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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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2
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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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3
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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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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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5
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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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6
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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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7
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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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8
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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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9
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Hannula SE, Morriën E, de Hollander M, van der Putten WH, van Veen JA, de Boer W. Shifts in rhizosphere fungal community during secondary succession following abandonment from agriculture. ISME J 2017; 11:2294-2304. [PMID: 28585935 PMCID: PMC5607372 DOI: 10.1038/ismej.2017.90] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 04/20/2017] [Accepted: 04/28/2017] [Indexed: 12/14/2022]
Abstract
Activities of rhizosphere microbes are key to the functioning of terrestrial ecosystems. It is commonly believed that bacteria are the major consumers of root exudates and that the role of fungi in the rhizosphere is mostly limited to plant-associated taxa, such as mycorrhizal fungi, pathogens and endophytes, whereas less is known about the role of saprotrophs. In order to test the hypothesis that the role of saprotrophic fungi in rhizosphere processes increases with increased time after abandonment from agriculture, we determined the composition of fungi that are active in the rhizosphere along a chronosequence of ex-arable fields in the Netherlands. Intact soil cores were collected from nine fields that represent three stages of land abandonment and pulse labeled with 13CO2. The fungal contribution to metabolization of plant-derived carbon was evaluated using phospholipid analysis combined with stable isotope probing (SIP), whereas fungal diversity was analyzed using DNA-SIP combined with 454-sequencing. We show that in recently abandoned fields most of the root-derived 13C was taken up by bacteria but that in long-term abandoned fields most of the root-derived 13C was found in fungal biomass. Furthermore, the composition of the active functional fungal community changed from one composed of fast-growing and pathogenic fungal species to one consisting of beneficial and slower-growing fungal species, which may have essential consequences for the carbon flow through the soil food web and consequently nutrient cycling and plant succession.
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Affiliation(s)
- S Emilia Hannula
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Elly Morriën
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
- Institute for Biodiversity and Ecosystem Dynamics, Department of Ecosytem and Landscape Dynamics (IBED-ELD), University of Amsterdam, Amsterdam, The Netherlands
| | - Mattias de Hollander
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Wim H van der Putten
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
- Department of Nematology, Wageningen University & Research, Wageningen, The Netherlands
| | - Johannes A van Veen
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
- Insititute of Biology, Leiden University, Leiden, The Netherlands
| | - Wietse de Boer
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
- Department of Soil Quality, Wageningen University & Research, Wageningen, The Netherlands
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10
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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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11
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Hannula SE, van Veen JA. Primer Sets Developed for Functional Genes Reveal Shifts in Functionality of Fungal Community in Soils. Front Microbiol 2016; 7:1897. [PMID: 27965632 PMCID: PMC5126076 DOI: 10.3389/fmicb.2016.01897] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [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: 04/07/2016] [Accepted: 11/11/2016] [Indexed: 12/16/2022] Open
Abstract
Phylogenetic diversity of soil microbes is a hot topic at the moment. However, the molecular tools for the assessment of functional diversity in the fungal community are less developed than tools based on genes encoding the ribosomal operon. Here 20 sets of primers targeting genes involved mainly in carbon cycling were designed and/or validated and the functioning of soil fungal communities along a chronosequence of land abandonment from agriculture was evaluated using them. We hypothesized that changes in fungal community structure during secondary succession would lead to difference in the types of genes present in soils and that these changes would be directional. We expected an increase in genes involved in degradation of recalcitrant organic matter in time since agriculture. Out of the investigated genes, the richness of the genes related to carbon cycling was significantly higher in fields abandoned for longer time. The composition of six of the genes analyzed revealed significant differences between fields abandoned for shorter and longer time. However, all genes revealed significant variance over the fields studied, and this could be related to other parameters than the time since agriculture such as pH, organic matter, and the amount of available nitrogen. Contrary to our initial hypothesis, the genes significantly different between fields were not related to the decomposition of more recalcitrant matter but rather involved in degradation of cellulose and hemicellulose.
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Affiliation(s)
- S. Emilia Hannula
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW)Wageningen, Netherlands
| | - Johannes A. van Veen
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW)Wageningen, Netherlands
- Insititute of Biology, Leiden UniversityLeiden, Netherlands
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12
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Kielak AM, Barreto CC, Kowalchuk GA, van Veen JA, Kuramae EE. The Ecology of Acidobacteria: Moving beyond Genes and Genomes. Front Microbiol 2016; 7:744. [PMID: 27303369 PMCID: PMC4885859 DOI: 10.3389/fmicb.2016.00744] [Citation(s) in RCA: 426] [Impact Index Per Article: 53.3] [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: 10/08/2015] [Accepted: 05/03/2016] [Indexed: 12/01/2022] Open
Abstract
The phylum Acidobacteria is one of the most widespread and abundant on the planet, yet remarkably our knowledge of the role of these diverse organisms in the functioning of terrestrial ecosystems remains surprisingly rudimentary. This blatant knowledge gap stems to a large degree from the difficulties associated with the cultivation of these bacteria by classical means. Given the phylogenetic breadth of the Acidobacteria, which is similar to the metabolically diverse Proteobacteria, it is clear that detailed and functional descriptions of acidobacterial assemblages are necessary. Fortunately, recent advances are providing a glimpse into the ecology of members of the phylum Acidobacteria. These include novel cultivation and enrichment strategies, genomic characterization and analyses of metagenomic DNA from environmental samples. Here, we couple the data from these complementary approaches for a better understanding of their role in the environment, thereby providing some initial insights into the ecology of this important phylum. All cultured acidobacterial type species are heterotrophic, and members of subdivisions 1, 3, and 4 appear to be more versatile in carbohydrate utilization. Genomic and metagenomic data predict a number of ecologically relevant capabilities for some acidobacteria, including the ability to: use of nitrite as N source, respond to soil macro-, micro nutrients and soil acidity, express multiple active transporters, degrade gellan gum and produce exopolysaccharide (EPS). Although these predicted properties allude to a competitive life style in soil, only very few of these prediction shave been confirmed via physiological studies. The increased availability of genomic and physiological information, coupled to distribution data in field surveys and experiments, should direct future progress in unraveling the ecology of this important but still enigmatic phylum.
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Affiliation(s)
- Anna M Kielak
- Department of Microbial Ecology, The Netherlands Institute of Ecology - Koninklijke Nederlandse Akademie van Wetenschappen Wageningen, Netherlands
| | - Cristine C Barreto
- Graduate Program in Genomic Sciences and Biotechnology, Universidade Católica de Brasília Brasília, Brazil
| | - George A Kowalchuk
- Ecology and Biodiversity Group, University of Utrecht Utrecht, Netherlands
| | - Johannes A van Veen
- Department of Microbial Ecology, The Netherlands Institute of Ecology - Koninklijke Nederlandse Akademie van Wetenschappen Wageningen, Netherlands
| | - Eiko E Kuramae
- Department of Microbial Ecology, The Netherlands Institute of Ecology - Koninklijke Nederlandse Akademie van Wetenschappen Wageningen, Netherlands
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13
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Kielak AM, Scheublin TR, Mendes LW, van Veen JA, Kuramae EE. Bacterial Community Succession in Pine-Wood Decomposition. Front Microbiol 2016; 7:231. [PMID: 26973611 PMCID: PMC4771932 DOI: 10.3389/fmicb.2016.00231] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [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: 10/07/2015] [Accepted: 02/15/2016] [Indexed: 11/17/2022] Open
Abstract
Though bacteria and fungi are common inhabitants of decaying wood, little is known about the relationship between bacterial and fungal community dynamics during natural wood decay. Based on previous studies involving inoculated wood blocks, strong fungal selection on bacteria abundance and community composition was expected to occur during natural wood decay. Here, we focused on bacterial and fungal community compositions in pine wood samples collected from dead trees in different stages of decomposition. We showed that bacterial communities undergo less drastic changes than fungal communities during wood decay. Furthermore, we found that bacterial community assembly was a stochastic process at initial stage of wood decay and became more deterministic in later stages, likely due to environmental factors. Moreover, composition of bacterial communities did not respond to the changes in the major fungal species present in the wood but rather to the stage of decay reflected by the wood density. We concluded that the shifts in the bacterial communities were a result of the changes in wood properties during decomposition and largely independent of the composition of the wood-decaying fungal communities.
