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Li T, Zhu K, Wang L, Dong Y, Huang J. Stabilization by Chaperone GroEL in Biogenic Selenium Nanoparticles Produced from Bifidobacterium animalis H15 for the Treatment of DSS-Induced Colitis. ACS APPLIED MATERIALS & INTERFACES 2024; 16:13439-13452. [PMID: 38456847 DOI: 10.1021/acsami.3c16340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/09/2024]
Abstract
Inflammatory bowel diseases have a high rate of mortality and pose a serious threat to global public health. Selenium is an essential trace element, which has been shown to play important roles in redox control and antioxidant defense. Microorganisms play important roles in the reduction of toxic inorganic selenium (selenite and selenate) to less-toxic biogenic selenium nanoparticles (Bio-SeNPs), which have higher biocompatibility. In the present study, novel Bio-SeNPs with high stability were synthesized using probiotic Bifidobacterium animalis subsp. lactis H15, which was isolated from breastfed infant feces. The Bio-SeNPs with a size of 122 nm showed stability at various ionic strengths, temperatures, and in simulated gastrointestinal fluid, while chemosynthetic SeNPs underwent aggregation. The main surface protein in the Bio-SeNPs was identified as chaperone GroEL by liquid chromatography-tandem mass spectrometry. The overexpression and purification of GroEL demonstrated that GroEL controlled the assembly of Bio-SeNPs both in vitro and in vivo. In vivo, oral administration of Bio-SeNPs could alleviate dextran sulfate sodium-induced colitis by decreasing cell apoptosis, increasing antioxidant capacity and the number of proliferating cells, and improving the function of the intestinal mucosal barrier. In vitro experiments verified that Bio-SeNPs inhibited lipopolysaccharide-induced toll-like receptor 4/NF-κB signaling pathway activation. These results suggest that the Bio-SeNPs with high stability could have potential as a nutritional supplement for the treatment of colitis in nanomedicine applications.
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Affiliation(s)
- Tong Li
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100083, China
| | - Kongdi Zhu
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100083, China
| | - Lianshun Wang
- College of Fisheries and Life Science, Dalian Ocean University, Dalian, Liaoning 116023, China
| | - Yulan Dong
- College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Jiaqiang Huang
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100083, China
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Krin E, Baharoglu Z, Sismeiro O, Varet H, Coppée JY, Mazel D. Systematic transcriptome analysis allows the identification of new type I and type II Toxin/Antitoxin systems located in the superintegron of Vibrio cholerae. Res Microbiol 2023; 174:103997. [PMID: 36347445 DOI: 10.1016/j.resmic.2022.103997] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/27/2022] [Accepted: 10/28/2022] [Indexed: 11/07/2022]
Abstract
Vibrio cholerae N16961 genome encodes 18 type II Toxin/Antitoxin (TA) systems, all but one located inside gene cassettes of its chromosomal superintegron (SI). This study aims to investigate additional TA systems in this genome. We screened for all two-genes operons of uncharacterized function by analyzing previous RNAseq data. Assays on nine candidates, revealed one additional functional type II TA encoded by the VCA0497-0498 operon, carried inside a SI cassette. We showed that VCA0498 antitoxin alone and in complex with VCA0497 represses its own operon promoter. VCA0497-0498 is the second element of the recently identified dhiT/dhiA superfamily uncharacterized type II TA system. RNAseq analysis revealed that another SI cassette encodes a novel type I TA system: VCA0495 gene and its two associated antisense non-coding RNAs, ncRNA495 and ncRNA496. Silencing of both antisense ncRNAs lead to cell death, demonstrating the type I TA function. Both VCA0497 and VCA0495 toxins do not show any homology to functionally characterized toxins, however our preliminary data suggest that their activity may end up in mRNA degradation, directly or indirectly. Our findings increase the TA systems number carried in this SI to 19, preferentially located in its distal end, confirming their importance in this large cassette array.
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Affiliation(s)
- Evelyne Krin
- Institut Pasteur, Université Paris Cité, CNRS UMR 3525, Unité de Plasticité du Génome Bactérien, 28 rue du Docteur Roux, F-75015 Paris, France.
| | - Zeynep Baharoglu
- Institut Pasteur, Université Paris Cité, CNRS UMR 3525, Unité de Plasticité du Génome Bactérien, 28 rue du Docteur Roux, F-75015 Paris, France.
| | - Odile Sismeiro
- Institut Pasteur, Université Paris Cité, Transcriptome and EpiGenome, Biomics Center for Innovation and Technological Research, 28 rue du Docteur Roux, F-75015 Paris, France.
| | - Hugo Varet
- Institut Pasteur, Université Paris Cité, Transcriptome and EpiGenome, Biomics Center for Innovation and Technological Research, 28 rue du Docteur Roux, F-75015 Paris, France.
| | - Jean-Yves Coppée
- Institut Pasteur, Université Paris Cité, Transcriptome and EpiGenome, Biomics Center for Innovation and Technological Research, 28 rue du Docteur Roux, F-75015 Paris, France.
| | - Didier Mazel
- Institut Pasteur, Université Paris Cité, CNRS UMR 3525, Unité de Plasticité du Génome Bactérien, 28 rue du Docteur Roux, F-75015 Paris, France.
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Biogenesis of selenium nanospheres using Halomonas venusta strain GUSDM4 exhibiting potent environmental applications. Arch Microbiol 2022; 204:372. [PMID: 35672607 DOI: 10.1007/s00203-022-02977-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 04/26/2022] [Accepted: 05/11/2022] [Indexed: 11/02/2022]
Abstract
Selenite reducing bacterial strain (GUSDM4) isolated from Mandovi estuary of Goa, India was identified as Halomonas venusta based on 16S rRNA gene sequence analysis. Its maximum tolerance level for sodium selenite (Na2SeO3) was 100 mM. The 2, 3-diaminonaphthalene-based spectroscopic analysis demonstrated 96 and 93% reduction of 2 and 4 mM Na2SeO3 respectively to elemental selenium (Se0) during the late stationary growth phase. Biosynthesis of Se nanoparticles (SeNPs) commenced within 4 h during the log phase, which was evident from the brick red color in the growth medium and a characteristic peak at 265 nm revealed by UV-Vis spectrophotometry. The intracellular periplasmic synthesis of SeNPs in GUSDM4 was confirmed by transmission electron microscopy (TEM). Characterization of SeNPs by X-ray crystallography, TEM and energy-dispersive X-ray analysis (EDAX) clearly demonstrated spherical SeNPs of 20-80 nm diameter with hexagonal crystal lattice. SeNPs (0.8 and 1 mg/L) primed seeds under arsenate [As(V)] stress showed increase in shoot length, root length and biomass by 1.4-, 1.5- and 1.1-fold respectively, as compared to As(V) primed seeds alone. The proline and phenolic content in seeds primed with SeNPs under arsenate stress showed alleviated levels proving its ameliorative potential. SeNPs also demonstrated anti-biofilm activity at 20 µg/mL against human pathogens which was evident by scanning electron microscopic (SEM) analysis. SeNPs interestingly revealed mosquito larvicidal activity also. Therefore, these studies have clearly demonstrated amazing potential of the marine bacterium, Halomonas venusta in biosynthesis of SeNPs and their applications as ameliorative, anti-biofilm and mosquito larvicidal agents which is the first report of its kind.
