Discovery Institute, Clayton, Victoria, Australia
| |
Collapse
|
15
|
Zheng Q, Hu Y, Zhang S, Noll L, Böckle T, Dietrich M, Herbold CW, Eichorst SA, Woebken D, Richter A, Wanek W. Soil multifunctionality is affected by the soil environment and by microbial community composition and diversity. Soil Biol Biochem 2019; 136:107521. [PMID: 31700196 PMCID: PMC6837881 DOI: 10.1016/j.soilbio.2019.107521] [Citation(s) in RCA: 100] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Microorganisms are critical in mediating carbon (C) and nitrogen (N) cycling processes in soils. Yet, it has long been debated whether the processes underlying biogeochemical cycles are affected by the composition and diversity of the soil microbial community or not. The composition and diversity of soil microbial communities can be influenced by various environmental factors, which in turn are known to impact biogeochemical processes. The objectives of this study were to test effects of multiple edaphic drivers individually and represented as the multivariate soil environment interacting with microbial community composition and diversity, and concomitantly on multiple soil functions (i.e. soil enzyme activities, soil C and N processes). We employed high-throughput sequencing (Illumina MiSeq) to analyze bacterial/archaeal and fungal community composition by targeting the 16S rRNA gene and the ITS1 region of soils collected from three land uses (cropland, grassland and forest) deriving from two bedrock forms (silicate and limestone). Based on this data set we explored single and combined effects of edaphic variables on soil microbial community structure and diversity, as well as on soil enzyme activities and several soil C and N processes. We found that both bacterial/archaeal and fungal communities were shaped by the same edaphic factors, with most single edaphic variables and the combined soil environment representation exerting stronger effects on bacterial/archaeal communities than on fungal communities, as demonstrated by (partial) Mantel tests. We also found similar edaphic controls on the bacterial/archaeal/fungal richness and diversity. Soil C processes were only directly affected by the soil environment but not affected by microbial community composition. In contrast, soil N processes were significantly related to bacterial/archaeal community composition and bacterial/archaeal/fungal richness/diversity but not directly affected by the soil environment. This indicates direct control of the soil environment on soil C processes and indirect control of the soil environment on soil N processes by structuring the microbial communities. The study further highlights the importance of edaphic drivers and microbial communities (i.e. composition and diversity) on important soil C and N processes.
Collapse
Affiliation(s)
- Qing Zheng
- University of Vienna, Center for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Terrestrial Ecosystem Research, Althanstrasse 14, 1090 Vienna, Austria
| | - Yuntao Hu
- University of Vienna, Center for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Terrestrial Ecosystem Research, Althanstrasse 14, 1090 Vienna, Austria
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Shasha Zhang
- University of Vienna, Center for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Terrestrial Ecosystem Research, Althanstrasse 14, 1090 Vienna, Austria
| | - Lisa Noll
- University of Vienna, Center for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Terrestrial Ecosystem Research, Althanstrasse 14, 1090 Vienna, Austria
| | - Theresa Böckle
- University of Vienna, Center for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Terrestrial Ecosystem Research, Althanstrasse 14, 1090 Vienna, Austria
| | - Marlies Dietrich
- University of Vienna, Center for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Althanstrasse 14, 1090 Vienna, Austria
| | - Craig W. Herbold
- University of Vienna, Center for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Althanstrasse 14, 1090 Vienna, Austria
| | - Stephanie A. Eichorst
- University of Vienna, Center for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Althanstrasse 14, 1090 Vienna, Austria
| | - Dagmar Woebken
- University of Vienna, Center for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Althanstrasse 14, 1090 Vienna, Austria
| | - Andreas Richter
- University of Vienna, Center for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Terrestrial Ecosystem Research, Althanstrasse 14, 1090 Vienna, Austria
| | - Wolfgang Wanek
- University of Vienna, Center for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Terrestrial Ecosystem Research, Althanstrasse 14, 1090 Vienna, Austria
- Corresponding author. (W. Wanek)
| |
Collapse
|
16
|
Schneider S, Schintlmeister A, Becana M, Wagner M, Woebken D, Wienkoop S. Sulfate is transported at significant rates through the symbiosome membrane and is crucial for nitrogenase biosynthesis. Plant Cell Environ 2019; 42:1180-1189. [PMID: 30443991 PMCID: PMC6446814 DOI: 10.1111/pce.13481] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 11/04/2018] [Accepted: 11/05/2018] [Indexed: 05/03/2023]
Abstract
Legume-rhizobia symbioses play a major role in food production for an ever growing human population. In this symbiosis, dinitrogen is reduced ("fixed") to ammonia by the rhizobial nitrogenase enzyme complex and is secreted to the plant host cells, whereas dicarboxylic acids derived from photosynthetically produced sucrose are transported into the symbiosomes and serve as respiratory substrates for the bacteroids. The symbiosome membrane contains high levels of SST1 protein, a sulfate transporter. Sulfate is an essential nutrient for all living organisms, but its importance for symbiotic nitrogen fixation and nodule metabolism has long been underestimated. Using chemical imaging, we demonstrate that the bacteroids take up 20-fold more sulfate than the nodule host cells. Furthermore, we show that nitrogenase biosynthesis relies on high levels of imported sulfate, making sulfur as essential as carbon for the regulation and functioning of symbiotic nitrogen fixation. Our findings thus establish the importance of sulfate and its active transport for the plant-microbe interaction that is most relevant for agriculture and soil fertility.