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Affiliation(s)
- Anna M Kielak
- Department of Microbial Ecology, Netherlands Institute of Ecology Wageningen, Netherlands
| | - Tanja R Scheublin
- Department of Microbial Ecology, Netherlands Institute of Ecology Wageningen, Netherlands
| | - Lucas W Mendes
- Department of Microbial Ecology, Netherlands Institute of Ecology Wageningen, Netherlands
| | - Johannes A van Veen
- Department of Microbial Ecology, Netherlands Institute of Ecology Wageningen, Netherlands
| | - Eiko E Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology Wageningen, Netherlands
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14
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Song C, Schmidt R, de Jager V, Krzyzanowska D, Jongedijk E, Cankar K, Beekwilder J, van Veen A, de Boer W, van Veen JA, Garbeva P. Exploring the genomic traits of fungus-feeding bacterial genus Collimonas. BMC Genomics 2015; 16:1103. [PMID: 26704531 PMCID: PMC4690342 DOI: 10.1186/s12864-015-2289-3] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [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: 07/08/2015] [Accepted: 12/11/2015] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Collimonas is a genus belonging to the class of Betaproteobacteria and consists mostly of soil bacteria with the ability to exploit living fungi as food source (mycophagy). Collimonas strains differ in a range of activities, including swimming motility, quorum sensing, extracellular protease activity, siderophore production, and antimicrobial activities. RESULTS In order to reveal ecological traits possibly related to Collimonas lifestyle and secondary metabolites production, we performed a comparative genomics analysis based on whole-genome sequencing of six strains representing 3 recognized species. The analysis revealed that the core genome represents 43.1 to 52.7% of the genomes of the six individual strains. These include genes coding for extracellular enzymes (chitinase, peptidase, phospholipase), iron acquisition and type II secretion systems. In the variable genome, differences were found in genes coding for secondary metabolites (e.g. tripropeptin A and volatile terpenes), several unknown orphan polyketide synthase-nonribosomal peptide synthetase (PKS-NRPS), nonribosomal peptide synthetase (NRPS) gene clusters, a new lipopeptide and type III and type VI secretion systems. Potential roles of the latter genes in the interaction with other organisms were investigated. Mutation of a gene involved in tripropeptin A biosynthesis strongly reduced the antibacterial activity against Staphylococcus aureus, while disruption of a gene involved in the biosynthesis of the new lipopeptide had a large effect on the antifungal/oomycetal activities. CONCLUSIONS Overall our results indicated that Collimonas genomes harbour many genes encoding for novel enzymes and secondary metabolites (including terpenes) important for interactions with other organisms and revealed genomic plasticity, which reflect the behaviour, antimicrobial activity and lifestylesof Collimonas spp.
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Affiliation(s)
- Chunxu Song
- Netherlands Institute of Ecology, Department of Microbial Ecology, Droevendaalsesteeg 10, Wageningen, 6708 PB, The Netherlands.
| | - Ruth Schmidt
- Netherlands Institute of Ecology, Department of Microbial Ecology, Droevendaalsesteeg 10, Wageningen, 6708 PB, The Netherlands.
| | - Victor de Jager
- Netherlands Institute of Ecology, Department of Microbial Ecology, Droevendaalsesteeg 10, Wageningen, 6708 PB, The Netherlands.
| | - Dorota Krzyzanowska
- Laboratory of Biological Plant Protection, Intercollegiate Faculty of Biotechnology UG&MUG, Kladki 24, Gdansk, 80-822, Poland.
| | - Esmer Jongedijk
- Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, Wageningen, 6708 PB, The Netherlands.
| | - Katarina Cankar
- Business Unit Bioscience, Plant Research International, Wageningen University and Research Centre, Wageningen, The Netherlands.
| | - Jules Beekwilder
- Business Unit Bioscience, Plant Research International, Wageningen University and Research Centre, Wageningen, The Netherlands.
| | - Anouk van Veen
- Netherlands Institute of Ecology, Department of Microbial Ecology, Droevendaalsesteeg 10, Wageningen, 6708 PB, The Netherlands.
| | - Wietse de Boer
- Netherlands Institute of Ecology, Department of Microbial Ecology, Droevendaalsesteeg 10, Wageningen, 6708 PB, The Netherlands.
| | - Johannes A van Veen
- Netherlands Institute of Ecology, Department of Microbial Ecology, Droevendaalsesteeg 10, Wageningen, 6708 PB, The Netherlands.
| | - Paolina Garbeva
- Netherlands Institute of Ecology, Department of Microbial Ecology, Droevendaalsesteeg 10, Wageningen, 6708 PB, The Netherlands.
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15
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Ballhausen MB, van Veen JA, Hundscheid MPJ, de Boer W. Methods for Baiting and Enriching Fungus-Feeding (Mycophagous) Rhizosphere Bacteria. Front Microbiol 2015; 6:1416. [PMID: 26733962 PMCID: PMC4687392 DOI: 10.3389/fmicb.2015.01416] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [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: 07/28/2015] [Accepted: 11/27/2015] [Indexed: 01/01/2023] Open
Abstract
Mycophagous soil bacteria are able to obtain nutrients from living fungal hyphae. However, with exception of the soil bacterial genus Collimonas, occurrence of this feeding strategy has not been well examined. Evaluation of the importance of mycophagy in soil bacterial communities requires targeted isolation methods. In this study, we compared two different approaches to obtain mycophagous bacteria from rhizospheric soil. A short-term method based on baiting for bacteria that can rapidly adhere to fungal hyphae and a long-term method based on the enrichment of bacteria on fungal hyphae via repeated transfer. Hyphae-adhering bacteria were isolated, identified by 16S rDNA sequencing and tested for antifungal activity and the ability to feed on fungi as the sole source of carbon. Both methods yielded a range of potentially mycophagous bacterial isolates with little phylogenetic overlap. We also found indications for feeding preferences among the potentially mycophagous bacteria. Our results indicate that mycophagy could be an important growth strategy for rhizosphere bacteria. To our surprise, we found several potential plant pathogenic bacteria among the mycophagous isolates. We discuss the possible benefits that these bacteria might gain from colonizing fungal hyphae.
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Affiliation(s)
- Max-Bernhard Ballhausen
- Department of Microbial Ecology, Netherlands Institute of EcologyWageningen, Netherlands
- Department of Plant Health, Institute for Vegetable and Ornamental CropsGroßbeeren, Germany
| | - Johannes A. van Veen
- Department of Microbial Ecology, Netherlands Institute of EcologyWageningen, Netherlands
- Institute of Biology Leiden, Leiden UniversityLeiden, Netherlands
| | - Maria P. J. Hundscheid
- Department of Microbial Ecology, Netherlands Institute of EcologyWageningen, Netherlands
| | - Wietse de Boer
- Department of Microbial Ecology, Netherlands Institute of EcologyWageningen, Netherlands
- Department of Soil Quality, Wageningen UniversityWageningen, Netherlands
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16
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de Boer W, Hundscheid MPJ, Klein Gunnewiek PJA, de Ridder-Duine AS, Thion C, van Veen JA, van der Wal A. Antifungal Rhizosphere Bacteria Can increase as Response to the Presence of Saprotrophic Fungi. PLoS One 2015; 10:e0137988. [PMID: 26393509 PMCID: PMC4578881 DOI: 10.1371/journal.pone.0137988] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 08/24/2015] [Indexed: 01/26/2023] Open
Abstract
Knowledge on the factors that determine the composition of bacterial communities in the vicinity of roots (rhizosphere) is essential to understand plant-soil interactions. Plant species identity, plant growth stage and soil properties have been indicated as major determinants of rhizosphere bacterial community composition. Here we show that the presence of saprotrophic fungi can be an additional factor steering rhizosphere bacterial community composition and functioning. We studied the impact of presence of two common fungal rhizosphere inhabitants (Mucor hiemalis and Trichoderma harzianum) on the composition of cultivable bacterial communities developing in the rhizosphere of Carex arenaria (sand sedge) in sand microcosms. Identification and phenotypic characterization of bacterial isolates revealed clear shifts in the rhizosphere bacterial community composition by the presence of two fungal strains (M. hiemalis BHB1 and T. harzianum PvdG2), whereas another M. hiemalis strain did not show this effect. Presence of both M. hiemalis BHB1 and T. harzianum PvdG2 resulted in a significant increase of chitinolytic and (in vitro) antifungal bacteria. The latter was most pronounced for M. hiemalis BHB1, an isolate from Carex roots, which stimulated the development of the bacterial genera Achromobacter and Stenotrophomonas. In vitro tests showed that these genera were strongly antagonistic against M. hiemalis but also against the plant-pathogenic fungus Rhizoctonia solani. The most likely explanation for fungal-induced shifts in the composition of rhizosphere bacteria is that bacteria are being selected which are successful in competing with fungi for root exudates. Based on the results we propose that measures increasing saprotrophic fungi in agricultural soils should be explored as an alternative approach to enhance natural biocontrol against soil-borne plant-pathogenic fungi, namely by stimulating indigenous antifungal rhizosphere bacteria.
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Affiliation(s)
- Wietse de Boer
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, 6708 PB, the Netherlands
- Department of Soil Quality, Wageningen University, Wageningen, 6708 PB, the Netherlands
| | - Maria P. J. Hundscheid
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, 6708 PB, the Netherlands
| | | | - Annelies S. de Ridder-Duine
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, 6708 PB, the Netherlands
| | - Cecile Thion
- School of Biological Science, University of Aberdeen, Aberdeen, AB24 3UU, United Kingdom
| | - Johannes A. van Veen
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, 6708 PB, the Netherlands
- Insititute of Biology, Leiden University, Leiden, 2333 BE, the Netherlands
| | - Annemieke van der Wal
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, 6708 PB, the Netherlands
- * E-mail:
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17
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Mendes LW, Tsai SM, Navarrete AA, de Hollander M, van Veen JA, Kuramae EE. Soil-borne microbiome: linking diversity to function. Microb Ecol 2015; 70:255-65. [PMID: 25586384 DOI: 10.1007/s00248-014-0559-2] [Citation(s) in RCA: 119] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Accepted: 12/19/2014] [Indexed: 05/25/2023]
Abstract
Soil microorganisms are sensitive to environment disturbances, and such alterations have consequences on microbial diversity and functions. Our hypothesis is that alpha diversity of microbial communities and functional diversity decrease from undisturbed to disturbed soils, with consequences for functional redundancy in the soil ecosystem. To test this hypothesis, we used soil DNA shotgun metagenomics approach to assess the soil microbiome in a chronosequence of land-use from a native tropical forest, followed by deforestation and cultivation of soybean croplands and pasture in different seasons. Agriculture and pasture soils were among the most diverse and presented higher functional redundancy, which is important to maintain the ecosystem functioning after the forest conversion. On the other hand, the ecosystem equilibrium in forest is maintained based on a lower alpha diversity but higher abundance of microorganisms. Our results indicate that land-use change alters the structure and composition of microbial communities; however, ecosystem functionality is overcome by different strategies based on the abundance and diversity of the communities.
