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Nebauer DJ, Pearson LA, Neilan BA. Critical steps in an environmental metaproteomics workflow. Environ Microbiol 2024; 26:e16637. [PMID: 38760994 DOI: 10.1111/1462-2920.16637] [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: 02/01/2024] [Accepted: 04/30/2024] [Indexed: 05/20/2024]
Abstract
Environmental metaproteomics is a rapidly advancing field that provides insights into the structure, dynamics, and metabolic activity of microbial communities. As the field is still maturing, it lacks consistent workflows, making it challenging for non-expert researchers to navigate. This review aims to introduce the workflow of environmental metaproteomics. It outlines the standard practices for sample collection, processing, and analysis, and offers strategies to overcome the unique challenges presented by common environmental matrices such as soil, freshwater, marine environments, biofilms, sludge, and symbionts. The review also highlights the bottlenecks in data analysis that are specific to metaproteomics samples and provides suggestions for researchers to obtain high-quality datasets. It includes recent benchmarking studies and descriptions of software packages specifically built for metaproteomics analysis. The article is written without assuming the reader's familiarity with single-organism proteomic workflows, making it accessible to those new to proteomics or mass spectrometry in general. This primer for environmental metaproteomics aims to improve accessibility to this exciting technology and empower researchers to tackle challenging and ambitious research questions. While it is primarily a resource for those new to the field, it should also be useful for established researchers looking to streamline or troubleshoot their metaproteomics experiments.
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Affiliation(s)
- Daniel J Nebauer
- School of Environmental and Life Sciences, The University of Newcastle, Callaghan, New South Wales, Australia
- Centre of Excellence in Synthetic Biology, Australian Research Council, Sydney, New South Wales, Australia
| | - Leanne A Pearson
- School of Environmental and Life Sciences, The University of Newcastle, Callaghan, New South Wales, Australia
- Centre of Excellence in Synthetic Biology, Australian Research Council, Sydney, New South Wales, Australia
| | - Brett A Neilan
- School of Environmental and Life Sciences, The University of Newcastle, Callaghan, New South Wales, Australia
- Centre of Excellence in Synthetic Biology, Australian Research Council, Sydney, New South Wales, Australia
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2
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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.
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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
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Zhang M, Li Y, Mu Q, Feng F, Yu X, Ge J, Zhang Y, Nie J. Effects of chlorpyrifos on the metabolic profiling of Bacillus megaterium strain RRB. CHEMOSPHERE 2022; 297:134189. [PMID: 35248589 DOI: 10.1016/j.chemosphere.2022.134189] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 02/12/2022] [Accepted: 03/01/2022] [Indexed: 06/14/2023]
Abstract
Many microorganisms have been reported to degrade organic pollutants in the environment and plants, however, the specific information about the effect of organic pollutants on the metabolism of microorganisms is poorly investigated. In the present study, the effect of the pesticide chlorpyrifos on the metabolic profiling of Bacillus megaterium strain RRB was investigated using metabolomics. Our data show that chlorpyrifos acting as an energy source was readily concentrated in the strain RRB from the culture medium. During early cultivation, the shift in energy sources from tryptic soy broth to chlorpyrifos may temporarily cause the strain RRB to enter the starvation stage, where some synthesis-related amino acids and intermediates in the pathways of TCA cycle and pyridoxine metabolism were decreased. The increase of nucleotides and lysine may help the strain RRB cope with the starvation stage. During later cultivation, many metabolites including organic acids, nucleosides and sugar phosphates were gradually accumulated, which indicates that chlorpyrifos could be utilized by the stain RRB to generate metabolites bacteria needed. In addition, arginine acting as a nitrogen-storage amino acid was gradually decreased with later cultivation, suggesting that chlorpyrifos could not provide enough nitrogen for bacteria.
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Affiliation(s)
- Mingxia Zhang
- College of Chemistry and Bioengineering, Guilin University of Technology, Guilin, 541004, China; Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, 50 Zhongling Street, Nanjing, 210014, China
| | - Yong Li
- Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, 50 Zhongling Street, Nanjing, 210014, China; School of Food and Biological Engineering, Jiangsu University, 301 Zhenjiang City University Road, Zhenjiang, 212001, China.
| | - Qi'e Mu
- College of Chemistry and Bioengineering, Guilin University of Technology, Guilin, 541004, China; Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, 50 Zhongling Street, Nanjing, 210014, China
| | - Fayun Feng
- Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, 50 Zhongling Street, Nanjing, 210014, China
| | - Xiangyang Yu
- Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, 50 Zhongling Street, Nanjing, 210014, China
| | - Jing Ge
- Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, 50 Zhongling Street, Nanjing, 210014, China
| | - Yun Zhang
- College of Chemistry and Bioengineering, Guilin University of Technology, Guilin, 541004, China
| | - Jinfang Nie
- College of Chemistry and Bioengineering, Guilin University of Technology, Guilin, 541004, China.
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Rajczewski AT, Jagtap PD, Griffin TJ. An overview of technologies for MS-based proteomics-centric multi-omics. Expert Rev Proteomics 2022; 19:165-181. [PMID: 35466851 PMCID: PMC9613604 DOI: 10.1080/14789450.2022.2070476] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
INTRODUCTION Mass spectrometry-based proteomics reveals dynamic molecular signatures underlying phenotypes reflecting normal and perturbed conditions in living systems. Although valuable on its own, the proteome has only one level of moleclar information, with the genome, epigenome, transcriptome, and metabolome, all providing complementary information. Multi-omic analysis integrating information from one or more of these other domains with proteomic information provides a more complete picture of molecular contributors to dynamic biological systems. AREAS COVERED Here, we discuss the improvements to mass spectrometry-based technologies, focused on peptide-based, bottom-up approaches that have enabled deep, quantitative characterization of complex proteomes. These advances are facilitating the integration of proteomics data with other 'omic information, providing a more complete picture of living systems. We also describe the current state of bioinformatics software and approaches for integrating proteomics and other 'omics data, critical for enabling new discoveries driven by multi-omics. EXPERT COMMENTARY Multi-omics, centered on the integration of proteomics information with other 'omic information, has tremendous promise for biological and biomedical studies. Continued advances in approaches for generating deep, reliable proteomic data and bioinformatics tools aimed at integrating data across 'omic domains will ensure the discoveries offered by these multi-omic studies continue to increase.
