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Pu T, Zhang N, Wang J, Zhao Z, Tan W, Li C, Song Y. Organic management pattern improves microbial community diversity and alters microbial network structure in karst tea plantation. Heliyon 2024; 10:e31528. [PMID: 38826734 PMCID: PMC11141352 DOI: 10.1016/j.heliyon.2024.e31528] [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: 02/26/2024] [Revised: 05/16/2024] [Accepted: 05/17/2024] [Indexed: 06/04/2024] Open
Abstract
Soil microbiomes play a crucial role in enhancing plant growth, health, and overall agricultural productivity. Nevertheless, the influence of distinct agricultural management practices on the microbial diversity and community structure within tea (Camellia sinensis) plantations has remained enigmatic. This study postulates that organic agricultural management models can enhance microbial diversity and optimise the microbial community structure within tea plantations, indirectly augmenting soil fertility and tea quality. We employed metagenome technology and conducted molecular ecological network analysis to explore the impact of organic management, pollution-free management, and conventional management on the microbial network structure of tea plantation soil in Weng'an County in the southwestern karst region. Soils subjected to organic management exhibited a higher relative abundance of soil microbial and carbohydrate-active enzyme functional genes than those subjected to other management regimes. Additionally, the relative abundance and diversity of dominant bacteria and keystone species were notably higher under organic management than under the other management regimes. Correlation analysis showed that soil microorganisms were closely related to soil fertility and tea quality, respectively. One-way analysis of variance and the structural equation modelling results showed significant variability in soil fertility under the three agricultural management modes and that soil fertility and soil microbial diversity had a direct impact on tea quality (P > 0.05). In conclusion, this study underscores the profound impact of management modes on microbial diversity and community structure within tea plantations. These management practices alter the soil microbial network structure and potential function, ultimately regulating the microecological dynamics of the soil community in tea plantations.
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Affiliation(s)
- Tianyi Pu
- School of Karst Science, Guizhou Normal University/State Engineering Technology Institute for Karst Desertification Control, Guiyang, 550001, China
- Guizhou Provincial Key Laboratory for Rare Animal and Economic Insect of the Mountainous Region, Guiyang University, Guiyang, Guizhou, 550001, China
| | - Ni Zhang
- School of Karst Science, Guizhou Normal University/State Engineering Technology Institute for Karst Desertification Control, Guiyang, 550001, China
| | - Jinqiu Wang
- School of Karst Science, Guizhou Normal University/State Engineering Technology Institute for Karst Desertification Control, Guiyang, 550001, China
- Guizhou Provincial Key Laboratory for Rare Animal and Economic Insect of the Mountainous Region, Guiyang University, Guiyang, Guizhou, 550001, China
| | - Zhibing Zhao
- School of Karst Science, Guizhou Normal University/State Engineering Technology Institute for Karst Desertification Control, Guiyang, 550001, China
| | - Weiwen Tan
- School of Karst Science, Guizhou Normal University/State Engineering Technology Institute for Karst Desertification Control, Guiyang, 550001, China
- Guizhou Provincial Key Laboratory for Rare Animal and Economic Insect of the Mountainous Region, Guiyang University, Guiyang, Guizhou, 550001, China
| | - Can Li
- Guizhou Provincial Key Laboratory for Rare Animal and Economic Insect of the Mountainous Region, Guiyang University, Guiyang, Guizhou, 550001, China
| | - Yuehua Song
- School of Karst Science, Guizhou Normal University/State Engineering Technology Institute for Karst Desertification Control, Guiyang, 550001, China
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Benalcazar P, Seuradge B, Diochon AC, Kolka RK, Phillips LA. Conversion of boreal forests to agricultural systems: soil microbial responses along a land-conversion chronosequence. ENVIRONMENTAL MICROBIOME 2024; 19:32. [PMID: 38734653 PMCID: PMC11088160 DOI: 10.1186/s40793-024-00576-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 05/02/2024] [Indexed: 05/13/2024]
Abstract
BACKGROUND Boreal regions are warming at more than double the global average, creating opportunities for the northward expansion of agriculture. Expanding agricultural production in these regions will involve the conversion of boreal forests to agricultural fields, with cumulative impacts on soil microbial communities and associated biogeochemical cycling processes. Understanding the magnitude or rate of change that will occur with these biological processes will provide information that will enable these regions to be developed in a more sustainable manner, including managing carbon and nitrogen losses. This study, based in the southern boreal region of Canada where agricultural expansion has been occurring for decades, used a paired forest-adjacent agricultural field approach to quantify how soil microbial communities and functions were altered at three different stages post-conversion (< 10, > 10 and < 50, and > 50 years). Soil microbial functional capacity was assessed by quantitative PCR of genes associated with carbon (C), nitrogen, and phosphorous (P) cycling; microbial taxonomic diversity and community structure was assessed by amplicon sequencing. RESULTS Fungal alpha diversity did not change, but communities shifted from Basidiomycota to Ascomycota dominant within the first decade. Bacterial alpha diversity increased, with Gemmatimonadota groups generally increasing and Actinomycetota groups generally decreasing in agricultural soils. These altered communities led to altered functional capacity. Functional genes associated with nitrification and low molecular weight C cycling potential increased after conversion, while those associated with organic P mineralization potential decreased. Stable increases in most N cycling functions occurred within the first decade, but C cycling functions were still changing 50 years post conversion. CONCLUSIONS Microbial communities underwent a rapid shift in the first decade, followed by several decades of slower transition until stabilizing 50 years post conversion. Understanding how the microbial communities respond at different stages post-conversion improves our ability to predict C and N losses from emerging boreal agricultural systems, and provides insight into how best to manage these soils in a way that is sustainable at the local level and within a global context.
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Affiliation(s)
- Paul Benalcazar
- Faculty of Natural Resources Management, Lakehead University, Thunder Bay, ON, Canada
| | - Brent Seuradge
- Agriculture and Agri-Food Canada, Harrow Research and Development Centre, Harrow, ON, Canada
| | - Amanda C Diochon
- Department of Geology, Lakehead University, Thunder Bay, ON, Canada
| | - Randall K Kolka
- USDA Forest Services Northern Research Station, Grand Rapid, MN, 55744, USA
| | - Lori A Phillips
- Agriculture and Agri-Food Canada, Harrow Research and Development Centre, Harrow, ON, Canada.
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Wentzien NM, Fernández-González AJ, Villadas PJ, Valverde-Corredor A, Mercado-Blanco J, Fernández-López M. Thriving beneath olive trees: The influence of organic farming on microbial communities. Comput Struct Biotechnol J 2023; 21:3575-3589. [PMID: 37520283 PMCID: PMC10372477 DOI: 10.1016/j.csbj.2023.07.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 07/11/2023] [Accepted: 07/11/2023] [Indexed: 08/01/2023] Open
Abstract
Soil health and root-associated microbiome are interconnected factors involved in plant health. The use of manure amendment on agricultural fields exerts a direct benefit on soil nutrient content and water retention, among others. However, little is known about the impact of manure amendment on the root-associated microbiome, particularly in woody species. In this study, we aimed to evaluate the effects of ovine manure on the microbial communities of the olive rhizosphere and root endosphere. Two adjacent orchards subjected to conventional (CM) and organic (OM) management were selected. We used metabarcoding sequencing to assess the bacterial and fungal communities. Our results point out a clear effect of manure amendment on the microbial community. Fungal richness and diversity were increased in the rhizosphere. The fungal biomass in the rhizosphere was more than doubled, ranging from 1.72 × 106 ± 1.62 × 105 (CM) to 4.54 × 106 ± 8.07 × 105 (OM) copies of the 18 S rRNA gene g-1 soil. Soil nutrient content was also enhanced in the OM orchard. Specifically, oxidable organic matter, total nitrogen, nitrate, phosphorous, potassium and sulfate concentrations were significantly increased in the OM orchard. Moreover, we predicted a higher abundance of bacteria in OM with metabolic functions involved in pollutant degradation and defence against pathogens. Lastly, microbial co-occurrence network showed more positive interactions, complexity and shorter geodesic distance in the OM orchard. According to our results, manure amendment on olive orchards represents a promising tool for positively modulating the microbial community in direct contact with the plant.
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Affiliation(s)
- Nuria M. Wentzien
- Soil and Plant Microbiology Department, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), 18008 Granada, Spain
| | - Antonio J. Fernández-González
- Soil and Plant Microbiology Department, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), 18008 Granada, Spain
| | - Pablo J. Villadas
- Soil and Plant Microbiology Department, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), 18008 Granada, Spain
| | | | - Jesús Mercado-Blanco
- Soil and Plant Microbiology Department, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), 18008 Granada, Spain
- Crop Protection Department, Instituto de Agricultura Sostenible (CSIC), 14004 Córdoba, Spain
| | - Manuel Fernández-López
- Soil and Plant Microbiology Department, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), 18008 Granada, Spain
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Soares-Castro P, Soares F, Reis F, Lino-Neto T, Santos PM. Bioprospection of the bacterial β-myrcene-biotransforming trait in the rhizosphere. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12650-w. [PMID: 37405434 PMCID: PMC10386936 DOI: 10.1007/s00253-023-12650-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 06/06/2023] [Accepted: 06/16/2023] [Indexed: 07/06/2023]
Abstract
The biocatalysis of β-myrcene into value-added compounds, with enhanced organoleptic/therapeutic properties, may be performed by resorting to specialized enzymatic machinery of β-myrcene-biotransforming bacteria. Few β-myrcene-biotransforming bacteria have been studied, limiting the diversity of genetic modules/catabolic pathways available for biotechnological research. In our model Pseudomonas sp. strain M1, the β-myrcene catabolic core-code was identified in a 28-kb genomic island (GI). The lack of close homologs of this β-myrcene-associated genetic code prompted a bioprospection of cork oak and eucalyptus rhizospheres, from 4 geographic locations in Portugal, to evaluate the environmental diversity and dissemination of the β-myrcene-biotransforming genetic trait (Myr+). Soil microbiomes were enriched in β-myrcene-supplemented cultures, from which β-myrcene-biotransforming bacteria were isolated, belonging to Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, and Sphingobacteriia classes. From a panel of representative Myr+ isolates that included 7 bacterial genera, the production of β-myrcene derivatives previously reported in strain M1 was detected in Pseudomonas spp., Cupriavidus sp., Sphingobacterium sp., and Variovorax sp. A comparative genomics analysis against the genome of strain M1 found the M1-GI code in 11 new Pseudomonas genomes. Full nucleotide conservation of the β-myrcene core-code was observed throughout a 76-kb locus in strain M1 and all 11 Pseudomonas spp., resembling the structure of an integrative and conjugative element (ICE), despite being isolated from different niches. Furthermore, the characterization of isolates not harboring the Myr+-related 76-kb locus suggested that they may biotransform β-myrcene via alternative catabolic loci, being thereby a novel source of enzymes and biomolecule catalogue for biotechnological exploitation. KEY POINTS: • The isolation of 150 Myr+ bacteria hints the ubiquity of such trait in the rhizosphere. • The Myr+ trait is spread across different bacterial taxonomic classes. • The core-code for the Myr+ trait was detected in a novel ICE, only found in Pseudomonas spp.
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Affiliation(s)
- Pedro Soares-Castro
- CBMA - Centre of Molecular and Environmental Biology, University of Minho, Campus de Gualtar, Braga, Portugal
- Faculdade de Medicina, Instituto de Medicina Molecular, Universidade de Lisboa, Av. Prof. Egas Moniz, Lisbon, Portugal
| | - Filipa Soares
- CBMA - Centre of Molecular and Environmental Biology, University of Minho, Campus de Gualtar, Braga, Portugal
| | - Francisca Reis
- CBMA - Centre of Molecular and Environmental Biology, University of Minho, Campus de Gualtar, Braga, Portugal
| | - Teresa Lino-Neto
- CBMA - Centre of Molecular and Environmental Biology, University of Minho, Campus de Gualtar, Braga, Portugal
| | - Pedro M Santos
- CBMA - Centre of Molecular and Environmental Biology, University of Minho, Campus de Gualtar, Braga, Portugal.
