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Valenzuela JJ, Immanuel SRC, Wilson J, Turkarslan S, Ruiz M, Gibbons SM, Hunt KA, Stopnisek N, Auer M, Zemla M, Stahl DA, Baliga NS. Origin of biogeographically distinct ecotypes during laboratory evolution. Nat Commun 2024; 15:7451. [PMID: 39198408 PMCID: PMC11358416 DOI: 10.1038/s41467-024-51759-y] [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: 06/05/2023] [Accepted: 08/15/2024] [Indexed: 09/01/2024] Open
Abstract
Resource partitioning is central to the incredible productivity of microbial communities, including gigatons in annual methane emissions through syntrophic interactions. Previous work revealed how a sulfate reducer (Desulfovibrio vulgaris, Dv) and a methanogen (Methanococcus maripaludis, Mm) underwent evolutionary diversification in a planktonic context, improving stability, cooperativity, and productivity within 300-1000 generations. Here, we show that mutations in just 15 Dv and 7 Mm genes within a minimal assemblage of this evolved community gave rise to co-existing ecotypes that were spatially enriched within a few days of culturing in a fluidized bed reactor. The spatially segregated communities partitioned resources in the simulated subsurface environment, with greater lactate utilization by attached Dv but partial utilization of resulting H2 by low affinity hydrogenases of Mm in the same phase. The unutilized H2 was scavenged by high affinity hydrogenases of planktonic Mm, producing copious amounts of methane. Our findings show how a few mutations can drive resource partitioning amongst niche-differentiated ecotypes, whose interplay synergistically improves productivity of the entire mutualistic community.
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Affiliation(s)
| | | | - James Wilson
- Institute for Systems Biology, Seattle, WA, 98109, USA
| | | | - Maryann Ruiz
- Institute for Systems Biology, Seattle, WA, 98109, USA
| | - Sean M Gibbons
- Institute for Systems Biology, Seattle, WA, 98109, USA
- Department of Bioengineering, University of Washington, Seattle, WA, 98195, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA
- eScience Institute, University of Washington, Seattle, WA, 98195, USA
| | - Kristopher A Hunt
- Civil and Environmental Engineering, University of Washington, Seattle, WA, 98195, USA
| | - Nejc Stopnisek
- Civil and Environmental Engineering, University of Washington, Seattle, WA, 98195, USA
| | - Manfred Auer
- Department of Biomedical Engineering, School of Biological Sciences and Medical Engineering, Southeast University, Nanjing, China
| | - Marcin Zemla
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - David A Stahl
- Civil and Environmental Engineering, University of Washington, Seattle, WA, 98195, USA
| | - Nitin S Baliga
- Institute for Systems Biology, Seattle, WA, 98109, USA.
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Department of Biology, University of Washington, Seattle, WA, USA.
- Department of Microbiology, University of Washington, Seattle, WA, USA.
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA.
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Marbehan X, Roger M, Fournier F, Infossi P, Guedon E, Delecourt L, Lebrun R, Giudici-Orticoni MT, Delaunay S. Combining metabolic flux analysis with proteomics to shed light on the metabolic flexibility: the case of Desulfovibrio vulgaris Hildenborough. Front Microbiol 2024; 15:1336360. [PMID: 38463485 PMCID: PMC10920352 DOI: 10.3389/fmicb.2024.1336360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 01/24/2024] [Indexed: 03/12/2024] Open
Abstract
Introduction Desulfovibrio vulgaris Hildenborough is a gram-negative anaerobic bacterium belonging to the sulfate-reducing bacteria that exhibits highly versatile metabolism. By switching from one energy mode to another depending on nutrients availability in the environments" it plays a central role in shaping ecosystems. Despite intensive efforts to study D. vulgaris energy metabolism at the genomic, biochemical and ecological level, bioenergetics in this microorganism remain far from being fully understood. Alternatively, metabolic modeling is a powerful tool to understand bioenergetics. However, all the current models for D. vulgaris appeared to be not easily adaptable to various environmental conditions. Methods To lift off these limitations, here we constructed a novel transparent and robust metabolic model to explain D. vulgaris bioenergetics by combining whole-cell proteomic analysis with modeling approaches (Flux Balance Analysis). Results The iDvu71 model showed over 0.95 correlation with experimental data. Further simulations allowed a detailed description of D. vulgaris metabolism in various conditions of growth. Altogether, the simulations run in this study highlighted the sulfate-to-lactate consumption ratio as a pivotal factor in D. vulgaris energy metabolism. Discussion In particular, the impact on the hydrogen/formate balance and biomass synthesis is discussed. Overall, this study provides a novel insight into D. vulgaris metabolic flexibility.
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Affiliation(s)
| | - Magali Roger
- BIP-UMR 7281, Laboratoire de Bioénergétique et Ingénierie des Protéines, Aix-Marseille Université, CNRS, Marseille, France
| | | | - Pascale Infossi
- BIP-UMR 7281, Laboratoire de Bioénergétique et Ingénierie des Protéines, Aix-Marseille Université, CNRS, Marseille, France
| | | | - Louis Delecourt
- BIP-UMR 7281, Laboratoire de Bioénergétique et Ingénierie des Protéines, Aix-Marseille Université, CNRS, Marseille, France
- LISM-UMR 7255, Laboratoire d’Ingénierie des Systèmes Macromoléculaires, Aix-Marseille Université, CNRS, Marseille, France
| | - Régine Lebrun
- IMM-FR3479, Marseille Protéomique, Aix-Marseille Université, CNRS, Marseille, France
| | - Marie-Thérèse Giudici-Orticoni
- BIP-UMR 7281, Laboratoire de Bioénergétique et Ingénierie des Protéines, Aix-Marseille Université, CNRS, Marseille, France
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3
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Jawaharraj K, Peta V, Dhiman SS, Gnimpieba EZ, Gadhamshetty V. Transcriptome-wide marker gene expression analysis of stress-responsive sulfate-reducing bacteria. Sci Rep 2023; 13:16181. [PMID: 37758719 PMCID: PMC10533852 DOI: 10.1038/s41598-023-43089-8] [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: 03/09/2023] [Accepted: 09/19/2023] [Indexed: 09/29/2023] Open
Abstract
Sulfate-reducing bacteria (SRB) are terminal members of any anaerobic food chain. For example, they critically influence the biogeochemical cycling of carbon, nitrogen, sulfur, and metals (natural environment) as well as the corrosion of civil infrastructure (built environment). The United States alone spends nearly $4 billion to address the biocorrosion challenges of SRB. It is important to analyze the genetic mechanisms of these organisms under environmental stresses. The current study uses complementary methodologies, viz., transcriptome-wide marker gene panel mapping and gene clustering analysis to decipher the stress mechanisms in four SRB. Here, the accessible RNA-sequencing data from the public domains were mined to identify the key transcriptional signatures. Crucial transcriptional candidate genes of Desulfovibrio spp. were accomplished and validated the gene cluster prediction. In addition, the unique transcriptional signatures of Oleidesulfovibrio alaskensis (OA-G20) at graphene and copper interfaces were discussed using in-house RNA-sequencing data. Furthermore, the comparative genomic analysis revealed 12,821 genes with translation, among which 10,178 genes were in homolog families and 2643 genes were in singleton families were observed among the 4 genomes studied. The current study paves a path for developing predictive deep learning tools for interpretable and mechanistic learning analysis of the SRB gene regulation.
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Affiliation(s)
- Kalimuthu Jawaharraj
- Civil and Environmental Engineering, South Dakota Mines, 501 E. St. Joseph Street, Rapid City, SD, 57701, USA
- 2D-Materials for Biofilm Engineering, Science and Technology (2D BEST) Center, South Dakota Mines, 501 E. St. Joseph Street, Rapid City, SD, 57701, USA
- Data-Driven Materials Discovery for Bioengineering Innovation Center, South Dakota Mines, 501 E. St. Joseph Street, Rapid City, SD, 57701, USA
| | - Vincent Peta
- Biomedical Engineering, University of South Dakota, 4800 N Career Ave, Sioux Falls, SD, 57107, USA
| | - Saurabh Sudha Dhiman
- Civil and Environmental Engineering, South Dakota Mines, 501 E. St. Joseph Street, Rapid City, SD, 57701, USA
- Data-Driven Materials Discovery for Bioengineering Innovation Center, South Dakota Mines, 501 E. St. Joseph Street, Rapid City, SD, 57701, USA
- Chemistry, Biology and Health Sciences, South Dakota Mines, 501 E. St. Joseph Street, Rapid City, SD, 57701, USA
| | - Etienne Z Gnimpieba
- 2D-Materials for Biofilm Engineering, Science and Technology (2D BEST) Center, South Dakota Mines, 501 E. St. Joseph Street, Rapid City, SD, 57701, USA.
- Data-Driven Materials Discovery for Bioengineering Innovation Center, South Dakota Mines, 501 E. St. Joseph Street, Rapid City, SD, 57701, USA.
- Biomedical Engineering, University of South Dakota, 4800 N Career Ave, Sioux Falls, SD, 57107, USA.
| | - Venkataramana Gadhamshetty
- Civil and Environmental Engineering, South Dakota Mines, 501 E. St. Joseph Street, Rapid City, SD, 57701, USA.
- 2D-Materials for Biofilm Engineering, Science and Technology (2D BEST) Center, South Dakota Mines, 501 E. St. Joseph Street, Rapid City, SD, 57701, USA.
- Data-Driven Materials Discovery for Bioengineering Innovation Center, South Dakota Mines, 501 E. St. Joseph Street, Rapid City, SD, 57701, USA.
