1
|
Yu F, Zhang B, Liu Y, Luo W, Chen H, Gao J, Ye X, Li J, Xie Q, Peng T, Wang H, Huang T, Hu Z. Biotransformation of HBCDs by the microbial communities enriched from mangrove sediments. JOURNAL OF HAZARDOUS MATERIALS 2024; 469:134036. [PMID: 38493623 DOI: 10.1016/j.jhazmat.2024.134036] [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: 11/15/2023] [Revised: 02/29/2024] [Accepted: 03/12/2024] [Indexed: 03/19/2024]
Abstract
1,2,5,6,9,10-Hexabromocyclododecanes (HBCDs) are a sort of persistent organic pollutants (POPs). This research investigated 12 microbial communities enriched from sediments of four mangroves in China to transform HBCDs. Six microbial communities gained high transformation rates (27.5-97.7%) after 12 generations of serial transfer. Bacteria were the main contributors to transform HBCDs rather than fungi. Analyses on the bacterial compositions and binning genomes showed that Alcanivorax (55.246-84.942%) harboring haloalkane dehalogenase genes dadAH and dadBH dominated the microbial communities with high transformation rates. Moreover, expressions of dadAH and dadBH in the microbial communities and Alcanivorax isolate could be induced by HBCDs. Further, it was found that purified proteins DadAH and DadBH showed high conversion rates on HBCDs in 36 h (91.9 ± 7.4 and 101.0 ± 1.8%, respectively). The engineered Escherichia coli BL21 strains harbored two genes could convert 5.7 ± 0.4 and 35.1 ± 0.1% HBCDs, respectively, lower than their cell-free crude extracts (61.2 ± 5.2 and 56.5 ± 8.7%, respectively). The diastereoisomer-specific transforming trend by both microbial communities and enzymes were γ- > α- > β-HBCD, differed from α- > β- > γ-HBCD by the Alcanivorax isolate. The identified transformation products indicated that HBCDs were dehalogenated via HBr elimination (dehydrobromination), hydrolytic and reductive debromination pathways in the enriched cultures. Two enzymes converted HBCDs via hydrolytic debromination. The present research provided theoretical bases for the biotransformation of HBCDs by microbial community and the bioremediation of HBCDs contamination in the environment.
Collapse
Affiliation(s)
- Fei Yu
- Department of Biology, College of Science, Shantou University, Shantou 515063, Guangdong Province, China
| | - Bing Zhang
- Department of Biology, College of Science, Shantou University, Shantou 515063, Guangdong Province, China
| | - Yongjin Liu
- Department of Biology, College of Science, Shantou University, Shantou 515063, Guangdong Province, China
| | - Wenqi Luo
- Department of Biology, College of Science, Shantou University, Shantou 515063, Guangdong Province, China
| | - Haonan Chen
- Department of Biology, College of Science, Shantou University, Shantou 515063, Guangdong Province, China
| | - Jun'na Gao
- Department of Biology, College of Science, Shantou University, Shantou 515063, Guangdong Province, China
| | - Xueying Ye
- School of Life Sciences, Huizhou University, Huizhou 516007, Guangdong Province, China
| | - Jin Li
- Guangdong Provincial Key Laboratory of Marine Disaster Prediction and Prevention, Shantou University, Shantou 515063, Guangdong Province, China
| | - Qingyi Xie
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Tao Peng
- Department of Biology, College of Science, Shantou University, Shantou 515063, Guangdong Province, China
| | - Hui Wang
- Department of Biology, College of Science, Shantou University, Shantou 515063, Guangdong Province, China
| | - Tongwang Huang
- Department of Biology, College of Science, Shantou University, Shantou 515063, Guangdong Province, China
| | - Zhong Hu
- Department of Biology, College of Science, Shantou University, Shantou 515063, Guangdong Province, China.
| |
Collapse
|
2
|
Cao S, Duan M, Zhang X, Yang Z, Zhuo R. Bacterial community structure analysis of sludge from Taozi lake and isolation of an efficient 17β-Estradiol (E2) degrading strain Sphingobacterium sp. GEMB-CSS-01. CHEMOSPHERE 2024; 355:141806. [PMID: 38548087 DOI: 10.1016/j.chemosphere.2024.141806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 01/28/2024] [Accepted: 03/24/2024] [Indexed: 04/08/2024]
Abstract
Environmental challenges arising from organic pollutants pose a significant problem for modern societies. Efficient microbial resources for the degradation of these pollutants are highly valuable. In this study, the bacterial community structure of sludge samples from Taozi Lake (polluted by urban sewage) was studied using 16S rRNA sequencing. The bacterial phyla Proteobacteria, Bacteroidetes, and Chloroflexi, which are potentially important in organic matter degradation by previous studies, were identified as the predominant phyla in our samples, with relative abundances of 48.5%, 8.3%, and 6.6%, respectively. Additionally, the FAPROTAX and co-occurrence network analysis suggested that the core microbial populations in the samples may be closely associated with organic matter metabolism. Subsequently, sludge samples from Taozi Lake were subjected to enrichment cultivation to isolate organic pollutant-degrading microorganisms. The strain Sphingobacterium sp. GEMB-CSS-01, tolerant to sulfanilamide, was successfully isolated. Subsequent investigations demonstrated that Sphingobacterium sp. GEMB-CSS-01 efficiently degraded the endocrine-disrupting compound 17β-Estradiol (E2). It achieved degradation efficiencies of 80.0% and 53.5% for E2 concentrations of 10 mg/L and 20 mg/L, respectively, within 10 days. Notably, despite a reduction in degradation efficiency, Sphingobacterium sp. GEMB-CSS-01 retained its ability to degrade E2 even in the presence of sulfanilamide concentrations ranging from 50 to 200 mg/L. The findings of this research identify potential microbial resources for environmental bioremediation, and concurrently provide valuable information about the microbial community structure and patterns within Taozi Lake.
Collapse
Affiliation(s)
- Shanshan Cao
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha, 410082, PR China; Hunan Provincial Certified Enterprise Technology Center, Hunan Xiangjiao Liquor Industry Co., Ltd., Shaoyang, 422000, PR China
| | - Mifang Duan
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha, 410082, PR China
| | - Xuan Zhang
- State Key Laboratory of Utilization of Woody Oil Resource, Hunan Academy of Forestry, Changsha, 410004, PR China
| | - Zhilong Yang
- Hunan Provincial Certified Enterprise Technology Center, Hunan Xiangjiao Liquor Industry Co., Ltd., Shaoyang, 422000, PR China
| | - Rui Zhuo
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha, 410082, PR China; Hunan Provincial Certified Enterprise Technology Center, Hunan Xiangjiao Liquor Industry Co., Ltd., Shaoyang, 422000, PR China.
| |
Collapse
|
3
|
Klaes S, Madan S, Deobald D, Cooper M, Adrian L. GroEL-Proteotyping of Bacterial Communities Using Tandem Mass Spectrometry. Int J Mol Sci 2023; 24:15692. [PMID: 37958676 PMCID: PMC10649880 DOI: 10.3390/ijms242115692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 10/24/2023] [Accepted: 10/25/2023] [Indexed: 11/15/2023] Open
Abstract
Profiling bacterial populations in mixed communities is a common task in microbiology. Sequencing of 16S small subunit ribosomal-RNA (16S rRNA) gene amplicons is a widely accepted and functional approach but relies on amplification primers and cannot quantify isotope incorporation. Tandem mass spectrometry proteotyping is an effective alternative for taxonomically profiling microorganisms. We suggest that targeted proteotyping approaches can complement traditional population analyses. Therefore, we describe an approach to assess bacterial community compositions at the family level using the taxonomic marker protein GroEL, which is ubiquitously found in bacteria, except a few obligate intracellular species. We refer to our method as GroEL-proteotyping. GroEL-proteotyping is based on high-resolution tandem mass spectrometry of GroEL peptides and identification of GroEL-derived taxa via a Galaxy workflow and a subsequent Python-based analysis script. Its advantage is that it can be performed with a curated and extendable sample-independent database and that GroEL can be pre-separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) to reduce sample complexity, improving GroEL identification while simultaneously decreasing the instrument time. GroEL-proteotyping was validated by employing it on a comprehensive raw dataset obtained through a metaproteome approach from synthetic microbial communities as well as real human gut samples. Our data show that GroEL-proteotyping enables fast and straightforward profiling of highly abundant taxa in bacterial communities at reasonable taxonomic resolution.
Collapse
Affiliation(s)
- Simon Klaes
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research (UFZ), 04318 Leipzig, Germany; (S.K.); (D.D.)
- Faculty III Process Sciences, Institute of Biotechnology, Chair of Geobiotechnology, Technische Universität Berlin, 13355 Berlin, Germany
| | - Shobhit Madan
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research (UFZ), 04318 Leipzig, Germany; (S.K.); (D.D.)
- Faculty of Engineering, Ansbach University of Applied Sciences, 91522 Ansbach, Germany
| | - Darja Deobald
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research (UFZ), 04318 Leipzig, Germany; (S.K.); (D.D.)
| | - Myriel Cooper
- Faculty III Process Sciences, Institute of Environmental Technology, Chair of Environmental Microbiology, Technische Universität Berlin, 10587 Berlin, Germany
| | - Lorenz Adrian
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research (UFZ), 04318 Leipzig, Germany; (S.K.); (D.D.)
- Faculty III Process Sciences, Institute of Biotechnology, Chair of Geobiotechnology, Technische Universität Berlin, 13355 Berlin, Germany
| |
Collapse
|
4
|
Heinze BM, Küsel K, Jehmlich N, von Bergen M, Taubert M. Metabolic versatility enables sulfur-oxidizers to dominate primary production in groundwater. WATER RESEARCH 2023; 244:120426. [PMID: 37597444 DOI: 10.1016/j.watres.2023.120426] [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: 05/13/2023] [Revised: 07/25/2023] [Accepted: 07/27/2023] [Indexed: 08/21/2023]
Abstract
High rates of CO2 fixation and the genetic potential of various groundwater microbes for autotrophic activity have shown that primary production is an important source of organic C in groundwater ecosystems. However, the contribution of specific chemolithoautotrophic groups such as S-oxidizing bacteria (SOB) to groundwater primary production and their adaptation strategies remain largely unknown. Here, we stimulated anoxic groundwater microcosms with reduced S and sampled the microbial community after 1, 3 and 6 weeks. Genome-resolved metaproteomics was combined with 50at-% 13CO2 stable isotope probing to follow the C flux through the microbial food web and infer traits expressed by active SOB in the groundwater microcosms. Already after 7 days, 90% of the total microbial biomass C in the microcosms was replaced by CO2-derived C, increasing to 97% at the end of incubation. Stable Isotope Cluster Analysis revealed active autotrophs, characterized by a uniform 13C-incorporation of 45% in their peptides, to dominate the microbial community throughout incubation. Mixo- and heterotrophs, characterized by 10 to 40% 13C-incorporation, utilized the primarily produced organic C. Interestingly, obligate autotrophs affiliated with Sulfuricella and Sulfuritalea contained traits enabling the storage of elemental S in globules to maintain primary production under energy limitation. Others related to Sulfurimonas seemed to rapidly utilize substrates for fast proliferation, and most autotrophs further maximized their energy yield via efficient denitrification and the potential for H2 oxidation. Mixotrophic SOB, belonging to Curvibacter or Polaromonas, enhanced metabolic flexibility by using organic compounds to satisfy their C requirements. Time series data spanning eight years further revealed that key taxa of our microcosms composed up to 15% of the microbial groundwater community, demonstrating their in-situ importance. This showed that SOB, by using different metabolic strategies, are able to account for high rates of primary production in groundwater, especially at sites limited to geogenic nutrient sources. The widespread presence of SOB with traits such as S storage, H2 oxidation, and organic C utilization in many aquatic habitats further suggested that metabolic versatility governs S-fueled primary production in the environment.
Collapse
Affiliation(s)
- Beatrix M Heinze
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger Str. 159, Jena 07743, Germany
| | - Kirsten Küsel
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger Str. 159, Jena 07743, Germany; The German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstr. 4, Leipzig 04103, Germany; Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany
| | - Nico Jehmlich
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research, UFZ, Permoserstr. 15, Leipzig 04318, Germany
| | - Martin von Bergen
- The German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstr. 4, Leipzig 04103, Germany; Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research, UFZ, Permoserstr. 15, Leipzig 04318, Germany; Faculty of Biosciences, Pharmacy and Psychology, Institute of Biochemistry, University of Leipzig, Brüderstr. 32, Leipzig 04103, Germany
| | - Martin Taubert
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger Str. 159, Jena 07743, Germany; Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany.
| |
Collapse
|
5
|
Khan N, Muge E, Mulaa FJ, Wamalwa B, von Bergen M, Jehmlich N, Wick LY. Mycelial nutrient transfer promotes bacterial co-metabolic organochlorine pesticide degradation in nutrient-deprived environments. THE ISME JOURNAL 2023; 17:570-578. [PMID: 36707614 PMCID: PMC10030463 DOI: 10.1038/s41396-023-01371-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 01/10/2023] [Accepted: 01/13/2023] [Indexed: 01/28/2023]
Abstract
Biotransformation of soil organochlorine pesticides (OCP) is often impeded by a lack of nutrients relevant for bacterial growth and/or co-metabolic OCP biotransformation. By providing space-filling mycelia, fungi promote contaminant biodegradation by facilitating bacterial dispersal and the mobilization and release of nutrients in the mycosphere. We here tested whether mycelial nutrient transfer from nutrient-rich to nutrient-deprived areas facilitates bacterial OCP degradation in a nutrient-deficient habitat. The legacy pesticide hexachlorocyclohexane (HCH), a non-HCH-degrading fungus (Fusarium equiseti K3), and a co-metabolically HCH-degrading bacterium (Sphingobium sp. S8) isolated from the same HCH-contaminated soil were used in spatially structured model ecosystems. Using 13C-labeled fungal biomass and protein-based stable isotope probing (protein-SIP), we traced the incorporation of 13C fungal metabolites into bacterial proteins while simultaneously determining the biotransformation of the HCH isomers. The relative isotope abundance (RIA, 7.1-14.2%), labeling ratio (LR, 0.13-0.35), and the shape of isotopic mass distribution profiles of bacterial peptides indicated the transfer of 13C-labeled fungal metabolites into bacterial proteins. Distinct 13C incorporation into the haloalkane dehalogenase (linB) and 2,5-dichloro-2,5-cyclohexadiene-1,4-diol dehydrogenase (LinC), as key enzymes in metabolic HCH degradation, underpin the role of mycelial nutrient transport and fungal-bacterial interactions for co-metabolic bacterial HCH degradation in heterogeneous habitats. Nutrient uptake from mycelia increased HCH removal by twofold as compared to bacterial monocultures. Fungal-bacterial interactions hence may play an important role in the co-metabolic biotransformation of OCP or recalcitrant micropollutants (MPs).
