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Kakouridis A, Yuan M, Nuccio EE, Hagen JA, Fossum CA, Moore ML, Estera-Molina KY, Nico PS, Weber PK, Pett-Ridge J, Firestone MK. Arbuscular mycorrhiza convey significant plant carbon to a diverse hyphosphere microbial food web and mineral-associated organic matter. THE NEW PHYTOLOGIST 2024; 242:1661-1675. [PMID: 38358052 DOI: 10.1111/nph.19560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Accepted: 12/04/2023] [Indexed: 02/16/2024]
Abstract
Arbuscular mycorrhizal fungi (AMF) transport substantial plant carbon (C) that serves as a substrate for soil organisms, a precursor of soil organic matter (SOM), and a driver of soil microbial dynamics. Using two-chamber microcosms where an air gap isolated AMF from roots, we 13CO2-labeled Avena barbata for 6 wk and measured the C Rhizophagus intraradices transferred to SOM and hyphosphere microorganisms. NanoSIMS imaging revealed hyphae and roots had similar 13C enrichment. SOM density fractionation, 13C NMR, and IRMS showed AMF transferred 0.77 mg C g-1 of soil (increasing total C by 2% relative to non-mycorrhizal controls); 33% was found in occluded or mineral-associated pools. In the AMF hyphosphere, there was no overall change in community diversity but 36 bacterial ASVs significantly changed in relative abundance. With stable isotope probing (SIP)-enabled shotgun sequencing, we found taxa from the Solibacterales, Sphingobacteriales, Myxococcales, and Nitrososphaerales (ammonium oxidizing archaea) were highly enriched in AMF-imported 13C (> 20 atom%). Mapping sequences from 13C-SIP metagenomes to total ASVs showed at least 92 bacteria and archaea were significantly 13C-enriched. Our results illustrate the quantitative and ecological impact of hyphal C transport on the formation of potentially protective SOM pools and microbial roles in the AMF hyphosphere soil food web.
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Affiliation(s)
- Anne Kakouridis
- University of California Berkeley, Berkeley, CA, 94720, USA
- Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Mengting Yuan
- University of California Berkeley, Berkeley, CA, 94720, USA
| | - Erin E Nuccio
- Lawrence Livermore National Laboratory, Livermore, 94550, CA, USA
| | - John A Hagen
- University of California Berkeley, Berkeley, CA, 94720, USA
| | | | - Madeline L Moore
- University of California Berkeley, Berkeley, CA, 94720, USA
- Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Katerina Y Estera-Molina
- University of California Berkeley, Berkeley, CA, 94720, USA
- Lawrence Livermore National Laboratory, Livermore, 94550, CA, USA
| | - Peter S Nico
- Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Peter K Weber
- Lawrence Livermore National Laboratory, Livermore, 94550, CA, USA
| | - Jennifer Pett-Ridge
- Lawrence Livermore National Laboratory, Livermore, 94550, CA, USA
- University of California Merced, Merced, 95343, CA, USA
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Musa OI, Akande SA, Ijah UJJ, Abioye OP, Maude AM, Samuel JO, Mustapha A, Abdulrahim AM, Gusdanis ACG. Biofilms communities in the soil: characteristic and interactions using mathematical model. Res Microbiol 2024; 175:104149. [PMID: 37923049 DOI: 10.1016/j.resmic.2023.104149] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 10/17/2023] [Accepted: 10/22/2023] [Indexed: 11/07/2023]
Abstract
There are many different kinds of microorganisms in the soil, and many of them are biofilms because they can make supracellular compounds. Surface-associated microorganisms in a biofilm are encased in a hydrated extracellular polymeric substance that aids in adherence and survival. Numerous different kinds of microorganisms call the soil home. Strong interactions with and among species are made possible by biofilms; this, in turn, might increase the effectiveness with which organic compounds and poisons in soil are degraded. This encouraged us to take a close look at soil biofilm ecosystems, which we do in this paper. In this research, we will look at how soil biofilms arise and how that affects the composition of microbial communities and their function in the soil. Recent years have seen an uptick in interest in questions about biofilm structure and the social interactions of various bacteria. Many concepts elucidating the underlying mathematics of biofilm growth are also presented. Since biofilms are so widespread, this breakthrough in soil biofilm inquiry might help scientists understand soil microbiomes better. Mathematical models further extrapolate the relationships between microbial communities and gives a more precise information as to what is happening in a biofilm. Biofilms can help plants cope with a variety of environmental challenges. Soil quality, plant nourishment, plant protection, bioremediation, and climate change are all influenced by the interplay of biofilm communities. Thus, biofilms play an important role in the development of environmentally friendly and sustainable agriculture.
