1
|
Pan H, Wattiez R, Gillan D. Soil Metaproteomics for Microbial Community Profiling: Methodologies and Challenges. Curr Microbiol 2024; 81:257. [PMID: 38955825 DOI: 10.1007/s00284-024-03781-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 06/21/2024] [Indexed: 07/04/2024]
Abstract
Soil represents a complex and dynamic ecosystem, hosting a myriad of microorganisms that coexist and play vital roles in nutrient cycling and organic matter transformation. Among these microorganisms, bacteria and fungi are key members of the microbial community, profoundly influencing the fate of nitrogen, sulfur, and carbon in terrestrial environments. Understanding the intricacies of soil ecosystems and the biological processes orchestrated by microbial communities necessitates a deep dive into their composition and metabolic activities. The advent of next-generation sequencing and 'omics' techniques, such as metagenomics and metaproteomics, has revolutionized our understanding of microbial ecology and the functional dynamics of soil microbial communities. Metagenomics enables the identification of microbial community composition in soil, while metaproteomics sheds light on the current biological functions performed by these communities. However, metaproteomics presents several challenges, both technical and computational. Factors such as the presence of humic acids and variations in extraction methods can influence protein yield, while the absence of high-resolution mass spectrometry and comprehensive protein databases limits the depth of protein identification. Notwithstanding these limitations, metaproteomics remains a potent tool for unraveling the intricate biological processes and functions of soil microbial communities. In this review, we delve into the methodologies and challenges of metaproteomics in soil research, covering aspects such as protein extraction, identification, and bioinformatics analysis. Furthermore, we explore the applications of metaproteomics in soil bioremediation, highlighting its potential in addressing environmental challenges.
Collapse
Affiliation(s)
- Haixia Pan
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Chemical Engineering, Ocean and Life Sciences, Dalian University of Technology (Panjin Campus), Panjin, China.
- Proteomics and Microbiology Department, University of Mons, Avenue du champ de Mars 6, 7000, Mons, Belgium.
| | - Ruddy Wattiez
- Proteomics and Microbiology Department, University of Mons, Avenue du champ de Mars 6, 7000, Mons, Belgium
| | - David Gillan
- Proteomics and Microbiology Department, University of Mons, Avenue du champ de Mars 6, 7000, Mons, Belgium
| |
Collapse
|
2
|
Toma L, Vignali G, Maffioli E, Tambuzzi S, Giaccari R, Mattarozzi M, Nonnis S, Milioli M, Franceschetti L, Paredi G, Negri A, Riccardi B, Cattaneo C, Careri M, Tedeschi G, Bruno S. Mass spectrometry-based proteomic strategy for ecchymotic skin examination in forensic pathology. Sci Rep 2023; 13:6116. [PMID: 37059833 PMCID: PMC10104867 DOI: 10.1038/s41598-023-32520-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 03/28/2023] [Indexed: 04/16/2023] Open
Abstract
Mass spectrometry (MS)-based proteomics has recently attracted the attention from forensic pathologists. This work is the first report of the development of a shotgun bottom-up proteomic approach based on rapid protein extraction and nano-liquid chromatography/high-resolution mass spectrometry applied to full-thickness human skin for the differential analysis of normal and ecchymotic tissues to identify new biomarkers for bruise characterization and dating. We identified around 2000 proteins from each pooled extract. The method showed excellent precision on independent replicates, with Pearson correlation coefficients always higher than 95%. Glycophorin A, a known biomarker of vital wounds from immunochemical studies, was identified only in ecchymotic tissues, as confirmed by Western blotting analysis. This finding suggests that this protein can be used as a MS-detectable biomarker of wound vitality. By focusing on skin samples from individuals with known wound dating, besides Glycophorin A, other proteins differentially expressed in ecchymotic samples and dependant on wound age were identified, although further analysis on larger datasets are needed to validate these findings. This study paves the way for an in-depth investigation of the potential of MS-based techniques for wound examination in forensic pathology, overcoming the limitations of immunochemical assays.
Collapse
Affiliation(s)
- Lorenzo Toma
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124, Parma, Italy
| | - Giulia Vignali
- Institute of Legal Medicine, Department of Biomedical Sciences for Health, University of Milan, 20133, Milan, Italy
| | - Elisa Maffioli
- Department of Veterinary Medicine and Animal Science, University of Milan, 26900, Lodi, Italy
| | - Stefano Tambuzzi
- Institute of Legal Medicine, Department of Biomedical Sciences for Health, University of Milan, 20133, Milan, Italy
| | - Roberta Giaccari
- Food and Drug Department, University of Parma, 43124, Parma, Italy
| | - Monica Mattarozzi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124, Parma, Italy.
| | - Simona Nonnis
- Department of Veterinary Medicine and Animal Science, University of Milan, 26900, Lodi, Italy.
- CRC Innovation for Well-Being and Environment (I-WE), University of Milan, 20133, Milan, Italy.
| | - Marco Milioli
- Department of Pharmacokinetic, Biochemistry and Metabolism, Global Research and Preclinical Development, Chiesi Farmaceutici Spa, 43122, Parma, Italy
| | - Lorenzo Franceschetti
- Institute of Legal Medicine, Department of Biomedical Sciences for Health, University of Milan, 20133, Milan, Italy
| | - Gianluca Paredi
- Food and Drug Department, University of Parma, 43124, Parma, Italy
| | - Armando Negri
- Department of Veterinary Medicine and Animal Science, University of Milan, 26900, Lodi, Italy
| | - Benedetta Riccardi
- Department of Pharmacokinetic, Biochemistry and Metabolism, Global Research and Preclinical Development, Chiesi Farmaceutici Spa, 43122, Parma, Italy
| | - Cristina Cattaneo
- Institute of Legal Medicine, Department of Biomedical Sciences for Health, University of Milan, 20133, Milan, Italy
| | - Maria Careri
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124, Parma, Italy
| | - Gabriella Tedeschi
- Department of Veterinary Medicine and Animal Science, University of Milan, 26900, Lodi, Italy
- CRC Innovation for Well-Being and Environment (I-WE), University of Milan, 20133, Milan, Italy
| | - Stefano Bruno
- Food and Drug Department, University of Parma, 43124, Parma, Italy
| |
Collapse
|
3
|
Tiwari P, Bae H. Trends in Harnessing Plant Endophytic Microbiome for Heavy Metal Mitigation in Plants: A Perspective. PLANTS (BASEL, SWITZERLAND) 2023; 12:1515. [PMID: 37050141 PMCID: PMC10097340 DOI: 10.3390/plants12071515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/08/2023] [Accepted: 03/27/2023] [Indexed: 06/19/2023]
Abstract
Plant microbiomes represent dynamic entities, influenced by the environmental stimuli and stresses in the surrounding conditions. Studies have suggested the benefits of commensal microbes in improving the overall fitness of plants, besides beneficial effects on plant adaptability and survival in challenging environmental conditions. The concept of 'Defense biome' has been proposed to include the plant-associated microbes that increase in response to plant stress and which need to be further explored for their role in plant fitness. Plant-associated endophytes are the emerging candidates, playing a pivotal role in plant growth, adaptability to challenging environmental conditions, and productivity, as well as showing tolerance to biotic and abiotic stresses. In this article, efforts have been made to discuss and understand the implications of stress-induced changes in plant endophytic microbiome, providing key insights into the effects of heavy metals on plant endophytic dynamics and how these beneficial microbes provide a prospective solution in the tolerance and mitigation of heavy metal in contaminated sites.