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Kalntremtziou M, Papaioannou IA, Vangalis V, Polemis E, Pappas KM, Zervakis GI, Typas MA. Evaluation of the lignocellulose degradation potential of Mediterranean forests soil microbial communities through diversity and targeted functional metagenomics. Front Microbiol 2023; 14:1121993. [PMID: 36922966 PMCID: PMC10008878 DOI: 10.3389/fmicb.2023.1121993] [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: 12/12/2022] [Accepted: 01/31/2023] [Indexed: 02/28/2023] Open
Abstract
The enzymatic arsenal of several soil microorganisms renders them particularly suitable for the degradation of lignocellulose, a process of distinct ecological significance with promising biotechnological implications. In this study, we investigated the spatiotemporal diversity and distribution of bacteria and fungi with 16S and Internally Trascribed Spacer (ITS) ribosomal RNA next-generation-sequencing (NGS), focusing on forest mainland Abies cephalonica and insular Quercus ilex habitats of Greece. We analyzed samples during winter and summer periods, from different soil depths, and we applied optimized and combined targeted meta-omics approaches aiming at the peroxidase-catalase family enzymes to gain insights into the lignocellulose degradation process at the soil microbial community level. The microbial communities recorded showed distinct patterns of response to season, soil depth and vegetation type. Overall, in both forests Proteobacteria, Actinobacteria, Acidobacteria were the most abundant bacteria phyla, while the other phyla and the super-kingdom of Archaea were detected in very low numbers. Members of the orders Agaricales, Russulales, Sebacinales, Gomphales, Geastrales, Hysterangiales, Thelephorales, and Trechisporales (Basidiomycota), and Pezizales, Sordariales, Eurotiales, Pleosporales, Helotiales, and Diaporthales (Ascomycota) were the most abundant for Fungi. By using optimized "universal" PCR primers that targeted the peroxidase-catalase enzyme family, we identified several known and novel sequences from various Basidiomycota, even from taxa appearing at low abundance. The majority of the sequences recovered were manganese peroxidases from several genera of Agaricales, Hysterangiales, Gomphales, Geastrales, Russulales, Hymenochaetales, and Trechisporales, while lignin -and versatile-peroxidases were limited to two to eight species, respectively. Comparisons of the obtained sequences with publicly available data allowed a detailed structural analysis of polymorphisms and functionally relevant amino-acid residues at phylogenetic level. The targeted metagenomics applied here revealed an important role in lignocellulose degradation of hitherto understudied orders of Basidiomycota, such as the Hysterangiales and Gomphales, while it also suggested the auxiliary activity of particular members of Proteobacteria, Actinobacteria, Acidobacteria, Verrucomicrobia, and Gemmatimonadetes. The application of NGS-based metagenomics approaches allows a better understanding of the complex process of lignocellulolysis at the microbial community level as well as the identification of candidate taxa and genes for targeted functional investigations and genetic modifications.
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Affiliation(s)
- Maria Kalntremtziou
- Department of Genetics and Biotechnology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Ioannis A Papaioannou
- Zentrum für Molekulare Biologie der Universität Heidelberg, ZMBH, University of Heidelberg, Heidelberg, Germany
| | - Vasileios Vangalis
- Department of Genetics and Biotechnology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Elias Polemis
- Laboratory of General and Agricultural Microbiology, Agricultural University of Athens, Athens, Greece
| | - Katherine M Pappas
- Department of Genetics and Biotechnology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Georgios I Zervakis
- Laboratory of General and Agricultural Microbiology, Agricultural University of Athens, Athens, Greece
| | - Milton A Typas
- Department of Genetics and Biotechnology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
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Bora SS, Naorem RS, Hazarika DJ, Dasgupta A, Churaman A, Gogoi M, Barooah M. Agricultural Land Use Influences Bacteriophage Community Diversity, Richness, and Heterogeneity. Curr Microbiol 2022; 80:10. [PMID: 36445553 DOI: 10.1007/s00284-022-03129-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 11/23/2022] [Indexed: 11/30/2022]
Abstract
The last two decades have witnessed a large-scale conversion of crop cultivation areas into small and mid-sized tea plantations in Assam, India. Agricultural land-use pattern positively or negatively influences native hydrology and above- and belowground biodiversity. Very little is known about the effect of agricultural land-use patterns on the soil virus (especially, bacteriophage) community structure and function. This metagenomic-based study evaluated the rhizosphere viral community structure of three interlinked cultivation areas, viz., mixed cropping area (coded as CP1), tea-seed orchard (CP2), and monocropping tea cultivation (CP3). The bacteriophages belonged to four major classes with the dominance of Malgrandaviricetes (CP1: 79.37%; CP2: 64.62%; CP3: 4.85%) followed by Caudoviricetes (CP1: 20.49%; CP2: 35.22%; CP3: 90.29%), Faserviricetes (CP1: 0.03%; CP2: 0.08%; CP3: 3.88%), and Tectiliviricetes (CP1: 0.12%; CP2: 0.07%; CP3: 0.97%). Microviruses dominated the phage population in both CP1 and CP2, representing 79.35% and 64.59% of total bacteriophage abundance. Both CP1 and CP2 had higher bacteriophage richness (species richness, R in CP1: 65; R in CP2: 66) and lower evenness (Pielou's evenness index, J in CP1: 0.531; J in CP2: 0.579) compared to the CP3 (R: 30; J: 0.902). Principal component analysis of edaphic soil factors and bacteriophage community structure showed a reverse-proportional correlation between the levels of Al saturation, and exchangeable Al3+ ions with that of soil pH, and bacteriophage abundance. Our study indicates that monocropping tea cultivation soil bears less viral richness, abundance, and heterogeneity.
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Affiliation(s)
- Sudipta Sankar Bora
- DBT-North East Centre for Agricultural Biotechnology (DBT-NECAB), Assam Agricultural University, Jorhat, Assam, India
| | - Romen Singh Naorem
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
| | - Dibya Jyoti Hazarika
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
| | - Abhisek Dasgupta
- DBT-North East Centre for Agricultural Biotechnology (DBT-NECAB), Assam Agricultural University, Jorhat, Assam, India
| | - Amrita Churaman
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
| | - Manuranjan Gogoi
- Department of Tea Husbandry and Technology, Assam Agricultural University, Jorhat, Assam, India
| | - Madhumita Barooah
- DBT-North East Centre for Agricultural Biotechnology (DBT-NECAB), Assam Agricultural University, Jorhat, Assam, India. .,Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India.
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Fulazzaky MA, Ismail I, Harlen H, Sukendi S, Roestamy M, Siregar YI. Evaluation of change in the peat soil properties affected by different fire severities. ENVIRONMENTAL MONITORING AND ASSESSMENT 2022; 194:783. [PMID: 36098855 DOI: 10.1007/s10661-022-10430-z] [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: 04/05/2022] [Accepted: 08/30/2022] [Indexed: 06/15/2023]
Abstract
The tropical peatland ecosystems of Indonesia provide direct economic benefits to local communities and act to maintain local weather patterns. The impact of burning tropical peat swamp forests of land clearing for palm oil plantations can have significant consequences on the change in the characteristics of peat soil. The aim of this study was to determine the physical, chemical, and biological properties of peat soils by field and laboratory testing and analysis to understand changes in the nature and characteristics of peatlands at four locations in the Pelalawan Regency of Riau Province. The results showed that the effect of burning peat swamp forests can lead to a change in the physical, chemical, and biological properties of the peat soils. Soil permeability and the soil microbial population can significantly decrease with increasing fire severity. The effect of different fire severities on the characteristics of peat soil is verified to contribute to advanced management of the tropical peatland in the future.
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Affiliation(s)
- Mohamad Ali Fulazzaky
- School of Postgraduate Studies, Universitas Djuanda, Jalan Tol Ciawi No. 1, Ciawi, Bogor, 16720, Indonesia.
- School of Civil Engineering, Faculty of Engineering, Universiti Teknologi Malaysia, 81310 UTM, Skudai, Johor Bahru, Malaysia.
| | - Ibrahim Ismail
- Postgraduate School of Environmental Science, Universitas Riau, Jalan Pattimura No. 9, Gobah Pekanbaru 28125, Riau, Indonesia
| | - Harlen Harlen
- Faculty of Economics, Universitas Riau, Jalan Pattimura No. 9, Gobah, 28125, Riau, Indonesia
| | - Sukendi Sukendi
- Faculty of Economics, Universitas Riau, Jalan Pattimura No. 9, Gobah, 28125, Riau, Indonesia
| | - Martin Roestamy
- School of Postgraduate Studies, Universitas Djuanda, Jalan Tol Ciawi No. 1, Ciawi, Bogor, 16720, Indonesia
| | - Yusni Ikhwan Siregar
- Faculty of Fishery and Marine, Universitas Riau, Jalan Pattimura No. 9, Gobah, 28125, Riau, Indonesia
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Brooks L, Subramanian S, Dranow DM, Mayclin SJ, Myler PJ, Asojo OA. Crystal structures of glutamyl-tRNA synthetase from Elizabethkingia anopheles and E. meningosepticum. Acta Crystallogr F Struct Biol Commun 2022; 78:306-312. [PMID: 35924598 PMCID: PMC9350836 DOI: 10.1107/s2053230x22007555] [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: 05/26/2022] [Accepted: 07/25/2022] [Indexed: 11/24/2022] Open
Abstract
Elizabethkingia bacteria cause opportunistic infections in neonates, the elderly and the immunocompromised with mortality rates of up to 40%. The high-resolution structures of glutamyl-tRNA synthetase (GluRS) from E. meningosepticum and E. anopheles reveal similarities to bacterial GluRSs that can be exploited to accelerate rational drug discovery for these globally important emerging infectious Gram-negative bacteria. Elizabethkingia bacteria are globally emerging pathogens that cause opportunistic and nosocomial infections, with up to 40% mortality among the immunocompromised. Elizabethkingia species are in the pipeline of organisms for high-throughput structural analysis at the Seattle Structural Genomics Center for Infectious Disease (SSGCID). These efforts include the structure–function analysis of potential therapeutic targets. Glutamyl-tRNA synthetase (GluRS) is essential for tRNA aminoacylation and is under investigation as a bacterial drug target. The SSGCID produced, crystallized and determined high-resolution structures of GluRS from E. meningosepticum (EmGluRS) and E. anopheles (EaGluRS). EmGluRS was co-crystallized with glutamate, while EaGluRS is an apo structure. EmGluRS shares ∼97% sequence identity with EaGluRS but less than 39% sequence identity with any other structure in the Protein Data Bank. EmGluRS and EaGluRS have the prototypical bacterial GluRS topology. EmGluRS and EaGluRS have similar binding sites and tertiary structures to other bacterial GluRSs that are promising drug targets. These structural similarities can be exploited for drug discovery.
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Singh U, Choudhary AK, Sharma S. A 3-year field study reveals that agri-management practices drive the dynamics of dominant bacterial taxa in the rhizosphere of Cajanus cajan. Symbiosis 2022. [DOI: 10.1007/s13199-022-00834-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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10
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Gray DB, Gagnon V, Button M, Farooq AJ, Patch DJ, Wallace SJ, Koch I, O'Carroll DM, Weber KP. Silver nanomaterials released from commercial textiles have minimal impacts on soil microbial communities at environmentally relevant concentrations. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 806:151248. [PMID: 34715213 DOI: 10.1016/j.scitotenv.2021.151248] [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: 07/08/2021] [Revised: 09/30/2021] [Accepted: 10/22/2021] [Indexed: 06/13/2023]
Abstract
Silver nanomaterials (Ag NMs) have been used in a variety of commercial products to take advantage of their antimicrobial properties. However, there are concerns that these AgNMs can be released during/after use and enter wastewater streams, potentially impacting aquatic systems or accumulating in wastewater biosolids. Biosolids, which are a residual of wastewater treatment processes, have been found to contain AgNMs and are frequently used as agricultural fertilizer. Since the function of soil microbial communities is imperative to nutrient cycling and agricultural productivity, it is important to characterize and assess the effects that silver nanomaterials could have in agricultural soils. In this study agricultural soil was amended with pristine engineered (PVP-coated or uncoated AgNMs), aged silver (sulphidized or released from textiles) nanomaterials, and ionic silver to determine the fate and toxicity over the course of three months. Exposures were carried out at various environmentally relevant concentrations (1 and 10 mg Ag/kg soil) representing between 30 to over 800 years of equivalent biosolid loadings. Over thirteen different methodologies and measures were used throughout this study to assess for potential effects of the silver nanomaterials on soil, including microbial community composition, average well colour development (AWCD) and enzymatic activity. Overall, the AgNM exposures did not exhibit significant toxic effects to the soil microbial communities in terms of density, activity, function and diversity. However, the positive ionic silver treatment (100 mg Ag/kg soil) resulted in suppression to microbial activity while also resulting in significantly higher populations of Frankia alni (nitrogen-fixer) and Arenimonas malthae (phytopathogen) as compared to the negative control (p < 0.05, Tukey HSD) which warrants further investigation.