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Affiliation(s)
- Ojeba Innocent Musa
- Department of Microbiology, Skyline University Nigeria, Kano State, Nigeria.
| | | | | | - Olabisi Peter Abioye
- Department of Microbiology, Federal University of Technology, Minna Niger State, Nigeria
| | - Asmau Mohammed Maude
- Department of Microbiology, Federal University of Technology, Minna Niger State, Nigeria
| | - Job Oloruntoba Samuel
- Department of Microbiology, Federal University of Technology, Minna Niger State, Nigeria
| | - Adamu Mustapha
- Department of Microbiology, Federal University of Technology, Minna Niger State, Nigeria
| | - Al-Musbahu Abdulrahim
- Department of Mathematics, Federal University of Technology, Minna Niger State, Nigeria
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3
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Chen X, Tang L, Wu K, Mo Y, Tang Q, Li G, Zhu Y. Combined contribution of biochar and introduced AM fungi on lead stability and microbial community in polluted agricultural soil. Front Microbiol 2023; 14:1284321. [PMID: 38033595 PMCID: PMC10684681 DOI: 10.3389/fmicb.2023.1284321] [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: 08/28/2023] [Accepted: 10/30/2023] [Indexed: 12/02/2023] Open
Abstract
Introduction Lead (Pb) pollution in agricultural soil has been accelerated by industrial development and human activities, and poses a major threat to agricultural ecosystems. Both biochar and arbuscular mycorrhiza (AM) fungi are considered to play an important role in remediation of Pb contaminated soil. Methods The combined remediation effects of introduced AM fungi and biochar on soil properties, Pb availability, microbial community and functional profiles were systematically investigated in unsterilized Pb-polluted agricultural soil. Results Results indicated that soil nutrients were significantly improved through the combined application of biochar and introduced AM fungi. The introduced AM fungi combined with biochar prepared at 400°C and 500°C promoted the transformation of Pb to a more stable state with low bioavailability. Moreover, the addition of AM fungi and biochar affected the relative abundances of dominant bacteria and fungi at the phylum and genus levels. Biochar mainly affected soil bacterial community and obviously increased the relative abundance of Actinobacteria and Blastococcus. The interactions between biochar and introduced AM fungi mainly affected fungal community, and increased the abundance of Ascomycota and Botryotrichum. Further, PICRUSt analysis indicated biochar amendment supported stronger bacterial metabolic functional potentials. Discussion Therefore, the combined application of biochar and Therefore, the combined application of biochar and introduced AM fungi could improve soil nutrients, reduce Pb introduced AM fungi could improve soil nutrients, reduce Pb availability, availability, and show and show a positive effect on a positive effect on indigenous microbial communities and indigenous microbial communities and metabolic functions in metabolic functions in farmland soil.
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Affiliation(s)
- Xuedong Chen
- College of Life Science, Luoyang Normal University, Luoyang, Henan, China
| | - Lin Tang
- College of Life Science, Luoyang Normal University, Luoyang, Henan, China
| | - Kongyang Wu
- College of Life Science, Luoyang Normal University, Luoyang, Henan, China
| | - Yifan Mo
- College of Life Science, Luoyang Normal University, Luoyang, Henan, China
| | - Qian Tang
- College of Life Science, Luoyang Normal University, Luoyang, Henan, China
| | - Gaojie Li
- School of Physics and Engineering, Henan University of Science and Technology, Luoyang, Henan, China
| | - Ying Zhu
- College of Life Science, Luoyang Normal University, Luoyang, Henan, China
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Pang W, Zhang P, Zhang Y, Zhang X, Huang Y, Zhang T, Liu B. The Ectomycorrhizal Fungi and Soil Bacterial Communities of the Five Typical Tree Species in the Junzifeng National Nature Reserve, Southeast China. PLANTS (BASEL, SWITZERLAND) 2023; 12:3853. [PMID: 38005750 PMCID: PMC10675191 DOI: 10.3390/plants12223853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 10/28/2023] [Accepted: 10/31/2023] [Indexed: 11/26/2023]
Abstract
To explore the contribution of microorganisms to forest ecosystem function, we studied the ectomycorrhizal (ECM) fungal and soil bacterial community of the five typical tree species (Pinus massoniana, PM; Castanopsis carlesii, CC; Castanopsis eyrei, CE; Castanopsis fargesii, CF; and Keteleeria cyclolepis, KC) at the Junzifeng National Nature Reserve. The results indicated that the ECM fungal and soil bacterial diversity of CC and CF was similar, and the diversity rates of CC and CF were higher than those of PM, CE, and KC. Cenococcum geophilum and unclassified_Cortinariaceae II were the most prevalent occurring ECM fungi species in the five typical tree species, followed by unclassified_Cortinariaceae I and Lactarius atrofuscus. In bacteria, the dominant bacterial genera were Acidothermus, Bradyrhizobium, Acidibacter, Candidatus_Solibacter, Candidatus_Koribacter, Roseiarcus, and Bryobacter. EMF fungi and soil bacteria were correlated with edaphic factors, especially the soil pH, TP, and TK, caused by stand development. The results show that the community characteristics of ECM fungi and bacteria in the typical tree species of the Junzifeng National Nature Reserve reflect the critical role of soil microorganisms in stabilizing forest ecosystems.