Collapse
|
4
|
Koner S, Chen JS, Rathod J, Hussain B, Hsu BM. Unravelling the ultramafic rock-driven serpentine soil formation leading to the geo-accumulation of heavy metals: An impact on the resident microbiome, biogeochemical cycling and acclimatized eco-physiological profiles. ENVIRONMENTAL RESEARCH 2023; 216:114664. [PMID: 36336091 DOI: 10.1016/j.envres.2022.114664] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/13/2022] [Accepted: 10/24/2022] [Indexed: 06/16/2023]
Abstract
In the present study, we have underpinned the serpentine rock, serpentinized ultramafic soil and rhizosphere's microbial communities, signifying their heavy metals-exposed taxa signatures and functional repertoires in comparison to non-serpentine soils. The results revealed that the serpentine rock embedded soil highlighted the geo-accumulation of higher amount of Cr and Ni impacting soil microbial diversity negatively by metal stress-driven selection. Biolog Ecoplate CLPP defined a restricted spectrum of C-utilization in the higher heavy metal-containing serpentine samples compared to non-serpentine. The linear discriminant analysis (LDA) score identified a higher abundance of Desulfobacterota, Opitutales, and Bacteroidales in low Cr and Ni-stressed non-serpentine-exposed samples. Whereas the abundance of Propionibacteriales and Actinobacteriota were significantly enriched in the serpentine niche. Further, the C, N, S, Fe, and methane biogeochemical cycles linked functional members were identified, and showing higher functional diversity in low Cr and Ni concentration-containing rhizosphere JS-soils. The Pearson correlation coefficient (r) value confirmed the abundance of functional members linked to specific biogeochemical cycle, positively correlated with relevant pathway enrichment. Ultimately, this study highlighted the heavy metal stress within a serpentine setting that could limit the resident microbial community's metabolic diversity and further select the bacteria that could thrive in the serpentine-associated heavy metal-stressed soils. These acclimatized microbes could pave the way for the future applications in the soil conservation and management.
Collapse
Affiliation(s)
- Suprokash Koner
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi, Taiwan; Department of Biomedical Sciences, National Chung Cheng University, Chiayi, Taiwan
| | - Jung-Sheng Chen
- Department of Medical Research, E-Da Hospital, Kaohsiung, Taiwan
| | - Jagat Rathod
- Department of Environmental Biotechnology, Gujarat Biotechnology University, Near Gujarat International Finance and Tec (GIFT)-City, Gandhinagar, 382355, Gujarat, India
| | - Bashir Hussain
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi, Taiwan; Department of Biomedical Sciences, National Chung Cheng University, Chiayi, Taiwan
| | - Bing-Mu Hsu
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi, Taiwan; Center for Innovative on Aging Society, National Chung Cheng University, Chiayi County, Taiwan.
| |
Collapse
|
5
|
Koner S, Tsai HC, Chen JS, Hussain B, Rajendran SK, Hsu BM. Exploration of pristine plate-tectonic plains and mining exposure areas for indigenous microbial communities and its impact on the mineral-microbial geochemical weathering process in ultramafic setting. ENVIRONMENTAL RESEARCH 2022; 214:113802. [PMID: 35810813 DOI: 10.1016/j.envres.2022.113802] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/27/2022] [Accepted: 06/29/2022] [Indexed: 06/15/2023]
Abstract
Heavy metal release from harsh ultramafic settings influences microbial diversity and function in soil ecology. This study aimed to determine how serpentine mineralosphere bacterial assemblies and their functions differed in two different plate-tectonic plains and mining exposure sites under heavy metal release conditions. The results showed that the Proteobacteria, Actinobacteria, Cyanobacteria, Planctomycetes, and Chloroflexi were the most abundant bacterial groups among all the sites. The log10-based LDA scores highlighted that some specific groups of bacterial assemblies were enriched in plate-tectonic plains and mining activity areas of the serpentine mineralosphere. Functional prediction revealed that the abundance of heavy metal (Cr and Ni) resistance and biogeochemical cycles involving functional KEGG orthology varied in samples from plate-tectonic plains and mining activity sites. The bipartite plot showed that the enrichment of the biogeochemical cycle and heavy metal resistance functional genes correlated with the abundance of serpentine mineralosphere bacterial groups at a 0.005% confidence level. The co-occurrence network plot revealed that the interconnection pattern of the indigenous bacterial assemblies changed in different plate-tectonic plains and mining exposure areas. Finally, this study concluded that due to heavy metal release, the variation in bacterial assemblies, their functioning, and intercommunity co-occurrence patterns were clarified the synergetic effect of mineral-microbial geochemical weathering process in serpentine mining areas.
