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Sivojienė D, Masevičienė A, Žičkienė L, Ražukas A, Kačergius A. Soil Microbial Community Structure and Carbon Stocks Following Fertilization with Organic Fertilizers and Biological Inputs. BIOLOGY 2024; 13:534. [PMID: 39056726 PMCID: PMC11273871 DOI: 10.3390/biology13070534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Revised: 07/07/2024] [Accepted: 07/15/2024] [Indexed: 07/28/2024]
Abstract
The application of organic fertilizers and biological inputs to soil inevitably affects its quality, agrochemical indicators, and microbiota. Sustainable agriculture is based on continuously learning about how to properly manage available soil, water, and biological resources. The aim of the study was to determine changes in microorganism communities and carbon stocks in infertile soils for fertilization using different organic fertilizers and their combinations with bio-inputs. Genetic analysis of microorganism populations was performed using the NGS approach. Our study showed that the application of organic fertilizers affects the soil microbiota and the taxonomic structure of its communities. Specific groups of bacteria, such as Bacillota, were promoted by organic fertilization, meanwhile the abundance of Pseudomonadota and Ascomycota decreased in most treatments after the application of poultry manure. Metagenomic analysis confirmed that the use of bio-inputs increased the relative abundance of Trichoderma spp. fungi; meanwhile, a significant change was not found in the representatives of Azotobacter compared to the treatments where the bio-inputs were not used. The positive influence of fertilization appeared on all the studied agrochemical indicators. Higher concentrations of Corg and Nmin accumulated in the soil when we used granulated poultry manure, and pHKCl when we used cattle manure.
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Affiliation(s)
- Diana Sivojienė
- Lithuanian Research Centre for Agriculture and Forestry, Kėdainiai District, LT-58344 Akademija, Lithuania; (A.M.); (L.Ž.); (A.R.); (A.K.)
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2
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Stanojković-Sebić A, Miladinović V, Pivić R. Response of Arugula to Integrated Use of Biological, Inorganic, and Organic Fertilization. Microorganisms 2024; 12:1334. [PMID: 39065102 PMCID: PMC11278703 DOI: 10.3390/microorganisms12071334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Revised: 06/25/2024] [Accepted: 06/26/2024] [Indexed: 07/28/2024] Open
Abstract
This study evaluated the effects of solely and integrated application of inorganic (NPK), commercial organic (NC), and biological (MIX, mixed strains Ensifer meliloti and Azotobacter chroococcum) fertilizers on the chemical characteristics of arugula biomass and its yield, as well as changes in soil microbiological parameters after the experiment in relation to the control treatment (Ø). The experiment was performed in semi-controlled greenhouse conditions, in pots, from the 4th decade of March to the 2nd decade of September, in 2023, at three cutting times/swaths, during one agricultural season, with Vertisol soil. For soil characterization, the following parameters were analysed: granulometric composition using sieving and sedimentation procedure; soil acidity-potentiometrically; SOM-soil organic matter by Kotzmann method; total N using CNS analyser; available P-spectrophotometrically; available K-flame photometrically; total number of microorganisms on an agarized soil extract medium; fungi on a solid Czapek agar; actinomycetes on a solid Krasiljnikov agar with saccharose; Azotobacter spp. on a liquid Fyodorov medium with mannitol; ammonifiers on a liquid medium with asparagine; and dehydrogenase activity-spectrophotometrically. For plant characterization, the following parameters were determined: N and C, both on CNS analyser; P on spectrophotometer; K on flame photometer; air-dried yield biomass. A stimulative effect on all microbiological parameters was found in the treatment with integrated use of organic and biological fertilizer, except for fungi, which grew better in the treatments with separate inorganic and organic fertilizers. Generally, the stimulative impact on plant chemical parameters manifested in combined inorganic and biological, organic and biological, and inorganic and organic fertilization treatments, and was inhibited in treatment without fertilization, in all three swaths, which could also be stated for the plant yield. Positive influence of all fertilization treatments on chemical parameters was observed for the second swath in relation to the first and the third. The total yield in the NPK+MIX treatment was 121%, and in the NC+MIX treatment, it was 87% higher compared to the control (Ø). In general, integrated use of inorganic and biological, organic and biological, and inorganic and organic fertilizers, respectively, could be proposed as an optimal fertilization treatment in arugula cultivation.
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Affiliation(s)
| | - Vladimir Miladinović
- Institute for Vegetable Crops, Karadjordjeva 71, 11420 Smederevska Palanka, Serbia;
| | - Radmila Pivić
- Institute of Soil Science, Teodora Drajzera 7, 11000 Belgrade, Serbia;
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Lei Y, Ding D, Duan J, Luo Y, Huang F, Kang Y, Chen Y, Li S. Soil Microbial Community Characteristics and Their Effect on Tea Quality under Different Fertilization Treatments in Two Tea Plantations. Genes (Basel) 2024; 15:610. [PMID: 38790239 PMCID: PMC11121415 DOI: 10.3390/genes15050610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 05/03/2024] [Accepted: 05/07/2024] [Indexed: 05/26/2024] Open
Abstract
Fertilization is an essential aspect of tea plantation management that supports a sustainable tea production and drastically influences soil microbial communities. However, few research studies have focused on the differences of microbial communities and the variation in tea quality in response to different fertilization treatments. In this work, the soil fertility, tea quality, and soil microbial communities were investigated in two domestic tea plantations following the application of chemical and organic fertilizers. We determined the content of mineral elements in the soil, including nitrogen, phosphorus, and potassium, and found that the supplementation of chemical fertilizer directly increased the content of mineral elements. However, the application of organic fertilizer significantly improved the accumulation of tea polyphenols and reduced the content of caffeine. Furthermore, amplicon sequencing results showed that the different ways of applying fertilizer have limited effect on the alpha diversity of the microbial community in the soil while the beta diversity was remarkably influenced. This work also suggests that the bacterial community structure and abundance were also relatively constant while the fungal community structure and abundance were dramatically influenced; for example, Chaetomiaceae at the family level, Hypocreaceae at the order level, Trichoderma at the genus level, and Fusarium oxysporum at the species level were predominantly enriched in the tea plantation applying organic fertilizer. Moreover, the bacterial and fungal biomarkers were also analyzed and it was found that Proteobacteria and Gammaproteobacteria (bacteria) and Tremellomycetes (fungi) were potentially characterized as biomarkers in the plantation under organic fertilization. These results provide a valuable basis for the application of organic fertilizer to improve the soil of tea plantations in the future.
