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Mara P, Geller-McGrath D, Suter E, Taylor GT, Pachiadaki MG, Edgcomb VP. Plasmid-Borne Biosynthetic Gene Clusters within a Permanently Stratified Marine Water Column. Microorganisms 2024; 12:929. [PMID: 38792759 PMCID: PMC11123730 DOI: 10.3390/microorganisms12050929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Revised: 04/22/2024] [Accepted: 04/29/2024] [Indexed: 05/26/2024] Open
Abstract
Plasmids are mobile genetic elements known to carry secondary metabolic genes that affect the fitness and survival of microbes in the environment. Well-studied cases of plasmid-encoded secondary metabolic genes in marine habitats include toxin/antitoxin and antibiotic biosynthesis/resistance genes. Here, we examine metagenome-assembled genomes (MAGs) from the permanently-stratified water column of the Cariaco Basin for integrated plasmids that encode biosynthetic gene clusters of secondary metabolites (smBGCs). We identify 16 plasmid-borne smBGCs in MAGs associated primarily with Planctomycetota and Pseudomonadota that encode terpene-synthesizing genes, and genes for production of ribosomal and non-ribosomal peptides. These identified genes encode for secondary metabolites that are mainly antimicrobial agents, and hence, their uptake via plasmids may increase the competitive advantage of those host taxa that acquire them. The ecological and evolutionary significance of smBGCs carried by prokaryotes in oxygen-depleted water columns is yet to be fully elucidated.
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Affiliation(s)
- Paraskevi Mara
- Geology & Geophysics Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA;
| | - David Geller-McGrath
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA; (D.G.-M.); (M.G.P.)
| | - Elizabeth Suter
- Biology, Chemistry and Environmental Science Department, Molloy University, New York, NY 11570, USA;
| | - Gordon T. Taylor
- School of Marine, Atmospheric and Sustainability Sciences, Stony Brook University, New York, NY 11794, USA;
| | - Maria G. Pachiadaki
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA; (D.G.-M.); (M.G.P.)
| | - Virginia P. Edgcomb
- Geology & Geophysics Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA;
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2
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Gwak JH, Rhee SK, Park JW. Bacteria involved in the sulfur cycle in tarballs collected from the Alabama Gulf Coast. FEMS Microbiol Lett 2024; 371:fnae003. [PMID: 38228401 DOI: 10.1093/femsle/fnae003] [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: 11/12/2023] [Revised: 01/04/2024] [Accepted: 01/15/2024] [Indexed: 01/18/2024] Open
Abstract
Tarballs are formed from released or discharged crude oil containing sulfur compounds. A considerable amount and variety of sulfate-reducing bacteria (SRB) and sulfur-oxidizing bacteria (SOB) were identified in tarballs collected from the intertidal and supratidal zones of Alabama's Gulf beaches. Amplicon sequencing of the bacterial 16S rRNA gene showed that SRB were more abundantly distributed in the core than on the surface of tarballs, while no significant differences were observed in the distribution of SOB. To our best knowledge, this is the first report on the spatial distribution of diverse SRB and SOB in tarballs.
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Affiliation(s)
- Joo-Han Gwak
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Seowon-Gu, Cheongju 28644, Republic of Korea
| | - Sung-Keun Rhee
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Seowon-Gu, Cheongju 28644, Republic of Korea
| | - Joong-Wook Park
- Department of Biological and Environmental Sciences, Troy University, Troy, AL 36082, United States
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Deng Z, Chen H, Wang J, Zhang N, Han Z, Xie Y, Zhang X, Fang X, Yu H, Zhang D, Yue Z, Zhang C. Marine Dehalogenator and Its Chaperones: Microbial Duties and Responses in 2,4,6-Trichlorophenol Dechlorination. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023. [PMID: 37478352 DOI: 10.1021/acs.est.3c03738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/23/2023]
Abstract
Marine environments contain diverse halogenated organic compounds (HOCs), both anthropogenic and natural, nourishing a group of versatile organohalide-respiring bacteria (OHRB). Here, we identified a novel OHRB (Peptococcaceae DCH) with conserved motifs but phylogenetically diverse reductive dehalogenase catalytic subunit (RdhAs) from marine enrichment culture. Further analyses clearly demonstrate the horizontal gene transfer of rdhAs among marine OHRB. Moreover, 2,4,6-trichlorophenol (TCP) was dechlorinated to 2,4-dichlorophenol and terminated at 4-chlorophenol in culture. Dendrosporobacter and Methanosarcina were the two dominant genera, and the constructed and verified metabolic pathways clearly demonstrated that the former provided various substrates for other microbes, while the latter drew nutrients, but might provide little benefit to microbial dehalogenation. Furthermore, Dendrosporobacter could readily adapt to TCP, and sporulation-related proteins of Dendrosporobacter were significantly upregulated in TCP-free controls, whereas other microbes (e.g., Methanosarcina and Aminivibrio) became more active, providing insights into how HOCs shape microbial communities. Additionally, sulfate could affect the dechlorination of Peptococcaceae DCH, but not debromination. Considering their electron accessibility and energy generation, the results clearly demonstrate that bromophenols are more suitable than chlorophenols for the enrichment of OHRB in marine environments. This study will greatly enhance our understanding of marine OHRB (rdhAs), auxiliary microbes, and microbial HOC adaptive mechanisms.
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Affiliation(s)
- Zhaochao Deng
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan 316021, Zhejiang, China
| | - Haixin Chen
- BGI-Sanya, BGI-Shenzhen, Sanya 572025, China
| | - Jun Wang
- BGI-Sanya, BGI-Shenzhen, Sanya 572025, China
| | - Ning Zhang
- Department of Environmental Engineering, School of Chemical Engineering and Pharmacy, Henan University of Science and Technology, Luoyang 471000, Henan, China
| | - Zhiqiang Han
- Department of Marine Resources and Environment, Fishery College, Zhejiang Ocean University, Zhoushan 316002, Zhejiang, China
| | - Yeting Xie
- College of Environmental Science and Engineering, Guilin University of Technology, Guilin 541006, Guangxi, China
| | - Xiaoyan Zhang
- College of Environmental Science and Engineering, Guilin University of Technology, Guilin 541006, Guangxi, China
| | | | - Hao Yu
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan 316021, Zhejiang, China
| | - Dongdong Zhang
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan 316021, Zhejiang, China
| | - Zhen Yue
- BGI-Sanya, BGI-Shenzhen, Sanya 572025, China
| | - Chunfang Zhang
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan 316021, Zhejiang, China
- College of Environmental Science and Engineering, Guilin University of Technology, Guilin 541006, Guangxi, China
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Kimisto A, Muia AW, Ong'ondo GO, Ndung'u K. Molecular characterization of microorganisms with industrial potential for methane production in sludge from Kangemi sewage treatment plant, Nyeri county-Kenya. Heliyon 2023; 9:e15715. [PMID: 37234610 PMCID: PMC10205513 DOI: 10.1016/j.heliyon.2023.e15715] [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: 10/05/2022] [Revised: 04/18/2023] [Accepted: 04/20/2023] [Indexed: 05/28/2023] Open
Abstract
Microbial consortia under anaerobic conditions are involved in oxidizing organic matter in the sludge to produce methane gas. However, in developing countries like Kenya, these microbes have not been fully identified to target them for the efficient harnessing of biofuel. This study collected wet sludge from two anaerobic digestion lagoons 1 and 2 that were operational during sampling at Kangemi Sewage Treatment Plant, in Nyeri County, Kenya. DNA was extracted from samples using commercially available ZymoBIOMICS™ DNA Miniprep Kit and sequenced using Shotgun metagenomics. Samples were analyzed using MG-RAST software (Project ID: mgp100988), which allowed for identifying microorganisms directly involved in various stages of methanogenesis pathways. The study found hydrogenotrophic methanogens, such as Methanospirillum (32%), Methanobacterium (27%), Methanobrevibacter (27%), and Methanosarcina (32%), being predominant in the lagoon communities, whereas acetoclastic microorganisms such as the Methanoregula (22%) and the acetate oxidazing bacteria such as Clostridia (68%) were the key microbes for that pathway in the sewage digester sludge. Furthermore, Methanothermobacter (18%), Methanosarcina (21%), Methanosaeta (15%), and Methanospirillum (13%) carried out the methylotrophic pathway. In contrast, Methanosarcina (23%),Methanoregula (14%), methanosaeta (13%), and methnanoprevibacter (13%) seemed to play an important role in the final step of methane release. This study concluded that the sludge produced from the Nyeri-Kangemi WWTP harbors microbes with significant potential for biogas production. The study recommends a pilot study to investigate the efficiency of the identified microbes for biogas production.
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Affiliation(s)
- Allan.K. Kimisto
- Department of Biological Sciences, Egerton University, P.O Box 536- 20115 Egerton, Kenya
| | - Anastasia W. Muia
- Department of Biological Sciences, Egerton University, P.O Box 536- 20115 Egerton, Kenya
| | - Geoffrey O. Ong'ondo
- Department of Biological Sciences, Egerton University, P.O Box 536- 20115 Egerton, Kenya
| | - Kimani.C. Ndung'u
- Kenya Agricultural and Livestock Research Organisation (KALRO), Njoro Station, Private Bag 20107 Njoro, Kenya
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Prakash O, Mostafa A, Im S, Song YC, Kang S, Kim DH. Enhanced anaerobic treatment of sulfate-rich wastewater by electrical voltage application. BIORESOURCE TECHNOLOGY 2023; 369:128430. [PMID: 36464001 DOI: 10.1016/j.biortech.2022.128430] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 11/29/2022] [Accepted: 11/30/2022] [Indexed: 06/17/2023]
Abstract
Treatment of sulfate-rich wastewater with high methane recovery is a major concern due to sulfide inhibition. Here, an electrical voltage (EV) aims to enhance methanogenesis and sulfidogenesis to treat sulfate-rich wastewater. Two (control and EV-applied) reactors were operated with a gradual decrease in chemical oxygen demand (COD)/SO42- ratios (CSR). EV-applied reactor (EVR) demonstrated an increase of ∼30 % in methane production and ∼40 % in sulfate removal, compared to the control till CSR of 2.0. At CSR 1.0, the control failed, while EVR still exhibited a stable performance of 50 % COD-methane recovery. Microbial community results showed that the relative abundance of sulfate-reducing bacteria in EVR was 1.5 times higher than the control. Furthermore, higher relative abundance of dissimilatory sulfate reductase (>50 %) and Ni/Fe hydrogenase (x15) genes demonstrated an improved tolerance against H2S toxicity. This study highlights the importance of EV application by minimizing the byproduct inhibition in sulfate-rich wastewater.
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Affiliation(s)
- Om Prakash
- Department of Smart-city Engineering, Inha University, 100 Inha-ro, Michuhol-gu, Incheon 22212, Republic of Korea
| | - Alsayed Mostafa
- Department of Smart-city Engineering, Inha University, 100 Inha-ro, Michuhol-gu, Incheon 22212, Republic of Korea
| | - Seongwon Im
- Department of Smart-city Engineering, Inha University, 100 Inha-ro, Michuhol-gu, Incheon 22212, Republic of Korea
| | - Young-Chae Song
- Department of Environmental Engineering, Korea Maritime and Ocean University, Busan 49112, Republic of Korea
| | - Seoktae Kang
- Department of Civil and Environmental Engineering, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Dong-Hoon Kim
- Department of Smart-city Engineering, Inha University, 100 Inha-ro, Michuhol-gu, Incheon 22212, Republic of Korea.
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Denise R, Babor J, Gerlt JA, de Crécy-Lagard V. Pyridoxal 5'-phosphate synthesis and salvage in Bacteria and Archaea: predicting pathway variant distributions and holes. Microb Genom 2023; 9:mgen000926. [PMID: 36729913 PMCID: PMC9997740 DOI: 10.1099/mgen.0.000926] [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: 07/26/2022] [Accepted: 11/04/2022] [Indexed: 02/03/2023] Open
Abstract
Pyridoxal 5’-phosphate or PLP is a cofactor derived from B6 vitamers and essential for growth in all known organisms. PLP synthesis and salvage pathways are well characterized in a few model species even though key components, such as the vitamin B6 transporters, are still to be identified in many organisms including the model bacteria Escherichia coli or Bacillus subtilis . Using a comparative genomic approach, PLP synthesis and salvage pathways were predicted in 5840 bacterial and archaeal species with complete genomes. The distribution of the two known de novo biosynthesis pathways and previously identified cases of non-orthologous displacements were surveyed in the process. This analysis revealed that several PLP de novo pathway genes remain to be identified in many organisms, either because sequence similarity alone cannot be used to discriminate among several homologous candidates or due to non-orthologous displacements. Candidates for some of these pathway holes were identified using published TnSeq data, but many remain. We find that ~10 % of the analysed organisms rely on salvage but further analyses will be required to identify potential transporters. This work is a starting point to model the exchanges of B6 vitamers in communities, predict the sensitivity of a given organism to drugs targeting PLP synthesis enzymes, and identify numerous gaps in knowledge that will need to be tackled in the years to come.