Collapse
Affiliation(s)
- Sebastian Schneider
- Division of Molecular Systems Biology, Department of Ecogenomics and Systems BiologyUniversity of ViennaViennaAustria
| | - Arno Schintlmeister
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network “Chemistry Meets Microbiology”University of ViennaViennaAustria
- Large‐Instrument Facility for Advanced Isotope ResearchUniversity of ViennaViennaAustria
| | | | - Michael Wagner
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network “Chemistry Meets Microbiology”University of ViennaViennaAustria
- Large‐Instrument Facility for Advanced Isotope ResearchUniversity of ViennaViennaAustria
| | - Dagmar Woebken
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network “Chemistry Meets Microbiology”University of ViennaViennaAustria
| | - Stefanie Wienkoop
- Division of Molecular Systems Biology, Department of Ecogenomics and Systems BiologyUniversity of ViennaViennaAustria
| |
Collapse
|
17
|
Gorka S, Dietrich M, Mayerhofer W, Gabriel R, Wiesenbauer J, Martin V, Zheng Q, Imai B, Prommer J, Weidinger M, Schweiger P, Eichorst SA, Wagner M, Richter A, Schintlmeister A, Woebken D, Kaiser C. Rapid Transfer of Plant Photosynthates to Soil Bacteria via Ectomycorrhizal Hyphae and Its Interaction With Nitrogen Availability. Front Microbiol 2019; 10:168. [PMID: 30863368 PMCID: PMC6399413 DOI: 10.3389/fmicb.2019.00168] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 01/22/2019] [Indexed: 01/03/2023] Open
Abstract
Plant roots release recent photosynthates into the rhizosphere, accelerating decomposition of organic matter by saprotrophic soil microbes ("rhizosphere priming effect") which consequently increases nutrient availability for plants. However, about 90% of all higher plant species are mycorrhizal, transferring a significant fraction of their photosynthates directly to their fungal partners. Whether mycorrhizal fungi pass on plant-derived carbon (C) to bacteria in root-distant soil areas, i.e., incite a "hyphosphere priming effect," is not known. Experimental evidence for C transfer from mycorrhizal hyphae to soil bacteria is limited, especially for ectomycorrhizal systems. As ectomycorrhizal fungi possess enzymatic capabilities to degrade organic matter themselves, it remains unclear whether they cooperate with soil bacteria by providing photosynthates, or compete for available nutrients. To investigate a possible C transfer from ectomycorrhizal hyphae to soil bacteria, and its response to changing nutrient availability, we planted young beech trees (Fagus sylvatica) into "split-root" boxes, dividing their root systems into two disconnected soil compartments. Each of these compartments was separated from a litter compartment by a mesh penetrable for fungal hyphae, but not for roots. Plants were exposed to a 13C-CO2-labeled atmosphere, while 15N-labeled ammonium and amino acids were added to one side of the split-root system. We found a rapid transfer of recent photosynthates via ectomycorrhizal hyphae to bacteria in root-distant soil areas. Fungal and bacterial phospholipid fatty acid (PLFA) biomarkers were significantly enriched in hyphae-exclusive compartments 24 h after 13C-CO2-labeling. Isotope imaging with nanometer-scale secondary ion mass spectrometry (NanoSIMS) allowed for the first time in situ visualization of plant-derived C and N taken up by an extraradical fungal hypha, and in microbial cells thriving on hyphal surfaces. When N was added to the litter compartments, bacterial biomass, and the amount of incorporated 13C strongly declined. Interestingly, this effect was also observed in adjacent soil compartments where added N was only available for bacteria through hyphal transport, indicating that ectomycorrhizal fungi were acting on soil bacteria. Together, our results demonstrate that (i) ectomycorrhizal hyphae rapidly transfer plant-derived C to bacterial communities in root-distant areas, and (ii) this transfer promptly responds to changing soil nutrient conditions.
Collapse
Affiliation(s)
- Stefan Gorka
- Department of Microbiology and Ecosystem Science, Research Network “Chemistry meets Microbiology”, University of Vienna, Vienna, Austria
| | - Marlies Dietrich
- Department of Microbiology and Ecosystem Science, Research Network “Chemistry meets Microbiology”, University of Vienna, Vienna, Austria
| | - Werner Mayerhofer
- Department of Microbiology and Ecosystem Science, Research Network “Chemistry meets Microbiology”, University of Vienna, Vienna, Austria
| | - Raphael Gabriel
- Department of Microbiology and Ecosystem Science, Research Network “Chemistry meets Microbiology”, University of Vienna, Vienna, Austria
| | - Julia Wiesenbauer
- Department of Microbiology and Ecosystem Science, Research Network “Chemistry meets Microbiology”, University of Vienna, Vienna, Austria
| | - Victoria Martin
- Department of Microbiology and Ecosystem Science, Research Network “Chemistry meets Microbiology”, University of Vienna, Vienna, Austria
| | - Qing Zheng
- Department of Microbiology and Ecosystem Science, Research Network “Chemistry meets Microbiology”, University of Vienna, Vienna, Austria
| | - Bruna Imai
- Department of Microbiology and Ecosystem Science, Research Network “Chemistry meets Microbiology”, University of Vienna, Vienna, Austria
| | - Judith Prommer
- Department of Microbiology and Ecosystem Science, Research Network “Chemistry meets Microbiology”, University of Vienna, Vienna, Austria
| | - Marieluise Weidinger
- Core Facility Cell Imaging and Ultrastructure Research, University of Vienna, Vienna, Austria
| | - Peter Schweiger
- Department of Microbiology and Ecosystem Science, Research Network “Chemistry meets Microbiology”, University of Vienna, Vienna, Austria
| | - Stephanie A. Eichorst
- Department of Microbiology and Ecosystem Science, Research Network “Chemistry meets Microbiology”, University of Vienna, Vienna, Austria
| | - Michael Wagner
- Department of Microbiology and Ecosystem Science, Research Network “Chemistry meets Microbiology”, University of Vienna, Vienna, Austria
- Large-Instrument Facility for Advanced Isotope Research, University of Vienna, Vienna, Austria
| | - Andreas Richter
- Department of Microbiology and Ecosystem Science, Research Network “Chemistry meets Microbiology”, University of Vienna, Vienna, Austria
- Large-Instrument Facility for Advanced Isotope Research, University of Vienna, Vienna, Austria
| | - Arno Schintlmeister
- Department of Microbiology and Ecosystem Science, Research Network “Chemistry meets Microbiology”, University of Vienna, Vienna, Austria
- Large-Instrument Facility for Advanced Isotope Research, University of Vienna, Vienna, Austria
| | - Dagmar Woebken
- Department of Microbiology and Ecosystem Science, Research Network “Chemistry meets Microbiology”, University of Vienna, Vienna, Austria
| | - Christina Kaiser
- Department of Microbiology and Ecosystem Science, Research Network “Chemistry meets Microbiology”, University of Vienna, Vienna, Austria
| |
Collapse
|
18
|
Walker TWN, Kaiser C, Strasser F, Herbold CW, Leblans NIW, Woebken D, Janssens IA, Sigurdsson BD, Richter A. Microbial temperature sensitivity and biomass change explain soil carbon loss with warming. Nat Clim Chang 2018. [PMID: 30288176 DOI: 10.1038/s41558-018-0322-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Soil microorganisms control carbon losses from soils to the atmosphere1-3, yet their responses to climate warming are often short-lived and unpredictable4-7. Two mechanisms, microbial acclimation and substrate depletion, have been proposed to explain temporary warming effects on soil microbial activity8-10. However, empirical support for either mechanism is unconvincing. Here we used geothermal temperature gradients (> 50 years of field warming)11 and a short-term experiment to show that microbial activity (gross rates of growth, turnover, respiration and carbon uptake) is intrinsically temperature sensitive and does not acclimate to warming (+ 6 ºC) over weeks or decades. Permanently accelerated microbial activity caused carbon loss from soil. However, soil carbon loss was temporary because substrate depletion reduced microbial biomass and constrained the influence of microbes over the ecosystem. A microbial biogeochemical model12-14 showed that these observations are reproducible through a modest, but permanent, acceleration in microbial physiology. These findings reveal a mechanism by which intrinsic microbial temperature sensitivity and substrate depletion together dictate warming effects on soil carbon loss via their control over microbial biomass. We thus provide a framework for interpreting the links between temperature, microbial activity and soil carbon loss on timescales relevant to Earth's climate system.