Collapse
Affiliation(s)
- Suprokash Koner
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi County, Taiwan; Department of Biomedical Sciences, National Chung Cheng University, Chiayi County, Taiwan
| | - Hsin-Chi Tsai
- Department of Psychiatry, School of Medicine, Tzu Chi University, Hualien, Taiwan; Department of Psychiatry, Tzu Chi General Hospital, Hualien, Taiwan
| | - Jung-Sheng Chen
- Department of Medical Research, E-Da Hospital, Kaohsiung, Taiwan
| | - Bashir Hussain
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi County, Taiwan; Department of Biomedical Sciences, National Chung Cheng University, Chiayi County, Taiwan
| | - Senthil Kumar Rajendran
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi County, Taiwan
| | - Bing-Mu Hsu
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi County, Taiwan; Center for Innovative on Aging Society, National Chung Cheng University, Chiayi County, Taiwan.
| |
Collapse
|
6
|
Appidi MR, Bible AN, Carper DL, Jawdy SS, Giannone RJ, Hettich RL, Morrell-Falvey J, Abraham PE. Development of an Experimental Approach to Achieve Spatially Resolved Plant Root-Associated Metaproteomics Using an Agar-Plate System. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2022; 35:639-649. [PMID: 35349304 DOI: 10.1094/mpmi-01-22-0011-ta] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Plant-microbe interactions in the rhizosphere play a vital role in plant health and productivity. The composition and function of root-associated microbiomes is strongly influenced by their surrounding environment, which is often customized by their host. How microbiomes change with respect to space and time across plant roots remains poorly understood, and methodologies that facilitate spatiotemporal metaproteomic studies of root-associated microbiomes are yet to be realized. Here, we developed a method that provides spatially resolved metaproteome measurements along plant roots embedded in agar-plate culture systems, which have long been used to study plants. Spatially defined agar "plugs" of interest were excised and subsequently processed using a novel peptide extraction method prior to metaproteomics, which was used to infer both microbial community composition and function. As a proof-of-principle, a previously studied 10-member community constructed from a Populus root system was grown in an agar plate with a 3-week-old Populus trichocarpa plant. Metaproteomics was performed across two time points (24 and 48 h) for three distinct locations (root base, root tip, and a region distant from the root). The spatial resolution of these measurements provides evidence that microbiome composition and expression changes across the plant root interface. Interrogation of the individual microbial proteomes revealed functional profiles related to their behavioral associations with the plant root, in which chemotaxis and augmented metabolism likely supported predominance of the most abundant member. This study demonstrated a novel peptide extraction method for studying plant agar-plate culture systems, which was previously unsuitable for (meta)proteomic measurements.
Collapse
Affiliation(s)
- Manasa R Appidi
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, U.S.A
- Department of Genome Science and Technology, University of Tennessee-Knoxville, Knoxville, TN 37996, U.S.A
| | - Amber N Bible
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, U.S.A
| | - Dana L Carper
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, U.S.A
| | - Sara S Jawdy
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, U.S.A
| | - Richard J Giannone
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, U.S.A
| | - Robert L Hettich
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, U.S.A
| | | | - Paul E Abraham
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, U.S.A
| |
Collapse
|
7
|
Hassan S, Sabreena, Khurshid Z, Bhat SA, Kumar V, Ameen F, Ganai BA. Marine Bacteria and Omic Approaches: A Novel and Potential Repository for Bioremediation Assessment. J Appl Microbiol 2022; 133:2299-2313. [PMID: 35818751 DOI: 10.1111/jam.15711] [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: 04/05/2022] [Revised: 06/15/2022] [Accepted: 07/01/2022] [Indexed: 10/17/2022]
Abstract
Marine environments accommodating diverse assortments of life constitute a great pool of differentiated natural resources. The cumulative need to remedy unpropitious effects of anthropogenic activities on estuaries, and coastal marine ecosystems has propelled the development of effective bioremediation strategies. Marine bacteria producing biosurfactants are promising agents for bio-remediating oil pollution in marine environments, making them prospective candidates for enhancing oil recovery. Molecular omics technologies are considered an emerging field of research in ecological and diversity assessment owing to their utility in environmental surveillance and bioremediation of polluted sites. A thorough literature review was undertaken to understand the applicability of different omic techniques employed for bioremediation assessment using marine bacteria. This review further establishes that for bioremediation of environmental pollutants (i.e., heavy metals, hydrocarbons, xenobiotic and numerous recalcitrant compounds), organisms isolated from marine environments can be better utilized for their removal. The literature survey shows that omics approaches can provide exemplary knowledge about microbial communities and their role in the bioremediation of environmental pollutants. This review centres on applications of marine bacteria in enhanced bioremediation, utilizing the omics approaches that can be a vital biological contrivance in environmental monitoring to tackle environmental degradation. The paper aims to identify the gaps in investigations involving marine bacteria to help researchers, ecologists, and decision-makers to develop a holistic understanding regarding their utility in bioremediation assessment.
Collapse
Affiliation(s)
- Shahnawaz Hassan
- Department of Environmental Science, University of Kashmir, India
| | - Sabreena
- Department of Environmental Science, University of Kashmir, India
| | | | | | - Vineet Kumar
- Department of Botany, Guru Ghasidas Vishwavidyalaya (A Central University), Bilaspur, Chhattisgarh-495009, India
| | - Fuad Ameen
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | | |
Collapse
|
8
|
Phurailatpam L, Dalal VK, Singh N, Mishra S. Heavy Metal Stress Alleviation Through Omics Analysis of Soil and Plant Microbiome. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2022. [DOI: 10.3389/fsufs.2021.817932] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Heavy metal (HM) contamination of soil and water resources is a global concern, which not only limits crop yield and quality, but also has serious environmental effects. Due to the non-biodegradable nature and toxicity, high concentration of HMs in food and environment is a serious threat to the entire ecosystem. Moreover, the target of supplying safe and quality food to the rising human population (expected to reach ~9–10 bn by the year 2050), necessitates effective treatment of the HM-contaminated soil. Various microbe-mediated bioremediation strategies such as biosorption, bioprecipiation, biostimulation, etc., have been found to be effective in uptake and conversion of HMs to less toxic forms. Further, in the past few years, the use of soil and plant-associated microbiome for HM stress alleviation is gaining attention among the scientific community. In general, microbes are spectacular in being dynamic and more responsive to environmental conditions in comparison to their host plants. Moreover, with the advancements in high throughput sequencing technologies, the focus is eventually shifting from just structural characterization to functional insights into the microbiome. The microbes inhabiting the HM-contaminated environments or associated with HM-tolerant plants are a source for exploring HM-tolerant microbial communities, which could be used for enhancing bioremediation efficiency and conferring HM tolerance in plants. This review discusses the application of omics techniques including metagenomics, metatranscriptomics, metaproteomics, and metabolomics, for rapid and robust identification of HM-tolerant microbial communities, mining novel HM resistance genes, and fabricating the HM resistome.
