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Steinberger Y, Doniger T, Applebaum I, Sherman C, Rotbart N. Effects of Vineyard Agro-management Practices on Soil Bacterial Community Composition, and Diversity. MICROBIAL ECOLOGY 2023; 87:17. [PMID: 38110747 DOI: 10.1007/s00248-023-02315-6] [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: 06/06/2023] [Accepted: 11/12/2023] [Indexed: 12/20/2023]
Abstract
Changes in land use strongly affect soil biological and physico-chemical structure and characteristics, which are strongly related to agricultural conversion of natural habitats to man-made usage. These are among the most important and not always beneficial changes, affecting loss of habitats. In Golan Heights basaltic soils, vineyards are currently a driving force in land-use change. Such changes could have an important effect on soil microbial community that play an important role in maintaining stable functioning of soil ecosystems. This study investigated the microbial communities in five different agro-managements using molecular tools that can clarify the differences in microbial community structure and function. Significant differences in soil microbial community composition were found. However, no differences in alpha diversity or functionality were found between the treatments. To the best of our knowledge, this is the first report indicating that the bacterial community in different agro-managements provide an insight into the potential function of a vineyard system.
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Affiliation(s)
- Yosef Steinberger
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, 5290002, Ramat Gan, Israel.
| | - Tirza Doniger
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, 5290002, Ramat Gan, Israel
| | - Itaii Applebaum
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, 5290002, Ramat Gan, Israel
| | - Chen Sherman
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, 5290002, Ramat Gan, Israel
| | - Nativ Rotbart
- Shamir Research Institute, University of Haifa, Haifa, Israel.
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2
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Chi Y, Song S, Xiong K. Effects of different grassland use patterns on soil bacterial communities in the karst desertification areas. Front Microbiol 2023; 14:1208971. [PMID: 37720153 PMCID: PMC10500843 DOI: 10.3389/fmicb.2023.1208971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 08/07/2023] [Indexed: 09/19/2023] Open
Abstract
Soil bacteria are closely related to soil environmental factors, and their community structure is an important indicator of ecosystem health and sustainability. A large number of artificial grasslands have been established to control rocky desertification in the karst areas of southern China, but the influence of different use patterns on the soil bacterial community in artificial grasslands is not clear. In this study, three grassland use patterns [i.e., grazing (GG), mowing (MG), and enclosure (EG)] were used to investigate the effects of different use patterns on the soil bacterial community in artificial grassland by using 16S rDNA Illumina sequencing and 12 soil environmental indicators. It was found that, compared with EG, GG significantly changed soil pH, increased alkaline hydrolyzable nitrogen (AN) content (P < 0.05), and decreased soil total phosphorus (TP) content (P < 0.05). However, MG significantly decreased the contents of soil organic carbon (SOC), total phosphorus (TP), available nitrogen (AN), ammonium nitrogen (NH4+-N), β-1,4-glucosidase (BG), and N-acetyl-β-D-glucamosonidase (NAG) (P < 0.05). The relative abundance of chemoheterotrophy was significantly decreased by GG and MG (P < 0.05). GG significantly increased the relative abundance of Acidobacteria and Gemmatimonadota (P < 0.05) and significantly decreased the relative abundance of Proteobacteria (P < 0.05), but the richness index (Chao 1) and diversity index (Shannon) of the bacterial community in GG, MG, and EG were not significantly different (P > 0.05). The pH (R2 = 0.79, P = 0.029) was the main factor affecting the bacterial community structure. This finding can provide a scientific reference for ecological restoration and sustainable utilization of grasslands in the karst desertification areas.
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Affiliation(s)
- Yongkuan Chi
- School of Karst Science, Guizhou Normal University, Guiyang, China
- Guizhou Engineering Laboratory for Karst Desertification Control and Eco-Industry, Guiyang, China
| | - Shuzhen Song
- School of Karst Science, Guizhou Normal University, Guiyang, China
| | - Kangning Xiong
- School of Karst Science, Guizhou Normal University, Guiyang, China
- Guizhou Engineering Laboratory for Karst Desertification Control and Eco-Industry, Guiyang, China
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Mula-Michel H, White P, Hale A. Immediate impacts of soybean cover crop on bacterial community composition and diversity in soil under long-term Saccharum monoculture. PeerJ 2023; 11:e15754. [PMID: 37637164 PMCID: PMC10452624 DOI: 10.7717/peerj.15754] [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: 02/02/2023] [Accepted: 06/26/2023] [Indexed: 08/29/2023] Open
Abstract
Saccharum yield decline results from long-term monoculture practices. Changes in cropping management can improve soil health and productivity. Below-ground bacterial community diversity and composition across soybean (Glycine max (L.) Merr) cover crop, Saccharum monoculture (30+ year) and fallowed soil were determined. Near full length (~1,400 base pairs) of 16S rRNA gene sequences were extracted from the rhizospheres of sugarcane and soybean and fallowed soil were compared. Higher soil bacterial diversity was observed in the soybean cover crop than sugarcane monoculture across all measured indices (observed operationational taxonomic units, Chao1, Shannon, reciprocal Simpson and Jackknife). Acidocateria, Proteobacteria, Bacteroidetes and Planctomycetes were the most abundant bacterial phyla across the treatments. Indicator species analysis identified nine indicator phyla. Planctomycetes, Armatimonadetes and candidate phylum FBP were associated with soybean; Proteobacteria and Firmicutes were linked with sugarcane and Gemmatimonadetes, Nitrospirae, Rokubacteria and unclassified bacteria were associated with fallowed soil. Non-metric multidimensional scaling analysis showed distinct groupings of bacterial operational taxonomic units (97% identity) according to management system (soybean, sugarcane or fallow) indicating compositional differences among treatments. This is confirmed by the results of the multi-response permutation procedures (A = 0.541, p = 0.00045716). No correlation between soil parameters and bacterial community structure was observed according to Mantel test (r = 211865, p = 0.14). Use of soybean cover-crop fostered bacterial diversity and altered community structure. This indicates cover crops could have a restorative effect and potentially promote sustainability in long-term Saccharum production systems.
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Affiliation(s)
- Himaya Mula-Michel
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, USDA-ARS, Sugarcane Research Unit, Houma, LA, USA
| | - Paul White
- USDA-ARS, Sugarcane Research Unit, Houma, LA, USA
| | - Anna Hale
- USDA-ARS, Sugarcane Research Unit, Houma, LA, USA
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Rolls RJ, Deane DC, Johnson SE, Heino J, Anderson MJ, Ellingsen KE. Biotic homogenisation and differentiation as directional change in beta diversity: synthesising driver-response relationships to develop conceptual models across ecosystems. Biol Rev Camb Philos Soc 2023; 98:1388-1423. [PMID: 37072381 DOI: 10.1111/brv.12958] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 03/23/2023] [Accepted: 03/28/2023] [Indexed: 04/20/2023]
Abstract
Biotic homogenisation is defined as decreasing dissimilarity among ecological assemblages sampled within a given spatial area over time. Biotic differentiation, in turn, is defined as increasing dissimilarity over time. Overall, changes in the spatial dissimilarities among assemblages (termed 'beta diversity') is an increasingly recognised feature of broader biodiversity change in the Anthropocene. Empirical evidence of biotic homogenisation and biotic differentiation remains scattered across different ecosystems. Most meta-analyses quantify the prevalence and direction of change in beta diversity, rather than attempting to identify underlying ecological drivers of such changes. By conceptualising the mechanisms that contribute to decreasing or increasing dissimilarity in the composition of ecological assemblages across space, environmental managers and conservation practitioners can make informed decisions about what interventions may be required to sustain biodiversity and can predict potential biodiversity outcomes of future disturbances. We systematically reviewed and synthesised published empirical evidence for ecological drivers of biotic homogenisation and differentiation across terrestrial, marine, and freshwater realms to derive conceptual models that explain changes in spatial beta diversity. We pursued five key themes in our review: (i) temporal environmental change; (ii) disturbance regime; (iii) connectivity alteration and species redistribution; (iv) habitat change; and (v) biotic and trophic interactions. Our first conceptual model highlights how biotic homogenisation and differentiation can occur as a function of changes in local (alpha) diversity or regional (gamma) diversity, independently of species invasions and losses due to changes in species occurrence among assemblages. Second, the direction and magnitude of change in beta diversity depends on the interaction between spatial variation (patchiness) and temporal variation (synchronicity) of disturbance events. Third, in the context of connectivity and species redistribution, divergent beta diversity outcomes occur as different species have different dispersal characteristics, and the magnitude of beta diversity change associated with species invasions also depends strongly on alpha and gamma diversity prior to species invasion. Fourth, beta diversity is positively linked with spatial environmental variability, such that biotic homogenisation and differentiation occur when environmental heterogeneity decreases or increases, respectively. Fifth, species interactions can influence beta diversity via habitat modification, disease, consumption (trophic dynamics), competition, and by altering ecosystem productivity. Our synthesis highlights the multitude of mechanisms that cause assemblages to be more or less spatially similar in composition (taxonomically, functionally, phylogenetically) through time. We consider that future studies should aim to enhance our collective understanding of ecological systems by clarifying the underlying mechanisms driving homogenisation or differentiation, rather than focusing only on reporting the prevalence and direction of change in beta diversity, per se.
