1
|
Dietrich M, Panhölzl C, Angel R, Giguere AT, Randi D, Hausmann B, Herbold CW, Pötsch EM, Schaumberger A, Eichorst SA, Woebken D. Plant roots affect free-living diazotroph communities in temperate grassland soils despite decades of fertilization. Commun Biol 2024; 7:846. [PMID: 38987659 PMCID: PMC11237082 DOI: 10.1038/s42003-024-06522-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 06/28/2024] [Indexed: 07/12/2024] Open
Abstract
Fixation of atmospheric N2 by free-living diazotrophs accounts for an important proportion of nitrogen naturally introduced to temperate grasslands. The effect of plants or fertilization on the general microbial community has been extensively studied, yet an understanding of the potential combinatorial effects on the community structure and activity of free-living diazotrophs is lacking. In this study we provide a multilevel assessment of the single and interactive effects of different long-term fertilization treatments, plant species and vicinity to roots on the free-living diazotroph community in relation to the general microbial community in grassland soils. We sequenced the dinitrogenase reductase (nifH) and the 16S rRNA genes of bulk soil and root-associated compartments (rhizosphere soil, rhizoplane and root) of two grass species (Arrhenatherum elatius and Anthoxanthum odoratum) and two herb species (Galium album and Plantago lanceolata) growing in Austrian grassland soils treated with different fertilizers (N, P, NPK) since 1960. Overall, fertilization has the strongest effect on the diazotroph and general microbial community structure, however with vicinity to the root, the plant effect increases. Despite the long-term fertilization, plants strongly influence the diazotroph communities emphasizing the complexity of soil microbial communities' responses to changing nutrient conditions in temperate grasslands.
Collapse
Affiliation(s)
- Marlies Dietrich
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Christopher Panhölzl
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, 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
- Institute of Soil Biology and Biogeochemistry, Biology Centre CAS, České Budějovice, Czechia
| | - Andrew T Giguere
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Dania Randi
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Bela Hausmann
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
- Division of Clinical Microbiology, Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Craig W Herbold
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Te Kura Pūtaiao Koiora, School of Biological Sciences, Te Whare Wānanga o Waitaha, University of Canterbury, Christchurch, New Zealand
| | - Erich M Pötsch
- Institute of Plant Production and Cultural Landscape, Agricultural Research and Education Centre, Raumberg-Gumpenstein, Austria
| | - Andreas Schaumberger
- Institute of Plant Production and Cultural Landscape, Agricultural Research and Education Centre, Raumberg-Gumpenstein, Austria
| | - Stephanie A Eichorst
- 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.
| |
Collapse
|
2
|
Chowdhury S, Berthelot H, Baudet C, González-Santana D, Reeder CF, L'Helguen S, Maguer JF, Löscher CR, Singh A, Blain S, Cassar N, Bonnet S, Planquette H, Benavides M. Fronts divide diazotroph communities in the Southern Indian Ocean. FEMS Microbiol Ecol 2024; 100:fiae095. [PMID: 38992179 DOI: 10.1093/femsec/fiae095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2024] Open
Abstract
Dinitrogen (N2) fixation represents a key source of reactive nitrogen in marine ecosystems. While the process has been rather well explored in low latitudes of the Atlantic and Pacific Oceans, other higher latitude regions and particularly the Indian Ocean have been chronically overlooked. Here we characterize N2 fixation and diazotroph community composition across nutrient and trace metals gradients spanning the multi-frontal system separating the oligotrophic waters of the Indian Ocean subtropical gyre from the high nutrient low chlorophyll waters of the Southern Ocean. We found a sharp contrasting distribution of diazotroph groups across the frontal system. Notably, cyanobacterial diazotrophs dominated north of fronts, driving elevated N2 fixation rates (up to 13.96 nmol N l-1 d-1) with notable peaks near the South African coast. South of the fronts non-cyanobacterial diazotrophs prevailed without significant N2 fixation activity being detected. Our results provide new crucial insights into high latitude diazotrophy in the Indian Ocean, which should contribute to improved climate model parameterization and enhanced constraints on global net primary productivity projections.
Collapse
Affiliation(s)
- Subhadeep Chowdhury
- Aix Marseille Université, CNRS, Université de Toulon, IRD, OSU Pythéas, Mediterranean Institute of Oceanography (MIO), UM 110, 13288 Marseille, France
- Turing Center for Living Systems, Aix-Marseille University, Marseille, France
| | - Hugo Berthelot
- IFREMER, DYNECO, Pelagos Laboratory, Plouzané, France
- Laboratoire des Sciences de l'Environnement Marin, IUEM, Université de Brest-UMR 6539 CNRS/UBO/IRD, Technopole Brest-Iroise, 29280 Plouzané, France
| | - Corentin Baudet
- Laboratoire des Sciences de l'Environnement Marin, IUEM, Université de Brest-UMR 6539 CNRS/UBO/IRD, Technopole Brest-Iroise, 29280 Plouzané, France
| | - David González-Santana
- Univ Brest, CNRS, IRD, Ifremer, LEMAR, F-29280 Plouzané, France
- Instituto de Oceanografía y Cambio Global, IOCAG, Universidad de Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Spain
| | - Christian Furbo Reeder
- Aix Marseille Université, CNRS, Université de Toulon, IRD, OSU Pythéas, Mediterranean Institute of Oceanography (MIO), UM 110, 13288 Marseille, France
- Turing Center for Living Systems, Aix-Marseille University, Marseille, France
| | - Stéphane L'Helguen
- Laboratoire des Sciences de l'Environnement Marin, IUEM, Université de Brest-UMR 6539 CNRS/UBO/IRD, Technopole Brest-Iroise, 29280 Plouzané, France
| | - Jean-François Maguer
- Laboratoire des Sciences de l'Environnement Marin, IUEM, Université de Brest-UMR 6539 CNRS/UBO/IRD, Technopole Brest-Iroise, 29280 Plouzané, France
| | - Carolin R Löscher
- Nordcee, Department of Biology, University of Southern Denmark, Odense 5230, Denmark
| | - Arvind Singh
- Geosciences Division, Physical Research Laboratory, Ahmedabad 380009, India
| | - Stéphane Blain
- Sorbonne Université, CNRS, Laboratoire d'Océanographie Microbienne (LOMIC), Observatoire Océanologique de Banyuls, 66650 Banyuls/mer, France
| | - Nicolas Cassar
- Laboratoire des Sciences de l'Environnement Marin, IUEM, Université de Brest-UMR 6539 CNRS/UBO/IRD, Technopole Brest-Iroise, 29280 Plouzané, France
- Division of Earth and Climate Sciences, Nicholas School of the Environment, Duke University, Durham, NC 27708, USA
| | - Sophie Bonnet
- Aix Marseille Université, CNRS, Université de Toulon, IRD, OSU Pythéas, Mediterranean Institute of Oceanography (MIO), UM 110, 13288 Marseille, France
| | - Hélène Planquette
- Aix Marseille Université, CNRS, Université de Toulon, IRD, OSU Pythéas, Mediterranean Institute of Oceanography (MIO), UM 110, 13288 Marseille, France
| | - Mar Benavides
- Aix Marseille Université, CNRS, Université de Toulon, IRD, OSU Pythéas, Mediterranean Institute of Oceanography (MIO), UM 110, 13288 Marseille, France
- Turing Center for Living Systems, Aix-Marseille University, Marseille, France
| |
Collapse
|
3
|
Sorochkina K, Martens-Habbena W, Reardon CL, Inglett PW, Strauss SL. Nitrogen-fixing bacterial communities differ between perennial agroecosystem crops. FEMS Microbiol Ecol 2024; 100:fiae064. [PMID: 38637314 DOI: 10.1093/femsec/fiae064] [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: 10/11/2023] [Revised: 03/28/2024] [Accepted: 04/17/2024] [Indexed: 04/20/2024] Open
Abstract
Biocrusts, common in natural ecosystems, are specific assemblages of microorganisms at or on the soil surface with associated microorganisms extending into the top centimeter of soil. Agroecosystem biocrusts have similar rates of nitrogen (N) fixation as those in natural ecosystems, but it is unclear how agricultural management influences their composition and function. This study examined the total bacterial and diazotrophic communities of biocrusts in a citrus orchard and a vineyard that shared a similar climate and soil type but differed in management. To contrast climate and soil type, these biocrusts were also compared with those from an apple orchard. Unlike natural ecosystem biocrusts, these agroecosystem biocrusts were dominated by proteobacteria and had a lower abundance of cyanobacteria. All of the examined agroecosystem biocrust diazotroph communities were dominated by N-fixing cyanobacteria from the Nostocales order, similar to natural ecosystem cyanobacterial biocrusts. Lower irrigation and fertilizer in the vineyard compared with the citrus orchard could have contributed to biocrust microbial composition, whereas soil type and climate could have differentiated the apple orchard biocrust. Season did not influence the bacterial and diazotrophic community composition of any of these agroecosystem biocrusts. Overall, agricultural management and climatic and edaphic factors potentially influenced the community composition and function of these biocrusts.