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Affiliation(s)
- Lucas W Mendes
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, CENA, University of Sao Paulo USP, Piracicaba, SP, Brazil
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18
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Navarrete AA, Tsai SM, Mendes LW, Faust K, de Hollander M, Cassman NA, Raes J, van Veen JA, Kuramae EE. Soil microbiome responses to the short-term effects of Amazonian deforestation. Mol Ecol 2015; 24:2433-48. [PMID: 25809788 DOI: 10.1111/mec.13172] [Citation(s) in RCA: 119] [Impact Index Per Article: 13.2] [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: 01/07/2015] [Accepted: 03/19/2015] [Indexed: 12/21/2022]
Abstract
Slash-and-burn clearing of forest typically results in increase in soil nutrient availability. However, the impact of these nutrients on the soil microbiome is not known. Using next generation sequencing of 16S rRNA gene and shotgun metagenomic DNA, we compared the structure and the potential functions of bacterial community in forest soils to deforested soils in the Amazon region and related the differences to soil chemical factors. Deforestation decreased soil organic matter content and factors linked to soil acidity and raised soil pH, base saturation and exchangeable bases. Concomitant to expected changes in soil chemical factors, we observed an increase in the alpha diversity of the bacterial microbiota and relative abundances of putative copiotrophic bacteria such as Actinomycetales and a decrease in the relative abundances of bacterial taxa such as Chlamydiae, Planctomycetes and Verrucomicrobia in the deforested soils. We did not observe an increase in genes related to microbial nutrient metabolism in deforested soils. However, we did observe changes in community functions such as increases in DNA repair, protein processing, modification, degradation and folding functions, and these functions might reflect adaptation to changes in soil characteristics due to forest clear-cutting and burning. In addition, there were changes in the composition of the bacterial groups associated with metabolism-related functions. Co-occurrence microbial network analysis identified distinct phylogenetic patterns for forest and deforested soils and suggested relationships between Planctomycetes and aluminium content, and Actinobacteria and nitrogen sources in Amazon soils. The results support taxonomic and functional adaptations in the soil bacterial community following deforestation. We hypothesize that these microbial adaptations may serve as a buffer to drastic changes in soil fertility after slash-and-burning deforestation in the Amazon region.
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Affiliation(s)
- Acacio A Navarrete
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture CENA, University of São Paulo USP, Avenida Centenário 303, 13400-970, Piracicaba, SP, Brazil; Department of Microbial Ecology, Netherlands Institute of Ecology NIOO-KNAW, Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
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19
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Tyc O, van den Berg M, Gerards S, van Veen JA, Raaijmakers JM, de Boer W, Garbeva P. Impact of interspecific interactions on antimicrobial activity among soil bacteria. Front Microbiol 2014; 5:567. [PMID: 25389421 PMCID: PMC4211544 DOI: 10.3389/fmicb.2014.00567] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [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: 08/19/2014] [Accepted: 10/08/2014] [Indexed: 11/13/2022] Open
Abstract
Certain bacterial species produce antimicrobial compounds only in the presence of a competing species. However, little is known on the frequency of interaction-mediated induction of antibiotic compound production in natural communities of soil bacteria. Here we developed a high-throughput method to screen for the production of antimicrobial activity by monocultures and pair-wise combinations of 146 phylogenetically different bacteria isolated from similar soil habitats. Growth responses of two human pathogenic model organisms, Escherichia coli WA321 and Staphylococcus aureus 533R4, were used to monitor antimicrobial activity. From all isolates, 33% showed antimicrobial activity only in monoculture and 42% showed activity only when tested in interactions. More bacterial isolates were active against S. aureus than against E. coli. The frequency of interaction-mediated induction of antimicrobial activity was 6% (154 interactions out of 2798) indicating that only a limited set of species combinations showed such activity. The screening revealed also interaction-mediated suppression of antimicrobial activity for 22% of all combinations tested. Whereas all patterns of antimicrobial activity (non-induced production, induced production and suppression) were seen for various bacterial classes, interaction-mediated induction of antimicrobial activity was more frequent for combinations of Flavobacteria and alpha- Proteobacteria. The results of our study give a first indication on the frequency of interference competitive interactions in natural soil bacterial communities which may forms a basis for selection of bacterial groups that are promising for the discovery of novel, cryptic antibiotics.
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Affiliation(s)
- Olaf Tyc
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW) Wageningen, Netherlands
| | - Marlies van den Berg
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW) Wageningen, Netherlands
| | - Saskia Gerards
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW) Wageningen, Netherlands
| | - Johannes A van Veen
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW) Wageningen, Netherlands
| | - Jos M Raaijmakers
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW) Wageningen, Netherlands
| | - Wietse de Boer
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW) Wageningen, Netherlands ; Department of Soil Quality, Wageningen University and Research Centre Wageningen, Netherlands
| | - Paolina Garbeva
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW) Wageningen, Netherlands
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20
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Abstract
Corrosion is the result of a series of chemical, physical and (micro) biological processes leading to the deterioration of materials such as steel and stone. It is a world-wide problem with great societal and economic consequences. Current corrosion control strategies based on chemically produced products are under increasing pressure of stringent environmental regulations. Furthermore, they are rather inefficient. Therefore, there is an urgent need for environmentally friendly and sustainable corrosion control strategies. The mechanisms of microbially influenced corrosion and microbially influenced corrosion inhibition are not completely understood, because they cannot be linked to a single biochemical reaction or specific microbial species or groups. Corrosion is influenced by the complex processes of different microorganisms performing different electrochemical reactions and secreting proteins and metabolites that can have secondary effects. Information on the identity and role of microbial communities that are related to corrosion and corrosion inhibition in different materials and in different environments is scarce. As some microorganisms are able to both cause and inhibit corrosion, we pay particular interest to their potential role as corrosion-controlling agents. We show interesting interfaces in which scientists from different disciplines such as microbiology, engineering and art conservation can collaborate to find solutions to the problems caused by corrosion.
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Affiliation(s)
- Nardy Kip
- 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
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21
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Pan Y, Cassman N, de Hollander M, Mendes LW, Korevaar H, Geerts RHEM, van Veen JA, Kuramae EE. Impact of long-term N, P, K, and NPK fertilization on the composition and potential functions of the bacterial community in grassland soil. FEMS Microbiol Ecol 2014; 90:195-205. [PMID: 25046442 DOI: 10.1111/1574-6941.12384] [Citation(s) in RCA: 153] [Impact Index Per Article: 15.3] [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: 03/29/2014] [Revised: 07/07/2014] [Accepted: 07/09/2014] [Indexed: 01/09/2023] Open
Abstract
Soil abiotic and biotic interactions govern important ecosystem processes. However, the mechanisms behind these interactions are complex, and the links between specific environmental factors, microbial community structures, and functions are not well understood. Here, we applied DNA shotgun metagenomic techniques to investigate the effect of inorganic fertilizers N, P, K, and NPK on the bacterial community composition and potential functions in grassland soils in a 54-year experiment. Differences in total and available nutrients were found in the treatment soils; interestingly, Al, As, Mg, and Mn contents were variable in N, P, K, and NPK treatments. Bacterial community compositions shifted and Actinobacteria were overrepresented under the four fertilization treatments compared to the control. Redundancy analysis of the soil parameters and the bacterial community profiles showed that Mg, total N, Cd, and Al were linked to community variation. Using correlation analysis, Acidobacteria, Bacteroidetes, and Verrucomicrobia were linked similarly to soil parameters, and Actinobacteria and Proteobacteria were linked separately to different suites of parameters. Surprisingly, we found no fertilizers effect on microbial functional profiles which supports functional redundancy as a mechanism for stabilization of functions during changes in microbial composition. We suggest that functional profiles are more resistant to environmental changes than community compositions in the grassland ecosystem.
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Affiliation(s)
- Yao Pan
- Department of Microbial Ecology, Netherlands Institute of Ecology NIOO-KNAW, Wageningen, The Netherlands
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Mendes LW, Kuramae EE, Navarrete AA, van Veen JA, Tsai SM. Taxonomical and functional microbial community selection in soybean rhizosphere. ISME J 2014; 8:1577-87. [PMID: 24553468 PMCID: PMC4817605 DOI: 10.1038/ismej.2014.17] [Citation(s) in RCA: 332] [Impact Index Per Article: 33.2] [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: 10/23/2013] [Revised: 01/10/2014] [Accepted: 01/14/2014] [Indexed: 11/08/2022]
Abstract
This study addressed the selection of the rhizospheric microbial community from the bulk soil reservoir under agricultural management of soybean in Amazon forest soils. We used a shotgun metagenomics approach to investigate the taxonomic and functional diversities of microbial communities in the bulk soil and in the rhizosphere of soybean plants and tested the validity of neutral and niche theories to explain the rhizosphere community assembly processes. Our results showed a clear selection at both taxonomic and functional levels operating in the assembly of the soybean rhizosphere community. The taxonomic analysis revealed that the rhizosphere community is a subset of the bulk soil community. Species abundance in rhizosphere fits the log-normal distribution model, which is an indicator of the occurrence of niche-based processes. In addition, the data indicate that the rhizosphere community is selected based on functional cores related to the metabolisms of nitrogen, iron, phosphorus and potassium, which are related to benefits to the plant, such as growth promotion and nutrition. The network analysis including bacterial groups and functions was less complex in rhizosphere, suggesting the specialization of some specific metabolic pathways. We conclude that the assembly of the microbial community in the rhizosphere is based on niche-based processes as a result of the selection power of the plant and other environmental factors.