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Affiliation(s)
- Devon B Gray
- Environmental Sciences Group, Department of Chemistry and Chemical Engineering, Royal Military College of Canada, Kingston, ON K7K 7B4, Canada
| | - Vincent Gagnon
- Environmental Sciences Group, Department of Chemistry and Chemical Engineering, Royal Military College of Canada, Kingston, ON K7K 7B4, Canada
| | - Mark Button
- Environmental Sciences Group, Department of Chemistry and Chemical Engineering, Royal Military College of Canada, Kingston, ON K7K 7B4, Canada; Fipke Laboratory for Trace Element Research, University of British Columbia Okanagan, Kelowna, V1V 1V7, British Columbia, Canada
| | - Anbareen J Farooq
- Environmental Sciences Group, Department of Chemistry and Chemical Engineering, Royal Military College of Canada, Kingston, ON K7K 7B4, Canada
| | - David J Patch
- Environmental Sciences Group, Department of Chemistry and Chemical Engineering, Royal Military College of Canada, Kingston, ON K7K 7B4, Canada
| | - Sarah J Wallace
- Environmental Sciences Group, Department of Chemistry and Chemical Engineering, Royal Military College of Canada, Kingston, ON K7K 7B4, Canada
| | - Iris Koch
- Environmental Sciences Group, Department of Chemistry and Chemical Engineering, Royal Military College of Canada, Kingston, ON K7K 7B4, Canada
| | - Denis M O'Carroll
- School of Civil and Environmental Engineering, UNSW Water Research Laboratory, University of New South Wales Sydney, Manly Vale, NSW 2093, Australia
| | - Kela P Weber
- Environmental Sciences Group, Department of Chemistry and Chemical Engineering, Royal Military College of Canada, Kingston, ON K7K 7B4, Canada.
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Cork Oak Forests Soil Bacteria: Potential for Sustainable Agroforest Production. Microorganisms 2021; 9:microorganisms9091973. [PMID: 34576868 PMCID: PMC8472395 DOI: 10.3390/microorganisms9091973] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Revised: 09/09/2021] [Accepted: 09/14/2021] [Indexed: 11/18/2022] Open
Abstract
Plant growth promoting rhizobacteria (PGPR) are in increasing demand due to their role in promoting sustainable practices, not only in agriculture but also in forestry. Keeping in mind the future application of PGPR for increasing cork oak sustainability, the aim of this study was to find cork oak PGPR isolates with increased nutrient solubilisation traits, able to promote root morphological changes and/or antagonize cork oak bark phytopathogens. Soils from three cork oak forests with distinct bioclimates (humid, semi-humid and semi-arid) were used for isolating bacteria. From the 7634 colony-forming units, 323 bacterial isolates were biochemically assayed for PGPR traits (siderophores production, phosphate solubilizing and organic acids production), and 51 were found to display all these traits. These PGPR were able to induce root morphological changes on Arabidopsis thaliana, like suppression of primary root growth, increase of lateral roots or root hairs formation. However, the most proficient PGPR displayed specific ability in changing a single root morphological trait. This ability was related not only to bacterial genotype, but also with the environment where bacteria thrived and isolation temperature. Bacteria from semi-arid environments (mainly Bacillus megaterium isolates) could hold a promising tool to enhance plant development. Other isolates (Serratia quinivorens or B. cereus) could be further explored for biocontrol purposes.
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Global Change and Forest Disturbances in the Mediterranean Basin: Breakthroughs, Knowledge Gaps, and Recommendations. FORESTS 2021. [DOI: 10.3390/f12050603] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Forest ecosystems in the Mediterranean Basin are mostly situated in the north of the Basin (mesic). In the most southern and dry areas, the forest can only exist where topography and/or altitude favor a sufficient availability of water to sustain forest biomass. We have conducted a thorough review of recent literature (2000–2021) that clearly indicates large direct and indirect impacts of increasing drought conditions on the forests of the Mediterranean Basin, their changes in surface and distribution areas, and the main impacts they have suffered. We have focused on the main trends that emerge from the current literature and have highlighted the main threatens and management solution for the maintenance of these forests. The results clearly indicate large direct and indirect impacts of increasing drought conditions on the forests of the Mediterranean Basin. These increasing drought conditions together with over-exploitation, pest expansion, fire and soil degradation, are synergistically driving to forest regression and dieback in several areas of this Mediterranean Basin. These environmental changes have triggered responses in tree morphology, physiology, growth, reproduction, and mortality. We identified at least seven causes of the changes in the last three decades that have led to the current situation and that can provide clues for projecting the future of these forests: (i) The direct effect of increased aridity due to more frequent and prolonged droughts, which has driven Mediterranean forest communities to the limit of their capacity to respond to drought and escape to wetter sites, (ii) the indirect effects of drought, mainly by the spread of pests and fires, (iii) the direct and indirect effects of anthropogenic activity associated with general environmental degradation, including soil degradation and the impacts of fire, species invasion and pollution, (iv) human pressure and intense management of water resources, (v) agricultural land abandonment in the northern Mediterranean Basin without adequate management of new forests, (vi) very high pressure on forested areas of northern Africa coupled with the demographic enhancement, the expansion of crops and higher livestock pressure, and the more intense and overexploitation of water resources uses on the remaining forested areas, and (vii) scarcity and inequality of human management and policies, depending on the national and/or regional governments and agencies, being unable to counteract the previous changes. We identified appropriate measures of management intervention, using the most adequate techniques and processes to counteract these impacts and thus to conserve the health, service capacity, and biodiversity of Mediterranean forests. Future policies should, moreover, promote research to improve our knowledge of the mechanisms of, and the effects on, nutrient and carbon plant-soil status concurrent with the impacts of aridity and leaching due to the effects of current changes. Finally, we acknowledge the difficulty to obtain an accurate quantification of the impacts of increasing aridity rise that warrants an urgent investment in more focused research to further develop future tools in order to counteract the negative effects of climate change on Mediterranean forests.
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Griggs RG, Steenwerth KL, Mills DA, Cantu D, Bokulich NA. Sources and Assembly of Microbial Communities in Vineyards as a Functional Component of Winegrowing. Front Microbiol 2021; 12:673810. [PMID: 33927711 PMCID: PMC8076609 DOI: 10.3389/fmicb.2021.673810] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 03/22/2021] [Indexed: 01/05/2023] Open
Abstract
Microbiomes are integral to viticulture and winemaking – collectively termed winegrowing – where diverse fungi and bacteria can exert positive and negative effects on grape health and wine quality. Wine is a fermented natural product, and the vineyard serves as a key point of entry for quality-modulating microbiota, particularly in wine fermentations that are conducted without the addition of exogenous yeasts. Thus, the sources and persistence of wine-relevant microbiota in vineyards critically impact its quality. Site-specific variations in microbiota within and between vineyards may contribute to regional wine characteristics. This includes distinctions in microbiomes and microbiota at the strain level, which can contribute to wine flavor and aroma, supporting the role of microbes in the accepted notion of terroir as a biological phenomenon. Little is known about the factors driving microbial biodiversity within and between vineyards, or those that influence annual assembly of the fruit microbiome. Fruit is a seasonally ephemeral, yet annually recurrent product of vineyards, and as such, understanding the sources of microbiota in vineyards is critical to the assessment of whether or not microbial terroir persists with inter-annual stability, and is a key factor in regional wine character, as stable as the geographic distances between vineyards. This review examines the potential sources and vectors of microbiota within vineyards, general rules governing plant microbiome assembly, and how these factors combine to influence plant-microbe interactions relevant to winemaking.
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Affiliation(s)
- Reid G Griggs
- Department of Viticulture and Enology, Robert Mondavi Institute for Wine and Food Science, University of California, Davis, Davis, CA, United States
| | - Kerri L Steenwerth
- USDA-ARS, Crops Pathology and Genetics Research Unit, Department of Land, Air and Water Resources, University of California, Davis, Davis, CA, United States
| | - David A Mills
- Department of Viticulture and Enology, Robert Mondavi Institute for Wine and Food Science, University of California, Davis, Davis, CA, United States.,Department of Food Science and Technology, Robert Mondavi Institute for Wine and Food Science, University of California, Davis, Davis, CA, United States.,Foods for Health Institute, University of California, Davis, Davis, CA, United States
| | - Dario Cantu
- Department of Viticulture and Enology, Robert Mondavi Institute for Wine and Food Science, University of California, Davis, Davis, CA, United States
| | - Nicholas A Bokulich
- Laboratory of Food Systems Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
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14
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Gong X, Shi J, Zhou X, Yuan T, Gao D, Wu F. Crop Rotation With Cress Increases Cucumber Yields by Regulating the Composition of the Rhizosphere Soil Microbial Community. Front Microbiol 2021; 12:631882. [PMID: 33776961 PMCID: PMC7994511 DOI: 10.3389/fmicb.2021.631882] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Accepted: 02/23/2021] [Indexed: 12/30/2022] Open
Abstract
Paddy-upland rotation is an effective agricultural management practice for alleviating soil sickness. However, the effect of varying degrees of flooding on the soil microbial community and crop performance remains unclear. We conducted a pot experiment to determine the effects of two soil water content (SWC) and two flooding durations on the soil microbial community attributes and yield in cucumber. In the pot experiment, cucumber was rotated with cress single (45 days) or double (90 days) under 100 or 80% SWC. Then, the soil microbial were inoculated into sterilized soil to verified the relationship between cucumber growth and microorganisms. The results indicated single cress rotation resulted in a higher cucumber yield than double cress rotation and control. Cress rotation under 80% SWC had higher soil microbial diversity than cress rotation under 100% SWC and control. Flooding duration and SWC led to differences in the structure of soil microbial communities. Under 80% SWC, single cress rotation increased the relative abundance of potentially beneficial microorganisms, including Roseiflexus and Pseudallescheria spp., in cucumber rhizosphere. Under 100% SWC, single cress rotation increased the relative abundance of potentially beneficial bacteria, such as Haliangium spp., and decreased potential pathogenic fungi, such as Fusarium and Monographella spp., compared with double cress rotation and control. Varying degrees of flooding were causing the difference in diversity, structure and composition of soil microbial communities in the cucumber rhizosphere, which have a positive effect on cucumber growth and development.
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Affiliation(s)
- Xiaoya Gong
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin, China.,College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Jibo Shi
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin, China.,College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Xingang Zhou
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin, China.,College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Tao Yuan
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin, China.,College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Danmei Gao
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin, China.,College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Fengzhi Wu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin, China.,College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
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15
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Radu E, Woegerbauer M, Rab G, Oismüller M, Strauss P, Hufnagl P, Gottsberger RA, Krampe J, Weyermair K, Kreuzinger N. Resilience of agricultural soils to antibiotic resistance genes introduced by agricultural management practices. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 756:143699. [PMID: 33307498 DOI: 10.1016/j.scitotenv.2020.143699] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 10/11/2020] [Accepted: 11/01/2020] [Indexed: 06/12/2023]
Abstract
Antimicrobial resistance (AR) represents a global threat in human and veterinary medicine. In that regard, AR proliferation and dissemination in agricultural soils after manure application raises concerns on the enrichment of endogenous soil bacterial population with allochthonous antibiotic resistance genes (ARGs). Natural resilience of agricultural soils and background concentrations of ARGs play key roles in the mitigation of AR propagation in natural environments. In the present study, we carried out a longitudinal sampling campaign for two crop vegetation periods to monitor spatial and temporal changes in the abundance of seven clinically relevant ARGs (sul1, ermB, vanA, aph(3')-IIa, aph(3')-IIIa, blaTEM-1 and tet(W)) and ribosomal 16S RNA. The absolute and relative abundances of the selected ARGs were quantified in total community DNA extracted from agricultural (manured and non-manured) and forest soils, fresh pig faeces and manure slurry. We observed that ARG concentrations return to background levels after manure-induced exposure within a crop growing season, highlighting the resilience capacity of soil. Naturally occurring high background concentrations of ARGs can be found in forest soil in due distance under low anthropogenic influences. It was observed that pesticide application increases the concentrations of three out of seven ARGs tested (ermB, aph(3')-IIIa and tet(W)). Moreover, we noticed that the absolute abundances of sul1, vanA, ermB and blaTEM-1 resistance genes show an increase by 100- to 10,000- fold, from maturation of fresh pig faeces to manure. Outcomes of our study suggest that agricultural soil environments show a strong capacity to alleviate externally induced disturbances in endogenous ARG concentrations. Naturally occurring high concentrations of ARGs are present also in low human impacted environments represented by the indigenous resistome.