Collapse
Affiliation(s)
- Kira Sorochkina
- Department of Soil, Water, and Ecosystem Sciences, University of Florida, Gainesville, FL, United States
- Southwest Research and Education Center, University of Florida, Immokalee, FL, United States
| | - Willm Martens-Habbena
- Fort Lauderdale Research and Education Center, University of Florida, Fort Lauderdale, FL, United States
| | - Catherine L Reardon
- Soil and Water Conservation Research Unit, U.S. Department of Agriculture, Agricultural Research Service (USDA-ARS), Pendleton, OR, United States
| | - Patrick W Inglett
- Department of Soil, Water, and Ecosystem Sciences, University of Florida, Gainesville, FL, United States
| | - Sarah L Strauss
- Department of Soil, Water, and Ecosystem Sciences, University of Florida, Gainesville, FL, United States
- Southwest Research and Education Center, University of Florida, Immokalee, FL, United States
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
Cho A, Joshi A, Hur HG, Lee JH. Nodulation Experiment by Cross-Inoculation of Nitrogen-Fixing Bacteria Isolated from Root Nodules of Several Leguminous Plants. J Microbiol Biotechnol 2024; 34:570-579. [PMID: 38213271 PMCID: PMC11016771 DOI: 10.4014/jmb.2310.10025] [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: 10/19/2023] [Revised: 12/13/2023] [Accepted: 12/21/2023] [Indexed: 01/13/2024]
Abstract
Root-nodule nitrogen-fixing bacteria are known for being specific to particular legumes. This study isolated the endophytic root-nodule bacteria from the nodules of legumes and examined them to determine whether they could be used to promote the formation of nodules in other legumes. Forty-six isolates were collected from five leguminous plants and screened for housekeeping (16S rRNA), nitrogen fixation (nifH), and nodulation (nodC) genes. Based on the 16S rRNA gene sequencing and phylogenetic analysis, the bacterial isolates WC15, WC16, WC24, and GM5 were identified as Rhizobium, Sphingomonas, Methylobacterium, and Bradyrhizobium, respectively. The four isolates were found to have the nifH gene, and the study confirmed that one isolate (GM5) had both the nifH and nodC genes. The Salkowski method was used to measure the isolated bacteria for their capacity to produce phytohormone indole acetic acid (IAA). Additional experiments were performed to examine the effect of the isolated bacteria on root morphology and nodulation. Among the four tested isolates, both WC24 and GM5 induced nodulation in Glycine max. The gene expression studies revealed that GM5 had a higher expression of the nifH gene. The existence and expression of the nitrogen-fixing genes implied that the tested strain had the ability to fix the atmospheric nitrogen. These findings demonstrated that a nitrogen-fixing bacterium, Methylobacterium (WC24), isolated from a Trifolium repens, induced the formation of root nodules in non-host leguminous plants (Glycine max). This suggested the potential application of these rhizobia as biofertilizer. Further studies are required to verify the N2-fixing efficiency of the isolates.
Collapse
Affiliation(s)
- Ahyeon Cho
- Department of Agricultural Chemistry, Jeonbuk National University, Jeonju 54896, Republic of Korea
| | - Alpana Joshi
- Department of Bioenvironmental Chemistry, Jeonbuk National University, Jeonju 54896, Republic of Korea
- Department of Agriculture Technology & Agri-Informatics, Shobhit Institute of Engineering & Technology, Meerut 250110, India
| | - Hor-Gil Hur
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea
| | - Ji-Hoon Lee
- Department of Agricultural Chemistry, Jeonbuk National University, Jeonju 54896, Republic of Korea
- Department of Bioenvironmental Chemistry, Jeonbuk National University, Jeonju 54896, Republic of Korea
| |
Collapse
|
6
|
Jung P, Briegel-Williams L, Werner L, Jost E, Schultz M, Nürnberg DJ, Grube M, Lakatos M. A direct PCR approach with low-biomass insert opens new horizons for molecular sciences on cryptogam communities. Appl Environ Microbiol 2024; 90:e0002424. [PMID: 38349146 PMCID: PMC10952543 DOI: 10.1128/aem.00024-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 01/19/2024] [Indexed: 03/21/2024] Open
Abstract
Molecular sequence data have transformed research on cryptogams (e.g., lichens, microalgae, fungi, and symbionts thereof) but methods are still strongly hampered by the small size and intermingled growth of the target organisms, poor cultivability and detrimental effects of their secondary metabolites. Here, we aim to showcase examples on which a modified direct PCR approach for diverse aspects of molecular work on environmental samples concerning biocrusts, biofilms, and cryptogams gives new options for the research community. Unlike traditional approaches, this methodology only requires biomass equivalent to colonies and fragments of 0.2 mm in diameter, which can be picked directly from the environmental sample, and includes a quick DNA lysis followed by a standardized PCR cycle that allows co-cycling of various organisms/target regions in the same run. We demonstrate that this modified method can (i) amplify the most widely used taxonomic gene regions and those used for applied and environmental sciences from single colonies and filaments of free-living cyanobacteria, bryophytes, fungi, and lichens, including their mycobionts, chlorobionts, and cyanobionts from both isolates and in situ material during co-cycling; (ii) act as a tool to confirm that the dominant lichen photobiont was isolated from the original sample; and (iii) optionally remove inhibitory secondary lichen substances. Our results represent examples which highlight the method's potential for future applications covering mycology, phycology, biocrusts, and lichenology, in particular.IMPORTANCECyanobacteria, green algae, lichens, and other cryptogams play crucial roles in complex microbial systems such as biological soil crusts of arid biomes or biofilms in caves. Molecular investigations on environmental samples or isolates of these microorganisms are often hampered by their dense aggregation, small size, or metabolism products which complicate DNA extraction and subsequent PCRs. Our work presents various examples of how a direct DNA extraction and PCR method relying on low biomass inserts can overcome these common problems and discusses additional applications of the workflow including adaptations.
Collapse
Affiliation(s)
- Patrick Jung
- Department of Integrative Biotechnology, University of Applied Sciences Kaiserslautern, Pirmasens, Germany
| | - Laura Briegel-Williams
- Department of Integrative Biotechnology, University of Applied Sciences Kaiserslautern, Pirmasens, Germany
| | - Lina Werner
- Department of Integrative Biotechnology, University of Applied Sciences Kaiserslautern, Pirmasens, Germany
| | - Emily Jost
- Department of Integrative Biotechnology, University of Applied Sciences Kaiserslautern, Pirmasens, Germany
| | - Matthias Schultz
- Institute for Plant Science and Microbiology, Herbarium Hamburgense, University of Hamburg, Hamburg, Germany
| | - Dennis J. Nürnberg
- Institute of Experimental Physics, Freie Universität Berlin, Berlin, Germany
- Dahlem Centre for Plant Sciences, Freie Universität Berlin, Berlin, Germany
| | - Martin Grube
- Institute of Biology, University of Graz, Graz, Austria
| | - Michael Lakatos
- Department of Integrative Biotechnology, University of Applied Sciences Kaiserslautern, Pirmasens, Germany
| |
Collapse
|
7
|
Si Y, Zhu Y, Sanders I, Kinkel DB, Purdy KJ, Trimmer M. Direct biological fixation provides a freshwater sink for N 2O. Nat Commun 2023; 14:6775. [PMID: 37880204 PMCID: PMC10600110 DOI: 10.1038/s41467-023-42481-2] [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: 05/03/2023] [Accepted: 10/12/2023] [Indexed: 10/27/2023] Open
Abstract
Nitrous oxide (N2O) is a potent climate gas, with its strong warming potential and ozone-depleting properties both focusing research on N2O sources. Although a sink for N2O through biological fixation has been observed in the Pacific, the regulation of N2O-fixation compared to canonical N2-fixation is unknown. Here we show that both N2O and N2 can be fixed by freshwater communities but with distinct seasonalities and temperature dependencies. N2O fixation appears less sensitive to temperature than N2 fixation, driving a strong sink for N2O in colder months. Moreover, by quantifying both N2O and N2 fixation we show that, rather than N2O being first reduced to N2 through denitrification, N2O fixation is direct and could explain the widely reported N2O sinks in natural waters. Analysis of the nitrogenase (nifH) community suggests that while only a subset is potentially capable of fixing N2O they maintain a strong, freshwater sink for N2O that could be eroded by warming.