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Trotter VV, Shatsky M, Price MN, Juba TR, Zane GM, De León KB, Majumder ELW, Gui Q, Ali R, Wetmore KM, Kuehl JV, Arkin AP, Wall JD, Deutschbauer AM, Chandonia JM, Butland GP. Large-scale genetic characterization of the model sulfate-reducing bacterium, Desulfovibrio vulgaris Hildenborough. Front Microbiol 2023; 14:1095191. [PMID: 37065130 PMCID: PMC10102598 DOI: 10.3389/fmicb.2023.1095191] [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: 11/10/2022] [Accepted: 03/10/2023] [Indexed: 04/03/2023] Open
Abstract
Sulfate-reducing bacteria (SRB) are obligate anaerobes that can couple their growth to the reduction of sulfate. Despite the importance of SRB to global nutrient cycles and their damage to the petroleum industry, our molecular understanding of their physiology remains limited. To systematically provide new insights into SRB biology, we generated a randomly barcoded transposon mutant library in the model SRB Desulfovibrio vulgaris Hildenborough (DvH) and used this genome-wide resource to assay the importance of its genes under a range of metabolic and stress conditions. In addition to defining the essential gene set of DvH, we identified a conditional phenotype for 1,137 non-essential genes. Through examination of these conditional phenotypes, we were able to make a number of novel insights into our molecular understanding of DvH, including how this bacterium synthesizes vitamins. For example, we identified DVU0867 as an atypical L-aspartate decarboxylase required for the synthesis of pantothenic acid, provided the first experimental evidence that biotin synthesis in DvH occurs via a specialized acyl carrier protein and without methyl esters, and demonstrated that the uncharacterized dehydrogenase DVU0826:DVU0827 is necessary for the synthesis of pyridoxal phosphate. In addition, we used the mutant fitness data to identify genes involved in the assimilation of diverse nitrogen sources and gained insights into the mechanism of inhibition of chlorate and molybdate. Our large-scale fitness dataset and RB-TnSeq mutant library are community-wide resources that can be used to generate further testable hypotheses into the gene functions of this environmentally and industrially important group of bacteria.
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Affiliation(s)
- Valentine V. Trotter
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Maxim Shatsky
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Morgan N. Price
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Thomas R. Juba
- Department of Biochemistry, University of Missouri, Columbia, MO, United States
| | - Grant M. Zane
- Department of Biochemistry, University of Missouri, Columbia, MO, United States
| | - Kara B. De León
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, United States
| | - Erica L.-W. Majumder
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, United States
| | - Qin Gui
- Department of Biochemistry, University of Missouri, Columbia, MO, United States
| | - Rida Ali
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Kelly M. Wetmore
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Jennifer V. Kuehl
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Adam P. Arkin
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, United States
| | - Judy D. Wall
- Department of Biochemistry, University of Missouri, Columbia, MO, United States
| | - Adam M. Deutschbauer
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
| | - John-Marc Chandonia
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Gareth P. Butland
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
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5
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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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [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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6
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Su Z, Zhang Y, Zhao R, Zhou J. Enhancement of dissimilatory nitrate/nitrite reduction to ammonium of Escherichia coli sp. SZQ1 by ascorbic acid: Mechanism and performance. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 853:158423. [PMID: 36055483 DOI: 10.1016/j.scitotenv.2022.158423] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 08/26/2022] [Accepted: 08/26/2022] [Indexed: 06/15/2023]
Abstract
Dissimilatory nitrate reduction to ammonium (DNRA) can be used for nitrogen recovery. However, due to the low conversion efficiency of the DNRA process of microorganisms, the process cannot be industrially applied. Ascorbic acid (ASA) can improve DNRA efficiency of Escherichia coli sp. SZQ1 (E. coli). Experimental studies suggest that 10 g L-1 ASA promoted DNRA process of E. coli at high concentrations of nitrite (10-20 mM). In the 5 g L-1 ASA system, 9.2 mM nitrite was reduced to 8.21 mM ammonium by E. coli in 120 h. Mechanistic studies reveal that ASA reduced the oxidation-reduction potential (ORP) of the system and scavenged reactive oxygen species (ROS) in the cell of E. coli. Meanwhile, ASA was utilized by E. coli as the sole carbon source and provided electrons to DNRA process through ASA metabolic pathways. This study proposes a new strategy for increasing the efficiency of DNRA.
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Affiliation(s)
- Zhiqiang Su
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), School of Environmental Science and Technology, Dalian University of Technology, Linggong Road 2, Dalian 116024, PR China
| | - Yu Zhang
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), School of Environmental Science and Technology, Dalian University of Technology, Linggong Road 2, Dalian 116024, PR China.
| | - Ruizhi Zhao
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), School of Environmental Science and Technology, Dalian University of Technology, Linggong Road 2, Dalian 116024, PR China
| | - Jiti Zhou
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), School of Environmental Science and Technology, Dalian University of Technology, Linggong Road 2, Dalian 116024, PR China.
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7
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Barnes RJ, Voegtlin SP, Naik SR, Gomes R, Hubert CRJ, Larter SR, Bryant SL. Inhibition of Sulfate Reduction and Cell Division by Desulfovibrio desulfuricans Coated in Palladium Metal. Appl Environ Microbiol 2022; 88:e0058022. [PMID: 35638843 PMCID: PMC9238422 DOI: 10.1128/aem.00580-22] [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: 04/02/2022] [Accepted: 05/04/2022] [Indexed: 11/20/2022] Open
Abstract
The growth of sulfate-reducing bacteria (SRB) and associated hydrogen sulfide production can be problematic in a range of industries such that inhibition strategies are needed. A range of SRB can reduce metal ions, a strategy that has been utilized for bioremediation, metal recovery, and synthesis of precious metal catalysts. In some instances, the metal remains bound to the cell surface, and the impact of this coating on bacterial cell division and metabolism has not previously been reported. In this study, Desulfovibrio desulfuricans cells (1g dry weight) enabled the reduction of up to 1500 mmol (157.5 g) palladium (Pd) ions, resulting in cells being coated in approximately 1 μm of metal. Thickly coated cells were no longer able to metabolize or divide, ultimately leading to the death of the population. Increasing Pd coating led to prolonged inhibition of sulfate reduction, which ceased completely after cells had been coated with 1200 mmol Pd g-1 dry cells. Less Pd nanoparticle coating permitted cells to carry out sulfate reduction and divide, allowing the population to recover over time as surface-associated Pd diminished. Overcoming inhibition in this way was more rapid using lactate as the electron donor, compared to formate. When using formate as an electron donor, preferential Pd(II) reduction took place in the presence of 100 mM sulfate. The inhibition of important metabolic pathways using a biologically enabled casing in metal highlights a new mechanism for the development of microbial control strategies. IMPORTANCE Microbial reduction of sulfate to hydrogen sulfide is highly undesirable in several industrial settings. Some sulfate-reducing bacteria are also able to transform metal ions in their environment into metal phases that remain attached to their outer cell surface. This study demonstrates the remarkable extent to which Desulfovibrio desulfuricans can be coated with locally generated metal nanoparticles, with individual cells carrying more than 100 times their mass of palladium metal. Moreover, it reveals the effect of metal coating on metabolism and replication for a wide range of metal loadings, with bacteria unable to reduce sulfate to sulfide beyond a specific threshold. These findings present a foundation for a novel means of modulating the activity of sulfate-reducing bacteria.
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Affiliation(s)
- Robert J. Barnes
- Department of Chemical and Petroleum Engineering, University of Calgary, Calgary, Alberta, Canada
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Stephen P. Voegtlin
- Department of Chemical and Petroleum Engineering, University of Calgary, Calgary, Alberta, Canada
| | - Shiv R. Naik
- Department of Chemical and Petroleum Engineering, University of Calgary, Calgary, Alberta, Canada
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
| | - Renessa Gomes
- Department of Chemical and Petroleum Engineering, University of Calgary, Calgary, Alberta, Canada
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
| | - Casey R. J. Hubert
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Stephen R. Larter
- Department of Geosciences, PRG, University of Calgary, Calgary, Alberta, Canada
| | - Steven L. Bryant
- Department of Chemical and Petroleum Engineering, University of Calgary, Calgary, Alberta, Canada
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Kayastha K, Katsyv A, Himmrich C, Welsch S, Schuller JM, Ermler U, Müller V. Structure-based electron-confurcation mechanism of the Ldh-EtfAB complex. eLife 2022; 11:77095. [PMID: 35748623 PMCID: PMC9232219 DOI: 10.7554/elife.77095] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 05/22/2022] [Indexed: 01/22/2023] Open
Abstract
Lactate oxidation with NAD+ as electron acceptor is a highly endergonic reaction. Some anaerobic bacteria overcome the energetic hurdle by flavin-based electron bifurcation/confurcation (FBEB/FBEC) using a lactate dehydrogenase (Ldh) in concert with the electron-transferring proteins EtfA and EtfB. The electron cryo-microscopically characterized (Ldh-EtfAB)2 complex of Acetobacterium woodii at 2.43 Å resolution consists of a mobile EtfAB shuttle domain located between the rigid central Ldh and the peripheral EtfAB base units. The FADs of Ldh and the EtfAB shuttle domain contact each other thereby forming the D (dehydrogenation-connected) state. The intermediary Glu37 and Glu139 may harmonize the redox potentials between the FADs and the pyruvate/lactate pair crucial for FBEC. By integrating Alphafold2 calculations a plausible novel B (bifurcation-connected) state was obtained allowing electron transfer between the EtfAB base and shuttle FADs. Kinetic analysis of enzyme variants suggests a correlation between NAD+ binding site and D-to-B-state transition implicating a 75° rotation of the EtfAB shuttle domain. The FBEC inactivity when truncating the ferredoxin domain of EtfA substantiates its role as redox relay. Lactate oxidation in Ldh is assisted by the catalytic base His423 and a metal center. On this basis, a comprehensive catalytic mechanism of the FBEC process was proposed.