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Affiliation(s)
- Andrew T. Rajczewski
- Department of Biochemistry, Molecular and Cell Biology Building, University of Minnesota, 420 Washington Ave SE 7-129, Minneapolis, MN, 55455, USA
| | - Pratik D. Jagtap
- Department of Biochemistry, Molecular and Cell Biology Building, University of Minnesota, 420 Washington Ave SE 7-129, Minneapolis, MN, 55455, USA,Coauthor, Research Department of Biochemistry, Molecular and Cell Biology Building, University of Minnesota, 420 Washington Ave SE 7-129, Minneapolis, MN, 55455, USA
| | - Timothy J. Griffin
- Department of Biochemistry, Molecular and Cell Biology Building, University of Minnesota, 420 Washington Ave SE 7-129, Minneapolis, MN, 55455, USA,Department of Biochemistry, Molecular and Cell Biology Building, University of Minnesota, 420 Washington Ave SE 7-129, Minneapolis, MN, 55455, USA
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Sieradzki ET, Morando M, Fuhrman JA. Metagenomics and Quantitative Stable Isotope Probing Offer Insights into Metabolism of Polycyclic Aromatic Hydrocarbon Degraders in Chronically Polluted Seawater. mSystems 2021; 6:e00245-21. [PMID: 33975968 PMCID: PMC8125074 DOI: 10.1128/msystems.00245-21] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 04/12/2021] [Indexed: 11/21/2022] Open
Abstract
Bacterial biodegradation is a significant contributor to remineralization of polycyclic aromatic hydrocarbons (PAHs)-toxic and recalcitrant components of crude oil as well as by-products of partial combustion chronically introduced into seawater via atmospheric deposition. The Deepwater Horizon oil spill demonstrated the speed at which a seed PAH-degrading community maintained by chronic inputs responds to acute pollution. We investigated the diversity and functional potential of a similar seed community in the chronically polluted Port of Los Angeles (POLA), using stable isotope probing with naphthalene, deep-sequenced metagenomes, and carbon incorporation rate measurements at the port and in two sites in the San Pedro Channel. We demonstrate the ability of the community of degraders at the POLA to incorporate carbon from naphthalene, leading to a quick shift in microbial community composition to be dominated by the normally rare Colwellia and Cycloclasticus We show that metagenome-assembled genomes (MAGs) belonged to these naphthalene degraders by matching their 16S-rRNA gene with experimental stable isotope probing data. Surprisingly, we did not find a full PAH degradation pathway in those genomes, even when combining genes from the entire microbial community, leading us to hypothesize that promiscuous dehydrogenases replace canonical naphthalene degradation enzymes in this site. We compared metabolic pathways identified in 29 genomes whose abundance increased in the presence of naphthalene to generate genomic-based recommendations for future optimization of PAH bioremediation at the POLA, e.g., ammonium as opposed to urea, heme or hemoproteins as an iron source, and polar amino acids.IMPORTANCE Oil spills in the marine environment have a devastating effect on marine life and biogeochemical cycles through bioaccumulation of toxic hydrocarbons and oxygen depletion by hydrocarbon-degrading bacteria. Oil-degrading bacteria occur naturally in the ocean, especially where they are supported by chronic inputs of oil or other organic carbon sources, and have a significant role in degradation of oil spills. Polycyclic aromatic hydrocarbons are the most persistent and toxic component of crude oil. Therefore, the bacteria that can break those molecules down are of particular importance. We identified such bacteria at the Port of Los Angeles (POLA), one of the busiest ports worldwide, and characterized their metabolic capabilities. We propose chemical targets based on those analyses to stimulate the activity of these bacteria in case of an oil spill in the Port POLA.
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Affiliation(s)
- Ella T Sieradzki
- Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
| | - Michael Morando
- Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
| | - Jed A Fuhrman
- Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
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6
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Reid T, Bergsveinson J. How Do the Players Play? A Post-Genomic Analysis Paradigm to Understand Aquatic Ecosystem Processes. Front Mol Biosci 2021; 8:662888. [PMID: 34026835 PMCID: PMC8138469 DOI: 10.3389/fmolb.2021.662888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 04/26/2021] [Indexed: 12/01/2022] Open
Abstract
Culture-independent and meta-omics sequencing methods have shed considerable light on the so-called “microbial dark matter” of Earth’s environmental microbiome, improving our understanding of phylogeny, the tree of life, and the vast functional diversity of microorganisms. This influx of sequence data has led to refined and reimagined hypotheses about the role and importance of microbial biomass, that paradoxically, sequencing approaches alone are unable to effectively test. Post-genomic approaches such as metabolomics are providing more sensitive and insightful data to unravel the fundamental operations and intricacies of microbial communities within aquatic systems. We assert that the implementation of integrated post-genomic approaches, specifically metabolomics and metatranscriptomics, is the new frontier of environmental microbiology and ecology, expanding conventional assessments toward a holistic systems biology understanding. Progressing beyond siloed phylogenetic assessments and cataloging of metabolites, toward integrated analysis of expression (metatranscriptomics) and activity (metabolomics) is the most effective approach to provide true insight into microbial contributions toward local and global ecosystem functions. This data in turn creates opportunity for improved regulatory guidelines, biomarker discovery and better integration of modeling frameworks. To that end, critical aquatic environmental issues related to climate change, such as ocean warming and acidification, contamination mitigation, and macro-organism health have reasonable opportunity of being addressed through such an integrative approach. Lastly, we argue that the “post-genomics” paradigm is well served to proactively address the systemic technical issues experienced throughout the genomics revolution and focus on collaborative assessment of field-wide experimental standards of sampling, bioinformatics and statistical treatments.
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Affiliation(s)
- Thomas Reid
- Canada Centre for Inland Waters, Environment and Climate Change Canada, Burlington, ON, Canada
| | - Jordyn Bergsveinson
- National Hydrology Research Centre, Environment and Climate Change Canada, Saskatoon, SK, Canada
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Wu B, Zhou M, Song L, Xu Q, Dai X, Chai X. Mechanism insights into polyhydroxyalkanoate-regulated denitrification from the perspective of pericytoplasmic nitrate reductase expression. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 754:142083. [PMID: 32920393 DOI: 10.1016/j.scitotenv.2020.142083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 08/27/2020] [Accepted: 08/28/2020] [Indexed: 06/11/2023]
Abstract
For enhanced biological nutrient removal (BNR) process, the polyhydroxyalkanoate (PHA) can be used as an eco-friendly internal as well as external substrate for regulating the growth of heterotrophic denitrifiers and promoting the denitrification process for deep nitrogen removal from wastewater. However, the exact mechanisms by which PHA impacts bacterial metabolism and affects the electron transfer of denitrification remain unknown. In this study, the in-depth mechanism investigation for PHA-mediated denitrification based on the jointly applied transcriptomic, proteomic and Western Blotting techniques was performed on a model denitrifier, Pseudomonas stutzeri. Results showed that PHA dramatically fostered the growth of Pseudomonas stutzeri, resulting in improved nitrate removal efficiency from 32.8% to 45.8%. Comparison of protein expression profiles indicated that PHA promoted the expression of enzyme NapB and NapA by approximately 10.34 and 20.01 times, respectively, which were both in charge of reduction from nitrate to nitrite. Based on transcriptional sequencing and Tandem Mass Tags, the correlation results also showed that differential proteins and genes with the same expression trend were positively correlated (R2 = 0.427, p-value<0.033). Western Blotting approach was further developed to confirm the up-regulated expression of target protein with the higher proportion of PHA in carbon source of the medium, which proved the reliability of proteomics results. All the findings presented here are believed to deepen the understanding of microbial mechanism about PHA-enhanced denitrification from the novel perspective of associated electron-transfer enzymatic proteins.