Collapse
Affiliation(s)
- Yueyue Si
- School of Biological and Behavioural Sciences, Queen Mary, University of London, London, E1 4NS, UK
| | - Yizhu Zhu
- School of Biological and Behavioural Sciences, Queen Mary, University of London, London, E1 4NS, UK
| | - Ian Sanders
- School of Biological and Behavioural Sciences, Queen Mary, University of London, London, E1 4NS, UK
| | - Dorothee B Kinkel
- School of Biological and Behavioural Sciences, Queen Mary, University of London, London, E1 4NS, UK
| | - Kevin J Purdy
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Mark Trimmer
- School of Biological and Behavioural Sciences, Queen Mary, University of London, London, E1 4NS, UK.
| |
Collapse
|
8
|
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.
Collapse
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
| |
Collapse
|
9
|
Stefani F, Beguin J, Paré D, Morency MJ, Martineau C, Fortin JA, Thiffault N, Séguin A. Does wood mulch trigger microbially mediated positive plant-soil feedback in degraded boreal forest sites? A post hoc study. FRONTIERS IN PLANT SCIENCE 2023; 14:1122445. [PMID: 37206972 PMCID: PMC10191178 DOI: 10.3389/fpls.2023.1122445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 03/15/2023] [Indexed: 05/21/2023]
Abstract
Introduction Reforestation of degraded lands in the boreal forest is challenging and depends on the direction and strength of the plant-soil feedback (PSF). Methods Using a gradient in tree productivity (null, low and high) from a long-term, spatially replicated reforestation experiment of borrow pits in the boreal forest, we investigated the interplay between microbial communities and soil and tree nutrient stocks and concentrations in relation to a positive PSF induced by wood mulch amendment. Results Three levels of mulch amendment underlie the observed gradient in tree productivity, and plots that had been amended with a continuous layer of mulch 17 years earlier showed a positive PSF with trees up to 6 m tall, a closed canopy, and a developing humus layer. The average taxonomic and functional composition of the bacterial and fungal communities differed markedly betweenlow- and high-productivity plots. Trees in high-productivity plots recruited a specialized soil microbiome that was more efficient at nutrient mobilization and acquisition. These plots showed increases in carbon (C), calcium (Ca), nitrogen (N), potassium (K), and phosphorus (P) stocks and as well as bacterial and fungal biomass. The soil microbiome was dominated by taxa from the fungal genus Cortinarius and the bacterial family Chitinophagaceae, and a complex microbial network with higher connectivity and more keystone species supported tree productivity in reforested plots compared to unproductive plots. Discussion Therefore, mulching of plots resulted in a microbially mediated PSF that enhances mineral weathering and non-symbiotic N fixation, and in turn helps transform unproductive plots into productive plots to ensure rapid restoration of the forest ecosystem in a harsh boreal environment.
Collapse
Affiliation(s)
- Franck Stefani
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, Canada
- *Correspondence: Franck Stefani, ; David Paré,
| | - Julien Beguin
- Institut de recherche sur les forêts, Université du Québec en Abitibi-Témiscamingue, Rouyn-Noranda, QC, Canada
| | - David Paré
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, QC, Canada
- *Correspondence: Franck Stefani, ; David Paré,
| | - Marie-Josée Morency
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, QC, Canada
| | - Christine Martineau
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, QC, Canada
| | - J. André Fortin
- Université Laval, Faculté de foresterie, de géographie et de géomatique, Département des sciences du bois et de la forêt, Québec, QC, Canada
| | - Nelson Thiffault
- Natural Resources Canada, Canadian Forest Service, Canadian Wood Fibre Centre, Québec, QC, Canada
| | - Armand Séguin
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, QC, Canada
| |
Collapse
|
10
|
Benavides M, Bonnet S, Le Moigne FAC, Armin G, Inomura K, Hallstrøm S, Riemann L, Berman-Frank I, Poletti E, Garel M, Grosso O, Leblanc K, Guigue C, Tedetti M, Dupouy C. Sinking Trichodesmium fixes nitrogen in the dark ocean. THE ISME JOURNAL 2022; 16:2398-2405. [PMID: 35835942 PMCID: PMC9478103 DOI: 10.1038/s41396-022-01289-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/29/2022] [Accepted: 07/05/2022] [Indexed: 01/04/2023]
Abstract
The photosynthetic cyanobacterium Trichodesmium is widely distributed in the surface low latitude ocean where it contributes significantly to N2 fixation and primary productivity. Previous studies found nifH genes and intact Trichodesmium colonies in the sunlight-deprived meso- and bathypelagic layers of the ocean (200-4000 m depth). Yet, the ability of Trichodesmium to fix N2 in the dark ocean has not been explored. We performed 15N2 incubations in sediment traps at 170, 270 and 1000 m at two locations in the South Pacific. Sinking Trichodesmium colonies fixed N2 at similar rates than previously observed in the surface ocean (36-214 fmol N cell-1 d-1). This activity accounted for 40 ± 28% of the bulk N2 fixation rates measured in the traps, indicating that other diazotrophs were also active in the mesopelagic zone. Accordingly, cDNA nifH amplicon sequencing revealed that while Trichodesmium accounted for most of the expressed nifH genes in the traps, other diazotrophs such as Chlorobium and Deltaproteobacteria were also active. Laboratory experiments simulating mesopelagic conditions confirmed that increasing hydrostatic pressure and decreasing temperature reduced but did not completely inhibit N2 fixation in Trichodesmium. Finally, using a cell metabolism model we predict that Trichodesmium uses photosynthesis-derived stored carbon to sustain N2 fixation while sinking into the mesopelagic. We conclude that sinking Trichodesmium provides ammonium, dissolved organic matter and biomass to mesopelagic prokaryotes.
Collapse
Affiliation(s)
- Mar Benavides
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France.
- Turing Center for Living Systems, Aix-Marseille University, 13009, Marseille, France.
| | - Sophie Bonnet
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France
| | - Frédéric A C Le Moigne
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France
- LEMAR, Laboratoire des Sciences de l'Environnement Marin, UMR6539, CNRS, UBO, IFREMER, IRD, 29280, Plouzané, Technopôle Brest-Iroise, France
| | - Gabrielle Armin
- Graduate School of Oceanography, University of Rhode Island, South Kingstown, RI, USA
| | - Keisuke Inomura
- Graduate School of Oceanography, University of Rhode Island, South Kingstown, RI, USA
| | - Søren Hallstrøm
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - Lasse Riemann
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - Ilana Berman-Frank
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Mt, Carmel, Haifa, Israel
| | - Emilie Poletti
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France
| | - Marc Garel
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France
| | - Olivier Grosso
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France
| | - Karine Leblanc
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France
| | - Catherine Guigue
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France
| | - Marc Tedetti
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France
| | - Cécile Dupouy
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France
| |
Collapse
|
11
|
Renaudin M, Laforest-Lapointe I, Bellenger JP. Unraveling global and diazotrophic bacteriomes of boreal forest floor feather mosses and their environmental drivers at the ecosystem and at the plant scale in North America. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 837:155761. [PMID: 35533858 DOI: 10.1016/j.scitotenv.2022.155761] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 04/29/2022] [Accepted: 05/03/2022] [Indexed: 06/14/2023]
Abstract
Feather mosses are abundant cryptogams of the boreal forest floor and shelter a broad diversity of bacteria who have important ecological functions (e.g., decomposition, nutrient cycling). In particular, nitrogen (N2-) fixation performed by feather moss-associated diazotrophs constitutes an important entry of nitrogen in the boreal forest ecosystem. However, the composition of the feather moss bacteriome and its environmental drivers are still unclear. Using cDNA amplicon sequencing of the 16S rRNA and nifH genes and cyanobacterial biomass quantification, we explored the active global and diazotrophic bacterial communities of two dominant feather moss species (i) at the ecosystem scale, along a 500-km climatic and nutrient deposition gradient in the North American boreal forest, and (ii) at the plant scale, along the moss shoot senescence gradient. We found that cyanobacteria were major actors of the feather moss bacteriome, accounting for 33% of global bacterial communities and 65% of diazotrophic communities, and that several cyanobacterial and methanotrophic genera were contributing to N2-fixation. Moreover, we showed that bacteria were occupying ecological niches along the moss shoot, with phototrophs being dominant in the apical part and methanotrophs being dominant in the basal part. Finally, climate (temperature, precipitation), environmental variables (moss species, month, tree density) and nutrients (nitrogen, phosphorus, molybdenum, vanadium, iron) strongly shaped global and diazotrophic bacteriomes. In summary, this work presents evidence that the feather moss bacteriome plays crucial roles in supporting moss growth, health, and decomposition, as well as in the boreal forest carbon and nitrogen cycles. This study also highlights the substantial effects of climate and nutrients on the feather moss bacteriome, suggesting the importance of understanding the impacts of global change on moss-associated bacterial growth and activity.