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Affiliation(s)
- Elena Radu
- Institute for Water Quality and Resource Management, University of Technology Vienna, Austria; Austrian Agency for Health and Food Safety AGES, Division of Data, Statistics and Risk Assessment, Department for Integrative Risk Assessment, Vienna, Austria; Institute of Virology Stefan S. Nicolau, Romanian Academy of Science, Bucharest, Romania.
| | - Markus Woegerbauer
- Austrian Agency for Health and Food Safety AGES, Division of Data, Statistics and Risk Assessment, Department for Integrative Risk Assessment, Vienna, Austria
| | - Gerhard Rab
- Institute of Hydraulic Engineering and Water Resources Management, University of Technology Vienna, Austria; Institute for Land and Water Management Research, Federal Agency for Water Management, Petzenkirchen, Austria
| | - Matthias Oismüller
- Institute of Hydraulic Engineering and Water Resources Management, University of Technology Vienna, Austria; Institute for Land and Water Management Research, Federal Agency for Water Management, Petzenkirchen, Austria
| | - Peter Strauss
- Institute for Land and Water Management Research, Federal Agency for Water Management, Petzenkirchen, Austria
| | - Peter Hufnagl
- Austrian Agency for Health and Food Safety AGES, Department for Medical Microbiology and Hygiene, Vienna, Austria
| | - Richard A Gottsberger
- Austrian Agency for Health and Food Safety AGES, Department for Molecular Diagnostic of Plant Diseases, Vienna, Austria
| | - Jörg Krampe
- Institute for Water Quality and Resource Management, University of Technology Vienna, Austria
| | - Karin Weyermair
- Austrian Agency for Health and Food Safety AGES, Division of Data, Statistics and Risk Assessment, Department of Statistics and Analytical Epidemiology, Graz, Austria
| | - Norbert Kreuzinger
- Institute for Water Quality and Resource Management, University of Technology Vienna, Austria
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16
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Bioremediation of hydrocarbon-contaminated soil from Carlini Station, Antarctica: effectiveness of different nutrient sources as biostimulation agents. Polar Biol 2021. [DOI: 10.1007/s00300-020-02787-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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17
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Influence of Acacia mangium on Soil Fertility and Bacterial Community in Eucalyptus Plantations in the Congolese Coastal Plains. SUSTAINABILITY 2020. [DOI: 10.3390/su12218763] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Productivity and sustainability of tropical forest plantations greatly rely on regulation of ecosystem functioning and nutrient cycling, i.e., the link between plant growth, nutrient availability, and the microbial community structure. So far, these interactions have never been evaluated in the Acacia and Eucalyptus forest planted on infertile soils in the Congolese coastal plains. In the present work, the soil bacterial community has been investigated by metabarcoding of the 16S rRNA bacterial gene in different stands of monoculture and mixed-species plantation to evaluate the potential of nitrogen-fixing trees on nutrient and bacterial structure. At the phylum level, the soil bacterial community was dominated by Actinobacteria, followed by Proteobacteria, Firmicutes, and Acidobacteria. A principal coordinate analysis revealed that bacterial communities from pure Eucalyptus, compared to those from plantations containing Acacia in pure and mixed-species stands, showed different community composition (beta-diversity). Regardless of the large variability of the studied soils, the prevalence of Firmicutes phylum, and lower bacterial richness and phylogenic diversity were reported in stands containing Acacia relative to the pure Eucalyptus. Distance-based redundancy analysis revealed a positive correlation of available phosphorus (P) and carbon/nitrogen (C/N) ratio with bacterial community structure. However, the Spearman correlation test revealed a broad correlation between the relative abundance of bacterial taxa and soil attributes, in particular with sulfur (S) and carbon (C), suggesting the important role of soil bacterial community in nutrient cycling in this type of forest management. Concerning mixed plantations, a shift in bacterial community structure was observed, probably linked to other changes, i.e., improvement in soil fertility (enhanced P and C dynamics in forest floor and soil, and increase in soil N status), and C sequestration in both soil and stand wood biomass with the great potential impact to mitigate climate change. Overall, our findings highlight the role of soil attributes, especially C, S, available P, and C/N ratio at a lesser extent, in driving the soil bacterial community in mixed-species plantations and its potential to improve soil fertility and to sustain Eucalyptus plantations established on the infertile and sandy soils of the Congolese coastal plains.
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Definition of Core Bacterial Taxa in Different Root Compartments of Dactylis glomerata, Grown in Soil under Different Levels of Land Use Intensity. DIVERSITY 2020. [DOI: 10.3390/d12100392] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Plant-associated bacterial assemblages are critical for plant fitness. Thus, identifying a consistent plant-associated core microbiome is important for predicting community responses to environmental changes. Our target was to identify the core bacterial microbiome of orchard grass Dactylis glomerata L. and to assess the part that is most sensitive to land management. Dactylis glomerata L. samples were collected from grassland sites with contrasting land use intensities but comparable soil properties at three different timepoints. To assess the plant-associated bacterial community structure in the compartments rhizosphere, bulk soil and endosphere, a molecular barcoding approach based on high throughput 16S rRNA amplicon sequencing was used. A distinct composition of plant-associated core bacterial communities independent of land use intensity was identified. Pseudomonas, Rhizobium and Bradyrhizobium were ubiquitously found in the root bacterial core microbiome. In the rhizosphere, the majority of assigned genera were Rhodoplanes, Methylibium, Kaistobacter and Bradyrhizobium. Due to the frequent occurrence of plant-promoting abilities in the genera found in the plant-associated core bacterial communities, our study helps to identify “healthy” plant-associated bacterial core communities. The variable part of the plant-associated microbiome, represented by the fluctuation of taxa at the different sampling timepoints, was increased under low land use intensity. This higher compositional variation in samples from plots with low land use intensity indicates a more selective recruitment of bacteria with traits required at different timepoints of plant development compared to samples from plots with high land use intensity.
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19
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Kirubakaran R, ArulJothi KN, Revathi S, Shameem N, Parray JA. Emerging priorities for microbial metagenome research. BIORESOURCE TECHNOLOGY REPORTS 2020; 11:100485. [PMID: 32835181 PMCID: PMC7319936 DOI: 10.1016/j.biteb.2020.100485] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 06/23/2020] [Accepted: 06/24/2020] [Indexed: 12/20/2022]
Abstract
Overwhelming anthropogenic activities lead to deterioration of natural resources and the environment. The microorganisms are considered desirable, due to their suitability for easy genetic manipulation and handling. With the aid of modern biotechnological techniques, the culturable microorganisms have been widely exploited for the benefit of mankind. Metagenomics, a powerful tool to access the abundant biodiversity of the environmental samples including the unculturable microbes, to determine microbial diversity and population structure, their ecological roles and expose novel genes of interest. This review focuses on the microbial adaptations to the adverse environmental conditions, metagenomic techniques employed towards microbial biotechnology. Metagenomic approach helps to understand microbial ecology and to identify useful microbial derivatives like antibiotics, toxins, and enzymes with diverse and enhanced function. It also summarizes the application of metagenomics in clinical diagnosis, improving microbial ecology, therapeutics, xenobiotic degradation and impact on agricultural crops.
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Affiliation(s)
| | - K N ArulJothi
- Department of Genetic Engineering, SRM Institute of Science and Technology, Chennai, India
- Department of Human Biology, University of Cape Town, Cape Town, South Africa
| | | | - Nowsheen Shameem
- Department of Environmental Science, Cluster University Srinagar, J&K, India
| | - Javid A Parray
- Department of Environmental Science, Govt SAM Degree College Budgam, J&K, India
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20
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Fernández-González AJ, Wentzien NM, Villadas PJ, Valverde-Corredor A, Lasa AV, Gómez-Lama Cabanás C, Mercado-Blanco J, Fernández-López M. Comparative study of neighboring Holm oak and olive trees-belowground microbial communities subjected to different soil management. PLoS One 2020; 15:e0236796. [PMID: 32780734 PMCID: PMC7418964 DOI: 10.1371/journal.pone.0236796] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 07/13/2020] [Indexed: 11/22/2022] Open
Abstract
It is well-known that different plant species, and even plant varieties, promote different assemblages of the microbial communities associated with them. Here, we investigate how microbial communities (bacteria and fungi) undergo changes within the influence of woody plants (two olive cultivars, one tolerant and another susceptible to the soilborne fungal pathogen Verticillium dahliae, plus wild Holm oak) grown in the same soil but with different management (agricultural versus native). By the use of metabarcoding sequencing we determined that the native Holm oak trees rhizosphere bacterial communities were different from its bulk soil, with differences in some genera like Gp4, Gp6 and Solirubrobacter. Moreover, the agricultural management used in the olive orchard led to belowground microbiota differences with respect to the natural conditions both in bulk soils and rhizospheres. Indeed, Gemmatimonas and Fusarium were more abundant in olive orchard soils. However, agricultural management removed the differences in the microbial communities between the two olive cultivars, and these differences were minor respect to the olive bulk soil. According to our results, and at least under the agronomical conditions here examined, the composition and structure of the rhizospheric microbial communities do not seem to play a major role in olive tolerance to V. dahliae.
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Affiliation(s)
- Antonio J Fernández-González
- Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
| | - Nuria M Wentzien
- Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
| | - Pablo J Villadas
- Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
| | | | - Ana V Lasa
- Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
| | | | - Jesús Mercado-Blanco
- Departamento de Protección de Cultivos, Instituto de Agricultura Sostenible, CSIC, Córdoba, Spain
| | - Manuel Fernández-López
- Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
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21
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Köberl M, Wagner P, Müller H, Matzer R, Unterfrauner H, Cernava T, Berg G. Unraveling the Complexity of Soil Microbiomes in a Large-Scale Study Subjected to Different Agricultural Management in Styria. Front Microbiol 2020; 11:1052. [PMID: 32523580 PMCID: PMC7261914 DOI: 10.3389/fmicb.2020.01052] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 04/28/2020] [Indexed: 12/31/2022] Open
Abstract
Healthy soil microbiomes are crucial for achieving high productivity in combination with crop quality, but our understanding of microbial diversity is still limited. In a large-scale study including 116 composite samples from vineyards, orchards and other crops from all over Styria (south-east Austria), agricultural management as well as distinct soil parameters were identified as drivers of the indigenous microbial communities in agricultural soils. The analysis of the soil microbiota based on microbial profiling of prokaryotic 16S rRNA gene fragments and fungal ITS regions revealed high bacterial and fungal diversity within Styrian agricultural soils; 206,596 prokaryotic and 53,710 fungal OTUs. Vineyards revealed a significantly higher diversity and distinct composition of soil fungi over orchards and other agricultural soils, whereas the prokaryotic diversity was unaffected. Soil pH was identified as one of the most important edaphic modulators of microbial community structure in both, vineyard and orchard soils. In general, the acid-base balance, disorders in the soil sorption complex, content and quality of organic substance as well as individual nutrients were identified as important drivers of the microbial community structure of Styrian vineyard and orchard soils. However, responses to distinct parameters differed in orchards and vineyards, and prokaryotic and fungal community responded differently to the same abiotic factor. In comparison to orchards, the microbiome of vineyard soils maintained a higher stability when herbicides were applied. Orchard soils exhibited drastic shifts within community composition; herbicides seem to have a substantial impact on the bacterial order Chthoniobacterales as well as potential plant growth promoters and antagonists of phytopathogens (Flavobacterium, Monographella), with a decreased abundance in herbicide-treated soils. Moreover, soils of herbicide-treated orchards revealed a significantly higher presence of potential apple pathogenic fungi (Nectria, Thelonectria). These findings provide the basis to adapt soil management practices in the future in order to maintain a healthy microbiome in agricultural soils.
