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Mahmood S, Fahad Z, Bolou-Bi EB, King K, Köhler SJ, Bishop K, Ekblad A, Finlay RD. Ectomycorrhizal fungi integrate nitrogen mobilisation and mineral weathering in boreal forest soil. THE NEW PHYTOLOGIST 2024; 242:1545-1560. [PMID: 37697631 DOI: 10.1111/nph.19260] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 08/24/2023] [Indexed: 09/13/2023]
Abstract
Tree growth in boreal forests is driven by ectomycorrhizal fungal mobilisation of organic nitrogen and mineral nutrients in soils with discrete organic and mineral horizons. However, there are no studies of how ectomycorrhizal mineral weathering and organic nitrogen mobilisation processes are integrated across the soil profile. We studied effects of organic matter (OM) availability on ectomycorrhizal functioning by altering the proportions of natural organic and mineral soil in reconstructed podzol profiles containing Pinus sylvestris plants, using 13CO2 pulse labelling, patterns of naturally occurring stable isotopes (26Mg and 15N) and high-throughput DNA sequencing of fungal amplicons. Reduction in OM resulted in nitrogen limitation of plant growth and decreased allocation of photosynthetically derived carbon and mycelial growth in mineral horizons. Fractionation patterns of 26Mg indicated that magnesium mobilisation and uptake occurred primarily in the deeper mineral horizon and was driven by carbon allocation to ectomycorrhizal mycelium. In this horizon, relative abundance of ectomycorrhizal fungi, carbon allocation and base cation mobilisation all increased with increased OM availability. Allocation of carbon through ectomycorrhizal fungi integrates organic nitrogen mobilisation and mineral weathering across soil horizons, improving the efficiency of plant nutrient acquisition. Our findings have fundamental implications for sustainable forest management and belowground carbon sequestration.
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Affiliation(s)
- Shahid Mahmood
- Department of Forest Mycology and Plant Pathology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Box 7026, SE-750 07, Uppsala, Sweden
| | - Zaenab Fahad
- Department of Forest Mycology and Plant Pathology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Box 7026, SE-750 07, Uppsala, Sweden
| | - Emile B Bolou-Bi
- UFR des Sciences de la Terre et des Ressources Minières, Département des Sciences du sol, Université Felix Houphouët-Boigny, 22 BP 582, Abidjan, Côte d'Ivoire
| | - Katharine King
- Department of Forest Mycology and Plant Pathology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Box 7026, SE-750 07, Uppsala, Sweden
| | - Stephan J Köhler
- Department of Aquatic Sciences and Assessment, Soil-Water-Environment Center, Swedish University of Agricultural Sciences, Box 7050, SE-750 07, Uppsala, Sweden
| | - Kevin Bishop
- Department of Aquatic Sciences and Assessment, Soil-Water-Environment Center, Swedish University of Agricultural Sciences, Box 7050, SE-750 07, Uppsala, Sweden
| | - Alf Ekblad
- School of Science and Technology, Örebro University, SE-701 82, Örebro, Sweden
| | - Roger D Finlay
- Department of Forest Mycology and Plant Pathology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Box 7026, SE-750 07, Uppsala, Sweden
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2
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Auer L, Buée M, Fauchery L, Lombard V, Barry KW, Clum A, Copeland A, Daum C, Foster B, LaButti K, Singan V, Yoshinaga Y, Martineau C, Alfaro M, Castillo FJ, Imbert JB, Ramírez L, Castanera R, Pisabarro AG, Finlay R, Lindahl B, Olson A, Séguin A, Kohler A, Henrissat B, Grigoriev IV, Martin FM. Metatranscriptomics sheds light on the links between the functional traits of fungal guilds and ecological processes in forest soil ecosystems. THE NEW PHYTOLOGIST 2024; 242:1676-1690. [PMID: 38148573 DOI: 10.1111/nph.19471] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 11/23/2023] [Indexed: 12/28/2023]
Abstract
