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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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Lee J, Kang YJ, Kim YK, Choi JY, Shin SM, Shin MC. Exploring the Influence of Growth-Associated Host Genetics on the Initial Gut Microbiota in Horses. Genes (Basel) 2023; 14:1354. [PMID: 37510259 PMCID: PMC10379381 DOI: 10.3390/genes14071354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 06/23/2023] [Accepted: 06/25/2023] [Indexed: 07/30/2023] Open
Abstract
The influences of diet and environmental factors on gut microbial profiles have been widely acknowledged; however, the specific roles of host genetics remain uncertain. To unravel host genetic effects, we raised 47 Jeju crossbred (Jeju × Thoroughbred) foals that exhibited higher genetic diversity. Foals were raised under identical environmental conditions and diets. Microbial composition revealed that Firmicutes, Bacteroidetes, and Spirochaetes were the predominant phyla. We identified 31 host-microbiome associations by utilizing 47,668 single nucleotide polymorphisms (SNPs) and 734 taxa with quantitative trait locus (QTL) information related to horse growth. The taxa involved in 31 host-microbiome associations were functionally linked to carbohydrate metabolism, energy metabolic processes, short-chain fatty acid (SCFA) production, and lactic acid production. Abundances of these taxa were affected by specific SNP genotypes. Most growth-associated SNPs are found between genes. The rs69057439 and rs69127732 SNPs are located within the introns of the VWA8 and MFSD6 genes, respectively. These genes are known to affect energy balance and metabolism. These discoveries emphasize the significant effect of host SNPs on the development of the intestinal microbiome during the initial phases of life and provide insights into the influence of gut microbial composition on horse growth.
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Affiliation(s)
- Jongan Lee
- Subtropical Livestock Research Institute, National Institute of Animal Science, RDA, Jeju 63242, Republic of Korea
| | - Yong-Jun Kang
- Subtropical Livestock Research Institute, National Institute of Animal Science, RDA, Jeju 63242, Republic of Korea
| | - Yoo-Kyung Kim
- Subtropical Livestock Research Institute, National Institute of Animal Science, RDA, Jeju 63242, Republic of Korea
| | - Jae-Young Choi
- Subtropical Livestock Research Institute, National Institute of Animal Science, RDA, Jeju 63242, Republic of Korea
| | - Sang-Min Shin
- Subtropical Livestock Research Institute, National Institute of Animal Science, RDA, Jeju 63242, Republic of Korea
| | - Moon-Cheol Shin
- Planning and Coordination Division, National Institute of Animal Science, RDA, Wanju 55365, Republic of Korea
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Moura JJG. The History of Desulfovibrio gigas Aldehyde Oxidoreductase-A Personal View. Molecules 2023; 28:4229. [PMID: 37241969 PMCID: PMC10223205 DOI: 10.3390/molecules28104229] [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: 04/18/2023] [Revised: 05/17/2023] [Accepted: 05/19/2023] [Indexed: 05/28/2023] Open
Abstract
A story going back almost 40 years is presented in this manuscript. This is a different and more challenging way of reporting my research and I hope it will be useful to and target a wide-ranging audience. When preparing the manuscript and collecting references on the subject of this paper-aldehyde oxidoreductase from Desulfovibrio gigas-I felt like I was travelling back in time (and space), bringing together the people that have contributed most to this area of research. I sincerely hope that I can give my collaborators the credit they deserve. This study is not presented as a chronologic narrative but as a grouping of topics, the development of which occurred over many years.
