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Carrascal M, Sánchez-Jiménez E, Fang J, Pérez-López C, Ginebreda A, Barceló D, Abian J. Sewage Protein Information Mining: Discovery of Large Biomolecules as Biomarkers of Population and Industrial Activities. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023. [PMID: 37463250 PMCID: PMC10399289 DOI: 10.1021/acs.est.3c00535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
Wastewater-based epidemiology has been revealed as a powerful approach for surveying the health and lifestyle of a population. In this context, proteins have been proposed as potential biomarkers that complement the information provided by currently available methods. However, little is known about the range of molecular species and dynamics of proteins in wastewater and the information hidden in these protein profiles is still to be uncovered. In this study, we investigated the protein composition of wastewater from 10 municipalities in Catalonia with diverse populations and industrial activities at three different times of the year. The soluble fraction of this material was analyzed using liquid chromatography high-resolution tandem mass spectrometry using a shotgun proteomics approach. The complete proteomic profile, distribution among different organisms, and semiquantitative analysis of the main constituents are described. Excreta (urine and feces) from humans, and blood and other residues from livestock were identified as the two main protein sources. Our findings provide new insights into the characterization of wastewater proteomics that allow for the proposal of specific bioindicators for wastewater-based environmental monitoring. This includes human and animal population monitoring, most notably for rodent pest control (immunoglobulins (Igs) and amylases) and livestock processing industry monitoring (albumins).
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Affiliation(s)
- Montserrat Carrascal
- Biological and Environmental Proteomics Group, Institute of Biomedical Research of Barcelona, Spanish National Research Council (IIBB-CSIC/IDIBAPS), Rosellón 161, E-08036 Barcelona, Spain
| | - Ester Sánchez-Jiménez
- Biological and Environmental Proteomics Group, Institute of Biomedical Research of Barcelona, Spanish National Research Council (IIBB-CSIC/IDIBAPS), Rosellón 161, E-08036 Barcelona, Spain
- Department of Environmental Chemistry, Institute of Environmental Assessment and Water Studies (IDAEA-CSIC), Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Jie Fang
- Biological and Environmental Proteomics Group, Institute of Biomedical Research of Barcelona, Spanish National Research Council (IIBB-CSIC/IDIBAPS), Rosellón 161, E-08036 Barcelona, Spain
- Department of Environmental Chemistry, Institute of Environmental Assessment and Water Studies (IDAEA-CSIC), Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Carlos Pérez-López
- Biological and Environmental Proteomics Group, Institute of Biomedical Research of Barcelona, Spanish National Research Council (IIBB-CSIC/IDIBAPS), Rosellón 161, E-08036 Barcelona, Spain
- Department of Environmental Chemistry, Institute of Environmental Assessment and Water Studies (IDAEA-CSIC), Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Antoni Ginebreda
- Department of Environmental Chemistry, Institute of Environmental Assessment and Water Studies (IDAEA-CSIC), Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Damià Barceló
- Department of Environmental Chemistry, Institute of Environmental Assessment and Water Studies (IDAEA-CSIC), Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Joaquin Abian
- Biological and Environmental Proteomics Group, Institute of Biomedical Research of Barcelona, Spanish National Research Council (IIBB-CSIC/IDIBAPS), Rosellón 161, E-08036 Barcelona, Spain
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Körner P. Hydrothermal Degradation of Amino Acids. CHEMSUSCHEM 2021; 14:4947-4957. [PMID: 34498812 PMCID: PMC9292971 DOI: 10.1002/cssc.202101487] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 09/09/2021] [Indexed: 05/05/2023]
Abstract
Within the past years, hydrothermal processes have gathered much attention as promising conversion technologies for especially wet biomass. Amino acids are an integral component of biomass, zoo biomass in particular. However, what happens to them during hydrothermal treatment? Reviewing the available literature going back to the mid of the 20th century revealed an astonishing, but still fragmentary view. In fact, two universal degradation reactions could be identified (i. e., deamination and decarboxylation), competing with each other. Thereby, small structural differences may obviously have huge impacts on the fate of individual amino acids. Nevertheless, the amount of available experimental data is relatively scarce in many cases. In this work, the available knowledge about the degradation of 20 proteinogenic amino acids under hydrothermal conditions was presented and discussed critically. The hydrothermal conversion of proteinaceus biomass as well as the Maillard reaction, both extensively reviewed elsewhere, were only touched on.
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Affiliation(s)
- Paul Körner
- DBFZ - Deutsches Biomasseforschungszentrum gemeinnützige GmbH Biorefineries DepartmentTorgauer Straße 11604347LeipzigGermany
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Hashemi S, Hashemi SE, Lien KM, Lamb JJ. Molecular Microbial Community Analysis as an Analysis Tool for Optimal Biogas Production. Microorganisms 2021; 9:microorganisms9061162. [PMID: 34071282 PMCID: PMC8226781 DOI: 10.3390/microorganisms9061162] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 05/17/2021] [Accepted: 05/26/2021] [Indexed: 11/16/2022] Open
Abstract
The microbial diversity in anaerobic digestion (AD) is important because it affects process robustness. High-throughput sequencing offers high-resolution data regarding the microbial diversity and robustness of biological systems including AD; however, to understand the dynamics of microbial processes, knowing the microbial diversity is not adequate alone. Advanced meta-omic techniques have been established to determine the activity and interactions among organisms in biological processes like AD. Results of these methods can be used to identify biomarkers for AD states. This can aid a better understanding of system dynamics and be applied to producing comprehensive models for AD. The paper provides valuable knowledge regarding the possibility of integration of molecular methods in AD. Although meta-genomic methods are not suitable for on-line use due to long operating time and high costs, they provide extensive insight into the microbial phylogeny in AD. Meta-proteomics can also be explored in the demonstration projects for failure prediction. However, for these methods to be fully realised in AD, a biomarker database needs to be developed.
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Affiliation(s)
- Seyedbehnam Hashemi
- Department of Energy and Process Engineering & Enersense, Norwegian University of Science and Technology (NTNU), 7034 Trondheim, Norway; (S.H.); (S.E.H.); (K.M.L.)
| | - Sayed Ebrahim Hashemi
- Department of Energy and Process Engineering & Enersense, Norwegian University of Science and Technology (NTNU), 7034 Trondheim, Norway; (S.H.); (S.E.H.); (K.M.L.)
| | - Kristian M. Lien
- Department of Energy and Process Engineering & Enersense, Norwegian University of Science and Technology (NTNU), 7034 Trondheim, Norway; (S.H.); (S.E.H.); (K.M.L.)
| | - Jacob J. Lamb
- Department of Energy and Process Engineering & Enersense, Norwegian University of Science and Technology (NTNU), 7034 Trondheim, Norway; (S.H.); (S.E.H.); (K.M.L.)
- Department of Electronic Systems, Norwegian University of Science and Technology (NTNU), 7034 Trondheim, Norway
- Correspondence:
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Carrascal M, Abian J, Ginebreda A, Barceló D. Discovery of large molecules as new biomarkers in wastewater using environmental proteomics and suitable polymer probes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 747:141145. [PMID: 32791406 DOI: 10.1016/j.scitotenv.2020.141145] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 07/16/2020] [Accepted: 07/19/2020] [Indexed: 05/24/2023]
Abstract
The capability of monitoring large molecules as possible biomarkers in wastewater will be an important contribution to the new field of sewage epidemiology. Here, we explore the use of polymer probes together with untargeted proteomics for large scale protein analysis in sewage and treated water. Polymeric probes were immersed in the influent, anoxic reactor and effluent waters of a Spanish WWTP during 11 days. Proteins sorbed were extracted and identified by mass spectrometry. A total of 690 proteins from bacteria, plants and animals, including human, were identified showing different proteome profiles in the different sites. Bacterial proteins (510) pointed at 175 genera distributed in 22 bacterial classes. The most abundant were EF-Tu, GroEL and ATP synthase which were contributed by a high number of species. Human was the species contributing the greatest number of identified proteins (57), some in high abundance like keratins. Human proteins dominated in the influent water and were efficiently removed at the effluent. Several of the proteins identified (S100A8, uromodulin, defensins) are known disease biomarkers. This study provides the first insight into the proteome profiles present in real wastewater.