Soil fungi belonging to different functional guilds, such as saprotrophs, pathogens, and mycorrhizal symbionts, play key roles in forest ecosystems. To date, no study has compared the actual gene expression of these guilds in different forest soils. We used metatranscriptomics to study the competition for organic resources by these fungal groups in boreal, temperate, and Mediterranean forest soils. Using a dedicated mRNA annotation pipeline combined with the JGI MycoCosm database, we compared the transcripts of these three fungal guilds, targeting enzymes involved in C- and N mobilization from plant and microbial cell walls. Genes encoding enzymes involved in the degradation of plant cell walls were expressed at a higher level in saprotrophic fungi than in ectomycorrhizal and pathogenic fungi. However, ectomycorrhizal and saprotrophic fungi showed similarly high expression levels of genes encoding enzymes involved in fungal cell wall degradation. Transcripts for N-related transporters were more highly expressed in ectomycorrhizal fungi than in other groups. We showed that ectomycorrhizal and saprotrophic fungi compete for N in soil organic matter, suggesting that their interactions could decelerate C cycling. Metatranscriptomics provides a unique tool to test controversial ecological hypotheses and to better understand the underlying ecological processes involved in soil functioning and carbon stabilization.
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Affiliation(s)
- Lucas Auer
- Université de Lorraine, INRAE, UMR Interactions Arbres-Microorganismes, Nancy, F-54000, France
| | - Marc Buée
- Université de Lorraine, INRAE, UMR Interactions Arbres-Microorganismes, Nancy, F-54000, France
| | - Laure Fauchery
- Université de Lorraine, INRAE, UMR Interactions Arbres-Microorganismes, Nancy, F-54000, France
| | - Vincent Lombard
- Architecture et Fonction des Macromolécules Biologiques, CNRS and Aix-Marseille Université, Marseille, 13288, France
- INRAE, USC1408 Architecture et Fonction des Macromolécules Biologiques, Marseille, 13009, France
| | - Kerry W Barry
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Alicia Clum
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Alex Copeland
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Chris Daum
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Brian Foster
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Kurt LaButti
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Vasanth Singan
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Yuko Yoshinaga
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Christine Martineau
- Laurentian Forestry Centre, Natural Resources Canada, Canadian Forest Service, Quebec, G1V4C7, QC, Canada
| | - Manuel Alfaro
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Public University of Navarra (UPNA), Pamplona, 31006, Spain
| | - Federico J Castillo
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Public University of Navarra (UPNA), Pamplona, 31006, Spain
| | - J Bosco Imbert
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Public University of Navarra (UPNA), Pamplona, 31006, Spain
| | - Lucia Ramírez
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Public University of Navarra (UPNA), Pamplona, 31006, Spain
| | - Raúl Castanera
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Public University of Navarra (UPNA), Pamplona, 31006, Spain
| | - Antonio G Pisabarro
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Public University of Navarra (UPNA), Pamplona, 31006, Spain
| | - Roger Finlay
- Department of Forest Mycology and Pathology, Swedish University of Agricultural Sciences, Uppsala, 75007, Sweden
| | - Björn Lindahl
- Department of Forest Mycology and Pathology, Swedish University of Agricultural Sciences, Uppsala, 75007, Sweden
| | - Ake Olson
- Department of Forest Mycology and Pathology, Swedish University of Agricultural Sciences, Uppsala, 75007, Sweden
| | - Armand Séguin
- Laurentian Forestry Centre, Natural Resources Canada, Canadian Forest Service, Quebec, G1V4C7, QC, Canada
| | - Annegret Kohler
- Université de Lorraine, INRAE, UMR Interactions Arbres-Microorganismes, Nancy, F-54000, France
| | - Bernard Henrissat
- DTU Bioengineering, Denmarks Tekniske Universitet, Copenhagen, 2800, Denmark
- Department of Biological Sciences, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Francis M Martin
