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He J, Zeng G, Liu Z, Guo Z, Zhang W, Li Y, Zhou Y, Xu H. Replacing traditional nursery soil with spent mushroom substrate improves rice seedling quality and soil substrate properties. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:39625-39636. [PMID: 38824472 DOI: 10.1007/s11356-024-33723-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Accepted: 05/15/2024] [Indexed: 06/03/2024]
Abstract
Currently, large quantities of spent mushroom substrate (SMS) are produced annually. Because SMS has high water retention and nutrients, it has great potential to replace traditional topsoil for raising seedlings in agricultural production. However, few studies have examined the effects of substituting SMS for paddy soil on rice seedling growth and soil nutrients. SMS was mixed with rice soil in different proportions (20%, 50%, and 80%), and chemical fertilizer, organic fertilizer, and peat substrate were added in addition to equivalent nitrogen as a traditional seedling nursery method for comparison. Compared to traditional paddy soil (CK), the seedling qualities of the three SMS ratio treatments were all higher. Adding SMS at different ratios promoted rice seedling root growth, elevated the soluble protein concentration, and amplified the superoxide dismutase (SOD) enzymatic action in rice seedlings. Total porosity and aeration porosity of the soil increased by 17.40% and 32.90%, respectively. Soil organic carbon (SOC), total nitrogen (TN), and total phosphorus (TP) increased by 21.26-118.48%, 50.44-71.68%, and 23.08-80.17%, respectively. Besides, the relative abundance of Bacillus, Bacteroidetes, and other bacteria as well as the abundance of Ascomycota were all significantly increased. Adding 50% SMS increased the abundance of Pseudomonas by 8.42 times. The seedling quality of the 50% SMS treatment was even higher than chemical fertilizer and organic fertilizer treatments, only second to the peat substrate treatment. In summary, partial substitution of paddy soil with SMS can ameliorate substrate properties, improve seedling quality, and increase microbial diversity, indicating the suitability of SMS as a replacement for rice soil in seedling substrates. The 50% SMS ratio is the best. This study provides a basis for SMS to replace traditional rice soil in seedling cultivation.
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Affiliation(s)
- Jinfeng He
- College of Environment and Ecology, Hunan Agricultural University and Hunan Provincial Key Laboratory of Rural Ecosystem Health in Dongting Lake Area, Changsha, 410128, People's Republic of China
| | - Guiyang Zeng
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, People's Republic of China
| | - Zhihui Liu
- College of Environment and Ecology, Hunan Agricultural University and Hunan Provincial Key Laboratory of Rural Ecosystem Health in Dongting Lake Area, Changsha, 410128, People's Republic of China
| | - Zhangliang Guo
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, People's Republic of China
| | - Wenzhuo Zhang
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, People's Republic of China
| | - Yici Li
- College of Environment and Ecology, Hunan Agricultural University and Hunan Provincial Key Laboratory of Rural Ecosystem Health in Dongting Lake Area, Changsha, 410128, People's Republic of China
| | - Yaoyu Zhou
- College of Environment and Ecology, Hunan Agricultural University and Hunan Provincial Key Laboratory of Rural Ecosystem Health in Dongting Lake Area, Changsha, 410128, People's Republic of China
| | - Huaqin Xu
- College of Environment and Ecology, Hunan Agricultural University and Hunan Provincial Key Laboratory of Rural Ecosystem Health in Dongting Lake Area, Changsha, 410128, People's Republic of China.
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Guo J, Xie Z, Meng Q, Xu H, Peng Q, Wang B, Dong D, Yang J, Jia S. Distribution of rhizosphere fungi of Kobresia humilis on the Qinghai-Tibet Plateau. PeerJ 2024; 12:e16620. [PMID: 38406296 PMCID: PMC10885805 DOI: 10.7717/peerj.16620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 11/16/2023] [Indexed: 02/27/2024] Open
Abstract
Kobresia humilis is a major species in the alpine meadow communities of the Qinghai-Tibet Plateau (QTP); it plays a crucial role in maintaining the ecological balance of these meadows. Nevertheless, little is known about the rhizosphere fungi associated with K. humilis on the Qinghai Tibet Plateau. In this study, we used Illumina Miseq to investigate the fungal diversity, community structure, and ecological types in the root and rhizosphere soil of K. humilis across eight areas on the QTP and analyzed the correlation between rhizosphere fungi of K. humilis and environmental factors. A total of 19,423 and 25,101 operational taxonomic units (OTUs) were obtained from the roots and rhizosphere soil of K. humilis. These were classified into seven phyla, 25 classes, 68 orders, 138 families, and 316 genera in the roots, and nine phyla, 31 classes, 76 orders, 152 families, and 407 genera in the rhizosphere soil. There were 435 and 415 core OTUs identified in root and rhizosphere soil, respectively, which were categorized into 68 and 59 genera, respectively, with 25 shared genera. Among them, the genera with a relative abundance >1% included Mortierella, Microscypha, Floccularia, Cistella, Gibberella, and Pilidium. Compared with the rhizosphere soil, the roots showed five differing fungal community characteristics, as well as differences in ecological type, and in the main influencing environmental factors. First, the diversity, abundance, and total number of OTUs in the rhizosphere soil of K. humilis were higher than for the endophytic fungi in the roots by 11.85%, 9.85%, and 22.62%, respectively. The composition and diversity of fungal communities also differed between the eight areas. Second, although saprotroph-symbiotrophs were the main ecological types in both roots and rhizosphere soil; there were 62.62% fewer pathotrophs in roots compared to the rhizosphere soil. Thirdly, at the higher altitude sites (3,900-4,410 m), the proportion of pathotroph fungi in K. humilis was found to be lower than at the lower altitude sites (3,200-3,690 m). Fourthly, metacommunity-scale network analysis showed that during the long-term evolutionary process, ZK (EICZK = 1) and HY (EICHY = 1) were critical sites for development of the fungal community structure in the roots and rhizosphere soil of K. humilis, respectively. Fifthly, canonical correspondence analysis (CCA) showed that key driving factors in relation to the fungal community were longitude (R2 = 0.5410) for the root community and pH (R2 = 0.5226) for the rhizosphere soil community. In summary, these results show that K. humilis fungal communities are significantly different in the root and rhizosphere soil and at the eight areas investigated, indicating that roots select for specific microorganisms in the soil. This is the first time that the fungal distribution of K. humilis on the QTP in relation to long-term evolutionary processes has been investigated. These findings are critical for determining the effects of environmental variables on K. humilis fungal communities and could be valuable when developing guidance for ecological restoration and sustainable utilization of the biological resources of the QTP.
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Affiliation(s)
- Jing Guo
- School of Ecology and Environmental Science, Qinghai University of Science and Technology, Xining, China
| | - Zhanling Xie
- College of Ecological and Environment Engineering, Qinghai University, Xining, China
- State Key Laboratory Breeding Base for Innovation and Utilization of Plateau Crop Germplasm, Qinghai University, Xining, China
| | - Qing Meng
- College of Ecological and Environment Engineering, Qinghai University, Xining, China
- State Key Laboratory Breeding Base for Innovation and Utilization of Plateau Crop Germplasm, Qinghai University, Xining, China
| | - Hongyan Xu
- Academy of Agriculture and Forestry Sciences, Qinghai University, Xining, China
| | - Qingqing Peng
- College of Ecological and Environment Engineering, Qinghai University, Xining, China
- State Key Laboratory Breeding Base for Innovation and Utilization of Plateau Crop Germplasm, Qinghai University, Xining, China
| | - Bao Wang
- College of Ecological and Environment Engineering, Qinghai University, Xining, China
| | - Deyu Dong
- College of Ecological and Environment Engineering, Qinghai University, Xining, China
| | - Jiabao Yang
- College of Ecological and Environment Engineering, Qinghai University, Xining, China
| | - Shunbin Jia
- Department of Ecological Restoration at Qinghai Grassland Station, Xining, China
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Oliveira MCO, Ragonezi C, Valente S, de Freitas JGR, Pinheiro de Carvalho MAA. Microorganism community structure: A characterisation of agrosystems from Madeira Archipelago. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13227. [PMID: 38268303 PMCID: PMC10866076 DOI: 10.1111/1758-2229.13227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 12/04/2023] [Indexed: 01/26/2024]
Abstract
Microbial diversity profoundly influences soil ecosystem functions, making it vital to monitor community dynamics to comprehend its structure. Our study focused on six agrosystems in Madeira Archipelago, analysing bacteria, archaea, fungi and AMF through classical microbiology and molecular techniques. Despite distinct edaphoclimatic conditions and management practices, bacterial structures exhibited similarities, with Alphaproteobacteria at 18%-20%, Bacilli at 11%-18% and Clostridia at 9%-14%. The predominance of copiothrophic groups suggested that soil nutrient content was the driver of these communities. Regarding archaea, the communities changed among sites, and it was evident that agrosystems provided niches for methanogens. The Crenarchaeota varied between 15% and 29%, followed by two classes of Euryarchaeota, Methanomicrobia (17%-25%) and Methanococci (4%-32%). Fungal communities showed consistent composition at the class level but had differing diversity indices due to management practices and soil texture. Sordaryomycetes (21%-28%) and Agaricomycetes (15%-23%) were predominant. Conversely, AMF communities appeared to be also influenced by the agrosystem, with Glomus representing over 50% of the community in all agrosystems. These insights into microbial groups' susceptibilities to environmental conditions are crucial for maintaining healthy soil and predicting climate change effects on agrosystems' productivity, resilience and sustainability. Additionally, our findings enable the development of more robust prediction models for agricultural practices.
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Affiliation(s)
- Maria Cristina O. Oliveira
- ISOPlexis ‐ Centre of Sustainable Agriculture and Food Technology, Campus da Penteada, University of MadeiraFunchalPortugal
| | - Carla Ragonezi
- ISOPlexis ‐ Centre of Sustainable Agriculture and Food Technology, Campus da Penteada, University of MadeiraFunchalPortugal
- Centre for the Research and Technology of Agro‐Environmental and Biological Sciences (CITAB), Inov4Agro – Institute for Innovation, Capacity Building and Sustainability of Agri‐Food ProductionUniversity of Trás‐os‐Montes and Alto DouroVila RealPortugal
- Faculty of Life Sciences, Campus da PenteadaUniversity of MadeiraFunchalPortugal
| | - Sofia Valente
- ISOPlexis ‐ Centre of Sustainable Agriculture and Food Technology, Campus da Penteada, University of MadeiraFunchalPortugal
| | - José G. R. de Freitas
- ISOPlexis ‐ Centre of Sustainable Agriculture and Food Technology, Campus da Penteada, University of MadeiraFunchalPortugal
| | - Miguel A. A. Pinheiro de Carvalho
- ISOPlexis ‐ Centre of Sustainable Agriculture and Food Technology, Campus da Penteada, University of MadeiraFunchalPortugal
- Centre for the Research and Technology of Agro‐Environmental and Biological Sciences (CITAB), Inov4Agro – Institute for Innovation, Capacity Building and Sustainability of Agri‐Food ProductionUniversity of Trás‐os‐Montes and Alto DouroVila RealPortugal
- Faculty of Life Sciences, Campus da PenteadaUniversity of MadeiraFunchalPortugal
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Christel A, Dequiedt S, Chemidlin-Prevost-Bouré N, Mercier F, Tripied J, Comment G, Djemiel C, Bargeot L, Matagne E, Fougeron A, Mina Passi JB, Ranjard L, Maron PA. Urban land uses shape soil microbial abundance and diversity. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 883:163455. [PMID: 37062324 DOI: 10.1016/j.scitotenv.2023.163455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 04/07/2023] [Accepted: 04/07/2023] [Indexed: 06/03/2023]
Abstract
Soil microbial biodiversity provides many useful services in cities. However, the ecology of microbial communities in urban soils remains poorly documented, and studies are required to better predict the impact of urban land use. We characterized microbial communities (archea/bacteria and fungi) in urban soils in Dijon (Burgundy, France). Three main land uses were considered - public leisure, traffic, and urban agriculture - sub-categorized in sub-land uses according to urban indexes and management practices. Microbial biomass and diversity were determined by quantifying and high-throughput sequencing of soil DNA. Variation partitioning analysis was used to rank soil physicochemical characteristics and land uses according to their relative contribution to the variation of soil microbial communities. Urban soils in Dijon harbored high levels of microbial biomass and diversity that varied according to land uses. Microbial biomass was 1.8 times higher in public leisure and traffic sites than in urban agriculture sites. Fungal richness increased by 25 % in urban agriculture soils, and bacterial richness was lower (by 20 %) in public leisure soils. Partitioning models explained 25.7 %, 46.2 % and 75.6 % of the variance of fungal richness, bacterial richness and microbial biomass, respectively. The organic carbon content and the C/N ratio were the best predictors of microbial biomass, whereas soil bacterial diversity was mainly explained by soil texture and land use. Neither metal trace elements nor polycyclic aromatic hydrocarbons contents explained variations of microbial communities, probably due to their very low concentration in the soils. The microbial composition results highlighted that leisure sites represented a stabilized habitat favoring specialized microbial groups and microbial plant symbionts, as opposed to urban agriculture sites that stimulated opportunistic populations able to face the impact of agricultural practices. Altogether, our results provide evidence that there is scope for urban planners to drive soil microbial diversity through sustainable urban land use and associated management practices.
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Affiliation(s)
- Amélie Christel
- AgroParisTech, 75732 Paris, France; Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
| | - Samuel Dequiedt
- Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
| | | | - Florian Mercier
- Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
| | - Julie Tripied
- Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
| | - Gwendoline Comment
- Platforme GenoSol, INRAE-Université de Bourgogne, CMSE, 21000 Dijon, France
| | - Christophe Djemiel
- Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
| | | | - Eric Matagne
- AGARIC-IG, 144 Rue Rambuteau, 71000 Macon, France
| | - Agnès Fougeron
- Jardin de l'Arquebuse Mairie de Dijon, CS 73310, 21033 Dijon Cedex, France
| | | | - Lionel Ranjard
- Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
| | - Pierre-Alain Maron
- Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France.
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Schüller A, Studt-Reinhold L, Berger H, Silvestrini L, Labuda R, Güldener U, Gorfer M, Bacher M, Doppler M, Gasparotto E, Gattesco A, Sulyok M, Strauss J. Genome analysis of Cephalotrichum gorgonifer and identification of the biosynthetic pathway for rasfonin, an inhibitor of KRAS dependent cancer. Fungal Biol Biotechnol 2023; 10:13. [PMID: 37355668 PMCID: PMC10290801 DOI: 10.1186/s40694-023-00158-x] [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: 11/08/2022] [Accepted: 04/28/2023] [Indexed: 06/26/2023] Open
Abstract
BACKGROUND Fungi are important sources for bioactive compounds that find their applications in many important sectors like in the pharma-, food- or agricultural industries. In an environmental monitoring project for fungi involved in soil nitrogen cycling we also isolated Cephalotrichum gorgonifer (strain NG_p51). In the course of strain characterisation work we found that this strain is able to naturally produce high amounts of rasfonin, a polyketide inducing autophagy, apoptosis, necroptosis in human cell lines and showing anti-tumor activity in KRAS-dependent cancer cells. RESULTS In order to elucidate the biosynthetic pathway of rasfonin, the strain was genome sequenced, annotated, submitted to transcriptome analysis and genetic transformation was established. Biosynthetic gene cluster (BGC) prediction revealed the existence of 22 BGCs of which the majority was not expressed under our experimental conditions. In silico prediction revealed two BGCs with a suite of enzymes possibly involved in rasfonin biosynthesis. Experimental verification by gene-knock out of the key enzyme genes showed that one of the predicted BGCs is indeed responsible for rasfonin biosynthesis. CONCLUSIONS This study identified a biosynthetic gene cluster containing a key-gene responsible for rasfonin production. Additionally, molecular tools were established for the non-model fungus Cephalotrichum gorgonifer which allows strain engineering and heterologous expression of the BGC for high rasfonin producing strains and the biosynthesis of rasfonin derivates for diverse applications.