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Affiliation(s)
- José J G Moura
- LAQV, NOVA School of Science and Technology|FCT NOVA, 2829-516 Caparica, Portugal
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Gao P, Zhang X, Huang X, Chen Z, Marietou A, Holmkvist L, Qu L, Finster K, Gong X. Genomic insight of sulfate reducing bacterial genus Desulfofaba reveals their metabolic versatility in biogeochemical cycling. BMC Genomics 2023; 24:209. [PMID: 37076818 PMCID: PMC10116758 DOI: 10.1186/s12864-023-09297-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 04/04/2023] [Indexed: 04/21/2023] Open
Abstract
BACKGROUND Sulfate-reducing bacteria (SRB) drive the ocean sulfur and carbon cycling. They constitute a diverse phylogenetic and physiological group and are widely distributed in anoxic marine environments. From a physiological viewpoint, SRB's can be categorized as complete or incomplete oxidizers, meaning that they either oxidize their carbon substrate completely to CO2 or to a stoichiometric mix of CO2 and acetate. Members of Desulfofabaceae family are incomplete oxidizers, and within that family, Desulfofaba is the only genus with three isolates that are classified into three species. Previous physiological experiments revealed their capability of respiring oxygen. RESULTS Here, we sequenced the genomes of three isolates in Desulfofaba genus and reported on a genomic comparison of the three species to reveal their metabolic potentials. Based on their genomic contents, they all could oxidize propionate to acetate and CO2. We confirmed their phylogenetic position as incomplete oxidizers based on dissimilatory sulfate reductase (DsrAB) phylogeny. We found the complete pathway for dissimilatory sulfate reduction, but also different key genes for nitrogen cycling, including nitrogen fixation, assimilatory nitrate/nitrite reduction, and hydroxylamine reduction to nitrous oxide. Their genomes also contain genes that allow them to cope with oxygen and oxidative stress. They have genes that encode for diverse central metabolisms for utilizing different substrates with the potential for more strains to be isolated in the future, yet their distribution is limited. CONCLUSIONS Results based on marker gene search and curated metagenome assembled genomes search suggest a limited environmental distribution of this genus. Our results reveal a large metabolic versatility within the Desulfofaba genus which establishes their importance in biogeochemical cycling of carbon in their respective habitats, as well as in the support of the entire microbial community through releasing easily degraded organic matters.
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Affiliation(s)
- Ping Gao
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources (MNR), 266061, Qingdao, PR China
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, 266237, Qingdao, PR China
| | - Xiaoting Zhang
- Institute of Marine Science and Technology, Shandong University, 266237, Qingdao, PR China
| | - Xiaomei Huang
- Institute of Marine Science and Technology, Shandong University, 266237, Qingdao, PR China
| | - Zhiyi Chen
- Institute of Marine Science and Technology, Shandong University, 266237, Qingdao, PR China
| | - Angeliki Marietou
- Section for Microbiology, Department of Biology, Aarhus University, 8000, Aarhus, Denmark
- Department of Biological and Chemical Engineering, Aarhus University, 8000, Aarhus, Denmark
| | - Lars Holmkvist
- Section for Microbiology, Department of Biology, Aarhus University, 8000, Aarhus, Denmark
| | - Lingyun Qu
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources (MNR), 266061, Qingdao, PR China
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, 266237, Qingdao, PR China
| | - Kai Finster
- Section for Microbiology, Department of Biology, Aarhus University, 8000, Aarhus, Denmark
- Stellar Astrophysics Center, Department of Physics and Astronomy, Aarhus University, 8000, Aarhus, Denmark
| | - Xianzhe Gong
- Institute of Marine Science and Technology, Shandong University, 266237, Qingdao, PR China.
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Barton LL, Duarte AG, Staicu LC. Genomic insight into iron acquisition by sulfate-reducing bacteria in microaerophilic environments. Biometals 2023; 36:339-350. [PMID: 35767096 DOI: 10.1007/s10534-022-00410-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 06/08/2022] [Indexed: 11/30/2022]
Abstract
Historically, sulfate-reducing bacteria (SRB) have been considered to be strict anaerobes, but reports in the past couple of decades indicate that SRB tolerate exposure to O2 and can even grow in aerophilic environments. With the transition from anaerobic to microaerophilic conditions, the uptake of Fe(III) from the environment by SRB would become important. In evaluating the metabolic capability for the uptake of iron, the genomes of 26 SRB, representing eight families, were examined. All SRB reviewed carry genes (feoA and feoB) for the ferrous uptake system to transport Fe(II) across the plasma membrane into the cytoplasm. In addition, all of the SRB genomes examined have putative genes for a canonical ABC transporter that may transport ferric siderophore or ferric chelated species from the environment. Gram-negative SRB have additional machinery to import ferric siderophores and ferric chelated species since they have the TonB system that can work alongside any of the outer membrane porins annotated in the genome. Included in this review is the discussion that SRB may use the putative siderophore uptake system to import metals other than iron.