Collapse
|
9
|
Nadarajah K, Abdul Rahman NSN. Plant-Microbe Interaction: Aboveground to Belowground, from the Good to the Bad. Int J Mol Sci 2021; 22:ijms221910388. [PMID: 34638728 PMCID: PMC8508622 DOI: 10.3390/ijms221910388] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 09/14/2021] [Accepted: 09/17/2021] [Indexed: 02/06/2023] Open
Abstract
Soil health and fertility issues are constantly addressed in the agricultural industry. Through the continuous and prolonged use of chemical heavy agricultural systems, most agricultural lands have been impacted, resulting in plateaued or reduced productivity. As such, to invigorate the agricultural industry, we would have to resort to alternative practices that will restore soil health and fertility. Therefore, in recent decades, studies have been directed towards taking a Magellan voyage of the soil rhizosphere region, to identify the diversity, density, and microbial population structure of the soil, and predict possible ways to restore soil health. Microbes that inhabit this region possess niche functions, such as the stimulation or promotion of plant growth, disease suppression, management of toxicity, and the cycling and utilization of nutrients. Therefore, studies should be conducted to identify microbes or groups of organisms that have assigned niche functions. Based on the above, this article reviews the aboveground and below-ground microbiomes, their roles in plant immunity, physiological functions, and challenges and tools available in studying these organisms. The information collected over the years may contribute toward future applications, and in designing sustainable agriculture.
Collapse
|
10
|
Basit A, Shah ST, Ullah I, Muntha ST, Mohamed HI. Microbe-assisted phytoremediation of environmental pollutants and energy recycling in sustainable agriculture. Arch Microbiol 2021; 203:5859-5885. [PMID: 34545411 DOI: 10.1007/s00203-021-02576-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 08/25/2021] [Accepted: 09/12/2021] [Indexed: 01/17/2023]
Abstract
The perception of phytoremediation is efficiently utilized as an eco-friendly practice of green plants combating and cleaning up the stressed environment without harming it. The industrial revolution was followed by the green revolution which fulfilled the food demands of the growing population caused an increase in yield per unit area in crop production, but it also increased the use of synthetic fertilizers in agriculture. Globally, the intensive use of inorganic fertilizers in agriculture has led to serious health problems and irreversible environmental damage. Biofertilizers improve the growth of the plant and can be applied as an alternative to chemical/synthetic fertilizers. Cyanobacteria, bacteria, and fungi are known as some of the principal microbe groups used to produce biofertilizers that form symbiotic associations with plants. Microorganisms perform a key role in phosphate solubilization and mobilization, nitrogen fixation, nutrient management, biotic elicitors and probiotics, and pollution management (biodegradation agents), specifically bacteria which also help in atmospheric nitrogen fixation and are thus available for the growth of the plant. Management or biodegradation of hazardous chemical residues and heavy metals produced by a huge number of large-scale industries should be given primary importance to be transformed by various bacterial strains, fungi, algae. Currently, modern omics technologies such as metagenomic, transcriptomic, and proteomic are being used to develop strategies for studying the ecology of microorganisms, as well as their use in environmental monitoring and bioremediation. This review briefly discusses some of the major groups of microorganisms that can perform different functions responsible for plant health, crop production, phytoremediation and also focus on the omics techniques reportedly used in environmental monitoring to tackle the pollution load.
Collapse
Affiliation(s)
- Abdul Basit
- Department of Horticulture, Faculty of Crop Production, The University of Agriculture Peshawar, Peshawar, 25120, Pakistan
| | - Syed Tanveer Shah
- Department of Horticulture, Faculty of Crop Production, The University of Agriculture Peshawar, Peshawar, 25120, Pakistan
| | - Izhar Ullah
- Department of Horticulture, Faculty of Crop Production, The University of Agriculture Peshawar, Peshawar, 25120, Pakistan
| | - Sidra Tul Muntha
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Heba I Mohamed
- Department of Biological and Geological Sciences, Faculty of Education, Ain Shams University, Cairo, Egypt.
| |
Collapse
|
11
|
Herruzo-Ruiz AM, Fuentes-Almagro CA, Jiménez-Pastor JM, Pérez-Rosa VM, Blasco J, Michán C, Alhama J. Meta-omic evaluation of bacterial microbial community structure and activity for the environmental assessment of soils: overcoming protein extraction pitfalls. Environ Microbiol 2021; 23:4706-4725. [PMID: 34258847 DOI: 10.1111/1462-2920.15673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 07/08/2021] [Accepted: 07/11/2021] [Indexed: 11/27/2022]
Abstract
Microorganisms play unique, essential and integral roles in the biosphere. This work aims to assess the utility of soil's metaomics for environmental diagnosis. Doñana National Park (DNP) was selected as a natural lab since it contains a strictly protected core that is surrounded by numerous threats of pollution. Culture-independent high-throughput molecular tools were used to evaluate the alterations of the global structure and metabolic activities of the microbiome. 16S rRNA sequencing shows lower bacterial abundance and diversity in areas historically exposed to contamination that surround DNP. For metaproteomics, an innovative post-alkaline protein extraction protocol was developed. After NaOH treatment, successive washing with Tris-HCl buffer supplemented with glycerol was essential to eliminate interferences. Starting from soils with different physicochemical characteristics, the method renders proteins with a remarkable resolution on SDS-PAGE gels. The proteins extracted were analysed by using an in-house database constructed from the rRNA data. LC-MS/MS analysis identified 2182 non-redundant proteins with 135 showing significant differences in relative abundance in the soils around DNP. Relevant global biological processes were altered in response to the environmental changes, such as protective and antioxidant mechanisms, translation, folding and homeostasis of proteins, membrane transport and aerobic respiratory metabolism.