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Affiliation(s)
- Boran Wu
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Meng Zhou
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Liyan Song
- Environmental Microbiology and Ecology Research Center, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Science (CAS), 266 Fangzheng Avenue, Chongqing 400714, China
| | - Qinqin Xu
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Xiaohu Dai
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China.
| | - Xiaoli Chai
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China.
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8
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Hoang SA, Lamb D, Seshadri B, Sarkar B, Choppala G, Kirkham MB, Bolan NS. Rhizoremediation as a green technology for the remediation of petroleum hydrocarbon-contaminated soils. JOURNAL OF HAZARDOUS MATERIALS 2021; 401:123282. [PMID: 32634659 DOI: 10.1016/j.jhazmat.2020.123282] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 06/18/2020] [Accepted: 06/19/2020] [Indexed: 05/22/2023]
Abstract
Rhizoremediation is increasingly becoming a green and sustainable alternative to physico-chemical methods for remediation of contaminated environments through the utilization of symbiotic relationship between plants and their associated soil microorganisms in the root zone. The overall efficiency can be enhanced by identifying suitable plant-microbe combinations for specific contaminants and supporting the process with the application of appropriate soil amendments. This approach not only involves promoting the existing activity of plants and soil microbes, but also introduces an adequate number of microorganisms with specific catabolic activity. Here, we reviewed recent literature on the main mechanisms and key factors in the rhizoremediation process with a particular focus on soils contaminated with total petroleum hydrocarbon (TPH). We then discuss the potential of different soil amendments to accelerate the remediation efficiency based on biostimulation and bioaugmentation processes. Notwithstanding some successes in well-controlled environments, rhizoremediation of TPH under field conditions is still not widespread and considered less attractive than physico-chemical methods. We catalogued the major pitfalls of this remediation approach at the field scale in TPH-contaminated sites and, provide some applicable situations for the future successful use of in situ rhizoremediation of TPH-contaminated soils.
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Affiliation(s)
- Son A Hoang
- Global Centre for Environmental Remediation (GCER), Advanced Technology Centre (ATC) Building, Faculty of Science, The University of Newcastle, University Drive, Callaghan, NSW 2308, Australia; Division of Urban Infrastructural Engineering, Mien Trung University of Civil Engineering, Phu Yen 56000, Viet Nam
| | - Dane Lamb
- Global Centre for Environmental Remediation (GCER), Advanced Technology Centre (ATC) Building, Faculty of Science, The University of Newcastle, University Drive, Callaghan, NSW 2308, Australia
| | - Balaji Seshadri
- Global Centre for Environmental Remediation (GCER), Advanced Technology Centre (ATC) Building, Faculty of Science, The University of Newcastle, University Drive, Callaghan, NSW 2308, Australia
| | - Binoy Sarkar
- Lancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, United Kingdom
| | - Girish Choppala
- Global Centre for Environmental Remediation (GCER), Advanced Technology Centre (ATC) Building, Faculty of Science, The University of Newcastle, University Drive, Callaghan, NSW 2308, Australia
| | - M B Kirkham
- Department of Agronomy, Kansas State University, Manhattan, KS, United States
| | - Nanthi S Bolan
- Global Centre for Environmental Remediation (GCER), Advanced Technology Centre (ATC) Building, Faculty of Science, The University of Newcastle, University Drive, Callaghan, NSW 2308, Australia.
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Laczi K, Erdeiné Kis Á, Szilágyi Á, Bounedjoum N, Bodor A, Vincze GE, Kovács T, Rákhely G, Perei K. New Frontiers of Anaerobic Hydrocarbon Biodegradation in the Multi-Omics Era. Front Microbiol 2020; 11:590049. [PMID: 33304336 PMCID: PMC7701123 DOI: 10.3389/fmicb.2020.590049] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 10/26/2020] [Indexed: 12/17/2022] Open
Abstract
The accumulation of petroleum hydrocarbons in the environment substantially endangers terrestrial and aquatic ecosystems. Many microbial strains have been recognized to utilize aliphatic and aromatic hydrocarbons under aerobic conditions. Nevertheless, most of these pollutants are transferred by natural processes, including rain, into the underground anaerobic zones where their degradation is much more problematic. In oxic zones, anaerobic microenvironments can be formed as a consequence of the intensive respiratory activities of (facultative) aerobic microbes. Even though aerobic bioremediation has been well-characterized over the past few decades, ample research is yet to be done in the field of anaerobic hydrocarbon biodegradation. With the emergence of high-throughput techniques, known as omics (e.g., genomics and metagenomics), the individual biodegraders, hydrocarbon-degrading microbial communities and metabolic pathways, interactions can be described at a contaminated site. Omics approaches provide the opportunity to examine single microorganisms or microbial communities at the system level and elucidate the metabolic networks, interspecies interactions during hydrocarbon mineralization. Metatranscriptomics and metaproteomics, for example, can shed light on the active genes and proteins and functional importance of the less abundant species. Moreover, novel unculturable hydrocarbon-degrading strains and enzymes can be discovered and fit into the metabolic networks of the community. Our objective is to review the anaerobic hydrocarbon biodegradation processes, the most important hydrocarbon degraders and their diverse metabolic pathways, including the use of various terminal electron acceptors and various electron transfer processes. The review primarily focuses on the achievements obtained by the current high-throughput (multi-omics) techniques which opened new perspectives in understanding the processes at the system level including the metabolic routes of individual strains, metabolic/electric interaction of the members of microbial communities. Based on the multi-omics techniques, novel metabolic blocks can be designed and used for the construction of microbial strains/consortia for efficient removal of hydrocarbons in anaerobic zones.