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Affiliation(s)
- Larry L Barton
- Department of Biology, University of New Mexico, MSCO3 2020, Albuquerque, NM, 87131, USA
| | - Americo G Duarte
- Instituto de Tecnologia Química E Biológica António Xavier/Universidade NOVA de Lisboa, Av. República, Estação Agronómica Nacional, 2780-157, Oeiras, Portugal
| | - Lucian C Staicu
- Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland.
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Longitudinal Study of the Effects of Flammulina velutipes Stipe Wastes on the Cecal Microbiota of Laying Hens. mSystems 2023; 8:e0083522. [PMID: 36511708 PMCID: PMC9948703 DOI: 10.1128/msystems.00835-22] [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] [Indexed: 12/15/2022] Open
Abstract
Because antibiotics have been phased out of use in poultry feed, measures to improve intestinal health have been sought. Dietary fiber may be beneficial to intestinal health by modulating gut microbial composition, but the exact changes it induces remain unclear. In this study, we evaluated the effect of Flammulina velutipes stipe wastes (FVW) on the cecal microbiotas of laying chickens at ages spanning birth to 490 days. Using clonal sequencing and 16S rRNA high-throughput sequencing, we showed that FVW improved the microbial diversity when they under fluctuated. The evolvement of the microbiota enhanced the physiological development of laying hens. Supplementation of FVW enriched the relative abundance of Sutterella, Ruminiclostridium, Synergistes, Anaerostipes, and Rikenellaceae, strengthened the positive connection between Firmicutes and Bacteroidetes, and increased the concentration of short-chain fatty acids (SCFAs) in early life. FVW maintains gut microbiota homeostasis by regulating Th1, Th2, and Th17 balance and secretory IgA (S-IgA) level. In conclusion, we showed that FVW induces microbial changes that are potentially beneficial for intestinal immunity. IMPORTANCE Dietary fiber is popularly used in poultry farming to improve host health and metabolism. Microbial composition is known to be influenced by dietary fiber use, although the exact FVW-induced changes remain unclear. This study provided a first comparison of the effects of FVW and the most commonly used antibiotic growth promoter (flavomycin) on the cecal microbiotas of laying hens from birth to 490 days of age. We found that supplementation with FVW altered cecal microbial composition, thereby affecting the correlation network between members of the microbiota, and subsequently affecting the intestinal immune homeostasis.
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Park MJ, Kim YJ, Park M, Yu J, Namirimu T, Roh YR, Kwon KK. Establishment of Genome Based Criteria for Classification of the Family Desulfovibrionaceae and Proposal of Two Novel Genera, Alkalidesulfovibrio gen. nov. and Salidesulfovibrio gen. nov. Front Microbiol 2022; 13:738205. [PMID: 35694308 PMCID: PMC9174804 DOI: 10.3389/fmicb.2022.738205] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 04/11/2022] [Indexed: 01/14/2023] Open
Abstract
Bacteria in the Desulfovibrionaceae family, which contribute to S element turnover as sulfate-reducing bacteria (SRB) and disproportionation of partially oxidized sulfoxy anions, have been extensively investigated since the importance of the sulfur cycle emerged. Novel species belonging to this taxon are frequently reported, because they exist in various environments and are easy to culture using established methods. Due to the rapid expansion of the taxon, correction and reclassification have been conducted. The development of high-throughput sequencing facilitated rapid expansion of genome sequence database. Genome-based criteria, based on these databases, proved to be potential classification standard by overcoming the limitations of 16S rRNA-based phylogeny. Although standards methods for taxogenomics are being established, the addition of a novel genus requires extensive calculations with taxa, including many species, such as Desulfovibrionaceae. Thus, the genome-based criteria for classification of Desulfovibrionaceae were established and validated in this study. The average amino-acid identity (AAI) cut-off value, 63.43 ± 0.01, was calculated to be an appropriate criterion for genus delineation of the family Desulfovibrionaceae. By applying the AAI cut-off value, 88 genomes of the Desulfovibrionaceae were divided into 27 genera, which follows the core gene phylogeny results. In this process, two novel genera (Alkalidesulfovibrio and Salidesulfovibrio) and one former invalid genus (“Psychrodesulfovibrio”) were officially proposed. Further, by applying the 95–96% average nucleotide identity (ANI) standard and the 70% digital DNA–DNA hybridization standard values for species delineation of strains that were classified as the same species, five strains have the potential to be newly classified. After verifying that the classification was appropriately performed through relative synonymous codon usage analysis, common characteristics were listed by group. In addition, by detecting metal resistance related genes via in silico analysis, it was confirmed that most strains display metal tolerance.