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Affiliation(s)
- Robert J Rolls
- School of Environmental and Rural Sciences, University of New England, Armidale, New South Wales, 2351, Australia
| | - David C Deane
- School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, Victoria, 3086, Australia
| | - Sarah E Johnson
- Natural Resources Department, Northland College, Ashland, WI, 54891, USA
| | - Jani Heino
- Geography Research Unit, University of Oulu, P.O. Box 8000, Oulu, FI-90014, Finland
| | - Marti J Anderson
- New Zealand Institute for Advanced Study (NZIAS), Massey University, Albany Campus, Auckland, New Zealand
| | - Kari E Ellingsen
- Norwegian Institute for Nature Research (NINA), Fram Centre, P.O. Box 6606 Langnes, Tromsø, 9296, Norway
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Bai Z, Zheng L, Bai Z, Jia A, Wang M. Long-term cultivation alter soil bacterial community in a forest-grassland transition zone. Front Microbiol 2022; 13:1001781. [PMID: 36246280 PMCID: PMC9557053 DOI: 10.3389/fmicb.2022.1001781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 09/13/2022] [Indexed: 11/13/2022] Open
Abstract
Changes in land use types can significantly affect soil porperties and microbial community composition in many areas. However, the underlying mechanism of shift in bacterial communities link to soil properties is still unclear. In this study, Illumina high-throughput sequencing was used to analyze the changes of soil bacterial communities in different land use types in a forest-grassland transition zone, North China. There are two different land use types: grassland (G) and cultivated land (CL). Meanwhile, cultivated land includes cultivated of 10 years (CL10) or 20 years (CL20). Compared with G, CL decreased soil pH, SOC and TN, and significantly increased soil EC, P and K, and soil properties varied significantly with different cultivation years. Grassland reclamation increases the diversity of bacterial communities, the relative abundance of Proteobacteria, Gemmatimonadetes and Bacteroidetes increased, while that of Actinobacteria, Acidobacteria, Rokubacteria and Verrucomicrobia decreased. However, the relative abundance of Proteobacteria decreased and the relative abundance of Chloroflexi and Nitrospirae increased with the increase of cultivated land years. Mantel test and RDA analysis showed that TP, AP, SOC and EC were the main factors affecting the diversity of composition of bacterial communities. In conclusion, soil properties and bacterial communities were significantly altered after long-term cultivation. This study provides data support for land use and grassland ecological protection in this region.
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Cofré N, Marro N, Grilli G, Soteras F. Arbuscular Mycorrhizal Fungi in Agroecosystems of East-Central Argentina: Two Agricultural Practices Effects on Taxonomic Groups. Fungal Biol 2022. [DOI: 10.1007/978-3-031-12994-0_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Rokubacteria in Northern Peatlands: Habitat Preferences and Diversity Patterns. Microorganisms 2021; 10:microorganisms10010011. [PMID: 35056460 PMCID: PMC8780371 DOI: 10.3390/microorganisms10010011] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 12/16/2021] [Accepted: 12/20/2021] [Indexed: 01/04/2023] Open
Abstract
Rokubacteria is a phylogenetic clade of as-yet-uncultivated prokaryotes, which are detected in diverse terrestrial habitats and are commonly addressed as members of the rare biosphere. This clade was originally described as a candidate phylum; however, based on the results of comparative genome analysis, was later defined as the order-level lineage, Rokubacteriales, within the phylum Methylomirabilota. The physiology and lifestyles of these bacteria are poorly understood. A dataset of 16S rRNA gene reads retrieved from four boreal raised bogs and six eutrophic fens was examined for the presence of the Rokubacteriales; the latter were detected exclusively in fens. Their relative abundance varied between 0.2 and 4% of all bacteria and was positively correlated with pH, total nitrogen content, and availability of Ca and Mg. To test an earlier published hypothesis regarding the presence of methanotrophic capabilities in Rokubacteria, peat samples were incubated with 10% methane for four weeks. No response to methane availability was detected for the Rokubacteriales, while clear a increase in relative abundance was observed for the conventional Methylococcales methanotrophs. The search for methane monooxygenase encoding genes in 60 currently available Rokubacteriales metagenomes yielded negative results, although copper-containing monooxygenases were encoded by some members of this order. This study suggests that peat-inhabiting Rokubacteriales are neutrophilic non-methanotrophic bacteria that colonize nitrogen-rich wetlands.
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Rios-Galicia B, Villagómez-Garfias C, De la Vega-Camarillo E, Guerra-Camacho JE, Medina-Jaritz N, Arteaga-Garibay RI, Villa-Tanaca L, Hernández-Rodríguez C. The Mexican giant maize of Jala landrace harbour plant-growth-promoting rhizospheric and endophytic bacteria. 3 Biotech 2021; 11:447. [PMID: 34631348 DOI: 10.1007/s13205-021-02983-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 09/04/2021] [Indexed: 01/02/2023] Open
Abstract
The giant landrace of maize Jala is a native crop cultured in Nayarit and Jalisco States in the occident of México. In this study, after screening 374 rhizospheric and endophytic bacteria isolated from rhizospheric soil, root, and seed tissues of maize Jala, a total of 16 bacterial strains were selected for their plant-growth-promoting potential and identified by 16S rRNA phylogenetic analysis. The isolates exhibited different combinations of phenotypic traits, including solubilisation of phosphate from hydroxyapatite, production of a broad spectrum of siderophores such as cobalt, iron, molybdenum, vanadium, or zinc (Co2+, Fe3+, Mo2 +, V5+, Zn2+), and nitrogen fixation capabilities, which were detected in both rhizospheric and endophytic strains. Additional traits such as production of 1-aminocyclopropane-1-carboxylate deaminase and a high-rate production of Indoleacetic Acid were exclusively detected on endophytic isolates. Among the selected strains, the rhizospheric Burkholderia sp., and Klebsiella variicola, and the endophytic Pseudomonas protegens significantly improved the growth of maize plants in greenhouse assays and controlled the infection against Fusarium sp. 50 on fresh maize cobs. These results present the first deep approach on handling autochthonous microorganisms from native maize with a potential biotechnological application in sustainable agriculture as biofertilizers or biopesticides.
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Affiliation(s)
- Bibiana Rios-Galicia
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala s/n, Colonia Santo Tomás, 11340 Ciudad de México, Mexico
| | - Catalina Villagómez-Garfias
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala s/n, Colonia Santo Tomás, 11340 Ciudad de México, Mexico
| | - Esaú De la Vega-Camarillo
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala s/n, Colonia Santo Tomás, 11340 Ciudad de México, Mexico
| | - Jairo Eder Guerra-Camacho
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala s/n, Colonia Santo Tomás, 11340 Ciudad de México, Mexico
| | - Nora Medina-Jaritz
- Departamento de Botánica, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala s/n, Colonia Santo Tomás, 11340 Ciudad de México, Mexico
| | - Ramón Ignacio Arteaga-Garibay
- Laboratorio de Recursos Genéticos Microbianos, Centro Nacional de Recursos Genéticos, Instituto Nacional de Investigaciones Forestales Agrícolas y Pecuarias, Boulevard de la Biodiversidad No. 400, Rancho Las Cruces, 47600 Tepatitlán de Morelos, Jalisco Mexico
| | - Lourdes Villa-Tanaca
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala s/n, Colonia Santo Tomás, 11340 Ciudad de México, Mexico
| | - César Hernández-Rodríguez
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala s/n, Colonia Santo Tomás, 11340 Ciudad de México, Mexico
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Effects of Abiotic Stress on Soil Microbiome. Int J Mol Sci 2021; 22:ijms22169036. [PMID: 34445742 PMCID: PMC8396473 DOI: 10.3390/ijms22169036] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/13/2021] [Accepted: 08/17/2021] [Indexed: 02/07/2023] Open
Abstract
Rhizospheric organisms have a unique manner of existence since many factors can influence the shape of the microbiome. As we all know, harnessing the interaction between soil microbes and plants is critical for sustainable agriculture and ecosystems. We can achieve sustainable agricultural practice by incorporating plant-microbiome interaction as a positive technology. The contribution of this interaction has piqued the interest of experts, who plan to do more research using beneficial microorganism in order to accomplish this vision. Plants engage in a wide range of interrelationship with soil microorganism, spanning the entire spectrum of ecological potential which can be mutualistic, commensal, neutral, exploitative, or competitive. Mutualistic microorganism found in plant-associated microbial communities assist their host in a number of ways. Many studies have demonstrated that the soil microbiome may provide significant advantages to the host plant. However, various soil conditions (pH, temperature, oxygen, physics-chemistry and moisture), soil environments (drought, submergence, metal toxicity and salinity), plant types/genotype, and agricultural practices may result in distinct microbial composition and characteristics, as well as its mechanism to promote plant development and defence against all these stressors. In this paper, we provide an in-depth overview of how the above factors are able to affect the soil microbial structure and communities and change above and below ground interactions. Future prospects will also be discussed.
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Fei X, Lina W, Jiayang C, Meng F, Guodong W, Yaping Y, Langjun C. Variations of microbial community in Aconitum carmichaeli Debx. rhizosphere soilin a short-term continuous cropping system. J Microbiol 2021; 59:481-490. [PMID: 33779961 DOI: 10.1007/s12275-021-0515-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 01/27/2021] [Accepted: 02/01/2021] [Indexed: 12/31/2022]
Abstract
Aconitum carmichaeli Debx. (Ranunculaceae) is a potential source of an important herbal drug named "Fuzi", which is derived from the lateral root of the plant. Increased therapeutic usage resulted in the great demand for artificial cultivation of A. carmichaeli, however, the obstacles caused by continuous cropping is a serious problem. Continuous cropping has shown to affect the soil biological and non-biological factors. The current study attempted to discover the variations of microbial communities and soil properties in short-term continuous cropping of A. carmichaeli. An experimental procedure with A. carmichaeli planted two years continuously was established. The variation of the soil microbial community, disease incidence, soil properties, and the correlation between soil microbe and disease incidence were investigated. The disease incidence increased during the continuous cropping of A. carmichaeli. The PCoA and LefSe results indicated that fungal communities in rhizosphere soil were altered during the short-term continuous croppingand the bacterial community was disturbed by the cultivation of A. carmichaeli, however, in the following two years of continuous cropping period, the soil bacterial community has not changed obviously. Proportions of some fungal and bacterial genera were varied significantly (p < 0.05), and some genera of microflora showed a significant correlation with adisease incidence of A. carmichaeli. Microorganisms contributing to community composition discrepancy were also elucidated. Continuous cropping of A. carmichaeli disturbed the rhizosphere soil microbial community and altered the soil chemical parameters and soil pH. These variations in soil may be related to the occurrence of plant diseases. The current study will not only provide theoretical and experimental evidence for the A. carmichaeli continuous cropping obstacles but will also contribute to A. carmichaeli agricultural production and soil improvement.
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Affiliation(s)
- Xia Fei
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, The Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, The Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, 710119, China
- School of Food and Biological Engineering, Shaanxi University of Science & Technology, Xi'An, 710021, China
| | - Wang Lina
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, The Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, The Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, 710119, China
| | - Chen Jiayang
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, The Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, The Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, 710119, China
| | - Fu Meng
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, The Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, The Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, 710119, China
| | - Wang Guodong
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, The Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, The Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, 710119, China
| | - Yan Yaping
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, The Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, The Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, 710119, China
| | - Cui Langjun
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, The Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, The Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, 710119, China.
