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Brodersen KE, Mosshammer M, Bittner MJ, Hallstrøm S, Santner J, Riemann L, Kühl M. Seagrass-mediated rhizosphere redox gradients are linked with ammonium accumulation driven by diazotrophs. Microbiol Spectr 2024; 12:e0333523. [PMID: 38426746 PMCID: PMC10986515 DOI: 10.1128/spectrum.03335-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 01/24/2024] [Indexed: 03/02/2024] Open
Abstract
Seagrasses can enhance nutrient mobilization in their rhizosphere via complex interactions with sediment redox conditions and microbial populations. Yet, limited knowledge exists on how seagrass-derived rhizosphere dynamics affect nitrogen cycling. Using optode and gel-sampler-based chemical imaging, we show that radial O2 loss (ROL) from rhizomes and roots leads to the formation of redox gradients around below-ground tissues of seagrass (Zostera marina), which are co-localized with regions of high ammonium concentrations in the rhizosphere. Combining such chemical imaging with fine-scale sampling for microbial community and gene expression analyses indicated that multiple biogeochemical pathways and microbial players can lead to high ammonium concentration within the oxidized regions of the seagrass rhizosphere. Symbiotic N2-fixing bacteria (Bradyrhizobium) were particularly abundant and expressed the diazotroph functional marker gene nifH in Z. marina rhizosphere areas with high ammonium concentrations. Such an association between Z. marina and Bradyrhizobium can facilitate ammonium mobilization, the preferred nitrogen source for seagrasses, enhancing seagrass productivity within nitrogen-limited environments. ROL also caused strong gradients of sulfide at anoxic/oxic interfaces in rhizosphere areas, where we found enhanced nifH transcription by sulfate-reducing bacteria. Furthermore, we found a high abundance of methylotrophic and sulfide-oxidizing bacteria in rhizosphere areas, where O2 was released from seagrass rhizomes and roots. These bacteria could play a beneficial role for the plants in terms of their methane and sulfide oxidation, as well as their formation of growth factors and phytohormones. ROL from below-ground tissues of seagrass, thus, seems crucial for ammonium production in the rhizosphere via stimulation of multiple diazotrophic associations. IMPORTANCE Seagrasses are important marine habitats providing several ecosystem services in coastal waters worldwide, such as enhancing marine biodiversity and mitigating climate change through efficient carbon sequestration. Notably, the fitness of seagrasses is affected by plant-microbe interactions. However, these microscale interactions are challenging to study and large knowledge gaps prevail. Our study shows that redox microgradients in the rhizosphere of seagrass select for a unique microbial community that can enhance the ammonium availability for seagrass. We provide first experimental evidence that Rhizobia, including the symbiotic N2-fixing bacteria Bradyrhizobium, can contribute to the bacterial ammonium production in the seagrass rhizosphere. The release of O2 from rhizomes and roots also caused gradients of sulfide in rhizosphere areas with enhanced nifH transcription by sulfate-reducing bacteria. O2 release from seagrass root systems thus seems crucial for ammonium production in the rhizosphere via stimulation of multiple diazotrophic associations.
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Affiliation(s)
| | - Maria Mosshammer
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - Meriel J. Bittner
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - Søren Hallstrøm
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - Jakob Santner
- Department of Crop Sciences, Institute of Agronomy, University of Natural Resources and Life Sciences Vienna, Tulln an der Donau, Austria
| | - Lasse Riemann
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - Michael Kühl
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
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Jabir T, Jain A, Vipindas PV, Krishnan KP. Stochastic Processes Dominate in the Water Mass-Based Segregation of Diazotrophs in a High Arctic Fjord (Svalbard). MICROBIAL ECOLOGY 2023; 86:2733-2746. [PMID: 37532947 DOI: 10.1007/s00248-023-02276-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 07/24/2023] [Indexed: 08/04/2023]
Abstract
Nitrogen-fixing or diazotrophic microbes fix atmospheric nitrogen (N2) to ammonia (NH3+) using nitrogenase enzyme and play a crucial role in regulating marine primary productivity and carbon dioxide sequestration. However, there is a lack of information about the diversity, structure, and environmental regulations of the diazotrophic communities in the high Arctic fjords, such as Kongsfjorden. Here, we employed nifH gene sequencing to clarify variations in composition, community structure, and assembly mechanism among the diazotrophs of the salinity-driven stratified waters of Kongsfjorden. The principal environmental and ecological drivers of the observed variations were identified. The majority of the nifH gene sequences obtained in the present study belonged to cluster I and cluster III nifH phylotypes, accounting for 65% and 25% of the total nifH gene sequences. The nifH gene diversity and composition, irrespective of the size fractions (free-living and particle attached), showed a clear separation among water mass types, i.e., Atlantic-influenced versus glacier-influenced water mass. Higher nifH gene diversity and relative abundances of non-cyanobacterial nifH OTUs, affiliated with uncultured Rhizobiales, Burkholderiales, Alteromonadaceae, Gallionellaceae (cluster I) and uncultured Deltaproteobacteria including Desulfuromonadaceae (cluster III), were prevalent in GIW while uncultured Gammaproteobacteria and Desulfobulbaceae were abundant in AIW. The diazotrophic community assembly was dominated by stochastic processes, principally ecological drift, and to lesser degrees dispersal limitation and homogeneous dispersal. Differences in the salinity and dissolved oxygen content lead to the vertical segregation of diazotrophs among water mass types. These findings suggest that water column stratification affects the composition and assembly mechanism of diazotrophic communities and thus could affect nitrogen fixation in the Arctic fjord.