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Affiliation(s)
- Mi-Jeong Park
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Busan, South Korea
- Department of Applied Ocean Science, University of Science and Technology, Daejeon, South Korea
| | - Yun Jae Kim
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Busan, South Korea
| | - Myeongkyu Park
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, South Korea
| | - Jihyun Yu
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Busan, South Korea
- Department of Applied Ocean Science, University of Science and Technology, Daejeon, South Korea
| | - Teddy Namirimu
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Busan, South Korea
- Department of Applied Ocean Science, University of Science and Technology, Daejeon, South Korea
| | - Yoo-Rim Roh
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Busan, South Korea
- Department of Applied Ocean Science, University of Science and Technology, Daejeon, South Korea
| | - Kae Kyoung Kwon
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Busan, South Korea
- Department of Applied Ocean Science, University of Science and Technology, Daejeon, South Korea
- *Correspondence: Kae Kyoung Kwon,
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Dai S, Korth B, Schwab L, Aulenta F, Vogt C, Harnisch F. Deciphering the fate of sulfate in one- and two-chamber bioelectrochemical systems. Electrochim Acta 2022. [DOI: 10.1016/j.electacta.2022.139942] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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9
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Massazza D, Robledo AJ, Rodriguez Simón CN, Busalmen JP, Bonanni S. Energetics, electron uptake mechanisms and limitations of electroautotrophs growing on biocathodes - A review. BIORESOURCE TECHNOLOGY 2021; 342:125893. [PMID: 34537530 DOI: 10.1016/j.biortech.2021.125893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Revised: 08/31/2021] [Accepted: 09/03/2021] [Indexed: 06/13/2023]
Abstract
Electroautotrophs are microorganisms that can take the electrons needed for energy generation, CO2 fixation and other metabolic reactions from a polarized electrode. They have been the focus of intense research for its application in wastewater treatment, bioelectrosynthetic processes and hydrogen generation. As a general trend, current densities produced by the electron uptake of these microorganisms are low, limiting their applicability at large scale. In this work, the electron uptake mechanisms that may operate in electroautotrophs are reviewed, aiming at finding possible causes for this low performance. Biomass yields, growth rates and electron uptake rates observed when these microorganisms use chemical electron donors are compared with those typically obtained with electrodes, to explore limitations and advantages inherent to the electroautotrophic metabolism. Also, the factors affecting biofilm development are analysed to show how interfacial interactions condition bacterial adhesion, biofilm growth and electrons uptake. Finally, possible strategies to overcome these limitations are described.
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Affiliation(s)
- Diego Massazza
- División Ingeniería de Interfases y Bioprocesos, INTEMA (Conicet, Universidad Nacional de Mar del Plata), Av. Colón 10850, Mar del Plata 7600, Argentina
| | - Alejandro Javier Robledo
- División Ingeniería de Interfases y Bioprocesos, INTEMA (Conicet, Universidad Nacional de Mar del Plata), Av. Colón 10850, Mar del Plata 7600, Argentina
| | - Carlos Norberto Rodriguez Simón
- División Ingeniería de Interfases y Bioprocesos, INTEMA (Conicet, Universidad Nacional de Mar del Plata), Av. Colón 10850, Mar del Plata 7600, Argentina
| | - Juan Pablo Busalmen
- División Ingeniería de Interfases y Bioprocesos, INTEMA (Conicet, Universidad Nacional de Mar del Plata), Av. Colón 10850, Mar del Plata 7600, Argentina
| | - Sebastián Bonanni
- División Ingeniería de Interfases y Bioprocesos, INTEMA (Conicet, Universidad Nacional de Mar del Plata), Av. Colón 10850, Mar del Plata 7600, Argentina.