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Affiliation(s)
- Rémi Denise
- Department of Microbiology and Cell Sciences, Gainesville, USA
- Present address: APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Jill Babor
- Department of Microbiology and Cell Sciences, Gainesville, USA
| | | | - Valérie de Crécy-Lagard
- Department of Microbiology and Cell Sciences, Gainesville, USA
- Genetics Institute, University of Florida, Gainesville, FL 32611, USA
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Yang Y, Cao C, Gu N. Identifying magnetosome-associated genes in the extended CtrA regulon in Magnetospirillum magneticum AMB-1 using a combinational approach. Brief Funct Genomics 2023; 22:61-74. [PMID: 36424838 DOI: 10.1093/bfgp/elac039] [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: 06/12/2022] [Revised: 10/01/2022] [Accepted: 10/14/2022] [Indexed: 11/26/2022] Open
Abstract
Magnetotactic bacteria (MTB) are worth studying because of magnetosome biomineralization. Magnetosome biogenesis in MTB is controlled by multiple genes known as magnetosome-associated genes. Recent advances in bioinformatics provide a unique opportunity for studying functions of magnetosome-associated genes and networks that they are involved in. Furthermore, various types of bioinformatics analyses can also help identify genes associated with magnetosome biogenesis. To predict novel magnetosome-associated genes in the extended CtrA regulon, we analyzed expression data of Magnetospirillum magneticum AMB-1 in the GSE35625 dataset in NCBI GEO. We identified 10 potential magnetosome-associated genes using a combinational approach of differential expression analysis, Gene ontology and Kyoto encyclopedia of genes and genomes pathway enrichment analysis, protein-protein interaction network analysis and weighted gene co-expression network analysis. Meanwhile, we also discovered and compared two co-expression modules that most known magnetosome-associated genes belong to. Our comparison indicated the importance of energy on regulating co-expression module structures for magnetosome biogenesis. At the last stage of our research, we predicted at least four real magnetosome-associated genes out of 10 potential genes, based on a comparison of evolutionary trees between known and potential magnetosome-associated genes. Because of the discovery of common subtrees that the stressed species are enriched in, we proposed a hypothesis that multiple types of environmental stress can trigger magnetosome evolution in different waters, and therefore its evolution can recur at different times in various locations on earth. Overall, our research provides useful information for identifying new MTB species and understanding magnetosome biogenesis.
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Affiliation(s)
- Yizi Yang
- Department of Bioinformatics, School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing 211166, China
| | - Chen Cao
- Department of Bioinformatics, School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing 211166, China
| | - Ning Gu
- Department of Bioinformatics, School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing 211166, China.,Jiangsu Key Laboratory for Biomaterials and Devices, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China
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8
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Horn EJ, van Hille RP, Oyekola OO, Welz PJ. Functional Microbial Communities in Hybrid Linear Flow Channel Reactors for Desulfurization of Tannery Effluent. Microorganisms 2022; 10:2305. [PMID: 36422375 PMCID: PMC9695182 DOI: 10.3390/microorganisms10112305] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/19/2024] Open
Abstract
Recent research has demonstrated that hybrid linear flow channel reactors (HLFCRs) can desulfurize tannery effluent via sulfate reduction and concurrent oxidation of sulfide to elemental sulfur. The reactors can be used to pre-treat tannery effluent to improve the efficiency of downstream anaerobic digestion and recover sulfur. This study was conducted to gain insight into the bacterial communities in HLFCRs operated in series and identify structure-function relationships. This was accomplished by interpreting the results obtained from amplicon sequencing of the 16S rRNA gene and quantification of the dissimilatory sulfite reducing (dsrB) gene. In an effort to provide a suitable inoculum, microbial consortia were harvested from saline estuaries and enriched. However, it was found that bioaugmentation was not necessary because native communities from tannery wastewater were selected over exogenous communities from the enriched consortia. Overall, Dethiosulfovibrio sp. and Petrimonas sp. were strongly selected (maximum relative abundances of 29% and 26%, respectively), while Desulfobacterium autotrophicum (57%), and Desulfobacter halotolerans (27%) dominated the sulfate reducing bacteria. The presence of elemental sulfur reducing genera such as Dethiosulfovibrio and Petrimonas is not desirable in HLFCRs, and strategies to counter their selection need to be considered to ensure efficiency of these systems for pre-treatment of tannery effluent.
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Woehle C, Roy AS, Glock N, Michels J, Wein T, Weissenbach J, Romero D, Hiebenthal C, Gorb SN, Schönfeld J, Dagan T. Denitrification in foraminifera has an ancient origin and is complemented by associated bacteria. Proc Natl Acad Sci U S A 2022; 119:e2200198119. [PMID: 35704763 PMCID: PMC9231491 DOI: 10.1073/pnas.2200198119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 05/05/2022] [Indexed: 11/18/2022] Open
Abstract
Benthic foraminifera are unicellular eukaryotes that inhabit sediments of aquatic environments. Several foraminifera of the order Rotaliida are known to store and use nitrate for denitrification, a unique energy metabolism among eukaryotes. The rotaliid Globobulimina spp. has been shown to encode an incomplete denitrification pathway of bacterial origin. However, the prevalence of denitrification genes in foraminifera remains unknown, and the missing denitrification pathway components are elusive. Analyzing transcriptomes and metagenomes of 10 foraminiferal species from the Peruvian oxygen minimum zone, we show that denitrification genes are highly conserved in foraminifera. We infer the last common ancestor of denitrifying foraminifera, which enables us to predict the ability to denitrify for additional foraminiferal species. Additionally, an examination of the foraminiferal microbiota reveals evidence for a stable interaction with Desulfobacteraceae, which harbor genes that complement the foraminiferal denitrification pathway. Our results provide evidence that foraminiferal denitrification is complemented by the foraminifera-associated microbiome. The interaction of foraminifera with their resident bacteria is at the basis of foraminiferal adaptation to anaerobic environments that manifested in ecological success in oxygen depleted habitats.
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Affiliation(s)
- Christian Woehle
- Institute of General Microbiology, Kiel University, Kiel 24118, Germany
| | | | - Nicolaas Glock
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel 24148, Germany
| | - Jan Michels
- Zoological Institute, Kiel University, Kiel 24118, Germany
| | - Tanita Wein
- Institute of General Microbiology, Kiel University, Kiel 24118, Germany
| | - Julia Weissenbach
- Institute of General Microbiology, Kiel University, Kiel 24118, Germany
| | - Dennis Romero
- Dirección General de Investigaciones Oceanográficas y Cambio Climático, Instituto del Mar del Perú, Callao 01, Peru 17
| | - Claas Hiebenthal
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel 24148, Germany
| | | | - Joachim Schönfeld
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel 24148, Germany
| | - Tal Dagan
- Institute of General Microbiology, Kiel University, Kiel 24118, Germany
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Choi A, Lee TK, Cho H, Lee WC, Hyun JH. Shifts in benthic bacterial communities associated with farming stages and a microbiological proxy for assessing sulfidic sediment conditions at fish farms. MARINE POLLUTION BULLETIN 2022; 178:113603. [PMID: 35390629 DOI: 10.1016/j.marpolbul.2022.113603] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 02/22/2022] [Accepted: 03/20/2022] [Indexed: 06/14/2023]
Abstract
To assess the aquaculture-induced sediment conditions associated with sulfur cycles, shifts in bacterial communities across farming stages were investigated. The sulfate reduction rate (SRR), and concentrations of acid volatile sulfide (AVS) and H2S were significantly higher at the mid- and post-farming stages than at the early stage, indicating that the aquaculture effects persist even after harvest. Incomplete organic carbon-oxidizing sulfate-reducing bacteria (IO-SRB) affiliated with Desulfobulbaceae, and gammaproteobacterial sulfur oxidizing bacteria (SOB) (Thiohalobacter, Thioprofundum, and Thiohalomonas) were dominant during the early stage, whereas fermenting bacteria (Bacteroidetes and Firmicutes) and complete oxidizing SRB (CO-SRB) belonging to Desulfobacteraceae, and epsilonproteobacterial SOB (Sulfurovum) dominated during the mid- and post-stages. The shift in SRB and SOB communities well reflected the anoxic and sulfidic conditions of farm sediment. Especially, the Sulfurovum-like SOB correlated highly and positively with H2S, AVS, and SRR, suggesting that they could be relevant microbiological proxies to assess sulfidic conditions in farm sediment.
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Affiliation(s)
- Ayeon Choi
- Department of Marine Science and Convergence Technology, Hanyang University, 55 Hanyangdaehak-ro, Sangnok-gu, Ansan, Gyeonggi-do 15588, South Korea; Marine Biotechnology Research Center, Korean Institute of Ocean Science & Technology (KIOST), 385 Haeyang-ro, Yeongdo-gu, Busan Metropolitan City, South Korea
| | - Tae Kwon Lee
- Department of Environmental Engineering, Yonsei University,1Yonseidae-gil, Wonju, Gangwon-do 26493, South Korea
| | - Hyeyoun Cho
- Department of Marine Science and Convergence Technology, Hanyang University, 55 Hanyangdaehak-ro, Sangnok-gu, Ansan, Gyeonggi-do 15588, South Korea
| | - Won-Chan Lee
- Marine Environment Research Division, National Institute of Fisheries Science (NIFS), Busan 46083, South Korea
| | - Jung-Ho Hyun
- Department of Marine Science and Convergence Technology, Hanyang University, 55 Hanyangdaehak-ro, Sangnok-gu, Ansan, Gyeonggi-do 15588, South Korea.
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Phylogenetic diversity in sulphate-reducing bacterial communities from oxidised and reduced bottom sediments of the Barents Sea. Antonie van Leeuwenhoek 2022; 115:801-820. [DOI: 10.1007/s10482-022-01733-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 03/22/2022] [Indexed: 11/25/2022]
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12
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Response to substrate limitation by a marine sulfate-reducing bacterium. THE ISME JOURNAL 2022; 16:200-210. [PMID: 34285365 PMCID: PMC8692349 DOI: 10.1038/s41396-021-01061-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 07/04/2021] [Accepted: 07/06/2021] [Indexed: 02/07/2023]
Abstract
Sulfate-reducing microorganisms (SRM) in subsurface sediments live under constant substrate and energy limitation, yet little is known about how they adapt to this mode of life. We combined controlled chemostat cultivation and transcriptomics to examine how the marine sulfate reducer, Desulfobacterium autotrophicum, copes with substrate (sulfate or lactate) limitation. The half-saturation uptake constant (Km) for lactate was 1.2 µM, which is the first value reported for a marine SRM, while the Km for sulfate was 3 µM. The measured residual lactate concentration in our experiments matched values observed in situ in marine sediments, supporting a key role of SRM in the control of lactate concentrations. Lactate limitation resulted in complete lactate oxidation via the Wood-Ljungdahl pathway and differential overexpression of genes involved in uptake and metabolism of amino acids as an alternative carbon source. D. autotrophicum switched to incomplete lactate oxidation, rerouting carbon metabolism in response to sulfate limitation. The estimated free energy was significantly lower during sulfate limitation (-28 to -33 kJ mol-1 sulfate), suggesting that the observed metabolic switch is under thermodynamic control. Furthermore, we detected the upregulation of putative sulfate transporters involved in either high or low affinity uptake in response to low or high sulfate concentration.
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Mixotrophic bacteria for environmental detoxification of contaminated waste and wastewater. Appl Microbiol Biotechnol 2021; 105:6627-6648. [PMID: 34468802 DOI: 10.1007/s00253-021-11514-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/06/2021] [Accepted: 08/10/2021] [Indexed: 12/31/2022]
Abstract
Mixotrophic bacteria provide a desirable alternative to the use of classical heterotrophic or chemolithoautotrophic bacteria in environmental technology, particularly under limiting nutrients conditions. Their bi-modal ability of adapting to inorganic or organic carbon feed and sulfur, nitrogen, or even heavy metal stress conditions are attractive features to achieve efficient bacterial activity and favorable operation conditions for the environmental detoxification or remediation of contaminated waste and wastewater. This review provides an overview on the state of the art and summarizes the metabolic traits of the most promising and emerging non-model mixotrophic bacteria for the environmental detoxification of contaminated wastewater and waste containing excess amounts of limiting nutrients. Although mixotrophic bacteria usually function with low organic carbon sources, the unusual capabilities of mixotrophic electroactive exoelectrogens and electrotrophs in bioelectrochemical systems and in microbial electrosynthesis for accelerating simultaneous metabolism of inorganic or organic C and N, S or heavy metals are reviewed. The identification of the mixotrophic properties of electroactive bacteria and their capability to drive mono- or bidirectional electron transfer processes are highly exciting and promising aspects. These aspects provide an appealing potential for unearthing new mixotrophic exoelectrogens and electrotrophs, and thus inspire the next generation of microbial electrochemical technology and mixotrophic bacterial metabolic engineering. KEY POINTS: • Mixotrophic bacteria efficiently and simultaneously remove C and N, S or heavy metals. • Exoelectrogens and electrotrophs accelerate metabolism of C and N, S or heavy metals. • New mixotrophic exoelectrogens and electrotrophs should be discovered and exploited.
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14
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Kroeger ME, Meredith LK, Meyer KM, Webster KD, de Camargo PB, de Souza LF, Tsai SM, van Haren J, Saleska S, Bohannan BJM, Rodrigues JLM, Berenguer E, Barlow J, Nüsslein K. Rainforest-to-pasture conversion stimulates soil methanogenesis across the Brazilian Amazon. THE ISME JOURNAL 2021; 15:658-672. [PMID: 33082572 PMCID: PMC8027882 DOI: 10.1038/s41396-020-00804-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 09/03/2020] [Accepted: 10/02/2020] [Indexed: 01/30/2023]
Abstract
The Amazon rainforest is a biodiversity hotspot and large terrestrial carbon sink threatened by agricultural conversion. Rainforest-to-pasture conversion stimulates the release of methane, a potent greenhouse gas. The biotic methane cycle is driven by microorganisms; therefore, this study focused on active methane-cycling microorganisms and their functions across land-use types. We collected intact soil cores from three land use types (primary rainforest, pasture, and secondary rainforest) of two geographically distinct areas of the Brazilian Amazon (Santarém, Pará and Ariquemes, Rondônia) and performed DNA stable-isotope probing coupled with metagenomics to identify the active methanotrophs and methanogens. At both locations, we observed a significant change in the composition of the isotope-labeled methane-cycling microbial community across land use types, specifically an increase in the abundance and diversity of active methanogens in pastures. We conclude that a significant increase in the abundance and activity of methanogens in pasture soils could drive increased soil methane emissions. Furthermore, we found that secondary rainforests had decreased methanogenic activity similar to primary rainforests, and thus a potential to recover as methane sinks, making it conceivable for forest restoration to offset greenhouse gas emissions in the tropics. These findings are critical for informing land management practices and global tropical rainforest conservation.