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Affiliation(s)
- Yu Lei
- Tea Research Institute, Hunan Academy of Agricultural Science, Changsha 410125, China; (Y.L.); (D.D.); (J.D.); (Y.L.); (F.H.); (Y.K.); (Y.C.)
- National Medium and Small Leaf Tea Plant Germplasm Resource Repository (Changsha), Changsha 410125, China
- National Center for Tea Improvement, Hunan Branch/Hunan Tea Variety and Seedling Engineering Technology Research Center, Changsha 410125, China
| | - Ding Ding
- Tea Research Institute, Hunan Academy of Agricultural Science, Changsha 410125, China; (Y.L.); (D.D.); (J.D.); (Y.L.); (F.H.); (Y.K.); (Y.C.)
- National Medium and Small Leaf Tea Plant Germplasm Resource Repository (Changsha), Changsha 410125, China
- National Center for Tea Improvement, Hunan Branch/Hunan Tea Variety and Seedling Engineering Technology Research Center, Changsha 410125, China
| | - Jihua Duan
- Tea Research Institute, Hunan Academy of Agricultural Science, Changsha 410125, China; (Y.L.); (D.D.); (J.D.); (Y.L.); (F.H.); (Y.K.); (Y.C.)
- National Medium and Small Leaf Tea Plant Germplasm Resource Repository (Changsha), Changsha 410125, China
- National Center for Tea Improvement, Hunan Branch/Hunan Tea Variety and Seedling Engineering Technology Research Center, Changsha 410125, China
| | - Yi Luo
- Tea Research Institute, Hunan Academy of Agricultural Science, Changsha 410125, China; (Y.L.); (D.D.); (J.D.); (Y.L.); (F.H.); (Y.K.); (Y.C.)
- National Medium and Small Leaf Tea Plant Germplasm Resource Repository (Changsha), Changsha 410125, China
- National Center for Tea Improvement, Hunan Branch/Hunan Tea Variety and Seedling Engineering Technology Research Center, Changsha 410125, China
| | - Feiyi Huang
- Tea Research Institute, Hunan Academy of Agricultural Science, Changsha 410125, China; (Y.L.); (D.D.); (J.D.); (Y.L.); (F.H.); (Y.K.); (Y.C.)
- National Medium and Small Leaf Tea Plant Germplasm Resource Repository (Changsha), Changsha 410125, China
- National Center for Tea Improvement, Hunan Branch/Hunan Tea Variety and Seedling Engineering Technology Research Center, Changsha 410125, China
| | - Yankai Kang
- Tea Research Institute, Hunan Academy of Agricultural Science, Changsha 410125, China; (Y.L.); (D.D.); (J.D.); (Y.L.); (F.H.); (Y.K.); (Y.C.)
- National Medium and Small Leaf Tea Plant Germplasm Resource Repository (Changsha), Changsha 410125, China
- National Center for Tea Improvement, Hunan Branch/Hunan Tea Variety and Seedling Engineering Technology Research Center, Changsha 410125, China
| | - Yingyu Chen
- Tea Research Institute, Hunan Academy of Agricultural Science, Changsha 410125, China; (Y.L.); (D.D.); (J.D.); (Y.L.); (F.H.); (Y.K.); (Y.C.)
- National Medium and Small Leaf Tea Plant Germplasm Resource Repository (Changsha), Changsha 410125, China
- National Center for Tea Improvement, Hunan Branch/Hunan Tea Variety and Seedling Engineering Technology Research Center, Changsha 410125, China
| | - Saijun Li
- Tea Research Institute, Hunan Academy of Agricultural Science, Changsha 410125, China; (Y.L.); (D.D.); (J.D.); (Y.L.); (F.H.); (Y.K.); (Y.C.)
- National Medium and Small Leaf Tea Plant Germplasm Resource Repository (Changsha), Changsha 410125, China
- National Center for Tea Improvement, Hunan Branch/Hunan Tea Variety and Seedling Engineering Technology Research Center, Changsha 410125, China
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Gupta VVSR, Tiedje JM. Ranking environmental and edaphic attributes driving soil microbial community structure and activity with special attention to spatial and temporal scales. MLIFE 2024; 3:21-41. [PMID: 38827504 PMCID: PMC11139212 DOI: 10.1002/mlf2.12116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 01/05/2024] [Accepted: 02/05/2024] [Indexed: 06/04/2024]
Abstract
The incredibly complex soil microbial communities at small scales make their analysis and identification of reasons for the observed structures challenging. Microbial community structure is mainly a result of the inoculum (dispersal), the selective advantages of those organisms under the habitat-based environmental attributes, and the ability of those colonizers to sustain themselves over time. Since soil is protective, and its microbial inhabitants have long adapted to varied soil conditions, significant portions of the soil microbial community structure are likely stable. Hence, a substantial portion of the community will not correlate to often measured soil attributes. We suggest that the drivers be ranked on the basis of their importance to the fundamental needs of the microbes: (i) those that supply energy, i.e., organic carbon and electron acceptors; (ii) environmental effectors or stressors, i.e., pH, salt, drought, and toxic chemicals; (iii) macro-organism associations, i.e., plants and their seasonality, animals and their fecal matter, and soil fauna; and (iv) nutrients, in order, N, P, and probably of lesser importance, other micronutrients, and metals. The relevance of drivers also varies with spatial and time scales, for example, aggregate to field to regional, and persistent to dynamic populations to transcripts, and with the extent of phylogenetic difference, hence phenotypic differences in organismal groups. We present a summary matrix to provide guidance on which drivers are important for particular studies, with special emphasis on a wide range of spatial and temporal scales, and illustrate this with genomic and population (rRNA gene) data from selected studies.