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Affiliation(s)
- M Carrascal
- Proteomics Laboratory CSIC/UAB, Institute of Biomedical Research of Barcelona, Spanish National Research Council (IIBB-CSIC/IDIBAPS), Rosellón 161, E-08036 Barcelona, Spain
| | - J Abian
- Proteomics Laboratory CSIC/UAB, Institute of Biomedical Research of Barcelona, Spanish National Research Council (IIBB-CSIC/IDIBAPS), Rosellón 161, E-08036 Barcelona, Spain.
| | - A Ginebreda
- Institute of Environmental Assessment and Water Studies (IDAEA-CSIC), Department of Environmental Chemistry, Jordi Girona 18-26, 08034 Barcelona, Spain
| | - D Barceló
- Institute of Environmental Assessment and Water Studies (IDAEA-CSIC), Department of Environmental Chemistry, Jordi Girona 18-26, 08034 Barcelona, Spain; Catalan Institute for Water Research (ICRA), Emili Grahit 101, Parc Científic i Tecnològic de la Universitat de Girona, Edifici H2O, 17003 Girona, Spain
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Gierse LC, Meene A, Schultz D, Schwaiger T, Karte C, Schröder C, Wang H, Wünsche C, Methling K, Kreikemeyer B, Fuchs S, Bernhardt J, Becher D, Lalk M, Study Group K, Urich T, Riedel K. A Multi-Omics Protocol for Swine Feces to Elucidate Longitudinal Dynamics in Microbiome Structure and Function. Microorganisms 2020; 8:microorganisms8121887. [PMID: 33260576 PMCID: PMC7760263 DOI: 10.3390/microorganisms8121887] [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] [Received: 09/04/2020] [Revised: 11/03/2020] [Accepted: 11/27/2020] [Indexed: 12/19/2022] Open
Abstract
Swine are regarded as promising biomedical models, but the dynamics of their gastrointestinal microbiome have been much less investigated than that of humans or mice. The aim of this study was to establish an integrated multi-omics protocol to investigate the fecal microbiome of healthy swine. To this end, a preparation and analysis protocol including integrated sample preparation for meta-omics analyses of deep-frozen feces was developed. Subsequent data integration linked microbiome composition with function, and metabolic activity with protein inventories, i.e., 16S rRNA data and expressed proteins, and identified proteins with corresponding metabolites. 16S rRNA gene amplicon and metaproteomics analyses revealed a fecal microbiome dominated by Prevotellaceae, Lactobacillaceae, Lachnospiraceae, Ruminococcaceae and Clostridiaceae. Similar microbiome compositions in feces and colon, but not ileum samples, were observed, showing that feces can serve as minimal-invasive proxy for porcine colon microbiomes. Longitudinal dynamics in composition, e.g., temporal decreased abundance of Lactobacillaceae and Streptococcaceae during the experiment, were not reflected in microbiome function. Instead, metaproteomics and metabolomics showed a rather stable functional state, as evident from short-chain fatty acids (SCFA) profiles and associated metaproteome functions, pointing towards functional redundancy among microbiome constituents. In conclusion, our pipeline generates congruent data from different omics approaches on the taxonomy and functionality of the intestinal microbiome of swine.
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Affiliation(s)
- Laurin Christopher Gierse
- Institute of Microbiology, University of Greifswald, Felix-Hausdorff-Str. 8, 17489 Greifswald, Germany; (L.C.G.); (A.M.); (H.W.); (C.W.); (J.B.); (D.B.)
| | - Alexander Meene
- Institute of Microbiology, University of Greifswald, Felix-Hausdorff-Str. 8, 17489 Greifswald, Germany; (L.C.G.); (A.M.); (H.W.); (C.W.); (J.B.); (D.B.)
| | - Daniel Schultz
- Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17489 Greifswald, Germany; (D.S.); (K.M.); (M.L.)
| | - Theresa Schwaiger
- Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Südufer 10, 17493 Greifswald, Germany; (T.S.); (C.K.); (C.S.)
| | - Claudia Karte
- Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Südufer 10, 17493 Greifswald, Germany; (T.S.); (C.K.); (C.S.)
| | - Charlotte Schröder
- Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Südufer 10, 17493 Greifswald, Germany; (T.S.); (C.K.); (C.S.)
| | - Haitao Wang
- Institute of Microbiology, University of Greifswald, Felix-Hausdorff-Str. 8, 17489 Greifswald, Germany; (L.C.G.); (A.M.); (H.W.); (C.W.); (J.B.); (D.B.)
| | - Christine Wünsche
- Institute of Microbiology, University of Greifswald, Felix-Hausdorff-Str. 8, 17489 Greifswald, Germany; (L.C.G.); (A.M.); (H.W.); (C.W.); (J.B.); (D.B.)
| | - Karen Methling
- Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17489 Greifswald, Germany; (D.S.); (K.M.); (M.L.)
| | - Bernd Kreikemeyer
- Institute for Medical Microbiology, Virology and Hygiene, Rostock University Medical Centre, Schillingallee 70, 18055 Rostock, Germany;
| | - Stephan Fuchs
- Division of Nosocomial Pathogens and Antibiotic Resistance, Robert Koch Institute Wernigerode, Burgstraße 37, 38855 Wernigerode, Germany;
| | - Jörg Bernhardt
- Institute of Microbiology, University of Greifswald, Felix-Hausdorff-Str. 8, 17489 Greifswald, Germany; (L.C.G.); (A.M.); (H.W.); (C.W.); (J.B.); (D.B.)
| | - Dörte Becher
- Institute of Microbiology, University of Greifswald, Felix-Hausdorff-Str. 8, 17489 Greifswald, Germany; (L.C.G.); (A.M.); (H.W.); (C.W.); (J.B.); (D.B.)
| | - Michael Lalk
- Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17489 Greifswald, Germany; (D.S.); (K.M.); (M.L.)
| | | | - Tim Urich
- Institute of Microbiology, University of Greifswald, Felix-Hausdorff-Str. 8, 17489 Greifswald, Germany; (L.C.G.); (A.M.); (H.W.); (C.W.); (J.B.); (D.B.)
- Correspondence: (T.U.); (K.R.); Tel.: +49-3834-420-5904 (T.U.); +49-3834-420-5900 (K.R.)
| | - Katharina Riedel
- Institute of Microbiology, University of Greifswald, Felix-Hausdorff-Str. 8, 17489 Greifswald, Germany; (L.C.G.); (A.M.); (H.W.); (C.W.); (J.B.); (D.B.)
- Correspondence: (T.U.); (K.R.); Tel.: +49-3834-420-5904 (T.U.); +49-3834-420-5900 (K.R.)
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6
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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.