- Université de Lorraine, INRAE, UMR Interactions Arbres-Microorganismes, Nancy, F-54000, France
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Forsmark B, Bizjak T, Nordin A, Rosenstock NP, Wallander H, Gundale MJ. Shifts in microbial community composition and metabolism correspond with rapid soil carbon accumulation in response to 20 years of simulated nitrogen deposition. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 918:170741. [PMID: 38325494 DOI: 10.1016/j.scitotenv.2024.170741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/21/2023] [Accepted: 02/04/2024] [Indexed: 02/09/2024]
Abstract
Anthropogenic nitrogen (N) deposition and fertilization in boreal forests frequently reduces decomposition and soil respiration and enhances C storage in the topsoil. This enhancement of the C sink can be as strong as the aboveground biomass response to N additions and has implications for the global C cycle, but the mechanisms remain elusive. We hypothesized that this effect would be associated with a shift in the microbial community and its activity, and particularly by fungal taxa reported to be capable of lignin degradation and organic N acquisition. We sampled the organic layer below the intact litter of a Norway spruce (Picea abies (L.) Karst) forest in northern Sweden after 20 years of annual N additions at low (12.5 kg N ha-1 yr-1) and high (50 kg N ha-1 yr-1) rates. We measured microbial biomass using phospholipid fatty-acid analysis (PLFA) and ergosterol measurements and used ITS metagenomics to profile the fungal community of soil and fine-roots. We probed the metabolic activity of the soil community by measuring the activity of extracellular enzymes and evaluated its relationships with the most N responsive soil fungal species. Nitrogen addition decreased the abundance of fungal PLFA markers and changed the fungal community in humus and fine-roots. Specifically, the humus community changed in part due to a shift from Oidiodendron pilicola, Cenococcum geophilum, and Cortinarius caperatus to Tylospora fibrillosa and Russula griseascens. These microbial community changes were associated with decreased activity of Mn-peroxidase and peptidase, and an increase in the activity of C acquiring enzymes. Our results show that the rapid accumulation of C in the humus layer frequently observed in areas with high N deposition is consistent with a shift in microbial metabolism, where decomposition associated with organic N acquisition is downregulated when inorganic N forms are readily available.
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Affiliation(s)
- Benjamin Forsmark
- Department of Forest Ecology and Management, Swedish University of Agricultural Sciences, SE-901 83 Umeå, Sweden.
| | - Tinkara Bizjak
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, SE-901 83 Umeå, Sweden
| | - Annika Nordin
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, SE-901 83 Umeå, Sweden
| | - Nicholas P Rosenstock
- Center for Environmental and Climate Research, Lund University, SE-223 62 Lund, Sweden
| | - Håkan Wallander
- Department of Microbial Ecology, Lund University, SE-223 62 Lund, Sweden
| | - Michael J Gundale
- Department of Forest Ecology and Management, Swedish University of Agricultural Sciences, SE-901 83 Umeå, Sweden
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4
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Cao Y, Yang ZX, Yang DM, Lu N, Yu SZ, Meng JY, Chen XJ. Tobacco Root Microbial Community Composition Significantly Associated With Root-Knot Nematode Infections: Dynamic Changes in Microbiota and Growth Stage. Front Microbiol 2022; 13:807057. [PMID: 35222332 PMCID: PMC8863970 DOI: 10.3389/fmicb.2022.807057] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 01/07/2022] [Indexed: 01/28/2023] Open
Abstract
