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Rempfert KR, Bell SL, Kasanke CP, Zhao Q, Zhao X, Lipton AS, Hofmockel KS. Biomolecular budget of persistent, microbial-derived soil organic carbon: The importance of underexplored pools. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 932:172916. [PMID: 38697544 DOI: 10.1016/j.scitotenv.2024.172916] [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: 01/04/2024] [Revised: 04/25/2024] [Accepted: 04/29/2024] [Indexed: 05/05/2024]
Abstract
The details of how soil microorganisms contribute to stable soil organic carbon pools are a pressing knowledge gap with direct implications for soil health and climate mitigation. It is now recognized that microbial necromass contributes substantially to the formation of stable soil carbon. However, the quantification of necromass in soils has largely been limited to model molecules such as aminosugar biomarkers. The abundance and chemical composition of other persistent microbial residues remain unresolved, particularly concerning how these pools may vary with microbial community structure, soil texture, and management practices. Here we use yearlong soil incubation experiments with an isotopic tracer to quantify the composition of persistent residues derived from microbial communities inhabiting sand or silt dominated soil with annual (corn) or perennial (switchgrass) monocultures. Persistent microbial residues were recovered in diverse soil biomolecular pools including metabolites, proteins, lipids, and mineral-associated organic matter (MAOM). The relative abundances of microbial contributions to necromass pools were consistent across cropping systems and soil textures. The greatest residue accumulation was not recovered in MAOM but in the light density fraction of soil debris that persisted after extraction by chemical fractionation using organic solvents. Necromass abundance was positively correlated with microbial biomass abundance and revealed a possible role of cell wall morphology in enhancing microbial carbon persistence; while gram-negative bacteria accounted for the greatest contribution to microbial-derived carbon by mass at one year, residues from gram-positive Actinobacteria and Firmicutes showed greater durability. Together these results offer a quantitative assessment of the relative importance of diverse molecular classes for generating durable soil carbon.
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Affiliation(s)
| | - Sheryl L Bell
- Pacific Northwest National Laboratory, Richland, WA, USA
| | | | - Qian Zhao
- Pacific Northwest National Laboratory, Richland, WA, USA
| | - Xiaodong Zhao
- Pacific Northwest National Laboratory, Richland, WA, USA
| | | | - Kirsten S Hofmockel
- Pacific Northwest National Laboratory, Richland, WA, USA; Department of Agronomy, Iowa State University, Ames, IA, USA.
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Charakas C, Khokhani D. Expanded trade: tripartite interactions in the mycorrhizosphere. mSystems 2024:e0135223. [PMID: 38837330 DOI: 10.1128/msystems.01352-23] [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: 06/07/2024] Open
Abstract
Interactions between arbuscular mycorrhizal fungi (AMF), plants, and the soil microbial community have the potential to increase the availability and uptake of phosphorus (P) and nitrogen (N) in agricultural systems. Nutrient exchange between plant roots, AMF, and the adjacent soil microbes occurs at the interface between roots colonized by mycorrhizal fungi and soil, referred to as the mycorrhizosphere. Research on the P exchange focuses on plant-AMF or AMF-microbe interactions, lacking a holistic view of P exchange between the plants, AMF, and other microbes. Recently, N exchange at both interfaces revealed the synergistic role of AMF and bacterial community in N uptake by the host plant. Here, we highlight work carried out on each interface and build upon it by emphasizing research involving all members of the tripartite network. Both nutrient systems are challenging to study due to the complex chemical and biological nature of the mycorrhizosphere. We discuss some of the effective methods to identify important nutrient processes and the tripartite members involved in these processes. The extrapolation of in vitro studies into the field is often fraught with contradiction and noise. Therefore, we also suggest some approaches that can potentially bridge the gap between laboratory-generated data and their extrapolation to the field, improving the applicability and contextual relevance of data within the field of mycorrhizosphere interactions. Overall, we argue that the research community needs to adopt a holistic tripartite approach and that we have the means to increase the applicability and accuracy of in vitro data in the field.
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Affiliation(s)
- Christos Charakas
- Department of Plant and Microbial Biology, University of Minnesota, Twin Cities, Minnesota, USA
| | - Devanshi Khokhani
- Department of Plant Pathology, University of Minnesota, Twin Cities, Minnesota, USA
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Bell-Dereske LP, Benucci GMN, da Costa PB, Bonito G, Friesen ML, Tiemann LK, Evans SE. Regional biogeography versus intra-annual dynamics of the root and soil microbiome. ENVIRONMENTAL MICROBIOME 2023; 18:50. [PMID: 37287059 DOI: 10.1186/s40793-023-00504-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 05/17/2023] [Indexed: 06/09/2023]
Abstract
BACKGROUND Root and soil microbial communities constitute the below-ground plant microbiome, are drivers of nutrient cycling, and affect plant productivity. However, our understanding of their spatiotemporal patterns is confounded by exogenous factors that covary spatially, such as changes in host plant species, climate, and edaphic factors. These spatiotemporal patterns likely differ across microbiome domains (bacteria and fungi) and niches (root vs. soil). RESULTS To capture spatial patterns at a regional scale, we sampled the below-ground microbiome of switchgrass monocultures of five sites spanning > 3 degrees of latitude within the Great Lakes region. To capture temporal patterns, we sampled the below-ground microbiome across the growing season within a single site. We compared the strength of spatiotemporal factors to nitrogen addition determining the major drivers in our perennial cropping system. All microbial communities were most strongly structured by sampling site, though collection date also had strong effects; in contrast, nitrogen addition had little to no effect on communities. Though all microbial communities were found to have significant spatiotemporal patterns, sampling site and collection date better explained bacterial than fungal community structure, which appeared more defined by stochastic processes. Root communities, especially bacterial, were more temporally structured than soil communities which were more spatially structured, both across and within sampling sites. Finally, we characterized a core set of taxa in the switchgrass microbiome that persists across space and time. These core taxa represented < 6% of total species richness but > 27% of relative abundance, with potential nitrogen fixing bacteria and fungal mutualists dominating the root community and saprotrophs dominating the soil community. CONCLUSIONS Our results highlight the dynamic variability of plant microbiome composition and assembly across space and time, even within a single variety of a plant species. Root and soil fungal community compositions appeared spatiotemporally paired, while root and soil bacterial communities showed a temporal lag in compositional similarity suggesting active recruitment of soil bacteria into the root niche throughout the growing season. A better understanding of the drivers of these differential responses to space and time may improve our ability to predict microbial community structure and function under novel conditions.
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Affiliation(s)
- Lukas P Bell-Dereske
- W.K. Kellogg Biological Station, Michigan State University, Hickory Corners, MI, USA.
- The Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, USA.