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Affiliation(s)
- Thajudeen Jabir
- Arctic Ecology and Biogeochemistry, National Centre for Polar and Ocean Research, Ministry of Earth Sciences, Vasco da Gama, Goa, 403 804, India.
| | - Anand Jain
- Arctic Ecology and Biogeochemistry, National Centre for Polar and Ocean Research, Ministry of Earth Sciences, Vasco da Gama, Goa, 403 804, India
| | - Puthiya Veettil Vipindas
- Arctic Ecology and Biogeochemistry, National Centre for Polar and Ocean Research, Ministry of Earth Sciences, Vasco da Gama, Goa, 403 804, India
| | - Kottekkatu Padinchati Krishnan
- Arctic Ecology and Biogeochemistry, National Centre for Polar and Ocean Research, Ministry of Earth Sciences, Vasco da Gama, Goa, 403 804, India
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von Friesen LW, Paulsen ML, Müller O, Gründger F, Riemann L. Glacial meltwater and seasonality influence community composition of diazotrophs in Arctic coastal and open waters. FEMS Microbiol Ecol 2023; 99:fiad067. [PMID: 37349965 DOI: 10.1093/femsec/fiad067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 04/29/2023] [Accepted: 06/20/2023] [Indexed: 06/24/2023] Open
Abstract
The Arctic Ocean is particularly affected by climate change with unknown consequences for primary productivity. Diazotrophs-prokaryotes capable of converting atmospheric nitrogen to ammonia-have been detected in the often nitrogen-limited Arctic Ocean but distribution and community composition dynamics are largely unknown. We performed amplicon sequencing of the diazotroph marker gene nifH from glacial rivers, coastal, and open ocean regions and identified regionally distinct Arctic communities. Proteobacterial diazotrophs dominated all seasons, epi- to mesopelagic depths and rivers to open waters and, surprisingly, Cyanobacteria were only sporadically identified in coastal and freshwaters. The upstream environment of glacial rivers influenced diazotroph diversity, and in marine samples putative anaerobic sulphate-reducers showed seasonal succession with highest prevalence in summer to polar night. Betaproteobacteria (Burkholderiales, Nitrosomonadales, and Rhodocyclales) were typically found in rivers and freshwater-influenced waters, and Delta- (Desulfuromonadales, Desulfobacterales, and Desulfovibrionales) and Gammaproteobacteria in marine waters. The identified community composition dynamics, likely driven by runoff, inorganic nutrients, particulate organic carbon, and seasonality, imply diazotrophy a phenotype of ecological relevance with expected responsiveness to ongoing climate change. Our study largely expands baseline knowledge of Arctic diazotrophs-a prerequisite to understand underpinning of nitrogen fixation-and supports nitrogen fixation as a contributor of new nitrogen in the rapidly changing Arctic Ocean.
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Affiliation(s)
- Lisa W von Friesen
- Department of Biology, University of Copenhagen, Strandpromenaden 5, DK-3000 Helsingør, Denmark
| | - Maria L Paulsen
- Department of Biology, Aarhus University, Ny Munkegade 114-116, DK-8000 Aarhus, Denmark
| | - Oliver Müller
- Department of Biological Sciences, University of Bergen, Thormøhlens gate 53A, NO-5006 Bergen, Norway
| | - Friederike Gründger
- Department of Biology, Aarhus University, Ny Munkegade 114-116, DK-8000 Aarhus, Denmark
| | - Lasse Riemann
- Department of Biology, University of Copenhagen, Strandpromenaden 5, DK-3000 Helsingør, Denmark
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Arróniz-Crespo M, Bougoure J, Murphy DV, Cutler NA, Souza-Egipsy V, Chaput DL, Jones DL, Ostle N, Wade SC, Clode PL, DeLuca TH. Revealing the transfer pathways of cyanobacterial-fixed N into the boreal forest through the feather-moss microbiome. FRONTIERS IN PLANT SCIENCE 2022; 13:1036258. [PMID: 36570951 PMCID: PMC9780503 DOI: 10.3389/fpls.2022.1036258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 11/21/2022] [Indexed: 06/17/2023]
Abstract
INTRODUCTION Biological N2 fixation in feather-mosses is one of the largest inputs of new nitrogen (N) to boreal forest ecosystems; however, revealing the fate of newly fixed N within the bryosphere (i.e. bryophytes and their associated organisms) remains uncertain. METHODS Herein, we combined 15N tracers, high resolution secondary ion mass-spectrometry (NanoSIMS) and a molecular survey of bacterial, fungal and diazotrophic communities, to determine the origin and transfer pathways of newly fixed N2 within feather-moss (Pleurozium schreberi) and its associated microbiome. RESULTS NanoSIMS images reveal that newly fixed N2, derived from cyanobacteria, is incorporated into moss tissues and associated bacteria, fungi and micro-algae. DISCUSSION These images demonstrate that previous assumptions that newly fixed N2 is sequestered into moss tissue and only released by decomposition are not correct. We provide the first empirical evidence of new pathways for N2 fixed in feather-mosses to enter the boreal forest ecosystem (i.e. through its microbiome) and discuss the implications for wider ecosystem function.
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Affiliation(s)
- María Arróniz-Crespo
- School of Natural Sciences, Bangor University, Bangor, United Kingdom
- School of Agricultural Engineering, CEIGRAM, Universidad Politecnica de Madrid, Madrid, Spain
| | - Jeremy Bougoure
- School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia
| | - Daniel V. Murphy
- School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia
- Centre for Microscopy, Characterisation and Analysis, The University of Western Australia, Perth, WA, Australia
- Centre for Sustainable Farming Systems, Food Futures Institute, Murdoch University, Murdoch, WA, Australia
| | - Nick A. Cutler
- Department of Geography, Scott Polar Research Institute, Cambridge, United Kingdom
- School of Geography, Politics and Sociology, Newcastle University, Newcastle, United Kingdom
| | - Virginia Souza-Egipsy
- Servicio de Microscopıa Electronica, Instituto Ciencias Agrarias CSIC, Madrid, Spain
| | | | - Davey L. Jones
- School of Natural Sciences, Bangor University, Bangor, United Kingdom
- Centre for Sustainable Farming Systems, Food Futures Institute, Murdoch University, Murdoch, WA, Australia
| | - Nicholas Ostle
- Lancaster Environment Centre, Lancaster University, Lancaster, United Kingdom
| | - Stephen C. Wade
- Advanced Microscopy and Bioimaging, Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, United Kingdom
| | - Peta L. Clode
- Centre for Microscopy, Characterisation and Analysis, The University of Western Australia, Perth, WA, Australia
- School of Biological Sciences, The University of Western Australia, Perth, WA, Australia
| | - Thomas H. DeLuca
- Department of Forest Ecosystems & Society, College of Forestry, Oregon State University, Corvallis, OR, United States
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Limnospira fusiformis harbors dinitrogenase reductase (nifH)-like genes, but does not show N2 fixation activity. ALGAL RES 2022. [DOI: 10.1016/j.algal.2022.102771] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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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] [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.