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11
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Gabbarini LA, Figuerola E, Frene JP, Robledo NB, Ibarbalz FM, Babin D, Smalla K, Erijman L, Wall LG. Impacts of switching tillage to no-tillage and vice versa on soil structure, enzyme activities and prokaryotic community profiles in Argentinean semi-arid soils. FEMS Microbiol Ecol 2021; 97:6133470. [PMID: 33571359 DOI: 10.1093/femsec/fiab025] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 02/09/2021] [Indexed: 12/19/2022] Open
Abstract
The effects of tillage on soil structure, physiology and microbiota structure were studied in a long-term field experiment, with side-to-side plots, established to compare effects of conventional tillage (CT) vs no-till (NT) agriculture. After 27 years, part of the field under CT was switched to NT and vice versa. Soil texture, soil enzymatic profiles and the prokaryotic community structure (16S rRNA genes amplicon sequencing) were analyzed at two soil depths (0-5 and 5-10 cm) in samples taken 6, 18 and 30 months after switching tillage practices. Soil enzymatic activities were higher in NT than CT, and enzymatic profiles responded to the changes much earlier than the overall prokaryotic community structure. Beta diversity measurements of the prokaryotic community indicated that the levels of stratification observed in long-term NT soils were already recovered in the new NT soils 30 months after switching from CT to NT. Bacteria and Archaea OTUs that responded to NT were associated with coarse soil fraction, soil organic carbon and C cycle enzymes, while CT responders were related to fine soil fractions and S cycle enzymes. This study showed the potential of managing the soil prokaryotic community and soil health through changes in agricultural management practices.
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Affiliation(s)
- Luciano A Gabbarini
- Laboratorio de Bioquímica y Microbiología de Suelo, Centro de Bioquímica y Microbiología de Suelos, Universidad Nacional de Quilmes, B1876BXD Bernal, Buenos Aires, Argentina
| | - Eva Figuerola
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres" (INGEBI, CONICET), C1428ADN Buenos Aires, Argentina.,Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, C1428EGA Buenos Aires, Argentina
| | - Juan P Frene
- Laboratorio de Bioquímica y Microbiología de Suelo, Centro de Bioquímica y Microbiología de Suelos, Universidad Nacional de Quilmes, B1876BXD Bernal, Buenos Aires, Argentina
| | - Natalia B Robledo
- Laboratorio de Bioquímica y Microbiología de Suelo, Centro de Bioquímica y Microbiología de Suelos, Universidad Nacional de Quilmes, B1876BXD Bernal, Buenos Aires, Argentina
| | - Federico M Ibarbalz
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres" (INGEBI, CONICET), C1428ADN Buenos Aires, Argentina
| | - Doreen Babin
- Julius Kühn-Institut, Federal Research Centre for Cultivated Plants (JKI), Institute for Epidemiology and Pathogen Diagnostics, 38104 Braunschweig, Germany
| | - Kornelia Smalla
- Julius Kühn-Institut, Federal Research Centre for Cultivated Plants (JKI), Institute for Epidemiology and Pathogen Diagnostics, 38104 Braunschweig, Germany
| | - Leonardo Erijman
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres" (INGEBI, CONICET), C1428ADN Buenos Aires, Argentina.,Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, C1428EGA Buenos Aires, Argentina
| | - Luis G Wall
- Laboratorio de Bioquímica y Microbiología de Suelo, Centro de Bioquímica y Microbiología de Suelos, Universidad Nacional de Quilmes, B1876BXD Bernal, Buenos Aires, Argentina
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12
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Lynn TM, Zhran M, Wang LF, Ge T, Yu SS, Kyaw EP, Latt ZK, Htwe TM. Effect of land use on soil properties, microbial abundance and diversity of four different crop lands in central Myanmar. 3 Biotech 2021; 11:154. [PMID: 33747704 DOI: 10.1007/s13205-021-02705-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 02/23/2021] [Indexed: 11/29/2022] Open
Abstract
Changing land use systems impact on local edaphic factors and microbial abundance and diversity, however, the information on it in central Myanmar's soils is still lacking. Therefore, soils with four different land uses were analyzed; WAP (soil from perennial tree orchard), PNON (soil from crop rotation of peanut and onion), SESA (soil from mono-crop of sesame) and CHON (soil from mono-crop of onion for 3 years consecutively). Soil organic carbon (SOC), total nitrogen (TN), dissolved organic carbon (DOC), ammonium nitrogen (NH4 +-N) and pH showed the highest in PNON soil, which suggested crop rotation with high fertilizer input and irrigation had positive effect on the edaphic factors of soil. CHON soil showed the lowest in most soil properties and microbial abundance as a result of intensive use of fertilizer and irrigation, no crop rotation and no input of manures. Microbial community composition showed differences among tested soils and relative abundance of Chloroflexi was the highest in CHON soil whereas that of Basidiomycota was the highest in WAP soil. The abundances of bacteria and fungi were significantly affected by Olsen P, whereas the abundances of archaea were influenced by SOC. Our results suggested crop rotation and manure fertilization (PNON soil) enhanced soil properties and microbial abundance although long-time onion mono-crop (CHON soil) reduced soil fertility. This study can provide information to improve soil quality and sustainability of agro-ecosystems using appropriate agricultural management. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-02705-y.
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Affiliation(s)
- Tin Mar Lynn
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125 China
- Microbiology Division, Biotechnology Research Department, Ministry of Education, Kyaukse, Mandalay Region 100301 Myanmar
| | - Mostafa Zhran
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125 China
- Atomic Energy Authority, Nuclear Research Center, Soil & Water Research Department, Abou-Zaabl, 13759 Egypt
| | - Liu Fang Wang
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125 China
| | - Tida Ge
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125 China
| | - San San Yu
- Microbiology Division, Biotechnology Research Department, Ministry of Education, Kyaukse, Mandalay Region 100301 Myanmar
| | - Ei Phyu Kyaw
- Microbiology Division, Biotechnology Research Department, Ministry of Education, Kyaukse, Mandalay Region 100301 Myanmar
| | - Zaw Ko Latt
- Microbiology Division, Biotechnology Research Department, Ministry of Education, Kyaukse, Mandalay Region 100301 Myanmar
| | - Tin Mar Htwe
- Ministry of Education, Kyaing Tong Education College, Kyaing Tong, Shan State Myanmar
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13
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Babin D, Sommermann L, Chowdhury SP, Behr JH, Sandmann M, Neumann G, Nesme J, Sørensen SJ, Schellenberg I, Rothballer M, Geistlinger J, Smalla K, Grosch R. Distinct rhizomicrobiota assemblages and plant performance in lettuce grown in soils with different agricultural management histories. FEMS Microbiol Ecol 2021; 97:fiab027. [PMID: 33571366 DOI: 10.1093/femsec/fiab027] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 02/09/2021] [Indexed: 12/21/2022] Open
Abstract
A better understanding of factors shaping the rhizosphere microbiota is important for sustainable crop production. We hypothesized that the effect of agricultural management on the soil microbiota is reflected in the assemblage of the rhizosphere microbiota with implications for plant performance. We designed a growth chamber experiment growing the model plant lettuce under controlled conditions in soils of a long-term field experiment with contrasting histories of tillage (mouldboard plough vs cultivator tillage), fertilization intensity (intensive standard nitrogen (N) + pesticides/growth regulators vs extensive reduced N without fungicides/growth regulators), and last standing field crop (rapeseed vs winter wheat). High-throughput sequencing of bacterial and archaeal 16S rRNA genes and fungal ITS2 regions amplified from total community DNA showed that these factors shaped the soil and rhizosphere microbiota of lettuce, however, to different extents among the microbial domains. Pseudomonas and Olpidium were identified as major indicators for agricultural management in the rhizosphere of lettuce. Long-term extensive fertilization history of soils resulted in higher lettuce growth and increased expression of genes involved in plant stress responses compared to intensive fertilization. Our work adds to the increasing knowledge on how soil microbiota can be manipulated by agricultural management practices which could be harnessed for sustainable crop production.
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Affiliation(s)
- Doreen Babin
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104 Braunschweig, Germany
| | - Loreen Sommermann
- Anhalt University of Applied Sciences, Department of Agriculture, Ecotrophology and Landscape Development, Institute of Bioanalytical Sciences (IBAS), Strenzfelder Allee 28, 06406 Bernburg, Germany
| | - Soumitra Paul Chowdhury
- Institute of Network Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Jan H Behr
- Leibniz Institute of Vegetable and Ornamental Crops (IGZ), Plant-Microbe Systems, Theodor-Echtermeyer-Weg 1, 14979 Großbeeren, Germany
| | - Martin Sandmann
- Leibniz Institute of Vegetable and Ornamental Crops (IGZ), Plant-Microbe Systems, Theodor-Echtermeyer-Weg 1, 14979 Großbeeren, Germany
| | - Günter Neumann
- University of Hohenheim, Institute of Crop Science, Department of Nutritional Crop Physiology, Fruwirthstraße 20, 70599 Stuttgart, Germany
| | - Joseph Nesme
- University of Copenhagen, Department of Biology, Section of Microbiology, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Søren J Sørensen
- University of Copenhagen, Department of Biology, Section of Microbiology, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Ingo Schellenberg
- Anhalt University of Applied Sciences, Department of Agriculture, Ecotrophology and Landscape Development, Institute of Bioanalytical Sciences (IBAS), Strenzfelder Allee 28, 06406 Bernburg, Germany
| | - Michael Rothballer
- Institute of Network Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Joerg Geistlinger
- Anhalt University of Applied Sciences, Department of Agriculture, Ecotrophology and Landscape Development, Institute of Bioanalytical Sciences (IBAS), Strenzfelder Allee 28, 06406 Bernburg, Germany
| | - Kornelia Smalla
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104 Braunschweig, Germany
| | - Rita Grosch
- Leibniz Institute of Vegetable and Ornamental Crops (IGZ), Plant-Microbe Systems, Theodor-Echtermeyer-Weg 1, 14979 Großbeeren, Germany
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14
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Fernandez-Gnecco G, Smalla K, Maccario L, Sørensen SJ, Barbieri P, Consolo VF, Covacevich F, Babin D. Microbial community analysis of soils under different soybean cropping regimes in the Argentinean south-eastern Humid Pampas. FEMS Microbiol Ecol 2021; 97:fiab007. [PMID: 33444447 DOI: 10.1093/femsec/fiab007] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 01/12/2021] [Indexed: 12/13/2022] Open
Abstract
Soil microbial communities are key players of ecosystem processes and important for crop and soil health. The Humid Pampas region in Argentina concentrates 75% of the national soybean production, which is based on intensive use of agrochemicals, monocropping and no-till. A long-term field experiment under no-till management in the southeast of the Argentinean Pampas provides a unique opportunity to compare soybean under monocropping with cultivation including alternating cover crops or in a three-phase rotation. We hypothesized that cropping regimes and season affect soil microbial community composition and diversity. Amplicon sequencing of 16S rRNA genes and internal transcribed spacer fragments showed a stronger microbial seasonal dynamic in conservation regimes compared to monocropping. In addition, several bacterial (e.g. Catenulispora, Streptomyces and Bacillus) and fungal genera (e.g. Exophiala) with cropping regime-dependent differential relative abundances were identified. Despite a temporal shift in microbial and chemical parameters, this study shows that long-term cropping regimes shaped the soil microbiota. This might have important implications for soil quality and soybean performance and should therefore be considered in the development of sustainable agricultural managements.
