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Kawa D, Thiombiano B, Shimels MZ, Taylor T, Walmsley A, Vahldick HE, Rybka D, Leite MFA, Musa Z, Bucksch A, Dini-Andreote F, Schilder M, Chen AJ, Daksa J, Etalo DW, Tessema T, Kuramae EE, Raaijmakers JM, Bouwmeester H, Brady SM. The soil microbiome modulates the sorghum root metabolome and cellular traits with a concomitant reduction of Striga infection. Cell Rep 2024; 43:113971. [PMID: 38537644 PMCID: PMC11063626 DOI: 10.1016/j.celrep.2024.113971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 01/17/2024] [Accepted: 02/29/2024] [Indexed: 04/10/2024] Open
Abstract
Sorghum bicolor is among the most important cereals globally and a staple crop for smallholder farmers in sub-Saharan Africa. Approximately 20% of sorghum yield is lost annually in Africa due to infestation with the root parasitic weed Striga hermonthica. Existing Striga management strategies are not singularly effective and integrated approaches are needed. Here, we demonstrate the functional potential of the soil microbiome to suppress Striga infection in sorghum. We associate this suppression with microbiome-mediated induction of root endodermal suberization and aerenchyma formation and with depletion of haustorium-inducing factors, compounds required for the initial stages of Striga infection. We further identify specific bacterial taxa that trigger the observed Striga-suppressive traits. Collectively, our study describes the importance of the soil microbiome in the early stages of root infection by Striga and pinpoints mechanisms of Striga suppression. These findings open avenues to broaden the effectiveness of integrated Striga management practices.
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Affiliation(s)
- Dorota Kawa
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA 95616, USA; Plant Stress Resilience, Department of Biology, Utrecht University, 3508 TC Utrecht, the Netherlands; Environmental and Computational Plant Development, Department of Biology, Utrecht University, 3508 TC Utrecht, the Netherlands.
| | - Benjamin Thiombiano
- Plant Hormone Biology Group, Green Life Sciences Cluster, Swammerdam Institute for Life Science, University of Amsterdam, 1098 XH Amsterdam, the Netherlands
| | - Mahdere Z Shimels
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Microbial Ecology, 6708 PB Wageningen, the Netherlands
| | - Tamera Taylor
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA 95616, USA; Plant Biology Graduate Group, University of California, Davis, Davis, CA 95616, USA
| | - Aimee Walmsley
- Plant Hormone Biology Group, Green Life Sciences Cluster, Swammerdam Institute for Life Science, University of Amsterdam, 1098 XH Amsterdam, the Netherlands
| | - Hannah E Vahldick
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA 95616, USA
| | - Dominika Rybka
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Microbial Ecology, 6708 PB Wageningen, the Netherlands
| | - Marcio F A Leite
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Microbial Ecology, 6708 PB Wageningen, the Netherlands
| | - Zayan Musa
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA 95616, USA
| | - Alexander Bucksch
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA; Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA; Warnell School of Forestry and Natural Resources, University of Georgia, Athens, GA 30602, USA
| | - Francisco Dini-Andreote
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Microbial Ecology, 6708 PB Wageningen, the Netherlands; Department of Plant Science, The Pennsylvania State University, University Park, PA 16802, USA; Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Mario Schilder
- Plant Hormone Biology Group, Green Life Sciences Cluster, Swammerdam Institute for Life Science, University of Amsterdam, 1098 XH Amsterdam, the Netherlands
| | - Alexander J Chen
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA 95616, USA
| | - Jiregna Daksa
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA 95616, USA
| | - Desalegn W Etalo
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Microbial Ecology, 6708 PB Wageningen, the Netherlands; Wageningen University and Research, Laboratory of Phytopathology, Wageningen, the Netherlands
| | - Taye Tessema
- Ethiopian Institute of Agricultural Research, 3G53+6XC Holeta, Ethiopia
| | - Eiko E Kuramae
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Microbial Ecology, 6708 PB Wageningen, the Netherlands; Ecology and Biodiversity, Department of Biology, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Jos M Raaijmakers
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Microbial Ecology, 6708 PB Wageningen, the Netherlands
| | - Harro Bouwmeester
- Plant Hormone Biology Group, Green Life Sciences Cluster, Swammerdam Institute for Life Science, University of Amsterdam, 1098 XH Amsterdam, the Netherlands
| | - Siobhan M Brady
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA 95616, USA.
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Wang H, Pijl A, Liu B, Wamelink W, Korthals GW, Costa OYA, Kuramae EE. A Comparison of Different Protocols for the Extraction of Microbial DNA Inhabiting Synthetic Mars Simulant Soil. Microorganisms 2024; 12:760. [PMID: 38674704 PMCID: PMC11051824 DOI: 10.3390/microorganisms12040760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 04/02/2024] [Accepted: 04/04/2024] [Indexed: 04/28/2024] Open
Abstract
Compared with typical Earth soil, Martian soil and Mars simulant soils have distinct properties, including pH > 8.0 and high contents of silicates, iron-rich minerals, sulfates, and metal oxides. This unique soil matrix poses a major challenge for extracting microbial DNA. In particular, mineral adsorption and the generation of destructive hydroxyl radicals through cationic redox cycling may interfere with DNA extraction. This study evaluated different protocols for extracting microbial DNA from Mars Global Simulant (MGS-1), a Mars simulant soil. Two commercial kits were tested: the FastDNA SPIN Kit for soil ("MP kit") and the DNeasy PowerSoil Pro Kit ("PowerSoil kit"). MGS-1 was incubated with living soil for five weeks, and DNA was extracted from aliquots using the kits. After extraction, the DNA was quantified with a NanoDrop spectrophotometer and used as the template for 16S rRNA gene amplicon sequencing and qPCR. The MP kit was the most efficient, yielding approximately four times more DNA than the PowerSoil kit. DNA extracted using the MP kit with 0.5 g soil resulted in 28,642-37,805 16S rRNA gene sequence reads and 30,380-42,070 16S rRNA gene copies, whereas the 16S rRNA gene could not be amplified from DNA extracted using the PowerSoil kit. We suggest that the FastDNA SPIN Kit is the best option for studying microbial communities in Mars simulant soils.
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Affiliation(s)
- Han Wang
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, The Netherlands; (H.W.); (A.P.); (O.Y.A.C.)
- Ecology and Biodiversity, Institute of Environmental Biology, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Agata Pijl
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, The Netherlands; (H.W.); (A.P.); (O.Y.A.C.)
| | - Binbin Liu
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 286 Huaizhong Road, Shijiazhuang 050021, China;
| | - Wieger Wamelink
- Biodiversity and Policy, Wageningen University and Research, Droevendaalsesteeg 4, 6708 PB Wageningen, The Netherlands;
| | - Gerard W. Korthals
- Bioindications and Plant Health, Wageningen University and Research, Droevendaalsesteeg 4, 6708 PB Wageningen, The Netherlands;
| | - Ohana Y. A. Costa
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, The Netherlands; (H.W.); (A.P.); (O.Y.A.C.)
| | - Eiko E. Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, The Netherlands; (H.W.); (A.P.); (O.Y.A.C.)
- Ecology and Biodiversity, Institute of Environmental Biology, Utrecht University, 3584 CH Utrecht, The Netherlands
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Faller L, Leite MFA, Kuramae EE. Enhancing phosphate-solubilising microbial communities through artificial selection. Nat Commun 2024; 15:1649. [PMID: 38388537 PMCID: PMC10884399 DOI: 10.1038/s41467-024-46060-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 02/13/2024] [Indexed: 02/24/2024] Open
Abstract
Microbial communities, acting as key drivers of ecosystem processes, harbour immense potential for sustainable agriculture practices. Phosphate-solubilising microorganisms, for example, can partially replace conventional phosphate fertilisers, which rely on finite resources. However, understanding the mechanisms and engineering efficient communities poses a significant challenge. In this study, we employ two artificial selection methods, environmental perturbation, and propagation, to construct phosphate-solubilising microbial communities. To assess trait transferability, we investigate the community performance in different media and a hydroponic system with Chrysanthemum indicum. Our findings reveal a distinct subset of phosphate-solubilising bacteria primarily dominated by Klebsiella and Enterobacterales. The propagated communities consistently demonstrate elevated levels of phosphate solubilisation, surpassing the starting soil community by 24.2% in activity. The increased activity of propagated communities remains consistent upon introduction into the hydroponic system. This study shows the efficacy of community-level artificial selection, particularly through propagation, as a tool for successfully modifying microbial communities to enhance phosphate solubilisation.
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Affiliation(s)
- Lena Faller
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
- Utrecht University, Institute of Environmental Biology, Ecology and Biodiversity, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Marcio F A Leite
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
- Utrecht University, Institute of Environmental Biology, Ecology and Biodiversity, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Eiko E Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands.
- Utrecht University, Institute of Environmental Biology, Ecology and Biodiversity, Padualaan 8, 3584 CH, Utrecht, The Netherlands.
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Chen S, Kuramae EE, Jia Z, Liu B. Stable isotope probing reveals compositional and functional shifts in active denitrifying communities along the soil profile in an intensive agricultural area. Sci Total Environ 2024; 907:167968. [PMID: 37875201 DOI: 10.1016/j.scitotenv.2023.167968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 10/16/2023] [Accepted: 10/18/2023] [Indexed: 10/26/2023]
Abstract
Denitrifying microbial communities in the vadose zone play an essential role in eliminating the nitrate leached from agricultural practices. This nitrate could otherwise contaminate groundwater and threaten public health. Here, we utilized stable isotope probing combined with amplicon sequencing and functional gene quantification to inspect the composition and function of heterotrophic denitrifying microorganisms along a 9-m soil profile in an intensive agricultural area. Dramatic differences in the composition of the active denitrifiers were uncovered between the surface soil and deep layers of the vadose zone. The main denitrifying bacterial taxa identified from 13C-DNA fractions were Pseudomonadaceae (Pseudomonas), Rhodocyclaceae (Azoarcus), and Burkholderiaceae in the surface soil (0-0.2 m), and were Pseudomonadaceae (Pseudomonas), Burkholderiaceae, Bacillaceae (Bacillus), and Paenibacillaceae (Ammoniphilus) in the deep layers (0.5-9.0 m). Analysis of the functional genes (nirS, nirK, and nosZ) in isotope-labeled DNA revealed an upward nos/nir ratio with increasing soil depth, which may account for the higher nitrous oxide emission potential in the surface soil, as compared to the deeper sand-rich, low organic carbon layers. This study improves our understanding of active denitrifying microbes in the vadose zone and helps in developing techniques to reduce nitrate pollution in groundwater.
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Affiliation(s)
- Shuaimin Chen
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 286 Huaizhong Road, Shijiazhuang 050021, China; Institute of Agricultural Resource and Environment, Jilin Academy of Agricultural Sciences, 1363 Shengtai Street, Changchun 130033, China; Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 Wageningen, PB, Netherlands
| | - Eiko E Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 Wageningen, PB, Netherlands; Ecology and Biodiversity, Institute of Environmental Biology, Utrecht University, Padualaan 8, 10 3584 CH, Utrecht, the Netherlands
| | - Zhongjun Jia
- Key Laboratory of Mollisols Agroecology, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, PR China
| | - Binbin Liu
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 286 Huaizhong Road, Shijiazhuang 050021, China.
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Dong M, Kuramae EE, Zhao M, Li R, Shen Q, Kowalchuk GA. Tomato growth stage modulates bacterial communities across different soil aggregate sizes and disease levels. ISME Commun 2023; 3:104. [PMID: 37752280 PMCID: PMC10522649 DOI: 10.1038/s43705-023-00312-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 09/07/2023] [Accepted: 09/13/2023] [Indexed: 09/28/2023]
Abstract
Soil aggregates contain distinct physio-chemical properties across different size classes. These differences in micro-habitats support varied microbial communities and modulate the effect of plant on microbiome, which affect soil functions such as disease suppression. However, little is known about how the residents of different soil aggregate size classes are impacted by plants throughout their growth stages. Here, we examined how tomato plants impact soil aggregation and bacterial communities within different soil aggregate size classes. Moreover, we investigated whether aggregate size impacts the distribution of soil pathogen and their potential inhibitors. We collected samples from different tomato growth stages: before-planting, seedling, flowering, and fruiting stage. We measured bacterial density, community composition, and pathogen abundance using qPCR and 16 S rRNA gene sequencing. We found the development of tomato growth stages negatively impacted root-adhering soil aggregation, with a gradual decrease of large macro-aggregates (1-2 mm) and an increase of micro-aggregates (<0.25 mm). Additionally, changes in bacterial density and community composition varied across soil aggregate size classes. Furthermore, the pathogen exhibited a preference to micro-aggregates, while macro-aggregates hold a higher abundance of potential pathogen-inhibiting taxa and predicted antibiotic-associated genes. Our results indicate that the impacts of tomatoes on soil differ for different soil aggregate size classes throughout different plant growth stages, and plant pathogens and their potential inhibitors have different habitats within soil aggregate size classes. These findings highlight the importance of fine-scale heterogeneity of soil aggregate size classes in research on microbial ecology and agricultural sustainability, further research focuses on soil aggregates level could help identify candidate tax involved in suppressing pathogens in the virtual micro-habitats.
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Affiliation(s)
- Menghui Dong
- Key Lab of Organic-Based Fertilizers of China, Jiangsu Provincial Key Lab for 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, China
- Ecology and Biodiversity Group, Department of Biology, Institute of Environmental Biology, Utrecht University, 3584 CH, Utrecht, The Netherlands
| | - Eiko E Kuramae
- Ecology and Biodiversity Group, Department of Biology, Institute of Environmental Biology, Utrecht University, 3584 CH, Utrecht, The Netherlands
- Department of Microbial Ecology, Netherlands Institute of Ecology, 6708 PB, Wageningen, The Netherlands
| | - Mengli Zhao
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300, China
| | - Rong Li
- Key Lab of Organic-Based Fertilizers of China, Jiangsu Provincial Key Lab for 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, China.
| | - Qirong Shen
- Key Lab of Organic-Based Fertilizers of China, Jiangsu Provincial Key Lab for 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, China
| | - George A Kowalchuk
- Ecology and Biodiversity Group, Department of Biology, Institute of Environmental Biology, Utrecht University, 3584 CH, Utrecht, The Netherlands
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Bossolani JW, Leite MFA, Momesso L, Ten Berge H, Bloem J, Kuramae EE. Nitrogen input on organic amendments alters the pattern of soil-microbe-plant co-dependence. Sci Total Environ 2023:164347. [PMID: 37230351 DOI: 10.1016/j.scitotenv.2023.164347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 05/14/2023] [Accepted: 05/18/2023] [Indexed: 05/27/2023]
Abstract
The challenges of nitrogen (N) management in agricultural fields include minimizing N losses while maximizing profitability and soil health. Crop residues can alter N and carbon (C) cycle processes in the soil and modulate the responses of the subsequent crop and soil- microbe-plant interactions. Here, we aim to understand how organic amendments with low and high C/N ratio, combined or not with mineral N may change soil bacterial community and their activity on the soil. Organic amendments with different C/N ratios were combined or not with N fertilization as follows: i) unamended soil (control), ii) grass clover silage (GC; low C/N ratio), and iii) wheat straw (WS; high C/N ratio). The organic amendments modulated the bacterial community assemblage and increased microbial activity. WS amendment had the strongest effects on hot water extractable carbon, microbial biomass N and soil respiration, which were linked with changes in bacterial community composition compared with GC-amended and unamended soil. By contrast, N transformation processes in the soil were more pronounced in GC-amended and unamended soil than in WS-amended soil. These responses were stronger in the presence of mineral N input. WS amendment induced greater N immobilization in the soil, even with mineral N input, impairing crop development. Interestingly, N input in unamended soil altered the co-dependence between the soil and the bacterial community to favor a new co-dependence among the soil, plant and microbial activity. In GC-amended soil, N fertilization shifted the dependence of the crop plant from the bacterial community to soil characteristics. Finally, the combined N input with WS amendment (organic carbon input) placed microbial activity at the center of the interrelationships between the bacterial community, plant, and soil. This emphasizes the crucial importance of microorganisms in the functioning of agroecosystems. To achieve higher yields in crops managed with various organic amendments, it is essential to incorporate mineral N management practices. This becomes particularly crucial when the soil amendments have a high C/N ratio.
