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Zeng XC, Xu Y, Lu H, Xiong J, Xu H, Wu W. Contradictory Impacts of Nitrate on the Dissimilatory Arsenate-Respiring Prokaryotes-Induced Reductive Mobilization of Arsenic from Contaminated Sediments: Mechanism Insight from Metagenomic and Functional Analyses. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:13473-13486. [PMID: 37639510 DOI: 10.1021/acs.est.3c02190] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Dissimilatory arsenate-respiring prokaryotes (DARPs) are considered to be a key impetus of the reductive dissolution of solid-phase arsenic. However, little is known about the interaction between nitrate and DARPs so far. In this study, we showed that nitrate either inhibited or promoted the DARP population-catalyzed reductive mobilization of As in sediments. Metagenomic analysis of the microbial communities in the microcosms after seven days of As release assays suggested that microbes mainly consisted of: Type-I DARPs having potential to reduce NO3- into NO2- and Type-II DARPs having potential to reduce NO3- to NH4+. We further isolated two cultivable DARPs, Neobacillus sp. A01 and Paenibacillus sp. A02, which represent Type-I and -II DARPs, respectively. We observed that nitrate suppressed A01-mediated release of As(III) but promoted A02-mediated release of As(III). Furthermore, we demonstrated that this observation was due to the fact that nitrite, the end product of incomplete denitrification by Type-I DARPs, suppressed the arrA gene expression per cell and growth of all DARPs, whereas ammonium, the end product of dissimilatory nitrate reduction to ammonium (DNRA) by Type-II DARPs, enhanced the arrA gene expression per cell and significantly promoted the growth of all DARPs. These findings suggest that the actual effects of nitrate on DARP population-catalyzed reductive mobilization of arsenic, largely depend on the ratio of Type-I to Type-II DARPs in sediments.
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Affiliation(s)
- Xian-Chun Zeng
- State Key Laboratory of Biogeology and Environmental Geology & School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan 430079, People's Republic of China
| | - Yifan Xu
- State Key Laboratory of Biogeology and Environmental Geology & School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan 430079, People's Republic of China
| | - Hongyu Lu
- State Key Laboratory of Biogeology and Environmental Geology & School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan 430079, People's Republic of China
| | - Jianyu Xiong
- State Key Laboratory of Biogeology and Environmental Geology & School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan 430079, People's Republic of China
| | - Hai Xu
- Division of Endocrinology and Rheumatology, HuangPi People's Hospital, the Third Affiliated Hospital of Jianghan University, Wuhan 430300, China
| | - Weiwei Wu
- State Key Laboratory of Biogeology and Environmental Geology & School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan 430079, People's Republic of China
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Luo B, Su JY, Wang YN, Guan L, Dong KS, Niu HJ, Shen SF, Li Y. Shewanella subflava sp. nov., a novel multi-resistant bacterium, isolated from the estuary of the Fenhe River into the Yellow River. Antonie Van Leeuwenhoek 2023; 116:511-519. [PMID: 37022511 DOI: 10.1007/s10482-023-01829-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 03/29/2023] [Indexed: 04/07/2023]
Abstract
A aerobic, gram-negative, rod-shaped and polar-flagellum bacterial strain, designated as FYR11-62T, was isolated from the estuary of the Fenhe River into the Yellow River in Shanxi Province, China. The isolate was able to grow at 4-37 °C (optimum, 25 °C), pH 5.5-9.5 (optimum, pH 7.5) and in the presence of 0-7.0% (w/v) NaCl (optimum, 1.0% NaCl). Phylogenetic analyses based on 16S rRNA genes and 1597 single-copy orthologous clusters indicated that strain FYR11-62T affiliated with the genus Shewanella and shared the highest 16S rRNA gene sequence similarity to Shewanella aestuarii SC18T (98.3%) and Shewanella gaetbuli TF-27T (97.3%), respectively. The major fatty acids were summed feature 3 (C16:1 ω7c and/or C16:1 ω6c), C16:0 and iso-C15:0. The major polar lipids were phosphatidylethanolamine and phosphatidylglycerol. The main quinones were Q-7 and Q-8. The genomic DNA G + C content was 41.6%. Gene annotation showed that strain FYR11-62T possessed 30 antibiotic resistance genes, implying its multiple antidrug resistance. The average nucleotide identity and digital DNA-DNA hybridization values between strain FYR11-62T and its closely related species were all below the thresholds for species delineation. The phylogenetic position together with the results of the analysis of morphological, physiological and genomic features support the classification of strain FYR11-62T (= MCCC 1K07242T = KCTC 92244T) as a novel species of the genus Shewanella, for which the name Shewanella subflava sp. nov. is proposed.