Collapse
Affiliation(s)
- Nelson Khan
- University of Nairobi, Department of Biochemistry, 00200-30197, Nairobi, Kenya
- Helmholtz Centre for Environmental Research UFZ, Department of Environmental Microbiology, 04318, Leipzig, Germany
| | - Edward Muge
- University of Nairobi, Department of Biochemistry, 00200-30197, Nairobi, Kenya
| | - Francis J Mulaa
- University of Nairobi, Department of Biochemistry, 00200-30197, Nairobi, Kenya
| | - Benson Wamalwa
- University of Nairobi, Department of Chemistry, 00200-30197, Nairobi, Kenya
| | - Martin von Bergen
- Helmholtz Centre for Environmental Research UFZ, Department of Molecular Systems Biology, 04318, Leipzig, Germany
- German Centre for Integrative Biodiversity Research, (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103, Leipzig, Germany
- University of Leipzig, Faculty of Life Sciences, Institute of Biochemistry, Brüderstraße 34, 04103, Leipzig, Germany
| | - Nico Jehmlich
- Helmholtz Centre for Environmental Research UFZ, Department of Molecular Systems Biology, 04318, Leipzig, Germany
| | - Lukas Y Wick
- Helmholtz Centre for Environmental Research UFZ, Department of Environmental Microbiology, 04318, Leipzig, Germany.
| |
Collapse
|
6
|
Jameson E, Taubert M, Angel R, Coyotzi S, Chen Y, Eyice Ö, Schäfer H, Murrell JC, Neufeld JD, Dumont MG. DNA-, RNA-, and Protein-Based Stable-Isotope Probing for High-Throughput Biomarker Analysis of Active Microorganisms. Methods Mol Biol 2023; 2555:261-282. [PMID: 36306091 DOI: 10.1007/978-1-0716-2795-2_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Stable-isotope probing (SIP) enables researchers to target active populations within complex microbial communities, which is achieved by providing growth substrates enriched in heavy isotopes, usually in the form of 13C, 18O, or 15N. After growth on the substrate and subsequent extraction of microbial biomarkers, typically nucleic acids or proteins, the SIP technique is used for the recovery and analysis of isotope-labelled biomarkers from active microbial populations. In the years following the initial development of DNA- and RNA-based SIP, it was common practice to characterize labelled populations by targeted gene analysis. Such approaches usually involved fingerprint-based analyses or sequencing clone libraries containing 16S rRNA genes or functional marker gene amplicons. Although molecular fingerprinting remains a valuable approach for rapid confirmation of isotope labelling, recent advances in sequencing technology mean that it is possible to obtain affordable and comprehensive amplicon profiles, or even metagenomes and metatranscriptomes from SIP experiments. Not only can the abundance of microbial groups be inferred from metagenomes, but researchers can bin, assemble, and explore individual genomes to build hypotheses about the metabolic capabilities of labelled microorganisms. Analysis of labelled mRNA is a more recent advance that can provide independent metatranscriptome-based analysis of active microorganisms. The power of metatranscriptomics is that mRNA abundance often correlates closely with the corresponding activity of encoded enzymes, thus providing insight into microbial metabolism at the time of sampling. Together, these advances have improved the sensitivity of SIP methods and allowed using labelled substrates at environmentally relevant concentrations. Particularly as methods improve and costs continue to drop, we expect that the integration of SIP with multiple omics-based methods will become prevalent components of microbial ecology studies, leading to further breakthroughs in our understanding of novel microbial populations and elucidation of the metabolic function of complex microbial communities. In this chapter, we provide protocols for obtaining labelled DNA, RNA, and proteins that can be used for downstream omics-based analyses.
Collapse
Affiliation(s)
- Eleanor Jameson
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Martin Taubert
- Aquatic Geochemistry, Institute of Biodiversity, Friedrich Schiller University, Jena, Germany
| | - Roey Angel
- Soil & Water Research Infrastructure and Institute of Soil Biology, Biology Centre CAS, České Budějovice, Czechia
| | - Sara Coyotzi
- Department of Biology, University of Waterloo, Waterloo, Canada
| | - Yin Chen
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Özge Eyice
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Hendrik Schäfer
- School of Life Sciences, University of Warwick, Coventry, UK
| | - J Colin Murrell
- School of Environmental Sciences, University of East Anglia, Norwich, UK
| | - Josh D Neufeld
- Department of Biology, University of Waterloo, Waterloo, Canada
| | - Marc G Dumont
- School of Biological Sciences, University of Southampton, Southampton, UK.
| |
Collapse
|
7
|
Holland SI, Vázquez-Campos X, Ertan H, Edwards RJ, Manefield MJ, Lee M. Metaproteomics reveals methyltransferases implicated in dichloromethane and glycine betaine fermentation by ' Candidatus Formimonas warabiya' strain DCMF. Front Microbiol 2022; 13:1035247. [PMID: 36569084 PMCID: PMC9768040 DOI: 10.3389/fmicb.2022.1035247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 11/15/2022] [Indexed: 12/12/2022] Open
Abstract
Dichloromethane (DCM; CH2Cl2) is a widespread pollutant with anthropogenic and natural sources. Anaerobic DCM-dechlorinating bacteria use the Wood-Ljungdahl pathway, yet dechlorination reaction mechanisms remain unclear and the enzyme(s) responsible for carbon-chlorine bond cleavage have not been definitively identified. Of the three bacterial taxa known to carry out anaerobic dechlorination of DCM, 'Candidatus Formimonas warabiya' strain DCMF is the only organism that can also ferment non-chlorinated substrates, including quaternary amines (i.e., choline and glycine betaine) and methanol. Strain DCMF is present within enrichment culture DFE, which was derived from an organochlorine-contaminated aquifer. We utilized the metabolic versatility of strain DCMF to carry out comparative metaproteomics of cultures grown with DCM or glycine betaine. This revealed differential abundance of numerous proteins, including a methyltransferase gene cluster (the mec cassette) that was significantly more abundant during DCM degradation, as well as highly conserved amongst anaerobic DCM-degrading bacteria. This lends strong support to its involvement in DCM dechlorination. A putative glycine betaine methyltransferase was also discovered, adding to the limited knowledge about the fate of this widespread osmolyte in anoxic subsurface environments. Furthermore, the metagenome of enrichment culture DFE was assembled, resulting in five high quality and two low quality draft metagenome-assembled genomes. Metaproteogenomic analysis did not reveal any genes or proteins for utilization of DCM or glycine betaine in the cohabiting bacteria, supporting the previously held idea that they persist via necromass utilization.
Collapse
Affiliation(s)
- Sophie I. Holland
- Water Research Centre, School of Civil and Environmental Engineering, University of New South Wales, Sydney, NSW, Australia
| | - Xabier Vázquez-Campos
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Haluk Ertan
- School of Chemical Engineering, University of New South Wales, Sydney, NSW, Australia
- Department of Molecular Biology and Genetics, Istanbul University, Istanbul, Turkey
| | - Richard J. Edwards
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Michael J. Manefield
- Water Research Centre, School of Civil and Environmental Engineering, University of New South Wales, Sydney, NSW, Australia
- School of Chemical Engineering, University of New South Wales, Sydney, NSW, Australia
| | - Matthew Lee
- Water Research Centre, School of Civil and Environmental Engineering, University of New South Wales, Sydney, NSW, Australia
| |
Collapse
|
8
|
Macêdo WV, Poulsen JS, Zaiat M, Nielsen JL. Proteogenomics identification of TBBPA degraders in anaerobic bioreactor. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 310:119786. [PMID: 35872283 DOI: 10.1016/j.envpol.2022.119786] [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: 03/12/2022] [Revised: 06/29/2022] [Accepted: 07/12/2022] [Indexed: 06/15/2023]
Abstract
Tetrabromobisphenol A (TBBPA) is the most used flame retardant worldwide and has become a threat to aquatic ecosystems. Previous research into the degradation of this micropollutant in anaerobic bioreactors has suggested several identities of putative TBBPA degraders. However, the organisms actively degrading TBBPA under in situ conditions have so far not been identified. Protein-stable isotope probing (protein-SIP) has become a cutting-edge technique in microbial ecology for enabling the link between identity and function under in situ conditions. Therefore, it was hypothesized that combining protein-based stable isotope probing with metagenomics could be used to identify and provide genomic insight into the TBBPA-degrading organisms. The identified 13C-labelled peptides were found to belong to organisms affiliated to Phytobacter, Clostridium, Sporolactobacillus, and Klebsilla genera. The functional classification of identified labelled peptides revealed that TBBPA is not only transformed by cometabolic reactions, but also assimilated into the biomass. By application of the proteogenomics with labelled micropollutants (protein-SIP) and metagenome-assembled genomes, it was possible to extend the current perspective of the diversity of TBBPA degraders in wastewater and predict putative TBBPA degradation pathways. The study provides a link to the active TBBPA degraders and which organisms to favor for optimized biodegradation.
Collapse
Affiliation(s)
- Williane Vieira Macêdo
- Laboratory of Biological Processes, São Carlos School of Engineering, University of São Paulo (USP), 1100, João Dagnone Ave., Santa Angelina, Zip Code 13563-120, São Carlos, SP, Brazil; Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, DK-9220, Aalborg, Denmark
| | - Jan Struckmann Poulsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, DK-9220, Aalborg, Denmark
| | - Marcelo Zaiat
- Laboratory of Biological Processes, São Carlos School of Engineering, University of São Paulo (USP), 1100, João Dagnone Ave., Santa Angelina, Zip Code 13563-120, São Carlos, SP, Brazil
| | - Jeppe Lund Nielsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, DK-9220, Aalborg, Denmark.
| |
Collapse
|
9
|
Guo S, Toth CRA, Luo F, Chen X, Xiao J, Edwards EA. Transient Oxygen Exposure Causes Profound and Lasting Changes to a Benzene-Degrading Methanogenic Community. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:13036-13045. [PMID: 36083837 PMCID: PMC9496526 DOI: 10.1021/acs.est.2c02624] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 08/22/2022] [Accepted: 08/26/2022] [Indexed: 06/15/2023]
Abstract
We investigated the impact of oxygen on a strictly anaerobic, methanogenic benzene-degrading enrichment culture derived decades ago from oil-contaminated sediment. The culture includes a benzene fermenter from Deltaproteobacteria candidate clade Sva0485 (referred to as ORM2) and methanogenic archaea. A one-time injection of 0.1 mL air , simulating a small leak into 30 mL batch culture bottle, had no measurable impact on benzene degradation rates, although retrospectively, a tiny enrichment of aerobic taxa was detected. A subsequent 100 times larger injection of air stalled methanogenesis and caused drastic perturbation of the microbial community. A benzene-degrading Pseudomonas became highly enriched and consumed all available oxygen. Anaerobic benzene-degrading ORM2 cell numbers plummeted during this time; re-growth and associated recovery of methanogenic benzene degradation took almost 1 year. These results highlight the oxygen sensitivity of this methanogenic culture and confirm that the mechanism for anaerobic biotransformation of benzene is independent of oxygen, fundamentally different from established aerobic pathways, and is carried out by distinct microbial communities. The study also highlights the importance of including microbial decay in characterizing and modeling mixed microbial communities.
Collapse
Affiliation(s)
| | | | | | - Xu Chen
- Department of Chemical Engineering
and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada
| | - Johnny Xiao
- Department of Chemical Engineering
and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada
| | - Elizabeth A. Edwards
- Department of Chemical Engineering
and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada
| |
Collapse
|
10
|
Bacterial Necromass Is Rapidly Metabolized by Heterotrophic Bacteria and Supports Multiple Trophic Levels of the Groundwater Microbiome. Microbiol Spectr 2022; 10:e0043722. [PMID: 35699474 PMCID: PMC9431026 DOI: 10.1128/spectrum.00437-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Pristine groundwater is a highly stable environment with microbes adapted to dark, oligotrophic conditions. Input events like heavy rainfalls can introduce the excess particulate organic matter, including surface-derived microorganisms, thereby disturbing the groundwater microbiome. Some surface-derived bacteria will not survive this translocation, leading to an input of necromass to the groundwater. Here, we investigated the effects of necromass addition to the microbial community in fractured bedrock groundwater, using groundwater mesocosms as model systems. We followed the uptake of 13C-labeled necromass by the bacterial and eukaryotic groundwater community quantitatively and over time using a complementary protein-stable and DNA-stable isotope probing approach. Necromass was rapidly depleted in the mesocosms within 4 days, accompanied by a strong decrease in Shannon diversity and a 10-fold increase in bacterial 16S rRNA gene copy numbers. Species of Flavobacterium, Massilia, Rheinheimera, Rhodoferax, and Undibacterium dominated the microbial community within 2 days and were identified as key players in necromass degradation, based on a 13C incorporation of >90% in their peptides. Their proteomes comprised various proteins for uptake and transport functions and amino acid metabolization. After 4 and 8 days, the autotrophic and mixotrophic taxa Nitrosomonas, Limnohabitans, Paucibacter, and Acidovorax increased in abundance with a 13C incorporation between 0.5% and 23%. Likewise, eukaryotes assimilated necromass-derived carbon either directly or indirectly. Our data point toward a fast and exclusive uptake of labeled necromass by a few specialists followed by a concerted action of groundwater microorganisms, including autotrophs presumably fueled by released, reduced nitrogen and sulfur compounds generated during necromass degradation. IMPORTANCE Subsurface microbiomes provide essential ecosystem services, like the generation of drinking water. These ecosystems are devoid of light-driven primary production, and microbial life is adapted to the resulting oligotrophic conditions. Modern groundwater is most vulnerable to anthropogenic and climatic impacts. Heavy rainfalls, which will increase with climate change, can result in high surface inputs into shallow aquifers by percolation or lateral flow. These inputs include terrestrial organic matter and surface-derived microbes that are not all capable to flourish in aquatic subsurface habitats. Here, we investigated the response of groundwater mesocosms to the addition of bacterial necromass, simulating event-driven surface input. We found that the groundwater microbiome responds with a rapid bloom of only a few primary degraders, followed by the activation of typical groundwater autotrophs and mixotrophs, as well as eukaryotes. Our results suggest that this multiphase strategy is essential to maintain the balance of the groundwater microbiome to provide ecosystem services.