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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
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Schultz D, Zühlke D, Bernhardt J, Francis TB, Albrecht D, Hirschfeld C, Markert S, Riedel K. An optimized metaproteomics protocol for a holistic taxonomic and functional characterization of microbial communities from marine particles. ENVIRONMENTAL MICROBIOLOGY REPORTS 2020; 12:367-376. [PMID: 32281239 DOI: 10.1111/1758-2229.12842] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 04/03/2020] [Indexed: 06/11/2023]
Abstract
This study aimed to establish a robust and reliable metaproteomics protocol for an in-depth characterization of marine particle-associated (PA) bacteria. To this end, we compared six well-established protein extraction protocols together with different MS-sample preparation techniques using particles sampled during a North Sea spring algae bloom in 2009. In the final optimized workflow, proteins are extracted using a combination of SDS-containing lysis buffer and cell disruption by bead-beating, separated by SDS-PAGE, in-gel digested and analysed by LC-MS/MS, before MASCOT search against a metagenome-based database and data processing/visualization with the in-house-developed bioinformatics tools Prophane and Paver. As an application example, free-living (FL) and particulate communities sampled in April 2009 were analysed, resulting in an as yet unprecedented number of 9354 and 5034 identified protein groups for FL and PA bacteria, respectively. Our data suggest that FL and PA communities appeared similar in their taxonomic distribution, with notable exceptions: eukaryotic proteins and proteins assigned to Flavobacteriia, Cyanobacteria, and some proteobacterial genera were found more abundant on particles, whilst overall proteins belonging to Proteobacteria were more dominant in the FL fraction. Furthermore, our data points to functional differences including proteins involved in polysaccharide degradation, sugar- and phosphorus uptake, adhesion, motility, and stress response.
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Affiliation(s)
- Doreen Schultz
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Daniela Zühlke
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Jörg Bernhardt
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | | | - Dirk Albrecht
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Claudia Hirschfeld
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Stephanie Markert
- Institute of Pharmacy, University of Greifswald, Greifswald, Germany
| | - Katharina Riedel
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
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Krause JL, Schaepe SS, Fritz-Wallace K, Engelmann B, Rolle-Kampczyk U, Kleinsteuber S, Schattenberg F, Liu Z, Mueller S, Jehmlich N, Von Bergen M, Herberth G. Following the community development of SIHUMIx - a new intestinal in vitro model for bioreactor use. Gut Microbes 2020; 11:1116-1129. [PMID: 31918607 PMCID: PMC7524388 DOI: 10.1080/19490976.2019.1702431] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 10/21/2019] [Accepted: 12/03/2019] [Indexed: 02/03/2023] Open
Abstract
Diverse intestinal microbiota is frequently used in in vitro bioreactor models to study the effects of diet, chemical contaminations, or medication. However, the reproducible cultivation of fecal microbiota is challenging and the resultant communities behave highly dynamic. To approach the issue of reproducibility in in vitro models, we established an intestinal microbiota model community of reduced complexity, SIHUMIx, as a valuable model for in vitro use. The development of the SIHUMIx community was monitored over time with methods covering the cellular and the molecular level. We used microbial flow cytometry, intact protein profiling and terminal restriction fragment length polymorphism analysis to assess community structure. In parallel, we analyzed the functional level by targeted analysis of short-chain fatty acids and untargeted metabolomics. The stability properties constancy, resistance, and resilience were approached both on the structural and functional level of the community. We show that the SIHUMIx community is highly reproducible and constant since day 5 of cultivation. Furthermore, SIHUMIx has the ability to resist and recover from a pulsed perturbation, with changes in community structure recovered earlier than functional changes. Since community structure and function changed divergently, both levels need to be monitored at the same time to gain a full overview of the community development. All five methods are highly suitable to follow the community dynamics of SIHUMIx and indicated stability on day five. This makes SIHUMIx a suitable in vitro model to investigate the effects of e.g. medical, chemical, or dietary interventions.
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Affiliation(s)
- Jannike Lea Krause
- Department of Environmental Immunology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, German
| | - Stephanie Serena Schaepe
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Katarina Fritz-Wallace
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Beatrice Engelmann
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Ulrike Rolle-Kampczyk
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Sabine Kleinsteuber
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Florian Schattenberg
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Zishu Liu
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Susann Mueller
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Nico Jehmlich
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Martin Von Bergen
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
- Institute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, University of Leipzig, Leipzig, Germany
| | - Gunda Herberth
- Department of Environmental Immunology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, German
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9
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Salerno C, Berardi G, Laera G, Pollice A. Functional Response of MBR Microbial Consortia to Substrate Stress as Revealed by Metaproteomics. MICROBIAL ECOLOGY 2019; 78:873-884. [PMID: 30976843 DOI: 10.1007/s00248-019-01360-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 02/10/2019] [Indexed: 06/09/2023]
Abstract
Bacterial consortia have a primary role in the biological degradations occurring in activated sludge for wastewater treatment, for their capacities to metabolize the polluting matter. Therefore, the knowledge of the main metabolic pathways for the degradation of pollutants becomes critical for a correct design and operation of wastewater treatment plants. The metabolic activity of the different bacterial groups in activated sludge is commonly investigated through respirometry. Furthermore, in the last years, the development of "omic" approaches has offered more opportunities to integrate or substitute the conventional microbiological assays and to deeply understand the taxonomy and dynamics of complex microbial consortia. In the present work, an experimental membrane bioreactor (MBR) was set up and operated for the treatment of municipal wastewater, and the effects of a sudden decrease of the organic supply on the activated sludge were investigated. Both respirometric and metaproteomic approaches revealed a resistance of autotrophic bacteria to the substrate stress, and particularly of nitrifying bacteria. Furthermore, metaproteomics allowed the identification of the taxonomy of the microbial consortium based on its protein expression, unveiling the prevalence of Sorangium and Nitrosomonas genera both before and after the organic load decrease. Moreover, it confirmed the results obtained through respirometry and revealed a general expression of proteins involved in metabolism and transport of nitrogen, or belonging to nitrifying species like Nitrosomonas europeae, Nitrosomonas sp. AL212, or Nitrospira defluvii.
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Affiliation(s)
- Carlo Salerno
- IRSA CNR, Water Research Institute, Viale F. De Blasio 5, 70132, Bari, Italy.
| | - Giovanni Berardi
- IRSA CNR, Water Research Institute, Viale F. De Blasio 5, 70132, Bari, Italy
| | - Giuseppe Laera
- IRSA CNR, Water Research Institute, Viale F. De Blasio 5, 70132, Bari, Italy
| | - Alfieri Pollice
- IRSA CNR, Water Research Institute, Viale F. De Blasio 5, 70132, Bari, Italy
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11
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Sharma B, Sarkar A, Singh P, Singh RP. Agricultural utilization of biosolids: A review on potential effects on soil and plant grown. WASTE MANAGEMENT (NEW YORK, N.Y.) 2017; 64:117-132. [PMID: 28336334 DOI: 10.1016/j.wasman.2017.03.002] [Citation(s) in RCA: 127] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2016] [Revised: 01/30/2017] [Accepted: 03/01/2017] [Indexed: 05/20/2023]
Abstract
Environmental and economic implications linked with the proper ecofriendly disposal of modern day wastes, has made it essential to come up with alternative waste management practices that reduce the environmental pressures resulting from unwise disposal of such wastes. Urban wastes like biosolids are loaded with essential plant nutrients. In this view, agricultural use of biosolids would enable recycling of these nutrients and could be a sustainable approach towards management of this hugely generated waste. Therefore biosolids i.e. sewage sludge can serve as an important resource for agricultural utilization. Biosolids are characterized by the occurrence of beneficial plant nutrients (essential elements and micro and macronutrients) which can make help them to work as an effective soil amendment, thereby minimizing the reliance on chemical fertilizers. However, biosolids might contain toxic heavy metals that may limit its usage in the cropland. Heavy metals at higher concentration than the permissible limits may lead to food chain contamination and have fatal consequences. Biosolids amendment in soil can improve physical and nutrient property of soil depending on the quantity and portion of the mixture. Hence, biosolids can be a promising soil ameliorating supplement to increase plant productivity, reduce bioavailability of heavy metals and also lead to effective waste management.