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Affiliation(s)
- Andreas Schüller
- Department of Applied Genetics and Cell Biology, Institute of Microbial Genetics, University of Natural Resources and Life Sciences, Vienna (BOKU), Campus Tulln, Konrad Lorenz Strasse 24, 3430, Tulln an der Donau, Austria
| | - Lena Studt-Reinhold
- Department of Applied Genetics and Cell Biology, Institute of Microbial Genetics, University of Natural Resources and Life Sciences, Vienna (BOKU), Campus Tulln, Konrad Lorenz Strasse 24, 3430, Tulln an der Donau, Austria
| | - Harald Berger
- Department of Applied Genetics and Cell Biology, Institute of Microbial Genetics, University of Natural Resources and Life Sciences, Vienna (BOKU), Campus Tulln, Konrad Lorenz Strasse 24, 3430, Tulln an der Donau, Austria
| | - Lucia Silvestrini
- Department of Applied Genetics and Cell Biology, Institute of Microbial Genetics, University of Natural Resources and Life Sciences, Vienna (BOKU), Campus Tulln, Konrad Lorenz Strasse 24, 3430, Tulln an der Donau, Austria
- DGforLife, Operations - Research and Development, Via Albert Einstein, Marcallo c.C., 20010, Milan, Italy
| | - Roman Labuda
- Research Platform Bioactive Microbial Metabolites (BiMM), Konrad Lorenz Strasse 24, 3430, Tulln an der Donau, Austria
- Department for Farm Animals and Veterinary Public Health, Institute of Food Safety, Food Technology and Veterinary Public Health, Unit of Food Microbiology, University of Veterinary Medicine Vienna, Veterinaerplatz 1, 1210, Vienna, Austria
| | - Ulrich Güldener
- Department of Bioinformatics, Technical University of Munich, TUM School of Life Sciences Weihenstephan, Freising, Germany
- German Heart Center Munich, Technical University Munich, Lazarettstraße 36, 80636, Munich, Germany
| | - Markus Gorfer
- AIT Austrian Institute of Technology GmbH, Bioresources, 3430, Tulln, Austria
| | - Markus Bacher
- Research Platform Bioactive Microbial Metabolites (BiMM), Konrad Lorenz Strasse 24, 3430, Tulln an der Donau, Austria
- Department of Chemistry, Institute of Chemistry of Renewable Resources, University of Natural Resources and Life Sciences Vienna (BOKU), Konrad-LorenzStraße 24, 3430, Tulln, Austria
| | - Maria Doppler
- Department of Agrobiotechnology (IFA-Tulln), Institute of Bioanalytics and Agro-Metabolomics, University of Natural Resources and Life Sciences, Vienna (BOKU), Konrad Lorenz Strasse 20, 3430, Tulln an der Donau, Austria
- Core Facility Bioactive Molecules, Screening and Analysis, University of Natural Resources and Life Sciences, Vienna, 3430, Tulln an der Donau, Austria
| | - Erika Gasparotto
- Department of Applied Genetics and Cell Biology, Institute of Microbial Genetics, University of Natural Resources and Life Sciences, Vienna (BOKU), Campus Tulln, Konrad Lorenz Strasse 24, 3430, Tulln an der Donau, Austria
- Research Platform Bioactive Microbial Metabolites (BiMM), Konrad Lorenz Strasse 24, 3430, Tulln an der Donau, Austria
- Department of Biological Chemistry, Faculty of Chemistry, University of Vienna, Josef-Holaubek-Platz 2, 1090, Vienna, Austria
| | - Arianna Gattesco
- Department of Applied Genetics and Cell Biology, Institute of Microbial Genetics, University of Natural Resources and Life Sciences, Vienna (BOKU), Campus Tulln, Konrad Lorenz Strasse 24, 3430, Tulln an der Donau, Austria
- Research Platform Bioactive Microbial Metabolites (BiMM), Konrad Lorenz Strasse 24, 3430, Tulln an der Donau, Austria
| | - Michael Sulyok
- Department of Agrobiotechnology (IFA-Tulln), Institute of Bioanalytics and Agro-Metabolomics, University of Natural Resources and Life Sciences, Vienna (BOKU), Konrad Lorenz Strasse 20, 3430, Tulln an der Donau, Austria
| | - Joseph Strauss
- Department of Applied Genetics and Cell Biology, Institute of Microbial Genetics, University of Natural Resources and Life Sciences, Vienna (BOKU), Campus Tulln, Konrad Lorenz Strasse 24, 3430, Tulln an der Donau, Austria.
- Research Platform Bioactive Microbial Metabolites (BiMM), Konrad Lorenz Strasse 24, 3430, Tulln an der Donau, Austria.
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Luo Y, Chavez-Rico VS, Sechi V, Bezemer TM, Buisman CJN, Ter Heijne A. Effect of organic amendments obtained from different pretreatment technologies on soil microbial community. ENVIRONMENTAL RESEARCH 2023:116346. [PMID: 37295594 DOI: 10.1016/j.envres.2023.116346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 05/31/2023] [Accepted: 06/06/2023] [Indexed: 06/12/2023]
Abstract
The application of organic amendments (OAs) obtained from biological treatment technologies is a common agricultural practice to increase soil functionality and fertility. OAs and their respective pretreatment processes have been extensively studied. However, comparing the properties of OAs obtained from different pretreatment processes remains challenging. In most cases, the organic residues used to produce OAs exhibit intrinsic variability and differ in origin and composition. In addition, few studies have focused on comparing OAs from different pretreatment processes in the soil microbiome, and the extent to which OAs affect the soil microbial community remains unclear. This limits the design and implementation of effective pretreatments aimed at reusing organic residues and facilitating sustainable agricultural practices. In this study, we used the same model residues to produce OAs to enable meaningful comparisons among compost, digestate, and ferment. These three OAs contained different microbial communities. Compost had higher bacterial but lower fungal alpha diversity than ferment and digestate. Compost-associated microbes were more prevalent in the soil than ferment- and digestate-associated microbes. More than 80% of the bacterial ASVs and fungal OTUs from the compost were detected 3 months after incorporation into the soil. However, the addition of compost had less influence on the resulting soil microbial biomass and community composition than the addition of ferment or digestate. Specific native soil microbes, members from Chloroflexi, Acidobacteria, and Mortierellomycota, were absent after ferment and digestate application. The addition of OAs increased the soil pH, particularly in the compost-amended soil, whereas the addition of digestate enhanced the concentrations of dissolved organic carbon (DOC) and available nutrients (such as ammonium and potassium). These physicochemical variables were key factors that influenced soil microbial communities. This study furthers our understanding of the effective recycling of organic resources for the development of sustainable soils.
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Affiliation(s)
- Yujia Luo
- Environmental Technology, Department of Agrotechnology and Food Sciences, Wageningen University, P.O. Box 17, 6700, AA, Wageningen, the Netherlands; Wetsus, European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, 8911, MA, Leeuwarden, the Netherlands.
| | - Vania Scarlet Chavez-Rico
- Environmental Technology, Department of Agrotechnology and Food Sciences, Wageningen University, P.O. Box 17, 6700, AA, Wageningen, the Netherlands; Wetsus, European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, 8911, MA, Leeuwarden, the Netherlands
| | - Valentina Sechi
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, 8911, MA, Leeuwarden, the Netherlands
| | - T Martijn Bezemer
- Institute of Biology, Aboveground Belowground Interactions Group, Leiden University, P.O. Box 9505, 2300, RA, Leiden, the Netherlands; Netherlands Institute of Ecology (NIOO-KNAW), Department of Terrestrial Ecology, Droevendaalsesteeg 10, 6708, PB, Wageningen, the Netherlands
| | - Cees J N Buisman
- Environmental Technology, Department of Agrotechnology and Food Sciences, Wageningen University, P.O. Box 17, 6700, AA, Wageningen, the Netherlands; Wetsus, European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, 8911, MA, Leeuwarden, the Netherlands
| | - Annemiek Ter Heijne
- Environmental Technology, Department of Agrotechnology and Food Sciences, Wageningen University, P.O. Box 17, 6700, AA, Wageningen, the Netherlands
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Darriaut R, Antonielli L, Martins G, Ballestra P, Vivin P, Marguerit E, Mitter B, Masneuf-Pomarède I, Compant S, Ollat N, Lauvergeat V. Soil composition and rootstock genotype drive the root associated microbial communities in young grapevines. Front Microbiol 2022; 13:1031064. [PMID: 36439844 PMCID: PMC9685171 DOI: 10.3389/fmicb.2022.1031064] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 10/14/2022] [Indexed: 08/31/2023] Open
Abstract
Soil microbiota plays a significant role in plant development and health and appears to be a major component of certain forms of grapevine decline. A greenhouse experiment was conducted to study the impact of the microbiological quality of the soil and grapevine rootstock genotype on the root microbial community and development of young plants. Two rootstocks heterografted with the same scion were grown in two vineyard soils differing in microbial composition and activities. After 4 months, culture-dependent approaches and amplicon sequencing of bacterial 16S rRNA gene and fungal ITS were performed on roots, rhizosphere and bulk soil samples. The root mycorrhizal colonization and number of cultivable microorganisms in the rhizosphere compartment of both genotypes were clearly influenced by the soil status. The fungal diversity and richness were dependent on the soil status and the rootstock, whereas bacterial richness was affected by the genotype only. Fungal genera associated with grapevine diseases were more abundant in declining soil and related root samples. The rootstock affected the compartmentalization of microbial communities, underscoring its influence on microorganism selection. Fluorescence in situ hybridization (FISH) confirmed the presence of predominant root-associated bacteria. These results emphasized the importance of rootstock genotype and soil composition in shaping the microbiome of young vines.
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Affiliation(s)
- Romain Darriaut
- EGFV, Université de Bordeaux, Bordeaux Sciences Agro, Villenave d'Ornon, France
| | - Livio Antonielli
- Bioresources Unit, Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Tulln, Austria
| | - Guilherme Martins
- Univ. Bordeaux, Bordeaux INP, INRAE, OENO, UMR 1366, ISVV, Villenave d’Ornon, France
- Bordeaux Sciences Agro, Bordeaux INP, INRAE, OENO, UMR 1366, ISVV, Gradignan, France
| | - Patricia Ballestra
- Univ. Bordeaux, Bordeaux INP, INRAE, OENO, UMR 1366, ISVV, Villenave d’Ornon, France
- Bordeaux Sciences Agro, Bordeaux INP, INRAE, OENO, UMR 1366, ISVV, Gradignan, France
| | - Philippe Vivin
- EGFV, Université de Bordeaux, Bordeaux Sciences Agro, Villenave d'Ornon, France
| | - Elisa Marguerit
- EGFV, Université de Bordeaux, Bordeaux Sciences Agro, Villenave d'Ornon, France
| | - Birgit Mitter
- Bioresources Unit, Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Tulln, Austria
| | - Isabelle Masneuf-Pomarède
- Univ. Bordeaux, Bordeaux INP, INRAE, OENO, UMR 1366, ISVV, Villenave d’Ornon, France
- Bordeaux Sciences Agro, Bordeaux INP, INRAE, OENO, UMR 1366, ISVV, Gradignan, France
| | - Stéphane Compant
- Bioresources Unit, Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Tulln, Austria
| | - Nathalie Ollat
- EGFV, Université de Bordeaux, Bordeaux Sciences Agro, Villenave d'Ornon, France
| | - Virginie Lauvergeat
- EGFV, Université de Bordeaux, Bordeaux Sciences Agro, Villenave d'Ornon, France
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Perazzolli M, Vicelli B, Antonielli L, Longa CMO, Bozza E, Bertini L, Caruso C, Pertot I. Simulated global warming affects endophytic bacterial and fungal communities of Antarctic pearlwort leaves and some bacterial isolates support plant growth at low temperatures. Sci Rep 2022; 12:18839. [PMID: 36336707 PMCID: PMC9637742 DOI: 10.1038/s41598-022-23582-2] [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: 07/04/2022] [Accepted: 11/02/2022] [Indexed: 11/07/2022] Open
Abstract
Antarctica is one of the most stressful environments for plant life and the Antarctic pearlwort (Colobanthus quitensis) is adapted to the hostile conditions. Plant-associated microorganisms can contribute to plant survival in cold environments, but scarce information is available on the taxonomic structure and functional roles of C. quitensis-associated microbial communities. This study aimed at evaluating the possible impacts of climate warming on the taxonomic structure of C. quitensis endophytes and at investigating the contribution of culturable bacterial endophytes to plant growth at low temperatures. The culture-independent analysis revealed changes in the taxonomic structure of bacterial and fungal communities according to plant growth conditions, such as the collection site and the presence of open-top chambers (OTCs), which can simulate global warming. Plants grown inside OTCs showed lower microbial richness and higher relative abundances of biomarker bacterial genera (Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium, Aeromicrobium, Aureimonas, Hymenobacter, Novosphingobium, Pedobacter, Pseudomonas and Sphingomonas) and fungal genera (Alternaria, Cistella, and Vishniacozyma) compared to plants collected from open areas (OA), as a possible response to global warming simulated by OTCs. Culturable psychrotolerant bacteria of C. quitensis were able to endophytically colonize tomato seedlings and promote shoot growth at low temperatures, suggesting their potential contribution to plant tolerance to cold conditions.
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Affiliation(s)
- Michele Perazzolli
- grid.11696.390000 0004 1937 0351Centre Agriculture, Food and the Environment (C3A), University of Trento, Via E. Mach 1, 38098 San Michele all’Adige, Italy ,grid.424414.30000 0004 1755 6224Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38098 San Michele all’Adige, Italy
| | - Bianca Vicelli
- grid.11696.390000 0004 1937 0351Centre Agriculture, Food and the Environment (C3A), University of Trento, Via E. Mach 1, 38098 San Michele all’Adige, Italy
| | - Livio Antonielli
- grid.4332.60000 0000 9799 7097Center for Health and Bioresources, Bioresources Unit, AIT Austrian Institute of Technology GmbH, Konrad-Lorenz-Strasse 24, 3430 Tulln an der Donau, Austria
| | - Claudia M. O. Longa
- grid.424414.30000 0004 1755 6224Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38098 San Michele all’Adige, Italy
| | - Elisa Bozza
- grid.424414.30000 0004 1755 6224Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38098 San Michele all’Adige, Italy
| | - Laura Bertini
- grid.12597.380000 0001 2298 9743Department of Ecological and Biological Sciences, University of Tuscia, Largo dell’Università s.n.c., 01100 Viterbo, Italy
| | - Carla Caruso
- grid.12597.380000 0001 2298 9743Department of Ecological and Biological Sciences, University of Tuscia, Largo dell’Università s.n.c., 01100 Viterbo, Italy
| | - Ilaria Pertot
- grid.11696.390000 0004 1937 0351Centre Agriculture, Food and the Environment (C3A), University of Trento, Via E. Mach 1, 38098 San Michele all’Adige, Italy ,grid.424414.30000 0004 1755 6224Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38098 San Michele all’Adige, Italy
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9
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Lazar A, Mushinski RM, Bending GD. Landscape scale ecology of Tetracladium spp. fungal root endophytes. ENVIRONMENTAL MICROBIOME 2022; 17:40. [PMID: 35879740 PMCID: PMC9310467 DOI: 10.1186/s40793-022-00431-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 06/23/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND The genus Tetracladium De Wild. (Ascomycota) has been traditionally regarded as a group of Ingoldian fungi or aquatic hyphomycetes-a polyphyletic group of phylogenetically diverse fungi which grow on decaying leaves and plant litter in streams. Recent sequencing evidence has shown that Tetracladium spp. may also exist as root endophytes in terrestrial environments, and furthermore may have beneficial effects on the health and growth of their host. However, the diversity of Tetracladium spp. communities in terrestrial systems and the factors which shape their distribution are largely unknown. RESULTS Using a fungal community internal transcribed spacer amplicon dataset from 37 UK Brassica napus fields we found that soils contained diverse Tetracladium spp., most of which represent previously uncharacterised clades. The two most abundant operational taxonomic units (OTUs), related to previously described aquatic T. furcatum and T. maxilliforme, were enriched in roots relative to bulk and rhizosphere soil. For both taxa, relative abundance in roots, but not rhizosphere or bulk soil was correlated with B. napus yield. The relative abundance of T. furcatum and T. maxilliforme OTUs across compartments showed very similar responses with respect to agricultural management practices and soil characteristics. The factors shaping the relative abundance of OTUs homologous to T. furcatum and T. maxilliforme OTUs in roots were assessed using linear regression and structural equation modelling. Relative abundance of T. maxilliforme and T. furcatum in roots increased with pH, concentrations of phosphorus, and increased rotation frequency of oilseed rape. It decreased with increased soil water content, concentrations of extractable phosphorus, chromium, and iron. CONCLUSIONS The genus Tetracladium as a root colonising endophyte is a diverse and widely distributed part of the oilseed rape microbiome that positively correlates to crop yield. The main drivers of its community composition are crop management practices and soil nutrients.
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Affiliation(s)
- Anna Lazar
- School of Life Sciences, The University of Warwick, Coventry, CV4 7AL, UK.
| | - Ryan M Mushinski
- School of Life Sciences, The University of Warwick, Coventry, CV4 7AL, UK
| | - Gary D Bending
- School of Life Sciences, The University of Warwick, Coventry, CV4 7AL, UK
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10
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Hernández-Guzmán M, Pérez-Hernández V, Gómez-Acata S, Jiménez-Bueno N, Verhulst N, Muñoz-Arenas LC, Navarro-Noya YE, Luna-Guido ML, Dendooven L. Application of young maize plant residues alters the microbiome composition and its functioning in a soil under conservation agriculture: a metagenomics study. Arch Microbiol 2022; 204:458. [PMID: 35788780 DOI: 10.1007/s00203-022-03060-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 05/01/2022] [Accepted: 06/07/2022] [Indexed: 12/24/2022]
Abstract
To increase our knowledge on how application of organic material alters soil microbial populations and functionality, shotgun metagenomic sequencing was used to determine the microbial communities and their potential functionality in an arable soil amended with young maize plants (Zea mays L.) in a laboratory experiment after 3 days. The relative abundance of bacterial and viral groups was strongly affected by organic material application, whereas that of the archaeal, protist and fungal groups was less affected. Cellulose degraders with copiotrophic lifestyle (e.g., Betaproteobacteria) were enriched in the amended soil, whereas the groups with slow growing oligotrophic and chemolithoautotrophic metabolism within Bacteria and Archaea were greater in the unamended than in the amended soil. The soil viral structure and richness were also affected. Caudovirales was the dominant viral family, with members of Siphoviridae enriched in the amended soil and members of Myoviridae in the unamended soil. More specialized metabolic traits related to both the degradation of complex C compounds and denitrification related genes were enriched in the young maize plant amended soil than in the unamended soil, whereas nitrification related genes were enriched in the latter. Copiotrophic life-style bacterial groups were enriched in the amended soil, whereas oligotrophic life-style bacterial groups in the unamended soil. Many bacterial and viral phylotypes were affected by the application of young maize plants, but the number of soil fungi, archaea and protists affected was smaller. Metabolic functionality was affected by the application of organic material as the relative abundance of genes involved in the denitrification process was higher in the maize plant amended soil than in the unamended soil and those involved in the nitrification process was higher in the unamended soil.