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Affiliation(s)
- Wenbo Pang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (W.P.); (P.Z.); (Y.Z.)
| | - Panpan Zhang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (W.P.); (P.Z.); (Y.Z.)
| | - Yuhu Zhang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (W.P.); (P.Z.); (Y.Z.)
| | - Xiao Zhang
- Key Laboratory of Soil Ecosystem Health and Regulation of Fujian Provincial University, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
| | - Yanbin Huang
- Administration Bureau of Fujian Junzifeng National Nature Reserve, Mingxi 365200, China;
| | - Taoxiang Zhang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (W.P.); (P.Z.); (Y.Z.)
| | - Bao Liu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (W.P.); (P.Z.); (Y.Z.)
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Wang H, Du X, Zhang Z, Feng F, Zhang J. Rhizosphere interface microbiome reassembly by arbuscular mycorrhizal fungi weakens cadmium migration dynamics. IMETA 2023; 2:e133. [PMID: 38868220 PMCID: PMC10989832 DOI: 10.1002/imt2.133] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 07/14/2023] [Accepted: 08/08/2023] [Indexed: 06/14/2024]
Abstract
The prevalence of cadmium (Cd)-polluted agricultural soils is increasing globally, and arbuscular mycorrhizal fungi (AMF) can reduce the absorption of heavy metals by plants and improve mineral nutrition. However, the immobilization of the rhizosphere on cadmium is often overlooked. In this study, Glomus mosseae and Medicago sativa were established as symbiotes, and Cd migration and environmental properties in the rhizosphere were analyzed. AMF reduced Cd migration, and Cd2+ changed to an organic-bound state. AMF symbiosis treatment and Cd exposure resulted in microbial community variation, exhibiting a distinct deterministic process (|βNTI| > 2), which ultimately resulted in a core microbiome function of heavy metal resistance and nutrient cycling. AMF increased available N and P, extracellular enzyme activity (LaC, LiP, and CAT), organic matter content (TOC, EOC, and GRSP), and Eh of the rhizosphere soil, significantly correlating with decreased Cd migration (p < 0.05). Furthermore, AMF significantly affected root metabolism by upregulating 739 metabolites, with flavonoids being the main factor causing microbiome variation. The structural equation model and variance partial analysis revealed that the superposition of the root metabolites, microbial, and soil exhibited the maximum explanation rate for Cd migration reduction (42.4%), and the microbial model had the highest single explanation rate (15.5%). Thus, the AMF in the rhizosphere microenvironment can regulate metabolite-soil-microbial interactions, reducing Cd migration. In summary, the study provides a new scientific explanation for how AMF improves plant Cd tolerance and offers a sustainable solution that could benefit both the environment and human health.
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Affiliation(s)
- Hong‐Rui Wang
- College of Life ScienceNortheast Forestry UniversityHarbinChina
| | - Xin‐Ran Du
- College of Life ScienceNortheast Forestry UniversityHarbinChina
| | - Zhuo‐Yun Zhang
- College of Life ScienceNortheast Forestry UniversityHarbinChina
| | - Fu‐Juan Feng
- College of Life ScienceNortheast Forestry UniversityHarbinChina
| | - Jia‐Ming Zhang
- College of Life ScienceNortheast Forestry UniversityHarbinChina
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Langrand J, Lounès-Hadj Sahraoui A, Duclercq J, Raveau R, Laruelle F, Bert V, Facon N, Tisserant B, Fontaine J. Coriander ( Coriandrum sativum) Cultivation Combined with Arbuscular Mycorrhizal Fungi Inoculation and Steel Slag Application Influences Trace Elements-Polluted Soil Bacterial Functioning. PLANTS (BASEL, SWITZERLAND) 2023; 12:618. [PMID: 36771702 PMCID: PMC9920375 DOI: 10.3390/plants12030618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/19/2023] [Accepted: 01/23/2023] [Indexed: 06/18/2023]
Abstract
The cultivation of aromatic plants for the extraction of essential oils has been presented as an innovative and economically viable alternative for the remediation of areas polluted with trace elements (TE). Therefore, this study focuses on the contribution of the cultivation of coriander and the use of arbuscular mycorrhizal fungi (AMF) in combination with mineral amendments (steel slag) on the bacterial function of the rhizosphere, an aspect that is currently poorly understood and studied. The introduction of soil amendments, such as steel slag or mycorrhizal inoculum, had no significant effect on coriander growth. However, steel slag changed the structure of the bacterial community in the rhizosphere without affecting microbial function. In fact, Actinobacteria were significantly less abundant under slag-amended conditions, while the relative proportion of Gemmatimonadota increased. On the other hand, the planting of coriander affects the bacterial community structure and significantly increased the bacterial functional richness of the amended soil. Overall, these results show that planting coriander most affected the structure and functioning of bacterial communities in the TE-polluted soils and reversed the effects of mineral amendments on rhizosphere bacterial communities and their activities. This study highlights the potential of coriander, especially in combination with steel slag, for phytomanagement of TE-polluted soils, by improving soil quality and health.