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Affiliation(s)
- Marie E. Kroeger
- grid.266683.f0000 0001 2184 9220Department of Microbiology, University of Massachusetts Amherst, Amherst, MA USA ,grid.148313.c0000 0004 0428 3079Present Address: Bioenergy and Biome Sciences, Los Alamos National Laboratory, Los Alamos, NM USA
| | - Laura K. Meredith
- grid.134563.60000 0001 2168 186XSchool of Natural Resources and the Environment, University of Arizona, Tucson, AZ USA ,grid.134563.60000 0001 2168 186XBiosphere 2, University of Arizona, Tucson, AZ USA
| | - Kyle M. Meyer
- grid.170202.60000 0004 1936 8008Institute of Ecology and Evolution, University of Oregon, Eugene, OR USA ,grid.47840.3f0000 0001 2181 7878Department of Integrative Biology, University of California–Berkeley, Berkeley, CA USA
| | - Kevin D. Webster
- grid.423138.f0000 0004 0637 3991Planetary Science Institute, Tucson, AZ USA
| | - Plinio Barbosa de Camargo
- grid.11899.380000 0004 1937 0722Center for Nuclear Energy in Agriculture, University of São Paulo, São Paulo, SP Brazil
| | - Leandro Fonseca de Souza
- grid.11899.380000 0004 1937 0722Center for Nuclear Energy in Agriculture, University of São Paulo, São Paulo, SP Brazil
| | - Siu Mui Tsai
- grid.11899.380000 0004 1937 0722Center for Nuclear Energy in Agriculture, University of São Paulo, São Paulo, SP Brazil
| | - Joost van Haren
- grid.134563.60000 0001 2168 186XBiosphere 2, University of Arizona, Tucson, AZ USA ,grid.134563.60000 0001 2168 186XHonors College, University of Arizona, Tucson, AZ USA
| | - Scott Saleska
- grid.134563.60000 0001 2168 186XDepartment of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ USA
| | - Brendan J. M. Bohannan
- grid.170202.60000 0004 1936 8008Institute of Ecology and Evolution, University of Oregon, Eugene, OR USA
| | - Jorge L. Mazza Rodrigues
- grid.27860.3b0000 0004 1936 9684Department of Land, Air and Water Resources, University of California, Davis, CA USA
| | - Erika Berenguer
- grid.9835.70000 0000 8190 6402Lancaster Environment Centre, Lancaster University, Lancaster, UK ,grid.4991.50000 0004 1936 8948Environmental Change Institute, University of Oxford, Oxford, UK
| | - Jos Barlow
- grid.9835.70000 0000 8190 6402Lancaster Environment Centre, Lancaster University, Lancaster, UK
| | - Klaus Nüsslein
- grid.266683.f0000 0001 2184 9220Department of Microbiology, University of Massachusetts Amherst, Amherst, MA USA
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15
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Brunet M, de Bettignies F, Le Duff N, Tanguy G, Davoult D, Leblanc C, Gobet A, Thomas F. Accumulation of detached kelp biomass in a subtidal temperate coastal ecosystem induces succession of epiphytic and sediment bacterial communities. Environ Microbiol 2021; 23:1638-1655. [PMID: 33400326 PMCID: PMC8248336 DOI: 10.1111/1462-2920.15389] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 12/14/2020] [Accepted: 01/02/2021] [Indexed: 12/30/2022]
Abstract
Kelps are dominant primary producers in temperate coastal ecosystems. Large amounts of kelp biomass can be exported to the seafloor during the algal growth cycle or following storms, creating new ecological niches for the associated microbiota. Here, we investigated the bacterial community associated with the kelp Laminaria hyperborea during its accumulation and degradation on the seafloor. Kelp tissue, seawater and sediment were sampled during a 6-month in situ experiment simulating kelp detritus accumulation. Evaluation of the epiphytic bacterial community abundance, structure, taxonomic composition and predicted functional profiles evidenced a biphasic succession. Initially, dominant genera (Hellea, Litorimonas, Granulosicoccus) showed a rapid and drastic decrease in sequence abundance, probably outcompeted by algal polysaccharide-degraders such as Bacteroidia members which responded within 4 weeks. Acidimicrobiia, especially members of the Sva0996 marine group, colonized the degrading kelp biomass after 11 weeks. These secondary colonizers could act as opportunistic scavenger bacteria assimilating substrates exposed by early degraders. In parallel, kelp accumulation modified bacterial communities in the underlying sediment, notably favouring anaerobic taxa potentially involved in the sulfur and nitrogen cycles. Overall, this study provides insights into the bacterial degradation of algal biomass in situ, an important link in coastal trophic chains.
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Affiliation(s)
- Maéva Brunet
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR)Roscoff29680France
| | - Florian de Bettignies
- Sorbonne Université, CNRS, UMR 7144 AD2M, Station Biologique de Roscoff (SBR)Roscoff29680France
| | - Nolwen Le Duff
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR)Roscoff29680France
| | - Gwenn Tanguy
- Sorbonne Université, CNRS, FR2424, Genomer, Station Biologique de RoscoffRoscoff29680France
| | - Dominique Davoult
- Sorbonne Université, CNRS, UMR 7144 AD2M, Station Biologique de Roscoff (SBR)Roscoff29680France
| | - Catherine Leblanc
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR)Roscoff29680France
| | - Angélique Gobet
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR)Roscoff29680France
- MARBEC, Univ Montpellier, CNRS, Ifremer, IRDSèteFrance
| | - François Thomas
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR)Roscoff29680France
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16
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Schnaars V, Wöhlbrand L, Scheve S, Hinrichs C, Reinhardt R, Rabus R. Proteogenomic Insights into the Physiology of Marine, Sulfate-Reducing, Filamentous Desulfonema limicola and Desulfonema magnum. Microb Physiol 2021; 31:1-20. [PMID: 33611323 PMCID: PMC8315694 DOI: 10.1159/000513383] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 11/19/2020] [Indexed: 11/19/2022]
Abstract
The genus Desulfonema belongs to the deltaproteobacterial family Desulfobacteraceae and comprises marine, sulfate-reducing bacteria that form filaments and move by gliding. This study reports on the complete, manually annotated genomes of Dn. limicola 5ac10T (6.91 Mbp; 6,207 CDS) and Dn. magnum 4be13T (8.03 Mbp; 9,970 CDS), integrated with substrate-specific proteome profiles (8 vs. 11). The richness in mobile genetic elements is shared with other Desulfobacteraceae members, corroborating horizontal gene transfer as major driver in shaping the genomes of this family. The catabolic networks of Dn. limicola and Dn. magnum have the following general characteristics: 98 versus 145 genes assigned (having genomic shares of 1.7 vs. 2.2%), 92.5 versus 89.7% proteomic coverage, and scattered gene clusters for substrate degradation and energy metabolism. The Dn. magnum typifying capacity for aromatic compound degradation (e.g., p-cresol, 3-phenylpropionate) requires 48 genes organized in operon-like structures (87.7% proteomic coverage; no homologs in Dn. limicola). The protein complements for aliphatic compound degradation, central pathways, and energy metabolism are highly similar between both genomes and were identified to a large extent (69-96%). The differential protein profiles revealed a high degree of substrate-specificity for peripheral reaction sequences (forming central intermediates), agreeing with the high number of sensory/regulatory proteins predicted for both strains. By contrast, central pathways and modules of the energy metabolism were constitutively formed under the tested substrate conditions. In accord with their natural habitats that are subject to fluctuating changes of physicochemical parameters, both Desulfonema strains are well equipped to cope with various stress conditions. Next to superoxide dismutase and catalase also desulfoferredoxin and rubredoxin oxidoreductase are formed to counter exposure to molecular oxygen. A variety of proteases and chaperones were detected that function in maintaining cellular homeostasis upon heat or cold shock. Furthermore, glycine betaine/proline betaine transport systems can respond to hyperosmotic stress. Gliding movement probably relies on twitching motility via type-IV pili or adventurous motility. Taken together, this proteogenomic study demonstrates the adaptability of Dn. limicola and Dn. magnum to its dynamic habitats by means of flexible catabolism and extensive stress response capacities.
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Affiliation(s)
- Vanessa Schnaars
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Lars Wöhlbrand
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Sabine Scheve
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Christina Hinrichs
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Richard Reinhardt
- Max-Planck-Genome-Centre Cologne, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Ralf Rabus
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany,
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17
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Watanabe M, Higashioka Y, Kojima H, Fukui M. Proposal of Desulfosarcina ovata subsp. sediminis subsp. nov., a novel toluene-degrading sulfate-reducing bacterium isolated from tidal flat sediment of Tokyo Bay. Syst Appl Microbiol 2020; 43:126109. [PMID: 32847784 DOI: 10.1016/j.syapm.2020.126109] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 06/15/2020] [Accepted: 06/22/2020] [Indexed: 11/30/2022]
Abstract
Strain 28bB2TT is a sulfate-reducing bacterium isolated in a previous study, obtained from a p-xylene-degrading enrichment culture. Physiological, phylogenetic and genomic characterizations of strain 28bB2TT were performed to establish the taxonomic status of the strain. Cells of strain 28bB2TT were short oval-shaped (0.8-1.2×1.2-2.7μm), motile, and Gram-negative. For growth, the optimum pH was pH 6.5-7.0 and the optimum temperature was 28-32°C. Strain 28bB2TT oxidized toluene but could not utilize p-xylene. Sulfate and thiosulfate were used as electron acceptors. The G+C content of the genomic DNA was 53.8mol%. The genome consisted of an approximately 8.3 Mb of chromosome and two extrachromosomal elements. On the basis of 16S rRNA gene analysis, strain 28bB2TT was revealed to belong to the genus Desulfosarcina, with high sequence identities to Desulfosarcina ovata oXyS1T (99.5%) and Desulfosarcina cetonica DSM 7267T (98.7%). Results of Average Nucleotide Identity (ANI) calculation and digital DNA-DNA hybridization (dDDH) analysis showed that the strain 28bB2TT should be classified as a subspecies under D. ovata. Based on physiological and phylogenetic data, strain 28bB2TT (=NBRC 106234 =DSM 23484) is proposed as the type strain of a novel species in genus Desulfosarcina, Desulfosarcina ovata subsp. sediminis subsp. nov.
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Affiliation(s)
- Miho Watanabe
- Institute of Low Temperature Science, Hokkaido University, Sapporo, Hokkaido, Japan; Postdoctoral Research Fellow of the Japan Society for the Promotion of Science, Chiyoda-ku, Tokyo 102-8471, Japan; Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan; Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan.
| | - Yuriko Higashioka
- National Institute of Technology, Kochi College, 200-1 Otsu, Monobe, Nankoku-city, Kochi 783-8508, Japan
| | - Hisaya Kojima
- Institute of Low Temperature Science, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Manabu Fukui
- Institute of Low Temperature Science, Hokkaido University, Sapporo, Hokkaido, Japan
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18
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A New Thioalkalivibrio sp. Strain Isolated from Petroleum-Contaminated Brackish Estuary Sediments: A New Candidate for Bio-Based Application for Sulfide Oxidation in Halo-Alkaline Conditions. WATER 2020. [DOI: 10.3390/w12051385] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
A new halo-alkaline sulfur-oxidising bacterial strain was isolated from brackish estuary sediments contaminated by total petroleum hydrocarbon. The isolate was classified as a new strain of Thioalkalivibrio sulfidiphilus sp., showing a higher capability of adaptation to pH and a higher optimal sodium concentration for growth, when compared to Thioalkalivibrio sulfidiphilus sp. HL-EbGr7, type strain of the species. The strain was capable to grow in saline concentrations up to 1.5 M Na+ and pH up to 10. The genome of the new isolate was sequenced and annotated. The comparison with the genome of Thioalkalivibrio sulfidiphilus sp. HL-EbGr7 showed a duplication of an operon encoding for a putative primary sodium extruding pump and the presence of a sodium/proton antiporter with optimal efficiency at halo-alkaline conditions. The new strain was able to oxidize sulfide at halo-alkaline conditions at the rate of 1 mmol/mg-N/h, suitable for industrial applications dedicated to the recovery of alkaline scrubber for H2S emission absorption and abatement.
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19
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St. James AR, Richardson RE. Ecogenomics reveals community interactions in a long-term methanogenic bioreactor and a rapid switch to sulfate-reducing conditions. FEMS Microbiol Ecol 2020; 96:5809959. [DOI: 10.1093/femsec/fiaa050] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 03/17/2020] [Indexed: 01/13/2023] Open
Abstract
ABSTRACT
The anaerobic digestion of wastes is globally important in the production of methane (CH4) as a biofuel. When sulfate is present, sulfate-reducing bacteria (SRB) are stimulated, competing with methanogens for common substrates, which decreases CH4 production and results in the formation of corrosive, odorous hydrogen sulfide gas (H2S). Here, we show that a population of SRB within a methanogenic bioreactor fed only butyrate for years immediately (within hours) responded to sulfate availability and shifted the microbial community dynamics within the bioreactor. By mapping shotgun metatranscriptomes to metagenome-assembled genomes, we shed light on the transcriptomic responses of key community members in response to increased sulfate provision. We link these short-term transcriptional responses to long-term niche partitioning using comparative metagenomic analyses. Our results suggest that sulfate provision supports a syntrophic butyrate oxidation community that disfavors poly-β-hydroxyalkanoate storage and that hydrogenotrophic SRB populations effectively exclude obligately hydrogenotrophic, but not aceticlastic, methanogens when sulfate is readily available. These findings elucidate key ecological dynamics between SRB, methanogens and syntrophic butyrate-oxidizing bacteria, which can be applied to a variety of engineered and natural systems.