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Affiliation(s)
- Krisztián Laczi
- Department of Biotechnology, University of Szeged, Szeged, Hungary
| | - Ágnes Erdeiné Kis
- Department of Biotechnology, University of Szeged, Szeged, Hungary.,Institute of Biophysics, Biological Research Centre, Szeged, Hungary
| | - Árpád Szilágyi
- Department of Biotechnology, University of Szeged, Szeged, Hungary
| | - Naila Bounedjoum
- Department of Biotechnology, University of Szeged, Szeged, Hungary.,Institute of Environmental and Technological Sciences, University of Szeged, Szeged, Hungary
| | - Attila Bodor
- Department of Biotechnology, University of Szeged, Szeged, Hungary.,Institute of Biophysics, Biological Research Centre, Szeged, Hungary.,Institute of Environmental and Technological Sciences, University of Szeged, Szeged, Hungary
| | | | - Tamás Kovács
- Department of Biotechnology, Nanophagetherapy Center, Enviroinvest Corporation, Pécs, Hungary
| | - Gábor Rákhely
- Department of Biotechnology, University of Szeged, Szeged, Hungary.,Institute of Biophysics, Biological Research Centre, Szeged, Hungary.,Institute of Environmental and Technological Sciences, University of Szeged, Szeged, Hungary
| | - Katalin Perei
- Department of Biotechnology, University of Szeged, Szeged, Hungary.,Institute of Environmental and Technological Sciences, University of Szeged, Szeged, Hungary
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Chemical Profiling Provides Insights into the Metabolic Machinery of Hydrocarbon-Degrading Deep-Sea Microbes. mSystems 2020; 5:5/6/e00824-20. [PMID: 33172970 PMCID: PMC7657597 DOI: 10.1128/msystems.00824-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Marine microbes are known to degrade hydrocarbons; however, microbes inhabiting deep-sea sediments remain largely unexplored. Previous studies into the classical pathways of marine microbial metabolism reveal diverse chemistries; however, metabolic profiling of marine microbes cultured with hydrocarbons is limited. In this study, taxonomic (amplicon sequencing) profiles of two environmental deep-sea sediments (>1,200 m deep) were obtained, along with taxonomic and metabolomic (mass spectrometry-based metabolomics) profiles of microbes harbored in deep-sea sediments cultured with hydrocarbons as the sole energy source. Samples were collected from the Gulf of México (GM) and cultured for 28 days using simple (toluene, benzene, hexadecane, and naphthalene) and complex (petroleum API 40) hydrocarbon mixtures as the sole energy sources. The sediment samples harbored diverse microbial communities predominantly classified into Woeseiaceae and Kiloniellaceae families, whereas Pseudomonadaceae and Enterobacteriaceae families prevailed after sediments were cultured with hydrocarbons. Chemical profiling of microbial metabolomes revealed diverse chemical groups belonging primarily to the lipids and lipid-like molecules superclass, as well as the organoheterocyclic compound superclass (ClassyFire annotation). Metabolomic data and prediction of functional profiles indicated an increase in aromatic and alkane degradation in samples cultured with hydrocarbons. Previously unreported metabolites, identified as intermediates in the degradation of hydrocarbons, were annotated as hydroxylated polyunsaturated fatty acids and carboxylated benzene derivatives. In summary, this study used mass spectrometry-based metabolomics coupled to chemoinformatics to demonstrate how microbes from deep-sea sediments could be cultured in the presence of hydrocarbons. This study also highlights how this experimental approach can be used to increase the understanding of hydrocarbon degradation by deep-sea sediment microbes.IMPORTANCE High-throughput technologies and emerging informatics tools have significantly advanced knowledge of hydrocarbon metabolism by marine microbes. However, research into microbes inhabiting deep-sea sediments (>1,000 m) is limited compared to those found in shallow waters. In this study, a nontargeted and nonclassical approach was used to examine the diversity of bacterial taxa and the metabolic profiles of hydrocarbon-degrading deep-sea microbes. In conclusion, this study used metabolomics and chemoinformatics to demonstrate that microbes from deep-sea sediment origin thrive in the presence of toxic and difficult-to-metabolize hydrocarbons. Notably, this study provides evidence of previously unreported metabolites and the global chemical repertoire associated with the metabolism of hydrocarbons by deep-sea microbes.
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Qiu ZL, Wen Z, Yang K, Tian T, Qiao G, Hong Y, Wen XP. Comparative Proteomics Profiling Illuminates the Fruitlet Abscission Mechanism of Sweet Cherry as Induced by Embryo Abortion. Int J Mol Sci 2020; 21:ijms21041200. [PMID: 32054063 PMCID: PMC7072775 DOI: 10.3390/ijms21041200] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 02/07/2020] [Accepted: 02/08/2020] [Indexed: 12/14/2022] Open
Abstract
Sweet cherry (Prunus avium L.) is a delicious nutrient-rich fruit widely cultivated in countries such as China, America, Chile, and Italy. However, the yield often drops severely due to the frequently-abnormal fruitlet abscission, and few studies on the metabolism during its ripening process at the proteomic level have been executed so far. To get a better understanding regarding the sweet cherry abscission mechanism, proteomic analysis between the abscising carpopodium and non-abscising carpopodium of sweet cherry was accomplished using a newly developed Liquid chromatography-mass spectrometry/mass spectrometry with Tandem Mass Tag (TMT-LC-MS/MS) methodology. The embryo viability experiments showed that the vigor of the abscission embryos was significantly lower than that of retention embryo. The activity of cell wall degrading enzymes in abscising carpopodium was significantly higher than that in non-abscising carpopodium. The anatomy results suggested that cells in the abscission zone were small and separated. In total, 6280 proteins were identified, among which 5681 were quantified. It has been observed that differentially accumulated proteins (DAPs) influenced several biological functions and various subcellular localizations. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that plenty of metabolic pathways were notably enriched, particularly those involved in phytohormone biosynthesis, cell wall metabolism, and cytoskeletal metabolism, including 1-aminocyclopropane-1-carboxylate oxidase proteins which promote ethylene synthesis, and proteins promoting cell wall degradation, such as endoglucanases, pectinase, and polygalacturonase. Differential expression of proteins concerning phytohormone biosynthesis might activate the shedding regulation signals. Up-regulation of several cell wall degradation-related proteins possibly regulated the shedding of plant organs. Variations of the phytohormone biosynthesis and cell wall degradation-related proteins were explored during the abscission process. Furthermore, changes in cytoskeleton-associated proteins might contribute to the abscission of carpopodium. The current work represented the first study using comparative proteomics between abscising carpopodium and non-abscising carpopodium. These results indicated that embryo abortion might lead to phytohormone synthesis disorder, which effected signal transduction pathways, and hereby controlled genes involved in cell wall degradation and then caused the abscission of fruitlet. Overall, our data may give an intrinsic explanation of the variations in metabolism during the abscission of carpopodium.