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Affiliation(s)
- Julien Langrand
- Unité de Chimie Environnementale et Interactions sur le Vivant (UCEIV-UR 4492), Université Littoral Côte d’Opale, SFR Condorcet FR CNRS 3417, CS 80699, 62228 Calais, France
| | - Anissa Lounès-Hadj Sahraoui
- Unité de Chimie Environnementale et Interactions sur le Vivant (UCEIV-UR 4492), Université Littoral Côte d’Opale, SFR Condorcet FR CNRS 3417, CS 80699, 62228 Calais, France
| | - Jérôme Duclercq
- Unité Écologie et Dynamique des Systèmes Anthropisés (EDYSAN UMR CNRS 7058 CNRS), Université de Picardie Jules Verne, UFR des Sciences, 80029 Amiens, France
| | - Robin Raveau
- Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), UMR Santé et Agroécologie du Vignoble (SAVE), Bordeaux Sciences Agro, ISVV, 33882 Villenave d’Ornon, France
| | - Frédéric Laruelle
- Unité de Chimie Environnementale et Interactions sur le Vivant (UCEIV-UR 4492), Université Littoral Côte d’Opale, SFR Condorcet FR CNRS 3417, CS 80699, 62228 Calais, France
| | - Valérie Bert
- Unité Technologies Propres et Economie Circulaire, INERIS, Parc Technologique Alata, BP2, 60550 Verneuil en Halatte, France
| | - Natacha Facon
- Unité de Chimie Environnementale et Interactions sur le Vivant (UCEIV-UR 4492), Université Littoral Côte d’Opale, SFR Condorcet FR CNRS 3417, CS 80699, 62228 Calais, France
| | - Benoît Tisserant
- Unité de Chimie Environnementale et Interactions sur le Vivant (UCEIV-UR 4492), Université Littoral Côte d’Opale, SFR Condorcet FR CNRS 3417, CS 80699, 62228 Calais, France
| | - Joël Fontaine
- Unité de Chimie Environnementale et Interactions sur le Vivant (UCEIV-UR 4492), Université Littoral Côte d’Opale, SFR Condorcet FR CNRS 3417, CS 80699, 62228 Calais, France
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Amiour S, Chekroud K, Font-Verdera F, Anver S, Liébana R, Hafdi O, Viver T. Overview of the Diversity of Extremely Saline Soils from a Semi-Arid Region Using 16S rRNA Gene Sequencing: A Case Study of the Sebkhas in Algerian High Plateaus. Microbiology (Reading) 2022. [DOI: 10.1134/s0026261722100472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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Liu J, Ding C, Zhang W, Wei Y, Zhou Y, Zhu W. Litter mixing promoted decomposition rate through increasing diversities of phyllosphere microbial communities. Front Microbiol 2022; 13:1009091. [PMID: 36425041 PMCID: PMC9678933 DOI: 10.3389/fmicb.2022.1009091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 10/19/2022] [Indexed: 11/10/2022] Open
Abstract
Decomposition of forest litter is an essential process for returning nutrients to the soil, which is crucial for preserving soil fertility and fostering the regular biological cycle and nutrient balance of the forest ecosystem. About 70% of the land-based forest litter is made up primarily of leaf litter. However, research on the complex effects and key determinants of leaf litter decomposition is still lacking. In this study, we examined the characteristics of nutrient release and microbial diversity structure during the decomposition of three types of litter in arid and semi-arid regions using 16S rRNA and ITS sequencing technology as well as nutrient content determination. It was revealed that the nutrient content and rate of decomposition of mixed litters were significantly different from those of single species. Following litter mixing, the richness and diversity of the microbial community on leaves significantly increased. It was determined that there was a significant correlation between bacterial diversity and content (Total N, Total P, N/P, and C/P). This study provided a theoretical framework for investigating the decomposition mechanism of mixed litters by revealing the microbial mechanism of mixed decomposition of litters from the microbial community and nutrient levels.
