1
|
Kertesz V, Khalid M, Retterer ST, Cahill JF. Structure-Driven Liquid Microjunction Surface-Sampling Probe Mass Spectrometry. Anal Chem 2023; 95:14521-14525. [PMID: 37738474 DOI: 10.1021/acs.analchem.3c02370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/24/2023]
Abstract
The rhizosphere is the narrow region of soil surrounding the roots of plants that is influenced by root exudates, root secretions, and associated microbial communities. This region is crucial to plant growth and development and plays a critical role in nutrient uptake, disease resistance, and soil transformation. Understanding the function of exogenous compounds in the rhizosphere starts with determining the spatiotemporal distribution of these molecular components. Using liquid microjunction surface-sampling probe mass spectrometry (LMJ-SSP-MS) and microfluidic devices with attached microporous membranes enables in situ, nondisruptive, and nondestructive spatiotemporal measurement of exogenous compounds from plant roots. However, long imaging times (>2 h) can negatively affect plant heath and limit temporal studies. Here, we present a novel strategy to optimize the number and location of sampling sites on these microporous membrane-covered microfluidic devices. This novel, "structure-driven" sampling workflow takes into consideration the channel structure of the microfluidic device to maximize sampling from the channels and minimize acquisition time (∼4× less time in some cases while providing similar chemical image accuracy), thus reducing stress on plants during in situ LMJ-SSP-MS analysis.
Collapse
Affiliation(s)
- Vilmos Kertesz
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6131, United States
| | - Muneeba Khalid
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6131, United States
| | - Scott T Retterer
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6131, United States
| | - John F Cahill
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6131, United States
| |
Collapse
|
2
|
Colette M, Guentas L, Patrona LD, Ansquer D, Callac N. Dynamic of active microbial diversity in rhizosphere sediments of halophytes used for bioremediation of earthen shrimp ponds. ENVIRONMENTAL MICROBIOME 2023; 18:58. [PMID: 37438848 DOI: 10.1186/s40793-023-00512-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Accepted: 07/02/2023] [Indexed: 07/14/2023]
Abstract
BACKGROUND In New-Caledonia, at the end of each shrimp production cycle, earthen ponds are drained and dried to enhance microbial decomposition of nutrient-rich waste trapped in the sediment during the rearing. However, excessive ponds drying may not be suitable for the decomposition activities of microorganisms. Halophytes, salt tolerant plants, naturally grow at vicinity of shrimp ponds; due to their specificity, we explored whether halophytes cultivation during the pond drying period may be suitable for pond bioremediation. In addition, plants are closely associated with microorganisms, which may play a significant role in organic matter decomposition and therefore in bioremediation. Thus, in this study we aimed to determine the impact of 3 halophyte species (Suaeda australis, Sarcocornia quinqueflora and Atriplex jubata) on active sediment microbial communities and their implications on organic matter degradation. RESULTS Drying significantly decreased the microbial diversity index compared to those of wet sediment or sediment with halophytes. Microbial profiles varied significantly over time and according to the experimental conditions (wet, dry sediment or sediment with halophyte species). Halophytes species seemed to promote putative microbial metabolism activities in the sediment. Taxa related to nitrogen removal, carbon mineralisation, sulphur reduction and sulphide oxidation were significant biomarkers in sediment harbouring halophytes and may be relevant for bioremediation. Whereas microbial communities of dry sediment were marked by soil limited-moisture taxa with no identification of microbial metabolic functions. Nitrogen reduction in sediments was evidenced in wet sediment and in sediments with halophytes cultures, along with putative microbial denitrification activities. The greatest nitrogen reduction was observed in halophytes culture. CONCLUSION The efficiency of sediment bioremediation by halophytes appears to be the result of both rhizosphere microbial communities and plant nutrition. Their cultures during the pond drying period may be used as aquaculture diversification by being a sustainable system.
Collapse
Affiliation(s)
- Marie Colette
- French Institute for Research in the Science of the Sea (IFREMER), Research Institute for Development (IRD), University of New Caledonia, University of Reunion, CNRS, UMR 9220 ENTROPIE, Noumea, New Caledonia.
- Institute of Exact and Applied Sciences (ISEA), EA 7484, University of New Caledonia, Noumea, 98851, New Caledonia.
| | - Linda Guentas
- Institute of Exact and Applied Sciences (ISEA), EA 7484, University of New Caledonia, Noumea, 98851, New Caledonia
| | - Luc Della Patrona
- French Institute for Research in the Science of the Sea (IFREMER), Research Institute for Development (IRD), University of New Caledonia, University of Reunion, CNRS, UMR 9220 ENTROPIE, Noumea, New Caledonia
| | - Dominique Ansquer
- French Institute for Research in the Science of the Sea (IFREMER), Research Institute for Development (IRD), University of New Caledonia, University of Reunion, CNRS, UMR 9220 ENTROPIE, Noumea, New Caledonia
| | - Nolwenn Callac
- French Institute for Research in the Science of the Sea (IFREMER), Research Institute for Development (IRD), University of New Caledonia, University of Reunion, CNRS, UMR 9220 ENTROPIE, Noumea, New Caledonia
| |
Collapse
|
3
|
Nam JH, Thibodeau A, Qian YL, Qian MC, Park SH. Multidisciplinary evaluation of plant growth promoting rhizobacteria on soil microbiome and strawberry quality. AMB Express 2023; 13:18. [PMID: 36795258 PMCID: PMC9935790 DOI: 10.1186/s13568-023-01524-z] [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: 01/17/2023] [Accepted: 02/04/2023] [Indexed: 02/17/2023] Open
Abstract
The natural soil environment is considered one of the most diverse habitats containing numerous bacteria, fungi, and larger organisms such as nematodes, insects, or rodents. Rhizosphere bacteria play vital roles in plant nutrition and the growth promotion of their host plant. The aim of this study was to evaluate the effects of three plant growth-promoting rhizobacteria (PGPR), Bacillus subtilis, Bacillus amyloliquefaciens, and Pseudomonas monteilii for their potential role as a biofertilizer. The effect of the PGPR was examined at a commercial strawberry farm in Dayton, Oregon. The PGPR were applied to the soil of the strawberry (Fragaria × ananassa cultivar Hood) plants in two different concentrations of PGPR, T1 (0.24% PGPR) and T2 (0.48% PGPR), and C (no PGPR). A total of 450 samples from August 2020 to May 2021 were collected, and microbiome sequencing based on the V4 region of the 16S rRNA gene was conducted. The strawberry quality was measured by sensory evaluation, total acidity (TA), total soluble solids (TSS), color (lightness and chroma), and volatile compounds. Application of the PGPR significantly increased the populations of Bacillus and Pseudomonas and promoted the growth of nitrogen-fixing bacteria. The TSS and color evaluation showed that the PGPR presumptively behaved as a ripening enhancer. The PGPR contributed to the production of fruit-related volatile compounds, while the sensory evaluation did not show significant differences among the three groups. The major finding of this study suggests that the consortium of the three PGPR have a potential role as a biofertilizer by supporting the growth of other microorganisms (nitrogen-fixing bacteria) as part of a synergetic effect and strawberry quality such as sweetness and volatile compounds.
Collapse
Affiliation(s)
- Jun Haeng Nam
- grid.4391.f0000 0001 2112 1969Department of Food Science and Technology, Oregon State University, 3051 SW Campus Way, Corvallis, OR 97331 USA
| | - Alyssa Thibodeau
- grid.4391.f0000 0001 2112 1969Department of Food Science and Technology, Oregon State University, 3051 SW Campus Way, Corvallis, OR 97331 USA
| | - Yanping L. Qian
- grid.4391.f0000 0001 2112 1969Department of Food Science and Technology, Oregon State University, 3051 SW Campus Way, Corvallis, OR 97331 USA
| | - Michael C. Qian
- grid.4391.f0000 0001 2112 1969Department of Food Science and Technology, Oregon State University, 3051 SW Campus Way, Corvallis, OR 97331 USA
| | - Si Hong Park
- Department of Food Science and Technology, Oregon State University, 3051 SW Campus Way, Corvallis, OR, 97331, USA.
| |
Collapse
|
4
|
Przemieniecki SW, Oćwieja M, Ciesielski S, Halecki W, Matras E, Gorczyca A. Chemical Structure of Stabilizing Layers of Negatively Charged Silver Nanoparticles as an Effector of Shifts in Soil Bacterial Microbiome under Short-Term Exposure. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:14438. [PMID: 36361318 PMCID: PMC9658158 DOI: 10.3390/ijerph192114438] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 10/23/2022] [Accepted: 10/25/2022] [Indexed: 06/16/2023]
Abstract
In this work, we have assessed the exposure of soil bacteria from potato monoculture to three types of silver nanoparticles (AgNPs) as well as silver ions (Ag+ ions) delivered in the form of silver nitrate and a commercially available fungicide. The diversity of the soil microbial community, enzymatic activity, and carbon source utilization were evaluated. It was found that only the fungicide significantly limited the abundance and activity of soil bacteria. Silver ions significantly reduced bacterial metabolic activity. In turn, one type of AgNPs prepared with the use of tannic acid (TA) increased bacterial load and activity. There was found in all AgNPs treated soils (1) a greater proportion of all types of persistent bacteria, i.e., Bacillus, Paenibacillus, and Clostridium; (2) a visible decrease in the proportion of Nocardioides, Arthrobacter, and Candidatus Solibacter; (3) almost complete depletion of Pseudomonas; (4) increase in the number of low-frequency taxa and decrease in dominant taxa compared to the control soil. Despite the general trend of qualitative changes in the bacterial community, it was found that the differences in the chemical structure of the AgNP stabilizing layers had a significant impact on the specific metabolic activity resulting from qualitative changes in the microbiome.