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Affiliation(s)
- Lucas W Mendes
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture (CENA), University of Sao Paulo (USP), Piracicaba, Brazil
- 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
| | - Acácio A Navarrete
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture (CENA), University of Sao Paulo (USP), Piracicaba, Brazil
- 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
- Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Siu M Tsai
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture (CENA), University of Sao Paulo (USP), Piracicaba, Brazil
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Bai Y, Eijsink VGH, Kielak AM, van Veen JA, de Boer W. Genomic comparison of chitinolytic enzyme systems from terrestrial and aquatic bacteria. Environ Microbiol 2014; 18:38-49. [DOI: 10.1111/1462-2920.12545] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 06/12/2014] [Indexed: 12/01/2022]
Affiliation(s)
- Yani Bai
- Department of Microbial Ecology; Netherlands Institute of Ecology (NIOO-KNAW); P.O. Box 50 Wageningen 6700 AB The Netherlands
| | - Vincent G. H. Eijsink
- Department of Chemistry, Biotechnology and Food Science; Norwegian University of Life Sciences; Aas Norway
| | - Anna M. Kielak
- Department of Microbial Ecology; Netherlands Institute of Ecology (NIOO-KNAW); P.O. Box 50 Wageningen 6700 AB The Netherlands
| | - Johannes A. van Veen
- Department of Microbial Ecology; Netherlands Institute of Ecology (NIOO-KNAW); P.O. Box 50 Wageningen 6700 AB The Netherlands
- Institute of Biology; Faculty of Science; Leiden University; Leiden The Netherlands
| | - Wietse de Boer
- Department of Microbial Ecology; Netherlands Institute of Ecology (NIOO-KNAW); P.O. Box 50 Wageningen 6700 AB The Netherlands
- Soil Quality Group; Wageningen University; P.O. Box 9101 Wageningen 6700 HB The Netherlands
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Fritsche K, van den Berg M, de Boer W, van Beek TA, Raaijmakers JM, van Veen JA, Leveau JHJ. Biosynthetic genes and activity spectrum of antifungal polyynes fromCollimonas fungivorans Ter331. Environ Microbiol 2014; 16:1334-45. [DOI: 10.1111/1462-2920.12440] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Accepted: 01/16/2014] [Indexed: 01/13/2023]
Affiliation(s)
- Kathrin Fritsche
- Department of Microbial Ecology; Netherlands Institute of Ecology (NIOO-KNAW); Wageningen The Netherlands
- BioDetection Systems b.v.; Amsterdam The Netherlands
| | - Marlies van den Berg
- Department of Microbial Ecology; Netherlands Institute of Ecology (NIOO-KNAW); Wageningen The Netherlands
| | - Wietse de Boer
- Department of Microbial Ecology; Netherlands Institute of Ecology (NIOO-KNAW); Wageningen The Netherlands
| | - Teris A. van Beek
- Laboratory of Organic Chemistry; Wageningen University; Wageningen The Netherlands
| | - Jos M. Raaijmakers
- Department of Microbial Ecology; Netherlands Institute of Ecology (NIOO-KNAW); Wageningen The Netherlands
- Laboratory of Phytopathology; Wageningen University; Wageningen The Netherlands
| | - Johannes A. van Veen
- Department of Microbial Ecology; Netherlands Institute of Ecology (NIOO-KNAW); Wageningen The Netherlands
- Institute of Biology; Leiden University; Leiden The Netherlands
| | - Johan H. J. Leveau
- Department of Microbial Ecology; Netherlands Institute of Ecology (NIOO-KNAW); Wageningen The Netherlands
- Department of Plant Pathology; University of California; Davis CA USA
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Vasileiadis S, Puglisi E, Arena M, Cappa F, van Veen JA, Cocconcelli PS, Trevisan M. Soil microbial diversity patterns of a lowland spring environment. FEMS Microbiol Ecol 2013; 86:172-84. [DOI: 10.1111/1574-6941.12150] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Revised: 05/09/2013] [Accepted: 05/21/2013] [Indexed: 11/30/2022] Open
Affiliation(s)
- Sotirios Vasileiadis
- Institute of Agricultural and Environmental Chemistry; Universitá Cattolica del Sacro Cuore; Piacenza; Italy
| | - Edoardo Puglisi
- Institute of Microbiology; Università Cattolica del Sacro Cuore; Piacenza; Italy
| | - Maria Arena
- Institute of Agricultural and Environmental Chemistry; Universitá Cattolica del Sacro Cuore; Piacenza; Italy
| | - Fabrizio Cappa
- Institute of Microbiology; Università Cattolica del Sacro Cuore; Piacenza; Italy
| | | | - Pier S. Cocconcelli
- Institute of Microbiology; Università Cattolica del Sacro Cuore; Piacenza; Italy
| | - Marco Trevisan
- Institute of Agricultural and Environmental Chemistry; Universitá Cattolica del Sacro Cuore; Piacenza; Italy
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Navarrete AA, Kuramae EE, de Hollander M, Pijl AS, van Veen JA, Tsai SM. Acidobacterial community responses to agricultural management of soybean in Amazon forest soils. FEMS Microbiol Ecol 2013; 83:607-21. [PMID: 23013447 DOI: 10.1111/1574-6941.12018] [Citation(s) in RCA: 119] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2012] [Revised: 08/01/2012] [Accepted: 09/23/2012] [Indexed: 11/29/2022] Open
Abstract
This study focused on the impact of land-use changes and agricultural management of soybean in Amazon forest soils on the abundance and composition of the acidobacterial community. Quantitative real-time PCR (q-PCR) assays and pyrosequencing of 16S rRNA gene were applied to study the acidobacterial community in bulk soil samples from soybean croplands and adjacent native forests, and mesocosm soil samples from soybean rhizosphere. Based on qPCR measurements, Acidobacteria accounted for 23% in forest soils, 18% in cropland soils, and 14% in soybean rhizosphere of the total bacterial signals. From the 16S rRNA gene sequences of Bacteria domain, the phylum Acidobacteria represented 28% of the sequences from forest soils, 16% from cropland soils, and 17% from soybean rhizosphere. Acidobacteria subgroups 1-8, 10, 11, 13, 17, 18, 22, and 25 were detected with subgroup 1 as dominant among them. Subgroups 4, 6, and 7 were significantly higher in cropland soils than in forest soils, which subgroups responded to decrease in soil aluminum. Subgroups 6 and 7 responded to high content of soil Ca, Mg, Mn, and B. These results showed a differential response of the Acidobacteria subgroups to abiotic soil factors, and open the possibilities to explore acidobacterial subgroups as early-warning bioindicators of agricultural soil management effects in the Amazon area.
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Affiliation(s)
- Acácio A Navarrete
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture CENA, University of São Paulo USP, Piracicaba, SP, Brazil
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Drigo B, Kowalchuk GA, Knapp BA, Pijl AS, Boschker HTS, van Veen JA. Impacts of 3 years of elevated atmospheric CO2 on rhizosphere carbon flow and microbial community dynamics. Glob Chang Biol 2013; 19:621-36. [PMID: 23504797 DOI: 10.1111/gcb.12045] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2011] [Accepted: 07/24/2012] [Indexed: 05/13/2023]
Abstract
Carbon (C) uptake by terrestrial ecosystems represents an important option for partially mitigating anthropogenic CO2 emissions. Short-term atmospheric elevated CO2 exposure has been shown to create major shifts in C flow routes and diversity of the active soil-borne microbial community. Long-term increases in CO2 have been hypothesized to have subtle effects due to the potential adaptation of soil microorganism to the increased flow of organic C. Here, we studied the effects of prolonged elevated atmospheric CO2 exposure on microbial C flow and microbial communities in the rhizosphere. Carex arenaria (a nonmycorrhizal plant species) and Festuca rubra (a mycorrhizal plant species) were grown at defined atmospheric conditions differing in CO2 concentration (350 and 700 ppm) for 3 years. During this period, C flow was assessed repeatedly (after 6 months, 1, 2, and 3 years) by (13) C pulse-chase experiments, and label was tracked through the rhizosphere bacterial, general fungal, and arbuscular mycorrhizal fungal (AMF) communities. Fatty acid biomarker analyses and RNA-stable isotope probing (RNA-SIP), in combination with real-time PCR and PCR-DGGE, were used to examine microbial community dynamics and abundance. Throughout the experiment the influence of elevated CO2 was highly plant dependent, with the mycorrhizal plant exerting a greater influence on both bacterial and fungal communities. Biomarker data confirmed that rhizodeposited C was first processed by AMF and subsequently transferred to bacterial and fungal communities in the rhizosphere soil. Over the course of 3 years, elevated CO2 caused a continuous increase in the (13) C enrichment retained in AMF and an increasing delay in the transfer of C to the bacterial community. These results show that, not only do elevated atmospheric CO2 conditions induce changes in rhizosphere C flow and dynamics but also continue to develop over multiple seasons, thereby affecting terrestrial ecosystems C utilization processes.