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Affiliation(s)
| | | | - Selene Gómez-Acata
- Laboratory of Soil Ecology, ABACUS, CINVESTAV, 07360, Mexico City, Mexico
| | | | - Nele Verhulst
- International Maize and Wheat Improvement Center (CIMMYT), Carretera México-Veracruz Km. 45, El Batán, Texcoco, Mexico
| | | | | | - Marco L Luna-Guido
- Laboratory of Soil Ecology, ABACUS, CINVESTAV, 07360, Mexico City, Mexico
| | - Luc Dendooven
- Laboratory of Soil Ecology, ABACUS, CINVESTAV, 07360, Mexico City, Mexico.
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11
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Ercole E, Adamo M, Lumini E, Fusconi A, Mucciarelli M. Alpine constructed wetlands: A metagenomic analysis reveals microbial complementary structure. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 822:153640. [PMID: 35124050 DOI: 10.1016/j.scitotenv.2022.153640] [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: 10/01/2021] [Revised: 01/20/2022] [Accepted: 01/29/2022] [Indexed: 06/14/2023]
Abstract
Constructed wetlands (CWs) are used to water treatment worldwide, however their application at high-altitude is poorly studied. In order to survive mountain winters, CWs rely on native flora and associated microbial communities. However, the choice of plant-microbes pairs more suitable for water treatment is challenging in alpine environments. Using a metagenomic approach, we investigated the composition of prokaryotes and fungal communities, through extensive sampling inside a constructed wetland in the SW-Alps. Best performing plant species were searched among those hosting the most diverse and resilient microbial communities and to this goal, we analysed them in the natural environment also. Our results showed that microbial communities were less diverse in the CW than at natural conditions, and they differed from plant to plant, revealing a clear variation in taxonomic composition between forbs and gramineous plants. Carex rostrata, Deschampsia caespitosa and Rumex alpinus hosted bacteria very active in N-cycles. Moreover, fungal and prokaryotic communities associated to R. alpinus (Polygonaceae) turned to be the richest and stable among the studied species. In our opinion, this species should be prioritized in CWs at high elevations, also in consideration of its low maintenance requirements.
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Affiliation(s)
- Enrico Ercole
- University of Torino, Department of Life Sciences and Systems Biology, Torino, Italy
| | - Martino Adamo
- University of Torino, Department of Life Sciences and Systems Biology, Torino, Italy
| | - Erica Lumini
- Institute for Sustainable Plant Protection (IPSP), National Research Council (CNR), Torino, Italy
| | - Anna Fusconi
- University of Torino, Department of Life Sciences and Systems Biology, Torino, Italy
| | - Marco Mucciarelli
- University of Torino, Department of Life Sciences and Systems Biology, Torino, Italy.
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12
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Spinelli V, Brasili E, Sciubba F, Ceci A, Giampaoli O, Miccheli A, Pasqua G, Persiani AM. Biostimulant Effects of Chaetomium globosum and Minimedusa polyspora Culture Filtrates on Cichorium intybus Plant: Growth Performance and Metabolomic Traits. FRONTIERS IN PLANT SCIENCE 2022; 13:879076. [PMID: 35646045 PMCID: PMC9134003 DOI: 10.3389/fpls.2022.879076] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 04/11/2022] [Indexed: 06/12/2023]
Abstract
In this study, we investigated the biostimulant effect of fungal culture filtrates obtained from Chaetomium globosum and Minimedusa polyspora on growth performance and metabolomic traits of chicory (Cichorium intybus) plants. For the first time, we showed that M. polyspora culture filtrate exerts a direct plant growth-promoting effect through an increase of biomass, both in shoots and roots, and of the leaf area. Conversely, no significant effect on morphological traits and biomass yield was observed in C. intybus plants treated with C. globosum culture filtrate. Based on 1H-NMR metabolomics data, differential metabolites and their related metabolic pathways were highlighted. The treatment with C. globosum and M. polyspora culture filtrates stimulated a common response in C. intybus roots involving the synthesis of 3-OH-butyrate through the decrease in the synthesis of fatty acids and sterols, as a mechanism balancing the NADPH/NADP+ ratio. The fungal culture filtrates differently triggered the phenylpropanoid pathway in C. intybus plants: C. globosum culture filtrate increased phenylalanine and chicoric acid in the roots, whereas M. polyspora culture filtrate stimulated an increase of 4-OH-benzoate. Chicoric acid, whose biosynthetic pathway in the chicory plant is putative and still not well known, is a very promising natural compound playing an important role in plant defense. On the contrary, benzoic acids serve as precursors for a wide variety of essential compounds playing crucial roles in plant fitness and defense response activation. To the best of our knowledge, this is the first study that shows the biostimulant effect of C. globosum and M. polyspora culture filtrates on C. intybus growth and metabolome, increasing the knowledge on fungal bioresources for the development of biostimulants.
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Affiliation(s)
- Veronica Spinelli
- Department of Environmental Biology, Sapienza University of Rome, Rome, Italy
| | - Elisa Brasili
- Department of Environmental Biology, Sapienza University of Rome, Rome, Italy
- NMR-Based Metabolomics Laboratory (NMLab), Sapienza University of Rome, Rome, Italy
| | - Fabio Sciubba
- Department of Environmental Biology, Sapienza University of Rome, Rome, Italy
- NMR-Based Metabolomics Laboratory (NMLab), Sapienza University of Rome, Rome, Italy
| | - Andrea Ceci
- Department of Environmental Biology, Sapienza University of Rome, Rome, Italy
| | - Ottavia Giampaoli
- Department of Environmental Biology, Sapienza University of Rome, Rome, Italy
- NMR-Based Metabolomics Laboratory (NMLab), Sapienza University of Rome, Rome, Italy
| | - Alfredo Miccheli
- Department of Environmental Biology, Sapienza University of Rome, Rome, Italy
- NMR-Based Metabolomics Laboratory (NMLab), Sapienza University of Rome, Rome, Italy
| | - Gabriella Pasqua
- Department of Environmental Biology, Sapienza University of Rome, Rome, Italy
- NMR-Based Metabolomics Laboratory (NMLab), Sapienza University of Rome, Rome, Italy
| | - Anna Maria Persiani
- Department of Environmental Biology, Sapienza University of Rome, Rome, Italy
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13
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Wolińska A, Podlewski J, Słomczewski A, Grządziel J, Gałązka A, Kuźniar A. Fungal Indicators of Sensitivity and Resistance to Long-Term Maize Monoculture: A Culture-Independent Approach. Front Microbiol 2022; 12:799378. [PMID: 35046921 PMCID: PMC8761758 DOI: 10.3389/fmicb.2021.799378] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 12/07/2021] [Indexed: 01/04/2023] Open
Abstract
Although fungi are regarded as very important components of soils, the knowledge of their community in agricultural (monocultural) soils is still limited. This indicates that soil fungal communities are investigated less intensively than bacteria. Therefore, the main goal of this paper was to evaluate the fungal mycobiome structure in monoculture soils in a culture-independent approach. Firstly, the study was conducted to identify the core mycobiome composition and its variability at different stages of the maize growing season (spring, summer, and autumn). Secondly, we identified and recommended fungal indicators of both sensitivity and resistance to long-term maize monoculture. Two neighboring fields from the Potulicka Foundation area were selected for the study: K20 sown with a Gorzow mixture (intercropping mixture) to improve soil quality after a maize monoculture in 2020 and K21, where long-term (over 30 years) monoculture cultivation was continued. The basic chemical features [acidity, redox potential, total organic carbon (TOC), and moisture] of soils were determined, fungal genetic diversity was assessed by ITS next generation sequencing (NGS) analyses, and biodiversity indices were calculated. The results of the NGS technique facilitated recognition and classification of the fungal mycobiome to the taxonomic genus level and changes in the fungal structure in the three periods (spring, summer, and autumn) were assessed. It was evidenced that the mycobiome composition was dependent on both the seasons and the agricultural practices. It was also found that even a 1-year break in the monoculture in favor of an intercropping mixture improved soil properties thus contributing to higher biodiversity. Mortierella was recommended as a potential indicator of sensitivity to long-term maize cultivation, whereas Solicoccozyma and Exophiala were proposed as indicators of resistance to long-term maize cultivation. We proved that the precision farming principles applied on the Potulicka Foundation farm had a very positive effect on fungal biodiversity, which was high even in the long-term maize monoculture field. Therefore, the monoculture cultivation carried out in this way does not induce biological degradation of monoculture soils but preserves their good biological quality.
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Affiliation(s)
- Agnieszka Wolińska
- Department of Biology and Biotechnology of Microorganisms, Institute of Biological Sciences, The John Paul II Catholic University of Lublin, Lublin, Poland
| | | | | | - Jarosław Grządziel
- Department of Agriculture Microbiology, Institute of Soil Science and Plant Cultivation in Pulawy, Puławy, Poland
| | - Anna Gałązka
- Department of Agriculture Microbiology, Institute of Soil Science and Plant Cultivation in Pulawy, Puławy, Poland
| | - Agnieszka Kuźniar
- Department of Biology and Biotechnology of Microorganisms, Institute of Biological Sciences, The John Paul II Catholic University of Lublin, Lublin, Poland
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14
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Finn DR, Lee S, Lanzén A, Bertrand M, Nicol GW, Hazard C. Cropping systems impact changes in soil fungal, but not prokaryote, alpha-diversity and community composition stability over a growing season in a long-term field trial. FEMS Microbiol Ecol 2021; 97:6374554. [PMID: 34555173 DOI: 10.1093/femsec/fiab136] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 09/21/2021] [Indexed: 12/30/2022] Open
Abstract
Crop harvest followed by a fallow period can act as a disturbance on soil microbial communities. Cropping systems intended to improve alpha-diversity of communities may also confer increased compositional stability during succeeding growing seasons. Over a single growing season in a long-term (18 year) agricultural field experiment incorporating conventional (CON), conservation (CA), organic (ORG) and integrated (INT) cropping systems, temporal changes in prokaryote, fungal and arbuscular mycorrhizal fungi (AMF) communities were investigated overwinter, during crop growth and at harvest. While certain prokaryote phyla were influenced by cropping system (e.g. Acidobacteria), the community as a whole was primarily driven by temporal changes over the growing season as distinct overwinter and crop-associated communities, with the same trend observed regardless of cropping system. Species-rich prokaryote communities were most stable over the growing season. Cropping system exerted a greater effect on fungal communities, with alpha-diversity highest and temporal changes most stable under CA. CON was particularly detrimental for alpha-diversity in AMF communities, with AMF alpha-diversity and stability improved under all other cropping systems. Practices that promoted alpha-diversity tended to also increase the similarity and temporal stability of soil fungal (and AMF) communities during a growing season, while prokaryote communities were largely insensitive to management.
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Affiliation(s)
- Damien R Finn
- Thünen Institut für Biodiversität, 38116 Braunschweig, Germany.,Environmental Microbial Genomics, Laboratoire Ampère, École Centrale de Lyon, Université de Lyon, 69134 Écully, France
| | - Sungeun Lee
- Environmental Microbial Genomics, Laboratoire Ampère, École Centrale de Lyon, Université de Lyon, 69134 Écully, France
| | - Anders Lanzén
- NEIKER, Basque Institute of Agricultural Research and Development, c/ Berreaga 1, 48160 Derio, Spain
| | - Michel Bertrand
- UMR Agronomie, INRAE AgroParisTech Université Paris-Saclay, 78850 Thiverval-Grignon, France
| | - Graeme W Nicol
- Environmental Microbial Genomics, Laboratoire Ampère, École Centrale de Lyon, Université de Lyon, 69134 Écully, France
| | - Christina Hazard
- Environmental Microbial Genomics, Laboratoire Ampère, École Centrale de Lyon, Université de Lyon, 69134 Écully, France
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15
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Li F, Dong C, Yang T, Bao S, Fang W, Lucas WJ, Zhang Z. The tea plant CsLHT1 and CsLHT6 transporters take up amino acids, as a nitrogen source, from the soil of organic tea plantations. HORTICULTURE RESEARCH 2021; 8:178. [PMID: 34333546 PMCID: PMC8325676 DOI: 10.1038/s41438-021-00615-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 04/09/2021] [Accepted: 05/20/2021] [Indexed: 06/13/2023]
Abstract
Organic tea is more popular than conventional tea that originates from fertilized plants. Amino acids inorganic soils constitute a substantial pool nitrogen (N) available for plants. However, the amino-acid contents in soils of tea plantations and how tea plants take up these amino acids remain largely unknown. In this study, we show that the amino-acid content in the soil of an organic tea plantation is significantly higher than that of a conventional tea plantation. Glutamate, alanine, valine, and leucine were the most abundant amino acids in the soil of this tea plantation. When 15N-glutamate was fed to tea plants, it was efficiently absorbed and significantly increased the contents of other amino acids in the roots. We cloned seven CsLHT genes encoding amino-acid transporters and found that the expression of CsLHT1, CsLHT2, and CsLHT6 in the roots significantly increased upon glutamate feeding. Moreover, the expression of CsLHT1 or CsLHT6 in a yeast amino-acid uptake-defective mutant, 22∆10α, enabled growth on media with amino acids constituting the sole N source. Amino-acid uptake assays indicated that CsLHT1 and CsLHT6 are H+-dependent high- and low-affinity amino-acid transporters, respectively. We further demonstrated that CsLHT1 and CsLHT6 are highly expressed in the roots and are localized to the plasma membrane. Moreover, overexpression of CsLHT1 and CsLHT6 in Arabidopsis significantly improved the uptake of exogenously supplied 15N-glutamate and 15N-glutamine. Taken together, our findings are consistent with the involvement of CsLHT1 and CsLHT6 in amino-acid uptake from the soil, which is particularly important for tea plants grown inorganic tea plantations.
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Affiliation(s)
- Fang Li
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, Anhui, 230036, China
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Chunxia Dong
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, Anhui, 230036, China
| | - Tianyuan Yang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, Anhui, 230036, China
| | - Shilai Bao
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wanping Fang
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - William J Lucas
- Department of Plant Biology, College of Biological Sciences, University of California, Davis, CA, 95616, USA
| | - Zhaoliang Zhang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, Anhui, 230036, China.
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16
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Navarro-Noya YE, Montoya-Ciriaco N, Muñoz-Arenas LC, Hereira-Pacheco S, Estrada-Torres A, Dendooven L. Conversion of a High-Altitude Temperate Forest for Agriculture Reduced Alpha and Beta Diversity of the Soil Fungal Communities as Revealed by a Metabarcoding Analysis. Front Microbiol 2021; 12:667566. [PMID: 34234759 PMCID: PMC8255801 DOI: 10.3389/fmicb.2021.667566] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Accepted: 05/03/2021] [Indexed: 11/13/2022] Open
Abstract
Land-use change is one of the most important drivers of change in biodiversity. Deforestation for grazing or agriculture has transformed large areas of temperate forest in the central highlands of Mexico, but its impact on soil fungal communities is still largely unknown. In this study, we determined how deforestation of a high-altitude temperate forest for cultivation of maize (Zea mays L.) or husbandry altered the taxonomic, phylogenetic, functional, and beta diversity of soil fungal communities using a 18S rRNA metabarcoding analysis. The true taxonomic and phylogenetic diversity at order q = 1, i.e., considering frequent operational taxonomic units, decreased significantly in the arable, but not in the pasture soil. The beta diversity decreased in the order forest > pasture > arable soil. The ordination analysis showed a clear effect of intensity of land-use as the forest soil clustered closer to pasture than to the arable soil. The most abundant fungal phyla in the studied soils were Ascomycota, Basidiomycota, and Mucoromycota. Deforestation more than halved the relative abundance of Basidiomycota; mostly Agaricomycetes, such as Lactarius and Inocybe. The relative abundance of Glomeromycota decreased in the order pasture > forest > arable soil. Symbiotrophs, especially ectomycorrhizal fungi, were negatively affected by deforestation while pathotrophs, especially animal pathogens, were enriched in the pasture and arable soil. Ectomycorrhizal fungi were more abundant in the forest soil as they are usually associated with conifers. Arbuscular mycorrhizal fungi were more abundant in the pasture than in the arable soil as the higher plant diversity provided more suitable hosts. Changes in fungal communities resulting from land-use change can provide important information for soil management and the assessment of the environmental impact of deforestation and conversion of vulnerable ecosystems such as high-altitude temperate forests.