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Affiliation(s)
- Bi Luo
- Financial Assets Department, Shanxi Agricultural University, Taigu, 030801, China
| | - Jing-Yun Su
- College of Life Sciences, Shanxi Agricultural University, Taigu, 030801, China
| | - Ya-Nan Wang
- College of Life Sciences, Shanxi Agricultural University, Taigu, 030801, China
| | - Li Guan
- College of Life Sciences, Shanxi Agricultural University, Taigu, 030801, China
| | - Kai-Shi Dong
- College of Life Sciences, Shanxi Agricultural University, Taigu, 030801, China
| | - Hui-Jing Niu
- College of Animal Science, Shanxi Agricultural University, Taigu, 030801, China
| | - Shao-Fei Shen
- College of Life Sciences, Shanxi Agricultural University, Taigu, 030801, China.
| | - Yi Li
- College of Life Sciences, Shanxi Agricultural University, Taigu, 030801, China.
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3
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Zhang D, Ke T, Xiu W, Ren C, Chen G, Lloyd JR, Bassil NM, Richards LA, Polya DA, Wang G, Guo H. Quantifying sulfidization and non-sulfidization in long-term in-situ microbial colonized As(V)-ferrihydrite coated sand columns: Insights into As mobility. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 858:160066. [PMID: 36356776 DOI: 10.1016/j.scitotenv.2022.160066] [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: 06/27/2022] [Revised: 10/30/2022] [Accepted: 11/04/2022] [Indexed: 06/16/2023]
Abstract
Sulfide-induced reduction (sulfidization) of arsenic (As)-bearing Fe(III) (oxyhydro)oxides may lead to As mobilization in aquifer systems. However, little is known about the relative contributions of sulfidization and non-sulfidization of Fe(III) (oxyhydro)oxides reduction to As mobilization. To address this issue, high As groundwater with low sulfide (LS) and high sulfide (HS) concentrations were pumped through As(V)-bearing ferrihydrite-coated sand columns (LS-column and HS-column, respectively) being settled within wells in the western Hetao Basin, China. Sulfidization of As(V)-bearing ferrihydrite was evidenced by the increase in dissolved Fe(II) and the presence of solid Fe(II) and elemental sulfur (S0) in both the columns. A conceptual model was built using accumulated S0 and Fe(II) produced in the columns to calculate the proportions of sulfidization-induced Fe(III) (oxyhydro)oxide reduction and non-sulfidization-induced Fe(III) (oxyhydro)oxide reduction. Fe(III) reduction via sulfidization occurred preferentially in the inlet ends (LS-column, 31 %; HS-column, 86 %), while Fe(III) reduction via non-sulfidization processes predominated in the outlet ends (LS-column, 96 %; HS-column, 86 %), and was attributed to the metabolism of genera associated with Fe(III) reduction (including Shewanella, Ferribacterium, and Desulfuromonas). Arsenic was mobilized in the columns via sulfidization and non-sulfidization processes. More As was released from the solid of the HS-column than that of the LS-column due to the higher intensity of sulfidization in the presence of higher concentrations of dissolved S(-II). Overall, this study highlights the sulfidization of As-bearing Fe(III) (oxyhydro)oxides as an important As-mobilizing pathway in complex As-Fe-S bio-hydrogeochemical networks.
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Affiliation(s)
- Di Zhang
- State Key Laboratory of Biogeology and Environmental Geology and MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences, Beijing 100083, PR China; School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing 100083, PR China
| | - Tiantian Ke
- State Key Laboratory of Biogeology and Environmental Geology and MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences, Beijing 100083, PR China; School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing 100083, PR China
| | - Wei Xiu
- State Key Laboratory of Biogeology and Environmental Geology and MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences, Beijing 100083, PR China; Institute of Earth sciences, China University of Geosciences (Beijing), Beijing 100083, PR China; School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing 100083, PR China; Williamson Research Centre for Molecular Environmental Science, Department of Earth and Environmental Sciences, The University of Manchester, Manchester M13 9PL, United Kingdom.
| | - Cui Ren
- School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing 100083, PR China
| | - Guangyu Chen
- School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing 100083, PR China
| | - Jonathan R Lloyd
- Williamson Research Centre for Molecular Environmental Science, Department of Earth and Environmental Sciences, The University of Manchester, Manchester M13 9PL, United Kingdom
| | - Naji M Bassil
- Williamson Research Centre for Molecular Environmental Science, Department of Earth and Environmental Sciences, The University of Manchester, Manchester M13 9PL, United Kingdom
| | - Laura A Richards
- Williamson Research Centre for Molecular Environmental Science, Department of Earth and Environmental Sciences, The University of Manchester, Manchester M13 9PL, United Kingdom
| | - David A Polya
- Williamson Research Centre for Molecular Environmental Science, Department of Earth and Environmental Sciences, The University of Manchester, Manchester M13 9PL, United Kingdom
| | - Guangcai Wang
- State Key Laboratory of Biogeology and Environmental Geology and MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences, Beijing 100083, PR China; School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing 100083, PR China
| | - Huaming Guo
- State Key Laboratory of Biogeology and Environmental Geology and MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences, Beijing 100083, PR China; School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing 100083, PR China.