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Affiliation(s)
| | - James M. Tiedje
- Centre for Microbial EcologyMichigan State UniversityEast LansingMichiganUSA
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Guo S, Jiao Z, Yan Z, Yan X, Deng X, Xiong W, Tao C, Liu H, Li R, Shen Q, Kowalchuk GA, Geisen S. Predatory protists reduce bacteria wilt disease incidence in tomato plants. Nat Commun 2024; 15:829. [PMID: 38280866 PMCID: PMC10821857 DOI: 10.1038/s41467-024-45150-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 01/16/2024] [Indexed: 01/29/2024] Open
Abstract
Soil organisms are affected by the presence of predatory protists. However, it remains poorly understood how predatory protists can affect plant disease incidence and how fertilization regimes can affect these interactions. Here, we characterise the rhizosphere bacteria, fungi and protists over eleven growing seasons of tomato planting under three fertilization regimes, i.e conventional, organic and bioorganic, and with different bacterial wilt disease incidence levels. We find that predatory protists are negatively associated with disease incidence, especially two ciliophoran Colpoda OTUs, and that bioorganic fertilization enhances the abundance of predatory protists. In glasshouse experiments we find that the predatory protist Colpoda influences disease incidence by directly consuming pathogens and indirectly increasing the presence of pathogen-suppressive microorganisms in the soil. Together, we demonstrate that predatory protists reduce bacterial wilt disease incidence in tomato plants via direct and indirect reductions of pathogens. Our study provides insights on the role that predatory protists play in plant disease, which could be used to design more sustainable agricultural practices.
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Affiliation(s)
- Sai Guo
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China
- The Sanya Institute of the Nanjing Agricultural University, Sanya, Hainan Province, PR China
| | - Zixuan Jiao
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China
| | - Zhiguang Yan
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China
| | - Xinyue Yan
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China
| | - Xuhui Deng
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China
- The Sanya Institute of the Nanjing Agricultural University, Sanya, Hainan Province, PR China
| | - Wu Xiong
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China
- The Sanya Institute of the Nanjing Agricultural University, Sanya, Hainan Province, PR China
| | - Chengyuan Tao
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China
- The Sanya Institute of the Nanjing Agricultural University, Sanya, Hainan Province, PR China
| | - Hongjun Liu
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China
- The Sanya Institute of the Nanjing Agricultural University, Sanya, Hainan Province, PR China
| | - Rong Li
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China.
- The Sanya Institute of the Nanjing Agricultural University, Sanya, Hainan Province, PR China.
| | - Qirong Shen
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China
| | - George A Kowalchuk
- Ecology and Biodiversity Group, Department of Biology, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Stefan Geisen
- Laboratory of Nematology, Wageningen University, 6700 AA, Wageningen, The Netherlands
- Netherlands Department of Terrestrial Ecology, Netherlands Institute for Ecology, (NIOO-KNAW), 6708 PB, Wageningen, The Netherlands
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6
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Kruczyńska A, Kuźniar A, Banach A, Jurczyk S, Podlewski J, Słomczewski A, Marzec-Grządziel A, Sochaczewska A, Gałązka A, Wolińska A. Changes in the mycobiome structure in response to reduced nitrogen fertilization in two cropping systems of maize. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 904:166343. [PMID: 37591379 DOI: 10.1016/j.scitotenv.2023.166343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 08/13/2023] [Accepted: 08/14/2023] [Indexed: 08/19/2023]
Abstract
Nitrogen (N) is an essential element for plant productivity; hence, it is abundantly applied to the soil in the form of organic or chemical fertilizers, which consequently have a negative impact on the environment. Therefore, the main objective of our study was to investigate the structure and richness of the soil mycobiome in response to reduced nitrogen fertilization under two cropping systems: plowing (P) and no-till (NT). Moreover, the scope of the study perfectly falls into the EU "From Field to Table" strategy, which recommends a 20 % reduction of nitrogen fertilization of agricultural soils by 2030. In our study, the samples were collected twice during a single growing season: before maize sowing (without fertilization) and after harvesting the crop (four different fertilization rates). The mycobiome structure was identified based on the next generation sequencing (NGS) technique. Overall, our research has proved that the cropping system is important in terms of the formation of the fungal mycobiome structure and relative abundance. In addition, we confirmed that soil properties have a significant impact on fungal communities. We determined that a 20 % lower nitrogen fertilization rate (92.0 kg N ha-1) had a positive effect on the abundance of fungal communities. Moreover, the highest biodiversity at each of the taxonomic levels tested (phylum, class, genus) in the NT system and at the class and genus levels in the P system was also evidenced at the 20 % lower N fertilization rate. We also recommended potential indicators confirming the positive impact of reduced fertilization in two cropping systems: plowing - Epicoccum, Metarhizium, Mycosphaerella, and Paraconiothyrium and no-till - Peziza, Podospora, Metarhizium, Trechispora, and Umbelopsis.
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Affiliation(s)
- Anna Kruczyńska
- Department of Biology and Biotechnology of Microorganisms, The John Paul II Catholic University of Lublin, Konstantynów 1 I Str., Lublin, Poland.
| | - Agnieszka Kuźniar
- Department of Biology and Biotechnology of Microorganisms, The John Paul II Catholic University of Lublin, Konstantynów 1 I Str., Lublin, Poland.
| | - Artur Banach
- Department of Biology and Biotechnology of Microorganisms, The John Paul II Catholic University of Lublin, Konstantynów 1 I Str., Lublin, Poland.
| | - Sara Jurczyk
- Department of Artificial Intelligence, The John Paul II Catholic University of Lublin, Konstantynów 1 H Str., Lublin, Poland.
| | - Jacek Podlewski
- Potulicka Foundation Economic Center, Wojnowo 5, Sicienko, Poland.
| | | | - Anna Marzec-Grządziel
- Institute of Soil Science and Plant Cultivation, Department of Agriculture Microbiology, Czartoryskich 8 Str., 24-100 Puławy, Poland.
| | - Anna Sochaczewska
- Department of Biology and Biotechnology of Microorganisms, The John Paul II Catholic University of Lublin, Konstantynów 1 I Str., Lublin, Poland.
| | - Anna Gałązka
- Institute of Soil Science and Plant Cultivation, Department of Agriculture Microbiology, Czartoryskich 8 Str., 24-100 Puławy, Poland.
| | - Agnieszka Wolińska
- Department of Biology and Biotechnology of Microorganisms, The John Paul II Catholic University of Lublin, Konstantynów 1 I Str., Lublin, Poland.