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Affiliation(s)
- Andrew R St. James
- School of Civil and Environmental Engineering, Cornell University, 527 College Ave, Hollister Hall, Ithaca, NY, USA 14853
| | - Ruth E Richardson
- School of Civil and Environmental Engineering, Cornell University, 527 College Ave, Hollister Hall, Ithaca, NY, USA 14853
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20
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Abstract
Current understanding of the diversity, biology, and ecology of Archaea is very limited, especially considering how few of the known phyla have been cultured or genomically explored. The reconstruction of “Ca. Methanomixophus” MAGs not only expands the known range of metabolic versatility of the members of Archaeoglobi but also suggests that the phylogenetic distribution of MCR and MTR complexes is even wider than previously anticipated. Euryarchaeal lineages have been believed to have a methanogenic last common ancestor. However, members of euryarchaeal Archaeoglobi have long been considered nonmethanogenic and their evolutionary history remains elusive. Here, three high-quality metagenomic-assembled genomes (MAGs) retrieved from high-temperature oil reservoir and hot springs, together with three newly assembled Archaeoglobi MAGs from previously reported hot spring metagenomes, are demonstrated to represent a novel genus of Archaeoglobaceae, “Candidatus Methanomixophus.” All “Ca. Methanomixophus” MAGs encode an M methyltransferase (MTR) complex and a traditional type of methyl-coenzyme M reductase (MCR) complex, which is different from the divergent MCR complexes found in “Ca. Polytropus marinifundus.” In addition, “Ca. Methanomixophus dualitatem” MAGs preserve the genomic capacity for dissimilatory sulfate reduction. Comparative phylogenetic analysis supports a laterally transferred origin for an MCR complex and vertical heritage of the MTR complex in this lineage. Metatranscriptomic analysis revealed concomitant in situ activity of hydrogen-dependent methylotrophic methanogenesis and heterotrophic fermentation within populations of “Ca. Methanomixophus hydrogenotrophicum” in a high-temperature oil reservoir. IMPORTANCE Current understanding of the diversity, biology, and ecology of Archaea is very limited, especially considering how few of the known phyla have been cultured or genomically explored. The reconstruction of “Ca. Methanomixophus” MAGs not only expands the known range of metabolic versatility of the members of Archaeoglobi but also suggests that the phylogenetic distribution of MCR and MTR complexes is even wider than previously anticipated.
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21
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Effect of Quorum Sensing on the Ability of Desulfovibrio vulgaris To Form Biofilms and To Biocorrode Carbon Steel in Saline Conditions. Appl Environ Microbiol 2019; 86:AEM.01664-19. [PMID: 31628147 DOI: 10.1128/aem.01664-19] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Accepted: 10/13/2019] [Indexed: 11/20/2022] Open
Abstract
Sulfate-reducing bacteria (SRB) are key contributors to microbe-induced corrosion (MIC), which can lead to serious economic and environmental impact. The presence of a biofilm significantly increases the MIC rate. Inhibition of the quorum-sensing (QS) system is a promising alternative approach to prevent biofilm formation in various industrial settings, especially considering the significant ecological impact of conventional chemical-based mitigation strategies. In this study, the effect of the QS stimulation and inhibition on Desulfovibrio vulgaris is described in terms of anaerobic respiration, cell activity, biofilm formation, and biocorrosion of carbon steel. All these traits were repressed when bacteria were in contact with QS inhibitors but enhanced upon exposure to QS signal molecules compared to the control. The difference in the treatments was confirmed by transcriptomic analysis performed at different time points after treatment application. Genes related to lactate and pyruvate metabolism, sulfate reduction, electron transfer, and biofilm formation were downregulated upon QS inhibition. In contrast, QS stimulation led to an upregulation of the above-mentioned genes compared to the control. In summary, these results reveal the impact of QS on the activity of D. vulgaris, paving the way toward the prevention of corrosive SRB biofilm formation via QS inhibition.IMPORTANCE Sulfate-reducing bacteria (SRB) are considered key contributors to biocorrosion, particularly in saline environments. Biocorrosion imposes tremendous economic costs, and common approaches to mitigate this problem involve the use of toxic and hazardous chemicals (e.g., chlorine), which raise health and environmental safety concerns. Quorum-sensing inhibitors (QSIs) can be used as an alternative approach to inhibit biofilm formation and biocorrosion. However, this approach would only be effective if SRB rely on QS for the pathways associated with biocorrosion. These pathways would include biofilm formation, electron transfer, and metabolism. This study demonstrates the role of QS in Desulfovibrio vulgaris on the above-mentioned pathways through both phenotypic measurements and transcriptomic approach. The results of this study suggest that QSIs can be used to mitigate SRB-induced corrosion problems in ecologically sensitive areas.
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22
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Kraiselburd I, Brüls T, Heilmann G, Kaschani F, Kaiser M, Meckenstock RU. Metabolic reconstruction of the genome of candidate Desulfatiglans TRIP_1 and identification of key candidate enzymes for anaerobic phenanthrene degradation. Environ Microbiol 2019; 21:1267-1286. [PMID: 30680888 PMCID: PMC6849830 DOI: 10.1111/1462-2920.14527] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 12/12/2018] [Indexed: 11/30/2022]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are widely distributed pollutants. As oxygen is rapidly depleted in water‐saturated PAH‐contaminated sites, anaerobic microorganisms are crucial for their consumption. Here, we report the metabolic pathway for anaerobic degradation of phenanthrene by a sulfate‐reducing enrichment culture (TRIP) obtained from a natural asphalt lake. The dominant organism of this culture belongs to the Desulfobacteraceae family of Deltaproteobacteria and genome‐resolved metagenomics led to the reconstruction of its genome along with a handful of genomes from lower abundance bacteria. Proteogenomic analyses confirmed metabolic capabilities for dissimilatory sulfate reduction and indicated the presence of the Embden‐Meyerhof‐Parnas pathway, a complete tricarboxylic acid cycle as well as a complete Wood‐Ljungdahl pathway. Genes encoding enzymes putatively involved in the degradation of phenanthrene were identified. This includes two gene clusters encoding a multisubunit carboxylase complex likely involved in the activation of phenanthrene, as well as genes encoding reductases potentially involved in subsequent ring dearomatization and reduction steps. The predicted metabolic pathways were corroborated by transcriptome and proteome analyses, and provide the first insights into the metabolic pathway responsible for the anaerobic degradation of three‐ringed PAHs.
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Affiliation(s)
- Ivana Kraiselburd
- Biofilm Centre, Aquatic Microbiology Department, Faculty of Chemistry, University Duisburg-Essen, Essen, Germany
| | - Thomas Brüls
- CEA, DRF, Institut Jacob, Genoscope, Evry, France.,CNRS-UMR8030, Université Paris-Saclay, Evry, France
| | - Geronimo Heilmann
- Centre of Medical Biotechnology, Chemical Biology Department, Faculty of Biology, University Duisburg-Essen, Essen, Germany
| | - Farnusch Kaschani
- Centre of Medical Biotechnology, Chemical Biology Department, Faculty of Biology, University Duisburg-Essen, Essen, Germany
| | - Markus Kaiser
- Centre of Medical Biotechnology, Chemical Biology Department, Faculty of Biology, University Duisburg-Essen, Essen, Germany
| | - Rainer U Meckenstock
- Biofilm Centre, Aquatic Microbiology Department, Faculty of Chemistry, University Duisburg-Essen, Essen, Germany
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23
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Cabral L, Pereira de Sousa ST, Júnior GVL, Hawley E, Andreote FD, Hess M, de Oliveira VM. Microbial functional responses to long-term anthropogenic impact in mangrove soils. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2018; 160:231-239. [PMID: 29807296 DOI: 10.1016/j.ecoenv.2018.04.050] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 04/23/2018] [Accepted: 04/26/2018] [Indexed: 06/08/2023]
Abstract
Mangroves are coastal ecosystems of transition between terrestrial and marine environments, that have been particularly contaminated in the last decades. Organic compounds are part of these contaminants, which have increased in the environment due to industrial activities and accidental oil spills. These contaminants are toxic to higher organisms, but microorganisms can metabolize most of these compounds and thus offer a tool for bioremediation purposes. The aim of the present study was to characterize the microbial potential and activity for degradation of aromatic compounds in sediment samples from mangroves using metagenomic and metatranscriptomic approaches. Sediment samples were collected for DNA and RNA extraction from each of the mangrove sites: highly oil-impacted (Oil Mgv), anthropogenically impacted (Ant Mgv) and pristine (Prs Mgv) mangrove. Hydrocarbon concentrations in Oil Mgv sediments were higher than those observed in Ant Mgv and Prs Mgv. Genes and transcripts associated with aromatic compound degradation, particularly the meta and ortho-pathways, were more abundant in Oil Mgv and Ant Mgv suggesting that many of the aromatic compounds are being aerobically degraded by the microbiome in these sites. Functions involved in the degradation of aromatic compounds were also found in pristine site, although in lower abundance. Members of the genera Aromatoleum, Desulfococcus, Desulfatibacillum, Desulfitobacterium and Vibrio were actively involved in the detoxification of sediments affected by the oil spill. Results obtained from this study provided strong evidence that microbial degradation of aromatic compounds plays an active role in the biological response to mangrove sediment pollution and subsequent ecosystem recovery.
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Affiliation(s)
- Lucélia Cabral
- Research Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas (UNICAMP), Campinas, São Paulo, Brazil.
| | - Sanderson Tarciso Pereira de Sousa
- Research Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas (UNICAMP), Campinas, São Paulo, Brazil; Institute of Biology (IB) - University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Gileno Vieira Lacerda Júnior
- Research Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas (UNICAMP), Campinas, São Paulo, Brazil; Institute of Biology (IB) - University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Erik Hawley
- Washington State University, Pullman, WA, USA
| | - Fernando Dini Andreote
- Department of Soil Science, ''Luiz de Queiroz'' College of Agriculture, University of Sao Paulo, Piracicaba, São Paulo, Brazil
| | - Matthias Hess
- University of California, Davis, Department of Animal Science, Davis, CA, USA
| | - Valéria Maia de Oliveira
- Research Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
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24
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Wu J, Niu Q, Li L, Hu Y, Mribet C, Hojo T, Li YY. A gradual change between methanogenesis and sulfidogenesis during a long-term UASB treatment of sulfate-rich chemical wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 636:168-176. [PMID: 29704712 DOI: 10.1016/j.scitotenv.2018.04.172] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 04/03/2018] [Accepted: 04/12/2018] [Indexed: 06/08/2023]
Abstract
The competition between methane-producing archaea and sulfate-reducing bacteria is an important topic in anaerobic wastewater treatment. In this study, an Up-flow Anaerobic Sludge Blanket Reactor (UASB) was operated for 330 days to evaluate the treatment performance of sulfate-rich wastewater. The effects of competition change between methane production and sulfate reduction on the organic removal efficiency, methane production, and electrons allocation were investigated. Synthetic wastewater was composed of ethanol and acetate with a chemical oxygen demand (COD)/SO42- of 1.0. As a result, the COD removal efficiency achieved in long-term treatment was higher than 90%. During the initial stage, methane production was the dominant reaction. Sulfate-reducing bacteria (SRB) could only partially oxidize ethanol to acetate, and methane-producing archaea (MPA) utilized acetate for methane production. Methane production declined gradually over the long-term operation, whereas the sulfate-reducing efficiency increased. However, UASB performed well throughout the experiment because there was no significant inhibition. After the complete reduction of the sulfate, MPA converted the remaining COD into methane.
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Affiliation(s)
- Jiang Wu
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, 6-6-06 Aza-Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan
| | - Qigui Niu
- School of Environmental Science and Engineering, Shandong University, 27# Shanda South Road, Jinan 250100, China
| | - Lu Li
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, 6-6-06 Aza-Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan
| | - Yong Hu
- National Institute for Environmental Studies, Onogawa 16-2, Tsukuba, Ibaraki 305-0053, Japan
| | - Chaimaa Mribet
- Graduate School of Environmental Studies, Tohoku University, 6-6-06 Aoba, Sendai 980-8579, Japan
| | - Toshimasa Hojo
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, 6-6-06 Aza-Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan
| | - Yu-You Li
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, 6-6-06 Aza-Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan.
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Zaybak Z, Logan BE, Pisciotta JM. Electrotrophic activity and electrosynthetic acetate production by Desulfobacterium autotrophicum HRM2. Bioelectrochemistry 2018; 123:150-155. [PMID: 29753938 DOI: 10.1016/j.bioelechem.2018.04.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 04/26/2018] [Accepted: 04/29/2018] [Indexed: 10/17/2022]
Abstract
Electroautotrophic microorganisms accept electrons from a cathode as source of reducing equivalents to drive CO2 fixation by poorly understood mechanisms. Acetogenic bacteria were the first group found to possess the capability for electroautotrophic metabolism in pure culture with associated electrosynthesis of acetate as primary metabolite. Identification of additional electrotrophic species can contribute to our understanding of this unusual form of metabolism. Here, bioelectrochemical techniques, chemical analysis and microscopy were used to determine electrotrophic metabolism of Desulfobacterium autotrophicum HRM2. Chronoamperometry showed increasing current uptake over 21 days of incubation in duplicate bioelectrochemical system sets. Linear sweep voltammetry indicated peak current uptake at -243 mV. High performance liquid chromatography (HPLC) analysis quantified acetate accumulation in anaerobic minimal media containing inorganic carbon as sole carbon source, consistent with electrosynthesis. Scanning electron microscopy and live/dead staining by epifluorescence microscopy analysis indicated viable 1-2 μm cells after 76 days of cultivation under electroautotrophic conditions. The genome of Db. autotrophicum HRM2 is fully sequenced and, thus, could provide insight into the biochemical and physiological mechanisms by which electrotrophic cells utilize cathode-derived electrons. This research expands the diversity of facultative autotrophs capable of electrotrophic metabolism to include the sulfate-reducing marine bacterium Db. autotrophicum HRM2.
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Affiliation(s)
- Zehra Zaybak
- Department of Civil and Environmental Engineering, The Pennsylvania State University, 212 Sackett Building, University Park, PA 16802, USA; Department of Biology, West Chester University of Pennsylvania, West Chester, PA 19383, USA
| | - Bruce E Logan
- Department of Civil and Environmental Engineering, The Pennsylvania State University, 212 Sackett Building, University Park, PA 16802, USA
| | - John M Pisciotta
- Department of Civil and Environmental Engineering, The Pennsylvania State University, 212 Sackett Building, University Park, PA 16802, USA; Department of Biology, West Chester University of Pennsylvania, West Chester, PA 19383, USA.