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Affiliation(s)
- Kanwal Kayastha
- Departments of Molecular Membrane Biology of the Max-Planck-Institut for Biophysics, Frankfurt am Main, Germany
| | - Alexander Katsyv
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Goethe University, Frankfurt am Main, Germany
| | - Christina Himmrich
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Goethe University, Frankfurt am Main, Germany
| | - Sonja Welsch
- Central Electron Microscopy Facility, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Jan M Schuller
- SYNMICRO Research Center and Department of Chemistry, Philipps University, Marburg, Germany
| | - Ulrich Ermler
- Departments of Molecular Membrane Biology of the Max-Planck-Institut for Biophysics, Frankfurt am Main, Germany
| | - Volker Müller
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Goethe University, Frankfurt am Main, Germany
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Long-term daily high-protein, drained yoghurt consumption alters abundance of selected functional groups of the human gut microbiota and fecal short-chain fatty acid profiles in a cohort of overweight and obese women. J Funct Foods 2022. [DOI: 10.1016/j.jff.2022.105089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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10
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Biryukova EN, Arinbasarova AY, Medentsev AG. L-Lactate Oxidase Systems of Microorganisms. Microbiology (Reading) 2022. [DOI: 10.1134/s0026261722020035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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11
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Lee S, O'Loughlin EJ, Kwon MJ. Impact of organic acids and sulfate on the biogeochemical properties of soil from urban subsurface environments. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2021; 292:112756. [PMID: 33984641 DOI: 10.1016/j.jenvman.2021.112756] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 04/03/2021] [Accepted: 05/02/2021] [Indexed: 06/12/2023]
Abstract
Urban subsurface environments are often different from undisturbed subsurface environments due to the impacts of human activities. For example, deterioration of underground infrastructure can introduce elevated levels of Ca, Fe, and heavy metals into subsurface soils and groundwater. Likewise, leakage from sewer systems can lead to contamination by organic C, N, S, and P. However, the impact of these organic and inorganic compounds on biogeochemical processes including microbial redox reactions, mineral transformations, and microbial community transitions in urban subsurface environments is poorly understood. Here we conducted a microcosm experiment with soil samples from an urban construction site to investigate the possible biotic and abiotic processes impacted when sulfate and acetate or lactate were introduced into an urban subsurface environment. In the top-layer soil (0-0.3 m) microcosms, which were highly alkaline (pH > 10), the major impact was on abiotic processes such as secondary mineral precipitation. In the mid-layer (2-3 m) soil microcosms, the rate of Fe(III)-reduction and the amount of Fe(II) produced were greatly impacted by the specific organic acid added, and sulfate-reduction was not observed until after Fe(III)-reduction was complete. Near the end of the incubation, some genera related to syntrophic acetate oxidation and methanogenesis were observed in the lactate-amended microcosms. In the bottom-layer (7-8 m) soil microcosms, the rate of Fe(III)-reduction and the amount of Fe(II) produced were affected by the concentration of amended sulfate. Sulfate-reduction was concurrent with Fe(III)-reduction, suggesting that Fe(II) production was likely due to abiotic reduction of Fe(III) by sulfide produced by microbial sulfate reduction. The slightly acidic initial pH (~5.8) of the mid-soil system was a major factor controlling sequential microbial Fe(III) and sulfate reduction versus parallel Fe(III) and sulfate reduction in the bottom soil system, which had a neutral initial pH (~7.2). 16S rRNA gene-based community analysis revealed a variety of indigenous microbial groups including alkaliphiles, dissimilatory iron and sulfate reducers, syntrophes, and methanogens tightly coupled with, and impacted by, these complex abiotic and biogeochemical processes occurring in urban subsurface environments.
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Affiliation(s)
- Sunhui Lee
- Department of Earth and Environmental Sciences, Korea University, Seoul, South Korea
| | | | - Man Jae Kwon
- Department of Earth and Environmental Sciences, Korea University, Seoul, South Korea.
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12
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Tang WT, Hao TW, Chen GH. Comparative metabolic modeling of multiple sulfate-reducing prokaryotes reveals versatile energy conservation mechanisms. Biotechnol Bioeng 2021; 118:2676-2693. [PMID: 33844295 DOI: 10.1002/bit.27787] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 01/21/2021] [Accepted: 03/11/2021] [Indexed: 11/07/2022]
Abstract
Sulfate-reducing prokaryotes (SRPs) are crucial participants in the cycling of sulfur, carbon, and various metals in the natural environment and in engineered systems. Despite recent advances in genetics and molecular biology bringing a huge amount of information about the energy metabolism of SRPs, little effort has been made to link this important information with their biotechnological studies. This study aims to construct multiple metabolic models of SRPs that systematically compile genomic, genetic, biochemical, and molecular information about SRPs to study their energy metabolism. Pan-genome analysis was conducted to compare the genomes of SRPs, from which a list of orthologous genes related to central and energy metabolism was obtained. Twenty-four SRP metabolic models via the inference of pan-genome analysis were efficiently constructed. The metabolic model of the well-studied model SRP Desulfovibrio vulgaris Hildenborough (DvH) was validated via flux balance analysis (FBA). The DvH model predictions matched reported experimental growth and energy yields, which demonstrated that the core metabolic model worked successfully. Further, steady-state simulation of SRP metabolic models under different growth conditions showed how the use of different electron transfer pathways leads to energy generation. Three energy conservation mechanisms were identified, including menaquinone-based redox loop, hydrogen cycling, and proton pumping. Flavin-based electron bifurcation (FBEB) was also demonstrated to be an essential mechanism for supporting energy conservation. The developed models can be easily extended to other species of SRPs not examined in this study. More importantly, the present work develops an accurate and efficient approach for constructing metabolic models of multiple organisms, which can be applied to other critical microbes in environmental and industrial systems, thereby enabling the quantitative prediction of their metabolic behaviors to benefit relevant applications.
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Affiliation(s)
- Wen-Tao Tang
- Department of Civil and Environmental Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Tian-Wei Hao
- Department of Civil and Environmental Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China.,Department of Civil and Environmental Engineering, Faculty of Science and Technology, University of Macau, Macau, China
| | - Guang-Hao Chen
- Department of Civil and Environmental Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
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Aoyagi T, Mori Y, Nanao M, Matsuyama Y, Sato Y, Inaba T, Aizawa H, Hayakawa T, Moriya M, Higo Y, Habe H, Hori T. Effective Se reduction by lactate-stimulated indigenous microbial communities in excavated waste rocks. JOURNAL OF HAZARDOUS MATERIALS 2021; 403:123908. [PMID: 33264961 DOI: 10.1016/j.jhazmat.2020.123908] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 08/13/2020] [Accepted: 09/04/2020] [Indexed: 06/12/2023]
Abstract
Waste rocks generated from tunnel excavation contain the metalloid selenium (Se) and its concentration sometimes exceeds the environmental standards. The possibility and effectiveness of dissolved Se removal by the indigenous microorganisms are unknown. Chemical analyses and high-throughput 16S rRNA gene sequencing were implemented to investigate the functional and structural responses of the rock microbial communities to the Se and lactate amendment. During anaerobic incubation of the amended rock slurries from two distinct sites, dissolved Se concentrations decreased significantly, which coincided with lactate degradation to acetate and/or propionate. Sequencing indicated that relative abundances of Desulfosporosinus burensis increased drastically from 0.025 % and 0.022% to 67.584% and 63.716 %, respectively, in the sites. In addition, various Desulfosporosinus spp., Symbiobacterium-related species and Brevibacillus ginsengisoli, as well as the Se(VI)-reducing Desulfitobacterium hafniense, proliferated remarkably. They are capable of incomplete lactate oxidation to acetate as only organic metabolite, strongly suggesting their involvement in dissimilatory Se reduction. Furthermore, predominance of Pelosinus fermentans that ferments lactate to propionate and acetate implied that Se served as the electron sink for its fermentative lactate degradation. These results demonstrated that the indigenous microorganisms played vital roles in the lactate-stimulated Se reduction, leading to the biological Se immobilization treatment of waste rocks.
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Affiliation(s)
- Tomo Aoyagi
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba 395-8569, Japan
| | - Yoshihiko Mori
- Central Research Laboratory, Taiheiyo Cement Co., Ltd., 2-4-2 Osaku, Sakura, Chiba 285-8655, Japan
| | - Mai Nanao
- Central Research Laboratory, Taiheiyo Cement Co., Ltd., 2-4-2 Osaku, Sakura, Chiba 285-8655, Japan
| | - Yusuke Matsuyama
- Taiheiyo Cement Co., Ltd., BUNKYO GARDEN GATE TOWER, 1-1-1 Koishikawa, Bunkyo, Tokyo 112-8503, Japan
| | - Yuya Sato
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba 395-8569, Japan
| | - Tomohiro Inaba
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba 395-8569, Japan
| | - Hidenobu Aizawa
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba 395-8569, Japan
| | - Takayuki Hayakawa
- Central Research Laboratory, Taiheiyo Cement Co., Ltd., 2-4-2 Osaku, Sakura, Chiba 285-8655, Japan
| | - Masahiko Moriya
- Taiheiyo Cement Co., Ltd., BUNKYO GARDEN GATE TOWER, 1-1-1 Koishikawa, Bunkyo, Tokyo 112-8503, Japan
| | - Yasuhide Higo
- Taiheiyo Cement Co., Ltd., BUNKYO GARDEN GATE TOWER, 1-1-1 Koishikawa, Bunkyo, Tokyo 112-8503, Japan
| | - Hiroshi Habe
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba 395-8569, Japan
| | - Tomoyuki Hori
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba 395-8569, Japan.