Collapse
Affiliation(s)
- Ana M Herruzo-Ruiz
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Campus de Rabanales, Edificio Severo Ochoa, Córdoba, E-14071, Spain
| | | | - José M Jiménez-Pastor
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Campus de Rabanales, Edificio Severo Ochoa, Córdoba, E-14071, Spain
| | - Víctor M Pérez-Rosa
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Campus de Rabanales, Edificio Severo Ochoa, Córdoba, E-14071, Spain
| | - Julián Blasco
- Department of Ecology and Coastal Management, ICMAN-CSIC, Campus Rio San Pedro, Puerto Real, E-11510, Spain
| | - Carmen Michán
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Campus de Rabanales, Edificio Severo Ochoa, Córdoba, E-14071, Spain
| | - José Alhama
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Campus de Rabanales, Edificio Severo Ochoa, Córdoba, E-14071, Spain
| |
Collapse
|
12
|
Priya P, Aneesh B, Harikrishnan K. Genomics as a potential tool to unravel the rhizosphere microbiome interactions on plant health. J Microbiol Methods 2021; 185:106215. [PMID: 33839214 DOI: 10.1016/j.mimet.2021.106215] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 04/05/2021] [Accepted: 04/06/2021] [Indexed: 12/12/2022]
Abstract
Intense agricultural practices to meet rising food demands have caused ecosystem perturbations. For sustainable crop production, biological agents are gaining attention, but exploring their functional potential on a multi-layered complex ecosystem like the rhizosphere is challenging. This review explains the significance of genomics as a culture-independent molecular tool to understand the diversity and functional significance of the rhizosphere microbiome for sustainable agriculture. It discusses the recent significant studies in the rhizosphere environment carried out using evolving techniques like metagenomics, metatranscriptomics, and metaproteomics, their challenges, constraints infield application, and prospective solutions. The recent advances in techniques such as nanotechnology for the development of bioformulations and visualization techniques contemplating environmental safety were also discussed. The need for development of metagenomic data sets of regionally important crops, their plant microbial interactions and agricultural practices for narrowing down significant data from huge databases have been suggested. The role of taxonomical and functional diversity of soil microbiota in understanding soil suppression and part played by the microbial metabolites in the process have been analyzed and discussed in the context of 'omics' approach. 'Omics' studies have revealed important information about microbial diversity, their responses to various biotic and abiotic stimuli, and the physiology of disease suppression. This can be translated to crop sustainability and combinational approaches with advancing visualization and analysis methodologies fix the existing knowledge gap to a huge extend. With improved data processing and standardization of the methods, details of plant-microbe interactions can be successfully decoded to develop sustainable agricultural practices.
Collapse
Affiliation(s)
- P Priya
- Environmental Biology Lab, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India.
| | - B Aneesh
- Department of Marine Biology, Microbiology and Biochemistry, School of Marine Sciences Cochin University of Science and Technology, Cochin, Kerala, India.
| | - K Harikrishnan
- Environmental Biology Lab, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India.
| |
Collapse
|
13
|
Tartaglia M, Bastida F, Sciarrillo R, Guarino C. Soil Metaproteomics for the Study of the Relationships Between Microorganisms and Plants: A Review of Extraction Protocols and Ecological Insights. Int J Mol Sci 2020; 21:ijms21228455. [PMID: 33187080 PMCID: PMC7697097 DOI: 10.3390/ijms21228455] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 11/02/2020] [Accepted: 11/09/2020] [Indexed: 12/19/2022] Open
Abstract
Soil is a complex matrix where biotic and abiotic components establish a still unclear network involving bacteria, fungi, archaea, protists, protozoa, and roots that are in constant communication with each other. Understanding these interactions has recently focused on metagenomics, metatranscriptomics and less on metaproteomics studies. Metaproteomic allows total extraction of intracellular and extracellular proteins from soil samples, providing a complete picture of the physiological and functional state of the “soil community”. The advancement of high-performance mass spectrometry technologies was more rapid than the development of ad hoc extraction techniques for soil proteins. The protein extraction from environmental samples is biased due to interfering substances and the lower amount of proteins in comparison to cell cultures. Soil sample preparation and extraction methodology are crucial steps to obtain high-quality resolution and yields of proteins. This review focuses on the several soil protein extraction protocols to date to highlight the methodological challenges and critical issues for the application of proteomics to soil samples. This review concludes that improvements in soil protein extraction, together with the employment of ad hoc metagenome database, may enhance the identification of proteins with low abundance or from non-dominant populations and increase our capacity to predict functional changes in soil.
Collapse
Affiliation(s)
- Maria Tartaglia
- Department of Science and Technology, University of Sannio, via de Sanctis snc, 82100 Benevento, Italy; (M.T.); (R.S.)
| | - Felipe Bastida
- CEBAS-CSIC, Department of Soil and Water Conservation, Campus Universitario de Espinardo, 30100 Murcia, Spain;
| | - Rosaria Sciarrillo
- Department of Science and Technology, University of Sannio, via de Sanctis snc, 82100 Benevento, Italy; (M.T.); (R.S.)
| | - Carmine Guarino
- Department of Science and Technology, University of Sannio, via de Sanctis snc, 82100 Benevento, Italy; (M.T.); (R.S.)
- Correspondence: ; Tel.: +39-824-305145
| |
Collapse
|
14
|
Pinski A, Zur J, Hasterok R, Hupert-Kocurek K. Comparative Genomics of Stenotrophomonas maltophilia and Stenotrophomonas rhizophila Revealed Characteristic Features of Both Species. Int J Mol Sci 2020; 21:E4922. [PMID: 32664682 PMCID: PMC7404187 DOI: 10.3390/ijms21144922] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 07/01/2020] [Accepted: 07/09/2020] [Indexed: 12/22/2022] Open
Abstract
Although Stenotrophomonas maltophilia strains are efficient biocontrol agents, their field applications have raised concerns due to their possible threat to human health. The non-pathogenic Stenotrophomonas rhizophila species, which is closely related to S. maltophilia, has been proposed as an alternative. However, knowledge regarding the genetics of S. rhizophila is limited. Thus, the aim of the study was to define any genetic differences between the species and to characterise their ability to promote the growth of plant hosts as well as to enhance phytoremediation efficiency. We compared 37 strains that belong to both species using the tools of comparative genomics and identified 96 genetic features that are unique to S. maltophilia (e.g., chitin-binding protein, mechanosensitive channels of small conductance and KGG repeat-containing stress-induced protein) and 59 that are unique to S. rhizophila (e.g., glucosylglycerol-phosphate synthase, cold shock protein with the DUF1294 domain, and pteridine-dependent dioxygenase-like protein). The strains from both species have a high potential for biocontrol, which is mainly related to the production of keratinases (KerSMD and KerSMF), proteinases and chitinases. Plant growth promotion traits are attributed to the biosynthesis of siderophores, spermidine, osmoprotectants such as trehalose and glucosylglycerol, which is unique to S. rhizophila. In eight out of 37 analysed strains, the genes that are required to degrade protocatechuate were present. While our results show genetic differences between the two species, they had a similar growth promotion potential. Considering the information above, S. rhizophila constitutes a promising alternative for S. maltophilia for use in agricultural biotechnology.