Collapse
|
11
|
Cabugao KGM, Gushgari-Doyle S, Chacon SS, Wu X, Bhattacharyya A, Bouskill N, Chakraborty R. Characterizing Natural Organic Matter Transformations by Microbial Communities in Terrestrial Subsurface Ecosystems: A Critical Review of Analytical Techniques and Challenges. Front Microbiol 2022; 13:864895. [PMID: 35602028 PMCID: PMC9114703 DOI: 10.3389/fmicb.2022.864895] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 03/28/2022] [Indexed: 11/13/2022] Open
Abstract
Determining the mechanisms, traits, and pathways that regulate microbial transformation of natural organic matter (NOM) is critical to informing our understanding of the microbial impacts on the global carbon cycle. The capillary fringe of subsurface soils is a highly dynamic environment that remains poorly understood. Characterization of organo-mineral chemistry combined with a nuanced understanding of microbial community composition and function is necessary to understand microbial impacts on NOM speciation in the capillary fringe. We present a critical review of the popular analytical and omics techniques used for characterizing complex carbon transformation by microbial communities and focus on how complementary information obtained from the different techniques enable us to connect chemical signatures with microbial genes and pathways. This holistic approach offers a way forward for the comprehensive characterization of the formation, transformation, and mineralization of terrestrial NOM as influenced by microbial communities.
Collapse
Affiliation(s)
- Kristine Grace M Cabugao
- Department of Ecology, Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Sara Gushgari-Doyle
- Department of Ecology, Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Stephany S Chacon
- Department of Ecology, Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Xiaoqin Wu
- Department of Ecology, Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Amrita Bhattacharyya
- Department of Ecology, Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Nicholas Bouskill
- Department of Ecology, Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Romy Chakraborty
- Department of Ecology, Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| |
Collapse
|
12
|
Bolstering fitness via CO 2 fixation and organic carbon uptake: mixotrophs in modern groundwater. THE ISME JOURNAL 2022; 16:1153-1162. [PMID: 34876683 PMCID: PMC8941145 DOI: 10.1038/s41396-021-01163-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 11/11/2021] [Accepted: 11/22/2021] [Indexed: 12/04/2022]
Abstract
Current understanding of organic carbon inputs into ecosystems lacking photosynthetic primary production is predicated on data and inferences derived almost entirely from metagenomic analyses. The elevated abundances of putative chemolithoautotrophs in groundwaters suggest that dark CO2 fixation is an integral component of subsurface trophic webs. To understand the impact of autotrophically fixed carbon, the flux of CO2-derived carbon through various populations of subsurface microbiota must first be resolved, both quantitatively and temporally. Here we implement novel Stable Isotope Cluster Analysis to render a time-resolved and quantitative evaluation of 13CO2-derived carbon flow through a groundwater community in microcosms stimulated with reduced sulfur compounds. We demonstrate that mixotrophs, not strict autotrophs, were the most abundant active organisms in groundwater microcosms. Species of Hydrogenophaga, Polaromonas, Dechloromonas, and other metabolically versatile mixotrophs drove the production and remineralization of organic carbon. Their activity facilitated the replacement of 43% and 80% of total microbial carbon stores in the groundwater microcosms with 13C in just 21 and 70 days, respectively. The mixotrophs employed different strategies for satisfying their carbon requirements by balancing CO2 fixation and uptake of available organic compounds. These different strategies might provide fitness under nutrient-limited conditions, explaining the great abundances of mixotrophs in other oligotrophic habitats, such as the upper ocean and boreal lakes.
Collapse
|
13
|
Haddad PG, Mura J, Castéran F, Guignard M, Ranchou-Peyruse M, Sénéchal P, Larregieu M, Isaure MP, Svahn I, Moonen P, Le Hécho I, Hoareau G, Chiquet P, Caumette G, Dequidt D, Cézac P, Ranchou-Peyruse A. Biological, geological and chemical effects of oxygen injection in underground gas storage aquifers in the setting of biomethane deployment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 806:150690. [PMID: 34600980 DOI: 10.1016/j.scitotenv.2021.150690] [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: 07/04/2021] [Revised: 09/15/2021] [Accepted: 09/26/2021] [Indexed: 06/13/2023]
Abstract
The last few years have seen the proliferation of anaerobic digestion plants to produce biomethane. Oxygen (O2) traces added to biogas during the desulfurization process are co-injected in the gas network and can be stored in Underground Gas Storage (UGS). However, there are no data available for the undesirable effects of O2 on these anoxic environments, especially on deep aquifers. In addition to mineral alteration, O2 can have an impact on the anaerobic autochthonous microbial life. In our study, the storage conditions of an UGS aquifer were reproduced in a high-pressure reactor and bio-geo-chemical interactions between the aqueous, gas and solid phases were studied. Sulfate was depleted from the liquid phase for three consecutive times during the first 130 days of incubation reproducing the storage conditions (36 °C, 60 bar, methane with 1% CO2). Sulfate-reducers, such as Desulfovibrionaceae, were identified from the high-pressure system. Simulations with PHREEQC were used to determine the thermodynamic equilibrium to confirm any gas consumption. CO2 quantities decreased in the gas phase, suggesting its use as carbon source by microbial life. Benzene and toluene, hydrocarbons found in traces and known to be biodegradable in storages, were monitored and a decrease of toluene was revealed and associated to the Peptococcaceae family. Afterwards, O2 was added as 1% of the gas phase, corresponding to the maximum quantity found in biomethane after desulfurization process. Re-oxidation of sulfide to sulfate was observed along with the end of sulfate reducing activity and toluene biodegradation and the disappearance of most of the community. H2 surprisingly appeared and accumulated as soon as hydrogenotrophic sulfate-reducers decreased. H2 would be produced via the necromass fermentation accomplished by microorganisms able to resist the oxic conditions of 4.42·10-4 mol.Kgw-1 of O2. The solid phase composed essentially of quartz, presented no remarkable changes.
Collapse
Affiliation(s)
- Perla G Haddad
- Universite de Pau et Pays de l'Adour, E2S UPPA, LaTEP, Pau, France
| | - Jean Mura
- Universite de Pau et Pays de l'Adour, E2S UPPA, LaTEP, Pau, France
| | - Franck Castéran
- Universite de Pau et Pays de l'Adour, E2S UPPA, LaTEP, Pau, France; Joint Laboratory SEnGA, UPPA-E2S-Teréga, Pau, 64000 Pau, France
| | - Marion Guignard
- Universite de Pau et Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
| | - Magali Ranchou-Peyruse
- Universite de Pau et Pays de l'Adour, E2S UPPA, LaTEP, Pau, France; Joint Laboratory SEnGA, UPPA-E2S-Teréga, Pau, 64000 Pau, France; Universite de Pau et Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
| | - Pascale Sénéchal
- Universite de Pau et Pays de l'Adour, E2S UPPA, CNRS, DMEX, Pau, France
| | - Marie Larregieu
- Universite de Pau et Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
| | | | - Isabelle Svahn
- Bordeaux Imaging Center (BIC), CNRS, Université de Bordeaux, Bordeaux, France
| | - Peter Moonen
- Universite de Pau et Pays de l'Adour, E2S UPPA, CNRS, DMEX, Pau, France
| | - Isabelle Le Hécho
- Joint Laboratory SEnGA, UPPA-E2S-Teréga, Pau, 64000 Pau, France; Universite de Pau et Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
| | - Guilhem Hoareau
- Universite de Pau et Pays de l'Adour, E2S UPPA, CNRS, TOTAL, LFCR, Pau, France
| | - Pierre Chiquet
- Joint Laboratory SEnGA, UPPA-E2S-Teréga, Pau, 64000 Pau, France; Teréga, Pau, France
| | - Guilhem Caumette
- Joint Laboratory SEnGA, UPPA-E2S-Teréga, Pau, 64000 Pau, France; Teréga, Pau, France
| | - David Dequidt
- STORENGY - Geosciences Department, Bois-Colombes, France
| | - Pierre Cézac
- Universite de Pau et Pays de l'Adour, E2S UPPA, LaTEP, Pau, France; Joint Laboratory SEnGA, UPPA-E2S-Teréga, Pau, 64000 Pau, France
| | - Anthony Ranchou-Peyruse
- Joint Laboratory SEnGA, UPPA-E2S-Teréga, Pau, 64000 Pau, France; Universite de Pau et Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France.
| |
Collapse
|
14
|
Eziuzor SC, Corrêa FB, Peng S, Schultz J, Kleinsteuber S, da Rocha UN, Adrian L, Vogt C. Structure and functional capacity of a benzene-mineralizing, nitrate-reducing microbial community. J Appl Microbiol 2022; 132:2795-2811. [PMID: 34995421 DOI: 10.1111/jam.15443] [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: 09/29/2021] [Revised: 12/16/2021] [Accepted: 01/04/2022] [Indexed: 11/26/2022]
Abstract
AIMS How benzene is metabolized by microbes under anoxic conditions is not fully understood. Here, we studied the degradation pathways in a benzene-mineralizing, nitrate-reducing enrichment culture. METHODS AND RESULTS Benzene mineralization was dependent on the presence of nitrate and correlated to the enrichment of a Peptococcaceae phylotype only distantly related to known anaerobic benzene degraders of this family. Its relative abundance decreased after benzene mineralization had terminated, while other abundant taxa-Ignavibacteriaceae, Rhodanobacteraceae and Brocadiaceae-slightly increased. Generally, the microbial community remained diverse despite the amendment of benzene as single organic carbon source, suggesting complex trophic interactions between different functional groups. A subunit of the putative anaerobic benzene carboxylase previously detected in Peptococcaceae was identified by metaproteomic analysis suggesting that benzene was activated by carboxylation. Detection of proteins involved in anaerobic ammonium oxidation (anammox) indicates that benzene mineralization was accompanied by anammox, facilitated by nitrite accumulation and the presence of ammonium in the growth medium. CONCLUSIONS The results suggest that benzene was activated by carboxylation and further assimilated by a novel Peptococcaceae phylotype. SIGNIFICANCE AND IMPACT OF THE STUDY The results confirm the hypothesis that Peptococcaceae are important anaerobic benzene degraders.
Collapse
Affiliation(s)
- Samuel C Eziuzor
- Department of Isotope Biogeochemistry, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Felipe B Corrêa
- Department of Environmental Microbiology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Shuchan Peng
- Department of Isotope Biogeochemistry, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany.,Department of Environmental Science, Chongqing University, Chongqing, China
| | - Júnia Schultz
- Department of Environmental Microbiology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany.,Departamento de Microbiologia Geral, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil.,Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Sabine Kleinsteuber
- Department of Environmental Microbiology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Ulisses N da Rocha
- Department of Environmental Microbiology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Lorenz Adrian
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany.,Geobiotechnology, Technische Universität Berlin, Berlin, Germany
| | - Carsten Vogt
- Department of Isotope Biogeochemistry, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
| |
Collapse
|
15
|
Bin Hudari MS, Vogt C, Richnow HH. Sulfidic acetate mineralization at 45°C by an aquifer microbial community: key players and effects of heat changes on activity and community structure. Environ Microbiol 2021; 24:370-389. [PMID: 34859568 DOI: 10.1111/1462-2920.15852] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 11/09/2021] [Accepted: 11/12/2021] [Indexed: 11/28/2022]
Abstract
High-Temperature Aquifer Thermal Energy Storage (HT-ATES) is a sustainable approach for integrating thermal energy from various sources into complex energy systems. Temperatures ≥45°C, which are relevant in impact zones of HT-ATES systems, may dramatically influence the structure and activities of indigenous aquifer microbial communities. Here, we characterized an acetate-mineralizing, sulfate-reducing microbial community derived from an aquifer and adapted to 45°C. Acetate mineralization was strongly inhibited at temperatures ≤25°C and 60°C. Prolonged incubation at 12°C and 25°C resulted in acetate mineralization recovery after 40-80 days whereas acetate was not mineralized at 60°C within 100 days. Cultures pre-grown at 45°C and inhibited for 28 days by incubation at 12°C, 25°C, or 60°C recovered quickly after changing the temperature back to 45°C. Phylotypes affiliated to the order Spirochaetales and to endospore-forming sulfate reducers of the order Clostridiales were highly abundant in microcosms being active at 45°C highlighting their key role. In summary, prolonged incubation at 45°C resulted in active microbial communities mainly consisting of organisms adapted to temperatures between the typical temperature range of mesophiles and thermophiles and being resilient to temporary heat changes.
Collapse
Affiliation(s)
- Mohammad S Bin Hudari
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Carsten Vogt
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Hans H Richnow
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| |
Collapse
|
16
|
Ranchou-Peyruse M, Guignard M, Casteran F, Abadie M, Defois C, Peyret P, Dequidt D, Caumette G, Chiquet P, Cézac P, Ranchou-Peyruse A. Microbial Diversity Under the Influence of Natural Gas Storage in a Deep Aquifer. Front Microbiol 2021; 12:688929. [PMID: 34721313 PMCID: PMC8549729 DOI: 10.3389/fmicb.2021.688929] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 09/08/2021] [Indexed: 11/30/2022] Open
Abstract
Deep aquifers (up to 2km deep) contain massive volumes of water harboring large and diverse microbial communities at high pressure. Aquifers are home to microbial ecosystems that participate in physicochemical balances. These microorganisms can positively or negatively interfere with subsurface (i) energy storage (CH4 and H2), (ii) CO2 sequestration; and (iii) resource (water, rare metals) exploitation. The aquifer studied here (720m deep, 37°C, 88bar) is naturally oligotrophic, with a total organic carbon content of <1mg.L-1 and a phosphate content of 0.02mg.L-1. The influence of natural gas storage locally generates different pressures and formation water displacements, but it also releases organic molecules such as monoaromatic hydrocarbons at the gas/water interface. The hydrocarbon biodegradation ability of the indigenous microbial community was evaluated in this work. The in situ microbial community was dominated by sulfate-reducing (e.g., Sva0485 lineage, Thermodesulfovibriona, Desulfotomaculum, Desulfomonile, and Desulfovibrio), fermentative (e.g., Peptococcaceae SCADC1_2_3, Anaerolineae lineage and Pelotomaculum), and homoacetogenic bacteria ("Candidatus Acetothermia") with a few archaeal representatives (e.g., Methanomassiliicoccaceae, Methanobacteriaceae, and members of the Bathyarcheia class), suggesting a role of H2 in microenvironment functioning. Monoaromatic hydrocarbon biodegradation is carried out by sulfate reducers and favored by concentrated biomass and slightly acidic conditions, which suggests that biodegradation should preferably occur in biofilms present on the surfaces of aquifer rock, rather than by planktonic bacteria. A simplified bacterial community, which was able to degrade monoaromatic hydrocarbons at atmospheric pressure over several months, was selected for incubation experiments at in situ pressure (i.e., 90bar). These showed that the abundance of various bacterial genera was altered, while taxonomic diversity was mostly unchanged. The candidate phylum Acetothermia was characteristic of the community incubated at 90bar. This work suggests that even if pressures on the order of 90bar do not seem to select for obligate piezophilic organisms, modifications of the thermodynamic equilibria could favor different microbial assemblages from those observed at atmospheric pressure.