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Kessi J, Turner RJ, Zannoni D. Tellurite and Selenite: how can these two oxyanions be chemically different yet so similar in the way they are transformed to their metal forms by bacteria? Biol Res 2022; 55:17. [PMID: 35382884 PMCID: PMC8981825 DOI: 10.1186/s40659-022-00378-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 02/06/2022] [Indexed: 12/26/2022] Open
Abstract
This opinion review explores the microbiology of tellurite, TeO32- and selenite, SeO32- oxyanions, two similar Group 16 chalcogen elements, but with slightly different physicochemical properties that lead to intriguing biological differences. Selenium, Se, is a required trace element compared to tellurium, Te, which is not. Here, the challenges around understanding the uptake transport mechanisms of these anions, as reflected in the model organisms used by different groups, are described. This leads to a discussion around how these oxyanions are subsequently reduced to nanomaterials, which mechanistically, has controversies between ideas around the molecule chemistry, chemical reactions involving reduced glutathione and reactive oxygen species (ROS) production along with the bioenergetics at the membrane versus the cytoplasm. Of particular interest is the linkage of glutathione and thioredoxin chemistry from the cytoplasm through the membrane electron transport chain (ETC) system/quinones to the periplasm. Throughout the opinion review we identify open and unanswered questions about the microbial physiology under selenite and tellurite exposure. Thus, demonstrating how far we have come, yet the exciting research directions that are still possible. The review is written in a conversational manner from three long-term researchers in the field, through which to play homage to the late Professor Claudio Vásquez.
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Affiliation(s)
- Janine Kessi
- Until 2018 - Dept of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Raymond J. Turner
- Dept of Biological Sciences, University of Calgary, Calgary, AB Canada
| | - Davide Zannoni
- Dept of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
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Staicu LC, Barton LL. Selenium respiration in anaerobic bacteria: Does energy generation pay off? J Inorg Biochem 2021; 222:111509. [PMID: 34118782 DOI: 10.1016/j.jinorgbio.2021.111509] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/18/2021] [Accepted: 05/30/2021] [Indexed: 01/03/2023]
Abstract
Selenium (Se) respiration in bacteria was revealed for the first time at the end of 1980s. Although thermodynamically-favorable, energy-dense and documented in phylogenetically-diverse bacteria, this metabolic process appears to be accompanied by a number of challenges and numerous unanswered questions. Selenium oxyanions, SeO42- and SeO32-, are reduced to elemental Se (Se0) through anaerobic respiration, the end product being solid and displaying a considerable size (up to 500 nm) at the bacterial scale. Compared to other electron acceptors used in anaerobic respiration (e.g. N, S, Fe, Mn, and As), Se is one of the few elements whose end product is solid. Furthermore, unlike other known bacterial intracellular accumulations such as volutin (inorganic polyphosphate), S0, glycogen or magnetite, Se0 has not been shown to play a nutritional or ecological role for its host. In the context of anaerobic respiration of Se oxyanions, biogenic Se0 appears to be a by-product, a waste that needs proper handling, and this raises the question of the evolutionary implications of this process. Why would bacteria use a respiratory substrate that is useful, in the first place, and then highly detrimental? Interestingly, in certain artificial ecosystems (e.g. upflow bioreactors) Se0 might help bacterial cells to increase their density and buoyancy and thus avoid biomass wash-out, ensuring survival. This review article provides an in-depth analysis of selenium respiration (model selenium respiring bacteria, thermodynamics, respiratory enzymes, and genetic determinants), complemented by an extensive discussion about the evolutionary implications and the properties of biogenic Se0 using published and original/unpublished results.
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Affiliation(s)
- Lucian C Staicu
- Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland.
| | - Larry L Barton
- Department of Biology, University of New Mexico, MSCO3 2020, Albuquerque, NM 87131, USA
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Wells M, Stolz JF. Microbial selenium metabolism: a brief history, biogeochemistry and ecophysiology. FEMS Microbiol Ecol 2020; 96:5921172. [DOI: 10.1093/femsec/fiaa209] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 10/08/2020] [Indexed: 01/02/2023] Open
Abstract
ABSTRACTSelenium is an essential trace element for organisms from all three domains of life. Microorganisms, in particular, mediate reductive transformations of selenium that govern the element's mobility and bioavailability in terrestrial and aquatic environments. Selenium metabolism is not just ubiquitous but an ancient feature of life likely extending back to the universal common ancestor of all cellular lineages. As with the sulfur biogeochemical cycle, reductive transformations of selenium serve two metabolic functions: assimilation into macromolecules and dissimilatory reduction during anaerobic respiration. This review begins with a historical overview of how research in both aspects of selenium metabolism has developed. We then provide an overview of the global selenium biogeochemical cycle, emphasizing the central role of microorganisms in the cycle. This serves as a basis for a robust discussion of current models for the evolution of the selenium biogeochemical cycle over geologic time, and how knowledge of the evolution and ecophysiology of selenium metabolism can enrich and refine these models. We conclude with a discussion of the ecophysiological function of selenium-respiring prokaryotes within the cycle, and the tantalizing possibility of oxidative selenium transformations during chemolithoautotrophic growth.
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Affiliation(s)
- Michael Wells
- Department of Biological Sciences, Duquesne University, Pittsburgh, PA 15282, USA
| | - John F Stolz
- Department of Biological Sciences, Duquesne University, Pittsburgh, PA 15282, USA
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Bhagdikar D, Grundy FJ, Henkin TM. Transcriptional and translational S-box riboswitches differ in ligand-binding properties. J Biol Chem 2020; 295:6849-6860. [PMID: 32209653 DOI: 10.1074/jbc.ra120.012853] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 03/20/2020] [Indexed: 01/27/2023] Open
Abstract
There are a number of riboswitches that utilize the same ligand-binding domain to regulate transcription or translation. S-box (SAM-I) riboswitches, including the riboswitch present in the Bacillus subtilis metI gene, which encodes cystathionine γ-synthase, regulate the expression of genes involved in methionine metabolism in response to SAM, primarily at the level of transcriptional attenuation. A rarer class of S-box riboswitches is predicted to regulate translation initiation. Here we identified and characterized a translational S-box riboswitch in the metI gene from Desulfurispirillum indicum The regulatory mechanisms of riboswitches are influenced by the kinetics of ligand interaction. The half-life of the translational D. indicum metI RNA-SAM complex is significantly shorter than that of the transcriptional B. subtilis metI RNA. This finding suggests that, unlike the transcriptional RNA, the translational metI riboswitch can make multiple reversible regulatory decisions. Comparison of both RNAs revealed that the second internal loop of helix P3 in the transcriptional RNA usually contains an A residue, whereas the translational RNA contains a C residue that is conserved in other S-box RNAs that are predicted to regulate translation. Mutational analysis indicated that the presence of an A or C residue correlates with RNA-SAM complex stability. Biochemical analyses indicate that the internal loop sequence critically determines the stability of the RNA-SAM complex by influencing the flexibility of residues involved in SAM binding and thereby affects the molecular mechanism of riboswitch function.