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Key Enzymes for Anaerobic Lactate Metabolism in Geobacter sulfurreducens. Appl Environ Microbiol 2021; 87:AEM.01968-20. [PMID: 33158892 DOI: 10.1128/aem.01968-20] [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: 08/10/2020] [Accepted: 09/22/2020] [Indexed: 11/20/2022] Open
Abstract
Growth of Geobacter sulfurreducens PCA on lactate was enhanced by laboratory adaptive evolution. The enhanced growth was considered to be attributed to increased expression of the sucCD genes, encoding a succinyl-coenzyme A (CoA) synthetase. To further investigate the function of the succinyl-CoA synthetase, the sucCD genes were deleted from G. sulfurreducens The mutant showed defective growth on lactate but not on acetate. Introduction of the sucCD genes into the mutant restored the full potential to grow on lactate. These results verify the importance of the succinyl-CoA synthetase in growth on lactate. Genome analysis of Geobacter species identified candidate genes, GSU1623, GSU1624, and GSU1620, for lactate dehydrogenase. Deletion mutants of the identified genes for d-lactate dehydrogenase (ΔGSU1623 ΔGSU1624 mutant) or l-lactate dehydrogenase (ΔGSU1620 mutant) could not grow on d-lactate or l-lactate but could grow on acetate and l- or d-lactate, respectively. Introduction of the respective genes into the mutants allowed growth on the corresponding lactate stereoisomer. These results suggest that the identified genes were essential for d- or l-lactate utilization. The lacZ reporter assay demonstrated that the putative promoter regions were more active during growth on lactate than during growth on acetate, indicating that the genes for the lactate dehydrogenases were expressed more during growth on lactate than during growth on acetate. The gene deletion phenotypes and the expression profiles indicate that there are metabolic switches between lactate and acetate. This study advances the understanding of anaerobic lactate utilization in G. sulfurreducens IMPORTANCE Lactate is a microbial fermentation product as well as a source of carbon and electrons for microorganisms in the environment. Furthermore, lactate is a common amendment for stimulation of microbial growth in environmental biotechnology applications. However, anaerobic metabolism of lactate has been poorly studied for environmentally relevant microorganisms. Geobacter species are found in various environments and environmental biotechnology applications. By employing genomic and genetic approaches, succinyl-CoA synthetase and lactate dehydrogenase were identified as key enzymes in anaerobic metabolism of lactate in Geobacter sulfurreducens, a representative Geobacter species. Differential gene expression during growth on lactate and acetate was observed, demonstrating that G. sulfurreducens could metabolically switch to adapt to available substrates in the environment. The findings provide new insights into basic physiology in lactate metabolism as well as cellular responses to growth conditions in the environment and can be informative for the application of lactate in environmental biotechnology.
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Amin AB, Mao S. Influence of yeast on rumen fermentation, growth performance and quality of products in ruminants: A review. ACTA ACUST UNITED AC 2020; 7:31-41. [PMID: 33997329 PMCID: PMC8110857 DOI: 10.1016/j.aninu.2020.10.005] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 08/14/2020] [Accepted: 10/15/2020] [Indexed: 12/28/2022]
Abstract
This review aims to give an overview of the efficacy of yeast supplementation on growth performance, rumen pH, rumen microbiota, and their relationship to meat and milk quality in ruminants. The practice of feeding high grain diets to ruminants in an effort to increase growth rate and weight gain usually results in excess deposition of saturated fatty acids in animal products and increased incidence of rumen acidosis. The supplementation of yeast at the right dose and viability level could counteract the acidotic effects of these high grain diets in the rumen and positively modify the fatty acid composition of animal products. Yeast exerts its actions by competing with lactate-producing (Streptococcus bovis and Lactobacillus) bacteria for available sugar and encouraging the growth of lactate-utilising bacteria (Megasphaera elsdenii). M. elsdenii is known to convert lactate into butyrate and propionate leading to a decrease in the accumulation of lactate thereby resulting in higher rumen pH. Interestingly, this creates a conducive environment for the proliferation of vaccenic acid-producing bacteria (Butyrivibrio fibrisolvens) and ciliate protozoa, both of which have been reported to increase the ruminal concentration of trans-11 and cis-9, trans-11-conjugated linoleic acid (CLA) at a pH range between 5.6 and 6.3. The addition of yeast into the diet of ruminants has also been reported to positively modify rumen biohydrogenation pathway to synthesise more of the beneficial biohydrogenation intermediates (trans -11 and cis -9, trans -11). This implies that more dietary sources of linoleic acid, linolenic acid, and oleic acid along with beneficial biohydrogenation intermediates (cis-9, trans-11-CLA, and trans-11) would escape complete biohydrogenation in the rumen to be absorbed into milk and meat. However, further studies are required to substantiate our claim. Therefore, techniques like transcriptomics should be employed to identify the mRNA transcript expression levels of genes like stearoyl-CoA desaturase, fatty acid synthase, and elongase of very long chain fatty acids 6 in the muscle. Different strains of yeast need to be tested at different doses and viability levels on the fatty acid profile of animal products as well as its vaccenic acid and rumenic acid composition.
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Affiliation(s)
- Abdulmumini B. Amin
- Centre for Ruminant Nutrition and Feed Engineering Research, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
- Department of Animal Science, Federal University Dutse, P.M.B 7156, Dutse, Jigawa State, Nigeria
| | - Shengyong Mao
- Centre for Ruminant Nutrition and Feed Engineering Research, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
- Jilin Inter-Regional Cooperation Centre for the Scientific and Technological Innovation of Ruminant Precision Nutrition and Smart and Ecological Farming, 132109, Jilin, China
- Corresponding author.
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Bachochin MJ, Venegas JC, Singh G, Zhang L, Barber RD. Characterization of a butyrate kinase from Desulfovibrio vulgaris str. Hildenborough. FEMS Microbiol Lett 2020; 367:5804727. [PMID: 32166312 DOI: 10.1093/femsle/fnaa047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 03/10/2020] [Indexed: 11/13/2022] Open
Abstract
Short and branched chain fatty acid kinases participate in both bacterial anabolic and catabolic processes, including fermentation, through the reversible, ATP-dependent synthesis of acyl phosphates. This study reports biochemical properties of a predicted butyrate kinase from Desulfovibrio vulgaris str. Hildenborough (DvBuk) expressed heterologously and purified from Escherichia coli. Gel filtration chromatography indicates purified DvBuk is active as a dimer. The optimum temperature and pH for DvBuk activity is 44°C and 7.5, respectively. The enzyme displays enhanced thermal stability in the presence of substrates as observed for similar enzymes. Measurement of kcat and KM for various substrates reveals DvBuk exhibits the highest catalytic efficiencies for butyrate, valerate and isobutyrate. In particular, these measurements reveal this enzyme's apparent high affinity for C4 fatty acids relative to other butyrate kinases. These results have implications on structure and function relationships within the ASKHA superfamily of phosphotransferases, particularly regarding the acyl binding pocket, as well as potential physiological roles for this enzyme in Desulfovibrio vulgaris str. Hildenborough.
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Affiliation(s)
- Maxwell J Bachochin
- Department of Biological Sciences, College of Natural and Health Sciences, University of Wisconsin-Parkside, Room 355 Greenquist Hall; 900 Wood Rd., Kenosha, WI 53141-2000, USA
| | - Jessica Castillo Venegas
- Department of Biological Sciences, College of Natural and Health Sciences, University of Wisconsin-Parkside, Room 355 Greenquist Hall; 900 Wood Rd., Kenosha, WI 53141-2000, USA
| | - Gundeep Singh
- Department of Biological Sciences, College of Natural and Health Sciences, University of Wisconsin-Parkside, Room 355 Greenquist Hall; 900 Wood Rd., Kenosha, WI 53141-2000, USA
| | - Liyang Zhang
- Department of Biological Sciences, College of Natural and Health Sciences, University of Wisconsin-Parkside, Room 355 Greenquist Hall; 900 Wood Rd., Kenosha, WI 53141-2000, USA
| | - Robert D Barber
- Department of Biological Sciences, College of Natural and Health Sciences, University of Wisconsin-Parkside, Room 355 Greenquist Hall; 900 Wood Rd., Kenosha, WI 53141-2000, USA
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Organohalide-respiring Desulfoluna species isolated from marine environments. ISME JOURNAL 2020; 14:815-827. [PMID: 31896791 PMCID: PMC7031245 DOI: 10.1038/s41396-019-0573-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 12/16/2019] [Indexed: 12/17/2022]
Abstract
The genus Desulfoluna comprises two anaerobic sulfate-reducing strains, D. spongiiphila AA1T and D. butyratoxydans MSL71T, of which only the former was shown to perform organohalide respiration (OHR). Here we isolated a third strain, designated D. spongiiphila strain DBB, from marine intertidal sediment using 1,4-dibromobenzene and sulfate as the electron acceptors and lactate as the electron donor. Each strain harbors three reductive dehalogenase gene clusters (rdhABC) and corrinoid biosynthesis genes in their genomes, and dehalogenated brominated but not chlorinated organohalogens. The Desulfoluna strains maintained OHR in the presence of 20 mM sulfate or 20 mM sulfide, which often negatively affect other organohalide-respiring bacteria. Strain DBB sustained OHR with 2% oxygen in the gas phase, in line with its genetic potential for reactive oxygen species detoxification. Reverse transcription-quantitative PCR revealed differential induction of rdhA genes in strain DBB in response to 1,4-dibromobenzene or 2,6-dibromophenol. Proteomic analysis confirmed expression of rdhA1 with 1,4-dibromobenzene, and revealed a partially shared electron transport chain from lactate to 1,4-dibromobenzene and sulfate, which may explain accelerated OHR during concurrent sulfate reduction. Versatility in using electron donors, de novo corrinoid biosynthesis, resistance to sulfate, sulfide and oxygen, and concurrent sulfate reduction and OHR may confer an advantage to marine Desulfoluna strains.