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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
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Singh RK, Singh P, Sharma A, Guo DJ, Upadhyay SK, Song QQ, Verma KK, Li DP, Malviya MK, Song XP, Yang LT, Li YR. Unraveling Nitrogen Fixing Potential of Endophytic Diazotrophs of Different Saccharum Species for Sustainable Sugarcane Growth. Int J Mol Sci 2022; 23:ijms23116242. [PMID: 35682919 PMCID: PMC9181200 DOI: 10.3390/ijms23116242] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 05/29/2022] [Accepted: 05/30/2022] [Indexed: 02/06/2023] Open
Abstract
Sugarcane (Saccharum officinarum L.) is one of the world’s highly significant commercial crops. The amounts of synthetic nitrogen (N2) fertilizer required to grow the sugarcane plant at its initial growth stages are higher, which increases the production costs and adverse environmental consequences globally. To combat this issue, sustainable environmental and economic concerns among researchers are necessary. The endophytic diazotrophs can offer significant amounts of nitrogen to crops through the biological nitrogen fixation mediated nif gene. The nifH gene is the most extensively utilized molecular marker in nature for studying N2 fixing microbiomes. The present research intended to determine the existence of novel endophytic diazotrophs through culturable and unculturable bacterial communities (EDBCs). The EDBCs of different tissues (root, stem, and leaf) of five sugarcane cultivars (Saccharum officinarum L. cv. Badila, S. barberi Jesw.cv Pansahi, S. robustum, S. spontaneum, and S. sinense Roxb.cv Uba) were isolated and molecularly characterized to evaluate N2 fixation ability. The diversity of EDBCs was observed based on nifH gene Illumina MiSeq sequencing and a culturable approach. In this study, 319766 operational taxonomic units (OTUs) were identified from 15 samples. The minimum number of OTUs was recorded in leaf tissues of S. robustum and maximum reads in root tissues of S. spontaneum. These data were assessed to ascertain the structure, diversity, abundance, and relationship between the microbial community. A total of 40 bacterial families with 58 genera were detected in different sugarcane species. Bacterial communities exhibited substantially different alpha and beta diversity. In total, 16 out of 20 genera showed potent N2-fixation in sugarcane and other crops. According to principal component analysis (PCA) and hierarchical clustering (Bray–Curtis dis) evaluation of OTUs, bacterial microbiomes associated with root tissues differed significantly from stem and leaf tissues of sugarcane. Significant differences often were observed in EDBCs among the sugarcane tissues. We tracked and validated the plethora of individual phylum strains and assessed their nitrogenase activity with a culture-dependent technique. The current work illustrated the significant and novel results of many uncharted endophytic microbial communities in different tissues of sugarcane species, which provides an experimental system to evaluate the biological nitrogen fixation (BNF) mechanism in sugarcane. The novel endophytic microbial communities with N2-fixation ability play a remarkable and promising role in sustainable agriculture production.
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Affiliation(s)
- Rajesh Kumar Singh
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China; (R.K.S.); (A.S.); (D.-J.G.); (K.K.V.); (M.K.M.)
- Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning 530007, China; (X.-P.S.); (L.-T.Y.)
| | - Pratiksha Singh
- School of Marine Sciences and Biotechnology, Guangxi University for Nationalities, Nanning 530008, China;
| | - Anjney Sharma
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China; (R.K.S.); (A.S.); (D.-J.G.); (K.K.V.); (M.K.M.)
- Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning 530007, China; (X.-P.S.); (L.-T.Y.)
| | - Dao-Jun Guo
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China; (R.K.S.); (A.S.); (D.-J.G.); (K.K.V.); (M.K.M.)
- College of Agriculture, State Key Laboratory of Conservation and Utilization of Subtropical Agro-bio Resources, Guangxi University, Nanning 530005, China
| | - Sudhir K. Upadhyay
- Department of Environmental Science, V.B.S. Purvanchal University, Jaunpur 222003, India;
| | - Qi-Qi Song
- Guangxi Subtropical Crop Research Institute, Sugarcane Research Institute, Nanning 530001, China;
| | - Krishan K. Verma
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China; (R.K.S.); (A.S.); (D.-J.G.); (K.K.V.); (M.K.M.)
- Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning 530007, China; (X.-P.S.); (L.-T.Y.)
| | - Dong-Ping Li
- Microbiology Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China;
| | - Mukesh Kumar Malviya
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China; (R.K.S.); (A.S.); (D.-J.G.); (K.K.V.); (M.K.M.)
- Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning 530007, China; (X.-P.S.); (L.-T.Y.)
| | - Xiu-Peng Song
- Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning 530007, China; (X.-P.S.); (L.-T.Y.)
| | - Li-Tao Yang
- Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning 530007, China; (X.-P.S.); (L.-T.Y.)
- College of Agriculture, State Key Laboratory of Conservation and Utilization of Subtropical Agro-bio Resources, Guangxi University, Nanning 530005, China
| | - Yang-Rui Li
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China; (R.K.S.); (A.S.); (D.-J.G.); (K.K.V.); (M.K.M.)
- Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning 530007, China; (X.-P.S.); (L.-T.Y.)
- College of Agriculture, State Key Laboratory of Conservation and Utilization of Subtropical Agro-bio Resources, Guangxi University, Nanning 530005, China
- Correspondence: ; Tel.: +86-771-3899033
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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] [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.