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Sedano-Núñez VT, Boeren S, Stams AJM, Plugge CM. Comparative proteome analysis of propionate degradation by Syntrophobacter fumaroxidans in pure culture and in coculture with methanogens. Environ Microbiol 2018; 20:1842-1856. [PMID: 29611893 PMCID: PMC5947623 DOI: 10.1111/1462-2920.14119] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 03/20/2018] [Accepted: 03/24/2018] [Indexed: 11/28/2022]
Abstract
Syntrophobacter fumaroxidans is a sulfate-reducing bacterium able to grow on propionate axenically or in syntrophic interaction with methanogens or other sulfate-reducing bacteria. We performed a proteome analysis of S. fumaroxidans growing with propionate axenically with sulfate or fumarate, and in syntrophy with Methanospirillum hungatei, Methanobacterium formicicum or Desulfovibrio desulfuricans. Special attention was put on the role of hydrogen and formate in interspecies electron transfer (IET) and energy conservation. Formate dehydrogenase Fdh1 and hydrogenase Hox were the main confurcating enzymes used for energy conservation. In the periplasm, Fdh2 and hydrogenase Hyn play an important role in reverse electron transport associated with succinate oxidation. Periplasmic Fdh3 and Fdh5 were involved in IET. The sulfate reduction pathway was poorly regulated and many enzymes associated with sulfate reduction (Sat, HppA, AprAB, DsrAB and DsrC) were abundant even at conditions where sulfate was not present. Proteins similar to heterodisulfide reductases (Hdr) were abundant. Hdr/Flox was detected in all conditions while HdrABC/HdrL was exclusively detected when sulfate was available; these complexes most likely confurcate electrons. Our results suggest that S. fumaroxidans mainly used formate for electron release and that different confurcating mechanisms were used in its sulfidogenic metabolism.
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Affiliation(s)
- Vicente T Sedano-Núñez
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, Wageningen, The Netherlands
| | - Sjef Boeren
- Laboratory of Biochemistry, Wageningen University & Research, Stippeneng 4, Wageningen, The Netherlands
| | - Alfons J M Stams
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, Wageningen, The Netherlands.,Centre of Biological Engineering, University of Minho, Campus de Gualtar, Braga, 4710-057, Portugal
| | - Caroline M Plugge
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, Wageningen, The Netherlands
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Buckel W, Thauer RK. Flavin-Based Electron Bifurcation, Ferredoxin, Flavodoxin, and Anaerobic Respiration With Protons (Ech) or NAD + (Rnf) as Electron Acceptors: A Historical Review. Front Microbiol 2018; 9:401. [PMID: 29593673 PMCID: PMC5861303 DOI: 10.3389/fmicb.2018.00401] [Citation(s) in RCA: 199] [Impact Index Per Article: 33.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Accepted: 02/21/2018] [Indexed: 12/19/2022] Open
Abstract
Flavin-based electron bifurcation is a newly discovered mechanism, by which a hydride electron pair from NAD(P)H, coenzyme F420H2, H2, or formate is split by flavoproteins into one-electron with a more negative reduction potential and one with a more positive reduction potential than that of the electron pair. Via this mechanism microorganisms generate low- potential electrons for the reduction of ferredoxins (Fd) and flavodoxins (Fld). The first example was described in 2008 when it was found that the butyryl-CoA dehydrogenase-electron-transferring flavoprotein complex (Bcd-EtfAB) of Clostridium kluyveri couples the endergonic reduction of ferredoxin (E0′ = −420 mV) with NADH (−320 mV) to the exergonic reduction of crotonyl-CoA to butyryl-CoA (−10 mV) with NADH. The discovery was followed by the finding of an electron-bifurcating Fd- and NAD-dependent [FeFe]-hydrogenase (HydABC) in Thermotoga maritima (2009), Fd-dependent transhydrogenase (NfnAB) in various bacteria and archaea (2010), Fd- and H2-dependent heterodisulfide reductase (MvhADG-HdrABC) in methanogenic archaea (2011), Fd- and NADH-dependent caffeyl-CoA reductase (CarCDE) in Acetobacterium woodii (2013), Fd- and NAD-dependent formate dehydrogenase (HylABC-FdhF2) in Clostridium acidi-urici (2013), Fd- and NADP-dependent [FeFe]-hydrogenase (HytA-E) in Clostridium autoethanogrenum (2013), Fd(?)- and NADH-dependent methylene-tetrahydrofolate reductase (MetFV-HdrABC-MvhD) in Moorella thermoacetica (2014), Fd- and NAD-dependent lactate dehydrogenase (LctBCD) in A. woodii (2015), Fd- and F420H2-dependent heterodisulfide reductase (HdrA2B2C2) in Methanosarcina acetivorans (2017), and Fd- and NADH-dependent ubiquinol reductase (FixABCX) in Azotobacter vinelandii (2017). The electron-bifurcating flavoprotein complexes known to date fall into four groups that have evolved independently, namely those containing EtfAB (CarED, LctCB, FixBA) with bound FAD, a NuoF homolog (HydB, HytB, or HylB) harboring FMN, NfnB with bound FAD, or HdrA harboring FAD. All these flavoproteins are cytoplasmic except for the membrane-associated protein FixABCX. The organisms—in which they have been found—are strictly anaerobic microorganisms except for the aerobe A. vinelandii. The electron-bifurcating complexes are involved in a variety of processes such as butyric acid fermentation, methanogenesis, acetogenesis, anaerobic lactate oxidation, dissimilatory sulfate reduction, anaerobic- dearomatization, nitrogen fixation, and CO2 fixation. They contribute to energy conservation via the energy-converting ferredoxin: NAD+ reductase complex Rnf or the energy-converting ferredoxin-dependent hydrogenase complex Ech. This Review describes how this mechanism was discovered.
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Affiliation(s)
- Wolfgang Buckel
- Laboratory for Microbiology, Faculty of Biology, Philipps-Universität Marburg, Marburg, Germany
| | - Rudolf K Thauer
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
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Dörries M, Wöhlbrand L, Rabus R. Differential proteomic analysis of the metabolic network of the marine sulfate-reducer Desulfobacterium autotrophicum HRM2. Proteomics 2017; 16:2878-2893. [PMID: 27701823 DOI: 10.1002/pmic.201600041] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Revised: 08/24/2016] [Accepted: 09/30/2016] [Indexed: 01/30/2023]
Abstract
The marine sulfate-reducing bacterium Desulfobacterium autotrophicum HRM2 belongs to the deltaproteobacterial family Desulfobacteraceae and stands out for its capacity of facultative chemolithoautotrophic growth (next to heterotrophy). Here, proteomics-driven metabolic reconstruction was based on a combination of 2D-DIGE, shotgun proteomics, and analysis of the membrane protein enriched fraction applied to eight different substrate adaptation conditions (seven aliphatic compounds plus H2 /CO2 ). In total, 1344 different proteins were identified (∼27% of the 4947 genome-predicted), from which a complex metabolic network was reconstructed consisting of 136 proteins (124 detected; ∼91%). Peripheral degradation routes for organic substrates feed directly or via the methylmalonyl-CoA pathway into the Wood-Ljungdahl pathway (WLP) for terminal oxidation to CO2 . Chemolithoautotrophic growth apparently involves the periplasmic [Ni/Fe/Se]-containing hydrogenase HysAB (H2 oxidation), the reductively operating WLP (CO2 fixation), and classical gluconeogenesis. Diverse soluble proteins (e.g., Hdr, Etf) probably establish a fine balanced cytoplasmic electron transfer network connecting individual catabolic reactions with the membrane menaquinone pool. In addition, multiple membrane protein complexes (Nqr, Qmo, Qrc, Rnf1, Rnf2, and Tmc) provide ample routes for interacting with the reducing equivalent pool and delivering electrons to dissimilatory sulfate reduction (both localized in the cytoplasm). Overall, this study contributes to the molecular understanding of the habitat-relevant Desulfobacteraceae.
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Affiliation(s)
- Marvin Dörries
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Oldenburg, Germany
| | - Lars Wöhlbrand
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Oldenburg, Germany
| | - Ralf Rabus
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Oldenburg, Germany.,Department Microbiology, Max Planck Institute for Marine Microbiology, Bremen, Germany
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Descamps ECT, Monteil CL, Menguy N, Ginet N, Pignol D, Bazylinski DA, Lefèvre CT. Desulfamplus magnetovallimortis gen. nov., sp. nov., a magnetotactic bacterium from a brackish desert spring able to biomineralize greigite and magnetite, that represents a novel lineage in the Desulfobacteraceae. Syst Appl Microbiol 2017. [PMID: 28622795 DOI: 10.1016/j.syapm.2017.05.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A magnetotactic bacterium, designated strain BW-1T, was isolated from a brackish spring in Death Valley National Park (California, USA) and cultivated in axenic culture. The Gram-negative cells of strain BW-1T are relatively large and rod-shaped and possess a single polar flagellum (monotrichous). This strain is the first magnetotactic bacterium isolated in axenic culture capable of producing greigite and/or magnetite nanocrystals aligned in one or more chains per cell. Strain BW-1T is an obligate anaerobe that grows chemoorganoheterotrophically while reducing sulfate as a terminal electron acceptor. Optimal growth occurred at pH 7.0 and 28°C with fumarate as electron donor and carbon source. Based on its genome sequence, the G+C content is 40.72mol %. Phylogenomic and phylogenetic analyses indicate that strain BW-1T belongs to the Desulfobacteraceae family within the Deltaproteobacteria class. Based on average amino acid identity, strain BW-1T can be considered as a novel species of a new genus, for which the name Desulfamplus magnetovallimortis is proposed. The type strain of D. magnetovallimortis is BW-1T (JCM 18010T-DSM 103535T).
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Affiliation(s)
- Elodie C T Descamps
- CNRS/CEA/Aix-Marseille Université, UMR7265 Institut de biosciences et biotechnologies, Laboratoire de Bioénergétique Cellulaire, 13108 Saint Paul lez Durance, France
| | - Caroline L Monteil
- CNRS/CEA/Aix-Marseille Université, UMR7265 Institut de biosciences et biotechnologies, Laboratoire de Bioénergétique Cellulaire, 13108 Saint Paul lez Durance, France
| | - Nicolas Menguy
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, UMR 7590 CNRS-UPMC-MNHN-Sorbonne Université, 4 place Jussieu, 75252 Paris Cedex 05, France
| | - Nicolas Ginet
- CNRS/CEA/Aix-Marseille Université, UMR7265 Institut de biosciences et biotechnologies, Laboratoire de Bioénergétique Cellulaire, 13108 Saint Paul lez Durance, France; CNRS/Aix-Marseille Université, UMR7283 Laboratoire de Chimie Bactérienne, 13009 Marseille, France
| | - David Pignol
- CNRS/CEA/Aix-Marseille Université, UMR7265 Institut de biosciences et biotechnologies, Laboratoire de Bioénergétique Cellulaire, 13108 Saint Paul lez Durance, France
| | - Dennis A Bazylinski
- School of Life Sciences, University of Nevada at Las Vegas, Las Vegas, NV 89154-4004, USA
| | - Christopher T Lefèvre
- CNRS/CEA/Aix-Marseille Université, UMR7265 Institut de biosciences et biotechnologies, Laboratoire de Bioénergétique Cellulaire, 13108 Saint Paul lez Durance, France.
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Tarpgaard IH, Jørgensen BB, Kjeldsen KU, Røy H. The marine sulfate reducer Desulfobacterium autotrophicum HRM2 can switch between low and high apparent half-saturation constants for dissimilatory sulfate reduction. FEMS Microbiol Ecol 2017; 93:2966865. [DOI: 10.1093/femsec/fix012] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 02/01/2017] [Indexed: 12/22/2022] Open
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Hagen LH, Frank JA, Zamanzadeh M, Eijsink VGH, Pope PB, Horn SJ, Arntzen MØ. Quantitative Metaproteomics Highlight the Metabolic Contributions of Uncultured Phylotypes in a Thermophilic Anaerobic Digester. Appl Environ Microbiol 2017; 83:e01955-16. [PMID: 27815274 PMCID: PMC5203625 DOI: 10.1128/aem.01955-16] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 10/31/2016] [Indexed: 01/23/2023] Open
Abstract
In this study, we used multiple meta-omic approaches to characterize the microbial community and the active metabolic pathways of a stable industrial biogas reactor with food waste as the dominant feedstock, operating at thermophilic temperatures (60°C) and elevated levels of free ammonia (367 mg/liter NH3-N). The microbial community was strongly dominated (76% of all 16S rRNA amplicon sequences) by populations closely related to the proteolytic bacterium Coprothermobacter proteolyticus. Multiple Coprothermobacter-affiliated strains were detected, introducing an additional level of complexity seldom explored in biogas studies. Genome reconstructions provided metabolic insight into the microbes that performed biomass deconstruction and fermentation, including the deeply branching phyla Dictyoglomi and Planctomycetes and the candidate phylum "Atribacteria" These biomass degraders were complemented by a synergistic network of microorganisms that convert key fermentation intermediates (fatty acids) via syntrophic interactions with hydrogenotrophic methanogens to ultimately produce methane. Interpretation of the proteomics data also suggested activity of a Methanosaeta phylotype acclimatized to high ammonia levels. In particular, we report multiple novel phylotypes proposed as syntrophic acetate oxidizers, which also exert expression of enzymes needed for both the Wood-Ljungdahl pathway and β-oxidation of fatty acids to acetyl coenzyme A. Such an arrangement differs from known syntrophic oxidizing bacteria and presents an interesting hypothesis for future studies. Collectively, these findings provide increased insight into active metabolic roles of uncultured phylotypes and presents new synergistic relationships, both of which may contribute to the stability of the biogas reactor. IMPORTANCE Biogas production through anaerobic digestion of organic waste provides an attractive source of renewable energy and a sustainable waste management strategy. A comprehensive understanding of the microbial community that drives anaerobic digesters is essential to ensure stable and efficient energy production. Here, we characterize the intricate microbial networks and metabolic pathways in a thermophilic biogas reactor. We discuss the impact of frequently encountered microbial populations as well as the metabolism of newly discovered novel phylotypes that seem to play distinct roles within key microbial stages of anaerobic digestion in this stable high-temperature system. In particular, we draft a metabolic scenario whereby multiple uncultured syntrophic acetate-oxidizing bacteria are capable of syntrophically oxidizing acetate as well as longer-chain fatty acids (via the β-oxidation and Wood-Ljundahl pathways) to hydrogen and carbon dioxide, which methanogens subsequently convert to methane.