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Affiliation(s)
- Zhi-Lang Qiu
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Guizhou University), Ministry of Education, Institute of Agro-bioengineering/College of Life Sciences, Guizhou University, Guiyang 550025, China; (Z.-L.Q.); (Z.W.); (K.Y.); (G.Q.); (Y.H.)
| | - Zhuang Wen
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Guizhou University), Ministry of Education, Institute of Agro-bioengineering/College of Life Sciences, Guizhou University, Guiyang 550025, China; (Z.-L.Q.); (Z.W.); (K.Y.); (G.Q.); (Y.H.)
| | - Kun Yang
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Guizhou University), Ministry of Education, Institute of Agro-bioengineering/College of Life Sciences, Guizhou University, Guiyang 550025, China; (Z.-L.Q.); (Z.W.); (K.Y.); (G.Q.); (Y.H.)
| | - Tian Tian
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Guizhou University), Ministry of Education, Institute of Agro-bioengineering/College of Life Sciences, Guizhou University, Guiyang 550025, China; (Z.-L.Q.); (Z.W.); (K.Y.); (G.Q.); (Y.H.)
- Institute for Forest Resources & Environment of Guizhou, College of Forestry, Guizhou University, Guiyang 550025, China;
| | - Guang Qiao
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Guizhou University), Ministry of Education, Institute of Agro-bioengineering/College of Life Sciences, Guizhou University, Guiyang 550025, China; (Z.-L.Q.); (Z.W.); (K.Y.); (G.Q.); (Y.H.)
| | - Yi Hong
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Guizhou University), Ministry of Education, Institute of Agro-bioengineering/College of Life Sciences, Guizhou University, Guiyang 550025, China; (Z.-L.Q.); (Z.W.); (K.Y.); (G.Q.); (Y.H.)
| | - Xiao-Peng Wen
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Guizhou University), Ministry of Education, Institute of Agro-bioengineering/College of Life Sciences, Guizhou University, Guiyang 550025, China; (Z.-L.Q.); (Z.W.); (K.Y.); (G.Q.); (Y.H.)
- Institute for Forest Resources & Environment of Guizhou, College of Forestry, Guizhou University, Guiyang 550025, China;
- Correspondence: ; Tel.: +86-851-88290212
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Giovanella P, Vieira GAL, Ramos Otero IV, Pais Pellizzer E, de Jesus Fontes B, Sette LD. Metal and organic pollutants bioremediation by extremophile microorganisms. JOURNAL OF HAZARDOUS MATERIALS 2020; 382:121024. [PMID: 31541933 DOI: 10.1016/j.jhazmat.2019.121024] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 07/17/2019] [Accepted: 08/14/2019] [Indexed: 06/10/2023]
Abstract
Extremophiles comprise microorganisms that are able to grow and thrive in extreme environments, including in an acidic or alkaline pH, high or low temperatures, high concentrations of pollutants, and salts, among others. These organisms are promising for environmental biotechnology due to their unique physiological and enzymatic characteristics, which allow them to survive in harsh environments. Due to the stability and persistence of these microorganisms under adverse environmental conditions, they can be used for the bioremediation of environments contaminated with extremely recalcitrant pollutants. Here, we provide an overview of extremophiles and the role of "omics" in the field of bioremediation of environmental pollutants, including hydrocarbons, textile dyes and metals.
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Affiliation(s)
- Patricia Giovanella
- Departamento de Bioquímica e Microbiologia, Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho, Rio Claro, SP, Brazil.
| | - Gabriela A L Vieira
- Departamento de Bioquímica e Microbiologia, Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho, Rio Claro, SP, Brazil
| | - Igor V Ramos Otero
- Departamento de Bioquímica e Microbiologia, Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho, Rio Claro, SP, Brazil
| | - Elisa Pais Pellizzer
- Departamento de Bioquímica e Microbiologia, Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho, Rio Claro, SP, Brazil
| | - Bruno de Jesus Fontes
- Departamento de Bioquímica e Microbiologia, Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho, Rio Claro, SP, Brazil
| | - Lara D Sette
- Departamento de Bioquímica e Microbiologia, Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho, Rio Claro, SP, Brazil.
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Santisi S, Catalfamo M, Bonsignore M, Gentile G, Di Salvo E, Genovese M, Mahjoubi M, Cherif A, Mancini G, Hassanshahian M, Pioggia G, Cappello S. Biodegradation ability of two selected microbial autochthonous consortia from a chronically polluted marine coastal area (Priolo Gargallo, Italy). J Appl Microbiol 2019; 127:618-629. [PMID: 30848509 DOI: 10.1111/jam.14246] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 02/22/2019] [Accepted: 02/25/2019] [Indexed: 11/29/2022]
Abstract
The aims of this study were: (i) the characterization of the structure of the indigenous microbial community associated with the sediments under study; (ii) the isolation and characterization of microbial consortia able to degrade the aged hydrocarbons contaminating the sediments, and (iii) the assessment of related biodegradation capability of selected consortia. Samples of surface sediments were collected in Priolo Gargallo harbour (Sicily, Italy). The samples were analysed for physical, chemical (GC-FID analysis) and microbiological characteristics (qualitative (16S rDNA clone library) and quantitative (DAPI, CFU and MPN count) analysis). The sediment samples were used for the selection of two microbial consortia (indicated as PSO and PSM) with high biodegradation capacity for crude oil (∼95%) and PAHs (∼63%) respectively. Genetic analysis showed that Alcanivorax and Cycloclasticus were the dominant genera in both the PSO and PSM consortia. Oil-polluted environments naturally develop an elevated biorecovery potential. The presence of a highly specialized microbial flora (adapted to support the contamination) and their stimulation through favourable induced conditions provides a promising recovery strategy. The chance to identify and select indigenous bacteria and/or consortia with a high biodegradation capacity is fundamental for the development and optimization of bioaugmentation strategies especially for those concerning in situ applications.