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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
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Suquilanda-Pesántez JD, Aguiar Salazar ED, Almeida-Galárraga D, Salum G, Villalba-Meneses F, Gudiño Gomezjurado ME. NIFtHool: an informatics program for identification of NifH proteins using deep neural networks. F1000Res 2022; 11:164. [PMID: 35360826 PMCID: PMC8956849 DOI: 10.12688/f1000research.107925.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/04/2022] [Indexed: 11/20/2022] Open
Abstract
Atmospheric nitrogen fixation carried out by microorganisms has environmental and industrial importance, related to the increase of soil fertility and productivity. The present work proposes the development of a new high precision system that allows the recognition of amino acid sequences of the nitrogenase enzyme (NifH) as a promising way to improve the identification of diazotrophic bacteria. For this purpose, a database obtained from UniProt built a processed dataset formed by a set of 4911 and 4782 amino acid sequences of the NifH and non-NifH
proteins respectively. Subsequently, the feature extraction was developed using two methodologies: (i) k-mers counting and (ii) embedding layers to obtain numerical vectors of the amino acid chains. Afterward, for the embedding layer, the data was crossed by an external trainable convolutional layer, which received a uniform matrix and applied convolution using filters to obtain the feature maps of the model. Finally, a deep neural network was used as the primary model to classify the amino acid sequences as NifH protein or not. Performance evaluation experiments were carried out, and the results revealed an accuracy of 96.4%, a sensitivity of 95.2%, and a specificity of 96.7%. Therefore, an amino acid sequence-based feature extraction method that uses a neural network to detect N-fixing organisms is proposed and implemented. NIFtHool is available from:
https://nifthool.anvil.app/
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Affiliation(s)
| | - Evelyn Dayana Aguiar Salazar
- Escuela de Ciencias Biológicas e Ingeniería, Universidad de Investigación de Tecnología Experimental Yachay, Urcuquí, Imbabura, 100115, Ecuador
| | - Diego Almeida-Galárraga
- Escuela de Ciencias Biológicas e Ingeniería, Universidad de Investigación de Tecnología Experimental Yachay, Urcuquí, Imbabura, 100115, Ecuador
| | - Graciela Salum
- Escuela de Ciencias Biológicas e Ingeniería, Universidad de Investigación de Tecnología Experimental Yachay, Urcuquí, Imbabura, 100115, Ecuador
| | - Fernando Villalba-Meneses
- Escuela de Ciencias Biológicas e Ingeniería, Universidad de Investigación de Tecnología Experimental Yachay, Urcuquí, Imbabura, 100115, Ecuador
| | - Marco Esteban Gudiño Gomezjurado
- Escuela de Ciencias Biológicas e Ingeniería, Universidad de Investigación de Tecnología Experimental Yachay, Urcuquí, Imbabura, 100115, Ecuador
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10
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Rädecker N, Pogoreutz C, Gegner HM, Cárdenas A, Perna G, Geißler L, Roth F, Bougoure J, Guagliardo P, Struck U, Wild C, Pernice M, Raina JB, Meibom A, Voolstra CR. Heat stress reduces the contribution of diazotrophs to coral holobiont nitrogen cycling. THE ISME JOURNAL 2021; 16:1110-1118. [PMID: 34857934 PMCID: PMC8941099 DOI: 10.1038/s41396-021-01158-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 11/11/2021] [Accepted: 11/16/2021] [Indexed: 12/22/2022]
Abstract
Efficient nutrient cycling in the coral-algal symbiosis requires constant but limited nitrogen availability. Coral-associated diazotrophs, i.e., prokaryotes capable of fixing dinitrogen, may thus support productivity in a stable coral-algal symbiosis but could contribute to its breakdown when overstimulated. However, the effects of environmental conditions on diazotroph communities and their interaction with other members of the coral holobiont remain poorly understood. Here we assessed the effects of heat stress on diazotroph diversity and their contribution to holobiont nutrient cycling in the reef-building coral Stylophora pistillata from the central Red Sea. In a stable symbiotic state, we found that nitrogen fixation by coral-associated diazotrophs constitutes a source of nitrogen to the algal symbionts. Heat stress caused an increase in nitrogen fixation concomitant with a change in diazotroph communities. Yet, this additional fixed nitrogen was not assimilated by the coral tissue or the algal symbionts. We conclude that although diazotrophs may support coral holobiont functioning under low nitrogen availability, altered nutrient cycling during heat stress abates the dependence of the coral host and its algal symbionts on diazotroph-derived nitrogen. Consequently, the role of nitrogen fixation in the coral holobiont is strongly dependent on its nutritional status and varies dynamically with environmental conditions.