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Paradesulfovibrio onnuriensis gen. nov., sp. nov., a chemolithoautotrophic sulfate-reducing bacterium isolated from the Onnuri vent field of the Indian Ocean and reclassification of Desulfovibrio senegalensis as Paradesulfovibrio senegalensis comb. nov. J Microbiol 2020; 58:252-259. [DOI: 10.1007/s12275-020-9376-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 10/31/2019] [Accepted: 01/21/2020] [Indexed: 10/24/2022]
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Pinnell LJ, Turner JW. Shotgun Metagenomics Reveals the Benthic Microbial Community Response to Plastic and Bioplastic in a Coastal Marine Environment. Front Microbiol 2019; 10:1252. [PMID: 31231339 PMCID: PMC6566015 DOI: 10.3389/fmicb.2019.01252] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 05/20/2019] [Indexed: 11/23/2022] Open
Abstract
Plastic is incredibly abundant in marine environments but little is known about its effects on benthic microbiota and biogeochemical cycling. This study reports the shotgun metagenomic sequencing of biofilms fouling plastic and bioplastic microcosms staged at the sediment–water interface of a coastal lagoon. Community composition analysis revealed that plastic biofilms were indistinguishable in comparison to a ceramic biofilm control. By contrast, bioplastic biofilms were distinct and dominated by sulfate-reducing microorganisms (SRM). Analysis of bioplastic gene pools revealed the enrichment of esterases, depolymerases, adenylyl sulfate reductases (aprBA), and dissimilatory sulfite reductases (dsrAB). The nearly 20-fold enrichment of a phylogenetically diverse polyhydroxybutyrate (PHB) depolymerase suggests this gene was distributed across a mixed microbial assemblage. The metagenomic reconstruction of genomes identified novel species of Desulfovibrio, Desulfobacteraceae, and Desulfobulbaceae among the abundant SRM, and these genomes contained genes integral to both bioplastic degradation and sulfate reduction. Findings indicate that bioplastic promoted a rapid and significant shift in benthic microbial diversity and gene pools, selecting for microbes that participate in bioplastic degradation and sulfate reduction. If plastic pollution is traded for bioplastic pollution and sedimentary inputs are large, the microbial response could unintentionally affect benthic biogeochemical activities through the stimulation of sulfate reducers.
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Affiliation(s)
- Lee J Pinnell
- Department of Life Sciences, Texas A&M University - Corpus Christi, Corpus Christi, TX, United States
| | - Jeffrey W Turner
- Department of Life Sciences, Texas A&M University - Corpus Christi, Corpus Christi, TX, United States
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12
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Baffert C, Kpebe A, Avilan L, Brugna M. Hydrogenases and H 2 metabolism in sulfate-reducing bacteria of the Desulfovibrio genus. Adv Microb Physiol 2019; 74:143-189. [PMID: 31126530 DOI: 10.1016/bs.ampbs.2019.03.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Hydrogen metabolism plays a central role in sulfate-reducing bacteria of the Desulfovibrio genus and is based on hydrogenases that catalyze the reversible conversion of protons into dihydrogen. These metabolically versatile microorganisms possess a complex hydrogenase system composed of several enzymes of both [FeFe]- and [NiFe]-type that can vary considerably from one Desulfovibrio species to another. This review covers the molecular and physiological aspects of hydrogenases and H2 metabolism in Desulfovibrio but focuses particularly on our model bacterium Desulfovibrio fructosovorans. The search of hydrogenase genes in more than 30 sequenced genomes provides an overview of the distribution of these enzymes in Desulfovibrio. Our discussion will consider the significance of the involvement of electron-bifurcation in H2 metabolism.