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Affiliation(s)
- João W Bossolani
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Microbial Ecology, 6708 PB Wageningen, the Netherlands
| | - Márcio F A Leite
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Microbial Ecology, 6708 PB Wageningen, the Netherlands
| | - Letusa Momesso
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Microbial Ecology, 6708 PB Wageningen, the Netherlands
| | - Hein Ten Berge
- Wageningen University & Research (WUR), Wageningen Environmental Research, 6700 AA Wageningen, the Netherlands
| | - Jaap Bloem
- Wageningen University & Research (WUR), Wageningen Environmental Research, 6700 AA Wageningen, the Netherlands
| | - Eiko E Kuramae
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Microbial Ecology, 6708 PB Wageningen, the Netherlands; Utrecht University, Institute of Environmental Biology, Ecology and Biodiversity, 3584 CH Utrecht, the Netherlands.
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Li Y, Kuramae EE, Nasir F, Wang E, Zhang Z, Li J, Yao Z, Tian L, Sun Y, Luo S, Guo L, Ren G, Tian C. Addition of cellulose degrading bacterial agents promoting keystone fungal-mediated cellulose degradation during aerobic composting: Construction the complex co-degradation system. Bioresour Technol 2023; 381:129132. [PMID: 37149269 DOI: 10.1016/j.biortech.2023.129132] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 04/26/2023] [Accepted: 05/01/2023] [Indexed: 05/08/2023]
Abstract
To excavate a complex co-degradation system for decomposing cellulose more efficiently, cellulose-degrading bacteria, including Bacillus subtilis WF-8, Bacillus licheniformis WF-11, Bacillus Cereus WS-1 and Streptomyces Nogalater WF-10 were added during maize straw and cattle manure aerobic composting. Bacillus and Streptomyces successfully colonized, which improve cellulose degrading ability. Continuous colonization of cellulose-degrading bacteria can promote the fungi to produce more precursors for humus and promote the negative correlation with Ascomycota. In the current study, the addition of cellulose-degrading bacteria has resulted in the rapid development of Mycothermus and Remersonia in the phylum Ascomycota as keystone fungal genera which constitute the foundation of the co-degradation system. Network analysis reveals the complex co-degradation system of efficient cellulose bacteria and mature fungi to treat cellulose in the process of straw aerobic composting mainly related to the influence of total carbon (TC) /total nitrogen (TN) and humic acid (HA)/fulvic acid (FA). This research offers a complex co-degradation system more efficiently to decompose cellulose aiming to maintain the long-term sustainability of agriculture.
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Affiliation(s)
- Yingxin Li
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, Jilin, PR China; University of Chinese Academy of Sciences, Beijing 101408, PR China; Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, the Netherlands
| | - Eiko E Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, the Netherlands; Ecology and Biodiversity Group, Department of Biology, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Fahad Nasir
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, Jilin, PR China
| | - Enze Wang
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, Jilin, PR China; University of Chinese Academy of Sciences, Beijing 101408, PR China
| | - Zhengang Zhang
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, Jilin, PR China; University of Chinese Academy of Sciences, Beijing 101408, PR China
| | - Ji Li
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, Jilin, PR China; University of Chinese Academy of Sciences, Beijing 101408, PR China; Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, the Netherlands
| | - Zongmu Yao
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, Jilin, PR China; University of Chinese Academy of Sciences, Beijing 101408, PR China
| | - Lei Tian
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, Jilin, PR China
| | - Yu Sun
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, Jilin, PR China
| | - Shouyang Luo
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, Jilin, PR China; University of Chinese Academy of Sciences, Beijing 101408, PR China
| | - Lingling Guo
- Microbial Research Institute of Liaoning Province, Chaoyang, 122000, PR China
| | - Gaidi Ren
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, the Netherlands; Institute of Agricultural Resources and Environment, Nanjing, 210000, Jiangsu Academy of Sciences, PR China
| | - Chunjie Tian
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, Jilin, PR China.
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Chang J, Tian L, Leite MFA, Sun Y, Shi S, Xu S, Wang J, Chen H, Chen D, Zhang J, Tian C, Kuramae EE. Nitrogen, manganese, iron, and carbon resource acquisition are potential functions of the wild rice Oryza rufipogon core rhizomicrobiome. Microbiome 2022; 10:196. [PMID: 36419170 PMCID: PMC9682824 DOI: 10.1186/s40168-022-01360-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 08/31/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND The assembly of the rhizomicrobiome, i.e., the microbiome in the soil adhering to the root, is influenced by soil conditions. Here, we investigated the core rhizomicrobiome of a wild plant species transplanted to an identical soil type with small differences in chemical factors and the impact of these soil chemistry differences on the core microbiome after long-term cultivation. We sampled three natural reserve populations of wild rice (i.e., in situ) and three populations of transplanted in situ wild rice grown ex situ for more than 40 years to determine the core wild rice rhizomicrobiome. RESULTS Generalized joint attribute modeling (GJAM) identified a total of 44 amplicon sequence variants (ASVs) composing the core wild rice rhizomicrobiome, including 35 bacterial ASVs belonging to the phyla Actinobacteria, Chloroflexi, Firmicutes, and Nitrospirae and 9 fungal ASVs belonging to the phyla Ascomycota, Basidiomycota, and Rozellomycota. Nine core bacterial ASVs belonging to the genera Haliangium, Anaeromyxobacter, Bradyrhizobium, and Bacillus were more abundant in the rhizosphere of ex situ wild rice than in the rhizosphere of in situ wild rice. The main ecological functions of the core microbiome were nitrogen fixation, manganese oxidation, aerobic chemoheterotrophy, chemoheterotrophy, and iron respiration, suggesting roles of the core rhizomicrobiome in improving nutrient resource acquisition for rice growth. The function of the core rhizosphere bacterial community was significantly (p < 0.05) shaped by electrical conductivity, total nitrogen, and available phosphorus present in the soil adhering to the roots. CONCLUSION We discovered that nitrogen, manganese, iron, and carbon resource acquisition are potential functions of the core rhizomicrobiome of the wild rice Oryza rufipogon. Our findings suggest that further potential utilization of the core rhizomicrobiome should consider the effects of soil properties on the abundances of different genera. Video Abstract.
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Affiliation(s)
- Jingjing Chang
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, Jilin, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Department of Microbial Ecology, Netherlands Institute of Ecology NIOO-KNAW, 6708 PB, Wageningen, the Netherlands
| | - Lei Tian
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, Jilin, China
| | - Marcio F A Leite
- Department of Microbial Ecology, Netherlands Institute of Ecology NIOO-KNAW, 6708 PB, Wageningen, the Netherlands
- Ecology and Biodiversity, Institute of Environmental Biology, Utrecht University, 3584 CH, Utrecht, the Netherlands
| | - Yu Sun
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, Jilin, China
| | - Shaohua Shi
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, Jilin, China
| | - Shangqi Xu
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, Jilin, China
| | - Jilin Wang
- Jiangxi Super-rice Research and Development Center, National Engineering Laboratory for Rice, Nanchang, China
| | - Hongping Chen
- Jiangxi Super-rice Research and Development Center, National Engineering Laboratory for Rice, Nanchang, China
| | - Dazhou Chen
- Jiangxi Super-rice Research and Development Center, National Engineering Laboratory for Rice, Nanchang, China
| | - Jianfeng Zhang
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Chunjie Tian
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, Jilin, China.
| | - Eiko E Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology NIOO-KNAW, 6708 PB, Wageningen, the Netherlands.
- Ecology and Biodiversity, Institute of Environmental Biology, Utrecht University, 3584 CH, Utrecht, the Netherlands.
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9
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Chang J, van Veen JA, Tian C, Kuramae EE. A review on the impact of domestication of the rhizosphere of grain crops and a perspective on the potential role of the rhizosphere microbial community for sustainable rice crop production. Sci Total Environ 2022; 842:156706. [PMID: 35724776 DOI: 10.1016/j.scitotenv.2022.156706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Revised: 06/10/2022] [Accepted: 06/11/2022] [Indexed: 06/15/2023]
Abstract
The rhizosphere-associated microbiome impacts plant performance and tolerance to abiotic and biotic stresses. Despite increasing recognition of the enormous functional role of the rhizomicrobiome on the survival of wild plant species growing under harsh environmental conditions, such as nutrient, water, temperature, and pathogen stresses, the utilization of the rhizosphere microbial community in domesticated rice production systems has been limited. Better insight into how this role of the rhizomicrobiome for the performance and survival of wild plants has been changed during domestication and development of present domesticated crops, may help to assess the potential of the rhizomicrobial community to improve the sustainable production of these crops. Here, we review the current knowledge of the effect of domestication on the microbial rhizosphere community of rice and other crops by comparing its diversity, structure, and function in wild versus domesticated species. We also examine the existing information on the impact of the plant on their physico-chemical environment. We propose that a holobiont approach should be explored in future studies by combining detailed analysis of the dynamics of the physicochemical microenvironment surrounding roots to systematically investigate the microenvironment-plant-rhizomicrobe interactions during rice domestication, and suggest focusing on the use of beneficial microbes (arbuscular mycorrhizal fungi and Nitrogen fixers), denitrifiers and methane consumers to improve the sustainable production of rice.
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Affiliation(s)
- Jingjing Chang
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China; University of Chinese Academy of Sciences, Beijing 100049, China; Department of Microbial Ecology, Netherlands Institute of Ecology NIOO-KNAW, 6708 PB Wageningen, the Netherlands
| | - Johannes A van Veen
- Department of Microbial Ecology, Netherlands Institute of Ecology NIOO-KNAW, 6708 PB Wageningen, the Netherlands
| | - Chunjie Tian
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China.
| | - Eiko E Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology NIOO-KNAW, 6708 PB Wageningen, the Netherlands; Ecology and Biodiversity, Institute of Environmental Biology, Utrecht University, 3584 CH Utrecht, the Netherlands.
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10
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Leite MFA, van den Broek SWEB, Kuramae EE. Current Challenges and Pitfalls in Soil Metagenomics. Microorganisms 2022; 10:microorganisms10101900. [PMID: 36296177 PMCID: PMC9606969 DOI: 10.3390/microorganisms10101900] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/16/2022] [Accepted: 09/20/2022] [Indexed: 11/17/2022] Open
Abstract
Soil microbial communities are essential components of agroecological ecosystems that influence soil fertility, nutrient turnover, and plant productivity. Metagenomics data are increasingly easy to obtain, but studies of soil metagenomics face three key challenges: (1) accounting for soil physicochemical properties; (2) incorporating untreated controls; and (3) sharing data. Accounting for soil physicochemical properties is crucial for better understanding the changes in soil microbial community composition, mechanisms, and abundance. Untreated controls provide a good baseline to measure changes in soil microbial communities and separate treatment effects from random effects. Sharing data increases reproducibility and enables meta-analyses, which are important for investigating overall effects. To overcome these challenges, we suggest establishing standard guidelines for the design of experiments for studying soil metagenomics. Addressing these challenges will promote a better understanding of soil microbial community composition and function, which we can exploit to enhance soil quality, health, and fertility.
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Affiliation(s)
- Marcio F. A. Leite
- Department of Microbial Ecology, Netherlands Institute of Ecology, 6708 PB Wageningen, The Netherlands
- Ecology and Biodiversity, Institute of Environmental Biology, Utrecht University, 3584 CS Utrecht, The Netherlands
| | | | - Eiko E. Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology, 6708 PB Wageningen, The Netherlands
- Ecology and Biodiversity, Institute of Environmental Biology, Utrecht University, 3584 CS Utrecht, The Netherlands
- Correspondence:
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11
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Bulgarelli RG, Leite MFA, de Hollander M, Mazzafera P, Andrade SAL, Kuramae EE. Eucalypt species drive rhizosphere bacterial and fungal community assembly but soil phosphorus availability rearranges the microbiome. Sci Total Environ 2022; 836:155667. [PMID: 35513142 DOI: 10.1016/j.scitotenv.2022.155667] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Revised: 04/11/2022] [Accepted: 04/29/2022] [Indexed: 06/14/2023]
Abstract
Soil phosphorus (P) availability may limit plant growth and alter root-soil interactions and rhizosphere microbial community composition. The composition of the rhizosphere microbial community can also be shaped by plant genotype. In this study, we examined the rhizosphere microbial communities of young plants of 24 species of eucalypts (22 Eucalyptus and two Corymbia species) under low or sufficient soil P availability. The taxonomic diversity of the rhizosphere bacterial and fungal communities was assessed by 16S and 18S rRNA gene amplicon sequencing. The taxonomic modifications in response to low P availability were evaluated by principal component analysis, and co-inertia analysis was performed to identify associations between bacterial and fungal community structures and parameters related to plant growth and nutritional status under low and sufficient soil P availability. The sequencing results showed that while both soil P availability and eucalypt species influenced the microbial community assembly, eucalypt species was the stronger determinant. However, when the plants are subjected to low P-availability, the rhizosphere selection became strongest. In response to low P, the bacterial and fungal communities in the rhizosphere of some species showed significant changes, whereas in others remained relatively constant under low and sufficient P. Co-inertia analyses revealed a significant co-dependence between plant nutrient contents and bacterial and fungal community composition only under sufficient P. By contrast, under low P, bacterial community composition was related to plant biomass production. In conclusion, our study shows that eucalypt species identity was the main factor modulating rhizosphere microbial community composition; significant shifts due to P availability were observed only for some eucalypt species.
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Affiliation(s)
- R G Bulgarelli
- University of Campinas, Institute of Biology, Department of Plant Biology, Campinas, SP, Brazil; Netherlands Institute of Ecology NIOO-KNAW, Department of Microbial Ecology, Wageningen, Netherlands
| | - M F A Leite
- Netherlands Institute of Ecology NIOO-KNAW, Department of Microbial Ecology, Wageningen, Netherlands
| | - M de Hollander
- Netherlands Institute of Ecology NIOO-KNAW, Department of Microbial Ecology, Wageningen, Netherlands
| | - P Mazzafera
- University of Campinas, Institute of Biology, Department of Plant Biology, Campinas, SP, Brazil; University of São Paulo, School of Agriculture Luiz de Queiroz, Department of Crop Production, Piracicaba, SP, Brazil
| | - S A L Andrade
- University of Campinas, Institute of Biology, Department of Plant Biology, Campinas, SP, Brazil.
| | - E E Kuramae
- Netherlands Institute of Ecology NIOO-KNAW, Department of Microbial Ecology, Wageningen, Netherlands; Utrecht University, Ecology and Biodiversity, Institute of Environmental Biology, Utrecht, Netherlands.
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12
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Costa OYA, de Hollander M, Kuramae EE, Bodelier PLE. PhyloFunDB: A Pipeline to Create and Update Functional Gene Taxonomic Databases. Microorganisms 2022; 10:microorganisms10061093. [PMID: 35744611 PMCID: PMC9229802 DOI: 10.3390/microorganisms10061093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 05/17/2022] [Accepted: 05/23/2022] [Indexed: 12/04/2022] Open
Abstract
The increase in sequencing capacity has amplified the number of taxonomically unclassified sequences in most databases. The classification of such sequences demands phylogenetic tree construction and comparison to currently classified sequences, a process that demands the processing of large amounts of data and use of several different software. Here, we present PhyloFunDB, a pipeline for extracting, processing, and inferring phylogenetic trees from specific functional genes. The goal of our work is to decrease processing time and facilitate the grouping of sequences that can be used for improved taxonomic classification of functional gene datasets.