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Affiliation(s)
- S Santisi
- Institute for Biological Resources and Marine Biotechnology (IRBIM)-CNR of Messina, Messina, Italy.,Institute of Applied Sciences & Intelligent Systems "Eduardo Caianiello" (ISASI)-CNR of Messina, Messina, Italy
| | - M Catalfamo
- Institute for Biological Resources and Marine Biotechnology (IRBIM)-CNR of Messina, Messina, Italy
| | - M Bonsignore
- Faculty of Biological Sciences, University of Messina, Messina, Italy
| | - G Gentile
- Institute for Biological Resources and Marine Biotechnology (IRBIM)-CNR of Messina, Messina, Italy
| | - E Di Salvo
- Institute for Biological Resources and Marine Biotechnology (IRBIM)-CNR of Messina, Messina, Italy.,Institute of Applied Sciences & Intelligent Systems "Eduardo Caianiello" (ISASI)-CNR of Messina, Messina, Italy
| | - M Genovese
- Institute for Biological Resources and Marine Biotechnology (IRBIM)-CNR of Messina, Messina, Italy
| | - M Mahjoubi
- Higher Institute for Biotechnology - University of Manouba Biotechpole of Sidi Thabet, Ariana, Tunisia
| | - A Cherif
- Higher Institute for Biotechnology - University of Manouba Biotechpole of Sidi Thabet, Ariana, Tunisia
| | - G Mancini
- Dep. "Ingegneria Industriale", University of Catania, Catania, Italy
| | - M Hassanshahian
- Dep."Biology", Faculty of Sciences, Shahid Bahonar University of Kerman, Kerman, Iran
| | - G Pioggia
- Institute of Applied Sciences & Intelligent Systems "Eduardo Caianiello" (ISASI)-CNR of Messina, Messina, Italy
| | - S Cappello
- Institute for Biological Resources and Marine Biotechnology (IRBIM)-CNR of Messina, Messina, Italy.,Institute of Applied Sciences & Intelligent Systems "Eduardo Caianiello" (ISASI)-CNR of Messina, Messina, Italy
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van de Kamp J, Hook SE, Williams A, Tanner JE, Bodrossy L. Baseline characterization of aerobic hydrocarbon degrading microbial communities in deep-sea sediments of the Great Australian Bight, Australia. Environ Microbiol 2019; 21:1782-1797. [PMID: 30761716 DOI: 10.1111/1462-2920.14559] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 01/28/2019] [Accepted: 02/07/2019] [Indexed: 11/30/2022]
Abstract
Exploratory drilling for deep-sea oil and gas resources is planned for the Great Australian Bight (GAB). There is scant knowledge of the region's benthic ecosystems and no baseline information of the region's indigenous oil degrading bacteria. To address this knowledge gap, we used next generation sequencing (NGS) of three marker genes (alkB, c23o and pmoA) to detect and characterize the microbial communities capable of aerobic hydrocarbon degradation. Unique, highly novel microbial communities capable of degrading hydrocarbons occur in surface sediments at depths between 200 and 2800 m. Clustering at 97% demonstrated differences in community structure with depth, changing most markedly between 400 and 1000 m depth on the continental slope, and identified putative functional 'ecotypes' related to depth. Observed differences in community structure showed strong correlations with temperature, other physicochemical properties of the overlying water column and are further modulated by differences in sediment grain size. This study provides important baseline data on hydrocarbon degrading microbial communities prior to the start of petroleum resource extraction. Our data will inform future ecological monitoring of the GAB deep-sea ecosystem.
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Affiliation(s)
- Jodie van de Kamp
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation, Hobart, Tasmania, 7000, Australia
| | - Sharon E Hook
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation, Lucas Heights, New South Wales, 2234, Australia
| | - Alan Williams
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation, Hobart, Tasmania, 7000, Australia
| | - Jason E Tanner
- Aquatic Sciences, South Australian Research and Development Institute, West Beach, South Australia, 5024, Australia
| | - Levente Bodrossy
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation, Hobart, Tasmania, 7000, Australia
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15
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Baidoo EEK, Teixeira Benites V. Mass Spectrometry-Based Microbial Metabolomics: Techniques, Analysis, and Applications. Methods Mol Biol 2019; 1859:11-69. [PMID: 30421222 DOI: 10.1007/978-1-4939-8757-3_2] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The demand for understanding the roles genes play in biological systems has steered the biosciences into the direction the metabolome, as it closely reflects the metabolic activities within a cell. The importance of the metabolome is further highlighted by its ability to influence the genome, transcriptome, and proteome. Consequently, metabolomic information is being used to understand microbial metabolic networks. At the forefront of this work is mass spectrometry, the most popular metabolomics measurement technique. Mass spectrometry-based metabolomic analyses have made significant contributions to microbiological research in the environment and human disease. In this chapter, we break down the technical aspects of mass spectrometry-based metabolomics and discuss its application to microbiological research.
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Affiliation(s)
- Edward E K Baidoo
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
- Joint BioEnergy Institute, Emeryville, California, USA.
| | - Veronica Teixeira Benites
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Joint BioEnergy Institute, Emeryville, California, USA
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Dangi AK, Sharma B, Hill RT, Shukla P. Bioremediation through microbes: systems biology and metabolic engineering approach. Crit Rev Biotechnol 2018; 39:79-98. [DOI: 10.1080/07388551.2018.1500997] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Arun Kumar Dangi
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
| | - Babita Sharma
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
| | - Russell T. Hill
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD, USA
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
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17
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Malla MA, Dubey A, Yadav S, Kumar A, Hashem A, Abd Allah EF. Understanding and Designing the Strategies for the Microbe-Mediated Remediation of Environmental Contaminants Using Omics Approaches. Front Microbiol 2018; 9:1132. [PMID: 29915565 PMCID: PMC5994547 DOI: 10.3389/fmicb.2018.01132] [Citation(s) in RCA: 100] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 05/14/2018] [Indexed: 12/24/2022] Open
Abstract
Rapid industrialization and population explosion has resulted in the generation and dumping of various contaminants into the environment. These harmful compounds deteriorate the human health as well as the surrounding environments. Current research aims to harness and enhance the natural ability of different microbes to metabolize these toxic compounds. Microbial-mediated bioremediation offers great potential to reinstate the contaminated environments in an ecologically acceptable approach. However, the lack of the knowledge regarding the factors controlling and regulating the growth, metabolism, and dynamics of diverse microbial communities in the contaminated environments often limits its execution. In recent years the importance of advanced tools such as genomics, proteomics, transcriptomics, metabolomics, and fluxomics has increased to design the strategies to treat these contaminants in ecofriendly manner. Previously researchers has largely focused on the environmental remediation using single omics-approach, however the present review specifically addresses the integrative role of the multi-omics approaches in microbial-mediated bioremediation. Additionally, we discussed how the multi-omics approaches help to comprehend and explore the structural and functional aspects of the microbial consortia in response to the different environmental pollutants and presented some success stories by using these approaches.
