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Wang K, Zhao M, Zhang M, Fang X, Wang H, Lv J, Shi F. Topography- and depth-dependent rhizosphere microbial community characteristics drive ecosystem multifunctionality in Juglans mandshurica forest. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 949:175070. [PMID: 39084382 DOI: 10.1016/j.scitotenv.2024.175070] [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: 04/08/2024] [Revised: 07/24/2024] [Accepted: 07/25/2024] [Indexed: 08/02/2024]
Abstract
Rhizosphere microbial community characteristics and ecosystem multifunctionality (EMF), both affected by topographic factors, are closely correlated. However, more targeted exploration is yet required to fully understand the variations of rhizosphere microbial communities along topographic gradients in different soil layers, as well as whether and how they regulate EMF under specific site conditions. Here, we conducted relevant research on Juglans mandshurica forests at six elevation gradients and two slope positions ranging from 310 to 750 m in Tianjin Baxian Mountain. Results demonstrated that rhizosphere soil physicochemical properties and enzyme activities of both layers (0-20 cm and 20-40 cm) varied significantly with elevation, while only at top layer did slope position have significant impacts on most indicators. Bacterial richness and diversity were higher in the top layer at slope bottom and middle-high elevation, the difference in fungi was not as noticeable. Both topographic factors and soil depth significantly impacted microbial community structure, with Candidatus_Udaeobacter of bacteria, Mortierella, Sebacina, and Hygrocybe of fungi mainly contributing to the dissimilarity between communities. EMF rose with increasing elevation, bacteria were more critical drivers of this process than fungi, and topographic factors could affect EMF by altering bacterial diversity and dominant taxa abundance. For evaluating EMF, the aggregate structure of sub layer and the carbon cycle-related indicators of top layer were of higher importance. Our results revealed the depth-dependent characteristics of the rhizosphere microbial community along topographic gradients in studied stands, as well as the pivotal regulatory role of bacteria on EMF, while also highlighting depth as an important variable for analyzing soil properties and EMF. This work helps us better understand the response of individuals and communities of J. mandshurica to changing environmental conditions, further providing a scientific reference for the management and protection of secondary forests locally and in North China.
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Affiliation(s)
- Kefan Wang
- Department of Plant Biology and Ecology, College of Life Sciences, Nankai University, Weijin Road 94, Tianjin 300071, PR China.
| | - Mingyuan Zhao
- Department of Plant Biology and Ecology, College of Life Sciences, Nankai University, Weijin Road 94, Tianjin 300071, PR China.
| | - Mei Zhang
- Department of Plant Biology and Ecology, College of Life Sciences, Nankai University, Weijin Road 94, Tianjin 300071, PR China.
| | - Xin Fang
- Department of Plant Biology and Ecology, College of Life Sciences, Nankai University, Weijin Road 94, Tianjin 300071, PR China.
| | - Haomin Wang
- Department of Plant Biology and Ecology, College of Life Sciences, Nankai University, Weijin Road 94, Tianjin 300071, PR China.
| | - Juan Lv
- School of Environmental Science and Engineering, Tiangong University, Binshui West Road 399, Tianjin 300387, PR China.
| | - Fuchen Shi
- Department of Plant Biology and Ecology, College of Life Sciences, Nankai University, Weijin Road 94, Tianjin 300071, PR China.
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Shu D, Banerjee S, Mao X, Zhang J, Cui W, Zhang W, Zhang B, Chen S, Jiao S, Wei G. Conversion of monocropping to intercropping promotes rhizosphere microbiome functionality and soil nitrogen cycling. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 949:174953. [PMID: 39069174 DOI: 10.1016/j.scitotenv.2024.174953] [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: 03/28/2024] [Revised: 06/07/2024] [Accepted: 07/20/2024] [Indexed: 07/30/2024]
Abstract
Intercropping can increase soil nutrient availability and provide greater crop yields for intensive agroecosystems. Despite its multiple benefits, how intercropping influences rhizosphere microbiome assemblages, functionality, and complex soil nitrogen cycling is not fully understood. Here, a three-year field experiment was carried out on different cropping system with five fertilization treatments at the main soybean production regions. We found that soybean yields in intercropped systems were on average 17 % greater than in monocropping system, regardless of fertilization treatments. We also found that intercropping systems significant increased network modularity (by 46 %) and functional diversity (by 11 %) than monocropping systems. Metagenomics analyses further indicated intercropping promotes microbiome functional adaptation, particularly enriching core functions related to nitrogen metabolism. Cropping patterns had a stronger influence on the functional genes associated with soil nitrogen cycling (R2 = 0.499). Monocropping systems increased the abundance of functional genes related to organic nitrogen ammonification, nitrogen fixation, and denitrification, while functional guilds of nitrate assimilation (by 28 %), nitrification (by 31 %), and dissimilatory nitrate reduction (by 10.1 %) genes were enriched in intercropping systems. Furthermore, we found that abiotic factors (i.e. AP, pH, and Moisture) are important drivers in shaping soil microbial community assemblage and nitrogen cycling. The functional genes include hzsB, and nrfA, and nxrA that affected by these biotic and abiotic variables were strongly related to crop yield (R2 = 0.076 ~ R2 = 0.249), suggesting a key role for maintaining crop production. We demonstrated that land use conversion from maize monocropping to maize-soybean intercropping diversify rhizosphere microbiome and functionality signatures, and intercropping increased key gene abundance related to soil nitrogen cycling to maintain the advantage of crop yield. The results of this study significantly facilitate our understanding of the complex soil nitrogen cycling processes and lay the foundation for manipulating desired specific functional taxa for improved crop productivity under sustainable intensification.
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Affiliation(s)
- Duntao Shu
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China; Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Yangling, Shaanxi 712100, China.
| | - Samiran Banerjee
- Department of Microbiological Sciences, North Dakota State University, Fargo 58102, ND, USA
| | - Xinyi Mao
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China; Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Yangling, Shaanxi 712100, China
| | - Jiaqi Zhang
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China; Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Yangling, Shaanxi 712100, China
| | - Weili Cui
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China; Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Yangling, Shaanxi 712100, China
| | - Wu Zhang
- Heihe Branch, Heilongjiang Academy of Agricultural Sciences, Heihe, Heilongjiang 150086, China
| | - Baogang Zhang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
| | - Sanfeng Chen
- College of Biological Sciences, China Agricultural University, Beijing 100091, China
| | - Shuo Jiao
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China; Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Yangling, Shaanxi 712100, China
| | - Gehong Wei
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China; Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Yangling, Shaanxi 712100, China.
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3
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Adigoun RFR, Durand A, Tchokponhoué DA, Achigan-Dako EG, Aholoukpè HNS, Bokonon-Ganta AH, Benizri E. Drivers of the Sisrè berry plant [Synsepalum dulcificum (Schumach & Thonn.) Daniell] rhizosphere bacterial communities in Benin. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 938:173550. [PMID: 38810760 DOI: 10.1016/j.scitotenv.2024.173550] [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: 04/02/2024] [Revised: 05/23/2024] [Accepted: 05/24/2024] [Indexed: 05/31/2024]
Abstract
Each plant species has its own rhizobacteriome, whose activities determine both soil biological quality and plant growth. Little knowledge exists of the rhizosphere bacterial communities associated with opportunity crops with high economic potential such as Synsepalum dulcificum. Native to West Africa, this shrub is famous for its red berries representing the only natural source of miraculin, a glycoprotein, with sweetening properties, but also playing a role in the treatment of cancer and diabetes. This study aimed to characterize the structure and diversity of rhizobacterial communities associated with S. dulcificum and to identify the parameters determining this diversity. An initial sampling stage allowed the collection of rhizosphere soils from 29 S. dulcificum accessions, belonging to three distinct phenotypes, from 16 municipalities of Benin, located either on farms or in home gardens. The bacterial diversity of these rhizosphere soils was assessed by Illumina sequencing of the 16S rRNA gene after DNA extraction from these soils. Furthermore, an analysis of the physicochemical properties of these soils was carried out. All accessions combined, the most represented phylum appeared to be Actinobacteriota, with an average relative abundance of 43.5 %, followed by Proteobacteria (14.8 %), Firmicutes (14.3 %) and Chloroflexi (12.2 %), yet the relative abundance of dominant phyla varied significantly among accessions (p < 0.05). Plant phenotype, habitat, climate and soil physicochemical properties affected the bacterial communities, but our study pointed out that soil physicochemical parameters were the main driver of rhizobacterial communities' structure and diversity. Among them, the assimilable phosphorus, lead, potassium, arsenic and manganese contents, texture and cation exchange capacity of rhizosphere soils were the major determinants of the composition and diversity of rhizosphere bacterial communities. These results suggested the possibility of improving the growth conditions and productivity of S. dulcificum, by harnessing its associated bacteria of interest and better managing soil physicochemical properties.
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Affiliation(s)
- Rabiath F R Adigoun
- Université de Lorraine, INRAE, LSE, F-54000 Nancy, France; Genetics, Biotechnology and Seed Science Unit (GBioS), Laboratory of Plant Production, Physiology and Plant Breeding (PAGEV), Department of Plant Sciences, Faculty of Agronomic Sciences, University of Abomey-Calavi, Abomey-Calavi, Benin; Laboratoire d'Entomologie Agricole (LEAg), Department of Plant Sciences, Faculty of Agronomic Sciences, University of Abomey-Calavi, B.P. 526 Abomey-Calavi, Benin
| | - Alexis Durand
- Université de Lorraine, INRAE, LSE, F-54000 Nancy, France
| | - Dèdéou A Tchokponhoué
- Genetics, Biotechnology and Seed Science Unit (GBioS), Laboratory of Plant Production, Physiology and Plant Breeding (PAGEV), Department of Plant Sciences, Faculty of Agronomic Sciences, University of Abomey-Calavi, Abomey-Calavi, Benin
| | - Enoch G Achigan-Dako
- Genetics, Biotechnology and Seed Science Unit (GBioS), Laboratory of Plant Production, Physiology and Plant Breeding (PAGEV), Department of Plant Sciences, Faculty of Agronomic Sciences, University of Abomey-Calavi, Abomey-Calavi, Benin
| | - Hervé N S Aholoukpè
- Centre de Recherches Agricoles Plantes Pérennes (CRA-PP), Institut National des Recherches Agricoles du Bénin, BP 01 Pobè, Benin
| | - Aimé H Bokonon-Ganta
- Laboratoire d'Entomologie Agricole (LEAg), Department of Plant Sciences, Faculty of Agronomic Sciences, University of Abomey-Calavi, B.P. 526 Abomey-Calavi, Benin
| | - Emile Benizri
- Université de Lorraine, INRAE, LSE, F-54000 Nancy, France
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Shi Y, Gahagan AC, Morrison MJ, Gregorich E, Lapen DR, Chen W. Stratified Effects of Tillage and Crop Rotations on Soil Microbes in Carbon and Nitrogen Cycles at Different Soil Depths in Long-Term Corn, Soybean, and Wheat Cultivation. Microorganisms 2024; 12:1635. [PMID: 39203479 PMCID: PMC11356494 DOI: 10.3390/microorganisms12081635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2024] [Revised: 08/05/2024] [Accepted: 08/08/2024] [Indexed: 09/03/2024] Open
Abstract
Understanding the soil bacterial communities involved in carbon (C) and nitrogen (N) cycling can inform beneficial tillage and crop rotation practices for sustainability and crop production. This study evaluated soil bacterial diversity, compositional structure, and functions associated with C-N cycling at two soil depths (0-15 cm and 15-30 cm) under long-term tillage (conventional tillage [CT] and no-till [NT]) and crop rotation (monocultures of corn, soybean, and wheat and corn-soybean-wheat rotation) systems. The soil microbial communities were characterized by metabarcoding the 16S rRNA gene V4-V5 regions using Illumina MiSeq. The results showed that long-term NT reduced the soil bacterial diversity at 15-30 cm compared to CT, while no significant differences were found at 0-15 cm. The bacterial communities differed significantly at the two soil depths under NT but not under CT. Notably, over 70% of the tillage-responding KEGG orthologs (KOs) associated with C fixation (primarily in the reductive citric acid cycle) were more abundant under NT than under CT at both depths. The tillage practices significantly affected bacteria involved in biological nitrogen (N2) fixation at the 0-15 cm soil depth, as well as bacteria involved in denitrification at both soil depths. The crop type and rotation regimes had limited effects on bacterial diversity and structure but significantly affected specific C-N-cycling genes. For instance, three KOs associated with the Calvin-Benson cycle for C fixation and four KOs related to various N-cycling processes were more abundant in the soil of wheat than in that of corn or soybean. These findings indicate that the long-term tillage practices had a greater influence than crop rotation on the soil bacterial communities, particularly in the C- and N-cycling processes. Integrated management practices that consider the combined effects of tillage, crop rotation, and crop types on soil bacterial functional groups are essential for sustainable agriculture.
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Affiliation(s)
- Yichao Shi
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave., Ottawa, ON K1A 0C6, Canada; (Y.S.); (A.C.G.); (M.J.M.); (E.G.); (D.R.L.)
| | - Alison Claire Gahagan
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave., Ottawa, ON K1A 0C6, Canada; (Y.S.); (A.C.G.); (M.J.M.); (E.G.); (D.R.L.)
| | - Malcolm J. Morrison
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave., Ottawa, ON K1A 0C6, Canada; (Y.S.); (A.C.G.); (M.J.M.); (E.G.); (D.R.L.)
| | - Edward Gregorich
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave., Ottawa, ON K1A 0C6, Canada; (Y.S.); (A.C.G.); (M.J.M.); (E.G.); (D.R.L.)
| | - David R. Lapen
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave., Ottawa, ON K1A 0C6, Canada; (Y.S.); (A.C.G.); (M.J.M.); (E.G.); (D.R.L.)
| | - Wen Chen
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave., Ottawa, ON K1A 0C6, Canada; (Y.S.); (A.C.G.); (M.J.M.); (E.G.); (D.R.L.)
- Department of Biology, University of Ottawa, 60 Marie Curie Prv., Ottawa, ON K1N 6N5, Canada
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5
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Moukarzel R, Jones EE, Panda P, Larrouy J, Ramana JV, Guerin-Laguette A, Ridgway HJ. Vineyard management systems influence arbuscular mycorrhizal fungi recruitment by grapevine rootstocks in New Zealand. J Appl Microbiol 2024; 135:lxae211. [PMID: 39147565 DOI: 10.1093/jambio/lxae211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 08/08/2024] [Accepted: 08/13/2024] [Indexed: 08/17/2024]
Abstract
AIMS Arbuscular mycorrhizal fungi (AMF) can perform significant functions within sustainable agricultural ecosystems, including vineyards. Increased AMF diversity can be beneficial in promoting plant growth and increasing resilience to environmental changes. To effectively utilize AMF communities and their benefits in vineyard ecosystems, a better understanding of how management systems influence AMF community composition is needed. Moreover, it is unknown whether AMF communities in organically managed vineyards are distinct from those in conventionally managed vineyards. METHODS AND RESULTS In this study, vineyards were surveyed across the Marlborough region, New Zealand to identify the AMF communities colonizing the roots of different rootstocks grafted with Sauvignon Blanc and Pinot Noir in both conventional and organic systems. The AMF communities were identified based on spores isolated from trap cultures established with the collected grapevine roots, and by next-generation sequencing technologies (Illumina MiSeq). The identified AMF species/genera belonged to Glomeraceae, Entrophosporaceae, and Diversisporaceae. The results revealed a significant difference in AMF community composition between rootstocks and in their interaction with management systems. CONCLUSIONS These outcomes indicated that vineyard management systems influence AMF recruitment by rootstocks and some rootstocks may therefore be more suited to organic systems due to the AMF communities they support. This could provide an increased benefit to organic systems by supporting higher biodiversity.
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Affiliation(s)
- Romy Moukarzel
- Department of Pest-management and Conservation, Lincoln University, PO Box 85084, Lincoln 7647, New Zealand
| | - E Eirian Jones
- Department of Pest-management and Conservation, Lincoln University, PO Box 85084, Lincoln 7647, New Zealand
| | - Preeti Panda
- The New Zealand Institute for Plant and Food Research Ltd., Private Bag 4704, Christchurch 8140, New Zealand
| | - Justine Larrouy
- The New Zealand Institute for Plant and Food Research Ltd., Private Bag 4704, Christchurch 8140, New Zealand
| | - John V Ramana
- Bioprotection Aotearoa, School of Biological Sciences, University of Canterbury, Christchurch 8041, New Zealand
- Manaaki Whenua-Landcare Research, PO Box 69040, Lincoln 7640, New Zealand
| | | | - Hayley J Ridgway
- The New Zealand Institute for Plant and Food Research Ltd., Private Bag 4704, Christchurch 8140, New Zealand
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Moretti LG, Crusciol CAC, Leite MFA, Momesso L, Bossolani JW, Costa OYA, Hungria M, Kuramae EE. Diverse bacterial consortia: key drivers of rhizosoil fertility modulating microbiome functions, plant physiology, nutrition, and soybean grain yield. ENVIRONMENTAL MICROBIOME 2024; 19:50. [PMID: 39030648 PMCID: PMC11264919 DOI: 10.1186/s40793-024-00595-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 07/08/2024] [Indexed: 07/21/2024]
Abstract
Soybean cultivation in tropical regions relies on symbioses with nitrogen-fixing Bradyrhizobium and plant growth-promoting bacteria (PGPBs), reducing environmental impacts of N fertilizers and pesticides. We evaluate the effects of soybean inoculation with different bacterial consortia combined with PGPBs or microbial secondary metabolites (MSMs) on rhizosoil chemistry, plant physiology, plant nutrition, grain yield, and rhizosphere microbial functions under field conditions over three growing seasons with four treatments: standard inoculation of Bradyrhizobium japonicum and Bradyrhizobium diazoefficiens consortium (SI); SI plus foliar spraying with Bacillus subtilis (SI + Bs); SI plus foliar spraying with Azospirillum brasilense (SI + Az); and SI plus seed application of MSMs enriched in lipo-chitooligosaccharides extracted from B. diazoefficiens and Rhizobium tropici (SI + MSM). Rhizosphere microbial composition, diversity, and function was assessed by metagenomics. The relationships between rhizosoil chemistry, plant nutrition, grain yield, and the abundance of microbial taxa and functions were determined by generalized joint attribute modeling. The bacterial consortia had the most significant impact on rhizosphere soil fertility, which in turn affected the bacterial community, plant physiology, nutrient availability, and production. Cluster analysis identified microbial groups and functions correlated with shifts in rhizosoil chemistry and plant nutrition. Bacterial consortia positively modulated specific genera and functional pathways involved in biosynthesis of plant secondary metabolites, amino acids, lipopolysaccharides, photosynthesis, bacterial secretion systems, and sulfur metabolism. The effects of the bacterial consortia on the soybean holobiont, particularly the rhizomicrobiome and rhizosoil fertility, highlight the importance of selecting appropriate consortia for desired outcomes. These findings have implications for microbial-based agricultural practices that enhance crop productivity, quality, and sustainability.