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Affiliation(s)
- Yendi E Navarro-Noya
- Laboratory of Biotic Interactions, Centro de Investigación en Ciencias Biológicas, Universidad Autónoma de Tlaxcala, Tlaxcala, Mexico
| | - Nina Montoya-Ciriaco
- Doctorado en Ciencias Biológicas, Universidad Autónoma de Tlaxcala, Tlaxcala, Mexico
| | - Ligia C Muñoz-Arenas
- Doctorado en Ciencias Biológicas, Universidad Autónoma de Tlaxcala, Tlaxcala, Mexico.,Facultad de Ingeniería Ambiental, UPAEP, Puebla, Mexico
| | | | - Arturo Estrada-Torres
- Centro Tlaxcala de Biología de la Conducta, Universidad Autónoma de Tlaxcala, Tlaxcala, Mexico
| | - Luc Dendooven
- Laboratory of Soil Ecology, CINVESTAV-IPN, Ciudad de México, Mexico
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17
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Clary Sage Cultivation and Mycorrhizal Inoculation Influence the Rhizosphere Fungal Community of an Aged Trace-Element Polluted Soil. Microorganisms 2021; 9:microorganisms9061333. [PMID: 34205382 PMCID: PMC8234821 DOI: 10.3390/microorganisms9061333] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/16/2021] [Accepted: 06/17/2021] [Indexed: 11/17/2022] Open
Abstract
Soil fungal communities play a central role in natural systems and agroecosystems. As such, they have attracted significant research interest. However, the fungal microbiota of aromatic plants, such as clary sage (Salvia sclarea L.), remain unexplored. This is especially the case in trace element (TE)-polluted conditions and within the framework of phytomanagement approaches. The presence of high concentrations of TEs in soils can negatively affect not only microbial diversity and community composition but also plant establishment and growth. Hence, the objective of this study is to investigate the soil fungal and arbuscular mycorrhizal fungi (AMF) community composition and their changes over time in TE-polluted soils in the vicinity of a former lead smelter and under the cultivation of clary sage. We used Illumina MiSeq amplicon sequencing to evaluate the effects of in situ clary sage cultivation over two successive years, combined or not with exogenous AMF inoculation, on the rhizospheric soil and root fungal communities. We obtained 1239 and 569 fungal amplicon sequence variants (ASV), respectively, in the rhizospheric soil and roots of S. sclarea under TE-polluted conditions. Remarkably, 69 AMF species were detected at our experimental site, belonging to 12 AMF genera. Furthermore, the inoculation treatment significantly shaped the fungal communities in soil and increased the number of AMF ASVs in clary sage roots. In addition, clary sage cultivation over successive years could be one of the explanatory parameters for the inter-annual variation in both fungal and AMF communities in the soil and root biotopes. Our data provide new insights on fungal and AMF communities in the rhizospheric soil and roots of an aromatic plant, clary sage, grown in TE-polluted agricultural soil.
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18
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Orrù L, Canfora L, Trinchera A, Migliore M, Pennelli B, Marcucci A, Farina R, Pinzari F. How Tillage and Crop Rotation Change the Distribution Pattern of Fungi. Front Microbiol 2021; 12:634325. [PMID: 34220731 PMCID: PMC8247931 DOI: 10.3389/fmicb.2021.634325] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 05/13/2021] [Indexed: 12/13/2022] Open
Abstract
Massive sequencing of fungal communities showed that climatic factors, followed by edaphic and spatial variables, are feasible predictors of fungal richness and community composition. This study, based on a long-term field experiment with tillage and no-tillage management since 1995 and with a crop rotation introduced in 2009, confirmed that tillage practices shape soil properties and impact soil fungal communities. Results highlighted higher biodiversity of saprotrophic fungi in soil sites with low disturbance and an inverse correlation between the biodiversity of ectomycorrhizal and saprotrophic fungi. We speculated how their mutual exclusion could be due to a substrate-mediated niche partitioning or by space segregation. Moreover, where the soil was ploughed, the species were evenly distributed. There was higher spatial variability in the absence of ploughing, with fungal taxa distributed according to a small-scale pattern, corresponding to micro-niches that probably remained undisturbed and heterogeneously distributed. Many differentially represented OTUs in all the conditions investigated were unidentified species or OTUs matching at high taxa level (i.e., phylum, class, order). Among the fungi with key roles in all the investigated conditions, there were several yeast species known to have pronounced endemism in soil and are also largely unidentified. In addition to yeasts, other fungal species emerged as either indicator of a kind of management or as strongly associated with a specific condition. Plant residues played a substantial role in defining the assortment of species.
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Affiliation(s)
- Luigi Orrù
- Council for Agricultural Research and Economics, Research Centre for Genomics and Bioinformatics, Fiorenzuola d'Arda, Italy
| | - Loredana Canfora
- Council for Agricultural Research and Economics, Research Centre for Agriculture and Environment, Rome, Italy
| | - Alessandra Trinchera
- Council for Agricultural Research and Economics, Research Centre for Agriculture and Environment, Rome, Italy
| | - Melania Migliore
- Council for Agricultural Research and Economics, Research Centre for Agriculture and Environment, Rome, Italy
| | - Bruno Pennelli
- Council for Agricultural Research and Economics, Research Centre for Agriculture and Environment, Rome, Italy
| | - Andrea Marcucci
- Council for Agricultural Research and Economics, Research Centre for Agriculture and Environment, Rome, Italy
| | - Roberta Farina
- Council for Agricultural Research and Economics, Research Centre for Agriculture and Environment, Rome, Italy
| | - Flavia Pinzari
- National Research Council of Italy, Institute for Biological Systems, Rome, Italy
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19
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Yin C, Schlatter DC, Kroese DR, Paulitz TC, Hagerty CH. Responses of Soil Fungal Communities to Lime Application in Wheat Fields in the Pacific Northwest. Front Microbiol 2021; 12:576763. [PMID: 34093451 PMCID: PMC8174452 DOI: 10.3389/fmicb.2021.576763] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 04/21/2021] [Indexed: 11/15/2022] Open
Abstract
Liming is an effective agricultural practice and is broadly used to ameliorate soil acidification in agricultural ecosystems. Our understanding of the impacts of lime application on the soil fungal community is scarce. In this study, we explored the responses of fungal communities to liming at two locations with decreasing soil pH in Oregon in the Pacific Northwest using high-throughput sequencing (Illumina MiSeq). Our results revealed that the location and liming did not significantly affect soil fungal diversity and richness, and the impact of soil depth on fungal diversity varied among locations. In contrast, location and soil depth had a strong effect on the structure and composition of soil fungal communities, whereas the impact of liming was much smaller, and location- and depth-dependent. Interestingly, families Lasiosphaeriaceae, Piskurozymaceae, and Sordariaceae predominated in the surface soil (0–7.5 cm) and were positively correlated with soil OM and aluminum, and negatively correlated with pH. The family Kickxellaceae which predominated in deeper soil (15–22.5 cm), had an opposite response to soil OM. Furthermore, some taxa in Ascomycota, such as Hypocreales, Peziza and Penicillium, were increased by liming at one of the locations (Moro). In conclusion, these findings suggest that fungal community structure and composition rather than fungal diversity responded to location, soil depth and liming. Compared to liming, location and depth had a stronger effect on the soil fungal community, but some specific fungal taxa shifted with lime application.
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Affiliation(s)
- Chuntao Yin
- Department of Plant Pathology, Washington State University, Pullman, WA, United States.,Department of Botany and Plant Pathology, Oregon State University, Adams, OR, United States
| | - Daniel C Schlatter
- Wheat Health, Genetics and Quality Research Unit, United States Department of Agriculture - Agriculture Research Service, Pullman, WA, United States
| | - Duncan R Kroese
- Department of Botany and Plant Pathology, Oregon State University, Adams, OR, United States
| | - Timothy C Paulitz
- Department of Plant Pathology, Washington State University, Pullman, WA, United States.,Wheat Health, Genetics and Quality Research Unit, United States Department of Agriculture - Agriculture Research Service, Pullman, WA, United States
| | - Christina H Hagerty
- Department of Botany and Plant Pathology, Oregon State University, Adams, OR, United States
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20
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Heklau H, Schindler N, Buscot F, Eisenhauer N, Ferlian O, Prada Salcedo LD, Bruelheide H. Mixing tree species associated with arbuscular or ectotrophic mycorrhizae reveals dual mycorrhization and interactive effects on the fungal partners. Ecol Evol 2021; 11:5424-5440. [PMID: 34026018 PMCID: PMC8131788 DOI: 10.1002/ece3.7437] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 02/22/2021] [Accepted: 02/26/2021] [Indexed: 11/29/2022] Open
Abstract
Recent studies found that the majority of shrub and tree species are associated with both arbuscular mycorrhizal (AM) and ectomycorrhizal (EM) fungi. However, our knowledge on how different mycorrhizal types interact with each other is still limited. We asked whether the combination of hosts with a preferred association with either AM or EM fungi increases the host tree roots' mycorrhization rate and affects AM and EM fungal richness and community composition.We established a tree diversity experiment, where five tree species of each of the two mycorrhiza types were planted in monocultures, two-species and four-species mixtures. We applied morphological assessment to estimate mycorrhization rates and next-generation molecular sequencing to quantify mycobiont richness.Both the morphological and molecular assessment revealed dual-mycorrhizal colonization in 79% and 100% of the samples, respectively. OTU community composition strongly differed between AM and EM trees. While host tree species richness did not affect mycorrhization rates, we observed significant effects of mixing AM- and EM-associated hosts in AM mycorrhization rate. Glomeromycota richness was larger in monotypic AM tree combinations than in AM-EM mixtures, pointing to a dilution or suppression effect of AM by EM trees. We found a strong match between morphological quantification of AM mycorrhization rate and Glomeromycota richness. Synthesis. We provide evidence that the combination of hosts differing in their preferred mycorrhiza association affects the host's fungal community composition, thus revealing important biotic interactions among trees and their associated fungi.
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Affiliation(s)
- Heike Heklau
- Institute of Biology/Geobotany and Botanical GardenMartin Luther University Halle‐WittenbergHalle (Saale)Germany
| | - Nicole Schindler
- Institute of Biology/Geobotany and Botanical GardenMartin Luther University Halle‐WittenbergHalle (Saale)Germany
| | - François Buscot
- Department of Soil EcologyHelmholtz Centre for Environmental Research – UFZHalle (Saale)Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigLeipzigGermany
| | - Nico Eisenhauer
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigLeipzigGermany
- Institute of BiologyLeipzig UniversityLeipzigGermany
| | - Olga Ferlian
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigLeipzigGermany
- Institute of BiologyLeipzig UniversityLeipzigGermany
| | - Luis D. Prada Salcedo
- Department of Soil EcologyHelmholtz Centre for Environmental Research – UFZHalle (Saale)Germany
| | - Helge Bruelheide
- Institute of Biology/Geobotany and Botanical GardenMartin Luther University Halle‐WittenbergHalle (Saale)Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigLeipzigGermany
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21
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Ares A, Costa J, Joaquim C, Pintado D, Santos D, Messmer MM, Mendes-Moreira PM. Effect of Low-Input Organic and Conventional Farming Systems on Maize Rhizosphere in Two Portuguese Open-Pollinated Varieties (OPV), "Pigarro" (Improved Landrace) and "SinPre" (a Composite Cross Population). Front Microbiol 2021; 12:636009. [PMID: 33717028 PMCID: PMC7953162 DOI: 10.3389/fmicb.2021.636009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 01/19/2021] [Indexed: 11/13/2022] Open
Abstract
Maize is one of the most important crops worldwide and is the number one arable crop in Portugal. A transition from the conventional farming system to organic agriculture requires optimization of cultivars and management, the interaction of plant-soil rhizosphere microbiota being pivotal. The objectives of this study were to unravel the effect of population genotype and farming system on microbial communities in the rhizosphere of maize. Rhizosphere soil samples of two open-pollinated maize populations ("SinPre" and "Pigarro") cultivated under conventional and organic farming systems were taken during flowering and analyzed by next-generation sequencing (NGS). Phenological data were collected from the replicated field trial. A total of 266 fungi and 317 bacteria genera were identified in "SinPre" and "Pigarro" populations, of which 186 (69.9%) and 277 (87.4%) were shared among them. The microbiota of "Pigarro" showed a significant higher (P < 0.05) average abundance than the microbiota of "SinPre." The farming system had a statistically significant impact (P < 0.05) on the soil rhizosphere microbiota, and several fungal and bacterial taxa were found to be farming system-specific. The rhizosphere microbiota diversity in the organic farming system was higher than that in the conventional system for both varieties. The presence of arbuscular mycorrhizae (Glomeromycota) was mainly detected in the microbiota of the "SinPre" population under the organic farming systems and very rare under conventional systems. A detailed metagenome function prediction was performed. At the fungal level, pathotroph-saprotroph and pathotroph-symbiotroph lifestyles were modified by the farming system. For bacterial microbiota, the main functions altered by the farming system were membrane transport, transcription, translation, cell motility, and signal transduction. This study allowed identifying groups of microorganisms known for their role as plant growth-promoting rhizobacteria (PGPR) and with the capacity to improve crop tolerance for stress conditions, allowing to minimize the use of synthetic fertilizers and pesticides. Arbuscular mycorrhizae (phyla Glomeromycota) were among the most important functional groups in the fungal microbiota and Achromobacter, Burkholderia, Erwinia, Lysinibacillus, Paenibacillus, Pseudomonas, and Stenotrophomonas in the bacterial microbiota. In this perspective, the potential role of these microorganisms will be explored in future research.
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Affiliation(s)
- Aitana Ares
- Department of Life Sciences, Centre for Functional Ecology, University of Coimbra, Coimbra, Portugal.,Laboratory for Phytopathology, Instituto Pedro Nunes, Coimbra, Portugal
| | - Joana Costa
- Department of Life Sciences, Centre for Functional Ecology, University of Coimbra, Coimbra, Portugal.,Laboratory for Phytopathology, Instituto Pedro Nunes, Coimbra, Portugal
| | - Carolina Joaquim
- Centro de Recursos Naturais, Ambiente e Sociedade (CERNAS), Coimbra, Portugal
| | - Duarte Pintado
- Centro de Recursos Naturais, Ambiente e Sociedade (CERNAS), Coimbra, Portugal
| | - Daniela Santos
- Centro de Recursos Naturais, Ambiente e Sociedade (CERNAS), Coimbra, Portugal
| | - Monika M Messmer
- Research Institute of Organic Agriculture (FiBL), Frick, Switzerland
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22
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Nutrient availability is a dominant predictor of soil bacterial and fungal community composition after nitrogen addition in subtropical acidic forests. PLoS One 2021; 16:e0246263. [PMID: 33621258 PMCID: PMC7901772 DOI: 10.1371/journal.pone.0246263] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 01/17/2021] [Indexed: 11/19/2022] Open
Abstract
Nutrient addition to forest ecosystems significantly influences belowground microbial diversity, community structure, and ecosystem functioning. Nitrogen (N) addition in forests is common in China, especially in the southeast region. However, the influence of N addition on belowground soil microbial community diversity in subtropical forests remains unclear. In May 2018, we randomly selected 12 experimental plots in a Pinus taiwanensis forest within the Daiyun Mountain Nature Reserve, Fujian Province, China, and subjected them to N addition treatments for one year. We investigated the responses of the soil microbial communities and identified the major elements that influenced microbial community composition in the experimental plots. The present study included three N treatments, i.e., the control (CT), low N addition (LN, 40 kg N ha-1 yr-1), and high N addition (HN, 80 kg N ha-1 yr-1), and two depths, 0−10 cm (topsoil) and 10−20 cm (subsoil), which were all sampled in the growing season (May) of 2019. Soil microbial diversity and community composition in the topsoil and subsoil were investigated using high-throughput sequencing of bacterial 16S rDNA genes and fungal internal transcribed spacer sequences. According to our results, 1) soil dissolved organic carbon (DOC) significantly decreased after HN addition, and available nitrogen (AN) significantly declined after LN addition, 2) bacterial α-diversity in the subsoil significantly decreased with HN addition, which was affected significantly by the interaction between N addition and soil layer, and 3) soil DOC, rather than pH, was the dominant environmental factor influencing soil bacterial community composition, while AN and MBN were the best predictors of soil fungal community structure dynamics. Moreover, N addition influence both diversity and community composition of soil bacteria more than those of fungi in the subtropical forests. The results of the present study provide further evidence to support shifts in soil microbial community structure in acidic subtropical forests in response to increasing N deposition.