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Affiliation(s)
- Barbara Drigo
- Hawkesbury Institute for the Environment, University of Western Sydney, Penrith, NSW, Australia
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Krumins JA, van Oevelen D, Bezemer TM, De Deyn GB, Hol WHG, van Donk E, de Boer W, de Ruiter PC, Middelburg JJ, Monroy F, Soetaert K, Thébault E, van de Koppel J, van Veen JA, Viketoft M, van der Putten WH. Soil and Freshwater and Marine Sediment Food Webs: Their Structure and Function. Bioscience 2013. [DOI: 10.1525/bio.2013.63.1.8] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Mela F, Fritsche K, de Boer W, van Veen JA, de Graaff LH, van den Berg M, Leveau JHJ. Dual transcriptional profiling of a bacterial/fungal confrontation: Collimonas fungivorans versus Aspergillus niger. ISME J 2011; 5:1494-504. [PMID: 21614084 DOI: 10.1038/ismej.2011.29] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Interactions between bacteria and fungi cover a wide range of incentives, mechanisms and outcomes. The genus Collimonas consists of soil bacteria that are known for their antifungal activity and ability to grow at the expense of living fungi. In non-contact confrontation assays with the fungus Aspergillus niger, Collimonas fungivorans showed accumulation of biomass concomitant with inhibition of hyphal spread. Through microarray analysis of bacterial and fungal mRNA from the confrontation arena, we gained new insights into the mechanisms underlying the fungistatic effect and mycophagous phenotype of collimonads. Collimonas responded to the fungus by activating genes for the utilization of fungal-derived compounds and for production of a putative antifungal compound. In A. niger, differentially expressed genes included those involved in lipid and cell wall metabolism and cell defense, which correlated well with the hyphal deformations that were observed microscopically. Transcriptional profiles revealed distress in both partners: downregulation of ribosomal proteins and upregulation of mobile genetic elements in the bacteria and expression of endoplasmic reticulum stress and conidia-related genes in the fungus. Both partners experienced nitrogen shortage in each other's presence. Overall, our results indicate that the Collimonas/Aspergillus interaction is a complex interplay between trophism, antibiosis and competition for nutrients.
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Affiliation(s)
- Francesca Mela
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
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Joosten L, van Veen JA. Defensive properties of pyrrolizidine alkaloids against microorganisms. Phytochem Rev 2011; 10:127-136. [PMID: 21475390 PMCID: PMC3047671 DOI: 10.1007/s11101-010-9204-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2010] [Accepted: 11/04/2010] [Indexed: 05/26/2023]
Abstract
The understanding of the selection factors that drive chemical diversification of secondary metabolites of constitutive defence systems in plants, such as pyrrolizidine alkaloids (PAs), is still incomplete. Historically, plants always have been confronted with microorganisms. Long before herbivores existed on this planet, plants had to cope with microbial pathogens. Therefore, plant pathogenic microorganisms may have played an important role in the early evolution of the secondary metabolite diversity. In this review, we discuss the impact that plant-produced PAs have on plant-associated microorganisms. The objective of the review is to present the current knowledge on PAs with respect to anti-microbial activities, adaptation and detoxification by microorganisms, pathogenic fungi, root protection and PA induction. Many in vitro experiments showed effects of PAs on microorganisms. These results point to the potential of microorganisms to be important for the evolution of PAs. However, only a few in vivo studies have been published and support the results of the in vitro studies. In conclusion, the topics pointed out in this review need further exploration by carrying out ecological experiments and field studies.
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Affiliation(s)
- Lotte Joosten
- Plant Ecology and Phytochemistry, Institute of Biology, Leiden University, P.O. Box 9505, 2300 RA Leiden, The Netherlands
- Microbial Ecology, Netherlands Institute of Ecology, P.O. Box 40, 6666 ZG Heteren, The Netherlands
| | - Johannes A. van Veen
- Plant Ecology and Phytochemistry, Institute of Biology, Leiden University, P.O. Box 9505, 2300 RA Leiden, The Netherlands
- Microbial Ecology, Netherlands Institute of Ecology, P.O. Box 40, 6666 ZG Heteren, The Netherlands
- P.O. Box 9505, 2300 RA Leiden, The Netherlands
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Joosten L, Cheng D, Mulder PPJ, Vrieling K, van Veen JA, Klinkhamer PGL. The genotype dependent presence of pyrrolizidine alkaloids as tertiary amine in Jacobaea vulgaris. Phytochemistry 2011; 72:214-22. [PMID: 21159354 DOI: 10.1016/j.phytochem.2010.11.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2010] [Revised: 11/05/2010] [Accepted: 11/11/2010] [Indexed: 05/20/2023]
Abstract
Secondary metabolites such as pyrrolizidine alkaloids (PAs) play a crucial part in plant defense. PAs can occur in plants in two forms: tertiary amine (free base) and N-oxide. PA extraction and detection are of great importance for the understanding of the role of PAs as plant defense compounds, as the tertiary PA form is known for its stronger influence on several generalist insects, whereas the N-oxide form is claimed to be less deterrent. We measured PA N-oxides and their reduced tertiary amines by liquid chromatography-tandem mass spectrometry (LC-MS/MS). We show that the occurrence of tertiary PAs is not an artifact of the extraction and detection method. We found up to 50% of tertiary PAs in shoots of Jacobine - chemotype plants of Jacobaea vulgaris. Jacobine and its derivatives (jacoline, jaconine, jacozine and dehydrojaconine) may occur for more than 20% in reduced form in the shoots and more than 10% in the roots. For 22 PAs detected in F(2) hybrids (J. vulgaris × Jacobaea aquatica), we calculate the tertiary amine percentage (TA%=the tertiary amine concentration/(tertiary amine concentration+the corresponding N-oxide concentration) × 100). We found that the TA% for various PAs was genotype-dependent. Furthermore, TA% for the different PAs were correlated and the highest correlations occurred between PAs which share high structural similarity.
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Affiliation(s)
- Lotte Joosten
- Plant Ecology & Phytochemistry, Institute of Biology, Leiden University, Leiden, The Netherlands
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Czajkowski R, de Boer WJ, van Veen JA, van der Wolf JM. Downward vascular translocation of a green fluorescent protein-tagged strain of Dickeya sp. (Biovar 3) from stem and leaf inoculation sites on potato. Phytopathology 2010; 100:1128-1137. [PMID: 20932162 DOI: 10.1094/phyto-03-10-0093] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Translocation of a green fluorescent protein (GFP)-tagged Dickeya sp. from stems or from leaves to underground parts of potato plants was studied in greenhouse experiments. Thirty days after stem inoculation, 90% of plants expressed symptoms at the stem base and 95% of plants showed browning of internal stem tissue. The GFP-tagged Dickeya sp. was detected by dilution plating in extracts of the stem interiors (100%), stem bases (90%), roots (80%), stolons (55%), and progeny tubers (24%). In roots, the GFP-tagged Dickeya sp. was found inside and between parenchyma cells whereas, in stems and stolons, the GFP-tagged Dickeya sp. was found in the xylem vessels and protoxylem cells. In progeny tubers, this strain was detected in the stolon end. Thirty days after leaf inoculation, the GFP-tagged Dickeya sp. was detected in extracts of 75% of the leaves, 88% of the petioles, 63% of the axils, and inside 25% of the stems taken 15 cm above the ground level. UV microscopy confirmed the presence of the GFP-tagged Dickeya sp. inside petioles and in the main leaf veins. No blackleg or aerial stem rot and no translocation of the GFP-tagged Dickeya sp. to underground plant parts was observed. The implications for contamination of progeny tubers are discussed.
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Hol WHG, de Boer W, Termorshuizen AJ, Meyer KM, Schneider JHM, van Dam NM, van Veen JA, van der Putten WH. Reduction of rare soil microbes modifies plant-herbivore interactions. Ecol Lett 2010; 13:292-301. [DOI: 10.1111/j.1461-0248.2009.01424.x] [Citation(s) in RCA: 137] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Joosten L, Mulder PPJ, Vrieling K, van Veen JA, Klinkhamer PGL. The analysis of pyrrolizidine alkaloids in Jacobaea vulgaris; a comparison of extraction and detection methods. Phytochem Anal 2010; 21:197-204. [PMID: 19908215 DOI: 10.1002/pca.1183] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
INTRODUCTION Pyrrolizidine alkaloids (PAs) serve an important function in plant defence.Objective - To compare different extraction methods and detection techniques, namely gas chromatography with nitrogen phosphorus detection (GC-NPD) and liquid chromatography tandem mass spectrometry (LC-MS/MS) with quadrupole analysers for analysing PAs in Jacobaea vulgaris. METHODOLOGY Both formic acid and sulfuric acid were tested for PA extraction from dry plant material. For GC-NPD, reduction is required to transform PA N-oxides into tertiary amines. Zinc and sodium metabisulfite were compared as reducing agents. RESULTS The lowest PA concentration measured with GC-NPD was approximately 0.03 mg/g and with LC-MS/MS 0.002 mg/g. The detection of major PAs by both techniques was comparable but a number of minor PAs were not detected by GC-NPD. With the LC-MS/MS procedure higher concentrations were found in plant extracts, indicating that losses may have occurred during the sample preparation for the GC-NPD method. Zinc proved a more effective reducing agent than sodium metabisulfite. The sample preparation for LC-MS/MS analysis using formic acid extraction without any reduction and purification steps is far less complex and less time consuming compared to GC-NPD analysis with sulfuric acid extraction and PA N-oxide reduction with zinc and purification. CONCLUSIONS In terms of sensitivity and discrimination, formic acid extraction in combination with LC-MS/MS detection is the method of choice for analysing PAs (both free and N-oxides forms) in plant material.