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7
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Kravchenko I, Rayko M, Sokornova S, Tikhonova E, Konopkin A, Lapidus A. Analysis of rhizosphere fungal community of agricultural crops cultivated in laboratory experiments on Chernevaya taiga soil. World J Microbiol Biotechnol 2023; 40:27. [PMID: 38057541 DOI: 10.1007/s11274-023-03827-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 11/02/2023] [Indexed: 12/08/2023]
Abstract
Chernevaya taiga of Western Siberia, Russia, is a unique ecosystem characterized by fertile soil, exceptionally large herbaceous plant sizes, and extraordinarily rapid rates of plant residue degradation. We expected that growing crops on soil collected from Chernevaya taiga, which has never been used for agricultural purposes before, would result in a distinct rhizospheric fungal community. This community could potentially yield novel, potent biostimulators and biocontrol fungi for modern agriculture. To check this idea, we used high-throughput ITS sequencing to examine the microbial communities in the rhizosphere of spring wheat and radish grown in greenhouse experiments on Chernevaya and control soils. Additionally, representative fungal strains were isolated and assessed for their ability to promote growth in wheat seedlings. The study revealed that the most abundant phyla in the rhizospheric fungal community were Mortierellomycota, primarily consisting of Mortierella species, and Ascomycota. Mucor and Umbelopsis comprised the majority of Mucoromycota in the control soils. Fusarium and Oidiodendron, two potentially plant-pathogenic fungi, were only found in the rhizosphere of crops grown in the control soil. Conversely, Chernevaya soil contained a diverse range of potential biocontrol fungi for plants. Tested novel fungal isolates showed a stimulating effect on the development of wheat seedlings and positively affected their rate of biomass accumulation. The results of the study demonstrate that the soil of Chernevaya taiga do indeed contain fungi with prominent potential to stimulate agricultural plants growth.
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Affiliation(s)
- Irina Kravchenko
- Research Center of Biotechnology, Winogradsky Institute of Microbiology, Russian Academy of Sciences, 119071, Moscow, Russia.
| | - Mikhail Rayko
- Center for Bioinformatics and Algorithmic Biotechnology, St. Petersburg State University, 199034, Saint Petersburg, Russia
| | - Sophie Sokornova
- Department of Phytotoxicology and Biotechnology, All-Russian Institute of Plant Protection, 196608, Saint Petersburg, Russia
| | - Ekaterina Tikhonova
- Research Center of Biotechnology, Winogradsky Institute of Microbiology, Russian Academy of Sciences, 119071, Moscow, Russia
| | - Aleksey Konopkin
- Research Center of Biotechnology, Winogradsky Institute of Microbiology, Russian Academy of Sciences, 119071, Moscow, Russia
| | - Alla Lapidus
- Center for Bioinformatics and Algorithmic Biotechnology, St. Petersburg State University, 199034, Saint Petersburg, Russia
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8
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Fischer MS, Patel NJ, de Lorimier PJ, Traxler MF. Prescribed fire selects for a pyrophilous soil sub-community in a northern California mixed conifer forest. Environ Microbiol 2023; 25:2498-2515. [PMID: 37553729 DOI: 10.1111/1462-2920.16475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 07/20/2023] [Indexed: 08/10/2023]
Abstract
Prescribed fire is a critical strategy for mitigating the effects of catastrophic wildfires. While the above-ground response to fire has been well-documented, fewer studies have addressed the effect of prescribed fire on soil microorganisms. To understand how soil microbial communities respond to prescribed fire, we sampled four plots at a high temporal resolution (two burned, two controls), for 17 months, in a mixed conifer forest in northern California, USA. Using amplicon sequencing, we found that prescribed fire significantly altered both fungal and bacterial community structure. We found that most differentially abundant fungal taxa had a positive fold-change, while differentially abundant bacterial taxa generally had a negative fold-change. We tested the null hypothesis that these communities assembled due to neutral processes (i.e., drift and/or dispersal), finding that >90% of taxa fit this neutral prediction. However, a dynamic sub-community composed of burn-associated indicator taxa that were positively differentially abundant was enriched for non-neutral amplicon sequence variants, suggesting assembly via deterministic processes. In synthesizing these results, we identified 15 pyrophilous taxa with a significant and positive response to prescribed burns. Together, these results lay the foundation for building a process-driven understanding of microbial community assembly in the context of the classical disturbance regime of fire.
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Affiliation(s)
- Monika S Fischer
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA
| | - Neem J Patel
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA
| | - Phillip J de Lorimier
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA
| | - Matthew F Traxler
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA
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9
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Li M, Chen C, Zhang H, Wang Z, Song N, Li J, Liang X, Yi K, Gu Y, Guo X. Effects of biochar amendment and organic fertilizer on microbial communities in the rhizosphere soil of wheat in Yellow River Delta saline-alkaline soil. Front Microbiol 2023; 14:1250453. [PMID: 37808323 PMCID: PMC10556502 DOI: 10.3389/fmicb.2023.1250453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 09/11/2023] [Indexed: 10/10/2023] Open
Abstract
The biochar and organic fertilizer amendment have been used as an effective practice to increase soil fertility. Nevertheless, the mechanisms of microbial community response to organic fertilizer and biochar application on saline-alkali soil have not been clarified. This study investigated the effects at different concentrations of organic fertilizer and biochar on the microbial community of wheat rhizosphere soil under field experiment in the Yellow River Delta (China, YRD), using high-throughput sequencing technology. Biochar and organic fertilizer significantly influenced in most soil parameters (p < 0.05), apart from soil moisture content (M), pH, total nitrogen (TN) and soil total phosphorus (TP). Proteobacteria and Actinobacteriota were found in the rhizosphere soil as the main bacterial phyla, and the main fungal phyla were Ascomycota and Mortierellomycota. The soil bacterial and fungal communities under organic fertilizer were distinct from CK. Furthermore, redundancy analysis (RDA) directed that changes in bacterial communities were related to soil properties like pH, available phosphorus (AP), and total organic carbon (TOC), while pH, AP and TP, were crucial contributors in regulating fungal distribution. The correlation between soil parameters and bacteria or fungi varied with the application of biochar and organic fertilizers, and the interaction between the bacteria and fungi in organic fertilizer treatments formed more connections compared with biochar treatments. Our results indicated that biochar was superior to organic fertilizer under the contents set up in this study, and soil parameters increased with biochar and organic fertilizer application rate. The diversity and structure of soil bacteria and fungi differed with the application of biochar and organic fertilizer. The research provides a reference to rational application of organic fertilizer and biochar improvement in saline-alkali soil.