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Affiliation(s)
- Divyaa Bhagdikar
- Department of Microbiology and Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210
| | - Frank J Grundy
- Department of Microbiology and Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210
| | - Tina M Henkin
- Department of Microbiology and Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210
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8
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Lee S, Roh Y, Koh DC. Oxidation and reduction of redox-sensitive elements in the presence of humic substances in subsurface environments: A review. CHEMOSPHERE 2019; 220:86-97. [PMID: 30579952 DOI: 10.1016/j.chemosphere.2018.11.143] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 11/19/2018] [Accepted: 11/22/2018] [Indexed: 06/09/2023]
Abstract
The oxidation and reduction (redox) processes of redox-sensitive elements (RSE) in the presence of humic substances (HS) have become a significantly important issue in the terms of biogeochemical cycles. Redox processes are crucial for determining the speciation, mobility, toxicity, and bioavailability of RSE in natural environments. It is known that HS act as an effective redox mediator for accepting and donating electrons, and thereby transfers them to RSE. We review the recent progress in the field of the redox processes of RSE including As, Cr, Cu, Fe, Hg, and Se in the presence of HS. The extent and rate of the redox processes of these RSE are significantly affected by the concentration of functional groups and the chemical composition of HS. In subsurface environments, pH, ionic strength, and the presence of competitive components, microorganisms, and oxygen need to be considered to elucidate the redox processes of RSE in the presence of HS. In addition, improved analytical techniques for the characterization of HS has the potential to advance the study on the redox processes of RSE in the presence of HS. It may contribute to understanding the mechanism for the redox processes between RSE and HS in the biogeochemical cycles.
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Affiliation(s)
- Seyong Lee
- Groundwater Research Center, Korea Institute of Geoscience and Mineral Resources (KIGAM), Gwahak-ro, Yuseoung-gu, Daejeon 34132, Republic of Korea; Planning & Management Division, National Institute of Chemical Safety (NICS), 90 Gajeongbuk-ro, Yuseoung-gu, Daejeon 34111, Republic of Korea.
| | - Younghee Roh
- Institute for Korean Regional Studies, Seoul National University (SNU), 1 Gwanak-ro Gwanak-gu, Seoul 08826, Republic of Korea
| | - Dong-Chan Koh
- Groundwater Research Center, Korea Institute of Geoscience and Mineral Resources (KIGAM), Gwahak-ro, Yuseoung-gu, Daejeon 34132, Republic of Korea
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Respiratory Selenite Reductase from Bacillus selenitireducens Strain MLS10. J Bacteriol 2019; 201:JB.00614-18. [PMID: 30642986 DOI: 10.1128/jb.00614-18] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 01/03/2019] [Indexed: 11/20/2022] Open
Abstract
The putative respiratory selenite [Se(IV)] reductase (Srr) from Bacillus selenitireducens MLS10 has been identified through a polyphasic approach involving genomics, proteomics, and enzymology. Nondenaturing gel assays were used to identify Srr in cell fractions, and the active band was shown to contain a single protein of 80 kDa. The protein was identified through liquid chromatography-tandem mass spectrometry (LC-MS/MS) as a homolog of the catalytic subunit of polysulfide reductase (PsrA). It was found to be encoded as part of an operon that contains six genes that we designated srrE, srrA, srrB, srrC, srrD, and srrF SrrA is the catalytic subunit (80 kDa), with a twin-arginine translocation (TAT) leader sequence indicative of a periplasmic protein and one putative 4Fe-4S binding site. SrrB is a small subunit (17 kDa) with four putative 4Fe-4S binding sites, SrrC (43 kDa) is an anchoring subunit, and SrrD (24 kDa) is a chaperon protein. Both SrrE (38 kDa) and SrrF (45 kDa) were annotated as rhodanese domain-containing proteins. Phylogenetic analysis revealed that SrrA belonged to the PsrA/PhsA clade but that it did not define a distinct subgroup, based on the putative homologs that were subsequently identified from other known selenite-respiring bacteria (e.g., Desulfurispirillum indicum and Pyrobaculum aerophilum). The enzyme appeared to be specific for Se(IV), showing no activity with selenate, arsenate, or thiosulfate, with a Km of 145 ± 53 μM, a V max of 23 ± 2.5 μM min-1, and a k cat of 23 ± 2.68 s-1 These results further our understanding of the mechanisms of selenium biotransformation and its biogeochemical cycle.IMPORTANCE Selenium is an essential element for life, with Se(IV) reduction a key step in its biogeochemical cycle. This report identifies for the first time a dissimilatory Se(IV) reductase, Srr, from a known selenite-respiring bacterium, the haloalkalophilic Bacillus selenitireducens strain MLS10. The work extends the versatility of the complex iron-sulfur molybdoenzyme (CISM) superfamily in electron transfer involving chalcogen substrates with different redox potentials. Further, it underscores the importance of biochemical and enzymological approaches in establishing the functionality of these enzymes.
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Jahan MI, Tobe R, Mihara H. Characterization of a Novel Porin-Like Protein, ExtI, from Geobacter sulfurreducens and Its Implication in the Reduction of Selenite and Tellurite. Int J Mol Sci 2018. [PMID: 29534491 PMCID: PMC5877670 DOI: 10.3390/ijms19030809] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The extI gene in Geobacter sulfurreducens encodes a putative outer membrane channel porin, which resides within a cluster of extHIJKLMNOPQS genes. This cluster is highly conserved across the Geobacteraceae and includes multiple putative c-type cytochromes. In silico analyses of the ExtI sequence, together with Western blot analysis and proteinase protection assays, showed that it is an outer membrane protein. The expression level of ExtI did not respond to changes in osmolality and phosphate starvation. An extI-deficient mutant did not show any significant impact on fumarate or Fe(III) citrate reduction or sensitivity to β-lactam antibiotics, as compared with those of the wild-type strain. However, extI deficiency resulted in a decreased ability to reduce selenite and tellurite. Heme staining analysis revealed that extI deficiency affects certain heme-containing proteins in the outer and inner membranes, which may cause a decrease in the ability to reduce selenite and tellurite. Based on these observations, we discuss possible roles for ExtI in selenite and tellurite reduction in G. sulfurreducens.
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Affiliation(s)
- Mst Ishrat Jahan
- Department of Biotechnology, College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan.
| | - Ryuta Tobe
- Department of Biotechnology, College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan.
| | - Hisaaki Mihara
- Department of Biotechnology, College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan.