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Affiliation(s)
- Live H Hagen
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Jeremy A Frank
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Mirzaman Zamanzadeh
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Vincent G H Eijsink
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Phillip B Pope
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Svein J Horn
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Magnus Ø Arntzen
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
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Dörries M, Wöhlbrand L, Kube M, Reinhardt R, Rabus R. Genome and catabolic subproteomes of the marine, nutritionally versatile, sulfate-reducing bacterium Desulfococcus multivorans DSM 2059. BMC Genomics 2016; 17:918. [PMID: 27846794 PMCID: PMC5109826 DOI: 10.1186/s12864-016-3236-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 11/01/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Sulfate-reducing bacteria (SRB) are key players of the carbon- and sulfur-cycles in the sediments of the world's oceans. Habitat relevant SRBs are often members of the Desulfosarcina-Desulfococcus clade belonging to the deltaproteobacterial family of Desulfobacteraceae. Despite this environmental recognition, their molecular (genome-based) physiology and their potential to contribute to organic carbon mineralization as well as to adapt to changing environmental conditions have been scarcely investigated. A metabolically versatile representative of this family is Desulfococcus multivorans that is able to completely oxidize (to CO2) a variety of organic acids, including fatty acids up to C14, as well as aromatic compounds. RESULTS In this study the complete 4.46 Mbp and manually annotated genome of metabolically versatile Desulfococcus multivorans DSM 2059 is presented with particular emphasis on a proteomics-driven metabolic reconstruction. Proteomic profiling covered 17 substrate adaptation conditions (6 aromatic and 11 aliphatic compounds) and comprised 2D DIGE, shotgun proteomics and analysis of the membrane protein-enriched fractions. This comprehensive proteogenomic dataset allowed for reconstructing a metabolic network of degradation pathways and energy metabolism that consists of 170 proteins (154 detected; ~91 % coverage). Peripheral degradation routes feed via central benzoyl-CoA, (modified) β-oxidation or methylmalonyl-CoA pathways into the Wood-Ljungdahl pathway for complete oxidation of acetyl-CoA to CO2. Dissimilatory sulfate reduction is fueled by a complex electron transfer network composed of cytoplasmic components (e.g., electron transfer flavoproteins) and diverse membrane redox complexes (Dsr, Qmo, Hmc, Tmc, Qrc, Nuo and Rnf). Overall, a high degree of substrate-specific formation of catabolic enzymes was observed, while most complexes involved in electron transfer appeared to be constitutively formed. CONCLUSIONS A highly dynamic genome structure in combination with substrate-specifically formed catabolic subproteomes and a constitutive subproteome for energy metabolism and electron transfer appears to be a common trait of Desulfobacteraceae members.
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Affiliation(s)
- Marvin Dörries
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Oldenburg, Germany
| | - Lars Wöhlbrand
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Oldenburg, Germany
| | - Michael Kube
- Institute of Forest Genetics, Johann Heinrich von Thünen Institute, Waldsieversdorf, Germany
| | | | - Ralf Rabus
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Oldenburg, Germany
- Max Planck Institute for Marine Microbiology, Bremen, Germany
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Nutrient enrichment induces dormancy and decreases diversity of active bacteria in salt marsh sediments. Nat Commun 2016; 7:12881. [PMID: 27666199 PMCID: PMC5052679 DOI: 10.1038/ncomms12881] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 08/10/2016] [Indexed: 11/08/2022] Open
Abstract
Microorganisms control key biogeochemical pathways, thus changes in microbial diversity, community structure and activity can affect ecosystem response to environmental drivers. Understanding factors that control the proportion of active microbes in the environment and how they vary when perturbed is critical to anticipating ecosystem response to global change. Increasing supplies of anthropogenic nitrogen to ecosystems globally makes it imperative that we understand how nutrient supply alters active microbial communities. Here we show that nitrogen additions to salt marshes cause a shift in the active microbial community despite no change in the total community. The active community shift causes the proportion of dormant microbial taxa to double, from 45 to 90%, and induces diversity loss in the active portion of the community. Our results suggest that perturbations to salt marshes can drastically alter active microbial communities, however these communities may remain resilient by protecting total diversity through increased dormancy.
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Cabral L, Júnior GVL, Pereira de Sousa ST, Dias ACF, Lira Cadete L, Andreote FD, Hess M, de Oliveira VM. Anthropogenic impact on mangrove sediments triggers differential responses in the heavy metals and antibiotic resistomes of microbial communities. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2016; 216:460-469. [PMID: 27297401 DOI: 10.1016/j.envpol.2016.05.078] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Revised: 04/27/2016] [Accepted: 05/26/2016] [Indexed: 05/20/2023]
Abstract
Mangroves are complex and dynamic ecosystems highly dependent on diverse microbial activities. In the last decades, these ecosystems have been exposed to and affected by diverse human activities, such as waste disposal and accidental oil spills. Complex microbial communities inhabiting the soil and sediment of mangroves comprise microorganisms that have developed mechanisms to adapt to organic and inorganic contaminants. The resistance of these microbes to contaminants is an attractive property and also the reason why soil and sediment living microorganisms and their enzymes have been considered promising for environmental detoxification. The aim of the present study was to identify active microbial genes in heavy metals, i.e., Cu, Zn, Cd, Pb and Hg, and antibiotic resistomes of polluted and pristine mangrove sediments through the comparative analysis of metatranscriptome data. The concentration of the heavy metals Zn, Cr, Pb, Cu, Ni, Cd, and Hg and abundance of genes and transcripts involved in resistance to toxic compounds (the cobalt-zinc-cadmium resistance protein complex; the cobalt-zinc-cadmium resistance protein CzcA and the cation efflux system protein CusA) have been closely associated with sites impacted with petroleum, sludge and other urban waste. The taxonomic profiling of metatranscriptome sequences suggests that members of Gammaproteobacteria and Deltaproteobacteria classes contribute to the detoxification of the polluted soil. Desulfobacterium autotrophicum was the most abundant microorganism in the oil-impacted site and displayed specific functions related to heavy metal resistance, potentially playing a key role in the successful persistence of the microbial community of this site.
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Affiliation(s)
- Lucélia Cabral
- Research Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Gileno Vieira Lacerda Júnior
- Research Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | | | - Armando Cavalcante Franco Dias
- Department of Soil Science, ''Luiz de Queiroz'' College of Agriculture, University of Sao Paulo, Piracicaba, São Paulo, Brazil
| | - Luana Lira Cadete
- Department of Soil Science, ''Luiz de Queiroz'' College of Agriculture, University of Sao Paulo, Piracicaba, São Paulo, Brazil
| | - Fernando Dini Andreote
- Department of Soil Science, ''Luiz de Queiroz'' College of Agriculture, University of Sao Paulo, Piracicaba, São Paulo, Brazil
| | - Matthias Hess
- University of California, Davis, Department of Animal Science, Davis, CA, USA
| | - Valéria Maia de Oliveira
- Research Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
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Osburn MR, Dawson KS, Fogel ML, Sessions AL. Fractionation of Hydrogen Isotopes by Sulfate- and Nitrate-Reducing Bacteria. Front Microbiol 2016; 7:1166. [PMID: 27531993 PMCID: PMC4969296 DOI: 10.3389/fmicb.2016.01166] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 07/13/2016] [Indexed: 11/30/2022] Open
Abstract
Hydrogen atoms from water and food are incorporated into biomass during cellular metabolism and biosynthesis, fractionating the isotopes of hydrogen—protium and deuterium—that are recorded in biomolecules. While these fractionations are often relatively constant in plants, large variations in the magnitude of fractionation are observed for many heterotrophic microbes utilizing different central metabolic pathways. The correlation between metabolism and lipid δ2H provides a potential basis for reconstructing environmental and ecological parameters, but the calibration dataset has thus far been limited mainly to aerobes. Here we report on the hydrogen isotopic fractionations of lipids produced by nitrate-respiring and sulfate-reducing bacteria. We observe only small differences in fractionation between oxygen- and nitrate-respiring growth conditions, with a typical pattern of variation between substrates that is broadly consistent with previously described trends. In contrast, fractionation by sulfate-reducing bacteria does not vary significantly between different substrates, even when autotrophic and heterotrophic growth conditions are compared. This result is in marked contrast to previously published observations and has significant implications for the interpretation of environmental hydrogen isotope data. We evaluate these trends in light of metabolic gene content of each strain, growth rate, and potential flux and reservoir-size effects of cellular hydrogen, but find no single variable that can account for the differences between nitrate- and sulfate-respiring bacteria. The emerging picture of bacterial hydrogen isotope fractionation is therefore more complex than the simple correspondence between δ2H and metabolic pathway previously understood from aerobes. Despite the complexity, the large signals and rich variability of observed lipid δ2H suggest much potential as an environmental recorder of metabolism.
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Affiliation(s)
- Magdalena R Osburn
- Division of Geological and Planetary Sciences, California Institute of Technology Pasadena, CA, USA
| | - Katherine S Dawson
- Division of Geological and Planetary Sciences, California Institute of Technology Pasadena, CA, USA
| | - Marilyn L Fogel
- Life and Environmental Sciences, School of Natural Science, University of California at Merced Merced, CA, USA
| | - Alex L Sessions
- Division of Geological and Planetary Sciences, California Institute of Technology Pasadena, CA, USA
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Winkel M, Salman-Carvalho V, Woyke T, Richter M, Schulz-Vogt HN, Flood BE, Bailey JV, Mußmann M. Single-cell Sequencing of Thiomargarita Reveals Genomic Flexibility for Adaptation to Dynamic Redox Conditions. Front Microbiol 2016; 7:964. [PMID: 27446006 PMCID: PMC4914600 DOI: 10.3389/fmicb.2016.00964] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2016] [Accepted: 06/03/2016] [Indexed: 11/25/2022] Open
Abstract
Large, colorless sulfur-oxidizing bacteria (LSB) of the family Beggiatoaceae form thick mats at sulfidic sediment surfaces, where they efficiently detoxify sulfide before it enters the water column. The genus Thiomargarita harbors the largest known free-living bacteria with cell sizes of up to 750 μm in diameter. In addition to their ability to oxidize reduced sulfur compounds, some Thiomargarita spp. are known to store large amounts of nitrate, phosphate and elemental sulfur internally. To date little is known about their energy yielding metabolic pathways, and how these pathways compare to other Beggiatoaceae. Here, we present a draft single-cell genome of a chain-forming “Candidatus Thiomargarita nelsonii Thio36”, and conduct a comparative analysis to five draft and one full genome of other members of the Beggiatoaceae. “Ca. T. nelsonii Thio36” is able to respire nitrate to both ammonium and dinitrogen, which allows them to flexibly respond to environmental changes. Genes for sulfur oxidation and inorganic carbon fixation confirmed that “Ca. T. nelsonii Thio36” can function as a chemolithoautotroph. Carbon can be fixed via the Calvin–Benson–Bassham cycle, which is common among the Beggiatoaceae. In addition we found key genes of the reductive tricarboxylic acid cycle that point toward an alternative CO2 fixation pathway. Surprisingly, “Ca. T. nelsonii Thio36” also encodes key genes of the C2-cycle that convert 2-phosphoglycolate to 3-phosphoglycerate during photorespiration in higher plants and cyanobacteria. Moreover, we identified a novel trait of a flavin-based energy bifurcation pathway coupled to a Na+-translocating membrane complex (Rnf). The coupling of these pathways may be key to surviving long periods of anoxia. As other Beggiatoaceae “Ca. T. nelsonii Thio36” encodes many genes similar to those of (filamentous) cyanobacteria. In summary, the genome of “Ca. T. nelsonii Thio36” provides additional insight into the ecology of giant sulfur-oxidizing bacteria, and reveals unique genomic features for the Thiomargarita lineage within the Beggiatoaceae.
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Affiliation(s)
- Matthias Winkel
- Molecular Ecology Group, Department of Molecular Ecology, Max Planck Institute for Marine MicrobiologyBremen, Germany; Section Geomicrobiology, GFZ German Research Centre for Geoscience, Helmholtz Centre PotsdamPotsdam, Germany
| | - Verena Salman-Carvalho
- HGF MPG Joint Research Group for Deep-sea Ecology and Technology, Max Planck Institute for Marine Microbiology Bremen, Germany
| | - Tanja Woyke
- Department of Energy Joint Genome Institute, Walnut Creek CA, USA
| | - Michael Richter
- Microbial Genomics and Bioinformatics Group, Department of Molecular Ecology, Max Planck Institute for Marine Microbiology Bremen, Germany
| | | | - Beverly E Flood
- Department of Earth Sciences, University of Minnesota, Minneapolis MN, USA
| | - Jake V Bailey
- Department of Earth Sciences, University of Minnesota, Minneapolis MN, USA
| | - Marc Mußmann
- Molecular Ecology Group, Department of Molecular Ecology, Max Planck Institute for Marine Microbiology Bremen, Germany
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Kirkegaard RH, Dueholm MS, McIlroy SJ, Nierychlo M, Karst SM, Albertsen M, Nielsen PH. Genomic insights into members of the candidate phylum Hyd24-12 common in mesophilic anaerobic digesters. ISME JOURNAL 2016; 10:2352-64. [PMID: 27058503 PMCID: PMC5030696 DOI: 10.1038/ismej.2016.43] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 02/15/2016] [Accepted: 02/22/2016] [Indexed: 12/13/2022]
Abstract
Members of the candidate phylum Hyd24-12 are globally distributed, but no genomic information or knowledge about their morphology, physiology or ecology is available. In this study, members of the Hyd24-12 lineage were shown to be present and abundant in full-scale mesophilic anaerobic digesters at Danish wastewater treatment facilities. In some samples, a member of the Hyd24-12 lineage was one of the most abundant genus-level bacterial taxa, accounting for up to 8% of the bacterial biomass. Three closely related and near-complete genomes were retrieved using metagenome sequencing of full-scale anaerobic digesters. Genome annotation and metabolic reconstruction showed that they are Gram-negative bacteria likely involved in acidogenesis, producing acetate and hydrogen from fermentation of sugars, and may play a role in the cycling of sulphur in the digesters. Fluorescence in situ hybridization revealed single rod-shaped cells dispersed within the flocs. The genomic information forms a foundation for a more detailed understanding of their role in anaerobic digestion and provides the first insight into a hitherto undescribed branch in the tree of life.