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Affiliation(s)
- Meng Li
- Shandong Institute of Sericulture, Shandong Academy of Agricultural Sciences, Yantai, China
| | - Chuanjie Chen
- Shandong Institute of Sericulture, Shandong Academy of Agricultural Sciences, Yantai, China
| | - Haiyang Zhang
- Shandong Institute of Sericulture, Shandong Academy of Agricultural Sciences, Yantai, China
| | - Zongshuai Wang
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Ningning Song
- School of Resources and Environment, Qingdao Agricultural University, Qingdao, China
| | - Junlin Li
- Shandong Institute of Sericulture, Shandong Academy of Agricultural Sciences, Yantai, China
| | - Xiaoyan Liang
- Shandong Institute of Sericulture, Shandong Academy of Agricultural Sciences, Yantai, China
| | - Kuihua Yi
- Shandong Institute of Sericulture, Shandong Academy of Agricultural Sciences, Yantai, China
| | - Yinyu Gu
- Shandong Institute of Sericulture, Shandong Academy of Agricultural Sciences, Yantai, China
| | - Xiaohong Guo
- School of Resources and Environmental Engineering, Ludong University, Yantai, China
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10
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Wentzien NM, Fernández-González AJ, Villadas PJ, Valverde-Corredor A, Mercado-Blanco J, Fernández-López M. Thriving beneath olive trees: The influence of organic farming on microbial communities. Comput Struct Biotechnol J 2023; 21:3575-3589. [PMID: 37520283 PMCID: PMC10372477 DOI: 10.1016/j.csbj.2023.07.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 07/11/2023] [Accepted: 07/11/2023] [Indexed: 08/01/2023] Open
Abstract
Soil health and root-associated microbiome are interconnected factors involved in plant health. The use of manure amendment on agricultural fields exerts a direct benefit on soil nutrient content and water retention, among others. However, little is known about the impact of manure amendment on the root-associated microbiome, particularly in woody species. In this study, we aimed to evaluate the effects of ovine manure on the microbial communities of the olive rhizosphere and root endosphere. Two adjacent orchards subjected to conventional (CM) and organic (OM) management were selected. We used metabarcoding sequencing to assess the bacterial and fungal communities. Our results point out a clear effect of manure amendment on the microbial community. Fungal richness and diversity were increased in the rhizosphere. The fungal biomass in the rhizosphere was more than doubled, ranging from 1.72 × 106 ± 1.62 × 105 (CM) to 4.54 × 106 ± 8.07 × 105 (OM) copies of the 18 S rRNA gene g-1 soil. Soil nutrient content was also enhanced in the OM orchard. Specifically, oxidable organic matter, total nitrogen, nitrate, phosphorous, potassium and sulfate concentrations were significantly increased in the OM orchard. Moreover, we predicted a higher abundance of bacteria in OM with metabolic functions involved in pollutant degradation and defence against pathogens. Lastly, microbial co-occurrence network showed more positive interactions, complexity and shorter geodesic distance in the OM orchard. According to our results, manure amendment on olive orchards represents a promising tool for positively modulating the microbial community in direct contact with the plant.
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Affiliation(s)
- Nuria M. Wentzien
- Soil and Plant Microbiology Department, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), 18008 Granada, Spain
| | - Antonio J. Fernández-González
- Soil and Plant Microbiology Department, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), 18008 Granada, Spain
| | - Pablo J. Villadas
- Soil and Plant Microbiology Department, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), 18008 Granada, Spain
| | | | - Jesús Mercado-Blanco
- Soil and Plant Microbiology Department, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), 18008 Granada, Spain
- Crop Protection Department, Instituto de Agricultura Sostenible (CSIC), 14004 Córdoba, Spain
| | - Manuel Fernández-López
- Soil and Plant Microbiology Department, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), 18008 Granada, Spain
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11
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Marín-Guirao JI, García-García MDC, Martín-Expósito E, de Cara-García M. Continued Organic Fertigation after Basal Manure Application Does Not Impact Soil Fungal Communities, Tomato Yield or Soil Fertility. Microorganisms 2023; 11:1715. [PMID: 37512888 PMCID: PMC10386759 DOI: 10.3390/microorganisms11071715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 06/21/2023] [Accepted: 06/26/2023] [Indexed: 07/30/2023] Open
Abstract
There is currently a limited understanding of the complex response of fungal microbiota diversity to organic fertigation. In this work, a 2-year field trial with organic tomato crops in a soil previously amended with fresh sheep manure was conducted. Two hypotheses were compared: (i) fertigation with organic liquid fertilizers versus (ii) irrigation with water. At the end of both years, soils were analyzed for physical-chemical parameters and mycobiome variables. Plate culture and DNA metabarcoding methods were performed in order to obtain a detailed understanding of soil fungal communities. Fertigation did not increase any of the physical-chemical parameters. Concerning soil fungal communities, differences were only found regarding the identification of biomarkers. The class Leotiomycetes and the family Myxotrichaceae were identified as biomarkers in the soil fungal community analyzed by means of DNA metabarcoding of the "fertigation" treatment at the end of Year 1. The Mortierella genus was detected as a biomarker in the "water" treatment, and Mucor was identified in the "fertigation" treatment in the cultivable soil fungi at the end of Year 2. In both years, tomato yield and fruit quality did not consistently differ between treatments, despite the high cost of the fertilizers added through fertigation.