Collapse
Affiliation(s)
- Marie Renaudin
- Centre Sève, Département de Chimie, Université de Sherbrooke, J1K 2R1 Sherbrooke, QC, Canada.
| | | | - Jean-Philippe Bellenger
- Centre Sève, Département de Chimie, Université de Sherbrooke, J1K 2R1 Sherbrooke, QC, Canada.
| |
Collapse
|
12
|
Pi HW, Lin JJ, Chen CA, Wang PH, Chiang YR, Huang CC, Young CC, Li WH. Origin and evolution of nitrogen fixation in prokaryotes. Mol Biol Evol 2022; 39:6673025. [PMID: 35993177 PMCID: PMC9447857 DOI: 10.1093/molbev/msac181] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
The origin of nitrogen fixation is an important issue in evolutionary biology. While nitrogen is required by all living organisms, only a small fraction of bacteria and archaea can fix nitrogen. The prevailing view is that nitrogen fixation first evolved in archaea and was later transferred to bacteria. However, nitrogen-fixing (Nif) bacteria are far larger in number and far more diverse in ecological niches than Nif archaea. We, therefore, propose the bacteria-first hypothesis, which postulates that nitrogen fixation first evolved in bacteria and was later transferred to archaea. As >30,000 prokaryotic genomes have been sequenced, we conduct an in-depth comparison of the two hypotheses. We first identify the six genes involved in nitrogen fixation in all sequenced prokaryotic genomes and then reconstruct phylogenetic trees using the six Nif proteins individually or in combination. In each of these trees, the earliest lineages are bacterial Nif protein sequences and in the oldest clade (group) the archaeal sequences are all nested inside bacterial sequences, suggesting that the Nif proteins first evolved in bacteria. The bacteria-first hypothesis is further supported by the observation that the majority of Nif archaea carry the major bacterial Mo (molybdenum) transporter (ModABC) rather than the archaeal Mo transporter (WtpABC). Moreover, in our phylogeny of all available ModA and WtpA protein sequences, the earliest lineages are bacterial sequences while archaeal sequences are nested inside bacterial sequences. Furthermore, the bacteria-first hypothesis is supported by available isotopic data. In conclusion, our study strongly supports the bacteria-first hypothesis.
Collapse
Affiliation(s)
- Hong Wei Pi
- Ph.D. Program in Microbial Genomics, National Chung Hsing University and Academia Sinica, Taiwan.,Biodiversity Research Center, Academia Sinica, Taipei, Taiwan 11529
| | - Jinn Jy Lin
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan 11529
| | - Chi An Chen
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan 11529.,Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei 10617, Taiwan
| | - Po Hsiang Wang
- Graduate Institute of Environmental Engineering, National Central University, Taoyuan, Taiwan 32001.,Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan 145-0061
| | - Yin Ru Chiang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan 11529
| | - Chieh Chen Huang
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan 402
| | - Chiu Chung Young
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan 402
| | - Wen Hsiung Li
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan 11529.,Department of Ecology and Evolution, University of Chicago, Chicago 60637, USA
| |
Collapse
|
13
|
Rui J, Hu J, Wang F, Zhao Y, Li C. Altitudinal niches of symbiotic, associative and free-living diazotrophs driven by soil moisture and temperature in the alpine meadow on the Tibetan Plateau. ENVIRONMENTAL RESEARCH 2022; 211:113033. [PMID: 35276191 DOI: 10.1016/j.envres.2022.113033] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 02/22/2022] [Accepted: 02/24/2022] [Indexed: 06/14/2023]
Abstract
Legume-associated symbiotic diazotrophs contribute more to nitrogen (N) fixation than non-symbiotic diazotrophs in many terrestrial ecosystems. However, the percentage of legume biomass is low in alpine meadows on the Tibetan Plateau. Therefore, non-symbiotic diazotrophs may play important roles in N fixation in alpine meadow soils. Moreover, Tibetan alpine meadows are fragile and sensitive to global climate change, and the investigating of the key factor driving soil diazotrophic community still entails several challenges. To address these issues, we investigated diazotrophic spatial distribution and diversity along the elevational gradient between 3200 and 4200 m in the alpine meadow using amplicon sequencing of nifH gene. The result clearly showed that soil moisture and temperature were key factors driving soil diazotrophic community structures. Both altitude and soil depth significantly differentiated diazotrophic community composition. Alpha diversity indices of diazotrophic communities showed unimodal distribution along elevation gradient, strongly affected by soil moisture. Altitudinal niches were occupied by different diazotrophs. Soils at lower elevations were dominated by symbiotic diazotrophs and associative diazotrophs related to high biomass of plant hosts, while those at higher elevations were dominated by free-living psychrophiles such as Polaromonas. Furthermore, high moisture stimulated free-living anaerobes at middle elevations, such as Geobacter and Anaeromyxobacter, while suppressed legumes and symbiotic Mezorhizobium. Soil temperature not only directly affected temperature-sensitive diazotrophs, but also indirectly affected them through plants and soil properties such as pH and ammonium content. Our results suggest that climate change may strongly affect biological nitrogen fixation (BNF), and free-living diazotrophs may play important roles in BNF of alpine meadow system on the Tibetan Plateau.
Collapse
Affiliation(s)
- Junpeng Rui
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, 730000, China; Center for Grassland Microbiome, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730000, China.
| | - Jingjing Hu
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Fuxin Wang
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Yuwei Zhao
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Chao Li
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| |
Collapse
|
14
|
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.
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
|
15
|
Alcamán-Arias ME, Cifuentes-Anticevic J, Castillo-Inaipil W, Farías L, Sanhueza C, Fernández-Gómez B, Verdugo J, Abarzua L, Ridley C, Tamayo-Leiva J, Díez B. Dark Diazotrophy during the Late Summer in Surface Waters of Chile Bay, West Antarctic Peninsula. Microorganisms 2022; 10:microorganisms10061140. [PMID: 35744658 PMCID: PMC9227844 DOI: 10.3390/microorganisms10061140] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 05/28/2022] [Accepted: 05/29/2022] [Indexed: 11/16/2022] Open
Abstract
Although crucial for the addition of new nitrogen in marine ecosystems, dinitrogen (N2) fixation remains an understudied process, especially under dark conditions and in polar coastal areas, such as the West Antarctic Peninsula (WAP). New measurements of light and dark N2 fixation rates in parallel with carbon (C) fixation rates, as well as analysis of the genetic marker nifH for diazotrophic organisms, were conducted during the late summer in the coastal waters of Chile Bay, South Shetland Islands, WAP. During six late summers (February 2013 to 2019), Chile Bay was characterized by high NO3− concentrations (~20 µM) and an NH4+ content that remained stable near 0.5 µM. The N:P ratio was approximately 14.1, thus close to that of the Redfield ratio (16:1). The presence of Cluster I and Cluster III nifH gene sequences closely related to Alpha-, Delta- and, to a lesser extent, Gammaproteobacteria, suggests that chemosynthetic and heterotrophic bacteria are primarily responsible for N2 fixation in the bay. Photosynthetic carbon assimilation ranged from 51.18 to 1471 nmol C L−1 d−1, while dark chemosynthesis ranged from 9.24 to 805 nmol C L−1 d−1. N2 fixation rates were higher under dark conditions (up to 45.40 nmol N L−1 d−1) than under light conditions (up to 7.70 nmol N L−1 d−1), possibly contributing more than 37% to new nitrogen-based production (≥2.5 g N m−2 y−1). Of all the environmental factors measured, only PO43- exhibited a significant correlation with C and N2 rates, being negatively correlated (p < 0.05) with dark chemosynthesis and N2 fixation under the light condition, revealing the importance of the N:P ratio for these processes in Chile Bay. This significant contribution of N2 fixation expands the ubiquity and biological potential of these marine chemosynthetic diazotrophs. As such, this process should be considered along with the entire N cycle when further reviewing highly productive Antarctic coastal waters and the diazotrophic potential of the global marine ecosystem.
Collapse
Affiliation(s)
- María E. Alcamán-Arias
- Departamento de Oceanografía, Universidad de Concepción, Concepción 4030000, Chile; (M.E.A.-A.); (L.F.); (L.A.)
- Center for Climate and Resilience Research (CR)2, Universidad de Chile, Blanco Encalada 2002, Santiago 8320000, Chile; (C.R.); (J.T.-L.)