Collapse
Affiliation(s)
- Artur Pinski
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, 28 Jagiellonska Street, 40-032 Katowice, Poland; (J.Z.); (R.H.)
| | | | | | - Katarzyna Hupert-Kocurek
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, 28 Jagiellonska Street, 40-032 Katowice, Poland; (J.Z.); (R.H.)
| |
Collapse
|
15
|
Chen W, Wang Z, Xu W, Tian R, Zeng J. Dibutyl phthalate contamination accelerates the uptake and metabolism of sugars by microbes in black soil. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 262:114332. [PMID: 32182534 DOI: 10.1016/j.envpol.2020.114332] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 02/21/2020] [Accepted: 03/04/2020] [Indexed: 06/10/2023]
Abstract
Dibutyl phthalate (DBP) is widely used as plasticizer and has been detected in the environment, posing a threat to animal health. However, the effects of DBP on agricultural microbiomes are not known. In this study, DBP levels in black soil were evaluated, and the impact of DBP contamination on the uptake and metabolism of sugars in microbes was assessed by glucose absorption tests, metaproteomics, metabolomics, enzyme activity assays and computational simulation analysis. The results indicated that DBP contamination accelerated glucose consumption and upregulated the expression of porins and periplasmic monosaccharide ATP-binding cassette (ABC) transporter solute-binding proteins (SBPs). DBP and its metabolic intermediates (carboxymuconate and butanol) may form a stable complex with sugar transporters and enhance the rigidity and stability of these proteins. Sugar metabolism resulting in the generation of ATP and reducing agent (NADPH), as well as the expression of some key enzymes (dehydrogenases) were also upregulated by DBP treatment. Moreover, a diverse bacterial community appears to utilize sugar, suggesting that there are widespread effects of DBP contamination on soil microbial ecosystems. The results of this study provide a theoretical basis for investigating the toxicological effects of DBP on microbes in black soil.
Collapse
Affiliation(s)
- Wenjing Chen
- Center for Ecological Research, Northeast Forestry University, Heilongjiang Province, Harbin, 150040, China; Heilongjiang Provincial Technology Innovation Center of Agromicrobial Preparation Industrialization, Qiqihar, 161006, China; College of Life Sciences, Agriculture and Forestry, Qiqihar University, Heilongjiang Province, Qiqihar, 161006, China.
| | - Zhigang Wang
- Heilongjiang Provincial Technology Innovation Center of Agromicrobial Preparation Industrialization, Qiqihar, 161006, China; College of Life Sciences, Agriculture and Forestry, Qiqihar University, Heilongjiang Province, Qiqihar, 161006, China.
| | - Weihui Xu
- Heilongjiang Provincial Technology Innovation Center of Agromicrobial Preparation Industrialization, Qiqihar, 161006, China; College of Life Sciences, Agriculture and Forestry, Qiqihar University, Heilongjiang Province, Qiqihar, 161006, China.
| | - Renmao Tian
- Institute for Food Safety and Health, Illinois Institute of Technology, Chicago, IL, 60501, USA.
| | - Jin Zeng
- Nanjing Institute of Geography & Limnology, Chinese Academy of Sciences, Nanjing, 210008, China.
| |
Collapse
|
16
|
Khatabi B, Gharechahi J, Ghaffari MR, Liu D, Haynes PA, McKay MJ, Mirzaei M, Salekdeh GH. Plant-Microbe Symbiosis: What Has Proteomics Taught Us? Proteomics 2020; 19:e1800105. [PMID: 31218790 DOI: 10.1002/pmic.201800105] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 05/04/2019] [Indexed: 11/08/2022]
Abstract
Beneficial microbes have a positive impact on the productivity and fitness of the host plant. A better understanding of the biological impacts and underlying mechanisms by which the host derives these benefits will help to address concerns around global food production and security. The recent development of omics-based technologies has broadened our understanding of the molecular aspects of beneficial plant-microbe symbiosis. Specifically, proteomics has led to the identification and characterization of several novel symbiosis-specific and symbiosis-related proteins and post-translational modifications that play a critical role in mediating symbiotic plant-microbe interactions and have helped assess the underlying molecular aspects of the symbiotic relationship. Integration of proteomic data with other "omics" data can provide valuable information to assess hypotheses regarding the underlying mechanism of symbiosis and help define the factors affecting the outcome of symbiosis. Herein, an update is provided on the current and potential applications of symbiosis-based "omic" approaches to dissect different aspects of symbiotic plant interactions. The application of proteomics, metaproteomics, and secretomics as enabling approaches for the functional analysis of plant-associated microbial communities is also discussed.
Collapse
Affiliation(s)
- Behnam Khatabi
- Department of Agriculture, Food and Resource Sciences, University of Maryland Eastern Shore, Princess Anne, MD, 21853, USA
| | - Javad Gharechahi
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education, and Extension Organization (AREEO), Karaj, Iran
| | - Mohammad Reza Ghaffari
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education, and Extension Organization (AREEO), Karaj, Iran
| | - Dilin Liu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, P. R. China.,Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangzhou, P. R. China
| | - Paul A Haynes
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Matthew J McKay
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia.,Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW, 2109, Australia
| | - Mehdi Mirzaei
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia.,Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW, 2109, Australia
| | - Ghasem Hosseini Salekdeh
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education, and Extension Organization (AREEO), Karaj, Iran.,Department of Molecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| |
Collapse
|
17
|
Chiapello M, Zampieri E, Mello A. A Small Effort for Researchers, a Big Gain for Soil Metaproteomics. Front Microbiol 2020; 11:88. [PMID: 32117118 PMCID: PMC7010931 DOI: 10.3389/fmicb.2020.00088] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 01/15/2020] [Indexed: 11/23/2022] Open
Affiliation(s)
- Marco Chiapello
- Institute for Sustainable Plant Protection, National Research Council, Turin, Italy
| | - Elisa Zampieri
- Council for Agricultural Research and Economics Research Centre for Cereal and Industrial Crops (CREA-CI), Vercelli, Italy
| | - Antonietta Mello
- Institute for Sustainable Plant Protection, National Research Council, Turin, Italy
| |
Collapse
|
18
|
Kavamura VN, Robinson RJ, Hughes D, Clark I, Rossmann M, Melo ISD, Hirsch PR, Mendes R, Mauchline TH. Wheat dwarfing influences selection of the rhizosphere microbiome. Sci Rep 2020; 10:1452. [PMID: 31996781 PMCID: PMC6989667 DOI: 10.1038/s41598-020-58402-y] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 01/14/2020] [Indexed: 12/23/2022] Open
Abstract
The development of dwarf wheat cultivars combined with high levels of agrochemical inputs during the green revolution resulted in high yielding cropping systems. However, changes in wheat cultivars were made without considering impacts on plant and soil microbe interactions. We studied the effect of these changes on root traits and on the assembly of rhizosphere bacterial communities by comparing eight wheat cultivars ranging from tall to semi-dwarf plants grown under field conditions. Wheat breeding influenced root diameter and specific root length (SRL). Rhizosphere bacterial communities from tall cultivars were distinct from those associated with semi-dwarf cultivars, with higher differential abundance of Actinobacteria, Bacteroidetes and Proteobacteria in tall cultivars, compared with a higher differential abundance of Verrucomicrobia, Planctomycetes and Acidobacteria in semi-dwarf cultivars. Predicted microbial functions were also impacted and network analysis revealed a greater level of connectedness between microbial communities in the tall cultivars relative to semi-dwarf cultivars. Taken together, results suggest that the development of semi-dwarf plants might have affected the ability of plants to recruit and sustain a complex bacterial community network in the rhizosphere.