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Affiliation(s)
- Lotte Joosten
- Ecology and Phytochemistry, Institute of Biology, Leiden University, PO Box 9505, 2300 RA Leiden, The Netherlands.
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Abstract
The genus Collimonas consists of soil bacteria that have the potential to grow at the expense of living fungal hyphae. However, the consequences of this mycophagous ability for soil fungi are unknown. Here we report on the development of fungal communities after introduction of collimonads in a soil that had a low abundance of indigenous collimonads. Development of fungal communities was stimulated by addition of cellulose or by introducing plants (Plantago lanceolata). Community composition of total fungi in soil and rhizosphere and of arbuscular mycorrhizal fungi in roots was examined by PCR-DGGE. The introduction of collimonads altered the composition of all fungal communities studied but had no effects on fungal biomass increase, cellulose degrading activity or plant performance. The most likely explanation for these results is that differences in sensitivity of fungal species to the presence of collimonads result in competitive replacement of species. The lab and greenhouse experiments were complemented with a field experiment. Mesh bags containing sterile sand with or without collimonads were buried in an ex-arable field and a forest. The presence of collimonads had an effect on the composition of fungi invading these bags in the ex-arable site but not in the forest site.
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Affiliation(s)
- Sachie Höppener-Ogawa
- Centre for Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Heteren, The Netherlands
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van der Wal A, de Boer W, Klein Gunnewiek PJA, van Veen JA. Possible Mechanism for Spontaneous Establishment ofCalluna vulgarisin a Recently Abandoned Agricultural Field. Restor Ecol 2009. [DOI: 10.1111/j.1526-100x.2007.00349.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Abstract
Although Acidobacteria represent the most abundant bacterial phylum in many soils, knowledge of acidobacterial diversity is still rather incomplete. We, therefore, examined the diversity of 16S rRNA genes affiliated with this phylum in a former arable soil via three independent approaches: (1) screening of a fosmid metagenome library for inserts containing Acidobacteria-like 16S rRNA genes; (2) PCR-cloning using general bacterial primers; and (3) PCR-cloning with acidobacterial-specific primers. Bacterial-specific libraries compared rhizosphere versus bulk soil samples, revealing a higher proportion of acidobacterial sequences in bulk soil libraries (P<0.001). Bacterial libraries recovered the greatest diversity, and sequence examination suggested that sequence mismatches with the Acidobacteria-specific primers limited the coverage of the metagenome library screening and specific library approaches. Together, these results expand knowledge of the distribution and diversity of Acidobacteria in soil environments and highlight important technical considerations in the molecular analysis of Acidobacteria diversity.
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Affiliation(s)
- Anna Kielak
- Department of Terrestrial Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Heteren, The Netherlands
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Höppener-Ogawa S, Leveau JHJ, van Veen JA, De Boer W. Mycophagous growth of Collimonas bacteria in natural soils, impact on fungal biomass turnover and interactions with mycophagous Trichoderma fungi. ISME J 2008; 3:190-8. [PMID: 18923455 DOI: 10.1038/ismej.2008.97] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Bacteria of the genus Collimonas are widely distributed in soils, although at low densities. In the laboratory, they were shown to be mycophagous, that is, they are able to grow at the expense of living hyphae. However, so far the importance of mycophagy for growth and survival of collimonads in natural soil habitats is unknown. Using a Collimonas-specific real-time PCR assay, we show here that the invasion of field soils by fungal hyphae (Absidia sp.) resulted in a short-term, significant increase (average fourfold) of indigenous collimonads. No such responses were observed for other soil bacteria studied (Pseudomonas, Burkholderia, PCR-denaturing gradient gel electrophoresis patterns of total bacteria and Burkholderia). Hence, it appears that the stimulation of growth of Collimonas bacteria by fungal hyphae is not common among other soil bacteria. In the same field soils, Trichoderma, a fungal genus known for mycophagous (mycoparasitic) growth, increased upon introduction of Absidia hyphae. Hence, mycophagous growth by Collimonas and Trichoderma can occur in the same soils. However, in controlled experiments (sand microcosms), collimonads appeared to have a negative effect on mycophagous growth of a Trichoderma strain. The effect of mycophagous growth of collimonads on fungal biomass dynamics was studied in sand microcosms using the same Absidia sp. as a test fungus. The growth of collimonads did not cause a significant reduction in the Absidia biomass. Overall, the study indicates that mycophagous nutrition may be important for collimonads in natural soils, but the impact on fungal biomass turnover is likely to be minor.
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Affiliation(s)
- Sachie Höppener-Ogawa
- Centre for Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Heteren, The Netherlands
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Fritsche K, de Boer W, Gerards S, van den Berg M, van Veen JA, Leveau JHJ. Identification and characterization of genes underlying chitinolysis in Collimonas fungivorans Ter331. FEMS Microbiol Ecol 2008; 66:123-35. [PMID: 18671744 DOI: 10.1111/j.1574-6941.2008.00547.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Through a combinatorial approach of plasposon mutagenesis, genome mining, and heterologous expression, we identified genes contributing to the chitinolytic phenotype of bacterium Collimonas fungivorans Ter331. One of five mutants with abolished ability to hydrolyze colloidal chitin carried its plasposon in the chiI gene coding for an extracellular endochitinase. Two mutants were affected in the promoter of chiP-II coding for an outer-membrane transporter of chitooligosaccharides. The remaining two mutations were linked to chitobiose/N-acetylglucosamine uptake. Thus, our model for the Collimonas chitinolytic system assumes a positive feedback regulation of chitinase activity by chitin degradation products. A second chitinase gene, chiII, coded for an exochitinase that preferentially released chitobiose from chitin analogs. Genes hexI and hexII showed coding resemblance to N-acetylglucosaminidases, and the activity of purified HexI protein towards chitin analogs suggested its role in converting chitobiose to N-acetylglucosamine. The hexI gene clustered with chiI, chiII, and chiP-II in one locus, while chitobiose/N-acetylglucosamine uptake genes colocalized in another. Both loci contained genes for conversion of N-acetylglucosamine to fructose-6-phosphate, confirming that C. fungivorans Ter331 features a complete chitin pathway. No link could be established between chitinolysis and antifungal activity of C. fungivorans Ter331, suggesting that the bacterium's reported antagonism towards fungi relies on other mechanisms.
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Affiliation(s)
- Kathrin Fritsche
- Netherlands Institute of Ecology (NIOO-KNAW), Heteren, The Netherlands
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Mela F, Fritsche K, Boersma H, van Elsas JD, Bartels D, Meyer F, de Boer W, van Veen JA, Leveau JHJ. Comparative genomics of the pIPO2/pSB102 family of environmental plasmids: sequence, evolution, and ecology of pTer331 isolated from Collimonas fungivorans Ter331. FEMS Microbiol Ecol 2008; 66:45-62. [PMID: 18355297 DOI: 10.1111/j.1574-6941.2008.00472.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Plasmid pTer331 from the bacterium Collimonas fungivorans Ter331 is a new member of the pIPO2/pSB102 family of environmental plasmids. The 40 457-bp sequence of pTer331 codes for 44 putative ORFs, most of which represent genes involved in replication, partitioning and transfer of the plasmid. We confirmed that pTer331 is stably maintained in its native host. Deletion analysis identified a mini-replicon capable of replicating autonomously in Escherichia coli and Pseudomonas putida. Furthermore, plasmid pTer331 was able to mobilize and retromobilize IncQ plasmid pSM1890 at typical rates of 10(-4) and 10(-8), respectively. Analysis of the 91% DNA sequence identity between pTer331 and pIPO2 revealed functional conservation of coding sequences, the deletion of DNA fragments flanked by short direct repeats (DR), and sequence preservation of long DRs. In addition, we experimentally established that pTer331 has no obvious contribution in several of the phenotypes that are characteristic of its host C. fungivorans Ter331, including the ability to efficiently colonize plant roots. Based on our findings, we hypothesize that cryptic plasmids such as pTer331 and pIPO2 might not confer an individual advantage to bacteria, but, due to their broad-host-range and ability to retromobilize, benefit bacterial populations by accelerating the intracommunal dissemination of the mobile gene pool.
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Affiliation(s)
- Francesca Mela
- Centre for Terrestrial Ecology, Netherlands Institute of Ecology, NIOO-KNAW, Heteren, The Netherlands
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Kielak A, Pijl AS, van Veen JA, Kowalchuk GA. Differences in vegetation composition and plant species identity lead to only minor changes in soil-borne microbial communities in a former arable field. FEMS Microbiol Ecol 2008; 63:372-82. [PMID: 18205817 DOI: 10.1111/j.1574-6941.2007.00428.x] [Citation(s) in RCA: 111] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
To examine the relationship between plant species composition and microbial community diversity and structure, we carried out a molecular analysis of microbial community structure and diversity in two field experiments. In the first experiment, we examined bacterial community structure in bulk and rhizosphere soils in fields exposed to different plant diversity treatments, via a 16S rRNA gene clone library approach. Clear differences were observed between bacterial communities of the bulk soil and the rhizosphere, with the latter containing lower bacterial diversity. The second experiment focused on the influence of 12 different native grassland plant species on bacterial community size and structure in the rhizosphere, as well as the structure of Acidobacteria and Verrucomicrobia community structures. In general, bacterial and phylum-specific quantitative PCR and PCR-denaturing gradient gel electrophoresis revealed only weak influences of plant species on rhizosphere communities. Thus, although plants did exert an influence on microbial species composition and diversity, these interactions were not specific and selective enough to lead to major impacts of vegetation composition and plant species on below-ground microbial communities.