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Lv PL, Zhong L, Dong QY, Yang SL, Shen WW, Zhu QS, Lai CY, Luo AC, Tang Y, Zhao HP. The effect of electron competition on chromate reduction using methane as electron donor. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:6609-6618. [PMID: 29255986 DOI: 10.1007/s11356-017-0937-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 12/03/2017] [Indexed: 06/07/2023]
Abstract
We studied the effect of electron competition on chromate (Cr(VI)) reduction in a methane (CH4)-based membrane biofilm reactor (MBfR), since the reduction rate was usually limited by electron supply. A low surface loading of SO42- promoted Cr(VI) reduction. The Cr(VI) removal percentage increased from 60 to 70% when the SO42- loading increased from 0 to 4.7 mg SO42-/m2-d. After the SO42- loading decreased back to zero, the Cr(VI) removal further increased to 90%, suggesting that some sulfate-reducing bacteria (SRB) stayed in the reactor to reduce Cr(VI). However, a high surface loading of SO42- (26.6 mg SO42-/m2-d) significantly slowed down the Cr(VI) reduction to 40% removal, which was probably due to competition between Cr(VI) and SO42- reduction. Similarly, when 0.5 mg/L of Se(VI) was introduced into the MBfR, Cr(VI) removal percentage slightly decreased to 60% and then increased to 80% when input Se(VI) was removed again. The microbial community strongly depended on the loadings of Cr(VI) and SO42-. In the sulfate effect experiment, three genera were dominant. Based on the correlation between the abundances of the three genera and the loadings of Cr(VI) and SO42-, we conclude that Methylocystis, a type II methanotroph, reduced both Cr(VI) and sulfate, Meiothermus only reduced Cr(VI), and Ferruginibacter only reduced SO42-.
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Affiliation(s)
- Pan-Long Lv
- College of Environmental and Resource Science, Zhejiang University, Hangzhou, China
| | - Liang Zhong
- College of Environmental and Resource Science, Zhejiang University, Hangzhou, China
| | - Qiu-Yi Dong
- College of Environmental and Resource Science, Zhejiang University, Hangzhou, China
| | - Shi-Lei Yang
- College of Environmental and Resource Science, Zhejiang University, Hangzhou, China
| | - Wei-Wei Shen
- College of Environmental and Resource Science, Zhejiang University, Hangzhou, China
| | - Quan-Song Zhu
- College of Environmental and Resource Science, Zhejiang University, Hangzhou, China
| | - Chun-Yu Lai
- College of Environmental and Resource Science, Zhejiang University, Hangzhou, China.
| | - An-Cheng Luo
- College of Environmental and Resource Science, Zhejiang University, Hangzhou, China
- Zhejiang Province Key Lab Water Pollut Control & Envi, Zhejiang University, Hangzhou, Zhejiang, China
- Ministry of Education Key Laboratory of Environmental Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Youneng Tang
- Department of Civil and Environmental Engineering, FAMU-FSU College of Engineering, Florida State University, Tallahassee, FL, 32310-6046, USA
| | - He-Ping Zhao
- College of Environmental and Resource Science, Zhejiang University, Hangzhou, China.
- Zhejiang Province Key Lab Water Pollut Control & Envi, Zhejiang University, Hangzhou, Zhejiang, China.
- Ministry of Education Key Laboratory of Environmental Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China.
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12
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Selenium reducing Citrobacter fruendii strain KP6 from Mandovi estuary and its potential application in selenium nanoparticle synthesis. ACTA ACUST UNITED AC 2016. [DOI: 10.1007/s40011-016-0815-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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13
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Dessì P, Jain R, Singh S, Seder-Colomina M, van Hullebusch ED, Rene ER, Ahammad SZ, Carucci A, Lens PNL. Effect of temperature on selenium removal from wastewater by UASB reactors. WATER RESEARCH 2016; 94:146-154. [PMID: 26938500 DOI: 10.1016/j.watres.2016.02.007] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Revised: 01/19/2016] [Accepted: 02/06/2016] [Indexed: 06/05/2023]
Abstract
The effect of temperature on selenium (Se) removal by upflow anaerobic sludge blanket (UASB) reactors treating selenate and nitrate containing wastewater was investigated by comparing the performance of a thermophilic (55 °C) versus a mesophilic (30 °C) UASB reactor. When only selenate (50 μM) was fed to the UASB reactors (pH 7.3; hydraulic retention time 8 h) with excess electron donor (lactate at 1.38 mM corresponding to an organic loading rate of 0.5 g COD L(-1) d(-1)), the thermophilic UASB reactor achieved a higher total Se removal efficiency (94.4 ± 2.4%) than the mesophilic UASB reactor (82.0 ± 3.8%). When 5000 μM nitrate was further added to the influent, total Se removal was again better under thermophilic (70.1 ± 6.6%) when compared to mesophilic (43.6 ± 8.8%) conditions. The higher total effluent Se concentration in the mesophilic UASB reactor was due to the higher concentrations of biogenic elemental Se nanoparticles (BioSeNPs). The shape of the BioSeNPs observed in both UASB reactors was different: nanospheres and nanorods, respectively, in the mesophilic and thermophilic UASB reactors. Microbial community analysis showed the presence of selenate respirers as well as denitrifying microorganisms.
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Affiliation(s)
- Paolo Dessì
- UNESCO-IHE, Institute for Water Education, Westvest 7, 2611AX, Delft, The Netherlands; DICAAR, Dept. of Civil-Environmental Engineering and Architecture, Piazza d'Armi, 09123, Cagliari, Italy; Department of Chemistry and Bioengineering, Tampere University of Technology, Korkeakoulunkatu 10, FI-33720, Tampere, Finland
| | - Rohan Jain
- UNESCO-IHE, Institute for Water Education, Westvest 7, 2611AX, Delft, The Netherlands; Université Paris-Est, Laboratoire Géomatériaux et Environnement (EA 4508), UPEM, 5, Boulevard Descartes - Champs sur Marne, 77454, Marne-la-Vallée, France; Department of Chemistry and Bioengineering, Tampere University of Technology, Korkeakoulunkatu 10, FI-33720, Tampere, Finland.