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Affiliation(s)
- Jose Ignacio Marín-Guirao
- Andalusian Institute of Agricultural and Fisheries Research Training (IFAPA) La Mojonera, Camino San Nicolás, 1, 04745 Almería, Spain
| | - María Del Carmen García-García
- Andalusian Institute of Agricultural and Fisheries Research Training (IFAPA) La Mojonera, Camino San Nicolás, 1, 04745 Almería, Spain
| | - Emilio Martín-Expósito
- Andalusian Institute of Agricultural and Fisheries Research Training (IFAPA) La Mojonera, Camino San Nicolás, 1, 04745 Almería, Spain
| | - Miguel de Cara-García
- Andalusian Institute of Agricultural and Fisheries Research Training (IFAPA) La Mojonera, Camino San Nicolás, 1, 04745 Almería, Spain
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12
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Schlatter DC, Gamble JD, Castle S, Rogers J, Wilson M. Abiotic and Biotic Drivers of Soil Fungal Communities in Response to Dairy Manure Amendment. Appl Environ Microbiol 2023; 89:e0193122. [PMID: 37212685 PMCID: PMC10304672 DOI: 10.1128/aem.01931-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 04/24/2023] [Indexed: 05/23/2023] Open
Abstract
Modern agriculture often relies on large inputs of synthetic fertilizers to maximize crop yield potential, yet their intensive use has led to nutrient losses and impaired soil health. Alternatively, manure amendments provide plant available nutrients, build organic carbon, and enhance soil health. However, we lack a clear understanding of how consistently manure impacts fungal communities, the mechanisms via which manure impacts soil fungi, and the fate of manure-borne fungi in soils. We assembled soil microcosms using five soils to investigate how manure amendments impact fungal communities over a 60-day incubation. Further, we used autoclaving treatments of soils and manure to determine if observed changes in soil fungal communities were due to abiotic or biotic properties, and if indigenous soil communities constrained colonization of manure-borne fungi. We found that manure amended soil fungal communities diverged from nonamended communities over time, often in concert with a reduction in diversity. Fungal communities responded to live and autoclaved manure in a similar manner, suggesting that abiotic forces are primarily responsible for the observed dynamics. Finally, manure-borne fungi declined quickly in both live and autoclaved soil, indicating that the soil environment is unsuitable for their survival. IMPORTANCE Manure amendments in agricultural systems can impact soil microbial communities via supplying growth substrates for indigenous microbes or by introducing manure-borne taxa. This study explores the consistency of these impacts on soil fungal communities and the relative importance of abiotic and biotic drivers across distinct soils. Different fungal taxa responded to manure among distinct soils, and shifts in soil fungal communities were driven largely by abiotic factors, rather than introduced microbes. This work demonstrates that manure may have inconsistent impacts on indigenous soil fungi, and that abiotic properties of soils render them largely resistant to invasion by manure-borne fungi.
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Affiliation(s)
| | - Joshua D. Gamble
- USDA-ARS Plant Science Research Unit, Saint Paul, Minnesota, USA
| | - Sarah Castle
- USDA-ARS Plant Science Research Unit, Saint Paul, Minnesota, USA
| | - Julia Rogers
- Department of Soil, Water, and Climate, University of Minnesota, Saint Paul, Minnesota, USA
| | - Melissa Wilson
- Department of Soil, Water, and Climate, University of Minnesota, Saint Paul, Minnesota, USA
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13
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Aranguren R, Voyron S, Ungaro F, Cañón J, Lumini E. Metabarcoding Reveals Impact of Different Land Uses on Fungal Diversity in the South-Eastern Region of Antioquia, Colombia. PLANTS (BASEL, SWITZERLAND) 2023; 12:1126. [PMID: 36903986 PMCID: PMC10005449 DOI: 10.3390/plants12051126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 02/20/2023] [Accepted: 02/28/2023] [Indexed: 06/18/2023]
Abstract
Changes in soil fungal communities caused by land use have not been sufficiently studied in South American Andosols, which are considered key food production areas. Since fungal communities play an important role in soil functionality, this study analysed 26 soil samples of Andosols collected from locations devoted to conservation, agriculture and mining activities in Antioquia, Colombia, to establish differences between fungal communities as indicators of soil biodiversity loss using Illumina MiSeq metabarcoding on nuclear ribosomal ITS2 region. A non-metric multidimensional scaling allowed to explore driver factors of changes in fungal communities, while the significance of these variations was assessed by PERMANOVA. Furthermore, the effect size of land use over relevant taxa was quantified. Our results suggest a good coverage of fungal diversity with a detection of 353,312 high-quality ITS2 sequences. We found strong correlations of Shannon and Fisher indexes with dissimilarities on fungal communities (r = 0.94). These correlations allow grouping soil samples according to land use. Variations in temperature, air humidity and organic matter content lead to changes in abundances of relevant orders (Wallemiales and Trichosporonales). The study highlights specific sensitivities of fungal biodiversity features in tropical Andosols, which may serve as a basis for robust assessments of soil quality in the region.
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Affiliation(s)
- Raul Aranguren
- GAIA Research Group, Universidad de Antioquia, Medellín 050010, Colombia
| | - Samuele Voyron
- Department of Life Sciences and Systems Biology, University of Turin, 10124 Turin, Italy
- Institute for Sustainable Plant Protection (IPSP), National Research Council (CNR), 10125 Turin, Italy
| | - Fabrizio Ungaro
- Institute for Bio-Economy (IBE), National Research Council (CNR), 50018 Florence, Italy
| | - Julio Cañón
- GAIA Research Group, Universidad de Antioquia, Medellín 050010, Colombia
| | - Erica Lumini
- Institute for Sustainable Plant Protection (IPSP), National Research Council (CNR), 10125 Turin, Italy
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14
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Diversity, Ecological Characteristics and Identification of Some Problematic Phytopathogenic Fusarium in Soil: A Review. DIVERSITY 2023. [DOI: 10.3390/d15010049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The genus Fusarium includes many pathogenic species causing a wide range of plant diseases that lead to high economic losses. In this review, we describe how the Fusarium taxonomy has changed with the development of microbiological methods. We specify the ecological traits of this genus and the methods of its identification in soils, particularly the detection of phytopathogenic representatives of Fusarium and the mycotoxins produced by them. The negative effects of soil-borne phytopathogenic Fusarium on agricultural plants and current methods for its control are discussed. Due to the high complexity and polymorphism of Fusarium species, integrated approaches for the risk assessment of Fusarium diseases are necessary.