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Affiliation(s)
- Bhavisha Sharma
- Institute of Environment and Sustainable Development, Banaras Hindu University, Varanasi, India
| | - Abhijit Sarkar
- Laboratory of Applied Stress Biology, Department of Botany, University of Gour Banga, Malda 732 103, West Bengal, India.
| | - Pooja Singh
- Institute of Environment and Sustainable Development, Banaras Hindu University, Varanasi, India
| | - Rajeev Pratap Singh
- Institute of Environment and Sustainable Development, Banaras Hindu University, Varanasi, India; Department of Civil Engineering, University of Nebraska Lincoln, Lincoln, USA.
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12
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Chen X, Zhao J, Bao L, Wang L, Zhang Y. The investigation of different pollutants and operation processes on sludge toxicity in sequencing batch bioreactors. ENVIRONMENTAL TECHNOLOGY 2016; 37:2048-2057. [PMID: 26914341 DOI: 10.1080/09593330.2016.1140813] [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] [Indexed: 06/05/2023]
Abstract
The influence of different target pollutants and operation modes in sequencing batch bioreactors (SBRs) on sludge toxicity was compared in this study. Sludge toxicity was characterized by the inhibiting luminosity through using luminescent bacterium Photobacterium phosphoreum (P. phosphoreum) during either gradual acclimation or impaction processes with synthetic wastewater containing high-strength bisphenol A (BPA) or N, N-dimethylformamide (DMF). When the activated sludge was first acclimated with either 120 mg/L DMF or 20 mg/L BPA, and then respectively increased to 200 mg/L DMF and 40 mg/L BPA it was defined as gradual acclimation process, whereas when the activated sludge was, respectively, injected with 200 mg/L DMF and 40 mg/L BPA directly it was defined as impaction process. Results showed that the toxicity of the impacted sludge was greater than that of the gradual acclimated sludge, especially in the initial stage before 10 d. Activated sludge treating BPA synthetic wastewater exhibited higher toxicity due to the more inhibition of BPA to sludge activity compared to that of DMF. The proteomics analysis indicated that the stress responses of activated sludge to DMF and BPA stimulation were both significant. In turn, the secretions from two kinds of sludge under stress conditions contributed to sludge toxicity.
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Affiliation(s)
- Xiurong Chen
- a State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process , East China University of Science and Technology , Shanghai 200237 , People's Republic of China
| | - Jianguo Zhao
- a State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process , East China University of Science and Technology , Shanghai 200237 , People's Republic of China
- b Key Laboratory for Yellow River and Huai River Water Environment and Pollution Control, Ministry of Education , Henan Key Laboratory for Environmental Pollution Control, Henan Normal University , Xinxiang 453007 , People's Republic of China
| | - Linlin Bao
- b Key Laboratory for Yellow River and Huai River Water Environment and Pollution Control, Ministry of Education , Henan Key Laboratory for Environmental Pollution Control, Henan Normal University , Xinxiang 453007 , People's Republic of China
| | - Lu Wang
- a State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process , East China University of Science and Technology , Shanghai 200237 , People's Republic of China
| | - Yuying Zhang
- a State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process , East China University of Science and Technology , Shanghai 200237 , People's Republic of China
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13
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Heyer R, Benndorf D, Kohrs F, De Vrieze J, Boon N, Hoffmann M, Rapp E, Schlüter A, Sczyrba A, Reichl U. Proteotyping of biogas plant microbiomes separates biogas plants according to process temperature and reactor type. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:155. [PMID: 27462366 PMCID: PMC4960849 DOI: 10.1186/s13068-016-0572-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 07/12/2016] [Indexed: 05/23/2023]
Abstract
BACKGROUND Methane yield and biogas productivity of biogas plants (BGPs) depend on microbial community structure and function, substrate supply, and general biogas process parameters. So far, however, relatively little is known about correlations between microbial community function and process parameters. To close this knowledge gap, microbial communities of 40 samples from 35 different industrial biogas plants were evaluated by a metaproteomics approach in this study. RESULTS Liquid chromatography coupled to tandem mass spectrometry (Orbitrap Elite™ Hybrid Ion Trap-Orbitrap Mass Spectrometer) of all 40 samples as triplicate enabled the identification of 3138 different metaproteins belonging to 162 biological processes and 75 different taxonomic orders. The respective database searches were performed against UniProtKB/Swiss-Prot and seven metagenome databases. Subsequent clustering and principal component analysis of these data allowed for the identification of four main clusters associated with mesophile and thermophile process conditions, the use of upflow anaerobic sludge blanket reactors and BGP feeding with sewage sludge. Observations confirm a previous phylogenetic study of the same BGP samples that was based on 16S rRNA gene sequencing by De Vrieze et al. (Water Res 75:312-323, 2015). In particular, we identified similar microbial key players of biogas processes, namely Bacillales, Enterobacteriales, Bacteriodales, Clostridiales, Rhizobiales and Thermoanaerobacteriales as well as Methanobacteriales, Methanosarcinales and Methanococcales. For the elucidation of the main biomass degradation pathways, the most abundant 1 % of metaproteins was assigned to the KEGG map 1200 representing the central carbon metabolism. Additionally, the effect of the process parameters (i) temperature, (ii) organic loading rate (OLR), (iii) total ammonia nitrogen (TAN), and (iv) sludge retention time (SRT) on these pathways was investigated. For example, high TAN correlated with hydrogenotrophic methanogens and bacterial one-carbon metabolism, indicating syntrophic acetate oxidation. CONCLUSIONS This is the first large-scale metaproteome study of BGPs. Proteotyping of BGPs reveals general correlations between the microbial community structure and its function with process parameters. The monitoring of changes on the level of microbial key functions or even of the microbial community represents a well-directed tool for the identification of process problems and disturbances.Graphical abstractCorrelation between the different orders and process parameter, as well as principle component analysis of all investigated biogas plants based on the identified metaproteins.
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Affiliation(s)
- R. Heyer
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstraße 1, 39106 Magdeburg, Germany
- Bioprocess Engineering, Otto von Guericke University Magdeburg, Universitätsplatz 2, 39106 Magdeburg, Germany
| | - D. Benndorf
- Bioprocess Engineering, Otto von Guericke University Magdeburg, Universitätsplatz 2, 39106 Magdeburg, Germany
| | - F. Kohrs
- Bioprocess Engineering, Otto von Guericke University Magdeburg, Universitätsplatz 2, 39106 Magdeburg, Germany
| | - J. De Vrieze
- Laboratory of Microbial Technology and Ecology (LabMET), Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - N. Boon
- Laboratory of Microbial Technology and Ecology (LabMET), Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - M. Hoffmann
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstraße 1, 39106 Magdeburg, Germany
| | - E. Rapp
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstraße 1, 39106 Magdeburg, Germany
| | - Andreas Schlüter
- Center for Biotechnology, Genome Research of Industrial Microorganisms, Universität Bielefeld, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Alexander Sczyrba
- Center for Biotechnology, Computational Metagenomics, Universität Bielefeld, Universitätsstr. 25, 33615 Bielefeld, Germany
| | - U. Reichl
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstraße 1, 39106 Magdeburg, Germany
- Bioprocess Engineering, Otto von Guericke University Magdeburg, Universitätsplatz 2, 39106 Magdeburg, Germany
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14
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Salerno C, Benndorf D, Kluge S, Palese LL, Reichl U, Pollice A. Metaproteomics Applied to Activated Sludge for Industrial Wastewater Treatment Revealed a Dominant Methylotrophic Metabolism of Hyphomicrobium zavarzinii. MICROBIAL ECOLOGY 2016; 72:9-13. [PMID: 27090901 DOI: 10.1007/s00248-016-0769-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 04/06/2016] [Indexed: 06/05/2023]
Abstract
In biological wastewater treatments, microbial populations of the so-called activated sludge work together in the abatement of pollutants. In this work, the metabolic behavior of the biomass of a lab-scale plant treating industrial pharmaceutical wastewater was investigated through a metaproteomic approach. The complete treatment process included a membrane biological reactor (MBR) coupled with an advanced oxidation process (AOP) for partial breakdown of non-biodegradable molecules. Proteins from biomass samples collected pre- and post-AOP application were investigated by two-dimensional gel electrophoresis (2DE), mass spectrometry (MS), and finally identified by database search. Results showed that most proteins remained constant between pre- and post-AOP. Methanol dehydrogenase (MDH) belonging to Hyphomicrobium zavarzinii appeared as the most constantly expressed protein in the studied consortium. Other identified proteins belonging to Hyphomicrobium spp. revealed a predominant methylotrophic metabolism, and H. zavarzinii appeared as a key actor in the studied microbial community.