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Affiliation(s)
- Ohana Y. A. Costa
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, The Netherlands; (O.Y.A.C.); (M.d.H.); (E.E.K.)
| | - Mattias de Hollander
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, The Netherlands; (O.Y.A.C.); (M.d.H.); (E.E.K.)
- Department of Terrestrial Ecology Bioinformatics Unit, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, The Netherlands
| | - Eiko E. Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, The Netherlands; (O.Y.A.C.); (M.d.H.); (E.E.K.)
- Ecology and Biodiversity Group, Department of Biology, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Paul L. E. Bodelier
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, The Netherlands; (O.Y.A.C.); (M.d.H.); (E.E.K.)
- Correspondence:
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13
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Rotoni C, Leite MFA, Pijl A, Kuramae EE. Rhizosphere microbiome response to host genetic variability: a trade-off between bacterial and fungal community assembly. FEMS Microbiol Ecol 2022; 98:6590037. [PMID: 35595468 DOI: 10.1093/femsec/fiac061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 05/13/2022] [Accepted: 05/17/2022] [Indexed: 11/14/2022] Open
Abstract
Rhizosphere microbial community composition is strongly influenced by plant species and cultivar. However, our understanding of the impact of plant cultivar genetic variability on microbial assembly composition remains limited. Here, we took advantage of vegetatively propagated chrysanthemum (Chrysanthemum indicum L.) as a plant model and induced roots in five commercial cultivars: Barolo, Chic, Chic 45, Chic Cream, and Haydar. We observed strong rhizosphere selection for the bacterial community but weaker selection for the fungal community. The genetic distance between cultivars explained 42.83% of the total dissimilarity between the bacteria selected by the different cultivars. By contrast, rhizosphere fungal selection was not significantly linked to plant genetic dissimilarity. Each chrysanthemum cultivar selected unique bacterial and fungal genera in the rhizosphere. We also observed a trade-off in the rhizosphere selection of bacteria and fungi in which the cultivar with the strongest selection of fungal communities showed the weakest bacterial selection. Finally, bacterial and fungal family taxonomic groups consistently selected by all cultivars were identified (bacteria Chitinophagaceae, Beijerinckiaceae, and Acidobacteriaceae and fungi Pseudeurotiaceae and Chrysozymaceae). Taken together, our findings suggest that chrysanthemum cultivars select distinct rhizosphere microbiomes and share a common core of microbes partially explained by the genetic dissimilarity between cultivars.
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Affiliation(s)
- Cristina Rotoni
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands.,Ecology and Biodiversity, Institute of Environmental Biology, Utrecht University, Utrecht, Netherlands
| | - Marcio F A Leite
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands.,Ecology and Biodiversity, Institute of Environmental Biology, Utrecht University, Utrecht, Netherlands
| | - Agata Pijl
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
| | - Eiko E Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands.,Ecology and Biodiversity, Institute of Environmental Biology, Utrecht University, Utrecht, Netherlands
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14
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Yang S, Poorter L, Kuramae EE, Sass-Klaassen U, Leite MFA, Costa OYA, Kowalchuk GA, Cornelissen JHC, van Hal J, Goudzwaard L, Hefting MM, van Logtestijn RSP, Sterck FJ. Stem traits, compartments, and tree species affect fungal communities on decaying wood. Environ Microbiol 2022; 24:3625-3639. [PMID: 35229433 PMCID: PMC9544286 DOI: 10.1111/1462-2920.15953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 01/12/2022] [Accepted: 02/23/2022] [Indexed: 12/01/2022]
Abstract
Dead wood quantity and quality is important for forest biodiversity, by determining wood‐inhabiting fungal assemblages. We therefore evaluated how fungal communities were regulated by stem traits and compartments (i.e. bark, outer‐ and inner wood) of 14 common temperate tree species. Fresh logs were incubated in a common garden experiment in a forest site in the Netherlands. After 1 and 4 years of decay, the fungal composition of different compartments was assessed using Internal Transcribed Spacer amplicon sequencing. We found that fungal alpha diversity differed significantly across tree species and stem compartments, with bark showing significantly higher fungal diversity than wood. Gymnosperms and Angiosperms hold different fungal communities, and distinct fungi were found between inner wood and other compartments. Stem traits showed significant afterlife effects on fungal communities; traits associated with accessibility (e.g. conduit diameter), stem chemistry (e.g. C, N, lignin) and physical defence (e.g. density) were important factors shaping fungal community structure in decaying stems. Overall, stem traits vary substantially across stem compartments and tree species, thus regulating fungal communities and the long‐term carbon dynamics of dead trees.
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Affiliation(s)
- Shanshan Yang
- Forest Ecology and Forest Management Group, Wageningen University and Research, P.O. Box 47, 6700, AA, Wageningen, The Netherlands
| | - Lourens Poorter
- Forest Ecology and Forest Management Group, Wageningen University and Research, P.O. Box 47, 6700, AA, Wageningen, The Netherlands
| | - Eiko E Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708, PB, Wageningen, the Netherlands.,Ecology and Biodiversity Group, Department of Biology, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands
| | - Ute Sass-Klaassen
- Forest Ecology and Forest Management Group, Wageningen University and Research, P.O. Box 47, 6700, AA, Wageningen, The Netherlands
| | - Marcio F A Leite
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708, PB, Wageningen, the Netherlands.,Ecology and Biodiversity Group, Department of Biology, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands
| | - Ohana Y A Costa
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708, PB, Wageningen, the Netherlands
| | - George A Kowalchuk
- Ecology and Biodiversity Group, Department of Biology, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands
| | - Johannes H C Cornelissen
- Systems Ecology, Department of Ecological Science, VU University (Vrije Universiteit) Amsterdam, De Boelelaan 1085, 1081, HV, Amsterdam, The Netherlands
| | - Jurgen van Hal
- Systems Ecology, Department of Ecological Science, VU University (Vrije Universiteit) Amsterdam, De Boelelaan 1085, 1081, HV, Amsterdam, The Netherlands
| | - Leo Goudzwaard
- Forest Ecology and Forest Management Group, Wageningen University and Research, P.O. Box 47, 6700, AA, Wageningen, The Netherlands
| | - Mariet M Hefting
- Ecology and Biodiversity Group, Department of Biology, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands
| | - Richard S P van Logtestijn
- Systems Ecology, Department of Ecological Science, VU University (Vrije Universiteit) Amsterdam, De Boelelaan 1085, 1081, HV, Amsterdam, The Netherlands
| | - Frank J Sterck
- Forest Ecology and Forest Management Group, Wageningen University and Research, P.O. Box 47, 6700, AA, Wageningen, The Netherlands
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15
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Su L, Qiu P, Fang Z, Sun J, Mo X, Liu Y, Kuramae EE, Zhang R, Shen B, Shen Q. Potassium Phosphite Enhances the Antagonistic Capability of Bacillus amyloliquefaciens to Manage Tomato Bacterial Wilt. Plant Dis 2022; 106:654-660. [PMID: 34491099 DOI: 10.1094/pdis-08-21-1601-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Bacterial wilt caused by Ralstonia solanacearum is a distributed and worldwide soilborne disease. The application of biocontrol microbes or agricultural chemicals has been widely used to manage tomato bacterial wilt. However, whether and how agricultural chemicals affect the antagonistic ability of biocontrol microbes is still unknown. Here, we combined potassium phosphite (K-Phite), an environmentally friendly agricultural chemical, and the biocontrol agent Bacillus amyloliquefaciens QPF8 (strain F8) to manage tomato bacterial wilt disease. First, K-Phite at a concentration of 0.05% (wt/vol) could significantly inhibit the growth of R. solanacearum. Second, 0.05% K-Phite enhanced the antagonistic capability of B. amyloliquefaciens F8. Third, the greenhouse soil experiments showed that the control efficiency for tomato bacterial wilt in the combined treatment was significantly higher than that of the application of B. amyloliquefaciens F8 or K-Phite alone. Overall, our results highlighted a novel strategy for the control of tomato bacterial wilt disease via application and revealed a new integrated pattern depending on the enhancement of the antagonistic capability of biocontrol microbes by K-Phite.
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Affiliation(s)
- Lv Su
- 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, P.R. China
- Key Laboratory of Agricultural Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, P.R. China
| | - Pengfei Qiu
- 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, P.R. China
| | - Zhiying Fang
- 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, P.R. China
| | - Juan Sun
- 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, P.R. China
| | - Xingxia Mo
- 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, P.R. China
| | - Yunpeng Liu
- Key Laboratory of Agricultural Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, P.R. China
| | - Eiko E Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
- Ecology and Biodiversity, Institute of Environmental Biology, Utrecht University, Utrecht, The Netherlands
| | - Ruifu Zhang
- 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, P.R. China
- Key Laboratory of Agricultural Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, P.R. China
| | - Biao 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, P.R. 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, P.R. China
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16
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Tian L, Chang J, Shi S, Ji L, Zhang J, Sun Y, Li X, Li X, Xie H, Cai Y, Chen D, Wang J, van Veen JA, Kuramae EE, Tran LSP, Tian C. Comparison of methane metabolism in the rhizomicrobiomes of wild and related cultivated rice accessions reveals a strong impact of crop domestication. Sci Total Environ 2022; 803:150131. [PMID: 34788940 DOI: 10.1016/j.scitotenv.2021.150131] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 06/28/2021] [Accepted: 08/31/2021] [Indexed: 06/13/2023]
Abstract
Microbial communities from rhizosphere (rhizomicrobiomes) have been significantly impacted by domestication as evidenced by a comparison of the rhizomicrobiomes of wild and related cultivated rice accessions. While there have been many published studies focusing on the structure of the rhizomicrobiome, studies comparing the functional traits of the microbial communities in the rhizospheres of wild rice and cultivated rice accessions are not yet available. In this study, we used metagenomic data from experimental rice plots to analyze the potential functional traits of the microbial communities in the rhizospheres of wild rice accessions originated from Africa and Asia in comparison with their related cultivated rice accessions. The functional potential of rhizosphere microbial communities involved in alanine, aspartate and glutamate metabolism, methane metabolism, carbon fixation pathways, citrate cycle (TCA cycle), pyruvate metabolism and lipopolysaccharide biosynthesis pathways were found to be enriched in the rhizomicrobiomes of wild rice accessions. Notably, methane metabolism in the rhizomicrobiomes of wild and cultivated rice accessions clearly differed. Key enzymes involved in methane production and utilization were overrepresented in the rhizomicrobiome samples obtained from wild rice accessions, suggesting that the rhizomicrobiomes of wild rice maintain a different ecological balance for methane production and utilization compared with those of the related cultivated rice accessions. A novel assessment of the impact of rice domestication on the primary metabolic pathways associated with microbial taxa in the rhizomicrobiomes was performed. Results indicated a strong impact of rice domestication on methane metabolism; a process that represents a critical function of the rhizosphere microbial community of rice. The findings of this study provide important information for future breeding of rice varieties with reduced methane emission during cultivation for sustainable agriculture.
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Affiliation(s)
- Lei Tian
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, Jilin 130102, China
| | - Jingjing Chang
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, Jilin 130102, China; University of Chinese Academy of Sciences, Beijing 100049, China; Department of Microbial Ecology, Netherlands Institute of Ecology NIOO-KNAW, Wageningen, the Netherlands; Ecology and Biodiversity, Institute of Environmental Biology, Utrecht University, Utrecht, the Netherlands
| | - Shaohua Shi
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, Jilin 130102, China
| | - Li Ji
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, Jilin 130102, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianfeng Zhang
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Yu Sun
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, Jilin 130102, China
| | - Xiaojie Li
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, Jilin 130102, China
| | - Xiujun Li
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, Jilin 130102, China
| | - Hongwei Xie
- Jiangxi Super-rice Research and Development Center, National Engineering Laboratory for Rice, Nanchang, China
| | - Yaohui Cai
- Jiangxi Super-rice Research and Development Center, National Engineering Laboratory for Rice, Nanchang, China
| | - Dazhou Chen
- Jiangxi Super-rice Research and Development Center, National Engineering Laboratory for Rice, Nanchang, China
| | - Jilin Wang
- Jiangxi Super-rice Research and Development Center, National Engineering Laboratory for Rice, Nanchang, China
| | - Johannes A van Veen
- Department of Microbial Ecology, Netherlands Institute of Ecology NIOO-KNAW, Wageningen, the Netherlands
| | - Eiko E Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology NIOO-KNAW, Wageningen, the Netherlands; Ecology and Biodiversity, Institute of Environmental Biology, Utrecht University, Utrecht, the Netherlands.
| | - Lam-Son Phan Tran
- Institute of Research and Development, Duy Tan University, Da Nang 550000, Viet Nam; Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, TX 79409, USA.
| | - Chunjie Tian
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, Jilin 130102, China.
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17
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Kim B, Westerhuis JA, Smilde AK, Floková K, Suleiman AKA, Kuramae EE, Bouwmeester HJ, Zancarini A. OUP accepted manuscript. FEMS Microbiol Ecol 2022; 98:6524125. [PMID: 35137050 PMCID: PMC8902685 DOI: 10.1093/femsec/fiac010] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 02/02/2022] [Accepted: 02/04/2022] [Indexed: 12/03/2022] Open
Abstract
Strigolactones are endogenous plant hormones regulating plant development and are exuded into the rhizosphere when plants experience nutrient deficiency. There, they promote the mutualistic association of plants with arbuscular mycorrhizal fungi that help the plant with the uptake of nutrients from the soil. This shows that plants actively establish—through the exudation of strigolactones—mutualistic interactions with microbes to overcome inadequate nutrition. The signaling function of strigolactones could possibly extend to other microbial partners, but the effect of strigolactones on the global root and rhizosphere microbiome remains poorly understood. Therefore, we analyzed the bacterial and fungal microbial communities of 16 rice genotypes differing in their root strigolactone exudation. Using multivariate analyses, distinctive differences in the microbiome composition were uncovered depending on strigolactone exudation. Moreover, the results of regression modeling showed that structural differences in the exuded strigolactones affected different sets of microbes. In particular, orobanchol was linked to the relative abundance of Burkholderia–Caballeronia–Paraburkholderia and Acidobacteria that potentially solubilize phosphate, while 4-deoxyorobanchol was associated with the genera Dyella and Umbelopsis. With this research, we provide new insight into the role of strigolactones in the interplay between plants and microbes in the rhizosphere.