Collapse
Affiliation(s)
- Tom W N Walker
- Department of Microbiology & Ecosystem Science, Division of Terrestrial Ecosystem Research, University of Vienna, 1090 Vienna, Austria
- Department of Ecology & Evolution, Université de Lausanne, CH-1015, Switzerland
| | - Christina Kaiser
- Department of Microbiology & Ecosystem Science, Division of Terrestrial Ecosystem Research, University of Vienna, 1090 Vienna, Austria
- Institute of Applied Systems Analysis, 2361 Laxenburg, Austria
| | - Florian Strasser
- Department of Microbiology & Ecosystem Science, Division of Microbial Ecology, University of Vienna, 1090 Vienna, Austria
| | - Craig W Herbold
- Department of Microbiology & Ecosystem Science, Division of Microbial Ecology, University of Vienna, 1090 Vienna, Austria
| | - Niki I W Leblans
- Department of Biology, University of Antwerp, 2610 Wilrijk, Antwerp, Belgium
- Agricultural University of Iceland, Hvanneyri, 311 Borgarnes, Iceland
| | - Dagmar Woebken
- Department of Microbiology & Ecosystem Science, Division of Microbial Ecology, University of Vienna, 1090 Vienna, Austria
| | - Ivan A Janssens
- Department of Biology, University of Antwerp, 2610 Wilrijk, Antwerp, Belgium
| | | | - Andreas Richter
- Department of Microbiology & Ecosystem Science, Division of Terrestrial Ecosystem Research, University of Vienna, 1090 Vienna, Austria
- Institute of Applied Systems Analysis, 2361 Laxenburg, Austria
| |
Collapse
|
19
|
Walker TWN, Kaiser C, Strasser F, Herbold CW, Leblans NIW, Woebken D, Janssens IA, Sigurdsson BD, Richter A. Microbial temperature sensitivity and biomass change explain soil carbon loss with warming. Nat Clim Chang 2018; 8:885-889. [PMID: 30288176 PMCID: PMC6166784 DOI: 10.1038/s41558-018-0259-x] [Citation(s) in RCA: 98] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 07/19/2018] [Indexed: 05/25/2023]
Abstract
Soil microorganisms control carbon losses from soils to the atmosphere1-3, yet their responses to climate warming are often short-lived and unpredictable4-7. Two mechanisms, microbial acclimation and substrate depletion, have been proposed to explain temporary warming effects on soil microbial activity8-10. However, empirical support for either mechanism is unconvincing. Here we used geothermal temperature gradients (> 50 years of field warming)11 and a short-term experiment to show that microbial activity (gross rates of growth, turnover, respiration and carbon uptake) is intrinsically temperature sensitive and does not acclimate to warming (+ 6 ºC) over weeks or decades. Permanently accelerated microbial activity caused carbon loss from soil. However, soil carbon loss was temporary because substrate depletion reduced microbial biomass and constrained the influence of microbes over the ecosystem. A microbial biogeochemical model12-14 showed that these observations are reproducible through a modest, but permanent, acceleration in microbial physiology. These findings reveal a mechanism by which intrinsic microbial temperature sensitivity and substrate depletion together dictate warming effects on soil carbon loss via their control over microbial biomass. We thus provide a framework for interpreting the links between temperature, microbial activity and soil carbon loss on timescales relevant to Earth's climate system.
Collapse
Affiliation(s)
- Tom W. N. Walker
- Department of Microbiology & Ecosystem Science, Division of Terrestrial Ecosystem Research, University of Vienna, 1090 Vienna, Austria
- Department of Ecology & Evolution, Université de Lausanne, CH-1015, Switzerland
| | - Christina Kaiser
- Department of Microbiology & Ecosystem Science, Division of Terrestrial Ecosystem Research, University of Vienna, 1090 Vienna, Austria
- Institute of Applied Systems Analysis, 2361 Laxenburg, Austria
| | - Florian Strasser
- Department of Microbiology & Ecosystem Science, Division of Microbial Ecology, University of Vienna, 1090 Vienna, Austria
| | - Craig W. Herbold
- Department of Microbiology & Ecosystem Science, Division of Microbial Ecology, University of Vienna, 1090 Vienna, Austria
| | - Niki I. W. Leblans
- Department of Biology, University of Antwerp, 2610 Wilrijk, Antwerp, Belgium
- Agricultural University of Iceland, Hvanneyri, 311 Borgarnes, Iceland
| | - Dagmar Woebken
- Department of Microbiology & Ecosystem Science, Division of Microbial Ecology, University of Vienna, 1090 Vienna, Austria
| | - Ivan A. Janssens
- Department of Biology, University of Antwerp, 2610 Wilrijk, Antwerp, Belgium
| | | | - Andreas Richter
- Department of Microbiology & Ecosystem Science, Division of Terrestrial Ecosystem Research, University of Vienna, 1090 Vienna, Austria
- Institute of Applied Systems Analysis, 2361 Laxenburg, Austria
| |
Collapse
|
20
|
Zumstein MT, Schintlmeister A, Nelson TF, Baumgartner R, Woebken D, Wagner M, Kohler HPE, McNeill K, Sander M. Biodegradation of synthetic polymers in soils: Tracking carbon into CO 2 and microbial biomass. Sci Adv 2018; 4:eaas9024. [PMID: 30050987 PMCID: PMC6059733 DOI: 10.1126/sciadv.aas9024] [Citation(s) in RCA: 159] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 06/18/2018] [Indexed: 05/22/2023]
Abstract
Plastic materials are widely used in agricultural applications to achieve food security for the growing world population. The use of biodegradable instead of nonbiodegradable polymers in single-use agricultural applications, including plastic mulching, promises to reduce plastic accumulation in the environment. We present a novel approach that allows tracking of carbon from biodegradable polymers into CO2 and microbial biomass. The approach is based on 13C-labeled polymers and on isotope-specific analytical methods, including nanoscale secondary ion mass spectrometry (NanoSIMS). Our results unequivocally demonstrate the biodegradability of poly(butylene adipate-co-terephthalate) (PBAT), an important polyester used in agriculture, in soil. Carbon from each monomer unit of PBAT was used by soil microorganisms, including filamentous fungi, to gain energy and to form biomass. This work advances both our conceptual understanding of polymer biodegradation and the methodological capabilities to assess this process in natural and engineered environments.
Collapse
Affiliation(s)
| | - Arno Schintlmeister
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network “Chemistry Meets Biology”, University of Vienna, Vienna 1090, Austria
- Large-Instrument Facility for Advanced Isotope Research, University of Vienna, Vienna 1090, Austria
| | | | - Rebekka Baumgartner
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich, 8092 Zürich, Switzerland
| | - Dagmar Woebken
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network “Chemistry Meets Biology”, University of Vienna, Vienna 1090, Austria
| | - Michael Wagner
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network “Chemistry Meets Biology”, University of Vienna, Vienna 1090, Austria
- Large-Instrument Facility for Advanced Isotope Research, University of Vienna, Vienna 1090, Austria
| | - Hans-Peter E. Kohler
- Environmental Biochemistry Group; Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), 8600 Dübendorf, Switzerland
| | - Kristopher McNeill
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich, 8092 Zürich, Switzerland
| | - Michael Sander
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich, 8092 Zürich, Switzerland
- Corresponding author.