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Affiliation(s)
- Carlo Salerno
- Water Research Institute, Viale F. De Blasio 5, 70132, Bari, Italy.
| | - Dirk Benndorf
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Sandtorstraße 1, 39106, Magdeburg, Germany
| | - Sabine Kluge
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Sandtorstraße 1, 39106, Magdeburg, Germany
| | - Luigi Leonardo Palese
- Department of Basic Medical Sciences, Neurosciences and Sense Organs, University of Bari, Policlinico, P.zza G. Cesare 11, 70124, Bari, Italy
| | - Udo Reichl
- Otto-von-Guericke University, Bioprocess Engineering, Universitätsplatz 2, 39106, Magdeburg, Germany
| | - Alfieri Pollice
- Water Research Institute, Viale F. De Blasio 5, 70132, Bari, Italy
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15
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Hanson AJ, Guho NM, Paszczynski AJ, Coats ER. Community proteomics provides functional insight into polyhydroxyalkanoate production by a mixed microbial culture cultivated on fermented dairy manure. Appl Microbiol Biotechnol 2016; 100:7957-76. [PMID: 27147532 DOI: 10.1007/s00253-016-7576-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2016] [Revised: 04/15/2016] [Accepted: 04/21/2016] [Indexed: 10/21/2022]
Abstract
Polyhydroxyalkanoates (PHAs) are bio-based, biodegradable polyesters that can be produced from organic-rich waste streams using mixed microbial cultures (MMCs). To maximize PHA production, MMCs are enriched for bacteria with a high polymer storage capacity through the application of aerobic dynamic feeding (ADF) in a sequencing batch reactor (SBR), which consequently induces a feast-famine metabolic response. Though the feast-famine response is generally understood empirically at a macro-level, the molecular level is less refined. The objective of this study was to investigate the microbial community composition and proteome profile of an enriched MMC cultivated on fermented dairy manure. The enriched MMC exhibited a feast-famine response and was capable of producing up to 40 % (wt. basis) PHA in a fed-batch reactor. High-throughput 16S rRNA gene sequencing revealed a microbial community dominated by Meganema, a known PHA-producing genus not often observed in high abundance in enrichment SBRs. The application of the proteomic methods two-dimensional electrophoresis and LC-MS/MS revealed PHA synthesis, energy generation, and protein synthesis prominently occurring during the feast phase, corroborating bulk solution variable observations and theoretical expectations. During the famine phase, nutrient transport, acyl-CoA metabolism, additional energy generation, and housekeeping functions were more pronounced, informing previously under-determined MMC functionality under famine conditions. During fed-batch PHA production, acetyl-CoA acetyltransferase and PHA granule-bound phasin proteins were in increased abundance relative to the SBR, supporting the higher PHA content observed. Collectively, the results provide unique microbial community structural and functional insight into feast-famine PHA production from waste feedstocks using MMCs.
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Affiliation(s)
- Andrea J Hanson
- Department of Biological Sciences, University of Idaho, Moscow, ID, 83844-3051, USA
| | - Nicholas M Guho
- Department of Civil Engineering, University of Idaho, 875 Perimeter Dr. MS1022, Moscow, ID, 83844-1022, USA
| | - Andrzej J Paszczynski
- Food Research Center, University of Idaho and Washington State University School of Food Science, Moscow, ID, 83844-1052, USA
| | - Erik R Coats
- Department of Civil Engineering, University of Idaho, 875 Perimeter Dr. MS1022, Moscow, ID, 83844-1022, USA.
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16
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Herbst FA, Lünsmann V, Kjeldal H, Jehmlich N, Tholey A, von Bergen M, Nielsen JL, Hettich RL, Seifert J, Nielsen PH. Enhancing metaproteomics--The value of models and defined environmental microbial systems. Proteomics 2016; 16:783-98. [PMID: 26621789 DOI: 10.1002/pmic.201500305] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Revised: 11/03/2015] [Accepted: 11/26/2015] [Indexed: 12/24/2022]
Abstract
Metaproteomics--the large-scale characterization of the entire protein complement of environmental microbiota at a given point in time--has provided new features to study complex microbial communities in order to unravel these "black boxes." New technical challenges arose that were not an issue for classical proteome analytics before that could be tackled by the application of different model systems. Here, we review different current and future model systems for metaproteome analysis. Following a short introduction to microbial communities and metaproteomics, we introduce model systems for clinical and biotechnological research questions including acid mine drainage, anaerobic digesters, and activated sludge. Model systems are useful to evaluate the challenges encountered within (but not limited to) metaproteomics, including species complexity and coverage, biomass availability, or reliable protein extraction. The implementation of model systems can be considered as a step forward to better understand microbial community responses and ecological functions of single member organisms. In the future, improvements are necessary to fully explore complex environmental systems by metaproteomics.
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Affiliation(s)
- Florian-Alexander Herbst
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark
| | - Vanessa Lünsmann
- Department of Proteomics, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany.,Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Henrik Kjeldal
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark
| | - Nico Jehmlich
- Department of Proteomics, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Andreas Tholey
- Systematic Proteome Research and Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Martin von Bergen
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark.,Department of Proteomics, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Jeppe Lund Nielsen
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark
| | - Robert L Hettich
- Chemical Sciences Division, Oak Ridge National Lab, Oak Ridge, TN, USA
| | - Jana Seifert
- Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
| | - Per Halkjaer Nielsen
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark
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17
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Heyer R, Kohrs F, Reichl U, Benndorf D. Metaproteomics of complex microbial communities in biogas plants. Microb Biotechnol 2015; 8:749-63. [PMID: 25874383 PMCID: PMC4554464 DOI: 10.1111/1751-7915.12276] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Revised: 02/05/2015] [Accepted: 02/11/2015] [Indexed: 11/29/2022] Open
Abstract
Production of biogas from agricultural biomass or organic wastes is an important source of renewable energy. Although thousands of biogas plants (BGPs) are operating in Germany, there is still a significant potential to improve yields, e.g. from fibrous substrates. In addition, process stability should be optimized. Besides evaluating technical measures, improving our understanding of microbial communities involved into the biogas process is considered as key issue to achieve both goals. Microscopic and genetic approaches to analyse community composition provide valuable experimental data, but fail to detect presence of enzymes and overall metabolic activity of microbial communities. Therefore, metaproteomics can significantly contribute to elucidate critical steps in the conversion of biomass to methane as it delivers combined functional and phylogenetic data. Although metaproteomics analyses are challenged by sample impurities, sample complexity and redundant protein identification, and are still limited by the availability of genome sequences, recent studies have shown promising results. In the following, the workflow and potential pitfalls for metaproteomics of samples from full-scale BGP are discussed. In addition, the value of metaproteomics to contribute to the further advancement of microbial ecology is evaluated. Finally, synergistic effects expected when metaproteomics is combined with advanced imaging techniques, metagenomics, metatranscriptomics and metabolomics are addressed.