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23
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Marčiulynienė D, Marčiulynas A, Lynikienė J, Vaičiukynė M, Gedminas A, Menkis A. DNA-Metabarcoding of Belowground Fungal Communities in Bare-Root Forest Nurseries: Focus on Different Tree Species. Microorganisms 2021; 9:150. [PMID: 33440909 PMCID: PMC7827201 DOI: 10.3390/microorganisms9010150] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 12/29/2020] [Accepted: 01/08/2021] [Indexed: 11/20/2022] Open
Abstract
The production of tree seedlings in forest nurseries and their use in the replanting of clear-cut forest sites is a common practice in the temperate and boreal forests of Europe. Although conifers dominate on replanted sites, in recent years, deciduous tree species have received more attention due to their often-higher resilience to abiotic and biotic stress factors. The aim of the present study was to assess the belowground fungal communities of bare-root cultivated seedlings of Alnus glutinosa , Betula pendula, Pinus sylvestris, Picea abies and Quercus robur in order to gain a better understanding of the associated fungi and oomycetes, and their potential effects on the seedling performance in forest nurseries and after outplanting. The study sites were at the seven largest bare-root forest nurseries in Lithuania. The sampling included the roots and adjacent soil of 2-3 year old healthy-looking seedlings. Following the isolation of the DNA from the individual root and soil samples, these were amplified using ITS rRNA as a marker, and subjected to high-throughput PacBio sequencing. The results showed the presence of 161,302 high-quality sequences, representing 2003 fungal and oomycete taxa. The most common fungi were Malassezia restricta (6.7% of all of the high-quality sequences), Wilcoxina mikolae (5.0%), Pustularia sp. 3993_4 (4.6%), and Fusarium oxysporum (3.5%). The most common oomycetes were Pythium ultimum var. ultimum (0.6%), Pythium heterothallicum (0.3%), Pythium spiculum (0.3%), and Pythium sylvaticum (0.2%). The coniferous tree species (P. abies and P. sylvestris) generally showed a higher richness of fungal taxa and a rather distinct fungal community composition compared to the deciduous tree species (A. glutinosa, B. pendula , and Q. robur). The results demonstrated that the seedling roots and the rhizosphere soil in forest nurseries support a high richness of fungal taxa. The seedling roots were primarily inhabited by saprotrophic and mycorrhizal fungi, while fungal pathogens and oomycetes were less abundant, showing that the cultivation practices used in forest nurseries secured both the production of high-quality planting stock and disease control.
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Affiliation(s)
- Diana Marčiulynienė
- Institute of Forestry, Lithuanian Research Centre for Agriculture and Forestry, Liepų Str. 1, Girionys, LT-53101 Kaunas District, Lithuania; (A.M.); (J.L.); (M.V.); (A.G.)
| | - Adas Marčiulynas
- Institute of Forestry, Lithuanian Research Centre for Agriculture and Forestry, Liepų Str. 1, Girionys, LT-53101 Kaunas District, Lithuania; (A.M.); (J.L.); (M.V.); (A.G.)
| | - Jūratė Lynikienė
- Institute of Forestry, Lithuanian Research Centre for Agriculture and Forestry, Liepų Str. 1, Girionys, LT-53101 Kaunas District, Lithuania; (A.M.); (J.L.); (M.V.); (A.G.)
| | - Miglė Vaičiukynė
- Institute of Forestry, Lithuanian Research Centre for Agriculture and Forestry, Liepų Str. 1, Girionys, LT-53101 Kaunas District, Lithuania; (A.M.); (J.L.); (M.V.); (A.G.)
| | - Artūras Gedminas
- Institute of Forestry, Lithuanian Research Centre for Agriculture and Forestry, Liepų Str. 1, Girionys, LT-53101 Kaunas District, Lithuania; (A.M.); (J.L.); (M.V.); (A.G.)
| | - Audrius Menkis
- Department of Forest Mycology and Plant Pathology, Uppsala BioCenter, Swedish University of Agricultural Sciences, P.O. Box 7026, SE-75007 Uppsala, Sweden;
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24
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Galitskaya P, Biktasheva L, Blagodatsky S, Selivanovskaya S. Response of bacterial and fungal communities to high petroleum pollution in different soils. Sci Rep 2021; 11:164. [PMID: 33420266 PMCID: PMC7794381 DOI: 10.1038/s41598-020-80631-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 12/21/2020] [Indexed: 01/29/2023] Open
Abstract
Petroleum pollution of soils is a major environmental problem. Soil microorganisms can decompose a significant fraction of petroleum hydrocarbons in soil at low concentrations (1-5%). This characteristic can be used for soil remediation after oil pollution. Microbial community dynamics and functions are well studied in cases of moderate petroleum pollution, while cases with heavy soil pollution have received much less attention. We studied bacterial and fungal successions in three different soils with high petroleum contents (6 and 25%) in a laboratory experiment. The proportion of aliphatic and aromatic compounds decreased by 4-7% in samples with 6% pollution after 120 days of incubation but remained unchanged in samples with 25% hydrocarbons. The composition of the microbial community changed significantly in all cases. Oil pollution led to an increase in the relative abundance of bacteria such as Actinobacteria and the candidate TM7 phylum (Saccaribacteria) and to a decrease in that of Bacteroidetes. The gene abundance (number of OTUs) of oil-degrading bacteria (Rhodococcus sp., candidate class TM7-3 representative) became dominant in all soil samples, irrespective of the petroleum pollution level and soil type. The fungal communities in unpolluted soil samples differed more significantly than the bacterial communities. Nonmetric multidimensional scaling revealed that in the polluted soil, successions of fungal communities differed between soils, in contrast to bacterial communities. However, these successions showed similar trends: fungi capable of lignin and cellulose decomposition, e.g., from the genera Fusarium and Mortierella, were dominant during the incubation period.
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Affiliation(s)
- Polina Galitskaya
- grid.77268.3c0000 0004 0543 9688Institute of Environmental Sciences, Kazan Federal University, Kazan, 420008 Russia
| | - Liliya Biktasheva
- grid.77268.3c0000 0004 0543 9688Institute of Environmental Sciences, Kazan Federal University, Kazan, 420008 Russia
| | - Sergey Blagodatsky
- grid.9464.f0000 0001 2290 1502Institute of Plant Production and Agroecology in the Tropics and Subtropics, University of Hohenheim, 70599 Stuttgart, Germany ,grid.451005.5Institute of Physico-Chemical and Biological Problems of Soil Science, Pushchino, 142290 Russia
| | - Svetlana Selivanovskaya
- grid.77268.3c0000 0004 0543 9688Institute of Environmental Sciences, Kazan Federal University, Kazan, 420008 Russia
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25
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Gorshkov V, Osipova E, Ponomareva M, Ponomarev S, Gogoleva N, Petrova O, Gogoleva O, Meshcherov A, Balkin A, Vetchinkina E, Potapov K, Gogolev Y, Korzun V. Rye Snow Mold-Associated Microdochium nivale Strains Inhabiting a Common Area: Variability in Genetics, Morphotype, Extracellular Enzymatic Activities, and Virulence. J Fungi (Basel) 2020; 6:E335. [PMID: 33287447 PMCID: PMC7761817 DOI: 10.3390/jof6040335] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 11/29/2020] [Accepted: 11/30/2020] [Indexed: 12/16/2022] Open
Abstract
Snow mold is a severe plant disease caused by psychrophilic or psychrotolerant fungi, of which Microdochium species are the most harmful. A clear understanding of Microdochium biology has many gaps; the pathocomplex and its dynamic are poorly characterized, virulence factors are unknown, genome sequences are not available, and the criteria of plant snow mold resistance are not elucidated. Our study aimed to identify comprehensive characteristics of a local community of snow mold-causing Microdochium species colonizing a particular crop culture. By using the next-generation sequencing (NGS) technique, we characterized fungal and bacterial communities of pink snow mold-affected winter rye (Secale cereale) plants within a given geographical location shortly after snowmelt. Twenty-one strains of M. nivale were isolated, classified on the basis of internal transcribed spacer 2 (ITS2) region, and characterized by morphology, synthesis of extracellular enzymes, and virulence. Several types of extracellular enzymatic activities, the level of which had no correlations with the degree of virulence, were revealed for Microdochium species for the first time. Our study shows that genetically and phenotypically diverse M. nivale strains simultaneously colonize winter rye plants within a common area, and each strain is likely to utilize its own, unique strategy to cause the disease using "a personal" pattern of extracellular enzymes.
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Affiliation(s)
- Vladimir Gorshkov
- Laboratory of Plant Infectious Diseases, FRC Kazan Scientific Center of RAS, ul. Lobachevskogo, 2/31, 420111 Kazan, Russia; (E.O.); (M.P.); (S.P.); (N.G.); (O.P.); (O.G.); (A.M.); (A.B.); (K.P.); (Y.G.); (V.K.)
| | - Elena Osipova
- Laboratory of Plant Infectious Diseases, FRC Kazan Scientific Center of RAS, ul. Lobachevskogo, 2/31, 420111 Kazan, Russia; (E.O.); (M.P.); (S.P.); (N.G.); (O.P.); (O.G.); (A.M.); (A.B.); (K.P.); (Y.G.); (V.K.)
| | - Mira Ponomareva
- Laboratory of Plant Infectious Diseases, FRC Kazan Scientific Center of RAS, ul. Lobachevskogo, 2/31, 420111 Kazan, Russia; (E.O.); (M.P.); (S.P.); (N.G.); (O.P.); (O.G.); (A.M.); (A.B.); (K.P.); (Y.G.); (V.K.)
| | - Sergey Ponomarev
- Laboratory of Plant Infectious Diseases, FRC Kazan Scientific Center of RAS, ul. Lobachevskogo, 2/31, 420111 Kazan, Russia; (E.O.); (M.P.); (S.P.); (N.G.); (O.P.); (O.G.); (A.M.); (A.B.); (K.P.); (Y.G.); (V.K.)
| | - Natalia Gogoleva
- Laboratory of Plant Infectious Diseases, FRC Kazan Scientific Center of RAS, ul. Lobachevskogo, 2/31, 420111 Kazan, Russia; (E.O.); (M.P.); (S.P.); (N.G.); (O.P.); (O.G.); (A.M.); (A.B.); (K.P.); (Y.G.); (V.K.)
| | - Olga Petrova
- Laboratory of Plant Infectious Diseases, FRC Kazan Scientific Center of RAS, ul. Lobachevskogo, 2/31, 420111 Kazan, Russia; (E.O.); (M.P.); (S.P.); (N.G.); (O.P.); (O.G.); (A.M.); (A.B.); (K.P.); (Y.G.); (V.K.)
| | - Olga Gogoleva
- Laboratory of Plant Infectious Diseases, FRC Kazan Scientific Center of RAS, ul. Lobachevskogo, 2/31, 420111 Kazan, Russia; (E.O.); (M.P.); (S.P.); (N.G.); (O.P.); (O.G.); (A.M.); (A.B.); (K.P.); (Y.G.); (V.K.)
| | - Azat Meshcherov
- Laboratory of Plant Infectious Diseases, FRC Kazan Scientific Center of RAS, ul. Lobachevskogo, 2/31, 420111 Kazan, Russia; (E.O.); (M.P.); (S.P.); (N.G.); (O.P.); (O.G.); (A.M.); (A.B.); (K.P.); (Y.G.); (V.K.)
| | - Alexander Balkin
- Laboratory of Plant Infectious Diseases, FRC Kazan Scientific Center of RAS, ul. Lobachevskogo, 2/31, 420111 Kazan, Russia; (E.O.); (M.P.); (S.P.); (N.G.); (O.P.); (O.G.); (A.M.); (A.B.); (K.P.); (Y.G.); (V.K.)
| | - Elena Vetchinkina
- Institute of Biochemistry and Physiology of Plants and Microorganisms, Russian Academy of Sciences (IBPPM RAS), 13 Prospekt Entuziastov, 410049 Saratov, Russia;
| | - Kim Potapov
- Laboratory of Plant Infectious Diseases, FRC Kazan Scientific Center of RAS, ul. Lobachevskogo, 2/31, 420111 Kazan, Russia; (E.O.); (M.P.); (S.P.); (N.G.); (O.P.); (O.G.); (A.M.); (A.B.); (K.P.); (Y.G.); (V.K.)
| | - Yuri Gogolev
- Laboratory of Plant Infectious Diseases, FRC Kazan Scientific Center of RAS, ul. Lobachevskogo, 2/31, 420111 Kazan, Russia; (E.O.); (M.P.); (S.P.); (N.G.); (O.P.); (O.G.); (A.M.); (A.B.); (K.P.); (Y.G.); (V.K.)
| | - Viktor Korzun
- Laboratory of Plant Infectious Diseases, FRC Kazan Scientific Center of RAS, ul. Lobachevskogo, 2/31, 420111 Kazan, Russia; (E.O.); (M.P.); (S.P.); (N.G.); (O.P.); (O.G.); (A.M.); (A.B.); (K.P.); (Y.G.); (V.K.)
- KWS SAAT SE & Co. KGaA, Grimsehlstr. 31, 37555 Einbeck, Germany
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Protistan and fungal diversity in soils and freshwater lakes are substantially different. Sci Rep 2020; 10:20025. [PMID: 33208814 PMCID: PMC7675990 DOI: 10.1038/s41598-020-77045-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 11/04/2020] [Indexed: 11/14/2022] Open
Abstract
Freshwater and soil habitats hold rich microbial communities. Here we address commonalities and differences between both habitat types. While freshwater and soil habitats differ considerably in habitat characteristics organismic exchange may be high and microbial communities may even be inoculated by organisms from the respective other habitat. We analyze diversity pattern and the overlap of taxa of eukaryotic microbial communities in freshwater and soil based on Illumina HiSeq high-throughput sequencing of the amplicon V9 diversity. We analyzed corresponding freshwater and soil samples from 30 locations, i.e. samples from different lakes across Germany and soil samples from the respective catchment areas. Aside from principle differences in the community composition of soils and freshwater, in particular with respect to the relative contribution of fungi and algae, soil habitats have a higher richness. Nevertheless, community similarity between different soil sites is considerably lower as compared to the similarity between different freshwater sites. We show that the overlap of organisms co-occurring in freshwater and soil habitats is surprisingly low. Even though closely related taxa occur in both habitats distinct OTUs were mostly habitat–specific and most OTUs occur exclusively in either soil or freshwater. The distribution pattern of the few co-occurring lineages indicates that even most of these are presumably rather habitat-specific. Their presence in both habitat types seems to be based on a stochastic drift of particularly abundant but habitat-specific taxa rather than on established populations in both types of habitats.
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Frąc M, Lipiec J, Usowicz B, Oszust K, Brzezińska M. Structural and functional microbial diversity of sandy soil under cropland and grassland. PeerJ 2020; 8:e9501. [PMID: 32953254 PMCID: PMC7474522 DOI: 10.7717/peerj.9501] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 06/17/2020] [Indexed: 02/06/2023] Open
Abstract
Background Land use change significantly alters soil organic carbon content and the microbial community. Therefore, in the present study, the effect of changing cropland to grassland on structural and functional soil microbial diversity was evaluated. The specific aims were (i) to identify the most prominent members of the fungal communities and their relevant ecological guild groups; (ii) to assess changes in the diversity of ammonia-oxidizing archaea; (iii) to determine the relationships between microbial diversity and selected physical and chemical properties. Methods We investigated microbial diversity and activity indicators, bulk density and the water-holding capacity of sandy soil under both cropland and 25-year-old grassland (formerly cropland) in Trzebieszów, in the Podlasie Region, Poland. Microbial diversity was assessed by: the relative abundance of ammonia-oxidizing archaea, fungal community composition and functional diversity. Microbial activity was assessed by soil enzyme (dehydrogenase, β-glucosidase) and respiration tests. Results It was shown that compared to cropland, grassland has a higher soil organic carbon content, microbial biomass, basal respiration, rate of enzyme activity, richness and diversity of the microbial community, water holding capacity and the structure of the fungal and ammonia-oxidizing archaea communities was also altered. The implications of these results for soil quality and soil health are also discussed. The results suggest that grassland can have a significant phytosanitary capacity with regard to ecosystem services, due to the prominent presence of beneficial and antagonistic microbes. Moreover, the results also suggest that grassland use may improve the status of soil organic carbon and nitrogen dynamics, thereby increasing the relative abundance of fungi and ammonia-oxidizing archaea.
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Affiliation(s)
- Magdalena Frąc
- Institute of Agrophysics, Polish Academy of Sciences, Lublin, Poland
| | - Jerzy Lipiec
- Institute of Agrophysics, Polish Academy of Sciences, Lublin, Poland
| | - Bogusław Usowicz
- Institute of Agrophysics, Polish Academy of Sciences, Lublin, Poland
| | - Karolina Oszust
- Institute of Agrophysics, Polish Academy of Sciences, Lublin, Poland
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Friberg H, Persson P, Jensen DF, Bergkvist G. Preceding crop and tillage system affect winter survival of wheat and the fungal communities on young wheat roots and in soil. FEMS Microbiol Lett 2020; 366:5561442. [PMID: 31504475 PMCID: PMC6759068 DOI: 10.1093/femsle/fnz189] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 09/02/2019] [Indexed: 12/02/2022] Open
Abstract
Agricultural practices like tillage and cropping sequence have profound influence on soil-living and plant-associated fungi, and thereby on plant growth. In a field experiment, we studied the effects of preceding crop and tillage on fungal communities in the soil and on young winter wheat roots in relation to plant winter survival and grain yield. We hypothesized that plant performance and fungal communities (described by amplicon sequencing) differ depending on tillage system and preceding crop; that the effect of preceding crop differs depending on tillage system, and that differences in fungal communities are reflected in plant performance. In line with our hypotheses, effects of preceding crop on plant growth and fungal communities on plant roots and in soil were more pronounced under non-inversion tillage than under inversion tillage (ploughing). Fungal communities on plant roots in treatments with low winter survival were different from those with better survival. In soil, several fungal OTUs (operational taxonomic units) differed significantly between tillage systems. OTUs representing putative plant pathogens were either more abundant (Parastagonospora sp._27) or less abundant (Fusarium culmorum/graminearum_5) after non-inversion tillage. Our findings highlight the influence of cultural practices on fungal communities and thereby on plant health and yield.