- Escuela de Medicina, Universidad Espíritu Santo, Guayaquil 0901952, Ecuador
| | - Jerónimo Cifuentes-Anticevic
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile; (J.C.-A.); (W.C.-I.); (C.S.); (B.F.-G.)
| | - Wilson Castillo-Inaipil
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile; (J.C.-A.); (W.C.-I.); (C.S.); (B.F.-G.)
| | - Laura Farías
- Departamento de Oceanografía, Universidad de Concepción, Concepción 4030000, Chile; (M.E.A.-A.); (L.F.); (L.A.)
- Center for Climate and Resilience Research (CR)2, Universidad de Chile, Blanco Encalada 2002, Santiago 8320000, Chile; (C.R.); (J.T.-L.)
| | - Cynthia Sanhueza
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile; (J.C.-A.); (W.C.-I.); (C.S.); (B.F.-G.)
| | - Beatriz Fernández-Gómez
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile; (J.C.-A.); (W.C.-I.); (C.S.); (B.F.-G.)
- Instituto de Oceanografía y Cambio Global (IOCAG), Universidad de Las Palmas de Gran Canaria (ULPGC), 35001 Las Palmas, Spain
| | - Josefa Verdugo
- Alfred-Wegener-Institute, Helmholtz Centre for Polar and Marine Research, 27570 Bremerhaven, Germany;
| | - Leslie Abarzua
- Departamento de Oceanografía, Universidad de Concepción, Concepción 4030000, Chile; (M.E.A.-A.); (L.F.); (L.A.)
| | - Christina Ridley
- Center for Climate and Resilience Research (CR)2, Universidad de Chile, Blanco Encalada 2002, Santiago 8320000, Chile; (C.R.); (J.T.-L.)
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile; (J.C.-A.); (W.C.-I.); (C.S.); (B.F.-G.)
| | - Javier Tamayo-Leiva
- Center for Climate and Resilience Research (CR)2, Universidad de Chile, Blanco Encalada 2002, Santiago 8320000, Chile; (C.R.); (J.T.-L.)
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile; (J.C.-A.); (W.C.-I.); (C.S.); (B.F.-G.)
- Center for Genome Regulation (CRG), Universidad de Chile, Blanco Encalada 2085, Santiago 8320000, Chile
| | - Beatriz Díez
- Center for Climate and Resilience Research (CR)2, Universidad de Chile, Blanco Encalada 2002, Santiago 8320000, Chile; (C.R.); (J.T.-L.)
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile; (J.C.-A.); (W.C.-I.); (C.S.); (B.F.-G.)
- Center for Genome Regulation (CRG), Universidad de Chile, Blanco Encalada 2085, Santiago 8320000, Chile
- Correspondence:
| |
Collapse
|
16
|
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.
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
|
17
|
Unraveling the Tropaeolum majus L. (Nasturtium) Root-Associated Bacterial Community in Search of Potential Biofertilizers. Microorganisms 2022; 10:microorganisms10030638. [PMID: 35336212 PMCID: PMC8950702 DOI: 10.3390/microorganisms10030638] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 03/14/2022] [Accepted: 03/15/2022] [Indexed: 01/27/2023] Open
Abstract
Although Tropaeolum majus (nasturtium) is an agriculturally and economically important plant, especially due to the presence of edible flowers and its medicinal properties, its microbiome is quite unexplored. Here, the structure of the total bacterial community associated with the rhizosphere, endosphere and bulk soil of T. majus was determined by 16S rRNA amplicon metagenomic sequencing. A decrease in diversity and richness from bulk soil to the rhizosphere and from the rhizosphere to the endosphere was observed in the alpha diversity analyses. The phylum Proteobacteria was the most dominant in the bacteriome of the three sites evaluated, whereas the genera Pseudomonas and Ralstonia showed a significantly higher relative abundance in the rhizosphere and endosphere communities, respectively. Plant growth-promoting bacteria (236 PGPB) were also isolated from the T. majus endosphere, and 76 strains belonging to 11 different genera, mostly Serratia, Raoultella and Klebsiella, showed positive results for at least four out of six plant growth-promoting tests performed. The selection of PGPB associated with T. majus can result in the development of a biofertilizer with activity against phytopathogens and capable of favoring the development of this important plant.
Collapse
|
18
|
Djemiel C, Maron PA, Terrat S, Dequiedt S, Cottin A, Ranjard L. Inferring microbiota functions from taxonomic genes: a review. Gigascience 2022; 11:giab090. [PMID: 35022702 PMCID: PMC8756179 DOI: 10.1093/gigascience/giab090] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 12/02/2021] [Accepted: 12/02/2021] [Indexed: 12/13/2022] Open
Abstract
Deciphering microbiota functions is crucial to predict ecosystem sustainability in response to global change. High-throughput sequencing at the individual or community level has revolutionized our understanding of microbial ecology, leading to the big data era and improving our ability to link microbial diversity with microbial functions. Recent advances in bioinformatics have been key for developing functional prediction tools based on DNA metabarcoding data and using taxonomic gene information. This cheaper approach in every aspect serves as an alternative to shotgun sequencing. Although these tools are increasingly used by ecologists, an objective evaluation of their modularity, portability, and robustness is lacking. Here, we reviewed 100 scientific papers on functional inference and ecological trait assignment to rank the advantages, specificities, and drawbacks of these tools, using a scientific benchmarking. To date, inference tools have been mainly devoted to bacterial functions, and ecological trait assignment tools, to fungal functions. A major limitation is the lack of reference genomes-compared with the human microbiota-especially for complex ecosystems such as soils. Finally, we explore applied research prospects. These tools are promising and already provide relevant information on ecosystem functioning, but standardized indicators and corresponding repositories are still lacking that would enable them to be used for operational diagnosis.
Collapse
Affiliation(s)
- Christophe Djemiel
- Agroécologie, AgroSup Dijon, INRAE, Université de Bourgogne, Université de Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Pierre-Alain Maron
- Agroécologie, AgroSup Dijon, INRAE, Université de Bourgogne, Université de Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Sébastien Terrat
- Agroécologie, AgroSup Dijon, INRAE, Université de Bourgogne, Université de Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Samuel Dequiedt
- Agroécologie, AgroSup Dijon, INRAE, Université de Bourgogne, Université de Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Aurélien Cottin
- Agroécologie, AgroSup Dijon, INRAE, Université de Bourgogne, Université de Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Lionel Ranjard
- Agroécologie, AgroSup Dijon, INRAE, Université de Bourgogne, Université de Bourgogne Franche-Comté, F-21000 Dijon, France
| |
Collapse
|
19
|
Mise K, Masuda Y, Senoo K, Itoh H. Undervalued Pseudo- nifH Sequences in Public Databases Distort Metagenomic Insights into Biological Nitrogen Fixers. mSphere 2021; 6:e0078521. [PMID: 34787447 PMCID: PMC8597730 DOI: 10.1128/msphere.00785-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 11/03/2021] [Indexed: 12/16/2022] Open
Abstract
Nitrogen fixation, a distinct process incorporating the inactive atmospheric nitrogen into the active biological processes, has been a major topic in biological and geochemical studies. Currently, insights into diversity and distribution of nitrogen-fixing microbes are dependent upon homology-based analyses of nitrogenase genes, especially the nifH gene, which are broadly conserved in nitrogen-fixing microbes. Here, we report the pitfall of using nifH as a marker of microbial nitrogen fixation. We exhaustively analyzed genomes in RefSeq (231,908 genomes) and KEGG (6,509 genomes) and cooccurrence and gene order patterns of nitrogenase genes (including nifH) therein. Up to 20% of nifH-harboring genomes lacked nifD and nifK, which encode essential subunits of nitrogenase, within 10 coding sequences upstream or downstream of nifH or on the same genome. According to a phenotypic database of prokaryotes, no species and strains harboring only nifH possess nitrogen-fixing activities, which shows that these nifH genes are "pseudo"-nifH genes. Pseudo-nifH sequences mainly belong to anaerobic microbes, including members of the class Clostridia and methanogens. We also detected many pseudo-nifH reads from metagenomic sequences of anaerobic environments such as animal guts, wastewater, paddy soils, and sediments. In some samples, pseudo-nifH overwhelmed the number of "true" nifH reads by 50% or 10 times. Because of the high sequence similarity between pseudo- and true-nifH, pronounced amounts of nifH-like reads were not confidently classified. Overall, our results encourage reconsideration of the conventional use of nifH for detecting nitrogen-fixing microbes, while suggesting that nifD or nifK would be a more reliable marker. IMPORTANCE Nitrogen-fixing microbes affect biogeochemical cycling, agricultural productivity, and microbial ecosystems, and their distributions have been investigated intensively using genomic and metagenomic sequencing. Currently, insights into nitrogen fixers in the environment have been acquired by homology searches against nitrogenase genes, particularly the nifH gene, in public databases. Here, we report that public databases include a significant amount of incorrectly annotated nifH sequences (pseudo-nifH). We exhaustively investigated the genomic structures of nifH-harboring genomes and found hundreds of pseudo-nifH sequences in RefSeq and KEGG. Over half of these pseudo-nifH sequences belonged to members of the class Clostridia, which is supposed to be a prominent nitrogen-fixing clade. We also found that the abundance of nitrogen fixers in metagenomes could be overestimated by 1.5 to >10 times due to pseudo-nifH recorded in public databases. Our results encourage reconsideration of the prevalent use of nifH as a marker of nitrogen-fixing microbes.