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Affiliation(s)
- Nils Rädecker
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia. .,Department of Biology, University of Konstanz, Konstanz, Germany. .,Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
| | - Claudia Pogoreutz
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.,Department of Biology, University of Konstanz, Konstanz, Germany
| | - Hagen M Gegner
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.,Metabolomics Core Technology Platform, Centre for Organismal Studies, University of Heidelberg, Heidelberg, Germany
| | - Anny Cárdenas
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.,Department of Biology, University of Konstanz, Konstanz, Germany
| | - Gabriela Perna
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.,Department of Biology, University of Konstanz, Konstanz, Germany
| | - Laura Geißler
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Florian Roth
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.,Baltic Sea Centre, Stockholm University, Stockholm, Sweden.,Faculty of Biological and Environmental Sciences, Tvärminne Zoological Station, University of Helsinki, Helsinki, Finland
| | - Jeremy Bougoure
- Centre for Microscopy, Characterisation and Analysis, University of Western Australia, Perth, WA, Australia
| | - Paul Guagliardo
- Centre for Microscopy, Characterisation and Analysis, University of Western Australia, Perth, WA, Australia
| | - Ulrich Struck
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany.,Department of Earth Sciences, Freie Universität Berlin, Berlin, Germany
| | - Christian Wild
- Faculty of Biology and Chemistry, Marine Ecology Department, University of Bremen, Bremen, Germany
| | - Mathieu Pernice
- Climate Change Cluster, University of Technology Sydney, Sydney, NSW, Australia
| | - Jean-Baptiste Raina
- Climate Change Cluster, University of Technology Sydney, Sydney, NSW, Australia
| | - Anders Meibom
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.,Center for Advanced Surface Analysis, Institute of Earth Sciences, Université de Lausanne, Lausanne, Switzerland
| | - Christian R Voolstra
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.,Department of Biology, University of Konstanz, Konstanz, Germany
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11
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Meunier V, Geissler L, Bonnet S, Rädecker N, Perna G, Grosso O, Lambert C, Rodolfo-Metalpa R, Voolstra CR, Houlbrèque F. Microbes support enhanced nitrogen requirements of coral holobionts in a high CO 2 environment. Mol Ecol 2021; 30:5888-5899. [PMID: 34473860 DOI: 10.1111/mec.16163] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 08/24/2021] [Accepted: 08/27/2021] [Indexed: 12/24/2022]
Abstract
Ocean acidification is posing a threat to calcifying organisms due to the increased energy requirements of calcification under high CO2 conditions. The ability of scleractinian corals to cope with future ocean conditions will thus depend on their ability to fulfil their carbon requirement. However, the primary productivity of coral holobionts is limited by low nitrogen (N) availability in coral reef waters. Here, we employed CO2 seeps of Tutum Bay (Papua New Guinea) as a natural laboratory to understand how coral holobionts offset their increased energy requirements under high CO2 conditions. Our results demonstrate for the first time that under high pCO2 conditions, N assimilation pathways of Pocillopora damicornis are jointly modified. We found that diazotroph-derived N assimilation rates in the Symbiodiniaceae were significantly higher in comparison to an ambient CO2 control site, concomitant with a restructured diazotroph community and the specific prevalence of an alpha-proteobacterium. Further, corals at the high CO2 site also had increased feeding rates on picoplankton and in particular exhibited selective feeding on Synechococcus sp., known to be rich in N. Given the high abundance of picoplankton in oligotrophic waters at large, our results suggest that corals exhibiting flexible diazotrophic communities and capable of exploiting N-rich picoplankton sources to offset their increased N requirements may be able to cope better in a high pCO2 world.
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Affiliation(s)
- Valentine Meunier
- Centre IRD Nouméa, UMR ENTROPIE (IRD, Université de La Réunion, CNRS, Université de La Nouvelle-Calédonie, Ifremer), Nouméa, New Caledonia
| | - Laura Geissler
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Sophie Bonnet
- Aix-Marseille Université, Université de Toulon, CNRS, IRD, Marseille, France
| | - Nils Rädecker
- Department of Biology, University of Konstanz, Konstanz, Germany.,Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Gabriela Perna
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Olivier Grosso
- Aix-Marseille Université, Université de Toulon, CNRS, IRD, Marseille, France
| | | | - Riccardo Rodolfo-Metalpa
- Centre IRD Nouméa, UMR ENTROPIE (IRD, Université de La Réunion, CNRS, Université de La Nouvelle-Calédonie, Ifremer), Nouméa, New Caledonia
| | | | - Fanny Houlbrèque
- Centre IRD Nouméa, UMR ENTROPIE (IRD, Université de La Réunion, CNRS, Université de La Nouvelle-Calédonie, Ifremer), Nouméa, New Caledonia
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12
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Hampel JJ, McCarthy MJ, Aalto SL, Newell SE. Hurricane Disturbance Stimulated Nitrification and Altered Ammonia Oxidizer Community Structure in Lake Okeechobee and St. Lucie Estuary (Florida). Front Microbiol 2020; 11:1541. [PMID: 32754132 PMCID: PMC7366250 DOI: 10.3389/fmicb.2020.01541] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 06/12/2020] [Indexed: 01/01/2023] Open
Abstract
Nitrification is an important biological link between oxidized and reduced forms of nitrogen (N). The efficiency of nitrification plays a key role in mitigating excess N in eutrophic systems, including those with cyanobacterial harmful algal blooms (cyanoHABs), since it can be closely coupled with denitrification and removal of excess N. Recent work suggests that competition for ammonium (NH4+) between ammonia oxidizers and cyanoHABs can help determine microbial community structure. Nitrification rates and ammonia-oxidizing archaeal (AOA) and bacterial (AOB) community composition and gene abundances were quantified in Lake Okeechobee and St. Lucie Estuary in southern Florida (United States). We sampled during cyanobacterial (Microcystis) blooms in July 2016 and August 2017 (2 weeks before Hurricane Irma) and 10 days after Hurricane Irma made landfall. Nitrification rates were low during cyanobacterial blooms in Lake Okeechobee and St. Lucie Estuary, while low bloom conditions in St. Lucie Estuary coincided with greater nitrification rates. Nitrification rates in the lake were correlated (R2 = 0.94; p = 0.006) with AOA amoA abundance. Following the hurricane, nitrification rates increased by an order of magnitude, suggesting that nitrifiers outcompeted cyanobacteria for NH4+ under turbid, poor light conditions. After Irma, AOA and AOB abundances increased in St. Lucie Estuary, while only AOB increased in Lake Okeechobee. AOA sequences clustered into three major lineages: Nitrosopumilales (NP), Nitrososphaerales (NS), and Nitrosotaleales (NT). Many of the lake OTUs placed within the uncultured and uncharacterized NS δ and NT β clades, suggesting that these taxa are ecologically important along this eutrophic, lacustrine to estuarine continuum. After the hurricane, the AOA community shifted toward dominance by freshwater clades in St. Lucie Estuary and terrestrial genera in Lake Okeechobee, likely due to high rainfall and subsequent increased turbidity and freshwater loading from the lake into the estuary. AOB community structure was not affected by the disturbance. AOA communities were consistently more diverse than AOB, despite fewer sequences recovered, including new, unclassified, eutrophic ecotypes, suggesting a wider ecological biogeography than the oligotrophic niche originally posited. These results and other recent reports contradict the early hypothesis that AOB dominate ammonia oxidation in high-nutrient or terrestrial-influenced systems.