- Laboratory of Environmental Microbiology, Institute of Microbiology, Czech Academy of Sciences, Vídeňská, Prague 4, 1083, 142 20, Czech Republic.
| | - Gian Maria Niccolò Benucci
- The Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, USA
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA
- Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - Pedro Beschoren da Costa
- Laboratory of Entomology, Department of Plant Sciences, Wageningen University & Research, Wageningen, The Netherlands
| | - Gregory Bonito
- The Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, USA
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA
- Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - Maren L Friesen
- Department of Plant Pathology, Department of Crop and Soil Sciences, Washington State University, Pullman, WA, USA
| | - Lisa K Tiemann
- The Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, USA
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA
| | - Sarah E Evans
- W.K. Kellogg Biological Station, Michigan State University, Hickory Corners, MI, USA
- The Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, USA
- Department of Integrative Biology, Michigan State University, East Lansing, MI, USA
- Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI, USA
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Bahulikar RA. Prevalence of Deltaproteobacterial sequences in nifH gene pools associated with the rhizosphere of native switchgrass from Tall Grass Prairie (Oklahoma, USA). 3 Biotech 2023; 13:210. [PMID: 37251732 PMCID: PMC10209375 DOI: 10.1007/s13205-023-03640-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 05/15/2023] [Indexed: 05/31/2023] Open
Abstract
The potential nitrogen-fixing bacterial diversity in the rhizospheric soil of the native switchgrass (Panicum virgatum L.) from Tall Grass Prairies of Northern Oklahoma was studied using a partial region of nitrogenase structural gene-nifH. Eleven clone libraries constructed from nifH amplicons gave 407 good-quality sequences. More than 70% of sequences showed similarity of nifH with uncultured bacteria (< 98%). The dominance of sequences affiliated with Deltaproteobacterial nifH was observed, followed by Betaproteobacterial nifH sequences. The nifH gene library was dominated by the genera Geobacter, Rhizobacter, Paenibacillus, and Azoarcus. Sequences affiliated with rhizobia, such as Bradyrhizobium, Methylocystis, Ensifer, etc., were also in the rhizosphere in small numbers. From Deltaproteobacteria, five genera, namely Geobacter, Pelobacter, Geomonas, Desulfovibrio, and Anaeromyxobacter, contributed to 48% of the total sequences suggesting the dominance of group Deltaproteobacteria in the rhizosphere of native switchgrass. Considering the percent similarity of the nifH sequences with cultivated bacteria, this study demonstrated the presence of novel bacterial species in switchgrass rhizospheric soil from Tall Grass Prairie.
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Affiliation(s)
- Rahul A. Bahulikar
- Noble Research Institute, 2510 Sam Noble Parkway, Ardmore, OK 73401 USA
- Present Address: BAIF Development Research Foundation, Central Research Station, Urali Kanchan, Pune, 412 202 India
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Seasonal activities of the phyllosphere microbiome of perennial crops. Nat Commun 2023; 14:1039. [PMID: 36823152 PMCID: PMC9950430 DOI: 10.1038/s41467-023-36515-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 02/03/2023] [Indexed: 02/25/2023] Open
Abstract
Understanding the interactions between plants and microorganisms can inform microbiome management to enhance crop productivity and resilience to stress. Here, we apply a genome-centric approach to identify ecologically important leaf microbiome members on replicated plots of field-grown switchgrass and miscanthus, and to quantify their activities over two growing seasons for switchgrass. We use metagenome and metatranscriptome sequencing and curate 40 medium- and high-quality metagenome-assembled-genomes (MAGs). We find that classes represented by these MAGs (Actinomycetia, Alpha- and Gamma- Proteobacteria, and Bacteroidota) are active in the late season, and upregulate transcripts for short-chain dehydrogenase, molybdopterin oxidoreductase, and polyketide cyclase. Stress-associated pathways are expressed for most MAGs, suggesting engagement with the host environment. We also detect seasonally activated biosynthetic pathways for terpenes and various non-ribosomal peptide pathways that are poorly annotated. Our findings support that leaf-associated bacterial populations are seasonally dynamic and responsive to host cues.
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Yu Y, Liu H, Zhang L, Sun Z, Lei B, Miao Y, Chu H, Han S, Shi Y, Zheng J. Distinct response patterns of plants and soil microorganisms to agronomic practices and seasonal variation in a floodplain ecosystem. Front Microbiol 2023; 14:1094750. [PMID: 36778881 PMCID: PMC9909268 DOI: 10.3389/fmicb.2023.1094750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 01/09/2023] [Indexed: 01/27/2023] Open
Abstract
Introduction Climate change and anthropogenic activities are the greatest threats to floodplain ecosystems. A growing body of literature shows that floodplain ecosystems have experienced increased chemical fertilizer and pesticide loads, which will disturb the above and belowground ecosystems. However, we lack knowledge regarding the effects of such human activities on the vegetation and soil microbiomes in these ecosystems. Methods In the present study, plant functional traits and Illumina Mi-Seq sequencing were to assess the impact of nitrogen fertilizer and glyphosate addition on the structure and function of the vegetation and soil microbiomes (bacteria, fungi, and protists) in a floodplain ecosystem, and to assess the influence of seasonal variation. Results We identified distinct response mechanisms of plant and microbial communities to the addition of nitrogen fertilizer and glyphosate, and seasonal variation. Nitrogen fertilizer and glyphosate significantly affected plant diversity, aboveground and underground biomass, and C and N content and significantly changed the leaf area and plant stature of dominant plants. However, the addition of nitrogen fertilizer and glyphosate did not significantly affect the diversity and structure of bacterial, fungal, and protist communities. The application of nitrogen fertilizer could improve the negative effects of glyphosate on the functional traits of plant communities. The seasonal variation of floodplain has significantly changed the soil's physical, chemical, and biological properties. Our results showed that compared with that in summer, the soil ecosystem multifunctionality of the floodplain ecosystem in autumn was significantly lower. Seasonal variation had a significant effect on plant diversity and functional traits. Moreover, seasonal variation significantly affected the community compositions, diversity, and structure of bacteria, fungi, and protists. Seasonal variation had a stronger impact on fungal community assembly than on that of bacteria and protists. In summer, the assembly of the fungal community was dominated by a deterministic process, while in autumn, it is dominated by a stochastic process. In addition, the negative association among bacteria, fungi, and protists has been strengthened in autumn and formed a more robust network to cope with external changes. Discussion These results extended our understanding of the ecological patterns of soil microbiomes in floodplain ecosystems and provided support for enhancing the ecological barrier function and the service potential of floodplain ecosystems.
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Affiliation(s)
- Yanyan Yu
- International Joint Research Laboratory for Global Change Ecology, School of Life Sciences, Henan University, Kaifeng, Henan, China
- School of Science and Technology, Xinyang College, Xinyang, Henan, China
- Yellow River Floodplain Ecosystems Research Station, Henan University, Kaifeng, Henan, China
| | - Hao Liu
- International Joint Research Laboratory for Global Change Ecology, School of Life Sciences, Henan University, Kaifeng, Henan, China
- Yellow River Floodplain Ecosystems Research Station, Henan University, Kaifeng, Henan, China
| | - Lanlan Zhang
- International Joint Research Laboratory for Global Change Ecology, School of Life Sciences, Henan University, Kaifeng, Henan, China
- Yellow River Floodplain Ecosystems Research Station, Henan University, Kaifeng, Henan, China
| | - Zhongjie Sun
- International Joint Research Laboratory for Global Change Ecology, School of Life Sciences, Henan University, Kaifeng, Henan, China
- Yellow River Floodplain Ecosystems Research Station, Henan University, Kaifeng, Henan, China
| | - Binghai Lei
- International Joint Research Laboratory for Global Change Ecology, School of Life Sciences, Henan University, Kaifeng, Henan, China
- Yellow River Floodplain Ecosystems Research Station, Henan University, Kaifeng, Henan, China
| | - Yuan Miao
- International Joint Research Laboratory for Global Change Ecology, School of Life Sciences, Henan University, Kaifeng, Henan, China
- Yellow River Floodplain Ecosystems Research Station, Henan University, Kaifeng, Henan, China
| | - Haiyan Chu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Shijie Han
- International Joint Research Laboratory for Global Change Ecology, School of Life Sciences, Henan University, Kaifeng, Henan, China
- Yellow River Floodplain Ecosystems Research Station, Henan University, Kaifeng, Henan, China
| | - Yu Shi
- International Joint Research Laboratory for Global Change Ecology, School of Life Sciences, Henan University, Kaifeng, Henan, China
- Yellow River Floodplain Ecosystems Research Station, Henan University, Kaifeng, Henan, China
| | - Junqiang Zheng
- International Joint Research Laboratory for Global Change Ecology, School of Life Sciences, Henan University, Kaifeng, Henan, China
- Yellow River Floodplain Ecosystems Research Station, Henan University, Kaifeng, Henan, China
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Chiaranunt P, White JF. Plant Beneficial Bacteria and Their Potential Applications in Vertical Farming Systems. PLANTS (BASEL, SWITZERLAND) 2023; 12:400. [PMID: 36679113 PMCID: PMC9861093 DOI: 10.3390/plants12020400] [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] [Revised: 01/12/2023] [Accepted: 01/12/2023] [Indexed: 06/17/2023]
Abstract
In this literature review, we discuss the various functions of beneficial plant bacteria in improving plant nutrition, the defense against biotic and abiotic stress, and hormonal regulation. We also review the recent research on rhizophagy, a nutrient scavenging mechanism in which bacteria enter and exit root cells on a cyclical basis. These concepts are covered in the contexts of soil agriculture and controlled environment agriculture, and they are also used in vertical farming systems. Vertical farming-its advantages and disadvantages over soil agriculture, and the various climatic factors in controlled environment agriculture-is also discussed in relation to plant-bacterial relationships. The different factors under grower control, such as choice of substrate, oxygenation rates, temperature, light, and CO2 supplementation, may influence plant-bacterial interactions in unintended ways. Understanding the specific effects of these environmental factors may inform the best cultural practices and further elucidate the mechanisms by which beneficial bacteria promote plant growth.