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Affiliation(s)
- Hanna Friberg
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, P.O. Box 7026, 75007 Uppsala , Sweden
| | - Paula Persson
- Department of Crop Production Ecology, Swedish University of Agricultural Sciences, P.O. Box 7043, 75007 Uppsala , Sweden
| | - Dan Funck Jensen
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, P.O. Box 7026, 75007 Uppsala , Sweden
| | - Göran Bergkvist
- Department of Crop Production Ecology, Swedish University of Agricultural Sciences, P.O. Box 7043, 75007 Uppsala , Sweden
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Fungal Planet description sheets: 1042-1111. Persoonia - Molecular Phylogeny and Evolution of Fungi 2020; 44:301-459. [PMID: 33116344 PMCID: PMC7567971 DOI: 10.3767/persoonia.2020.44.11] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 05/30/2020] [Indexed: 12/31/2022]
Abstract
Novel species of fungi described in this study include those from various countries as follows: Antarctica, Cladosporium arenosum from marine sediment sand. Argentina, Kosmimatamyces alatophylus (incl. Kosmimatamyces gen. nov.) from soil. Australia, Aspergillus banksianus, Aspergillus kumbius, Aspergillus luteorubrus, Aspergillus malvicolor and Aspergillus nanangensis from soil, Erysiphe medicaginis from leaves of Medicago polymorpha, Hymenotorrendiella communis on leaf litter of Eucalyptus bicostata, Lactifluus albopicri and Lactifluus austropiperatus on soil, Macalpinomyces collinsiae on Eriachne benthamii, Marasmius vagus on soil, Microdochium dawsoniorum from leaves of Sporobolus natalensis, Neopestalotiopsis nebuloides from leaves of Sporobolus elongatus, Pestalotiopsis etonensis from leaves of Sporobolus jacquemontii, Phytophthora personensis from soil associated with dying Grevillea mccutcheonii.Brazil, Aspergillus oxumiae from soil, Calvatia baixaverdensis on soil, Geastrum calycicoriaceum on leaf litter, Greeneria kielmeyerae on leaf spots of Kielmeyera coriacea. Chile, Phytophthora aysenensis on collar rot and stem of Aristotelia chilensis.Croatia, Mollisia gibbospora on fallen branch of Fagus sylvatica.Czech Republic, Neosetophoma hnaniceana from Buxus sempervirens.Ecuador, Exophiala frigidotolerans from soil. Estonia, Elaphomyces bucholtzii in soil. France, Venturia paralias from leaves of Euphorbia paralias.India, Cortinarius balteatoindicus and Cortinarius ulkhagarhiensis on leaf litter. Indonesia, Hymenotorrendiella indonesiana on Eucalyptus urophylla leaf litter. Italy, Penicillium taurinense from indoor chestnut mill. Malaysia, Hemileucoglossum kelabitense on soil, Satchmopsis pini on dead needles of Pinus tecunumanii.Poland, Lecanicillium praecognitum on insects’ frass. Portugal, Neodevriesia aestuarina from saline water. Republic of Korea, Gongronella namwonensis from freshwater. Russia, Candida pellucida from Exomias pellucidus, Heterocephalacria septentrionalis as endophyte from Cladonia rangiferina, Vishniacozyma phoenicis from dates fruit, Volvariella paludosa from swamp. Slovenia, Mallocybe crassivelata on soil. South Africa, Beltraniella podocarpi, Hamatocanthoscypha podocarpi, Coleophoma podocarpi and Nothoseiridium podocarpi (incl. Nothoseiridium gen. nov.) from leaves of Podocarpus latifolius, Gyrothrix encephalarti from leaves of Encephalartos sp., Paraphyton cutaneum from skin of human patient, Phacidiella alsophilae from leaves of Alsophila capensis, and Satchmopsis metrosideri on leaf litter of Metrosideros excelsa.Spain, Cladophialophora cabanerensis from soil, Cortinarius paezii on soil, Cylindrium magnoliae from leaves of Magnolia grandiflora, Trichophoma cylindrospora (incl. Trichophoma gen. nov.) from plant debris, Tuber alcaracense in calcareus soil, Tuber buendiae in calcareus soil. Thailand, Annulohypoxylon spougei on corticated wood, Poaceascoma filiforme from leaves of unknown Poaceae.UK, Dendrostoma luteum on branch lesions of Castanea sativa, Ypsilina buttingtonensis from heartwood of Quercus sp. Ukraine, Myrmecridium phragmiticola from leaves of Phragmites australis.USA, Absidia pararepens from air, Juncomyces californiensis (incl. Juncomyces gen. nov.) from leaves of Juncus effusus, Montagnula cylindrospora from a human skin sample, Muriphila oklahomaensis (incl. Muriphila gen. nov.) on outside wall of alcohol distillery, Neofabraea eucalyptorum from leaves of Eucalyptus macrandra, Diabolocovidia claustri (incl. Diabolocovidia gen. nov.) from leaves of Serenoa repens, Paecilomyces penicilliformis from air, Pseudopezicula betulae from leaves of leaf spots of Populus tremuloides. Vietnam, Diaporthe durionigena on branches of Durio zibethinus and Roridomyces pseudoirritans on rotten wood. Morphological and culture characteristics are supported by DNA barcodes.
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Köberl M, Wagner P, Müller H, Matzer R, Unterfrauner H, Cernava T, Berg G. Unraveling the Complexity of Soil Microbiomes in a Large-Scale Study Subjected to Different Agricultural Management in Styria. Front Microbiol 2020; 11:1052. [PMID: 32523580 PMCID: PMC7261914 DOI: 10.3389/fmicb.2020.01052] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 04/28/2020] [Indexed: 12/31/2022] Open
Abstract
Healthy soil microbiomes are crucial for achieving high productivity in combination with crop quality, but our understanding of microbial diversity is still limited. In a large-scale study including 116 composite samples from vineyards, orchards and other crops from all over Styria (south-east Austria), agricultural management as well as distinct soil parameters were identified as drivers of the indigenous microbial communities in agricultural soils. The analysis of the soil microbiota based on microbial profiling of prokaryotic 16S rRNA gene fragments and fungal ITS regions revealed high bacterial and fungal diversity within Styrian agricultural soils; 206,596 prokaryotic and 53,710 fungal OTUs. Vineyards revealed a significantly higher diversity and distinct composition of soil fungi over orchards and other agricultural soils, whereas the prokaryotic diversity was unaffected. Soil pH was identified as one of the most important edaphic modulators of microbial community structure in both, vineyard and orchard soils. In general, the acid-base balance, disorders in the soil sorption complex, content and quality of organic substance as well as individual nutrients were identified as important drivers of the microbial community structure of Styrian vineyard and orchard soils. However, responses to distinct parameters differed in orchards and vineyards, and prokaryotic and fungal community responded differently to the same abiotic factor. In comparison to orchards, the microbiome of vineyard soils maintained a higher stability when herbicides were applied. Orchard soils exhibited drastic shifts within community composition; herbicides seem to have a substantial impact on the bacterial order Chthoniobacterales as well as potential plant growth promoters and antagonists of phytopathogens (Flavobacterium, Monographella), with a decreased abundance in herbicide-treated soils. Moreover, soils of herbicide-treated orchards revealed a significantly higher presence of potential apple pathogenic fungi (Nectria, Thelonectria). These findings provide the basis to adapt soil management practices in the future in order to maintain a healthy microbiome in agricultural soils.
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Affiliation(s)
- Martina Köberl
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Philipp Wagner
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Henry Müller
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Robert Matzer
- ARGE obst.wein, Association of Weinbauverband Steiermark and Verband Steirischer Erwerbsobstbauern, Graz, Austria
| | | | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
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31
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Keuschnig C, Gorfer M, Li G, Mania D, Frostegård Å, Bakken L, Larose C. NO and N 2 O transformations of diverse fungi in hypoxia: evidence for anaerobic respiration only in Fusarium strains. Environ Microbiol 2020; 22:2182-2195. [PMID: 32157782 DOI: 10.1111/1462-2920.14980] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 02/21/2020] [Accepted: 03/07/2020] [Indexed: 11/30/2022]
Abstract
Fungal denitrification is claimed to produce non-negligible amounts of N2 O in soils, but few tested species have shown significant activity. We hypothesized that denitrifying fungi would be found among those with assimilatory nitrate reductase, and tested 20 such batch cultures for their respiratory metabolism, including two positive controls, Fusarium oxysporum and Fusarium lichenicola, throughout the transition from oxic to anoxic conditions in media supplemented with NO 2 - . Enzymatic reduction of NO 2 - (NIR) and NO (NOR) was assessed by correcting measured NO- and N2 O-kinetics for abiotic NO- and N2 O-production (sterile controls). Significant anaerobic respiration was only confirmed for the positive controls and for two of three Fusarium solani cultures. The NO kinetics in six cultures showed NIR but not NOR activity, observed through the accumulation of NO. Others had NOR but not NIR activity, thus reducing abiotically produced NO to N2 O. The presence of candidate genes (nirK and p450nor) was confirmed in the positive controls, but not in some of the NO or N2 O accumulating cultures. Based on our results, we conclude that only the Fusarium cultures were able to sustain anaerobic respiration and produced low amounts of N2 O as a response to an abiotic NO production from the medium.
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Affiliation(s)
- Christoph Keuschnig
- Environmental Microbial Genomics, Laboratoire Ampère, CNRS UMR 5005, Ecole Centrale de Lyon, Université de Lyon, 69134, Ecully Cedex, France
| | - Markus Gorfer
- Bioresources, AIT Austrian Institute of Technology GmbH, Tulln, Austria
| | - Guofen Li
- Bioresources, AIT Austrian Institute of Technology GmbH, Tulln, Austria
| | - Daniel Mania
- Faculty of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, 1432, Aas, Norway
| | - Åsa Frostegård
- Faculty of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, 1432, Aas, Norway
| | - Lars Bakken
- Faculty of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, 1432, Aas, Norway
| | - Catherine Larose
- Environmental Microbial Genomics, Laboratoire Ampère, CNRS UMR 5005, Ecole Centrale de Lyon, Université de Lyon, 69134, Ecully Cedex, France
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32
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Jamil A, Yang JY, Su DF, Tong JY, Chen SY, Luo ZW, Shen XM, Wei SJ, Cui XL. Rhizospheric soil fungal community patterns of Duchesnea indica in response to altitude gradient in Yunnan, southwest China. Can J Microbiol 2020; 66:359-367. [PMID: 32053399 DOI: 10.1139/cjm-2019-0589] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The magnitude of the impact of altitude gradient on microbial community and diversity has been studied in recent decades. Whereas bacteria have been the focus of most studies, fungi have been given relatively less attention. As a vital part of the macro- and microscopic ecosystem, rhizosphere fungi play a key role in organic matter decomposition and relative abundance of plant species and have an impact on plant growth and development. Using Duchesnea indica as the host plant, we examined the rhizosphere soil fungal community patterns across the altitude gradient in 15 sites of Yunnan province by sequencing the fungal ITS2 region with the Illumina MiSeq platform. We determined the fungal community composition and structure. We found that, surprisingly, rhizosphere soil fungal diversity of D. indica increased with altitudinal gradient. There was a slight difference in diversity between samples from high- and medium-altitude sites, with medium-altitude sites having the greater diversity. Furthermore, the rhizosphere soil fungal community composition and structure kept changing along the altitudinal gradient. Taxonomic results showed that the extent of phylum diversity was greatest at high-altitude sites, with Ascomycota, Basidiomycota, Zygomycota, and Glomeromycota as the most dominant fungal phyla.
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Affiliation(s)
- Arslan Jamil
- Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming, Yunnan 650091, People's Republic of China.,State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, Yunnan 650091, People's Republic of China
| | - Jun-Yu Yang
- Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming, Yunnan 650091, People's Republic of China.,State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, Yunnan 650091, People's Republic of China
| | - Dai-Fa Su
- Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming, Yunnan 650091, People's Republic of China.,State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, Yunnan 650091, People's Republic of China
| | - Jiang-Yun Tong
- Kunming Academy of Agricultural Science, Kunming, Yunnan 650034, People's Republic of China
| | - Shan-Yan Chen
- Kunming Academy of Agricultural Science, Kunming, Yunnan 650034, People's Republic of China
| | - Zhi-Wei Luo
- Kunming Academy of Agricultural Science, Kunming, Yunnan 650034, People's Republic of China
| | - Xue-Mei Shen
- Kunming Academy of Agricultural Science, Kunming, Yunnan 650034, People's Republic of China
| | - Shi-Jie Wei
- Kunming Academy of Agricultural Science, Kunming, Yunnan 650034, People's Republic of China
| | - Xiao-Long Cui
- Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming, Yunnan 650091, People's Republic of China.,State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, Yunnan 650091, People's Republic of China
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33
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Karlsson E, Johansson AM, Ahlinder J, Lundkvist MJ, Singh NJ, Brodin T, Forsman M, Stenberg P. Airborne microbial biodiversity and seasonality in Northern and Southern Sweden. PeerJ 2020; 8:e8424. [PMID: 32025374 PMCID: PMC6991134 DOI: 10.7717/peerj.8424] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 12/17/2019] [Indexed: 01/04/2023] Open
Abstract
Microorganisms are essential constituents of ecosystems. To improve our understanding of how various factors shape microbial diversity and composition in nature it is important to study how microorganisms vary in space and time. Factors shaping microbial communities in ground level air have been surveyed in a limited number of studies, indicating that geographic location, season and local climate influence the microbial communities. However, few have surveyed more than one location, at high latitude or continuously over more than a year. We surveyed the airborne microbial communities over two full consecutive years in Kiruna, in the Arctic boreal zone, and Ljungbyhed, in the Southern nemoral zone of Sweden, by using a unique collection of archived air filters. We mapped both geographic and seasonal differences in bacterial and fungal communities and evaluated environmental factors that may contribute to these differences and found that location, season and weather influence the airborne communities. Location had stronger influence on the bacterial community composition compared to season, while location and season had equal influence on the fungal community composition. However, the airborne bacterial and fungal diversity showed overall the same trend over the seasons, regardless of location, with a peak during the warmer parts of the year, except for the fungal seasonal trend in Ljungbyhed, which fluctuated more within season. Interestingly, the diversity and evenness of the airborne communities were generally lower in Ljungbyhed. In addition, both bacterial and fungal communities varied significantly within and between locations, where orders like Rhizobiales, Rhodospirillales and Agaricales dominated in Kiruna, whereas Bacillales, Clostridiales and Sordariales dominated in Ljungbyhed. These differences are a likely reflection of the landscape surrounding the sampling sites where the landscape in Ljungbyhed is more homogenous and predominantly characterized by artificial and agricultural surroundings. Our results further indicate that local landscape, as well as seasonal variation, shapes microbial communities in air.
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Affiliation(s)
- Edvin Karlsson
- Department of Molecular Biology, Umeå University, Umeå, Sweden.,Department of Biological Agents, Division of CBRN Defense and Security, Swedish Defense Research Agency, Umeå, Sweden
| | | | - Jon Ahlinder
- Department of Biological Agents, Division of CBRN Defense and Security, Swedish Defense Research Agency, Umeå, Sweden
| | - Moa J Lundkvist
- Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Navinder J Singh
- Department of Wildlife, Fish, and Environmental Studies, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Tomas Brodin
- Department of Wildlife, Fish, and Environmental Studies, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Mats Forsman
- Department of Biological Agents, Division of CBRN Defense and Security, Swedish Defense Research Agency, Umeå, Sweden
| | - Per Stenberg
- Department of Biological Agents, Division of CBRN Defense and Security, Swedish Defense Research Agency, Umeå, Sweden.,Department of Ecology and Environmental Sciences, Umeå University, Umeå, Sweden
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Das S, Lee JG, Cho SR, Song HJ, Kim PJ. Silicate Fertilizer Amendment Alters Fungal Communities and Accelerates Soil Organic Matter Decomposition. Front Microbiol 2019; 10:2950. [PMID: 31921092 PMCID: PMC6932956 DOI: 10.3389/fmicb.2019.02950] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 12/09/2019] [Indexed: 11/26/2022] Open
Abstract
Soil microorganisms play a crucial role in organic matter decomposition and nutrient cycling in cropping systems. Compared to bacteria, fungal community composition and the role of fungi in organic matter decomposition and nutrient cycling in agro-systems are, however, elusive. Silicon (Si) fertilization is essential to improve agronomic performance of rice. The effects of the Si fertilizer application on the soil fungal community composition and their contribution in soil organic matter (SOM) decomposition are not yet studied. We investigated the short-term (120 days) slag silicate fertilizer (SSF) amendment impacts on plant photosynthesis and soil biochemical changes, soil fungal communities (assessed by ITS amplicon illumina sequencing), hydrolytic and oxidase enzyme activities, CO2 emissions, and bacterial and fungal respiration in diverse eco-geographic races of rice (Oryza sativa L.), i.e., Japonica rice (O. sativa japonica) and Indica rice (O. sativa indica). The short-term SSF amendment significantly increased the relative abundance of saprotrophic fungi and accelerated organic matter decomposition. The increase in saprotrophic fungi was mostly attributed to greater labile C availability and Si availability. Higher organic matter decomposition was accompanied by an increase in both hydrolytic and oxidative enzyme activities in response to the SSF amendment. The stimulation of oxidative enzyme activities was explained by an increase in root oxidase activities and iron redox cycling, whereas stimulation of hydrolytic enzyme activities was explained by the greater labile C availability under SSF fertilization. We conclude that the short-term SSF amendment increases saprotrophic fungal communities and soil hydrolytic and oxidative enzyme activities, which in turn stimulates SOM mineralization and thus could have negative feedback impacts on soil C storage in submerged rice paddies.