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Affiliation(s)
- Justyna J Hampel
- School of Ocean Science and Engineering, The University of Southern Mississippi, Ocean Springs, MS, United States.,Department of Earth and Environmental Sciences, Wright State University, Dayton, OH, United States
| | - Mark J McCarthy
- Department of Earth and Environmental Sciences, Wright State University, Dayton, OH, United States
| | - Sanni L Aalto
- Section for Aquaculture, The North Sea Research Centre, DTU Aqua, Technical University of Denmark, Hirtshals, Denmark
| | - Silvia E Newell
- Department of Earth and Environmental Sciences, Wright State University, Dayton, OH, United States
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13
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Fan K, Delgado-Baquerizo M, Guo X, Wang D, Wu Y, Zhu M, Yu W, Yao H, Zhu YG, Chu H. Suppressed N fixation and diazotrophs after four decades of fertilization. MICROBIOME 2019; 7:143. [PMID: 31672173 PMCID: PMC6824023 DOI: 10.1186/s40168-019-0757-8] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 10/02/2019] [Indexed: 05/06/2023]
Abstract
BACKGROUND N fixation is one of the most important microbially driven ecosystem processes on Earth, allowing N to enter the soil from the atmosphere, and regulating plant productivity. A question that remains to be answered is whether such a fundamental process would still be that important in an over-fertilized world, as the long-term effects of fertilization on N fixation and associated diazotrophic communities remain to be tested. Here, we used a 35-year fertilization experiment, and investigated the changes in N fixation rates and the diazotrophic community in response to long-term inorganic and organic fertilization. RESULTS It was found that N fixation was drastically reduced (dropped by 50%) after almost four decades of fertilization. Our results further indicated that functionality losses were associated with reductions in the relative abundance of keystone and phylogenetically clustered N fixers such as Geobacter spp. CONCLUSIONS Our work suggests that long-term fertilization might have selected against N fixation and specific groups of N fixers. Our study provides solid evidence that N fixation and certain groups of diazotrophic taxa will be largely suppressed in a more and more fertilized world, with implications for soil biodiversity and ecosystem functions.
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Affiliation(s)
- Kunkun Fan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing, 210008 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Manuel Delgado-Baquerizo
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO 80309 USA
- Departamento de Biología y Geología, Física y Química Inorgánica, Escuela Superior de Ciencias Experimentales y Tecnología, Universidad Rey Juan Carlos, c/ Tulipán s/n, 28933 Móstoles, Spain
| | - Xisheng Guo
- Institute of Soil and Fertilizer Research, Anhui Academy of Agricultural Sciences, 40 South Nongke Road, Hefei, 230031 China
| | - Daozhong Wang
- Institute of Soil and Fertilizer Research, Anhui Academy of Agricultural Sciences, 40 South Nongke Road, Hefei, 230031 China
| | - Yanying Wu
- High School Affiliated to Nanjing Normal University, Nanjing, 210003 China
| | - Mo Zhu
- High School Affiliated to Nanjing Normal University, Nanjing, 210003 China
| | - Wei Yu
- High School Affiliated to Nanjing Normal University, Nanjing, 210003 China
| | - Huaiying Yao
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021 China
- School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan, 430205 China
| | - Yong-guan Zhu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021 China
| | - Haiyan Chu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing, 210008 China
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14
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Pedersen JN, Bombar D, Paerl RW, Riemann L. Diazotrophs and N 2-Fixation Associated With Particles in Coastal Estuarine Waters. Front Microbiol 2018; 9:2759. [PMID: 30505296 PMCID: PMC6250843 DOI: 10.3389/fmicb.2018.02759] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 10/29/2018] [Indexed: 11/13/2022] Open
Abstract
Putative heterotrophic bacteria carrying out N2-fixation, so-called non-cyanobacterial diazotrophs (NCDs), are widely distributed in marine waters, but details of how the O2-inhibited N2-fixation process is promoted in the oxic water column remains ambiguous. Here we carried out two experiments with water from a eutrophic temperate fjord to examine whether low-oxygen microenvironments within particulate organic matter could be loci suitable for N2-fixation. First, water enriched with natural particles or sediment showed higher N2-fixation rates than bulk water, and nitrogenase genes (nifH) revealed that specific diazotrophs were affiliated with the particulate matter. Second, pristine artificial surfaces were rapidly colonized by diverse bacteria, while putative diazotrophs emerged relatively late (after 80 h) during the colonization, and phylotypes related to Pseudomonas and to anaerobic bacteria became dominant with time. Our study pinpoints natural particles as sites of N2-fixation, and indicates that resuspension of sediment material can elevate pelagic N2-fixation. Moreover, we show that diverse natural diazotrophs can colonize artificial surfaces, but colonization by “pioneer” bacterioplankton that more rapidly associate with surfaces appears to be a prerequisite. Whereas our experimental study supports the idea of pelagic particles as sites of N2-fixation by heterotrophic bacteria, future in situ studies are needed in order to establish identity, activity and ecology of particle associated NCDs as a function of individual particle characteristics.