Collapse
Affiliation(s)
- Vanessa N Kavamura
- Sustainable Agriculture Sciences, Rothamsted Research, Harpenden, Hertfordshire, United Kingdom
| | - Rebekah J Robinson
- Plant Pathology Laboratory, Royal Horticultural Society, RHS Garden Wisley, Woking, Surrey, GU23 6QB, United Kingdom
| | - David Hughes
- Computational and Analytical Sciences, Rothamsted Research, Harpenden, Hertfordshire, United Kingdom
| | - Ian Clark
- Sustainable Agriculture Sciences, Rothamsted Research, Harpenden, Hertfordshire, United Kingdom
| | - Maike Rossmann
- Laboratory of Environmental Microbiology, Embrapa Environment, Jaguariúna-SP, Brazil
| | - Itamar Soares de Melo
- Laboratory of Environmental Microbiology, Embrapa Environment, Jaguariúna-SP, Brazil
| | - Penny R Hirsch
- Sustainable Agriculture Sciences, Rothamsted Research, Harpenden, Hertfordshire, United Kingdom
| | - Rodrigo Mendes
- Laboratory of Environmental Microbiology, Embrapa Environment, Jaguariúna-SP, Brazil
| | - Tim H Mauchline
- Sustainable Agriculture Sciences, Rothamsted Research, Harpenden, Hertfordshire, United Kingdom.
| |
Collapse
|
19
|
Chandra AK, Kumar A, Bharati A, Joshi R, Agrawal A, Kumar S. Microbial-assisted and genomic-assisted breeding: a two way approach for the improvement of nutritional quality traits in agricultural crops. 3 Biotech 2020; 10:2. [PMID: 31824813 DOI: 10.1007/s13205-019-1994-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 11/18/2019] [Indexed: 12/19/2022] Open
Abstract
Both human and animals, for their nutritional requirements, mainly rely on the plant-based foods, which provide a wide range of nutrients. Minerals, proteins, vitamins are among the nutrients which are essential and need to be available in adequate amount in edible portion of the staple crops. Increasing nutritional content in staple crops either through agronomic biofortification or through conventional plant-breeding strategies continue to be a huge task for scientists around the globe. Although some success has been achieved in recent past, in most cases, we have fallen short of expected targets. To maximize the nutrient uptake and partitioning to different economic part of plants, scientists have employed and tailored several biofortification strategies. But in present agricultural and environmental concerns, these approaches are not much effective. Henceforth, we are highlighting the recent developments and promising aspects of microbial-assisted and genomic-assisted breeding as candidate biofortification approach, that have contributed significantly in increasing nutritional content in grains of different crops. The methods used to date to accomplish nutrient enrichment with recently emerging strategies that we believe could be the most promising and holistic approach for future biofortification program. Results are encouraging, but for future perspective, the existing knowledge about the strategies needs to be confined. Concerted scientific investment are required to widen up these biofortification strategies, so that it could play an important role in ensuring nutritional security of ever-growing population in growing agricultural and environmental constraints.
Collapse
|
20
|
DalCorso G, Fasani E, Manara A, Visioli G, Furini A. Heavy Metal Pollutions: State of the Art and Innovation in Phytoremediation. Int J Mol Sci 2019; 20:E3412. [PMID: 31336773 PMCID: PMC6679171 DOI: 10.3390/ijms20143412] [Citation(s) in RCA: 119] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 07/09/2019] [Accepted: 07/10/2019] [Indexed: 12/12/2022] Open
Abstract
Mineral nutrition of plants greatly depends on both environmental conditions, particularly of soils, and the genetic background of the plant itself. Being sessile, plants adopted a range of strategies for sensing and responding to nutrient availability to optimize development and growth, as well as to protect their metabolisms from heavy metal toxicity. Such mechanisms, together with the soil environment, meaning the soil microorganisms and their interaction with plant roots, have been extensively studied with the goal of exploiting them to reclaim polluted lands; this approach, defined phytoremediation, will be the subject of this review. The main aspects and innovations in this field are considered, in particular with respect to the selection of efficient plant genotypes, the application of improved cultural strategies, and the symbiotic interaction with soil microorganisms, to manage heavy metal polluted soils.