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Affiliation(s)
- Gabriela Fernandez-Gnecco
- Instituto de Investigaciones en Biodiversidad y Biotecnología, CONICET- Fundación para Investigaciones Biológicas Aplicadas (INBIOTEC, CONICET-FIBA), Vieytes 3103, B7602FCK Mar del Plata, Buenos Aires, Argentina
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104 Braunschweig, Germany
- Instituto Nacional de Tecnología Agropecuaria, Estación Experimental Agropecuaria Balcarce - CONICET (INTA, EEA Balcarce - CONICET), Ruta 226 Km 73.5, 7620 Balcarce, Buenos Aires, Argentina
| | - Kornelia Smalla
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104 Braunschweig, Germany
| | - Lorrie Maccario
- Department of Biology, University of Copenhagen, Section of Microbiology, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Søren J Sørensen
- Department of Biology, University of Copenhagen, Section of Microbiology, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Pablo Barbieri
- National Scientific and Technical Research Council (CONICET), Argentina
- Instituto Nacional de Tecnología Agropecuaria, Estación Experimental Agropecuaria Balcarce - CONICET (INTA, EEA Balcarce - CONICET), Ruta 226 Km 73.5, 7620 Balcarce, Buenos Aires, Argentina
| | - Veronica F Consolo
- Instituto de Investigaciones en Biodiversidad y Biotecnología, CONICET- Fundación para Investigaciones Biológicas Aplicadas (INBIOTEC, CONICET-FIBA), Vieytes 3103, B7602FCK Mar del Plata, Buenos Aires, Argentina
- National Scientific and Technical Research Council (CONICET), Argentina
| | - Fernanda Covacevich
- Instituto de Investigaciones en Biodiversidad y Biotecnología, CONICET- Fundación para Investigaciones Biológicas Aplicadas (INBIOTEC, CONICET-FIBA), Vieytes 3103, B7602FCK Mar del Plata, Buenos Aires, Argentina
- National Scientific and Technical Research Council (CONICET), Argentina
- Instituto Nacional de Tecnología Agropecuaria, Estación Experimental Agropecuaria Balcarce - CONICET (INTA, EEA Balcarce - CONICET), Ruta 226 Km 73.5, 7620 Balcarce, Buenos Aires, Argentina
| | - Doreen Babin
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104 Braunschweig, Germany
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15
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Chiba A, Uchida Y, Kublik S, Vestergaard G, Buegger F, Schloter M, Schulz S. Soil Bacterial Diversity Is Positively Correlated with Decomposition Rates during Early Phases of Maize Litter Decomposition. Microorganisms 2021; 9:microorganisms9020357. [PMID: 33670245 PMCID: PMC7916959 DOI: 10.3390/microorganisms9020357] [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: 01/26/2021] [Revised: 02/07/2021] [Accepted: 02/09/2021] [Indexed: 12/16/2022] Open
Abstract
This study aimed to investigate the effects of different levels of soil- and plant-associated bacterial diversity on the rates of litter decomposition, and bacterial community dynamics during its early phases. We performed an incubation experiment where soil bacterial diversity (but not abundance) was manipulated by autoclaving and reinoculation. Natural or autoclaved maize leaves were applied to the soils and incubated for 6 weeks. Bacterial diversity was assessed before and during litter decomposition using 16S rRNA gene metabarcoding. We found a positive correlation between litter decomposition rates and soil bacterial diversity. The soil with the highest bacterial diversity was dominated by oligotrophic bacteria including Acidobacteria, Nitrospiraceae, and Gaiellaceae, and its community composition did not change during the incubation. In the less diverse soils, those taxa were absent but were replaced by copiotrophic bacteria, such as Caulobacteraceae and Beijerinckiaceae, until the end of the incubation period. SourceTracker analysis revealed that litter-associated bacteria, such as Beijerinckiaceae, only became part of the bacterial communities in the less diverse soils. This suggests a pivotal role of oligotrophic bacteria during the early phases of litter decomposition and the predominance of copiotrophic bacteria at low diversity.
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Affiliation(s)
- Akane Chiba
- Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan; (A.C.); (Y.U.)
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, German Research Centre for Environmental Health, 85764 Neuherberg, Germany; (S.K.); (G.V.); (M.S.)
- Crop Physiology, TUM School of Life Science, Technical University of Munich, 85354 Freising, Germany
| | - Yoshitaka Uchida
- Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan; (A.C.); (Y.U.)
| | - Susanne Kublik
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, German Research Centre for Environmental Health, 85764 Neuherberg, Germany; (S.K.); (G.V.); (M.S.)
| | - Gisle Vestergaard
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, German Research Centre for Environmental Health, 85764 Neuherberg, Germany; (S.K.); (G.V.); (M.S.)
- Section of Bioinformatics, Department of Health Technology, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Franz Buegger
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, German Research Centre for Environmental Health, 85764 Neuherberg, Germany;
| | - Michael Schloter
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, German Research Centre for Environmental Health, 85764 Neuherberg, Germany; (S.K.); (G.V.); (M.S.)
- TUM School of Life Science, Technical University of Munich, 85354 Freising, Germany
| | - Stefanie Schulz
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, German Research Centre for Environmental Health, 85764 Neuherberg, Germany; (S.K.); (G.V.); (M.S.)
- Correspondence: ; Tel.: +49-(0)89-3187-3054
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16
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Soil bacterial communities remain altered after 30 years of agriculture abandonment in Pampa grasslands. Oecologia 2020; 193:959-968. [PMID: 32851494 DOI: 10.1007/s00442-020-04736-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 08/18/2020] [Indexed: 10/23/2022]
Abstract
Old fields are spreading in the world because of agriculture abandonment, and they show a persistence of exotic plant species with little recovery towards the original vegetation composition. Soil biota may also differ between old fields and native grasslands, but were comparatively less studied than plant communities, despite their importance in biogeochemical processes. Here we compared soil bacterial communities of exotic-dominated old fields with those of remnants of native grasslands in the Inland Pampa, Argentina, using the 16S rRNA gene amplicon sequencing approach. We also characterized plant communities, soil physico-chemical properties, and soil respiration. We expected more diverse soil bacterial communities, with higher heterogeneity, in remnant grasslands than in old fields because of a more diverse and more heterogeneous plant community. However, our results showed that soil bacterial communities had higher Shannon diversity in old fields than in remnant grasslands, but richness was not significantly different. Also we found different bacterial community compositions between grasslands even at a low taxonomic level. On the other hand, old fields harbored less heterogeneous bacterial communities than remnants, and bacteria and plant beta diversity were correlated. Despite contrasting plant and bacterial composition between old fields and remnant grasslands, soil physico-chemical properties were quite similar between grasslands. Overall, our results showed that bacterial communities in grassland soils were associated with changes in plant communities after agricultural abandonment. Plant-microbial feedbacks might regulate plant and soil bacterial community assemblage in old fields, yet further research is needed to demonstrate this potential feedback mechanism.
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17
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Tibbett M, Fraser TD, Duddigan S. Identifying potential threats to soil biodiversity. PeerJ 2020; 8:e9271. [PMID: 32566399 PMCID: PMC7295018 DOI: 10.7717/peerj.9271] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 05/11/2020] [Indexed: 12/31/2022] Open
Abstract
A decline in soil biodiversity is generally considered to be the reduction of forms of life living in soils, both in terms of quantity and variety. Where soil biodiversity decline occurs, it can significantly affect the soils' ability to function, respond to perturbations and recover from a disturbance. Several soil threats have been identified as having negative effects on soil biodiversity, including human intensive exploitation, land-use change and soil organic matter decline. In this review we consider what we mean by soil biodiversity, and why it is important to monitor. After a thorough review of the literature identified on a Web of Science search concerning threats to soil biodiversity (topic search: threat* "soil biodiversity"), we compiled a table of biodiversity threats considered in each paper including climate change, land use change, intensive human exploitation, decline in soil health or plastic; followed by detailed listings of threats studied. This we compared to a previously published expert assessment of threats to soil biodiversity. In addition, we identified emerging threats, particularly microplastics, in the 10 years following these knowledge based rankings. We found that many soil biodiversity studies do not focus on biodiversity sensu stricto, rather these studies examined either changes in abundance and/or diversity of individual groups of soil biota, instead of soil biodiversity as a whole, encompassing all levels of the soil food web. This highlights the complexity of soil biodiversity which is often impractical to assess in all but the largest studies. Published global scientific activity was only partially related to the threats identified by the expert panel assessment. The number of threats and the priority given to the threats (by number of publications) were quite different, indicating a disparity between research actions versus perceived threats. The lack of research effort in key areas of high priority in the threats to soil biodiversity are a concerning finding and requires some consideration and debate in the research community.