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Affiliation(s)
- Jeppe N Pedersen
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - Deniz Bombar
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - Ryan W Paerl
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - Lasse Riemann
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
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15
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Farnelid H, Turk-Kubo K, Ploug H, Ossolinski JE, Collins JR, Van Mooy BAS, Zehr JP. Diverse diazotrophs are present on sinking particles in the North Pacific Subtropical Gyre. ISME JOURNAL 2018; 13:170-182. [PMID: 30116043 PMCID: PMC6299005 DOI: 10.1038/s41396-018-0259-x] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 07/03/2018] [Accepted: 07/26/2018] [Indexed: 11/09/2022]
Abstract
Sinking particles transport carbon and nutrients from the surface ocean into the deep sea and are considered hot spots for bacterial diversity and activity. In the oligotrophic oceans, nitrogen (N2)-fixing organisms (diazotrophs) are an important source of new N but the extent to which these organisms are present and exported on sinking particles is not well known. Sinking particles were collected every 6 h over a 2-day period using net traps deployed at 150 m in the North Pacific Subtropical Gyre. The bacterial community and composition of diazotrophs associated with individual and bulk sinking particles was assessed using 16S rRNA and nifH gene amplicon sequencing. The bacterial community composition in bulk particles remained remarkably consistent throughout time and space while large variations of individually picked particles were observed. This difference suggests that unique biogeochemical conditions within individual particles may offer distinct ecological niches for specialized bacterial taxa. Compared to surrounding seawater, particle samples were enriched in different size classes of globally significant N2-fixing cyanobacteria including Trichodesmium, symbionts of diatoms, and the unicellular cyanobacteria Crocosphaera and UCYN-A. The particles also contained nifH gene sequences of diverse non-cyanobacterial diazotrophs suggesting that particles could be loci for N2 fixation by heterotrophic bacteria. The results demonstrate that diverse diazotrophs were present on particles and that new N may thereby be directly exported from surface waters on sinking particles.
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Affiliation(s)
- Hanna Farnelid
- Ocean Sciences Department, University of California at Santa Cruz, Santa Cruz, CA, USA. .,Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden.
| | - Kendra Turk-Kubo
- Ocean Sciences Department, University of California at Santa Cruz, Santa Cruz, CA, USA
| | - Helle Ploug
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Justin E Ossolinski
- Department of Marine Chemistry & Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - James R Collins
- Department of Marine Chemistry & Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA.,MIT/WHOI Joint Program in Oceanography, University of Washington, Seattle, WA, USA.,School of Oceanography and eScience Institute, University of Washington, Seattle, WA, USA
| | - Benjamin A S Van Mooy
- Department of Marine Chemistry & Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Jonathan P Zehr
- Ocean Sciences Department, University of California at Santa Cruz, Santa Cruz, CA, USA
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16
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Delmont TO, Quince C, Shaiber A, Esen ÖC, Lee ST, Rappé MS, McLellan SL, Lücker S, Eren AM. Nitrogen-fixing populations of Planctomycetes and Proteobacteria are abundant in surface ocean metagenomes. Nat Microbiol 2018; 3:804-813. [PMID: 29891866 PMCID: PMC6792437 DOI: 10.1038/s41564-018-0176-9] [Citation(s) in RCA: 234] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 05/15/2018] [Indexed: 01/28/2023]
Abstract
Nitrogen fixation in the surface ocean impacts global marine nitrogen bioavailability and thus microbial primary productivity. Until now, cyanobacterial populations have been viewed as the main suppliers of bioavailable nitrogen in this habitat. Although PCR amplicon surveys targeting the nitrogenase reductase gene have revealed the existence of diverse non-cyanobacterial diazotrophic populations, subsequent quantitative PCR surveys suggest that they generally occur in low abundance. Here, we use state-of-the-art metagenomic assembly and binning strategies to recover nearly one thousand non-redundant microbial population genomes from the TARA Oceans metagenomes. Among these, we provide the first genomic evidence for non-cyanobacterial diazotrophs inhabiting surface waters of the open ocean, which correspond to lineages within the Proteobacteria and, most strikingly, the Planctomycetes. Members of the latter phylum are prevalent in aquatic systems, but have never been linked to nitrogen fixation previously. Moreover, using genome-wide quantitative read recruitment, we demonstrate that the discovered diazotrophs were not only widespread but also remarkably abundant (up to 0.3% of metagenomic reads for a single population) in both the Pacific Ocean and the Atlantic Ocean northwest. Our results extend decades of PCR-based gene surveys, and substantiate the importance of heterotrophic bacteria in the fixation of nitrogen in the surface ocean.
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Affiliation(s)
- Tom O Delmont
- Department of Medicine, University of Chicago, Chicago, IL, USA.
| | | | - Alon Shaiber
- Graduate Program in the Biophysical Sciences, University of Chicago, Chicago, IL, USA
| | - Özcan C Esen
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Sonny Tm Lee
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Michael S Rappé
- Hawaii Institute of Marine Biology, University of Hawaii at Manoa, Kaneohe, HI, USA
| | - Sandra L McLellan
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Sebastian Lücker
- Department of Microbiology, Radboud University, Nijmegen, The Netherlands
| | - A Murat Eren
- Department of Medicine, University of Chicago, Chicago, IL, USA. .,Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA, USA. .,Committee on Microbiology, University of Chicago, Chicago, IL, USA.
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17
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Meher PK, Sahu TK, Mohanty J, Gahoi S, Purru S, Grover M, Rao AR. nifPred: Proteome-Wide Identification and Categorization of Nitrogen-Fixation Proteins of Diaztrophs Based on Composition-Transition-Distribution Features Using Support Vector Machine. Front Microbiol 2018; 9:1100. [PMID: 29896173 PMCID: PMC5986947 DOI: 10.3389/fmicb.2018.01100] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 05/08/2018] [Indexed: 11/13/2022] Open
Abstract
As inorganic nitrogen compounds are essential for basic building blocks of life (e.g., nucleotides and amino acids), the role of biological nitrogen-fixation (BNF) is indispensible. All nitrogen fixing microbes rely on the same nitrogenase enzyme for nitrogen reduction, which is in fact an enzyme complex consists of as many as 20 genes. However, the occurrence of six genes viz., nifB, nifD, nifE, nifH, nifK, and nifN has been proposed to be essential for a functional nitrogenase enzyme. Therefore, identification of these genes is important to understand the mechanism of BNF as well as to explore the possibilities for improving BNF from agricultural sustainability point of view. Further, though the computational tools are available for the annotation and phylogenetic analysis of nifH gene sequences alone, to the best of our knowledge no tool is available for the computational prediction of the above mentioned six categories of nitrogen-fixation (nif) genes or proteins. Thus, we proposed an approach, which is first of its kind for the computational identification of nif proteins encoded by the six categories of nif genes. Sequence-derived features were employed to map the input sequences into vectors of numeric observations that were subsequently fed to the support vector machine as input. Two types of classifier were constructed: (i) a binary classifier for classification of nif and non-nitrogen-fixation (non-nif) proteins, and (ii) a multi-class classifier for classification of six categories of nif proteins. Higher accuracies were observed for the combination of composition-transition-distribution (CTD) feature set and radial kernel, as compared to the other feature-kernel combinations. The overall accuracies were observed >90% in both binary and multi-class classifications. The developed approach further achieved >92% accuracy, while evaluated with blind (independent) test datasets. The developed approach also produced higher accuracy in identifying nif proteins, while evaluated using proteome-wide datasets of several species. Furthermore, we established a prediction server nifPred (http://webapp.cabgrid.res.in/nifPred) to assist the scientific community for proteome-wide identification of six categories of nif proteins. Besides, the source code of nifPred is also available at https://github.com/PrabinaMeher/nifPred. The developed web server is expected to supplement the transcriptional profiling and comparative genomics studies for the identification and functional annotation of genes related to BNF.