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Affiliation(s)
- Carole Baffert
- Aix-Marseille University, CNRS, BIP, 31 Chemin Joseph Aiguier, 13402 Marseille, France
| | - Arlette Kpebe
- Aix-Marseille University, CNRS, BIP, 31 Chemin Joseph Aiguier, 13402 Marseille, France
| | - Luisana Avilan
- Aix-Marseille University, CNRS, BIP, 31 Chemin Joseph Aiguier, 13402 Marseille, France
| | - Myriam Brugna
- Aix-Marseille University, CNRS, BIP, 31 Chemin Joseph Aiguier, 13402 Marseille, France
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Qian Z, Tianwei H, Mackey HR, van Loosdrecht MCM, Guanghao C. Recent advances in dissimilatory sulfate reduction: From metabolic study to application. WATER RESEARCH 2019; 150:162-181. [PMID: 30508713 DOI: 10.1016/j.watres.2018.11.018] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 10/25/2018] [Accepted: 11/08/2018] [Indexed: 05/24/2023]
Abstract
Sulfate-reducing bacteria (SRB) are a group of diverse anaerobic microorganisms omnipresent in natural habitats and engineered environments that use sulfur compounds as the electron acceptor for energy metabolism. Dissimilatory sulfate reduction (DSR)-based techniques mediated by SRB have been utilized in many sulfate-containing wastewater treatment systems worldwide, particularly for acid mine drainage, groundwater, sewage and industrial wastewater remediation. However, DSR processes are often operated suboptimally and disturbances are common in practical application. To improve the efficiency and robustness of SRB-based processes, it is necessary to study SRB metabolism and operational conditions. In this review, the mechanisms of DSR processes are reviewed and discussed focusing on intracellular and extracellular electron transfer with different electron donors (hydrogen, organics, methane and electrodes). Based on the understanding of the metabolism of SRB, responses of SRB to environmental stress (pH-, temperature-, and salinity-related stress) are summarized at the species and community levels. Application in these stressed conditions is discussed and future research is proposed. The feasibility of recovering energy and resources such as biohydrogen, hydrocarbons, polyhydroxyalkanoates, magnetite and metal sulfides through the use of SRB were investigated but some long-standing questions remain unanswered. Linking the existing scientific understanding and observations to practical application is the challenge as always for promotion of SRB-based techniques.
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Affiliation(s)
- Zeng Qian
- Department of Civil and Environmental Engineering, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Hao Tianwei
- Department of Civil and Environmental Engineering, Faculty of Science and Technology, University of Macau, Macau, China; Department of Civil and Environmental Engineering, The Hong Kong University of Science and Technology, Hong Kong, China.
| | - Hamish Robert Mackey
- Division of Sustainable Development, College of Science and Engineering, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar
| | | | - Chen Guanghao
- Department of Civil and Environmental Engineering, The Hong Kong University of Science and Technology, Hong Kong, China; Water Technology Center, The Hong Kong University of Science and Technology, Hong Kong, China; Hong Kong Branch of Chinese National Engineering Research Center for Control & Treatment of Heavy Metal Pollution, The Hong Kong University of Science and Technology, Hong Kong, China; Wastewater Treatment Laboratory, FYT Graduate School, The Hong Kong University of Science and Technology, Nansha, Guangzhou, China.
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Marietou A, Røy H, Jørgensen BB, Kjeldsen KU. Sulfate Transporters in Dissimilatory Sulfate Reducing Microorganisms: A Comparative Genomics Analysis. Front Microbiol 2018; 9:309. [PMID: 29551997 PMCID: PMC5840216 DOI: 10.3389/fmicb.2018.00309] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Accepted: 02/09/2018] [Indexed: 12/31/2022] Open
Abstract
The first step in the sulfate reduction pathway is the transport of sulfate across the cell membrane. This uptake has a major effect on sulfate reduction rates. Much of the information available on sulfate transport was obtained by studies on assimilatory sulfate reduction, where sulfate transporters were identified among several types of protein families. Despite our growing knowledge on the physiology of dissimilatory sulfate-reducing microorganisms (SRM) there are no studies identifying the proteins involved in sulfate uptake in members of this ecologically important group of anaerobes. We surveyed the complete genomes of 44 sulfate-reducing bacteria and archaea across six phyla and identified putative sulfate transporter encoding genes from four out of the five surveyed protein families based on homology. We did not find evidence that ABC-type transporters (SulT) are involved in the uptake of sulfate in SRM. We speculate that members of the CysP sulfate transporters could play a key role in the uptake of sulfate in thermophilic SRM. Putative CysZ-type sulfate transporters were present in all genomes examined suggesting that this overlooked group of sulfate transporters might play a role in sulfate transport in dissimilatory sulfate reducers alongside SulP. Our in silico analysis highlights several targets for further molecular studies in order to understand this key step in the metabolism of SRMs.