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4
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Current Trends in Metal Biomining with a Focus on Genomics Aspects and Attention to Arsenopyrite Leaching-A Review. Microorganisms 2023; 11:microorganisms11010186. [PMID: 36677478 PMCID: PMC9864737 DOI: 10.3390/microorganisms11010186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 01/06/2023] [Accepted: 01/09/2023] [Indexed: 01/15/2023] Open
Abstract
The presented review is based on scientific microbiological articles and patents in the field of biomining valuable metals. The main attention is paid to publications of the last two decades, which illustrate some shifts in objects of interest and modern trends both in general and applied microbiology. The review demonstrates that microbial bioleaching continues to develop actively, despite various problems in its industrial application. The previous classic trends in the microbial bioleaching persist and remain unchanged, including (i) the search for and selection of new effective species and strains and (ii) technical optimization of the bioleaching process. Moreover, new trends were formed during the last decades with an emphasis on the phylogeny of leaching microbiota and on genomes of the leaching microorganisms. This area of genomics provides new, interesting information and forms a basis for the subsequent construction of new leaching strains. For example, this review mentions some changed strains with increased resistance to toxic compounds. Additionally, the review considers some problems of bioleaching valuable metals from toxic arsenopyrite.
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5
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Cerbino GN, Traglia GM, Ayala Nuñez T, Parmeciano Di Noto G, Ramírez MS, Centrón D, Iriarte A, Quiroga C. Comparative genome analysis of the genus Shewanella unravels the association of key genetic traits with known and potential pathogenic lineages. Front Microbiol 2023; 14:1124225. [PMID: 36925471 PMCID: PMC10011109 DOI: 10.3389/fmicb.2023.1124225] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 02/06/2023] [Indexed: 03/06/2023] Open
Abstract
Shewanella spp. are Gram-negative rods widely disseminated in aquatic niches that can also be found in human-associated environments. In recent years, reports of infections caused by these bacteria have increased significantly. Mobilome and resistome analysis of a few species showed that they are versatile; however, comprehensive comparative studies in the genus are lacking. Here, we analyzed the genetic traits of 144 genomes from Shewanella spp. isolates focusing on the mobilome, resistome, and virulome to establish their evolutionary relationship and detect unique features based on their genome content and habitat. Shewanella spp. showed a great diversity of mobile genetic elements (MGEs), most of them associated with monophyletic lineages of clinical isolates. Furthermore, 79/144 genomes encoded at least one antimicrobial resistant gene with their highest occurrence in clinical-related lineages. CRISPR-Cas systems, which confer immunity against MGEs, were found in 41 genomes being I-E and I-F the more frequent ones. Virulome analysis showed that all Shewanella spp. encoded different virulence genes (motility, quorum sensing, biofilm, adherence, etc.) that may confer adaptive advantages for survival against hosts. Our data revealed that key accessory genes are frequently found in two major clinical-related groups, which encompass the opportunistic pathogens Shewanella algae and Shewanella xiamenensis together with several other species. This work highlights the evolutionary nature of Shewanella spp. genomes, capable of acquiring different key genetic traits that contribute to their adaptation to different niches and facilitate the emergence of more resistant and virulent isolates that impact directly on human and animal health.
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Affiliation(s)
- Gabriela N Cerbino
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Tecnológicas, Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPAM), Facultad de Medicina, Buenos Aires, Argentina
| | - German M Traglia
- Laboratorio de Biología Computacional, Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Teolincacihuatl Ayala Nuñez
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Tecnológicas, Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPAM), Facultad de Medicina, Buenos Aires, Argentina
| | - Gisela Parmeciano Di Noto
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Tecnológicas, Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPAM), Facultad de Medicina, Buenos Aires, Argentina
| | - María Soledad Ramírez
- Center for Applied Biotechnology Studies, Department of Biological Science, California State University, Fullerton, Fullerton, CA, United States
| | - Daniela Centrón
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Tecnológicas, Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPAM), Facultad de Medicina, Buenos Aires, Argentina
| | - Andrés Iriarte
- Laboratorio de Biología Computacional, Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Cecilia Quiroga
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Tecnológicas, Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPAM), Facultad de Medicina, Buenos Aires, Argentina
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6
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Topić Popović N, Kazazić S, Bilić B, Babić S, Bojanić K, Bujak M, Tartaro Bujak I, Jadan M, Strunjak-Perović I, Kepec S, Čož-Rakovac R. Shewanella spp. from wastewater treatment plant-affected environment: isolation and characterization. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:82986-83003. [PMID: 35761132 DOI: 10.1007/s11356-022-21573-4] [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: 01/17/2022] [Accepted: 06/15/2022] [Indexed: 06/15/2023]
Abstract
Bacteria from the genus Shewanella are inhabitants of marine and freshwater ecosystems, recognized fish spoilage bacteria, but less known as fish disease agents. Shewanella spp. isolated from fish living in waters close to effluents of a wastewater treatment plant (WWTP) were not previously characterized. We have tested Shewanella isolates from WWTP-affected waters and related fish. Genotypic characterization identified most strains as S. baltica and S. oneidensis. In order to investigate the sensibility and accuracy of their MALDI-TOF MS identification, they were grown on two culture media enriched by various NaCl concentrations, incubated at different temperatures and duration. We analyzed their antimicrobial susceptibility on a panel of antimicrobial drugs and capacity for biofilm production. With a view to demonstrate their capacity to produce fatty acids, we assessed the impact of different culture media on their lipid profile. We performed zebrafish embryotoxicity tests to simulate the environmental infection of the earliest life stages in S. baltica-contaminated waters. The best MALDI-TOF MS identification scores were for strains cultivated on TSA for 24 h at 22 °C and with supplementation of 1.5% NaCl. Less than 17% of isolates demonstrated antimicrobial resistance. Most isolates were weak biofilm producers. Strain-to-strain variation of MIC and MBC was low. The major fatty acids were C15:0, C16:0, C16:1, C17:1, and iC15:0. Exposure of Danio rerio to different S. baltica concentrations induced severe effects on zebrafish development: decreased heartbeat rate, locomotor activity, and melanin pigmentation. S. baltica passed through chorionic pores of zebrafish.