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Affiliation(s)
- Rasmus Hansen Kirkegaard
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Morten Simonsen Dueholm
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Simon Jon McIlroy
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Marta Nierychlo
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Søren Michael Karst
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Mads Albertsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Per Halkjær Nielsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
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Krukenberg V, Harding K, Richter M, Glöckner FO, Gruber-Vodicka HR, Adam B, Berg JS, Knittel K, Tegetmeyer HE, Boetius A, Wegener G. CandidatusDesulfofervidus auxilii, a hydrogenotrophic sulfate-reducing bacterium involved in the thermophilic anaerobic oxidation of methane. Environ Microbiol 2016; 18:3073-91. [DOI: 10.1111/1462-2920.13283] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 02/23/2016] [Accepted: 02/24/2016] [Indexed: 01/20/2023]
Affiliation(s)
| | - Katie Harding
- Max Planck Institute for Marine Microbiology; Bremen Germany
| | - Michael Richter
- Max Planck Institute for Marine Microbiology; Bremen Germany
| | - Frank Oliver Glöckner
- Max Planck Institute for Marine Microbiology; Bremen Germany
- Jacobs University Bremen gGmbH; Bremen Germany
| | | | - Birgit Adam
- Max Planck Institute for Marine Microbiology; Bremen Germany
| | - Jasmine S. Berg
- Max Planck Institute for Marine Microbiology; Bremen Germany
| | - Katrin Knittel
- Max Planck Institute for Marine Microbiology; Bremen Germany
| | - Halina E. Tegetmeyer
- Alfred Wegener Institute, Helmholtz Center for Polar and Marine Research; Bremerhaven Germany
- Center for Biotechnology, Bielefeld University; Bielefeld Germany
| | - Antje Boetius
- Max Planck Institute for Marine Microbiology; Bremen Germany
- Alfred Wegener Institute, Helmholtz Center for Polar and Marine Research; Bremerhaven Germany
- MARUM, Center for Marine Environmental Sciences, University Bremen; Bremen Germany
| | - Gunter Wegener
- Max Planck Institute for Marine Microbiology; Bremen Germany
- MARUM, Center for Marine Environmental Sciences, University Bremen; Bremen Germany
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39
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Bargiela R, Herbst FA, Martínez-Martínez M, Seifert J, Rojo D, Cappello S, Genovese M, Crisafi F, Denaro R, Chernikova TN, Barbas C, von Bergen M, Yakimov MM, Ferrer M, Golyshin PN. Metaproteomics and metabolomics analyses of chronically petroleum-polluted sites reveal the importance of general anaerobic processes uncoupled with degradation. Proteomics 2015; 15:3508-20. [PMID: 26201687 PMCID: PMC4973819 DOI: 10.1002/pmic.201400614] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2014] [Revised: 05/21/2015] [Accepted: 07/20/2015] [Indexed: 11/24/2022]
Abstract
Crude oil is one of the most important natural assets for humankind, yet it is a major environmental pollutant, notably in marine environments. One of the largest crude oil polluted areas in the word is the semi-enclosed Mediterranean Sea, in which the metabolic potential of indigenous microbial populations towards the large-scale chronic pollution is yet to be defined, particularly in anaerobic and micro-aerophilic sites. Here, we provide an insight into the microbial metabolism in sediments from three chronically polluted marine sites along the coastline of Italy: the Priolo oil terminal/refinery site (near Siracuse, Sicily), harbour of Messina (Sicily) and shipwreck of MT Haven (near Genoa). Using shotgun metaproteomics and community metabolomics approaches, the presence of 651 microbial proteins and 4776 metabolite mass features have been detected in these three environments, revealing a high metabolic heterogeneity between the investigated sites. The proteomes displayed the prevalence of anaerobic metabolisms that were not directly related with petroleum biodegradation, indicating that in the absence of oxygen, biodegradation is significantly suppressed. This suppression was also suggested by examining the metabolome patterns. The proteome analysis further highlighted the metabolic coupling between methylotrophs and sulphate reducers in oxygen-depleted petroleum-polluted sediments.
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Affiliation(s)
- Rafael Bargiela
- Consejo Superior de Investigaciones Científicas (CSIC), Institute of Catalysis, Madrid, Spain
| | - Florian-Alexander Herbst
- Department of Proteomics, UFZ - Helmholtz Centre for Environmental Research, Leipzig, Germany
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | | | - Jana Seifert
- Department of Proteomics, UFZ - Helmholtz Centre for Environmental Research, Leipzig, Germany
- Institute of Animal Science, Universität Hohenheim, Stuttgart, Germany
| | - David Rojo
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Madrid, Spain
| | - Simone Cappello
- Institute for Coastal Marine Environment, CNR, Messina, Italy
| | - María Genovese
- Institute for Coastal Marine Environment, CNR, Messina, Italy
| | | | - Renata Denaro
- Institute for Coastal Marine Environment, CNR, Messina, Italy
| | | | - Coral Barbas
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Madrid, Spain
| | - Martin von Bergen
- Department of Proteomics, UFZ - Helmholtz Centre for Environmental Research, Leipzig, Germany
- Department of Metabolomics, UFZ - Helmholtz Centre for Environmental Research, Leipzig, Germany
| | | | - Manuel Ferrer
- Consejo Superior de Investigaciones Científicas (CSIC), Institute of Catalysis, Madrid, Spain
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40
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A Post-Genomic View of the Ecophysiology, Catabolism and Biotechnological Relevance of Sulphate-Reducing Prokaryotes. Adv Microb Physiol 2015. [PMID: 26210106 DOI: 10.1016/bs.ampbs.2015.05.002] [Citation(s) in RCA: 174] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Dissimilatory sulphate reduction is the unifying and defining trait of sulphate-reducing prokaryotes (SRP). In their predominant habitats, sulphate-rich marine sediments, SRP have long been recognized to be major players in the carbon and sulphur cycles. Other, more recently appreciated, ecophysiological roles include activity in the deep biosphere, symbiotic relations, syntrophic associations, human microbiome/health and long-distance electron transfer. SRP include a high diversity of organisms, with large nutritional versatility and broad metabolic capacities, including anaerobic degradation of aromatic compounds and hydrocarbons. Elucidation of novel catabolic capacities as well as progress in the understanding of metabolic and regulatory networks, energy metabolism, evolutionary processes and adaptation to changing environmental conditions has greatly benefited from genomics, functional OMICS approaches and advances in genetic accessibility and biochemical studies. Important biotechnological roles of SRP range from (i) wastewater and off gas treatment, (ii) bioremediation of metals and hydrocarbons and (iii) bioelectrochemistry, to undesired impacts such as (iv) souring in oil reservoirs and other environments, and (v) corrosion of iron and concrete. Here we review recent advances in our understanding of SRPs focusing mainly on works published after 2000. The wealth of publications in this period, covering many diverse areas, is a testimony to the large environmental, biogeochemical and technological relevance of these organisms and how much the field has progressed in these years, although many important questions and applications remain to be explored.
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41
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Ramos AR, Grein F, Oliveira GP, Venceslau SS, Keller KL, Wall JD, Pereira IAC. The FlxABCD-HdrABC proteins correspond to a novel NADH dehydrogenase/heterodisulfide reductase widespread in anaerobic bacteria and involved in ethanol metabolism in Desulfovibrio vulgaris Hildenborough. Environ Microbiol 2015; 17:2288-305. [PMID: 25367508 DOI: 10.1111/1462-2920.12689] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2014] [Accepted: 10/23/2014] [Indexed: 11/29/2022]
Abstract
Flavin-based electron bifurcation (FBEB) is an important mechanism for the energy metabolism of anaerobes. A new family of NADH dehydrogenases, the flavin oxidoreductase (FlxABCD, previously called FloxABCD), was proposed to perform FBEB in sulphate-reducing organisms coupled with heterodisulfide reductase (HdrABC). We found that the hdrABC-flxABCD gene cluster is widespread among anaerobic bacteria, pointing to a general and important role in their bioenergetics. In this work, we studied FlxABCD of Desulfovibrio vulgaris Hildenborough. The hdr-flx genes are part of the same transcriptional unit and are increased in transcription during growth in ethanol-sulfate, and to a less extent during pyruvate fermentation. Two mutant strains were generated: one where expression of the hdr-flx genes was interrupted and another lacking the flxA gene. Both strains were unable to grow with ethanol-sulfate, whereas growth was restored in a flxA-complemented strain. The mutant strains also produced very reduced amounts of ethanol compared with the wild type during pyruvate fermentation. Our results show that in D. vulgaris, the FlxABCD-HdrABC proteins are essential for NADH oxidation during growth on ethanol, probably involving a FBEB mechanism that leads to reduction of ferredoxin and the small protein DsrC, while in fermentation they operate in reverse, reducing NAD(+) for ethanol production.
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Affiliation(s)
- Ana Raquel Ramos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, 2780-157, Portugal
| | - Fabian Grein
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, 2780-157, Portugal
| | - Gonçalo P Oliveira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, 2780-157, Portugal
| | - Sofia S Venceslau
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, 2780-157, Portugal
| | - Kimberly L Keller
- Biochemistry Department, University of Missouri, Columbia, MO, USA.,ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies), Berkeley, CA, USA
| | - Judy D Wall
- Biochemistry Department, University of Missouri, Columbia, MO, USA.,ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies), Berkeley, CA, USA
| | - Inês A C Pereira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, 2780-157, Portugal
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42
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Justice NB, Norman A, Brown CT, Singh A, Thomas BC, Banfield JF. Comparison of environmental and isolate Sulfobacillus genomes reveals diverse carbon, sulfur, nitrogen, and hydrogen metabolisms. BMC Genomics 2014; 15:1107. [PMID: 25511286 PMCID: PMC4378227 DOI: 10.1186/1471-2164-15-1107] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 11/27/2014] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Bacteria of the genus Sulfobacillus are found worldwide as members of microbial communities that accelerate sulfide mineral dissolution in acid mine drainage environments (AMD), acid-rock drainage environments (ARD), as well as in industrial bioleaching operations. Despite their frequent identification in these environments, their role in biogeochemical cycling is poorly understood. RESULTS Here we report draft genomes of five species of the Sulfobacillus genus (AMDSBA1-5) reconstructed by cultivation-independent sequencing of biofilms sampled from the Richmond Mine (Iron Mountain, CA). Three of these species (AMDSBA2, AMDSBA3, and AMDSBA4) have no cultured representatives while AMDSBA1 is a strain of S. benefaciens, and AMDSBA5 a strain of S. thermosulfidooxidans. We analyzed the diversity of energy conservation and central carbon metabolisms for these genomes and previously published Sulfobacillus genomes. Pathways of sulfur oxidation vary considerably across the genus, including the number and type of subunits of putative heterodisulfide reductase complexes likely involved in sulfur oxidation. The number and type of nickel-iron hydrogenase proteins varied across the genus, as does the presence of different central carbon pathways. Only the AMDSBA3 genome encodes a dissimilatory nitrate reducatase and only the AMDSBA5 and S. thermosulfidooxidans genomes encode assimilatory nitrate reductases. Within the genus, AMDSBA4 is unusual in that its electron transport chain includes a cytochrome bc type complex, a unique cytochrome c oxidase, and two distinct succinate dehydrogenase complexes. CONCLUSIONS Overall, the results significantly expand our understanding of carbon, sulfur, nitrogen, and hydrogen metabolism within the Sulfobacillus genus.
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Affiliation(s)
- Nicholas B Justice
- />Department of Earth and Planetary Science, University of California, Berkeley, CA 94720 USA
- />Physical Biosciences Division, Lawrence Berkeley National Lab, Berkeley, CA USA
| | - Anders Norman
- />Department of Earth and Planetary Science, University of California, Berkeley, CA 94720 USA
- />Section for Infection Microbiology, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Christopher T Brown
- />Department of Earth and Planetary Science, University of California, Berkeley, CA 94720 USA
| | - Andrea Singh
- />Department of Earth and Planetary Science, University of California, Berkeley, CA 94720 USA
| | - Brian C Thomas
- />Department of Earth and Planetary Science, University of California, Berkeley, CA 94720 USA
| | - Jillian F Banfield
- />Department of Earth and Planetary Science, University of California, Berkeley, CA 94720 USA
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Abstract
Environmental bacteria play a central role in the Earth's elemental cycles and represent a mostly untapped reservoir for novel metabolic capacities and biocatalysts. Over the last 15 years, the author's laboratory has focused on three major switches in the breakdown of organic carbon defined by the abundance and recalcitrance of the substrates: carbohydrates and amino acids by aerobic heterotrophs, fermentation end products by sulphate reducers and anaerobic degradation of aromatic compounds and hydrocarbons by denitrifiers and sulphate reducers. As these bacteria are novel isolates mostly not accessibly by molecular genetics, genomics combined with differential proteomics was early on applied to obtain molecular-functional insights into degradation pathways, catabolic and regulatory networks, as well as mechanisms and strategies for adapting to changing environmental conditions. This review provides some background on research motivations and briefly summarizes insights into studied model organisms, e.g. "Aromatoleum aromaticum" EbN1, Desulfobacula toluolica Tol2 and Phaeobacter inhibens DSM 17395.
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Affiliation(s)
- R Rabus
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), University Oldenburg , Oldenburg , Germany
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44
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Rothery RA, Weiner JH. Shifting the metallocentric molybdoenzyme paradigm: the importance of pyranopterin coordination. J Biol Inorg Chem 2014; 20:349-72. [PMID: 25267303 DOI: 10.1007/s00775-014-1194-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 09/15/2014] [Indexed: 01/10/2023]
Abstract
In this review, we test the hypothesis that pyranopterin coordination plays a critical role in defining substrate reactivities in the four families of mononuclear molybdenum and tungsten enzymes (Mo/W-enzymes). Enzyme families containing a single pyranopterin dithiolene chelate have been demonstrated to have reactivity towards two (sulfite oxidase, SUOX-fold) and five (xanthine dehydrogenase, XDH-fold) types of substrate, whereas the major family of enzymes containing a bis-pyranopterin dithiolene chelate (dimethylsulfoxide reductase, DMSOR-fold) is reactive towards eight types of substrate. A second bis-pyranopterin enzyme (aldehyde oxidoreductase, AOR-fold) family catalyzes a single type of reaction. The diversity of reactions catalyzed by each family correlates with active site variability, and also with the number of pyranopterins and their coordination by the protein. In the case of the AOR-fold enzymes, inflexibility of pyranopterin coordination correlates with their limited substrate specificity (oxidation of aldehydes). In examples of the SUOX-fold and DMSOR-fold enzymes, we observe three types of histidine-containing charge-transfer relays that can: (1) connect the piperazine ring of the pyranopterin to the substrate-binding site (SUOX-fold enzymes); (2) provide inter-pyranopterin communication (DMSOR-fold enzymes); and (3) connect a pyran ring oxygen to deeply buried water molecules (the DMSOR-fold NarGHI-type nitrate reductases). Finally, sequence data mining reveals a number of bacterial species whose predicted proteomes contain large numbers (up to 64) of Mo/W-enzymes, with the DMSOR-fold enzymes being dominant. These analyses also reveal an inverse correlation between Mo/W-enzyme content and pathogenicity.