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Affiliation(s)
- Bora Kim
- Plant Hormone Biology Group, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Johan A Westerhuis
- Biosystems Data Analysis Group, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Age K Smilde
- Biosystems Data Analysis Group, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Kristýna Floková
- Plant Hormone Biology Group, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Afnan K A Suleiman
- Department of Microbial Ecology, Netherlands Institute for Ecology (NIOO-KNAW), 6708 PB Wageningen, The Netherlands
- Soil Health Group, Bioclear Earth B.V., 9727 DL Groningen, The Netherlands
| | - Eiko E Kuramae
- Department of Microbial Ecology, Netherlands Institute for Ecology (NIOO-KNAW), 6708 PB Wageningen, The Netherlands
- Ecology and Biodiversity Group, Institute of Environmental Biology, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Harro J Bouwmeester
- Corresponding author: Plant Hormone Biology Group, Swammerdam Institute for Life Sciences, University of Amsterdam, Postbus 1210, 1000 BE Amsterdam, The Netherlands. Tel: +31-20-525-6476; E-mail:
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Leite MFA, Dimitrov MR, Freitas-Iório RP, de Hollander M, Cipriano MAP, Andrade SAL, da Silveira APD, Kuramae EE. Rearranging the sugarcane holobiont via plant growth-promoting bacteria and nitrogen input. Sci Total Environ 2021; 800:149493. [PMID: 34426366 DOI: 10.1016/j.scitotenv.2021.149493] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 07/22/2021] [Accepted: 08/02/2021] [Indexed: 06/13/2023]
Abstract
The development and productivity of plants are governed by their genetic background, nutrient input, and the microbial communities they host, i.e. the holobiont. Accordingly, engineering beneficial root microbiomes has emerged as a novel and sustainable approach to crop production with reduced nutrient input. Here, we tested the effects of six bacterial strains isolated from sugarcane stalks on sugarcane growth and physiology as well as the dynamics of prokaryote community assembly in the rhizosphere and root endosphere under two N fertilization regimes. All six strains, Paraburkholderia caribensis IAC/BECa 88, Kosakonia oryzae IAC/BECa 90, Kosakonia radicincitans IAC/BECa 95, Paraburkholderia tropica IAC/BECa 135, Pseudomonas fluorescens IAC/BECa 141 and Herbaspirillum frisingense IAC/BECa 152, increased in shoot and root dry mass, and influenced the concentration and accumulation of important macro- and micronutrients. However, N input reduced the impact of inoculation by shifting the sugarcane microbiome (rhizosphere and root endosphere) and weakening the co-dependence between soil microbes and sugarcane biomass and nutrients. The results show that these beneficial microbes improved plant nutrient uptake conditioned to a reduced N nutrient input. Therefore, reduced fertilization is not only desirable consequence of bacterial inoculation but essential for higher impact of these beneficial bacteria on the sugarcane microbiome.
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Affiliation(s)
- Marcio F A Leite
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, the Netherlands; Ecology and Biodiversity, Institute of Environmental Biology, Utrecht University, Utrecht, the Netherlands
| | - Mauricio R Dimitrov
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, the Netherlands
| | | | - Mattias de Hollander
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, the Netherlands
| | - Matheus A P Cipriano
- Center of Soil and Environmental Resources, Agronomic Institute (IAC), Campinas, Brazil
| | - Sara A L Andrade
- Department of Plant Biology, Institute of Biology, State University of Campinas, Campinas, Brazil
| | | | - Eiko E Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, the Netherlands; Ecology and Biodiversity, Institute of Environmental Biology, Utrecht University, Utrecht, the Netherlands.
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19
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Zhou X, Leite MFA, Zhang Z, Tian L, Chang J, Ma L, Li X, van Veen JA, Tian C, Kuramae EE. Facilitation in the soil microbiome does not necessarily lead to niche expansion. Environ Microbiome 2021; 16:4. [PMID: 33902741 PMCID: PMC8067652 DOI: 10.1186/s40793-021-00373-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Accepted: 01/21/2021] [Indexed: 05/24/2023]
Abstract
BACKGROUND The soil microbiome drives soil ecosystem function, and soil microbial functionality is directly linked to interactions between microbes and the soil environment. However, the context-dependent interactions in the soil microbiome remain largely unknown. RESULTS Using latent variable models (LVMs), we disentangle the biotic and abiotic interactions of soil bacteria, fungi and environmental factors using the Qinghai-Tibetan Plateau soil ecosystem as a model. Our results show that soil bacteria and fungi not only interact with each other but also shift from competition to facilitation or vice versa depending on environmental variation; that is, the nature of their interactions is context-dependent. CONCLUSIONS Overall, elevation is the environmental gradient that most promotes facilitative interactions among microbes but is not a major driver of soil microbial community composition, as evidenced by variance partitioning. The larger the tolerance of a microbe to a specific environmental gradient, the lesser likely it is to interact with other soil microbes, which suggests that facilitation does not necessarily lead to niche expansion.
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Affiliation(s)
- Xue Zhou
- College of Resources and Environment, Jilin Agricultural University, Changchun, China
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Márcio F A Leite
- Department of Microbial Ecology, Netherlands Institute of Ecology NIOO-KNAW, Wageningen, the Netherlands
| | - Zhenqing Zhang
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Lei Tian
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Jingjing Chang
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Lina Ma
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Xiujun Li
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Johannes A van Veen
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
- Department of Microbial Ecology, Netherlands Institute of Ecology NIOO-KNAW, Wageningen, the Netherlands
| | - Chunjie Tian
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China.
| | - Eiko E Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology NIOO-KNAW, Wageningen, the Netherlands.
- Ecology and biodiversity, Institute of Environmental Biology, Utrecht University, Utrecht, The Netherlands.
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20
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Chang J, Sun Y, Tian L, Ji L, Luo S, Nasir F, Kuramae EE, Tian C. The Structure of Rhizosphere Fungal Communities of Wild and Domesticated Rice: Changes in Diversity and Co-occurrence Patterns. Front Microbiol 2021; 12:610823. [PMID: 33613482 PMCID: PMC7890246 DOI: 10.3389/fmicb.2021.610823] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 01/06/2021] [Indexed: 01/16/2023] Open
Abstract
The rhizosphere fungal community affects the ability of crops to acquire nutrients and their susceptibility to pathogen invasion. However, the effects of rice domestication on the diversity and interactions of rhizosphere fungal community still remain largely unknown. Here, internal transcribed spacer amplicon sequencing was used to systematically analyze the structure of rhizosphere fungal communities of wild and domesticated rice. The results showed that domestication increased the alpha diversity indices of the rice rhizosphere fungal community. The changes of alpha diversity index may be associated with the enrichment of Acremonium, Lecythophora, and other specific rare taxa in the rhizosphere of domesticated rice. The co-occurrence network showed that the complexity of wild rice rhizosphere fungal community was higher than that of the domesticated rice rhizosphere fungal community. Arbuscular mycorrhizal fungi (AMF) and soilborne fungi were positively and negatively correlated with more fungi in the wild rice rhizosphere, respectively. For restructuring the rhizomicrobial community of domesticated crops, we hypothesize that microbes that hold positive connections with AMF and negative connections with soilborne fungi can be used as potential sources for bio-inoculation. Our findings provide a scientific basis for reshaping the structure of rhizomicrobial community and furthermore create potential for novel intelligent and sustainable agricultural solutions.
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Affiliation(s)
- Jingjing Chang
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Yu Sun
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Lei Tian
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Li Ji
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Shasha Luo
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Fahad Nasir
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Eiko E. Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology NIOO-KNAW, Wageningen, Netherlands
- Ecology and Biodiversity, Institute of Environmental Biology, Utrecht University, Utrecht, Netherlands
| | - Chunjie Tian
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
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21
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Costa OYA, Kuramae EE. The influence of agar brands and micronutrients in the growth optimization of Granulicella sp. (Acidobacteriota). J Microbiol Methods 2021; 181:106148. [PMID: 33484740 DOI: 10.1016/j.mimet.2021.106148] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 01/04/2021] [Accepted: 01/12/2021] [Indexed: 11/25/2022]
Abstract
Acidobacteriota are highly abundant in soils, however, few cultured representatives are available. The purity of the reagents can influence microbial growth in laboratory conditions and successful isolation. Here we investigated the impact of different agar brands in culture medium and advocate that agar origin should be carefully considered for Acidobacteriota strains growth and microbial isolation.
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Affiliation(s)
- Ohana Y A Costa
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Microbial Ecology, Droevendaalsesteeg 10, 6708, PB, Wageningen, the Netherlands.
| | - Eiko E Kuramae
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Microbial Ecology, Droevendaalsesteeg 10, 6708, PB, Wageningen, the Netherlands; Institute of Environmental Biology, Ecology and Biodiversity, Utrecht University, 3584, CH, Utrecht, the Netherlands
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22
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Kuramae EE, Dimitrov MR, da Silva GHR, Lucheta AR, Mendes LW, Luz RL, Vet LEM, Fernandes TV. On-Site Blackwater Treatment Fosters Microbial Groups and Functions to Efficiently and Robustly Recover Carbon and Nutrients. Microorganisms 2020; 9:E75. [PMID: 33396683 PMCID: PMC7824102 DOI: 10.3390/microorganisms9010075] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 12/23/2020] [Accepted: 12/24/2020] [Indexed: 12/04/2022] Open
Abstract
Wastewater is considered a renewable resource water and energy. An advantage of decentralized sanitation systems is the separation of the blackwater (BW) stream, contaminated with human pathogens, from the remaining household water. However, the composition and functions of the microbial community in BW are not known. In this study, we used shotgun metagenomics to assess the dynamics of microbial community structure and function throughout a new BW anaerobic digestion system installed at The Netherlands Institute of Ecology. Samples from the influent (BW), primary effluent (anaerobic digested BW), sludge and final effluent of the pilot upflow anaerobic sludge blanket (UASB) reactor and microalgae pilot tubular photobioreactor (PBR) were analyzed. Our results showed a decrease in microbial richness and diversity followed by a decrease in functional complexity and co-occurrence along the different modules of the bioreactor. The microbial diversity and function decrease were reflected both changes in substrate composition and wash conditions. Our wastewater treatment system also decreased microbial functions related to pathogenesis. In summary, the new sanitation system studied here fosters microbial groups and functions that allow the system to efficiently and robustly recover carbon and nutrients while reducing pathogenic groups, ultimately generating a final effluent safe for discharge and reuse.
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Affiliation(s)
- Eiko E. Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands; (M.R.D.); (A.R.L.); (L.W.M.); (R.L.L.)
- Ecology and Biodiversity, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Mauricio R. Dimitrov
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands; (M.R.D.); (A.R.L.); (L.W.M.); (R.L.L.)
| | - Gustavo H. R. da Silva
- Department of Environmental and Civil Engineering, São Paulo State University (UNESP), Bauru 17033-360, Brazil;
| | - Adriano R. Lucheta
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands; (M.R.D.); (A.R.L.); (L.W.M.); (R.L.L.)
| | - Lucas W. Mendes
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands; (M.R.D.); (A.R.L.); (L.W.M.); (R.L.L.)
| | - Ronildson L. Luz
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands; (M.R.D.); (A.R.L.); (L.W.M.); (R.L.L.)
| | - Louise E. M. Vet
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands;
| | - Tania V. Fernandes
- Department of Aquatic Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands;
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Costa OYA, Oguejiofor C, Zühlke D, Barreto CC, Wünsche C, Riedel K, Kuramae EE. Impact of Different Trace Elements on the Growth and Proteome of Two Strains of Granulicella, Class "Acidobacteriia". Front Microbiol 2020; 11:1227. [PMID: 32625179 PMCID: PMC7315648 DOI: 10.3389/fmicb.2020.01227] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 05/14/2020] [Indexed: 12/24/2022] Open
Abstract
Acidobacteria represents one of the most dominant bacterial groups across diverse ecosystems. However, insight into their ecology and physiology has been hampered by difficulties in cultivating members of this phylum. Previous cultivation efforts have suggested an important role of trace elements for the proliferation of Acidobacteria, however, the impact of these metals on their growth and metabolism is not known. In order to gain insight into this relationship, we evaluated the effect of trace element solution SL10 on the growth of two strains (5B5 and WH15) of Acidobacteria belonging to the genus Granulicella and studied the proteomic responses to manganese (Mn). Granulicella species had highest growth with the addition of Mn, as well as higher tolerance to this metal compared to seven other metal salts. Variations in tolerance to metal salt concentrations suggests that Granulicella sp. strains possess different mechanisms to deal with metal ion homeostasis and stress. Furthermore, Granulicella sp. 5B5 might be more adapted to survive in an environment with higher concentration of several metal ions when compared to Granulicella sp. WH15. The proteomic profiles of both strains indicated that Mn was more important in enhancing enzymatic activity than to protein expression regulation. In the genomic analyses, we did not find the most common transcriptional regulation of Mn homeostasis, but we found candidate transporters that could be potentially involved in Mn homeostasis for Granulicella species. The presence of such transporters might be involved in tolerance to higher Mn concentrations, improving the adaptability of bacteria to metal enriched environments, such as the decaying wood-rich Mn environment from which these two Granulicella strains were isolated.
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Affiliation(s)
- Ohana Y A Costa
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands.,Institute of Biology Leiden, Leiden University, Leiden, Netherlands
| | - Chidinma Oguejiofor
- Department of Soil Science and Meteorology, Michael Okpara University of Agriculture, Umudike, Nigeria
| | - Daniela Zühlke
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Cristine C Barreto
- Genomic Sciences and Biotechnology Program, Catholic University of Brasilia, Distrito Federal, Brazil
| | - Christine Wünsche
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Katharina Riedel
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Eiko E Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands.,Ecology and Biodiversity, Institute of Environmental Biology, Utrecht University, Utrecht, Netherlands
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Costa OYA, de Hollander M, Pijl A, Liu B, Kuramae EE. Cultivation-independent and cultivation-dependent metagenomes reveal genetic and enzymatic potential of microbial community involved in the degradation of a complex microbial polymer. Microbiome 2020; 8:76. [PMID: 32482164 PMCID: PMC7265232 DOI: 10.1186/s40168-020-00836-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 03/31/2020] [Indexed: 05/04/2023]
Abstract
BACKGROUND Cultivation-independent methods, including metagenomics, are tools for the exploration and discovery of biotechnological compounds produced by microbes in natural environments. Glycoside hydrolases (GHs) enzymes are extremely desired and important in the industry of production for goods and biofuel and removal of problematic biofilms and exopolysaccharide (EPS). Biofilms and EPS are complex, requiring a wide range of enzymes for a complete degradation. The aim of this study was to identify potential GH microbial producers and GH genes with biotechnological potential, using EPS-complex structure (WH15EPS) of Acidobacteria Granulicella sp. strain WH15 as an enrichment factor, in cultivation-independent and cultivation-dependent methods. We performed stable isotope probing (SIP) combined with metagenomics on topsoil litter amended with WH15EPS and coupled solid culture-EPS amended medium with metagenomics. RESULTS SIP metagenome analysis of the soil litter demonstrated that phyla Proteobacteria, Actinobacteria, Acidobacteria, and Planctomycetes were the most abundant in WH15EPS amended and unamended treatments. The enrichment cultures in solid culture medium coupled to metagenomics demonstrated an enrichment in Proteobacteria, and the metagenome assembly of this enrichment cultures resulted in 4 metagenome-assembled genomes (MAGs) of microbes with low identity (42-86%) to known microorganisms. Among all carbohydrate-active enzymes (CAZymes) retrieved genes, glycoside transferase (GT) was the most abundant family, either in culture-independent or culture-based metagenome datasets. Within the glycoside hydrolases (GHs), GH13 was the most abundant family in both metagenome datasets. In the "heavy" fraction of the culture-independent metagenome SIP dataset, GH109 (α-N-acetylgalactosaminidases), GH117 (agarases), GH50 (agarases), GH32 (invertases and inulinases), GH17 (endoglucanases), and GH71 (mutanases) families were more abundant in comparison with the controls. Those GH families are affiliated to microorganism that are probably capable to degrade WH15EPS and potentially applicable for biofilm deconstruction. Subsequent in culture-based metagenome, the assembled 4 MAGs (unclassified Proteobacteria) also contained GH families of interest, involving mannosidases, lysozymes, galactosidases, and chitinases. CONCLUSIONS We demonstrated that functional diversity induced by the presence of WH15EPS in both culture-independent and culture-dependent approaches was enriched in GHs, such as amylases and endoglucanases that could be applied in chemical, pharmaceutical, and food industrial sectors. Furthermore, WH15EPS may be used for the investigation and isolation of yet unknown taxa, such as unclassified Proteobacteria and Planctomycetes, increasing the number of current cultured bacterial representatives with potential biotechnological traits. Video Abstract.