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Affiliation(s)
- Jiaying Liu
- College of Forestry, Shenyang Agriculture University, Shenyang, China
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Research Station of Liaohe-River Plain Forest Ecosystem, Chinese Forest Ecosystem Research Network (CFERN), Shenyang Agricultural University, Tieling, China
| | - Changjun Ding
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- *Correspondence: Changjun Ding,
| | - Weixi Zhang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Yawei Wei
- College of Forestry, Shenyang Agriculture University, Shenyang, China
- Research Station of Liaohe-River Plain Forest Ecosystem, Chinese Forest Ecosystem Research Network (CFERN), Shenyang Agricultural University, Tieling, China
| | - Yongbin Zhou
- College of Forestry, Shenyang Agriculture University, Shenyang, China
- Research Station of Liaohe-River Plain Forest Ecosystem, Chinese Forest Ecosystem Research Network (CFERN), Shenyang Agricultural University, Tieling, China
| | - Wenxu Zhu
- College of Forestry, Shenyang Agriculture University, Shenyang, China
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
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Recreating in vitro tripartite mycorrhizal associations through functional bacterial biofilms. Appl Microbiol Biotechnol 2022; 106:4237-4250. [DOI: 10.1007/s00253-022-11996-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 05/14/2022] [Accepted: 05/16/2022] [Indexed: 12/19/2022]
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Li H, Gao MY, Mo CH, Wong MH, Chen XW, Wang JJ. Potential use of arbuscular mycorrhizal fungi for simultaneous mitigation of arsenic and cadmium accumulation in rice. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:50-67. [PMID: 34610119 DOI: 10.1093/jxb/erab444] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 09/30/2021] [Indexed: 06/13/2023]
Abstract
Rice polluted by metal(loid)s, especially arsenic (As) and cadmium (Cd), imposes serious health risks. Numerous studies have demonstrated that the obligate plant symbionts arbuscular mycorrhizal fungi (AMF) can reduce As and Cd concentrations in rice. The behaviours of metal(loid)s in the soil-rice-AMF system are of significant interest for scientists in the fields of plant biology, microbiology, agriculture, and environmental science. We review the mechanisms of As and Cd accumulation in rice with and without the involvement of AMF. In the context of the soil-rice-AMF system, we assess and discuss the role of AMF in affecting soil ion mobility, chemical forms, transport pathways (including the symplast and apoplast), and genotype variation. A potential strategy for AMF application in rice fields is considered, followed by future research directions to improve theoretical understanding and encourage field application.
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Affiliation(s)
- Hui Li
- Guangdong Provincial Research Centre for Environment Pollution Control and Remediation Materials, Department of Ecology, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Meng Ying Gao
- Guangdong Provincial Research Centre for Environment Pollution Control and Remediation Materials, Department of Ecology, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Ce Hui Mo
- Guangdong Provincial Research Centre for Environment Pollution Control and Remediation Materials, Department of Ecology, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Ming Hung Wong
- Guangdong Provincial Research Centre for Environment Pollution Control and Remediation Materials, Department of Ecology, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
- State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China
- Consortium on Health, Environment, Education and Research (CHEER), The Education University of Hong Kong, Tai Po, Hong Kong, China
| | - Xun Wen Chen
- State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Jun-Jian Wang
- State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China
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Suppression of Arbuscular Mycorrhizal Fungi Aggravates the Negative Interactive Effects of Warming and Nitrogen Addition on Soil Bacterial and Fungal Diversity and Community Composition. Appl Environ Microbiol 2021; 87:e0152321. [PMID: 34469189 DOI: 10.1128/aem.01523-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We examined the impacts of warming, nitrogen (N) addition, and suppression of arbuscular mycorrhizal fungi (AMF) on soil bacterial and fungal richness and community composition in a field experiment. AMF root colonization and the concentration of an AMF-specific phospholipid fatty acid (PLFA) were significantly reduced after the application of the fungicide benomyl as a soil drench. Warming and N addition had no independent effects but interactively decreased soil fungal richness, while warming, N addition, and AMF suppression together reduced soil bacterial richness. Soil bacterial and fungal species diversity was lower with AMF suppression, indicating that AMF suppression has a negative effect on microbial diversity. Warming and N addition decreased the net loss of plant species and the plant species richness, respectively. AMF suppression reduced plant species richness and the net gain of plant species but enhanced the net loss of plant species. Structural equation modeling (SEM) demonstrated that the soil bacterial community responded to the increased soil temperature (ST) induced by warming and the increased soil available N (AN) induced by N addition through changes in AMF colonization and plant species richness; ST directly affected the bacterial community, but AN affected both the soil bacterial and fungal communities via AMF colonization. In addition, higher mycorrhizal colonization increased the plant species richness by increasing the net gains in plant species under warming and N addition. IMPORTANCE AMF can influence the composition and diversity of plant communities. Previous studies have shown that climate warming and N deposition reduce the effectiveness of AMF. However, how AMF affect soil bacterial and fungal communities under these global change drivers is still poorly understood. A 4-year field study revealed that AMF suppression decreased bacterial and fungal diversity irrespective of warming or N addition, while AMF suppression interacted with warming or N addition to reduce bacterial and fungal richness. In addition, bacterial and fungal community compositions were determined by mycorrhizal colonization, which was regulated by soil AN and ST. These results suggest that AMF suppression can aggravate the severe losses to native soil microbial diversity and functioning caused by global changes; thus, AMF play a vital role in maintaining belowground ecosystem stability in the future.