The root-knot nematode (RKN) is an important pathogen that affects the growth of many crops. Exploring the interaction of biocontrol bacteria-pathogens-host root microbes is the theoretical basis for improving colonization and controlling the effect of biocontrol bacteria in the rhizosphere. Therefore, 16S and 18S rRNA sequencing technology was used to explore the microbial composition and diversity of tobacco roots (rhizosphere and endophytic) at different growth stages in typical tobacco RKN-infected areas for 2 consecutive years. We observed that RKN infection changed the α-diversity and microbial composition of root microorganisms and drove the transformation of microorganisms from bacteria to fungi. The abundance of Sphingomonas decreased significantly from 18% to less than 3%, while the abundance of Rhizobiaceae increased from 4 to 15% at the early growth stage during the first planting year, and it promoted the proliferation of Chryseobacterium at the late growth stage in rhizosphere microorganisms with the highest abundance of 17%. The overall trend of rhizosphere microorganisms changed in the early growth stage with increasing growth time. The specific results were as follows: (1) Rhizobiaceae and Chryseobacterium increased rapidly after 75 days, became the main abundant bacteria in the rhizosphere microorganisms. (2) The dominant flora in fungi were Fusarium and Setophoma. (3) Comparing the root microbes in 2017 and 2018, RKN infection significantly promoted the proliferation of Pseudomonas and Setophoma in both the rhizosphere and endophytes during the second year of continuous tobacco planting, increasing the relative abundance of Pseudomonas from 2 to 25%. Pseudomonas was determined to play an important role in plant pest control. Finally, a total of 32 strains of growth-promoting bacteria were screened from tobacco rhizosphere bacteria infected with RKN through a combination of 16S rRNA sequencing and life-promoting tests. The results of this research are helpful for analyzing the relationship between RKNs and bacteria in plants, providing reference data for elucidating the pathogenesis of RKNs and new ideas for the biological control of RKNs. ![]()
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Affiliation(s)
- Yi Cao
- Guizhou Academy of Tobacco Science, Guiyang, China
| | | | | | - Ning Lu
- Guizhou Academy of Tobacco Science, Guiyang, China
| | - Shi-Zhou Yu
- Guizhou Academy of Tobacco Science, Guiyang, China
| | - Jian-Yu Meng
- Guizhou Academy of Tobacco Science, Guiyang, China
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Liang P, Jingan X, Liying S. The effects of reclaimed water irrigation on the soil characteristics and microbial populations of plant rhizosphere. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:17570-17579. [PMID: 34669129 DOI: 10.1007/s11356-021-16983-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 10/06/2021] [Indexed: 06/13/2023]
Abstract
In this paper, the effects of irrigation with different water qualities on the soil characteristics of 8 kinds of garden plants were analyzed. The results showed that soil pH (ranging at 7.76-8.73) had no significant difference in different soils compared with the contrast treatment. Under the reclaimed water irrigation, the content of soil total salinity, chloride ions, and water soluble sodium in soil of most plants was averagely 160.3%, 83.3%, and 67.5% higher than that of tap water, respectively. The influences of reclaimed water irrigation on soil nutrients were changed with the types of plants. The content of soil organic matter and the available potassium showed no significant differences in most plants. Compared with the tap water irrigation, the content of alkaline nitrogen in 5 plants increased (averagely 25.8%) after 5-year irrigation with reclaimed water. In terms of soil microorganism, the increase of soil microbial population, including bacteria, fungus and actinomycetes, has been promoted by different levels of reclaimed water irrigation, which is closely related with soil nutrients.
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Affiliation(s)
- Pei Liang
- Key Laboratory of Water Cycle and Related Land Surface Processes, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Xiao Jingan
- Key Laboratory of Water Cycle and Related Land Surface Processes, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Sun Liying
- Key Laboratory of Water Cycle and Related Land Surface Processes, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China.