Collapse
Affiliation(s)
- Magali Ranchou-Peyruse
- IPREM, Institut des Sciences Analytiques et de Physico-Chimie pour l’Environnement et les Matériaux, Université de Pau & Pays Adour/E2S-UPPA, Pau, France
- Laboratoire de thermique, énergétique et procédés IPRA, EA1932, Université de Pau & Pays Adour/E2S-UPPA, Pau, France
- Joint Laboratory SEnGA, UPPA-E2S-Teréga, Pau, France
| | - Marion Guignard
- IPREM, Institut des Sciences Analytiques et de Physico-Chimie pour l’Environnement et les Matériaux, Université de Pau & Pays Adour/E2S-UPPA, Pau, France
| | - Franck Casteran
- Laboratoire de thermique, énergétique et procédés IPRA, EA1932, Université de Pau & Pays Adour/E2S-UPPA, Pau, France
| | - Maïder Abadie
- IPREM, Institut des Sciences Analytiques et de Physico-Chimie pour l’Environnement et les Matériaux, Université de Pau & Pays Adour/E2S-UPPA, Pau, France
| | - Clémence Defois
- Université Clermont Auvergne, INRAE, UMR 0454 MEDIS, Clermont-Ferrand, France
| | - Pierre Peyret
- Université Clermont Auvergne, INRAE, UMR 0454 MEDIS, Clermont-Ferrand, France
| | - David Dequidt
- STORENGY – Geosciences Department, Bois-Colombes, France
| | - Guilhem Caumette
- Joint Laboratory SEnGA, UPPA-E2S-Teréga, Pau, France
- Teréga, Pau, France
| | - Pierre Chiquet
- Joint Laboratory SEnGA, UPPA-E2S-Teréga, Pau, France
- Teréga, Pau, France
| | - Pierre Cézac
- Laboratoire de thermique, énergétique et procédés IPRA, EA1932, Université de Pau & Pays Adour/E2S-UPPA, Pau, France
- Joint Laboratory SEnGA, UPPA-E2S-Teréga, Pau, France
| | - Anthony Ranchou-Peyruse
- IPREM, Institut des Sciences Analytiques et de Physico-Chimie pour l’Environnement et les Matériaux, Université de Pau & Pays Adour/E2S-UPPA, Pau, France
- Joint Laboratory SEnGA, UPPA-E2S-Teréga, Pau, France
| |
Collapse
|
17
|
Saha A, Mohapatra B, Kazy SK, Sar P. Variable response of arsenic contaminated groundwater microbial community to electron acceptor regime revealed by microcosm based high-throughput sequencing approach. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART A, TOXIC/HAZARDOUS SUBSTANCES & ENVIRONMENTAL ENGINEERING 2021; 56:804-817. [PMID: 34284694 DOI: 10.1080/10934529.2021.1930448] [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: 02/17/2021] [Revised: 05/10/2021] [Accepted: 05/11/2021] [Indexed: 06/13/2023]
Abstract
Arsenic (As) mobilization in alluvial aquifers is facilitated by microbially catalyzed redox transformations that depend on the availability of electron acceptors (EAs). In this study, the response of an As-contaminated groundwater microbial community from West Bengal, India towards varied EAs was elucidated through microcosm based 16S rRNA gene amplicon sequencing. Acinetobacter, Deinococcus, Nocardioides, etc., and several unclassified bacteria (Ignavibacteria) and archaea (Bathyarchaeia, Micrarchaeia) previously not reported from As-contaminated groundwater of West Bengal, characterized the groundwater community. Distinct shifts in community composition were observed in response to various EAs. Enrichment of operational taxonomic units (OTUs) affiliated to Denitratisoma (NO3-), Spirochaetaceae (Mn4+), Deinococcus (As5+), Ruminiclostridium (Fe3+), Macellibacteroides (SO42-), Holophagae-Subgroup 7 (HCO3-), Dechloromonas and Geobacter (EA mixture) was noted. Alternatively, As3+ amendment as electron donor allowed predominance of Rhizobium. Taxonomy based functional profiling highlighted the role of chemoorganoheterotrophs capable of concurrent reduction of NO3-, Fe3+, SO42-, and As biotransformation in As-contaminated groundwater of West Bengal. Our analysis revealed two major aspects of the community, (a) taxa selective toward responding to the EAs, and (b) multifaceted nature of taxa appearing in abundance in response to multiple substrates. Thus, the results emphasized the potential of microbial community members to influence the biogeochemical cycling of As and other dominant anions/cations.
Collapse
Affiliation(s)
- Anumeha Saha
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, India
| | - Balaram Mohapatra
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, India
| | - Sufia Khannam Kazy
- Department of Biotechnology, National Institute of Technology Durgapur, Durgapur, West Bengal, India
| | - Pinaki Sar
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, India
| |
Collapse
|
18
|
Insights into Autotrophic Activities and Carbon Flow in Iron-Rich Pelagic Aggregates (Iron Snow). Microorganisms 2021; 9:microorganisms9071368. [PMID: 34201891 PMCID: PMC8305228 DOI: 10.3390/microorganisms9071368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 06/18/2021] [Accepted: 06/21/2021] [Indexed: 11/17/2022] Open
Abstract
Pelagic aggregates function as biological carbon pumps for transporting fixed organic carbon to sediments. In iron-rich (ferruginous) lakes, photoferrotrophic and chemolithoautotrophic bacteria contribute to CO2 fixation by oxidizing reduced iron, leading to the formation of iron-rich pelagic aggregates (iron snow). The significance of iron oxidizers in carbon fixation, their general role in iron snow functioning and the flow of carbon within iron snow is still unclear. Here, we combined a two-year metatranscriptome analysis of iron snow collected from an acidic lake with protein-based stable isotope probing to determine general metabolic activities and to trace 13CO2 incorporation in iron snow over time under oxic and anoxic conditions. mRNA-derived metatranscriptome of iron snow identified four key players (Leptospirillum, Ferrovum, Acidithrix, Acidiphilium) with relative abundances (59.6-85.7%) encoding ecologically relevant pathways, including carbon fixation and polysaccharide biosynthesis. No transcriptional activity for carbon fixation from archaea or eukaryotes was detected. 13CO2 incorporation studies identified active chemolithoautotroph Ferrovum under both conditions. Only 1.0-5.3% relative 13C abundances were found in heterotrophic Acidiphilium and Acidocella under oxic conditions. These data show that iron oxidizers play an important role in CO2 fixation, but the majority of fixed C will be directly transported to the sediment without feeding heterotrophs in the water column in acidic ferruginous lakes.
Collapse
|
19
|
Aoyagi T, Katayama Y, Aizawa H, Takasaki M, Hori T. Nitrate-Driven Trophic Association of Sulfur-Cycling Microorganisms in Tsunami-Deposited Marine Sediment Revealed by High-Sensitivity 13C-Bicarbonate Probing. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:8410-8421. [PMID: 34078080 DOI: 10.1021/acs.est.0c08191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Although denitrification-dependent chemolithotrophic sulfur oxidizers proliferated in tsunami-deposited marine sediment with nitrate amendment, their ecophysiological roles in biogeochemical carbon transfer are not addressed. We employed time-resolved high-sensitivity 13C-bicarbonate probing of rRNA to unveil the carbon fixation and resulting trophic relationship of the nitrate-amended sediment microorganisms. Nitrate reduction and sulfur oxidation co-occurred along with significant decreases in the 13CO2 and dissolved bicarbonate concentrations for the first 4 days of the incubation, during which the denitrification-dependent sulfur-oxidizing chemolithotrophs, i.e., the Sulfurimonas sp. HDS01 and Thioalkalispira sp. HDS22 relatives, and the sulfate-reducing heterotrophs, i.e., the Desulfobulbus spp. and Desulfofustis glycolicus relatives, actively incorporated 13C. These indicated that the sulfur oxidizers and sulfate reducers were tightly associated with each other through the direct carbon transfer. Relatives of the fermentative Thalassomonas sediminis and the hydrolytic Pararheinheimera aquatica, in addition to various sulfur-cycling microorganisms, significantly assimilated 13C at day 14. Although the incorporation of 13C was not detected, a syntrophic volatile-fatty-acid oxidizer and hydrogenotrophic methanogens significantly expressed their 16S rRNA molecules at day 21, indicating the metabolic activation of these final decomposers under the latter nutrient-limited conditions. The results demonstrated the nitrate-driven trophic association of sulfur-cycling microorganisms and the subsequent microbial activation and diversification, triggering the restoration of the marine ecosystem function.
Collapse
Affiliation(s)
- Tomo Aoyagi
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology, 16-1 Onogawa, Tsukuba, Ibaraki 305-8569, Japan
| | - Yoko Katayama
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
| | - Hidenobu Aizawa
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology, 16-1 Onogawa, Tsukuba, Ibaraki 305-8569, Japan
| | - Mitsuru Takasaki
- Department of Food and Environmental Sciences, Faculty of Science and Engineering, Ishinomaki Senshu University, 1 Shinmito Minamisakai, Ishinomaki, Miyagi 986-8580, Japan
| | - Tomoyuki Hori
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology, 16-1 Onogawa, Tsukuba, Ibaraki 305-8569, Japan
| |
Collapse
|
20
|
Yu F, Li Y, Wang H, Peng T, Wu YR, Hu Z. Microbial debromination of hexabromocyclododecanes. Appl Microbiol Biotechnol 2021; 105:4535-4550. [PMID: 34076715 DOI: 10.1007/s00253-021-11095-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 12/22/2020] [Accepted: 01/03/2021] [Indexed: 11/29/2022]
Abstract
Hexabromocyclododecanes (HBCDs), a new sort of brominated flame retardants (BFRs), are globally prevalent and recalcitrant toxic environmental pollutants. HBCDs have been found in many environmental media and even in the human body, leading to serious health concerns. HBCDs are biodegradable in the environment. By now, dozens of bacteria have been discovered with the ability to transform HBCDs. Microbial debromination of HBCDs is via HBr-elimination, HBr-dihaloelimination, and hydrolytic debromination. Biotic transformation of HBCDs yields many hydroxylated and lower brominated compounds which lack assessment of ecological toxicity. Bioremediation of HBCD pollution has only been applied in the laboratory. Here, we review the current knowledge about microbial debromination of HBCDs, aiming to promote the bioremediation applied in HBCD contaminated sites. KEY POINTS: • Microbial debromination of HBCDs is via hydrolytic debromination, HBr-elimination, and HBr-dihaloelimination. • Newly occurred halogenated contaminants such as HBCDs hitch the degradation pathway tamed by previously discharged anthropogenic organohalides. • Strategy that combines bioaugmentation with phytoremediation for bioremediation of HBCD pollution is promising.
Collapse
Affiliation(s)
- Fei Yu
- Department of Biology, Science College, Shantou University, Shantou, 515063, Guangdong Province, People's Republic of China
| | - Yuyang Li
- Department of Biology, Science College, Shantou University, Shantou, 515063, Guangdong Province, People's Republic of China
| | - Hui Wang
- Department of Biology, Science College, Shantou University, Shantou, 515063, Guangdong Province, People's Republic of China
| | - Tao Peng
- Department of Biology, Science College, Shantou University, Shantou, 515063, Guangdong Province, People's Republic of China
| | - Yi-Rui Wu
- Department of Biology, Science College, Shantou University, Shantou, 515063, Guangdong Province, People's Republic of China
| | - Zhong Hu
- Department of Biology, Science College, Shantou University, Shantou, 515063, Guangdong Province, People's Republic of China.
| |
Collapse
|
21
|
Melkonian C, Fillinger L, Atashgahi S, da Rocha UN, Kuiper E, Olivier B, Braster M, Gottstein W, Helmus R, Parsons JR, Smidt H, van der Waals M, Gerritse J, Brandt BW, Röling WFM, Molenaar D, van Spanning RJM. High biodiversity in a benzene-degrading nitrate-reducing culture is sustained by a few primary consumers. Commun Biol 2021; 4:530. [PMID: 33953314 PMCID: PMC8099898 DOI: 10.1038/s42003-021-01948-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 03/03/2021] [Indexed: 01/04/2023] Open
Abstract
A key question in microbial ecology is what the driving forces behind the persistence of large biodiversity in natural environments are. We studied a microbial community with more than 100 different types of species which evolved in a 15-years old bioreactor with benzene as the main carbon and energy source and nitrate as the electron acceptor. Using genome-centric metagenomics plus metatranscriptomics, we demonstrate that most of the community members likely feed on metabolic left-overs or on necromass while only a few of them, from families Rhodocyclaceae and Peptococcaceae, are candidates to degrade benzene. We verify with an additional succession experiment using metabolomics and metabarcoding that these few community members are the actual drivers of benzene degradation. As such, we hypothesize that high species richness is maintained and the complexity of a natural community is stabilized in a controlled environment by the interdependencies between the few benzene degraders and the rest of the community members, ultimately resulting in a food web with different trophic levels.
