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Lewin S, Wende S, Wehrhan M, Verch G, Ganugi P, Sommer M, Kolb S. Cereals rhizosphere microbiome undergoes host selection of nitrogen cycle guilds correlated to crop productivity. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 911:168794. [PMID: 38000749 DOI: 10.1016/j.scitotenv.2023.168794] [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: 05/30/2023] [Revised: 08/31/2023] [Accepted: 11/20/2023] [Indexed: 11/26/2023]
Abstract
Sustainable transformation of agricultural plant production requires the reduction of nitrogen (N) fertilizer application. Such a reduced N fertilizer application may impede crop production due to an altered symbiosis of crops and their rhizosphere microbiome, since reduced N input may affect the competition and synergisms with the plant. The assessment of such changes in the crop microbiome functionalities at spatial scales relevant for agricultural management remains challenging. We investigated in a field plot experiment how and if the N cycling guilds of the rhizosphere of globally relevant cereal crops - winter barley, wheat and rye - are influenced by reduced N fertilization. Crop productivity was assessed by remote sensing of the shoot biomass. Microbial N cycling guilds were investigated by metagenomics targeting diazotrophs, nitrifiers, denitrifiers and the dissimilatory nitrate to ammonium reducing guild (DNRA). The functional composition of microbial N cycling guilds was explained by crop productivity parameters and soil pH, and diverged substantially between the crop species. The responses of individual microbial N cycling guild abundances to shoot dry weight and rhizosphere nitrate content was modulated by the N fertilization treatments and the crop species, which was identified based on regression analyses. Thus, characteristic shifts in the microbial N cycling guild acquisition associated with the crop host species were resolved. Particularly, the rhizosphere of rye was enriched with potentially N-preserving microbial guilds - diazotrophs and the DNRA guild - when no fertilizer was applied. We speculate that the acquisition of microbial N cycling guilds was the result of plant species-specific acquisition strategies. Thus, the investigated cereal crop holobionts have likely different symbiotic strategies that make them differently resilient against reduced N fertilizer inputs. Furthermore, we demonstrated that these belowground patterns of N cycling guilds from the rhizosphere microbiome are linked to remotely sensed aboveground plant productivity.
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Affiliation(s)
- Simon Lewin
- Working Group Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Centre for Agricultural Landscape Research e.V. (ZALF), Müncheberg, Germany
| | - Sonja Wende
- Working Group Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Centre for Agricultural Landscape Research e.V. (ZALF), Müncheberg, Germany
| | - Marc Wehrhan
- Working Group Landscape Pedology, Research Area Landscape Functioning, Leibniz Centre for Agricultural Landscape Research e.V. (ZALF), Müncheberg, Germany
| | - Gernot Verch
- Experimental Station Dedelow, Experimental Infrastructure Platform, Leibniz Centre for Agricultural Landscape Research e.V. (ZALF), Müncheberg, Germany
| | - Paola Ganugi
- Department of Agricultural, Forest and Food sciences, University of Turin, Grugliasco, Italy
| | - Michael Sommer
- Working Group Landscape Pedology, Research Area Landscape Functioning, Leibniz Centre for Agricultural Landscape Research e.V. (ZALF), Müncheberg, Germany; Institute of Environmental Science & Geography, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - Steffen Kolb
- Working Group Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Centre for Agricultural Landscape Research e.V. (ZALF), Müncheberg, Germany; Thaer Institute, Faculty of Life Sciences, Humboldt University of Berlin, Berlin, Germany.
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Soil Chemistry and Soil History Significantly Structure Oomycete Communities in Brassicaceae Crop Rotations. Appl Environ Microbiol 2023; 89:e0131422. [PMID: 36629416 PMCID: PMC9888183 DOI: 10.1128/aem.01314-22] [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: 01/12/2023] Open
Abstract
Oomycetes are critically important in soil microbial communities, especially for agriculture, where they are responsible for major declines in yields. Unfortunately, oomycetes are vastly understudied compared to bacteria and fungi. As such, our understanding of how oomycete biodiversity and community structure vary through time in the soil remains poor. Soil history established by previous crops is one factor known to structure other soil microbes, but this has not been investigated for its influence on oomycetes. In this study, we established three different soil histories in field trials; the following year, these plots were planted with five different Brassicaceae crops. We hypothesized that the previously established soil histories would structure different oomycete communities, regardless of their current Brassicaceae crop host, in both the roots and rhizosphere. We used a nested internal transcribed spacer amplicon strategy incorporated with MiSeq metabarcoding, where the sequencing data was used to infer amplicon sequence variants of the oomycetes present in each sample. This allowed us to determine the impact of different soil histories on the structure and biodiversity of the oomycete root and rhizosphere communities from the five different Brassicaceae crops. We found that each soil history structured distinct oomycete rhizosphere communities, regardless of different Brassicaceae crop hosts, while soil chemistry structured the oomycete communities more during a dry year. Interestingly, soil history appeared specific to oomycetes but was less influential for bacterial communities previously identified from the same samples. These results advance our understanding of how different agricultural practices and inputs can alter edaphic factors to impact future oomycete communities. Examining how different soil histories endure and impact oomycete biodiversity will help clarify how these important communities may be assembled in agricultural soils. IMPORTANCE Oomycetes cause global plant diseases that result in substantial losses, yet they are highly understudied compared to other microbes, like fungi and bacteria. We wanted to investigate how past soil events, like changing crops in rotation, would impact subsequent oomycete communities. We planted different oilseed crops in three different soil histories and found that each soil history structured a distinct oomycete community regardless of which new oilseed crop was planted, e.g., oomycete communities from last year's lentil plots were still detected the following year regardless of which new oilseed crops we planted. This study demonstrated how different agricultural practices can impact future microbial communities differently. Our results also highlight the need for continued monitoring of oomycete biodiversity and quantification.