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Affiliation(s)
- Mark Tibbett
- Department of Sustainable Land Management and Soil Research Centre, School of Agriculture Policy and Development, University of Reading, Reading, Berkshire, United Kingdom
| | - Tandra D. Fraser
- Department of Sustainable Land Management and Soil Research Centre, School of Agriculture Policy and Development, University of Reading, Reading, Berkshire, United Kingdom
| | - Sarah Duddigan
- Department of Sustainable Land Management and Soil Research Centre, School of Agriculture Policy and Development, University of Reading, Reading, Berkshire, United Kingdom
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18
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Hermans SM, Buckley HL, Case BS, Curran-Cournane F, Taylor M, Lear G. Using soil bacterial communities to predict physico-chemical variables and soil quality. MICROBIOME 2020; 8:79. [PMID: 32487269 PMCID: PMC7268603 DOI: 10.1186/s40168-020-00858-1] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 05/08/2020] [Indexed: 05/19/2023]
Abstract
BACKGROUND Soil ecosystems consist of complex interactions between biological communities and physico-chemical variables, all of which contribute to the overall quality of soils. Despite this, changes in bacterial communities are ignored by most soil monitoring programs, which are crucial to ensure the sustainability of land management practices. We applied 16S rRNA gene sequencing to determine the bacterial community composition of over 3000 soil samples from 606 sites in New Zealand. Sites were classified as indigenous forests, exotic forest plantations, horticulture, or pastoral grasslands; soil physico-chemical variables related to soil quality were also collected. The composition of soil bacterial communities was then used to predict the land use and soil physico-chemical variables of each site. RESULTS Soil bacterial community composition was strongly linked to land use, to the extent where it could correctly determine the type of land use with 85% accuracy. Despite the inherent variation introduced by sampling across ~ 1300 km distance gradient, the bacterial communities could also be used to differentiate sites grouped by key physico-chemical properties with up to 83% accuracy. Further, individual soil variables such as soil pH, nutrient concentrations and bulk density could be predicted; the correlations between predicted and true values ranged from weak (R2 value = 0.35) to strong (R2 value = 0.79). These predictions were accurate enough to allow bacterial communities to assign the correct soil quality scores with 50-95% accuracy. CONCLUSIONS The inclusion of biological information when monitoring soil quality is crucial if we wish to gain a better, more accurate understanding of how land management impacts the soil ecosystem. We have shown that soil bacterial communities can provide biologically relevant insights on the impacts of land use on soil ecosystems. Furthermore, their ability to indicate changes in individual soil parameters shows that analysing bacterial DNA data can be used to screen soil quality. Video Abstract.
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Affiliation(s)
- Syrie M Hermans
- School of Biological Sciences, University of Auckland, 3A Symonds Street, Auckland, 1010, New Zealand
| | - Hannah L Buckley
- School of Science, Auckland University of Technology, 46 Wakefield St, Auckland, 1010, New Zealand
| | - Bradley S Case
- School of Science, Auckland University of Technology, 46 Wakefield St, Auckland, 1010, New Zealand
| | - Fiona Curran-Cournane
- Ministry for the Environment - Manatū Mō Te Taiao, 45 Queen Street, Auckland, 1010, New Zealand
| | - Matthew Taylor
- Waikato Regional Council, 401 Grey Street, Hamilton, 3216, New Zealand
| | - Gavin Lear
- School of Biological Sciences, University of Auckland, 3A Symonds Street, Auckland, 1010, New Zealand.
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Sun Y, Luo C, Jiang L, Song M, Zhang D, Li J, Li Y, Ostle NJ, Zhang G. Land-use changes alter soil bacterial composition and diversity in tropical forest soil in China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 712:136526. [PMID: 31945538 DOI: 10.1016/j.scitotenv.2020.136526] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 01/02/2020] [Accepted: 01/03/2020] [Indexed: 06/10/2023]
Abstract
Tropical forests, under pressure from human activities, are important reservoirs of biodiversity and regulators of global biogeochemical cycles. Land-use and management are influential drivers of environmental change and ecosystem sustainability. However, only limited studies have analysed the impacts of planting age and vegetation type under land-use change on soil microbial community in tropical forests simultaneously. Here, we assessed soil bacterial community composition and diversity under different land-use in Hainan Province, China, using high-throughput sequencing combined with PICRUSt analysis. Land-use included natural forest, 5-year-old cropland, young (5-year-old) rubber tree plantation, and old (30-year-old) rubber tree plantation. Land-use changes altered the soil bacterial community composition but had a non-significant influence on alpha diversity (P > .05). We found that bacterial beta-diversity significantly decreased in young rubber tree plantation soils and cropland soils compared to natural forest as a control. In contrast, soil bacterial beta-diversity increased in old rubber tree plantation soils, indicating the effects of time since planting. There was no difference in microbial beta-diversity between soils from cropland and young rubber tree plantation. Soil bulk density and moisture, not pH, were the main environmental factors explaining the variability in microbial diversity. PICRUSt analysis of soil bacterial predicted gene abundances within metabolic pathways and indicated that land-use change altered soil functional traits, e.g., amino acid-related enzymes, ribosomes, DNA repair/recombination proteins and oxidative phosphorylation. Also, vegetation type, not planting age, had significant impacts on soil functional traits. Overall, planting age had the greatest influence on soil bacterial beta-diversity, while vegetation type was more crucial for soil functional traits (P < .05).
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Affiliation(s)
- Yingtao Sun
- State Key Laboratory of Organic Geochemistry and Guangdong Key Laboratory of Environmental Protection and Resources Utilization, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100049, China
| | - Chunling Luo
- State Key Laboratory of Organic Geochemistry and Guangdong Key Laboratory of Environmental Protection and Resources Utilization, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China.
| | - Longfei Jiang
- State Key Laboratory of Organic Geochemistry and Guangdong Key Laboratory of Environmental Protection and Resources Utilization, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Mengke Song
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
| | - Dayi Zhang
- School of Environment, Tsinghua University, Beijing 100084, PR China
| | - Jun Li
- State Key Laboratory of Organic Geochemistry and Guangdong Key Laboratory of Environmental Protection and Resources Utilization, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Yongtao Li
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
| | - Nicholas J Ostle
- Lancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, UK
| | - Gan Zhang
- State Key Laboratory of Organic Geochemistry and Guangdong Key Laboratory of Environmental Protection and Resources Utilization, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
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20
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Lopez S, van der Ent A, Sumail S, Sugau JB, Buang MM, Amin Z, Echevarria G, Morel JL, Benizri E. Bacterial community diversity in the rhizosphere of nickel hyperaccumulator plant species from Borneo Island (Malaysia). Environ Microbiol 2020; 22:1649-1665. [PMID: 32128926 DOI: 10.1111/1462-2920.14970] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 02/27/2020] [Accepted: 03/01/2020] [Indexed: 12/01/2022]
Abstract
The Island of Borneo is a major biodiversity hotspot, and in the Malaysian state of Sabah, ultramafic soils are extensive and home to more than 31 endemic nickel hyperaccumulator plants. The aim of this study was to characterize the structure and the diversity of the rhizosphere bacterial communities of several of these nickel hyperaccumulator plants and factors that affect these bacterial communities in Sabah. The most abundant phyla were Proteobacteria, Acidobacteria and Actinobacteria. At family level, Burkholderiaceae and Xanthobacteraceae (Proteobacteria phylum) were the most abundant families in the hyperaccumulator rhizospheres. Redundancy analysis based on soil chemical analyses and relative abundances of the major bacterial phyla showed that abiotic factors of the studied sites drove the bacterial diversity. For all R. aff. bengalensis rhizosphere soil samples, irrespective of studied site, the bacterial diversity was similar. Moreover, the Saprospiraceae family showed a high representativeness in the R. aff. bengalensis rhizosphere soils and was linked with the nickel availability in soils. The ability of R. aff. bengalensis to concentrate nickel in its rhizosphere appears to be the major factor driving the rhizobacterial community diversity unlike for other hyperaccumulator species.
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Affiliation(s)
- Séverine Lopez
- Université de Lorraine, INRAE, Laboratoire Sols et Environnement, 54000, Nancy, France
| | - Antony van der Ent
- Université de Lorraine, INRAE, Laboratoire Sols et Environnement, 54000, Nancy, France.,Centre for Mined Land Rehabilitation, Sustainable Minerals Institute, The University of Queensland, St Lucia, 4072, QLD, Australia
| | | | | | - Matsain Mohd Buang
- Forest Research Centre, Sabah Forestry Department, Sandakan, Sabah, Malaysia
| | - Zarina Amin
- Biotechnology Research Institute, Universiti Malaysia Sabah, Kota Kinabalu, Sabah, Malaysia
| | - Guillaume Echevarria
- Université de Lorraine, INRAE, Laboratoire Sols et Environnement, 54000, Nancy, France.,Centre for Mined Land Rehabilitation, Sustainable Minerals Institute, The University of Queensland, St Lucia, 4072, QLD, Australia
| | - Jean Louis Morel
- Université de Lorraine, INRAE, Laboratoire Sols et Environnement, 54000, Nancy, France
| | - Emile Benizri
- Université de Lorraine, INRAE, Laboratoire Sols et Environnement, 54000, Nancy, France
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Castle SC, Samac DA, Sadowsky MJ, Rosen CJ, Gutknecht JLM, Kinkel LL. Impacts of Sampling Design on Estimates of Microbial Community Diversity and Composition in Agricultural Soils. MICROBIAL ECOLOGY 2019; 78:753-763. [PMID: 30852638 DOI: 10.1007/s00248-019-01318-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 01/03/2019] [Indexed: 06/09/2023]
Abstract
Soil microbiota play important and diverse roles in agricultural crop nutrition and productivity. Yet, despite increasing efforts to characterize soil bacterial and fungal assemblages, it is challenging to disentangle the influences of sampling design on assessments of communities. Here, we sought to determine whether composite samples-often analyzed as a low cost and effort alternative to replicated individual samples-provide representative summary estimates of microbial communities. At three Minnesota agricultural research sites planted with an oat cover crop, we conducted amplicon sequencing for soil bacterial and fungal communities (16SV4 and ITS2) of replicated individual or homogenized composite soil samples. We compared soil microbiota from within and among plots and then among agricultural sites using both sampling strategies. Results indicated that single or multiple replicated individual samples, or a composite sample from each plot, were sufficient for distinguishing broad site-level macroecological differences among bacterial and fungal communities. Analysis of a single sample per plot captured only a small fraction of the distinct OTUs, diversity, and compositional variability detected in the analysis of multiple individual samples or a single composite sample. Likewise, composite samples captured only a fraction of the diversity represented by the six individual samples from which they were formed, and, on average, analysis of two or three individual samples offered greater compositional coverage (i.e., greater number of OTUs) than a single composite sample. We conclude that sampling design significantly impacts estimates of bacterial and fungal communities even in homogeneously managed agricultural soils, and our findings indicate that while either strategy may be sufficient for broad macroecological investigations, composites may be a poor substitute for replicated samples at finer spatial scales.