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12
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Wu N, Li Z, Tang M. Impact of salt and exogenous AM inoculation on indigenous microbial community structure in the rhizosphere of dioecious plant, Populus cathayana. Sci Rep 2021; 11:18403. [PMID: 34526541 PMCID: PMC8443550 DOI: 10.1038/s41598-021-97674-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 08/27/2021] [Indexed: 12/03/2022] Open
Abstract
The sex-specific physical and biochemical responses in dioecious plants to abiotic stresses could result in gender imbalance, and how to ease the current situation by microorganisms is still unclear. Using native soil where poplars were grown, growth parameters, soil physicochemical properties in the rhizosphere soil of different sexes of Populus cathayana exposed to salt stress and exogenous arbuscular mycorrhizal (AM) inoculation were tested. Besides, the sex-specific microbial community structures in the rhizosphere soil of different sexes of Populus cathayana were compared under salt stress. To identify the sex-specific microbial community characteristics related to salinity and AM symbiosis, a combined qPCR and DGGE method was used to monitor microbial community diversity. Seedlings suffered severe pressure by salt stress, reflected in limited growth, biomass, and nutrient element accumulation, especially on females. Exogenous AM inoculation treatment alleviated these negative effects, especially under salt treatment of 75 mM. Compared with salt effect, exogenous AM inoculation treatment showed a greater effect on soil physical-chemical properties of both sexes. Based on DGGE results, salt stress negatively affected fungal richness but positively affected fungal Simpson diversity index, while exogenous AM inoculation treatment showed the opposite effect. Structural equation modeling (SEM) was performed to show the causal relationships between salt and exogenous AM inoculation treatments with biomass accumulation and microbial community: salt and exogenous AM inoculation treatment showed complicated effects on elementary concentrations, soil properties, which resulted in different relationship with biomass accumulation and microbial community. Salt stress had a negative effect on soil properties and microbial community structure in the rhizosphere soil of P. cathayana, whereas exogenous AM inoculation showed positive impacts on most of the soil physical-chemical properties and microbial community status.
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Affiliation(s)
- Na Wu
- Institute of Applied Biotechnology, School of Life Science, Shanxi Datong University, Datong, 037009, Shanxi, China
| | - Zhen Li
- Institute of Applied Biotechnology, School of Life Science, Shanxi Datong University, Datong, 037009, Shanxi, China
| | - Ming Tang
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-bioresources, Lingnan Guangdong Laboratory of Modern Agriculture, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, Guangdong, China.
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Zhu Q, Wang N, Duan B, Wang Q, Wang Y. Rhizosphere bacterial and fungal communities succession patterns related to growth of poplar fine roots. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 756:143839. [PMID: 33298322 DOI: 10.1016/j.scitotenv.2020.143839] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 10/12/2020] [Accepted: 11/05/2020] [Indexed: 06/12/2023]
Abstract
Understanding the succession patterns of microbial community along root growth provides deep insights into interaction between fine roots and microbes. In the study, we investigated this issue using fine roots from poplar trees and grouped these fine roots into three growth stages: newborn white roots (WR), mature yellow roots (YR) and aging brown roots (BR). Root surface traits were observed under a scanning electron microscopy (SEM). Adhered soils on roots of the three growth stages were grouped into the three soil compartments, correspondingly. The 16S rRNA and ITS1 region were sequenced for bacteria and fungi inhabiting rhizosphere soils, respectively. Phospholipid fatty acid (PLFA) technology was employed to examine the biomass of bacterial and fungal communities. The anatomical traits of fine roots show apparent differences among the WR, YR and BR. Both bacteria and fungi have 25 dominant genera with a relative abundance over 1%, of which, four genera of the bacteria (Bacillus, Burkholderia, Ralstonia and Dyella) differ in abundance among the WR, YR and BR soil compartments and four genera of the fungi (Fusarium, Chaetomium, Penicillium and Scleroderma) differ in abundance among these soil compartments. The operational taxonomic units (OTUs) showed the highest richness in the WR soil compartment for bacteria and in the YR soil compartment for fungi, indicating a different succession pattern between the bacterial and fungal communities. Furthermore, the biomass of bacterial community is larger than the fungal community according to PLFAs, and both decreased along fine root growth. The total carbon (TC) in the soil increases along root growth while the dissolved organic carbon (DOC) decreases. Redundancy analysis (RDA) shows a close correlation between twelve dominant bacteria genera and the total organic carbon (TOC), the readily oxidizable organic carbon (ROC) and DOC and ten dominant fungi genera with the TOC and ROC. In conclusion, our results indicate that fine roots growth has shaped the composition and structure of root associated bacterial and fungal communities.
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Affiliation(s)
- Qiliang Zhu
- Taishan Forest Ecosystem Research Station of State Forestry Administration, College of Forestry, Shandong Agricultural University, Tai'an 271018, PR China
| | - Nian Wang
- Taishan Forest Ecosystem Research Station of State Forestry Administration, College of Forestry, Shandong Agricultural University, Tai'an 271018, PR China
| | - Baoli Duan
- Institute of Mountain Hazards and Environments, Chinese Academy of Sciences, Chengdu 610041, PR China
| | - Qingkui Wang
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110164, PR China
| | - Yanping Wang
- Taishan Forest Ecosystem Research Station of State Forestry Administration, College of Forestry, Shandong Agricultural University, Tai'an 271018, PR China.