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Affiliation(s)
- Natalija Topić Popović
- Laboratory for Aquaculture Biotechnology, Ruđer Bošković Institute, Bijenička 54, 10 000, Zagreb, Croatia
- Center of Excellence for Marine Bioprospecting-BioProCro, Ruđer Bošković Institute, Zagreb, Croatia
| | - Snježana Kazazić
- Laboratory for Mass Spectrometry and Functional Proteomics, Ruđer Bošković Institute, Zagreb, Croatia.
| | - Branka Bilić
- Laboratory for Mass Spectrometry and Functional Proteomics, Ruđer Bošković Institute, Zagreb, Croatia
| | - Sanja Babić
- Laboratory for Aquaculture Biotechnology, Ruđer Bošković Institute, Bijenička 54, 10 000, Zagreb, Croatia
- Center of Excellence for Marine Bioprospecting-BioProCro, Ruđer Bošković Institute, Zagreb, Croatia
| | - Krunoslav Bojanić
- Laboratory for Aquaculture Biotechnology, Ruđer Bošković Institute, Bijenička 54, 10 000, Zagreb, Croatia
- Center of Excellence for Marine Bioprospecting-BioProCro, Ruđer Bošković Institute, Zagreb, Croatia
| | - Maro Bujak
- Laboratory for Aquaculture Biotechnology, Ruđer Bošković Institute, Bijenička 54, 10 000, Zagreb, Croatia
- Center of Excellence for Marine Bioprospecting-BioProCro, Ruđer Bošković Institute, Zagreb, Croatia
| | - Ivana Tartaro Bujak
- Radiation Chemistry and Dosimetry Laboratory, Ruđer Bošković Institute, Zagreb, Croatia
| | - Margita Jadan
- Laboratory for Aquaculture Biotechnology, Ruđer Bošković Institute, Bijenička 54, 10 000, Zagreb, Croatia
- Center of Excellence for Marine Bioprospecting-BioProCro, Ruđer Bošković Institute, Zagreb, Croatia
| | - Ivančica Strunjak-Perović
- Laboratory for Aquaculture Biotechnology, Ruđer Bošković Institute, Bijenička 54, 10 000, Zagreb, Croatia
- Center of Excellence for Marine Bioprospecting-BioProCro, Ruđer Bošković Institute, Zagreb, Croatia
| | - Slavko Kepec
- Virkom d.o.o., Public Water Supply and Wastewater Services, 33 000, Virovitica, Croatia
| | - Rozelindra Čož-Rakovac
- Laboratory for Aquaculture Biotechnology, Ruđer Bošković Institute, Bijenička 54, 10 000, Zagreb, Croatia
- Center of Excellence for Marine Bioprospecting-BioProCro, Ruđer Bošković Institute, Zagreb, Croatia
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Domínguez-Maqueda M, Pérez-Gómez O, Grande-Pérez A, Esteve C, Seoane P, Tapia-Paniagua ST, Balebona MC, Moriñigo MA. Pathogenic strains of Shewanella putrefaciens contain plasmids that are absent in the probiotic strain Pdp11. PeerJ 2022; 10:e14248. [PMID: 36312754 PMCID: PMC9610664 DOI: 10.7717/peerj.14248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 09/26/2022] [Indexed: 01/24/2023] Open
Abstract
Shewanella putrefaciens Pdp11 is a strain described as a probiotic for use in aquaculture. However, S. putrefaciens includes strains reported to be pathogenic or saprophytic to fish. Although the probiotic trait has been related to the presence of a group of genes in its genome, the existence of plasmids that could determine the probiotic or pathogenic character of this bacterium is unknown. In the present work, we searched for plasmids in several strains of S. putrefaciens that differ in their pathogenic and probiotic character. Under the different conditions tested, plasmids were only found in two of the five pathogenic strains, but not in the probiotic strain nor in the two saprophytic strains tested. Using a workflow integrating Sanger and Illumina reads, the complete consensus sequences of the plasmids were obtained. Plasmids differed in one ORF and encoded a putative replication initiator protein of the repB family, as well as proteins related to plasmid stability and a toxin-antitoxin system. Phylogenetic analysis showed some similarity to functional repB proteins of other Shewanella species. The implication of these plasmids in the probiotic or pathogenic nature of S. putrefaciens is discussed.