| | - Satyendra Singh
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, Delhi, Hauz-Khas, 110016, New Delhi, India
| | - Marina Seder-Colomina
- Université Paris-Est, Laboratoire Géomatériaux et Environnement (EA 4508), UPEM, 5, Boulevard Descartes - Champs sur Marne, 77454, Marne-la-Vallée, France; Institut de Minéralogie, de Physique des Matériaux, et de Cosmochimie (IMPMC). Sorbonne Universités - UPMC Univ Paris 06, UMR CNRS, 7590, Muséum National d'Histoire Naturelle, IRD UMR 206, Paris, France
| | - Eric D van Hullebusch
- Université Paris-Est, Laboratoire Géomatériaux et Environnement (EA 4508), UPEM, 5, Boulevard Descartes - Champs sur Marne, 77454, Marne-la-Vallée, France
| | - Eldon R Rene
- UNESCO-IHE, Institute for Water Education, Westvest 7, 2611AX, Delft, The Netherlands
| | - Shaikh Ziauddin Ahammad
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, Delhi, Hauz-Khas, 110016, New Delhi, India
| | - Alessandra Carucci
- DICAAR, Dept. of Civil-Environmental Engineering and Architecture, Piazza d'Armi, 09123, Cagliari, Italy
| | - Piet N L Lens
- UNESCO-IHE, Institute for Water Education, Westvest 7, 2611AX, Delft, The Netherlands; Department of Chemistry and Bioengineering, Tampere University of Technology, Korkeakoulunkatu 10, FI-33720, Tampere, Finland
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14
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Marreiros BC, Calisto F, Castro PJ, Duarte AM, Sena FV, Silva AF, Sousa FM, Teixeira M, Refojo PN, Pereira MM. Exploring membrane respiratory chains. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:1039-1067. [PMID: 27044012 DOI: 10.1016/j.bbabio.2016.03.028] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 03/16/2016] [Accepted: 03/18/2016] [Indexed: 01/20/2023]
Abstract
Acquisition of energy is central to life. In addition to the synthesis of ATP, organisms need energy for the establishment and maintenance of a transmembrane difference in electrochemical potential, in order to import and export metabolites or to their motility. The membrane potential is established by a variety of membrane bound respiratory complexes. In this work we explored the diversity of membrane respiratory chains and the presence of the different enzyme complexes in the several phyla of life. We performed taxonomic profiles of the several membrane bound respiratory proteins and complexes evaluating the presence of their respective coding genes in all species deposited in KEGG database. We evaluated 26 quinone reductases, 5 quinol:electron carriers oxidoreductases and 18 terminal electron acceptor reductases. We further included in the analyses enzymes performing redox or decarboxylation driven ion translocation, ATP synthase and transhydrogenase and we also investigated the electron carriers that perform functional connection between the membrane complexes, quinones or soluble proteins. Our results bring a novel, broad and integrated perspective of membrane bound respiratory complexes and thus of the several energetic metabolisms of living systems. This article is part of a Special Issue entitled 'EBEC 2016: 19th European Bioenergetics Conference, Riva del Garda, Italy, July 2-6, 2016', edited by Prof. Paolo Bernardi.
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Affiliation(s)
- Bruno C Marreiros
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157 Oeiras, Portugal
| | - Filipa Calisto
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157 Oeiras, Portugal
| | - Paulo J Castro
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157 Oeiras, Portugal
| | - Afonso M Duarte
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157 Oeiras, Portugal
| | - Filipa V Sena
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157 Oeiras, Portugal
| | - Andreia F Silva
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157 Oeiras, Portugal
| | - Filipe M Sousa
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157 Oeiras, Portugal
| | - Miguel Teixeira
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157 Oeiras, Portugal
| | - Patrícia N Refojo
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157 Oeiras, Portugal
| | - Manuela M Pereira
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157 Oeiras, Portugal.
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15
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Wen LL, Lai CY, Yang Q, Chen JX, Zhang Y, Ontiveros-Valencia A, Zhao HP. Quantitative detection of selenate-reducing bacteria by real-time PCR targeting the selenate reductase gene. Enzyme Microb Technol 2016; 85:19-24. [DOI: 10.1016/j.enzmictec.2016.01.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 01/04/2016] [Accepted: 01/04/2016] [Indexed: 12/26/2022]
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16
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Maltman C, Walter G, Yurkov V. A Diverse Community of Metal(loid) Oxide Respiring Bacteria Is Associated with Tube Worms in the Vicinity of the Juan de Fuca Ridge Black Smoker Field. PLoS One 2016; 11:e0149812. [PMID: 26914590 PMCID: PMC4767881 DOI: 10.1371/journal.pone.0149812] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 02/04/2016] [Indexed: 01/24/2023] Open
Abstract
Epibiotic bacteria associated with tube worms living in the vicinity of deep sea hydrothermal vents of the Juan de Fuca Ridge in the Pacific Ocean were investigated for the ability to respire anaerobically on tellurite, tellurate, selenite, selenate, metavanadate and orthovanadate as terminal electron acceptors. Out of 107 isolates tested, 106 were capable of respiration on one or more of these oxides, indicating that metal(loid) oxide based respiration is not only much more prevalent in nature than is generally believed, but also is an important mode of energy generation in the habitat. Partial 16S rRNA gene sequencing revealed the bacterial community to be rich and highly diverse, containing many potentially new species. Furthermore, it appears that the worms not only possess a close symbiotic relationship with chemolithotrophic sulfide-oxidizing bacteria, but also with the metal(loid) oxide transformers. Possibly they protect the worms through reduction of the toxic compounds that would otherwise be harmful to the host.
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Affiliation(s)
- Chris Maltman
- Department of Microbiology, University of Manitoba, Winnipeg, Canada
| | - Graham Walter
- Department of Microbiology, University of Manitoba, Winnipeg, Canada
| | - Vladimir Yurkov
- Department of Microbiology, University of Manitoba, Winnipeg, Canada
- * E-mail:
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17
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Maltman C, Piercey-Normore MD, Yurkov V. Tellurite-, tellurate-, and selenite-based anaerobic respiration by strain CM-3 isolated from gold mine tailings. Extremophiles 2015; 19:1013-9. [PMID: 26254805 DOI: 10.1007/s00792-015-0776-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 07/23/2015] [Indexed: 12/20/2022]
Abstract
The newly discovered strain CM-3, a Gram-negative, rod-shaped bacterium from gold mine tailings of the Central Mine in Nopiming Provincial Park, Canada, is capable of dissimilatory anaerobic reduction of tellurite, tellurate, and selenite. CM-3 possesses very high level resistance to these oxides, both aerobically and anaerobically. During aerobic growth, tellurite and tellurate resistance was up to 1500 and 1000 µg/ml, respectively. In the presence of selenite, growth occurred at the highest concentration tested, 7000 µg/ml. Under anaerobic conditions, resistance was decreased to 800 µg/ml for the Te oxides; however, much like under aerobic conditions, growth with selenite still took place at 7000 µg/ml. In the absence of oxygen, CM-3 couples oxide reduction to an increase in biomass. Following an initial drop in viable cells, due to switching from aerobic to anaerobic conditions, there was an increase in CFU/ml greater than one order of magnitude in the presence of tellurite (6.6 × 10(3)-8.6 × 10(4) CFU/ml), tellurate (4.6 × 10(3)-1.4 × 10(5) CFU/ml), and selenite (2.7 × 10(5)-5.6 × 10(6) CFU/ml). A control culture without metalloid oxides showed a steady decrease in CFU/ml with no recovery. ATP production was also increased in the presence of each oxide, further indicating anaerobic respiration. Partial 16S rRNA gene sequencing revealed a 99.0 % similarity of CM-3 to Pseudomonas reactans.
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Affiliation(s)
- Chris Maltman
- Department of Microbiology, University of Manitoba, Winnipeg, MB, Canada
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18
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Abstract
In nature, selenium is actively cycled between oxic and anoxic habitats, and this cycle plays an important role in carbon and nitrogen mineralization through bacterial anaerobic respiration. Selenium-respiring bacteria (SeRB) are found in geographically diverse, pristine or contaminated environments and play a pivotal role in the selenium cycle. Unlike its structural analogues oxygen and sulfur, the chalcogen selenium and its microbial cycling have received much less attention by the scientific community. This review focuses on microorganisms that use selenate and selenite as terminal electron acceptors, in parallel to the well-studied sulfate-reducing bacteria. It overviews the significant advancements made in recent years on the role of SeRB in the biological selenium cycle and their ecological role, phylogenetic characterization, and metabolism, as well as selenium biomineralization mechanisms and environmental biotechnological applications.