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Affiliation(s)
- Luiz Gustavo Moretti
- College of Agricultural Sciences, Department of Crop Science, São Paulo State University (UNESP), Botucatu, São Paulo, 18610-034, Brazil
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, 6708 PB, The Netherlands
| | - Carlos Alexandre Costa Crusciol
- College of Agricultural Sciences, Department of Crop Science, São Paulo State University (UNESP), Botucatu, São Paulo, 18610-034, Brazil
| | - Marcio Fernandes Alves Leite
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, 6708 PB, The Netherlands
| | - Letusa Momesso
- School of Agriculture, Federal University of Goiás (UFG), 74690-900, Goiânia, Goiás, Brazil
| | - João William Bossolani
- College of Agricultural Sciences, Department of Crop Science, São Paulo State University (UNESP), Botucatu, São Paulo, 18610-034, Brazil
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, 6708 PB, The Netherlands
| | - Ohana Yonara Assis Costa
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, 6708 PB, The Netherlands
| | - Mariangela Hungria
- Embrapa Soybean, Carlos João Strass Highway, Post Office Box 231, Londrina, Paraná, 86001-970, Brazil
| | - Eiko Eurya Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, 6708 PB, The Netherlands.
- Institute of Environmental Biology, Ecology and Biodiversity, Utrecht University, Padualaan 8, Utrecht, 3584 CH, The Netherlands.
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7
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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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8
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Gao C, Bezemer TM, de Vries FT, van Bodegom PM. Trade-offs in soil microbial functions and soil health in agroecosystems. Trends Ecol Evol 2024:S0169-5347(24)00138-1. [PMID: 38910081 DOI: 10.1016/j.tree.2024.05.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 04/24/2024] [Accepted: 05/31/2024] [Indexed: 06/25/2024]
Abstract
Soil microbial communities play pivotal roles in maintaining soil health in agroecosystems. However, how the delivery of multiple microbial functions in agroecosystems is maintained remains poorly understood. This may put us at risk of incurring unexpected trade-offs between soil functions. We elucidate how interactions between soil microbes can lead to trade-offs in the functioning of agricultural soils. Interactions within soil microbial communities can result in not only positive but also neutral and negative relationships among soil functions. Altering soil conditions through soil health-improving agricultural management can alleviate these functional trade-offs by promoting the diversity and interrelationships of soil microbes, which can help to achieve more productive and sustainable agroecosystems.
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Affiliation(s)
- Chenguang Gao
- Environmental Biology, Institute of Environmental Sciences, Leiden University, Einsteinweg 2, 2333 CC Leiden, The Netherlands.
| | - Thiemo Martijn Bezemer
- Institute of Biology, Above-Belowground Interactions Group, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Franciska T de Vries
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Science Park 904, 1090 GE Amsterdam, The Netherlands
| | - Peter M van Bodegom
- Environmental Biology, Institute of Environmental Sciences, Leiden University, Einsteinweg 2, 2333 CC Leiden, The Netherlands
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9
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de Celis M, Fernández-Alonso MJ, Belda I, García C, Ochoa-Hueso R, Palomino J, Singh BK, Yin Y, Wang JT, Abdala-Roberts L, Alfaro FD, Angulo-Pérez D, Arthikala MK, Corwin J, Gui-Lan D, Hernandez-Lopez A, Nanjareddy K, Pasari B, Quijano-Medina T, Rivera DS, Shaaf S, Trivedi P, Yang Q, Zaady E, Zhu YG, Delgado-Baquerizo M, Milla R, García-Palacios P. The abundant fraction of soil microbiomes regulates the rhizosphere function in crop wild progenitors. Ecol Lett 2024; 27:e14462. [PMID: 39031813 DOI: 10.1111/ele.14462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 04/30/2024] [Accepted: 05/27/2024] [Indexed: 07/22/2024]
Abstract
The rhizosphere influence on the soil microbiome and function of crop wild progenitors (CWPs) remains virtually unknown, despite its relevance to develop microbiome-oriented tools in sustainable agriculture. Here, we quantified the rhizosphere influence-a comparison between rhizosphere and bulk soil samples-on bacterial, fungal, protists and invertebrate communities and on soil multifunctionality across nine CWPs at their sites of origin. Overall, rhizosphere influence was higher for abundant taxa across the four microbial groups and had a positive influence on rhizosphere soil organic C and nutrient contents compared to bulk soils. The rhizosphere influence on abundant soil microbiomes was more important for soil multifunctionality than rare taxa and environmental conditions. Our results are a starting point towards the use of CWPs for rhizosphere engineering in modern crops.
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Affiliation(s)
- Miguel de Celis
- Departamento de Suelo, Planta y Calidad Ambiental, Instituto de Ciencias Agrarias, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - María José Fernández-Alonso
- Area of Biodiversity and Conservation, Department of Biology and Geology, Physics and Inorganic Chemistry, Universidad Rey Juan Carlos, Móstoles, Spain
- Departamento de Geología y Geoquímica, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - Ignacio Belda
- Department of Genetics, Physiology and Microbiology, Microbiology Unit, Faculty of Biology, Complutense University of Madrid, Madrid, Spain
| | - Carlos García
- Department of Soil and Water Conservation and Organic Waste Management, CEBAS-CSIC, Murcia, Spain
| | - Raúl Ochoa-Hueso
- Department of Biology, IVAGRO, University of Cádiz, Cádiz, Spain
| | - Javier Palomino
- Area of Biodiversity and Conservation, Department of Biology and Geology, Physics and Inorganic Chemistry, Universidad Rey Juan Carlos, Móstoles, Spain
| | - Brajesh K Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia
- Global Centre for Land-Based Innovation, Western Sydney University, Penrith, New South Wales, Australia
| | - Yue Yin
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Jun-Tao Wang
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia
- Global Centre for Land-Based Innovation, Western Sydney University, Penrith, New South Wales, Australia
| | - Luis Abdala-Roberts
- Departamento de Ecología Tropical, Universidad Autónoma de Yucatán, Mérida, Yucatán, Mexico
| | - Fernando D Alfaro
- GEMA Center for Genomics, Ecology and Environment, Universidad Mayor, Santiago, Chile
| | - Diego Angulo-Pérez
- Unidad de Recursos Naturales, Centro de Investigación Científica de Yucatán, A.C., Mérida, Yucatán, Mexico
| | - Manoj-Kumar Arthikala
- Ciencias Agrogenómicas, Escuela Nacional de Estudios Superiores Unidad León-Universidad Nacional Autónoma de México (UNAM), León, Guanajuato, Mexico
| | - Jason Corwin
- Microbiome Network and Department of Agricultural Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Duan Gui-Lan
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Antonio Hernandez-Lopez
- Escuela Nacional de Estudios Superiores Unidad León, Universidad Nacional Autónoma de México, Guanajuato, Mexico
| | - Kalpana Nanjareddy
- Ciencias Agrogenómicas, Escuela Nacional de Estudios Superiores Unidad León-Universidad Nacional Autónoma de México (UNAM), León, Guanajuato, Mexico
| | - Babak Pasari
- Department of Agronomy and Plant Breeding, Sanandaj Branch, Islamic Azad University, Sanandaj, Iran
| | - Teresa Quijano-Medina
- Departamento de Ecología Tropical, Universidad Autónoma de Yucatán, Mérida, Yucatán, Mexico
| | - Daniela S Rivera
- GEMA Center for Genomics, Ecology and Environment, Universidad Mayor, Santiago, Chile
| | - Salar Shaaf
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Pankaj Trivedi
- Microbiome Network and Department of Agricultural Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Qingwen Yang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Eli Zaady
- Department of Natural Resources, Agricultural Research Organization, Gilat Research Center, Institute of Plant Sciences, Mobile Post Negev, Israel
| | - Yong-Guan Zhu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Sevilla, Spain
| | - Rubén Milla
- Area of Biodiversity and Conservation, Department of Biology and Geology, Physics and Inorganic Chemistry, Universidad Rey Juan Carlos, Móstoles, Spain
- Global Change Research Institute, Universidad Rey Juan Carlos, Móstoles, Spain
| | - Pablo García-Palacios
- Departamento de Suelo, Planta y Calidad Ambiental, Instituto de Ciencias Agrarias, Consejo Superior de Investigaciones Científicas, Madrid, Spain
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
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10
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Wang T, Gao M, Shao W, Wang L, Yang C, Wang X, Yao S, Zhang B. Dissecting the role of soybean rhizosphere-enriched bacterial taxa in modulating nitrogen-cycling functions. Appl Microbiol Biotechnol 2024; 108:347. [PMID: 38805033 PMCID: PMC11133221 DOI: 10.1007/s00253-024-13184-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 04/30/2024] [Accepted: 05/15/2024] [Indexed: 05/29/2024]
Abstract
Crop roots selectively recruit certain microbial taxa that are essential for supporting their growth. Within the recruited microbes, some taxa are consistently enriched in the rhizosphere across various locations and crop genotypes, while others are unique to specific planting sites or genotypes. Whether these differentially enriched taxa are different in community composition and how they interact with nutrient cycling need further investigation. Here, we sampled bulk soil and the rhizosphere soil of five soybean varieties grown in Shijiazhuang and Xuzhou, categorized the rhizosphere-enriched microbes into shared, site-specific, and variety-specific taxa, and analyzed their correlation with the diazotrophic communities and microbial genes involved in nitrogen (N) cycling. The shared taxa were dominated by Actinobacteria and Thaumarchaeota, the site-specific taxa were dominated by Actinobacteria in Shijiazhuang and by Nitrospirae in Xuzhou, while the variety-specific taxa were more evenly distributed in several phyla and contained many rare operational taxonomic units (OTUs). The rhizosphere-enriched taxa correlated with most diazotroph orders negatively but with eight orders including Rhizobiales positively. Each group within the shared, site-specific, and variety-specific taxa negatively correlated with bacterial amoA and narG in Shijiazhuang and positively correlated with archaeal amoA in Xuzhou. These results revealed that the shared, site-specific, and variety-specific taxa are distinct in community compositions but similar in associations with rhizosphere N-cycling functions. They exhibited potential in regulating the soybean roots' selection for high-efficiency diazotrophs and the ammonia-oxidizing and denitrification processes. This study provides new insights into soybean rhizosphere-enriched microbes and their association with N cycling. KEY POINTS: • Soybean rhizosphere affected diazotroph community and enriched nifH, amoA, and nosZ. • Shared and site- and variety-specific taxa were dominated by different phyla. • Rhizosphere-enriched taxa were similarly associated with N-cycle functions.
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Affiliation(s)
- Tianshu Wang
- State Key Laboratory of Efficient Utilization of Arid and Semi-Arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Miao Gao
- State Key Laboratory of Efficient Utilization of Arid and Semi-Arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Weiwei Shao
- State Key Laboratory of Efficient Utilization of Arid and Semi-Arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Li Wang
- State Key Laboratory of Efficient Utilization of Arid and Semi-Arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Chunyan Yang
- The Key Laboratory of Crop Genetics and Breeding of Hebei, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, 050031, China
| | - Xing Wang
- Jiangsu Xuhuai Regional Institute of Agricultural Sciences, Xuzhou, 221131, China
| | - Shuihong Yao
- State Key Laboratory of Efficient Utilization of Arid and Semi-Arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Bin Zhang
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China.
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11
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Hirpara KR, Hinsu AT, Kothari RK. Metagenomic evaluation of peanut rhizosphere microbiome from the farms of Saurashtra regions of Gujarat, India. Sci Rep 2024; 14:10525. [PMID: 38720057 PMCID: PMC11079051 DOI: 10.1038/s41598-024-61343-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Accepted: 05/05/2024] [Indexed: 05/12/2024] Open
Abstract
The narrow zone of soil around the plant roots with maximum microbial activity termed as rhizosphere. Rhizospheric bacteria promote the plant growth directly or indirectly by providing the nutrients and producing antimicrobial compounds. In this study, the rhizospheric microbiota of peanut plants was characterized from different farms using an Illumina-based partial 16S rRNA gene sequencing to evaluate microbial diversity and identify the core microbiome through culture-independent (CI) approach. Further, all rhizospheric bacteria that could grow on various nutrient media were identified, and the diversity of those microbes through culture-dependent method (CD) was then directly compared with their CI counterparts. The microbial population profiles showed a significant correlation with organic carbon and concentration of phosphate, manganese, and potassium in the rhizospheric soil. Genera like Sphingomicrobium, Actinoplanes, Aureimonas _A, Chryseobacterium, members from Sphingomonadaceae, Burkholderiaceae, Pseudomonadaceae, Enterobacteriaceae family, and Bacilli class were found in the core microbiome of peanut plants. As expected, the current study demonstrated more bacterial diversity in the CI method. However, a higher number of sequence variants were exclusively present in the CD approach compared to the number of sequence variants shared between both approaches. These CD-exclusive variants belonged to organisms that are more typically found in soil. Overall, this study portrayed the changes in the rhizospheric microbiota of peanuts in different rhizospheric soil and environmental conditions and gave an idea about core microbiome of peanut plant and comparative bacterial diversity identified through both approaches.
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Affiliation(s)
- Krunal R Hirpara
- Department of Biosciences, Saurashtra University, Rajkot, Gujarat, 360005, India
| | - Ankit T Hinsu
- Department of Biosciences, Saurashtra University, Rajkot, Gujarat, 360005, India
- Royal Veterinary College, London, AL9 7TA, UK
| | - Ramesh K Kothari
- Department of Biosciences, Saurashtra University, Rajkot, Gujarat, 360005, India.
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12
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Juliyanti V, Itakura R, Kotani K, Lim SY, Suzuki G, Chong CW, Song BK, Rahman S. Comparative analysis of root associated microbes in tropical cultivated and weedy rice (Oryza spp.) and temperate cultivated rice. Sci Rep 2024; 14:9656. [PMID: 38671238 PMCID: PMC11053024 DOI: 10.1038/s41598-024-60384-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 04/22/2024] [Indexed: 04/28/2024] Open
Abstract
Weedy rice is a major problem in paddy fields around the world. It is well known that weedy rice appears to grow faster and mature earlier than cultivated rice. It is possible that differences in the root microbial genetics are correlated with this characteristic. This study incorporated 16S rRNA amplicon sequencing to study the microbial composition in the rhizosphere and endosphere of rice root. No significant difference was found between the microbiota associated with weedy and cultivated rice lines grown in the same field. It was found that the endosphere had less microbial diversity compared to the rhizosphere. The major groups of bacteria found in the endosphere are from the phylum Proteobacteria, Myxococcota, Chloroflexota, and Actinobacteria. In addition, by analyzing the microbiome of japonica rice grown in the field in a temperate climate, we found that despite differences in genotype and location, some bacterial taxa were found to be common and these members of the putative rice core microbiome can also be detected by in situ hybridization. The delineation of a core microbiome in the endosphere of rice suggests that these bacterial taxa might be important in the life cycle of a wide range of rice types.
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Affiliation(s)
- Vani Juliyanti
- School of Science, Monash University Malaysia, Bandar Sunway, Malaysia
| | - Ryota Itakura
- Division of Natural Science, Osaka Kyoiku University, Kashiwara, 582-8582, Japan
| | - Kanta Kotani
- Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Shu Yong Lim
- Genomics Facility, Monash University Malaysia, Bandar Sunway, Malaysia
| | - Go Suzuki
- Division of Natural Science, Osaka Kyoiku University, Kashiwara, 582-8582, Japan
| | - Chun Wie Chong
- School of Pharmacy, Monash University Malaysia, Bandar Sunway, Malaysia
| | - Beng Kah Song
- School of Science, Monash University Malaysia, Bandar Sunway, Malaysia
| | - Sadequr Rahman
- School of Science, Monash University Malaysia, Bandar Sunway, Malaysia.
- Tropical Medicine and Biology Multidisciplinary Platform, Monash University Malaysia, Bandar Sunway, Malaysia.