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Competitive Exclusion and Metabolic Dependency among Microorganisms Structure the Cellulose Economy of an Agricultural Soil. mBio 2021; 12:mBio.03099-20. [PMID: 33402535 PMCID: PMC8545098 DOI: 10.1128/mbio.03099-20] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Microorganisms that degrade cellulose utilize extracellular reactions that yield free by-products which can promote interactions with noncellulolytic organisms. We hypothesized that these interactions determine the ecological and physiological traits governing the fate of cellulosic carbon (C) in soil. We performed comparative genomics with genome bins from a shotgun metagenomic-stable isotope probing experiment to characterize the attributes of cellulolytic and noncellulolytic taxa accessing 13C from cellulose. We hypothesized that cellulolytic taxa would exhibit competitive traits that limit access, while noncellulolytic taxa would display greater metabolic dependency, such as signatures of adaptive gene loss. We tested our hypotheses by evaluating genomic traits indicative of competitive exclusion or metabolic dependency, such as antibiotic production, growth rate, surface attachment, biomass degrading potential, and auxotrophy. The most 13C-enriched taxa were cellulolytic Cellvibrio (Gammaproteobacteria) and Chaetomium (Ascomycota), which exhibited a strategy of self-sufficiency (prototrophy), rapid growth, and competitive exclusion via antibiotic production. Auxotrophy was more prevalent in cellulolytic Actinobacteria than in cellulolytic Proteobacteria, demonstrating differences in dependency among cellulose degraders. Noncellulolytic taxa that accessed 13C from cellulose (Planctomycetales, Verrucomicrobia, and Vampirovibrionales) were also more dependent, as indicated by patterns of auxotrophy and 13C labeling (i.e., partial labeling or labeling at later stages). Major 13C-labeled cellulolytic microbes (e.g., Sorangium, Actinomycetales, Rhizobiales, and Caulobacteraceae) possessed adaptations for surface colonization (e.g., gliding motility, hyphae, attachment structures) signifying the importance of surface ecology in decomposing particulate organic matter. Our results demonstrated that access to cellulosic C was accompanied by ecological trade-offs characterized by differing degrees of metabolic dependency and competitive exclusion.
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Raveau R, Fontaine J, Hijri M, Lounès-Hadj Sahraoui A. The Aromatic Plant Clary Sage Shaped Bacterial Communities in the Roots and in the Trace Element-Contaminated Soil More Than Mycorrhizal Inoculation - A Two-Year Monitoring Field Trial. Front Microbiol 2020; 11:586050. [PMID: 33424786 PMCID: PMC7794003 DOI: 10.3389/fmicb.2020.586050] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 10/14/2020] [Indexed: 01/04/2023] Open
Abstract
To cope with soil contamination by trace elements (TE), phytomanagement has attracted much attention as being an eco-friendly and cost-effective green approach. In this context, aromatic plants could represent a good option not only to immobilize TE, but also to use their biomass to extract essential oils, resulting in high added-value products suitable for non-food valorization. However, the influence of aromatic plants cultivation on the bacterial community structure and functioning in the rhizosphere microbiota remains unknown. Thus, the present study aims at determining in TE-aged contaminated soil (Pb - 394 ppm, Zn - 443 ppm, and Cd - 7ppm, respectively, 11, 6, and 17 times higher than the ordinary amounts in regional agricultural soils) the effects of perennial clary sage (Salvia sclarea L.) cultivation, during two successive years of growth and inoculated with arbuscular mycorrhizal fungi, on rhizosphere bacterial diversity and community structure. Illumina MiSeq amplicon sequencing targeting bacterial 16S rRNA gene was used to assess bacterial diversity and community structure changes. Bioinformatic analysis of sequencing datasets resulted in 4691 and 2728 bacterial Amplicon Sequence Variants (ASVs) in soil and root biotopes, respectively. Our findings have shown that the cultivation of clary sage displayed a significant year-to-year effect, on both bacterial richness and community structures. We found that the abundance of plant-growth promoting rhizobacteria significantly increased in roots during the second growing season. However, we didn't observe any significant effect of mycorrhizal inoculation neither on bacterial diversity nor on community structure. Our study brings new evidence in TE-contaminated areas of the effect of a vegetation cover with clary sage cultivation on the microbial soil functioning.