Collapse
Affiliation(s)
- Sebastian Wojciech Przemieniecki
- Department of Entomology, Phytopathology and Molecular Diagnostics, University of Warmia and Mazury in Olsztyn, Prawochenskiego 17, PL-10721 Olsztyn, Poland
| | - Magdalena Oćwieja
- Jerzy Haber Institute of Catalysis and Surface Chemistry Polish Academy of Sciences, Niezapominajek 8, PL-30239 Krakow, Poland
| | - Sławomir Ciesielski
- Department of Environmental Biotechnology, University of Warmia and Mazury in Olsztyn, Słoneczna 45G, PL-10719 Olsztyn, Poland
| | - Wiktor Halecki
- Institute of Nature Conservation, Polish Academy of Sciences, Mickiewicza 33, PL-31120 Kraków, Poland
| | - Ewelina Matras
- Department of Microbiology and Biomonitoring, University of Agriculture in Krakow, Mickiewicza 21, PL-31120 Krakow, Poland
| | - Anna Gorczyca
- Department of Microbiology and Biomonitoring, University of Agriculture in Krakow, Mickiewicza 21, PL-31120 Krakow, Poland
| |
Collapse
|
5
|
Mansour A, Mannaa M, Hewedy O, Ali MG, Jung H, Seo YS. Versatile Roles of Microbes and Small RNAs in Rice and Planthopper Interactions. THE PLANT PATHOLOGY JOURNAL 2022; 38:432-448. [PMID: 36221916 PMCID: PMC9561162 DOI: 10.5423/ppj.rw.07.2022.0090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 07/21/2022] [Accepted: 07/22/2022] [Indexed: 06/16/2023]
Abstract
Planthopper infestation in rice causes direct and indirect damage through feeding and viral transmission. Host microbes and small RNAs (sRNAs) play essential roles in regulating biological processes, such as metabolism, development, immunity, and stress responses in eukaryotic organisms, including plants and insects. Recently, advanced metagenomic approaches have facilitated investigations on microbial diversity and its function in insects and plants, highlighting the significance of microbiota in sustaining host life and regulating their interactions with the environment. Recent research has also suggested significant roles for sRNA-regulated genes during rice-planthopper interactions. The response and behavior of the rice plant to planthopper feeding are determined by changes in the host transcriptome, which might be regulated by sRNAs. In addition, the roles of microbial symbionts and sRNAs in the host response to viral infection are complex and involve defense-related changes in the host transcriptomic profile. This review reviews the structure and potential functions of microbes and sRNAs in rice and the associated planthopper species. In addition, the involvement of the microbiota and sRNAs in the rice-planthopper-virus interactions during planthopper infestation and viral infection are discussed.
Collapse
Affiliation(s)
- Abdelaziz Mansour
- Department of Integrated Biological Science, Pusan National University, Busan 46241,
Korea
- Department of Economic Entomology and Pesticides, Faculty of Agriculture, Cairo University, Giza 12613,
Egypt
| | - Mohamed Mannaa
- Department of Integrated Biological Science, Pusan National University, Busan 46241,
Korea
- Department of Plant Pathology, Cairo University, Giza 12613,
Egypt
| | - Omar Hewedy
- Department of Plant Agriculture, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1,
Canada
- Department of Genetics, Faculty of Agriculture, Menoufia University, Shibin El-Kom 32514,
Egypt
| | - Mostafa G. Ali
- Department of Botany and Microbiology, Faculty of Science, Benha University, Benha 13518,
Egypt
| | - Hyejung Jung
- Department of Integrated Biological Science, Pusan National University, Busan 46241,
Korea
| | - Young-Su Seo
- Department of Integrated Biological Science, Pusan National University, Busan 46241,
Korea
| |
Collapse
|
6
|
Walton CL, Khalid M, Bible AN, Kertesz V, Retterer ST, Morrell-Falvey J, Cahill JF. In Situ Detection of Amino Acids from Bacterial Biofilms and Plant Root Exudates by Liquid Microjunction Surface-Sampling Probe Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:1615-1625. [PMID: 35904879 DOI: 10.1021/jasms.2c00081] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The plant rhizosphere is a complex and dynamic chemical environment where the exchange of molecular signals between plants, microbes, and fungi drives the development of the entire biological system. Exogenous compounds in the rhizosphere are known to affect plant-microbe organization, interactions between organisms, and ultimately, growth and survivability. The function of exogenous compounds in the rhizosphere is still under much investigation, specifically with respect to their roles in plant growth and development, the assembly of the associated microbial community, and the spatiotemporal distribution of molecular components. A major challenge for spatiotemporal measurements is developing a nondisruptive and nondestructive technique capable of analyzing the exogenous compounds contained within the environment. A methodology using liquid microjunction-surface sampling probe-mass spectrometry (LMJ-SSP-MS) and microfluidic devices with attached microporous membranes was developed for in situ, spatiotemporal measurement of amino acids (AAs) from bacterial biofilms and plant roots. Exuded arginine was measured from a living Pantoea YR343 biofilm, which resulted in a chemical image indicative of biofilm growth within the device. Spot sampling along the roots of Populus trichocarpa with the LMJ-SSP-MS resulted in the detection of 15 AAs. Variation in AA concentrations across the root system was observed, indicating that exudation is not homogeneous and may be linked to local rhizosphere architecture and different biological processes along the root.
Collapse
Affiliation(s)
- Courtney L Walton
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6131, United States
| | - Muneeba Khalid
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6131, United States
| | - Amber N Bible
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6131, United States
| | - Vilmos Kertesz
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6131, United States
| | - Scott T Retterer
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6131, United States
| | - Jennifer Morrell-Falvey
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6131, United States
| | - John F Cahill
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6131, United States
| |
Collapse
|
7
|
Djemiel C, Dequiedt S, Karimi B, Cottin A, Horrigue W, Bailly A, Boutaleb A, Sadet-Bourgeteau S, Maron PA, Chemidlin Prévost-Bouré N, Ranjard L, Terrat S. Potential of Meta-Omics to Provide Modern Microbial Indicators for Monitoring Soil Quality and Securing Food Production. Front Microbiol 2022; 13:889788. [PMID: 35847063 PMCID: PMC9280627 DOI: 10.3389/fmicb.2022.889788] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 06/06/2022] [Indexed: 01/02/2023] Open
Abstract
Soils are fundamental resources for agricultural production and play an essential role in food security. They represent the keystone of the food value chain because they harbor a large fraction of biodiversity—the backbone of the regulation of ecosystem services and “soil health” maintenance. In the face of the numerous causes of soil degradation such as unsustainable soil management practices, pollution, waste disposal, or the increasing number of extreme weather events, it has become clear that (i) preserving the soil biodiversity is key to food security, and (ii) biodiversity-based solutions for environmental monitoring have to be developed. Within the soil biodiversity reservoir, microbial diversity including Archaea, Bacteria, Fungi and protists is essential for ecosystem functioning and resilience. Microbial communities are also sensitive to various environmental drivers and to management practices; as a result, they are ideal candidates for monitoring soil quality assessment. The emergence of meta-omics approaches based on recent advances in high-throughput sequencing and bioinformatics has remarkably improved our ability to characterize microbial diversity and its potential functions. This revolution has substantially filled the knowledge gap about soil microbial diversity regulation and ecology, but also provided new and robust indicators of agricultural soil quality. We reviewed how meta-omics approaches replaced traditional methods and allowed developing modern microbial indicators of the soil biological quality. Each meta-omics approach is described in its general principles, methodologies, specificities, strengths and drawbacks, and illustrated with concrete applications for soil monitoring. The development of metabarcoding approaches in the last 20 years has led to a collection of microbial indicators that are now operational and available for the farming sector. Our review shows that despite the recent huge advances, some meta-omics approaches (e.g., metatranscriptomics or meta-proteomics) still need developments to be operational for environmental bio-monitoring. As regards prospects, we outline the importance of building up repositories of soil quality indicators. These are essential for objective and robust diagnosis, to help actors and stakeholders improve soil management, with a view to or to contribute to combining the food and environmental quality of next-generation farming systems in the context of the agroecological transition.