Collapse
Affiliation(s)
- Chrats Melkonian
- Department of Molecular Cell Biology, AIMMS, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
| | - Lucas Fillinger
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Siavash Atashgahi
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Ulisses Nunes da Rocha
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Esther Kuiper
- Department of Molecular Cell Biology, AIMMS, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Brett Olivier
- Department of Molecular Cell Biology, AIMMS, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Martin Braster
- Department of Molecular Cell Biology, AIMMS, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Willi Gottstein
- Department of Molecular Cell Biology, AIMMS, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Rick Helmus
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - John R Parsons
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | | | - Jan Gerritse
- Unit Subsurface and Groundwater Systems, Deltares, Utrecht, The Netherlands
| | - Bernd W Brandt
- Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam, University of Amsterdam and Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Wilfred F M Röling
- Department of Molecular Cell Biology, AIMMS, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Douwe Molenaar
- Department of Molecular Cell Biology, AIMMS, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Rob J M van Spanning
- Department of Molecular Cell Biology, AIMMS, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
| |
Collapse
|
22
|
Lee K, Ulrich A. Indigenous microbial communities in Albertan sediments are capable of anaerobic benzene biodegradation under methanogenic, sulfate-reducing, nitrate-reducing, and iron-reducing redox conditions. WATER ENVIRONMENT RESEARCH : A RESEARCH PUBLICATION OF THE WATER ENVIRONMENT FEDERATION 2021; 93:524-534. [PMID: 32892398 DOI: 10.1002/wer.1454] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 08/13/2020] [Accepted: 08/28/2020] [Indexed: 06/11/2023]
Abstract
Alberta is a major center for oil and gas production, and correspondingly harbors hundreds of unresolved contamination sites by environmental hazards such as benzene (C6 H6 ). Due to its cost-effectiveness, bioremediation has become a promising strategy for C6 H6 removal. Contamination sites typically take on an anaerobic context, which complicates the energetics of contamination sites and is a subject that is scarcely broached in studies of Albertan sediments. This study examines the innate potential for indigenous microbial communities in Albertan sediments to remove C6 H6 in a multitude of reduced conditions. Community profiles of these sediments were analyzed by 16S rRNA gene amplicon sequencing, and removal rates and reaction stoichiometries were observed by gas chromatography and ion chromatography. Organisms belonging to known primary degrader taxa were identified, including Geobacter (iron-reducing), and Peptococcaceae (nitrate-reducing). Furthermore, benzene removal patterns of the cultures were similar to those observed in previously reported microcosms, with lag times between 70 and 168 days and removal rates between 3.27 and 12.70 µM/day. Such information could support a more comprehensive survey of Albertan sediment consortia, which may eventually be utilized in informing future remediation efforts in the province. PRACTITIONER POINTS: ●Clay and sand sediments originating from Northern Alberta could remove benzene under methanogenic, sulfate-reducing, iron-reducing, and nitrate-reducing conditions. ●Degradation profiles were broadly comparable to those of reported cultures from other geographical locales. ●Key degrader taxa observed included Geobacter (Fe3+ -reducing) and Peptococcaceae ( NO 3 - -reducing). ●Knowledge gained can be the start of a more extensive survey of Albertan sediments. Eventually, this collection of information can be used to generate robust C6 H6 -degrading cultures that can be implemented for bioaugmentation and be implemented in informing remediation strategies in soil and water matrices for priority contamination cases such as leaking underground storage tanks and orphan wells.
Collapse
Affiliation(s)
- Korris Lee
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Alberta, Canada
| | - Ania Ulrich
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Alberta, Canada
| |
Collapse
|
23
|
Müller C, Knöller K, Lucas R, Kleinsteuber S, Trabitzsch R, Weiß H, Stollberg R, Richnow HH, Vogt C. Benzene degradation in contaminated aquifers: Enhancing natural attenuation by injecting nitrate. JOURNAL OF CONTAMINANT HYDROLOGY 2021; 238:103759. [PMID: 33461044 DOI: 10.1016/j.jconhyd.2020.103759] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 12/11/2020] [Accepted: 12/21/2020] [Indexed: 06/12/2023]
Abstract
Natural attenuation processes depend on the availability of suitable electron acceptors. At the megasite Zeitz, concentrations of the main contaminant benzene were observed to increase constantly in the lower aquifer to levels of more than 2.5 mM. This was accompanied by decreasing concentrations of sulphate (SO42-), which has been previously shown to be the main electron acceptor for benzene oxidation at this site, resulting in an electron acceptor-limited, sulphidic benzene plume. Therefore, a field experiment was conducted to stimulate benzene biodegradation by injecting nitrate (NO3-) into the sulphidic benzene plume aiming (i) to recycle sulphate by nitrate-dependent sulphide oxidation, and (ii) to serve as direct electron acceptor for benzene oxidation. Within 60 days, 6.74 tons sodium nitrate (NaNO3) were injected into the lower aquifer, and the resulting biogeochemical effects within the benzene plume were monitored for more than one year by chemical and microbiological analyses of groundwater samples taken from various depths of ten monitoring wells located in three observation lines downstream of nitrate injection. Nitrate was microbiologically consumed, as shown by changes in δ15N-NO3- and δ18O-NO3- values, partial nitrite accumulation, and changing ratios of Na+/NO3-. Main electron donors for nitrate reduction were reduced sulphur compounds, verified by changing δ34S-SO42- and δ18O-SO42- values, partially increasing sulphate concentrations, and strongly increasing abundances of typical sulphur-oxidizing, nitrate-reducing bacterial taxa within the nitrate plume. The general absent hydrogen isotope fractionation of benzene, also in the sulphidic, nitrate-free part of the plume, indicates that benzene was not biodegraded by sulphate-reducing consortia. However, detected small carbon isotope fractionation of benzene points to in situ benzene biodegradation processes in the plume, probably supported by nitrate. In conclusion, nitrate injection resulted in changing redox conditions and recycling of sulphate in the sulphidic, sulphate-depleted benzene plume due to microbial oxidation of reduced sulphur species, leading to presumably favored conditions for in situ benzene biodegradation.
Collapse
Affiliation(s)
- Christin Müller
- Helmholtz-Centre for Environmental Research UFZ, Department Catchment Hydrology, Germany.
| | - Kay Knöller
- Helmholtz-Centre for Environmental Research UFZ, Department Catchment Hydrology, Germany
| | - Rico Lucas
- Helmholtz-Centre for Environmental Research UFZ, Department Environmental Microbiology, Germany
| | - Sabine Kleinsteuber
- Helmholtz-Centre for Environmental Research UFZ, Department Environmental Microbiology, Germany
| | - Ralf Trabitzsch
- Helmholtz-Centre for Environmental Research UFZ, Department Environmental Informatics, Germany
| | - Holger Weiß
- Helmholtz-Centre for Environmental Research UFZ, Department Environmental Informatics, Germany
| | - Reiner Stollberg
- Helmholtz-Centre for Environmental Research UFZ, Department Environmental Informatics, Germany
| | - Hans Hermann Richnow
- Helmholtz-Centre for Environmental Research UFZ, Department Isotope Biogeochemistry, Germany
| | - Carsten Vogt
- Helmholtz-Centre for Environmental Research UFZ, Department Isotope Biogeochemistry, Germany
| |
Collapse
|
24
|
Starke R, Schäpe SS, Jehmlich N, von Bergen M. Protein stable isotope probing with H 2 18 O differentiated cold stress response at permissive temperatures from general growth at optimal conditions in Escherichia coli K12. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2021; 35:e8941. [PMID: 32885498 DOI: 10.1002/rcm.8941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 08/26/2020] [Accepted: 08/29/2020] [Indexed: 06/11/2023]
Abstract
RATIONALE Tracing isotopically labeled water into proteins allows for the detection of species-specific metabolic activity in complex communities. However, a stress response may alter the newly synthesized proteins. METHODS We traced 18-oxygen from heavy water into proteins of Escherichia coli K12 grown from permissive to retardant temperatures. All samples were analyzed using UPLC/Orbitrap Q-Exactive-MS/MS operating in positive electrospray ionization mode. RESULTS We found that warmer temperatures resulted in significantly (P-value < 0.05) higher incorporation of 18-oxygen as seen by both substrate utilization as relative isotope abundance (RIA) and growth as labeling ratio (LR). However, the absolute number of peptides with incorporation of 18-oxygen showed no significant correlation to temperature, potentially caused by the synthesis of different proteins at low temperatures, namely, proteins related to cold stress response. CONCLUSIONS Our results unveil the species-specific cold stress response of E. coli K12 that could be misinterpreted as general growth; this is why the quantity as RIA and LR but also the quality as absolute number of peptides with incorporation (relative abundance, RA) and their function must be considered to fully understand the activity of microbial communities.
Collapse
Affiliation(s)
- Robert Starke
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Stephanie Serena Schäpe
- Department of Molecular Systems Biology, 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
| |
Collapse
|
25
|
Bin Hudari MS, Vogt C, Richnow HH. Effect of Temperature on Acetate Mineralization Kinetics and Microbial Community Composition in a Hydrocarbon-Affected Microbial Community During a Shift From Oxic to Sulfidogenic Conditions. Front Microbiol 2021; 11:606565. [PMID: 33391229 PMCID: PMC7773710 DOI: 10.3389/fmicb.2020.606565] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 11/23/2020] [Indexed: 01/04/2023] Open
Abstract
Aquifer thermal energy storage (ATES) allows for the seasonal storage and extraction of heat in the subsurface thus reducing reliance on fossil fuels and supporting decarbonization of the heating and cooling sector. However, the impacts of higher temperatures toward biodiversity and ecosystem services in the subsurface environment remain unclear. Here, we conducted a laboratory microcosm study comprising a hydrocarbon-degrading microbial community from a sulfidic hydrocarbon-contaminated aquifer spiked with 13C-labeled acetate and incubated at temperatures between 12 and 80°C to evaluate (i) the extent and rates of acetate mineralization and (ii) the resultant temperature-induced shifts in the microbial community structure. We observed biphasic mineralization curves at 12, 25, 38, and 45°C, arising from immediate and fast aerobic mineralization due to an initial oxygen exposure, followed by slower mineralization at sulfidogenic conditions. At 60°C and several replicates at 45°C, acetate was only aerobically mineralized. At 80°C, no mineralization was observed within 178 days. Rates of acetate mineralization coupled to sulfate reduction at 25 and 38°C were six times faster than at 12°C. Distinct microbial communities developed in oxic and strictly anoxic phases of mineralization as well as at different temperatures. Members of the Alphaproteobacteria were dominant in the oxic mineralization phase at 12–38°C, succeeded by a more diverse community in the anoxic phase composed of Deltaproteobacteria, Clostridia, Spirochaetia, Gammaproteobacteria and Anaerolinea, with varying abundances dependent on the temperature. In the oxic phases at 45 and 60°C, phylotypes affiliated to spore-forming Bacilli developed. In conclusion, temperatures up to 38°C allowed aerobic and anaerobic acetate mineralization albeit at varying rates, while mineralization occurred mainly aerobically between 45 and 60°C; thermophilic sulfate reducers being active at temperatures > 45°C were not detected. Hence, temperature may affect dissolved organic carbon mineralization rates in ATES while the variability in the microbial community composition during the transition from micro-oxic to sulfidogenic conditions highlights the crucial role of electron acceptor availability when combining ATES with bioremediation.
Collapse
Affiliation(s)
| | - Carsten Vogt
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Hans Hermann Richnow
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research, Leipzig, Germany
| |
Collapse
|
26
|
Figueroa-Gonzalez PA, Bornemann TLV, Adam PS, Plewka J, Révész F, von Hagen CA, Táncsics A, Probst AJ. Saccharibacteria as Organic Carbon Sinks in Hydrocarbon-Fueled Communities. Front Microbiol 2020; 11:587782. [PMID: 33424787 PMCID: PMC7786006 DOI: 10.3389/fmicb.2020.587782] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 12/03/2020] [Indexed: 01/05/2023] Open
Abstract
Organisms of the candidate phylum Saccharibacteria have frequently been detected as active members of hydrocarbon degrading communities, yet their actual role in hydrocarbon degradation remained unclear. Here, we analyzed three enrichment cultures of hydrocarbon-amended groundwater samples using genome-resolved metagenomics to unravel the metabolic potential of indigenous Saccharibacteria. Community profiling based on ribosomal proteins revealed high variation in the enrichment cultures suggesting little reproducibility although identical cultivation conditions were applied. Only 17.5 and 12.5% of the community members were shared between the three enrichment cultures based on ribosomal protein clustering and read mapping of reconstructed genomes, respectively. In one enrichment, two Saccharibacteria strains dominated the community with 16.6% in relative abundance and we were able to recover near-complete genomes for each of them. A detailed analysis of their limited metabolism revealed the capacity for peptide degradation, lactate fermentation from various hexoses, and suggests a scavenging lifestyle with external retrieval of molecular building blocks. In contrast to previous studies suggesting that Saccharibacteria are directly involved in hydrocarbon degradation, our analyses provide evidence that these organisms can be highly abundant scavengers acting rather as organic carbon sinks than hydrocarbon degraders in these communities.
Collapse
Affiliation(s)
- Perla Abigail Figueroa-Gonzalez
- Group for Aquatic Microbial Ecology, Environmental Microbiology and Biotechnology, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany
| | - Till L V Bornemann
- Group for Aquatic Microbial Ecology, Environmental Microbiology and Biotechnology, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany
| | - Panagiotis S Adam
- Group for Aquatic Microbial Ecology, Environmental Microbiology and Biotechnology, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany
| | - Julia Plewka
- Group for Aquatic Microbial Ecology, Environmental Microbiology and Biotechnology, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany
| | - Fruzsina Révész
- Regional University Center of Excellence in Environmental Industry, Szent István University, Gödöllõ, Hungary.,Department of Environmental Protection and Environmental Safety, Szent István University, Gödöllõ, Hungary
| | - Christian A von Hagen
- Group for Aquatic Microbial Ecology, Environmental Microbiology and Biotechnology, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany
| | - András Táncsics
- Regional University Center of Excellence in Environmental Industry, Szent István University, Gödöllõ, Hungary.,Department of Environmental Protection and Environmental Safety, Szent István University, Gödöllõ, Hungary
| | - Alexander J Probst
- Group for Aquatic Microbial Ecology, Environmental Microbiology and Biotechnology, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany
| |
Collapse
|
27
|
Starke R, Oliphant K, Jehmlich N, Schäpe SS, Sachsenberg T, Kohlbacher O, Allen-Vercoe E, von Bergen M. Tracing incorporation of heavy water into proteins for species-specific metabolic activity in complex communities. J Proteomics 2020; 222:103791. [PMID: 32335296 DOI: 10.1016/j.jprot.2020.103791] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 04/08/2020] [Accepted: 04/19/2020] [Indexed: 02/07/2023]
Abstract
Stable isotope probing (SIP) approaches are a suitable tool to identify active organisms in bacterial communities, but adding isotopically labeled substrate can alter both the structure and the functionality of the community. Here, we validated and demonstrated a substrate-independent protein-SIP protocol using isotopically labeled water that captures the entire microbial activity of a community. We found that 18O yielded a higher incorporation rate into peptides and thus comprised a higher sensitivity. We then applied the method to an in vitro model of a human distal gut microbial ecosystem grown in two medium formulations, to evaluate changes in microbial activity between a high-fiber and high-protein diet. We showed that only little changes are seen in the community structure but the functionality varied between the diets. In conclusion, our approach can detect species-specific metabolic activity in complex bacterial communities and more specifically to quantify the amount of amino acid synthesis. Heavy water makes possible to analyze the activity of bacterial communities for which adding an isotopically labeled energy and nutrient sources is not easily feasible. SIGNIFICANCE: Heavy stable isotopes allow for the detection of active key players in complex ecosystems where many organisms are thought to be dormant. Opposed to the labelling with energy or nutrient sources, heavy water could be a suitable replacement to trace activity, which has been shown for DNA and RNA. Here we validate, quantify and compare the incorporation of heavy water either labeled with deuterium or 18‑oxygen into proteins of Escherichia coli K12 and of an in vitro model of a human gut microbial ecosystem. The significance of our research is in providing a freely available pipeline to analyze the incorporation of deuterium and 18‑oxygen into proteins together with the validation of the applicability of tracing heavy water as a proxy for activity. Our approach unveils the relative functional contribution of microbiota in complex ecosystems, which will improve our understanding of both animal- and environment-associated microbiomes and in vitro models.