| |
Collapse
|
21
|
Hausmann B, Pelikan C, Herbold CW, Köstlbacher S, Albertsen M, Eichorst SA, Glavina Del Rio T, Huemer M, Nielsen PH, Rattei T, Stingl U, Tringe SG, Trojan D, Wentrup C, Woebken D, Pester M, Loy A. Peatland Acidobacteria with a dissimilatory sulfur metabolism. ISME J 2018; 12:1729-1742. [PMID: 29476143 PMCID: PMC6018796 DOI: 10.1038/s41396-018-0077-1] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 12/21/2017] [Accepted: 01/20/2018] [Indexed: 12/25/2022]
Abstract
Sulfur-cycling microorganisms impact organic matter decomposition in wetlands and consequently greenhouse gas emissions from these globally relevant environments. However, their identities and physiological properties are largely unknown. By applying a functional metagenomics approach to an acidic peatland, we recovered draft genomes of seven novel Acidobacteria species with the potential for dissimilatory sulfite (dsrAB, dsrC, dsrD, dsrN, dsrT, dsrMKJOP) or sulfate respiration (sat, aprBA, qmoABC plus dsr genes). Surprisingly, the genomes also encoded DsrL, which so far was only found in sulfur-oxidizing microorganisms. Metatranscriptome analysis demonstrated expression of acidobacterial sulfur-metabolism genes in native peat soil and their upregulation in diverse anoxic microcosms. This indicated an active sulfate respiration pathway, which, however, might also operate in reverse for dissimilatory sulfur oxidation or disproportionation as proposed for the sulfur-oxidizing Desulfurivibrio alkaliphilus. Acidobacteria that only harbored genes for sulfite reduction additionally encoded enzymes that liberate sulfite from organosulfonates, which suggested organic sulfur compounds as complementary energy sources. Further metabolic potentials included polysaccharide hydrolysis and sugar utilization, aerobic respiration, several fermentative capabilities, and hydrogen oxidation. Our findings extend both, the known physiological and genetic properties of Acidobacteria and the known taxonomic diversity of microorganisms with a DsrAB-based sulfur metabolism, and highlight new fundamental niches for facultative anaerobic Acidobacteria in wetlands based on exploitation of inorganic and organic sulfur molecules for energy conservation.
Collapse
Affiliation(s)
- Bela Hausmann
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, Vienna, Austria
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Claus Pelikan
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, Vienna, Austria
| | - Craig W Herbold
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, Vienna, Austria
| | - Stephan Köstlbacher
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, Vienna, Austria
| | - Mads Albertsen
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark
| | - Stephanie A Eichorst
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, Vienna, Austria
| | | | - Martin Huemer
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, Vienna, Austria
| | - Per H Nielsen
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark
| | - Thomas Rattei
- Division of Computational Systems Biology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, Vienna, Austria
| | - Ulrich Stingl
- Department for Microbiology and Cell Science, Fort Lauderdale Research and Education Center, UF/IFAS, University of Florida, Davie, FL, USA
| | - Susannah G Tringe
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Daniela Trojan
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, Vienna, Austria
| | - Cecilia Wentrup
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, Vienna, Austria
| | - Dagmar Woebken
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, Vienna, Austria
| | - Michael Pester
- Department of Biology, University of Konstanz, Konstanz, Germany.
- Leibniz Institute DSMZ, Braunschweig, Germany.
| | - Alexander Loy
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, Vienna, Austria
| |
Collapse
|
22
|
Angel R, Nepel M, Panhölzl C, Schmidt H, Herbold CW, Eichorst SA, Woebken D. Evaluation of Primers Targeting the Diazotroph Functional Gene and Development of NifMAP - A Bioinformatics Pipeline for Analyzing nifH Amplicon Data. Front Microbiol 2018; 9:703. [PMID: 29760683 PMCID: PMC5936773 DOI: 10.3389/fmicb.2018.00703] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Accepted: 03/27/2018] [Indexed: 11/13/2022] Open
Abstract
Diazotrophic microorganisms introduce biologically available nitrogen (N) to the global N cycle through the activity of the nitrogenase enzyme. The genetically conserved dinitrogenase reductase (nifH) gene is phylogenetically distributed across four clusters (I-IV) and is widely used as a marker gene for N2 fixation, permitting investigators to study the genetic diversity of diazotrophs in nature and target potential participants in N2 fixation. To date there have been limited, standardized pipelines for analyzing the nifH functional gene, which is in stark contrast to the 16S rRNA gene. Here we present a bioinformatics pipeline for processing nifH amplicon datasets - NifMAP ("NifH MiSeq Illumina Amplicon Analysis Pipeline"), which as a novel aspect uses Hidden-Markov Models to filter out homologous genes to nifH. By using this pipeline, we evaluated the broadly inclusive primer pairs (Ueda19F-R6, IGK3-DVV, and F2-R6) that target the nifH gene. To evaluate any systematic biases, the nifH gene was amplified with the aforementioned primer pairs in a diverse collection of environmental samples (soils, rhizosphere and roots samples, biological soil crusts and estuarine samples), in addition to a nifH mock community consisting of six phylogenetically diverse members. We noted that all primer pairs co-amplified nifH homologs to varying degrees; up to 90% of the amplicons were nifH homologs with IGK3-DVV in some samples (rhizosphere and roots from tall oat-grass). In regards to specificity, we observed some degree of bias across the primer pairs. For example, primer pair F2-R6 discriminated against cyanobacteria (amongst others), yet captured many sequences from subclusters IIIE and IIIL-N. These aforementioned subclusters were largely missing by the primer pair IGK3-DVV, which also tended to discriminate against Alphaproteobacteria, but amplified sequences within clusters IIIC (affiliated with Clostridia) and clusters IVB and IVC. Primer pair Ueda19F-R6 exhibited the least bias and successfully captured diazotrophs in cluster I and subclusters IIIE, IIIL, IIIM, and IIIN, but tended to discriminate against Firmicutes and subcluster IIIC. Taken together, our newly established bioinformatics pipeline, NifMAP, along with our systematic evaluations of nifH primer pairs permit more robust, high-throughput investigations of diazotrophs in diverse environments.
Collapse
Affiliation(s)
- Roey Angel
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network ‘Chemistry meets Microbiology’, University of Vienna, Vienna, Austria
| | | | | | | | | | | | - Dagmar Woebken
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network ‘Chemistry meets Microbiology’, University of Vienna, Vienna, Austria
| |
Collapse
|
23
|
Eichorst SA, Trojan D, Roux S, Herbold C, Rattei T, Woebken D. Genomic insights into the Acidobacteria reveal strategies for their success in terrestrial environments. Environ Microbiol 2018; 20:1041-1063. [PMID: 29327410 PMCID: PMC5900883 DOI: 10.1111/1462-2920.14043] [Citation(s) in RCA: 134] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 12/16/2017] [Accepted: 01/08/2018] [Indexed: 12/11/2022]
Abstract
Members of the phylum Acidobacteria are abundant and ubiquitous across soils. We performed a large-scale comparative genome analysis spanning subdivisions 1, 3, 4, 6, 8 and 23 (n = 24) with the goal to identify features to help explain their prevalence in soils and understand their ecophysiology. Our analysis revealed that bacteriophage integration events along with transposable and mobile elements influenced the structure and plasticity of these genomes. Low- and high-affinity respiratory oxygen reductases were detected in multiple genomes, suggesting the capacity for growing across different oxygen gradients. Among many genomes, the capacity to use a diverse collection of carbohydrates, as well as inorganic and organic nitrogen sources (such as via extracellular peptidases), was detected - both advantageous traits in environments with fluctuating nutrient environments. We also identified multiple soil acidobacteria with the potential to scavenge atmospheric concentrations of H2 , now encompassing mesophilic soil strains within the subdivision 1 and 3, in addition to a previously identified thermophilic strain in subdivision 4. This large-scale acidobacteria genome analysis reveal traits that provide genomic, physiological and metabolic versatility, presumably allowing flexibility and versatility in the challenging and fluctuating soil environment.