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Xiong C, Lu Y. Microbiomes in agroecosystem: Diversity, function and assembly mechanisms. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:833-849. [PMID: 36184075 DOI: 10.1111/1758-2229.13126] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 09/08/2022] [Indexed: 06/16/2023]
Abstract
Soils are a main repository of biodiversity harbouring immense diversity of microbial species that plays a central role in fundamental ecological processes and acts as the seed bank for emergence of the plant microbiome in cropland ecosystems. Crop-associated microbiomes play an important role in shaping plant performance, which includes but not limited to nutrient uptake, disease resistance, and abiotic stress tolerance. Although our understanding of structure and function of soil and plant microbiomes has been rapidly advancing, most of our knowledge comes from ecosystems in natural environment. In this review, we present an overview of the current knowledge of diversity and function of microbial communities along the soil-plant continuum in agroecosystems. To characterize the ecological mechanisms for community assembly of soil and crop microbiomes, we explore how crop host and environmental factors such as plant species and developmental stage, pathogen invasion, and land management shape microbiome structure, microbial co-occurrence patterns, and crop-microbiome interactions. Particularly, the relative importance of deterministic and stochastic processes in microbial community assembly is illustrated under different environmental conditions, and potential sources and keystone taxa of the crop microbiome are described. Finally, we highlight a few important questions and perspectives in future crop microbiome research.
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Affiliation(s)
- Chao Xiong
- College of Urban and Environmental Sciences, Peking University, Beijing, People's Republic of China
| | - Yahai Lu
- College of Urban and Environmental Sciences, Peking University, Beijing, People's Republic of China
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Blakney AJC, Bainard LD, St-Arnaud M, Hijri M. Brassicaceae host plants mask the feedback from the previous year's soil history on bacterial communities, except when they experience drought. Environ Microbiol 2022; 24:3529-3548. [PMID: 35590462 DOI: 10.1111/1462-2920.16046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 05/09/2022] [Accepted: 05/10/2022] [Indexed: 11/27/2022]
Abstract
Soil history operates through time to influence the structure and biodiversity of soil bacterial communities. Examining how different soil histories endure will help clarify the rules of bacterial community assembly. In this study, we established three different soil histories in field trials; the following year these plots were planted with five different Brassicaceae species. We hypothesized that the previously established soil histories would continue to structure the subsequent Brassicaceae bacterial root and rhizosphere communities. We used a MiSeq 16S rRNA metabarcoding strategy to determine the impact of different soil histories on the structure and biodiversity of the bacterial root and rhizosphere communities from the five different Brassicaceae host plants. We found that the Brassicaceae hosts were consistently significant factors in structuring the bacterial communities. Four host plants (Sinapis alba, Brassica napus, B. juncea, B. carinata) formed similar bacterial communities, regardless of different soil histories. Camelina sativa host plants structured phylogenetically distinct bacterial communities compared to the other hosts, particularly in their roots. Soil history established the previous year was only a significant factor for bacterial community structure when the feedback of the Brassicaceae host plants was weakened, potentially due to limited soil moisture during a dry year. Understanding how soil history is involved in the structure and biodiversity of bacterial communities through time is a limitation in microbial ecology and is required for employing microbiome technologies in improving agricultural systems. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Andrew J C Blakney
- Institut de recherche en biologie végétale, Département de Sciences Biologiques, Université de Montréal and Jardin botanique de Montréal, Montréal, QC, Canada
| | - Luke D Bainard
- Agassiz Research and Development Centre, AgricuSlture and Agri-Food Canada, Agassiz, BC, V0M 1A2, Canada
| | - Marc St-Arnaud
- Institut de recherche en biologie végétale, Département de Sciences Biologiques, Université de Montréal and Jardin botanique de Montréal, Montréal, QC, Canada