Collapse
Affiliation(s)
- Robert Starke
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany; Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic.
| | - Kaitlyn Oliphant
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada.
| | - Nico Jehmlich
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany.
| | - Stephanie Serena Schäpe
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany.
| | - Timo Sachsenberg
- Applied Bioinformatics, Dept. of Computer Science, University of Tübingen, Tübingen, Germany; Center for Bioinformatics, University of Tübingen, Germany
| | - Oliver Kohlbacher
- Applied Bioinformatics, Dept. of Computer Science, University of Tübingen, Tübingen, Germany; Center for Bioinformatics, University of Tübingen, Germany; Biomolecular Interactions, Max Planck Institute for Developmental Biology, Tübingen, Germany; Institute for Translational Bioinformatics, University Hospital Tübingen, Tübingen, Germany.
| | - Emma Allen-Vercoe
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada.
| | - 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.
| |
Collapse
|
28
|
Low A, Zhao S, Rogers MJ, Zemb O, Lee M, He J, Manefield M. Isolation, characterization and bioaugmentation of an acidotolerant 1,2-dichloroethane respiring Desulfitobacterium species from a low pH aquifer. FEMS Microbiol Ecol 2020; 95:5454739. [PMID: 30980656 DOI: 10.1093/femsec/fiz055] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2018] [Accepted: 04/11/2019] [Indexed: 01/14/2023] Open
Abstract
A Desulfitobacterium sp. strain AusDCA of the Peptococcaceae family capable of respiring 1,2-dichloroethane (1,2-DCA) to ethene anaerobically with ethanol or hydrogen as electron donor at pH 5.0 with optimal range between pH 6.5-7.5 was isolated from an acidic aquifer near Sydney, Australia. Strain AusDCA is distant (94% nucleotide identity) from its nearest phylogenetic neighbor, D. metallireducens, and could represent a new species. Reference gene-based quantification of growth indicated a doubling time of 2 days in cultures buffered at pH 7.2, and a yield of 7.66 (± 4.0) × 106 cells µmol-1 of 1,2-DCA. A putative 1,2-DCA reductive dehalogenase was translated from a dcaAB locus and had high amino acid identity (97.3% for DcaA and 100% for DcaB) to RdhA1B1 of the 1,2-DCA respiring Dehalobacter strain WL. Proteomic analysis confirmed DcaA expression in the pure culture. Dehalogenation of 1,2-DCA (1.6 mM) was observed in batch cultures established from groundwater at pH 5.5 collected 38 days after in situ bioaugmentation but not in cultures established with groundwater collected at the same time from wells not receiving bioaugmentation. Overall, strain AusDCA can tolerate lower pH than previously characterized organohalide respiring bacteria and remained viable in groundwater at pH 5.5.
Collapse
Affiliation(s)
- Adrian Low
- Genome Structural Biology, Temasek Lifesciences Laboratory, 1 Research Link, Singapore 117604, Singapore
| | - Siyan Zhao
- Department of Civil and Environmental Engineering, National University of Singapore, Block E2-02-13, 1 Engineering Drive 3, Singapore 117576, Singapore
| | - Matthew J Rogers
- Department of Civil and Environmental Engineering, National University of Singapore, Block E2-02-13, 1 Engineering Drive 3, Singapore 117576, Singapore
| | - Olivier Zemb
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Castanet Tolosan, France
| | - Matthew Lee
- School of Civil and Environmental Engineering, Water Research Centre, University of New South Wales, Sydney, NSW 2052, Australia
| | - Jianzhong He
- Department of Civil and Environmental Engineering, National University of Singapore, Block E2-02-13, 1 Engineering Drive 3, Singapore 117576, Singapore
| | - Mike Manefield
- School of Chemical Engineering, School of Civil and Environmental Engineering, University of New South Wales, Sydney, NSW 2052, Australia
| |
Collapse
|
29
|
Lohmann P, Schäpe SS, Haange SB, Oliphant K, Allen-Vercoe E, Jehmlich N, Von Bergen M. Function is what counts: how microbial community complexity affects species, proteome and pathway coverage in metaproteomics. Expert Rev Proteomics 2020; 17:163-173. [PMID: 32174200 DOI: 10.1080/14789450.2020.1738931] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Introduction: Metaproteomics is an established method to obtain a comprehensive taxonomic and functional view of microbial communities. After more than a decade, we are now able to describe the promise, reality, and perspectives of metaproteomics and provide useful information about the choice of method, applications, and potential improvement strategies.Areas covered: In this article, we will discuss current challenges of species and proteome coverage, and also highlight functional aspects of metaproteomics analysis of microbial communities with different levels of complexity. To do this, we re-analyzed data from microbial communities with low to high complexity (8, 72, 200 and >300 species). High species diversity leads to a reduced number of protein group identifications in a complex community, and thus the number of species resolved is underestimated. Ultimately, low abundance species remain undiscovered in complex communities. However, we observed that the main functional categories were better represented within complex microbiomes when compared to species coverage.Expert opinion: Our findings showed that even with low species coverage, metaproteomics has the potential to reveal habitat-specific functional features. Finally, we exploit this information to highlight future research avenues that are urgently needed to enhance our understanding of taxonomic composition and functions of complex microbiomes.
Collapse
Affiliation(s)
- Patrick Lohmann
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Stephanie Serena Schäpe
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Sven-Bastiaan Haange
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Kaitlyn Oliphant
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - Emma Allen-Vercoe
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - 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, University of Leipzig, Leipzig, Germany
| |
Collapse
|
30
|
Taubert M, Grob C, Crombie A, Howat AM, Burns OJ, Weber M, Lott C, Kaster AK, Vollmers J, Jehmlich N, von Bergen M, Chen Y, Murrell JC. Communal metabolism by Methylococcaceae and Methylophilaceae is driving rapid aerobic methane oxidation in sediments of a shallow seep near Elba, Italy. Environ Microbiol 2019; 21:3780-3795. [PMID: 31267680 DOI: 10.1111/1462-2920.14728] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 06/14/2019] [Accepted: 06/29/2019] [Indexed: 11/29/2022]
Abstract
The release of abiotic methane from marine seeps into the atmosphere is a major source of this potent greenhouse gas. Methanotrophic microorganisms in methane seeps use methane as carbon and energy source, thus significantly mitigating global methane emissions. Here, we investigated microbial methane oxidation at the sediment-water interface of a shallow marine methane seep. Metagenomics and metaproteomics, combined with 13 C-methane stable isotope probing, demonstrated that various members of the gammaproteobacterial family Methylococcaceae were the key players for methane oxidation, catalysing the first reaction step to methanol. We observed a transfer of carbon to methanol-oxidizing methylotrophs of the betaproteobacterial family Methylophilaceae, suggesting an interaction between methanotrophic and methylotrophic microorganisms that allowed for rapid methane oxidation. From our microcosms, we estimated methane oxidation rates of up to 871 nmol of methane per gram sediment per day. This implies that more than 50% of methane at the seep is removed by microbial oxidation at the sediment-water interface, based on previously reported in situ methane fluxes. The organic carbon produced was further assimilated by different heterotrophic microbes, demonstrating that the methane-oxidizing community supported a complex trophic network. Our results provide valuable eco-physiological insights into this specialized microbial community performing an ecosystem function of global relevance.
Collapse
Affiliation(s)
- Martin Taubert
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger Str. 159 07743, Jena, Germany.,School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Carolina Grob
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Andrew Crombie
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Alexandra M Howat
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Oliver J Burns
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Miriam Weber
- HYDRA Marine Sciences GmbH, Sinzheim, Germany.,HYDRA Field Station Elba, Italy.,Microsensor Group, Max Plank Institute for Marine Microbiology, 28359, Celsiusstr. 1, Bremen, Germany
| | - Christian Lott
- HYDRA Marine Sciences GmbH, Sinzheim, Germany.,HYDRA Field Station Elba, Italy.,Department of Symbiosis, Max Plank Institute for Marine Microbiology, 28359, Celsiusstr. 1, Bremen, Germany
| | - Anne-Kristin Kaster
- Institute for Biological Interfaces (IBG5), Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Karlsruhe, Germany.,Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, 38124, Inhoffenstrasse 7B, Braunschweig, Germany
| | - John Vollmers
- Institute for Biological Interfaces (IBG5), Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Karlsruhe, Germany.,Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, 38124, Inhoffenstrasse 7B, Braunschweig, 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, 04103, Brüderstraße 32, Leipzig, Germany.,Department of Chemistry and Bioscience, University of Aalborg, 9220, Fredrik Bajers Vej 7H, Aalborg East, Denmark
| | - Yin Chen
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - John Colin Murrell
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| |
Collapse
|
31
|
Ouyang WY, Su JQ, Richnow HH, Adrian L. Identification of dominant sulfamethoxazole-degraders in pig farm-impacted soil by DNA and protein stable isotope probing. ENVIRONMENT INTERNATIONAL 2019; 126:118-126. [PMID: 30797101 DOI: 10.1016/j.envint.2019.02.001] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 01/31/2019] [Accepted: 02/01/2019] [Indexed: 05/27/2023]
Abstract
Increasing introduction of antibiotic residues from humans and animal farming into the environment impacts the functioning of natural ecosystems and significantly contributes to the propagation of antibiotic resistance. Microbial degradation is the major sink of antibiotics in soil but the identification of in situ degrading populations is challenging. Here, we investigated sulfamethoxazole-degrading bacteria in soil microcosms by culture-independent DNA and protein stable isotope probing. 0.5% of the carbon from 13C6-labeled sulfamethoxazole amended to soil microcosms was transformed to 13CO2 demonstrating partial mineralization of the antibiotic. DNA stable isotope probing revealed incorporation of 13C from 13C6-labeled sulfamethoxazole into Actinobacteria and among them into the families Intrasporangiaceae, Nocardioidaceae, and Gaiellaceae and the order Solirubrobacterales. Protein stable isotope probing demonstrated the incorporation of 13C from 13C6-labeled sulfamethoxazole into proteins of bacteria of the families Intrasporangiaceae, Nocardioidaceae and the order Solirubrobacterales, which is consistent with the results of DNA stable isotope probing. The 13C abundance of 60 to 80% in several taxonomically relevant proteins indicated that Intrasporangiaceae directly acquired carbon from 13C6-labeled sulfamethoxazole. The results highlight the crucial role of yet-uncultivated indigenous bacteria for antibiotics degradation, and the potential of cultivation-independent stable isotope based molecular approaches to elucidate the structure of antibiotic-degrading populations in complex microbial communities under natural conditions.
Collapse
Affiliation(s)
- Wei-Ying Ouyang
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany; Chair of Geobiotechnology, Technische Universität Berlin, Berlin, Germany
| | - Jian-Qiang Su
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China.
| | - Hans H Richnow
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Lorenz Adrian
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany; Chair of Geobiotechnology, Technische Universität Berlin, Berlin, Germany
| |
Collapse
|
32
|
Using proteins to study how microbes contribute to soil ecosystem services: The current state and future perspectives of soil metaproteomics. J Proteomics 2019; 198:50-58. [DOI: 10.1016/j.jprot.2018.11.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 11/08/2018] [Accepted: 11/12/2018] [Indexed: 02/07/2023]
|
33
|
Blue carbon potential of coastal wetland restoration varies with inundation and rainfall. Sci Rep 2019; 9:4368. [PMID: 30867475 PMCID: PMC6416304 DOI: 10.1038/s41598-019-40763-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 02/19/2019] [Indexed: 01/29/2023] Open
Abstract
There is a growing interest in how the management of 'blue carbon' sequestered by coastal wetlands can influence global greenhouse gas (GHG) budgets. A promising intervention is through restoring tidal exchange to impounded coastal wetlands for reduced methane (CH4) emissions. We monitored an impounded wetland's GHG flux (CO2 and CH4) prior to and following tidal reinstatement. We found that biogeochemical responses varied across an elevation gradient. The low elevation zone experienced a greater increase in water level and an associated greater marine transition in the sediment microbial community (16 S rRNA) than the high elevation zone. The low elevation zone's GHG emissions had a reduced sustained global warming potential of 264 g m-2 yr-1 CO2-e over 100 years, and it increased to 351 g m-2 yr-1 with the removal of extreme rain events. However, emission benefits were achieved through a reduction in CO2 emissions, not CH4 emissions. Overall, the wetland shifted from a prior CH4 sink (-0.07 to -1.74 g C m-2 yr-1) to a variable sink or source depending on the elevation site and rainfall. This highlights the need to consider a wetland's initial GHG emissions, elevation and future rainfall trends when assessing the efficacy of tidal reinstatement for GHG emission control.
Collapse
|
34
|
Abstract
Stable isotope probing combined with metaproteomics enables the detection and characterization of active key species in microbial populations under near-natural conditions, which greatly helps to understand the metabolic functions of complex microbial communities. This is achieved by providing growth substrates labeled with heavy isotopes such as 13C, which will be assimilated into microbial biomass. After subsequent extraction of proteins and proteolytic cleavage into peptides, the heavy isotope enrichment can be detected by high-resolution mass spectrometric analysis, and linked to the functional and taxonomic characterization of these biomarkers. Here we provide protocols for obtaining isotopically labeled proteins and for downstream SIP-metaproteomics analysis.