Collapse
Affiliation(s)
- Christophe Djemiel
- Agroécologie, INRAE, Institut Agro, Université Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
| | - Samuel Dequiedt
- Agroécologie, INRAE, Institut Agro, Université Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
| | - Battle Karimi
- Agroécologie, INRAE, Institut Agro, Université Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
- Novasol Experts, Dijon, France
| | - Aurélien Cottin
- Agroécologie, INRAE, Institut Agro, Université Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
| | - Walid Horrigue
- Agroécologie, INRAE, Institut Agro, Université Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
| | - Arthur Bailly
- Agroécologie, INRAE, Institut Agro, Université Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
| | - Ali Boutaleb
- Agroécologie, INRAE, Institut Agro, Université Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
| | - Sophie Sadet-Bourgeteau
- Agroécologie, INRAE, Institut Agro, Université Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
| | - Pierre-Alain Maron
- Agroécologie, INRAE, Institut Agro, Université Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
| | | | - Lionel Ranjard
- Agroécologie, INRAE, Institut Agro, Université Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
- Lionel Ranjard,
| | - Sébastien Terrat
- Agroécologie, INRAE, Institut Agro, Université Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
- *Correspondence: Sébastien Terrat,
| |
Collapse
|
8
|
The Rhizosphere Microbiome of Ginseng. Microorganisms 2022; 10:microorganisms10061152. [PMID: 35744670 PMCID: PMC9231392 DOI: 10.3390/microorganisms10061152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 05/30/2022] [Accepted: 06/01/2022] [Indexed: 12/04/2022] Open
Abstract
The rhizosphere of ginseng contains a wide range of microorganisms that can have beneficial or harmful effects on the plant. Root exudates of ginseng, particularly ginsenosides and phenolic acids, appear to select for particular microbial populations through their stimulatory and inhibitory activities, which may account for the similarities between the rhizosphere microbiomes of different cultivated species of Panax. Many practices of cultivation attempt to mimic the natural conditions of ginseng as an understory plant in hilly forested areas. However, these practices are often disruptive to soil, and thus the soil microbiome differs between wild and cultivated ginseng. Changes in the microbiome during cultivation can be harmful as they have been associated with negative changes of the soil physiochemistry as well as the promotion of plant diseases. However, isolation of a number of beneficial microbes from the ginseng rhizosphere indicates that many have the potential to improve ginseng production. The application of high-throughput sequencing to study the rhizosphere microbiome of ginseng grown under a variety of conditions continues to greatly expand our knowledge of the diversity and abundance of those organisms as well as their impacts of cultivation. While there is much more to be learnt, many aspects of the ginseng rhizosphere microbiome have already been revealed.
Collapse
|
9
|
Lahlali R, Ibrahim DS, Belabess Z, Kadir Roni MZ, Radouane N, Vicente CS, Menéndez E, Mokrini F, Barka EA, Galvão de Melo e Mota M, Peng G. High-throughput molecular technologies for unraveling the mystery of soil microbial community: challenges and future prospects. Heliyon 2021; 7:e08142. [PMID: 34693062 PMCID: PMC8515249 DOI: 10.1016/j.heliyon.2021.e08142] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 08/08/2021] [Accepted: 10/04/2021] [Indexed: 12/12/2022] Open
Abstract
Soil microbial communities play a crucial role in soil fertility, sustainability, and plant health. However, intensive agriculture with increasing chemical inputs and changing environments have influenced native soil microbial communities. Approaches have been developed to study the structure, diversity, and activity of soil microbes to better understand the biology and plant-microbe interactions in soils. Unfortunately, a good understanding of soil microbial community remains a challenge due to the complexity of community composition, interactions of the soil environment, and limitations of technologies, especially related to the functionality of some taxa rarely detected using conventional techniques. Culture-based methods have been shown unable and sometimes are biased for assessing soil microbial communities. To gain further knowledge, culture-independent methods relying on direct analysis of nucleic acids, proteins, and lipids are worth exploring. In recent years, metagenomics, metaproteomics, metatranscriptomics, and proteogenomics have been increasingly used in studying microbial ecology. In this review, we examined the importance of microbial community to soil quality, the mystery of rhizosphere and plant-microbe interactions, and the biodiversity and multi-trophic interactions that influence the soil structure and functionality. The impact of the cropping system and climate change on the soil microbial community was also explored. Importantly, progresses in molecular biology, especially in the development of high-throughput biotechnological tools, were extensively assessed for potential uses to decipher the diversity and dynamics of soil microbial communities, with the highlighted advantages/limitations.
Collapse
Affiliation(s)
- Rachid Lahlali
- Plant Pathology Unit, Department of Plant Protection, Ecole Nationale d’Agriculture de Meknes, BP S/40, 50001, Meknes, Morocco
| | - Dina S.S. Ibrahim
- Department of Nematodes Diseases and Central Lab of Biotechnology, Plant Pathology Research Institute, Agricultural Research Center (ARC), 12619, Egypt
| | - Zineb Belabess
- Plant Protection Laboratory. Regional Center of Agricultural Research of Oujda, National Institute of Agricultural Research, Avenue Mohamed VI, BP428 60000 Oujda, Morocco
| | - Md Zohurul Kadir Roni
- Tropical Agriculture Research Front, Japan International Research Center for Agricultural Sciences (JIRCAS), 1091-1 Maezato-Kawarabaru, Ishigaki, Okinawa, 907-0002, Japan
| | - Nabil Radouane
- Plant Pathology Unit, Department of Plant Protection, Ecole Nationale d’Agriculture de Meknes, BP S/40, 50001, Meknes, Morocco
- Department of Biology, Laboratory of Functional Ecology and Environmental Engineering, FST-Fez, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Cláudia S.L. Vicente
- MED – Mediterranean Institute for Agriculture, Environment and Development, Institute for Advanced Studies and Research (IIFA), Universidade de Évora, Pólo da Mitra, Ap. 94, 7006-554 Évora, Portugal
- INIAV, I.P. - Instituto Nacional de Investigação Agrária e Veterinária, Quinta do Marquês, 2780-159 Oeiras, Portugal
| | - Esther Menéndez
- INIAV, I.P. - Instituto Nacional de Investigação Agrária e Veterinária, Quinta do Marquês, 2780-159 Oeiras, Portugal
- Department of Microbiology and Genetics / Spanish-Portuguese Institute for Agricultural Research (CIALE). University of Salamanca, 37007, Salamanca, Spain
| | - Fouad Mokrini
- Plant Protection Laboratory, INRA, Centre Régional de la Recherche Agronomique (CRRA), Rabat, Morocco
| | - Essaid Ait Barka
- Unité de Recherche Résistance Induite et Bio-protection des Plantes, EA 4707, USC, INRAe1488, Université de Reims Champagne-Ardenne, France
| | - Manuel Galvão de Melo e Mota
- NemaLab, MED – Mediterranean Institute for Agriculture, Environment and Development & Department of Biology, Escola de Ciências e Tecnologia, Universidade de Évora, Pólo da Mitra, Ap. 94, 7006-554 Évora, Portugal
| | - Gary Peng
- Saskatoon Research Development Centre, Agriculture and Agri-Food, Saskatchewan, Canada
| |
Collapse
|
10
|
Guijarro B, Casals C, Teixidó N, Larena I, Melgarejo P, De Cal A. Balance between resilient fruit surface microbial community and population of Monilinia spp. after biopesticide field applications of Penicillium frequentans. Int J Food Microbiol 2020; 333:108788. [PMID: 32711131 DOI: 10.1016/j.ijfoodmicro.2020.108788] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 06/30/2020] [Accepted: 07/08/2020] [Indexed: 11/28/2022]
Abstract
The microbial variability on the host plant surface must be maintained because population diversity and quantity are essential to avoid disease development. It would be necessary to examine the patterns and mechanisms associated with the massive and reiterative introduction of a microbial pest control agent. The effect of inundative releases of biopesticide formulations containing Penicillium frequentans for the control of Monilinia spp. populations, and the effect on fruit surface microbiota on 18 stone fruit field experiments located in four European countries for more than two crop seasons against brown rot were studied. P. frequentans was monitored after application in order to assess whether it was persistent or not in the environment. Hydrolysis of fluorescein diacetate and denaturing gradient gel electrophoresis were used to study the effects of P. frequentans on fungal and bacterial non-target populations on fruit surface. The effect of P. frequentans formulations on the populations of Monilinia spp. on fruit was also assessed in different orchards. P. frequentans population on stone fruit surfaces showed ranged from 100 to 10,000 CFU cm-2, and postharvest recovered populations were more than 10-100-fold higher than preharvest recovered populations. The population of P. frequentans varied among orchards and years, rather than by the type of formulation. P. frequentans formulation reduced Monilinia spp. population and brown rot and latent infections caused by this pathogen both before and at harvest, while stabilizing or increasing antagonist populations and avoiding non-target microorganisms. However, fungicides reduced significantly the microbial activity on nectarine surfaces.
Collapse
Affiliation(s)
- Belén Guijarro
- Department of Plant Protection, INIA, Ctra. de La Coruña Km. 7, 28040, Madrid, Spain
| | - Carla Casals
- IRTA, XaRTA-Postharvest, Edifici Fruitcentre, Parc Científic i Tecnologic Agroalimentari de Lleida, 25003 Lleida, Spain
| | - Neus Teixidó
- IRTA, XaRTA-Postharvest, Edifici Fruitcentre, Parc Científic i Tecnologic Agroalimentari de Lleida, 25003 Lleida, Spain
| | - Inmaculada Larena
- Department of Plant Protection, INIA, Ctra. de La Coruña Km. 7, 28040, Madrid, Spain
| | - Paloma Melgarejo
- Department of Plant Protection, INIA, Ctra. de La Coruña Km. 7, 28040, Madrid, Spain
| | - Antonieta De Cal
- Department of Plant Protection, INIA, Ctra. de La Coruña Km. 7, 28040, Madrid, Spain.
| |
Collapse
|
11
|
Gryta A, Frąc M. Methodological Aspects of Multiplex Terminal Restriction Fragment Length Polymorphism-Technique to Describe the Genetic Diversity of Soil Bacteria, Archaea and Fungi. SENSORS 2020; 20:s20113292. [PMID: 32527006 PMCID: PMC7309186 DOI: 10.3390/s20113292] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 06/05/2020] [Accepted: 06/07/2020] [Indexed: 01/24/2023]
Abstract
The molecular fingerprinting methods used to evaluate soil microbial diversity could also be used as effective biosensors for the purposes of monitoring ecological soil status. The biodiversity of microorganisms is a relevant index of soil activity and there is a necessity to develop tools to generate reliable results for an emerging approach in the field of environmental control using microbial diversity biosensors. This work reports a method under development for determining soil microbial diversity using high efficiency Multiplex PCR-Terminal Restriction Fragment Length Polymorphism (M-T-RFLP) for the simultaneous detection of bacteria, archaea and fungi. Three different primer sets were used in the reaction and the analytical conditions were optimized. Optimal analytical conditions were achieved using 0.5 µM of primer for bacteria and 1 µM for archaea and fungi, 4 ng of soil DNA template, and HaeIII restriction enzyme. Comparative tests using the proposed analytical approach and a single analysis of each microorganism group were carried out to indicate that both genetic profiles were similar. The Jaccard similarity coefficient between single and multiplexing approach ranged from 0.773 to 0.850 for bacteria and fungi, and 0.208 to 0.905 for archaea. In conclusion, the multiplexing and pooling approaches significantly reduced the costs and time required to perform the analyses, while maintaining a proper effectiveness.