| | - Mohamed Hijri
- Institut de recherche en biologie végétale, Département de Sciences Biologiques, Université de Montréal and Jardin botanique de Montréal, Montréal, QC, Canada.,African Genome Center, Mohammed VI Polytechnic University (UM6P), Lot 660, Hay Moulay Rachid, Ben Guerir, 43150, Morocco
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Zhang M, Li X, Xing F, Li Z, Liu X, Li Y. Soil Microbial Legacy Overrides the Responses of a Dominant Grass and Nitrogen-Cycling Functional Microbes in Grassland Soil to Nitrogen Addition. PLANTS (BASEL, SWITZERLAND) 2022; 11:1305. [PMID: 35631730 PMCID: PMC9145027 DOI: 10.3390/plants11101305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 05/03/2022] [Accepted: 05/12/2022] [Indexed: 06/15/2023]
Abstract
Both atmospheric nitrogen (N) deposition and soil microbial legacy (SML) can affect plant performance, the activity of soil N-cycling functional microbes and the relative abundance of N-cycling functional genes (NCFGs). In the grassland vegetation successional process, how the interaction of SML and N deposition affects the performance of dominant grass and NCFGs remains unclear. Therefore, we planted Leymus chinensis, a dominant grass in the Songnen grassland, in the soil taken from the early, medium, late, and stable successional stages. We subjected the plants to soil sterilization and N addition treatments and measured the plant traits and NCFG abundances (i.e., nifH, AOB amoA, nirS, and nirK). Our results showed the biomass and ramet number of L. chinensis in sterilized soil were significantly higher than those in non-sterilized soil, indicating that SML negatively affects the growth of L. chinensis. However, N addition increased the plant biomass and the AOB amoA gene abundance only in sterilized soils, implying that SML overrode the N addition effects because SML buffered the effects of increasing soil N availability on NCFGs. Therefore, we emphasize the potential role of SML in assessing the effects of N deposition on dominant plant performance and NCFGs in the grassland vegetation succession.
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Affiliation(s)
- Minghui Zhang
- Key Laboratory of Vegetation Ecology, Ministry of Education, Jilin Songnen Grassland Ecosystem National Observation and Research Station, Institute of Grassland Science, Northeast Normal University, Changchun 130024, China; (M.Z.); (X.L.); (Z.L.); (X.L.); (Y.L.)
- Jilin Provincial Key Laboratory of Ecological Restoration and Ecosystem Management, Northeast Normal University, Changchun 130024, China
| | - Xueli Li
- Key Laboratory of Vegetation Ecology, Ministry of Education, Jilin Songnen Grassland Ecosystem National Observation and Research Station, Institute of Grassland Science, Northeast Normal University, Changchun 130024, China; (M.Z.); (X.L.); (Z.L.); (X.L.); (Y.L.)
- Jilin Provincial Key Laboratory of Ecological Restoration and Ecosystem Management, Northeast Normal University, Changchun 130024, China
| | - Fu Xing
- Key Laboratory of Vegetation Ecology, Ministry of Education, Jilin Songnen Grassland Ecosystem National Observation and Research Station, Institute of Grassland Science, Northeast Normal University, Changchun 130024, China; (M.Z.); (X.L.); (Z.L.); (X.L.); (Y.L.)
- Jilin Provincial Key Laboratory of Ecological Restoration and Ecosystem Management, Northeast Normal University, Changchun 130024, China
| | - Zhuo Li
- Key Laboratory of Vegetation Ecology, Ministry of Education, Jilin Songnen Grassland Ecosystem National Observation and Research Station, Institute of Grassland Science, Northeast Normal University, Changchun 130024, China; (M.Z.); (X.L.); (Z.L.); (X.L.); (Y.L.)
- Jilin Provincial Key Laboratory of Ecological Restoration and Ecosystem Management, Northeast Normal University, Changchun 130024, China
| | - Xiaowei Liu
- Key Laboratory of Vegetation Ecology, Ministry of Education, Jilin Songnen Grassland Ecosystem National Observation and Research Station, Institute of Grassland Science, Northeast Normal University, Changchun 130024, China; (M.Z.); (X.L.); (Z.L.); (X.L.); (Y.L.)
- Jilin Provincial Key Laboratory of Ecological Restoration and Ecosystem Management, Northeast Normal University, Changchun 130024, China
| | - Yanan Li
- Key Laboratory of Vegetation Ecology, Ministry of Education, Jilin Songnen Grassland Ecosystem National Observation and Research Station, Institute of Grassland Science, Northeast Normal University, Changchun 130024, China; (M.Z.); (X.L.); (Z.L.); (X.L.); (Y.L.)
- Jilin Provincial Key Laboratory of Ecological Restoration and Ecosystem Management, Northeast Normal University, Changchun 130024, China
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