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Alex A, Antunes A. Comparative Genomics Reveals Metabolic Specificity of Endozoicomonas Isolated from a Marine Sponge and the Genomic Repertoire for Host-Bacteria Symbioses. Microorganisms 2019; 7:microorganisms7120635. [PMID: 31801294 PMCID: PMC6955870 DOI: 10.3390/microorganisms7120635] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Revised: 11/19/2019] [Accepted: 11/27/2019] [Indexed: 11/29/2022] Open
Abstract
The most recently described bacterial members of the genus Endozoicomonas have been found in association with a wide variety of marine invertebrates. Despite their ubiquity in the host holobiont, limited information is available on the molecular genomic signatures of the symbiotic association of Endozoicomonas with marine sponges. Here, we generated a draft genome of Endozoicomonas sp. OPT23 isolated from the intertidal marine sponge Ophlitaspongia papilla and performed comprehensive comparative genomics analyses. Genome-specific analysis and metabolic pathway comparison of the members of the genus Endozoicomonas revealed the presence of gene clusters encoding for unique metabolic features, such as the utilization of carbon sources through lactate, L-rhamnose metabolism, and a phenylacetic acid degradation pathway in Endozoicomonas sp. OPT23. Moreover, the genome harbors genes encoding for eukaryotic-like proteins, such as ankyrin repeats, tetratricopeptide repeats, and Sel1 repeats, which likely facilitate sponge-bacterium attachment. The genome also encodes major secretion systems and homologs of effector molecules that seem to enable the sponge-associated bacterium to interact with the sponge and deliver the virulence factors for successful colonization. In conclusion, the genome analysis of Endozoicomonas sp. OPT23 revealed the presence of adaptive genomic signatures that might favor their symbiotic lifestyle within the sponge host.
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Affiliation(s)
- Anoop Alex
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, 4450-208 Porto, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
- Correspondence: (A.Al.); (A.An.); Tel.: +351-22-340-1813 (A.Al.); +351-22-340-1813 (A.An.)
| | - Agostino Antunes
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, 4450-208 Porto, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
- Correspondence: (A.Al.); (A.An.); Tel.: +351-22-340-1813 (A.Al.); +351-22-340-1813 (A.An.)
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Recovery of Metals from Waste Lithium Ion Battery Leachates Using Biogenic Hydrogen Sulfide. MINERALS 2019. [DOI: 10.3390/min9090563] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Lithium ion battery (LIB) waste is increasing globally and contains an abundance of valuable metals that can be recovered for re-use. This study aimed to evaluate the recovery of metals from LIB waste leachate using hydrogen sulfide generated by a consortium of sulfate-reducing bacteria (SRB) in a lactate-fed fluidised bed reactor (FBR). The microbial community analysis showed Desulfovibrio as the most abundant genus in a dynamic and diverse bioreactor consortium. During periods of biogenic hydrogen sulfide production, the average dissolved sulfide concentration was 507 mg L−1 and the average volumetric sulfate reduction rate was 278 mg L−1 d−1. Over 99% precipitation efficiency was achieved for Al, Ni, Co, and Cu using biogenic sulfide and NaOH, accounting for 96% of the metal value contained in the LIB waste leachate. The purity indices of the precipitates were highest for Co, being above 0.7 for the precipitate at pH 10. However, the process was not selective for individual metals due to simultaneous precipitation and the complexity of the metal content of the LIB waste. Overall, the process facilitated the production of high value mixed metal precipitates, which could be purified further or used as feedstock for other processes, such as the production of steel.
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Effects of live yeast on differential genetic and functional attributes of rumen microbiota in beef cattle. J Anim Sci Biotechnol 2019; 10:68. [PMID: 31508230 PMCID: PMC6724239 DOI: 10.1186/s40104-019-0378-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 07/09/2019] [Indexed: 12/13/2022] Open
Abstract
Several studies have evaluated the effects of live yeast supplementation on rumen microbial population; however, its effect on differential microbial genes and their functional potential has not been described. Thus, this study applied shotgun metagenomic sequencing to evaluate the effects of live yeast supplementation on genetic and functional potential of the rumen microbiota in beef cattle. Eight rumen-cannulated Holstein steers were randomly assigned to two treatments in a cross-over design with two 25-day experimental periods and a 10-day wash-out between the two periods. The steers were housed in individual pens and fed 50% concentrate-mix and 50% red clover/orchard hay ad libitum. Treatments were (1) control (CON; basal diet without additive) and (2) yeast (YEA; basal diet plus 15 g/d of live yeast product). Rumen fluid samples were collected at 3, 6, and 9 h after feeding on the last d of each period. Sequencing was done on an Illumina HiSeq 2500 platform. Dietary yeast supplementation increased the relative abundance of carbohydrate-fermenting bacteria (such as Ruminococcus albus, R. champanellensis, R. bromii, and R. obeum) and lactate-utilizing bacteria (such as Megasphaera elsdenii, Desulfovibrio desulfuricans, and D. vulgaris). A total of 154 differentially abundant genes (DEGs) were obtained (false discovery rate < 0.01). Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation analysis of the DEGs revealed that 10 pathways, including amino sugar and nucleotide sugar metabolism, oxidative phosphorylation, lipopolysaccharide biosynthesis, pantothenate and coenzyme A biosynthesis, glutathione metabolism, beta-alanine metabolism, polyketide sugar unit biosynthesis, protein export, ribosome, and bacterial secretory system, were enriched in steers fed YEA. Annotation analysis of the DEGs in the carbohydrate-active enzymes (CAZy) database revealed that the abundance of genes coding for enzymes belonging to glycoside hydrolases, glycosyltransferases, and carbohydrate binding modules were enriched in steers fed YEA. These results confirm the effectiveness of a live S. cerevisiae product for improving rumen function in beef steers by increasing the abundance of cellulolytic bacteria, lactic acid-utilizing bacteria, and carbohydrate-active enzymes in the rumen.
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Sato Y, Hamai T, Hori T, Aoyagi T, Inaba T, Kobayashi M, Habe H, Sakata T. Desulfosporosinus spp. were the most predominant sulfate-reducing bacteria in pilot- and laboratory-scale passive bioreactors for acid mine drainage treatment. Appl Microbiol Biotechnol 2019; 103:7783-7793. [DOI: 10.1007/s00253-019-10063-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 07/22/2019] [Accepted: 07/24/2019] [Indexed: 11/29/2022]
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Gao SH, Ho JY, Fan L, Nouwens A, Hoelzle RD, Schulz B, Guo J, Zhou J, Yuan Z, Bond PL. A comparative proteomic analysis of Desulfovibrio vulgaris Hildenborough in response to the antimicrobial agent free nitrous acid. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 672:625-633. [PMID: 30974354 DOI: 10.1016/j.scitotenv.2019.03.442] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 03/12/2019] [Accepted: 03/28/2019] [Indexed: 06/09/2023]
Abstract
Sulfate reducing bacteria (SRB) can contribute to facilitating serious concrete corrosion through the production of hydrogen sulfide in sewers. Recently, free nitrous acid (FNA) was discovered as a promising antimicrobial agent to inhibit SRB activities thereby limiting hydrogen sulfide production in sewers. However, knowledge of the bacterial response to increasing levels of the antimicrobial agent is unknown. Here we report the proteomic response of Desulfovibrio vulgaris Hildenborough and reveal that the antimicrobial effect of FNA is multi-targeted and dependent on the FNA levels. This was achieved using a sequential window acquisition of all theoretical mass spectrometry analysis to determine protein abundance variations in D. vulgaris during exposure to different FNA concentrations. When exposed to 1.0 μg N/L FNA, nitrite reduction (nitrite reductase) related proteins and nitrosative stress related proteins, including the hybrid cluster protein, showed distinct increased abundances. When exposed to 4.0 and 8.0 μg N/L FNA, increased abundance was detected for proteins putatively involved in nitrite reduction. Abundance of proteins involved in the sulfate reduction pathway (from adenylylphophosulfate to sulfite) and lactate oxidation pathway (from pyruvate to acetate) were initially inhibited in response to FNA at 8 h incubation, and then recovered at 12 h incubation. Lowered ribosomal protein abundance in D. vulgaris was detected, however, total cellular protein levels were mostly constant in the presence or absence of FNA. In addition, this study indicates that proteins coded by genes DVU2543, DVU0772, and DVU3212 potentially participate in resisting oxidative stress with FNA exposure. These findings share new insights for understanding the dynamic responses of D. vulgaris to FNA and could be useful to guide and improve the practical applications of FNA-based technologies for control of sewer corrosion.
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Affiliation(s)
- Shu-Hong Gao
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia; Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA
| | - Jun Yuan Ho
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Lu Fan
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Amanda Nouwens
- School of Chemistry & Molecular Biosciences, The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia
| | - Robert D Hoelzle
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia; Australian Centre for Ecogenomics, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Benjamin Schulz
- School of Chemistry & Molecular Biosciences, The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia
| | - Jianhua Guo
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Jizhong Zhou
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA
| | - Zhiguo Yuan
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Philip L Bond
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia.