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Cleveland CC, Reis CRG, Perakis SS, Dynarski KA, Batterman SA, Crews TE, Gei M, Gundale MJ, Menge DNL, Peoples MB, Reed SC, Salmon VG, Soper FM, Taylor BN, Turner MG, Wurzburger N. Exploring the Role of Cryptic Nitrogen Fixers in Terrestrial Ecosystems: A Frontier in Nitrogen Cycling Research. Ecosystems 2022. [DOI: 10.1007/s10021-022-00804-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Soil Origin and Plant Genotype Modulate Switchgrass Aboveground Productivity and Root Microbiome Assembly. mBio 2022; 13:e0007922. [PMID: 35384699 PMCID: PMC9040762 DOI: 10.1128/mbio.00079-22] [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] [Indexed: 11/20/2022] Open
Abstract
Switchgrass (Panicum virgatum) is a model perennial grass for bioenergy production that can be productive in agricultural lands that are not suitable for food production. There is growing interest in whether its associated microbiome may be adaptive in low- or no-input cultivation systems. However, the relative impact of plant genotype and soil factors on plant microbiome and biomass are a challenge to decouple. To address this, a common garden greenhouse experiment was carried out using six common switchgrass genotypes, which were each grown in four different marginal soils collected from long-term bioenergy research sites in Michigan and Wisconsin. We characterized the fungal and bacterial root communities with high-throughput amplicon sequencing of the ITS and 16S rDNA markers, and collected phenological plant traits during plant growth, as well as soil chemical traits. At harvest, we measured the total plant aerial dry biomass. Significant differences in richness and Shannon diversity across soils but not between plant genotypes were found. Generalized linear models showed an interaction between soil and genotype for fungal richness but not for bacterial richness. Community structure was also strongly shaped by soil origin and soil origin × plant genotype interactions. Overall, plant genotype effects were significant but low. Random Forest models indicate that important factors impacting switchgrass biomass included NO3−, Ca2+, PO43−, and microbial biodiversity. We identified 54 fungal and 52 bacterial predictors of plant aerial biomass, which included several operational taxonomic units belonging to Glomeraceae and Rhizobiaceae, fungal and bacterial lineages that are involved in provisioning nutrients to plants.
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Zhang X, Tong J, Dong M, Akhtar K, He B. Isolation, identification and characterization of nitrogen fixing endophytic bacteria and their effects on cassava production. PeerJ 2022; 10:e12677. [PMID: 35127278 PMCID: PMC8796710 DOI: 10.7717/peerj.12677] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 12/02/2021] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Cassava (Manibot esculenta Crantz) is one of the most important among tuber crops. The amount of nitrogen fertilizer used for cassava production is relatively high (400 kg ha-1), but there are few studies on biological nitrogen fixation in this crop. Therefore, it is particularly important to study whether cassava and microorganisms have the associated nitrogen-fixing and other promoting effects of endophytic bacteria. METHODS We screened 10 endophytic bacteria using the nitrogen-free culture method from the roots of seven cassava cultivars, and the nitrogenase activity of the A02 strain was the highest 95.81 nmol mL-1 h-1. The A02 strain was confirmed as Microbacteriaceae, Curtobacterium using 16S rRNA sequence alignment. The biological and morphological characteristics of strain A02 were further analyzed. RESULTS The experimental results showed that the biomass of roots, stems, and leaves of cassava inoculated with A02 increased by 17.6%, 12.6%, and 10.3%, respectively, compared to that of the control (without A02 inoculation). These results were not only related to the secretion of auxin (IAA) and solubilization of phosphate but also in the promotion of biological nitrogen fixation of cassava leaves by strain A02. Moreover, the highest 95.81 nmol mL-1h-1 of nitrogenase activity was reported in strain A02, and thus more nitrogen fixation was observed in strain A02. In conclusion, A02 is a newly discovered endophytic nitrogen-fixing bacteria in cassava that can be further used in the research of biological bacterial fertilizers.
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Affiliation(s)
- Xiao Zhang
- College of Agriculture, Guangxi University, Guangxi, Nanning, China
| | - Juanjuan Tong
- College of Agriculture, Guangxi University, Guangxi, Nanning, China
| | - Mengmeng Dong
- College of Agriculture, Guangxi University, Guangxi, Nanning, China
| | - Kashif Akhtar
- College of Life Science and Technology, Guangxi University, Guangxi, Nanning, China
| | - Bing He
- College of Agriculture, Guangxi University, Guangxi, Nanning, China
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Freschet GT, Pagès L, Iversen CM, Comas LH, Rewald B, Roumet C, Klimešová J, Zadworny M, Poorter H, Postma JA, Adams TS, Bagniewska‐Zadworna A, Bengough AG, Blancaflor EB, Brunner I, Cornelissen JHC, Garnier E, Gessler A, Hobbie SE, Meier IC, Mommer L, Picon‐Cochard C, Rose L, Ryser P, Scherer‐Lorenzen M, Soudzilovskaia NA, Stokes A, Sun T, Valverde‐Barrantes OJ, Weemstra M, Weigelt A, Wurzburger N, York LM, Batterman SA, Gomes de Moraes M, Janeček Š, Lambers H, Salmon V, Tharayil N, McCormack ML. A starting guide to root ecology: strengthening ecological concepts and standardising root classification, sampling, processing and trait measurements. THE NEW PHYTOLOGIST 2021; 232:973-1122. [PMID: 34608637 PMCID: PMC8518129 DOI: 10.1111/nph.17572] [Citation(s) in RCA: 89] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 03/22/2021] [Indexed: 05/17/2023]
Abstract
In the context of a recent massive increase in research on plant root functions and their impact on the environment, root ecologists currently face many important challenges to keep on generating cutting-edge, meaningful and integrated knowledge. Consideration of the below-ground components in plant and ecosystem studies has been consistently called for in recent decades, but methodology is disparate and sometimes inappropriate. This handbook, based on the collective effort of a large team of experts, will improve trait comparisons across studies and integration of information across databases by providing standardised methods and controlled vocabularies. It is meant to be used not only as starting point by students and scientists who desire working on below-ground ecosystems, but also by experts for consolidating and broadening their views on multiple aspects of root ecology. Beyond the classical compilation of measurement protocols, we have synthesised recommendations from the literature to provide key background knowledge useful for: (1) defining below-ground plant entities and giving keys for their meaningful dissection, classification and naming beyond the classical fine-root vs coarse-root approach; (2) considering the specificity of root research to produce sound laboratory and field data; (3) describing typical, but overlooked steps for studying roots (e.g. root handling, cleaning and storage); and (4) gathering metadata necessary for the interpretation of results and their reuse. Most importantly, all root traits have been introduced with some degree of ecological context that will be a foundation for understanding their ecological meaning, their typical use and uncertainties, and some methodological and conceptual perspectives for future research. Considering all of this, we urge readers not to solely extract protocol recommendations for trait measurements from this work, but to take a moment to read and reflect on the extensive information contained in this broader guide to root ecology, including sections I-VII and the many introductions to each section and root trait description. Finally, it is critical to understand that a major aim of this guide is to help break down barriers between the many subdisciplines of root ecology and ecophysiology, broaden researchers' views on the multiple aspects of root study and create favourable conditions for the inception of comprehensive experiments on the role of roots in plant and ecosystem functioning.