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Affiliation(s)
- Prabina K Meher
- Division of Statistical Genetics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Tanmaya K Sahu
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Jyotilipsa Mohanty
- Division of Statistical Genetics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India.,Department of Bioinformatics, Orissa University of Agriculture and Technology, Bhubaneswar, India
| | - Shachi Gahoi
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Supriya Purru
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Monendra Grover
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Atmakuri R Rao
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
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18
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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] [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.
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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
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Gaby JC, Rishishwar L, Valderrama-Aguirre LC, Green SJ, Valderrama-Aguirre A, Jordan IK, Kostka JE. Diazotroph Community Characterization via a High-Throughput nifH Amplicon Sequencing and Analysis Pipeline. Appl Environ Microbiol 2018; 84:e01512-17. [PMID: 29180374 PMCID: PMC5795091 DOI: 10.1128/aem.01512-17] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 11/21/2017] [Indexed: 11/20/2022] Open
Abstract
The dinitrogenase reductase gene (nifH) is the most widely established molecular marker for the study of nitrogen-fixing prokaryotes in nature. A large number of PCR primer sets have been developed for nifH amplification, and the effective deployment of these approaches should be guided by a rapid, easy-to-use analysis protocol. Bioinformatic analysis of marker gene sequences also requires considerable expertise. In this study, we advance the state of the art for nifH analysis by evaluating nifH primer set performance, developing an improved amplicon sequencing workflow, and implementing a user-friendly bioinformatics pipeline. The developed amplicon sequencing workflow is a three-stage PCR-based approach that uses established technologies for incorporating sample-specific barcode sequences and sequencing adapters. Based on our primer evaluation, we recommend the Ando primer set be used with a modified annealing temperature of 58°C, as this approach captured the largest diversity of nifH templates, including paralog cluster IV/V sequences. To improve nifH sequence analysis, we developed a computational pipeline which infers taxonomy and optionally filters out paralog sequences. In addition, we employed an empirical model to derive optimal operational taxonomic unit (OTU) cutoffs for the nifH gene at the species, genus, and family levels. A comprehensive workflow script named TaxADivA (TAXonomy Assignment and DIVersity Assessment) is provided to ease processing and analysis of nifH amplicons. Our approach is then validated through characterization of diazotroph communities across environmental gradients in beach sands impacted by the Deepwater Horizon oil spill in the Gulf of Mexico, in a peat moss-dominated wetland, and in various plant compartments of a sugarcane field.IMPORTANCE Nitrogen availability often limits ecosystem productivity, and nitrogen fixation, exclusive to prokaryotes, comprises a major source of nitrogen input that sustains food webs. The nifH gene, which codes for the iron protein of the nitrogenase enzyme, is the most widely established molecular marker for the study of nitrogen-fixing microorganisms (diazotrophs) in nature. In this study, a flexible sequencing/analysis pipeline, named TaxADivA, was developed for nifH amplicons produced by Illumina paired-end sequencing, and it enables an inference of taxonomy, performs clustering, and produces output in formats that may be used by programs that facilitate data exploration and analysis. Diazotroph diversity and community composition are linked to ecosystem functioning, and our results advance the phylogenetic characterization of diazotroph communities by providing empirically derived nifH similarity cutoffs for species, genus, and family levels. The utility of our pipeline is validated for diazotroph communities in a variety of ecosystems, including contaminated beach sands, peatland ecosystems, living plant tissues, and rhizosphere soil.
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Affiliation(s)
- John Christian Gaby
- School of Biology, The Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Lavanya Rishishwar
- School of Biology, The Georgia Institute of Technology, Atlanta, Georgia, USA
- Applied Bioinformatics Laboratory, Atlanta, Georgia, USA
- PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia
| | - Lina C Valderrama-Aguirre
- Laboratory of Microorganismal Production (Bioinoculums), Department of Field Research in Sugarcane, Incauca S.A.S, Cali, Valle del Cauca, Colombia
- School of Natural Resources and Environmental Engineering, PhD Program in Sanitary and Environmental Engineering, Universidad del Valle, Cali, Valle del Cauca, Colombia
| | - Stefan J Green
- DNA Services Facility, Research Resources Center, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Augusto Valderrama-Aguirre
- PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia
- Biomedical Research Institute, Universidad Libre, Cali, Valle del Cauca, Colombia
- Regenerar, Center of Excellence for Regenerative and Personalized Medicine, Valle del Cauca, Colombia
| | - I King Jordan
- School of Biology, The Georgia Institute of Technology, Atlanta, Georgia, USA
- Applied Bioinformatics Laboratory, Atlanta, Georgia, USA
- PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia
| | - Joel E Kostka
- School of Biology, The Georgia Institute of Technology, Atlanta, Georgia, USA
- PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia
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