Collapse
Affiliation(s)
- Kazumori Mise
- National Institute of Advanced Industrial Science and Technology (AIST) Hokkaido, Sapporo, Hokkaido, Japan
| | - Yoko Masuda
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Keishi Senoo
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan
| | - Hideomi Itoh
- National Institute of Advanced Industrial Science and Technology (AIST) Hokkaido, Sapporo, Hokkaido, Japan
| |
Collapse
|
20
|
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.
Collapse
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
| |
Collapse
|
21
|
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.
Collapse
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
| |
Collapse
|
22
|
Smercina DN, Evans SE, Friesen ML, Tiemann LK. Impacts of nitrogen addition on switchgrass root-associated diazotrophic community structure and function. FEMS Microbiol Ecol 2021; 96:5920613. [PMID: 33038234 DOI: 10.1093/femsec/fiaa208] [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: 06/22/2020] [Accepted: 10/08/2020] [Indexed: 02/02/2023] Open
Abstract
Cellulosic bioenergy crops, like switchgrass (Panicum virgatum), have potential for growth on lands unsuitable for food production coupled with potential for climate mitigation. Sustainability of these systems lies in identifying conditions that promote high biomass yields on marginal lands under low-input agricultural practices. Associative nitrogen fixation (ANF) is a potentially important nitrogen (N) source for these crops, yet ANF contributions to plant N, especially under fertilizer N addition are unclear. In this study, we assess structure (nifH) and function (ANF) of switchgrass root-associated diazotrophic communities to long-term and short-term N additions using soil from three marginal land sites. ANF rates were variable and often unexpectedly high, sometimes 10× greater than reported in the literature, and did not respond in repeatable ways to long-term or short-term N. We found few impacts of N addition on root-associated diazotrophic community structure or membership. Instead, we found a very consistent root-associated diazotrophic community even though switchgrass seeds were germinated in soil from field sites with distinct diazotrophic communities. Ultimately, this work demonstrates that root-associated diazotrophic communities have the potential to contribute to switchgrass N demands, independent of N addition, and this may be driven by selection of the diazotrophic community by switchgrass roots.
Collapse
Affiliation(s)
- Darian N Smercina
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA
| | - Sarah E Evans
- W.K. Kellogg Biological Station, Department of Integrative Biology, Michigan State University, Hickory Corners, MI 49060, USA
| | - Maren L Friesen
- Department of Plant Pathology, Washington State University, Pullman, WA 99164, USA.,Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164, USA
| | - Lisa K Tiemann
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA
| |
Collapse
|
23
|
Kapili BJ, Dekas AE. PPIT: an R package for inferring microbial taxonomy from nifH sequences. Bioinformatics 2021; 37:2289-2298. [PMID: 33580675 DOI: 10.1093/bioinformatics/btab100] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 07/22/2020] [Accepted: 02/11/2021] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Linking microbial community members to their ecological functions is a central goal of environmental microbiology. When assigned taxonomy, amplicon sequences of metabolic marker genes can suggest such links, thereby offering an overview of the phylogenetic structure underpinning particular ecosystem functions. However, inferring microbial taxonomy from metabolic marker gene sequences remains a challenge, particularly for the frequently sequenced nitrogen fixation marker gene, nitrogenase reductase (nifH). Horizontal gene transfer in recent nifH evolutionary history can confound taxonomic inferences drawn from the pairwise identity methods used in existing software. Other methods for inferring taxonomy are not standardized and require manual inspection that is difficult to scale. RESULTS We present Phylogenetic Placement for Inferring Taxonomy (PPIT), an R package that infers microbial taxonomy from nifH amplicons using both phylogenetic and sequence identity approaches. After users place query sequences on a reference nifH gene tree provided by PPIT (n = 6317 full-length nifH sequences), PPIT searches the phylogenetic neighborhood of each query sequence and attempts to infer microbial taxonomy. An inference is drawn only if references in the phylogenetic neighborhood are: (1) taxonomically consistent and (2) share sufficient pairwise identity with the query, thereby avoiding erroneous inferences due to known horizontal gene transfer events. We find that PPIT returns a higher proportion of correct taxonomic inferences than BLAST-based approaches at the cost of fewer total inferences. We demonstrate PPIT on deep-sea sediment and find that Deltaproteobacteria are the most abundant potential diazotrophs. Using this dataset we show that emending PPIT inferences based on visual inspection of query sequence placement can achieve taxonomic inferences for nearly all sequences in a query set. We additionally discuss how users can apply PPIT to the analysis of other marker genes. AVAILABILITY PPIT is freely available to non-commercial users at https://github.com/bkapili/ppit. Installation includes a vignette that demonstrates package use and reproduces the nifH amplicon analysis discussed here. The raw nifH amplicon sequence data have been deposited in the GenBank, EMBL, and DDBJ databases under BioProject number PRJEB37167. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Bennett J Kapili
- Department of Earth System Science, Stanford University, Stanford, CA, 94305, USA
| | - Anne E Dekas
- Department of Earth System Science, Stanford University, Stanford, CA, 94305, USA
| |
Collapse
|
24
|
Coyne KJ, Parker AE, Lee CK, Sohm JA, Kalmbach A, Gunderson T, León-Zayas R, Capone DG, Carpenter EJ, Cary SC. The distribution and relative ecological roles of autotrophic and heterotrophic diazotrophs in the McMurdo Dry Valleys, Antarctica. FEMS Microbiol Ecol 2020; 96:5714082. [PMID: 31967635 PMCID: PMC7043275 DOI: 10.1093/femsec/fiaa010] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Accepted: 01/21/2020] [Indexed: 12/13/2022] Open
Abstract
The McMurdo Dry Valleys (MDV) in Antarctica harbor a diverse assemblage of mat-forming diazotrophic cyanobacteria that play a key role in nitrogen cycling. Prior research showed that heterotrophic diazotrophs also make a substantial contribution to nitrogen fixation in MDV. The goals of this study were to survey autotrophic and heterotrophic diazotrophs across the MDV to investigate factors that regulate the distribution and relative ecological roles of each group. Results indicated that diazotrophs were present only in samples with mats, suggesting a metabolic coupling between autotrophic and heterotrophic diazotrophs. Analysis of 16S rRNA and nifH gene sequences also showed that diazotrophs were significantly correlated to the broader bacterial community, while co-occurrence network analysis revealed potential interspecific interactions. Consistent with previous studies, heterotrophic diazotrophs in MDV were diverse, but largely limited to lakes and their outlet streams, or other environments protected from desiccation. Despite the limited distribution, heterotrophic diazotrophs may make a substantial contribution to the nitrogen budget of MDV due to larger surface area and longer residence times of lakes. This work contributes to our understanding of key drivers of bacterial community structure in polar deserts and informs future efforts to investigate the contribution of nitrogen fixation to MDV ecosystems.