Collapse
Affiliation(s)
- Stephanie A. Eichorst
- Division of Microbial Ecology, Department of Microbiology and Ecosystem ScienceResearch Network “Chemistry Meets Biology”, University of ViennaViennaAustria
| | - Daniela Trojan
- Division of Microbial Ecology, Department of Microbiology and Ecosystem ScienceResearch Network “Chemistry Meets Biology”, University of ViennaViennaAustria
| | - Simon Roux
- Department of EnergyJoint Genome InstituteWalnut CreekCAUSA
| | - Craig Herbold
- Division of Microbial Ecology, Department of Microbiology and Ecosystem ScienceResearch Network “Chemistry Meets Biology”, University of ViennaViennaAustria
| | - Thomas Rattei
- Division of Computational Systems Biology, Department of Microbiology and Ecosystem ScienceResearch Network “Chemistry Meets Biology”, University of ViennaViennaAustria
| | - Dagmar Woebken
- Division of Microbial Ecology, Department of Microbiology and Ecosystem ScienceResearch Network “Chemistry Meets Biology”, University of ViennaViennaAustria
| |
Collapse
|
24
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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
| |
Collapse
|
25
|
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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 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.
Collapse
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
| |
Collapse
|
26
|
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: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [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.
Collapse
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
| |
Collapse
|
27
|
Woebken D, Burow LC, Behnam F, Mayali X, Schintlmeister A, Fleming ED, Prufert-Bebout L, Singer SW, Cortés AL, Hoehler TM, Pett-Ridge J, Spormann AM, Wagner M, Weber PK, Bebout BM. Revisiting N₂ fixation in Guerrero Negro intertidal microbial mats with a functional single-cell approach. ISME J 2015; 9:485-96. [PMID: 25303712 PMCID: PMC4303640 DOI: 10.1038/ismej.2014.144] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2014] [Revised: 06/15/2014] [Accepted: 06/29/2014] [Indexed: 11/09/2022]
Abstract
Photosynthetic microbial mats are complex, stratified ecosystems in which high rates of primary production create a demand for nitrogen, met partially by N₂ fixation. Dinitrogenase reductase (nifH) genes and transcripts from Cyanobacteria and heterotrophic bacteria (for example, Deltaproteobacteria) were detected in these mats, yet their contribution to N2 fixation is poorly understood. We used a combined approach of manipulation experiments with inhibitors, nifH sequencing and single-cell isotope analysis to investigate the active diazotrophic community in intertidal microbial mats at Laguna Ojo de Liebre near Guerrero Negro, Mexico. Acetylene reduction assays with specific metabolic inhibitors suggested that both sulfate reducers and members of the Cyanobacteria contributed to N₂ fixation, whereas (15)N₂ tracer experiments at the bulk level only supported a contribution of Cyanobacteria. Cyanobacterial and nifH Cluster III (including deltaproteobacterial sulfate reducers) sequences dominated the nifH gene pool, whereas the nifH transcript pool was dominated by sequences related to Lyngbya spp. Single-cell isotope analysis of (15)N₂-incubated mat samples via high-resolution secondary ion mass spectrometry (NanoSIMS) revealed that Cyanobacteria were enriched in (15)N, with the highest enrichment being detected in Lyngbya spp. filaments (on average 4.4 at% (15)N), whereas the Deltaproteobacteria (identified by CARD-FISH) were not significantly enriched. We investigated the potential dilution effect from CARD-FISH on the isotopic composition and concluded that the dilution bias was not substantial enough to influence our conclusions. Our combined data provide evidence that members of the Cyanobacteria, especially Lyngbya spp., actively contributed to N₂ fixation in the intertidal mats, whereas support for significant N₂ fixation activity of the targeted deltaproteobacterial sulfate reducers could not be found.
Collapse
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
| |
Collapse
|
28
|
Burow LC, Woebken D, Marshall IPG, Singer SW, Pett-Ridge J, Prufert-Bebout L, Spormann AM, Bebout BM, Weber PK, Hoehler TM. Identification of Desulfobacterales as primary hydrogenotrophs in a complex microbial mat community. Geobiology 2014; 12:221-230. [PMID: 24730641 DOI: 10.1111/gbi.12080] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Accepted: 01/22/2014] [Indexed: 06/03/2023]
Abstract
Hypersaline microbial mats have been shown to produce significant quantities of H2 under dark, anoxic conditions via cyanobacterial fermentation. This flux of a widely accessible microbial substrate has potential to significantly influence the ecology of the mat, and any consumption will affect the net efflux of H2 that might otherwise be captured as a resource. Here, we focus on H2 consumption in a microbial mat from Elkhorn Slough, California, USA, for which H2 production has been previously characterized. Active biologic H2 consumption in this mat is indicated by a significant time-dependent decrease in added H2 compared with a killed control. Inhibition of sulfate reduction, as indicated by a decrease in hydrogen sulfide production relative to controls, resulted in a significant increase in H2 efflux, suggesting that sulfate-reducing bacteria (SRB) are important hydrogenotrophs. Low methane efflux under these same conditions indicated that methanogens are likely not important hydrogenotrophs. Analyses of genes and transcripts that encode for rRNA or dissimilatory sulfite reductase, using both PCR-dependent and PCR-independent metatranscriptomic sequencing methods, demonstrated that Desulfobacterales are the dominant, active SRB in the upper, H2-producing layer of the mat (0-2 mm). This hypothesis was further supported by the identification of transcripts encoding hydrogenases derived from Desulfobacterales capable of H2 oxidation. Analysis of molecular data provided no evidence for the activity of hydrogenotrophic methanogens. The combined biogeochemical and molecular data strongly indicate that SRB belonging to the Desulfobacterales are the quantitatively important hydrogenotrophs in the Elkhorn Slough mat.
Collapse
Affiliation(s)
- L C Burow
- Departments of Chemical, Civil and Environmental Engineering, Stanford University, Stanford, CA, USA; Exobiology Branch, NASA Ames Research Center, Moffett Field, CA, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
29
|
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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 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.
Collapse
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
| |
Collapse
|
30
|
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 Announc 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] [What about the content of this article? (0)] [Affiliation(s)] [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%.