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Affiliation(s)
- Martina Köberl
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Philipp Wagner
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Henry Müller
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Robert Matzer
- ARGE obst.wein, Association of Weinbauverband Steiermark and Verband Steirischer Erwerbsobstbauern, Graz, Austria
| | | | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
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Abis L, Loubet B, Ciuraru R, Lafouge F, Houot S, Nowak V, Tripied J, Dequiedt S, Maron PA, Sadet-Bourgeteau S. Reduced microbial diversity induces larger volatile organic compound emissions from soils. Sci Rep 2020; 10:6104. [PMID: 32269288 PMCID: PMC7142124 DOI: 10.1038/s41598-020-63091-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 02/29/2020] [Indexed: 12/11/2022] Open
Abstract
Microorganisms in soil are known to be a source and a sink of volatile organic compounds (VOCs). The role of the microbial VOCs on soil ecosystem regulation has been increasingly demonstrated in the recent years. Nevertheless, little is known about the influence of the microbial soil community structure and diversity on VOC emissions. This novel study analyzed the effect of reduced microbial diversity in soil on VOC emissions. We found that reduced levels of microbial diversity in soil increased VOC emissions from soils, while the number of different VOCs emitted decreased. Furthermore, we found that Proteobacteria, Bacteroidetes and fungi phyla were positively correlated to VOC emissions, and other prokaryotic phyla were either negatively correlated or very slightly positively correlated to VOCs emissions. Our interpretation is that Proteobacteria, Bacteroidetes and fungi were VOC producers while the other prokaryotic phyla were consumers. Finally, we discussed the possible role of VOCs as mediators of microbial interactions in soil.
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Affiliation(s)
- Letizia Abis
- Sorbonne Université, UPMC, Paris, France.
- INRA, UMR ECOSYS, INRA, AgroParisTech, Université Paris-Saclay, 78850, Thiverval-Grignon, France.
- Technische Universität Berlin, Umweltchemie und Luftrinhaltunz, Straße des 17. Juni 135, Berlin, 10623, Germany.
| | - Benjamin Loubet
- INRA, UMR ECOSYS, INRA, AgroParisTech, Université Paris-Saclay, 78850, Thiverval-Grignon, France
| | - Raluca Ciuraru
- INRA, UMR ECOSYS, INRA, AgroParisTech, Université Paris-Saclay, 78850, Thiverval-Grignon, France
| | - Florence Lafouge
- INRA, UMR ECOSYS, INRA, AgroParisTech, Université Paris-Saclay, 78850, Thiverval-Grignon, France
| | - Sabine Houot
- INRA, UMR ECOSYS, INRA, AgroParisTech, Université Paris-Saclay, 78850, Thiverval-Grignon, France
| | - Virginie Nowak
- INRA, UMR AgroEcologie, AgroSup Dijon, BP 87999, 21079, Dijon, cedex, France
| | - Julie Tripied
- INRA, UMR AgroEcologie, AgroSup Dijon, BP 87999, 21079, Dijon, cedex, France
| | - Samuel Dequiedt
- INRA, UMR AgroEcologie, AgroSup Dijon, BP 87999, 21079, Dijon, cedex, France
| | - Pierre Alain Maron
- INRA, UMR AgroEcologie, AgroSup Dijon, BP 87999, 21079, Dijon, cedex, France
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Piazza G, Ercoli L, Nuti M, Pellegrino E. Interaction Between Conservation Tillage and Nitrogen Fertilization Shapes Prokaryotic and Fungal Diversity at Different Soil Depths: Evidence From a 23-Year Field Experiment in the Mediterranean Area. Front Microbiol 2019; 10:2047. [PMID: 31551981 PMCID: PMC6737287 DOI: 10.3389/fmicb.2019.02047] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 08/20/2019] [Indexed: 01/20/2023] Open
Abstract
Soil biodiversity accomplishes key roles in agro-ecosystem services consisting in preserving and enhancing soil fertility and nutrient cycling, crop productivity and environmental protection. Thus, the improvement of knowledge on the effect of conservation practices, related to tillage and N fertilization, on soil microbial communities is critical to better understand the role and function of microorganisms in regulating agro-ecosystems. In the Mediterranean area, vulnerable to climate change and suffering for management-induced losses of soil fertility, the impact of conservation practices on soil microbial communities is of special interest for building mitigation and adaptation strategies to climate change. A long-term experiment, originally designed to investigate the effect of tillage and N fertilization on crop yield and soil organic carbon, was utilized to understand the effect of these management practices on soil prokaryotic and fungal community diversity. The majority of prokaryotic and fungal taxa were common to all treatments at both soil depths, whereas few bacterial taxa (Cloacimonates, Spirochaetia and Berkelbacteria) and a larger number of fungal taxa (i.e., Coniphoraceae, Debaryomycetaceae, Geastraceae, Cordicypitaceae and Steccherinaceae) were unique to specific management practices. Soil prokaryotic and fungal structure was heavily influenced by the interaction of tillage and N fertilization: the prokaryotic community structure of the fertilized conventional tillage system was remarkably different respect to the unfertilized conservation and conventional systems in the surface layer. In addition, the effect of N fertilization in shaping the fungal community structure of the surface layer was higher under conservation tillage systems than under conventional tillage systems. Soil microbial community was shaped by soil depth irrespective of the effect of plowing and N addition. Finally, chemical and enzymatic parameters of soil and crop yields were significantly related to fungal community structure along the soil profile. The findings of this study gave new insights on the identification of management practices supporting and suppressing beneficial and detrimental taxa, respectively. This highlights the importance of managing soil microbial diversity through agro-ecological intensified systems in the Mediterranean area.
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Chen H, Yang ZK, Yip D, Morris RH, Lebreux SJ, Cregger MA, Klingeman DM, Hui D, Hettich RL, Wilhelm SW, Wang G, Löffler FE, Schadt CW. One-time nitrogen fertilization shifts switchgrass soil microbiomes within a context of larger spatial and temporal variation. PLoS One 2019; 14:e0211310. [PMID: 31211785 PMCID: PMC6581249 DOI: 10.1371/journal.pone.0211310] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 05/28/2019] [Indexed: 12/21/2022] Open
Abstract
Soil microbiome responses to short-term nitrogen (N) inputs remain uncertain when compared with previous research that has focused on long-term fertilization responses. Here, we examined soil bacterial/archaeal and fungal communities pre- and post-N fertilization in an 8 year-old switchgrass field, in which twenty-four plots received N fertilization at three levels (0, 100, and 200 kg N ha-1 as NH4NO3) for the first time since planting. Soils were collected at two depths, 0–5 and 5–15 cm, for DNA extraction and amplicon sequencing of 16S rRNA genes and ITS regions for assessment of microbial community composition. Baseline assessments prior to fertilization revealed no significant pre-existing divergence in either bacterial/archaeal or fungal communities across plots. The one-time N fertilizations increased switchgrass yields and tissue N content, and the added N was nearly completely removed from the soil of fertilized plots by the end of the growing season. Both bacterial/archaeal and fungal communities showed large spatial (by depth) and temporal variation (by season) within each plot, accounting for 17 and 12–22% of the variation as calculated from the Sq. root of PERMANOVA tests for bacterial/archaeal and fungal community composition, respectively. While N fertilization effects accounted for only ~4% of overall variation, some specific microbial groups, including the bacterial genus Pseudonocardia and the fungal genus Archaeorhizomyces, were notably repressed by fertilization at 200 kg N ha-1. Bacterial groups varied with both depth in the soil profile and time of sampling, while temporal variability shaped the fungal community more significantly than vertical heterogeneity in the soil. These results suggest that short-term effects of N fertilization are significant but subtle, and other sources of variation will need to be carefully accounted for study designs including multiple intra-annual sampling dates, rather than one-time “snapshot” analyses that are common in the literature. Continued analyses of these trends over time with fertilization and management are needed to understand how these effects may persist or change over time.
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Affiliation(s)
- Huaihai Chen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Zamin K. Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Dan Yip
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Reese H. Morris
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Steven J. Lebreux
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Melissa A. Cregger
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Dawn M. Klingeman
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Dafeng Hui
- Department of Biological Sciences, Tennessee State University, Nashville, Tennessee, United States of America
| | - Robert L. Hettich
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Steven W. Wilhelm
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Gangsheng Wang
- Environmental Science Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
- Institute for Environmental Genomics and Department of Microbiology & Plant Biology, University of Oklahoma, Norman, Oklahoma, United States of America
| | - Frank E. Löffler
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Christopher W. Schadt
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, United States of America
- * E-mail:
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Makino A, Xu J, Nishimura J, Isogai E. Detection of Clostridium perfringens in tsunami deposits after the Great East Japan Earthquake. Microbiol Immunol 2019; 63:179-185. [PMID: 31045261 DOI: 10.1111/1348-0421.12682] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Revised: 04/02/2019] [Accepted: 04/09/2019] [Indexed: 11/27/2022]
Abstract
The Great East Japan Earthquake struck off the Tohoku and caused a tsunami in 2011. Most of the microbial characteristics of tsunami-affected soil remain unknown and no published study has shown how a tsunami affects the risk of infection by Clostridium perfringens living in soil. In 2011 and 2015, C. perfringens was assessed in deposits in soil from tsunami-damaged areas and undamaged areas of Miyagi. It was found that the number of C. perfringens was overwhelmingly greater in 2011 than in 2015 in the tsunami-damaged areas. According to real-time PCR, the prevalence C. perfringens organisms (%) was 103 fold greater in the damaged than in the undamaged areas.
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Affiliation(s)
- Asuka Makino
- Laboratory of Animal Microbiology, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Jun Xu
- Laboratory of Animal Microbiology, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Junko Nishimura
- Department of Life and Environmental Science, Hachinohe Institute of Technology, Hachinohe, Japan.,Cluster of Agricultural Sciences, Fukushima University, Kanayagawa, Fukushima, Japan
| | - Emiko Isogai
- Laboratory of Animal Microbiology, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
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Chaudhary DK, Khulan A, Kim J. Development of a novel cultivation technique for uncultured soil bacteria. Sci Rep 2019; 9:6666. [PMID: 31040339 PMCID: PMC6491550 DOI: 10.1038/s41598-019-43182-x] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 04/16/2019] [Indexed: 01/18/2023] Open
Abstract
In this study, a new diffusion bioreactor was developed to cultivate hidden bacterial communities in their natural environment. The newly developed method was investigated to cultivate microbial communities from the forest soil, and the results were evaluated against traditional culture methods and compared to the results of a pyrosequencing-based molecular survey. The molecular analysis revealed that a diverse bacterial population was present in the soil sample. However, both the newly developed method and the traditional method recovered more than 400 isolates, which belonged to only four phyla: Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes. Although these isolates were distributed over only four major phyla, the use of the newly developed technique resulted in the successful cultivation of 35 previously uncultured strains, whereas no such strains were successfully cultivated by the traditional method. Furthermore, the study also found that the recovery of uncultured bacteria and novel isolates was related to sampling season, incubation period, and cultivation media. The use of soil collected in summer, a prolonged incubation period, and low-substrate modified media increased the recovery of uncultured and novel isolates. Overall, the results indicate that the newly designed diffusion bioreactor can mimic the natural environment, which permits the cultivation of previously uncultured bacteria.
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Affiliation(s)
| | - Altankhuu Khulan
- Ecology Laboratory, Department of Life Science, Kyonggi University, Suwon, South Korea
| | - Jaisoo Kim
- Ecology Laboratory, Department of Life Science, Kyonggi University, Suwon, South Korea.
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The Influence of Herbicide Underdosage on the Composition and Diversity of Weeds in Oilseed Rape (Brassica napus L. var. oleifera D.C.) Mediterranean Fields. SUSTAINABILITY 2019. [DOI: 10.3390/su11061653] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Weed flora is considered harmful for crop growth and yield, but it is fundamental for preserving biodiversity in agroecosystems. Two three-year trials were conducted in Italy (two different sites) to assess the effect of six herbicide treatments on the weed flora structure of an oilseed rape crop. We applied metazachlor during the pre-emergence stage at 25%, 50%, 75%, and 100% of the labelled dose (M25, M50, M75, M100); trifluralin (during the first growing season); post-emergence treatment (PE); and a weedy control (W). Species richness, and diversity indices were used to characterize weed flora composition and to evaluate the effect of herbicide treatments on the considered variables. Results highlighted that the weed community is characterized by a higher diversity in underdosed than in M100 treated plots. Raphanus raphanistrum and Sinapis arvensis were the most common species in M75 and M100 treatments in both sites, while more weed species were detected in underdosed treatments and in weedy plots. The highest Shannon index values were observed in the underdosed treatments. In general, only a slightly similar trend was observed between sites, weed abundance and diversity being positively affected both by low-input herbicide management and by environmental factors (e.g., pedoclimatic situation and previous crop).