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13
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Jiang W, Cheng Z, Zhai W, Ma X, Gao J, Liu X, Liu D, Zhou Z, Wang P. Oxytetracycline Increases the Residual Risk of Imidacloprid in Radish ( Raphanus sativus) and Disturbs the Plant-Rhizosphere Microbiome Holobiont Homeostasis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:6167-6177. [PMID: 38500001 DOI: 10.1021/acs.jafc.4c00271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
Antibiotics can be accidentally introduced into farmland by wastewater irrigation, and the environmental effects are still unclear. In this study, the effects of oxytetracycline on the residue of imidacloprid in soil and radishes were investigated. Besides, the rhizosphere microbiome and radish metabolome were analyzed. It showed that the persistence of imidacloprid in soil was unchanged, but the content of olefin-imidacloprid was increased by oxytetracycline. The residue of imidacloprid in radishes was increased by nearly 1.5 times, and the hazard index of imidacloprid was significantly raised by 1.5-4 times. Oxytetracycline remodeled the rhizosphere microbiome, including Actinobe, Elusimic, and Firmicutes, and influenced the metabolome of radishes. Especially, some amino acid metabolic pathways in radish were downregulated, which might be involved in imidacloprid degradation. It can be assumed that oxytetracycline increased the imidacloprid residue in radish through disturbing the plant-rhizosphere microbiome holobiont and, thus, increased the pesticide dietary risk.
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Affiliation(s)
- Wenqi Jiang
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210093, China
- Department of Applied Chemistry, China Agricultural University, Beijing 100094, China
| | - Zheng Cheng
- Department of Applied Chemistry, China Agricultural University, Beijing 100094, China
| | - Wangjing Zhai
- Department of Applied Chemistry, China Agricultural University, Beijing 100094, China
| | - Xiaoran Ma
- Department of Applied Chemistry, China Agricultural University, Beijing 100094, China
| | - Jing Gao
- Department of Applied Chemistry, China Agricultural University, Beijing 100094, China
| | - Xueke Liu
- Department of Applied Chemistry, China Agricultural University, Beijing 100094, China
| | - Donghui Liu
- Department of Applied Chemistry, China Agricultural University, Beijing 100094, China
| | - Zhiqiang Zhou
- Department of Applied Chemistry, China Agricultural University, Beijing 100094, China
| | - Peng Wang
- Department of Applied Chemistry, China Agricultural University, Beijing 100094, China
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14
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Paina C, Fois M, Asp T, Jensen J, Hansen PB, Rohde PD. The soil microbiome of Lolium perenne L. depends on host genotype, is modified by nitrogen level and varies across season. Sci Rep 2024; 14:5767. [PMID: 38459164 PMCID: PMC10923896 DOI: 10.1038/s41598-024-56353-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 03/05/2024] [Indexed: 03/10/2024] Open
Abstract
Genotype by environment interactions (G × E) are frequently observed in herbage production. Understanding the underlying biological mechanisms is important for achieving stable and predictive outputs across production environments. The microbiome is gaining increasing attention as a significant contributing factor to G × E. Here, we focused on the soil microbiome of perennial ryegrass (Lolium perenne L.) grown under field conditions and investigated the soil microbiome variation across different ryegrass varieties to assess whether environmental factors, such as seasonality and nitrogen levels, affect the microbial community. We identified bacteria, archaea, and fungi operational taxonomic units (OTUs) and showed that seasonality and ryegrass variety were the two factors explaining the largest fraction of the soil microbiome diversity. The strong and significant variety-by-treatment-by-seasonal cut interaction for ryegrass dry matter was associated with the number of unique OTUs within each sample. We identified seven OTUs associated with ryegrass dry matter variation. An OTU belonging to the Solirubrobacterales (Thermoleophilales) order was associated with increased plant biomass, supporting the possibility of developing engineered microbiomes for increased plant yield. Our results indicate the importance of incorporating different layers of biological data, such as genomic and soil microbiome data to improve the prediction accuracy of plant phenotypes grown across heterogeneous environments.
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Affiliation(s)
- Cristiana Paina
- Department of Agroecology, Aarhus University, Forsøgsvej 1, 4200, Slagelse, Denmark
| | - Mattia Fois
- Center for Quantitative Genetics and Genomics, Aarhus University, Forsøgsvej 1, 4200, Slagelse, Denmark
| | - Torben Asp
- Center for Quantitative Genetics and Genomics, Aarhus University, Forsøgsvej 1, 4200, Slagelse, Denmark
| | - Just Jensen
- Center for Quantitative Genetics and Genomics, Aarhus University, C. F. Møllers Allé 3, Bldg. 1130, 8000, Aarhus, Denmark.
| | - Pernille Bjarup Hansen
- Center for Quantitative Genetics and Genomics, Aarhus University, Forsøgsvej 1, 4200, Slagelse, Denmark
| | - Palle Duun Rohde
- Genomic Medicine, Department of Health Science and Technology, Aalborg University, Selma Lagerløfs Vej 249, 9260, Gistrup, Denmark
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15
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Liu Z, Xia Q, Cai J, Wang Z, Yang K, Chen D, Wei J, Chen C, Liu C, Chang W, Li Z, Li X, Yang Y, Yang L, Tan X. Nitrogen Fertilizers Affect Microbial Hitchhiking to the Plant Roots. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:4639-4648. [PMID: 38377485 DOI: 10.1021/acs.jafc.3c07623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
The phenomenon of microbial hitchhiking, where nonmotile microbes utilize transspecies motility to navigate within their environment, has been observed. However, the underlying factors driving microbial hitchhiking remain unclear. Our study explored how nitrogen fertilizers affect microbial hitchhiking in soil through an in situ planting experiment. We established twelve treatments encompassing the presence and absence of plants, the presence and absence of a filter membrane that is used to prevent hitchhiking, and three nitrogen levels. Results showed that nitrogen influenced bacterial diversity in all soils, an effect thwarted by filter membranes. In the presence of plants, nitrogen significantly affected the bacterial mobility, Bacillus abundance, and plant biomass, but these effects vanished when filters were used. The correlation between motile Bacillus and rhizosphere bacteria was strong without filters at the proper nitrogen levels but weakened with membrane treatments. Thus, plants and nitrogen together, not nitrogen alone, alter the soil microbiome via hitchhiking.
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Affiliation(s)
- Zhibin Liu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China
| | - Qini Xia
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China
| | - Jing Cai
- West China School of Pharmacy, Sichuan University, Chengdu, Sichuan 610041, China
| | - Ziyuan Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China
| | - Kexin Yang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China
| | - Dixu Chen
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China
| | - Jiahong Wei
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China
| | - Cun Chen
- College of Chemistry and Life Science, Chengdu Normal University, Chengdu, Sichuan 611130, China
| | - Chao Liu
- State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, Sichuan 610065, China
- College of Water Resource and Hydropower, Sichuan University, Chengdu, Sichuan 610065, China
| | - Wei Chang
- Vegetable Germplasm Innovation and Variety Improvement Key Laboratory of Sichuan Province/Horticulture Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China
| | - Zhi Li
- Vegetable Germplasm Innovation and Variety Improvement Key Laboratory of Sichuan Province/Horticulture Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China
| | - Xufeng Li
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China
| | - Yi Yang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China
| | - Liang Yang
- Vegetable Germplasm Innovation and Variety Improvement Key Laboratory of Sichuan Province/Horticulture Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China
| | - Xiao Tan
- State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, Sichuan 610065, China
- College of Water Resource and Hydropower, Sichuan University, Chengdu, Sichuan 610065, China
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16
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Pan C, Sun C, Qu X, Yu W, Guo J, Yu Y, Li X. Microbial community interactions determine the mineralization of soil organic phosphorus in subtropical forest ecosystems. Microbiol Spectr 2024; 12:e0135523. [PMID: 38334388 PMCID: PMC10913379 DOI: 10.1128/spectrum.01355-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 01/18/2024] [Indexed: 02/10/2024] Open
Abstract
In subtropical forest ecosystems with few phosphorus (P) inputs, P availability and forest productivity depend on soil organic P (Po) mineralization. However, the mechanisms by which the microbial community determines the status and fate of soil Po mineralization remain unclear. In the present study, soils were collected from three typical forest types: secondary natural forest (SNF), mixed planting, and monoculture forest of Chinese fir. The P fractions, Po-mineralization ability, and microbial community in the soils of different forest types were characterized. In addition, we defined Po-mineralizing taxa with the potential to interact with the soil microbial community to regulate Po mineralization. We found that a higher labile P content persisted in SNF and was positively associated with the Po-mineralization capacity of the soil microbial community. In vitro cultures of soil suspensions revealed that soil Po mineralization of three forest types was distinguished by differences in the composition of fungal communities. We further identified broad phylogenetic lineages of Po-mineralizing fungi with a high intensity of positive interactions with the soil microbial community, implying that the facilitation of Po-mineralizing taxa is crucial for soil P availability. Our dilution experiments to weaken microbial interactions revealed that in SNF soil, which had the highest interaction intensity of Po-mineralizing taxa with the community, Po-mineralization capacity was irreversibly lost after dilution, highlighting the importance of microbial diversity protection in forest soils. In summary, this study demonstrates that the interactions of Po-mineralizing microorganisms with the soil microbial community are critical for P availability in subtropical forests.IMPORTANCEIn subtropical forest ecosystems with few phosphorus inputs, phosphorus availability and forest productivity depend on soil organic phosphorus mineralization. However, the mechanisms by which the microbial community interactions determine the mineralization of soil organic phosphorus remain unclear. In the present study, soils were collected from three typical forest types: secondary natural forest, mixed planting, and monoculture forest of Chinese fir. We found that a higher soil labile phosphorus content was positively associated with the organic phosphorus mineralization capacity of the soil microbial community. Soil organic phosphorus mineralization of three forest types was distinguished by the differences in the composition of fungal communities. The positive interactions between organic phosphorus-mineralizing fungi and the rest of the soil microbial community facilitated organic phosphorus mineralization. This study highlights the importance of microbial diversity protection in forest soils and reveals the microbial mechanism of phosphorus availability maintenance in subtropical forest ecosystems.
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Affiliation(s)
- Chang Pan
- College of Ecology and Environment, Nanjing Forestry University, Nanjing, China
- School of Life Sciences, Anqing Normal University, Anqing, China
| | - Chenchen Sun
- College of Ecology and Environment, Nanjing Forestry University, Nanjing, China
| | - Xinjing Qu
- College of Ecology and Environment, Nanjing Forestry University, Nanjing, China
| | - Wenruinan Yu
- College of Ecology and Environment, Nanjing Forestry University, Nanjing, China
| | - Jiahuan Guo
- College of Ecology and Environment, Nanjing Forestry University, Nanjing, China
| | - Yuanchun Yu
- College of Ecology and Environment, Nanjing Forestry University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Xiaogang Li
- College of Ecology and Environment, Nanjing Forestry University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
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17
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Matteoli FP, Silva AMM, de Araújo VLVP, Feiler HP, Cardoso EJBN. Organic farming promotes the abundance of fungi keystone taxa in bacteria-fungi interkingdom networks. World J Microbiol Biotechnol 2024; 40:119. [PMID: 38429532 DOI: 10.1007/s11274-024-03926-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 02/14/2024] [Indexed: 03/03/2024]
Abstract
Soil bacteria-fungi interactions are essential in the biogeochemical cycles of several nutrients, making these microbes major players in agroecosystems. While the impact of the farming system on microbial community composition has been extensively reported in the literature, whether sustainable farming approaches can promote associations between bacteria and fungi is still unclear. To study this, we employed 16S, ITS, and 18S DNA sequencing to uncover how microbial interactions were affected by conventional and organic farming systems on maize crops. The Bray-Curtis index revealed that bacterial, fungal, and arbuscular mycorrhizal fungi communities were significantly different between the two farming systems. Several taxa known to thrive in healthy soils, such as Nitrosophaerales, Orbiliales, and Glomus were more abundant in the organic farming system. Constrained ordination revealed that the organic farming system microbial community was significantly correlated with the β-glucosidase activity, whereas the conventional farming system microbial community significantly correlated with soil pH. Both conventional and organic co-occurrence interkingdom networks exhibited a parallel node count, however, the former had a higher number of edges, thus being denser than the latter. Despite the similar amount of fungal nodes in the co-occurrence networks, the organic farming system co-occurrence network exhibited more than 3-fold the proportion of fungal taxa as keystone nodes than the conventional co-occurrence network. The genera Bionectria, Cercophora, Geastrum, Penicillium, Preussia, Metarhizium, Myceliophthora, and Rhizophlyctis were among the fungal keystone nodes of the organic farming system network. Altogether, our results uncover that beyond differences in microbial community composition between the two farming systems, fungal keystone nodes are far more relevant in the organic farming system, thus suggesting that bacteria-fungi interactions are more frequent in organic farming systems, promoting a more functional microbial community.
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Affiliation(s)
- Filipe Pereira Matteoli
- Laboratory of Microbial Bioinformatics, Department of Biological Sciences, Faculty of Sciences, São Paulo State University, Bauru, Brazil.
| | - Antonio M M Silva
- Department of Soil Sciences, University of São Paulo, "Luiz de Queiroz" College of Agriculture, Piracicaba, Brazil
| | - Victor L V P de Araújo
- Department of Soil Sciences, University of São Paulo, "Luiz de Queiroz" College of Agriculture, Piracicaba, Brazil
| | - Henrique P Feiler
- Department of Soil Sciences, University of São Paulo, "Luiz de Queiroz" College of Agriculture, Piracicaba, Brazil
| | - Elke J B N Cardoso
- Department of Soil Sciences, University of São Paulo, "Luiz de Queiroz" College of Agriculture, Piracicaba, Brazil
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18
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Zhou G, Fan K, Gao S, Chang D, Li G, Liang T, Liang H, Li S, Zhang J, Che Z, Cao W. Green manuring relocates microbiomes in driving the soil functionality of nitrogen cycling to obtain preferable grain yields in thirty years. SCIENCE CHINA. LIFE SCIENCES 2024; 67:596-610. [PMID: 38057623 DOI: 10.1007/s11427-023-2432-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Accepted: 08/05/2023] [Indexed: 12/08/2023]
Abstract
Fertilizers are widely used to produce more food, inevitably altering the diversity and composition of soil organisms. The role of soil biodiversity in controlling multiple ecosystem services remains unclear, especially after decades of fertilization. Here, we assess the contribution of the soil functionalities of carbon (C), nitrogen (N), and phosphorus (P) cycling to crop production and explore how soil organisms control these functionalities in a 33-year field fertilization experiment. The long-term application of green manure or cow manure produced wheat yields equivalent to those obtained with chemical N, with the former providing higher soil functions and allowing the functionality of N cycling (especially soil N mineralization and biological N fixation) to control wheat production. The keystone phylotypes within the global network rather than the overall microbial community dominated the soil multifunctionality and functionality of C, N, and P cycling across the soil profile (0-100 cm). We further confirmed that these keystone phylotypes consisted of many metabolic pathways of nutrient cycling and essential microbes involved in organic C mineralization, N2O release, and biological N fixation. The chemical N, green manure, and cow manure resulted in the highest abundances of amoB, nifH, and GH48 genes and Nitrosomonadaceae, Azospirillaceae, and Sphingomonadaceae within the keystone phylotypes, and these microbes were significantly and positively correlated with N2O release, N fixation, and organic C mineralization, respectively. Moreover, our results demonstrated that organic fertilization increased the effects of the network size and keystone phylotypes on the subsoil functions by facilitating the migration of soil microorganisms across the soil profiles and green manure with the highest migration rates. This study highlights the importance of the functionality of N cycling in controlling crop production and keystone phylotypes in regulating soil functions, and provides selectable fertilization strategies for maintaining crop production and soil functions across soil profiles in agricultural ecosystems.
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Affiliation(s)
- Guopeng Zhou
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China/Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Kunkun Fan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Songjuan Gao
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Danna Chang
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China/Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Guilong Li
- Institute of Soil & Fertilizer and Resource & Environment, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200, China
| | - Ting Liang
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China/Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Hai Liang
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shun Li
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jiudong Zhang
- Institute of Soil and Fertilizer and Water-saving Agriculture, Gansu Academy of Agricultural Sciences, Lanzhou, 730070, China
| | - Zongxian Che
- Institute of Soil and Fertilizer and Water-saving Agriculture, Gansu Academy of Agricultural Sciences, Lanzhou, 730070, China.
| | - Weidong Cao
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China/Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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Lewin S, Wende S, Wehrhan M, Verch G, Ganugi P, Sommer M, Kolb S. Cereals rhizosphere microbiome undergoes host selection of nitrogen cycle guilds correlated to crop productivity. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 911:168794. [PMID: 38000749 DOI: 10.1016/j.scitotenv.2023.168794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 08/31/2023] [Accepted: 11/20/2023] [Indexed: 11/26/2023]
Abstract
Sustainable transformation of agricultural plant production requires the reduction of nitrogen (N) fertilizer application. Such a reduced N fertilizer application may impede crop production due to an altered symbiosis of crops and their rhizosphere microbiome, since reduced N input may affect the competition and synergisms with the plant. The assessment of such changes in the crop microbiome functionalities at spatial scales relevant for agricultural management remains challenging. We investigated in a field plot experiment how and if the N cycling guilds of the rhizosphere of globally relevant cereal crops - winter barley, wheat and rye - are influenced by reduced N fertilization. Crop productivity was assessed by remote sensing of the shoot biomass. Microbial N cycling guilds were investigated by metagenomics targeting diazotrophs, nitrifiers, denitrifiers and the dissimilatory nitrate to ammonium reducing guild (DNRA). The functional composition of microbial N cycling guilds was explained by crop productivity parameters and soil pH, and diverged substantially between the crop species. The responses of individual microbial N cycling guild abundances to shoot dry weight and rhizosphere nitrate content was modulated by the N fertilization treatments and the crop species, which was identified based on regression analyses. Thus, characteristic shifts in the microbial N cycling guild acquisition associated with the crop host species were resolved. Particularly, the rhizosphere of rye was enriched with potentially N-preserving microbial guilds - diazotrophs and the DNRA guild - when no fertilizer was applied. We speculate that the acquisition of microbial N cycling guilds was the result of plant species-specific acquisition strategies. Thus, the investigated cereal crop holobionts have likely different symbiotic strategies that make them differently resilient against reduced N fertilizer inputs. Furthermore, we demonstrated that these belowground patterns of N cycling guilds from the rhizosphere microbiome are linked to remotely sensed aboveground plant productivity.