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Gui X, Xu W, Cao H, Ning P, Zhang Y, Li Y, Sheng Y. A novel phenol and ammonia recovery process for coal gasification wastewater altering the bacterial community and increasing pollutants removal in anaerobic/anoxic/aerobic system. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 661:203-211. [PMID: 30669053 DOI: 10.1016/j.scitotenv.2019.01.126] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2018] [Revised: 01/11/2019] [Accepted: 01/11/2019] [Indexed: 06/09/2023]
Abstract
Coal gasification wastewater (CGWW) is a typical toxic and refractory industrial wastewater. Here, a novel phenol and ammonia recovery process (IPE) was employed for CGWW pretreatment, and the coupled system assemble by the IPE process with A2/O system (IPE-A2/O) were operated to enhance the treatment performance of CGWW. The results showed that the IPE pre-treated effluent had a higher BOD5/COD ratio and lower refractory compounds compared to a typical process (MIBK). Subsequent A2/O biological treatment indicated that the A2/O-p system (A2/O system followed IPE process) obtained a higher average COD removal of 92% compared to 87.7% of the control (A2/O-m, A2/O system followed MIBK). The GC-MS analysis suggested that the content of alkanes in the IPE-A2/O effluent was lower than that of the MIBK-A2/O. The high-throughput sequencing revealed Levilinea, Alcaligenes, Acinetobacter, Thauera and Thiobacillus were the core genera in A2/O system. The genera Alcaligenes, Acinetobacter, Thauera and Thiobacillus in the degrading consortium were enriched in the A2/O-p system, leading to increased removals of organic pollutants and TN. These results suggested that the IPE process was a feasible pretreatment method, and the coupled IPE-A2/O system was an alternative technique for treating CGWW.
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Affiliation(s)
- Xuefei Gui
- School of Chemical and Environmental Engineering, China University of Mining and Technology (Beijing), Beijing 100083, PR China; CAS Interdisciplinary Innovation Team, Chinese Academy of Sciences, Beijing 100190, PR China
| | - Weichao Xu
- School of Chemical and Environmental Engineering, China University of Mining and Technology (Beijing), Beijing 100083, PR China
| | - Hongbin Cao
- CAS Interdisciplinary Innovation Team, Chinese Academy of Sciences, Beijing 100190, PR China; National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China
| | - Pengge Ning
- CAS Interdisciplinary Innovation Team, Chinese Academy of Sciences, Beijing 100190, PR China.
| | - Yuxiu Zhang
- School of Chemical and Environmental Engineering, China University of Mining and Technology (Beijing), Beijing 100083, PR China.
| | - Yuping Li
- CAS Interdisciplinary Innovation Team, Chinese Academy of Sciences, Beijing 100190, PR China
| | - Yuxing Sheng
- CAS Interdisciplinary Innovation Team, Chinese Academy of Sciences, Beijing 100190, PR China; National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China
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24
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Leavitt WD, Venceslau SS, Waldbauer J, Smith DA, Pereira IAC, Bradley AS. Proteomic and Isotopic Response of Desulfovibrio vulgaris to DsrC Perturbation. Front Microbiol 2019; 10:658. [PMID: 31031715 PMCID: PMC6470260 DOI: 10.3389/fmicb.2019.00658] [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: 11/25/2018] [Accepted: 03/15/2019] [Indexed: 11/30/2022] Open
Abstract
Dissimilatory sulfate reduction is a microbial energy metabolism that can produce sulfur isotopic fractionations over a large range in magnitude. Calibrating sulfur isotopic fractionation in laboratory experiments allows for better interpretations of sulfur isotopes in modern sediments and ancient sedimentary rocks. The proteins involved in sulfate reduction are expressed in response to environmental conditions, and are collectively responsible for the net isotopic fractionation between sulfate and sulfide. We examined the role of DsrC, a key component of the sulfate reduction pathway, by comparing wildtype Desulfovibrio vulgaris DSM 644T to strain IPFG07, a mutant deficient in DsrC production. Both strains were cultivated in parallel chemostat reactors at identical turnover times and cell specific sulfate reduction rates. Under these conditions, sulfur isotopic fractionations between sulfate and sulfide of 17.3 ± 0.5‰ or 12.6 ± 0.5‰ were recorded for the wildtype or mutant, respectively. The enzymatic machinery that produced these different fractionations was revealed by quantitative proteomics. Results are consistent with a cellular-level response that throttled the supply of electrons and sulfur supply through the sulfate reduction pathway more in the mutant relative to the wildtype, independent of rate. We conclude that the smaller fractionation observed in the mutant strain is a consequence of sulfate reduction that proceeded at a rate that consumed a greater proportion of the strains overall capacity for sulfate reduction. These observations have consequences for models of sulfate reducer metabolism and how it yields different isotopic fractionations, notably, the role of DsrC in central energy metabolism.
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Affiliation(s)
- William D. Leavitt
- Department of Earth Sciences, Dartmouth College, Hanover, NH, United States
- Department of Earth and Planetary Sciences, Washington University in St. Louis, St. Louis, MO, United States
- Department of Biological Sciences, Dartmouth College, Hanover, NH, United States
- Department of Chemistry, Dartmouth College, Hanover, NH, United States
| | - Sofia S. Venceslau
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Jacob Waldbauer
- Department of the Geophysical Sciences, University of Chicago, Chicago, IL, United States
| | - Derek A. Smith
- Department of Earth and Planetary Sciences, Washington University in St. Louis, St. Louis, MO, United States
| | - Inês A. Cardoso Pereira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Alexander S. Bradley
- Department of Earth and Planetary Sciences, Washington University in St. Louis, St. Louis, MO, United States
- Division of Biology and Biomedical Sciences, Washington University in St. Louis, St. Louis, MO, United States
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25
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Rajeev L, Luning EG, Zane GM, Juba TR, Kazakov AE, Novichkov PS, Wall JD, Mukhopadhyay A. LurR is a regulator of the central lactate oxidation pathway in sulfate-reducing Desulfovibrio species. PLoS One 2019; 14:e0214960. [PMID: 30964892 PMCID: PMC6456213 DOI: 10.1371/journal.pone.0214960] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 03/22/2019] [Indexed: 11/18/2022] Open
Abstract
The central carbon/lactate utilization pathway in the model sulfate-reducing bacterium, Desulfovibrio vulgaris Hildenborough, is encoded by the highly conserved operon DVU3025-3033. Our earlier in vitro genome-wide study had suggested a network of four two-component system regulators that target this large operon; however, how these four regulators control this operon was not known. Here, we probe the regulation of the lactate utilization operon with mutant strains and DNA-protein binding assays. We show that the LurR response regulator is required for optimal growth and complete lactate utilization, and that it activates the DVU3025-3033 lactate oxidation operon as well as DVU2451, a lactate permease gene, in the presence of lactate. We show by electrophoretic mobility shift assays that LurR binds to three sites in the upstream region of DVU3025, the first gene of the operon. NrfR, a response regulator that is activated under nitrite stress, and LurR share similar binding site motifs and bind the same sites upstream of DVU3025. The DVU3025 promoter also has a binding site motif (Pho box) that is bound by PhoB, a two-component response regulator activated under phosphate limitation. The lactate utilization operon, the regulator LurR, and LurR binding sites are conserved across the order Desulfovibrionales whereas possible modulation of the lactate utilization genes by additional regulators such as NrfR and PhoB appears to be limited to D. vulgaris.
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Affiliation(s)
- Lara Rajeev
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Eric G. Luning
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Grant M. Zane
- Department of Biochemistry, University of Missouri, Columbia, Missouri, United States of America
| | - Thomas R. Juba
- Department of Biochemistry, University of Missouri, Columbia, Missouri, United States of America
| | - Alexey E. Kazakov
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Pavel S. Novichkov
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Judy D. Wall
- Department of Biochemistry, University of Missouri, Columbia, Missouri, United States of America
| | - Aindrila Mukhopadhyay
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- * E-mail:
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26
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Schoeffler M, Gaudin AL, Ramel F, Valette O, Denis Y, Hania WB, Hirschler-Réa A, Dolla A. Growth of an anaerobic sulfate-reducing bacterium sustained by oxygen respiratory energy conservation after O 2 -driven experimental evolution. Environ Microbiol 2018; 21:360-373. [PMID: 30394641 DOI: 10.1111/1462-2920.14466] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 10/25/2018] [Accepted: 10/31/2018] [Indexed: 11/30/2022]
Abstract
Desulfovibrio species are representatives of microorganisms at the boundary between anaerobic and aerobic lifestyles, since they contain the enzymatic systems required for both sulfate and oxygen reduction. However, the latter has been shown to be solely a protective mechanism. By implementing the oxygen-driven experimental evolution of Desulfovibrio vulgaris Hildenborough, we have obtained strains that have evolved to grow with energy derived from oxidative phosphorylation linked to oxygen reduction. We show that a few mutations are sufficient for the emergence of this phenotype and reveal two routes of evolution primarily involving either inactivation or overexpression of the gene encoding heterodisulfide reductase. We propose that the oxygen respiration for energy conservation that sustains the growth of the O2 -evolved strains is associated with a rearrangement of metabolite fluxes, especially NAD+ /NADH, leading to an optimized O2 reduction. These evolved strains are the first sulfate-reducing bacteria that exhibit a demonstrated oxygen respiratory process that enables growth.