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Affiliation(s)
- Robert Heyer
- Bioprocess Engineering, Otto von Guericke University MagdeburgUniversitätsplatz 2, Magdeburg, 39106, Germany
- Max Planck Institute for Dynamics of Complex Technical SystemsSandtorstr. 1, Magdeburg, 39106, Germany
| | - Fabian Kohrs
- Bioprocess Engineering, Otto von Guericke University MagdeburgUniversitätsplatz 2, Magdeburg, 39106, Germany
- Max Planck Institute for Dynamics of Complex Technical SystemsSandtorstr. 1, Magdeburg, 39106, Germany
| | - Udo Reichl
- Bioprocess Engineering, Otto von Guericke University MagdeburgUniversitätsplatz 2, Magdeburg, 39106, Germany
- Max Planck Institute for Dynamics of Complex Technical SystemsSandtorstr. 1, Magdeburg, 39106, Germany
| | - Dirk Benndorf
- Bioprocess Engineering, Otto von Guericke University MagdeburgUniversitätsplatz 2, Magdeburg, 39106, Germany
- Max Planck Institute for Dynamics of Complex Technical SystemsSandtorstr. 1, Magdeburg, 39106, Germany
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18
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Arsène-Ploetze F, Bertin PN, Carapito C. Proteomic tools to decipher microbial community structure and functioning. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2015; 22:13599-13612. [PMID: 25475614 PMCID: PMC4560766 DOI: 10.1007/s11356-014-3898-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 11/20/2014] [Indexed: 06/04/2023]
Abstract
Recent advances in microbial ecology allow studying microorganisms in their environment, without laboratory cultivation, in order to get access to the large uncultivable microbial community. With this aim, environmental proteomics has emerged as an appropriate complementary approach to metagenomics providing information on key players that carry out main metabolic functions and addressing the adaptation capacities of living organisms in situ. In this review, a wide range of proteomic approaches applied to investigate the structure and functioning of microbial communities as well as recent examples of such studies are presented.
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Affiliation(s)
- Florence Arsène-Ploetze
- Génétique moléculaire, Génomique et Microbiologie, Université de Strasbourg, UMR7156 CNRS, Strasbourg, France,
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19
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Püttker S, Kohrs F, Benndorf D, Heyer R, Rapp E, Reichl U. Metaproteomics of activated sludge from a wastewater treatment plant - A pilot study. Proteomics 2015. [DOI: 10.1002/pmic.201400559] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Sebastian Püttker
- Bioprocess Engineering; Otto von Guericke University Magdeburg; Magdeburg Germany
| | - Fabian Kohrs
- Bioprocess Engineering; Otto von Guericke University Magdeburg; Magdeburg Germany
| | - Dirk Benndorf
- Bioprocess Engineering; Otto von Guericke University Magdeburg; Magdeburg Germany
| | - Robert Heyer
- Bioprocess Engineering; Otto von Guericke University Magdeburg; Magdeburg Germany
| | - Erdmann Rapp
- Bioprocess Engineering; Max Planck Institute for Dynamics of Complex Technical Systems; Magdeburg Germany
| | - Udo Reichl
- Bioprocess Engineering; Otto von Guericke University Magdeburg; Magdeburg Germany
- Bioprocess Engineering; Max Planck Institute for Dynamics of Complex Technical Systems; Magdeburg Germany
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20
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Muth T, Behne A, Heyer R, Kohrs F, Benndorf D, Hoffmann M, Lehtevä M, Reichl U, Martens L, Rapp E. The MetaProteomeAnalyzer: A Powerful Open-Source Software Suite for Metaproteomics Data Analysis and Interpretation. J Proteome Res 2015; 14:1557-65. [DOI: 10.1021/pr501246w] [Citation(s) in RCA: 124] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Thilo Muth
- Max Planck Institute
for Dynamics of Complex Technical Systems, 39106 Magdeburg, Germany
| | - Alexander Behne
- Chair
of Bioprocess Engineering, Otto von Guericke University Magdeburg, 39106 Magdeburg, Germany
| | - Robert Heyer
- Chair
of Bioprocess Engineering, Otto von Guericke University Magdeburg, 39106 Magdeburg, Germany
| | - Fabian Kohrs
- Chair
of Bioprocess Engineering, Otto von Guericke University Magdeburg, 39106 Magdeburg, Germany
| | - Dirk Benndorf
- Chair
of Bioprocess Engineering, Otto von Guericke University Magdeburg, 39106 Magdeburg, Germany
| | - Marcus Hoffmann
- Max Planck Institute
for Dynamics of Complex Technical Systems, 39106 Magdeburg, Germany
| | - Miro Lehtevä
- Department
of Medical Protein Research, VIB, B-9000 Ghent, Belgium
- Department
of Biochemistry, Ghent University, B-9000 Ghent, Belgium
| | - Udo Reichl
- Max Planck Institute
for Dynamics of Complex Technical Systems, 39106 Magdeburg, Germany
- Chair
of Bioprocess Engineering, Otto von Guericke University Magdeburg, 39106 Magdeburg, Germany
| | - Lennart Martens
- Department
of Medical Protein Research, VIB, B-9000 Ghent, Belgium
- Department
of Biochemistry, Ghent University, B-9000 Ghent, Belgium
| | - Erdmann Rapp
- Max Planck Institute
for Dynamics of Complex Technical Systems, 39106 Magdeburg, Germany
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21
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Zhou Z, Meng F, He X, Chae SR, An Y, Jia X. Metaproteomic analysis of biocake proteins to understand membrane fouling in a submerged membrane bioreactor. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:1068-1077. [PMID: 25517759 DOI: 10.1021/es504489r] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Metaproteomic analyses, including two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) separation and matrix-assisted laser desorption/ionization (MALDI)-time-of-flight (TOF)/TOF mass spectrometer (MS) detection, were used to trace and identify biocake proteins on membranes in a bench-scale submerged membrane bioreactor (MBR). 2D-PAGE images showed that proteins in the biocake (S3) at a low transmembrane pressure (TMP) level (i.e., before the TMP jump) had larger gray intensities in the pH 5.5–7.0 region regardless of the membrane flux, similar to soluble microbial product (SMP) proteins. However, the biocake (S2 and S4) at a high TMP level (i.e., after the TMP jump) had many more proteins in the pH range of 4.0–5.5, similar to extracellular polymeric substance (EPS) proteins. Such similarities between biocake proteins and SMP or EPS proteins can be useful for tracing the sources of proteins resulting in membrane fouling. In total, 183 differentially abundant protein spots were marked in the three biocakes (S2, S3, and S4). However, only 32 protein spots co-occurred in the 2D gels of the three biocakes, indicating that membrane fluxes and TMP evolution levels had significant effects on the abundance of biocake proteins. On the basis of the MS and MS/MS data, 23 of 71 protein spots were successfully identified. Of the 23 proteins, outer membrane proteins (Omp) were a major contributor (60.87%). These Omps were mainly from potential surface colonizers such as Aeromonas, Enterobacter, Pseudomonas, and Thauera. Generally, the metaproteomic analysis is a useful alternative to trace the sources and compositions of biocake proteins on the levels of molecules and bacteria species that can provide new insight into membrane fouling.