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Affiliation(s)
- Simon Lewin
- Working Group Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Centre for Agricultural Landscape Research e.V. (ZALF), Müncheberg, Germany
| | - Sonja Wende
- Working Group Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Centre for Agricultural Landscape Research e.V. (ZALF), Müncheberg, Germany
| | - Marc Wehrhan
- Working Group Landscape Pedology, Research Area Landscape Functioning, Leibniz Centre for Agricultural Landscape Research e.V. (ZALF), Müncheberg, Germany
| | - Gernot Verch
- Experimental Station Dedelow, Experimental Infrastructure Platform, Leibniz Centre for Agricultural Landscape Research e.V. (ZALF), Müncheberg, Germany
| | - Paola Ganugi
- Department of Agricultural, Forest and Food sciences, University of Turin, Grugliasco, Italy
| | - Michael Sommer
- Working Group Landscape Pedology, Research Area Landscape Functioning, Leibniz Centre for Agricultural Landscape Research e.V. (ZALF), Müncheberg, Germany; Institute of Environmental Science & Geography, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - Steffen Kolb
- Working Group Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Centre for Agricultural Landscape Research e.V. (ZALF), Müncheberg, Germany; Thaer Institute, Faculty of Life Sciences, Humboldt University of Berlin, Berlin, Germany.
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20
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Higo M, Kang DJ, Isobe K. Root-associated microbial community and diversity in napiergrass across radiocesium-contaminated lands after the Fukushima-Daiichi nuclear disaster in Japan. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 342:123051. [PMID: 38043771 DOI: 10.1016/j.envpol.2023.123051] [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: 07/08/2023] [Revised: 11/18/2023] [Accepted: 11/25/2023] [Indexed: 12/05/2023]
Abstract
The microbiome derived from soil associated with plant roots help in plant growth and stress resistance. It exhibits potential benefits for soil remediation and restoration of radioactive-cesium (137Cs)-contaminated soils. However, there is still limited information about the community and diversity of root-associated microbiome in 137Cs-contaminated soil after the Fukushima-Daiichi Nuclear Power Plant (FDNPP) disaster. To address this, a comparative analysis of communities and diversity of root-associated microbiomes was conducted in two field types after the FDNPP disaster. In 2013, we investigated the community and diversity of indigenous root-associated microbiome of napiergrass (Pennisetum purpureum) grown in both grassland and paddy fields of 137Cs-contaminated land-use type within a 30-km radius around the FDNPP. Results showed that the root-associated bacterial communities in napiergrass belonged to 32 phyla, 75 classes, 174 orders, 284 families, and 521 genera, whereas the root-associated fungal communities belonged to 5 phyla, 11 classes, 31 orders, 59 families, and 64 genera. The most frequently observed phylum in both grassland and paddy field was Proteobacteria (47.4% and 55.9%, respectively), followed by Actinobacteriota (23.8% and 27.9%, respectively) and Bacteroidota (10.1% and 11.3%, respectively). The dominant fungal phylum observed in both grassland and paddy field was Basidiomycota (75.9% and 94.2%, respectively), followed by Ascomycota (24.0% and 5.8%, respectively). Land-use type significantly affected the bacterial and fungal communities that colonize the roots of napiergrass. Several 137Cs-tolerant bacterial and fungal taxa were also identified, which may be potentially applied for the phytoremediation of 137Cs-contaminated areas around FDNPP. These findings contribute to a better understanding of the distribution of microbial communities in 137Cs-contaminated lands and their long-term ecosystem benefits for phytoremediation efforts.
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Affiliation(s)
- Masao Higo
- College of Bioresource Sciences, Nihon University, Kameino, 1866, Fujisawa, Kanagawa, 252-0880, Japan.
| | - Dong-Jin Kang
- Teaching and Research Center for Bio-coexistence, Faculty of Agriculture and Life Sciences, Hirosaki University, Gosyogawara, Aomori, 037-0202, Japan.
| | - Katsunori Isobe
- College of Bioresource Sciences, Nihon University, Kameino, 1866, Fujisawa, Kanagawa, 252-0880, Japan
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21
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Guo S, Jiao Z, Yan Z, Yan X, Deng X, Xiong W, Tao C, Liu H, Li R, Shen Q, Kowalchuk GA, Geisen S. Predatory protists reduce bacteria wilt disease incidence in tomato plants. Nat Commun 2024; 15:829. [PMID: 38280866 PMCID: PMC10821857 DOI: 10.1038/s41467-024-45150-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 01/16/2024] [Indexed: 01/29/2024] Open
Abstract
Soil organisms are affected by the presence of predatory protists. However, it remains poorly understood how predatory protists can affect plant disease incidence and how fertilization regimes can affect these interactions. Here, we characterise the rhizosphere bacteria, fungi and protists over eleven growing seasons of tomato planting under three fertilization regimes, i.e conventional, organic and bioorganic, and with different bacterial wilt disease incidence levels. We find that predatory protists are negatively associated with disease incidence, especially two ciliophoran Colpoda OTUs, and that bioorganic fertilization enhances the abundance of predatory protists. In glasshouse experiments we find that the predatory protist Colpoda influences disease incidence by directly consuming pathogens and indirectly increasing the presence of pathogen-suppressive microorganisms in the soil. Together, we demonstrate that predatory protists reduce bacterial wilt disease incidence in tomato plants via direct and indirect reductions of pathogens. Our study provides insights on the role that predatory protists play in plant disease, which could be used to design more sustainable agricultural practices.
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Affiliation(s)
- Sai Guo
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China
- The Sanya Institute of the Nanjing Agricultural University, Sanya, Hainan Province, PR China
| | - Zixuan Jiao
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China
| | - Zhiguang Yan
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China
| | - Xinyue Yan
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China
| | - Xuhui Deng
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China
- The Sanya Institute of the Nanjing Agricultural University, Sanya, Hainan Province, PR China
| | - Wu Xiong
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China
- The Sanya Institute of the Nanjing Agricultural University, Sanya, Hainan Province, PR China
| | - Chengyuan Tao
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China
- The Sanya Institute of the Nanjing Agricultural University, Sanya, Hainan Province, PR China
| | - Hongjun Liu
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China
- The Sanya Institute of the Nanjing Agricultural University, Sanya, Hainan Province, PR China
| | - Rong Li
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China.
- The Sanya Institute of the Nanjing Agricultural University, Sanya, Hainan Province, PR China.
| | - Qirong Shen
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China
| | - George A Kowalchuk
- Ecology and Biodiversity Group, Department of Biology, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Stefan Geisen
- Laboratory of Nematology, Wageningen University, 6700 AA, Wageningen, The Netherlands
- Netherlands Department of Terrestrial Ecology, Netherlands Institute for Ecology, (NIOO-KNAW), 6708 PB, Wageningen, The Netherlands
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22
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Elhawat N, Kovács AB, Antal G, Kurucz E, Domokos-Szabolcsy É, Fári MG, Alshaal T. Living mulch enhances soil enzyme activities, nitrogen pools and water retention in giant reed (Arundo donax L.) plantations. Sci Rep 2024; 14:1704. [PMID: 38242963 PMCID: PMC10798950 DOI: 10.1038/s41598-024-51491-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 01/05/2024] [Indexed: 01/21/2024] Open
Abstract
Giant reed (Arundo donax L.) is one of the most well-studied perennial biomass crops because of its high productivity and potential to store carbon. Yet, little information on controlling weeds in giant reed plantations and their influences on the soil ecosystem is available. In the present study, three different weed control methods, i.e., intercropping (living mulch) with sweet clover (Melilotus officinalis L.), herbicide (glyphosate), and hoeing, were investigated in a 2-year giant reed farm. The intercropping presented significantly higher values (on average) of all the tested soil properties than herbicide and hoeing, except for the catalase activity and pH. The dehydrogenase, phosphatase, and urease activities in the soil under intercropping were higher than the herbicide by 75%, 65%, and 80% (on average), respectively. Also, the soil under intercropping had higher soil organic matter (SOM) and soil respiration than the herbicide by 20% and 25%, respectively. Intercropping also increased the content of N pools, i.e., NO3--N, NH4+-N, Org-N, and Total-N by 517%, 356%, 38%, and 137%, respectively, compared to herbicide. These findings illustrated that controlling weeds in biomass plantations through legume intercropping brings benefits not only to soil properties but also to biomass productivity.
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Affiliation(s)
- Nevien Elhawat
- Department of Applied Plant Biology; Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, Böszörményi str. 138, 4032, Debrecen, Hungary.
- Department of Biological and Environmental Sciences, Faculty of Home Economic, Al-Azhar University, Tanta, 31732, Egypt.
| | - Andrea Balla Kovács
- Institute of Agricultural Chemistry and Soil Science, FAFSEM, University of Debrecen, 4032, Debrecen, Hungary
| | - Gabriella Antal
- Institute of Horticulture University of Debrecen, 4032, Debrecen, Hungary
| | - Erika Kurucz
- Institute of Horticulture University of Debrecen, 4032, Debrecen, Hungary
| | - Éva Domokos-Szabolcsy
- Department of Applied Plant Biology; Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, Böszörményi str. 138, 4032, Debrecen, Hungary
| | - Miklós Gábor Fári
- Department of Applied Plant Biology; Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, Böszörményi str. 138, 4032, Debrecen, Hungary
| | - Tarek Alshaal
- Department of Applied Plant Biology; Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, Böszörményi str. 138, 4032, Debrecen, Hungary
- Soil and Water Department, Faculty of Agriculture, University of Kafrelsheikh, Kafr El-Sheikh, 33516, Egypt
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23
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Wu C, Zhang X, Fan Y, Ye J, Dong L, Wang Y, Ren Y, Yong H, Liu R, Wang A. Vertical transfer and functional characterization of cotton seed core microbiome. Front Microbiol 2024; 14:1323342. [PMID: 38264479 PMCID: PMC10803423 DOI: 10.3389/fmicb.2023.1323342] [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: 10/17/2023] [Accepted: 12/22/2023] [Indexed: 01/25/2024] Open
Abstract
Introduction Microbiome within plant tissues is pivotal for co-evolution with host plants. This microbiome can colonize the plant, with potential transmission via seeds between parents and offspring, affecting seedling growth and host plant adaptability to the environment. Methods We employed 16S rRNA gene amplicon analysis to investigate the vertical distribution of core microbiome in cotton seeds across ecological niches [rhizosphere, root, stem, leaf, seed and seed-P (parental seed)] of the three cotton genotypes. Results The findings demonstrated a significant decrease in microbiome diversity and network complexity from roots, stems, and leaves to seeds. The microenvironment exerted a more substantial influence on the microbiome structure of cotton than the genotypes. The core endophytic microorganisms in cotton seeds comprised 29 amplicon sequence variants (ASVs) affiliated with Acidimicrobiia, Alphaproteobacteria, Bacilli, Bacteroidia, Clostridia, Gammaproteobacteria, and unclassified_Proteobacteria. These vertically transmitted taxa are widely distributed in cotton plants. Through 16S rRNA gene-based function prediction analysis of the cotton microbiome, we preliminarily understood that there are potential differences in metabolic capabilities and phenotypic traits among microbiomes in different microhabitats. Discussion In conclusion, this study demonstrated the crucial role of the microenvironment in influencing the cotton microbiome and offered insights into the structures and functions of the cotton seed microbiome, facilitating future crop yield enhancement through core seed microbiome regulation.
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Affiliation(s)
- Chongdie Wu
- College of Life Sciences, Shihezi University, Shihezi, China
- Xinjiang Production and Construction Corps, Key Laboratory of Oasis Town and Mountain-basin System Ecology, Shihezi, China
| | - Xin Zhang
- College of Life Sciences, Shihezi University, Shihezi, China
| | - Yongbin Fan
- College of Life Sciences, Shihezi University, Shihezi, China
- Xinjiang Production and Construction Corps, Key Laboratory of Oasis Town and Mountain-basin System Ecology, Shihezi, China
| | - Jingyi Ye
- College of Life Sciences, Shihezi University, Shihezi, China
- Xinjiang Production and Construction Corps, Key Laboratory of Oasis Town and Mountain-basin System Ecology, Shihezi, China
| | - Lingjun Dong
- College of Life Sciences, Shihezi University, Shihezi, China
| | - YuXiang Wang
- College of Life Sciences, Shihezi University, Shihezi, China
| | - YinZheng Ren
- College of Life Sciences, Shihezi University, Shihezi, China
| | - HongHong Yong
- College of Life Sciences, Shihezi University, Shihezi, China
| | - Ruina Liu
- College of Life Sciences, Shihezi University, Shihezi, China
- Xinjiang Production and Construction Corps, Key Laboratory of Oasis Town and Mountain-basin System Ecology, Shihezi, China
| | - Aiying Wang
- College of Life Sciences, Shihezi University, Shihezi, China
- Xinjiang Production and Construction Corps, Key Laboratory of Oasis Town and Mountain-basin System Ecology, Shihezi, China
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24
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Zhang Y, Zhan J, Ma C, Liu W, Huang H, Yu H, Christie P, Li T, Wu L. Root-associated bacterial microbiome shaped by root selective effects benefits phytostabilization by Athyrium wardii (Hook.). ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 269:115739. [PMID: 38016191 DOI: 10.1016/j.ecoenv.2023.115739] [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: 08/20/2023] [Revised: 11/18/2023] [Accepted: 11/22/2023] [Indexed: 11/30/2023]
Abstract
The root-associated microbiome assembly substantially promotes (hyper)accumulator plant growth and metal accumulation and is influenced by multiple factors, especially host species and environmental stress. Athyrium wardii (Hook.) is a phytostabilizer that grows in lead (Pb)-zinc (Zn) mine tailings and shows high root Pb accumulation. However, there remains little information on the assembly of the root-associated microbiome of A. wardii and its role in phytostabilization. A field study investigated the structural and functional variation in the root-associated bacterial microbiome of Athyrium wardii (Hook.) exposed to different levels of contamination in Pb-Zn mine tailings. The root compartment dominated the variation in the root-associated bacterial microbiome but the levels of contaminants showed less impact. Bacterial co-occurrence was enhanced in the rhizosphere soil and rhizoplane but tended to be much simpler in the endosphere in terms of network complexity and connectivity. This indicates that the microbial community assembly of A. wardii was non-random and shaped by root selective effects. Proteobacteria, Chloroflexi, Actinobacteria, Cyanobacteria, and Acidobacteriota were generally the dominant bacterial phyla. The genera Crossiella and Bradyrhizobium were enriched in the rhizosphere and cyanobacterial genera were enriched in the endosphere, demonstrating substantial advantages to plant survival and adaptation in the harsh mine environment. Functional categories involved in amino acid and carbohydrate metabolism were abundant in the rhizosphere soil, thus contributing to metal solubility and bioavailability in the rhizosphere. Membrane transporters, especially ATP-binding cassette transporters, were enriched in the endosphere, indicating a potential role in metal tolerance and transportation in A. wardii. The study shows substantial variation in the structure and function of microbiomes colonizing different compartments, with the rhizosphere and endophytic microbiota potentially involved in plant metal tolerance and accumulation during phytostabilization.
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Affiliation(s)
- Yunhong Zhang
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; College of Resources, Sichuan Agricultural University, 211 Huimin Road, Chengdu 611130, China
| | - Juan Zhan
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Chuang Ma
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Wuxing Liu
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Huagang Huang
- College of Resources, Sichuan Agricultural University, 211 Huimin Road, Chengdu 611130, China
| | - Haiying Yu
- College of Resources, Sichuan Agricultural University, 211 Huimin Road, Chengdu 611130, China
| | - Peter Christie
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Tingxuan Li
- College of Resources, Sichuan Agricultural University, 211 Huimin Road, Chengdu 611130, China.
| | - Longhua Wu
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China.
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25
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Yang Y, Qiu K, Xie Y, Li X, Zhang S, Liu W, Huang Y, Cui L, Wang S, Bao P. Geographical, climatic, and soil factors control the altitudinal pattern of rhizosphere microbial diversity and its driving effect on root zone soil multifunctionality in mountain ecosystems. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 904:166932. [PMID: 37690759 DOI: 10.1016/j.scitotenv.2023.166932] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 09/05/2023] [Accepted: 09/06/2023] [Indexed: 09/12/2023]
Abstract
Shifts in rhizosphere soil microorganisms of dominant plants' response to climate change profoundly impact mountain soil ecosystem multifunctionality; relatively little is known about the relationship between them and how they depend on long-term environmental drivers. Here, we conducted analyses of rhizosphere microbial altitudinal pattern, community assembly, and co-occurrence network of 6 dominant plants in six typical vegetation zones ranging from 1350 to 2900 m (a.s.l.) in Helan Mountains by absolute quantitative sequencing technology, and finally related the microbiomes to root zone soil multifunctionality ('soil multifunctionality' hereafter), the environmental dependence of the relationship was explored. It was found that the altitudinal pattern of rhizosphere soil bacterial and fungal diversities differed significantly. Higher co-occurrence and more potential interactions of Stipa breviflora and Carex coninux were found at the lowest and highest altitudes. Bacterial α diversity, the identity of some dominant bacterial and fungal taxa, had significant positive or negative effects on soil multifunctionality. The effect sizes of positive effects of microbial diversity on soil multifunctionality were greater than those of negative effects. These results indicated that the balance of positive and negative effects of microbes determines the impact of microbial diversity on soil multifunctionality. As the number of microbes at the phylum level increases, there will be a net gain in soil multifunctionality. Our study reveals that geographical and climatic factors can directly or modulate the effects of soil properties on rhizosphere microbial diversity, thereby affecting the driving effect of microbial diversity on soil multifunctionality, and points to the rhizosphere bacterial diversity rather than the fungi being strongly associated with soil multifunctionality. This work has important ecological implications for predicting how multiple environment-plant-soil-microorganisms interactions in mountain ecosystems will respond to future climate change.