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Affiliation(s)
- Ohana Y A Costa
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Microbial Ecology, Droevendaalsesteeg 10, 6708 PB, Wageningen, Netherlands
- Institute of Biology (IBL), Leiden University, Leiden, The Netherlands
| | - Mattias de Hollander
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Microbial Ecology, Droevendaalsesteeg 10, 6708 PB, Wageningen, Netherlands
| | - Agata Pijl
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Microbial Ecology, Droevendaalsesteeg 10, 6708 PB, Wageningen, Netherlands
| | - Binbin Liu
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050021, Hebei, China.
| | - Eiko E Kuramae
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Microbial Ecology, Droevendaalsesteeg 10, 6708 PB, Wageningen, Netherlands.
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Kuramae EE, Derksen S, Schlemper TR, Dimitrov MR, Costa OYA, da Silveira APD. Sorghum Growth Promotion by Paraburkholderia tropica and Herbaspirillum frisingense: Putative Mechanisms Revealed by Genomics and Metagenomics. Microorganisms 2020; 8:E725. [PMID: 32414048 PMCID: PMC7285511 DOI: 10.3390/microorganisms8050725] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 05/08/2020] [Accepted: 05/11/2020] [Indexed: 01/11/2023] Open
Abstract
Bacteria from the genera Paraburkholderia and Herbaspirillum can promote the growth of Sorghum bicolor, but the underlying mechanisms are not yet known. In a pot experiment, sorghum plants grown on sterilized substrate were inoculated with Paraburkholderia tropica strain IAC/BECa 135 and Herbaspirillum frisingense strain IAC/BECa 152 under phosphate-deficient conditions. These strains significantly increased Sorghum bicolor cultivar SRN-39 root and shoot biomass. Shotgun metagenomic analysis of the rhizosphere revealed successful colonization by both strains; however, the incidence of colonization was higher in plants inoculated with P. tropica strain IAC/BECa 135 than in those inoculated with H. frisingense strain IAC/BECa 152. Conversely, plants inoculated with H. frisingense strain IAC/BECa 152 showed the highest increase in biomass. Genomic analysis of the two inoculants implied a high degree of rhizosphere fitness of P. tropica strain IAC/BECa 135 through environmental signal processing, biofilm formation, and nutrient acquisition. Both genomes contained genes related to plant growth-promoting bacterial (PGPB) traits, including genes related to indole-3-acetate (IAA) synthesis, nitrogen fixation, nodulation, siderophore production, and phosphate solubilization, although the P. tropica strain IAC/BECa 135 genome contained a slightly more extensive repertoire. This study provides evidence that complementary mechanisms of growth promotion in Sorghum might occur, i.e., that P. tropica strain IAC/BECa 135 acts in the rhizosphere and increases the availability of nutrients, while H. frisingense strain IAC/BECa 152 influences plant hormone signaling. While the functional and taxonomic profiles of the rhizobiomes were similar in all treatments, significant differences in plant biomass were observed, indicating that the rhizobiome and the endophytic microbial community may play equally important roles in the complicated plant-microbial interplay underlying increased host plant growth.
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Affiliation(s)
- Eiko E. Kuramae
- Netherlands Institute of Ecology (NIOO-KNAW), Microbial Ecology Department, Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands; (S.D.); (T.R.S.); (M.R.D.); (O.Y.A.C.)
- Utrecht University, Institute of Environmental Biology, Ecology and biodiversity, 3508 TC Utrecht, The Netherlands
| | - Stan Derksen
- Netherlands Institute of Ecology (NIOO-KNAW), Microbial Ecology Department, Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands; (S.D.); (T.R.S.); (M.R.D.); (O.Y.A.C.)
| | - Thiago R. Schlemper
- Netherlands Institute of Ecology (NIOO-KNAW), Microbial Ecology Department, Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands; (S.D.); (T.R.S.); (M.R.D.); (O.Y.A.C.)
| | - Maurício R. Dimitrov
- Netherlands Institute of Ecology (NIOO-KNAW), Microbial Ecology Department, Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands; (S.D.); (T.R.S.); (M.R.D.); (O.Y.A.C.)
| | - Ohana Y. A. Costa
- Netherlands Institute of Ecology (NIOO-KNAW), Microbial Ecology Department, Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands; (S.D.); (T.R.S.); (M.R.D.); (O.Y.A.C.)
| | - Adriana P. D. da Silveira
- Center of Soil and Environmental Resources, Agronomic Institute of Campinas (IAC), Av. Barão de Itapura 1481, 13020-902 Campinas, Brazil
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Costa OY, Zerillo MM, Zühlke D, Kielak AM, Pijl A, Riedel K, Kuramae EE. Responses of Acidobacteria Granulicella sp. WH15 to High Carbon Revealed by Integrated Omics Analyses. Microorganisms 2020; 8:E244. [PMID: 32059463 PMCID: PMC7074687 DOI: 10.3390/microorganisms8020244] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 02/08/2020] [Accepted: 02/10/2020] [Indexed: 01/18/2023] Open
Abstract
The phylum Acidobacteria is widely distributed in soils, but few representatives have been cultured. In general, Acidobacteria are oligotrophs and exhibit slow growth under laboratory conditions. We sequenced the genome of Granulicella sp. WH15, a strain obtained from decaying wood, and determined the bacterial transcriptome and proteome under growth in poor medium with a low or high concentration of sugar. We detected the presence of 217 carbohydrate-associated enzymes in the genome of strain WH15. Integrated analysis of the transcriptomic and proteomic profiles showed that high sugar triggered a stress response. As part of this response, transcripts related to cell wall stress, such as sigma factor σW and toxin-antitoxin (TA) systems, were upregulated, as were several proteins involved in detoxification and repair, including MdtA and OprM. KEGG metabolic pathway analysis indicated the repression of carbon metabolism (especially the pentose phosphate pathway) and the reduction of protein synthesis, carbohydrate metabolism, and cell division, suggesting the arrest of cell activity and growth. In summary, the stress response of Granulicella sp. WH15 induced by the presence of a high sugar concentration in the medium resulted in the intensification of secretion functions to eliminate toxic compounds and the reallocation of resources to cell maintenance instead of growth.
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Affiliation(s)
- Ohana Y.A. Costa
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands (M.M.Z.); (A.M.K.); (A.P.)
| | - Marcelo M. Zerillo
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands (M.M.Z.); (A.M.K.); (A.P.)
| | - Daniela Zühlke
- Institute of Microbiology, University of Greifswald, Felix-Hausdorff-Strasse 8, 17487 Greifswald, Germany; (D.Z.); (K.R.)
| | - Anna M. Kielak
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands (M.M.Z.); (A.M.K.); (A.P.)
| | - Agata Pijl
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands (M.M.Z.); (A.M.K.); (A.P.)
| | - Katharina Riedel
- Institute of Microbiology, University of Greifswald, Felix-Hausdorff-Strasse 8, 17487 Greifswald, Germany; (D.Z.); (K.R.)
| | - Eiko E. Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands (M.M.Z.); (A.M.K.); (A.P.)
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Suleiman AKA, Harkes P, van den Elsen S, Holterman M, Korthals GW, Helder J, Kuramae EE. Organic amendment strengthens interkingdom associations in the soil and rhizosphere of barley (Hordeum vulgare). Sci Total Environ 2019; 695:133885. [PMID: 31756853 DOI: 10.1016/j.scitotenv.2019.133885] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 07/25/2019] [Accepted: 08/10/2019] [Indexed: 06/10/2023]
Abstract
Anthropogenic modification of soil systems has diverse impacts on food web interactions and ecosystem functioning. To understand the positive, neutral or adverse effects of agricultural practices on the associations of community members of soil microbes and microfaunal biomes, we characterized the effects of different fertilization types (organic, inorganic and a combination of organic and inorganic) on the food web active communities in the bulk soil and rhizosphere compartments in field conditions. We examined the influence of fertilization on (i) individual groups (bacteria, protozoa and fungi as microbe representatives and metazoans as microfauna representatives) and (ii) inter-kingdom interactions (focusing on the interactions between bacteria and eukaryotic groups) both neglecting and considering environmental factors in our analysis in combination with the microbial compositional data. Our results revealed different patterns of biota communities under organic versus inorganic fertilization, which shaped food web associations in both the bulk and rhizosphere compartments. Overall, organic fertilization increased the complexity of microbial-microfaunal ecological associations with inter- and intra- connections among categories of primary decomposers (bacteria and fungi) and predators (protozoa and microfauna) and differences in potential function in the soil food web in both the bulk and rhizosphere compartments. Furthermore, the inter-connections between primary decomposers and predators in bulk soil were more pronounced when environmental factors were considered. We suggest that organic fertilization selects bacterial orders with different potential ecological functions and interactions as survival, predation and cooperation due to more complex environment than those of inorganic or combined fertilization. Our findings support the importance of a comprehensive understanding of trophic food web patterns for soil management systems.
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Affiliation(s)
- Afnan K A Suleiman
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Microbial Ecology, Wageningen, the Netherlands.
| | - Paula Harkes
- Wageningen University and Research Centre (WUR), Laboratory of Nematology, Wageningen, the Netherlands.
| | - Sven van den Elsen
- Wageningen University and Research Centre (WUR), Laboratory of Nematology, Wageningen, the Netherlands.
| | - Martijn Holterman
- Wageningen University and Research Centre (WUR), Laboratory of Nematology, Wageningen, the Netherlands.
| | - Gerard W Korthals
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Microbial Ecology, Wageningen, the Netherlands; Wageningen University and Research Centre (WUR), Laboratory of Nematology, Wageningen, the Netherlands.
| | - Johannes Helder
- Wageningen University and Research Centre (WUR), Laboratory of Nematology, Wageningen, the Netherlands
| | - Eiko E Kuramae
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Microbial Ecology, Wageningen, the Netherlands.
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Chen S, Waghmode TR, Sun R, Kuramae EE, Hu C, Liu B. Root-associated microbiomes of wheat under the combined effect of plant development and nitrogen fertilization. Microbiome 2019; 7:136. [PMID: 31640813 PMCID: PMC6806522 DOI: 10.1186/s40168-019-0750-2] [Citation(s) in RCA: 151] [Impact Index Per Article: 30.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Accepted: 09/13/2019] [Indexed: 05/20/2023]
Abstract
BACKGROUND Plant roots assemble microbial communities both inside the roots and in the rhizosphere, and these root-associated microbiomes play pivotal roles in plant nutrition and productivity. Although it is known that increased synthetic fertilizer input in Chinese farmlands over the past 50 years has resulted in not only increased yields but also environmental problems, we lack a comprehensive understanding of how crops under elevated nutrient input shape root-associated microbial communities, especially through adjusting the quantities and compositions of root metabolites and exudates. METHODS The compositions of bacterial and fungal communities from the roots and rhizosphere of wheat (Triticum aestivum L.) under four levels of long-term inorganic nitrogen (N) fertilization were characterized at the tillering, jointing and ripening stages. The root-released organic carbon (ROC), organic acids in the root exudates and soil organic carbon (SOC) and soil active carbon (SAC) in the rhizosphere were quantified. RESULTS ROC levels varied dramatically across wheat growth stages and correlated more with the bacterial community than with the fungal community. Rhizosphere SOC and SAC levels were elevated by long-term N fertilization but varied only slightly across growth stages. Variation in the microbial community structure across plant growth stages showed a decreasing trend with N fertilization level in the rhizosphere. In addition, more bacterial and fungal genera were significantly correlated in the jointing and ripening stages than in the tillering stage in the root samples. A number of bacterial genera that shifted in response to N fertilization, including Arthrobacter, Bacillus and Devosia, correlated significantly with acetic acid, oxalic acid, succinic acid and tartaric acid levels. CONCLUSIONS Our results indicate that both plant growth status and N input drive changes in the microbial community structure in the root zone of wheat. Plant growth stage demostrated a stronger influence on bacterial than on fungal community composition. A number of bacterial genera that have been described as plant growth-promoting rhizobacteria (PGPR) responded positively to N fertilization, and their abundance correlated significantly with the organic acid level, suggesting that the secretion of organic acids may be a strategy developed by plants to recruit beneficial microbes in the root zone to cope with high N input. These results provide novel insight into the associations among increased N input, altered carbon availability, and shifts in microbial communities in the plant roots and rhizosphere of intensive agricultural ecosystems.
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Affiliation(s)
- Shuaimin Chen
- Key Laboratory of Agricultural Water Resources, Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 286 Huaizhong Road, Shijiazhuang, 050021, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Tatoba R Waghmode
- Key Laboratory of Agricultural Water Resources, Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 286 Huaizhong Road, Shijiazhuang, 050021, China
| | - Ruibo Sun
- Key Laboratory of Agricultural Water Resources, Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 286 Huaizhong Road, Shijiazhuang, 050021, China
| | - Eiko E Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708, Wageningen, PB, Netherlands
| | - Chunsheng Hu
- Key Laboratory of Agricultural Water Resources, Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 286 Huaizhong Road, Shijiazhuang, 050021, China.
| | - Binbin Liu
- Key Laboratory of Agricultural Water Resources, Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 286 Huaizhong Road, Shijiazhuang, 050021, China.
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Harkes P, Suleiman AKA, van den Elsen SJJ, de Haan JJ, Holterman M, Kuramae EE, Helder J. Conventional and organic soil management as divergent drivers of resident and active fractions of major soil food web constituents. Sci Rep 2019; 9:13521. [PMID: 31534146 PMCID: PMC6751164 DOI: 10.1038/s41598-019-49854-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 08/27/2019] [Indexed: 11/09/2022] Open
Abstract
Conventional agricultural production systems, typified by large inputs of mineral fertilizers and pesticides, reduce soil biodiversity and may negatively affect ecosystem services such as carbon fixation, nutrient cycling and disease suppressiveness. Organic soil management is thought to contribute to a more diverse and stable soil food web, but data detailing this effect are sparse and fragmented. We set out to map both the resident (rDNA) and the active (rRNA) fractions of bacterial, fungal, protozoan and metazoan communities under various soil management regimes in two distinct soil types with barley as the main crop. Contrasts between resident and active communities explained 22%, 14%, 21% and 25% of the variance within the bacterial, fungal, protozoan, and metazoan communities. As the active fractions of organismal groups define the actual ecological functioning of soils, our findings underline the relevance of characterizing both resident and active pools. All four major organismal groups were affected by soil management (p < 0.01), and most taxa showed both an increased presence and an enlarged activity under the organic regime. Hence, a prolonged organic soil management not only impacts the primary decomposers, bacteria and fungi, but also major representatives of the next trophic level, protists and metazoa.
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Affiliation(s)
- Paula Harkes
- Laboratory of Nematology, Dept. Plant Sciences, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Afnan K A Suleiman
- Department Microbial Ecology, Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
- KWR Watercycle Research Institute, Groningenhaven 7, 3433, PE, Nieuwegein, The Netherlands
| | - Sven J J van den Elsen
- Laboratory of Nematology, Dept. Plant Sciences, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Johannes J de Haan
- Wageningen University & Research Open Teelten, Edelhertweg 10, Lelystad, The Netherlands
| | - Martijn Holterman
- Laboratory of Nematology, Dept. Plant Sciences, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Eiko E Kuramae
- Department Microbial Ecology, Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
| | - Johannes Helder
- Laboratory of Nematology, Dept. Plant Sciences, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
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De Tender C, Mesuere B, Van der Jeugt F, Haegeman A, Ruttink T, Vandecasteele B, Dawyndt P, Debode J, Kuramae EE. Peat substrate amended with chitin modulates the N-cycle, siderophore and chitinase responses in the lettuce rhizobiome. Sci Rep 2019; 9:9890. [PMID: 31289280 PMCID: PMC6617458 DOI: 10.1038/s41598-019-46106-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 06/19/2019] [Indexed: 11/09/2022] Open
Abstract
Chitin is a valuable peat substrate amendment by increasing lettuce growth and reducing the survival of the zoonotic pathogen Salmonella enterica on lettuce leaves. The production of chitin-catabolic enzymes (chitinases) play a crucial role and are mediated through the microbial community. A higher abundance of plant-growth promoting microorganisms and genera involved in N and chitin metabolism are present in a chitin-enriched substrate. In this study, we hypothesize that chitin addition to peat substrate stimulates the microbial chitinase production. The degradation of chitin leads to nutrient release and the production of small chitin oligomers that are related to plant growth promotion and activation of the plant's defense response. First a shotgun metagenomics approach was used to decipher the potential rhizosphere microbial functions then the nutritional content of the peat substrate was measured. Our results show that chitin addition increases chitin-catabolic enzymes, bacterial ammonium oxidizing and siderophore genes. Lettuce growth promotion can be explained by a cascade degradation of chitin to N-acetylglucosamine and eventually ammonium. The occurrence of increased ammonium oxidizing bacteria, Nitrosospira, and amoA genes results in an elevated concentration of plant-available nitrate. In addition, the increase in chitinase and siderophore genes may have stimulated the plant's systemic resistance.