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Affiliation(s)
| | | | - Ana Grande-Pérez
- Área de Genética, Universidad de Málaga, Málaga, Spain,Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”-Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Universidad de Málaga, Málaga, Spain
| | - Consuelo Esteve
- Departmento de Microbiología y Ecología, Universidad de Valencia, Valencia, Spain
| | - Pedro Seoane
- Centro de Investigación Biomédica en Red de Enfermedades Raras, CIBERER, Madrid, Spain,Departmento de Biología Molecular y Bioquímica, Universidad de Málaga, Málaga, Spain
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Staicu LC, Wójtowicz PJ, Molnár Z, Ruiz-Agudo E, Gallego JLR, Baragaño D, Pósfai M. Interplay between arsenic and selenium biomineralization in Shewanella sp. O23S. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 306:119451. [PMID: 35569621 DOI: 10.1016/j.envpol.2022.119451] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 05/04/2022] [Accepted: 05/07/2022] [Indexed: 06/15/2023]
Abstract
Bacteria play crucial roles in the biogeochemical cycle of arsenic (As) and selenium (Se) as these elements are metabolized via detoxification, energy generation (anaerobic respiration) and biosynthesis (e.g. selenocysteine) strategies. To date, arsenic and selenium biomineralization in bacteria were studied separately. In this study, the anaerobic metabolism of As and Se in Shewanella sp. O23S was investigated separately and mixed, with an emphasis put on the biomineralization products of this process. Multiple analytical techniques including ICP-MS, TEM-EDS, XRD, Micro-Raman, spectrophotometry and surface charge (zeta potential) were employed. Shewanella sp. O23S is capable of reducing selenate (SeO42-) and selenite (SeO32-) to red Se(-S)0, and arsenate (AsO43-) to arsenite (AsO33-). The release of H2S from cysteine led to the precipitation of AsS minerals: nanorod AsS and granular As2S3. When As and Se oxyanions were mixed, both As-S and Se(-S)0 biominerals were synthesized. All biominerals were extracellular, amorphous and presented a negative surface charge (-24 to -38 mV). Kinetic analysis indicated the following reduction yields: SeO32- (90%), AsO43- (60%), and SeO42- (<10%). The mix of SeO32- with AsO43- led to a decrease in As removal to 30%, while Se reduction yield was unaffected (88%). Interestingly, SeO42- incubated with AsO43- boosted the Se removal (71%). The exclusive extracellular formation of As and Se biominerals might indicate an extracellular respiratory process characteristic of various Shewanella species and strains. This is the first study documenting a complex interplay between As and Se oxyanions: selenite decreased arsenate reduction, whereas arsenate stimulated selenate reduction. Further investigation needs to clarify whether Shewanella sp. O23S employs multi-substrate respiratory enzymes or separate, high affinity enzymes for As and Se oxyanion respiration.
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Affiliation(s)
- Lucian C Staicu
- Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland.
| | - Paulina J Wójtowicz
- Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland
| | - Zsombor Molnár
- Research Institute of Biomolecular and Chemical Engineering, University of Pannonia, Egyetem u. 10, H-8200, Veszprém, Hungary; ELKH-PE Environmental Mineralogy Research Group, University of Pannonia, Egyetem u. 10, H-8200, Veszprém, Hungary
| | | | - José Luis R Gallego
- Environmental Biogeochemistry & Raw Materials Group and INDUROT, Campus de Mieres, University of Oviedo, C/Gonzalo Gutiérrez Quirós. S/N, 33600, Mieres, Spain
| | - Diego Baragaño
- Environmental Biogeochemistry & Raw Materials Group and INDUROT, Campus de Mieres, University of Oviedo, C/Gonzalo Gutiérrez Quirós. S/N, 33600, Mieres, Spain
| | - Mihály Pósfai
- Research Institute of Biomolecular and Chemical Engineering, University of Pannonia, Egyetem u. 10, H-8200, Veszprém, Hungary; ELKH-PE Environmental Mineralogy Research Group, University of Pannonia, Egyetem u. 10, H-8200, Veszprém, Hungary
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9
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Bacterial Arsenic Metabolism and Its Role in Arsenic Bioremediation. Curr Microbiol 2022; 79:131. [PMID: 35290506 DOI: 10.1007/s00284-022-02810-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 02/14/2022] [Indexed: 11/03/2022]
Abstract
Arsenic contaminations, often adversely influencing the living organisms, including plants, animals, and the microbial communities, are of grave apprehension. Many physical, chemical, and biological techniques are now being explored to minimize the adverse affects of arsenic toxicity. Bioremediation of arsenic species using arsenic loving bacteria has drawn much attention. Arsenate and arsenite are mostly uptaken by bacteria through aquaglycoporins and phosphate transporters. After entering arsenic inside bacterial cell arsenic get metabolized (e.g., reduction, oxidation, methylation, etc.) into different forms. Arsenite is sequentially methylated into monomethyl arsenic acid (MMA) and dimethyl arsenic acid (DMA), followed by a transformation of less toxic, volatile trimethyl arsenic acid (TMA). Passive remediation techniques, including adsorption, biomineralization, bioaccumulation, bioleaching, and so on are exploited by bacteria. Rhizospheric bacterial association with some specific plants enhances phytoextraction process. Arsenic-resistant rhizospheric bacteria have immense role in enhancement of crop plant growth and development, but their applications are not well studied till date. Emerging techniques like phytosuction separation (PS-S) have a promising future, but still light to be focused on these techniques. Plant-associated bioremediation processes like phytoextraction and phytosuction separation (PS-S) techniques might be modified by treating with potent bacteria for furtherance.