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Affiliation(s)
- Yi Yang
- College of Forestry and Prataculture, Ningxia University, Yinchuan, China; Ningxia Grassland and Animal Husbandry Engineering Technology Research Center, Yinchuan, China; Breeding Base for State Key Laboratory of Land Degradation and Ecological Restoration of Northwest China, Yinchuan, China; Key Laboratory for Model Innovation in Forage Production Efficiency, Ministry of Agriculture and Rural Affairs, Ningxia University, Yinchuan, China
| | - Kaiyang Qiu
- College of Forestry and Prataculture, Ningxia University, Yinchuan, China; Ningxia Grassland and Animal Husbandry Engineering Technology Research Center, Yinchuan, China; Breeding Base for State Key Laboratory of Land Degradation and Ecological Restoration of Northwest China, Yinchuan, China; Key Laboratory for Model Innovation in Forage Production Efficiency, Ministry of Agriculture and Rural Affairs, Ningxia University, Yinchuan, China.
| | - Yingzhong Xie
- College of Forestry and Prataculture, Ningxia University, Yinchuan, China; Ningxia Grassland and Animal Husbandry Engineering Technology Research Center, Yinchuan, China; Breeding Base for State Key Laboratory of Land Degradation and Ecological Restoration of Northwest China, Yinchuan, China; Key Laboratory for Model Innovation in Forage Production Efficiency, Ministry of Agriculture and Rural Affairs, Ningxia University, Yinchuan, China
| | - Xiaocong Li
- College of Forestry and Prataculture, Ningxia University, Yinchuan, China; Ningxia Grassland and Animal Husbandry Engineering Technology Research Center, Yinchuan, China; Breeding Base for State Key Laboratory of Land Degradation and Ecological Restoration of Northwest China, Yinchuan, China; Key Laboratory for Model Innovation in Forage Production Efficiency, Ministry of Agriculture and Rural Affairs, Ningxia University, Yinchuan, China
| | - Shuo Zhang
- College of Forestry and Prataculture, Ningxia University, Yinchuan, China; Ningxia Grassland and Animal Husbandry Engineering Technology Research Center, Yinchuan, China; Breeding Base for State Key Laboratory of Land Degradation and Ecological Restoration of Northwest China, Yinchuan, China; Key Laboratory for Model Innovation in Forage Production Efficiency, Ministry of Agriculture and Rural Affairs, Ningxia University, Yinchuan, China
| | - Wangsuo Liu
- College of Forestry and Prataculture, Ningxia University, Yinchuan, China; Ningxia Grassland and Animal Husbandry Engineering Technology Research Center, Yinchuan, China; Breeding Base for State Key Laboratory of Land Degradation and Ecological Restoration of Northwest China, Yinchuan, China; Key Laboratory for Model Innovation in Forage Production Efficiency, Ministry of Agriculture and Rural Affairs, Ningxia University, Yinchuan, China
| | - Yeyun Huang
- College of Forestry and Prataculture, Ningxia University, Yinchuan, China; Ningxia Grassland and Animal Husbandry Engineering Technology Research Center, Yinchuan, China; Breeding Base for State Key Laboratory of Land Degradation and Ecological Restoration of Northwest China, Yinchuan, China; Key Laboratory for Model Innovation in Forage Production Efficiency, Ministry of Agriculture and Rural Affairs, Ningxia University, Yinchuan, China
| | - Luyao Cui
- College of Forestry and Prataculture, Ningxia University, Yinchuan, China; Ningxia Grassland and Animal Husbandry Engineering Technology Research Center, Yinchuan, China; Breeding Base for State Key Laboratory of Land Degradation and Ecological Restoration of Northwest China, Yinchuan, China; Key Laboratory for Model Innovation in Forage Production Efficiency, Ministry of Agriculture and Rural Affairs, Ningxia University, Yinchuan, China
| | - Siyao Wang
- College of Forestry and Prataculture, Ningxia University, Yinchuan, China; Ningxia Grassland and Animal Husbandry Engineering Technology Research Center, Yinchuan, China; Breeding Base for State Key Laboratory of Land Degradation and Ecological Restoration of Northwest China, Yinchuan, China; Key Laboratory for Model Innovation in Forage Production Efficiency, Ministry of Agriculture and Rural Affairs, Ningxia University, Yinchuan, China
| | - Pingan Bao
- College of Forestry and Prataculture, Ningxia University, Yinchuan, China; Ningxia Grassland and Animal Husbandry Engineering Technology Research Center, Yinchuan, China; Breeding Base for State Key Laboratory of Land Degradation and Ecological Restoration of Northwest China, Yinchuan, China; Key Laboratory for Model Innovation in Forage Production Efficiency, Ministry of Agriculture and Rural Affairs, Ningxia University, Yinchuan, China
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Chen S, Wang Y, Gao J, Chen X, Qi J, Peng Z, Chen B, Pan H, Liang C, Liu J, Wang Y, Wei G, Jiao S. Agricultural tillage practice and rhizosphere selection interactively drive the improvement of soybean plant biomass. PLANT, CELL & ENVIRONMENT 2023; 46:3542-3557. [PMID: 37564021 DOI: 10.1111/pce.14694] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 07/30/2023] [Accepted: 08/03/2023] [Indexed: 08/12/2023]
Abstract
Rhizosphere microbes play key roles in plant growth and productivity in agricultural systems. One of the critical issues is revealing the interaction of agricultural management (M) and rhizosphere selection effects (R) on soil microbial communities, root exudates and plant productivity. Through a field management experiment, we found that bacteria were more sensitive to the M × R interaction effect than fungi, and the positive effect of rhizosphere bacterial diversity on plant biomass existed in the bacterial three two-tillage system. In addition, inoculation experiments demonstrated that the nitrogen cycle-related isolate Stenotrophomonas could promote plant growth and alter the activities of extracellular enzymes N-acetyl- d-glucosaminidase and leucine aminopeptidase in rhizosphere soil. Microbe-metabolites network analysis revealed that hubnodes Burkholderia-Caballeronia-Paraburkholderia and Pseudomonas were recruited by specific root metabolites under the M × R interaction effect, and the inoculation of 10 rhizosphere-matched isolates further proved that these microbes could promote the growth of soybean seedlings. Kyoto Encyclopaedia of Genes and Genomes pathway analysis indicated that the growth-promoting mechanisms of these beneficial genera were closely related to metabolic pathways such as amino acid metabolism, melatonin biosynthesis, aerobactin biosynthesis and so on. This study provides field observation and experimental evidence to reveal the close relationship between beneficial rhizosphere microbes and plant productivity under the M × R interaction effect.
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Affiliation(s)
- Shi Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Yang Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Jiamin Gao
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Xingyu Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Jiejun Qi
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Ziheng Peng
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Beibei Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Haibo Pan
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Chunling Liang
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Jiai Liu
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Yihe Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Gehong Wei
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Shuo Jiao
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
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Fudjoe SK, Li L, Anwar S, Shi S, Xie J, Yeboah FK, Wang L. The impact of fertilization on ammonia-oxidizing bacteria and comammox Nitrospira communities and the subsequent effect on N 2O emission and maize yield in a semi-arid region. Front Microbiol 2023; 14:1249668. [PMID: 37840719 PMCID: PMC10570556 DOI: 10.3389/fmicb.2023.1249668] [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: 06/29/2023] [Accepted: 09/06/2023] [Indexed: 10/17/2023] Open
Abstract
The control of nitrous oxide (N2O) emissions through nitrification and the optimization of maize yield are important in agricultural systems. However, within the semi-arid region, the impact of fertilization on the function of nitrification communities and its connection with N2O emissions in the rhizosphere soil is still unclear. Our study investigates the influence of fertilization treatments on the communities of ammonia-oxidizing bacteria (AOB) and the complete ammonia oxidizers of the Nitrospira known as comammox (CAOB) in a maize agroecosystem. Nitrous oxide production, potential nitrification activity (PNA), maize yield, and nitrogen use efficiency (NUE) were determined for the same samples. The fertilizer treatments included a control group without fertilization (NA), inorganic fertilizer (CF), organic fertilizer (SM), combined inorganic and organic fertilizer (SC), and maize straw (MS). The SC treatment indicated a lower cumulative N2O emission than the CF treatment in the 2020 and 2021 cropping seasons. The AOB community under the CF, MS, and SM treatments was predominantly composed of Nitrosospira cluster 3b, while the SC treatment was associated with the comammox Nitrospira clade A.1 lineage, related to key species such as Ca. Nitrospira inopinata and Ca. Nitrospira nitrificans. Network analysis demonstrated a positive potential for competitive interaction between hub taxonomy and distinct keystone taxa among AOB and comammox Nitrospira nitrifiers. The structural equation model further revealed a significant positive association between AOB nitrifiers and N2O emission, PNA, soil pH, SOC, NO 3 - -N, and DON under organic fertilization. The keystone taxa in the comammox Nitrospira nitrifier and network Module II exhibited a positive correlation with maize productivity and NUE, likely due to their functional activities stimulated by the SC treatment. It is noteworthy that the AOB community played a more significant role in driving nitrification compared to the composition of comammox Nitrospira. Collectively, combined inorganic and organic fertilizer (SC) treatment exhibits high potential for reducing N2O emissions, enhancing maize productivity, increasing NUE, and increasing the sustainability of the nitrogen dynamics of maize agroecosystems in the semi-arid Loess Plateau.
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Affiliation(s)
- Setor Kwami Fudjoe
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Lingling Li
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Sumera Anwar
- Department of Botany, Government College Women University Faisalabad, Faisalabad, Pakistan
| | - Shangli Shi
- College of Grassland Science, Gansu Agricultural University, Lanzhou, China
| | - Junhong Xie
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Frederick Kwame Yeboah
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Beijing Normal University, Beijing, China
| | - Linlin Wang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
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28
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Guo M, Yang G, Meng X, Zhang T, Li C, Bai S, Zhao X. Illuminating plant-microbe interaction: How photoperiod affects rhizosphere and pollutant removal in constructed wetland? ENVIRONMENT INTERNATIONAL 2023; 179:108144. [PMID: 37586276 DOI: 10.1016/j.envint.2023.108144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Revised: 07/18/2023] [Accepted: 08/11/2023] [Indexed: 08/18/2023]
Abstract
Rhizosphere is a crucial area in comprehending the interaction between plants and microorganisms in constructed wetlands (CWs). However, influence of photoperiod, a key factor that regulates photosynthesis and rhizosphere microbial activity, remains largely unknown. This study investigated the effect of photoperiod (9, 12, 15 h/day) on pollutant removal and underlying mechanisms. Results showed that 15-hour photoperiod treatment exhibited the highest removal efficiencies for COD (87.26%), TN (63.32%), and NO3--N (97.79%). This treatment enhanced photosynthetic pigmentation and root activity, which increased transport of oxygen and soluble organic carbon to rhizosphere, thus promoting microbial nitrification and denitrification. Microbial community analysis revealed a more stable co-occurrence network due to increased complexity and aggregation in the 15-hour photoperiod treatment. Phaselicystis was identified as a key connector, which was responsible for transferring necessary carbon sources, ATP, and electron donors that supported and optimized nitrogen metabolism in the CWs. Structural equation model analysis emphasized the importance of plant-microbe interactions in pollutant removal through increased substance, information, and energy exchange. These findings offer valuable insights for CWs design and operation in various latitudes and rural areas for small-scale decentralized systems.
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Affiliation(s)
- Mengran Guo
- College of Resource and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Genji Yang
- College of Resource and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Xiangwei Meng
- College of Resource and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Tuoshi Zhang
- College of Resource and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Chunyan Li
- College of Resource and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Shunwen Bai
- School of Environment, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Xinyue Zhao
- College of Resource and Environment, Northeast Agricultural University, Harbin 150030, China.
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Li J, Meng F, Jiang M, Zhang H, Chu G, Tao R. Assembly and co-occurrence patterns of rhizosphere bacterial communities are closely linked to soil fertility during continuous cropping of cut chrysanthemum (Chrysanthemum morifolium Ramat). J Appl Microbiol 2023; 134:lxad175. [PMID: 37537151 DOI: 10.1093/jambio/lxad175] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 07/27/2023] [Accepted: 08/03/2023] [Indexed: 08/05/2023]
Abstract
AIMS Continuous cropping is known to have profound effects on the soil microbial community in different planting systems. However, we lack an understanding of how different years of continuous cropping affects rhizosphere soil bacterial community co-occurrence pattern and assembly processes in the cut chrysanthemum (Chrysanthemum morifolium Ramat.) field. METHODS AND RESULTS We collected the soils from cut chrysanthemum rhizospheres with planting for 1 year (PY1) and continuous cropping for 6 years (CY6) and 12 years (CY12). Real-time quantitative PCR and flow cytometry (FCM) techniques were used to test the 16S rRNA gene copy number and bacterial cell count, respectively. The bacterial community structure was analysed by using high-throughput sequencing technology. The CY12 had a significantly decreased soil fertility index and rhizosphere bacterial living cell counts and gene copy numbers compared to CY6 and PY1 (P < 0.05). The rhizosphere bacterial community dissimilarity increased as the continuous cropping years increased. Three main ecological clusters (modules #1, #2, and #3) were observed in the bacterial co-occurrence network across all samples, and only the relative abundance of module #1 (enriched in the CY12) was significantly correlated with soil fertility (P < 0.05). Moreover, the rhizosphere bacterial community assembly was primarily governed by the deterministic process under 12 years of continuous cropping. CONCLUSIONS Soil fertility decline correlates with ecological network modularization and the deterministic assembly process of the rhizosphere bacterial community of cut chrysanthemum during continuous cropping.
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Affiliation(s)
- Jun Li
- School of Life Science, Shaoxing University, Zhejiang 312000, P. R. China
| | - Feng Meng
- Shaoxing Service Center for Environmental Protection Science and Technology, Zhejiang 312000, P. R. China
| | - Maibo Jiang
- Ningbo City College of Vocational Technology, Ningbo, Zhejiang 315100, P. R. China
| | - Hanjie Zhang
- School of Life Science, Shaoxing University, Zhejiang 312000, P. R. China
| | - Guixin Chu
- School of Life Science, Shaoxing University, Zhejiang 312000, P. R. China
| | - Rui Tao
- School of Life Science, Shaoxing University, Zhejiang 312000, P. R. China
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30
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Shi Z, Yang Y, Fan Y, He Y, Li T. Dynamic Responses of Rhizosphere Microorganisms to Biogas Slurry Combined with Chemical Fertilizer Application during the Whole Life Cycle of Rice Growth. Microorganisms 2023; 11:1755. [PMID: 37512927 PMCID: PMC10386682 DOI: 10.3390/microorganisms11071755] [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: 05/19/2023] [Revised: 06/14/2023] [Accepted: 07/01/2023] [Indexed: 07/30/2023] Open
Abstract
Biogas slurry combined with chemical fertilizer (BCF) is widely used as a fertilizer in paddy fields and rhizosphere microorganisms are key players in plant growth and reproduction. However, the dynamic responses of rhizosphere microorganisms of field-grown rice to BCF application still remain largely unknown. In this study, a field experiment was conducted in two proximate paddy fields in Chongming Island to study the impacts of BCF on the changes in rhizosphere microorganisms during the whole rice growth, including seedling, tillering, booting, and grain-filling stages, with solely chemical fertilizer (CF) treatment as control. The results showed BCF could increase the N-, P-, and C- levels in paddy water as well as the rhizosphere microbial abundance and diversity compared with control. In particular, the phosphate-solubilizing- and cellulose-decomposing-bacteria (e.g., Bacillus) and fungi (e.g., Mortierella) were more abundant in the rhizosphere of BCF than those of CF. Moreover, these microbes increased markedly at the booting and grain-filling stages in BCF, which could promote rice to obtain available nutrients (P and C). It was noted that denitrifying-like bacteria (e.g., Steroidobacteraceae) decreased and dissimilatory nitrate reduction to ammonia-related bacteria (e.g., Geobacter, Anaeromyxobacter, and Ignavibacterium) increased at the booting and filling stages, which could promote N-availability. TP in paddy water of BCF was most correlated to the bacteria, while COD was the most critical regulator for the fungi. Furthermore, correlation network analysis showed nutrient-cycling-related microorganisms were more closely interconnected in BCF than those in CF. These findings showed the application of biogas slurry plus chemical fertilizer could regulate rhizosphere microorganisms towards a beneficial fertilizer use for rice growth.