Collapse
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
| |
Collapse
|
31
|
van de Vossenberg J, Woebken D, Maalcke WJ, Wessels HJCT, Dutilh BE, Kartal B, Janssen-Megens EM, Roeselers G, Yan J, Speth D, Gloerich J, Geerts W, van der Biezen E, Pluk W, Francoijs KJ, Russ L, Lam P, Malfatti SA, Tringe SG, Haaijer SCM, Op den Camp HJM, Stunnenberg HG, Amann R, Kuypers MMM, Jetten MSM. The metagenome of the marine anammox bacterium 'Candidatus Scalindua profunda' illustrates the versatility of this globally important nitrogen cycle bacterium. Environ Microbiol 2013; 15:1275-89. [PMID: 22568606 PMCID: PMC3655542 DOI: 10.1111/j.1462-2920.2012.02774.x] [Citation(s) in RCA: 153] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2012] [Revised: 04/11/2012] [Accepted: 04/12/2012] [Indexed: 11/28/2022]
Abstract
Anaerobic ammonium-oxidizing (anammox) bacteria are responsible for a significant portion of the loss of fixed nitrogen from the oceans, making them important players in the global nitrogen cycle. To date, marine anammox bacteria found in marine water columns and sediments worldwide belong almost exclusively to the 'Candidatus Scalindua' species, but the molecular basis of their metabolism and competitive fitness is presently unknown. We applied community sequencing of a marine anammox enrichment culture dominated by 'Candidatus Scalindua profunda' to construct a genome assembly, which was subsequently used to analyse the most abundant gene transcripts and proteins. In the S. profunda assembly, 4756 genes were annotated, and only about half of them showed the highest identity to the only other anammox bacterium of which a metagenome assembly had been constructed so far, the freshwater 'Candidatus Kuenenia stuttgartiensis'. In total, 2016 genes of S. profunda could not be matched to the K. stuttgartiensis metagenome assembly at all, and a similar number of genes in K.stuttgartiensis could not be found in S. profunda. Most of these genes did not have a known function but 98 expressed genes could be attributed to oligopeptide transport, amino acid metabolism, use of organic acids and electron transport. On the basis of the S. profunda metagenome, and environmental metagenome data, we observed pronounced differences in the gene organization and expression of important anammox enzymes, such as hydrazine synthase (HzsAB), nitrite reductase (NirS) and inorganic nitrogen transport proteins. Adaptations of Scalindua to the substrate limitation of the ocean may include highly expressed ammonium, nitrite and oligopeptide transport systems and pathways for the transport, oxidation, and assimilation of small organic compounds that may allow a more versatile lifestyle contributing to the competitive fitness of Scalindua in the marine realm.
Collapse
Affiliation(s)
- Jack van de Vossenberg
- Department of Microbiology, IWWR, Radboud University Nijmegen6525 AJ Nijmegen, the Netherlands
| | - Dagmar Woebken
- Max Planck Institute for Marine MicrobiologyCelsiusstrasse 1, Bremen, Germany
| | - Wouter J Maalcke
- Department of Microbiology, IWWR, Radboud University Nijmegen6525 AJ Nijmegen, the Netherlands
| | - Hans J C T Wessels
- Nijmegen Centre for Mitochondrial Disorders, Nijmegen Proteomics Facility, Department of Laboratory Medicine, Laboratory of Genetic, Endocrine and Metabolic disease, Radboud University Nijmegen Medical CentreNijmegen, the Netherlands
| | - Bas E Dutilh
- CMBI, Radboud University Nijmegen Medical CentreNijmegen, the Netherlands
| | - Boran Kartal
- Department of Microbiology, IWWR, Radboud University Nijmegen6525 AJ Nijmegen, the Netherlands
| | - Eva M Janssen-Megens
- Nijmegen Center for Molecular Life Sciences, Department of Molecular Biology, Radboud University NijmegenNijmegen, the Netherlands
| | - Guus Roeselers
- Department of Microbiology, IWWR, Radboud University Nijmegen6525 AJ Nijmegen, the Netherlands
| | - Jia Yan
- Department of Microbiology, IWWR, Radboud University Nijmegen6525 AJ Nijmegen, the Netherlands
| | - Daan Speth
- Department of Microbiology, IWWR, Radboud University Nijmegen6525 AJ Nijmegen, the Netherlands
| | - Jolein Gloerich
- Nijmegen Proteomics Facility, Department of Laboratory Medicine, Laboratory of Genetic, Endocrine and Metabolic disease, Radboud University Nijmegen Medical CentreNijmegen, the Netherlands
| | - Wim Geerts
- Department of Microbiology, IWWR, Radboud University Nijmegen6525 AJ Nijmegen, the Netherlands
| | - Erwin van der Biezen
- Department of Microbiology, IWWR, Radboud University Nijmegen6525 AJ Nijmegen, the Netherlands
| | - Wendy Pluk
- Nijmegen Proteomics Facility, Department of Laboratory Medicine, Laboratory of Genetic, Endocrine and Metabolic disease, Radboud University Nijmegen Medical CentreNijmegen, the Netherlands
| | - Kees-Jan Francoijs
- Nijmegen Center for Molecular Life Sciences, Department of Molecular Biology, Radboud University NijmegenNijmegen, the Netherlands
| | - Lina Russ
- Department of Microbiology, IWWR, Radboud University Nijmegen6525 AJ Nijmegen, the Netherlands
| | - Phyllis Lam
- Max Planck Institute for Marine MicrobiologyCelsiusstrasse 1, Bremen, Germany
| | | | | | - Suzanne C M Haaijer
- Department of Microbiology, IWWR, Radboud University Nijmegen6525 AJ Nijmegen, the Netherlands
| | - Huub J M Op den Camp
- Department of Microbiology, IWWR, Radboud University Nijmegen6525 AJ Nijmegen, the Netherlands
| | - Henk G Stunnenberg
- Nijmegen Center for Molecular Life Sciences, Department of Molecular Biology, Radboud University NijmegenNijmegen, the Netherlands
| | - Rudi Amann
- Max Planck Institute for Marine MicrobiologyCelsiusstrasse 1, Bremen, Germany
| | - Marcel M M Kuypers
- Max Planck Institute for Marine MicrobiologyCelsiusstrasse 1, Bremen, Germany
| | - Mike S M Jetten
- Department of Microbiology, IWWR, Radboud University Nijmegen6525 AJ Nijmegen, the Netherlands
- Department of Biotechnology, Delft University of TechnologyDelft, the Netherlands
| |
Collapse
|
32
|
Woebken D, Burow LC, Prufert-Bebout L, Bebout BM, Hoehler TM, Pett-Ridge J, Spormann AM, Weber PK, Singer SW. Identification of a novel cyanobacterial group as active diazotrophs in a coastal microbial mat using NanoSIMS analysis. ISME J 2012; 6:1427-39. [PMID: 22237543 DOI: 10.1038/ismej.2011.200] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
N(2) fixation is a key process in photosynthetic microbial mats to support the nitrogen demands associated with primary production. Despite its importance, groups that actively fix N(2) and contribute to the input of organic N in these ecosystems still remain largely unclear. To investigate the active diazotrophic community in microbial mats from the Elkhorn Slough estuary, Monterey Bay, CA, USA, we conducted an extensive combined approach, including biogeochemical, molecular and high-resolution secondary ion mass spectrometry (NanoSIMS) analyses. Detailed analysis of dinitrogenase reductase (nifH) transcript clone libraries from mat samples that fixed N(2) at night indicated that cyanobacterial nifH transcripts were abundant and formed a novel monophyletic lineage. Independent NanoSIMS analysis of (15)N(2)-incubated samples revealed significant incorporation of (15)N into small, non-heterocystous cyanobacterial filaments. Mat-derived enrichment cultures yielded a unicyanobacterial culture with similar filaments (named Elkhorn Slough Filamentous Cyanobacterium-1 (ESFC-1)) that contained nifH gene sequences grouping with the novel cyanobacterial lineage identified in the transcript clone libraries, displaying up to 100% amino-acid sequence identity. The 16S rRNA gene sequence recovered from this enrichment allowed for the identification of related sequences from Elkhorn Slough mats and revealed great sequence diversity in this cluster. Furthermore, by combining (15)N(2) tracer experiments, fluorescence in situ hybridization and NanoSIMS, in situ N(2) fixation activity by the novel ESFC-1 group was demonstrated, suggesting that this group may be the most active cyanobacterial diazotroph in the Elkhorn Slough mat. Pyrotag sequences affiliated with ESFC-1 were recovered from mat samples throughout 2009, demonstrating the prevalence of this group. This work illustrates that combining standard and single-cell analyses can link phylogeny and function to identify previously unknown key functional groups in complex ecosystems.