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Affiliation(s)
- Y V Nancharaiah
- Environmental Engineering and Water Technology Department, UNESCO-IHE Institute for Water Education, Delft, The Netherlands Biofouling and Biofilm Processes Section, Water and Steam Chemistry Division, Bhabha Atomic Research Centre, Kalpakkam, Tamil Nadu, India
| | - P N L Lens
- Environmental Engineering and Water Technology Department, UNESCO-IHE Institute for Water Education, Delft, The Netherlands
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19
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Shi L, Fredrickson JK, Zachara JM. Genomic analyses of bacterial porin-cytochrome gene clusters. Front Microbiol 2014; 5:657. [PMID: 25505896 PMCID: PMC4245776 DOI: 10.3389/fmicb.2014.00657] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 11/13/2014] [Indexed: 11/13/2022] Open
Abstract
The porin-cytochrome (Pcc) protein complex is responsible for trans-outer membrane electron transfer during extracellular reduction of Fe(III) by the dissimilatory metal-reducing bacterium Geobacter sulfurreducens PCA. The identified and characterized Pcc complex of G. sulfurreducens PCA consists of a porin-like outer-membrane protein, a periplasmic 8-heme c-type cytochrome (c-Cyt) and an outer-membrane 12-heme c-Cyt, and the genes encoding the Pcc proteins are clustered in the same regions of genome (i.e., the pcc gene clusters) of G. sulfurreducens PCA. A survey of additionally microbial genomes has identified the pcc gene clusters in all sequenced Geobacter spp. and other bacteria from six different phyla, including Anaeromyxobacter dehalogenans 2CP-1, A. dehalogenans 2CP-C, Anaeromyxobacter sp. K, Candidatus Kuenenia stuttgartiensis, Denitrovibrio acetiphilus DSM 12809, Desulfurispirillum indicum S5, Desulfurivibrio alkaliphilus AHT2, Desulfurobacterium thermolithotrophum DSM 11699, Desulfuromonas acetoxidans DSM 684, Ignavibacterium album JCM 16511, and Thermovibrio ammonificans HB-1. The numbers of genes in the pcc gene clusters vary, ranging from two to nine. Similar to the metal-reducing (Mtr) gene clusters of other Fe(III)-reducing bacteria, such as Shewanella spp., additional genes that encode putative c-Cyts with predicted cellular localizations at the cytoplasmic membrane, periplasm and outer membrane often associate with the pcc gene clusters. This suggests that the Pcc-associated c-Cyts may be part of the pathways for extracellular electron transfer reactions. The presence of pcc gene clusters in the microorganisms that do not reduce solid-phase Fe(III) and Mn(IV) oxides, such as D. alkaliphilus AHT2 and I. album JCM 16511, also suggests that some of the pcc gene clusters may be involved in extracellular electron transfer reactions with the substrates other than Fe(III) and Mn(IV) oxides.
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Affiliation(s)
- Liang Shi
- Pacific Northwest National Laboratory Richland, WA, USA
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20
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Welsh A, Chee-Sanford JC, Connor LM, Löffler FE, Sanford RA. Refined NrfA phylogeny improves PCR-based nrfA gene detection. Appl Environ Microbiol 2014; 80:2110-9. [PMID: 24463965 PMCID: PMC3993153 DOI: 10.1128/aem.03443-13] [Citation(s) in RCA: 111] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Accepted: 01/16/2014] [Indexed: 11/20/2022] Open
Abstract
Dissimilatory nitrate reduction to ammonium (DNRA) and denitrification are contrasting microbial processes in the terrestrial nitrogen (N) cycle, in that the former promotes N retention and the latter leads to N loss (i.e., the formation of gaseous products). The nitrite reductase NrfA catalyzes nitrite reduction to ammonium, the enzyme associated with respiratory nitrite ammonification and the key step in DNRA. Although well studied biochemically, the diversity and phylogeny of this enzyme had not been rigorously analyzed. A phylogenetic analysis of 272 full-length NrfA protein sequences distinguished 18 NrfA clades with robust statistical support (>90% Bayesian posterior probabilities). Three clades possessed a CXXCH motif in the first heme-binding domain, whereas all other clades had a CXXCK motif in this location. The analysis further identified a KXRH or KXQH motif between the third and fourth heme-binding motifs as a conserved and diagnostic feature of all pentaheme NrfA proteins. PCR primers targeting a portion of the heme-binding motifs that flank this diagnostic region yielded the expected 250-bp-long amplicons with template DNA from eight pure cultures and 16 new nrfA-containing isolates. nrfA amplicons obtained with template DNA from two geomorphically distinct agricultural soils could be assigned to one of the 18 NrfA clades, providing support for this expanded classification. The extended NrfA phylogeny revealed novel diagnostic features of DNRA populations and will be useful to assess nitrate/nitrite fate in natural and engineered ecosystems.
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Affiliation(s)
- Allana Welsh
- University of Illinois at Urbana Champaign, Urbana, Illinois, USA
| | - Joanne C. Chee-Sanford
- University of Illinois at Urbana Champaign, Urbana, Illinois, USA
- USDA-ARS, Urbana, Illinois, USA
| | | | - Frank E. Löffler
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, USA
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee, USA
- University of Tennessee and Oak Ridge National Laboratory (UT-ORNL) Joint Institute for Biological Sciences (JIBS) and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
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21
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Lai CY, Yang X, Tang Y, Rittmann BE, Zhao HP. Nitrate shaped the selenate-reducing microbial community in a hydrogen-based biofilm reactor. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2014; 48:3395-3402. [PMID: 24579788 DOI: 10.1021/es4053939] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
To study the effect of nitrate (NO3(-)) on selenate (SeO4(2-)) reduction, we tested a H2-based biofilm with a range of influent NO3(-) loadings. When SeO4(2-) was the only electron acceptor (stage 1), 40% of the influent SeO4(2-) was reduced to insoluble elemental selenium (Se(0)). SeO4(2-) reduction was dramatically inhibited when NO3(-) was added at a surface loading larger than 1.14 g of N m(-2) day(-1), when H2 delivery became limiting and only 80% of the input NO3(-) was reduced (stage 2). In stage 3, when NO3(-) was again removed from the influent, SeO4(2-) reduction was re-established and increased to 60% conversion to Se(0). SeO4(2-) reduction remained stable at 60% in stages 4 and 5, when the NO3(-) surface loading was re-introduced at ≤ 0.53 g of N m(-2) day(-1), allowing for complete NO3(-) reduction. The selenate-reducing microbial community was significantly reshaped by the high NO3(-) surface loading in stage 2, and it remained stable through stages 3-5. In particular, the abundance of α-Proteobacteria decreased from 30% in stage 1 to less than 10% of total bacteria in stage 2. β-Proteobacteria, which represented about 55% of total bacteria in the biofilm in stage 1, increased to more than 90% of phylotypes in stage 2. Hydrogenophaga, an autotrophic denitrifier, was positively correlated with NO3(-) flux. Thus, introducing a NO3(-) loading high enough to cause H2 limitation and suppress SeO4(2-) reduction had a long-lasting effect on the microbial community structure, which was confirmed by principal coordinate analysis, although SeO4(2-) reduction remained intact.