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Affiliation(s)
- Richard A Rothery
- Department of Biochemistry, University of Alberta, Edmonton, AB, T6G 2H7, Canada
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45
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Dalla Vecchia E, Shao PP, Suvorova E, Chiappe D, Hamelin R, Bernier-Latmani R. Characterization of the surfaceome of the metal-reducing bacterium Desulfotomaculum reducens. Front Microbiol 2014; 5:432. [PMID: 25191310 PMCID: PMC4137172 DOI: 10.3389/fmicb.2014.00432] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Accepted: 07/31/2014] [Indexed: 11/13/2022] Open
Abstract
Desulfotomaculum reducens strain MI-1 is a Gram-positive, sulfate-reducing bacterium also capable of reducing Fe(III). Metal reduction in Gram-positive bacteria is poorly understood. Here, we investigated Fe(III) reduction with lactate, a non-fermentable substrate, as the electron donor. Lactate consumption is concomitant to Fe(III) reduction, but does not support significant growth, suggesting that little energy can be conserved from this process and that it may occur fortuitously. D. reducens can reduce both soluble [Fe(III)-citrate] and insoluble (hydrous ferric oxide, HFO) Fe(III). Because physically inaccessible HFO was not reduced, we concluded that reduction requires direct contact under these experimental conditions. This implies the presence of a surface exposed reductase capable of transferring electrons from the cell to the extracellular electron acceptor. With the goal of characterizing the role of surface proteins in D. reducens and of identifying candidate Fe(III) reductases, we carried out an investigation of the surface proteome (surfaceome) of D. reducens. Cell surface exposed proteins were extracted by trypsin cell shaving or by lysozyme treatment, and analyzed by liquid chromatography-tandem mass spectrometry. This investigation revealed that the surfaceome fulfills many functions, including solute transport, protein export, maturation and hydrolysis, peptidoglycan synthesis and modification, and chemotaxis. Furthermore, a few redox-active proteins were identified. Among these, three are putatively involved in Fe(III) reduction, i.e., a membrane-bound hydrogenase 4Fe-4S cluster subunit (Dred_0462), a heterodisulfide reductase subunit A (Dred_0143) and a protein annotated as alkyl hydroperoxide reductase but likely functioning as a thiol-disulfide oxidoreductase (Dred_1533).
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Affiliation(s)
- Elena Dalla Vecchia
- Environmental Microbiology Laboratory, Environmental Engineering Institute, École Polytechnique Fédérale de Lausanne Lausanne, Switzerland
| | - Paul P Shao
- Environmental Microbiology Laboratory, Environmental Engineering Institute, École Polytechnique Fédérale de Lausanne Lausanne, Switzerland
| | - Elena Suvorova
- Environmental Microbiology Laboratory, Environmental Engineering Institute, École Polytechnique Fédérale de Lausanne Lausanne, Switzerland
| | - Diego Chiappe
- Proteomics Core Facility, Core Facility PTECH, École Polytechnique Fédérale de Lausanne Lausanne, Switzerland
| | - Romain Hamelin
- Proteomics Core Facility, Core Facility PTECH, École Polytechnique Fédérale de Lausanne Lausanne, Switzerland
| | - Rizlan Bernier-Latmani
- Environmental Microbiology Laboratory, Environmental Engineering Institute, École Polytechnique Fédérale de Lausanne Lausanne, Switzerland
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46
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Bozinovski D, Taubert M, Kleinsteuber S, Richnow HH, von Bergen M, Vogt C, Seifert J. Metaproteogenomic analysis of a sulfate-reducing enrichment culture reveals genomic organization of key enzymes in the m-xylene degradation pathway and metabolic activity of proteobacteria. Syst Appl Microbiol 2014; 37:488-501. [PMID: 25156802 DOI: 10.1016/j.syapm.2014.07.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Revised: 06/02/2014] [Accepted: 07/15/2014] [Indexed: 10/24/2022]
Abstract
This study aimed to ascertain the functional and phylogenetic relationships within an m-xylene degrading sulfate-reducing enrichment culture, which had been maintained for several years in the laboratory with m-xylene as the sole source of carbon and energy. Previous studies indicated that a phylotype affiliated to the Desulfobacteraceae was the main m-xylene assimilating organism. In the present study, genes and gene products were identified by a metaproteogenomic approach using LC-MS/MS analysis of the microbial community, and 2426 peptides were identified from 576 proteins. In the metagenome of the community, gene clusters encoding enzymes involved in fumarate addition to a methyl moiety of m-xylene (nms, bss), as well as gene clusters coding for enzymes involved in modified beta-oxidation to (3-methyl)benzoyl-CoA (bns), were identified in two separate contigs. Additionally, gene clusters containing homologues to bam genes encoding benzoyl-CoA reductase (Bcr) class II, catalyzing the dearomatization of (3-methyl)benzoyl-CoA, were identified. Time-resolved protein stable isotope probing (protein-SIP) experiments using (13)C-labeled m-xylene showed that the respective gene products were highly (13)C-labeled. The present data suggested the identification of gene products that were similar to those involved in methylnaphthalene degradation even though the consortium was not capable of growing in the presence of naphthalene, methylnaphthalene or toluene as substrates. Thus, a novel branch of enzymes was found that was probably specific for anaerobic m-xylene degradation.
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Affiliation(s)
- Dragana Bozinovski
- UFZ-Helmholtz Centre for Environmental Research, Department of Proteomics, 04318 Leipzig, Germany
| | - Martin Taubert
- UFZ-Helmholtz Centre for Environmental Research, Department of Proteomics, 04318 Leipzig, Germany; School of Environmental Sciences, University of East Anglia, Norwich NR4 7TJ, UK
| | - Sabine Kleinsteuber
- UFZ-Helmholtz Centre for Environmental Research, Department of Environmental Microbiology, 04318 Leipzig, Germany
| | - Hans-Hermann Richnow
- UFZ-Helmholtz Centre for Environmental Research, Department of Isotope Biogeochemistry, 04318 Leipzig, Germany
| | - Martin von Bergen
- UFZ-Helmholtz Centre for Environmental Research, Department of Proteomics, 04318 Leipzig, Germany; UFZ-Helmholtz Centre for Environmental Research, Department of Metabolomics, 04318 Leipzig, Germany; Aalborg University, Department of Biotechnology, Chemistry and Environmental Engineering, Aalborg University, 9000 Aalborg, Denmark
| | - Carsten Vogt
- UFZ-Helmholtz Centre for Environmental Research, Department of Isotope Biogeochemistry, 04318 Leipzig, Germany
| | - Jana Seifert
- UFZ-Helmholtz Centre for Environmental Research, Department of Proteomics, 04318 Leipzig, Germany; University of Hohenheim, Institute of Animal Nutrition, 70599 Stuttgart, Germany.
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Gutiérrez Acosta OB, Schleheck D, Schink B. Acetone utilization by sulfate-reducing bacteria: draft genome sequence of Desulfococcus biacutus and a proteomic survey of acetone-inducible proteins. BMC Genomics 2014; 15:584. [PMID: 25012398 PMCID: PMC4103992 DOI: 10.1186/1471-2164-15-584] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Accepted: 07/03/2014] [Indexed: 11/30/2022] Open
Abstract
Background The sulfate-reducing bacterium Desulfococcus biacutus is able to utilize acetone for growth by an inducible degradation pathway that involves a novel activation reaction for acetone with CO as a co-substrate. The mechanism, enzyme(s) and gene(s) involved in this acetone activation reaction are of great interest because they represent a novel and yet undefined type of activation reaction under strictly anoxic conditions. Results In this study, a draft genome sequence of D. biacutus was established. Sequencing, assembly and annotation resulted in 159 contigs with 5,242,029 base pairs and 4773 predicted genes; 4708 were predicted protein-encoding genes, and 3520 of these had a functional prediction. Proteins and genes were identified that are specifically induced during growth with acetone. A thiamine diphosphate-requiring enzyme appeared to be highly induced during growth with acetone and is probably involved in the activation reaction. Moreover, a coenzyme B12- dependent enzyme and proteins that are involved in redox reactions were also induced during growth with acetone. Conclusions We present for the first time the genome of a sulfate reducer that is able to grow with acetone. The genome information of this organism represents an important tool for the elucidation of a novel reaction mechanism that is employed by a sulfate reducer in acetone activation. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-584) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | - Bernhard Schink
- Department of Biology and Konstanz Research School Chemical Biology, University of Konstanz, D-78457 Konstanz, Germany.
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-Biao Guo F, Lin Y, -Ling Chen L. Recognition of Protein-coding Genes Based on Z-curve Algorithms. Curr Genomics 2014; 15:95-103. [PMID: 24822027 PMCID: PMC4009845 DOI: 10.2174/1389202915999140328162724] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2013] [Revised: 11/19/2013] [Accepted: 11/20/2013] [Indexed: 01/18/2023] Open
Abstract
Recognition of protein-coding genes, a classical bioinformatics issue, is an absolutely needed step for annotating newly sequenced genomes. The Z-curve algorithm, as one of the most effective methods on this issue, has been successfully applied in annotating or re-annotating many genomes, including those of bacteria, archaea and viruses. Two Z-curve based ab initio gene-finding programs have been developed: ZCURVE (for bacteria and archaea) and ZCURVE_V (for viruses and phages). ZCURVE_C (for 57 bacteria) and Zfisher (for any bacterium) are web servers for re-annotation of bacterial and archaeal genomes. The above four tools can be used for genome annotation or re-annotation, either independently or combined with the other gene-finding programs. In addition to recognizing protein-coding genes and exons, Z-curve algorithms are also effective in recognizing promoters and translation start sites. Here, we summarize the applications of Z-curve algorithms in gene finding and genome annotation.
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Affiliation(s)
- Feng -Biao Guo
- Center of Bioinformatics and Key Laboratory for NeuroInformation of the Ministry of Education, University of Elec-tronic Science and Technology of China, Chengdu, 610054, China
| | - Yan Lin
- Department of Physics, Tianjin University, Tianjin 300072, China
| | - Ling -Ling Chen
- cCollege of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
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Origin and evolution of the sodium -pumping NADH: ubiquinone oxidoreductase. PLoS One 2014; 9:e96696. [PMID: 24809444 PMCID: PMC4014512 DOI: 10.1371/journal.pone.0096696] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Accepted: 04/11/2014] [Indexed: 11/27/2022] Open
Abstract
The sodium -pumping NADH: ubiquinone oxidoreductase (Na+-NQR) is the main ion pump and the primary entry site for electrons into the respiratory chain of many different types of pathogenic bacteria. This enzymatic complex creates a transmembrane gradient of sodium that is used by the cell to sustain ionic homeostasis, nutrient transport, ATP synthesis, flagellum rotation and other essential processes. Comparative genomics data demonstrate that the nqr operon, which encodes all Na+-NQR subunits, is found in a large variety of bacterial lineages with different habitats and metabolic strategies. Here we studied the distribution, origin and evolution of this enzymatic complex. The molecular phylogenetic analyses and the organizations of the nqr operon indicate that Na+-NQR evolved within the Chlorobi/Bacteroidetes group, after the duplication and subsequent neofunctionalization of the operon that encodes the homolog RNF complex. Subsequently, the nqr operon dispersed through multiple horizontal transfer events to other bacterial lineages such as Chlamydiae, Planctomyces and α, β, γ and δ -proteobacteria. Considering the biochemical properties of the Na+-NQR complex and its physiological role in different bacteria, we propose a detailed scenario to explain the molecular mechanisms that gave rise to its novel redox- dependent sodium -pumping activity. Our model postulates that the evolution of the Na+-NQR complex involved a functional divergence from its RNF homolog, following the duplication of the rnf operon, the loss of the rnfB gene and the recruitment of the reductase subunit of an aromatic monooxygenase.
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50
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Zhang R, Zhang CT. A Brief Review: The Z-curve Theory and its Application in Genome Analysis. Curr Genomics 2014; 15:78-94. [PMID: 24822026 PMCID: PMC4009844 DOI: 10.2174/1389202915999140328162433] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2013] [Revised: 10/16/2013] [Accepted: 10/16/2013] [Indexed: 11/22/2022] Open
Abstract
In theoretical physics, there exist two basic mathematical approaches, algebraic and geometrical methods, which, in most cases, are complementary. In the area of genome sequence analysis, however, algebraic approaches have been widely used, while geometrical approaches have been less explored for a long time. The Z-curve theory is a geometrical approach to genome analysis. The Z-curve is a three-dimensional curve that represents a given DNA sequence in the sense that each can be uniquely reconstructed given the other. The Z-curve, therefore, contains all the information that the corresponding DNA sequence carries. The analysis of a DNA sequence can then be performed through studying the corresponding Z-curve. The Z-curve method has found applications in a wide range of areas in the past two decades, including the identifications of protein-coding genes, replication origins, horizontally-transferred genomic islands, promoters, translational start sides and isochores, as well as studies on phylogenetics, genome visualization and comparative genomics. Here, we review the progress of Z-curve studies from aspects of both theory and applications in genome analysis.
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Affiliation(s)
- Ren Zhang
- Center for Molecular Medicine and Genetics, Wayne State University Medical School, Detroit, MI 48201, USA
| | - Chun-Ting Zhang
- Department of Physics, Tianjin University, Tianjin 300072, China
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