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Affiliation(s)
- Marine Schoeffler
- Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - Anne-Laure Gaudin
- Aix Marseille Université, CNRS, LCB, Marseille, France.,GERME SA, Technopôle de Château Gombert, Marseille, France
| | - Fanny Ramel
- Aix Marseille Université, CNRS, LCB, Marseille, France
| | - Odile Valette
- Aix Marseille Université, CNRS, LCB, Marseille, France
| | - Yann Denis
- Aix Marseille Université, CNRS, IMM, Marseille, France
| | - Wagdi Ben Hania
- Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - Agnès Hirschler-Réa
- Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - Alain Dolla
- Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO, Marseille, France
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27
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Flowers JJ, Richards MA, Baliga N, Meyer B, Stahl DA. Constraint-based modelling captures the metabolic versatility of Desulfovibrio vulgaris. ENVIRONMENTAL MICROBIOLOGY REPORTS 2018; 10:190-201. [PMID: 29377633 DOI: 10.1111/1758-2229.12619] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 01/18/2018] [Indexed: 06/07/2023]
Abstract
A refined Desulfovibrio vulgaris Hildenborough flux balance analysis (FBA) model (iJF744) was developed, incorporating 1016 reactions that include 744 genes and 951 metabolites. A draft model was first developed through automatic model reconstruction using the ModelSeed Server and then curated based on existing literature. The curated model was further refined by incorporating three recently proposed redox reactions involving the Hdr-Flx and Qmo complexes and a lactate dehydrogenase (LdhAB, DVU 3027-3028) indicated by mutation and transcript analyses to serve electron transfer reactions central to syntrophic and respiratory growth. Eight different variations of this model were evaluated by comparing model predictions to experimental data determined for four different growth conditions - three for sulfate respiration (with lactate, pyruvate or H2 /CO2 -acetate) and one for fermentation in syntrophic coculture. The final general model supports (i) a role for Hdr-Flx in the oxidation of DsrC and ferredoxin, and reduction of NAD+ in a flavin-based electron confurcating reaction sequence, (ii) a function of the Qmo complex in receiving electrons from the menaquinone pool and potentially from ferredoxin to reduce APS and (iii) a reduction of the soluble DsrC by LdhAB and a function of DsrC in electron transfer reactions other than sulfite reduction.
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Affiliation(s)
- Jason J Flowers
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
| | | | | | - Birte Meyer
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
| | - David A Stahl
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
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28
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Chen Z, Lu J, Gao SH, Jin M, Bond PL, Yang P, Yuan Z, Guo J. Silver nanoparticles stimulate the proliferation of sulfate reducing bacterium Desulfovibrio vulgaris. WATER RESEARCH 2018; 129:163-171. [PMID: 29149671 DOI: 10.1016/j.watres.2017.11.021] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 11/06/2017] [Accepted: 11/07/2017] [Indexed: 06/07/2023]
Abstract
The intensive use of silver nanoparticles (AgNPs) in cosmetics and textiles causes their release into sewer networks of urban water systems. Although a few studies have investigated antimicrobial activities of nanoparticles against environmental bacteria, little is known about potential impacts of the released AgNPs on sulfate reducing bacteria in sewers. Here, we investigated the effect of AgNPs on Desulfovibrio vulgaris Hidenborough (D. vulgaris), a typical sulfate-reducing bacterium (SRB) in sewer systems. We found AgNPs stimulated the proliferation of D. vulgaris, rather than exerting inhibitory or biocidal effects. Based on flow cytometer detections, both the cell growth rate and the viable cell ratio of D. vulgaris increased during exposure to AgNPs at concentrations of up to 100 mg/L. The growth stimulation was dependent on the AgNP concentration. These results imply that the presence of AgNPs in sewage may affect SRB abundance in sewer networks. Our findings also shed new lights on the interactions of nanoparticles and bacteria.
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Affiliation(s)
- Zhaoyu Chen
- Advanced Water Management Centre, The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia; Department of Environmental Science & Engineering, Sichuan University, Chengdu, Sichuan 610065, China
| | - Ji Lu
- Advanced Water Management Centre, The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia
| | - Shu-Hong Gao
- Advanced Water Management Centre, The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia
| | - Min Jin
- Advanced Water Management Centre, The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia
| | - Philip L Bond
- Advanced Water Management Centre, The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia
| | - Ping Yang
- Department of Environmental Science & Engineering, Sichuan University, Chengdu, Sichuan 610065, China
| | - Zhiguo Yuan
- Advanced Water Management Centre, The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia
| | - Jianhua Guo
- Advanced Water Management Centre, The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia.
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29
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Detman A, Mielecki D, Pleśniak Ł, Bucha M, Janiga M, Matyasik I, Chojnacka A, Jędrysek MO, Błaszczyk MK, Sikora A. Methane-yielding microbial communities processing lactate-rich substrates: a piece of the anaerobic digestion puzzle. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:116. [PMID: 29721040 PMCID: PMC5910564 DOI: 10.1186/s13068-018-1106-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 04/04/2018] [Indexed: 05/02/2023]
Abstract
BACKGROUND Anaerobic digestion, whose final products are methane and carbon dioxide, ensures energy flow and circulation of matter in ecosystems. This naturally occurring process is used for the production of renewable energy from biomass. Lactate, a common product of acidic fermentation, is a key intermediate in anaerobic digestion of biomass in the environment and biogas plants. Effective utilization of lactate has been observed in many experimental approaches used to study anaerobic digestion. Interestingly, anaerobic lactate oxidation and lactate oxidizers as a physiological group in methane-yielding microbial communities have not received enough attention in the context of the acetogenic step of anaerobic digestion. This study focuses on metabolic transformation of lactate during the acetogenic and methanogenic steps of anaerobic digestion in methane-yielding bioreactors. RESULTS Methane-yielding microbial communities instead of pure cultures of acetate producers were used to process artificial lactate-rich media to methane and carbon dioxide in up-flow anaerobic sludge blanket reactors. The media imitated the mixture of acidic products found in anaerobic environments/digesters where lactate fermentation dominates in acidogenesis. Effective utilization of lactate and biogas production was observed. 16S rRNA profiling was used to examine the selected methane-yielding communities. Among Archaea present in the bioreactors, the order Methanosarcinales predominated. The acetoclastic pathway of methane formation was further confirmed by analysis of the stable carbon isotope composition of methane and carbon dioxide. The domain Bacteria was represented by Bacteroidetes, Firmicutes, Proteobacteria, Synergistetes, Actinobacteria, Spirochaetes, Tenericutes, Caldithrix, Verrucomicrobia, Thermotogae, Chloroflexi, Nitrospirae, and Cyanobacteria. Available genome sequences of species and/or genera identified in the microbial communities were searched for genes encoding the lactate-oxidizing metabolic machinery homologous to those of Acetobacterium woodii and Desulfovibrio vulgaris. Furthermore, genes for enzymes of the reductive acetyl-CoA pathway were present in the microbial communities. CONCLUSIONS The results indicate that lactate is oxidized mainly to acetate during the acetogenic step of AD and this comprises the acetotrophic pathway of methanogenesis. The genes for lactate utilization under anaerobic conditions are widespread in the domain Bacteria. Lactate oxidation to the substrates for methanogens is the most energetically attractive process in comparison to butyrate, propionate, or ethanol oxidation.
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Affiliation(s)
- Anna Detman
- Department of Molecular Biology, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Damian Mielecki
- Department of Molecular Biology, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Łukasz Pleśniak
- Department of Molecular Biology, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Michał Bucha
- Faculty of Earth Sciences, University of Silesia in Katowice, Sosnowiec, Poland
| | - Marek Janiga
- Oil and Gas Institute, National Research Institute, Cracow, Poland
| | - Irena Matyasik
- Oil and Gas Institute, National Research Institute, Cracow, Poland
| | - Aleksandra Chojnacka
- Department of Molecular Biology, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | | | | | - Anna Sikora
- Department of Molecular Biology, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
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30
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Miran W, Jang J, Nawaz M, Shahzad A, Jeong SE, Jeon CO, Lee DS. Mixed sulfate-reducing bacteria-enriched microbial fuel cells for the treatment of wastewater containing copper. CHEMOSPHERE 2017; 189:134-142. [PMID: 28934653 DOI: 10.1016/j.chemosphere.2017.09.048] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 08/31/2017] [Accepted: 09/11/2017] [Indexed: 06/07/2023]
Abstract
Microbial fuel cells (MFCs) have been widely investigated for organic-based waste/substrate conversion to electricity. However, toxic compounds such as heavy metals are ubiquitous in organic waste and wastewater. In this work, a sulfate reducing bacteria (SRB)-enriched anode is used to study the impact of Cu2+ on MFC performance. This study demonstrates that MFC performance is slightly enhanced at concentrations of up to 20 mg/L of Cu2+, owing to the stimulating effect of metals on biological reactions. Cu2+ removal involves the precipitation of metalloids out of the solution, as metal sulfide, after they react with the sulfide produced by SRB. Simultaneous power generation of 224.1 mW/m2 at lactate COD/SO42- mass ratio of 2.0 and Cu2+ of 20 mg/L, and high Cu2+ removal efficiency, at >98%, are demonstrated in the anodic chamber of a dual-chamber MFC. Consistent MFC performance at 20 mg/L of Cu2+ for ten successive cycles shows the excellent reproducibility of this system. In addition, total organic content and sulfate removal efficiencies greater than 85% and 70%, respectively, are achieved up to 20 mg/L of Cu2+ in 48 h batches. However, higher metal concentration and very low pH at <4.0 inhibit the SRB MFC system. Microbial community analysis reveals that Desulfovibrio is the most abundant SRB in anode biofilm at the genus level, at 38.1%. The experimental results demonstrate that biological treatment of low-concentration metal-containing wastewater with SRB in MFCs can be an attractive technique for the bioremediation of this type of medium with simultaneous energy generation.