Collapse
|
12
|
Yang J, Wei S, Su D, Zhang Z, Chen S, Luo Z, Shen X, Lai Y, Jamil A, Tong J, Cui X. Comparison of the Rhizosphere Soil Microbial Community Structure and Diversity Between Powdery Mildew-Infected and Noninfected Strawberry Plants in a Greenhouse by High-Throughput Sequencing Technology. Curr Microbiol 2020; 77:1724-1736. [PMID: 32314037 DOI: 10.1007/s00284-020-01948-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 03/09/2020] [Indexed: 10/24/2022]
Abstract
The aim of this study was to compare the microbial community structure and diversity in powdery mildew-infected and noninfected strawberry plant rhizosphere soils in the greenhouse based on variations in the 16S rRNA gene V3-V4 and fungal ITS2 regions by Illumina amplicon sequencing. Powdery mildew infection reduced the number of operational taxonomic units (OTUs) and prokaryotic and fungal community richness/diversity indexes in the rhizosphere soils compared with those in healthy plant soils. Furthermore, 3543 prokaryotic and 581 fungal OTUs were obtained at the 97% similarity level. Proteobacteria, Actinobacteria, Bacteroidetes, Acidobacteria, and Chloroflexi were the dominant bacterial phyla; Woesearchaeota_DHVEG-6, Bathyarchaeota, and Thaumarchaeota were the dominant archaea; and Ascomycota, Basidiomycota, unclassified_fungi, and Zygomycota were the dominant fungal phyla. Their proportions differed significantly among samples. Wolbachia, Devosia, Pseudolabrys, Streptomyces, and Rhizomicrobium were the most abundant bacterial genera; their proportions differed significantly among samples. Most Pseudomonas, Streptomyces, and 'norank' group members might be potential antagonistic microorganisms of powdery mildew pathogens, and Wolbachia and Rickettsia might be pathogen-transmitting vectors. Microascus, Clitopilus, and Ciliophora were the dominant fungi, and their community structures and abundances significantly differed among samples. Microascus, Talaromyces, Zopfiella, and Cryptococcus were relatively more abundant in the powdery mildew-infected strawberry plant rhizosphere soils. Fusarium, Trichoderma, Clitopilus, and 'unclassified' group members may be potential antagonistic populations. The results suggested that powdery mildew-infected strawberry fruits and plants cannot be consumed. This report is the first study to illustrate differences in the rhizosphere soil prokaryotic and fungal communities between powdery mildew-infected and noninfected strawberry plants in a greenhouse.
Collapse
Affiliation(s)
- Junyu Yang
- School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, Yunnan, People's Republic of China.,State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, Yunnan, People's Republic of China
| | - Shijie Wei
- Kunming Academy of Agricultural Science, Kunming, 650034, Yunnan, People's Republic of China
| | - Daifa Su
- School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, Yunnan, People's Republic of China.,State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, Yunnan, People's Republic of China
| | - Zhengrong Zhang
- Kunming Academy of Agricultural Science, Kunming, 650034, Yunnan, People's Republic of China
| | - Shanyan Chen
- Kunming Academy of Agricultural Science, Kunming, 650034, Yunnan, People's Republic of China
| | - Zhiwei Luo
- Kunming Academy of Agricultural Science, Kunming, 650034, Yunnan, People's Republic of China
| | - Xuemei Shen
- Kunming Academy of Agricultural Science, Kunming, 650034, Yunnan, People's Republic of China
| | - Yonghong Lai
- School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, Yunnan, People's Republic of China
| | - Arslan Jamil
- School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, Yunnan, People's Republic of China.,State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, Yunnan, People's Republic of China
| | - Jiangyun Tong
- Kunming Academy of Agricultural Science, Kunming, 650034, Yunnan, People's Republic of China.
| | - Xiaolong Cui
- School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, Yunnan, People's Republic of China. .,State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, Yunnan, People's Republic of China.
| |
Collapse
|
13
|
Jaiswal S, Gautam RK, Singh RK, Krishnamurthy SL, Ali S, Sakthivel K, Iquebal MA, Rai A, Kumar D. Harmonizing technological advances in phenomics and genomics for enhanced salt tolerance in rice from a practical perspective. RICE (NEW YORK, N.Y.) 2019; 12:89. [PMID: 31802312 PMCID: PMC6892996 DOI: 10.1186/s12284-019-0347-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 11/06/2019] [Indexed: 05/12/2023]
Abstract
Half of the global human population is dependent on rice as a staple food crop and more than 25% increase in rice productivity is required to feed the global population by 2030. With increase in irrigation, global warming and rising sea level, rising salinity has become one of the major challenges to enhance the rice productivity. Since the loss on this account is to the tune of US$12 billion per annum, it necessitates the global attention. In the era of technological advancement, substantial progress has been made on phenomics and genomics data generation but reaping benefit of this in rice salinity variety development in terms of cost, time and precision requires their harmonization. There is hardly any comprehensive holistic review for such combined approach. Present review describes classical salinity phenotyping approaches having morphological, physiological and biochemical components. It also gives a detailed account of invasive and non-invasive approaches of phenomic data generation and utilization. Classical work of rice salinity QLTs mapping in the form of chromosomal atlas has been updated. This review describes how QTLs can be further dissected into QTN by GWAS and transcriptomic approaches. Opportunities and progress made by transgenic, genome editing, metagenomics approaches in combating rice salinity problems are discussed. Major aim of this review is to provide a comprehensive over-view of hitherto progress made in rice salinity tolerance research which is required to understand bridging of phenotype based breeding with molecular breeding. This review is expected to assist rice breeders in their endeavours by fetching greater harmonization of technological advances in phenomics and genomics for better pragmatic approach having practical perspective.
Collapse
Affiliation(s)
- Sarika Jaiswal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistical Research Institute, PUSA, New Delhi, 110012, India
| | - R K Gautam
- Division of Field Crop Improvement & Protection, ICAR-Central Island Agricultural Research Institute, Port Blair, Andaman and Nicobar Islands, 744105, India.
| | - R K Singh
- Division of Plant Breeding Genetics and Biotechnology, International Rice Research Institute, DAPO Box 7777, Los Banos, Metro Manila, Philippines
| | - S L Krishnamurthy
- Division of Crop Improvement, ICAR-Central Soil Salinity Research Institute, Karnal, Haryana, 132001, India
| | - S Ali
- Division of Crop Improvement, ICAR-Central Soil Salinity Research Institute, Karnal, Haryana, 132001, India
| | - K Sakthivel
- Division of Field Crop Improvement & Protection, ICAR-Central Island Agricultural Research Institute, Port Blair, Andaman and Nicobar Islands, 744105, India
| | - M A Iquebal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistical Research Institute, PUSA, New Delhi, 110012, India
| | - Anil Rai
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistical Research Institute, PUSA, New Delhi, 110012, India
| | - Dinesh Kumar
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistical Research Institute, PUSA, New Delhi, 110012, India.
| |
Collapse
|
14
|
Madigan AP, Egidi E, Bedon F, Franks AE, Plummer KM. Bacterial and Fungal Communities Are Differentially Modified by Melatonin in Agricultural Soils Under Abiotic Stress. Front Microbiol 2019; 10:2616. [PMID: 31849848 PMCID: PMC6901394 DOI: 10.3389/fmicb.2019.02616] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 10/28/2019] [Indexed: 12/29/2022] Open
Abstract
An extensive body of evidence from the last decade has indicated that melatonin enhances plant resistance to a range of biotic and abiotic stressors. This has led to an interest in the application of melatonin in agriculture to reduce negative physiological effects from environmental stresses that affect yield and crop quality. However, there are no reports regarding the effects of melatonin on soil microbial communities under abiotic stress, despite the importance of microbes for plant root health and function. Three agricultural soils associated with different land usage histories (pasture, canola or wheat) were placed under abiotic stress by cadmium (100 or 280 mg kg-1 soil) or salt (4 or 7 g kg-1 soil) and treated with melatonin (0.2 and 4 mg kg-1 soil). Automated Ribosomal Intergenic Spacer Analysis (ARISA) was used to generate Operational Taxonomic Units (OTU) for microbial community analysis in each soil. Significant differences in richness (α diversity) and community structures (β diversity) were observed between bacterial and fungal assemblages across all three soils, demonstrating the effect of melatonin on soil microbial communities under abiotic stress. The analysis also indicated that the microbial response to melatonin is governed by the type of soil and history. The effects of melatonin on soil microbes need to be regarded in potential future agricultural applications.