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An F, Li H, Diao Z, Lv J. The soil bacterial community in cropland is vulnerable to Cd contamination in winter rather than in summer. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2019; 26:114-125. [PMID: 30382516 DOI: 10.1007/s11356-018-3531-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Accepted: 07/03/2018] [Indexed: 06/08/2023]
Abstract
Potentially toxic metal contamination exerts a significant impact on soil microbes, thus deteriorating soil quality. The seasonality also has effects in shaping soil microbial community. The soil microbial community is a crucial factor representing soil health. However, whether the influence of potentially toxic metals on the microbial community differs in different seasons are still unknown. In this study, we established nine mesocosms of three cadmium treatments to investigate the impact of Cd amendments on the bacterial community of croplands in winter and summer. High bacterial diversity was revealed from the soil samples with 31 phyla. In winter, the abundance of dominant phylum Bacteroidetes, Gemmatimonadetes, and Verrucomicrobia increased, but Firmicutes decreased in Cd-contaminated soil in winter. Meanwhile, the abundance of Actinobacteria, Planctomycetes, and Chloroflexi showed Cd dose-dependent pattern in winter. In summer, the phylum Gemmatimonadetes and Verrucomicrobia decreased along with Cd dosing, while the dose-effect of Cd was found on the abundance of Actinobacteria and Chloroflexi. At the genus level, 55 genera of bacteria were significantly affected by Cd stress in winter, 24 genera decreased, 11 genera increased along with Cd gradients, and 20 genera changed depending on Cd dosage. In particular, genera Lactococcus, Psychrobacter, Brochothrix, Enhydrobacter, and Carnobacterium disappeared in Cd treatments, suggesting high sensitivity to Cd stress in winter. In summer, one genus decreased, seven genera increased with Cd dosing, and three genera were dose-dependent. The contrasting effects of Cd on soil bacterial community could be due to different edaphic factors in winter (moisture, available phosphorus, and total Cd) and summer (available Cd). Collectively, the winter-induced multiple stressors increase the impact of Cd on bacterial community in cropland. In further studies, the seasonal factor should be taken into consideration during the sampling stage.
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Affiliation(s)
- Fengqiu An
- College of Natural Resources and Environment, Ministry of Agriculture Key Laboratory of Plant Nutrition and Agri-environment in Northwest China, Northwest A&F University, Yangling, 712100, China
- College of Environmental and Chemical Engineering, Polytechnic University, Xi'an, 710048, China
| | - Haihong Li
- College of Environmental and Chemical Engineering, Polytechnic University, Xi'an, 710048, China
| | - Zhan Diao
- College of Natural Resources and Environment, Ministry of Agriculture Key Laboratory of Plant Nutrition and Agri-environment in Northwest China, Northwest A&F University, Yangling, 712100, China
- Law School & Intellectual Property School, JiNan University, Guangzhou, 510632, China
| | - Jialong Lv
- College of Natural Resources and Environment, Ministry of Agriculture Key Laboratory of Plant Nutrition and Agri-environment in Northwest China, Northwest A&F University, Yangling, 712100, China.
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29
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Wei Z, Feng K, Li S, Zhang Y, Chen H, Yin H, Xu M, Deng Y. Exploring abundance, diversity and variation of a widespread antibiotic resistance gene in wastewater treatment plants. ENVIRONMENT INTERNATIONAL 2018; 117:186-195. [PMID: 29753149 DOI: 10.1016/j.envint.2018.05.009] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 04/24/2018] [Accepted: 05/03/2018] [Indexed: 06/08/2023]
Abstract
An updated sul1 gene sequence database was constructed and new degenerate primers were designed to better investigate the abundance, diversity, and variation of a ubiquitous antibiotic resistance gene, sul1, with PCR-based methods in activated sludge from wastewater treatment plants (WWTPs). The newly designed degenerate primers showed high specificity and higher coverage in both in-silico evaluations and activated sludge samples compared to previous sul1 primers. Using the new primers, the abundance and diversity of sul1 gene, together with 16S rRNA gene, in activated sludge from five WWTPs in summer and winter were determined by quantitative PCR and MiSeq sequencing. The sul1 gene was found to be prevalent and displayed a comparable abundance (0.081 copies per bacterial cell in average) to the total bacteria across all samples. However, compared to the significant seasonal and geographical divergences in the quantity and diversity of bacterial communities in WWTPs, there were no significant seasonal or geographical variations of representative clusters of sul1 gene in most cases. Additionally, the representative sul1 clusters showed fairly close phylogeny and there was no obvious correlation between sul1 gene and the dominant bacterial genera, as well as the int1 gene, suggesting that bacterial hosts of sul1 gene is not stable, the sul1 gene may be carried by mobile genetic elements, sometimes integrated with class 1 integrons and sometimes not. Thus mobile genetic elements likely play a greater role than specific microbial taxa in determining the composition of sul1 gene in WWTPs.
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Affiliation(s)
- Ziyan Wei
- Key Laboratory of Environmental Biotechnology of CAS, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kai Feng
- Key Laboratory of Environmental Biotechnology of CAS, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuzhen Li
- Key Laboratory of Environmental Biotechnology of CAS, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; State Key Laboratory of Industrial Ecology and Environmental Engineering, Ministry of Education, School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Yu Zhang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongrui Chen
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China
| | - Meiying Xu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangzhou 510070, China
| | - Ye Deng
- Key Laboratory of Environmental Biotechnology of CAS, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China.
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30
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Mercado-Blanco J, Abrantes I, Barra Caracciolo A, Bevivino A, Ciancio A, Grenni P, Hrynkiewicz K, Kredics L, Proença DN. Belowground Microbiota and the Health of Tree Crops. Front Microbiol 2018; 9:1006. [PMID: 29922245 PMCID: PMC5996133 DOI: 10.3389/fmicb.2018.01006] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 04/30/2018] [Indexed: 11/13/2022] Open
Abstract
Trees are crucial for sustaining life on our planet. Forests and land devoted to tree crops do not only supply essential edible products to humans and animals, but also additional goods such as paper or wood. They also prevent soil erosion, support microbial, animal, and plant biodiversity, play key roles in nutrient and water cycling processes, and mitigate the effects of climate change acting as carbon dioxide sinks. Hence, the health of forests and tree cropping systems is of particular significance. In particular, soil/rhizosphere/root-associated microbial communities (known as microbiota) are decisive to sustain the fitness, development, and productivity of trees. These benefits rely on processes aiming to enhance nutrient assimilation efficiency (plant growth promotion) and/or to protect against a number of (a)biotic constraints. Moreover, specific members of the microbial communities associated with perennial tree crops interact with soil invertebrate food webs, underpinning many density regulation mechanisms. This review discusses belowground microbiota interactions influencing the growth of tree crops. The study of tree-(micro)organism interactions taking place at the belowground level is crucial to understand how they contribute to processes like carbon sequestration, regulation of ecosystem functioning, and nutrient cycling. A comprehensive understanding of the relationship between roots and their associate microbiota can also facilitate the design of novel sustainable approaches for the benefit of these relevant agro-ecosystems. Here, we summarize the methodological approaches to unravel the composition and function of belowground microbiota, the factors influencing their interaction with tree crops, their benefits and harms, with a focus on representative examples of Biological Control Agents (BCA) used against relevant biotic constraints of tree crops. Finally, we add some concluding remarks and suggest future perspectives concerning the microbiota-assisted management strategies to sustain tree crops.
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Affiliation(s)
- Jesús Mercado-Blanco
- Department of Crop Protection, Agencia Estatal Consejo Superior de Investigaciones Científicas, Institute for Sustainable Agriculture, Córdoba, Spain
| | - Isabel Abrantes
- Department of Life Sciences, Centre for Functional Ecology, University of Coimbra, Coimbra, Portugal
| | | | - Annamaria Bevivino
- Department for Sustainability of Production and Territorial Systems, Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), Rome, Italy
| | - Aurelio Ciancio
- Institute for Sustainable Plant Protection, National Research Council, Bari, Italy
| | - Paola Grenni
- Water Research Institute (CNR-IRSA), National Research Council, Rome, Italy
| | - Katarzyna Hrynkiewicz
- Department of Microbiology, Faculty of Biology and Environmental Protection, Nicolaus Copernicus University, Toruń, Poland
| | - László Kredics
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Diogo N. Proença
- Centre for Mechanical Engineering, Materials and Processes (CEMMPRE) and Department of Life Sciences, University of Coimbra, Coimbra, Portugal
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31
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Drylands soil bacterial community is affected by land use change and different irrigation practices in the Mezquital Valley, Mexico. Sci Rep 2018; 8:1413. [PMID: 29362388 PMCID: PMC5780513 DOI: 10.1038/s41598-018-19743-x] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 01/03/2018] [Indexed: 11/09/2022] Open
Abstract
Dryland agriculture nourishes one third of global population, although crop irrigation is often mandatory. As freshwater sources are scarce, treated and untreated wastewater is increasingly used for irrigation. Here, we investigated how the transformation of semiarid shrubland into rainfed farming or irrigated agriculture with freshwater, dam-stored or untreated wastewater affects the total (DNA-based) and active (RNA-based) soil bacterial community composition, diversity, and functionality. To do this we collected soil samples during the dry and rainy seasons and isolated DNA and RNA. Soil moisture, sodium content and pH were the strongest drivers of the bacterial community composition. We found lineage-specific adaptations to drought and sodium content in specific land use systems. Predicted functionality profiles revealed gene abundances involved in nitrogen, carbon and phosphorous cycles differed among land use systems and season. Freshwater irrigated bacterial community is taxonomically and functionally susceptible to seasonal environmental changes, while wastewater irrigated ones are taxonomically susceptible but functionally resistant to them. Additionally, we identified potentially harmful human and phytopathogens. The analyses of 16 S rRNA genes, its transcripts and deduced functional profiles provided extensive understanding of the short-term and long-term responses of bacterial communities associated to land use, seasonality, and water quality used for irrigation in drylands.
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Francaviglia R, Ledda L, Farina R. Organic Carbon and Ecosystem Services in Agricultural Soils of the Mediterranean Basin. SUSTAINABLE AGRICULTURE REVIEWS 28 2018. [DOI: 10.1007/978-3-319-90309-5_6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Francaviglia R, Renzi G, Ledda L, Benedetti A. Organic carbon pools and soil biological fertility are affected by land use intensity in Mediterranean ecosystems of Sardinia, Italy. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 599-600:789-796. [PMID: 28499227 DOI: 10.1016/j.scitotenv.2017.05.021] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 05/02/2017] [Accepted: 05/02/2017] [Indexed: 06/07/2023]
Abstract
Soil quality is mainly studied from the chemical and physical point of view, whereas soil biochemical and microbiological parameters are relatively more scarcely explored to assess the effect of management practices. This study aimed to evaluate soil organic carbon (SOC) and its pools; soil microbial activity parameters; and the Biological Fertility Index (BFI), in six land uses characteristics of the Mediterranean basin in north-eastern Sardinia. These land uses differed in management intensity and consisted of: tilled vineyard (TV), no tilled grassed vineyard (GV), former vineyards (FV), hay crop and pasture (HC and PA), cork oak forest (CO). Significant differences among ecosystems were found in most cases in (SOC), the related pools (total extractable carbon, humic and fulvic acids, not humified, not extractable), humification parameters (degree, rate and index of humification), and soil microbial activity (microbial carbon, respiration, metabolic quotient, and mineralization quotient). Pasture and cork oak forest showed in average a better soil quality for most biochemical and microbial parameters in comparison with the other ecosystems. The index of soil biological fertility (BFI) was higher under cork oak forest which is supposed to be the most sustainable ecosystem in the long term in this environment, able to maintain soil biological fertility and microbial diversity.