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Affiliation(s)
- Waheed Miran
- Department of Environmental Engineering, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu, 41566, Republic of Korea
| | - Jiseon Jang
- Department of Environmental Engineering, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu, 41566, Republic of Korea
| | - Mohsin Nawaz
- Department of Environmental Engineering, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu, 41566, Republic of Korea
| | - Asif Shahzad
- Department of Environmental Engineering, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu, 41566, Republic of Korea
| | - Sang Eun Jeong
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Che Ok Jeon
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Dae Sung Lee
- Department of Environmental Engineering, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu, 41566, Republic of Korea.
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31
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Valette O, Tran TTT, Cavazza C, Caudeville E, Brasseur G, Dolla A, Talla E, Pieulle L. Biochemical Function, Molecular Structure and Evolution of an Atypical Thioredoxin Reductase from Desulfovibrio vulgaris. Front Microbiol 2017; 8:1855. [PMID: 29033913 PMCID: PMC5627308 DOI: 10.3389/fmicb.2017.01855] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 09/11/2017] [Indexed: 11/19/2022] Open
Abstract
Thioredoxin reductase (TR) regulates the intracellular redox environment by reducing thioredoxin (Trx). In anaerobes, recent findings indicate that the Trx redox network is implicated in the global redox regulation of metabolism but also actively participates in protecting cells against O2. In the anaerobe Desulfovibrio vulgaris Hildenborough (DvH), there is an intriguing redundancy of the Trx system which includes a classical system using NADPH as electron source, a non-canonical system using NADH and an isolated TR (DvTRi). The functionality of DvTRi was questioned due to its lack of reactivity with DvTrxs. Structural analysis shows that DvTRi is a NAD(P)H-independent TR but its reducer needs still to be identified. Moreover, DvTRi reduced by an artificial electron source is able to reduce in turn DvTrx1 and complexation experiments demonstrate a direct interaction between DvTRi and DvTrx1. The deletion mutant tri exhibits a higher sensitivity to disulfide stress and the gene tri is upregulated by O2 exposure. Having DvTRi in addition to DvTR1 as electron source for reducing DvTrx1 must be an asset to combat oxidative stress. Large-scale phylogenomics analyses show that TRi homologs are confined within the anaerobes. All TRi proteins displayed a conserved TQ/NGK motif instead of the HRRD motif, which is selective for the binding of the 2′-phosphate group of NADPH. The evolutionary history of TRs indicates that tr1 is the common gene ancestor in prokaryotes, affected by both gene duplications and horizontal gene events, therefore leading to the appearance of TRi through subfunctionalization over the evolutionary time.
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Affiliation(s)
| | - Tam T T Tran
- Aix-Marseille Univ, CNRS, LCB, Marseille, France
| | - Christine Cavazza
- Laboratoire de Chimie et Biologie des Métaux, Université Grenoble Alpes, Grenoble, France.,UMR 5249, Laboratoire de Chimie et Biologie des Métaux, Centre National de la Recherche Scientifique, Grenoble, France.,DRF/BIG/CBM, CEA-Grenoble, Grenoble, France
| | | | | | - Alain Dolla
- Aix-Marseille Univ, CNRS, LCB, Marseille, France
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32
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Viala JP, Prima V, Puppo R, Agrebi R, Canestrari MJ, Lignon S, Chauvin N, Méresse S, Mignot T, Lebrun R, Bouveret E. Acylation of the Type 3 Secretion System Translocon Using a Dedicated Acyl Carrier Protein. PLoS Genet 2017; 13:e1006556. [PMID: 28085879 PMCID: PMC5279801 DOI: 10.1371/journal.pgen.1006556] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 01/30/2017] [Accepted: 12/29/2016] [Indexed: 12/18/2022] Open
Abstract
Bacterial pathogens often deliver effectors into host cells using type 3 secretion systems (T3SS), the extremity of which forms a translocon that perforates the host plasma membrane. The T3SS encoded by Salmonella pathogenicity island 1 (SPI-1) is genetically associated with an acyl carrier protein, IacP, whose role has remained enigmatic. In this study, using tandem affinity purification, we identify a direct protein-protein interaction between IacP and the translocon protein SipB. We show, by mass spectrometry and radiolabelling, that SipB is acylated, which provides evidence for a modification of the translocon that has not been described before. A unique and conserved cysteine residue of SipB is identified as crucial for this modification. Although acylation of SipB was not essential to virulence, we show that this posttranslational modification promoted SipB insertion into host-cell membranes and pore-forming activity linked to the SPI-1 T3SS. Cooccurrence of acyl carrier and translocon proteins in several γ- and β-proteobacteria suggests that acylation of the translocon is conserved in these other pathogenic bacteria. These results also indicate that acyl carrier proteins, known for their involvement in metabolic pathways, have also evolved as cofactors of new bacterial protein lipidation pathways. Acyl carrier proteins are small ubiquitous proteins involved in the synthesis of hydrocarbon based molecules. Notably, they are essential for the synthesis of fatty acids, which are the precursors of membrane phospholipids. They can also be involved in secondary metabolism, for example for the synthesis of molecules with antibacterial properties. Although acyl carrier proteins are widespread, the specific role of each individual protein seems comparatively poorly explored. In this study, we investigate the role of an acyl carrier protein genetically associated with a type 3 secretion system (T3SS). Many Gram-negative bacterial pathogens use T3SS to deliver effectors directly into the cytoplasm of eukaryotic host cells and to subvert host cellular pathways. For this purpose, the translocon, which is the terminal part of T3SS, forms a pore inserted into the host-cell membrane. Here we show that the acyl carrier protein associated with the T3SS has specialized to allow acylation of the translocon. The novel posttranslational modification of the translocon that we describe optimizes insertion into the host-cell membrane and pore-forming activity. This mechanism is likely to be conserved in other pathogenic bacteria given the conserved genetic association between T3SS and acyl carrier protein in several bacteria.
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Affiliation(s)
- Julie P. Viala
- Aix Marseille Univ, CNRS, IMM, LISM, Marseille, France
- * E-mail:
| | - Valérie Prima
- Aix Marseille Univ, CNRS, IMM, LISM, Marseille, France
| | - Rémy Puppo
- Aix Marseille Univ, CNRS, IMM, Proteomic Platform- IBISA, Marseille, France
| | - Rym Agrebi
- Aix Marseille Univ, CNRS, IMM, LCB, Marseille, France
| | | | - Sabrina Lignon
- Aix Marseille Univ, CNRS, IMM, Proteomic Platform- IBISA, Marseille, France
| | | | | | - Tâm Mignot
- Aix Marseille Univ, CNRS, IMM, LCB, Marseille, France
| | - Régine Lebrun
- Aix Marseille Univ, CNRS, IMM, Proteomic Platform- IBISA, Marseille, France
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33
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Antimicrobial Effects of Free Nitrous Acid on Desulfovibrio vulgaris: Implications for Sulfide-Induced Corrosion of Concrete. Appl Environ Microbiol 2016; 82:5563-75. [PMID: 27371588 DOI: 10.1128/aem.01655-16] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 06/28/2016] [Indexed: 01/04/2023] Open
Abstract
Hydrogen sulfide produced by sulfate-reducing bacteria (SRB) in sewers causes odor problems and asset deterioration due to the sulfide-induced concrete corrosion. Free nitrous acid (FNA) was recently demonstrated as a promising antimicrobial agent to alleviate hydrogen sulfide production in sewers. However, details of the antimicrobial mechanisms of FNA are largely unknown. Here, we report the multiple-targeted antimicrobial effects of FNA on the SRB Desulfovibrio vulgaris Hildenborough by determining the growth, physiological, and gene expression responses to FNA exposure. The activities of growth, respiration, and ATP generation were inhibited when exposed to FNA. These changes were reflected in the transcript levels detected during exposure. The removal of FNA was evident by nitrite reduction that likely involved nitrite reductase and the poorly characterized hybrid cluster protein, and the genes coding for these proteins were highly expressed. During FNA exposure, lowered ribosome activity and protein production were detected. Additionally, conditions within the cells were more oxidizing, and there was evidence of oxidative stress. Based on an interpretation of the measured responses, we present a model depicting the antimicrobial effects of FNA on D. vulgaris These findings provide new insight for understanding the responses of D. vulgaris to FNA and will provide a foundation for optimal application of this antimicrobial agent for improved control of sewer corrosion and odor management.IMPORTANCE Hydrogen sulfide produced by SRB in sewers causes odor problems and results in serious deterioration of sewer assets that requires very costly and demanding rehabilitation. Currently, there is successful application of the antimicrobial agent free nitrous acid (FNA), the protonated form of nitrite, for the control of sulfide levels in sewers (G. Jiang et al., Water Res 47:4331-4339, 2013, http://dx.doi.org/10.1016/j.watres.2013.05.024). However, the details of the antimicrobial mechanisms of FNA are largely unknown. In this study, we identified the key responses (decreased anaerobic respiration, reducing FNA, combating oxidative stress, and shutting down protein synthesis) of Desulfovibrio vulgaris Hildenborough, a model sewer corrosion bacterium, to FNA exposure by examining the growth, physiological, and gene expression changes. These findings provide new insight and underpinning knowledge for understanding the responses of D. vulgaris to FNA exposure, thereby benefiting the practical application of FNA for improved control of sewer corrosion and odor.
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