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Affiliation(s)
- Muneer A Malla
- Department of Zoology, Dr. Harisingh Gour University, Sagar, India
| | - Anamika Dubey
- Metagenomics and Secretomics Research Laboratory, Department of Botany, Dr. Harisingh Gour University, Sagar, India
| | - Shweta Yadav
- Department of Zoology, Dr. Harisingh Gour University, Sagar, India
| | - Ashwani Kumar
- Metagenomics and Secretomics Research Laboratory, Department of Botany, Dr. Harisingh Gour University, Sagar, India
| | - Abeer Hashem
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Elsayed Fathi Abd Allah
- Department of Plant Production, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
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18
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Catania V, Cappello S, Di Giorgi V, Santisi S, Di Maria R, Mazzola A, Vizzini S, Quatrini P. Microbial communities of polluted sub-surface marine sediments. MARINE POLLUTION BULLETIN 2018; 131:396-406. [PMID: 29886964 DOI: 10.1016/j.marpolbul.2018.04.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 03/08/2018] [Accepted: 04/09/2018] [Indexed: 06/08/2023]
Abstract
Microbial communities of coastal marine sediment play a key role in degradation of petroleum contaminants. Here the bacterial and archaeal communities of sub-surface sediments (5-10 cm) of the chronically polluted Priolo Bay (eastern coast of Sicily, Italy), contaminated mainly by n-alkanes and biodegraded/weathered oils, were characterized by cultural and molecular approaches. 16S-PCR-DGGE analysis at six stations, revealed that bacterial communities are highly divergent and display lower phylogenetic diversity than the surface sediment; sub-surface communities respond to oil supplementation in microcosms with a significant reduction in biodiversity and a shift in composition; they retain high biodegradation capacities and host hydrocarbon (HC) degraders that were isolated and identified. HC-degrading Alfa, Gamma and Epsilon proteobacteria together with Clostridia and Archaea are a common feature of sub-surface communities. These assemblages show similarities with that of subsurface petroleum reservoirs also characterized by the presence of biodegraded and weathered oils where anaerobic or microaerophilic syntrophic HC metabolism has been proposed.
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Affiliation(s)
- Valentina Catania
- Dept. of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Palermo, Italy
| | - Simone Cappello
- Institute for Coastal Marine Environment (IAMC)-CNR of Messina, Messina, Italy
| | - Vincenzo Di Giorgi
- Dept. of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Palermo, Italy
| | - Santina Santisi
- Institute for Coastal Marine Environment (IAMC)-CNR of Messina, Messina, Italy
| | - Roberta Di Maria
- Dept. of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Palermo, Italy
| | - Antonio Mazzola
- Dept. of Earth and Marine Sciences (DISTEM) University of Palermo, Palermo, Italy; Consorzio Nazionale Interuniversitario per le Scienze del Mare (CoNISMa), Roma, Italy
| | - Salvatrice Vizzini
- Dept. of Earth and Marine Sciences (DISTEM) University of Palermo, Palermo, Italy; Consorzio Nazionale Interuniversitario per le Scienze del Mare (CoNISMa), Roma, Italy
| | - Paola Quatrini
- Dept. of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Palermo, Italy.
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Metabolomic Profiles of a Midge (Procladius villosimanus, Kieffer) Are Associated with Sediment Contamination in Urban Wetlands. Metabolites 2017; 7:metabo7040064. [PMID: 29258276 PMCID: PMC5746744 DOI: 10.3390/metabo7040064] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 12/14/2017] [Accepted: 12/16/2017] [Indexed: 02/04/2023] Open
Abstract
Metabolomic techniques are powerful tools for investigating organism-environment interactions. Metabolite profiles have the potential to identify exposure or toxicity before populations are disrupted and can provide useful information for environmental assessment. However, under complex environmental scenarios, metabolomic responses to exposure can be distorted by background and/or organismal variation. In the current study, we use LC-MS (liquid chromatography-mass spectrometry) and GC-MS (gas chromatography-mass spectrometry) to measure metabolites of the midge Procladius villosimanus inhabiting 21 urban wetlands. These metabolites were tested against common sediment contaminants using random forest models and metabolite enrichment analysis. Sediment contaminant concentrations in the field correlated with several P. villosimanus metabolites despite natural environmental and organismal variation. Furthermore, enrichment analysis indicated that metabolite sets implicated in stress responses were enriched, pointing to specific cellular functions affected by exposure. Methionine metabolism, sugar metabolism and glycerolipid metabolism associated with total petroleum hydrocarbon and metal concentrations, while mitochondrial electron transport and urea cycle sets associated only with bifenthrin. These results demonstrate the potential for metabolomics approaches to provide useful information in field-based environmental assessments.
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Wöhlbrand L, Feenders C, Nachbaur J, Freund H, Engelen B, Wilkes H, Brumsack HJ, Rabus R. Impact of Extraction Methods on the Detectable Protein Complement of Metaproteomic Analyses of Marine Sediments. Proteomics 2017; 17. [DOI: 10.1002/pmic.201700241] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 08/21/2017] [Indexed: 11/11/2022]
Affiliation(s)
- Lars Wöhlbrand
- General and Molecular Microbiology; Institute for Chemistry and Biology of the Marine Environment (ICBM); Carl von Ossietzky University of Oldenburg; Oldenburg Germany
| | - Christoph Feenders
- Mathematical Modelling; Institute for Chemistry and Biology of the Marine Environment (ICBM); Carl von Ossietzky University of Oldenburg; Oldenburg Germany
| | - Jessica Nachbaur
- General and Molecular Microbiology; Institute for Chemistry and Biology of the Marine Environment (ICBM); Carl von Ossietzky University of Oldenburg; Oldenburg Germany
| | - Holger Freund
- Geoecology; Institute for Chemistry and Biology of the Marine Environment (ICBM); Carl von Ossietzky University of Oldenburg; Oldenburg Germany
| | - Bert Engelen
- Paleomicrobiology; Institute for Chemistry and Biology of the Marine Environment (ICBM); Carl von Ossietzky University of Oldenburg; Oldenburg Germany
| | - Heinz Wilkes
- Organic Geochemistry; Institute for Chemistry and Biology of the Marine Environment (ICBM); Carl von Ossietzky University of Oldenburg; Oldenburg Germany
| | - Hans-Jürgen Brumsack
- Microbiogeochemistry; Institute for Chemistry and Biology of the Marine Environment (ICBM); Carl von Ossietzky University of Oldenburg; Oldenburg Germany
| | - Ralf Rabus
- General and Molecular Microbiology; Institute for Chemistry and Biology of the Marine Environment (ICBM); Carl von Ossietzky University of Oldenburg; Oldenburg Germany
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Mesuere B, Van der Jeugt F, Willems T, Naessens T, Devreese B, Martens L, Dawyndt P. High-throughput metaproteomics data analysis with Unipept: A tutorial. J Proteomics 2017; 171:11-22. [PMID: 28552653 DOI: 10.1016/j.jprot.2017.05.022] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 05/15/2017] [Accepted: 05/22/2017] [Indexed: 02/06/2023]
Abstract
In recent years, shotgun metaproteomics has established itself as an important tool to study the composition of complex ecosystems and microbial communities. Two key steps in metaproteomics data analysis are the inference of proteins from the identified peptides, and the determination of the taxonomic origin and function of these proteins. This tutorial therefore introduces the Unipept command line interface (http://unipept.ugent.be/clidocs) as a platform-independent tool for such metaproteomics data analyses. First, a detailed overview is given of the available Unipept commands and their functions. Next, the power of the Unipept command line interface is illustrated using two case studies that analyze a single tryptic peptide, and a set of peptides retrieved from a shotgun metaproteomics experiment, respectively. Finally, the analysis results obtained using these command line tools are compared with the interactive taxonomic analysis that is available on the Unipept website.