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Genome Study of a Novel Virulent Phage vB_SspS_KASIA and Mu-like Prophages of Shewanella sp. M16 Provides Insights into the Genetic Diversity of the Shewanella Virome. Int J Mol Sci 2021; 22:ijms222011070. [PMID: 34681734 PMCID: PMC8541194 DOI: 10.3390/ijms222011070] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 09/28/2021] [Accepted: 10/10/2021] [Indexed: 12/19/2022] Open
Abstract
Shewanella is a ubiquitous bacterial genus of aquatic ecosystems, and its bacteriophages are also isolated from aquatic environments (oceans, lakes, ice, and wastewater). In this study, the isolation and characterization of a novel virulent Shewanella phage vB_SspS_KASIA and the identification of three prophages of its host, Shewanella sp. M16, including a mitomycin-inducible Mu-like siphovirus, vB_SspS_MuM16-1, became the starting point for comparative analyses of phages infecting Shewanella spp. and the determination of their position among the known bacterial viruses. A similarity networking analysis revealed the high diversity of Shewanella phages in general, with vB_SspS_KASIA clustering exclusively with Colwellia phage 9A, with which it forms a single viral cluster composed of two separate viral subclusters. Furthermore, vB_SspS_MuM16-1 presented itself as being significantly different from the phages deposited in public databases, expanding the diversity of the known Mu-like phages and giving potential molecular markers for the identification of Mu-like prophages in bacterial genomes. Moreover, the functional analysis performed for vB_SspS_KASIA suggested that, despite the KASIA host, the M16 strain grows better in a rich medium and at 30 °C the phage replication cycle seems to be optimal in restrictive culture conditions mimicking their natural environment, the Zloty Stok gold and arsenic mine.
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Staicu LC, Wόjtowicz PJ, Baragaño D, Pόsfai M, Molnár Z, Ruiz-Agudo E, Gallego JLR. Bioremediation of a polymetallic, arsenic-dominated reverse osmosis reject stream. Lett Appl Microbiol 2021; 75:1084-1092. [PMID: 34608662 DOI: 10.1111/lam.13578] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 09/13/2021] [Accepted: 09/30/2021] [Indexed: 12/01/2022]
Abstract
The treatment of metal-laden industrial effluents by reverse osmosis is gaining in popularity worldwide due to its high performance. However, this process generates a polymetallic concentrate (retentate) stream in need of efficient post-treatment prior to environmental discharge. This paper presents results on the bioremediation (in batch mode) of a metal-laden, arsenic-dominated retentate using Shewanella sp. O23S as inoculum. The incubation of the retentate for 14 days under anoxic conditions resulted in the following removal yields: As (8%), Co (11%), Mo (3%), Se (62%), Sb (30%) and Zn (40%). The addition of 1 mmol l-1 cysteine increased the removal rate as follows: As (27%), Co (80%), Mo (78%), Se (88%), Sb (83%) and Zn (90%). The contribution of cysteine as a source of H2 S to enhancing the removal yield was confirmed by its addition after 7 days of incubations initially lacking it. Additionally, the cysteine-sourced H2 S was confirmed by its capture onto headspace-mounted Pb-acetate test strips that were analysed by X-ray diffraction. We show that real metal-laden industrial effluents can be treated to medium-to-high efficiency using a biological system (naturally sourced inocula) and inexpensive reagents (yeast extract, lactate and cysteine).