Collapse
Affiliation(s)
- Andrew P. Madigan
- Department of Animal, Plant and Soil Sciences, AgriBio, La Trobe University, Melbourne, VIC, Australia
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Melbourne, VIC, Australia
| | - Eleonora Egidi
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, Australia
| | - Frank Bedon
- Department of Animal, Plant and Soil Sciences, AgriBio, La Trobe University, Melbourne, VIC, Australia
| | - Ashley E. Franks
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Melbourne, VIC, Australia
- Centre for Future Landscapes, School of Life Sciences, La Trobe University, Melbourne, VIC, Australia
| | - Kim M. Plummer
- Department of Animal, Plant and Soil Sciences, AgriBio, La Trobe University, Melbourne, VIC, Australia
| |
Collapse
|
15
|
Fernandez M, Pereira PP, Agostini E, González PS. How the bacterial community of a tannery effluent responds to bioaugmentation with the consortium SFC 500-1. Impact of environmental variables. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2019; 247:46-56. [PMID: 31229785 DOI: 10.1016/j.jenvman.2019.06.055] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 05/17/2019] [Accepted: 06/11/2019] [Indexed: 06/09/2023]
Abstract
Bioaugmentation with the consortium SFC 500-1 is a promising alternative to remediate wastewaters, such as tannery effluents. With the aim of assessing the changes produced in response to bioaugmentation, bacterial 16S rDNA genes were sequenced with Illumina MiSeq Platform. Additionally, bacterial and fungal groups were analyzed through standard culture dependent methods. The impact of diverse physico-chemical and microbiological parameters on the prokaryotic diversity was also evaluated throughout. Bacteroidetes, Firmicutes and Proteobacteria, represented together up to 91% of the total number of sequences obtained from the tannery effluent. Diversity decreased immediately after inoculation, due to an increase in the representation of the taxa to which the added consortium belongs. However, bioaugmentation produced no greater variations since only a 10% of unique operational taxonomic units were found in the inoculated treatment. An increase in the abundance of Myroides and a reduction in the representation of Proteiniclasticum and Halomonas were major observed variations. On the other hand, pH and dissolved oxygen constituted main environmental factors affecting the structure of the prokaryotic communities. In all treatments yeasts increased over time, to the detriment of filamentous fungi. Together, data from this report may contribute to the development of improved bioremediation strategies of industrial wastewaters.
Collapse
Affiliation(s)
- Marilina Fernandez
- Departamento de Biología Molecular, FCEFQyN, Universidad Nacional de Río Cuarto, 5800, Río Cuarto, Córdoba, Argentina; CONICET, UNRC, Instituto de Biotecnología Ambiental y Salud (INBIAS), Río Cuarto, Córdoba, Argentina.
| | - Paola P Pereira
- Departamento de Biología Molecular, FCEFQyN, Universidad Nacional de Río Cuarto, 5800, Río Cuarto, Córdoba, Argentina; CONICET, UNRC, Instituto de Biotecnología Ambiental y Salud (INBIAS), Río Cuarto, Córdoba, Argentina.
| | - Elizabeth Agostini
- Departamento de Biología Molecular, FCEFQyN, Universidad Nacional de Río Cuarto, 5800, Río Cuarto, Córdoba, Argentina; CONICET, UNRC, Instituto de Biotecnología Ambiental y Salud (INBIAS), Río Cuarto, Córdoba, Argentina.
| | - Paola S González
- Departamento de Biología Molecular, FCEFQyN, Universidad Nacional de Río Cuarto, 5800, Río Cuarto, Córdoba, Argentina; CONICET, UNRC, Instituto de Biotecnología Ambiental y Salud (INBIAS), Río Cuarto, Córdoba, Argentina.
| |
Collapse
|
16
|
A 16S rDNA PCR-based theoretical to actual delta approach on culturable mock communities revealed severe losses of diversity information. BMC Microbiol 2019; 19:74. [PMID: 30961521 PMCID: PMC6454784 DOI: 10.1186/s12866-019-1446-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 03/28/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Subunits of ribosomal RNA genes (rDNAs) characterized by PCR-based protocols have been the proxy for studies in microbial taxonomy, phylogenetics, evolution and ecology. However, relevant factors have shown to interfere in the experimental outputs in a variety of systems. In this work, a 'theoretical' to 'actual' delta approach was applied to data on culturable mock bacterial communities (MBCs) to study the levels of losses in operational taxonomic units (OTUs) detectability. Computational and lab-bench strategies based on 16S rDNA amplification by 799F and U1492R primers were employed, using a fingerprinting method with highly improved detectability of fragments as a case-study tool. MBCs were of two major types: in silico MBCs, assembled with database-retrieved sequences, and in vitro MBCs, with AluI digestions of PCR data generated from culturable endophytes isolated from cacao trees. RESULTS Interfering factors for the 16 s rDNA amplifications, such as the type of template, direct and nested PCR, proportion of chloroplast DNA from a tropical plant source (Virola officinalis), and biased-amplification by the primers resulted in altered bacterial 16S rDNA amplification, both on MBCs and V. officinalis leaf-extracted DNA. For the theoretical data, the maximum number of fragments for in silico and in vitro cuts were not significantly different from each other. Primers' preferences for certain sequences were detected, depending on the MBCs' composition prior to PCR. The results indicated overall losses from 2.3 up to 8.2 times in the number of OTUs detected from actual AluI digestions of MBCs when compared to in silico and in vitro theoretical data. CONCLUSIONS Due to all those effects, the final amplification profile of the bacterial community assembled was remarkably simplified when compared to the expected number of detectable fragments known to be present in the MBC. From these findings, the scope of hypotheses generation and conclusions from experiments based on PCR amplifications of bacterial communities was discussed.
Collapse
|
17
|
The Effects of Different Lead Pollution Levels on Soil Microbial Quantities and Metabolic Function with/without Salix integra Thunb. Planting. FORESTS 2019. [DOI: 10.3390/f10020077] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Background and Objectives: Salix integra Thunb., a fast-growing woody species, has been used in phytoremediation in recent years. It has the potential to accumulate high amounts of lead (Pb) in its growth, however, its effects on soil microbial community structure and function during its phytoextraction processes are not well understood, especially at different pollution levels. Materials and Methods: In our study, we set unplanted and planted Salix integra in areas with four levels of Pb treatments (0, 500, 1000, and 1500 mg/kg). After six months of planting, the rhizospheric soil, bulk soil, and unplanted soil were collected. Soil properties and microbes participating in nitrogen and phosphorus cycling were measured, following standard methods. Microbial metabolic functions were assessed using a Biolog-ECO microplate. Results: The bacteria (nitrogen-fixing bacteria, ammonifying bacteria, inorganic phosphorus-solubilizing bacteria, and nitrosobacteria) all increased in the 500 mg/kg treatment and decreased in the 1500 mg/kg treatment compared with the 0 mg/kg treatment, especially in rhizospheric soil. The microbial metabolisms decreased along with the increase of Pb levels, with the exception of the rhizospheric soil with a 500 mg/kg treatment. The metabolic patterns were relative to the pollution levels. The utilization of carbohydrates was decreased, and of amino acids or fatty acids was increased, in the 500 mg/kg treatment, while the opposite occurred in the 1500 mg/kg treatment. The values of soil properties, microbial quantities, and metabolic activities were higher in rhizospheric than bulk soil, while the differences between bulk and unplanted soil were different among the different Pb treatments. The soil properties had little effect on the microbial quantities and metabolic activities. Conclusions: S. integra planting and Pb levels had an interactive effect on the microbial community. In general, S. integra planting promoted microbial quantities and metabolic activity in rhizospheric soil. Lower Pb pollution increased microbial quantities and promoted the utilization of amino acids or fatty acids, while higher Pb concentrations decreased microbial quantities and metabolic activities, and promoted the utilization of carbohydrates.
Collapse
|
18
|
Mukhtar S, Mirza BS, Mehnaz S, Mirza MS, Mclean J, Malik KA. Impact of soil salinity on the microbial structure of halophyte rhizosphere microbiome. World J Microbiol Biotechnol 2018; 34:136. [PMID: 30128756 DOI: 10.1007/s11274-018-2509-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Accepted: 07/27/2018] [Indexed: 02/01/2023]
Abstract
The rhizosphere microbiome plays a significant role in the life of plants in promoting plant survival under adverse conditions. However, limited information is available about microbial diversity in saline environments. In the current study, we compared the composition of the rhizosphere microbiomes of the halophytes Urochloa, Kochia, Salsola, and Atriplex living in moderate and high salinity environments (Khewra salt mines; Pakistan) with that of the non-halophyte Triticum. Soil microbiomes analysis using pyrosequencing of 16S rRNA gene indicated that Actinobacteria were dominant in saline soil samples whereas Proteobacteria predominated in non-saline soil samples. Firmicutes, Acidobacteria, Bacteriodetes and Thaumarchaeota were predominant phyla in saline and non-saline soils, whereas Cyanobacteria, Verrucomicrobia, Gemmatimonadetes and the unclassified WPS-2 were less abundant. Sequences from Euryarchaeota, Ignavibacteriae, and Nanohaloarchaeota were identified only from the rhizosphere of halophytes. Dominant halophilic bacteria and archaea identified in this study included Agrococcus, Armatimonadetes gp4, Halalkalicoccus, Haloferula and Halobacterium. Our analysis showed that increases in soil salinity correlated with significant differences in the alpha and beta diversity of the microbial communities across saline and non-saline soil samples. Having a complete inventory of the soil bacteria from different saline environments in Pakistan will help in the discovery of potential inoculants for crops growing on salt-affected land.