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Affiliation(s)
- Grégoire T. Freschet
- CEFEUniv Montpellier, CNRS, EPHE, IRD1919 route de MendeMontpellier34293France
- Station d’Ecologie Théorique et ExpérimentaleCNRS2 route du CNRS09200MoulisFrance
| | - Loïc Pagès
- UR 1115 PSHCentre PACA, site AgroparcINRAE84914Avignon cedex 9France
| | - Colleen M. Iversen
- Environmental Sciences Division and Climate Change Science InstituteOak Ridge National LaboratoryOak RidgeTN37831USA
| | - Louise H. Comas
- USDA‐ARS Water Management Research Unit2150 Centre Avenue, Bldg D, Suite 320Fort CollinsCO80526USA
| | - Boris Rewald
- Department of Forest and Soil SciencesUniversity of Natural Resources and Life SciencesVienna1190Austria
| | - Catherine Roumet
- CEFEUniv Montpellier, CNRS, EPHE, IRD1919 route de MendeMontpellier34293France
| | - Jitka Klimešová
- Department of Functional EcologyInstitute of Botany CASDukelska 13537901TrebonCzech Republic
| | - Marcin Zadworny
- Institute of DendrologyPolish Academy of SciencesParkowa 562‐035KórnikPoland
| | - Hendrik Poorter
- Plant Sciences (IBG‐2)Forschungszentrum Jülich GmbHD‐52425JülichGermany
- Department of Biological SciencesMacquarie UniversityNorth RydeNSW2109Australia
| | | | - Thomas S. Adams
- Department of Plant SciencesThe Pennsylvania State UniversityUniversity ParkPA16802USA
| | - Agnieszka Bagniewska‐Zadworna
- Department of General BotanyInstitute of Experimental BiologyFaculty of BiologyAdam Mickiewicz UniversityUniwersytetu Poznańskiego 661-614PoznańPoland
| | - A. Glyn Bengough
- The James Hutton InstituteInvergowrie, Dundee,DD2 5DAUK
- School of Science and EngineeringUniversity of DundeeDundee,DD1 4HNUK
| | | | - Ivano Brunner
- Forest Soils and BiogeochemistrySwiss Federal Research Institute WSLZürcherstr. 1118903BirmensdorfSwitzerland
| | - Johannes H. C. Cornelissen
- Department of Ecological ScienceFaculty of ScienceVrije Universiteit AmsterdamDe Boelelaan 1085Amsterdam1081 HVthe Netherlands
| | - Eric Garnier
- CEFEUniv Montpellier, CNRS, EPHE, IRD1919 route de MendeMontpellier34293France
| | - Arthur Gessler
- Forest DynamicsSwiss Federal Research Institute WSLZürcherstr. 1118903BirmensdorfSwitzerland
- Institute of Terrestrial EcosystemsETH Zurich8092ZurichSwitzerland
| | - Sarah E. Hobbie
- Department of Ecology, Evolution and BehaviorUniversity of MinnesotaSt PaulMN55108USA
| | - Ina C. Meier
- Functional Forest EcologyUniversity of HamburgHaidkrugsweg 122885BarsbütelGermany
| | - Liesje Mommer
- Plant Ecology and Nature Conservation GroupDepartment of Environmental SciencesWageningen University and ResearchPO Box 476700 AAWageningenthe Netherlands
| | | | - Laura Rose
- Station d’Ecologie Théorique et ExpérimentaleCNRS2 route du CNRS09200MoulisFrance
- Senckenberg Biodiversity and Climate Research Centre (BiK-F)Senckenberganlage 2560325Frankfurt am MainGermany
| | - Peter Ryser
- Laurentian University935 Ramsey Lake RoadSudburyONP3E 2C6Canada
| | | | - Nadejda A. Soudzilovskaia
- Environmental Biology DepartmentInstitute of Environmental SciencesCMLLeiden UniversityLeiden2300 RAthe Netherlands
| | - Alexia Stokes
- INRAEAMAPCIRAD, IRDCNRSUniversity of MontpellierMontpellier34000France
| | - Tao Sun
- Institute of Applied EcologyChinese Academy of SciencesShenyang110016China
| | - Oscar J. Valverde‐Barrantes
- International Center for Tropical BotanyDepartment of Biological SciencesFlorida International UniversityMiamiFL33199USA
| | - Monique Weemstra
- CEFEUniv Montpellier, CNRS, EPHE, IRD1919 route de MendeMontpellier34293France
| | - Alexandra Weigelt
- Systematic Botany and Functional BiodiversityInstitute of BiologyLeipzig UniversityJohannisallee 21-23Leipzig04103Germany
| | - Nina Wurzburger
- Odum School of EcologyUniversity of Georgia140 E. Green StreetAthensGA30602USA
| | - Larry M. York
- Biosciences Division and Center for Bioenergy InnovationOak Ridge National LaboratoryOak RidgeTN37831USA
| | - Sarah A. Batterman
- School of Geography and Priestley International Centre for ClimateUniversity of LeedsLeedsLS2 9JTUK
- Cary Institute of Ecosystem StudiesMillbrookNY12545USA
| | - Moemy Gomes de Moraes
- Department of BotanyInstitute of Biological SciencesFederal University of Goiás1974690-900Goiânia, GoiásBrazil
| | - Štěpán Janeček
- School of Biological SciencesThe University of Western Australia35 Stirling HighwayCrawley (Perth)WA 6009Australia
| | - Hans Lambers
- School of Biological SciencesThe University of Western AustraliaCrawley (Perth)WAAustralia
| | - Verity Salmon
- Environmental Sciences Division and Climate Change Science InstituteOak Ridge National LaboratoryOak RidgeTN37831USA
| | - Nishanth Tharayil
- Department of Plant and Environmental SciencesClemson UniversityClemsonSC29634USA
| | - M. Luke McCormack
- Center for Tree ScienceMorton Arboretum, 4100 Illinois Rt. 53LisleIL60532USA
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Freschet GT, Pagès L, Iversen CM, Comas LH, Rewald B, Roumet C, Klimešová J, Zadworny M, Poorter H, Postma JA, Adams TS, Bagniewska-Zadworna A, Bengough AG, Blancaflor EB, Brunner I, Cornelissen JHC, Garnier E, Gessler A, Hobbie SE, Meier IC, Mommer L, Picon-Cochard C, Rose L, Ryser P, Scherer-Lorenzen M, Soudzilovskaia NA, Stokes A, Sun T, Valverde-Barrantes OJ, Weemstra M, Weigelt A, Wurzburger N, York LM, Batterman SA, Gomes de Moraes M, Janeček Š, Lambers H, Salmon V, Tharayil N, McCormack ML. A starting guide to root ecology: strengthening ecological concepts and standardising root classification, sampling, processing and trait measurements. THE NEW PHYTOLOGIST 2021. [PMID: 34608637 DOI: 10.1111/nph.17572.hal-03379708] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
In the context of a recent massive increase in research on plant root functions and their impact on the environment, root ecologists currently face many important challenges to keep on generating cutting-edge, meaningful and integrated knowledge. Consideration of the below-ground components in plant and ecosystem studies has been consistently called for in recent decades, but methodology is disparate and sometimes inappropriate. This handbook, based on the collective effort of a large team of experts, will improve trait comparisons across studies and integration of information across databases by providing standardised methods and controlled vocabularies. It is meant to be used not only as starting point by students and scientists who desire working on below-ground ecosystems, but also by experts for consolidating and broadening their views on multiple aspects of root ecology. Beyond the classical compilation of measurement protocols, we have synthesised recommendations from the literature to provide key background knowledge useful for: (1) defining below-ground plant entities and giving keys for their meaningful dissection, classification and naming beyond the classical fine-root vs coarse-root approach; (2) considering the specificity of root research to produce sound laboratory and field data; (3) describing typical, but overlooked steps for studying roots (e.g. root handling, cleaning and storage); and (4) gathering metadata necessary for the interpretation of results and their reuse. Most importantly, all root traits have been introduced with some degree of ecological context that will be a foundation for understanding their ecological meaning, their typical use and uncertainties, and some methodological and conceptual perspectives for future research. Considering all of this, we urge readers not to solely extract protocol recommendations for trait measurements from this work, but to take a moment to read and reflect on the extensive information contained in this broader guide to root ecology, including sections I-VII and the many introductions to each section and root trait description. Finally, it is critical to understand that a major aim of this guide is to help break down barriers between the many subdisciplines of root ecology and ecophysiology, broaden researchers' views on the multiple aspects of root study and create favourable conditions for the inception of comprehensive experiments on the role of roots in plant and ecosystem functioning.