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Affiliation(s)
- Zhenbao Shi
- State Key Laboratory of Pollution Control and Resource Reuse, Tongji University, Shanghai 200092, China
| | - Yanmei Yang
- Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, Shanghai Key Laboratory for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, Institute of Eco-Chongming, East China Normal University, Shanghai 200241, China
| | - Yehong Fan
- Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, Shanghai Key Laboratory for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, Institute of Eco-Chongming, East China Normal University, Shanghai 200241, China
| | - Yan He
- Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, Shanghai Key Laboratory for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, Institute of Eco-Chongming, East China Normal University, Shanghai 200241, China
| | - Tian Li
- State Key Laboratory of Pollution Control and Resource Reuse, Tongji University, Shanghai 200092, China
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31
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Moraga D, Latorre K, Muñoz-Torres P, Cárdenas S, Jofré-Quispe A, López-Cepeda J, Bustos L, Balada C, Argaluza MF, González P, Guzmán L. Diversity of Culturable Bacteria from Endemic Medicinal Plants of the Highlands of the Province of Parinacota, Chile. BIOLOGY 2023; 12:920. [PMID: 37508351 PMCID: PMC10376134 DOI: 10.3390/biology12070920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 06/14/2023] [Accepted: 06/15/2023] [Indexed: 07/30/2023]
Abstract
Endemic medicinal plants that grow at altitudes in northern Chile have been traditionally used for therapeutic applications by Aymara doctors. Several studies have analyzed the biological properties of these plants for therapeutic purposes. The aim was to characterize at molecular and biochemical levels the bacteria that live in the rhizosphere and roots from endemic medicinal plants that grow between 3681-5104 m.a.s.l. in the province of Parinacota. Thirty-nine bacteria were isolated from nine medicinal plants under our laboratory conditions. These bacteria were characterized by Gram stain, hydrolase production, plant-growth promotion, anti-fungal and antibacterial activities, and 16S rDNA sequencing. A phylogenetic study revealed the presence of three major phyla, Actinomycetota (46.2%), Bacillota (43.6%), and Pseudomonadota (10.3%). The rhizobacteria strains associated with the Aymara medicinal plant exhibited several interesting biological activities, such as hydrolytic enzymes, plant-growth-promoting traits, and antibacterial and antifungal properties, indicating their potential for developing new bio-based products for agricultural or clinical applications. These results are promising and highlight the need to point toward the search for explanations of the bio-molecular basis of the therapeutic effects of medicinal plants.
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Affiliation(s)
- Daniel Moraga
- Laboratorio de Fisiología, Departamento de Ciencias Biomédicas, Facultad de Medicina, Universidad de Tarapacá, Arica 1000000, Chile
| | - Katina Latorre
- Laboratorio de Microbiología, Departamento de Tecnología Médica, Facultad de Ciencias de la Salud, Universidad de Tarapacá, Arica 1000000, Chile
| | - Patricio Muñoz-Torres
- Laboratorio de Patología Vegetal y Bioproductos, Facultad de Ciencias Agronómicas, Universidad de Tarapacá, Arica 1000000, Chile
| | - Steffany Cárdenas
- Laboratorio de Patología Vegetal y Bioproductos, Facultad de Ciencias Agronómicas, Universidad de Tarapacá, Arica 1000000, Chile
| | - Alan Jofré-Quispe
- Departamento de Ciencias Históricas y Geográficas, Universidad de Tarapacá, Arica 1000000, Chile
| | - José López-Cepeda
- Departamento de Biología, Facultad de Ciencias, Universidad de Tarapacá, Arica 1000000, Chile
| | - Luis Bustos
- Subdepartamento de Gestión de Farmacia, Servicio de Salud Arica, Arica 1000871, Chile
| | - Cristóbal Balada
- Laboratorio de Química Biológica, Instituto de Química, Facultad de Ciencias, Pontificia Universidad Católica de Valparaíso, Valparaíso 2340001, Chile
| | - María Fernanda Argaluza
- Laboratorio de Química Biológica, Instituto de Química, Facultad de Ciencias, Pontificia Universidad Católica de Valparaíso, Valparaíso 2340001, Chile
| | - Pablo González
- Laboratorio de Química Biológica, Instituto de Química, Facultad de Ciencias, Pontificia Universidad Católica de Valparaíso, Valparaíso 2340001, Chile
| | - Leda Guzmán
- Laboratorio de Química Biológica, Instituto de Química, Facultad de Ciencias, Pontificia Universidad Católica de Valparaíso, Valparaíso 2340001, Chile
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32
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Bourak K, Sare AR, Allaoui A, Jijakli MH, Massart S. Impact of Two Phosphorus Fertilizer Formulations on Wheat Physiology, Rhizosphere, and Rhizoplane Microbiota. Int J Mol Sci 2023; 24:9879. [PMID: 37373026 DOI: 10.3390/ijms24129879] [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: 04/21/2023] [Revised: 05/29/2023] [Accepted: 06/05/2023] [Indexed: 06/29/2023] Open
Abstract
Phosphorus (P) is the second most important macronutrient for crop growth and a limiting factor in food production. Choosing the right P fertilizer formulation is important for crop production systems because P is not mobile in soils, and placing phosphate fertilizers is a major management decision. In addition, root microorganisms play an important role in helping phosphorus fertilization management by regulating soil properties and fertility through different pathways. Our study evaluated the impact of two phosphorous formulations (polyphosphates and orthophosphates) on physiological traits of wheat related to yield (photosynthetic parameters, biomass, and root morphology) and its associated microbiota. A greenhouse experiment was conducted using agricultural soil deficient in P (1.49%). Phenotyping technologies were used at the tillering, stem elongation, heading, flowering, and grain-filling stages. The evaluation of wheat physiological traits revealed highly significant differences between treated and untreated plants but not between phosphorous fertilizers. High-throughput sequencing technologies were applied to analyse the wheat rhizosphere and rhizoplane microbiota at the tillering and the grain-filling growth stages. The alpha- and beta-diversity analyses of bacterial and fungal microbiota revealed differences between fertilized and non-fertilized wheat, rhizosphere, and rhizoplane, and the tillering and grain-filling growth stages. Our study provides new information on the composition of the wheat microbiota in the rhizosphere and rhizoplane during growth stages (Z39 and Z69) under polyphosphate and orthophosphate fertilization. Hence, a deeper understanding of this interaction could provide better insights into managing microbial communities to promote beneficial plant-microbiome interactions for P uptake.
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Affiliation(s)
- Kaoutar Bourak
- Terra Research Center, Integrated and Urban Plant Pathology Laboratory, Liege University, Gembloux Agro-Bio-Tech, B-5030 Gembloux, Belgium
- Microbiology Laboratory, African Genome Center (AGC), Mohammed VI Polytechnic University, Lot 660, Hay Moulay Rachid, Ben Guerir 43150, Morocco
| | - Abdoul Razack Sare
- Terra Research Center, Integrated and Urban Plant Pathology Laboratory, Liege University, Gembloux Agro-Bio-Tech, B-5030 Gembloux, Belgium
| | - Abdelmounaaim Allaoui
- Microbiology Laboratory, African Genome Center (AGC), Mohammed VI Polytechnic University, Lot 660, Hay Moulay Rachid, Ben Guerir 43150, Morocco
| | - M Haissam Jijakli
- Terra Research Center, Integrated and Urban Plant Pathology Laboratory, Liege University, Gembloux Agro-Bio-Tech, B-5030 Gembloux, Belgium
| | - Sébastien Massart
- Terra Research Center, Integrated and Urban Plant Pathology Laboratory, Liege University, Gembloux Agro-Bio-Tech, B-5030 Gembloux, Belgium
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33
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Morales-Manzo II, Ribes-Moya AM, Pallotti C, Jimenez-Belenguer A, Moro CP, Raigón MD, Rodríguez-Burruezo A, Fita A. Root-Soil Interactions for Pepper Accessions Grown under Organic and Conventional Farming. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12091873. [PMID: 37176931 PMCID: PMC10180822 DOI: 10.3390/plants12091873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/12/2023] [Accepted: 04/28/2023] [Indexed: 05/15/2023]
Abstract
Modern agriculture has boosted the production of food based on the use of pesticides and fertilizers and improved plant varieties. However, the impact of some such technologies is high and not sustainable in the long term. Although the importance of rhizospheres in final plant performance, nutrient cycling, and ecosystems is well recognized, there is still a lack of information on the interactions of their main players. In this paper, four accessions of pepper are studied at the rhizosphere and root level under two farming systems: organic and conventional. Variations in soil traits, such as induced respiration, enzymatic activities, microbial counts, and metabolism of nitrogen at the rhizosphere and bulk soil, as well as measures of root morphology and plant production, are presented. The results showed differences for the evaluated traits between organic and conventional management, both at the rhizosphere and bulk soil levels. Organic farming showed higher microbial counts, enzymatic activities, and nitrogen mobilization. Our results also showed how some genotypes, such as Serrano or Piquillo, modified the properties of the rhizospheres in a very genotype-dependent way. This specificity of the soil-plant interaction should be considered for future breeding programs for soil-tailored agriculture.
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Affiliation(s)
- Ivan I Morales-Manzo
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Edificio 8E Escalera J, CPI, Universitat Politècnica de València, 46022 Valencia, Spain
| | - Ana M Ribes-Moya
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Edificio 8E Escalera J, CPI, Universitat Politècnica de València, 46022 Valencia, Spain
| | - Claudia Pallotti
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Edificio 8E Escalera J, CPI, Universitat Politècnica de València, 46022 Valencia, Spain
| | - Ana Jimenez-Belenguer
- Centro Avanzado de Microbiología Aplicada, Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain
| | - Clara Pérez Moro
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Edificio 8E Escalera J, CPI, Universitat Politècnica de València, 46022 Valencia, Spain
| | - María Dolores Raigón
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Edificio 8E Escalera J, CPI, Universitat Politècnica de València, 46022 Valencia, Spain
| | - Adrián Rodríguez-Burruezo
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Edificio 8E Escalera J, CPI, Universitat Politècnica de València, 46022 Valencia, Spain
| | - Ana Fita
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Edificio 8E Escalera J, CPI, Universitat Politècnica de València, 46022 Valencia, Spain
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Wang P, Nie J, Yang L, Zhao J, Wang X, Zhang Y, Zang H, Yang Y, Zeng Z. Plant growth stages covered the legacy effect of rotation systems on microbial community structure and function in wheat rhizosphere. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:59632-59644. [PMID: 37012567 DOI: 10.1007/s11356-023-26703-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 03/24/2023] [Indexed: 05/10/2023]
Abstract
Legume-based crop rotation is conducive to improve soil multifunctionality, but how the legacy effect of previous legumes influenced the rhizosphere microbial community of the following crops along with growth stages remains unclear. Here, the wheat rhizosphere microbial community was assessed at the regreening and filling stages with four previous legumes (mungbean, adzuki bean, soybean, and peanut), as well as cereal maize as a control. The composition and structure of both bacterial and fungal communities varied dramatically between two growth stages. The differences in fungal community structure among rotation systems were observed at both the regreening and filling stages, while the difference in bacterial community structure among rotation systems was observed only at the filling stage. The complexity and centrality of the microbial network decreased along with crop growth stages. The species associations were strengthened in legume-based rotation systems than in cereal-based rotation system at the filling stage. The abundance of KEGG orthologs (KOs) associated with carbon, nitrogen, phosphorus, and sulfur metabolism of bacterial community decreased from the regreening stage to the filling stage. However, there was no difference in the abundance of KOs among rotation systems. Together, our results showed that plant growth stages had a stronger impact than the legacy effect of rotation systems in shaping the wheat rhizosphere microbial community, and the differences among rotation systems were more obvious at the late growth stage. Such compositional, structural, and functional changes may provide predictable consequences of crop growth and soil nutrient cycling.
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Affiliation(s)
- Peixin Wang
- College of Agronomy and Biotechnology/Key Laboratory of Farming System of Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, 100193, China
- Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Jiangwen Nie
- College of Agronomy and Biotechnology/Key Laboratory of Farming System of Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, 100193, China
| | - Lei Yang
- College of Agronomy and Biotechnology/Key Laboratory of Farming System of Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, 100193, China
| | - Jie Zhao
- College of Agronomy and Biotechnology/Key Laboratory of Farming System of Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, 100193, China
| | - Xiquan Wang
- College of Agronomy and Biotechnology/Key Laboratory of Farming System of Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, 100193, China
- Institute of Agricultural Sources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yudan Zhang
- College of Agronomy and Biotechnology/Key Laboratory of Farming System of Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, 100193, China
- Jining Academy of Agricultural Sciences, Jining, 272000, China
| | - Huadong Zang
- College of Agronomy and Biotechnology/Key Laboratory of Farming System of Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, 100193, China
| | - Yadong Yang
- College of Agronomy and Biotechnology/Key Laboratory of Farming System of Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, 100193, China.
| | - Zhaohai Zeng
- College of Agronomy and Biotechnology/Key Laboratory of Farming System of Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, 100193, China
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Ding W, Li J, Hu B, Chu G, Tao R. Response of abundance, diversity, and network of rhizosphere fungal community to monoculture of cut chrysanthemum. Appl Microbiol Biotechnol 2023; 107:3673-3685. [PMID: 37115253 DOI: 10.1007/s00253-023-12542-z] [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: 12/18/2022] [Revised: 03/31/2023] [Accepted: 04/10/2023] [Indexed: 04/29/2023]
Abstract
The effects of different monoculture years on rhizosphere fungal communities (abundance, diversity, structure, and cooccurrence network) of cut chrysanthemum were determined. Three different monoculture years were (i) planting for only 1 year (Y1), (ii) continuous monoculture for 6 years (Y6), and (iii) continuous monoculture for 12 years (Y12). Compared to the Y1 treatment, the Y12 treatment significantly decreased the rhizosphere fungal gene copy numbers but increased the potential pathogen Fusarium oxysporum (P < 0.05). Both the Y6 and Y12 treatments significantly increased fungal diversity (Shannon and Simpson indices), but Y6 had great potential to enhance fungal richness (Chao1 index) relative to the Y12 treatment. Monoculture treatments decreased the relative abundance of Ascomycota but increased that of Mortierellomycota. Four ecological clusters (Modules 0, 3, 4, and 9) were observed in the fungal cooccurrence network across the Y1, Y6, and Y12 treatments, and only Module 0 was significantly enriched in the Y12 treatment and associated with soil properties (P < 0.05). RDA (redundancy analysis) and Mantel analysis showed that soil pH and soil nutrients (organic carbon, total nitrogen, and available phosphorus) were the key factors affecting fungal communities during monoculture of cut chrysanthemum. Overall, the changes in soil properties were responsible for shaping rhizospheric soil fungal communities in long-term rather than short-term monoculture systems. KEY POINTS: • Both short- and long-term monocultures reshaped the soil fungal community structure. • Long-term monoculture enhanced the network complexity of the fungal community. • Soil pH, C and N levels mainly drove modularization in the fungal community network.
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Affiliation(s)
- Wangying Ding
- Department of Environmental Science and Engineering, School of Life Science, Shaoxing University, Huancheng West Road 508, Shaoxing, 312000, People's Republic of China
| | - Jun Li
- Department of Environmental Science and Engineering, School of Life Science, Shaoxing University, Huancheng West Road 508, Shaoxing, 312000, People's Republic of China
| | - Baowei Hu
- Department of Environmental Science and Engineering, School of Life Science, Shaoxing University, Huancheng West Road 508, Shaoxing, 312000, People's Republic of China
| | - Guixin Chu
- Department of Environmental Science and Engineering, School of Life Science, Shaoxing University, Huancheng West Road 508, Shaoxing, 312000, People's Republic of China
| | - Rui Tao
- Department of Environmental Science and Engineering, School of Life Science, Shaoxing University, Huancheng West Road 508, Shaoxing, 312000, People's Republic of China.
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Gong X, Feng Y, Dang K, Jiang Y, Qi H, Feng B. Linkages of microbial community structure and root exudates: Evidence from microbial nitrogen limitation in soils of crop families. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 881:163536. [PMID: 37075993 DOI: 10.1016/j.scitotenv.2023.163536] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 04/12/2023] [Accepted: 04/12/2023] [Indexed: 05/03/2023]
Abstract
Rhizosphere microorganisms are critical for crop nutrient cycling and soil ecological functions in agroecosystem soils; however, there is limited information regarding the role of root exudates in determining soil microbial communities and functions in plant-soil systems, especially for microbial nutrient limitations. In the present study, rhizosphere soil samples were collected from the main food crop families, including maize, soybean, potato, and buckwheat, representing the cereals, Leguminosae, Solanaceae, and Polygonaceae families, in the northern Loess Plateau, China, to investigate soil microbial co-occurrences and assembly processes and the relationship between soil microbes and root exudates. The results showed that the crop families greatly regulated the soil microbial community composition and assembly, and all microorganisms of the four species were subjected to N limitation via the vector analysis. The topological properties of the soil microbial networks varied with the crop family, demonstrating that the ecological relationships of bacterial taxa are more complex than those of fungi. Stochastic processes were more important in stimulating assembly across the four crop families; the non-dominated process governed >60 % of the critical ecological turnover in community assembly, whereas dispersal limitation was the key factor influencing fungal community assembly. Furthermore, the metabolic profiles of root exudates in response to microbial N limitation varied by family. Microbial function and metabolic limitations were strongly associated with variations in root exudates, especially amino acids and organic acids, which were directly facilitated by crop families. Our results highlight the key roles of root exudates in stimulating microbial community structure and ecological functions from the perspective of microbial nutrient limitation and improve our understanding of plant-microbe interactions in agricultural ecosystems.
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Affiliation(s)
- Xiangwei Gong
- College of Agronomy, Shenyang Agricultural University, Shenyang, Liaoning 110866, PR China.
| | - Yu Feng
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A & F University, Yangling, Shaanxi 712100, PR China
| | - Ke Dang
- Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry of Water Resources, Yangling, Shaanxi 712100, PR China
| | - Ying Jiang
- College of Agronomy, Shenyang Agricultural University, Shenyang, Liaoning 110866, PR China
| | - Hua Qi
- College of Agronomy, Shenyang Agricultural University, Shenyang, Liaoning 110866, PR China
| | - Baili Feng
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A & F University, Yangling, Shaanxi 712100, PR China.