Collapse
Affiliation(s)
- Salma Mukhtar
- Department of Biological Sciences, Forman Christian College (A Chartered University), Ferozepur Road, Lahore, 54600, Pakistan
| | - Babur Saeed Mirza
- Department of Biology, Missouri State University, 901 S, National Ave, Springfield, MO, USA
| | - Samina Mehnaz
- Department of Biological Sciences, Forman Christian College (A Chartered University), Ferozepur Road, Lahore, 54600, Pakistan
| | - Muhammad Sajjad Mirza
- Environmental Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Jhang Road, Faisalabad, Pakistan
| | - Joan Mclean
- Utah Water Research Laboratory, Department of Civil and Environmental Engineering, Utah State University, Logan, UT, 84322-8200, USA
| | - Kauser Abdulla Malik
- Department of Biological Sciences, Forman Christian College (A Chartered University), Ferozepur Road, Lahore, 54600, Pakistan.
| |
Collapse
|
19
|
An F, Diao Z, Lv J. Microbial diversity and community structure in agricultural soils suffering from 4 years of Pb contamination. Can J Microbiol 2018; 64:305-316. [DOI: 10.1139/cjm-2017-0278] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Heavy metal pollution has become a widespread environmental problem due to rapid economic development. The phylogenetic diversity and structure of microbial communities in lead (Pb)-contaminated Lou soils were investigated using Illumina MiSeq sequencing of 16S rRNA genes. The presence of Pb2+ in soil showed weak impact on the diversity of soil bacteria community, but it influenced the abundance of some genera of bacteria, as well as soil physicochemical properties. We found significant differences in the relative abundances of heavy-metal-resistant bacteria such as Bacillus, Streptococcus, and Arthrobacter at the genus level. Available Pb and total Pb negatively correlated with soil organic matter but positively affected available phosphorus. The abundance of main bacteria phyla was highly correlated with total Pb. The relative abundance of Gemmatimonadetes, Nitrospirae, and Planctomycetes was negatively correlated with total Pb. Collectively, Pb influences both the microbial community composition and physicochemical properties of soil.
Collapse
Affiliation(s)
- Fengqiu An
- College of Natural Resources and Environment, Northwest A&F University, Ministry of Agriculture Key Laboratory of Plant Nutrition and Agri-environment in Northwest China, Yangling 712100, People’s Republic of China
- College of Environmental and Chemical Engineering, Polytechnic University, Xi’an 710048, People’s Republic of China
| | - Zhan Diao
- College of Natural Resources and Environment, Northwest A&F University, Ministry of Agriculture Key Laboratory of Plant Nutrition and Agri-environment in Northwest China, Yangling 712100, People’s Republic of China
- Law School & Intellectual Property School, JiNan University, Guangzhou 510632, People’s Republic of China
| | - Jialong Lv
- College of Natural Resources and Environment, Northwest A&F University, Ministry of Agriculture Key Laboratory of Plant Nutrition and Agri-environment in Northwest China, Yangling 712100, People’s Republic of China
| |
Collapse
|
20
|
Bonilla JO, Kurth DG, Cid FD, Ulacco JH, Gil RA, Villegas LB. Prokaryotic and eukaryotic community structure affected by the presence of an acid mine drainage from an abandoned gold mine. Extremophiles 2018; 22:699-711. [DOI: 10.1007/s00792-018-1030-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 04/20/2018] [Indexed: 12/11/2022]
|
21
|
Chagas FO, Pessotti RDC, Caraballo-Rodríguez AM, Pupo MT. Chemical signaling involved in plant-microbe interactions. Chem Soc Rev 2018; 47:1652-1704. [PMID: 29218336 DOI: 10.1039/c7cs00343a] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Microorganisms are found everywhere, and they are closely associated with plants. Because the establishment of any plant-microbe association involves chemical communication, understanding crosstalk processes is fundamental to defining the type of relationship. Although several metabolites from plants and microbes have been fully characterized, their roles in the chemical interplay between these partners are not well understood in most cases, and they require further investigation. In this review, we describe different plant-microbe associations from colonization to microbial establishment processes in plants along with future prospects, including agricultural benefits.
Collapse
Affiliation(s)
- Fernanda Oliveira Chagas
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo (FCFRP-USP), Avenida do Café, s/n, 14040-903, Ribeirão Preto-SP, Brazil.
| | | | | | | |
Collapse
|
22
|
Igiehon NO, Babalola OO. Rhizosphere Microbiome Modulators: Contributions of Nitrogen Fixing Bacteria towards Sustainable Agriculture. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2018; 15:ijerph15040574. [PMID: 29570619 PMCID: PMC5923616 DOI: 10.3390/ijerph15040574] [Citation(s) in RCA: 105] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 03/03/2018] [Accepted: 03/19/2018] [Indexed: 02/05/2023]
Abstract
Rhizosphere microbiome which has been shown to enhance plant growth and yield are modulated or influenced by a few environmental factors such as soil type, plant cultivar, climate change and anthropogenic activities. In particular, anthropogenic activity, such as the use of nitrogen-based chemical fertilizers, is associated with environmental destruction and this calls for a more ecofriendly strategy to increase nitrogen levels in agricultural land. This feat is attainable by harnessing nitrogen-fixing endophytic and free-living rhizobacteria. Rhizobium, Pseudomonas, Azospirillum and Bacillus, have been found to have positive impacts on crops by enhancing both above and belowground biomass and could therefore play positive roles in achieving sustainable agriculture outcomes. Thus, it is necessary to study this rhizosphere microbiome with more sophisticated culture-independent techniques such as next generation sequencing (NGS) with the prospect of discovering novel bacteria with plant growth promoting traits. This review is therefore aimed at discussing factors that can modulate rhizosphere microbiome with focus on the contributions of nitrogen fixing bacteria towards sustainable agricultural development and the techniques that can be used for their study.
Collapse
Affiliation(s)
- Nicholas Ozede Igiehon
- Food Security and Safety Niche, Faculty of Natural and Agricultural Science, Private Mail Bag X2046, North West University, Mmabatho 2735, South Africa.
| | - Olubukola Oluranti Babalola
- Food Security and Safety Niche, Faculty of Natural and Agricultural Science, Private Mail Bag X2046, North West University, Mmabatho 2735, South Africa.
| |
Collapse
|
23
|
Grün AL, Emmerling C. Long-term effects of environmentally relevant concentrations of silver nanoparticles on major soil bacterial phyla of a loamy soil. ENVIRONMENTAL SCIENCES EUROPE 2018; 30:31. [PMID: 30221103 PMCID: PMC6132800 DOI: 10.1186/s12302-018-0160-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 08/20/2018] [Indexed: 05/12/2023]
Abstract
BACKGROUND The growing production and use of engineered AgNP in industry and private households make increasing concentrations of AgNP in the environment unavoidable. Although we already know the harmful effects of AgNP on pivotal bacterial driven soil functions, information about the impact of silver nanoparticles (AgNP) on the soil bacterial community structure is rare. Hence, the aim of this study was to reveal the long-term effects of AgNP on major soil bacterial phyla in a loamy soil. The study was conducted as a laboratory incubation experiment over a period of 1 year using a loamy soil and AgNP concentrations ranging from 0.01 to 1 mg AgNP/kg soil. Effects were quantified using the taxon-specific 16S rRNA qPCR. RESULTS The short-term exposure of AgNP at environmentally relevant concentration of 0.01 mg AgNP/kg caused significant positive effects on Acidobacteria (44.0%), Actinobacteria (21.1%) and Bacteroidetes (14.6%), whereas beta-Proteobacteria population was minimized by 14.2% relative to the control (p ≤ 0.05). After 1 year of exposure to 0.01 mg AgNP/kg diminished Acidobacteria (p = 0.007), Bacteroidetes (p = 0.005) and beta-Proteobacteria (p = 0.000) by 14.5, 10.1 and 13.9%, respectively. Actino- and alpha-Proteobacteria were statistically unaffected by AgNP treatments after 1-year exposure. Furthermore, a statistically significant regression and correlation analysis between silver toxicity and exposure time confirmed loamy soils as a sink for silver nanoparticles and their concomitant silver ions. CONCLUSIONS Even very low concentrations of AgNP may cause disadvantages for the autotrophic ammonia oxidation (nitrification), the organic carbon transformation and the chitin degradation in soils by exerting harmful effects on the liable bacterial phyla.