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Affiliation(s)
- Grégoire T Freschet
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, 1919 route de Mende, Montpellier, 34293, France
- Station d'Ecologie Théorique et Expérimentale, CNRS, 2 route du CNRS, 09200, Moulis, France
| | - Loïc Pagès
- UR 1115 PSH, Centre PACA, site Agroparc, INRAE, 84914, Avignon cedex 9, France
| | - Colleen M Iversen
- Environmental Sciences Division and Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Louise H Comas
- USDA-ARS Water Management Research Unit, 2150 Centre Avenue, Bldg D, Suite 320, Fort Collins, CO, 80526, USA
| | - Boris Rewald
- Department of Forest and Soil Sciences, University of Natural Resources and Life Sciences, Vienna, 1190, Austria
| | - Catherine Roumet
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, 1919 route de Mende, Montpellier, 34293, France
| | - Jitka Klimešová
- Department of Functional Ecology, Institute of Botany CAS, Dukelska 135, 37901, Trebon, Czech Republic
| | - Marcin Zadworny
- Institute of Dendrology, Polish Academy of Sciences, Parkowa 5, 62-035, Kórnik, Poland
| | - Hendrik Poorter
- Plant Sciences (IBG-2), Forschungszentrum Jülich GmbH, D-52425, Jülich, Germany
- Department of Biological Sciences, Macquarie University, North Ryde, NSW, 2109, Australia
| | - Johannes A Postma
- Plant Sciences (IBG-2), Forschungszentrum Jülich GmbH, D-52425, Jülich, Germany
| | - Thomas S Adams
- Department of Plant Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Agnieszka Bagniewska-Zadworna
- Department of General Botany, Institute of Experimental Biology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland
| | - A Glyn Bengough
- The James Hutton Institute, Invergowrie, Dundee,, DD2 5DA, UK
- School of Science and Engineering, University of Dundee, Dundee,, DD1 4HN, UK
| | - Elison B Blancaflor
- Noble Research Institute, LLC, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
| | - Ivano Brunner
- Forest Soils and Biogeochemistry, Swiss Federal Research Institute WSL, Zürcherstr. 111, 8903, Birmensdorf, Switzerland
| | - Johannes H C Cornelissen
- Department of Ecological Science, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1085, Amsterdam, 1081 HV, the Netherlands
| | - Eric Garnier
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, 1919 route de Mende, Montpellier, 34293, France
| | - Arthur Gessler
- Forest Dynamics, Swiss Federal Research Institute WSL, Zürcherstr. 111, 8903, Birmensdorf, Switzerland
- Institute of Terrestrial Ecosystems, ETH Zurich, 8092, Zurich, Switzerland
| | - Sarah E Hobbie
- Department of Ecology, Evolution and Behavior, University of Minnesota, St Paul, MN, 55108, USA
| | - Ina C Meier
- Functional Forest Ecology, University of Hamburg, Haidkrugsweg 1, 22885, Barsbütel, Germany
| | - Liesje Mommer
- Plant Ecology and Nature Conservation Group, Department of Environmental Sciences, Wageningen University and Research, PO Box 47, 6700 AA, Wageningen, the Netherlands
| | | | - Laura Rose
- Station d'Ecologie Théorique et Expérimentale, CNRS, 2 route du CNRS, 09200, Moulis, France
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325, Frankfurt am Main, Germany
| | - Peter Ryser
- Laurentian University, 935 Ramsey Lake Road, Sudbury, ON, P3E 2C6, Canada
| | | | - Nadejda A Soudzilovskaia
- Environmental Biology Department, Institute of Environmental Sciences, CML, Leiden University, Leiden, 2300 RA, the Netherlands
| | - Alexia Stokes
- INRAE, AMAP, CIRAD, IRD, CNRS, University of Montpellier, Montpellier, 34000, France
| | - Tao Sun
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110016, China
| | - Oscar J Valverde-Barrantes
- International Center for Tropical Botany, Department of Biological Sciences, Florida International University, Miami, FL, 33199, USA
| | - Monique Weemstra
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, 1919 route de Mende, Montpellier, 34293, France
| | - Alexandra Weigelt
- Systematic Botany and Functional Biodiversity, Institute of Biology, Leipzig University, Johannisallee 21-23, Leipzig, 04103, Germany
| | - Nina Wurzburger
- Odum School of Ecology, University of Georgia, 140 E. Green Street, Athens, GA, 30602, USA
| | - Larry M York
- Biosciences Division and Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Sarah A Batterman
- School of Geography and Priestley International Centre for Climate, University of Leeds, Leeds, LS2 9JT, UK
- Cary Institute of Ecosystem Studies, Millbrook, NY, 12545, USA
| | - Moemy Gomes de Moraes
- Department of Botany, Institute of Biological Sciences, Federal University of Goiás, 19, 74690-900, Goiânia, Goiás, Brazil
| | - Štěpán Janeček
- School of Biological Sciences, The University of Western Australia, 35 Stirling Highway, Crawley (Perth), WA 6009, Australia
| | - Hans Lambers
- School of Biological Sciences, The University of Western Australia, Crawley (Perth), WA, Australia
| | - Verity Salmon
- Environmental Sciences Division and Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Nishanth Tharayil
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, 29634, USA
| | - M Luke McCormack
- Center for Tree Science, Morton Arboretum, 4100 Illinois Rt. 53, Lisle, IL, 60532, USA
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Fazal A, Wen Z, Yang M, Liao Y, Fu J, He C, Wang X, Jie W, Ali F, Hu D, Yin T, Hong Z, Lu G, Qi J, Yang Y. Deciphering the rhizobacterial assemblages under the influence of genetically engineered maize carrying mcry genes. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:60154-60166. [PMID: 34151402 DOI: 10.1007/s11356-021-14901-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 06/10/2021] [Indexed: 06/13/2023]
Abstract
Genetically engineered (GE) maize has been thoroughly studied regarding its agro-environmental impact; however, its concerns for the soil environment remain. This work was aimed to decode rhizosphere microbe interactions and potential ecological hazards associated with GE maize. Rhizobacterial communities of field grown transgenic insect-resistant 2A5 maize carrying mcry1Ab and mcry2Ab genes were compared with control Z58 using PacBio sequencing platform. Also full-length 16S rDNA gene sequencing was used to verify the partial (V3-V4) sequencing results obtained in 2017. Measures of α-diversity displayed transgenic 2A5 to be significantly lower in species richness at the flowering stage; however, diversity remained undisturbed. β-diversity was least affected by genetic modifications where similar community profiles were shared by transgenic 2A5 and control Z58. In addition, root exudation patterns were found to drive variations in bacterial assemblages based on developmental stages. For example, genus Massilia successfully colonized the rhizosphere at jointing stage, while Mucilaginobacter showed higher relative abundance in flowering stages of both 2A5 and Z58. These members are known to possess attributes related to plant growth. The impact of dual-transgene insertion on nifH gene abundance was also analyzed where no apparent significant difference in nifH gene copy number was observed. Our results confirmed that full-length 16S rDNA sequencing was sufficient to provide higher taxonomic resolution. Also, results of our 2-year field trials confirmed that there is no significant impact of mcry gene integration on belowground biomasses. Therefore, GE insect-resistant 2A5 maize carrying mcry1Ab and mcry2Ab genes can continue to benefit human populations by increasing crop productivity. In future, further research needs to be catalyzed to analyze the impact of Bt-insertion on microbial community structure across the years for ecosystem sustainability.