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Affiliation(s)
- Anna Kielak
- Department of Terrestrial Microbial Ecology, Netherlands Institute of Ecology , Heteren, The Netherlands
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Höppener-Ogawa S, Leveau JHJ, Smant W, van Veen JA, de Boer W. Specific detection and real-time PCR quantification of potentially mycophagous bacteria belonging to the genus Collimonas in different soil ecosystems. Appl Environ Microbiol 2007; 73:4191-7. [PMID: 17483278 PMCID: PMC1932782 DOI: 10.1128/aem.00387-07] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2007] [Accepted: 04/24/2007] [Indexed: 11/20/2022] Open
Abstract
The bacterial genus Collimonas has the remarkable characteristic that it grows at the expense of living fungal hyphae under laboratory conditions. Here, we report the first field inventory of the occurrence and abundance of Collimonas in soils (n = 45) with naturally different fungal densities, which was performed in order to test the null hypothesis that there is a relationship between the presence of Collimonas and fungal biomass. Estimates of fungal densities were based on ergosterol measurements. Each soil was also characterized in terms of its physical and chemical properties and vegetation and management types. Culturable Collimonas was identified in plate-spread soil samples by its ability to clear colloidal chitin, in combination with a Collimonas-specific restriction fragment length polymorphism analysis of 16S rRNA PCR amplified from individual colonies. Using this approach, we found culturable collimonads only in (semi)natural grasslands. A real-time PCR assay for the specific quantification of Collimonas 16S rRNA in total soil DNA was developed. Collimonas was detectable in 80% of the soil samples, with densities up to 10(5) cells g(-1) (dry weight) soil. The numbers of Collimonas cells per gram of soil were consistently lowest in fungus-poor arable soils and, surprisingly, also in fungus-rich organic layers of forest soils. When all soils were included, no significant correlation was observed between the number of Collimonas cells and ergosterol-based soil fungal biomass. Based on this result, we rejected our null hypothesis, and possible explanations for this were addressed.
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Affiliation(s)
- Sachie Höppener-Ogawa
- Netherlands Institute of Ecology (NIOO-KNAW), Centre for Terrestrial Ecology, Boterhoeksestraat 48, Heteren, The Netherlands.
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Kowalchuk GA, Speksnijder AGCL, Zhang K, Goodman RM, van Veen JA. Finding the needles in the metagenome haystack. Microb Ecol 2007; 53:475-85. [PMID: 17345132 PMCID: PMC1915608 DOI: 10.1007/s00248-006-9201-2] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2006] [Revised: 12/11/2006] [Accepted: 12/16/2006] [Indexed: 05/14/2023]
Abstract
In the collective genomes (the metagenome) of the microorganisms inhabiting the Earth's diverse environments is written the history of life on this planet. New molecular tools developed and used for the past 15 years by microbial ecologists are facilitating the extraction, cloning, screening, and sequencing of these genomes. This approach allows microbial ecologists to access and study the full range of microbial diversity, regardless of our ability to culture organisms, and provides an unprecedented access to the breadth of natural products that these genomes encode. However, there is no way that the mere collection of sequences, no matter how expansive, can provide full coverage of the complex world of microbial metagenomes within the foreseeable future. Furthermore, although it is possible to fish out highly informative and useful genes from the sea of gene diversity in the environment, this can be a highly tedious and inefficient procedure. Microbial ecologists must be clever in their pursuit of ecologically relevant, valuable, and niche-defining genomic information within the vast haystack of microbial diversity. In this report, we seek to describe advances and prospects that will help microbial ecologists glean more knowledge from investigations into metagenomes. These include technological advances in sequencing and cloning methodologies, as well as improvements in annotation and comparative sequence analysis. More significant, however, will be ways to focus in on various subsets of the metagenome that may be of particular relevance, either by limiting the target community under study or improving the focus or speed of screening procedures. Lastly, given the cost and infrastructure necessary for large metagenome projects, and the almost inexhaustible amount of data they can produce, trends toward broader use of metagenome data across the research community coupled with the needed investment in bioinformatics infrastructure devoted to metagenomics will no doubt further increase the value of metagenomic studies in various environments.
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Affiliation(s)
- George A Kowalchuk
- Centre for Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 40, 6666 ZG, Heteren, The Netherlands.
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de Boer W, Wagenaar AM, Klein Gunnewiek PJA, van Veen JA. In vitro suppression of fungi caused by combinations of apparently non-antagonistic soil bacteria. FEMS Microbiol Ecol 2007; 59:177-85. [PMID: 17233750 DOI: 10.1111/j.1574-6941.2006.00197.x] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
We hypothesized that apparently non-antagonistic soil bacteria may contribute to suppression of fungi during competitive interactions with other bacteria. Four soil bacteria (Brevundimonas sp., Luteibacter sp., Pedobacter sp. and Pseudomonas sp.) that exhibited little or no visible antifungal activity on different agar media were prescribed. Single and mixed strains of these species were tested for antagonism on a nutrient-poor agar medium against the plant pathogenic fungi Fusarium culmorum and Rhizoctonia solani and the saprotrophic fungus Trichoderma harzianum. Single bacterial strains caused little to moderate growth reduction of fungi (quantified as ergosterol), most probably due to nutrient withdrawal from the media. Growth reduction of fungi by the bacterial mixture was much stronger than that by the single strains. This appeared to be mostly due to competitive interactions between the Pseudomonas and Pedobacter strains. We argue that cohabitation of these strains triggered antibiotic production via interspecific interactions and that the growth reduction of fungi was a side-effect caused by the sensitivity of the fungi to bacterial secondary metabolites. Induction of gliding behavior in the Pedobacter strain by other strains was also observed. Our results indicate that apparently non-antagonistic soil bacteria may be important contributors to soil suppressiveness and fungistasis when in a community context.
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Affiliation(s)
- Wietse de Boer
- Netherlands Institute of Ecology (NIOO-KNAW), Centre for Terrestrial Ecology, ZG Heteren, The Netherlands.
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Leveau JHJ, Gerards S, Fritsche K, Zondag G, van Veen JA. Genomic flank-sequencing of plasposon insertion sites for rapid identification of functional genes. J Microbiol Methods 2006; 66:276-85. [PMID: 16457898 DOI: 10.1016/j.mimet.2005.12.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2005] [Revised: 12/02/2005] [Accepted: 12/13/2005] [Indexed: 10/25/2022]
Abstract
Plasposons are modified mini-Tn5 transposons for random mutagenesis of Gram-negative bacteria. Their unique design allows for the rescue cloning and sequencing of DNA that flanks insertion sites in plasposon mutants. However, this process can be laborious and time-consuming, as it involves genomic DNA isolation, restriction endonuclease treatment, subsequent religation, transformation of religated DNA into an Escherichia coli host, and re-isolation as a plasmid, which is then used as a template in sequencing reactions with primers that read from the plasposon ends into the flanking DNA regions. We describe here a method that produces flanking DNA sequences directly from genomic DNA that is isolated from plasposon mutants. By eliminating the need for rescue cloning, our protocol dramatically reduces time and effort, typically by 2 to 3 working days, as well as costs associated with digestion, ligation, transformation, and plasmid isolation. Furthermore, it allows for a high-throughput automated approach to analysis of the plasposome, i.e. the collective set of plasposon insertion sites in a plasposon mutant library. We have tested the utility of genomic flank-sequencing on three plasposon mutants of the soil bacterium Collimonas fungivorans with abolished ability to degrade chitin.
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Affiliation(s)
- Johan H J Leveau
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Terrestrial Microbial Ecology, Boterhoeksestraat 48, 6666 GA Heteren, The Netherlands.
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Leveau JHJ, Gerards S, de Boer W, van Veen JA. Phylogeny-function analysis of (meta)genomic libraries: screening for expression of ribosomal RNA genes by large-insert library fluorescent in situ hybridization (LIL-FISH). Environ Microbiol 2004; 6:990-8. [PMID: 15305924 DOI: 10.1111/j.1462-2920.2004.00673.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
We assessed the utility of fluorescent in situ hybridization (FISH) in the screening of clone libraries of (meta)genomic or environmental DNA for the presence and expression of bacterial ribosomal RNA (rRNA) genes. To establish proof-of-principle, we constructed a fosmid-based library in Escherichia coli of large-sized genomic DNA fragments of the mycophagous soil bacterium Collimonas fungivorans, and hybridized 768 library clones with the Collimonas-specific fluorescent probe CTE998-1015. Critical to the success of this approach (which we refer to as large-insert library FISH or LIL-FISH) was the ability to induce fosmid copy number, the exponential growth status of library clones in the FISH assay and the use of a simple pooling strategy to reduce the number of hybridizations. Twelve out of 768 E. coli clones were suspected to harbour and express Collimonas 16S rRNA genes based on their hybridization to CTE998-1015. This was confirmed by the finding that all 12 clones were also identified in an independent polymerase chain reaction-based screening of the same 768 clones using a primer set for the specific detection of Collimonas 16S ribosomal DNA (rDNA). Fosmids isolated from these clones were grouped by restriction analysis into two distinct contigs, confirming that C. fungivorans harbours at least two 16S rRNA genes. For one contig, representing 1-2% of the genome, the nucleotide sequence was determined, providing us with a narrow but informative view of Collimonas genome structure and content.