Collapse
Affiliation(s)
- Anna-Lena Grün
- Department of Soil Science, Faculty of Regional and Environmental Science, University of Trier, Campus II, Behringstraße 21, 54296 Trier, Germany
| | - Christoph Emmerling
- Department of Soil Science, Faculty of Regional and Environmental Science, University of Trier, Campus II, Behringstraße 21, 54296 Trier, Germany
| |
Collapse
|
24
|
Cao Q, Steinman AD, Su X, Xie L. Effects of microcystins contamination on soil enzyme activities and microbial community in two typical lakeside soils. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2017; 231:134-142. [PMID: 28797902 DOI: 10.1016/j.envpol.2017.08.013] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 08/02/2017] [Accepted: 08/03/2017] [Indexed: 06/07/2023]
Abstract
A 30-day indoor incubation experiment was conducted to investigate the effects of different concentrations of microcystin (1, 10, 100 and 1000 μg eq. MC-LR L-1) on soil enzyme activity, soil respiration, physiological profiles, potential nitrification, and microbial abundance (total bacteria, total fungi, ammonia-oxidizing bacteria and archaea) in two lakeside soils in China (Soil A from the lakeside of Lake Poyanghu at Jiujiang; Soil B from the lakeside of Lake Taihu at Suzhou). Of the enzymes tested, only phenol oxidase activity was negatively affected by microcystin application. In contrast, dehydrogenase activity was stimulated in the 1000 μg treatment, and a stimulatory effect also occurred with soil respiration in contaminated soil. The metabolic profiles of the microbial communities indicated that overall carbon metabolic activity in the soils treated with high microcystin concentrations was inhibited, and high concentrations of microcystin also led to different patterns of potential carbon utilization. High microcystin concentrations (100, 1000 μg eq. MC-LR L-1 in Soil A; 10, 100 1000 μg eq. MC-LR L-1 in Soil B) significantly decreased soil potential nitrification rate. Furthermore, the decrease in soil potential nitrification rate was positively correlated with the decrease of the amoA gene abundance, which corresponds to the ammonia-oxidizing bacterial community. We conclude that application of microcystin-enriched irrigation water can significantly impact soil microbial community structure and function.
Collapse
Affiliation(s)
- Qing Cao
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, 73 East Beijing Road, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Alan D Steinman
- Annis Water Resources Institute, Grand Valley State University, 740 West Shoreline Drive, Muskegon, MI 49441, USA
| | - Xiaomei Su
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, 73 East Beijing Road, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liqiang Xie
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, 73 East Beijing Road, Nanjing 210008, China.
| |
Collapse
|
25
|
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.
Collapse
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.
| |
Collapse
|
26
|
Kim K, Islam R, Benson A, Joe MM, Denver W, Chanratan M, Chatterjee P, Kang Y, Sa T. An Overview of Different Techniques on the Microbial Community Structure, and Functional Diversity of Plant Growth Promoting Bacteria. ACTA ACUST UNITED AC 2016. [DOI: 10.7745/kjssf.2016.49.2.144] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
27
|
Miao CP, Mi QL, Qiao XG, Zheng YK, Chen YW, Xu LH, Guan HL, Zhao LX. Rhizospheric fungi of Panax notoginseng: diversity and antagonism to host phytopathogens. J Ginseng Res 2016; 40:127-34. [PMID: 27158233 PMCID: PMC4845048 DOI: 10.1016/j.jgr.2015.06.004] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Revised: 05/04/2015] [Accepted: 06/14/2015] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Rhizospheric fungi play an essential role in the plant-soil ecosystem, affecting plant growth and health. In this study, we evaluated the fungal diversity in the rhizosphere soil of 2-yr-old healthy Panax notoginseng cultivated in Wenshan, China. METHODS Culture-independent Illumina MiSeq and culture-dependent techniques, combining molecular and morphological characteristics, were used to analyze the rhizospheric fungal diversity. A diffusion test was used to challenge the phytopathogens of P. notoginseng. RESULTS A total of 16,130 paired-end reads of the nuclear ribosomal internal transcribed spacer 2 were generated and clustered into 860 operational taxonomic units at 97% sequence similarity. All the operational taxonomic units were assigned to five phyla and 79 genera. Zygomycota (46.2%) and Ascomycota (37.8%) were the dominant taxa; Mortierella and unclassified Mortierellales accounted for a large proportion (44.9%) at genus level. The relative abundance of Fusarium and Phoma sequences was high, accounting for 12.9% and 5.5%, respectively. In total, 113 fungal isolates were isolated from rhizosphere soil. They were assigned to five classes, eight orders (except for an Incertae sedis), 26 genera, and 43 species based on morphological characteristics and phylogenetic analysis of the internal transcribed spacer. Fusarium was the most isolated genus with six species (24 isolates, 21.2%). The abundance of Phoma was also relatively high (8.0%). Thirteen isolates displayed antimicrobial activity against at least one test fungus. CONCLUSION Our results suggest that diverse fungi including potential pathogenic ones exist in the rhizosphere soil of 2-yr-old P. notoginseng and that antagonistic isolates may be useful for biological control of pathogens.
Collapse
Affiliation(s)
- Cui-Ping Miao
- Key Laboratory of Microbial Diversity in Southwest China of Ministry of Education and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, China
| | - Qi-Li Mi
- Key Laboratory of Microbial Diversity in Southwest China of Ministry of Education and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, China
- Technology Center, China Tobacco Yunnan Industrial Co., Ltd, Kunming, China
| | - Xin-Guo Qiao
- Key Laboratory of Microbial Diversity in Southwest China of Ministry of Education and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, China
| | - You-Kun Zheng
- Key Laboratory of Microbial Diversity in Southwest China of Ministry of Education and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, China
| | - You-Wei Chen
- Key Laboratory of Microbial Diversity in Southwest China of Ministry of Education and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, China
| | - Li-Hua Xu
- Key Laboratory of Microbial Diversity in Southwest China of Ministry of Education and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, China
| | - Hui-Lin Guan
- School of Energy and Environment Science, Yunnan Normal University, Kunming, China
| | - Li-Xing Zhao
- Key Laboratory of Microbial Diversity in Southwest China of Ministry of Education and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, China
| |
Collapse
|
28
|
Ramesh P, Reena P, Amitbikram M, Chaitanya J, Anju K. Insight into the transcriptome of Arthrobotrys conoides using high throughput sequencing. J Basic Microbiol 2015; 55:1394-405. [PMID: 26301953 DOI: 10.1002/jobm.201500237] [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: 05/07/2015] [Accepted: 07/20/2015] [Indexed: 11/09/2022]
Abstract
Arthrobotrys conoides is a nematode-trapping fungus belonging to Orbiliales, Ascomycota group, and traps prey nematodes by means of adhesive network. Fungus has a potential to be used as a biocontrol agent against plant parasitic nematodes. In the present study, we characterized the transcriptome of A. conoides using high-throughput sequencing technology and characterized its virulence unigenes. Total 7,255 cDNA contigs with an average length of 425 bp were generated and 6184 (61.81%) transcripts were functionally annotated and characterized. Majority of unigenes were found analogous to the genes of plant pathogenic fungi. A total of 1749 transcripts were found to be orthologous with eukaryotic proteins of KOG database. Several carbohydrate active enzymes and peptidases were identified. We also analyzed classically and nonclassically secreted proteins and confirmed by BLASTP against fungal secretome database. A total of 916 contigs were analogous to 556 unique proteins of Pathogen Host Interaction (PHI) database. Further, we identified 91 unigenes homologous to the database of fungal virulence factor (DFVF). A total of 104 putative protein kinases coding transcripts were identified by BLASTP against KinBase database, which are major players in signaling pathways. This study provides a comprehensive look at the transcriptome of A. conoides and the identified unigenes might have a role in catching and killing prey nematodes by A. conoides.
Collapse
Affiliation(s)
- Pandit Ramesh
- Ashok and Rita Patel Institute of Integrated Study and Research in Biotechnology and Allied Sciences, New V.V. Nagar, Anand, Gujarat, India.,Department of Animal Biotechnology, College of Veterinary Science and A.H., Anand Agricultural University, Anand, Gujarat, India
| | - Patel Reena
- Ashok and Rita Patel Institute of Integrated Study and Research in Biotechnology and Allied Sciences, New V.V. Nagar, Anand, Gujarat, India
| | - Mohapatra Amitbikram
- Department of Animal Biotechnology, College of Veterinary Science and A.H., Anand Agricultural University, Anand, Gujarat, India
| | - Joshi Chaitanya
- Department of Animal Biotechnology, College of Veterinary Science and A.H., Anand Agricultural University, Anand, Gujarat, India
| | - Kunjadia Anju
- Ashok and Rita Patel Institute of Integrated Study and Research in Biotechnology and Allied Sciences, New V.V. Nagar, Anand, Gujarat, India
| |
Collapse
|
29
|
Bharti N, Barnawal D, Maji D, Kalra A. Halotolerant PGPRs Prevent Major Shifts in Indigenous Microbial Community Structure Under Salinity Stress. MICROBIAL ECOLOGY 2015; 70:196-208. [PMID: 25542205 DOI: 10.1007/s00248-014-0557-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Accepted: 12/09/2014] [Indexed: 05/27/2023]
Abstract
The resilience of soil microbial populations and processes to environmental perturbation is of increasing interest as alteration in rhizosphere microbial community dynamics impacts the combined functions of plant-microbe interactions. The present study was conducted to investigate the effect of inoculation with halotolerant rhizobacteria Bacillus pumilus (STR2), Halomonas desiderata (STR8), and Exiguobacterium oxidotolerans (STR36) on the indigenous root-associated microbial (bacterial and fungal) communities in maize under non-saline and salinity stress. Plants inoculated with halotolerant rhizobacteria recorded improved growth as illustrated by significantly higher shoot and root dry weight and elongation in comparison to un-inoculated control plants under both non-saline and saline conditions. Additive main effect and multiplicative interaction ordination analysis revealed that plant growth promoting rhizobacteria (PGPR) inoculations as well as salinity are major drivers of microbial community shift in maize rhizosphere. Salinity negatively impacts microbial community as analysed through diversity indices; among the PGPR-inoculated plants, STR2-inoculated plants recorded higher values of diversity indices. As observed in the terminal-restriction fragment length polymorphism analysis, the inoculation of halotolerant rhizobacteria prevents major shift of the microbial community structure, thus enhancing the resilience capacity of the microbial communities.