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Affiliation(s)
- Bart Mesuere
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium; VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium; Department of Biochemistry, Ghent University, Ghent, Belgium.
| | - Felix Van der Jeugt
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
| | - Toon Willems
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
| | - Tom Naessens
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
| | - Bart Devreese
- Laboratory for Protein Biochemistry and Biomolecular Engineering, Ghent University, Ghent, Belgium
| | - Lennart Martens
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium; Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Peter Dawyndt
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
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Mapelli F, Scoma A, Michoud G, Aulenta F, Boon N, Borin S, Kalogerakis N, Daffonchio D. Biotechnologies for Marine Oil Spill Cleanup: Indissoluble Ties with Microorganisms. Trends Biotechnol 2017; 35:860-870. [PMID: 28511936 DOI: 10.1016/j.tibtech.2017.04.003] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 04/09/2017] [Accepted: 04/10/2017] [Indexed: 12/25/2022]
Abstract
The ubiquitous exploitation of petroleum hydrocarbons (HCs) has been accompanied by accidental spills and chronic pollution in marine ecosystems, including the deep ocean. Physicochemical technologies are available for oil spill cleanup, but HCs must ultimately be mineralized by microorganisms. How environmental factors drive the assembly and activity of HC-degrading microbial communities remains unknown, limiting our capacity to integrate microorganism-based cleanup strategies with current physicochemical remediation technologies. In this review, we summarize recent findings about microbial physiology, metabolism and ecology and describe how microbes can be exploited to create improved biotechnological solutions to clean up marine surface and deep waters, sediments and beaches.
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Affiliation(s)
- Francesca Mapelli
- Department of Food Environmental and Nutritional Sciences, University of Milan, 20133 Milan, Italy
| | - Alberto Scoma
- Center for Microbial Ecology and Technology (CMET), University of Gent, B 9000 Gent, Belgium
| | - Grégoire Michoud
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division, 23955-6900 Thuwal, Saudi Arabia
| | - Federico Aulenta
- Water Research Institute (IRSA), National Research Council (CNR), 00015 Monterotondo, Italy
| | - Nico Boon
- Center for Microbial Ecology and Technology (CMET), University of Gent, B 9000 Gent, Belgium
| | - Sara Borin
- Department of Food Environmental and Nutritional Sciences, University of Milan, 20133 Milan, Italy
| | - Nicolas Kalogerakis
- School of Environmental Engineering, Technical University of Crete, 73100 Chania, Greece
| | - Daniele Daffonchio
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division, 23955-6900 Thuwal, Saudi Arabia.
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23
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Matturro B, Frascadore E, Cappello S, Genovese M, Rossetti S. In situ detection of alkB2 gene involved in Alcanivorax borkumensis SK2(T) hydrocarbon biodegradation. MARINE POLLUTION BULLETIN 2016; 110:378-382. [PMID: 27315756 DOI: 10.1016/j.marpolbul.2016.06.038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 06/08/2016] [Accepted: 06/10/2016] [Indexed: 06/06/2023]
Abstract
This study aimed to develop a new assay based on the whole cell hybridization in order to monitor alkane hydroxylase genes (alkB system) of the marine bacterium Alcanivorax borkumensis SK2(T) commonly reported as the predominant microorganism responsible for the biodegradation of n-alkanes which are the major fraction of petroleum hydrocarbons. The assay based on the whole cell hybridization targeting alkB2 gene was successfully developed and calibrated on a pure culture of Alcanivorax borkumensis SK2(T) with a detection efficiency up to 80%. The approach was further successfully validated on hydrocarbon-contaminated seawater and provided cells abundance (6.74E+04alkB2-carryingcellsmL(-1)) higher of about one order of magnitude than those obtained by qPCR (4.96E+03alkB2genecopiesmL(-1)). This study highlights the validity of the assay for the detection at single cell level of key-functional genes involved in the biodegradation of n-alkanes.
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Affiliation(s)
- Bruna Matturro
- Water Research Institute, IRSA-CNR, Via Salaria km 29,300, Monterotondo, RM, Italy
| | - Emanuela Frascadore
- Water Research Institute, IRSA-CNR, Via Salaria km 29,300, Monterotondo, RM, Italy
| | - Simone Cappello
- Institute of Marine and Coastal Environments, IAMC-CNR, Spianata S. Raineri, 86, Messina, ME, Italy
| | - Mariella Genovese
- Institute of Marine and Coastal Environments, IAMC-CNR, Spianata S. Raineri, 86, Messina, ME, Italy
| | - Simona Rossetti
- Water Research Institute, IRSA-CNR, Via Salaria km 29,300, Monterotondo, RM, Italy.
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24
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Armengaud J. Next-generation proteomics faces new challenges in environmental biotechnology. Curr Opin Biotechnol 2016; 38:174-82. [DOI: 10.1016/j.copbio.2016.02.025] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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25
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Christie-Oleza JA, Armengaud J. Proteomics of theRoseobacterclade, a window to the marine microbiology landscape. Proteomics 2015; 15:3928-42. [DOI: 10.1002/pmic.201500222] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Revised: 08/24/2015] [Accepted: 09/22/2015] [Indexed: 11/07/2022]
Affiliation(s)
| | - Jean Armengaud
- CEA; DSV; IBiTec-S; SPI; Li2D; Laboratory “Innovative Technologies for Detection and Diagnostics”; Bagnols-sur-Cèze France
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