Collapse
Affiliation(s)
- Kathryn J Coyne
- College of Earth, Ocean, and Environment, University of Delaware, Lewes, DE 19958, USA
| | - Alexander E Parker
- Estuary and Ocean Science Center, San Francisco State University, Tiburon, CA 94920, USA
| | - Charles K Lee
- International Centre for Terrestrial Antarctic Research, School of Science, University of Waikato, Hamilton 3240, New Zealand
| | - Jill A Sohm
- Wrigley Institute for Environmental Studies and Department of Biological Sciences, University of Southern California, Los Angeles, CA 9008-037, USA
| | - Andrew Kalmbach
- Estuary and Ocean Science Center, San Francisco State University, Tiburon, CA 94920, USA
| | - Troy Gunderson
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 9008-037, USA
| | - Rosa León-Zayas
- Willamette University, Biology Department, Salem, OR 97301, USA
| | - Douglas G Capone
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 9008-037, USA
| | - Edward J Carpenter
- Estuary and Ocean Science Center, San Francisco State University, Tiburon, CA 94920, USA
| | - S Craig Cary
- College of Earth, Ocean, and Environment, University of Delaware, Lewes, DE 19958, USA.,International Centre for Terrestrial Antarctic Research, School of Science, University of Waikato, Hamilton 3240, New Zealand
| |
Collapse
|
25
|
Raggi L, García-Guevara F, Godoy-Lozano EE, Martínez-Santana A, Escobar-Zepeda A, Gutierrez-Rios RM, Loza A, Merino E, Sanchez-Flores A, Licea-Navarro A, Pardo-Lopez L, Segovia L, Juarez K. Metagenomic Profiling and Microbial Metabolic Potential of Perdido Fold Belt (NW) and Campeche Knolls (SE) in the Gulf of Mexico. Front Microbiol 2020; 11:1825. [PMID: 32903729 PMCID: PMC7438803 DOI: 10.3389/fmicb.2020.01825] [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: 05/14/2020] [Accepted: 07/10/2020] [Indexed: 01/04/2023] Open
Abstract
The Gulf of Mexico (GoM) is a particular environment that is continuously exposed to hydrocarbon compounds that may influence the microbial community composition. We carried out a metagenomic assessment of the bacterial community to get an overall view of this geographical zone. We analyzed both taxonomic and metabolic markers profiles to explain how the indigenous GoM microorganims participate in the biogeochemical cycling. Two geographically distant regions in the GoM, one in the north-west (NW) and one in the south-east (SE) of the GoM were analyzed and showed differences in their microbial composition and metabolic potential. These differences provide evidence the delicate equilibrium that sustains microbial communities and biogeochemical cycles. Based on the taxonomy and gene groups, the NW are more oxic sediments than SE ones, which have anaerobic conditions. Both water and sediments show the expected sulfur, nitrogen, and hydrocarbon metabolism genes, with particularly high diversity of the hydrocarbon-degrading ones. Accordingly, many of the assigned genera were associated with hydrocarbon degradation processes, Nitrospira and Sva0081 were the most abundant in sediments, while Vibrio, Alteromonas, and Alcanivorax were mostly detected in water samples. This basal-state analysis presents the GoM as a potential source of aerobic and anaerobic hydrocarbon degradation genes important for the ecological dynamics of hydrocarbons and the potential use for water and sediment bioremediation processes.
Collapse
Affiliation(s)
- Luciana Raggi
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico.,CONACYT-Laboratorio de Biotecnología Acuícola, Instituto de Investigaciones Agropecuarias y Forestales, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mexico
| | | | - E Ernestina Godoy-Lozano
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico.,Centro de Investigación Sobre Enfermedades Infecciosas, Departamento de Bioinformática en Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Mexico
| | | | | | | | - Antonio Loza
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Enrique Merino
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | | | - Alexei Licea-Navarro
- Laboratorio de Inmunología Molecular y Biotoxinas, Departamento de Innovación Biomedica, CICESE, Ensenada, Mexico
| | - Liliana Pardo-Lopez
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Lorenzo Segovia
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Katy Juarez
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| |
Collapse
|
26
|
Poret-Peterson AT, Sayed N, Glyzewski N, Forbes H, González-Orta ET, Kluepfel DA. Temporal Responses of Microbial Communities to Anaerobic Soil Disinfestation. MICROBIAL ECOLOGY 2020; 80:191-201. [PMID: 31873773 PMCID: PMC7338823 DOI: 10.1007/s00248-019-01477-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 12/16/2019] [Indexed: 06/10/2023]
Abstract
Anaerobic soil disinfestation (ASD) is an organic amendment-based management tool for controlling soil-borne plant diseases and is increasingly used in a variety of crops. ASD results in a marked decrease in soil redox potential and other physicochemical changes, and a turnover in the composition of the soil microbiome. Mechanisms of ASD-mediated pathogen control are not fully understood, but appear to depend on the carbon source used to initiate the process and involve a combination of biological (i.e., release of volatile organic compounds) and abiotic (i.e., lowered pH, release of metal ions) factors. In this study, we examined how the soil microbiome changes over time in response to ASD initiated with rice bran, tomato pomace, or red grape pomace as amendments using growth chamber mesocosms that replicate ASD-induced field soil redox conditions. Within 2 days, the soil microbiome rapidly shifted from a diverse assemblage of taxa to being dominated by members of the Firmicutes for all ASD treatments, whereas control mesocosms maintained diverse and more evenly distributed communities. Rice bran and tomato pomace amendments resulted in microbial communities with similar compositions and trajectories that were different from red grape pomace communities. Quantitative PCR showed nitrogenase gene abundances were higher in ASD communities and tended to increase over time, suggesting the potential for altering soil nitrogen availability. These results highlight the need for temporal and functional studies to understand how pathogen suppressive microbial communities assemble and function in ASD-treated soils.
Collapse
Affiliation(s)
| | - Nada Sayed
- USDA-ARS Crops Pathology and Genetics Research Unit, University of California, Davis, USA
- University of California Davis Medical Center, Sacramento, CA, USA
| | - Nathaniel Glyzewski
- USDA-ARS Crops Pathology and Genetics Research Unit, University of California, Davis, USA
- Green Leaf Lab, Sacramento, CA, USA
| | - Holly Forbes
- USDA-ARS Crops Pathology and Genetics Research Unit, University of California, Davis, USA
| | - Enid T González-Orta
- Department of Biological Sciences, California State University, Sacramento, CA, USA
| | - Daniel A Kluepfel
- USDA-ARS Crops Pathology and Genetics Research Unit, University of California, Davis, USA
| |
Collapse
|
27
|
Pankievicz VCS, Irving TB, Maia LGS, Ané JM. Are we there yet? The long walk towards the development of efficient symbiotic associations between nitrogen-fixing bacteria and non-leguminous crops. BMC Biol 2019; 17:99. [PMID: 31796086 PMCID: PMC6889567 DOI: 10.1186/s12915-019-0710-0] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 10/18/2019] [Indexed: 01/09/2023] Open
Abstract
Nitrogen is an essential element of life, and nitrogen availability often limits crop yields. Since the Green Revolution, massive amounts of synthetic nitrogen fertilizers have been produced from atmospheric nitrogen and natural gas, threatening the sustainability of global food production and degrading the environment. There is a need for alternative means of bringing nitrogen to crops, and taking greater advantage of biological nitrogen fixation seems a logical option. Legumes are used in most cropping systems around the world because of the nitrogen-fixing symbiosis with rhizobia. However, the world's three major cereal crops-rice, wheat, and maize-do not associate with rhizobia. In this review, we will survey how genetic approaches in rhizobia and their legume hosts allowed tremendous progress in understanding the molecular mechanisms controlling root nodule symbioses, and how this knowledge paves the way for engineering such associations in non-legume crops. We will also discuss challenges in bringing these systems into the field and how they can be surmounted by interdisciplinary collaborations between synthetic biologists, microbiologists, plant biologists, breeders, agronomists, and policymakers.
Collapse
Affiliation(s)
| | - Thomas B Irving
- Department of Bacteriology, University of Wisconsin, Madison, WI, USA
| | - Lucas G S Maia
- Department of Bacteriology, University of Wisconsin, Madison, WI, USA
| | - Jean-Michel Ané
- Department of Agronomy, University of Wisconsin, Madison, WI, USA.
- Department of Bacteriology, University of Wisconsin, Madison, WI, USA.
| |
Collapse
|
28
|
Gupta VVSR, Zhang B, Penton CR, Yu J, Tiedje JM. Diazotroph Diversity and Nitrogen Fixation in Summer Active Perennial Grasses in a Mediterranean Region Agricultural Soil. Front Mol Biosci 2019; 6:115. [PMID: 31750314 PMCID: PMC6848460 DOI: 10.3389/fmolb.2019.00115] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 10/11/2019] [Indexed: 12/16/2022] Open
Abstract
Summer-growing perennial grasses such as Panicum coloratum L. cv. Bambatsi (Bambatsi panic), Chloris gayana Kunth cv. Katambora (Rhodes grass) and Digitaria eriantha Steud. cv. Premier (Premier digit grass) growing in the poor fertility sandy soils in the Mediterranean regions of southern Australia and western Australia mainly depend upon soil N and biological N inputs through diazotrophic (free living or associative) N fixation. We investigated the community composition and diversity (nifH-amplicon sequencing), abundance (qPCR) and functional capacity (15N incubation assay) of the endophytic diazotrophic community in the below and above ground plant parts of field grown and unfertilized grasses. Results showed a diverse and abundant diazotrophic community inside plant both above and below-ground and there was a distinct diazotrophic assemblage in the different plant parts in all the three grasses. There was a limited difference in the diversity between leaves, stems and roots except that Panicum grass roots harbored greater species richness. Nitrogen fixation potentials ranged between 0.24 and 5.9 mg N kg-1 day-1 and N fixation capacity was found in both the above and below ground plant parts. Results confirmed previous reports of plant species-based variation and that Alpha-Proteobacteria were the dominant group of nifH-harboring taxa both in the belowground and aboveground parts of the three grass species. Results also showed a well-structured nifH-harboring community in all plant parts, an example for a functional endophytic community. Overall, the variation in the number and identity of module hubs and connectors among the different plant parts suggests that co-occurrence patterns within the nifH-harboring community specific to individual compartments and local environments of the niches within each plant part may dictate the overall composition of diazotrophs within a plant.