Collapse
Affiliation(s)
- Martin Taubert
- Faculty of Biological Sciences, Institute of Biodiversity, Friedrich Schiller University Jena, Jena, Germany.
| |
Collapse
|
35
|
Fermentative Spirochaetes mediate necromass recycling in anoxic hydrocarbon-contaminated habitats. ISME JOURNAL 2018; 12:2039-2050. [PMID: 29849169 PMCID: PMC6052044 DOI: 10.1038/s41396-018-0148-3] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Revised: 03/23/2018] [Accepted: 03/29/2018] [Indexed: 11/08/2022]
Abstract
Spirochaetes are frequently detected in anoxic hydrocarbon- and organohalide-polluted groundwater, but their role in such ecosystems has remained unclear. To address this, we studied a sulfate-reducing, naphthalene-degrading enrichment culture, mainly comprising the sulfate reducer Desulfobacterium N47 and the rod-shaped Spirochete Rectinema cohabitans HM. Genome sequencing and proteome analysis suggested that the Spirochete is an obligate fermenter that catabolizes proteins and carbohydrates, resulting in acetate, ethanol, and molecular hydrogen (H2) production. Physiological experiments inferred that hydrogen is an important link between the two bacteria in the enrichment culture, with H2 derived from fermentation by R. cohabitans used as reductant for sulfate reduction by Desulfobacterium N47. Differential proteomics and physiological experiments showed that R. cohabitans utilizes biomass (proteins and carbohydrates) released from dead cells of Desulfobacterium N47. Further comparative and community genome analyses indicated that other Rectinema phylotypes are widespread in contaminated environments and may perform a hydrogenogenic fermentative lifestyle similar to R. cohabitans. Together, these findings indicate that environmental Spirochaetes scavenge detrital biomass and in turn drive necromass recycling at anoxic hydrocarbon-contaminated sites and potentially other habitats.
Collapse
|
36
|
Keller AH, Kleinsteuber S, Vogt C. Anaerobic Benzene Mineralization by Nitrate-Reducing and Sulfate-Reducing Microbial Consortia Enriched From the Same Site: Comparison of Community Composition and Degradation Characteristics. MICROBIAL ECOLOGY 2018; 75:941-953. [PMID: 29124312 DOI: 10.1007/s00248-017-1100-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 10/26/2017] [Indexed: 05/22/2023]
Abstract
Benzene mineralization under nitrate-reducing conditions was successfully established in an on-site reactor continuously fed with nitrate and sulfidic, benzene-containing groundwater extracted from a contaminated aquifer. Filling material from the reactor columns was used to set up anoxic enrichment cultures in mineral medium with benzene as electron donor and sole organic carbon source and nitrate as electron acceptor. Benzene degradation characteristics and community composition under nitrate-reducing conditions were monitored and compared to those of a well-investigated benzene-mineralizing consortium enriched from the same column system under sulfate-reducing conditions. The nitrate-reducing cultures degraded benzene at a rate of 10.1 ± 1.7 μM d-1, accompanied by simultaneous reduction of nitrate to nitrite. The previously studied sulfate-reducing culture degraded benzene at similar rates. Carbon and hydrogen stable isotope enrichment factors determined for nitrate-dependent benzene degradation differed significantly from those of the sulfate-reducing culture (ΛH/C nitrate = 12 ± 3 compared to ΛH/C sulfate = 28 ± 3), indicating different benzene activation mechanisms under the two conditions. The nitrate-reducing community was mainly composed of Betaproteobacteria, Ignavibacteria, and Anaerolineae. Azoarcus and a phylotype related to clone Dok59 (Rhodocyclaceae) were the dominant genera, indicating an involvement in nitrate-dependent benzene degradation. The primary benzene degrader of the sulfate-reducing consortium, a phylotype belonging to the Peptococcaceae, was absent in the nitrate-reducing consortium.
Collapse
Affiliation(s)
- Andreas H Keller
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Permoserstraße 15, 04318, Leipzig, Germany
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Permoserstraße 15, 04318, Leipzig, Germany
| | - Sabine Kleinsteuber
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Permoserstraße 15, 04318, Leipzig, Germany
| | - Carsten Vogt
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Permoserstraße 15, 04318, Leipzig, Germany.
| |
Collapse
|
37
|
A benzene-degrading nitrate-reducing microbial consortium displays aerobic and anaerobic benzene degradation pathways. Sci Rep 2018. [PMID: 29540736 PMCID: PMC5852087 DOI: 10.1038/s41598-018-22617-x] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
In this study, we report transcription of genes involved in aerobic and anaerobic benzene degradation pathways in a benzene-degrading denitrifying continuous culture. Transcripts associated with the family Peptococcaceae dominated all samples (21-36% relative abundance) indicating their key role in the community. We found a highly transcribed gene cluster encoding a presumed anaerobic benzene carboxylase (AbcA and AbcD) and a benzoate-coenzyme A ligase (BzlA). Predicted gene products showed >96% amino acid identity and similar gene order to the corresponding benzene degradation gene cluster described previously, providing further evidence for anaerobic benzene activation via carboxylation. For subsequent benzoyl-CoA dearomatization, bam-like genes analogous to the ones found in other strict anaerobes were transcribed, whereas gene transcripts involved in downstream benzoyl-CoA degradation were mostly analogous to the ones described in facultative anaerobes. The concurrent transcription of genes encoding enzymes involved in oxygenase-mediated aerobic benzene degradation suggested oxygen presence in the culture, possibly formed via a recently identified nitric oxide dismutase (Nod). Although we were unable to detect transcription of Nod-encoding genes, addition of nitrite and formate to the continuous culture showed indication for oxygen production. Such an oxygen production would enable aerobic microbes to thrive in oxygen-depleted and nitrate-containing subsurface environments contaminated with hydrocarbons.
Collapse
|
38
|
Taubert M, Stöckel S, Geesink P, Girnus S, Jehmlich N, von Bergen M, Rösch P, Popp J, Küsel K. Tracking active groundwater microbes with D2O labelling to understand their ecosystem function. Environ Microbiol 2017; 20:369-384. [DOI: 10.1111/1462-2920.14010] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 11/16/2017] [Indexed: 11/30/2022]
Affiliation(s)
- Martin Taubert
- Aquatic Geomicrobiology, Institute of Biodiversity; Friedrich Schiller University Jena, Dornburger Str. 159; 07743 Jena Germany
| | - Stephan Stöckel
- Institute of Physical Chemistry and Abbe Center of Photonics; Friedrich Schiller University Jena, Helmholtzweg 4; 07743 Jena Germany
| | - Patricia Geesink
- Aquatic Geomicrobiology, Institute of Biodiversity; Friedrich Schiller University Jena, Dornburger Str. 159; 07743 Jena Germany
| | - Sophie Girnus
- Institute of Physical Chemistry and Abbe Center of Photonics; Friedrich Schiller University Jena, Helmholtzweg 4; 07743 Jena Germany
| | - Nico Jehmlich
- Department of Molecular Systems Biology; Helmholtz Centre for Environmental Research - UFZ, Permoserstrasse 15; 04318 Leipzig Germany
| | - Martin von Bergen
- Department of Molecular Systems Biology; Helmholtz Centre for Environmental Research - UFZ, Permoserstrasse 15; 04318 Leipzig Germany
- Institute of Biochemistry, Pharmacy and Psychology; University of Leipzig, Brüderstraße 32; 04103 Leipzig Germany
- Department of Chemistry and Bioscience; University of Aalborg, Fredrik Bajers Vej 7H; 9220 Aalborg East Denmark
| | - Petra Rösch
- Institute of Physical Chemistry and Abbe Center of Photonics; Friedrich Schiller University Jena, Helmholtzweg 4; 07743 Jena Germany
| | - Jürgen Popp
- Institute of Physical Chemistry and Abbe Center of Photonics; Friedrich Schiller University Jena, Helmholtzweg 4; 07743 Jena Germany
- Leibniz-Institute of Photonic Technology, Albert-Einstein-Straße 9; 07745 Jena Germany
| | - Kirsten Küsel
- Aquatic Geomicrobiology, Institute of Biodiversity; Friedrich Schiller University Jena, Dornburger Str. 159; 07743 Jena Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5E; 04103 Leipzig Germany
| |
Collapse
|
39
|
High reactivity of deep biota under anthropogenic CO 2 injection into basalt. Nat Commun 2017; 8:1063. [PMID: 29051484 PMCID: PMC5648843 DOI: 10.1038/s41467-017-01288-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 09/01/2017] [Indexed: 11/21/2022] Open
Abstract
Basalts are recognized as one of the major habitats on Earth, harboring diverse and active microbial populations. Inconsistently, this living component is rarely considered in engineering operations carried out in these environments. This includes carbon capture and storage (CCS) technologies that seek to offset anthropogenic CO2 emissions into the atmosphere by burying this greenhouse gas in the subsurface. Here, we show that deep ecosystems respond quickly to field operations associated with CO2 injections based on a microbiological survey of a basaltic CCS site. Acidic CO2-charged groundwater results in a marked decrease (by ~ 2.5–4) in microbial richness despite observable blooms of lithoautotrophic iron-oxidizing Betaproteobacteria and degraders of aromatic compounds, which hence impact the aquifer redox state and the carbon fate. Host-basalt dissolution releases nutrients and energy sources, which sustain the growth of autotrophic and heterotrophic species whose activities may have consequences on mineral storage. The impacts of carbon capture and storage (CCS) on subsurface microorganisms are poorly understood. Here, the authors show that deep ecosystems respond quickly to CO2 injections and that the environmental consequences of their metabolic activities need to be properly assessed for sustainable CCS in basalt.
Collapse
|
40
|
van der Waals MJ, Atashgahi S, da Rocha UN, van der Zaan BM, Smidt H, Gerritse J. Benzene degradation in a denitrifying biofilm reactor: activity and microbial community composition. Appl Microbiol Biotechnol 2017; 101:5175-5188. [PMID: 28321487 PMCID: PMC5486827 DOI: 10.1007/s00253-017-8214-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 02/27/2017] [Accepted: 03/04/2017] [Indexed: 11/26/2022]
Abstract
Benzene is an aromatic compound and harmful for the environment. Biodegradation of benzene can reduce the toxicological risk after accidental or controlled release of this chemical in the environment. In this study, we further characterized an anaerobic continuous biofilm culture grown for more than 14 years on benzene with nitrate as electron acceptor. We determined steady state degradation rates, microbial community composition dynamics in the biofilm, and the initial anaerobic benzene degradation reactions. Benzene was degraded at a rate of 0.15 μmol/mg protein/day and a first-order rate constant of 3.04/day which was fourfold higher than rates reported previously. Bacteria belonging to the Peptococcaceae were found to play an important role in this anaerobic benzene-degrading biofilm culture, but also members of the Anaerolineaceae were predicted to be involved in benzene degradation or benzene metabolite degradation based on Illumina MiSeq analysis of 16S ribosomal RNA genes. Biomass retention in the reactor using a filtration finger resulted in reduction of benzene degradation capacity. Detection of the benzene carboxylase encoding gene, abcA, and benzoic acid in the culture vessel indicated that benzene degradation proceeds through an initial carboxylation step.
Collapse
Affiliation(s)
- Marcelle J van der Waals
- Deltares, Subsurface and Groundwater Systems, Princetonlaan 6, 3584 CB, Utrecht, The Netherlands.
- Wageningen University & Research, Laboratory of Microbiology, Stippeneng 4, 6708 WE, Wageningen, The Netherlands.
| | - Siavash Atashgahi
- Wageningen University & Research, Laboratory of Microbiology, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Ulisses Nunes da Rocha
- VU University of Amsterdam, Department of Molecular Cell Physiology, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands
| | - Bas M van der Zaan
- Deltares, Subsurface and Groundwater Systems, Princetonlaan 6, 3584 CB, Utrecht, The Netherlands
| | - Hauke Smidt
- Wageningen University & Research, Laboratory of Microbiology, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Jan Gerritse
- Deltares, Subsurface and Groundwater Systems, Princetonlaan 6, 3584 CB, Utrecht, The Netherlands
| |
Collapse
|
41
|
Kantor RS, Huddy RJ, Iyer R, Thomas BC, Brown CT, Anantharaman K, Tringe S, Hettich RL, Harrison STL, Banfield JF. Genome-Resolved Meta-Omics Ties Microbial Dynamics to Process Performance in Biotechnology for Thiocyanate Degradation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:2944-2953. [PMID: 28139919 DOI: 10.1021/acs.est.6b04477] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Remediation of industrial wastewater is important for preventing environmental contamination and enabling water reuse. Biological treatment for one industrial contaminant, thiocyanate (SCN-), relies upon microbial hydrolysis, but this process is sensitive to high loadings. To examine the activity and stability of a microbial community over increasing SCN- loadings, we established and operated a continuous-flow bioreactor fed increasing loadings of SCN-. A second reactor was fed ammonium sulfate to mimic breakdown products of SCN-. Biomass was sampled from both reactors for metagenomics and metaproteomics, yielding a set of genomes for 144 bacteria and one rotifer that constituted the abundant community in both reactors. We analyzed the metabolic potential and temporal dynamics of these organisms across the increasing loadings. In the SCN- reactor, Thiobacillus strains capable of SCN- degradation were highly abundant, whereas the ammonium sulfate reactor contained nitrifiers and heterotrophs capable of nitrate reduction. Key organisms in the SCN- reactor expressed proteins involved in SCN- degradation, sulfur oxidation, carbon fixation, and nitrogen removal. Lower performance at higher loadings was linked to changes in microbial community composition. This work provides an example of how meta-omics can increase our understanding of industrial wastewater treatment and inform iterative process design and development.