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Affiliation(s)
- L C Staicu
- Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - P J Wόjtowicz
- Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - D Baragaño
- Environmental Biogeochemistry & Raw Materials Group and INDUROT, University of Oviedo, Mieres, Spain
| | - M Pόsfai
- Research Institute of Biomolecular and Chemical Engineering, Nanolab, University of Pannonia, Veszprém, Hungary
| | - Z Molnár
- Research Institute of Biomolecular and Chemical Engineering, Nanolab, University of Pannonia, Veszprém, Hungary
| | - E Ruiz-Agudo
- Department of Mineralogy and Petrology, University of Granada, Granada, Spain
| | - J L R Gallego
- Environmental Biogeochemistry & Raw Materials Group and INDUROT, University of Oviedo, Mieres, Spain
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Imchen M, Kumavath R. Shotgun metagenomics reveals a heterogeneous prokaryotic community and a wide array of antibiotic resistance genes in mangrove sediment. FEMS Microbiol Ecol 2021; 96:5897355. [PMID: 32845305 DOI: 10.1093/femsec/fiaa173] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 08/18/2020] [Indexed: 12/20/2022] Open
Abstract
Saline tolerant mangrove forests partake in vital biogeochemical cycles. However, they are endangered due to deforestation as a result of urbanization. In this study, we have carried out a metagenomic snapshot of the mangrove ecosystem from five countries to assess its taxonomic, functional and antibiotic resistome structure. Chao1 alpha diversity varied significantly (P < 0.001) between the countries (Brazil, Saudi Arabia, China, India and Malaysia). All datasets were composed of 33 phyla dominated by eight major phyla covering >90% relative abundance. Comparative analysis of mangrove with terrestrial and marine ecosystems revealed the strongest heterogeneity in the mangrove microbial community. We also observed that the mangrove community shared similarities to both the terrestrial and marine microbiome, forming a link between the two contrasting ecosystems. The antibiotic resistant genes (ARG) resistome was comprised of nineteen level 3 classifications dominated by multidrug resistance efflux pumps (46.7 ± 4.3%) and BlaR1 family regulatory sensor-transducer disambiguation (25.2 ± 4.8%). ARG relative abundance was significantly higher in Asian countries and in human intervention datasets at a global scale. Our study shows that the mangrove microbial community and its antibiotic resistance are affected by geography as well as human intervention and are unique to the mangrove ecosystem. Understanding changes in the mangrove microbiome and its ARG is significant for sustainable development and public health.
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Affiliation(s)
- Madangchanok Imchen
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Tejaswini Hills, Periya (P.O) Kasaragod, Kerala-671320, India
| | - Ranjith Kumavath
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Tejaswini Hills, Periya (P.O) Kasaragod, Kerala-671320, India
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Yang Z, Karczewska-Golec J, Styczynski M, Bajda T, Drewniak L. Characterization of Fe-based sediments received from chemical pre-treatment of hydrometallurgical waste leachate from the recycling of alkaline batteries. JOURNAL OF HAZARDOUS MATERIALS 2021; 403:123988. [PMID: 33265027 DOI: 10.1016/j.jhazmat.2020.123988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 04/21/2020] [Accepted: 09/12/2020] [Indexed: 06/12/2023]
Abstract
The waste leachate from the hydrometallurgical recycling of spent batteries contains a significant amount of undesirable iron that needs to be precipitated before the recovery of target metals. The produced Fe-sediments are usually disposed of or stored at the treatment site as waste and are often poorly managed. This work estimates the environmental stability and application potential of Fe-sediments produced from highly acidic hydrometallurgical leachate during the recycling of spent alkaline batteries. After pH neutralization of the leachate by Na2CO3, a primary Fe-sediment (PFS), mainly composed of highly unstable metal (i.e., Fe, Zn, and Mn) sulfates, was obtained. The subsequent rinsing of this unstable PFS sediment led to the production of a secondary Fe-sediment (SFS), which was composed of an amorphous-phased ferric iron sulfate hydrate - Fe16O16(SO4)3(OH)10·10H2O. The results of single extraction using chemical reagents and biological dissolution by iron-transforming bacteria confirmed that despite most of the ions in PFS were dissolvable, the processed SFS was environmentally safe. The sorption efficiency of SFS towards Pb(II) and As(V) (up to ~ 99% and 94%, respectively, with an initial concentration of 100 mg/L) was found to be promising, suggesting the high potential for economical reuse of SFS.
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Affiliation(s)
- Zhendong Yang
- Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Joanna Karczewska-Golec
- Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Michal Styczynski
- Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Tomasz Bajda
- AGH University of Science and Technology in Krakow, Faculty of Geology, Geophysics and Environmental Protection, al. A. Mickiewicza 30, 30-059 Krakow, Poland
| | - Lukasz Drewniak
- Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland.