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15
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Moneda APC, de Carvalho LAL, Teheran-Sierra LG, Funnicelli MIG, Pinheiro DG. Sugarcane cultivation practices modulate rhizosphere microbial community composition and structure. Sci Rep 2022; 12:19174. [PMID: 36357461 PMCID: PMC9649670 DOI: 10.1038/s41598-022-23562-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 11/02/2022] [Indexed: 11/12/2022] Open
Abstract
Sugarcane (Saccharum spp.) represents a crop of great economic importance, remarkably relevant in the food industry and energy supply chains from renewable sources. However, its conventional cultivation involves the intensive use of fertilizers, pesticides, and other agrochemical agents whose detrimental effects on the environment are notorious. Alternative systems, such as organic farming, have been presented as an environmentally friendly way of production. Still, the outcomes of different cropping systems on the microbiota associated with sugarcane-whose role in its health and growth is crucial-remain underexplored. Thus, we studied the rhizospheric microbiota of two adjacent sugarcane fields, which differ in terms of the type of farming system. For this, we used the sequencing of taxonomic markers of prokaryotes (gene 16S rRNA, subregions V3-V4) and fungi (Internal transcribed spacer 2) and evaluated the changes caused by the systems. Our results show a well-conserved microbiota composition among farming systems in the highest taxonomic ranks, such as phylum, class, and order. Also, both systems showed very similar alpha diversity indices and shared core taxa with growth-promoting capacities, such as bacteria from the Bacillus and Bradyrhizobium genera and the fungal genus Trichoderma. However, the composition at more specific levels denotes differences, such as the separation of the samples concerning beta diversity and the identification of 74 differentially abundant taxa between the systems. Of these, 60 were fungal taxa, indicating that this microbiota quota is more susceptible to changes caused by farming systems. The analysis of co-occurrence networks also showed the formation of peripheral sub-networks associated with the treatments-especially in fungi-and the presence of keystone taxa in terms of their ability to mediate relationships between other members of microbial communities. Considering that both crop fields used the same cultivar and had almost identical soil properties, we conclude that the observed findings are effects of the activities intrinsic to each system and can contribute to a better understanding of the effects of farming practices on the plant microbiome.
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Affiliation(s)
- Ana Paula Corrêa Moneda
- grid.410543.70000 0001 2188 478XLaboratory of Bioinformatics, Department of Agricultural, Livestock and Environmental Biotechnology, School of Agricultural and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, SP 14884-900 Brazil ,grid.410543.70000 0001 2188 478XGraduate Program in Agricultural and Livestock Microbiology, School of Agricultural and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, SP Brazil
| | - Lucas Amoroso Lopes de Carvalho
- grid.410543.70000 0001 2188 478XLaboratory of Bioinformatics, Department of Agricultural, Livestock and Environmental Biotechnology, School of Agricultural and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, SP 14884-900 Brazil ,grid.410543.70000 0001 2188 478XGraduate Program in Agricultural and Livestock Microbiology, School of Agricultural and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, SP Brazil
| | - Luis Guillermo Teheran-Sierra
- grid.410543.70000 0001 2188 478XLaboratory of Bioinformatics, Department of Agricultural, Livestock and Environmental Biotechnology, School of Agricultural and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, SP 14884-900 Brazil ,grid.410543.70000 0001 2188 478XGraduate Program in Agricultural and Livestock Microbiology, School of Agricultural and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, SP Brazil
| | - Michelli Inácio Gonçalves Funnicelli
- grid.410543.70000 0001 2188 478XLaboratory of Bioinformatics, Department of Agricultural, Livestock and Environmental Biotechnology, School of Agricultural and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, SP 14884-900 Brazil ,grid.410543.70000 0001 2188 478XGraduate Program in Agricultural and Livestock Microbiology, School of Agricultural and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, SP Brazil
| | - Daniel Guariz Pinheiro
- grid.410543.70000 0001 2188 478XLaboratory of Bioinformatics, Department of Agricultural, Livestock and Environmental Biotechnology, School of Agricultural and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, SP 14884-900 Brazil ,grid.410543.70000 0001 2188 478XGraduate Program in Agricultural and Livestock Microbiology, School of Agricultural and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, SP Brazil
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16
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Sommermann L, Babin D, Behr JH, Chowdhury SP, Sandmann M, Windisch S, Neumann G, Nesme J, Sørensen SJ, Schellenberg I, Rothballer M, Geistlinger J, Smalla K, Grosch R. Long-Term Fertilization Strategy Impacts Rhizoctonia solani–Microbe Interactions in Soil and Rhizosphere and Defense Responses in Lettuce. Microorganisms 2022; 10:microorganisms10091717. [PMID: 36144319 PMCID: PMC9501836 DOI: 10.3390/microorganisms10091717] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 08/04/2022] [Accepted: 08/17/2022] [Indexed: 11/16/2022] Open
Abstract
The long-term effects of agricultural management such as different fertilization strategies on soil microbiota and soil suppressiveness against plant pathogens are crucial. Therefore, the suppressiveness of soils differing in fertilization history was assessed using two Rhizoctonia solani isolates and their respective host plants (lettuce, sugar beet) in pot experiments. Further, the effects of fertilization history and the pathogen R. solani AG1-IB on the bulk soil, root-associated soil and rhizosphere microbiota of lettuce were analyzed based on amplicon sequencing of the 16S rRNA gene and ITS2 region. Organic fertilization history supported the spread of the soil-borne pathogens compared to long-term mineral fertilization. The fertilization strategy affected bacterial and fungal community composition in the root-associated soil and rhizosphere, respectively, but only the fungal community shifted in response to the inoculated pathogen. The potential plant-beneficial genus Talaromyces was enriched in the rhizosphere by organic fertilization and presence of the pathogen. Moreover, increased expression levels of defense-related genes in shoots of lettuce were observed in the soil with organic fertilization history, both in the absence and presence of the pathogen. This may reflect the enrichment of potential plant-beneficial microorganisms in the rhizosphere, but also pathogen infestation. However, enhanced defense responses resulted in retarded plant growth in the presence of R. solani (plant growth/defense tradeoff).