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Affiliation(s)
- Aliya Fazal
- Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Zhongling Wen
- Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Minkai Yang
- Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Yonghui Liao
- Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Jiangyan Fu
- Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Cong He
- Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Xuan Wang
- Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Wencai Jie
- Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Farman Ali
- Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Dongqing Hu
- Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Tongming Yin
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Zhi Hong
- Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Guihua Lu
- Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China.
- School of Life Sciences, Huaiyin Normal University, Huaian, 223300, China.
| | - Jinliang Qi
- Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China.
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China.
| | - Yonghua Yang
- Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China.
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China.
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14
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Mosier S, Córdova SC, Robertson GP. Restoring Soil Fertility on Degraded Lands to Meet Food, Fuel, and Climate Security Needs via Perennialization. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2021. [DOI: 10.3389/fsufs.2021.706142] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A continuously growing pressure to increase food, fiber, and fuel production to meet worldwide demand and achieve zero hunger has put severe pressure on soil resources. Abandoned, degraded, and marginal lands with significant agricultural constraints—many still used for agricultural production—result from inappropriately intensive management, insufficient attention to soil conservation, and climate change. Continued use for agricultural production will often require ever more external inputs such as fertilizers and herbicides, further exacerbating soil degradation and impeding nutrient recycling and retention. Growing evidence suggests that degraded lands have a large potential for restoration, perhaps most effectively via perennial cropping systems that can simultaneously provide additional ecosystem services. Here we synthesize the advantages of and potentials for using perennial vegetation to restore soil fertility on degraded croplands, by summarizing the principal mechanisms underpinning soil carbon stabilization and nitrogen and phosphorus availability and retention. We illustrate restoration potentials with example systems that deliver climate mitigation (cellulosic bioenergy), animal production (intensive rotational grazing), and biodiversity conservation (natural ecological succession). Perennialization has substantial promise for restoring fertility to degraded croplands, helping to meet future food security needs.
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15
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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.
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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
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16
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Differential Resilience of Soil Microbes and Ecosystem Functions Following Cessation of Long-Term Fertilization. Ecosystems 2021. [DOI: 10.1007/s10021-021-00633-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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17
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Gelfand I, Hamilton SK, Kravchenko AN, Jackson RD, Thelen KD, Robertson GP. Empirical Evidence for the Potential Climate Benefits of Decarbonizing Light Vehicle Transport in the U.S. with Bioenergy from Purpose-Grown Biomass with and without BECCS. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:2961-2974. [PMID: 32052964 DOI: 10.1021/acs.est.9b07019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Climate mitigation scenarios limiting global temperature increases to 1.5 °C rely on decarbonizing vehicle transport with bioenergy production plus carbon capture and storage (BECCS), but climate impacts for producing different bioenergy feedstocks have not been directly compared experimentally or for ethanol vs electric light-duty vehicles. A field experiment at two Midwest U.S. sites on contrasting soils revealed that feedstock yields of seven potential bioenergy cropping systems varied substantially within sites but little between. Bioenergy produced per hectare reflected yields: miscanthus > poplar > switchgrass > native grasses ≈ maize stover (residue) > restored prairie ≈ early successional. Greenhouse gas emission intensities for ethanol vehicles ranged from 20 to -179 g CO2e MJ-1: maize stover ≫ miscanthus ≈ switchgrass ≈ native grasses ≈ poplar > early successional ≥ restored prairie; direct climate benefits ranged from ∼80% (stover) to 290% (restored prairie) reductions in CO2e compared to petroleum and were similar for electric vehicles. With carbon capture and storage (CCS), reductions in emission intensities ranged from 204% (stover) to 416% (restored prairie) for ethanol vehicles and from 329 to 558% for electric vehicles, declining 27 and 15%, respectively, once soil carbon equilibrates within several decades of establishment. Extrapolation based on expected U.S. transportation energy use suggests that, once CCS potential is maximized with CO2 pipeline infrastructure, negative emissions from bioenergy with CCS for light-duty electric vehicles could capture >900 Tg CO2e year-1 in the U.S. In the future, as other renewable electricity sources become more important, electricity production from biomass would offset less fossil fuel electricity, and the advantage of electric over ethanol vehicles would decrease proportionately.
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Affiliation(s)
- Ilya Gelfand
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, Michigan 48824, United States
- W.K. Kellogg Biological Station, Michigan State University, Hickory Corners, Michigan 49060, United States
- The French Associates Institute for Agriculture and Biotechnology of Drylands, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Beer-Sheva 84990, Israel
| | - Stephen K Hamilton
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, Michigan 48824, United States
- W.K. Kellogg Biological Station, Michigan State University, Hickory Corners, Michigan 49060, United States
- Department of Integrative Biology, Michigan State University, East Lansing, Michigan 48824, United States
- Cary Institute of Ecosystem Studies, Millbrook, New York 12545, United States
| | - Alexandra N Kravchenko
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, Michigan 48824, United States
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, Michigan 48824, United States
| | - Randall D Jackson
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Department of Agronomy, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Kurt D Thelen
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, Michigan 48824, United States
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, Michigan 48824, United States
| | - G Philip Robertson
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, Michigan 48824, United States
- W.K. Kellogg Biological Station, Michigan State University, Hickory Corners, Michigan 49060, United States
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, Michigan 48824, United States
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18
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Jach-Smith LC, Jackson RD. Inorganic N addition replaces N supplied to switchgrass (Panicum virgatum) by arbuscular mycorrhizal fungi. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2020; 30:e02047. [PMID: 31758822 DOI: 10.1002/eap.2047] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 02/20/2019] [Accepted: 04/25/2019] [Indexed: 06/10/2023]
Abstract
Arbuscular mycorrhizal fungi (AMF) provide many benefits in agroecosystems including improved soil tilth, carbon sequestration, and water and nutrient transfer to plants. AMF are known to affect plant nitrogen (N) dynamics and transfer N to plants, but there have been few studies addressing whether the amount of N transferred to plants by AMF is agronomically relevant. We used δ15 N natural abundance methods and δ15 N mass balance equations to estimate the amount of plant N derived from AMF transfer in perennial grasses managed for bioenergy production under different N addition treatments (0, 56, and 196 kg N/ha). Differentiation of δ15 N among plant, soil N, and AMF pools was higher than anticipated leading to calculations of 34-55% of plant N transferred by AMF in the treatments receiving no N addition to 6-22% of plant N transferred to plants in high-N addition treatments. AMF extra-radical hyphae biomass was significantly reduced in the high-N (196 kg N/ha) addition treatments, which was negatively correlated to enriched plant δ15 N. Our results suggest that N addition decreases AMF N transfer to plants. When N was limiting to plant growth, AMF supplied agronomically significant amounts of plant N, and a higher proportion of overall plant N. Because differentiation between N pools was greater than expected, stable isotope measurements can be used to estimate N transfer to AMF plant hosts.