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Affiliation(s)
- C De Tender
- Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Burgemeester Van Gansberghelaan 92, 9820, Merelbeke, Belgium.
- Ghent University, Department of Applied Mathematics, Computer Science and Statistics, Krijgslaan 281 S9, 9000, Ghent, Belgium.
| | - B Mesuere
- Ghent University, Department of Applied Mathematics, Computer Science and Statistics, Krijgslaan 281 S9, 9000, Ghent, Belgium
- VIB-UGent Center for Medical Biotechnology, VIB, B-9000, Ghent, Belgium
| | - F Van der Jeugt
- Ghent University, Department of Applied Mathematics, Computer Science and Statistics, Krijgslaan 281 S9, 9000, Ghent, Belgium
| | - A Haegeman
- Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Burgemeester Van Gansberghelaan 92, 9820, Merelbeke, Belgium
| | - T Ruttink
- Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Burgemeester Van Gansberghelaan 92, 9820, Merelbeke, Belgium
| | - B Vandecasteele
- Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Burgemeester Van Gansberghelaan 92, 9820, Merelbeke, Belgium
| | - P Dawyndt
- Ghent University, Department of Applied Mathematics, Computer Science and Statistics, Krijgslaan 281 S9, 9000, Ghent, Belgium
| | - J Debode
- Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Burgemeester Van Gansberghelaan 92, 9820, Merelbeke, Belgium
| | - E E Kuramae
- Netherlands Institute of Ecology, department of Microbial Ecology, Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
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Kuramae EE, Leite MFA, Suleiman AKA, Gough CM, Castillo BT, Faller L, Franklin RB, Syring J. Wood Decay Characteristics and Interspecific Interactions Control Bacterial Community Succession in Populus grandidentata (Bigtooth Aspen). Front Microbiol 2019; 10:979. [PMID: 31143163 PMCID: PMC6520631 DOI: 10.3389/fmicb.2019.00979] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 04/18/2019] [Indexed: 02/01/2023] Open
Abstract
Few studies have investigated bacterial community succession and the role of bacterial decomposition over a continuum of wood decay. Here, we identified how (i) the diversity and abundance of bacteria changed along a chronosequence of decay in Populus grandidentata (bigtooth aspen); (ii) bacterial community succession was dependent on the physical and chemical characteristics of the wood; (iii) interspecific bacterial interactions may mediate community structure. Four hundred and fifty-nine taxa were identified through Illumina sequencing of 16S rRNA amplicons from samples taken along a continuum of decay, representing standing dead trees, downed wood, and soil. Community diversity increased as decomposition progressed, peaking in the most decomposed trees. While a small proportion of taxa displayed a significant pattern in regards to decay status of the host log, many bacterial taxa followed a stochastic distribution. Changes in the water availability and chemical composition of standing dead and downed trees and soil were strongly coupled with shifts in bacterial communities. Nitrogen was a major driver of succession and nitrogen-fixing taxa of the order Rhizobiales were abundant early in decomposition. Recently downed logs shared 65% of their bacterial abundance with the microbiomes of standing dead trees while only sharing 16% with soil. As decay proceeds, bacterial communities appear to respond less to shifting resource availability and more to interspecific bacterial interactions – we report an increase in both the proportion (+9.3%) and the intensity (+62.3%) of interspecific interactions in later stages of decomposition, suggesting the emergence of a more complex community structure as wood decay progresses.
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Affiliation(s)
- Eiko E Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, Netherlands
| | - Marcio F A Leite
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, Netherlands
| | - Afnan K A Suleiman
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, Netherlands
| | - Christopher M Gough
- Department of Biology, Virginia Commonwealth University, Richmond, VA, United States
| | - Buck T Castillo
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, United States
| | - Lewis Faller
- Department of Biology, Linfield College, McMinnville, OR, United States
| | - Rima B Franklin
- Department of Biology, Virginia Commonwealth University, Richmond, VA, United States
| | - John Syring
- Department of Biology, Linfield College, McMinnville, OR, United States
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Cipriano MAP, Suleiman AKA, da Silveira APD, do Carmo JB, Kuramae EE. Bacterial community composition and diversity of two different forms of an organic residue of bioenergy crop. PeerJ 2019; 7:e6768. [PMID: 31024771 PMCID: PMC6475576 DOI: 10.7717/peerj.6768] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 03/12/2019] [Indexed: 11/20/2022] Open
Abstract
The use of residue of sugarcane ethanol industry named vinasse in fertirrigation is an established and widespread practice in Brazil. Both non-concentrated vinasse (NCV) and concentrated vinasse (CV) are used in fertirrigation, particularly to replace the potassium fertilizer. Although studies on the chemical and organic composition of vinasse and their impact on nitrous oxide emissions when applied in soil have been carried out, no studies have evaluated the microbial community composition and diversity in different forms of vinasse. We assessed the bacterial community composition of NCV and CV by non-culturable and culturable approaches. The non-culturable bacterial community was assessed by next generation sequencing of the 16S rRNA gene and culturable community by isolation of bacterial strains and molecular and biochemical characterization. Additionally, we assessed in the bacterial strains the presence of genes of nitrogen cycle nitrification and denitrification pathways. The microbial community based on 16S rRNA sequences of NCV was overrepresented by Bacilli and Negativicutes while CV was mainly represented by Bacilli class. The isolated strains from the two types of vinasse belong to class Bacilli, similar to Lysinibacillus, encode for nirK gene related to denitrification pathway. This study highlights the bacterial microbial composition particularly in CV what residue is currently recycled and recommended as a sustainable practice in sugarcane cultivation in the tropics.
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Affiliation(s)
| | - Afnan K A Suleiman
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
| | | | | | - Eiko E Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
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Cassman NA, Soares JR, Pijl A, Lourenço KS, van Veen JA, Cantarella H, Kuramae EE. Nitrification inhibitors effectively target N 2 O-producing Nitrosospira spp. in tropical soil. Environ Microbiol 2019; 21:1241-1254. [PMID: 30735001 PMCID: PMC6850170 DOI: 10.1111/1462-2920.14557] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 01/09/2019] [Accepted: 02/04/2019] [Indexed: 01/01/2023]
Abstract
The nitrification inhibitors (NIs) 3,4-dimethylpyrazole (DMPP) and dicyandiamide (DCD) can effectively reduce N2 O emissions; however, which species are targeted and the effect of these NIs on the microbial nitrifier community is still unclear. Here, we identified the ammonia oxidizing bacteria (AOB) species linked to N2 O emissions and evaluated the effects of urea and urea with DCD and DMPP on the nitrifying community in a 258 day field experiment under sugarcane. Using an amoA AOB amplicon sequencing approach and mining a previous dataset of 16S rRNA sequences, we characterized the most likely N2 O-producing AOB as a Nitrosospira spp. and identified Nitrosospira (AOB), Nitrososphaera (archaeal ammonia oxidizer) and Nitrospira (nitrite-oxidizer) as the most abundant, present nitrifiers. The fertilizer treatments had no effect on the alpha and beta diversities of the AOB communities. Interestingly, we found three clusters of co-varying variables with nitrifier operational taxonomic units (OTUs): the N2 O-producing AOB Nitrosospira with N2 O, NO3 - , NH4 + , water-filled pore space (WFPS) and pH; AOA Nitrososphaera with NO3 - , NH4 + and pH; and AOA Nitrososphaera and NOB Nitrospira with NH4 + , which suggests different drivers. These results support the co-occurrence of non-N2 O-producing Nitrososphaera and Nitrospira in the unfertilized soils and the promotion of N2 O-producing Nitrosospira under urea fertilization. Further, we suggest that DMPP is a more effective NI than DCD in tropical soil under sugarcane.
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Affiliation(s)
- Noriko A. Cassman
- Department of Microbial EcologyNetherlands Institute for Ecology NIOO‐KNAWWageningenNetherlands
| | - Johnny R. Soares
- Department of Microbial EcologyNetherlands Institute for Ecology NIOO‐KNAWWageningenNetherlands
- Soil Sciences and Fertility, Soil and Environmental Resources Center, Agronomic Institute of CampinasP.O. Box 28, 13012‐970, CampinasSPBrazil
| | - Agata Pijl
- Department of Microbial EcologyNetherlands Institute for Ecology NIOO‐KNAWWageningenNetherlands
| | - Késia S. Lourenço
- Department of Microbial EcologyNetherlands Institute for Ecology NIOO‐KNAWWageningenNetherlands
- Soil Sciences and Fertility, Soil and Environmental Resources Center, Agronomic Institute of CampinasP.O. Box 28, 13012‐970, CampinasSPBrazil
| | - Johannes A. van Veen
- Department of Microbial EcologyNetherlands Institute for Ecology NIOO‐KNAWWageningenNetherlands
| | - Heitor Cantarella
- Soil Sciences and Fertility, Soil and Environmental Resources Center, Agronomic Institute of CampinasP.O. Box 28, 13012‐970, CampinasSPBrazil
| | - Eiko E. Kuramae
- Department of Microbial EcologyNetherlands Institute for Ecology NIOO‐KNAWWageningenNetherlands
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Lupatini M, Suleiman AKA, Jacques RJS, Lemos LN, Pylro VS, Van Veen JA, Kuramae EE, Roesch LFW. Moisture Is More Important than Temperature for Assembly of Both Potentially Active and Whole Prokaryotic Communities in Subtropical Grassland. Microb Ecol 2019; 77:460-470. [PMID: 30607437 DOI: 10.1007/s00248-018-1310-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 12/18/2018] [Indexed: 06/09/2023]
Abstract
Moisture and temperature play important roles in the assembly and functioning of prokaryotic communities in soil. However, how moisture and temperature regulate the function of niche- versus neutral-based processes during the assembly of these communities has not been examined considering both the total microbial community and the sole active portion with potential for growth in native subtropical grassland. We set up a well-controlled microcosm-based experiment to investigate the individual and combined effects of moisture and temperature on soil prokaryotic communities by simulating subtropical seasons in grassland. The prokaryotic populations with potential for growth and the total prokaryotic community were assessed by 16S rRNA transcript and 16S rRNA gene analyses, respectively. Moisture was the major factor influencing community diversity and structure, with a considerable effect of this factor on the total community. The prokaryotic populations with potential for growth and the total communities were influenced by the same assembly rules, with the niche-based mechanism being more influential in communities under dry condition. Our results provide new information regarding moisture and temperature in microbial communities of soil and elucidate how coexisting prokaryotic populations, under different physiological statuses, are shaped in native subtropical grassland soil.
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Affiliation(s)
- Manoeli Lupatini
- Departamento de Solos, Programa de Pós-graduação em Ciência do Solo, Universidade Federal de Santa Maria, Roraima, 1000, Santa Maria, 97105-900, Brazil
| | - Afnan K A Suleiman
- Departamento de Solos, Programa de Pós-graduação em Ciência do Solo, Universidade Federal de Santa Maria, Roraima, 1000, Santa Maria, 97105-900, Brazil
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
| | - Rodrigo J S Jacques
- Departamento de Solos, Programa de Pós-graduação em Ciência do Solo, Universidade Federal de Santa Maria, Roraima, 1000, Santa Maria, 97105-900, Brazil
| | - Leandro N Lemos
- Laboratório de Biologia Molecular e Celular, Centro de Energia Nuclear na Agricultura CENA, Universidade de São Paulo USP, Piracicaba, SP, Brazil
| | - Victor S Pylro
- Department of Biology, Federal University of Lavras - UFLA, Lavras, Minas Gerais, Brazil
| | - Johannes A Van Veen
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
| | - Eiko E Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
| | - Luiz F W Roesch
- Centro Interdisciplinar de Pesquisas em Biotecnologia - CIP-Biotec, Universidade Federal do Pampa, Campus São Gabriel, Avenida Antonio Trilha, 1847, São Gabriel, 97300-000, Brazil.
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Lupatini M, Korthals GW, Roesch LFW, Kuramae EE. Long-term farming systems modulate multi-trophic responses. Sci Total Environ 2019; 646:480-490. [PMID: 30056235 DOI: 10.1016/j.scitotenv.2018.07.323] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 07/12/2018] [Accepted: 07/23/2018] [Indexed: 06/08/2023]
Abstract
Soil microbiome and multi-trophic relationships are essential for the stability and functioning of agroecosystems. However, little is known about how farming systems and alternative methods for controlling plant pathogens modulate microbial communities, soil mesofauna and plant productivity. In this study, we assessed the composition of eukaryotic microbial groups using a high-throughput sequencing approach (18S rRNA gene marker), the populations of parasitic and free-living nematodes, plant productivity and their inter-relationships in long-term conventional and organic farming systems. The diversity of the fungal community increased in the organic farming system compared to the conventional farming system, whereas the diversity of the protist community was similar between the two farming systems. Compared to conventional farming, organic farming increased the population of free-living nematodes and suppressed plant parasitic nematodes belonging to Meloidogynidae and Pratylenchidae. Fungal diversity and community structure appeared to be related to nematode suppression in the system receiving organic fertilizer, which was characterized by component microbial groups known to be involved in the suppression of soil pathogens. Unraveling the microbiome and multi-trophic interactions in different farming systems may permit the management of the soil environment toward more sustainable control of plant pathogens.
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Affiliation(s)
- Manoeli Lupatini
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, the Netherlands
| | - Gerard W Korthals
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, the Netherlands
| | - Luiz F W Roesch
- Centro Interdisciplinar de Pesquisas em Biotecnologia, Universidade Federal do Pampa (UNIPAMPA), Avenida Antônio Trilha 1847, 97300-000 São Gabriel, Brazil
| | - Eiko E Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, the Netherlands.
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36
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Li X, Jousset A, de Boer W, Carrión VJ, Zhang T, Wang X, Kuramae EE. Legacy of land use history determines reprogramming of plant physiology by soil microbiome. ISME J 2018; 13:738-751. [PMID: 30368524 PMCID: PMC6461838 DOI: 10.1038/s41396-018-0300-0] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 08/25/2018] [Accepted: 10/04/2018] [Indexed: 01/01/2023]
Abstract
Microorganisms associated with roots are thought to be part of the so-called extended plant phenotypes with roles in the acquisition of nutrients, production of growth hormones, and defense against diseases. Since the crops selectively enrich most rhizosphere microbes out of the bulk soil, we hypothesized that changes in the composition of bulk soil communities caused by agricultural management affect the extended plant phenotype. In the current study, we performed shotgun metagenome sequencing of the rhizosphere microbiome of the peanut (Arachis hypogaea) and metatranscriptome analysis of the roots of peanut plants grown in the soil with different management histories, peanut monocropping and crop rotation. We found that the past planting record had a significant effect on the assembly of the microbial community in the peanut rhizosphere, indicating a soil memory effect. Monocropping resulted in a reduction of the rhizosphere microbial diversity, an enrichment of several rare species, and a reduced representation of traits related to plant performance, such as nutrients metabolism and phytohormone biosynthesis. Furthermore, peanut plants in monocropped soil exhibited a significant reduction in growth coinciding with a down-regulation of genes related to hormone production, mainly auxin and cytokinin, and up-regulation of genes related to the abscisic acid, salicylic acid, jasmonic acid, and ethylene pathways. These findings suggest that land use history affects crop rhizosphere microbiomes and plant physiology.