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Suhadolnik MLS, Costa PS, Castro GM, Lobo FP, Nascimento AMA. Comprehensive insights into arsenic- and iron-redox genes, their taxonomy and associated environmental drivers deciphered by a meta-analysis. ENVIRONMENT INTERNATIONAL 2021; 146:106234. [PMID: 33181412 DOI: 10.1016/j.envint.2020.106234] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 09/23/2020] [Accepted: 10/20/2020] [Indexed: 06/11/2023]
Abstract
In nature, arsenic (As) and iron (Fe) biotransformation are interconnected, influencing local As mobility and toxicity. While As- or Fe-metabolizing microorganisms are widely documented, knowledge concerning their cycling genes, associated with geophysicochemical data and taxonomic distribution, remains scarce. We performed a meta-analysis to explore the distribution and environmental importance of As- and Fe-redox genes (AsRGs and FeRGs) and predict their significant correlations and hosts. The most abundant and ubiquitous AsRGs and FeRGs were arsC and ccoN, respectively. The ccoN gene had the highest frequency at pH ≥ 9.1, in which dissolved Fe(II) is scarce, possibly contributing to enhanced host survival. Fe(III) oxidation genes iro and ccoN appear to be associated with As(V) detoxification in mesophilic environments. No correlation was observed between Fe(III) reduction gene omcB and arsenate reductase genes. Cytochromes with putative roles in Fe-redox reactions were identified (including yceJ and fbcH) and were significantly correlated with As(V) reduction genes under diverse geophysicochemical conditions. The taxonomies of AsRGs and FeRGs-carrying contigs revealed great diversity, among which various, such as Chlamydea (arsC) and Firmicutes (omcB), were previously undescribed. Nearly all (98.9%) of the AsRGs and FeRGs were not carried by any plasmid sequences. This meta-analysis expands our understanding of the global environmental, taxonomic and functional microbiome involved in As- and Fe-redox transformations. Moreover, these findings should help guide studies on putative in vivo functional roles of cytochromes in Fe-redox pathways.
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Affiliation(s)
- Maria Luíza S Suhadolnik
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Brazil
| | - Patrícia S Costa
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Brazil
| | - Giovanni M Castro
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Brazil
| | - Francisco P Lobo
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Brazil
| | - Andréa M A Nascimento
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Brazil.
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Bujak K, Decewicz P, Kaminski J, Radlinska M. Identification, Characterization, and Genomic Analysis of Novel Serratia Temperate Phages from a Gold Mine. Int J Mol Sci 2020; 21:ijms21186709. [PMID: 32933193 PMCID: PMC7556043 DOI: 10.3390/ijms21186709] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 09/04/2020] [Accepted: 09/10/2020] [Indexed: 12/14/2022] Open
Abstract
Bacteria of the genus Serratia inhabit a variety of ecological niches like water, soil, and the bodies of animals, and have a wide range of lifestyles. Currently, the complete genome sequences of 25 Serratia phages are available in the NCBI database. All of them were isolated from nutrient-rich environments like sewage, with the use of clinical Serratia strains as hosts. In this study, we identified a novel Serratia myovirus named vB_SspM_BZS1. Both the phage and its host Serratia sp. OS31 were isolated from the same oligotrophic environment, namely, an abandoned gold mine (Zloty Stok, Poland). The BZS1 phage was thoroughly characterized here in terms of its genomics, morphology, and infection kinetics. We also demonstrated that Serratia sp. OS31 was lysogenized by mitomycin-inducible siphovirus vB_SspS_OS31. Comparative analyses revealed that vB_SspM_BZS1 and vB_SspS_OS31 were remote from the known Serratia phages. Moreover, vB_SspM_BZS1 was only distantly related to other viruses. However, we discovered similar prophage sequences in genomes of various bacteria here. Additionally, a protein-based similarity network showed a high diversity of Serratia phages in general, as they were scattered across nineteen different clusters. In summary, this work broadened our knowledge on the diverse relationships of Serratia phages.
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McDermott TR, Stolz JF, Oremland RS. Arsenic and the gastrointestinal tract microbiome. ENVIRONMENTAL MICROBIOLOGY REPORTS 2020; 12:136-159. [PMID: 31773890 DOI: 10.1111/1758-2229.12814] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 11/23/2019] [Accepted: 11/25/2019] [Indexed: 06/10/2023]
Abstract
Arsenic is a toxin, ranking first on the Agency for Toxic Substances and Disease Registry and the Environmental Protection Agency Priority List of Hazardous Substances. Chronic exposure increases the risk of a broad range of human illnesses, most notably cancer; however, there is significant variability in arsenic-induced disease among exposed individuals. Human genetics is a known component, but it alone cannot account for the large inter-individual variability in the presentation of arsenicosis symptoms. Each part of the gastrointestinal tract (GIT) may be considered as a unique environment with characteristic pH, oxygen concentration, and microbiome. Given the well-established arsenic redox transformation activities of microorganisms, it is reasonable to imagine how the GIT microbiome composition variability among individuals could play a significant role in determining the fate, mobility and toxicity of arsenic, whether inhaled or ingested. This is a relatively new field of research that would benefit from early dialogue aimed at summarizing what is known and identifying reasonable research targets and concepts. Herein, we strive to initiate this dialogue by reviewing known aspects of microbe-arsenic interactions and placing it in the context of potential for influencing host exposure and health risks. We finish by considering future experimental approaches that might be of value.
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Affiliation(s)
- Timothy R McDermott
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, 59717, USA
| | - John F Stolz
- Department of Biological Sciences and Center for Environmental Research and Education, Duquesne University, Pittsburgh, PA, USA
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