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Affiliation(s)
- Laura C Jach-Smith
- Nelson Institute for Environmental Studies, University of Wisconsin-Madison, 550 North Park Street, Madison, Wisconsin, 53706, USA
- DOE-Great Lakes Bioenergy Research Center, 1552 University Avenue, Madison, Wisconsin, 53726, USA
| | - Randall D Jackson
- Nelson Institute for Environmental Studies, University of Wisconsin-Madison, 550 North Park Street, Madison, Wisconsin, 53706, USA
- DOE-Great Lakes Bioenergy Research Center, 1552 University Avenue, Madison, Wisconsin, 53726, USA
- Department of Agronomy, University of Wisconsin-Madison, 1575 Linden Drive, Madison, Wisconsin, 53706, USA
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19
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Blesh J. Feedbacks between nitrogen fixation and soil organic matter increase ecosystem functions in diversified agroecosystems. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2019; 29:e01986. [PMID: 31359515 DOI: 10.1002/eap.1986] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 07/01/2019] [Accepted: 07/12/2019] [Indexed: 05/25/2023]
Abstract
Nitrogen (N) losses from intensified agriculture are a major cause of global change, due to nitrate (NO3- ) export and the eutrophication of aquatic systems as well as emissions of nitrous oxide (N2 O) into the atmosphere. Diversified agroecosystems with legume cover crops couple N and carbon (C) inputs to soil and reduce N pollution, but there is a need to identify controls on legume N2 fixation across ecosystems with variable soil conditions. Here, I tested the hypothesis that N mineralization from turnover of soil organic matter (SOM) regulates legume N2 fixation across 10 farms that spanned a gradient of SOM levels. I separated soil samples into two SOM fractions, based on size and density, which are indicators of soil nutrient cycling and N availability (free particulate organic matter and intra-aggregate particulate organic matter [POM]). This study indicates downregulation of legume N2 fixation in diversified agroecosystems with increasing N availability in intra-aggregate POM and increasing N mineralization. Intercropping the legume with a grass weakened the relationship between N in POM and N2 fixation due to N assimilation by the grass. Further, mean rates of N and C mineralization across sites increased with two seasons of a legume-grass cover crop mixture, which could enhance this stabilizing feedback between soil N availability and N2 fixation over time. These results suggest a potential mechanism for the diversity-ecosystem-function relationships measured in long-term studies of agroecosystems, in which regular use of legume cover crops increases total soil organic C and N and reduces negative environmental impacts of crop production.
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Affiliation(s)
- Jennifer Blesh
- School for Environment and Sustainability, University of Michigan, 440 Church Street, Ann Arbor, Michigan, 48109, USA
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20
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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: 15] [Impact Index Per Article: 3.0] [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.
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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
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Yoneyama T, Terakado-Tonooka J, Bao Z, Minamisawa K. Molecular Analyses of the Distribution and Function of Diazotrophic Rhizobia and Methanotrophs in the Tissues and Rhizosphere of Non-Leguminous Plants. PLANTS 2019; 8:plants8100408. [PMID: 31614562 PMCID: PMC6843303 DOI: 10.3390/plants8100408] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Revised: 09/26/2019] [Accepted: 10/10/2019] [Indexed: 01/16/2023]
Abstract
Biological nitrogen fixation (BNF) by plants and its bacterial associations represent an important natural system for capturing atmospheric dinitrogen (N2) and processing it into a reactive form of nitrogen through enzymatic reduction. The study of BNF in non-leguminous plants has been difficult compared to nodule-localized BNF in leguminous plants because of the diverse sites of N2 fixation in non-leguminous plants. Identification of the involved N2-fixing bacteria has also been difficult because the major nitrogen fixers were often lost during isolation attempts. The past 20 years of molecular analyses has led to the identification of N2 fixation sites and active nitrogen fixers in tissues and the rhizosphere of non-leguminous plants. Here, we examined BNF hotspots in six reported non-leguminous plants. Novel rhizobia and methanotrophs were found to be abundantly present in the free-living state at sites where carbon and energy sources were predominantly available. In the carbon-rich apoplasts of plant tissues, rhizobia such as Bradyrhizobium spp. microaerobically fix N2. In paddy rice fields, methane molecules generated under anoxia are oxidized by xylem aerenchyma-transported oxygen with the simultaneous fixation of N2 by methane-oxidizing methanotrophs. We discuss the effective functions of the rhizobia and methanotrophs in non-legumes for the acquisition of fixed nitrogen in addition to research perspectives.
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Affiliation(s)
- Tadakatsu Yoneyama
- Department of Applied Biological Chemistry, University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan.
- National Agriculture and Food Research Organization, Kannondai 3-1-1, Tsukuba, Ibaraki 305-8666, Japan.
| | - Junko Terakado-Tonooka
- National Agriculture and Food Research Organization, Kannondai 3-1-1, Tsukuba, Ibaraki 305-8666, Japan.
| | - Zhihua Bao
- School of Ecology and Environment, Inner Mongolia University, 235 West University Blvd., Hohhot 010021, Inner Mongolia, China.
| | - Kiwamu Minamisawa
- Graduate School of Life Sciences, Tohoku University, Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan.
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Singer E, Bonnette J, Woyke T, Juenger TE. Conservation of Endophyte Bacterial Community Structure Across Two Panicum Grass Species. Front Microbiol 2019; 10:2181. [PMID: 31611851 PMCID: PMC6777145 DOI: 10.3389/fmicb.2019.02181] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 09/05/2019] [Indexed: 02/01/2023] Open
Abstract
Panicum represents a large genus of many North American prairie grass species. These include switchgrass (Panicum virgatum), a biofuel crop candidate with wide geographic range, as well as Panicum hallii, a close relative to switchgrass, which serves as a model system for the study of Panicum genetics due to its diploid genome and short growth cycles. For the advancement of switchgrass as a biofuel crop, it is essential to understand host microbiome interactions, which can be impacted by plant genetics and environmental factors inducing ecotype-specific phenotypic traits. We here compared rhizosphere and root endosphere bacterial communities of upland and lowland P. virgatum and P. hallii genotypes planted at two sites in Texas. Our analysis shows that sampling site predominantly contributed to bacterial community variance in the rhizosphere, however, impacted root endosphere bacterial communities much less. Instead we observed a relatively large core endophytic microbiome dominated by ubiquitously root-colonizing bacterial genera Streptomyces, Pseudomonas, and Bradyrhizobium. Endosphere communities displayed comparable diversity and conserved community structures across genotypes of both Panicum species. Functional insights into interactions between P. hallii and its root endophyte microbiome could hence inform testable hypotheses that are relevant for the improvement of switchgrass as a biofuel crop.