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Affiliation(s)
- Chun-Yu Lai
- Ministry of Education, Key Laboratory of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Science, Zhejiang University , Hangzhou 310029, People's Republic of China
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22
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Microbiota and metabolite profiling reveal specific alterations in bacterial community structure and environment in the cystic fibrosis airway during exacerbation. PLoS One 2013; 8:e82432. [PMID: 24358183 PMCID: PMC3866110 DOI: 10.1371/journal.pone.0082432] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Accepted: 10/23/2013] [Indexed: 01/04/2023] Open
Abstract
Chronic polymicrobial infections of the lung are the foremost cause of morbidity and mortality in cystic fibrosis (CF) patients. The composition of the microbial flora of the airway alters considerably during infection, particularly during patient exacerbation. An understanding of which organisms are growing, their environment and their behaviour in the airway is of importance for designing antibiotic treatment regimes and for patient prognosis. To this end, we have analysed sputum samples taken from separate cohorts of CF and non-CF subjects for metabolites and in parallel, and we have examined both isolated DNA and RNA for the presence of 16S rRNA genes and transcripts by high-throughput sequencing of amplicon or cDNA libraries. This analysis revealed that although the population size of all dominant orders of bacteria as measured by DNA- and RNA- based methods are similar, greater discrepancies are seen with less prevalent organisms, some of which we associated with CF for the first time. Additionally, we identified a strong relationship between the abundance of specific anaerobes and fluctuations in several metabolites including lactate and putrescine during patient exacerbation. This study has hence identified organisms whose occurrence within the CF microbiome has been hitherto unreported and has revealed potential metabolic biomarkers for exacerbation.
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23
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Rauschenbach I, Posternak V, Cantarella P, McConnell J, Starovoytov V, Häggblom MM. Seleniivibrio woodruffii gen. nov., sp. nov., a selenate- and arsenate-respiring bacterium in the
Deferribacteraceae. Int J Syst Evol Microbiol 2013; 63:3659-3665. [DOI: 10.1099/ijs.0.043547-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-type-negative, obligately anaerobic, selenate-respiring bacterium, strain S4T, was isolated from activated sludge of a wastewater treatment plant in New Jersey after enrichment with 10 mM selenate as the sole electron acceptor. In addition to its selenate-respiring capability, strain S4T also respired arsenate with acetate as carbon source and electron donor. Fermentative growth was not observed. The optimum growth temperature was 37 °C and optimum pH was pH 7. Phylogenetic analysis of the 16S rRNA gene sequence revealed that strain S4T is a novel member of the family
Deferribacteraceae
, with the type strain of
Denitrovibrio acetiphilus
as its closest cultivated relative, with 91.5 % sequence similarity. The cellular fatty acid profile was composed predominantly of straight-chain fatty acids C14 : 0, C15 : 0, C16 : 0, C17 : 0 and C18 : 0, which distinguishes this organism from its closest relatives. The DNA G+C content was 47.7 mol%. Together, these findings support the conclusion that strain S4T represents a novel genus and species, for which the name Seleniivibrio woodruffii gen. nov., sp. nov. is proposed. The type strain of Seleniivibrio woodruffii is S4T ( = DSM 24984T = ATCC BAA-2290T).
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Affiliation(s)
- Ines Rauschenbach
- Rutgers University, Department of Biochemistry and Microbiology, School of Environmental and Biological Sciences, 76 Lipman Drive, New Brunswick, NJ 08901, USA
| | - Valeriya Posternak
- Rutgers University, Department of Biochemistry and Microbiology, School of Environmental and Biological Sciences, 76 Lipman Drive, New Brunswick, NJ 08901, USA
| | - Pasquale Cantarella
- Rutgers University, Department of Biochemistry and Microbiology, School of Environmental and Biological Sciences, 76 Lipman Drive, New Brunswick, NJ 08901, USA
| | - Jennifer McConnell
- Rutgers University, Department of Biochemistry and Microbiology, School of Environmental and Biological Sciences, 76 Lipman Drive, New Brunswick, NJ 08901, USA
| | - Valentin Starovoytov
- Rutgers University, Department of Cell Biology and Neuroscience, 604 Allison Road, Piscataway, NJ 08854, USA
| | - Max M. Häggblom
- Rutgers University, Department of Biochemistry and Microbiology, School of Environmental and Biological Sciences, 76 Lipman Drive, New Brunswick, NJ 08901, USA
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24
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Mumford AC, Yee N, Young LY. Precipitation of alacranite (As8S9) by a novel As(V)-respiring anaerobe strain MPA-C3. Environ Microbiol 2013; 15:2748-60. [PMID: 23735175 DOI: 10.1111/1462-2920.12136] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Accepted: 03/20/2013] [Indexed: 01/15/2023]
Abstract
Strain MPA-C3 was isolated by incubating arsenic-bearing sediments under anaerobic, mesophilic conditions in minimal media with acetate as the sole source of energy and carbon, and As(V) as the sole electron acceptor. Following growth and the respiratory reduction of As(V) to As(III), a yellow precipitate formed in active cultures, while no precipitate was observed in autoclaved controls, or in uninoculated media supplemented with As(III). The precipitate was identified by X-ray diffraction as alacranite, As8 S9 , a mineral previously only identified in hydrothermal environments. Sequencing of the 16S rRNA gene indicated that strain MPA-C3 is a member of the Deferribacteres family, with relatively low (90%) identity to Denitrovibrio acetiphilus DSM 12809. The arsenate respiratory reductase gene, arrA, was sequenced, showing high homology to the arrA gene of Desulfitobacterium halfniense. In addition to As(V), strain MPA-C3 utilizes NO3(-), Se(VI), Se(IV), fumarate and Fe(III) as electron acceptors, and acetate, pyruvate, fructose and benzoate as sources of carbon and energy. Analysis of a draft genome sequence revealed multiple pathways for respiration and carbon utilization. The results of this work demonstrate that alacranite, a mineral previously thought to be formed only chemically under hydrothermal conditions, is precipitated under mesophilic conditions by the metabolically versatile strain MPA-C3.
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Affiliation(s)
- Adam C Mumford
- Department of Environmental Sciences, Rutgers University, New Brunswick, NJ, USA
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25
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Letzel AC, Pidot SJ, Hertweck C. A genomic approach to the cryptic secondary metabolome of the anaerobic world. Nat Prod Rep 2012; 30:392-428. [PMID: 23263685 DOI: 10.1039/c2np20103h] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
A total of 211 complete and published genomes from anaerobic bacteria are analysed for the presence of secondary metabolite biosynthesis gene clusters, in particular those tentatively coding for polyketide synthases (PKS) and non-ribosomal peptide synthetases (NRPS). We investigate the distribution of these gene clusters according to bacterial phylogeny and, if known, correlate these to the type of metabolic pathways they encode. The potential of anaerobes as secondary metabolite producers is highlighted.