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Affiliation(s)
- Xiaogang Li
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China.,Department of Microbial Ecology, Netherlands Institute of Ecology, NIOO-KNAW, Wageningen, 6708 PB, The Netherlands
| | - Alexandre Jousset
- Institute for Environmental Biology, Ecology & Biodiversity, Utrecht University, Utrecht, 3584 CH, The Netherlands
| | - Wietse de Boer
- Department of Microbial Ecology, Netherlands Institute of Ecology, NIOO-KNAW, Wageningen, 6708 PB, The Netherlands.,Soil Biology Group, Wageningen University, Wageningen, 6708 PB, The Netherlands
| | - Víctor J Carrión
- Department of Microbial Ecology, Netherlands Institute of Ecology, NIOO-KNAW, Wageningen, 6708 PB, The Netherlands
| | - Taolin Zhang
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Xingxiang Wang
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China. .,Experimental Station of Red Soil, Chinese Academy of Sciences, Yingtan, 335211, China.
| | - Eiko E Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology, NIOO-KNAW, Wageningen, 6708 PB, The Netherlands
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37
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Cassman NA, Lourenço KS, do Carmo JB, Cantarella H, Kuramae EE. Correction to: Genome-resolved metagenomics of sugarcane vinasse bacteria. Biotechnol Biofuels 2018; 11:270. [PMID: 30305843 PMCID: PMC6169111 DOI: 10.1186/s13068-018-1254-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
[This corrects the article DOI: 10.1186/s13068-018-1036-9.].
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Affiliation(s)
- Noriko A. Cassman
- Department of Microbial Ecology, Netherlands Institute of Ecology NIOO-KNAW, Wageningen, Netherlands
| | - Késia S. Lourenço
- Department of Microbial Ecology, Netherlands Institute of Ecology NIOO-KNAW, Wageningen, Netherlands
- Soils and Environmental Resources Center, Agronomic Institute of Campinas, P.O. Box 28, Campinas, SP 13012‑970 Brazil
| | - Janaína B. do Carmo
- Environmental Science Department, Federal University of São Carlos, Sorocaba, SP 18052‑780 Brazil
| | - Heitor Cantarella
- Soils and Environmental Resources Center, Agronomic Institute of Campinas, P.O. Box 28, Campinas, SP 13012‑970 Brazil
| | - Eiko E. Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology NIOO-KNAW, Wageningen, Netherlands
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38
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Lourenço KS, Suleiman AKA, Pijl A, van Veen JA, Cantarella H, Kuramae EE. Resilience of the resident soil microbiome to organic and inorganic amendment disturbances and to temporary bacterial invasion. Microbiome 2018; 6:142. [PMID: 30103819 PMCID: PMC6090642 DOI: 10.1186/s40168-018-0525-1] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 08/01/2018] [Indexed: 05/20/2023]
Abstract
BACKGROUND Vinasse, a by-product of sugarcane ethanol production, is recycled by sugarcane plantations as a fertilizer due to its rich nutrient content. However, the impacts of the chemical and microbial composition of vinasse on soil microbiome dynamics are unknown. Here, we evaluate the recovery of the native soil microbiome after multiple disturbances caused by the application of organic vinasse residue, inorganic nitrogen, or a combination of both during the sugarcane crop-growing season (389 days). Additionally, we evaluated the resistance of the resident soil microbial community to the vinasse microbiome. RESULTS Vinasse applied alone or 30 days prior to N resulted in similar changes in the soil microbial community. Furthermore, the impact of the application of vinasse together with N fertilizer on the soil microbial community differed from that of N fertilizer alone. Organic vinasse is a source of microbes, nutrients, and organic matter, and the combination of these factors drove the changes in the resident soil microbial community. However, these changes were restricted to a short period of time due to the capacity of the soil community to recover. The invasive bacteria present in the vinasse microbiome were unable to survive in the soil conditions and disappeared after 31 days, with the exception of the Acetobacteraceae (native in the soil) and Lactobacillaceae families. CONCLUSION Our analysis showed that the resident soil microbial community was not resistant to vinasse and inorganic N application but was highly resilient.
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Affiliation(s)
- Késia Silva Lourenço
- Microbial Ecology Department, Netherlands Institute of Ecology (NIOO), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
- Soils and Environmental Resources Center, Agronomic Institute of Campinas (IAC), Av. Barão de Itapura 1481, Campinas, SP, 13020-902, Brazil
- Institute of Biology Leiden, Leiden University, Leiden, Netherlands
| | - Afnan K A Suleiman
- Microbial Ecology Department, Netherlands Institute of Ecology (NIOO), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
| | - A Pijl
- Microbial Ecology Department, Netherlands Institute of Ecology (NIOO), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
| | - J A van Veen
- Microbial Ecology Department, Netherlands Institute of Ecology (NIOO), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
- Institute of Biology Leiden, Leiden University, Leiden, Netherlands
| | - H Cantarella
- Soils and Environmental Resources Center, Agronomic Institute of Campinas (IAC), Av. Barão de Itapura 1481, Campinas, SP, 13020-902, Brazil
| | - E E Kuramae
- Microbial Ecology Department, Netherlands Institute of Ecology (NIOO), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands.
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39
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Schlemper TR, Dimitrov MR, Silva Gutierrez FAO, van Veen JA, Silveira APD, Kuramae EE. Effect of Burkholderia tropica and Herbaspirillum frisingense strains on sorghum growth is plant genotype dependent. PeerJ 2018; 6:e5346. [PMID: 30065892 PMCID: PMC6063206 DOI: 10.7717/peerj.5346] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Accepted: 07/06/2018] [Indexed: 01/23/2023] Open
Abstract
Sorghum is a multipurpose crop that is cultivated worldwide. Plant growth-promoting bacteria (PGPB) have important roles in enhancing sorghum biomass and nutrient uptake and suppressing plant pathogens. The aim of this research was to test the effects of the endophytic bacterial species Kosakonia radicincitans strain IAC/BECa 99, Enterobacter asburiae strain IAC/BECa 128, Pseudomonas fluorescens strain IAC/BECa 141, Burkholderia tropica strain IAC/BECa 135 and Herbaspirillum frisingense strain IAC/BECa 152 on the growth and root architecture of four sorghum cultivars (SRN-39, Shanqui-Red, BRS330, BRS509), with different uses and strigolactone profiles. We hypothesized that the different bacterial species would trigger different growth plant responses in different sorghum cultivars. Burkholderia tropica and H. frisingense significantly increased the plant biomass of cultivars SRN-39 and BRS330. Moreover, cultivar BRS330 inoculated with either strain displayed isolates significant decrease in average root diameter. This study shows that Burkholderia tropica strain IAC/BECa 135 and H. frisingense strain IAC/BECa 152 are promising PGPB strains for use as inocula for sustainable sorghum cultivation.
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Affiliation(s)
- Thiago R Schlemper
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands.,Leiden University, Institute of Biology, Leiden, The Netherlands
| | - Maurício R Dimitrov
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | | | - Johannes A van Veen
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Adriana P D Silveira
- Center of Soil and Environmental Resources, Agronomic Institute of Campinas (IAC), Campinas, Sao Paulo, Brazil
| | - Eiko E Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
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40
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Costa OYA, Raaijmakers JM, Kuramae EE. Microbial Extracellular Polymeric Substances: Ecological Function and Impact on Soil Aggregation. Front Microbiol 2018; 9:1636. [PMID: 30083145 PMCID: PMC6064872 DOI: 10.3389/fmicb.2018.01636] [Citation(s) in RCA: 364] [Impact Index Per Article: 60.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 06/30/2018] [Indexed: 11/15/2022] Open
Abstract
A wide range of microorganisms produce extracellular polymeric substances (EPS), highly hydrated polymers that are mainly composed of polysaccharides, proteins, and DNA. EPS are fundamental for microbial life and provide an ideal environment for chemical reactions, nutrient entrapment, and protection against environmental stresses such as salinity and drought. Microbial EPS can enhance the aggregation of soil particles and benefit plants by maintaining the moisture of the environment and trapping nutrients. In addition, EPS have unique characteristics, such as biocompatibility, gelling, and thickening capabilities, with industrial applications. However, despite decades of research on the industrial potential of EPS, only a few polymers are widely used in different areas, especially in agriculture. This review provides an overview of current knowledge on the ecological functions of microbial EPSs and their application in agricultural soils to improve soil particle aggregation, an important factor for soil structure, health, and fertility.
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Affiliation(s)
- Ohana Y. A. Costa
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
- Institute of Biology, Leiden University, Leiden, Netherlands
| | - Jos M. Raaijmakers
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
- Institute of Biology, Leiden University, Leiden, Netherlands
| | - Eiko E. Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
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41
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Schlemper TR, van Veen JA, Kuramae EE. Co-Variation of Bacterial and Fungal Communities in Different Sorghum Cultivars and Growth Stages is Soil Dependent. Microb Ecol 2018; 76:205-214. [PMID: 29147973 PMCID: PMC6061463 DOI: 10.1007/s00248-017-1108-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 11/03/2017] [Indexed: 05/29/2023]
Abstract
Rhizosphere microbial community composition can be influenced by different biotic and abiotic factors. We investigated the composition and co-variation of rhizosphere bacterial and fungal communities from two sorghum genotypes (BRS330 and SRN-39) in three different plant growth stages (emergence of the second leaf, (day10), vegetative to reproductive differentiation point (day 35), and at the last visible emerged leaf (day 50)) in two different soil types, Clue field (CF) and Vredepeel (VD). We observed that either bacterial or fungal community had its composition stronger influenced by soil followed by plant growth stage and cultivar. However, the influence of plant growth stage was higher on fungal community composition than on the bacterial community composition. Furthermore, we showed that sorghum rhizosphere bacterial and fungal communities can affect each other's composition and structure. The decrease in relative abundance of the fungus genus Gibberella over plant growth stages was followed by decrease of the bacterial families Oxalobacteracea and Sphingobacteriacea. Although cultivar effect was not the major responsible for bacterial and fungal community composition, cultivar SRN-39 showed to promote a stronger co-variance between bacterial and fungal communities.
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Affiliation(s)
- Thiago R Schlemper
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
- Department of Biology, Leiden University, Leiden, The Netherlands
| | - Johannes A van Veen
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Eiko E Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands.
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42
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Armada E, Leite MFA, Medina A, Azcón R, Kuramae EE. Native bacteria promote plant growth under drought stress condition without impacting the rhizomicrobiome. FEMS Microbiol Ecol 2018; 94:4996783. [DOI: 10.1093/femsec/fiy092] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 05/13/2018] [Indexed: 12/20/2022] Open
Affiliation(s)
- Elisabeth Armada
- Estación Experimental del Zaidín, CSIC, Departamento de Microbiología del Suelo y Sistemas Simbióticos, Prof. Albareda 1, 18008, Granada, Spain
| | - Márcio F A Leite
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Microbial Ecology, Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
- Leiden University, Department of Biology, Leiden, 2311 EZ, The Netherlands
- Maranhão State University (UEMA), department of Agroecology, São Luís, Brazil
| | - Almudena Medina
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Microbial Ecology, Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
| | - Rosario Azcón
- Estación Experimental del Zaidín, CSIC, Departamento de Microbiología del Suelo y Sistemas Simbióticos, Prof. Albareda 1, 18008, Granada, Spain
| | - Eiko E Kuramae
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Microbial Ecology, Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
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43
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Lourenço KS, Cassman NA, Pijl AS, van Veen JA, Cantarella H, Kuramae EE. Nitrosospira sp. Govern Nitrous Oxide Emissions in a Tropical Soil Amended With Residues of Bioenergy Crop. Front Microbiol 2018; 9:674. [PMID: 29692763 PMCID: PMC5902487 DOI: 10.3389/fmicb.2018.00674] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Accepted: 03/22/2018] [Indexed: 11/13/2022] Open
Abstract
Organic vinasse, a residue produced during bioethanol production, increases nitrous oxide (N2O) emissions when applied with inorganic nitrogen (N) fertilizer in soil. The present study investigated the role of the ammonia-oxidizing bacteria (AOB) community on the N2O emissions in soils amended with organic vinasse (CV: concentrated and V: non-concentrated) plus inorganic N fertilizer. Soil samples and N2O emissions were evaluated at 11, 19, and 45 days after fertilizer application, and the bacterial and archaea gene (amoA) encoding the ammonia monooxygenase enzyme, bacterial denitrifier (nirK, nirS, and nosZ) genes and total bacteria were quantified by real time PCR. We also employed a deep amoA amplicon sequencing approach to evaluate the effect of treatment on the community structure and diversity of the soil AOB community. Both vinasse types applied with inorganic N application increased the total N2O emissions and the abundance of AOB. Nitrosospira sp. was the dominant AOB in the soil and was correlated with N2O emissions. However, the diversity and the community structure of AOB did not change with vinasse and inorganic N fertilizer amendment. The results highlight the importance of residues and fertilizer management in sustainable agriculture and can be used as a reference and an input tool to determine good management practices for organic fertilization.
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Affiliation(s)
- Késia S Lourenço
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, Netherlands.,Soils and Environmental Resources Center, Agronomic Institute of Campinas, Campinas, Brazil.,Institute of Biology Leiden, Leiden University, Leiden, Netherlands
| | - Noriko A Cassman
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, Netherlands.,Institute of Biology Leiden, Leiden University, Leiden, Netherlands
| | - Agata S Pijl
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, Netherlands
| | - Johannes A van Veen
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, Netherlands.,Institute of Biology Leiden, Leiden University, Leiden, Netherlands
| | - Heitor Cantarella
- Soils and Environmental Resources Center, Agronomic Institute of Campinas, Campinas, Brazil
| | - Eiko E Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, Netherlands
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44
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Benevenuto J, Teixeira-Silva NS, Kuramae EE, Croll D, Monteiro-Vitorello CB. Comparative Genomics of Smut Pathogens: Insights From Orphans and Positively Selected Genes Into Host Specialization. Front Microbiol 2018; 9:660. [PMID: 29681893 PMCID: PMC5897528 DOI: 10.3389/fmicb.2018.00660] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 03/21/2018] [Indexed: 12/20/2022] Open
Abstract
Host specialization is a key evolutionary process for the diversification and emergence of new pathogens. However, the molecular determinants of host range are poorly understood. Smut fungi are biotrophic pathogens that have distinct and narrow host ranges based on largely unknown genetic determinants. Hence, we aimed to expand comparative genomics analyses of smut fungi by including more species infecting different hosts and to define orphans and positively selected genes to gain further insights into the genetics basis of host specialization. We analyzed nine lineages of smut fungi isolated from eight crop and non-crop hosts: maize, barley, sugarcane, wheat, oats, Zizania latifolia (Manchurian rice), Echinochloa colona (a wild grass), and Persicaria sp. (a wild dicot plant). We assembled two new genomes: Ustilago hordei (strain Uhor01) isolated from oats and U. tritici (strain CBS 119.19) isolated from wheat. The smut genomes were of small sizes, ranging from 18.38 to 24.63 Mb. U. hordei species experienced genome expansions due to the proliferation of transposable elements and the amount of these elements varied among the two strains. Phylogenetic analysis confirmed that Ustilago is not a monophyletic genus and, furthermore, detected misclassification of the U. tritici specimen. The comparison between smut pathogens of crop and non-crop hosts did not reveal distinct signatures, suggesting that host domestication did not play a dominant role in shaping the evolution of smuts. We found that host specialization in smut fungi likely has a complex genetic basis: different functional categories were enriched in orphans and lineage-specific selected genes. The diversification and gain/loss of effector genes are probably the most important determinants of host specificity.