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Affiliation(s)
- Angeliki Marietou
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Hans Røy
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Bo B Jørgensen
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Kasper U Kjeldsen
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
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Wöhlbrand L, Ruppersberg HS, Feenders C, Blasius B, Braun HP, Rabus R. Analysis of membrane-protein complexes of the marine sulfate reducer Desulfobacula toluolica Tol2 by 1D blue native-PAGE complexome profiling and 2D blue native-/SDS-PAGE. Proteomics 2016; 16:973-88. [PMID: 26792001 DOI: 10.1002/pmic.201500360] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Revised: 12/16/2015] [Accepted: 12/30/2015] [Indexed: 02/03/2023]
Abstract
Sulfate-reducing bacteria (SRB) obtain energy from cytoplasmic reduction of sulfate to sulfide involving APS-reductase (AprAB) and dissimilatory sulfite reductase (DsrAB). These enzymes are predicted to obtain electrons from membrane redox complexes, i.e. the quinone-interacting membrane-bound oxidoreductase (QmoABC) and DsrMKJOP complexes. In addition to these conserved complexes, the genomes of SRB encode a large number of other (predicted) membrane redox complexes, the function and actual formation of which is unknown. This study reports the establishment of 1D Blue Native-PAGE complexome profiling and 2D BN-/SDS-PAGE for analysis of the membrane protein complexome of the marine sulfate reducer Desulfobacula toluolica Tol2. Analysis of normalized score profiles of >800 proteins in combination with hierarchical clustering and identification of 2D BN-/SDS-PAGE separated spots demonstrated separation of membrane complexes in their native form, e.g. ATP synthase. In addition to the QmoABC and DsrMKJOP complexes, other complexes were detected that constitute the basic membrane complexome of D. toluolica Tol2, e.g. transport proteins (e.g. sodium/sulfate symporters) or redox complexes involved in Na(+) -based bioenergetics (RnfABCDEG). Notably, size estimation indicates dimer and quadruple formation of the DsrMKJOP complex in vivo. Furthermore, cluster analysis suggests interaction of this complex with a rhodanese-like protein (Tol2_C05230) possibly representing a periplasmic electron transfer partner for DsrMKJOP.
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Affiliation(s)
- Lars Wöhlbrand
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Oldenburg, Germany
| | - Hanna S Ruppersberg
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Oldenburg, Germany
| | - Christoph Feenders
- Mathematical Modelling, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Oldenburg, Germany
| | - Bernd Blasius
- Mathematical Modelling, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Oldenburg, Germany
| | - Hans-Peter Braun
- Plant Proteomics, Institute of Plant Genetics, Leibniz University Hannover, Hannover, Germany
| | - Ralf Rabus
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Oldenburg, Germany
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Electron transfer pathways of formate-driven H2 production in Desulfovibrio. Appl Microbiol Biotechnol 2016; 100:8135-46. [DOI: 10.1007/s00253-016-7649-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 05/12/2016] [Accepted: 05/25/2016] [Indexed: 10/21/2022]
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Genome Sequence of the Piezophilic, Mesophilic Sulfate-Reducing Bacterium Desulfovibrio indicus J2T. GENOME ANNOUNCEMENTS 2016; 4:4/2/e00214-16. [PMID: 27056223 PMCID: PMC4824256 DOI: 10.1128/genomea.00214-16] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The complete genome sequence of Desulfovibrio indicus J2T, a member of the family Desulfovibrionaceae, consists of 3,966,573-bp in one contig and encodes 3,461 predicted genes, 5 noncoding RNAs, 3 rRNAs operons, and 52 tRNA-encoding genes. The genome is consistent with a heterotrophic, anaerobic lifestyle including the sulfate reduction pathway.
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da Silva SM, Amaral C, Neves SS, Santos C, Pimentel C, Rodrigues-Pousada C. An HcpR paralog of Desulfovibrio gigas provides protection against nitrosative stress. FEBS Open Bio 2015; 5:594-604. [PMID: 26273559 PMCID: PMC4534486 DOI: 10.1016/j.fob.2015.07.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 07/01/2015] [Indexed: 01/12/2023] Open
Abstract
Desulfovibrio gigas genome encodes two HcpR paralogs, HcpR1 and HcpR2. Cells lacking HcpR1 are less tolerant to NO. HcpR1 regulates the expression of several genes related to nitrogen metabolism. Phylogenetic analyses indicate that the presence of HcpR paralogs is a common finding among Desulfovibrio species.