Collapse
Affiliation(s)
- Rose S Kantor
- Department of Plant and Microbial Biology, University of California , Berkeley, California 94720, United States
| | - Robert J Huddy
- Centre for Bioprocess Engineering Research, Department of Chemical Engineering, University of Cape Town , Rondebosch, 7701, South Africa
| | - Ramsunder Iyer
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
- Graduate School of Genome Science and Technology, University of Tennessee , Knoxville, Tennessee 37996, United States
| | - Brian C Thomas
- Department of Earth and Planetary Sciences, University of California , Berkeley, California 94720, United States
| | - Christopher T Brown
- Department of Plant and Microbial Biology, University of California , Berkeley, California 94720, United States
| | - Karthik Anantharaman
- Department of Earth and Planetary Sciences, University of California , Berkeley, California 94720, United States
| | - Susannah Tringe
- Joint Genome Institute , Walnut Creek, California 94598, United States
| | - Robert L Hettich
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Susan T L Harrison
- Centre for Bioprocess Engineering Research, Department of Chemical Engineering, University of Cape Town , Rondebosch, 7701, South Africa
| | - Jillian F Banfield
- Department of Earth and Planetary Sciences, University of California , Berkeley, California 94720, United States
- Department of Environmental Science, Policy, and Management, University of California , Berkeley, California 94720, United States
| |
Collapse
|
42
|
Chiu H, Verpoort F, Liu J, Chang Y, Kao C. Using intrinsic bioremediation for petroleum–hydrocarbon contaminated groundwater cleanup and migration containment: Effectiveness and mechanism evaluation. J Taiwan Inst Chem Eng 2017. [DOI: 10.1016/j.jtice.2017.01.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
43
|
Ranchou‐Peyruse M, Gasc C, Guignard M, Aüllo T, Dequidt D, Peyret P, Ranchou‐Peyruse A. The sequence capture by hybridization: a new approach for revealing the potential of mono-aromatic hydrocarbons bioattenuation in a deep oligotrophic aquifer. Microb Biotechnol 2017; 10:469-479. [PMID: 27766749 PMCID: PMC5328808 DOI: 10.1111/1751-7915.12426] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 09/15/2016] [Accepted: 09/18/2016] [Indexed: 01/04/2023] Open
Abstract
The formation water of a deep aquifer (853 m of depth) used for geological storage of natural gas was sampled to assess the mono-aromatic hydrocarbons attenuation potential of the indigenous microbiota. The study of bacterial diversity suggests that Firmicutes and, in particular, sulphate-reducing bacteria (Peptococcaceae) predominate in this microbial community. The capacity of the microbial community to biodegrade toluene and m- and p-xylenes was demonstrated using a culture-based approach after several hundred days of incubation. In order to reveal the potential for biodegradation of these compounds within a shorter time frame, an innovative approach named the solution hybrid selection method, which combines sequence capture by hybridization and next-generation sequencing, was applied to the same original water sample. The bssA and bssA-like genes were investigated as they are considered good biomarkers for the potential of toluene and xylene biodegradation. Unlike a PCR approach which failed to detect these genes directly from formation water, this innovative strategy demonstrated the presence of the bssA and bssA-like genes in this oligotrophic ecosystem, probably harboured by Peptococcaceae. The sequence capture by hybridization shows significant potential to reveal the presence of genes of functional interest which have low-level representation in the biosphere.
Collapse
Affiliation(s)
- Magali Ranchou‐Peyruse
- Université de Pau et des Pays de l'AdourEquipe Environnement et Microbiologie, IPREM‐CNRS 5254F‐64013PauFrance
| | - Cyrielle Gasc
- Université d'AuvergneEA 4678 CIDAM63001Clermont‐FerrandFrance
| | - Marion Guignard
- Université de Pau et des Pays de l'AdourEquipe Environnement et Microbiologie, IPREM‐CNRS 5254F‐64013PauFrance
| | - Thomas Aüllo
- TIGF – Transport et Infrastructures Gaz France40 Avenue de l'Europe, CS2052264000PauFrance
| | - David Dequidt
- STORENGY – Geosciences DepartmentBois‐ColombesFrance
| | - Pierre Peyret
- Université d'AuvergneEA 4678 CIDAM63001Clermont‐FerrandFrance
| | - Anthony Ranchou‐Peyruse
- Université de Pau et des Pays de l'AdourEquipe Environnement et Microbiologie, IPREM‐CNRS 5254F‐64013PauFrance
| |
Collapse
|
44
|
Denitrification synergized with ANAMMOX for the anaerobic degradation of benzene: performance and microbial community structure. Appl Microbiol Biotechnol 2017; 101:4315-4325. [DOI: 10.1007/s00253-017-8166-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 01/25/2017] [Accepted: 02/05/2017] [Indexed: 12/21/2022]
|
45
|
Jameson E, Taubert M, Coyotzi S, Chen Y, Eyice Ö, Schäfer H, Murrell JC, Neufeld JD, Dumont MG. DNA-, RNA-, and Protein-Based Stable-Isotope Probing for High-Throughput Biomarker Analysis of Active Microorganisms. Methods Mol Biol 2017; 1539:57-74. [PMID: 27900684 DOI: 10.1007/978-1-4939-6691-2_5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Stable-isotope probing (SIP) enables researchers to target active populations within complex microbial communities, which is achieved by providing growth substrates enriched in heavy isotopes, usually in the form of 13C, 18O, or 15N. After growth on the substrate and subsequent extraction of microbial biomarkers, typically nucleic acids or proteins, the SIP technique is used for the recovery and analysis of isotope-labeled biomarkers from active microbial populations. In the years following the initial development of DNA- and RNA-based SIP, it was common practice to characterize labeled populations by targeted gene analysis. Such approaches usually involved fingerprint-based analyses or sequencing of clone libraries containing 16S rRNA genes or functional marker gene amplicons. Although molecular fingerprinting remains a valuable approach for rapid confirmation of isotope labeling, recent advances in sequencing technology mean that it is possible to obtain affordable and comprehensive amplicon profiles, metagenomes, or metatranscriptomes from SIP experiments. Not only can the abundance of microbial groups be inferred from metagenomes, but researchers can bin, assemble, and explore individual genomes to build hypotheses about the metabolic capabilities of labeled microorganisms. Analysis of labeled mRNA is a more recent advance that can provide independent metatranscriptome-based analysis of active microorganisms. The power of metatranscriptomics is that mRNA abundance often correlates closely with the corresponding activity of encoded enzymes, thus providing insight into microbial metabolism at the time of sampling. Together, these advances have improved the sensitivity of SIP methods and allow the use of labeled substrates at ecologically relevant concentrations. Particularly as methods improve and costs continue to drop, we expect that the integration of SIP with multiple omics-based methods will become prevalent components of microbial ecology studies, leading to further breakthroughs in our understanding of novel microbial populations and elucidation of the metabolic function of complex microbial communities. In this chapter we provide protocols for obtaining labeled DNA, RNA, and proteins that can be used for downstream omics-based analyses.
Collapse
Affiliation(s)
- Eleanor Jameson
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Martin Taubert
- Institute of Ecology, Friedrich Schiller University Jena, Jena, Germany
| | - Sara Coyotzi
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Yin Chen
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Özge Eyice
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Hendrik Schäfer
- School of Life Sciences, University of Warwick, Coventry, UK
| | - J Colin Murrell
- School of Environmental Sciences, University of East Anglia, Norwich, UK
| | - Josh D Neufeld
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Marc G Dumont
- Centre for Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK.
| |
Collapse
|
46
|
Lueders T. The ecology of anaerobic degraders of BTEX hydrocarbons in aquifers. FEMS Microbiol Ecol 2016; 93:fiw220. [PMID: 27810873 PMCID: PMC5400083 DOI: 10.1093/femsec/fiw220] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 06/10/2016] [Indexed: 12/24/2022] Open
Abstract
The degradation of benzene, toluene, ethylbenzene and xylene (BTEX) contaminants in groundwater relies largely on anaerobic processes. While the physiology and biochemistry of selected relevant microbes have been intensively studied, research has now started to take the generated knowledge back to the field, in order to trace the populations truly responsible for the anaerobic degradation of BTEX hydrocarbons in situ and to unravel their ecology in contaminated aquifers. Here, recent advances in our knowledge of the identity, diversity and ecology of microbes involved in these important ecosystem services are discussed. At several sites, distinct lineages within the Desulfobulbaceae, the Rhodocyclaceae and the Gram-positive Peptococcaceae have been shown to dominate the degradation of different BTEX hydrocarbons. Especially for the functional guild of anaerobic toluene degraders, specific molecular detection systems have been developed, allowing researchers to trace their diversity and distribution in contaminated aquifers. Their populations appear enriched in hot spots of biodegradation in situ. 13C-labelling experiments have revealed unexpected pathways of carbon sharing and obligate syntrophic interactions to be relevant in degradation. Together with feedback mechanisms between abiotic and biotic habitat components, this promotes an enhanced ecological perspective of the anaerobic degradation of BTEX hydrocarbons, as well as its incorporation into updated concepts for site monitoring and bioremediation.
Collapse
Affiliation(s)
- Tillmann Lueders
- Institute of Groundwater Ecology, Helmholtz Zentrum München-German Research Center for Environmental Health, 85764 Neuherberg, Germany
| |
Collapse
|
47
|
Kästner M, Nowak KM, Miltner A, Schäffer A. (Multiple) Isotope probing approaches to trace the fate of environmental chemicals and the formation of non-extractable ‘bound’ residues. Curr Opin Biotechnol 2016; 41:73-82. [DOI: 10.1016/j.copbio.2016.05.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 05/12/2016] [Accepted: 05/16/2016] [Indexed: 10/21/2022]
|
48
|
Mosbæk F, Kjeldal H, Mulat DG, Albertsen M, Ward AJ, Feilberg A, Nielsen JL. Identification of syntrophic acetate-oxidizing bacteria in anaerobic digesters by combined protein-based stable isotope probing and metagenomics. THE ISME JOURNAL 2016; 10:2405-18. [PMID: 27128991 PMCID: PMC5030692 DOI: 10.1038/ismej.2016.39] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Revised: 01/22/2016] [Accepted: 02/02/2016] [Indexed: 12/31/2022]
Abstract
Inhibition of anaerobic digestion through accumulation of volatile fatty acids occasionally occurs as the result of unbalanced growth between acidogenic bacteria and methanogens. A fast recovery is a prerequisite for establishing an economical production of biogas. However, very little is known about the microorganisms facilitating this recovery. In this study, we investigated the organisms involved by a novel approach of mapping protein-stable isotope probing (protein-SIP) onto a binned metagenome. Under simulation of acetate accumulation conditions, formations of (13)C-labeled CO2 and CH4 were detected immediately following incubation with [U-(13)C]acetate, indicating high turnover rate of acetate. The identified (13)C-labeled peptides were mapped onto a binned metagenome for improved identification of the organisms involved. The results revealed that Methanosarcina and Methanoculleus were actively involved in acetate turnover, as were five subspecies of Clostridia. The acetate-consuming organisms affiliating with Clostridia all contained the FTFHS gene for formyltetrahydrofolate synthetase, a key enzyme for reductive acetogenesis, indicating that these organisms are possible syntrophic acetate-oxidizing (SAO) bacteria that can facilitate acetate consumption via SAO, coupled with hydrogenotrophic methanogenesis (SAO-HM). This study represents the first study applying protein-SIP for analysis of complex biogas samples, a promising method for identifying key microorganisms utilizing specific pathways.
Collapse
Affiliation(s)
- Freya Mosbæk
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Henrik Kjeldal
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Daniel G Mulat
- Department of Engineering, Aarhus University, Aarhus, Denmark
| | - Mads Albertsen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Alastair J Ward
- Department of Engineering, Aarhus University, Aarhus, Denmark
| | - Anders Feilberg
- Department of Engineering, Aarhus University, Aarhus, Denmark
| | - Jeppe L Nielsen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| |
Collapse
|
49
|
Adrian L, Marco-Urrea E. Isotopes in geobiochemistry: tracing metabolic pathways in microorganisms of environmental relevance with stable isotopes. Curr Opin Biotechnol 2016; 41:19-25. [DOI: 10.1016/j.copbio.2016.03.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Revised: 03/02/2016] [Accepted: 03/18/2016] [Indexed: 11/25/2022]
|
50
|
Berlendis S, Ranchou-Peyruse M, Fardeau ML, Lascourrèges JF, Joseph M, Ollivier B, Aüllo T, Dequidt D, Magot M, Ranchou-Peyruse A. Desulfotomaculum aquiferis sp. nov. and Desulfotomaculum profundi sp. nov., isolated from a deep natural gas storage aquifer. Int J Syst Evol Microbiol 2016; 66:4329-4338. [PMID: 27473224 DOI: 10.1099/ijsem.0.001352] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Two novel strictly anaerobic bacteria, strains Bs105T and Bs107T, were isolated from a deep aquifer-derived hydrocarbonoclastic community. The cells were rod-shaped, not motile and had terminal spores. Phylogenetic affiliation and physiological properties revealed that these isolates belong to two novel species of the genus Desulfotomaculum. Optimal growth temperatures for strains Bs105T and Bs107T were 42 and 45 °C, respectively. The estimated G+C content of the genomic DNA was 42.9 and 48.7 mol%. For both strains, the major cellular fatty acid was palmitate (C16 : 0). Specific carbon fatty acid signatures of Gram-positive bacteria (iso-C17 : 0) and sulfate-reducing bacteria (C17 : 0cyc) were also detected. An insertion was revealed in one of the two 16S rRNA gene copies harboured by strain Bs107T. Similar insertions have previously been highlighted among moderately thermophilic species of the genus Desulfotomaculum. Both strains shared the ability to oxidize aromatic acids (Bs105T: hydroquinone, acetophenone, para-toluic acid, 2-phenylethanol, trans-cinnamic acid, 4-hydroxybenzaldehyde, benzyl alcohol, benzoic acid 4-hydroxybutyl ester; Bs107T: ortho-toluic acid, benzoic acid 4-hydroxybutyl ester). The names Desulfotomaculum aquiferis sp. nov. and Desulfotomaculum profundi sp. nov. are proposed for the type strains Bs105T (=DSM 24088T=JCM 31386T) and Bs107T (=DSM 24093T=JCM 31387T).
Collapse
Affiliation(s)
- Sabrina Berlendis
- Université de Pau et des Pays de l'Adour, CNRS, IPREM UMR 5254, Equipe Environnement et Microbiologie, Pau 64013, France.,School of Earth and Ocean Sciences, Main building, Park Place, Cardiff University, Cardiff CF10 3AT, UK
| | - Magali Ranchou-Peyruse
- Université de Pau et des Pays de l'Adour, CNRS, IPREM UMR 5254, Equipe Environnement et Microbiologie, Pau 64013, France
| | - Marie-Laure Fardeau
- Aix-Marseille Université, Université du Sud Toulon-Var, CNRS/INSU, IRD, MIO, UM 110, 13288 Marseille Cedex 09, France
| | | | - Manon Joseph
- Aix-Marseille Université, Université du Sud Toulon-Var, CNRS/INSU, IRD, MIO, UM 110, 13288 Marseille Cedex 09, France
| | - Bernard Ollivier
- Aix-Marseille Université, Université du Sud Toulon-Var, CNRS/INSU, IRD, MIO, UM 110, 13288 Marseille Cedex 09, France
| | - Thomas Aüllo
- TIGF - Transport et Infrastructures Gaz France, 40 Avenue de l'Europe, CS20522, Pau 64000, France
| | - David Dequidt
- Storengy - Geosciences Department, Bois-Colombes, France
| | - Michel Magot
- Université de Pau et des Pays de l'Adour, CNRS, IPREM UMR 5254, Equipe Environnement et Microbiologie, Pau 64013, France
| | - Anthony Ranchou-Peyruse
- Université de Pau et des Pays de l'Adour, CNRS, IPREM UMR 5254, Equipe Environnement et Microbiologie, Pau 64013, France
| |
Collapse
|