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Affiliation(s)
- Sarah C Castle
- Department of Plant Pathology, University of Minnesota, Minneapolis, USA.
| | - Deborah A Samac
- Department of Plant Pathology, University of Minnesota, Minneapolis, USA
- USDA-ARS, Plant Science Research Unit, Saint Paul, MN, USA
| | - Michael J Sadowsky
- Department of Soil, Water, and Climate, University of Minnesota, Minneapolis, MN, USA
- Biotechnology Institute, University of Minnesota, Minneapolis, MN, USA
| | - Carl J Rosen
- Department of Soil, Water, and Climate, University of Minnesota, Minneapolis, MN, USA
| | - Jessica L M Gutknecht
- Department of Soil, Water, and Climate, University of Minnesota, Minneapolis, MN, USA
| | - Linda L Kinkel
- Department of Plant Pathology, University of Minnesota, Minneapolis, USA
- Biotechnology Institute, University of Minnesota, Minneapolis, MN, USA
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22
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Altshuler I, Hamel J, Turney S, Magnuson E, Lévesque R, Greer CW, Whyte LG. Species interactions and distinct microbial communities in high Arctic permafrost affected cryosols are associated with the CH 4 and CO 2 gas fluxes. Environ Microbiol 2019; 21:3711-3727. [PMID: 31206918 DOI: 10.1111/1462-2920.14715] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Revised: 05/27/2019] [Accepted: 06/10/2019] [Indexed: 11/29/2022]
Abstract
Microbial metabolism of the thawing organic carbon stores in permafrost results in a positive feedback loop of greenhouse gas emissions. CO2 and CH4 fluxes and the associated microbial communities in Arctic cryosols are important in predicting future warming potential of the Arctic. We demonstrate that topography had an impact on CH4 and CO2 flux at a high Arctic ice-wedge polygon terrain site, with higher CO2 emissions and lower CH4 uptake at troughs compared to polygon interior soils. The pmoA sequencing suggested that USCα cluster of uncultured methanotrophs is likely responsible for observed methane sink. Community profiling revealed distinct assemblages across the terrain at different depths. Deeper soils contained higher abundances of Verrucomicrobia and Gemmatimonadetes, whereas the polygon interior had higher Acidobacteria and lower Betaproteobacteria and Deltaproteobacteria abundances. Genome sequencing of isolates from the terrain revealed presence of carbon cycling genes including ones involved in serine and ribulose monophosphate pathways. A novel hybrid network analysis identified key members that had positive and negative impacts on other species. Operational Taxonomic Units (OTUs) with numerous positive interactions corresponded to Proteobacteria, Candidatus Rokubacteria and Actinobacteria phyla, while Verrucomicrobia and Acidobacteria members had negative impacts on other species. Results indicate that topography and microbial interactions impact community composition.
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Affiliation(s)
- Ianina Altshuler
- Department of Natural Resource Sciences, Faculty of Agricultural and Environmental Sciences, Macdonald Campus, McGill University, 21111 Lakeshore Rd, Ste Anne-de-Bellevue, QC, H9X 3V9, Canada
| | - Jérémie Hamel
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, QC, Québec, Canada
| | - Shaun Turney
- Department of Natural Resource Sciences, Faculty of Agricultural and Environmental Sciences, Macdonald Campus, McGill University, 21111 Lakeshore Rd, Ste Anne-de-Bellevue, QC, H9X 3V9, Canada
| | - Elisse Magnuson
- Department of Natural Resource Sciences, Faculty of Agricultural and Environmental Sciences, Macdonald Campus, McGill University, 21111 Lakeshore Rd, Ste Anne-de-Bellevue, QC, H9X 3V9, Canada
| | - Roger Lévesque
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, QC, Québec, Canada
| | - Charles W Greer
- Department of Natural Resource Sciences, Faculty of Agricultural and Environmental Sciences, Macdonald Campus, McGill University, 21111 Lakeshore Rd, Ste Anne-de-Bellevue, QC, H9X 3V9, Canada.,National Research Council of Canada, 6100 Royalmount Avenue, Montreal, QC, H4P 2R2, Canada
| | - Lyle G Whyte
- Department of Natural Resource Sciences, Faculty of Agricultural and Environmental Sciences, Macdonald Campus, McGill University, 21111 Lakeshore Rd, Ste Anne-de-Bellevue, QC, H9X 3V9, Canada
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23
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Changes of paradigms in agriculture soil microbiology and new challenges in microbial ecology. ACTA OECOLOGICA-INTERNATIONAL JOURNAL OF ECOLOGY 2019. [DOI: 10.1016/j.actao.2019.02.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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24
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Enrichment of Verrucomicrobia, Actinobacteria and Burkholderiales drives selection of bacterial community from soil by maize roots in a traditional milpa agroecosystem. PLoS One 2018; 13:e0208852. [PMID: 30571782 PMCID: PMC6301694 DOI: 10.1371/journal.pone.0208852] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 11/19/2018] [Indexed: 01/19/2023] Open
Abstract
Milpas are rain-fed agroecosystems involving domesticated, semi-domesticated and tolerated plant species that combine maize with a large variety of other crop, tree or shrub species. Milpas are low input and low-tillage, yet highly productive agroecosystems, which have been maintained over millennia in indigenous communities in Mexico and other countries in Central America. Thus, milpas may retain ancient plant-microorganisms interactions, which could have been lost in modern high-tillage monocultures with large agrochemical input. In this work, we performed high-throughput 16S ribosomal DNA sequencing of soil adjacent to maize roots and bulk soil sampled at 30 cm from the base of the plants. We found that the bacterial communities of maize root soil had a lower alpha diversity, suggesting selection of microorganisms by maize-roots from the bulk-soil community. Beta diversity analysis confirmed that these environments harbor two distinct microbial communities; differences were driven by members of phyla Verrucomicrobia and Actinobacteria, as well as the order Burkholderiales (Betaproteobacteria), all of which had higher relative abundance in soil adjacent to the roots. Numerous studies have shown the influence of maize plants on bacterial communities found in soil attached tightly to the roots; here we further show that the influence of maize roots at milpas on bacterial communities is detectable even in plant-free soil collected nearby. We propose that members of Verrucomicrobia and other phyla found in the rhizosphere may establish beneficial plant-microbe interactions with maize roots in milpas, and propose to address their cultivation for future studies on ecology and potential use.
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25
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Balázs HE, Schmid CAO, Feher I, Podar D, Szatmari PM, Marincaş O, Balázs ZR, Schröder P. HCH phytoremediation potential of native plant species from a contaminated urban site in Turda, Romania. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2018; 223:286-296. [PMID: 29933144 DOI: 10.1016/j.jenvman.2018.06.018] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 05/09/2018] [Accepted: 06/07/2018] [Indexed: 06/08/2023]
Abstract
Current physical or chemical methods used for remediation of soils contaminated with hexachlocyclohexane (HCH), leave behind significant levels of pollutants. Given the compound's volatility and persistence in the environment, sites contaminated with HCH remain a concern for the population living in nearby areas. By making use of both the recovery capacity and the pollutant uptake ability of spontaneously growing vegetation, our study aimed to identify native plant species able to cover and moreover take up the HCH left at a former lindane production unit in Turda, Romania. The results showed that dominant species across the study site like Lotus tenuis, Artemisia vulgaris or Tanacetum vulgare, were capable of taking up HCH in their tissues, according to different patterns that combined at the scale of the plant community. Regardless of the proximity of the HCH contamination hotspots, the development of the plant cover was characteristic for vegetation succession on disturbed soils of the Central European region. Finally, we conclude that plant species which grow spontaneously at the HCH contaminated site in Turda and are capable of taking up the pollutant, represent a self-sustainable and low maintenance phytomanagement approach that would allow for the reintegration of the site in the urban or industrial circuit and nevertheless would reduce the toxicity risk to the neighboring human inhabitants.
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Affiliation(s)
- Helga E Balázs
- Helmholtz Zentrum München, Comparative Microbiome Analysis, Ingolstädter Landstr. 1, 85764, München, Germany; Botanical Garden "Alexandru Borza", 42 Republicii St., 400015, Cluj-Napoca, Romania
| | - Christoph A O Schmid
- Helmholtz Zentrum München, Comparative Microbiome Analysis, Ingolstädter Landstr. 1, 85764, München, Germany
| | - Ioana Feher
- National Institute for Research and Development of Isotopic and Molecular Technologies, 67-103 Donat St. 400293, Cluj-Napoca, Romania
| | - Dorina Podar
- Babeş-Bolyai University, Department of Molecular Biology and Biotechnology, 1 Kogălniceanu St., 400084, Cluj-Napoca, Romania
| | - Paul-Marian Szatmari
- Botanical Garden "Alexandru Borza", 42 Republicii St., 400015, Cluj-Napoca, Romania; Biological Research Center, Botanical Garden "Vasile Fati", 16 Wesselényi Miklós St., 455200, Jibou, Romania
| | - Olivian Marincaş
- National Institute for Research and Development of Isotopic and Molecular Technologies, 67-103 Donat St. 400293, Cluj-Napoca, Romania
| | - Zoltan R Balázs
- Babeş-Bolyai University, Department of Molecular Biology and Biotechnology, 1 Kogălniceanu St., 400084, Cluj-Napoca, Romania
| | - Peter Schröder
- Helmholtz Zentrum München, Comparative Microbiome Analysis, Ingolstädter Landstr. 1, 85764, München, Germany.