Desulfovibrio gigas belongs to the group of sulfate reducing bacteria (SRB). These ubiquitous and metabolically versatile microorganisms are often exposed to reactive nitrogen species (RNS). Nonetheless, the mechanisms and regulatory elements involved in nitrosative stress protection are still poorly understood. The transcription factor HcpR has emerged as a putative regulator of nitrosative stress response among anaerobic bacteria. HcpR is known to orchestrate the expression of the hybrid cluster protein gene, hcp, proposed to be involved in cellular defense against RNS. According to phylogenetic analyses, the occurrence of hcpR paralog genes is a common feature among several Desulfovibrio species. Within the D. gigas genome we have identified two HcpR-related sequences. One of these sequences, hcpR1, was found in the close vicinity of the hcp gene and this finding prompted us to proceed with its functional characterization. We observed that the growth of a D. gigas strain lacking hcpR1 is severely impaired under nitrosative stress. An in silico search revealed several putative targets of HcpR1 that were experimentally validated. The fact that HcpR1 regulates several genes encoding proteins involved in nitrite and nitrate metabolism, together with the sensitive growth phenotype to NO displayed by an hcpR1 mutant strain, strongly supports a relevant role of this factor under nitrosative stress. Moreover, the finding that several Desulfovibrio species possess HcpR paralogs, which have been transmitted vertically in the evolution and diversification of the genus, suggests that these sequences may confer adaptive or survival advantage to these organisms, possibly by increasing their tolerance to nitrosative stress.
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Key Words
- BI, Bayesian inference
- BS, bootstrap
- CRP/FNR, cAMP receptor protein/fumarate and nitrate reductase regulatory protein
- Desulfovibrio
- Frdx, ferredoxin
- GSNO, S-nitrosoglutathione
- HGT, horizontal gene transfer
- Hcp, hybrid cluster protein
- HcpR
- ML, maximum likelihood
- MP, maximum parsimony
- Molecular phylogeny
- NO, nitric oxide
- Nitrosative stress
- PP, posterior probability
- RNS, reactive nitrogen species
- ROO, rubredoxin oxygen reductase
- SRB, sulfate reducing bacteria
- Sulfate reducing bacteria
- Transcription regulation
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Affiliation(s)
- Sofia M da Silva
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Catarina Amaral
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Susana S Neves
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Cátia Santos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Catarina Pimentel
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Claudina Rodrigues-Pousada
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
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A Post-Genomic View of the Ecophysiology, Catabolism and Biotechnological Relevance of Sulphate-Reducing Prokaryotes. Adv Microb Physiol 2015. [PMID: 26210106 DOI: 10.1016/bs.ampbs.2015.05.002] [Citation(s) in RCA: 173] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Dissimilatory sulphate reduction is the unifying and defining trait of sulphate-reducing prokaryotes (SRP). In their predominant habitats, sulphate-rich marine sediments, SRP have long been recognized to be major players in the carbon and sulphur cycles. Other, more recently appreciated, ecophysiological roles include activity in the deep biosphere, symbiotic relations, syntrophic associations, human microbiome/health and long-distance electron transfer. SRP include a high diversity of organisms, with large nutritional versatility and broad metabolic capacities, including anaerobic degradation of aromatic compounds and hydrocarbons. Elucidation of novel catabolic capacities as well as progress in the understanding of metabolic and regulatory networks, energy metabolism, evolutionary processes and adaptation to changing environmental conditions has greatly benefited from genomics, functional OMICS approaches and advances in genetic accessibility and biochemical studies. Important biotechnological roles of SRP range from (i) wastewater and off gas treatment, (ii) bioremediation of metals and hydrocarbons and (iii) bioelectrochemistry, to undesired impacts such as (iv) souring in oil reservoirs and other environments, and (v) corrosion of iron and concrete. Here we review recent advances in our understanding of SRPs focusing mainly on works published after 2000. The wealth of publications in this period, covering many diverse areas, is a testimony to the large environmental, biogeochemical and technological relevance of these organisms and how much the field has progressed in these years, although many important questions and applications remain to be explored.
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