Collapse
Affiliation(s)
- Dagmar Woebken
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA.
| | | | | | | | | | | | | | | | | |
Collapse
|
33
|
Burow LC, Woebken D, Bebout BM, McMurdie PJ, Singer SW, Pett-Ridge J, Prufert-Bebout L, Spormann AM, Weber PK, Hoehler TM. Hydrogen production in photosynthetic microbial mats in the Elkhorn Slough estuary, Monterey Bay. ISME J 2011; 6:863-74. [PMID: 22011721 DOI: 10.1038/ismej.2011.142] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Hydrogen (H(2)) release from photosynthetic microbial mats has contributed to the chemical evolution of Earth and could potentially be a source of renewable H(2) in the future. However, the taxonomy of H(2)-producing microorganisms (hydrogenogens) in these mats has not been previously determined. With combined biogeochemical and molecular studies of microbial mats collected from Elkhorn Slough, Monterey Bay, California, we characterized the mechanisms of H(2) production and identified a dominant hydrogenogen. Net production of H(2) was observed within the upper photosynthetic layer (0-2 mm) of the mats under dark and anoxic conditions. Pyrosequencing of rRNA gene libraries generated from this layer demonstrated the presence of 64 phyla, with Bacteriodetes, Cyanobacteria and Proteobacteria dominating the sequences. Sequencing of rRNA transcripts obtained from this layer demonstrated that Cyanobacteria dominated rRNA transcript pyrotag libraries. An OTU affiliated to Microcoleus spp. was the most abundant OTU in both rRNA gene and transcript libraries. Depriving mats of sunlight resulted in an order of magnitude decrease in subsequent nighttime H(2) production, suggesting that newly fixed carbon is critical to H(2) production. Suppression of nitrogen (N(2))-fixation in the mats did not suppress H(2) production, which indicates that co-metabolic production of H(2) during N(2)-fixation is not an important contributor to H(2) production. Concomitant production of organic acids is consistent with fermentation of recently produced photosynthate as the dominant mode of H(2) production. Analysis of rRNA % transcript:% gene ratios and H(2)-evolving bidirectional [NiFe] hydrogenase % transcript:% gene ratios indicated that Microcoelus spp. are dominant hydrogenogens in the Elkhorn Slough mats.
Collapse
Affiliation(s)
- Luke C Burow
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA 94305, USA.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
34
|
Hoffmann F, Radax R, Woebken D, Holtappels M, Lavik G, Rapp HT, Schläppy ML, Schleper C, Kuypers MMM. Complex nitrogen cycling in the sponge Geodia barretti. Environ Microbiol 2009; 11:2228-43. [PMID: 19453700 DOI: 10.1111/j.1462-2920.2009.01944.x] [Citation(s) in RCA: 233] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Marine sponges constitute major parts of coral reefs and deep-water communities. They often harbour high amounts of phylogenetically and physiologically diverse microbes, which are so far poorly characterized. Many of these sponges regulate their internal oxygen concentration by modulating their ventilation behaviour providing a suitable habitat for both aerobic and anaerobic microbes. In the present study, both aerobic (nitrification) and anaerobic (denitrification, anammox) microbial processes of the nitrogen cycle were quantified in the sponge Geodia barretti and possible involved microbes were identified by molecular techniques. Nitrification rates of 566 nmol N cm(-3) sponge day(-1) were obtained when monitoring the production of nitrite and nitrate. In support of this finding, ammonia-oxidizing Archaea (crenarchaeotes) were found by amplification of the amoA gene, and nitrite-oxidizing bacteria of the genus Nitrospira were detected based on rRNA gene analyses. Incubation experiments with stable isotopes ((15)NO(3)(-) and (15)NH(4)(+)) revealed denitrification and anaerobic ammonium oxidation (anammox) rates of 92 nmol N cm(-3) sponge day(-1) and 3 nmol N cm(-3) sponge day(-1) respectively. Accordingly, sequences closely related to 'Candidatus Scalindua sorokinii' and 'Candidatus Scalindua brodae' were detected in 16S rRNA gene libraries. The amplification of the nirS gene revealed the presence of denitrifiers, likely belonging to the Betaproteobacteria. This is the first proof of anammox and denitrification in the same animal host, and the first proof of anammox and denitrification in sponges. The close and complex interactions of aerobic, anaerobic, autotrophic and heterotrophic microbial processes are fuelled by metabolic waste products of the sponge host, and enable efficient utilization and recirculation of nutrients within the sponge-microbe system. Since denitrification and anammox remove inorganic nitrogen from the environment, sponges may function as so far unrecognized nitrogen sinks in the ocean. In certain marine environments with high sponge cover, sponge-mediated nitrogen mineralization processes might even be more important than sediment processes.
Collapse
Affiliation(s)
- Friederike Hoffmann
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1,Bremen, Germany.
| | | | | | | | | | | | | | | | | |
Collapse
|
35
|
Schmid MC, Hooper AB, Klotz MG, Woebken D, Lam P, Kuypers MMM, Pommerening-Roeser A, Op den Camp HJM, Jetten MSM. Environmental detection of octahaem cytochrome c hydroxylamine/hydrazine oxidoreductase genes of aerobic and anaerobic ammonium-oxidizing bacteria. Environ Microbiol 2008; 10:3140-9. [PMID: 18973625 DOI: 10.1111/j.1462-2920.2008.01732.x] [Citation(s) in RCA: 131] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Bacterial aerobic ammonium oxidation and anaerobic ammonium oxidation (anammox) are important processes in the global nitrogen cycle. Key enzymes in both processes are the octahaem cytochrome c (OCC) proteins, hydroxylamine oxidoreductase (HAO) of aerobic ammonium-oxidizing bacteria (AOB), which catalyses the oxidation of hydroxylamine to nitrite, and hydrazine oxidoreductase (HZO) of anammox bacteria, which converts hydrazine to N(2). While the genomes of AOB encode up to three nearly identical copies of hao operons, genome analysis of Candidatus'Kuenenia stuttgartiensis' showed eight highly divergent octahaem protein coding regions as possible candidates for the HZO. Based on their phylogenetic relationship and biochemical characteristics, the sequences of these eight gene products grouped in three clusters. Degenerate primers were designed on the basis of available gene sequences with the aim to detect hao and hzo genes in various ecosystems. The hao primer pairs amplified gene fragments from 738 to 1172 bp and the hzo primer pairs amplified gene fragments from 289 to 876 bp in length, when tested on genomic DNA isolated from a variety of AOB and anammox bacteria. A selection of these primer pairs was also used successfully to amplify and analyse the hao and hzo genes in community DNA isolated from different ecosystems harbouring both AOB and anammox bacteria. We propose that OCC protein-encoding genes are suitable targets for molecular ecological studies on both aerobic and anaerobic ammonium-oxidizing bacteria.