Collapse
Affiliation(s)
- Giovanni DalCorso
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy.
| | - Elisa Fasani
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy
| | - Anna Manara
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy
| | - Giovanna Visioli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze, 11/A, 43124 Parma, Italy
| | - Antonella Furini
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy.
| |
Collapse
|
21
|
Using proteins to study how microbes contribute to soil ecosystem services: The current state and future perspectives of soil metaproteomics. J Proteomics 2019; 198:50-58. [DOI: 10.1016/j.jprot.2018.11.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 11/08/2018] [Accepted: 11/12/2018] [Indexed: 02/07/2023]
|
22
|
Blank C, Easterly C, Gruening B, Johnson J, Kolmeder CA, Kumar P, May D, Mehta S, Mesuere B, Brown Z, Elias JE, Hervey WJ, McGowan T, Muth T, Nunn B, Rudney J, Tanca A, Griffin TJ, Jagtap PD. Disseminating Metaproteomic Informatics Capabilities and Knowledge Using the Galaxy-P Framework. Proteomes 2018; 6:proteomes6010007. [PMID: 29385081 PMCID: PMC5874766 DOI: 10.3390/proteomes6010007] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 01/26/2018] [Accepted: 01/26/2018] [Indexed: 01/12/2023] Open
Abstract
The impact of microbial communities, also known as the microbiome, on human health and the environment is receiving increased attention. Studying translated gene products (proteins) and comparing metaproteomic profiles may elucidate how microbiomes respond to specific environmental stimuli, and interact with host organisms. Characterizing proteins expressed by a complex microbiome and interpreting their functional signature requires sophisticated informatics tools and workflows tailored to metaproteomics. Additionally, there is a need to disseminate these informatics resources to researchers undertaking metaproteomic studies, who could use them to make new and important discoveries in microbiome research. The Galaxy for proteomics platform (Galaxy-P) offers an open source, web-based bioinformatics platform for disseminating metaproteomics software and workflows. Within this platform, we have developed easily-accessible and documented metaproteomic software tools and workflows aimed at training researchers in their operation and disseminating the tools for more widespread use. The modular workflows encompass the core requirements of metaproteomic informatics: (a) database generation; (b) peptide spectral matching; (c) taxonomic analysis and (d) functional analysis. Much of the software available via the Galaxy-P platform was selected, packaged and deployed through an online metaproteomics "Contribution Fest" undertaken by a unique consortium of expert software developers and users from the metaproteomics research community, who have co-authored this manuscript. These resources are documented on GitHub and freely available through the Galaxy Toolshed, as well as a publicly accessible metaproteomics gateway Galaxy instance. These documented workflows are well suited for the training of novice metaproteomics researchers, through online resources such as the Galaxy Training Network, as well as hands-on training workshops. Here, we describe the metaproteomics tools available within these Galaxy-based resources, as well as the process by which they were selected and implemented in our community-based work. We hope this description will increase access to and utilization of metaproteomics tools, as well as offer a framework for continued community-based development and dissemination of cutting edge metaproteomics software.
Collapse
Affiliation(s)
- Clemens Blank
- Bioinformatics Group, Department of Computer Science, University of Freiburg, 79110 Freiburg im Breisgau, Germany.
| | - Caleb Easterly
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Bjoern Gruening
- Bioinformatics Group, Department of Computer Science, University of Freiburg, 79110 Freiburg im Breisgau, Germany.
| | - James Johnson
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Carolin A Kolmeder
- Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland.
| | - Praveen Kumar
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Damon May
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
| | - Subina Mehta
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Bart Mesuere
- Computational Biology Group, Ghent University, Krijgslaan 281, B-9000 Ghent, Belgium.
| | - Zachary Brown
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Joshua E Elias
- Department of Chemical & Systems Biology, Stanford University, Stanford, CA 94305, USA.
| | - W Judson Hervey
- Center for Bio/Molecular Science & Engineering, Naval Research Laboratory, Washington, DC 20375, USA.
| | - Thomas McGowan
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Thilo Muth
- Bioinformatics Unit (MF1), Department for Methods Development and Research Infrastructure, Robert Koch Institute, 13353 Berlin, Germany.
| | - Brook Nunn
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
| | - Joel Rudney
- Department of Diagnostic and Biological Sciences, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Alessandro Tanca
- Porto Conte Ricerche Science and Technology Park of Sardinia, 07041 Alghero, Italy.
| | - Timothy J Griffin
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Pratik D Jagtap
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.
| |
Collapse
|
23
|
Olaya-Abril A, Parras-Alcántara L, Lozano-García B, Obregón-Romero R. Soil organic carbon distribution in Mediterranean areas under a climate change scenario via multiple linear regression analysis. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 592:134-143. [PMID: 28319700 DOI: 10.1016/j.scitotenv.2017.03.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 03/02/2017] [Accepted: 03/02/2017] [Indexed: 06/06/2023]
Abstract
Over time, the interest on soil studies has increased due to its role in carbon sequestration in terrestrial ecosystems, which could contribute to decreasing atmospheric CO2 rates. In many studies, independent variables were related to soil organic carbon (SOC) alone, however, the contribution degree of each variable with the experimentally determined SOC content were not considered. In this study, samples from 612 soil profiles were obtained in a natural protected (Red Natura 2000) of Sierra Morena (Mediterranean area, South Spain), considering only the topsoil 0-25cm, for better comparison between results. 24 independent variables were used to define it relationship with SOC content. Subsequently, using a multiple linear regression analysis, the effects of these variables on the SOC correlation was considered. Finally, the best parameters determined with the regression analysis were used in a climatic change scenario. The model indicated that SOC in a future scenario of climate change depends on average temperature of coldest quarter (41.9%), average temperature of warmest quarter (34.5%), annual precipitation (22.2%) and annual average temperature (1.3%). When the current and future situations were compared, the SOC content in the study area was reduced a 35.4%, and a trend towards migration to higher latitude and altitude was observed.
Collapse
Affiliation(s)
- Alfonso Olaya-Abril
- Department of Agricultural Chemistry and Soil Science, Faculty of Science, Agrifood Campus of International Excellence - ceiA3, University of Cordoba, Cordoba, Spain; Department of Biochemistry and Molecular Biology, Faculty of Science, Campus of International Excellence - ceiA3, University of Cordoba, Cordoba, Spain
| | - Luis Parras-Alcántara
- Department of Agricultural Chemistry and Soil Science, Faculty of Science, Agrifood Campus of International Excellence - ceiA3, University of Cordoba, Cordoba, Spain; Sustainable Use and Management of Soils (SUMAS) Research Group, Spain.
| | - Beatriz Lozano-García
- Department of Agricultural Chemistry and Soil Science, Faculty of Science, Agrifood Campus of International Excellence - ceiA3, University of Cordoba, Cordoba, Spain; Sustainable Use and Management of Soils (SUMAS) Research Group, Spain
| | - Rafael Obregón-Romero
- Department of Botany, Ecology and Plant physiology, Faculty of Science, Campus of International Excellence - ceiA3, University of Cordoba, Cordoba, Spain
| |
Collapse
|