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Affiliation(s)
- Esther Singer
- US Department of Energy, Joint Genome Institute, Walnut Creek, CA, United States
| | - Jason Bonnette
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, United States
| | - Tanja Woyke
- US Department of Energy, Joint Genome Institute, Walnut Creek, CA, United States
| | - Thomas E Juenger
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, United States
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Hestrin R, Hammer EC, Mueller CW, Lehmann J. Synergies between mycorrhizal fungi and soil microbial communities increase plant nitrogen acquisition. Commun Biol 2019; 2:233. [PMID: 31263777 PMCID: PMC6588552 DOI: 10.1038/s42003-019-0481-8] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 05/28/2019] [Indexed: 01/03/2023] Open
Abstract
Nitrogen availability often restricts primary productivity in terrestrial ecosystems. Arbuscular mycorrhizal fungi are ubiquitous symbionts of terrestrial plants and can improve plant nitrogen acquisition, but have a limited ability to access organic nitrogen. Although other soil biota mineralize organic nitrogen into bioavailable forms, they may simultaneously compete for nitrogen, with unknown consequences for plant nutrition. Here, we show that synergies between the mycorrhizal fungus Rhizophagus irregularis and soil microbial communities have a highly non-additive effect on nitrogen acquisition by the model grass Brachypodium distachyon. These multipartite microbial synergies result in a doubling of the nitrogen that mycorrhizal plants acquire from organic matter and a tenfold increase in nitrogen acquisition compared to non-mycorrhizal plants grown in the absence of soil microbial communities. This previously unquantified multipartite relationship may contribute to more than 70 Tg of annually assimilated plant nitrogen, thereby playing a critical role in global nutrient cycling and ecosystem function.
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Affiliation(s)
- Rachel Hestrin
- Soil and Crop Sciences, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853 USA
| | - Edith C. Hammer
- Department of Biology, Lund University, Box 118, 22100 Lund, Sweden
| | - Carsten W. Mueller
- Lehrstuhl für Bodenkunde, TU München, 85356 Freising-Weihenstephan, Germany
| | - Johannes Lehmann
- Soil and Crop Sciences, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853 USA
- Atkinson Center for a Sustainable Future, Cornell University, Ithaca, NY 14853 USA
- Institute for Advanced Studies, TU München, 85748 Garching, Germany
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24
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To Fix or Not To Fix: Controls on Free-Living Nitrogen Fixation in the Rhizosphere. Appl Environ Microbiol 2019; 85:AEM.02546-18. [PMID: 30658971 DOI: 10.1128/aem.02546-18] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Free-living nitrogen fixation (FLNF) in the rhizosphere, or N fixation by heterotrophic bacteria living on/near root surfaces, is ubiquitous and a significant source of N in some terrestrial systems. FLNF is also of interest in crop production as an alternative to chemical fertilizer, potentially reducing production costs and ameliorating negative environmental impacts of fertilizer N additions. Despite this interest, a mechanistic understanding of controls (e.g., carbon, oxygen, nitrogen, and nutrient availability) on FLNF in the rhizosphere is lacking but necessary. FLNF is distinct from and occurs under more diverse and dynamic conditions than symbiotic N fixation; therefore, predicting FLNF rates and understanding controls on FLNF has proven difficult. This has led to large gaps in our understanding of FLNF, and studies aimed at identifying controls on FLNF are needed. Here, we provide a mechanistic overview of FLNF, including how various controls may influence FLNF in the rhizosphere in comparison with symbiotic N fixation occurring in plant nodules where environmental conditions are moderated by the plant. We apply this knowledge to a real-world example, the bioenergy crop switchgrass (Panicum virgatum), to provide context of how FLNF may function in a managed system. We also highlight future challenges to assessing FLNF and understanding how FLNF functions in the environment and significantly contributes to plant N availability and productivity.
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25
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White JF, Kingsley KL, Verma SK, Kowalski KP. Rhizophagy Cycle: An Oxidative Process in Plants for Nutrient Extraction from Symbiotic Microbes. Microorganisms 2018; 6:microorganisms6030095. [PMID: 30227634 PMCID: PMC6164190 DOI: 10.3390/microorganisms6030095] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 09/01/2018] [Accepted: 09/05/2018] [Indexed: 12/20/2022] Open
Abstract
In this paper, we describe a mechanism for the transfer of nutrients from symbiotic microbes (bacteria and fungi) to host plant roots that we term the ‘rhizophagy cycle.’ In the rhizophagy cycle, microbes alternate between a root intracellular endophytic phase and a free-living soil phase. Microbes acquire soil nutrients in the free-living soil phase; nutrients are extracted through exposure to host-produced reactive oxygen in the intracellular endophytic phase. We conducted experiments on several seed-vectored microbes in several host species. We found that initially the symbiotic microbes grow on the rhizoplane in the exudate zone adjacent the root meristem. Microbes enter root tip meristem cells—locating within the periplasmic spaces between cell wall and plasma membrane. In the periplasmic spaces of root cells, microbes convert to wall-less protoplast forms. As root cells mature, microbes continue to be subjected to reactive oxygen (superoxide) produced by NADPH oxidases (NOX) on the root cell plasma membranes. Reactive oxygen degrades some of the intracellular microbes, also likely inducing electrolyte leakage from microbes—effectively extracting nutrients from microbes. Surviving bacteria in root epidermal cells trigger root hair elongation and as hairs elongate bacteria exit at the hair tips, reforming cell walls and cell shapes as microbes emerge into the rhizosphere where they may obtain additional nutrients. Precisely what nutrients are transferred through rhizophagy or how important this process is for nutrient acquisition is still unknown.
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Affiliation(s)
- James F White
- Department of Plant Biology, Rutgers University, New Brunswick, NJ 08901, USA.
| | - Kathryn L Kingsley
- Department of Plant Biology, Rutgers University, New Brunswick, NJ 08901, USA.
| | - Satish K Verma
- Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi, UP 221005, India.
| | - Kurt P Kowalski
- U.S. Geological Survey, Great Lakes Science Center, 1451 Green Road, Ann Arbor, MI 48105-2807, USA.
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26
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Roley SS, Duncan DS, Liang D, Garoutte A, Jackson RD, Tiedje JM, Robertson GP. Associative nitrogen fixation (ANF) in switchgrass (Panicum virgatum) across a nitrogen input gradient. PLoS One 2018; 13:e0197320. [PMID: 29856843 PMCID: PMC5983442 DOI: 10.1371/journal.pone.0197320] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 04/29/2018] [Indexed: 11/23/2022] Open
Abstract
Associative N fixation (ANF), the process by which dinitrogen gas is converted to ammonia by bacteria in casual association with plants, has not been well-studied in temperate ecosystems. We examined the ANF potential of switchgrass (Panicum virgatum L.), a North American prairie grass whose productivity is often unresponsive to N fertilizer addition, via separate short-term 15N2 incubations of rhizosphere soils and excised roots four times during the growing season. Measurements occurred along N fertilization gradients at two sites with contrasting soil fertility (Wisconsin, USA Mollisols and Michigan, USA Alfisols). In general, we found that ANF potentials declined with long-term N addition, corresponding with increased soil N availability. Although we hypothesized that ANF potential would track plant N demand through the growing season, the highest root fixation rates occurred after plants senesced, suggesting that root diazotrophs exploit carbon (C) released during senescence, as C is translocated from aboveground tissues to roots for wintertime storage. Measured ANF potentials, coupled with mass balance calculations, suggest that ANF appears to be an important source of N to unfertilized switchgrass, and, by extension, to temperate grasslands in general.
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Affiliation(s)
- Sarah S. Roley
- WK Kellogg Biological Station, Michigan State University, Hickory Corners, Michigan, United States of America
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, Michigan, United States of America
- * E-mail:
| | - David S. Duncan
- Department of Agronomy, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Di Liang
- WK Kellogg Biological Station, Michigan State University, Hickory Corners, Michigan, United States of America
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, Michigan, United States of America
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, Michigan, United States of America
| | - Aaron Garoutte
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, Michigan, United States of America
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, United States of America
| | - Randall D. Jackson
- Department of Agronomy, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - James M. Tiedje
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, Michigan, United States of America
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, United States of America
| | - G. Philip Robertson
- WK Kellogg Biological Station, Michigan State University, Hickory Corners, Michigan, United States of America
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, Michigan, United States of America
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, Michigan, United States of America
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