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Michl K, Berg G, Cernava T. The microbiome of cereal plants: The current state of knowledge and the potential for future applications. ENVIRONMENTAL MICROBIOME 2023; 18:28. [PMID: 37004087 PMCID: PMC10064690 DOI: 10.1186/s40793-023-00484-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 03/16/2023] [Indexed: 06/19/2023]
Abstract
The plant microbiota fulfils various crucial functions related to host health, fitness, and productivity. Over the past years, the number of plant microbiome studies continued to steadily increase. Technological advancements not only allow us to produce constantly increasing datasets, but also to extract more information from them in order to advance our understanding of plant-microbe interactions. The growing knowledge base has an enormous potential to improve microbiome-based, sustainable agricultural practices, which are currently poorly understood and have yet to be further developed. Cereal plants are staple foods for a large proportion of the world's population and are therefore often implemented in microbiome studies. In the present review, we conducted extensive literature research to reflect the current state of knowledge in terms of the microbiome of the four most commonly cultivated cereal plants. We found that currently the majority of available studies are targeting the wheat microbiome, which is closely followed by studies on maize and rice. There is a substantial gap, in terms of published studies, addressing the barley microbiome. Overall, the focus of most microbiome studies on cereal plants is on the below-ground microbial communities, and there is more research on bacteria than on fungi and archaea. A meta-analysis conducted in the frame of this review highlights microbiome similarities across different cereal plants. Our review also provides an outlook on how the plant microbiota could be harnessed to improve sustainability of cereal crop production.
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Affiliation(s)
- Kristina Michl
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, Graz, 8010 Austria
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, Graz, 8010 Austria
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Max-Eyth Allee 100, 14469 Potsdam, Germany
- Institute for Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Golm, OT Germany
| | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, Graz, 8010 Austria
- School of Biological Sciences, Faculty of Environmental and Life Sciences, Southampton, SO17 1BJ UK
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Differences in Soil Microbial Communities between Healthy and Diseased Lycium barbarum cv. Ningqi-5 Plants with Root Rot. Microorganisms 2023; 11:microorganisms11030694. [PMID: 36985267 PMCID: PMC10054753 DOI: 10.3390/microorganisms11030694] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/15/2023] [Accepted: 03/06/2023] [Indexed: 03/11/2023] Open
Abstract
For a long time, the development of the Lycium barbarum industry has been seriously restricted by root rot disease. In general, the occurrence of plant root rot is considered to be closely related to the composition and diversity of the soil microbial community. It is critical to understand the relationship between the occurrence of root rot in L. barbarum and the soil microbial composition. In this study, samples of the rhizosphere, rhizoplane, and root zone were collected from diseased and healthy plants. The V3–V4 region of bacterial 16S rDNA and the fungal ITS1 fragment of the collected samples were sequenced using Illumina MiSeq high-throughput sequencing technology. The sequencing results were first quality controlled and then aligned with the relevant databases for annotation and analysis. The richness of fungal communities in the rhizoplane and root zone of the healthy plants was significantly higher than that of the diseased plants (p < 0.05), and the community evenness and diversity of all the rhizoplane samples were significantly different from those of the rhizosphere and root zone. The richness of the bacterial communities in the rhizosphere and root zone of healthy plants was significantly greater than those of diseased plants (p < 0.05). The community composition of the rhizoplane was quite different from the other parts. The abundance of Fusarium in the rhizoplane and rhizosphere soil of diseased plants was higher than that in the corresponding parts of healthy plants. The abundances of Mortierella and Ilyonectria in the three parts of the healthy plants were correspondingly higher than those in the three parts of the diseased plants, and Plectosphaerella was the most abundant in the rhizoplane of diseased plants. There was little difference in the composition of the dominant bacteria at the phylum and genus levels between healthy plants and diseased plants, but the abundances of these dominant bacteria were different between healthy and diseased plants. Functional prediction showed that the bacterial community had the largest proportion of functional abundance belonging to metabolism. The functional abundances of the diseased plants, such as metabolism and genetic information processing, were lower than those of the healthy plants. The fungal community function prediction showed that the Animal Pathogen-Endophyte-Lichen Parasite-Plant Pathogen-Soil Saprotroph-Wood Saprotroph group had the largest functional abundance, and the corresponding fungi were Fusarium. In this study, we mainly discussed the differences in the soil microbial communities and their functions between the healthy and diseased L. barbarum cv. Ningqi-5, and predicted the functional composition of the microbial community, which is of great significance to understanding the root rot of L. barbarum.
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Zhang Y, Cheng Z, Li Q, Dai Q, Hu J. Responses of rhizosphere bacterial communities in newly reclaimed mudflat paddies to rice genotype and nitrogen fertilizer rate. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:38761-38774. [PMID: 36586025 DOI: 10.1007/s11356-022-25020-2] [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: 07/25/2022] [Accepted: 12/23/2022] [Indexed: 06/17/2023]
Abstract
The rhizosphere microbiome plays a vital role in crop growth and adaptation. However, the effects of rice genotype, nitrogen (N) fertilization, and their interactions on the rhizosphere bacterial communities in low fertility soil remain poorly understood. In this study, a two-factor field experiment was performed in newly reclaimed mudflat paddies characterized by poor fertility to analyze bacterial communities in the rhizosphere of Yongyou 2640 (japonica/indica hybrid rice, JIH) and Huaidao No.5 (japonica conventional rice, JC) under different N fertilizer rates. Results showed that genotype, followed by N fertilizer rate, was the primary factor affecting rhizobacteria diversity. Rhizobacteria diversity was higher in JIH than in JC and that of JIH and JC did not significantly change overall as N fertilizer rates but increased and decreased at N fertilizer rates of over 300 kg N ha-1, respectively. The inconsistent response was probably attributed to the difference in the increase of ammonium and/or nitrate in the rhizosphere of JIH and JC. Genotype explained approximately 26% of the variation in rhizosphere bacterial communities. Rhizosphere bacterial communities with N fertilizer rates of over 300 kg N ha-1 were more dissimilar to those without N fertilization relative to those with N fertilizer rates of below 300 kg N ha-1, which was mainly attributed to changes in the concentration of ammonium and/or nitrate. The relative abundances of some potential beneficial genera such as Salinimicrobium, Salegentibacter, Gillisia, and Anaerolinea in the rhizosphere of JC and Salegentibacter, Lysobacter, Nocardioides, and Pontibacter in the rhizosphere of JIH were increased under N fertilizer rates of less than 300 kg N ha-1 and positively correlated with rice yields, which indicate that changes in bacterial communities caused by N fertilization might be strongly associated with the improvement of rice yield. Overall, rhizosphere bacterial communities were more sensitive to genotype in newly reclaimed mudflat paddies and showed a consistent response to N fertilizer rates.
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Affiliation(s)
- Yang Zhang
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou, 225127, China
- Key Laboratory of Arable Land Quality Monitoring and Evaluation, Ministry of Agriculture and Rural Affairs, Yangzhou University, Yangzhou, 225127, China
| | - Zhandou Cheng
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou, 225127, China
| | - Qing Li
- Jiangsu Key Laboratory of Crop Genetic and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Research Institute of Rice Industrial Engineering Technology, Yangzhou University, Yangzhou, 225009, China
| | - Qigen Dai
- Jiangsu Key Laboratory of Crop Genetic and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Research Institute of Rice Industrial Engineering Technology, Yangzhou University, Yangzhou, 225009, China.
| | - Jian Hu
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou, 225127, China
- Key Laboratory of Arable Land Quality Monitoring and Evaluation, Ministry of Agriculture and Rural Affairs, Yangzhou University, Yangzhou, 225127, China
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Miao Y, Zhang X, Zhang G, Feng Z, Pei J, Liu C, Huang L. From guest to host: parasite Cistanche deserticola shapes and dominates bacterial and fungal community structure and network complexity. ENVIRONMENTAL MICROBIOME 2023; 18:11. [PMID: 36814319 PMCID: PMC9945605 DOI: 10.1186/s40793-023-00471-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 02/10/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Rhizosphere and plant microbiota are assumed to play an essential role in deciding the well-being of hosts, but effects of parasites on their host microbiota have been rarely studied. Also, the characteristics of the rhizosphere and root microbiota of parasites and hosts under parasitism is relatively unknown. In this study, we used Cistanche deserticola and Haloxylon ammodendron from cultivated populations as our model parasites and host plants, respectively. We collected samples from BULK soil (BULK), rhizosphere soil of H. ammodendron not parasitized (NCD) and parasitized (RHA) to study how the parasite influenced the rhizosphere microbiota of the host. We also collected samples from the rhizosphere soil and roots of C. deserticola (RCD and ECD) and Haloxylon ammodendron (RHA and EHA) to explore the difference between the microbiota of the parasite and its host under parasitism. RESULTS The parasite reduced the compositional and co-occurrence network complexities of bacterial and fungal microbiota of RHA. Additionally, the parasite increased the proportion of stochastic processes mainly belonging to dispersal limitation in the bacterial microbiota of RHA. Based on the PCoA ordinations and permutational multivariate analysis of variance, the dissimilarity between microbiota of C. deserticola and H. ammodendron were rarely evident (bacteria, R2 = 0.29971; fungi, R2 = 0.15631). Interestingly, four hub nodes of H. ammodendron in endosphere fungal microbiota were identified, while one hub node of C. deserticola in endosphere fungal microbiota was identified. It indicated that H. ammodendron played a predominant role in the co-occurrence network of endosphere fungal microbiota. Source model of plant microbiome suggested the potential source percentage from the parasite to the host (bacteria: 52.1%; fungi: 16.7%) was lower than host-to-parasite (bacteria: 76.5%; fungi: 34.3%), illustrating that microbial communication was bidirectional, mainly from the host to the parasite. CONCLUSIONS Collectively, our results suggested that the parasite C. deserticola shaped the diversity, composition, co-occurrence network, and community assembly mechanisms of the rhizosphere microbiota of H. ammodendron. Additionally, the microbiota of C. deserticola and H. ammodendron were highly similar and shared. Our findings on parasite and host microbiota provided a novel line of evidence supporting the influence of parasites on the microbiota of their hosts.
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Affiliation(s)
- Yujing Miao
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
| | - Xinke Zhang
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
| | - Guoshuai Zhang
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
| | - Zhan Feng
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
- Jiangxi University of Traditional Chinese Medicine, Nanchang, 330000, Jiangxi, China
| | - Jin Pei
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, Sichuan, China
| | - Chang Liu
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
| | - Linfang Huang
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China.
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Pan Y, She D, Shi Z, Cao T, Xia Y, Shan J. Salinity and high pH reduce denitrification rates by inhibiting denitrifying gene abundance in a saline-alkali soil. Sci Rep 2023; 13:2155. [PMID: 36750752 PMCID: PMC9905596 DOI: 10.1038/s41598-023-29311-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 02/02/2023] [Indexed: 02/09/2023] Open
Abstract
Denitrification, as the main nitrogen (N) removal process in farmland drainage ditches in coastal areas, is significantly affected by saline-alkali conditions. To elucidate the effects of saline-alkali conditions on denitrification, incubation experiments with five salt and salt-alkali gradients and three nitrogen addition levels were conducted in a saline-alkali soil followed by determination of denitrification rates and the associated functional genes (i.e., nirK/nirS and nosZ Clade I) via N2/Ar technique in combination with qPCR. The results showed that denitrification rates were significantly decreased by 23.83-50.08%, 20.64-57.31% and 6.12-54.61% with salt gradient increasing from 1 to 3‰, 8‰, and 15‰ under 0.05‰, 0.10‰ and 0.15‰ urea addition conditions, respectively. Similarly, denitrification rates were significantly decreased by 44.57-63.24% with an increase of the salt-alkali gradient from 0.5 to 8‰. The abundance of nosZ decreased sharply in the saline condition, while a high salt level significantly decreased the abundance of nirK and nirS. In addition, the increase of nitrogen concentration attenuated the reduction of nirK, nirS and nosZ gene abundance. Partial least squares regression (PLSR) models demonstrated that salinity, dissolved oxygen (DO) in the overlying water, N concentration, and denitrifying gene abundance were key determinants of the denitrification rate in the saline environment, while pH was an additional determinant in the saline-alkali environment. Taken together, our results suggest that salinity and high pH levels decreased the denitrification rates by significantly inhibiting the abundance of the denitrifying genes nirK, nirS, and nosZ, whereas increasing nitrogen concentration could alleviate this effect. Our study provides helpful information on better understanding of reactive N removal and fertilizer application in the coastal areas.
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Affiliation(s)
- Yongchun Pan
- College of Agricultural Science and Engineering, Hohai University, Nanjing, 210098, China.,Jiangsu Province Engineering Research Center for Agricultural Soil-Water Efficient Utilization, Carbon Sequestration and Emission Reduction, Nanjing, 210098, China
| | - Dongli She
- College of Agricultural Science and Engineering, Hohai University, Nanjing, 210098, China. .,Jiangsu Province Engineering Research Center for Agricultural Soil-Water Efficient Utilization, Carbon Sequestration and Emission Reduction, Nanjing, 210098, China.
| | - Zhenqi Shi
- College of Agricultural Science and Engineering, Hohai University, Nanjing, 210098, China.,Jiangsu Province Engineering Research Center for Agricultural Soil-Water Efficient Utilization, Carbon Sequestration and Emission Reduction, Nanjing, 210098, China
| | - Taohong Cao
- College of Agricultural Science and Engineering, Hohai University, Nanjing, 210098, China.,Jiangsu Province Engineering Research Center for Agricultural Soil-Water Efficient Utilization, Carbon Sequestration and Emission Reduction, Nanjing, 210098, China
| | - Yongqiu Xia
- Key Laboratory of Soil and Sustainable Agriculture, Changshu National Agro-Ecosystem Observation and Research Station, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Jun Shan
- Key Laboratory of Soil and Sustainable Agriculture, Changshu National Agro-Ecosystem Observation and Research Station, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China.
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Guo W, Zhang J, Li MH, Qi L. Soil fungal community characteristics vary with bamboo varieties and soil compartments. Front Microbiol 2023; 14:1120679. [PMID: 36814565 PMCID: PMC9939831 DOI: 10.3389/fmicb.2023.1120679] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 01/16/2023] [Indexed: 02/09/2023] Open
Abstract
Soil fungi play an important role in nutrient cycling, mycorrhizal symbiosis, antagonism against pathogens, and organic matter decomposition. However, our knowledge about the community characteristics of soil fungi in relation to bamboo varieties is still limited. Here, we compared the fungal communities in different soil compartments (rhizosphere vs. bulk soil) of moso bamboo (Phyllostachys edulis) and its four varieties using ITS high-throughput sequencing technology. The fungal α diversity (Shannon index) in bulk soil was significantly higher than that in rhizosphere soil, but it was not affected by bamboo variety or interactions between the soil compartment and bamboo variety. Soil compartment and bamboo variety together explained 31.74% of the variation in fungal community diversity. Soil compartment and bamboo variety were the key factors affecting the relative abundance of the major fungal taxa at the phylum and genus levels. Soil compartment mainly affected the relative abundance of the dominant fungal phylum, while bamboo variety primarily influenced the dominant fungal genus. Network analysis showed that the fungal network in rhizosphere soil was more complex, stable, and connected than that in bulk soil. A FUNGuild database analysis indicated that both soil compartment and bamboo variety affect fungal functions. Our findings provide new insights into the roles of both soil compartments and plant species (including variety) in shaping soil fungal communities.
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Affiliation(s)
- Wen Guo
- Key Laboratory of National Forestry and Grassland Administration/Beijing Bamboo and Rattan Science and Technology, International Centre for Bamboo and Rattan, Beijing, China,Forest Dynamics, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Jian Zhang
- Key Laboratory of National Forestry and Grassland Administration/Beijing Bamboo and Rattan Science and Technology, International Centre for Bamboo and Rattan, Beijing, China
| | - Mai-He Li
- Forest Dynamics, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland,Key Laboratory of Geographical Processes and Ecological Security in Changbai Mountains, Ministry of Education, School of Geographical Sciences, Northeast Normal University, Changchun, China,School of Life Science, Hebei University, Baoding, China,*Correspondence: Mai-He Li,
| | - Lianghua Qi
- Key Laboratory of National Forestry and Grassland Administration/Beijing Bamboo and Rattan Science and Technology, International Centre for Bamboo and Rattan, Beijing, China,Sanya Research Base, International Centre for Bamboo and Rattan, Sanya, China,Lianghua Qi,
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Chen W, Wu Z, Liu C, Zhang Z, Liu X. Biochar combined with Bacillus subtilis SL-44 as an eco-friendly strategy to improve soil fertility, reduce Fusarium wilt, and promote radish growth. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 251:114509. [PMID: 36621032 DOI: 10.1016/j.ecoenv.2023.114509] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 12/29/2022] [Accepted: 01/02/2023] [Indexed: 06/17/2023]
Abstract
Bacillus subtilis as microbial fertilizers contribute to avoiding the harmful effects of traditional agricultural fertilizers and pesticides. However, there are many restrictions on the practical application of fertilizers. In this study, microbial biochar formulations (BCMs) were prepared by loading biochar with B. subtilis SL-44. Pot experiments were conducted to evaluate the effects of the BCMs on soil fertility, Fusarium wilt control, and radish plant growth. The application of BCMs dramatically improved soil properties and favored plant growth. Compared with SL-44 and biochar treatments, the BCMs treatments increased radish plant physical-chemical properties and activities of several enzymes in the soil. What's more, Fusarium wilt incidence had decreased by 59.88%. In addition, the BCMs treatments exhibited a significant increase in the abundance of bacterial genera in the rhizosphere soil of radish. Therefore, this study demonstrated that BCMs may be an eco-friendly strategy for improving soil fertility, reducing Fusarium wilt, and promoting radish plant growth.