Collapse
Affiliation(s)
- Markus C Schmid
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, the Netherlands.
| | | | | | | | | | | | | | | | | |
Collapse
|
36
|
Woebken D, Lam P, Kuypers MMM, Naqvi SWA, Kartal B, Strous M, Jetten MSM, Fuchs BM, Amann R. A microdiversity study of anammox bacteria reveals a novelCandidatusScalindua phylotype in marine oxygen minimum zones. Environ Microbiol 2008; 10:3106-19. [DOI: 10.1111/j.1462-2920.2008.01640.x] [Citation(s) in RCA: 217] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
37
|
Woebken D, Fuchs BM, Kuypers MMM, Amann R. Potential interactions of particle-associated anammox bacteria with bacterial and archaeal partners in the Namibian upwelling system. Appl Environ Microbiol 2007; 73:4648-57. [PMID: 17526789 PMCID: PMC1932835 DOI: 10.1128/aem.02774-06] [Citation(s) in RCA: 186] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Recent studies have shown that the anaerobic oxidation of ammonium by anammox bacteria plays an important role in catalyzing the loss of nitrogen from marine oxygen minimum zones (OMZ). However, in situ oxygen concentrations of up to 25 microM and ammonium concentrations close to or below the detection limit in the layer of anammox activity are hard to reconcile with the current knowledge of the physiology of anammox bacteria. We therefore investigated samples from the Namibian OMZ by comparative 16S rRNA gene analysis and fluorescence in situ hybridization. Our results showed that "Candidatus Scalindua" spp., the typical marine anammox bacteria, colonized microscopic particles that were likely the remains of either macroscopic marine snow particles or resuspended particles. These particles were slightly but significantly (P < 0.01) enriched in Gammaproteobacteria (11.8% +/- 5.0%) compared to the free-water phase (8.1% +/- 1.8%). No preference for the attachment to particles could be observed for members of the Alphaproteobacteria and Bacteroidetes, which were abundant (12 to 17%) in both habitats. The alphaproteobacterial SAR11 clade, the Euryarchaeota, and group I Crenarchaeota, were all significantly depleted in particles compared to their presence in the free-water phase (16.5% +/- 3.5% versus 2.6% +/- 1.7%, 2.7% +/- 1.9% versus <1%, and 14.9% +/- 4.6% versus 2.2% +/- 1.8%, respectively, all P < 0.001). Sequence analysis of the crenarchaeotal 16S rRNA genes showed a 99% sequence identity to the nitrifying "Nitrosopumilus maritimus." Even though we could not observe conspicuous consortium-like structures of anammox bacteria with particle-enriched bacterioplankton groups, we hypothesize that members of Gammaproteobacteria, Alphaproteobacteria, and Bacteroidetes play a critical role in extending the anammox reaction to nutrient-depleted suboxic water layers in the Namibian upwelling system by creating anoxic, nutrient-enriched microniches.
Collapse
MESH Headings
- Anaerobiosis
- Archaea/classification
- Archaea/growth & development
- Archaea/isolation & purification
- Archaea/metabolism
- Bacteria/classification
- Bacteria/growth & development
- Bacteria/isolation & purification
- Bacteria/metabolism
- Biodiversity
- DNA, Archaeal/chemistry
- DNA, Archaeal/genetics
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- In Situ Hybridization, Fluorescence
- Molecular Sequence Data
- Namibia
- Phylogeny
- Quaternary Ammonium Compounds/metabolism
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- Soil Microbiology
- Water Microbiology
Collapse
Affiliation(s)
- Dagmar Woebken
- Max Planck Institute for Marine Microbiology, Molecular Ecology, Celsiusstr. 1, 28359 Bremen, Germany
| | | | | | | |
Collapse
|
38
|
Bauer M, Kube M, Teeling H, Richter M, Lombardot T, Allers E, Würdemann CA, Quast C, Kuhl H, Knaust F, Woebken D, Bischof K, Mussmann M, Choudhuri JV, Meyer F, Reinhardt R, Amann RI, Glöckner FO. Whole genome analysis of the marine Bacteroidetes'Gramella forsetii' reveals adaptations to degradation of polymeric organic matter. Environ Microbiol 2007; 8:2201-13. [PMID: 17107561 DOI: 10.1111/j.1462-2920.2006.01152.x] [Citation(s) in RCA: 244] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Members of the Bacteroidetes, formerly known as the Cytophaga-Flavobacteria-Bacteroides (CFB) phylum, are among the major taxa of marine heterotrophic bacterioplankton frequently found on macroscopic organic matter particles (marine snow). In addition, they have been shown to also represent a significant part of free-living microbial assemblages in nutrient-rich microenvironments. Their abundance and distribution pattern in combination with enzymatic activity studies has led to the notion that organisms of this group are specialists for degradation of high molecular weight compounds in both the dissolved and particulate fraction of the marine organic matter pool, implying a major role of Bacteroidetes in the marine carbon cycle. Despite their ecological importance, comprehensive molecular data on organisms of this group have been scarce so far. Here we report on the first whole genome analysis of a marine Bacteroidetes representative, 'Gramella forsetii' KT0803. Functional analysis of the predicted proteome disclosed several traits which in joint consideration suggest a clear adaptation of this marine Bacteroidetes representative to the degradation of high molecular weight organic matter, such as a substantial suite of genes encoding hydrolytic enzymes, a predicted preference for polymeric carbon sources and a distinct capability for surface adhesion.
Collapse
Affiliation(s)
- Margarete Bauer
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen, Germany.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
39
|
Kuypers MMM, Lavik G, Woebken D, Schmid M, Fuchs BM, Amann R, Jørgensen BB, Jetten MSM. Massive nitrogen loss from the Benguela upwelling system through anaerobic ammonium oxidation. Proc Natl Acad Sci U S A 2005; 102:6478-83. [PMID: 15843458 PMCID: PMC556276 DOI: 10.1073/pnas.0502088102] [Citation(s) in RCA: 567] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In many oceanic regions, growth of phytoplankton is nitrogen-limited because fixation of N2 cannot make up for the removal of fixed inorganic nitrogen (NH4+, NO2-, and NO3-) by anaerobic microbial processes. Globally, 30-50% of the total nitrogen loss occurs in oxygen-minimum zones (OMZs) and is commonly attributed to denitrification (reduction of nitrate to N2 by heterotrophic bacteria). Here, we show that instead, the anammox process (the anaerobic oxidation of ammonium by nitrite to yield N2) is mainly responsible for nitrogen loss in the OMZ waters of one of the most productive regions of the world ocean, the Benguela upwelling system. Our in situ experiments indicate that nitrate is not directly converted to N2 by heterotrophic denitrification in the suboxic zone. In the Benguela system, nutrient profiles, anammox rates, abundances of anammox cells, and specific biomarker lipids indicate that anammox bacteria are responsible for massive losses of fixed nitrogen. We have identified and directly linked anammox bacteria to the removal of fixed inorganic nitrogen in the OMZ waters of an open-ocean setting. We hypothesize that anammox could also be responsible for substantial nitrogen loss from other OMZ waters of the ocean.
Collapse
Affiliation(s)
- Marcel M M Kuypers
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, 28359 Bremen, Germany.
| | | | | | | | | | | | | | | |
Collapse
|