Collapse
Affiliation(s)
| | - Bangzhou Zhang
- Institute for Microbial Ecology, School of Medicine, Xiamen University, Xiamen, China
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, United States
| | - Christopher Ryan Penton
- College of Integrative Sciences and Arts, Arizona State University, Mesa, AZ, United States
- Center for Fundamental and Applied Microbiomics, Biodesign Institute, Arizona State University, Tempe, AZ, United States
| | - Julian Yu
- College of Integrative Sciences and Arts, Arizona State University, Mesa, AZ, United States
- Center for Fundamental and Applied Microbiomics, Biodesign Institute, Arizona State University, Tempe, AZ, United States
| | - James M. Tiedje
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, United States
| |
Collapse
|
29
|
Lucaciu R, Pelikan C, Gerner SM, Zioutis C, Köstlbacher S, Marx H, Herbold CW, Schmidt H, Rattei T. A Bioinformatics Guide to Plant Microbiome Analysis. FRONTIERS IN PLANT SCIENCE 2019; 10:1313. [PMID: 31708944 PMCID: PMC6819368 DOI: 10.3389/fpls.2019.01313] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 09/20/2019] [Indexed: 05/18/2023]
Abstract
Recent evidence for intimate relationship of plants with their microbiota shows that plants host individual and diverse microbial communities that are essential for their survival. Understanding their relatedness using genome-based and high-throughput techniques remains a hot topic in microbiome research. Molecular analysis of the plant holobiont necessitates the application of specific sampling and preparatory steps that also consider sources of unwanted information, such as soil, co-amplified plant organelles, human DNA, and other contaminations. Here, we review state-of-the-art and present practical guidelines regarding experimental and computational aspects to be considered in molecular plant-microbiome studies. We discuss sequencing and "omics" techniques with a focus on the requirements needed to adapt these methods to individual research approaches. The choice of primers and sequence databases is of utmost importance for amplicon sequencing, while the assembly and binning of shotgun metagenomic sequences is crucial to obtain quality data. We discuss specific bioinformatic workflows to overcome the limitation of genome database resources and for covering large eukaryotic genomes such as fungi. In transcriptomics, it is necessary to account for the separation of host mRNA or dual-RNAseq data. Metaproteomics approaches provide a snapshot of the protein abundances within a plant tissue which requires the knowledge of complete and well-annotated plant genomes, as well as microbial genomes. Metabolomics offers a powerful tool to detect and quantify small molecules and molecular changes at the plant-bacteria interface if the necessary requirements with regard to (secondary) metabolite databases are considered. We highlight data integration and complementarity which should help to widen our understanding of the interactions among individual players of the plant holobiont in the future.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Hannes Schmidt
- Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Thomas Rattei
- Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| |
Collapse
|
30
|
Andreozzi A, Prieto P, Mercado-Blanco J, Monaco S, Zampieri E, Romano S, Valè G, Defez R, Bianco C. Efficient colonization of the endophytes Herbaspirillum huttiense RCA24 and Enterobacter cloacae RCA25 influences the physiological parameters of Oryza sativa L. cv. Baldo rice. Environ Microbiol 2019; 21:3489-3504. [PMID: 31106946 DOI: 10.1111/1462-2920.14688] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 05/15/2019] [Accepted: 05/17/2019] [Indexed: 11/26/2022]
Abstract
Several important bacterial characteristics, such as biological nitrogen fixation, phosphate solubilization, 1-aminocyclopropane-1-carboxylate deaminase activity and production of siderophores and phytohormones, can be assessed as plant growth promotion traits. Our aim was to evaluate the effects of nitrogen fixing and indole-3-acetic acid (IAA) producing endophytes in two Oryza sativa cultivars (Baldo and Vialone Nano). Three bacteria, Herbaspirillum huttiense RCA24, Enterobacter asburiae RCA23 and Staphylococcus sp. 377, producing different IAA levels, were tested for their ability to enhance nifH gene expression and nitrogenase activity in Enterobacter cloacae RCA25. Results showed that H. huttiense RCA24 performed best. Improvement in nitrogen fixation and changes in physiological parameters such as chlorophyll, nitrogen content and shoot dry weight were observed for plants co-inoculated with strains RCA25 and RCA24 in a 10:1 ratio. Based on confocal laser scanning microscopy analysis, strain RCA24 was the best colonizer of the root interior and the only IAA producer located in the same root niche occupied by RCA25 cells. This work shows that the choice of a bio-inoculum having the right composition is one of the key aspects to be considered for the inoculation of a specific host plant cultivar with microbial consortia.
Collapse
Affiliation(s)
- Anna Andreozzi
- Institute of Biosciences and BioResources, via P. Castellino 111, 80131 Naples, Italy
| | - Pilar Prieto
- Departamento de Mejora Genética, Instituto de Agricultura Sostenible (IAS), Consejo Superior de Investigaciones Científicas (CSIC), Campus 'Alameda del Obispo', Avd. Menéndez Pidal s/n, 14004 Córdoba, Spain
| | - Jesús Mercado-Blanco
- Departamento de Protección de Cultivos, Instituto de Agricultura Sostenible (IAS), Consejo Superior de Investigaciones Científicas (CSIC), Campus 'Alameda del Obispo', Avd. Menéndez Pidal s/n, 14004 Córdoba, Spain
| | - Stefano Monaco
- CREA - CI, Research Centre for Cereal and Industrial Crops, 13100, Vercelli, Italy
| | - Elisa Zampieri
- CREA - CI, Research Centre for Cereal and Industrial Crops, 13100, Vercelli, Italy
| | - Silvia Romano
- Institute of Biosciences and BioResources, via P. Castellino 111, 80131 Naples, Italy
| | - Gianpiero Valè
- DiSIT, Dipartimento di Scienze e Innovazione Tecnologica, Università del Piemonte Orientale, Piazza San Eusebio 5, I-13100 Vercelli, Italy
| | - Roberto Defez
- Institute of Biosciences and BioResources, via P. Castellino 111, 80131 Naples, Italy
| | - Carmen Bianco
- Institute of Biosciences and BioResources, via P. Castellino 111, 80131 Naples, Italy
| |
Collapse
|
31
|
A Nodulation-Proficient Nonrhizobial Inhabitant of Pueraria phaseoloides. ScientificWorldJournal 2019; 2019:9782684. [PMID: 31057340 PMCID: PMC6463565 DOI: 10.1155/2019/9782684] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 01/30/2019] [Accepted: 02/19/2019] [Indexed: 11/17/2022] Open
Abstract
Pueraria phaseoloides is a legume cover crop, found chiefly in the wet zone of Sri Lanka. Nitrogen fixation is performed by nodular inhabitants of this cover crop, comparable to the nodule-dwelling bacteria of most other legume plants. We isolated a bacterium (Sub1) from Pueraria phaseoloides, of coccobacillus cell shape, that showed nodulation, when assessed by hydroponics, showing nodules as early as 3 weeks after reinfection. When a nifH fragment from the genome of this bacterium was amplified using a pair of nifH primers, it yielded an amplicon of 360 bp that, when sequenced, helped us identify the bacterium, as belonging to a species of Pseudacidovorax intermedius, at 99% sequence identity. When we constructed a phylogenetic tree with neighboring sequences, we encountered nifH sequences of Pseudacidovorax, forming a monophyletic cluster, which too contained a single Azospirillum species. The genus Pseudacidovorax is a bacterium that, so far, has not been associated with legume nodules. Sub1 secreted a pair of enzymes to the extracellular medium to degrade cellulose and milk proteins. The Sub1 bacterium showed biofilm formation and secreted into the extracellular medium, indole acetic acid. Sub1 also showed a "bulls eye" swarming pattern for the chemoattractant proline, while showing no significant chemotaxis movement, for naringenin, quercetin, and glutamate. Sub1 too possesses the basic genetic foundation (nifH and nifD) to produce a molybdenum-dependent nitrogenase enzyme. We finally show that this rare nonrhizobial bacterium is able to impact, positively, nodulation and shoot length of Pueraria plants, demonstrating that this beta-proteobacterium can abet the biological vigor of this legume cover crop.
Collapse
|