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Affiliation(s)
- Loreen Sommermann
- Department of Agriculture, Ecotrophology and Landscape Development, Anhalt University of Applied Sciences, 06406 Bernburg, Germany
- Correspondence:
| | - Doreen Babin
- Julius Kühn-Institute (JKI)—Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, 38104 Braunschweig, Germany
| | - Jan Helge Behr
- Plant-Microbe Systems, Leibniz Institute of Vegetable and Ornamental Crops (IGZ), 14979 Großbeeren, Germany
| | - Soumitra Paul Chowdhury
- Institute of Network Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Martin Sandmann
- Plant-Microbe Systems, Leibniz Institute of Vegetable and Ornamental Crops (IGZ), 14979 Großbeeren, Germany
| | - Saskia Windisch
- Institute of Crop Science (340h), University of Hohenheim, 70599 Stuttgart, Germany
| | - Günter Neumann
- Institute of Crop Science (340h), University of Hohenheim, 70599 Stuttgart, Germany
| | - Joseph Nesme
- Section of Microbiology, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Søren J. Sørensen
- Section of Microbiology, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Ingo Schellenberg
- Department of Agriculture, Ecotrophology and Landscape Development, Anhalt University of Applied Sciences, 06406 Bernburg, Germany
| | - Michael Rothballer
- Institute of Network Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Joerg Geistlinger
- Department of Agriculture, Ecotrophology and Landscape Development, Anhalt University of Applied Sciences, 06406 Bernburg, Germany
| | - Kornelia Smalla
- Julius Kühn-Institute (JKI)—Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, 38104 Braunschweig, Germany
| | - Rita Grosch
- Plant-Microbe Systems, Leibniz Institute of Vegetable and Ornamental Crops (IGZ), 14979 Großbeeren, Germany
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17
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Sun J, Luo H, Yu Q, Kou B, Jiang Y, Weng L, Xiao C. Optimal NPK Fertilizer Combination Increases Panax ginseng Yield and Quality and Affects Diversity and Structure of Rhizosphere Fungal Communities. Front Microbiol 2022; 13:919434. [PMID: 35801112 PMCID: PMC9255912 DOI: 10.3389/fmicb.2022.919434] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 05/25/2022] [Indexed: 11/25/2022] Open
Abstract
Soil microorganisms affect crop rhizospheres via the transformation and transport of nutrients, which has important influences on soil fertility, carbon sequestration, and plant yield and health in agroecosystems. There are few reports on the effects of fertilizer application on the growth of Panax ginseng (C. A. Mey.) or the structure of its rhizosphere microbial communities. In this study, an orthogonal experimental design was used to explore the effects of nine different combinations of nitrogen (N), phosphorus (P), and potassium (K) fertilizers with different amounts and proportions on ginseng growth and accumulation of ginsenosides and the structure of rhizosphere soil fungal communities. Soil without fertilization was the control. With the combined application of NPK, ginseng growth and development increased. The fertilization scheme N3P1K3, with N fertilizer at 50 g·m−2, P fertilizer at 15 g·m−2, and K fertilizer at 60 g·m−2, had the most comprehensive benefit and significantly increased ginseng rhizome biomass and ginsenoside contents (Rg1, Re, Rf, Rg2, Rb1, Ro, Rc, Rb2, Rb3, and Rd). Amplicon sequencing showed that NPK application increased the diversity of fungal communities in ginseng rhizospheres, whereas richness was bidirectionally regulated by proportions and amounts of NPK. Ascomycota was the dominant fungal phylum in ginseng rhizosphere soil, and relative abundances decreased with combined NPK application. Combined NPK application increased the relative abundance of potential beneficial fungi, such as Mortierella, but decreased that of potentially pathogenic fungi, such as Fusarium. Correlation analysis showed that potential beneficial fungi were significantly positively correlated with ginseng rhizome yield and ginsenoside contents, whereas the opposite relation was observed with potential pathogenic fungi. Thus, in addition to directly increasing crop growth, precise NPK application can also increase crop adaptability to the environment by shaping specific microbial communities. The results of this study suggest that the combined effects of biotic and abiotic processes on agricultural production determine crop yield and quality.
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18
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Seasonal Dynamics of Organic Carbon and Nitrogen in Biomasses of Microorganisms in Arable Mollisols Affected by Different Tillage Systems. LAND 2022. [DOI: 10.3390/land11040486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Tillage has been reported to induce seasonal changes of organic carbon (Cmicro) and nitrogen (Nmicro) in the biomass of microorganisms. Soil microorganisms execute such ecosystem functions as it is an immediate sink of labile biophil elements; it is an agent of a conversion, catalysis and synthesis of humus substances; it transforms soil contaminants into nonhazardous wastes and it participates in soil aggregation and pedogenesis as a whole. However, the seasonal turnover of microorganisms on arable lands in temperate ecosystems has not been studied at a relevant level. Hence, we are aimed at studying the dynamics of such soil microbial biomass patterns as Cmicro, Nmicro, microbial index (MI = (Cmicro/CTOC)·100%) and CO2-C emissions against the background of 9 years of tillage and 22 years of abandoned (Ab) and fallow (F) usage. Our study was conducted on a long-term experimental site on a Mollisol in Northeast China. The maximum Cmicro and Nmicro contents were recorded at the beginning of the growing season at the 0–10-cm layer and mid-July at the 20–40-cm layer, while the minimum content was during August–October. The Cmicro content ranged from 577.79 to 381.79 mg−1 kg−1 using Ab in the spring to 229.53 to 272.86 mg−1 kg−1 in the autumn using CT (conventional tillage) and F in the 0–10- and 10–20-cm layers, respectively. The amplitude of Nmicro content changes were several times lower as compared with the Cmicro. The smallest quartile range (IQR0.25–0.75) of such changes was shown when using the following treatments: no till (NT) and Ab in the 0–10-, NT and F in the 10–20- and CT in the 20–40-cm layer. The widest Cmicro:Nmicro ratio was recorded at F and CT in the 0–20- and CT and rotational tillage (Rot) in the 20–40-cm layer. The MI dynamics were similar to the trends of Cmicro and Nmicro and changed from 0.72 ± 0.168 to 2.00 ± 0.030%. The highest share of Cmicro in CTOC was at Ab (1.82 ± 1.85%) and NT (1.66 ± 1.52 %) in the 0–10-, Ab (1.23 ± 1.27%) and NT (1.29 ± 1.32%) in the 10–20- and Ab (1.19 ± 1.09%) and F (1.11 ± 1.077%) in the 20–40-cm layer, correspondingly. The Pearson’s correlation coefficient between Cmicro and CTOC increased from the upper 0–10- to the lower 20–40-cm layer; it was “strong” and “high” between Cmicro and CTOC. Different uses of Mollisol affected the amplitude of the Cmicro and Nmicro seasonal changes, but it did not change their trend. Our results suggest the key role of Ab and NT technologies in Cmicro accumulation in the total organic carbon (TOC).
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