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22
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Boaro AA, Kim YM, Konopka AE, Callister SJ, Ahring BK. Integrated 'omics analysis for studying the microbial community response to a pH perturbation of a cellulose-degrading bioreactor culture. FEMS Microbiol Ecol 2014; 90:802-15. [PMID: 25290699 DOI: 10.1111/1574-6941.12435] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Revised: 08/11/2014] [Accepted: 09/30/2014] [Indexed: 01/14/2023] Open
Abstract
Integrated 'omics have been used on pure cultures and co-cultures, yet they have not been applied to complex microbial communities to examine questions of perturbation response. In this study, we used integrated 'omics to measure the perturbation response of a cellulose-degrading bioreactor community fed with microcrystalline cellulose (Avicel). We predicted that a pH decrease by addition of a pulse of acid would reduce microbial community diversity and temporarily reduce reactor function in terms of cellulose degradation. However, 16S rDNA gene pyrosequencing results revealed increased alpha diversity in the microbial community after the perturbation, and a persistence of the dominant community members over the duration of the experiment. Proteomics results showed a decrease in activity of proteins associated with Fibrobacter succinogenes 2 days after the perturbation followed by increased protein abundances 6 days after the perturbation. The decrease in cellulolytic activity suggested by the proteomics was confirmed by the accumulation of Avicel in the reactor. Metabolomics showed a pattern similar to that of the proteome, with amino acid production decreasing 2 days after the perturbation and increasing after 6 days. This study demonstrated that community 'omics data provide valuable information about the interactions and function of anaerobic cellulolytic community members after a perturbation.
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Affiliation(s)
- Amy A Boaro
- Bioproducts, Sciences and Engineering Laboratory, Washington State University Tri-cities, Richland, WA, USA
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23
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Hansen SH, Stensballe A, Nielsen PH, Herbst FA. Metaproteomics: Evaluation of protein extraction from activated sludge. Proteomics 2014; 14:2535-9. [DOI: 10.1002/pmic.201400167] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 07/14/2014] [Accepted: 08/08/2014] [Indexed: 11/06/2022]
Affiliation(s)
- Susan Hove Hansen
- Center for Microbial Communities; Department of Biotechnology; Chemistry and Environmental Engineering; Aalborg University; Aalborg Denmark
| | - Allan Stensballe
- Department of Health Science and Technology; Aalborg University; Aalborg Denmark
| | - Per Halkjaer Nielsen
- Center for Microbial Communities; Department of Biotechnology; Chemistry and Environmental Engineering; Aalborg University; Aalborg Denmark
| | - Florian-Alexander Herbst
- Center for Microbial Communities; Department of Biotechnology; Chemistry and Environmental Engineering; Aalborg University; Aalborg Denmark
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24
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Kohrs F, Heyer R, Magnussen A, Benndorf D, Muth T, Behne A, Rapp E, Kausmann R, Heiermann M, Klocke M, Reichl U. Sample prefractionation with liquid isoelectric focusing enables in depth microbial metaproteome analysis of mesophilic and thermophilic biogas plants. Anaerobe 2014; 29:59-67. [DOI: 10.1016/j.anaerobe.2013.11.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Revised: 11/22/2013] [Accepted: 11/25/2013] [Indexed: 12/20/2022]
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25
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Vanwonterghem I, Jensen PD, Ho DP, Batstone DJ, Tyson GW. Linking microbial community structure, interactions and function in anaerobic digesters using new molecular techniques. Curr Opin Biotechnol 2013; 27:55-64. [PMID: 24863897 DOI: 10.1016/j.copbio.2013.11.004] [Citation(s) in RCA: 209] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Revised: 11/06/2013] [Accepted: 11/06/2013] [Indexed: 01/08/2023]
Abstract
Over the last decade there has been a rapid development in culture-independent techniques for exploring microbial communities, which have led to new insights into their structure and function in both natural environments and engineered systems. This review focuses on some of the most important recent advances and their applications to the diverse microbial communities associated with anaerobic digestion. The use of these approaches in combination with complementary imaging techniques, chemical isotope analyses and detailed reactor performance measurements provides a new opportunity to develop a fundamental understanding of how microbial community dynamics, interactions and functionality influence digester efficiency and stability.
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Affiliation(s)
- Inka Vanwonterghem
- Advanced Water Management Center (AWMC), School of Chemical Engineering, The University of Queensland, St Lucia, QLD 4072, Australia; Australian Center for Ecogenomics (ACE), School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Paul D Jensen
- Advanced Water Management Center (AWMC), School of Chemical Engineering, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Dang P Ho
- Advanced Water Management Center (AWMC), School of Chemical Engineering, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Damien J Batstone
- Advanced Water Management Center (AWMC), School of Chemical Engineering, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Gene W Tyson
- Advanced Water Management Center (AWMC), School of Chemical Engineering, The University of Queensland, St Lucia, QLD 4072, Australia; Australian Center for Ecogenomics (ACE), School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD 4072, Australia.
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26
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Affiliation(s)
- Dirk Benndorf
- Department of Bioprocess Engineering; Otto von Guericke University Magdeburg; Magdeburg Germany
| | - Udo Reichl
- Department of Bioprocess Engineering; Otto von Guericke University Magdeburg; Magdeburg Germany
- Department of Bioprocess Engineering; Max Planck Institute for Dynamics of Complex Technical Systems; Magdeburg Germany
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Heyer R, Kohrs F, Benndorf D, Rapp E, Kausmann R, Heiermann M, Klocke M, Reichl U. Metaproteome analysis of the microbial communities in agricultural biogas plants. N Biotechnol 2013; 30:614-22. [DOI: 10.1016/j.nbt.2013.01.002] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Revised: 12/07/2012] [Accepted: 01/11/2013] [Indexed: 11/25/2022]
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Muth T, Benndorf D, Reichl U, Rapp E, Martens L. Searching for a needle in a stack of needles: challenges in metaproteomics data analysis. MOLECULAR BIOSYSTEMS 2013; 9:578-85. [PMID: 23238088 DOI: 10.1039/c2mb25415h] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
In the past years the integral study of microbial communities of varying complexity has gained increasing research interest. Mass spectrometry-driven metaproteomics enables the analysis of such communities on the functional level, but this fledgling field still faces various technical and semantic challenges regarding experimental data analysis and interpretation. In the present review, we outline the hurdles involved and attempt to cover the most valuable methods and software implementations available to researchers in the field today. Beyond merely focusing on protein identification, we provide an overview on different data pre- and post-processing steps, such as metabolic pathway analysis, that can be useful in a typical metaproteomics workflow. Finally, we briefly discuss directions for future work.
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Affiliation(s)
- Thilo Muth
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Magdeburg, Germany
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29
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Hanreich A, Schimpf U, Zakrzewski M, Schlüter A, Benndorf D, Heyer R, Rapp E, Pühler A, Reichl U, Klocke M. Metagenome and metaproteome analyses of microbial communities in mesophilic biogas-producing anaerobic batch fermentations indicate concerted plant carbohydrate degradation. Syst Appl Microbiol 2013; 36:330-8. [PMID: 23694815 DOI: 10.1016/j.syapm.2013.03.006] [Citation(s) in RCA: 112] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Revised: 03/01/2013] [Accepted: 03/07/2013] [Indexed: 11/27/2022]
Abstract
Microbial communities in biogas batch fermentations, using straw and hay as co-substrates, were analyzed at the gene and protein level by metagenomic and metaproteomic approaches. The analysis of metagenomic data revealed that the Clostridiales and Bacteroidales orders were prevalent in the community. However, the number of sequences assigned to the Clostridiales order decreased during fermentation, whereas the number of sequences assigned to the Bacteroidales order increased. In addition, changes at the functional level were monitored and the metaproteomic analyses detected transporter proteins and flagellins, which were expressed mainly by members of the Bacteroidetes and Firmicutes phyla. A high number of sugar transporters, expressed by members of the Bacteroidetes, proved their potential to take up various glycans efficiently. Metagenome data also showed that methanogenic organisms represented less than 4% of the community, while 20-30% of the identified proteins were of archeal origin. These data suggested that methanogens were disproportionally active. In conclusion, the community studied was capable of digesting the recalcitrant co-substrate. Members of the Firmicutes phylum seemed to be the main degraders of cellulose, even though expression of only a few glycoside hydrolases was detected. The Bacteroidetes phylum expressed a high number of sugar transporters and seemed to specialize in the digestion of other polysaccharides. Finally, it was found that key enzymes of methanogenesis were expressed in high quantities, indicating the high metabolic activity of methanogens, although they only represented a minor group within the microbial community.