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Affiliation(s)
- Rosa Francaviglia
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Centro di Ricerca Agricoltura e Ambiente, Via della Navicella 2-4, 00184 Rome, Italy.
| | - Gianluca Renzi
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Centro di Ricerca Agricoltura e Ambiente, Via della Navicella 2-4, 00184 Rome, Italy
| | - Luigi Ledda
- Università degli Studi di Sassari, Dipartimento di Agraria, Sezione di Agronomia, Coltivazioni erbacee e Genetica, Viale Italia 39, 07100 Sassari, Italy
| | - Anna Benedetti
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Centro di Ricerca Agricoltura e Ambiente, Via della Navicella 2-4, 00184 Rome, Italy
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Kalivas A, Ganopoulos I, Psomopoulos F, Grigoriadis I, Xanthopoulou A, Hatzigiannakis E, Osathanunkul M, Tsaftaris A, Madesis P. Comparative metagenomics reveals alterations in the soil bacterial community driven by N-fertilizer and Amino 16® application in lettuce. GENOMICS DATA 2017; 14:14-17. [PMID: 28794989 PMCID: PMC5547230 DOI: 10.1016/j.gdata.2017.07.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 07/24/2017] [Accepted: 07/30/2017] [Indexed: 12/03/2022]
Abstract
Nutrients in the form of fertilizers and/or other additives such as amino acids, dramatically influence plant development and growth, plant nutrient composition and the level of soil pollution. Moreover, the treatment of soil microbiota is emerging as a new strategy in plant breeding to achieve desirable traits. Thus, integrated study of fertilizer application and soil microbiota might lead to a better understanding of soil-plant interactions and inform the design of novel ways to fertilize plants. Herein we report metagenomics data for soil microbiota in lettuce (Lactuca sativa) treated with fertilizer, amino acids or their combinations as follows: N-fertilizer + Amino16®, Amino16®, N-fertilizer and no treatment control. Data have been deposited in the NCBI Sequence Read Archive (SRA) (accession number: PRJNA388765).
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Affiliation(s)
- Apostolos Kalivas
- Institute of Plant Breeding and Genetic Resources ELGO-DEMETER (ex NAGREF), Thermi, Thessaloniki GR-57001, Greece
| | - Ioannis Ganopoulos
- Institute of Plant Breeding and Genetic Resources ELGO-DEMETER (ex NAGREF), Thermi, Thessaloniki GR-57001, Greece
| | - Fotis Psomopoulos
- Institute of Applied Biosciences, CERTH, Thermi, Thessaloniki 570 01, Greece
| | - Ioannis Grigoriadis
- Institute of Plant Breeding and Genetic Resources ELGO-DEMETER (ex NAGREF), Thermi, Thessaloniki GR-57001, Greece
| | - Aliki Xanthopoulou
- Institute of Applied Biosciences, CERTH, Thermi, Thessaloniki 570 01, Greece
| | | | - Maslin Osathanunkul
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Athanasios Tsaftaris
- Institute of Applied Biosciences, CERTH, Thermi, Thessaloniki 570 01, Greece
- Perrotis College, American Farm School, Thessaloniki 55102, Greece
| | - Panagiotis Madesis
- Institute of Applied Biosciences, CERTH, Thermi, Thessaloniki 570 01, Greece
- Corresponding author.
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Campisano A, Albanese D, Yousaf S, Pancher M, Donati C, Pertot I. Temperature drives the assembly of endophytic communities' seasonal succession. Environ Microbiol 2017; 19:3353-3364. [PMID: 28654220 DOI: 10.1111/1462-2920.13843] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 06/16/2017] [Accepted: 06/17/2017] [Indexed: 12/19/2022]
Abstract
Endophytic microorganisms asymptomatically colonise plant tissues. Exploring the assembly dynamics of bacterial endophytic communities is essential to understand the functioning of the plant holobiont and to optimise their possible use as biopesticides or plant biostimulants. The variation in endophytic communities in above and below-ground organs in Vitis vinifera in the field were studied. To understand the specific effect of temperature on endophytic communities, a separate experiment was set up where grapevine cuttings were grown under controlled conditions at three different temperatures. The findings revealed the succession of endophytic communities over the year. Endophytic communities of roots and stems differ in terms of composition and dynamic response to temperature. Noticeably, compositional differences during the seasons affected bacterial taxa more in stems than in roots, suggesting that roots offer a more stable and less easily perturbed environment. Correlation abundance networks showed that the presence of several taxa (including Bradyrhizobium, Burkholderia, Dyella, Mesorhizobium, Propionibacterium and Ralstonia) is linked in both the field and the greenhouse.
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Affiliation(s)
- Andrea Campisano
- Department of Sustainable Agro-ecosystems and Bioresources, Research and Innovation Centre, Fondazione Edmund Mach (FEM), Via E. Mach 1, S. Michele all'Adige, TN, 38010, Italy
| | - Davide Albanese
- Fondazione Edmund Mach, Computational Biology Unit, Research and Innovation Centre, Via E. Mach 1, S. Michele all'Adige, TN, 38010, Italy
| | - Sohail Yousaf
- Department of Sustainable Agro-ecosystems and Bioresources, Research and Innovation Centre, Fondazione Edmund Mach (FEM), Via E. Mach 1, S. Michele all'Adige, TN, 38010, Italy.,Department of Environmental Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Michael Pancher
- Department of Sustainable Agro-ecosystems and Bioresources, Research and Innovation Centre, Fondazione Edmund Mach (FEM), Via E. Mach 1, S. Michele all'Adige, TN, 38010, Italy
| | - Claudio Donati
- Fondazione Edmund Mach, Computational Biology Unit, Research and Innovation Centre, Via E. Mach 1, S. Michele all'Adige, TN, 38010, Italy
| | - Ilaria Pertot
- Department of Sustainable Agro-ecosystems and Bioresources, Research and Innovation Centre, Fondazione Edmund Mach (FEM), Via E. Mach 1, S. Michele all'Adige, TN, 38010, Italy
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Effects of different nitrogen additions on soil microbial communities in different seasons in a boreal forest. Ecosphere 2017. [DOI: 10.1002/ecs2.1879] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
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Wu J, Jiao Z, Zhou J, Guo F, Ding Z, Qiu Z. Analysis of bacterial communities in rhizosphere soil of continuously cropped healthy and diseased konjac. World J Microbiol Biotechnol 2017; 33:134. [PMID: 28585167 DOI: 10.1007/s11274-017-2287-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 05/17/2017] [Indexed: 11/28/2022]
Abstract
The bacterial community and diversity in healthy and diseased konjac rhizosphere soils with different ages of continuous cropping were investigated using next-generation sequencing. The results demonstrated that the number of years of continuous cropping significantly altered soil bacterial community and diversity. Soil bacterial Shannon diversity index and Chao 1 index decreased with the increasing cropping years of konjac. After 1 year of cropping, the soil exhibited the highest bacterial relative abundance and diversity. Of the 44 bacterial genera (relative abundance ratio of genera greater than 0.3%), 14 were significantly affected by the duration of continuous cropping and plant status. With increasing continuous cropping, Alicyclobacillus decreased, while Achromobacter, Lactobacillus, Kaistobacter, Rhodoplanes increased after 3 years continuous cropping. Continuous cropping altered the structure and composition of the soil bacterial community, which led to the reduction in the beneficial bacteria and multiplication of harmful bacteria. These results will improve our understanding of soil microbial community regulation and soil health maintenance in konjac farm systems.
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Affiliation(s)
- Jinping Wu
- Hubei Academy of Agricultural Sciences, 43 Nanhu Road, Hongshan District, Wuhan City, 430064, Hubei Province, China
| | - Zhenbiao Jiao
- Hubei Academy of Agricultural Sciences, 43 Nanhu Road, Hongshan District, Wuhan City, 430064, Hubei Province, China
| | - Jie Zhou
- Hubei Academy of Agricultural Sciences, 43 Nanhu Road, Hongshan District, Wuhan City, 430064, Hubei Province, China
| | - Fengling Guo
- Hubei Academy of Agricultural Sciences, 43 Nanhu Road, Hongshan District, Wuhan City, 430064, Hubei Province, China
| | - Zili Ding
- Hubei Academy of Agricultural Sciences, 43 Nanhu Road, Hongshan District, Wuhan City, 430064, Hubei Province, China.
| | - Zhengming Qiu
- Hubei Academy of Agricultural Sciences, 43 Nanhu Road, Hongshan District, Wuhan City, 430064, Hubei Province, China
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38
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McGee CF, Storey S, Clipson N, Doyle E. Soil microbial community responses to contamination with silver, aluminium oxide and silicon dioxide nanoparticles. ECOTOXICOLOGY (LONDON, ENGLAND) 2017; 26:449-458. [PMID: 28197855 DOI: 10.1007/s10646-017-1776-5] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 02/04/2017] [Indexed: 05/14/2023]
Abstract
Soil microorganisms are key contributors to nutrient cycling and are essential for the maintenance of healthy soils and sustainable agriculture. Although the antimicrobial effects of a broad range of nanoparticulate substances have been characterised in vitro, little is known about the impact of these compounds on microbial communities in environments such as soil. In this study, the effect of three widely used nanoparticulates (silver, silicon dioxide and aluminium oxide) on bacterial and fungal communities in an agricultural pastureland soil was examined in a microcosm-based experiment using a combination of enzyme analysis, molecular fingerprinting and amplicon sequencing. A relatively low concentration of silver nanoparticles (AgNPs) significantly reduced total soil dehydrogenase and urease activity, while Al2O3 and SiO2 nanoparticles had no effect. Amplicon sequencing revealed substantial shifts in bacterial community composition in soils amended with AgNPs, with significant decreases in the relative abundance of Acidobacteria and Verrucomicrobia and an increase in Proteobacteria. In particular, the relative abundance of the Proteobacterial genus Dyella significantly increased in AgNP amended soil. The effects of Al2O3 and SiO2 NPs on bacterial community composition were less pronounced. AgNPs significantly reduced bacterial and archaeal amoA gene abundance in soil, with the archaea more susceptible than bacteria. AgNPs also significantly impacted soil fungal community structure, while Al2O3 and SiO2 NPs had no effect. Several fungal ribotypes increased in soil amended with AgNPs, compared to control soil. This study highlights the need to consider the effects of individual nanoparticles on soil microbial communities when assessing their environmental impact.
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Affiliation(s)
- C F McGee
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - S Storey
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - N Clipson
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - E Doyle
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland.
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Castañeda LE, Barbosa O. Metagenomic analysis exploring taxonomic and functional diversity of soil microbial communities in Chilean vineyards and surrounding native forests. PeerJ 2017; 5:e3098. [PMID: 28382231 PMCID: PMC5376117 DOI: 10.7717/peerj.3098] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 02/15/2017] [Indexed: 11/20/2022] Open
Abstract
Mediterranean biomes are biodiversity hotspots, and vineyards are important components of the Mediterranean landscape. Over the last few decades, the amount of land occupied by vineyards has augmented rapidly, thereby increasing threats to Mediterranean ecosystems. Land use change and agricultural management have important effects on soil biodiversity, because they change the physical and chemical properties of soil. These changes may also have consequences on wine production considering that soil is a key component of terroir. Here, we describe the taxonomic diversity and metabolic functions of bacterial and fungal communities present in forest and vineyard soils in Chile. To accomplish this goal, we collected soil samples from organic vineyards in central Chile and employed a shotgun metagenomic approach to sequence the microbial DNA. Additionally, we studied the surrounding native forest to obtain a baseline of the soil conditions in the area prior to the establishment of the vineyard. Our metagenomic analyses revealed that both habitats shared most of the soil microbial species. The most abundant genera in the two habitats were the bacteria Candidatus Solibacter and Bradyrhizobium and the fungus Gibberella. Our results suggest that the soil microbial communities are similar in these forests and vineyards. Therefore, we hypothesize that native forests surrounding the vineyards may be acting as a microbial reservoir buffering the effects of the land conversion. Regarding the metabolic diversity, we found that genes pertaining to the metabolism of amino acids, fatty acids, and nucleotides as well as genes involved in secondary metabolism were enriched in forest soils. On the other hand, genes related to miscellaneous functions were more abundant in vineyard soils. These results suggest that the metabolic function of microbes found in these habitats differs, though differences are not related to taxonomy. Finally, we propose that the implementation of environmentally friendly practices by the wine industry may help to maintain the microbial diversity and ecosystem functions associated with natural habitats.