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Affiliation(s)
- Johan H J Leveau
- Netherlands Institute of Ecology (NIOO-KNAW), Centre for Terrestrial Ecology, Boterhoeksestraat 48, 6666 GA Heteren, the Netherlands.
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de Boer W, Leveau JHJ, Kowalchuk GA, Gunnewiek PJAK, Abeln ECA, Figge MJ, Sjollema K, Janse JD, van Veen JA. Collimonas fungivorans gen. nov., sp. nov., a chitinolytic soil bacterium with the ability to grow on living fungal hyphae. Int J Syst Evol Microbiol 2004; 54:857-864. [PMID: 15143036 DOI: 10.1099/ijs.0.02920-0] [Citation(s) in RCA: 111] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A polyphasic approach was used to describe the phylogenetic position of 22 chitinolytic bacterial isolates that were able to grow at the expense of intact, living hyphae of several soil fungi. These isolates, which were found in slightly acidic dune soils in the Netherlands, were strictly aerobic, Gram-negative rods. Cells grown in liquid cultures were flagellated and possessed pili. A wide range of sugars, alcohols, organic acids and amino acids could be metabolized, whereas several di- and trisaccharides could not be used as substrates. The major cellular fatty acids were C(16 : 0), C(16 : 1)omega7c and C(18 : 1)omega7c. DNA G+C contents were 57-62 mol%. Analysis of nearly full-length 16S rDNA sequences showed that the isolates were related closely to each other (>98.6 % sequence similarity) and could be assigned to the beta-Proteobacteria, family 'Oxalobacteraceae', order 'Burkholderiales'. The most closely related species belonged to the genera Herbaspirillum and Janthinobacterium, exhibiting 95.9-96.7 % (Herbaspirillum species) and 94.3-95.6 % (Janthinobacterium species) 16S rDNA sequence similarity to the isolates. Several physiological and biochemical properties indicated that the isolates could be distinguished clearly from both of these genera. Therefore, it is proposed that the isolates described in this study are representatives of a novel genus, Collimonas gen. nov. Genomic fingerprinting (BOX-PCR), detailed analysis of 16S rDNA patterns and physiological characterization (Biolog) of the isolates revealed the existence of four subclusters. The name Collimonas fungivorans gen. nov., sp. nov. has been given to one subcluster (four isolates) that appears to be in the centre of the novel genus; isolates in the other subclusters have been tentatively named Collimonas sp. The type strain of Collimonas fungivorans gen. nov., sp. nov. is Ter6(T) (=NCCB 100033(T)=LMG 21973(T)).
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Affiliation(s)
- Wietse de Boer
- Netherlands Institute of Ecology, Centre for Terrestrial Ecology, Department of Plant-Microorganism Interactions, NL-6666 ZG Heteren, the Netherlands
| | - Johan H J Leveau
- Netherlands Institute of Ecology, Centre for Terrestrial Ecology, Department of Plant-Microorganism Interactions, NL-6666 ZG Heteren, the Netherlands
| | - George A Kowalchuk
- Netherlands Institute of Ecology, Centre for Terrestrial Ecology, Department of Plant-Microorganism Interactions, NL-6666 ZG Heteren, the Netherlands
| | - Paulien J A Klein Gunnewiek
- Netherlands Institute of Ecology, Centre for Terrestrial Ecology, Department of Plant-Microorganism Interactions, NL-6666 ZG Heteren, the Netherlands
| | - Edwin C A Abeln
- Netherlands Culture Collection of Bacteria, NL-3584 CT Utrecht, the Netherlands
| | - Marian J Figge
- Netherlands Culture Collection of Bacteria, NL-3584 CT Utrecht, the Netherlands
| | - Klaas Sjollema
- Eukaryotic Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, NL-9751 NN Haren, the Netherlands
| | - Jaap D Janse
- Plant Protection Service, Section Bacteriology, NL-6700 HC Wageningen, the Netherlands
| | - Johannes A van Veen
- Netherlands Institute of Ecology, Centre for Terrestrial Ecology, Department of Plant-Microorganism Interactions, NL-6666 ZG Heteren, the Netherlands
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de Souza FA, Kowalchuk GA, Leeflang P, van Veen JA, Smit E. PCR-denaturing gradient gel electrophoresis profiling of inter- and intraspecies 18S rRNA gene sequence heterogeneity is an accurate and sensitive method to assess species diversity of arbuscular mycorrhizal fungi of the genus Gigaspora. Appl Environ Microbiol 2004; 70:1413-24. [PMID: 15006761 PMCID: PMC368397 DOI: 10.1128/aem.70.3.1413-1424.2004] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2003] [Accepted: 11/19/2003] [Indexed: 11/20/2022] Open
Abstract
Despite the importance of arbuscular mycorrhizal fungi in the majority of terrestrial ecosystems, their ecology, genetics, and evolution are poorly understood, partly due to difficulties associated with detecting and identifying species. We explored the inter- and intraspecies variations of the 18S rRNA genes of the genus Gigaspora to assess the use of this marker for the discrimination of Gigaspora isolates and of Gigasporaceae populations from environmental samples. Screening of 48 Gigaspora isolates by PCR-denaturing gradient gel electrophoresis (DGGE) revealed that the V3-V4 region of the 18S rRNA gene contained insufficient variation to discriminate between different Gigaspora species. In contrast, the patterns of 18S ribosomal DNA (rDNA) heterogeneity within the V9 region of this marker could be used for reliable identification of all recognized species within this genus. PCR-DGGE patterns provided insight into some putative misidentifications and could be used to differentiate geographic isolates of G. albida, G. gigantea, and G. margarita but not G. rosea. Two major clusters were apparent based upon PCR-DGGE ribotype patterns, one containing G. albida, G. candida, G. ramisporophora, and G. rosea and the other containing G. decipiens and G. margarita. Dissection of the DGGE patterns by cloning, DGGE screening, and sequencing confirmed these groupings and revealed that some ribotypes were shared across species boundaries. Of the 48 isolates examined, only two displayed any spore-to-spore variation, and these exceptions may be indicative of coisolation of more than one species or subspecies within these cultures. Two Brazilian agricultural soils were also analyzed with a Gigasporaceae-specific nested PCR approach, revealing a dominance of G. margarita within this family.
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Affiliation(s)
- Francisco A de Souza
- Empresa Brasileira de Pesquisa Agropecuária, Embrapa Agrobiologia, Seropédica, Rio de Janeiro, Brazil.
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Folman LB, Postma J, van Veen JA. Characterisation of Lysobacter enzymogenes (Christensen and Cook 1978) strain 3.1T8, a powerful antagonist of fungal diseases of cucumber. Microbiol Res 2003; 158:107-15. [PMID: 12906383 DOI: 10.1078/0944-5013-00185] [Citation(s) in RCA: 93] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Isolate 3.1T8 of Lysobacter enzymogenes (Christensen and Cook 1978), originating from the rhizosphere of cucumber and shown to have the potential to control Pythium aphanidermatum, is described. The strain produces extracellular proteases and lipases and shows high levels of resistance against streptomycin, kanamycin and tetracycline, but not to chloramphenicol. It shows strong in vitro antibiosis against P. aphanidermatum and several other phytopathogenic fungi. In order to identify the isolate, a carbon substrate oxidation profile (Biolog) was generated, and fatty acid methyl ester (FAME) analysis was performed. Also, the 16S rRNA gene was cloned and sequenced. With Biolog and FAME analysis, no assignment to species level was possible, because the species was not in the respective databases. BLAST analysis of the obtained sequence, followed by phylogenetic analysis, using a number of related and unrelated sequences, showed that the isolate was most closely related to Lysobacter enzymogenes (Christensen and Cook 1978).
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Affiliation(s)
- Larissa B Folman
- Institute of Evolutionary and Ecological Sciences, University of Leiden, P.O. Box 9516, 2300 RA Leiden, The Netherlands.
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Abstract
Most soils inhibit fungal germination and growth to a certain extent, a phenomenon known as soil fungistasis. Previous observations have implicated microorganisms as the causal agents of fungistasis, with their action mediated either by available carbon limitation (nutrient deprivation hypothesis) or production of antifungal compounds (antibiosis hypothesis). To obtain evidence for either of these hypotheses, we measured soil respiration and microbial numbers (as indicators of nutrient stress) and bacterial community composition (as an indicator of potential differences in the composition of antifungal components) during the development of fungistasis. This was done for two fungistatic dune soils in which fungistasis was initially fully or partly relieved by partial sterilization treatment or nutrient addition. Fungistasis development was measured as restriction of the ability of the fungi Chaetomium globosum, Fusarium culmorum, Fusarium oxysporum, and Trichoderma harzianum to colonize soils. Fungistasis did not always reappear after soil treatments despite intense competition for carbon, suggesting that microbial community composition is important in the development of fungistasis. Both microbial community analysis and in vitro antagonism tests indicated that the presence of pseudomonads might be essential for the development of fungistasis. Overall, the results lend support to the antibiosis hypothesis.
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Affiliation(s)
- Wietse de Boer
- Department of Plant-Microorganism Interactions, Centre for Terrestrial Ecology, Netherlands Institute of Ecology, 6666 ZG Heteren, The Netherlands.
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