Collapse
Affiliation(s)
- Nidhi Bharti
- Microbial Technology Department, CSIR-Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, Lucknow, 226015, India
| | | | | | | |
Collapse
|
30
|
Damaso N, Martin L, Kushwaha P, Mills D. F-108 polymer and capillary electrophoresis easily resolves complex environmental DNA mixtures and SNPs. Electrophoresis 2014; 35:3208-11. [PMID: 25168595 DOI: 10.1002/elps.201400069] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Revised: 08/21/2014] [Accepted: 08/22/2014] [Indexed: 11/08/2022]
Abstract
Ecological studies of microbial communities often use profiling methods but the true community diversity can be underestimated in methods that separate amplicons based on sequence length using performance optimized polymer 4. Taxonomically, unrelated organisms can produce the same length amplicon even though the amplicons have different sequences. F-108 polymer has previously been shown to resolve same length amplicons by sequence polymorphisms. In this study, we showed F-108 polymer, using the ABI Prism 310 Genetic Analyzer and CE, resolved four bacteria that produced the same length amplicon for the 16S rRNA domain V3 but have variable nucleotide content. Second, a microbial mat community profile was resolved and supported by NextGen sequencing where the number of peaks in the F-108 profile was in concordance with the confirmed species numbers in the mat. Third, equine DNA was analyzed for SNPs. The F-108 polymer was able to distinguish heterozygous and homozygous individuals for the melanocortin 1 receptor coat color gene. The method proved to be rapid, inexpensive, reproducible, and uses common CE instruments. The potential for F-108 to resolve DNA mixtures or SNPs can be applied to various sample types-from SNPs to forensic mixtures to ecological communities.
Collapse
Affiliation(s)
- Natalie Damaso
- Department of Biological Sciences, Florida International University, Miami, FL, USA; International Forensic Research Institute, Florida International University, Miami, FL, USA; Department of Chemistry and Biochemistry, Florida International University, Miami, FL, USA
| | | | | | | |
Collapse
|
31
|
Lakshmanan V, Selvaraj G, Bais HP. Functional soil microbiome: belowground solutions to an aboveground problem. PLANT PHYSIOLOGY 2014; 166:689-700. [PMID: 25059708 PMCID: PMC4213098 DOI: 10.1104/pp.114.245811] [Citation(s) in RCA: 132] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Accepted: 07/23/2014] [Indexed: 05/07/2023]
Abstract
There is considerable evidence in the literature that beneficial rhizospheric microbes can alter plant morphology, enhance plant growth, and increase mineral content. Of late, there is a surge to understand the impact of the microbiome on plant health. Recent research shows the utilization of novel sequencing techniques to identify the microbiome in model systems such as Arabidopsis (Arabidopsis thaliana) and maize (Zea mays). However, it is not known how the community of microbes identified may play a role to improve plant health and fitness. There are very few detailed studies with isolated beneficial microbes showing the importance of the functional microbiome in plant fitness and disease protection. Some recent work on the cultivated microbiome in rice (Oryza sativa) shows that a wide diversity of bacterial species is associated with the roots of field-grown rice plants. However, the biological significance and potential effects of the microbiome on the host plants are completely unknown. Work performed with isolated strains showed various genetic pathways that are involved in the recognition of host-specific factors that play roles in beneficial host-microbe interactions. The composition of the microbiome in plants is dynamic and controlled by multiple factors. In the case of the rhizosphere, temperature, pH, and the presence of chemical signals from bacteria, plants, and nematodes all shape the environment and influence which organisms will flourish. This provides a basis for plants and their microbiomes to selectively associate with one another. This Update addresses the importance of the functional microbiome to identify phenotypes that may provide a sustainable and effective strategy to increase crop yield and food security.
Collapse
Affiliation(s)
- Venkatachalam Lakshmanan
- Department of Plant and Soil Sciences, University of Delaware, and Delaware Biotechnology Institute, Newark, Delaware 19711
| | - Gopinath Selvaraj
- Department of Plant and Soil Sciences, University of Delaware, and Delaware Biotechnology Institute, Newark, Delaware 19711
| | - Harsh P Bais
- Department of Plant and Soil Sciences, University of Delaware, and Delaware Biotechnology Institute, Newark, Delaware 19711
| |
Collapse
|
32
|
Khodakova AS, Smith RJ, Burgoyne L, Abarno D, Linacre A. Random whole metagenomic sequencing for forensic discrimination of soils. PLoS One 2014; 9:e104996. [PMID: 25111003 PMCID: PMC4128759 DOI: 10.1371/journal.pone.0104996] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Accepted: 07/15/2014] [Indexed: 11/19/2022] Open
Abstract
Here we assess the ability of random whole metagenomic sequencing approaches to discriminate between similar soils from two geographically distinct urban sites for application in forensic science. Repeat samples from two parklands in residential areas separated by approximately 3 km were collected and the DNA was extracted. Shotgun, whole genome amplification (WGA) and single arbitrarily primed DNA amplification (AP-PCR) based sequencing techniques were then used to generate soil metagenomic profiles. Full and subsampled metagenomic datasets were then annotated against M5NR/M5RNA (taxonomic classification) and SEED Subsystems (metabolic classification) databases. Further comparative analyses were performed using a number of statistical tools including: hierarchical agglomerative clustering (CLUSTER); similarity profile analysis (SIMPROF); non-metric multidimensional scaling (NMDS); and canonical analysis of principal coordinates (CAP) at all major levels of taxonomic and metabolic classification. Our data showed that shotgun and WGA-based approaches generated highly similar metagenomic profiles for the soil samples such that the soil samples could not be distinguished accurately. An AP-PCR based approach was shown to be successful at obtaining reproducible site-specific metagenomic DNA profiles, which in turn were employed for successful discrimination of visually similar soil samples collected from two different locations.
Collapse
Affiliation(s)
| | - Renee J. Smith
- School of Biological Sciences, Flinders University, Adelaide, Australia
| | - Leigh Burgoyne
- School of Biological Sciences, Flinders University, Adelaide, Australia
| | - Damien Abarno
- School of Biological Sciences, Flinders University, Adelaide, Australia
- Forensic Science South Australia, Adelaide, Australia
| | - Adrian Linacre
- School of Biological Sciences, Flinders University, Adelaide, Australia
| |
Collapse
|
33
|
Siles JA, Rachid CTCC, Sampedro I, García-Romera I, Tiedje JM. Microbial diversity of a Mediterranean soil and its changes after biotransformed dry olive residue amendment. PLoS One 2014; 9:e103035. [PMID: 25058610 PMCID: PMC4109964 DOI: 10.1371/journal.pone.0103035] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Accepted: 06/27/2014] [Indexed: 01/18/2023] Open
Abstract
The Mediterranean basin has been identified as a biodiversity hotspot, about whose soil microbial diversity little is known. Intensive land use and aggressive management practices are degrading the soil, with a consequent loss of fertility. The use of organic amendments such as dry olive residue (DOR), a waste produced by a two-phase olive-oil extraction system, has been proposed as an effective way to improve soil properties. However, before its application to soil, DOR needs a pre-treatment, such as by a ligninolytic fungal transformation, e.g. Coriolopsis floccosa. The present study aimed to describe the bacterial and fungal diversity in a Mediterranean soil and to assess the impact of raw DOR (DOR) and C. floccosa-transformed DOR (CORDOR) on function and phylogeny of soil microbial communities after 0, 30 and 60 days. Pyrosequencing of the 16S rRNA gene demonstrated that bacterial diversity was dominated by the phyla Proteobacteria, Acidobacteria, and Actinobacteria, while 28S-rRNA gene data revealed that Ascomycota and Basidiomycota accounted for the majority of phyla in the fungal community. A Biolog EcoPlate experiment showed that DOR and CORDOR amendments decreased functional diversity and altered microbial functional structures. These changes in soil functionality occurred in parallel with those in phylogenetic bacterial and fungal community structures. Some bacterial and fungal groups increased while others decreased depending on the relative abundance of beneficial and toxic substances incorporated with each amendment. In general, DOR was observed to be more disruptive than CORDOR.
Collapse
Affiliation(s)
- José A. Siles
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
- * E-mail:
| | - Caio T. C. C. Rachid
- Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Center for Microbial Ecology, Michigan State University, East Lansing, Michigan, United States of America
| | - Inmaculada Sampedro
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
- Thayer School of Engineering, Dartmouth College, Hanover, New Hampshire, United States of America
| | - Inmaculada García-Romera
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
| | - James M. Tiedje
- Center for Microbial Ecology, Michigan State University, East Lansing, Michigan, United States of America
| |
Collapse
|
34
|
Sharma B, Narzary D, Jha DK. Culture Independent Diversity Analysis of Soil Microbial Community and their Significance. SUSTAINABLE DEVELOPMENT AND BIODIVERSITY 2014. [DOI: 10.1007/978-3-319-05936-5_12] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
|