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Mackelprang R, Grube AM, Lamendella R, Jesus EDC, Copeland A, Liang C, Jackson RD, Rice CW, Kapucija S, Parsa B, Tringe SG, Tiedje JM, Jansson JK. Microbial Community Structure and Functional Potential in Cultivated and Native Tallgrass Prairie Soils of the Midwestern United States. Front Microbiol 2018; 9:1775. [PMID: 30158906 PMCID: PMC6104126 DOI: 10.3389/fmicb.2018.01775] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 07/16/2018] [Indexed: 11/19/2022] Open
Abstract
The North American prairie covered about 3.6 million-km2 of the continent prior to European contact. Only 1-2% of the original prairie remains, but the soils that developed under these prairies are some of the most productive and fertile in the world, containing over 35% of the soil carbon in the continental United States. Cultivation may alter microbial diversity and composition, influencing the metabolism of carbon, nitrogen, and other elements. Here, we explored the structure and functional potential of the soil microbiome in paired cultivated-corn (at the time of sampling) and never-cultivated native prairie soils across a three-states transect (Wisconsin, Iowa, and Kansas) using metagenomic and 16S rRNA gene sequencing and lipid analysis. At the Wisconsin site, we also sampled adjacent restored prairie and switchgrass plots. We found that agricultural practices drove differences in community composition and diversity across the transect. Microbial biomass in prairie samples was twice that of cultivated soils, but alpha diversity was higher with cultivation. Metagenome analyses revealed denitrification and starch degradation genes were abundant across all soils, as were core genes involved in response to osmotic stress, resource transport, and environmental sensing. Together, these data indicate that cultivation shifted the microbiome in consistent ways across different regions of the prairie, but also suggest that many functions are resilient to changes caused by land management practices - perhaps reflecting adaptations to conditions common to tallgrass prairie soils in the region (e.g., soil type, parent material, development under grasses, temperature and rainfall patterns, and annual freeze-thaw cycles). These findings are important for understanding the long-term consequences of land management practices to prairie soil microbial communities and their genetic potential to carry out key functions.
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Affiliation(s)
- Rachel Mackelprang
- Department of Biology, California State University, Northridge, Northridge, CA, United States
| | - Alyssa M. Grube
- Department of Biology, Juniata College, Huntingdon, PA, United States
| | - Regina Lamendella
- Department of Biology, Juniata College, Huntingdon, PA, United States
| | - Ederson da C. Jesus
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, United States
- Great Lakes Bioenergy Research Center, U.S. Department of Energy, University of Wisconsin–Madison, Madison, WI, United States
| | - Alex Copeland
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA, United States
| | - Chao Liang
- Great Lakes Bioenergy Research Center, U.S. Department of Energy, University of Wisconsin–Madison, Madison, WI, United States
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Randall D. Jackson
- Great Lakes Bioenergy Research Center, U.S. Department of Energy, University of Wisconsin–Madison, Madison, WI, United States
- Department of Agronomy, University of Wisconsin–Madison, Madison, WI, United States
| | - Charles W. Rice
- Department of Agronomy, Kansas State University, Manhattan, KS, United States
| | - Stefanie Kapucija
- Department of Biology, California State University, Northridge, Northridge, CA, United States
| | - Bayan Parsa
- Department of Biology, California State University, Northridge, Northridge, CA, United States
| | - Susannah G. Tringe
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA, United States
| | - James M. Tiedje
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, United States
- Great Lakes Bioenergy Research Center, U.S. Department of Energy, University of Wisconsin–Madison, Madison, WI, United States
| | - Janet K. Jansson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
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27
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Draghi WO, Degrossi J, Bialer M, Brelles-Mariño G, Abdian P, Soler-Bistué A, Wall L, Zorreguieta A. Biodiversity of cultivable Burkholderia species in Argentinean soils under no-till agricultural practices. PLoS One 2018; 13:e0200651. [PMID: 30001428 PMCID: PMC6042781 DOI: 10.1371/journal.pone.0200651] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 06/29/2018] [Indexed: 11/19/2022] Open
Abstract
No-tillage crop production has revolutionized the agriculture worldwide. In our country more than 30 Mha are currently cultivated under no-till schemes, stressing the importance of this management system for crop production. It is widely recognized that soil microbiota is altered under different soil managements. In this regard the structure of Burkholderia populations is affected by soils management practices such as tillage, fertilization, or crop rotation. The stability of these structures, however, has not been evaluated under sustainable schemes where the impact of land practices could be less deleterious to physicochemical soils characteristics. In order to assess the structure of Burkholderia spp. populations in no-till schemes, culturable Burkholderia spp. strains were quantified and their biodiversity evaluated. Results showed that Burkholderia spp. biodiversity, but not their abundance, clearly displayed a dependence on agricultural managements. We also showed that biodiversity was mainly influenced by two soil factors: Total Organic Carbon and Total Nitrogen. Results showed that no-till schemes are not per se sufficient to maintain a richer Burkholderia spp. soil microbiota, and additional traits should be considered when sustainability of productive soils is a goal to fulfil productive agricultural schemes.
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Affiliation(s)
- Walter Omar Draghi
- Fundación Instituto Leloir, IIBBA CONICET, Buenos Aires, Argentina
- Instituto de Biotecnología y Biología Molecular–CCT La Plata CONICET, Universidad Nacional de La Plata, La Plata, Argentina
- * E-mail: (AZ); (WOD)
| | - Jose Degrossi
- Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Magalí Bialer
- Fundación Instituto Leloir, IIBBA CONICET, Buenos Aires, Argentina
| | - Graciela Brelles-Mariño
- Center for Research and Development of Industrial Fermentations, (CINDEFI, CCT-LA PLATA-CONICET), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Patricia Abdian
- Fundación Instituto Leloir, IIBBA CONICET, Buenos Aires, Argentina
| | | | - Luis Wall
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Bernal, Argentina
| | - Angeles Zorreguieta
- Fundación Instituto Leloir, IIBBA CONICET, Buenos Aires, Argentina
- * E-mail: (AZ); (WOD)
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28
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Karasov TL, Almario J, Friedemann C, Ding W, Giolai M, Heavens D, Kersten S, Lundberg DS, Neumann M, Regalado J, Neher RA, Kemen E, Weigel D. Arabidopsis thaliana and Pseudomonas Pathogens Exhibit Stable Associations over Evolutionary Timescales. Cell Host Microbe 2018; 24:168-179.e4. [PMID: 30001519 PMCID: PMC6054916 DOI: 10.1016/j.chom.2018.06.011] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 05/16/2018] [Accepted: 06/21/2018] [Indexed: 11/23/2022]
Abstract
Crop disease outbreaks are often associated with clonal expansions of single pathogenic lineages. To determine whether similar boom-and-bust scenarios hold for wild pathosystems, we carried out a multi-year, multi-site survey of Pseudomonas in its natural host Arabidopsis thaliana. The most common Pseudomonas lineage corresponded to a ubiquitous pathogenic clade. Sequencing of 1,524 genomes revealed this lineage to have diversified approximately 300,000 years ago, containing dozens of genetically identifiable pathogenic sublineages. There is differentiation at the level of both gene content and disease phenotype, although the differentiation may not provide fitness advantages to specific sublineages. The coexistence of sublineages indicates that in contrast to crop systems, no single strain has been able to overtake the studied A. thaliana populations in the recent past. Our results suggest that selective pressures acting on a plant pathogen in wild hosts are likely to be much more complex than those in agricultural systems.
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Affiliation(s)
- Talia L Karasov
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Juliana Almario
- Max Planck Research Group Fungal Biodiversity, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829 Cologne, Germany; Interfaculty Institute of Microbiology and Infection Medicine Tübingen, IMITP, University of Tübingen, 72076 Tübingen, Germany
| | - Claudia Friedemann
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Wei Ding
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Michael Giolai
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany; Earlham Institute, Norwich Research Park Innovation Centre, Colney Lane, Norwich NR4 7UZ, UK
| | - Darren Heavens
- Earlham Institute, Norwich Research Park Innovation Centre, Colney Lane, Norwich NR4 7UZ, UK
| | - Sonja Kersten
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Derek S Lundberg
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Manuela Neumann
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Julian Regalado
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Richard A Neher
- University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland
| | - Eric Kemen
- Max Planck Research Group Fungal Biodiversity, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829 Cologne, Germany; Interfaculty Institute of Microbiology and Infection Medicine Tübingen, IMITP, University of Tübingen, 72076 Tübingen, Germany
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.
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29
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Becraft ED, Woyke T, Jarett J, Ivanova N, Godoy-Vitorino F, Poulton N, Brown JM, Brown J, Lau MCY, Onstott T, Eisen JA, Moser D, Stepanauskas R. Rokubacteria: Genomic Giants among the Uncultured Bacterial Phyla. Front Microbiol 2017; 8:2264. [PMID: 29234309 PMCID: PMC5712423 DOI: 10.3389/fmicb.2017.02264] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 11/02/2017] [Indexed: 01/08/2023] Open
Abstract
Recent advances in single-cell genomic and metagenomic techniques have facilitated the discovery of numerous previously unknown, deep branches of the tree of life that lack cultured representatives. Many of these candidate phyla are composed of microorganisms with minimalistic, streamlined genomes lacking some core metabolic pathways, which may contribute to their resistance to growth in pure culture. Here we analyzed single-cell genomes and metagenome bins to show that the "Candidate phylum Rokubacteria," formerly known as SPAM, represents an interesting exception, by having large genomes (6-8 Mbps), high GC content (66-71%), and the potential for a versatile, mixotrophic metabolism. We also observed an unusually high genomic heterogeneity among individual Rokubacteria cells in the studied samples. These features may have contributed to the limited recovery of sequences of this candidate phylum in prior cultivation and metagenomic studies. Our analyses suggest that Rokubacteria are distributed globally in diverse terrestrial ecosystems, including soils, the rhizosphere, volcanic mud, oil wells, aquifers, and the deep subsurface, with no reports from marine environments to date.