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Affiliation(s)
- Wumei Chen
- School of Environmental and Chemical Engineering, Xi'an Key Laboratory of Textile Chemical Engineering Auxiliaries, Xi'an Polytechnic University, Xi'an 710048, PR China
| | - Zhansheng Wu
- School of Environmental and Chemical Engineering, Xi'an Key Laboratory of Textile Chemical Engineering Auxiliaries, Xi'an Polytechnic University, Xi'an 710048, PR China.
| | - Changhao Liu
- School of Environmental and Chemical Engineering, Xi'an Key Laboratory of Textile Chemical Engineering Auxiliaries, Xi'an Polytechnic University, Xi'an 710048, PR China
| | - Ziyan Zhang
- School of Environmental and Chemical Engineering, Xi'an Key Laboratory of Textile Chemical Engineering Auxiliaries, Xi'an Polytechnic University, Xi'an 710048, PR China
| | - Xiaochen Liu
- School of Environmental and Chemical Engineering, Xi'an Key Laboratory of Textile Chemical Engineering Auxiliaries, Xi'an Polytechnic University, Xi'an 710048, PR China.
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Mang M, Maywald NJ, Li X, Ludewig U, Francioli D. Nitrogen Fertilizer Type and Genotype as Drivers of P Acquisition and Rhizosphere Microbiota Assembly in Juvenile Maize Plants. PLANTS (BASEL, SWITZERLAND) 2023; 12:544. [PMID: 36771628 PMCID: PMC9919524 DOI: 10.3390/plants12030544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/14/2023] [Accepted: 01/19/2023] [Indexed: 06/18/2023]
Abstract
Phosphorus (P) is an essential nutrient for plant growth and development, as well as an important factor limiting sustainable maize production. Targeted nitrogen (N) fertilization in the form of ammonium has been shown to positively affect Pi uptake under P-deficient conditions compared to nitrate. Nevertheless, its profound effects on root traits, P uptake, and soil microbial composition are still largely unknown. In this study, two maize genotypes F160 and F7 with different P sensitivity were used to investigate phosphorus-related root traits such as root hair length, root diameter, AMF association, and multiple P efficiencies under P limitation when fertilized either with ammonium or nitrate. Ammonium application improved phosphorous acquisition efficiency in the F7 genotype but not in F160, suggesting that the genotype plays an important role in how a particular N form affects P uptake in maize. Additionally, metabarcoding data showed that young maize roots were able to promote distinct microbial taxa, such as arbuscular mycorrhizal fungi, when fertilized with ammonium. Overall, the results suggest that the form of chemical nitrogen fertilizer can be instrumental in selecting beneficial microbial communities associated with phosphorus uptake and maize plant fitness.
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Alcalá-Herrera R, Moreno B, Aguirrebengoa M, Winter S, Robles-Cruz AB, Ramos-Font ME, Benítez E. Role of Agricultural Management in the Provision of Ecosystem Services in Warm Climate Vineyards: Functional Prediction of Genes Involved in Nutrient Cycling and Carbon Sequestration. PLANTS (BASEL, SWITZERLAND) 2023; 12:527. [PMID: 36771611 PMCID: PMC9919410 DOI: 10.3390/plants12030527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/19/2023] [Accepted: 01/20/2023] [Indexed: 06/18/2023]
Abstract
(1) Background: Maintaining soil fertility and crop productivity using natural microbial diversity could be a feasible approach for achieving sustainable development in agriculture. In this study, we compared soils from vineyards under organic and conventional management by predicting functional profiles through metagenomic analysis based on the 16S rRNA gene. (2) Methods: The structure, diversity and predictive functions of soil bacteria related to the biogeochemical cycle of the soil were analyzed, including oxidative and hydrolytic C-cycling enzymes, N-cycling enzymes and P-cycling enzymes. The inter-row spontaneous vegetation in the organic vineyards was also characterized. (3) Results: A clear effect of the farming system (organic vs. conventional) and cover management (herbicides plus tillage, mowing only and mowing plus tillage) on bacterial beta diversity and predicted functions was evidenced. While conventional viticulture increased the potential capacity of the soil to regulate the cycling of inorganic forms of N, organic viticulture in general enhanced those functions involving organic N, P and C substrates. Although the soil bacterial community responded differently to contrasting soil management strategies, nutrient cycling and carbon sequestration functions remained preserved, suggesting a high bacterial functional redundancy in the soil in any case. However, most of the predicted bacterial functions related to soil organic matter turnover were enhanced by organic management. (4) Conclusions: We posit the potential for organic viticulture to adequately address climate change adaptation in the context of sustainable agriculture.
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Affiliation(s)
- Rafael Alcalá-Herrera
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín, CSIC, c/Profesor Albareda 1, 18008 Granada, Spain
| | - Beatriz Moreno
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín, CSIC, c/Profesor Albareda 1, 18008 Granada, Spain
| | - Martin Aguirrebengoa
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín, CSIC, c/Profesor Albareda 1, 18008 Granada, Spain
| | - Silvia Winter
- Department of Crop Sciences, Institute of Plant Protection, University of Natural Resources and Life Sciences, Gregor-Mendel-Straße 33, 1180 Vienna, Austria
| | - Ana Belén Robles-Cruz
- Assessment, Restoration and Protection of Mediterranean Agrosystems Service (SERPAM), Estación Experimental del Zaidín, CSIC, c/Profesor Albareda, 1, 18008 Granada, Spain
| | - María Eugenia Ramos-Font
- Assessment, Restoration and Protection of Mediterranean Agrosystems Service (SERPAM), Estación Experimental del Zaidín, CSIC, c/Profesor Albareda, 1, 18008 Granada, Spain
| | - Emilio Benítez
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín, CSIC, c/Profesor Albareda 1, 18008 Granada, Spain
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Lian WH, Mohamad OAA, Dong L, Zhang LY, Wang D, Liu L, Han MX, Li S, Wang S, Antunes A, Fang BZ, Jiao JY, Li WJ. Culturomics- and metagenomics-based insights into the microbial community and function of rhizosphere soils in Sinai desert farming systems. ENVIRONMENTAL MICROBIOME 2023; 18:4. [PMID: 36639807 PMCID: PMC9840269 DOI: 10.1186/s40793-023-00463-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 01/08/2023] [Indexed: 06/12/2023]
Abstract
BACKGROUND The microbiome of the Sinai Desert farming system plays an important role in the adaptive strategy of growing crops in a harsh, poly-extreme, desert environment. However, the diversity and function of microbial communities under this unfavorable moisture and nutritional conditions have not yet been investigated. Based on culturomic and metagenomic methods, we analyzed the microbial diversity and function of a total of fourteen rhizosphere soil samples (collected from twelve plants in four farms of the Sinai desert), which may provide a valuable and meaningful guidance for the design of microbial inoculants. RESULTS The results revealed a wide range of microbial taxa, including a high proportion of novel undescribed lineages. The composition of the rhizosphere microbial communities differed according to the sampling sites, despite similarities or differences in floristics. Whereas, the functional features of rhizosphere microbiomes were significantly similar in different sampling sites, although the microbial communities and the plant hosts themselves were different. Importantly, microorganisms involved in ecosystem functions are different between the sampling sites, for example nitrogen fixation was prevalent in all sample sites while microorganisms responsible for this process were different. CONCLUSION Here, we provide the first characterization of microbial communities and functions of rhizosphere soil from the Sinai desert farming systems and highlight its unexpectedly high diversity. This study provides evidence that the key microorganisms involved in ecosystem functions are different between sampling sites with different environment conditions, emphasizing the importance of the functional microbiomes of rhizosphere microbial communities. Furthermore, we suggest that microbial inoculants to be used in future agricultural production should select microorganisms that can be involved in plant-microorganism interactions and are already adapted to a similar environmental setting.
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Affiliation(s)
- Wen-Hui Lian
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Osama Abdalla Abdelshafy Mohamad
- Department of Environmental Protection, Faculty of Environmental Agricultural Sciences, Arish University, Arish, 45511, Egypt
- State Key Laboratory of Lunar and Planetary Sciences, Macau University of Science and Technology (MUST), Macau, People's Republic of China
| | - Lei Dong
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Ling-Yu Zhang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Dong Wang
- College of Life Science and Technology, Honghe University, Mengzi, 661199, People's Republic of China
| | - Lan Liu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Ming-Xian Han
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Shuai Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Shuang Wang
- Heilongjiang Academy of Black Soil Conservation and Utilization, Harbin, 150086, People's Republic of China
| | - André Antunes
- State Key Laboratory of Lunar and Planetary Sciences, Macau University of Science and Technology (MUST), Macau, People's Republic of China
| | - Bao-Zhu Fang
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China
| | - Jian-Yu Jiao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China.
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Liu W, Wang N, Yao X, He D, Sun H, Ao X, Wang H, Zhang H, St. Martin S, Xie F, Wang J. Continuous-cropping-tolerant soybean cultivars alleviate continuous cropping obstacles by improving structure and function of rhizosphere microorganisms. Front Microbiol 2023; 13:1048747. [PMID: 36687563 PMCID: PMC9846356 DOI: 10.3389/fmicb.2022.1048747] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 12/07/2022] [Indexed: 01/05/2023] Open
Abstract
Introduction Soybean continuous cropping will change soil microorganisms and cause continuous cropping obstacles, resulting in a significant yield decline. Different soybean cultivars have different tolerances to continuous cropping, but the relationship between continuous cropping tolerance and soil microorganisms is not clear. Methods Two soybean cultivars with different tolerances to continuous cropping were used to study the effects of continuous cropping on soil physical and chemical properties, nitrogen and phosphorus cyclic enzyme activities, rhizosphere soil microbial community and function. Results The results showed that the yield reduction rate of a continuous-cropping-tolerant cultivar (L14) was lower than that of a continuous-cropping-sensitive cultivar (L10) under continuous cropping. At R1 and R6 growth stages, soil nutrient content (NH4 +-N, NO3 --N, AP, DOM, TK, and pH), nitrogen cycling enzyme (URE, NAG, LAP) activities, phosphorus cycling enzyme (ALP, NPA, ACP) activities, copy numbers of nitrogen functional genes (AOA, AOB, nirK, nirK) and phosphorus functional genes (phoA, phoB) in L14 were higher than those in L10. Soybean cultivar was an important factor affecting the structure and functional structure of bacterial community under continuous cropping. The relative abundances of Proteobacteria, Bacteroidota, Acidobacteriota and Verrucomicrobiota with L14 were significantly higher than those of L10. The complexity of the soil bacterial community co-occurrence network in L14 was higher than that in L10. Discussion The continuous-cropping-tolerant soybean cultivar recruited more beneficial bacteria, changed the structure and function of microbial community, improved soil nitrogen and phosphorus cycling, and reduced the impact of continuous cropping obstacles on grain yield.
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Affiliation(s)
- Wenbo Liu
- Soybean Research Institute, Shenyang Agricultural University, Shenyang, China
| | - Nan Wang
- Soybean Research Institute, Shenyang Agricultural University, Shenyang, China
| | - Xingdong Yao
- Soybean Research Institute, Shenyang Agricultural University, Shenyang, China,Postdoctoral Station of Agricultural Resources and Environment, Land and Environment College, Shenyang Agricultural University, Shenyang, China,Key Laboratory of Soybean Biology of Chinese Education Ministry, Soybean Research Institute, Northeast Agricultural University, Harbin, China,*Correspondence: Xingdong Yao, ✉
| | - Dexin He
- Soybean Research Institute, Shenyang Agricultural University, Shenyang, China
| | - Hexiang Sun
- Soybean Research Institute, Shenyang Agricultural University, Shenyang, China
| | - Xue Ao
- Soybean Research Institute, Shenyang Agricultural University, Shenyang, China
| | - Haiying Wang
- Soybean Research Institute, Shenyang Agricultural University, Shenyang, China
| | - Huijun Zhang
- Soybean Research Institute, Shenyang Agricultural University, Shenyang, China
| | - Steven St. Martin
- Department of Horticulture and Crop Science, The Ohio State University, Columbus, OH, United States
| | - Futi Xie
- Soybean Research Institute, Shenyang Agricultural University, Shenyang, China,Futi Xie, ✉
| | - Jingkuan Wang
- Postdoctoral Station of Agricultural Resources and Environment, Land and Environment College, Shenyang Agricultural University, Shenyang, China
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Bai S, Chen J, Guo M, Ren N, Zhao X. Vertical-scale spatial influence of radial oxygen loss on rhizosphere microbial community in constructed wetland. ENVIRONMENT INTERNATIONAL 2023; 171:107690. [PMID: 36516673 DOI: 10.1016/j.envint.2022.107690] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 12/04/2022] [Accepted: 12/08/2022] [Indexed: 06/17/2023]
Abstract
Complex interactions between plants and microorganisms form the basis of constructed wetlands (CWs) for pollutant removal. In the rhizosphere, radial oxygen loss (ROL) plays a key role in the activity and abundance of functional microorganisms. However, little has been done to explore how ROL would influence the niche differentiation of microbial communities at different vertical spatial scales. We demonstrate that ROL decreases with depth, promoting an oxidation-reduction rhizosphere microecosystem in CWs. The high level of ROL in the upper layer could support the oxygen supply for aerobic bacteria (Haliangium), facilitating the COD (60%) and NH4+-N (50%) removal, whereas the enrichment of denitrifiers (e.g., Hydrogenophaga and Ralstonia) and methanotrophs (Methanobaterium) in the lower layer could stimulate denitrification. The function prediction results further certified that the abundance of genes catalyzing nitrifying and denitrification processes were significantly enhanced in the upper and bottom layers, respectively, which was attributed to the oxygen concentration gradient in the rhizosphere. This study contributes to further unraveling the rhizosphere effect and enables an improved understanding of the decontamination mechanisms of CWs.
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Affiliation(s)
- Shunwen Bai
- School of Environment, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Juntong Chen
- College of Resource and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Mengran Guo
- College of Resource and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Nanqi Ren
- School of Environment, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Xinyue Zhao
- College of Resource and Environment, Northeast Agricultural University, Harbin 150030, China.
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Li X, Liu Y, Wang Z, Yang C, Zhang R, Luo Y, Ma Y, Deng Y. Microbiome analysis and biocontrol bacteria isolation from rhizosphere soils associated with different sugarcane root rot severity. Front Bioeng Biotechnol 2022; 10:1062351. [PMID: 36588942 PMCID: PMC9802638 DOI: 10.3389/fbioe.2022.1062351] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 12/07/2022] [Indexed: 12/23/2022] Open
Abstract
To explore the causal pathogen and the correlated rhizosphere soil microecology of sugarcane root rot, we sampled the sugarcane root materials displaying different disease severity, and the corresponding rhizosphere soil, for systematic root phenotype and microbial population analyses. We found that with increased level of disease severity reflected by above-ground parts of sugarcane, the total root length, total root surface area and total volume were significantly reduced, accompanied with changes in the microbial population diversity and structure in rhizosphere soil. Fungal community richness was significantly lower in the rhizosphere soil samples from mildly diseased plant than that from either healthy plant, or severely diseased plant. Particularly, we noticed that a peculiar decrease of potential pathogenic fungi in rhizosphere soil, including genera Fusarium, Talaromyces and Neocosmospora, with increased level of disease severity. As for bacterial community, Firmicutes was found to be of the highest level, while Acidobacteria and Chloroflexi of the lowest level, in rhizosphere soil from healthy plant compared to that from diseased plant of different severity. FUNGuild prediction showed that the proportion of saprophytic fungi was higher in the rhizosphere soil of healthy plants, while the proportion of pathogenic fungi was higher in the rhizosphere soil of diseased plants. By co-occurrence network analysis we demonstrated the Bacillus and Burkholderia were in a strong interaction with Fusarium pathogen(s). Consistently, the biocontrol and/or growth-promoting bacteria isolated from the rhizosphere soil were mostly (6 out of 7) belonging to Bacillus and Burkholderia species. By confrontation culture and pot experiments, we verified the biocontrol and/or growth-promoting property of the isolated bacterial strains. Overall, we demonstrated a clear correlation between sugarcane root rot severity and rhizosphere soil microbiome composition and function, and identified several promising biocontrol bacteria strains with strong disease suppression effect and growth-promoting properties.
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Affiliation(s)
- Xinyang Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresource, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, China
| | - Yue Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresource, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, China
- Laboratory of Crop Physiology and Field Ecology, Northwest A&F University, Yangling, China
| | - Ziting Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresource, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, China
| | - Chenglong Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresource, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, China
| | - Runzhi Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresource, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, China
| | - Yibao Luo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresource, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, China
| | - Yuming Ma
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Yizhen Deng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
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Characteristics of rhizosphere and endogenous bacterial community of Ulleung-sanmaneul, an endemic plant in Korea: application for alleviating salt stress. Sci Rep 2022; 12:21124. [PMID: 36476722 PMCID: PMC9729608 DOI: 10.1038/s41598-022-25731-z] [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: 04/27/2022] [Accepted: 12/05/2022] [Indexed: 12/12/2022] Open
Abstract
Microbes influence plant growth and fitness. However, the structure and function of microbiomes associated with rare and endemic plants remain underexplored. To investigate the bacterial community structure of Ulleung-sanmaneul (U-SMN), an endemic plant in Korea, samples were collected from natural and cultivated habitats, and their 16S rDNA was sequenced. The root bacterial community structure differed from those of bulk soil and rhizosphere in both habitats. Endogenous bacteria in cultivated plants were less diverse than wild plants, but Luteibacter rhizovicinus, Pseudomonas fulva, and Sphingomonas pruni were shared. Co-inoculation of Pseudoxanthomonas sp. JBCE485 and Variovorax paradoxus JBCE486 promoted growth and induced salt stress resistance in Arabidopsis and chive. Changes in growth promotion and phenotypes of plants by co-inoculation were mediated by increased auxin production. Each strain colonized the roots without niche competition. The results indicated that host selectivity was influential than environmental factors in formulating endophytic bacterial composition, and domestication simplified the bacterial community diversity. Our results will contribute to the growth and maintenance of endemic U-SMN plants.
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