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Affiliation(s)
- Suvendu Das
- Institute of Agriculture and Life Sciences, Gyeongsang National University, Jinju, South Korea
| | - Jeong Gu Lee
- Division of Applied Life Sciences, Gyeongsang National University, Jinju, South Korea
| | - Song Rae Cho
- Division of Applied Life Sciences, Gyeongsang National University, Jinju, South Korea
| | - Hyeon Ji Song
- Division of Applied Life Sciences, Gyeongsang National University, Jinju, South Korea
| | - Pil Joo Kim
- Institute of Agriculture and Life Sciences, Gyeongsang National University, Jinju, South Korea.,Division of Applied Life Sciences, Gyeongsang National University, Jinju, South Korea
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Harkes P, Suleiman AKA, van den Elsen SJJ, de Haan JJ, Holterman M, Kuramae EE, Helder J. Conventional and organic soil management as divergent drivers of resident and active fractions of major soil food web constituents. Sci Rep 2019; 9:13521. [PMID: 31534146 PMCID: PMC6751164 DOI: 10.1038/s41598-019-49854-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 08/27/2019] [Indexed: 11/09/2022] Open
Abstract
Conventional agricultural production systems, typified by large inputs of mineral fertilizers and pesticides, reduce soil biodiversity and may negatively affect ecosystem services such as carbon fixation, nutrient cycling and disease suppressiveness. Organic soil management is thought to contribute to a more diverse and stable soil food web, but data detailing this effect are sparse and fragmented. We set out to map both the resident (rDNA) and the active (rRNA) fractions of bacterial, fungal, protozoan and metazoan communities under various soil management regimes in two distinct soil types with barley as the main crop. Contrasts between resident and active communities explained 22%, 14%, 21% and 25% of the variance within the bacterial, fungal, protozoan, and metazoan communities. As the active fractions of organismal groups define the actual ecological functioning of soils, our findings underline the relevance of characterizing both resident and active pools. All four major organismal groups were affected by soil management (p < 0.01), and most taxa showed both an increased presence and an enlarged activity under the organic regime. Hence, a prolonged organic soil management not only impacts the primary decomposers, bacteria and fungi, but also major representatives of the next trophic level, protists and metazoa.
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Affiliation(s)
- Paula Harkes
- Laboratory of Nematology, Dept. Plant Sciences, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Afnan K A Suleiman
- Department Microbial Ecology, Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
- KWR Watercycle Research Institute, Groningenhaven 7, 3433, PE, Nieuwegein, The Netherlands
| | - Sven J J van den Elsen
- Laboratory of Nematology, Dept. Plant Sciences, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Johannes J de Haan
- Wageningen University & Research Open Teelten, Edelhertweg 10, Lelystad, The Netherlands
| | - Martijn Holterman
- Laboratory of Nematology, Dept. Plant Sciences, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Eiko E Kuramae
- Department Microbial Ecology, Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
| | - Johannes Helder
- Laboratory of Nematology, Dept. Plant Sciences, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
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Liang H, Wang X, Yan J, Luo L. Characterizing the Intra-Vineyard Variation of Soil Bacterial and Fungal Communities. Front Microbiol 2019; 10:1239. [PMID: 31214155 PMCID: PMC6554343 DOI: 10.3389/fmicb.2019.01239] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 05/17/2019] [Indexed: 12/20/2022] Open
Abstract
Vineyard soil microbial communities potentially mediate grapevine growth, grape production as well as wine terroir. Simultaneously assessing shifts of microbial community composition at the intra-vineyard scale allows us to decouple correlations among environmental variables, thus providing insights into vineyard management. Here we investigated bacterial and fungal community compositions and their relationships with edaphic properties in soils collected from a commercial vineyard at four different soil depths (0-5, 5-10, 10-20, and 20-40 cm). Soil organic carbon (SOC) content, invertase activity and phosphatase activity decreased along depth gradient in the 0-20 cm soil fraction (P < 0.001). The soil bacterial biomass and α-diversity were significantly higher than those of fungi (P ≤ 0.001). Statistical analyses revealed that SOC content, pH, C/N ratio and total phosphorus (TP) were significant determinants of soil bacterial (R = 0.494, P = 0.001) and fungal (R = 0.443, P = 0.001) community structure. The abundance of dominated bacterial phyla (Proteobacteria, Acidobacteria and Actinobacteria) and fungal phyla (Ascomycota, Zygomycota and Basidiomycota) slightly varied among all soil samples. Genus Lactococcus, which comprised 2.72% of the soil bacterial community, showed increasing pattern with depth. Importantly, Candidatus Nitrososphaera, Monographella and Fusarium were also detected with high abundances in soil samples, indicating their ecological function in soil nitrogen cycle and the potential risk in grapevine disease. Overall, this work detected the intra-vineyard variation of bacterial and fungal communities and their relationships with soil characteristics, which was beneficial to vineyard soil management and grapevine disease prevention.
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Affiliation(s)
- Hebin Liang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Xiaowen Wang
- Food Testing Institute, Shenzhen Academy of Metrology and Quality Inspection, Shenzhen, China.,National Nutrition Food Testing Center, Shenzhen, China
| | - Junwei Yan
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Lixin Luo
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
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Adamczyk M, Hagedorn F, Wipf S, Donhauser J, Vittoz P, Rixen C, Frossard A, Theurillat JP, Frey B. The Soil Microbiome of GLORIA Mountain Summits in the Swiss Alps. Front Microbiol 2019; 10:1080. [PMID: 31156590 PMCID: PMC6529532 DOI: 10.3389/fmicb.2019.01080] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 04/29/2019] [Indexed: 01/03/2023] Open
Abstract
While vegetation has intensively been surveyed on mountain summits, limited knowledge exists about the diversity and community structure of soil biota. Here, we study how climatic variables, vegetation, parent material, soil properties, and slope aspect affect the soil microbiome on 10 GLORIA (Global Observation Research Initiative in Alpine environments) mountain summits ranging from the lower alpine to the nival zone in Switzerland. At these summits we sampled soils from all four aspects and examined how the bacterial and fungal communities vary by using Illumina MiSeq sequencing. We found that mountain summit soils contain highly diverse microbial communities with a total of 10,406 bacterial and 6,291 fungal taxa. Bacterial α-diversity increased with increasing soil pH and decreased with increasing elevation, whereas fungal α-diversity did not change significantly. Soil pH was the strongest predictor for microbial β-diversity. Bacterial and fungal community structures exhibited a significant positive relationship with plant communities, indicating that summits with a more distinct plant composition also revealed more distinct microbial communities. The influence of elevation was stronger than aspect on the soil microbiome. Several microbial taxa responded to elevation and soil pH. Chloroflexi and Mucoromycota were significantly more abundant on summits at higher elevations, whereas the relative abundance of Basidiomycota and Agaricomycetes decreased with elevation. Most bacterial OTUs belonging to the phylum Acidobacteria were indicators for siliceous parent material and several OTUs belonging to the phylum Planctomycetes were associated with calcareous soils. The trends for fungi were less clear. Indicator OTUs belonging to the genera Mortierella and Naganishia showed a mixed response to parent material, demonstrating their ubiquitous and opportunistic behaviour in soils. Overall, fungal communities responded weakly to abiotic and biotic factors. In contrast, bacterial communities were strongly influenced by environmental changes suggesting they will be strongly affected by future climate change and associated temperature increase and an upward migration of vegetation. Our results provide the first insights into the soil microbiome of mountain summits in the European Alps that are shaped as a result of highly variable local environmental conditions and may help to predict responses of the soil biota to global climate change.
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Affiliation(s)
- Magdalene Adamczyk
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Frank Hagedorn
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Sonja Wipf
- Community Ecology, WSL Institute for Snow and Avalanche Research SLF, Davos, Switzerland
| | - Johanna Donhauser
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Pascal Vittoz
- Institute of Earth Surface Dynamics, University of Lausanne, Lausanne, Switzerland
| | - Christian Rixen
- Community Ecology, WSL Institute for Snow and Avalanche Research SLF, Davos, Switzerland
| | - Aline Frossard
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Jean-Paul Theurillat
- Fondation J.-M. Aubert, Champex-Lac, Switzerland.,Department of Botany and Plant Biology, University of Geneva, Chambésy, Switzerland
| | - Beat Frey
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
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38
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Mallet C, Romdhane S, Loiseau C, Béguet J, Martin-Laurent F, Calvayrac C, Barthelmebs L. Impact of Leptospermone, a Natural β-Triketone Herbicide, on the Fungal Composition and Diversity of Two Arable Soils. Front Microbiol 2019; 10:1024. [PMID: 31134038 PMCID: PMC6524154 DOI: 10.3389/fmicb.2019.01024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 04/24/2019] [Indexed: 01/10/2023] Open
Abstract
Impact of leptospermone, a β-triketone bioherbicide, was investigated on the fungal community which supports important soil ecological functions such as decomposition of organic matter and nutrients recycling. This study was done in a microcosm experiment using two French soils, Perpignan (P) and Saint-Jean-de-Fos (SJF), differing in their physicochemical properties and history treatment with synthetic β-triketones. Soil microcosms were treated with leptospermone at recommended dose and incubated under controlled conditions for 45 days. Untreated microcosms were used as control. Illumina MiSeq sequencing of the internal transcribed spacer region of the fungal rRNA revealed significant changes in fungal community structure and diversity in both soils. Xylariales, Hypocreales, Pleosporales and Capnodiales (Ascomycota phyla) fungi and those belonging to Sebacinales, Cantharellales, Agaricales, Polyporales, Filobasidiales and Tremellales orders (Basidiomycota phyla) were well represented in treated soil microcosms compared to control. Nevertheless, while for the treated SJF a complete recovery of the fungal community was observed at the end of the experiment, this was not the case for the P treated soil, although no more bioherbicide remained. Indeed, the relative abundance of most of the saprophytic fungi were lower in treated soil compared to control microcosms whereas fungi from parasitic fungi included in Spizellomycetales and Pezizales orders increased. To the best of our knowledge, this is the only study assessing the effect of the bioherbicide leptospermone on the composition and diversity of the fungal community in soil. This study showed that leptospermone has an impact on α- and β-diversity of the fungal community. It underlines the possible interest of microbial endpoints for environmental risk assessment of biopesticide.
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Affiliation(s)
- Clarisse Mallet
- Laboratoire Microorganismes : Génome et Environnement, CNRS, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Sana Romdhane
- AgroSup Dijon, INRA UMR1347 Agroécologie, Université de Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
- Biocapteurs-Analyses-Environnement, Université de Perpignan Via Domitia, Perpignan, France
| | - Camille Loiseau
- Laboratoire Microorganismes : Génome et Environnement, CNRS, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Jérémie Béguet
- AgroSup Dijon, INRA UMR1347 Agroécologie, Université de Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
| | - Fabrice Martin-Laurent
- AgroSup Dijon, INRA UMR1347 Agroécologie, Université de Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
| | - Christophe Calvayrac
- Biocapteurs-Analyses-Environnement, Université de Perpignan Via Domitia, Perpignan, France
- Laboratoire de Biodiversité et Biotechnologies Microbiennes, USR 3579 Sorbonne Universités (UPMC) Paris 6 et CNRS Observatoire Océanologique, Banyuls-sur-Mer, France
| | - Lise Barthelmebs
- Biocapteurs-Analyses-Environnement, Université de Perpignan Via Domitia, Perpignan, France
- Laboratoire de Biodiversité et Biotechnologies Microbiennes, USR 3579 Sorbonne Universités (UPMC) Paris 6 et CNRS Observatoire Océanologique, Banyuls-sur-Mer, France
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39
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Divergent national-scale trends of microbial and animal biodiversity revealed across diverse temperate soil ecosystems. Nat Commun 2019; 10:1107. [PMID: 30846683 PMCID: PMC6405921 DOI: 10.1038/s41467-019-09031-1] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 02/13/2019] [Indexed: 02/07/2023] Open
Abstract
Soil biota accounts for ~25% of global biodiversity and is vital to nutrient cycling and primary production. There is growing momentum to study total belowground biodiversity across large ecological scales to understand how habitat and soil properties shape belowground communities. Microbial and animal components of belowground communities follow divergent responses to soil properties and land use intensification; however, it is unclear whether this extends across heterogeneous ecosystems. Here, a national-scale metabarcoding analysis of 436 locations across 7 different temperate ecosystems shows that belowground animal and microbial (bacteria, archaea, fungi, and protists) richness follow divergent trends, whereas β-diversity does not. Animal richness is governed by intensive land use and unaffected by soil properties, while microbial richness was driven by environmental properties across land uses. Our findings demonstrate that established divergent patterns of belowground microbial and animal diversity are consistent across heterogeneous land uses and are detectable using a standardised metabarcoding approach.
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40
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Zhao Y, Xiong Z, Wu G, Bai W, Zhu Z, Gao Y, Parmar S, Sharma VK, Li H. Fungal Endophytic Communities of Two Wild Rosa Varieties With Different Powdery Mildew Susceptibilities. Front Microbiol 2018; 9:2462. [PMID: 30386316 PMCID: PMC6198141 DOI: 10.3389/fmicb.2018.02462] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 09/26/2018] [Indexed: 12/20/2022] Open
Abstract
Powdery mildew (PM) is one of the most devastating and wide spread fungal diseases of rose, which seriously decrease its productivity and commercial value. In the present study, the endophytic fungal communities of two wild Rosa varieties (Rosa multiflora Thunb and R. multiflora var. carnea Redouté and Thory) with different PM susceptibilities were studied through Illumina MiSeq sequencer. A total of 14,000,424 raw reads were obtained from 60 samples, and 6,862,953 tags were produced after merging paired-end reads. 4462 distinct OTUs were generated at a 97% similarity level. It was found that only 34.2% of OTUs shared between two plant varieties. All of the OTUs were assigned into four fungal phyla, 17 classes, 43 orders, 86 families, 157 genera, and 208 species. Members of Ascomycota were found to be the most common fungal endophytes (EF) among all plant samples (93.7% relative abundance), followed by Basidiomycota (4.7% relative abundance), while Zygomycota and Glomeromycota were found to be rare and incidental. At each developmental stage of plants, the diversity and community structure of EF between two Rosa varieties showed significant differences. Both PCoA plots and PERMANOVA analyses indicated that developmental stage was the major factor contributing to the difference between the Rosa varieties (R2 = 0.348, p < 0.001). In addition, plant varieties and tissues were also important factors contributing to the difference (R2 = 0.031, p < 0.05; R2 = 0.029, p < 0.05). Moreover, Neofusicoccum, Rhodosporidium, and Podosphaera, etc., were found to be significantly different between two Rosa varieties, and some of the endophytes may play a role in PM resistance. These finding are encouraging to testify the potential use of these fungi in the biocontrol of PM in future studies.
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Affiliation(s)
- Yi Zhao
- Medical School of Kunming University of Science and Technology, Kunming, China
| | - Zhi Xiong
- Medical School of Kunming University of Science and Technology, Kunming, China
| | - Guangli Wu
- Medical School of Kunming University of Science and Technology, Kunming, China
| | - Weixiao Bai
- Medical School of Kunming University of Science and Technology, Kunming, China
| | - Zhengqing Zhu
- Medical School of Kunming University of Science and Technology, Kunming, China
| | - Yonghan Gao
- Medical School of Kunming University of Science and Technology, Kunming, China
| | - Shobhika Parmar
- Medical School of Kunming University of Science and Technology, Kunming, China
| | - Vijay K Sharma
- Medical School of Kunming University of Science and Technology, Kunming, China
| | - Haiyan Li
- Medical School of Kunming University of Science and Technology, Kunming, China
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Metataxonomic comparison between internal transcribed spacer and 26S ribosomal large subunit (LSU) rDNA gene. Int J Food Microbiol 2018; 290:132-140. [PMID: 30340111 DOI: 10.1016/j.ijfoodmicro.2018.10.010] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 10/04/2018] [Accepted: 10/08/2018] [Indexed: 12/12/2022]
Abstract
Next-generation sequencing has been used to strengthen knowledge about taxonomic diversity and ecology of fungi within food ecosystems. However, primer amplification and identification bias could edge our understanding into the fungal ecology. The aim of this study is to compare the performance of two primer pairs over two nuclear ribosomal RNA (rRNA) regions of the fungal kingdom, namely the ITS2 and 26S regions. Fermented cocoa beans were employed as biological material and the fungal ecology during fermentation was studied using amplicon-based sequencing tools, making use of a manually curated 26S database constructed in this study, and validated with SILVA's database. To explore potential biases introduced by PCR amplification of fungal communities, a mock community of known composition was prepared and tested. The relative abundances observed for ITS2 suggest that species with longer amplification fragments are underestimated and concurrently species that render shorter amplification fragments are overestimated. However, this correlation between amplicon length and estimation is not valid for all the species analysed. Variability in the amplification lengths contributed to the preferential amplification phenomenon. DNA extracted from twenty fermented cocoa bean samples were used to assess the performance of the two target regions. Overall, the metataxonomic data set recovered similar taxonomic composition and provided consistent results in OTU richness among biological samples. However, 26S region provided higher alpha diversity index and greater fungal rRNA taxonomic depth and robustness results compared with ITS2. Based on the results of this study we suggest the use of the 26S region for targeting fungi. Furthermore, this study showed the efficacy of the manually curated reference database optimized for annotation of mycobiota by using the 26S as a gene target.