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Affiliation(s)
- Eric D Becraft
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States
| | - Tanja Woyke
- Joint Genome Institute, Walnut Creek, CA, United States
| | | | | | - Filipa Godoy-Vitorino
- Department of Natural Sciences, Inter American University of Puerto Rico, San Juan, Puerto Rico
| | - Nicole Poulton
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States
| | - Julia M Brown
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States
| | - Joseph Brown
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States
| | - M C Y Lau
- Department of Geosciences, Princeton University, Princeton, NJ, United States
| | - Tullis Onstott
- Department of Geosciences, Princeton University, Princeton, NJ, United States
| | - Jonathan A Eisen
- College of Biological Sciences, Genome Center, University of California, Davis, Davis, CA, United States
| | - Duane Moser
- Desert Research Institute, Las Vegas, NV, United States
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30
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Lichtenberg EM, Mendenhall CD, Brosi B. Foraging traits modulate stingless bee community disassembly under forest loss. J Anim Ecol 2017; 86:1404-1416. [DOI: 10.1111/1365-2656.12747] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 08/07/2017] [Indexed: 11/28/2022]
Affiliation(s)
- Elinor M. Lichtenberg
- Department of Ecology and Evolutionary Biology University of Arizona Tucson AZ USA
- Department of Integrative Biology University of Texas at Austin Austin TX USA
| | - Chase D. Mendenhall
- Department of Biology Stanford University Stanford CA USA
- Center for Conservation Biology Stanford University Stanford CA USA
- The Nature Conservancy Arlington VA USA
| | - Berry Brosi
- Department of Environmental Studies Emory University Atlanta GA USA
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31
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Andreote FD, Pereira e Silva MDC. Microbial communities associated with plants: learning from nature to apply it in agriculture. Curr Opin Microbiol 2017; 37:29-34. [DOI: 10.1016/j.mib.2017.03.011] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 03/22/2017] [Indexed: 01/20/2023]
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32
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Evaluation of the reproducibility of amplicon sequencing with Illumina MiSeq platform. PLoS One 2017; 12:e0176716. [PMID: 28453559 PMCID: PMC5409056 DOI: 10.1371/journal.pone.0176716] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 04/15/2017] [Indexed: 12/12/2022] Open
Abstract
Illumina’s MiSeq has become the dominant platform for gene amplicon sequencing in microbial ecology studies; however, various technical concerns, such as reproducibility, still exist. To assess reproducibility, 16S rRNA gene amplicons from 18 soil samples of a reciprocal transplantation experiment were sequenced on an Illumina MiSeq. The V4 region of 16S rRNA gene from each sample was sequenced in triplicate with each replicate having a unique barcode. The average OTU overlap, without considering sequence abundance, at a rarefaction level of 10,323 sequences was 33.4±2.1% and 20.2±1.7% between two and among three technical replicates, respectively. When OTU sequence abundance was considered, the average sequence abundance weighted OTU overlap was 85.6±1.6% and 81.2±2.1% for two and three replicates, respectively. Removing singletons significantly increased the overlap for both (~1–3%, p<0.001). Increasing the sequencing depth to 160,000 reads by deep sequencing increased OTU overlap both when sequence abundance was considered (95%) and when not (44%). However, if singletons were not removed the overlap between two technical replicates (not considering sequence abundance) plateaus at 39% with 30,000 sequences. Diversity measures were not affected by the low overlap as α-diversities were similar among technical replicates while β-diversities (Bray-Curtis) were much smaller among technical replicates than among treatment replicates (e.g., 0.269 vs. 0.374). Higher diversity coverage, but lower OTU overlap, was observed when replicates were sequenced in separate runs. Detrended correspondence analysis indicated that while there was considerable variation among technical replicates, the reproducibility was sufficient for detecting treatment effects for the samples examined. These results suggest that although there is variation among technical replicates, amplicon sequencing on MiSeq is useful for analyzing microbial community structure if used appropriately and with caution. For example, including technical replicates, removing spurious sequences and unrepresentative OTUs, using a clustering method with a high stringency for OTU generation, estimating treatment effects at higher taxonomic levels, and adapting the unique molecular identifier (UMI) and other newly developed methods to lower PCR and sequencing error and to identify true low abundance rare species all can increase reproducibility.
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Lupatini M, Korthals GW, de Hollander M, Janssens TKS, Kuramae EE. Soil Microbiome Is More Heterogeneous in Organic Than in Conventional Farming System. Front Microbiol 2017; 7:2064. [PMID: 28101080 PMCID: PMC5209367 DOI: 10.3389/fmicb.2016.02064] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 12/07/2016] [Indexed: 11/17/2022] Open
Abstract
Organic farming system and sustainable management of soil pathogens aim at reducing the use of agricultural chemicals in order to improve ecosystem health. Despite the essential role of microbial communities in agro-ecosystems, we still have limited understanding of the complex response of microbial diversity and composition to organic and conventional farming systems and to alternative methods for controlling plant pathogens. In this study we assessed the microbial community structure, diversity and richness using 16S rRNA gene next generation sequences and report that conventional and organic farming systems had major influence on soil microbial diversity and community composition while the effects of the soil health treatments (sustainable alternatives for chemical control) in both farming systems were of smaller magnitude. Organically managed system increased taxonomic and phylogenetic richness, diversity and heterogeneity of the soil microbiota when compared with conventional farming system. The composition of microbial communities, but not the diversity nor heterogeneity, were altered by soil health treatments. Soil health treatments exhibited an overrepresentation of specific microbial taxa which are known to be involved in soil suppressiveness to pathogens (plant-parasitic nematodes and soil-borne fungi). Our results provide a comprehensive survey on the response of microbial communities to different agricultural systems and to soil treatments for controlling plant pathogens and give novel insights to improve the sustainability of agro-ecosystems by means of beneficial microorganisms.
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Affiliation(s)
- Manoeli Lupatini
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW)Wageningen, Netherlands
| | - Gerard W. Korthals
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW)Wageningen, Netherlands
| | - Mattias de Hollander
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW)Wageningen, Netherlands
| | - Thierry K. S. Janssens
- MicroLife SolutionsAmsterdam, Netherlands
- Department of Ecological Science, Vrije Universiteit AmsterdamAmsterdam, Netherlands
| | - Eiko E. Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW)Wageningen, Netherlands
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Trivedi P, Delgado-Baquerizo M, Anderson IC, Singh BK. Response of Soil Properties and Microbial Communities to Agriculture: Implications for Primary Productivity and Soil Health Indicators. FRONTIERS IN PLANT SCIENCE 2016; 7:990. [PMID: 27462326 PMCID: PMC4940416 DOI: 10.3389/fpls.2016.00990] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2015] [Accepted: 06/22/2016] [Indexed: 05/05/2023]
Abstract
Agricultural intensification is placing tremendous pressure on the soil's capacity to maintain its functions leading to large-scale ecosystem degradation and loss of productivity in the long term. Therefore, there is an urgent need to find early indicators of soil health degradation in response to agricultural management. In recent years, major advances in soil meta-genomic and spatial studies on microbial communities and community-level molecular characteristics can now be exploited as 'biomarker' indicators of ecosystem processes for monitoring and managing sustainable soil health under global change. However, a continental scale, cross biome approach assessing soil microbial communities and their functional potential to identify the unifying principles governing the susceptibility of soil biodiversity to land conversion is lacking. We conducted a meta-analysis from a dataset generated from 102 peer-reviewed publications as well as unpublished data to explore how properties directly linked to soil nutritional health (total C and N; C:N ratio), primary productivity (NPP) and microbial diversity and composition (relative abundance of major bacterial phyla determined by next generation sequencing techniques) are affected in response to agricultural management across the main biomes of Earth (arid, continental, temperate and tropical). In our analysis, we found strong statistical trends in the relative abundance of several bacterial phyla in agricultural (e.g., Actinobacteria and Chloroflexi) and natural (Acidobacteria, Proteobacteria, and Cyanobacteria) systems across all regions and these trends correlated well with many soil properties. However, main effects of agriculture on soil properties and productivity were biome-dependent. Our meta-analysis provides evidence on the predictable nature of the microbial community responses to vegetation type. This knowledge can be exploited in future for developing a new set of indicators for primary productivity and soil health.
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Affiliation(s)
- Pankaj Trivedi
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith South, NSWAustralia
- *Correspondence: Pankaj Trivedi,
| | - Manuel Delgado-Baquerizo
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith South, NSWAustralia
| | - Ian C. Anderson
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith South, NSWAustralia
| | - Brajesh K. Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith South, NSWAustralia
- Global Centre for Land Based Innovation, Western Sydney University, Penrith South, NSWAustralia
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Pyrosequencing reveals changes in soil bacterial communities after conversion of Yungas forests to agriculture. PLoS One 2015; 10:e0119426. [PMID: 25793893 PMCID: PMC4368548 DOI: 10.1371/journal.pone.0119426] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Accepted: 01/13/2015] [Indexed: 11/19/2022] Open
Abstract
The Southern Andean Yungas in Northwest Argentina constitute one of the main biodiversity hotspots in the world. Considerable changes in land use have taken place in this ecoregion, predominantly related to forest conversion to croplands, inducing losses in above-ground biodiversity and with potential impact on soil microbial communities. In this study, we used high-throughput pyrosequencing of the 16S ribosomal RNA gene to assess whether land-use change and time under agriculture affect the composition and diversity of soil bacterial communities. We selected two areas dedicated to sugarcane and soybean production, comprising both short- and long-term agricultural sites, and used the adjacent native forest soils as a reference. Land-use change altered the composition of bacterial communities, with differences between productive areas despite the similarities between both forests. At the phylum level, only Verrucomicrobia and Firmicutes changed in abundance after deforestation for sugarcane and soybean cropping, respectively. In cultivated soils, Verrucomicrobia decreased sharply (~80%), while Firmicutes were more abundant. Despite the fact that local diversity was increased in sugarcane systems and was not altered by soybean cropping, phylogenetic beta diversity declined along both chronosequences, evidencing a homogenization of soil bacterial communities over time. In spite of the detected alteration in composition and diversity, we found a core microbiome resistant to the disturbances caused by the conversion of forests to cultivated lands and few or none exclusive OTUs for each land-use type. The overall changes in the relative abundance of copiotrophic and oligotrophic taxa may have an impact in soil ecosystem functionality. However, communities with many taxa in common may also share many functional attributes, allowing to maintain at least some soil ecosystem services after forest conversion to croplands.
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