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Affiliation(s)
- Robin Raveau
- Université du Littoral Côte d’Opale, Unité de Chimie Environnementale et Interactions sur le Vivant (UCEIV), Calais, France
| | - Joël Fontaine
- Université du Littoral Côte d’Opale, Unité de Chimie Environnementale et Interactions sur le Vivant (UCEIV), Calais, France
| | - Mohamed Hijri
- Institut de Recherche en Biologie Végétale (IRBV) de l’Université de Montréal, Montreal, QC, Canada
- AgroBioSciences, Mohammed VI Polytechnic University (UM6P), Ben Guerir, Morocco
| | - Anissa Lounès-Hadj Sahraoui
- Université du Littoral Côte d’Opale, Unité de Chimie Environnementale et Interactions sur le Vivant (UCEIV), Calais, France
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Pandit A, Adholeya A, Cahill D, Brau L, Kochar M. Microbial biofilms in nature: unlocking their potential for agricultural applications. J Appl Microbiol 2020; 129:199-211. [PMID: 32034822 DOI: 10.1111/jam.14609] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 01/23/2020] [Accepted: 02/05/2020] [Indexed: 12/17/2022]
Abstract
Soil environments are dynamic and the plant rhizosphere harbours a phenomenal diversity of micro-organisms which exchange signals and beneficial nutrients. Bipartite beneficial or symbiotic interactions with host roots, such as mycorrhizae and various bacteria, are relatively well characterized. In addition, a tripartite interaction also exists between plant roots, arbuscular mycorrhizal fungi (AMF) and associated bacteria. Bacterial biofilms exist as a sheet of bacterial cells in association with AMF structures, embedded within a self-produced exopolysaccharide matrix. Such biofilms may play important functional roles within these tripartite interactions. However, the details about such interactions in the rhizosphere and their relevant functional relationships have not been elucidated. This review explores the current understanding of naturally occurring microbial biofilms, and their interaction with biotic surfaces, especially AMF. The possible roles played by bacterial biofilms and the potential for their application for a more productive and sustainable agriculture is discussed in this review.
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Affiliation(s)
- A Pandit
- TERI Deakin Nanobiotechnology Centre, Sustainable Agriculture Division, The Energy and Resources Institute, TERI Gram, Gwal Pahari, Gurugram, Haryana, India
- School of Life and Environmental Sciences, Deakin University, Geelong, Vic, Australia
| | - A Adholeya
- TERI Deakin Nanobiotechnology Centre, Sustainable Agriculture Division, The Energy and Resources Institute, TERI Gram, Gwal Pahari, Gurugram, Haryana, India
| | - D Cahill
- School of Life and Environmental Sciences, Deakin University, Geelong, Vic, Australia
| | - L Brau
- School of Life and Environmental Sciences, Deakin University, Geelong, Vic, Australia
| | - M Kochar
- TERI Deakin Nanobiotechnology Centre, Sustainable Agriculture Division, The Energy and Resources Institute, TERI Gram, Gwal Pahari, Gurugram, Haryana, India
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Carrillo-Saucedo SM, Gavito ME. Resilience of soil aggregation and exocellular enzymatic functions associated with arbuscular mycorrhizal fungal communities along a successional gradient in a tropical dry forest. MYCORRHIZA 2020; 30:109-120. [PMID: 31836908 DOI: 10.1007/s00572-019-00928-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 11/20/2019] [Indexed: 06/10/2023]
Abstract
Arbuscular mycorrhizal (AM) fungi are well-known contributors to soil aggregation and nutrient cycling functions, but we still know little about their capacity to resist or recover from persistent disturbance. Rangeland management may deteriorate these functions by affecting the activity of soil biota, including AM fungi, among other consequences. If affected, some soil properties show recovery when management stops and natural regeneration is allowed. We conducted an experiment to evaluate if the functions related to soil aggregation and promotion of exocellular enzymatic activities associated with AM fungal communities had been affected by rangeland management and, if they had, whether they recovered with successional time when management stopped. AM fungal communities from ten sites with different successional ages in a tropical dry forest region were inoculated to the same host growing in pots divided by mesh into a plant compartment and an AM mycelium compartment. We examined soil stable aggregates fractions and enzymatic activities produced or promoted by AM fungi. Soil aggregation changed significantly only after the study had run for 3 years, was higher in the hyphosphere than in the root compartment, and showed a low but positive relation with the successional age of the communities. The activity of phosphatase, but not casein-protease and beta-glucosidase, increased with successional age. Therefore, soil aggregation and enzyme activities associated with AM fungal communities seemed resilient because casein-protease and beta-glucosidase were unchanged, and aggregation and phosphatase were reduced by rangeland management but recovered with successional time.
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Affiliation(s)
- Silvia Margarita Carrillo-Saucedo
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad, Universidad Nacional Autónoma de México, Antigua Carretera a Pátzcuaro No. 8701, Col. Exhacienda San José de la Huerta, C.P. 58190, Morelia, Michoacán, Mexico
| | - Mayra E Gavito
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad, Universidad Nacional Autónoma de México, Antigua Carretera a Pátzcuaro No. 8701, Col. Exhacienda San José de la Huerta, C.P. 58190, Morelia, Michoacán, Mexico.
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