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42
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Ma M, Jiang X, Wang Q, Ongena M, Wei D, Ding J, Guan D, Cao F, Zhao B, Li J. Responses of fungal community composition to long-term chemical and organic fertilization strategies in Chinese Mollisols. Microbiologyopen 2018; 7:e00597. [PMID: 29573192 PMCID: PMC6182557 DOI: 10.1002/mbo3.597] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 01/02/2018] [Accepted: 01/09/2018] [Indexed: 11/07/2022] Open
Abstract
How fungi respond to long-term fertilization in Chinese Mollisols as sensitive indicators of soil fertility has received limited attention. To broaden our knowledge, we used high-throughput pyrosequencing and quantitative PCR to explore the response of soil fungal community to long-term chemical and organic fertilization strategies. Soils were collected in a 35-year field experiment with four treatments: no fertilizer, chemical phosphorus, and potassium fertilizer (PK), chemical phosphorus, potassium, and nitrogen fertilizer (NPK), and chemical phosphorus and potassium fertilizer plus manure (MPK). All fertilization differently changed soil properties and fungal community. The MPK application benefited soil acidification alleviation and organic matter accumulation, as well as soybean yield. Moreover, the community richness indices (Chao1 and ACE) were higher under the MPK regimes, indicating the resilience of microbial diversity and stability. With regards to fungal community composition, the phylum Ascomycota was dominant in all samples, followed by Zygomycota, Basidiomycota, Chytridiomycota, and Glomeromycota. At each taxonomic level, the community composition dramatically differed under different fertilization strategies, leading to different soil quality. The NPK application caused a loss of Leotiomycetes but an increase in Eurotiomycetes, which might reduce the plant-fungal symbioses and increase nitrogen losses and greenhouse gas emissions. According to the linear discriminant analysis (LDA) coupled with effect size (LDA score > 3.0), the NPK application significantly increased the abundances of fungal taxa with known pathogenic traits, such as order Chaetothyriales, family Chaetothyriaceae and Pleosporaceae, and genera Corynespora, Bipolaris, and Cyphellophora. In contrast, these fungi were detected at low levels under the MPK regime. Soil organic matter and pH were the two most important contributors to fungal community composition.
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Affiliation(s)
- Mingchao Ma
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China.,Microbial Processes and Interactions Research Unit, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Xin Jiang
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China.,Laboratory of Quality & Safety Risk Assessment for Microbial Products, Ministry of Agriculture, Beijing, China
| | - Qingfeng Wang
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Marc Ongena
- Microbial Processes and Interactions Research Unit, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Dan Wei
- The Institute of Soil Fertility and Environmental Sources, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Jianli Ding
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China.,Laboratory of Quality & Safety Risk Assessment for Microbial Products, Ministry of Agriculture, Beijing, China
| | - Dawei Guan
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China.,Laboratory of Quality & Safety Risk Assessment for Microbial Products, Ministry of Agriculture, Beijing, China
| | - Fengming Cao
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China.,Laboratory of Quality & Safety Risk Assessment for Microbial Products, Ministry of Agriculture, Beijing, China
| | - Baisuo Zhao
- Laboratory of Quality & Safety Risk Assessment for Microbial Products, Ministry of Agriculture, Beijing, China
| | - Jun Li
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China.,Laboratory of Quality & Safety Risk Assessment for Microbial Products, Ministry of Agriculture, Beijing, China
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Keiblinger KM, Schneider M, Gorfer M, Paumann M, Deltedesco E, Berger H, Jöchlinger L, Mentler A, Zechmeister-Boltenstern S, Soja G, Zehetner F. Assessment of Cu applications in two contrasting soils-effects on soil microbial activity and the fungal community structure. ECOTOXICOLOGY (LONDON, ENGLAND) 2018; 27:217-233. [PMID: 29297133 PMCID: PMC5847031 DOI: 10.1007/s10646-017-1888-y] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 12/12/2017] [Indexed: 05/20/2023]
Abstract
Copper (Cu)-based fungicides have been used in viticulture to prevent downy mildew since the end of the 19th century, and are still used today to reduce fungal diseases. Consequently, Cu has built up in many vineyard soils, and it is still unclear how this affects soil functioning. The present study aimed to assess the short and medium-term effects of Cu contamination on the soil fungal community. Two contrasting agricultural soils, an acidic sandy loam and an alkaline silt loam, were used for an eco-toxicological greenhouse pot experiment. The soils were spiked with a Cu-based fungicide in seven concentrations (0-5000 mg Cu kg-1 soil) and alfalfa was grown in the pots for 3 months. Sampling was conducted at the beginning and at the end of the study period to test Cu toxicity effects on total microbial biomass, basal respiration and enzyme activities. Fungal abundance was analysed by ergosterol at both samplings, and for the second sampling, fungal community structure was evaluated via ITS amplicon sequences. Soil microbial biomass C as well as microbial respiration rate decreased with increasing Cu concentrations, with EC50 ranging from 76 to 187 mg EDTA-extractable Cu kg-1 soil. Oxidative enzymes showed a trend of increasing activity at the first sampling, but a decline in peroxidase activity was observed for the second sampling. We found remarkable Cu-induced changes in fungal community abundance (EC50 ranging from 9.2 to 94 mg EDTA-extractable Cu kg-1 soil) and composition, but not in diversity. A large number of diverse fungi were able to thrive under elevated Cu concentrations, though within the order of Hypocreales several species declined. A remarkable Cu-induced change in the community composition was found, which depended on the soil properties and, hence, on Cu availability.
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Affiliation(s)
- Katharina M Keiblinger
- Institute of Soil Research, University of Natural Resources and Life Sciences, Vienna, Austria.
| | - Martin Schneider
- Institute of Soil Research, University of Natural Resources and Life Sciences, Vienna, Austria
- AIT Austrian Institute of Technology, Center for Energy, Business Unit Environmental Resources & Technologies, Tulln, Austria
| | - Markus Gorfer
- AIT Austrian Institute of Technology, Center for Health and Bioresources, Business Unit Bioresources, Tulln, Austria
| | - Melanie Paumann
- Institute of Soil Research, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Evi Deltedesco
- Institute of Soil Research, University of Natural Resources and Life Sciences, Vienna, Austria
- AIT Austrian Institute of Technology, Center for Health and Bioresources, Business Unit Bioresources, Tulln, Austria
| | | | - Lisa Jöchlinger
- Institute of Soil Research, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Axel Mentler
- Institute of Soil Research, University of Natural Resources and Life Sciences, Vienna, Austria
| | | | - Gerhard Soja
- AIT Austrian Institute of Technology, Center for Energy, Business Unit Environmental Resources & Technologies, Tulln, Austria
| | - Franz Zehetner
- Institute of Soil Research, University of Natural Resources and Life Sciences, Vienna, Austria
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Gałązka A, Grządziel J. Fungal Genetics and Functional Diversity of Microbial Communities in the Soil under Long-Term Monoculture of Maize Using Different Cultivation Techniques. Front Microbiol 2018; 9:76. [PMID: 29441054 PMCID: PMC5797640 DOI: 10.3389/fmicb.2018.00076] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Accepted: 01/12/2018] [Indexed: 11/17/2022] Open
Abstract
Fungal diversity in the soil may be limited under natural conditions by inappropriate environmental factors such as: nutrient resources, biotic and abiotic factors, tillage system and microbial interactions that prevent the occurrence or survival of the species in the environment. The aim of this paper was to determine fungal genetic diversity and community level physiological profiling of microbial communities in the soil under long-term maize monoculture. The experimental scheme involved four cultivation techniques: direct sowing (DS), reduced tillage (RT), full tillage (FT), and crop rotation (CR). Soil samples were taken in two stages: before sowing of maize (DSBS-direct sowing, RTBS-reduced tillage, FTBS-full tillage, CRBS-crop rotation) and the flowering stage of maize growth (DSF-direct sowing, RTF-reduced tillage, FTF-full tillage, CRF-crop rotation). The following plants were used in the crop rotation: spring barley, winter wheat and maize. The study included fungal genetic diversity assessment by ITS-1 next generation sequencing (NGS) analyses as well as the characterization of the catabolic potential of microbial communities (Biolog EcoPlates) in the soil under long-term monoculture of maize using different cultivation techniques. The results obtained from the ITS-1 NGS technique enabled to classify and correlate the fungi species or genus to the soil metabolome. The research methods used in this paper have contributed to a better understanding of genetic diversity and composition of the population of fungi in the soil under the influence of the changes that have occurred in the soil under long-term maize cultivation. In all cultivation techniques, the season had a great influence on the fungal genetic structure in the soil. Significant differences were found on the family level (P = 0.032, F = 3.895), genus level (P = 0.026, F = 3.313) and on the species level (P = 0.033, F = 2.718). This study has shown that: (1) fungal diversity was changed under the influence different cultivation techniques; (2) techniques of maize cultivation and season were an important factors that can influence the biochemical activity of soil. Maize cultivated in direct sowing did not cause negative changes in the fungal structure, even making it more stable during seasonal changes; (3) full tillage and crop rotation may change fungal community and soil function.
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Affiliation(s)
- Anna Gałązka
- Department of Agricultural Microbiology, Institute of Soil Science and Plant Cultivation - State Research Institute, Puławy, Poland
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Panelli S, Capelli E, Comandatore F, Landinez-Torres A, Granata MU, Tosi S, Picco AM. A metagenomic-based, cross-seasonal picture of fungal consortia associated with Italian soils subjected to different agricultural managements. FUNGAL ECOL 2017. [DOI: 10.1016/j.funeco.2017.07.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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46
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Bhowmik A, Cloutier M, Ball E, Bruns MA. Underexplored microbial metabolisms for enhanced nutrient recycling in agricultural soils. AIMS Microbiol 2017; 3:826-845. [PMID: 31294192 PMCID: PMC6604955 DOI: 10.3934/microbiol.2017.4.826] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 09/21/2017] [Indexed: 01/03/2023] Open
Abstract
Worldwide, arable soils have been degraded through erosion and exhaustive cultivation, and substantial proportions of fertilizer nutrients are not taken up by crops. A central challenge in agriculture is to understand how soils and resident microbial communities can be managed to deliver nutrients to crops more efficiently with minimal losses to the environment. Throughout much of the twentieth century, intensive farming has caused substantial loss of organic matter and soil biological function. Today, more farmers recognize the importance of protecting soils and restoring organic matter through reduced tillage, diversified crop rotation, cover cropping, and increased organic amendments. Such management practices are expected to foster soil conditions more similar to those of undisturbed, native plant-soil systems by restoring soil biophysical integrity and re-establishing plant-microbe interactions that retain and recycle nutrients. Soil conditions which could contribute to desirable shifts in microbial metabolic processes include lower redox potentials, more diverse biogeochemical gradients, higher concentrations of labile carbon, and enrichment of carbon dioxide (CO2) and hydrogen gas (H2) in soil pores. This paper reviews recent literature on generalized and specific microbial processes that could become more operational once soils are no longer subjected to intensive tillage and organic matter depletion. These processes include heterotrophic assimilation of CO2; utilization of H2 as electron donor or reactant; and more diversified nitrogen uptake and dissimilation pathways. Despite knowledge of these processes occurring in laboratory studies, they have received little attention for their potential to affect nutrient and energy flows in soils. This paper explores how soil microbial processes could contribute to in situ nutrient retention, recycling, and crop uptake in agricultural soils managed for improved biological function.
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Affiliation(s)
- Arnab Bhowmik
- Department of Ecosystem Science and Management, The Pennsylvania State University, University Park, PA 16802, USA
| | - Mara Cloutier
- Department of Ecosystem Science and Management, The Pennsylvania State University, University Park, PA 16802, USA.,Dual-Title Graduate Program in Biogeochemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - Emily Ball
- Department of Ecosystem Science and Management, The Pennsylvania State University, University Park, PA 16802, USA
| | - Mary Ann Bruns
- Department of Ecosystem Science and Management, The Pennsylvania State University, University Park, PA 16802, USA.,Dual-Title Graduate Program in Biogeochemistry, The Pennsylvania State University, University Park, PA 16802, USA.,Intercollege Graduate Degree Program in Ecology, The Pennsylvania State University, University Park, PA 16802, USA
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Vera J, Gutiérrez MH, Palfner G, Pantoja S. Diversity of culturable filamentous Ascomycetes in the eastern South Pacific Ocean off Chile. World J Microbiol Biotechnol 2017; 33:157. [PMID: 28726124 DOI: 10.1007/s11274-017-2321-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 07/14/2017] [Indexed: 11/27/2022]
Abstract
Our study reports the diversity of culturable mycoplankton in the eastern South Pacific Ocean off Chile to contribute with novel knowledge on taxonomy of filamentous fungi isolated from distinct physicochemical and biological marine environments. We characterized spatial distribution of isolates, evaluated their viability and assessed the influence of organic substrate availability on fungal development. Thirty-nine Operational Taxonomic Units were identified from 99 fungal strains isolated from coastal and oceanic waters by using Automatic Barcode Gap Discovery. All Operational Taxonomic Units belonged to phylum Ascomycota and orders Eurotiales, Dothideales, Sordariales and Hypocreales, mainly Penicillium sp. (82%); 11 sequences did not match existing species in GenBank, suggesting occurrence of novel fungal taxa. Our results suggest that fungal communities in the South Pacific Ocean off Chile appear to thrive in a wide range of environmental conditions in the ocean and that substrate availability may be a factor influencing fungal viability in the ocean.
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Affiliation(s)
- Jeanett Vera
- Graduate Program in Oceanography, Department of Oceanography, University of Concepción, Concepción, Chile
| | - Marcelo H Gutiérrez
- Department of Oceanography and COPAS Sur-Austral, University of Concepción, Concepción, Chile
| | - Götz Palfner
- Department of Botany, University of Concepción, Concepción, Chile
| | - Silvio Pantoja
- Department of Oceanography and COPAS Sur-Austral, University of Concepción, Concepción, Chile.
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Wang Z, Li T, Wen X, Liu Y, Han J, Liao Y, DeBruyn JM. Fungal Communities in Rhizosphere Soil under Conservation Tillage Shift in Response to Plant Growth. Front Microbiol 2017; 8:1301. [PMID: 28744278 PMCID: PMC5504275 DOI: 10.3389/fmicb.2017.01301] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Accepted: 06/27/2017] [Indexed: 01/22/2023] Open
Abstract
Conservation tillage is an extensively used agricultural practice in northern China that alters soil texture and nutrient conditions, causing changes in the soil microbial community. However, how conservation tillage affects rhizosphere and bulk soil fungal communities during plant growth remains unclear. The present study investigated the effect of long-term (6 years) conservation (chisel plow, zero) and conventional (plow) tillage during wheat growth on the rhizosphere fungal community, using high-throughput sequencing of the internal transcribed spacer (ITS) gene and quantitative PCR. During tillering, fungal alpha diversity in both rhizosphere and bulk soil were significantly higher under zero tillage compared to other methods. Although tillage had no significant effect during the flowering stage, fungal alpha diversity at this stage was significantly different between rhizosphere and bulk soils, with bulk soil presenting the highest diversity. This was also reflected in the phylogenetic structure of the communities, as rhizosphere soil communities underwent a greater shift from tillering to flowering compared to bulk soil communities. In general, less variation in community structure was observed under zero tillage compared to plow and chisel plow treatments. Changes in the relative abundance of the fungal orders Capnodiales, Pleosporales, and Xylariales contributed the highest to the dissimilarities observed. Structural equation models revealed that the soil fungal communities under the three tillage regimes were likely influenced by the changes in soil properties associated with plant growth. This study suggested that: (1) differences in nutrient resources between rhizosphere and bulk soils can select for different types of fungi thereby increasing community variation during plant growth; (2) tillage can alter fungal communities' variability, with zero tillage promoting more stable communities. This work suggests that long-term changes in tillage regimes may result in unique soil fungal ecology, which might influence other aspects of soil functioning (e.g., decomposition).
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Affiliation(s)
- Ziting Wang
- College of Agronomy, Northwest A&F UniversityYangling, China
| | - Tong Li
- College of Agronomy, Northwest A&F UniversityYangling, China
| | - Xiaoxia Wen
- College of Agronomy, Northwest A&F UniversityYangling, China
| | - Yang Liu
- College of Agronomy, Northwest A&F UniversityYangling, China
| | - Juan Han
- College of Agronomy, Northwest A&F UniversityYangling, China
| | - Yuncheng Liao
- College of Agronomy, Northwest A&F UniversityYangling, China
| | - Jennifer M DeBruyn
- Department of Biosystems Engineering and Soil Science, The University of TennesseeKnoxville, TN, United States
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Effects of different nitrogen additions on soil microbial communities in different seasons in a boreal forest. Ecosphere 2017. [DOI: 10.1002/ecs2.1879] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
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Influence of agricultural activities in the structure and metabolic functionality of paramo soil samples in Colombia studied using a metagenomics analysis in dynamic state. Ecol Modell 2017. [DOI: 10.1016/j.ecolmodel.2017.02.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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