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Affiliation(s)
- Angelika Hanreich
- Leibniz-Institut für Agrartechnik Potsdam-Bornim e.V., Abteilung Bioverfahrenstechnik, Max-Eyth-Allee 100, 14469 Potsdam, Germany
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30
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Hettich RL, Pan C, Chourey K, Giannone RJ. Metaproteomics: harnessing the power of high performance mass spectrometry to identify the suite of proteins that control metabolic activities in microbial communities. Anal Chem 2013; 85:4203-14. [PMID: 23469896 PMCID: PMC3696428 DOI: 10.1021/ac303053e] [Citation(s) in RCA: 140] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The availability of extensive genome information for many different microbes, including unculturable species in mixed communities from environmental samples, has enabled systems-biology interrogation by providing a means to access genomic, transcriptomic, and proteomic information. To this end, metaproteomics exploits the power of high-performance mass spectrometry for extensive characterization of the complete suite of proteins expressed by a microbial community in an environmental sample.
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31
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Hawley AK, Kheirandish S, Mueller A, Leung HTC, Norbeck AD, Brewer HM, Pasa-Tolic L, Hallam SJ. Molecular tools for investigating microbial community structure and function in oxygen-deficient marine waters. Methods Enzymol 2013; 531:305-29. [PMID: 24060128 DOI: 10.1016/b978-0-12-407863-5.00016-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Water column oxygen (O2)-deficiency shapes food-web structure by progressively directing nutrients and energy away from higher trophic levels into microbial community metabolism resulting in fixed nitrogen loss and greenhouse gas production. Although respiratory O2 consumption during organic matter degradation is a natural outcome of a productive surface ocean, global-warming-induced stratification intensifies this process leading to oxygen minimum zone (OMZ) expansion. Here, we describe useful tools for detection and quantification of potential key microbial players and processes in OMZ community metabolism including quantitative polymerase chain reaction primers targeting Marine Group I Thaumarchaeota, SUP05, Arctic96BD-19, and SAR324 small-subunit ribosomal RNA genes and protein extraction methods from OMZ waters compatible with high-resolution mass spectrometry for profiling microbial community structure and functional dynamics.
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Affiliation(s)
- Alyse K Hawley
- Department of Microbiology & Immunology, University of British Columbia, Vancouver, British Columbia, Canada
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32
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Community and proteomic analysis of methanogenic consortia degrading terephthalate. Appl Environ Microbiol 2012; 79:105-12. [PMID: 23064332 DOI: 10.1128/aem.02327-12] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Degradation of terephthalate (TA) through microbial syntrophy under moderately thermophilic (46 to 50°C) methanogenic conditions was characterized by using a metagenomic approach (A. Lykidis et al., ISME J. 5:122-130, 2011). To further study the activities of key microorganisms responsible for the TA degradation, community analysis and shotgun proteomics were used. The results of hierarchical oligonucleotide primer extension analysis of PCR-amplified 16S rRNA genes indicated that Pelotomaculum, Methanosaeta, and Methanolinea were predominant in the TA-degrading biofilms. Metaproteomic analysis identified a total of 482 proteins and revealed a distinctive distribution pattern of microbial functions expressed in situ. The results confirmed that TA was degraded by Pelotomaculum spp. via the proposed decarboxylation and benzoyl-coenzyme A-dependent pathway. The intermediate by-products, including acetate, H(2)/CO(2), and butyrate, were produced to support the growth of methanogens, as well as other microbial populations that could further degrade butyrate. Proteins related to energy production and conservation, and signal transduction mechanisms (that is, chemotaxis, PAS/GGDEF regulators, and stress proteins) were highly expressed, and these mechanisms were important for growth in energy-limited syntrophic ecosystems.
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Hanreich A, Heyer R, Benndorf D, Rapp E, Pioch M, Reichl U, Klocke M. Metaproteome analysis to determine the metabolically active part of a thermophilic microbial community producing biogas from agricultural biomass. Can J Microbiol 2012; 58:917-22. [DOI: 10.1139/w2012-058] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Complex consortia of microorganisms are responsible for biogas production. A lot of information about the taxonomic structure and enzymatic potential of such communities has been collected by a variety of gene-based approaches, yet little is known about which of all the assumable metabolic pathways are active throughout the process of biogas formation. To tackle this problem, we established a protocol for the metaproteomic analysis of samples taken from biogas reactors fed with agricultural biomass. In contrast to previous studies where an anaerobic digester was fed with synthetic wastewater, the complex matrix in this study required the extraction of proteins with liquid phenol and the application of paper bridge loading for 2-dimensional gel electrophoresis. Proteins were subjected to nanoHPLC (high-performance liquid chromatography) coupled to tandem mass spectrometry for characterization. Several housekeeping proteins as well as methanogenesis-related enzymes were identified by a MASCOT search and de novo sequencing, which proved the feasibility of our approach. The establishment of such an approach is the basis for further metaproteomic studies of biogas-producing communities. In particular, the apparent status of metabolic activities within the communities can be monitored. The knowledge collected from such experiments could lead to further improvements of biogas production.
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Affiliation(s)
- Angelika Hanreich
- Leibniz-Institut für Agrartechnik Potsdam-Bornim e.V., Abteilung Bioverfahrenstechnik, Max-Eyth-Allee 100, 14469 Potsdam, Germany
| | - Robert Heyer
- Otto von Guericke University, Bioprocess Engineering, Universitätsplatz 2, 39106 Magdeburg, Germany
| | - Dirk Benndorf
- Otto von Guericke University, Bioprocess Engineering, Universitätsplatz 2, 39106 Magdeburg, Germany
| | - Erdmann Rapp
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Sandtor Straße 1, 39106 Magdeburg, Germany
| | - Markus Pioch
- Otto von Guericke University, Bioprocess Engineering, Universitätsplatz 2, 39106 Magdeburg, Germany
| | - Udo Reichl
- Otto von Guericke University, Bioprocess Engineering, Universitätsplatz 2, 39106 Magdeburg, Germany
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Sandtor Straße 1, 39106 Magdeburg, Germany
| | - Michael Klocke
- Leibniz-Institut für Agrartechnik Potsdam-Bornim e.V., Abteilung Bioverfahrenstechnik, Max-Eyth-Allee 100, 14469 Potsdam, Germany
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34
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Hettich RL, Sharma R, Chourey K, Giannone RJ. Microbial metaproteomics: identifying the repertoire of proteins that microorganisms use to compete and cooperate in complex environmental communities. Curr Opin Microbiol 2012; 15:373-80. [PMID: 22632760 DOI: 10.1016/j.mib.2012.04.008] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2012] [Accepted: 04/27/2012] [Indexed: 10/28/2022]
Abstract
The availability of genome information for microbial consortia, including unculturable species, from environmental samples has enabled systems-biology interrogation by providing a means to access genomic, transcriptomic, and proteomic information. This provides a unique opportunity to characterize the molecular activities and interactions of these microbial systems at a comprehensive level never before possible. Such information not only provides details about the organizational, functional, and metabolic activities of such systems, but also the untapped reserve of molecular activities that might be invoked and exploited under certain environmental conditions. Since bacteria naturally exist in complex ecosystems, it is imperative to develop and utilize analytical approaches that can provide molecular level details on systems consisting of mixed microbial membership. This is the realm of metaproteomics-the characterization of the complement of proteins expressed by a microbial community in an environmental sample.
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