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Affiliation(s)
- Anne-Catrin Letzel
- Leibniz Institute for Natural Product Research and Infection Biology HKI, Beutenbergstr. 11a, Jena, 07745, Germany
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26
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Rauschenbach I, Bini E, Häggblom MM, Yee N. Physiological response of Desulfurispirillum indicum S5 to arsenate and nitrate as terminal electron acceptors. FEMS Microbiol Ecol 2012; 81:156-62. [DOI: 10.1111/j.1574-6941.2012.01351.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2011] [Revised: 02/28/2012] [Accepted: 02/28/2012] [Indexed: 11/30/2022] Open
Affiliation(s)
- Ines Rauschenbach
- Department of Biochemistry and Microbiology; School of Environmental and Biological Sciences; Rutgers University; New Brunswick; NJ; USA
| | - Elisabetta Bini
- Department of Biochemistry and Microbiology; School of Environmental and Biological Sciences; Rutgers University; New Brunswick; NJ; USA
| | - Max M. Häggblom
- Department of Biochemistry and Microbiology; School of Environmental and Biological Sciences; Rutgers University; New Brunswick; NJ; USA
| | - Nathan Yee
- Department of Environmental Sciences; School of Environmental and Biological Sciences; Rutgers University; New Brunswick; NJ; USA
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27
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Bini E, Rauschenbach I, Narasingarao P, Starovoytov V, Hauser L, Jeffries CD, Land M, Bruce D, Detter C, Goodwin L, Han S, Held B, Tapia R, Copeland A, Ivanova N, Mikhailova N, Nolan M, Pati A, Pennacchio L, Pitluck S, Woyke T, Häggblom M. Complete genome sequence of Desulfurispirillum indicum strain S5(T). Stand Genomic Sci 2011; 5:371-8. [PMID: 22675586 PMCID: PMC3368425 DOI: 10.4056/sigs.2425302] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Desulfurispirillum indicum strain S5(T) is a strictly anaerobic bacterium isolated from river sediment in Chennai, India. D. indicum belongs to the deep branching phylum of Chrysiogenetes, which currently only includes three other cultured species. Strain S5(T) is the type strain of the species and it is capable of growth using selenate, selenite, arsenate, nitrate or nitrite as terminal electron acceptors. The 2,928,377 bp genome encodes 2,619 proteins and 49 RNA genes, and the information gained from its sequence will be relevant to the elucidation of microbially-mediated transformations of arsenic and selenium, in addition to deepening our knowledge of the underrepresented phylum of Chrysiogenetes.
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Affiliation(s)
- Elisabetta Bini
- Rutgers, The State University of New Jersey, Department of Biochemistry and Microbiology, School of Environmental and Biological Sciences, New Brunswick, New Jersey, USA
- Corresponding author: Elisabetta Bini,
| | - Ines Rauschenbach
- Rutgers, The State University of New Jersey, Department of Biochemistry and Microbiology, School of Environmental and Biological Sciences, New Brunswick, New Jersey, USA
| | - Priya Narasingarao
- Rutgers, The State University of New Jersey, Department of Biochemistry and Microbiology, School of Environmental and Biological Sciences, New Brunswick, New Jersey, USA
- Current address: Scripps Institution of Oceanography, San Diego, CA, USA
| | - Valentin Starovoytov
- Rutgers, The State University of New Jersey, Department of Cell Biology and Neuroscience, Piscataway, NJ, USA
| | - Lauren Hauser
- Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | | | - Miriam Land
- Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - David Bruce
- Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - Chris Detter
- Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - Lynne Goodwin
- Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - Shunsheng Han
- Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - Brittany Held
- Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - Roxanne Tapia
- Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | | | | | | | - Matt Nolan
- Joint Genome Institute, Walnut Creek, USA
| | | | | | | | | | - Max Häggblom
- Rutgers, The State University of New Jersey, Department of Biochemistry and Microbiology, School of Environmental and Biological Sciences, New Brunswick, New Jersey, USA
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Abstract
During selenate respiration by Thauera selenatis, the reduction of selenate results in the formation of intracellular selenium (Se) deposits that are ultimately secreted as Se nanospheres of approximately 150 nm in diameter. We report that the Se nanospheres are associated with a protein of approximately 95 kDa. Subsequent experiments to investigate the expression and secretion profile of this protein have demonstrated that it is up-regulated and secreted in response to increasing selenite concentrations. The protein was purified from Se nanospheres, and peptide fragments from a tryptic digest were used to identify the gene in the draft T. selenatis genome. A matched open reading frame was located, encoding a protein with a calculated mass of 94.5 kDa. N-terminal sequence analysis of the mature protein revealed no cleavable signal peptide, suggesting that the protein is exported directly from the cytoplasm. The protein has been called Se factor A (SefA), and homologues of known function have not been reported previously. The sefA gene was cloned and expressed in Escherichia coli, and the recombinant His-tagged SefA purified. In vivo experiments demonstrate that SefA forms larger (approximately 300 nm) Se nanospheres in E. coli when treated with selenite, and these are retained within the cell. In vitro assays demonstrate that the formation of Se nanospheres upon the reduction of selenite by glutathione are stabilized by the presence of SefA. The role of SefA in selenium nanosphere assembly has potential for exploitation in bionanomaterial fabrication.
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Biswas KC, Barton LL, Tsui WL, Shuman K, Gillespie J, Eze CS. A novel method for the measurement of elemental selenium produced by bacterial reduction of selenite. J Microbiol Methods 2011; 86:140-4. [PMID: 21536079 DOI: 10.1016/j.mimet.2011.04.009] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2011] [Revised: 04/13/2011] [Accepted: 04/13/2011] [Indexed: 11/17/2022]
Abstract
The measurement of elemental selenium (Se(0)) is needed to assess the rate and magnitude of bacteria reduction of selenite or selenate. We have developed a spectrophotometric method for the measurement Se(0) that is rapid and can be employed to measure the quantity of Se(0) produced by bacterial cultures. This method employs the use of 1M Na(2)S to convert the insoluble elemental selenium to a red-brown solution and with this method there is a direct correlation between concentration of elemental selenium and the absorption at 500nm. To demonstrate the utility of this assay, we have followed the reduction of selenite to Se(0) by Moraxella bovis, and by bacterial consortia in soil and water samples.
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Affiliation(s)
- Keka C Biswas
- Department of Science, Wesley College, Dover, DE 19901, USA
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30
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Rauschenbach I, Yee N, Häggblom MM, Bini E. Energy metabolism and multiple respiratory pathways revealed by genome sequencing ofDesulfurispirillum indicumstrain S5. Environ Microbiol 2011; 13:1611-21. [DOI: 10.1111/j.1462-2920.2011.02473.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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