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Affiliation(s)
- Luis E Castañeda
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile , Valdivia , Chile
| | - Olga Barbosa
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile; Instituto de Ecología y Biodiversidad (IEB-Chile), Santiago, Chile
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Estendorfer J, Stempfhuber B, Haury P, Vestergaard G, Rillig MC, Joshi J, Schröder P, Schloter M. The Influence of Land Use Intensity on the Plant-Associated Microbiome of Dactylis glomerata L. FRONTIERS IN PLANT SCIENCE 2017; 8:930. [PMID: 28680426 PMCID: PMC5478725 DOI: 10.3389/fpls.2017.00930] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 05/18/2017] [Indexed: 05/07/2023]
Abstract
In this study, we investigated the impact of different land use intensities (LUI) on the root-associated microbiome of Dactylis glomerata (orchardgrass). For this purpose, eight sampling sites with different land use intensity levels but comparable soil properties were selected in the southwest of Germany. Experimental plots covered land use levels from natural grassland up to intensively managed meadows. We used 16S rRNA gene based barcoding to assess the plant-associated community structure in the endosphere, rhizosphere and bulk soil of D. glomerata. Samples were taken at the reproductive stage of the plant in early summer. Our data indicated that roots harbor a distinct bacterial community, which clearly differed from the microbiome of the rhizosphere and bulk soil. Our results revealed Pseudomonadaceae, Enterobacteriaceae and Comamonadaceae as the most abundant endophytes independently of land use intensity. Rhizosphere and bulk soil were dominated also by Proteobacteria, but the most abundant families differed from those obtained from root samples. In the soil, the effect of land use intensity was more pronounced compared to root endophytes leading to a clearly distinct pattern of bacterial communities under different LUI from rhizosphere and bulk soil vs. endophytes. Overall, a change of community structure on the plant-soil interface was observed, as the number of shared OTUs between all three compartments investigated increased with decreasing land use intensity. Thus, our findings suggest a stronger interaction of the plant with its surrounding soil under low land use intensity. Furthermore, the amount and quality of available nitrogen was identified as a major driver for shifts in the microbiome structure in all compartments.
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Affiliation(s)
- Jennifer Estendorfer
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum MünchenNeuherberg, Germany
| | - Barbara Stempfhuber
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum MünchenNeuherberg, Germany
| | - Paula Haury
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum MünchenNeuherberg, Germany
| | - Gisle Vestergaard
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum MünchenNeuherberg, Germany
| | | | - Jasmin Joshi
- Biodiversity Research/Systematic Botany, Institute for Biochemistry und Biology, University of PotsdamPotsdam, Germany
| | - Peter Schröder
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum MünchenNeuherberg, Germany
- *Correspondence: Peter Schröder,
| | - Michael Schloter
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum MünchenNeuherberg, Germany
- Chair of Soil Science, Technical University of MunichFreising, Germany
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Shen F, Li Y, Zhang M, Awasthi MK, Ali A, Li R, Wang Q, Zhang Z. Atmospheric Deposition-Carried Zn and Cd from a Zinc Smelter and Their Effects on Soil Microflora as Revealed by 16S rDNA. Sci Rep 2016; 6:39148. [PMID: 27958371 PMCID: PMC5153631 DOI: 10.1038/srep39148] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 11/18/2016] [Indexed: 02/01/2023] Open
Abstract
In this study, we investigated the influence of heavy metals (HM) on total soil bacterial population and its diversity pattern from 10 km distance of a Zinc smelter in Feng County, Qinling Mountain, China. We characterized and identified the bacterial community in a HM polluted soil using 16S rDNA technology. Out results indicated that the maximum soil HM concentration and the minimum bacterial population were observed in S2 soil, whereas bacterial diversity raised with the sampling distance increased. The bacterial communities were dominated by the phyla Proteobacteria, Acidobacteria and Actinobacteria in cornfield soils, except Fimicutes phylum which dominated in hilly area soil. The soil CEC, humic acid (HA)/fulvic acid (FA) and microbial OTUs increased with the sampling distance increased. Shewanella, Halomonas and Escherichia genera were highly tolerant to HM stress in both cultivated and non-cultivated soil. Finally, we found a consistent correlation of bacterial diversity with total HM and SOM along the sampling distance surrounding the zinc smelter, which could provide a new insight into the bacterial community-assisted and phytoremediation of HM contaminated soils.
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MESH Headings
- Bacteria/drug effects
- Bacteria/genetics
- Bacteria/growth & development
- Benzopyrans/toxicity
- Biodiversity
- Cadmium/toxicity
- Cluster Analysis
- DNA, Bacterial/chemistry
- DNA, Bacterial/isolation & purification
- DNA, Bacterial/metabolism
- Humic Substances/toxicity
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 16S/isolation & purification
- RNA, Ribosomal, 16S/metabolism
- Sequence Analysis, DNA
- Soil Microbiology
- Soil Pollutants/chemistry
- Soil Pollutants/toxicity
- Zinc/toxicity
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Affiliation(s)
- Feng Shen
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, China
| | - Yanxia Li
- School of Environment, Beijing Normal University, Beijing, China
| | - Min Zhang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, China
| | - Mukesh Kumar Awasthi
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, China
| | - Amjad Ali
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, China
| | - Ronghua Li
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, China
| | - Quan Wang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, China
| | - Zengqiang Zhang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, China
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42
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Zhang W, Chen L, Zhang R, Lin K. High throughput sequencing analysis of the joint effects of BDE209-Pb on soil bacterial community structure. JOURNAL OF HAZARDOUS MATERIALS 2016; 301:1-7. [PMID: 26342145 DOI: 10.1016/j.jhazmat.2015.08.037] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Revised: 08/04/2015] [Accepted: 08/22/2015] [Indexed: 06/05/2023]
Abstract
Decabromodiphenyl ether (BDE209) and Lead (Pb) are the main pollutants at e-waste recycling sites (EWRSs). However, the impact on soil microorganism of joint exposure to the two chemicals remains almost unknown. Therefore, the indoor incubation tests were performed to determine the response of soil microbial biomass and activity as well as bacterial community structure in the presence of the two chemicals during 60 d incubation period. The results indicated that after Pb alone or BDE209-Pb exposure, soil microbial biomass C (Cmic) was significantly lower (p<0.01), and soil basal respiration (SBR) and metabolic quotient (qCO2) were enhanced, while BDE209 barely resulted in significant influence (p>0.05). 16S rRNA gene sequencing on the Illumina MiSeq platform demonstrated that a total 49,405 valid sequences widely represented the diversity of microbial community. Sequence analyses at phylum and genus taxonomic levels illustrated that 11 identified phyla and 297 genera were observed among all the soil samples, and the contaminants input had affected bacterial community structure, suggesting that Proteobacteria, Actinobacteria and Acidobacteria were the dominant phyla, and the genera Massilia and Bacillus were enriched in contaminated soil. BDE209 exposure alone in all the samples indicated a more similar community structure compared to the control. The results of these observations have provided a better understanding of ecotoxicological effects of BDE209 and Pb joint exposure on indigenous microorganisms in soil at EWRSs.
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Affiliation(s)
- Wei Zhang
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, Shanghai 200237, China; School of Resource and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, China.
| | - Lei Chen
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, Shanghai 200237, China; School of Resource and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, China; R&D Center, China Haisum Engineering Co., Ltd., Shanghai 201702, China
| | - Rong Zhang
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, Shanghai 200237, China; School of Resource and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Kuangfei Lin
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, Shanghai 200237, China; School of Resource and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, China
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Castañeda LE, Godoy K, Manzano M, Marquet PA, Barbosa O. Comparison of soil microbial communities inhabiting vineyards and native sclerophyllous forests in central Chile. Ecol Evol 2015; 5:3857-68. [PMID: 26445647 PMCID: PMC4588659 DOI: 10.1002/ece3.1652] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 07/06/2015] [Accepted: 07/09/2015] [Indexed: 11/09/2022] Open
Abstract
Natural ecosystems provide services to agriculture such as pest control, soil nutrients, and key microbial components. These services and others in turn provide essential elements that fuel biomass productivity. Responsible agricultural management and conservation of natural habitats can enhance these ecosystem services. Vineyards are currently driving land‐use changes in many Mediterranean ecosystems. These land‐use changes could have important effects on the supporting ecosystems services related to the soil properties and the microbial communities associated with forests and vineyard soils. Here, we explore soil bacterial and fungal communities present in sclerophyllous forests and organic vineyards from three different wine growing areas in central Chile. We employed terminal restriction fragment length polymorphisms (T‐RFLP) to describe the soil microbial communities inhabiting native forests and vineyards in central Chile. We found that the bacterial community changed between the sampled growing areas; however, the fungal community did not differ. At the local scale, our findings show that fungal communities differed between habitats because fungi species might be more sensitive to land‐use change compared to bacterial species, as bacterial communities did not change between forests and vineyards. We discuss these findings based on the sensitivity of microbial communities to soil properties and land‐use change. Finally, we focus our conclusions on the importance of naturally derived ecosystem services to vineyards.
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Affiliation(s)
- Luis E Castañeda
- Facultad de Ciencias Instituto de Ciencias Ambientales y Evolutivas Campus Isla Teja Universidad Austral de Chile Valdivia Chile ; Instituto de Ecología & Biodiversidad (IEB-Chile) Casilla 653 Santiago Chile
| | - Karina Godoy
- Facultad de Ciencias Instituto de Ciencias Ambientales y Evolutivas Campus Isla Teja Universidad Austral de Chile Valdivia Chile ; Instituto de Ecología & Biodiversidad (IEB-Chile) Casilla 653 Santiago Chile
| | - Marlene Manzano
- Instituto de Ecología & Biodiversidad (IEB-Chile) Casilla 653 Santiago Chile ; Departamento de Ecología Facultad de Ciencias Biológicas Pontificia Universidad Católica de Chile Alameda 340 Santiago Chile
| | - Pablo A Marquet
- Instituto de Ecología & Biodiversidad (IEB-Chile) Casilla 653 Santiago Chile ; Departamento de Ecología Facultad de Ciencias Biológicas Pontificia Universidad Católica de Chile Alameda 340 Santiago Chile ; The Santa Fe Institute Santa Fe New Mexico 87501 ; Laboratorio Internacional de Cambio Global Pontificia Universidad Católica de Chile Alameda 340 Santiago Chile ; Centro Cambio Global UC Pontificia Universidad Católica de Chile Av. Vicuña Mackenna 4860 Santiago Chile
| | - Olga Barbosa
- Facultad de Ciencias Instituto de Ciencias Ambientales y Evolutivas Campus Isla Teja Universidad Austral de Chile Valdivia Chile ; Instituto de Ecología & Biodiversidad (IEB-Chile) Casilla 653 Santiago Chile
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44
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Correction: Soil bacterial community response to differences in agricultural management along with seasonal changes in a Mediterranean region. PLoS One 2015; 10:e0124603. [PMID: 25860991 PMCID: PMC4393129 DOI: 10.1371/journal.pone.0124603] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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45
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Ponce-Soto GY, Aguirre-von-Wobeser E, Eguiarte LE, Elser JJ, Lee ZMP, Souza V. Enrichment experiment changes microbial interactions in an ultra-oligotrophic environment. Front Microbiol 2015; 6:246. [PMID: 25883593 PMCID: PMC4381637 DOI: 10.3389/fmicb.2015.00246] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Accepted: 03/13/2015] [Indexed: 11/13/2022] Open
Abstract
The increase of nutrients in water bodies, in particular nitrogen (N) and phosphorus (P) due to the recent expansion of agricultural and other human activities is accelerating environmental degradation of these water bodies, elevating the risk of eutrophication and reducing biodiversity. To evaluate the ecological effects of the influx of nutrients in an oligotrophic and stoichiometrically imbalanced environment, we performed a replicated in situ mesocosm experiment. We analyzed the effects of a N- and P-enrichment on the bacterial interspecific interactions in an experiment conducted in the Cuatro Cienegas Basin (CCB) in Mexico. This is a desert ecosystem comprised of several aquatic systems with a large number of microbial endemic species. The abundance of key nutrients in this basin exhibits strong stoichiometric imbalance (high N:P ratios), suggesting that species diversity is maintained mostly by competition for resources. We focused on the biofilm formation and antibiotic resistance of 960 strains of cultivated bacteria in two habitats, water and sediment, before and after 3 weeks of fertilization. The water habitat was dominated by Pseudomonas, while Halomonas dominated the sediment. Strong antibiotic resistance was found among the isolates at time zero in the nutrient-poor bacterial communities, but resistance declined in the bacteria isolated in the nutrient-rich environments, suggesting that in the nutrient-poor original environment, negative inter-specific interactions were important, while in the nutrient-rich environments, competitive interactions are not so important. In water, a significant increase in the percentage of biofilm-forming strains was observed for all treatments involving nutrient addition.
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Affiliation(s)
- Gabriel Y Ponce-Soto
- Laboratorio de Ecología Molecular y Experimental, Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México Coyoacán, México
| | | | - Luis E Eguiarte
- Laboratorio de Ecología Molecular y Experimental, Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México Coyoacán, México
| | - James J Elser
- School of Life Sciences, Arizona State University Tempe, AZ, USA
| | - Zarraz M-P Lee
- School of Life Sciences, Arizona State University Tempe, AZ, USA
| | - Valeria Souza
- Laboratorio de Ecología Molecular y Experimental, Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México Coyoacán, México
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