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Effects of Abiotic Stress on Soil Microbiome. Int J Mol Sci 2021; 22:ijms22169036. [PMID: 34445742 PMCID: PMC8396473 DOI: 10.3390/ijms22169036] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/13/2021] [Accepted: 08/17/2021] [Indexed: 02/07/2023] Open
Abstract
Rhizospheric organisms have a unique manner of existence since many factors can influence the shape of the microbiome. As we all know, harnessing the interaction between soil microbes and plants is critical for sustainable agriculture and ecosystems. We can achieve sustainable agricultural practice by incorporating plant-microbiome interaction as a positive technology. The contribution of this interaction has piqued the interest of experts, who plan to do more research using beneficial microorganism in order to accomplish this vision. Plants engage in a wide range of interrelationship with soil microorganism, spanning the entire spectrum of ecological potential which can be mutualistic, commensal, neutral, exploitative, or competitive. Mutualistic microorganism found in plant-associated microbial communities assist their host in a number of ways. Many studies have demonstrated that the soil microbiome may provide significant advantages to the host plant. However, various soil conditions (pH, temperature, oxygen, physics-chemistry and moisture), soil environments (drought, submergence, metal toxicity and salinity), plant types/genotype, and agricultural practices may result in distinct microbial composition and characteristics, as well as its mechanism to promote plant development and defence against all these stressors. In this paper, we provide an in-depth overview of how the above factors are able to affect the soil microbial structure and communities and change above and below ground interactions. Future prospects will also be discussed.
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Belluco S, Mancin M, Marzoli F, Bortolami A, Mazzetto E, Pezzuto A, Favretti M, Terregino C, Bonfante F, Piro R. Prevalence of SARS-CoV-2 RNA on inanimate surfaces: a systematic review and meta-analysis. Eur J Epidemiol 2021; 36:685-707. [PMID: 34313896 PMCID: PMC8313411 DOI: 10.1007/s10654-021-00784-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 06/29/2021] [Indexed: 02/07/2023]
Abstract
Coronavirus disease (COVID-19) is a respiratory disease affecting many people and able to be transmitted through direct and perhaps indirect contact. Direct contact transmission, mediated by aerosols or droplets, is widely demonstrated, whereas indirect transmission is only supported by collateral evidence such as virus persistence on inanimate surfaces and data from other similar viruses. The present systematic review aims to estimate SARS-CoV-2 prevalence on inanimate surfaces, identifying risk levels according to surface characteristics. Data were obtained from studies in published papers collected from two databases (PubMed and Embase) with the last search on 1 September 2020. Included studies had to be papers in English, had to deal with coronavirus and had to consider inanimate surfaces in real settings. Studies were coded according to our assessment of the risk that the investigated surfaces could be contaminated by SARS-CoV-2. A meta-analysis and a metaregression were carried out to quantify virus RNA prevalence and to identify important factors driving differences among studies. Thirty-nine out of forty retrieved paper reported studies carried out in healthcare settings on the prevalence of virus RNA, five studies carry out also analyses through cell culture and six tested the viability of isolated viruses. Overall prevalences of SARS-CoV-2 RNA on high-, medium- and low-risk surfaces were 0.22 (CI95 [0.152-0.296]), 0.04 (CI95 [0.007-0.090]), and 0.00 (CI95 [0.00-0.019]), respectively. The duration surfaces were exposed to virus sources (patients) was the main factor explaining differences in prevalence.
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Affiliation(s)
- Simone Belluco
- Department of Food Safety, Istituto Zooprofilattico Sperimentale Delle Venezie, Legnaro, Italy.
| | - Marzia Mancin
- Department of Food Safety, Istituto Zooprofilattico Sperimentale Delle Venezie, Legnaro, Italy
| | - Filippo Marzoli
- Department of Food Safety, Istituto Zooprofilattico Sperimentale Delle Venezie, Legnaro, Italy
| | - Alessio Bortolami
- Division of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale Delle Venezie, Legnaro, Italy
| | - Eva Mazzetto
- Division of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale Delle Venezie, Legnaro, Italy
| | - Alessandra Pezzuto
- Department of Food Safety, Istituto Zooprofilattico Sperimentale Delle Venezie, Legnaro, Italy
| | - Michela Favretti
- Department of Food Safety, Istituto Zooprofilattico Sperimentale Delle Venezie, Legnaro, Italy
| | - Calogero Terregino
- Division of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale Delle Venezie, Legnaro, Italy
| | - Francesco Bonfante
- Division of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale Delle Venezie, Legnaro, Italy
| | - Roberto Piro
- Department of Food Safety, Istituto Zooprofilattico Sperimentale Delle Venezie, Legnaro, Italy
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