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Affiliation(s)
- Juliana Benevenuto
- Microbial Genetics Laboratory, Department of Genetics, University of São Paulo/Luiz de Queiroz College of Agriculture (USP/ESALQ), Piracicaba, Brazil
| | - Natalia S. Teixeira-Silva
- Microbial Genetics Laboratory, Department of Genetics, University of São Paulo/Luiz de Queiroz College of Agriculture (USP/ESALQ), Piracicaba, Brazil
| | - Eiko E. Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel (UNINE), Neuchâtel, Switzerland
| | - Claudia B. Monteiro-Vitorello
- Microbial Genetics Laboratory, Department of Genetics, University of São Paulo/Luiz de Queiroz College of Agriculture (USP/ESALQ), Piracicaba, Brazil
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45
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Cassman NA, Lourenço KS, do Carmo JB, Cantarella H, Kuramae EE. Genome-resolved metagenomics of sugarcane vinasse bacteria. Biotechnol Biofuels 2018; 11:48. [PMID: 29483941 PMCID: PMC5822648 DOI: 10.1186/s13068-018-1036-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 01/30/2018] [Indexed: 05/28/2023]
Abstract
BACKGROUND The production of 1 L of ethanol from sugarcane generates up to 12 L of vinasse, which is a liquid waste containing an as-yet uncharacterized microbial assemblage. Most vinasse is destined for use as a fertilizer on the sugarcane fields because of the high organic and K content; however, increased N2O emissions have been observed when vinasse is co-applied with inorganic N fertilizers. Here we aimed to characterize the microbial assemblage of vinasse to determine the gene potential of vinasse microbes for contributing to negative environmental effects during fertirrigation and/or to the obstruction of bioethanol fermentation. RESULTS We measured chemical characteristics and extracted total DNA from six vinasse batches taken over 1.5 years from a bioethanol and sugar mill in Sao Paulo State. The vinasse microbial assemblage was characterized by low alpha diversity with 5-15 species across the six vinasses. The core genus was Lactobacillus. The top six represented bacterial genera across the samples were Lactobacillus, Megasphaera and Mitsuokella (Phylum Firmicutes, 35-97% of sample reads); Arcobacter and Alcaligenes (Phylum Proteobacteria, 0-40%); Dysgonomonas (Phylum Bacteroidetes, 0-53%); and Bifidobacterium (Phylum Actinobacteria, 0-18%). Potential genes for denitrification but not nitrification were identified in the vinasse metagenomes, with putative nirK and nosZ genes the most represented. Binning resulted in 38 large bins with between 36.0 and 99.3% completeness, and five small mobile element bins. Of the large bins, 53% could be classified at the phylum level as Firmicutes, 15% as Proteobacteria, 13% as unknown phyla, 13% as Bacteroidetes and 6% as Actinobacteria. The large bins spanned a range of potential denitrifiers; moreover, the genetic repertoires of all the large bins included the presence of genes involved in acetate, CO2, ethanol, H2O2, and lactose metabolism; for many of the large bins, genes related to the metabolism of mannitol, xylose, butyric acid, cellulose, sucrose, "3-hydroxy" fatty acids and antibiotic resistance were present based on the annotations. In total, 21 vinasse bacterial draft genomes were submitted to the genome repository. CONCLUSIONS Identification of the gene repertoires of vinasse bacteria and assemblages supported the idea that organic carbon and nitrogen present in vinasse together with microbiological variation of vinasse might lead to varying patterns of N2O emissions during fertirrigation. Furthermore, we uncovered draft genomes of novel strains of known bioethanol contaminants, as well as draft genomes unknown at the phylum level. This study will aid efforts to improve bioethanol production efficiency and sugarcane agriculture sustainability.
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Affiliation(s)
- Noriko A. Cassman
- Department of Microbial Ecology, Netherlands Institute of Ecology NIOO-KNAW, Wageningen, Netherlands
| | - Késia S. Lourenço
- Department of Microbial Ecology, Netherlands Institute of Ecology NIOO-KNAW, Wageningen, Netherlands
- Soils and Environmental Resources Center, Agronomic Institute of Campinas, P.O. Box 28, Campinas, SP 13012-970 Brazil
| | - Janaína B. do Carmo
- Environmental Science Department, Federal University of São Carlos, Sorocaba, SP 18052-780 Brazil
| | - Heitor Cantarella
- Soils and Environmental Resources Center, Agronomic Institute of Campinas, P.O. Box 28, Campinas, SP 13012-970 Brazil
| | - Eiko E. Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology NIOO-KNAW, Wageningen, Netherlands
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Schlemper TR, Leite MFA, Lucheta AR, Shimels M, Bouwmeester HJ, van Veen JA, Kuramae EE. Rhizobacterial community structure differences among sorghum cultivars in different growth stages and soils. FEMS Microbiol Ecol 2017; 93:4002672. [PMID: 28830071 DOI: 10.1093/femsec/fix096] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 07/20/2017] [Indexed: 11/14/2022] Open
Abstract
Plant genotype selects the rhizosphere microbiome. The success of plant-microbe interactions is dependent on factors that directly or indirectly influence the plant rhizosphere microbial composition. We investigated the rhizosphere bacterial community composition of seven different sorghum cultivars in two different soil types (abandoned (CF) and agricultural (VD)). The rhizosphere bacterial community was evaluated at four different plant growth stages: emergence of the second (day 10) and third leaves (day 20), the transition between the vegetative and reproductive stages (day 35), and the emergence of the last visible leaf (day 50). At early stages (days 10 and 20), the sorghum rhizosphere bacterial community composition was mainly driven by soil type, whereas at late stages (days 35 and 50), the bacterial community composition was also affected by the sorghum genotype. Although this effect of sorghum genotype was small, different sorghum cultivars assembled significantly different bacterial community compositions. In CF soil, the striga-resistant cultivar had significantly higher relative abundances of Acidobacteria GP1, Burkholderia, Cupriavidus (Burkholderiaceae), Acidovorax and Albidiferax (Comamonadaceae) than the other six cultivars. This study is the first to simultaneously investigate the contributions of plant genotype, plant growth stage and soil type in shaping sorghum rhizosphere bacterial community composition.
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Affiliation(s)
- Thiago R Schlemper
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Microbial Ecology, 6708 PB Wageningen, Netherlands.,Department of Biology, Leiden University, 2333 BE Leiden, The Netherlands
| | - Márcio F A Leite
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Microbial Ecology, 6708 PB Wageningen, Netherlands.,Department of Biology, Leiden University, 2333 BE Leiden, The Netherlands.,Department of Agroecology, Maranhão State University, 65055-970 São Luis, Brazil
| | - Adriano R Lucheta
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Microbial Ecology, 6708 PB Wageningen, Netherlands
| | - Mahdere Shimels
- Laboratory of Plant Physiology, Wageningen University, 6700 HB Wageningen, The Netherlands
| | - Harro J Bouwmeester
- Plant Hormone Biology Group, Swammerdam Institute for Life Sciences, University of Amsterdam (UVA), 1098 XH Amsterdam, The Netherlands
| | - Johannes A van Veen
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Microbial Ecology, 6708 PB Wageningen, Netherlands.,Department of Biology, Leiden University, 2333 BE Leiden, The Netherlands
| | - Eiko E Kuramae
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Microbial Ecology, 6708 PB Wageningen, Netherlands
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47
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Kip N, Jansen S, Leite MFA, de Hollander M, Afanasyev M, Kuramae EE, Veen JAV. Methanogens predominate in natural corrosion protective layers on metal sheet piles. Sci Rep 2017; 7:11899. [PMID: 28928457 PMCID: PMC5605657 DOI: 10.1038/s41598-017-11244-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 08/16/2017] [Indexed: 11/09/2022] Open
Abstract
Microorganisms are able to cause, but also to inhibit or protect against corrosion. Corrosion inhibition by microbial processes may be due to the formation of mineral deposition layers on metal objects. Such deposition layers have been found in archaeological studies on ancient metal objects, buried in soil, which were hardly corroded. Recent field investigations showed that natural mineral deposition layers can be found on sheet piles in soil. We investigated the microbial communities of these deposition layers and the adjacent soil. Our data, from five different sampling sites, all show striking differences between microbial communities of the deposition layer versus the adjacent soil over the depth profile. Bacterial species dominated in top soil while archaeal sequences increased in abundance with depth. All mineral deposition layers from the steel surface were dominated by Euryarchaeota, of which almost all sequences were phylogenetically related with the Methanobacteria genus. The mineral layer consisted of carbonate precipitates. Based on 16S rDNA gene sequencing data we hypothesize that the methanogens directly extract electrons from the metal surface, thereby, initially inducing mild corrosion, but simultaneously, inducing carbonate precipitation. This, will cause encrustation of the archaea, which drastically slow down their activity and create a natural protective layer against further corrosion.
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Affiliation(s)
- Nardy Kip
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
| | - Stefan Jansen
- Deltares, Princetonlaan 6, 3584 CB, Utrecht, The Netherlands
| | - Marcio F A Leite
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
| | - Mattias de Hollander
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
| | - Michael Afanasyev
- Department of Geoscience & Engineering, Delft University of Technology, Stevinweg 1, 2628 CN, Delft, The Netherlands
| | - Eiko E Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
| | - Johannes A Van Veen
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands.
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48
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Leite MFA, Pan Y, Bloem J, Berge HT, Kuramae EE. Organic nitrogen rearranges both structure and activity of the soil-borne microbial seedbank. Sci Rep 2017; 7:42634. [PMID: 28198425 PMCID: PMC5309777 DOI: 10.1038/srep42634] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 01/13/2017] [Indexed: 02/05/2023] Open
Abstract
Use of organic amendments is a valuable strategy for crop production. However, it remains unclear how organic amendments shape both soil microbial community structure and activity, and how these changes impact nutrient mineralization rates. We evaluated the effect of various organic amendments, which range in Carbon/Nitrogen (C/N) ratio and degradability, on the soil microbiome in a mesocosm study at 32, 69 and 132 days. Soil samples were collected to determine community structure (assessed by 16S and 18S rRNA gene sequences), microbial biomass (fungi and bacteria), microbial activity (leucine incorporation and active hyphal length), and carbon and nitrogen mineralization rates. We considered the microbial soil DNA as the microbial seedbank. High C/N ratio favored fungal presence, while low C/N favored dominance of bacterial populations. Our results suggest that organic amendments shape the soil microbial community structure through a feedback mechanism by which microbial activity responds to changing organic inputs and rearranges composition of the microbial seedbank. We hypothesize that the microbial seedbank composition responds to changing organic inputs according to the resistance and resilience of individual species, while changes in microbial activity may result in increases or decreases in availability of various soil nutrients that affect plant nutrient uptake.
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Affiliation(s)
- Márcio F A Leite
- Netherlands Institute of Ecology (NIOO/KNAW), Department of Microbial Ecology, Wageningen, The Netherlands.,Agroecology Program of Maranhão State University - UEMA, São Luís - MA, Brazil
| | - Yao Pan
- Netherlands Institute of Ecology (NIOO/KNAW), Department of Microbial Ecology, Wageningen, The Netherlands
| | | | - Hein Ten Berge
- Plant Research International, Wageningen UR, The Netherlands
| | - Eiko E Kuramae
- Netherlands Institute of Ecology (NIOO/KNAW), Department of Microbial Ecology, Wageningen, The Netherlands
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49
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Dimitrov MR, Veraart AJ, de Hollander M, Smidt H, van Veen JA, Kuramae EE. Successive DNA extractions improve characterization of soil microbial communities. PeerJ 2017; 5:e2915. [PMID: 28168105 PMCID: PMC5291099 DOI: 10.7717/peerj.2915] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 12/15/2016] [Indexed: 01/21/2023] Open
Abstract
Currently, characterization of soil microbial communities relies heavily on the use of molecular approaches. Independently of the approach used, soil DNA extraction is a crucial step, and success of downstream procedures will depend on how well DNA extraction was performed. Often, studies describing and comparing soil microbial communities are based on a single DNA extraction, which may not lead to a representative recovery of DNA from all organisms present in the soil. The use of successive DNA extractions might improve soil microbial characterization, but the benefit of this approach has only been limitedly studied. To determine whether successive DNA extractions of the same soil sample would lead to different observations in terms of microbial abundance and community composition, we performed three successive extractions, with two widely used commercial kits, on a range of clay and sandy soils. Successive extractions increased DNA yield considerably (1-374%), as well as total bacterial and fungal abundances in most of the soil samples. Analysis of the 16S and 18S ribosomal RNA genes using 454-pyrosequencing, revealed that microbial community composition (taxonomic groups) observed in the successive DNA extractions were similar. However, successive DNA extractions did reveal several additional microbial groups. For some soil samples, shifts in microbial community composition were observed, mainly due to shifts in relative abundance of a number of microbial groups. Our results highlight that performing successive DNA extractions optimize DNA yield, and can lead to a better picture of overall community composition.
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Affiliation(s)
- Mauricio R Dimitrov
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands; Laboratory of Microbiology, Wageningen University, Wageningen, Netherlands
| | - Annelies J Veraart
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW) , Wageningen , Netherlands
| | - Mattias de Hollander
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW) , Wageningen , Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University , Wageningen , Netherlands
| | - Johannes A van Veen
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW) , Wageningen , Netherlands
| | - Eiko E Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW) , Wageningen , Netherlands
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50
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Lupatini M, Korthals GW, de Hollander M, Janssens TKS, Kuramae EE. Soil Microbiome Is More Heterogeneous in Organic Than in Conventional Farming System. Front Microbiol 2017; 7:2064. [PMID: 28101080 PMCID: PMC5209367 DOI: 10.3389/fmicb.2016.02064] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 12/07/2016] [Indexed: 11/17/2022] Open
Abstract
Organic farming system and sustainable management of soil pathogens aim at reducing the use of agricultural chemicals in order to improve ecosystem health. Despite the essential role of microbial communities in agro-ecosystems, we still have limited understanding of the complex response of microbial diversity and composition to organic and conventional farming systems and to alternative methods for controlling plant pathogens. In this study we assessed the microbial community structure, diversity and richness using 16S rRNA gene next generation sequences and report that conventional and organic farming systems had major influence on soil microbial diversity and community composition while the effects of the soil health treatments (sustainable alternatives for chemical control) in both farming systems were of smaller magnitude. Organically managed system increased taxonomic and phylogenetic richness, diversity and heterogeneity of the soil microbiota when compared with conventional farming system. The composition of microbial communities, but not the diversity nor heterogeneity, were altered by soil health treatments. Soil health treatments exhibited an overrepresentation of specific microbial taxa which are known to be involved in soil suppressiveness to pathogens (plant-parasitic nematodes and soil-borne fungi). Our results provide a comprehensive survey on the response of microbial communities to different agricultural systems and to soil treatments for controlling plant pathogens and give novel insights to improve the sustainability of agro-ecosystems by means of beneficial microorganisms.
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Affiliation(s)
- Manoeli Lupatini
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW)Wageningen, Netherlands
| | - Gerard W. Korthals
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW)Wageningen, Netherlands
| | - Mattias de Hollander
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW)Wageningen, Netherlands
| | - Thierry K. S. Janssens
- MicroLife SolutionsAmsterdam, Netherlands
- Department of Ecological Science, Vrije Universiteit AmsterdamAmsterdam, Netherlands
| | - Eiko E. Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW)Wageningen, Netherlands
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