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Fatema K, Mahmud NU, Gupta DR, Siddiqui MN, Sakif TI, Sarker A, Sharpe AG, Islam T. Enhancing rice growth and yield with weed endophytic bacteria Alcaligenes faecalis and Metabacillus indicus under reduced chemical fertilization. PLoS One 2024; 19:e0296547. [PMID: 38753661 PMCID: PMC11098348 DOI: 10.1371/journal.pone.0296547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 03/22/2024] [Indexed: 05/18/2024] Open
Abstract
Endophytic bacteria, recognized as eco-friendly biofertilizers, have demonstrated the potential to enhance crop growth and yield. While the plant growth-promoting effects of endophytic bacteria have been extensively studied, the impact of weed endophytes remains less explored. In this study, we aimed to isolate endophytic bacteria from native weeds and assess their plant growth-promoting abilities in rice under varying chemical fertilization. The evaluation encompassed measurements of mineral phosphate and potash solubilization, as well as indole-3-acetic acid (IAA) production activity by the selected isolates. Two promising strains, tentatively identified as Alcaligenes faecalis (BTCP01) from Eleusine indica (Goose grass) and Metabacillus indicus (BTDR03) from Cynodon dactylon (Bermuda grass) based on 16S rRNA gene phylogeny, exhibited noteworthy phosphate and potassium solubilization activity, respectively. BTCP01 demonstrated superior phosphate solubilizing activity, while BTDR03 exhibited the highest potassium (K) solubilizing activity. Both isolates synthesized IAA in the presence of L-tryptophan, with the detection of nifH and ipdC genes in their genomes. Application of isolates BTCP01 and BTDR03 through root dipping and spraying at the flowering stage significantly enhanced the agronomic performance of rice variety CV. BRRI dhan29. Notably, combining both strains with 50% of recommended N, P, and K fertilizer doses led to a substantial increase in rice grain yields compared to control plants receiving 100% of recommended doses. Taken together, our results indicate that weed endophytic bacterial strains BTCP01 and BTDR03 hold promise as biofertilizers, potentially reducing the dependency on chemical fertilizers by up to 50%, thereby fostering sustainable rice production.
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Affiliation(s)
- Kaniz Fatema
- Institute of Biotechnology and Genetic Engineering (IBGE), Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| | - Nur Uddin Mahmud
- Institute of Biotechnology and Genetic Engineering (IBGE), Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| | - Dipali Rani Gupta
- Institute of Biotechnology and Genetic Engineering (IBGE), Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| | - Md. Nurealam Siddiqui
- Department of Biochemistry and Molecular Biology, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| | - Tahsin Islam Sakif
- Keck Graduate Institute, Claremont, California, United States of America
| | - Aniruddha Sarker
- Residual Chemical Assessment Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeollabuk-do, Republic of Korea
| | - Andrew G. Sharpe
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Tofazzal Islam
- Institute of Biotechnology and Genetic Engineering (IBGE), Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
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Sánchez-Arroyo A, Plaza-Vinuesa L, de Las Rivas B, Mancheño JM, Muñoz R. Structural and functional analysis of the key enzyme responsible for the degradation of ochratoxin A in the Alcaligenes genus. Int J Biol Macromol 2024; 267:131342. [PMID: 38574921 DOI: 10.1016/j.ijbiomac.2024.131342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 03/01/2024] [Accepted: 04/01/2024] [Indexed: 04/06/2024]
Abstract
The potential to degrade ochratoxin A (OTA), a highly poisonous mycotoxin, was investigated in cultures from Alcaligenes-type strains. Genome sequence analyses from different Alcaligenes species have permitted us to demonstrate a direct, causal link between the gene coding a known N-acyl-L-amino acid amidohydrolase from A. faecalis (AfOTH) and the OTA-degrading activity of this bacterium. In agreement with this finding, we found the gene coding AfOTH in two additional species included in the Alcaligenes genus, namely, A. pakistanensis, and A. aquatilis, which also degraded OTA. Notably, A. faecalis subsp. faecalis DSM 30030T was able to transform OTα, the product of OTA hydrolysis. AfOTH from A. faecalis subsp. phenolicus DSM 16503T was recombinantly over-produced and enzymatically characterized. AfOTH is a Zn2+-containing metalloenzyme that possesses structural features and conserved residues identified in the M20D family of enzymes. AfOTH is a tetramer in solution that shows both aminoacylase and carboxypeptidase activities. Using diverse potential substrates, namely, N-acetyl-L-amino acids and carbobenzyloxy-L-amino acids, a marked preference towards C-terminal Phe and Tyr residues could be deduced. The structural basis for this specificity has been determined by in silico molecular docking analyses. The amidase activity of AfOTH on C-terminal Phe residues structurally supports its OTA and OTB degradation activity.
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Affiliation(s)
- Ana Sánchez-Arroyo
- Bacterial Biotechnology Laboratory, Institute of Food Science, Technology and Nutrition (ICTAN), CSIC, José Antonio Novais 6, 28040 Madrid, Spain
| | - Laura Plaza-Vinuesa
- Bacterial Biotechnology Laboratory, Institute of Food Science, Technology and Nutrition (ICTAN), CSIC, José Antonio Novais 6, 28040 Madrid, Spain
| | - Blanca de Las Rivas
- Bacterial Biotechnology Laboratory, Institute of Food Science, Technology and Nutrition (ICTAN), CSIC, José Antonio Novais 6, 28040 Madrid, Spain
| | - José Miguel Mancheño
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry Blas Cabrera (IQF), CSIC, Serrano 119, 28006 Madrid, Spain.
| | - Rosario Muñoz
- Bacterial Biotechnology Laboratory, Institute of Food Science, Technology and Nutrition (ICTAN), CSIC, José Antonio Novais 6, 28040 Madrid, Spain.
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Pedrosa-Silva F, Venancio TM. Comparative Genomics Reveals Novel Species and Insights into the Biotechnological Potential, Virulence, and Resistance of Alcaligenes. Genes (Basel) 2023; 14:1783. [PMID: 37761923 PMCID: PMC10530903 DOI: 10.3390/genes14091783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 09/06/2023] [Accepted: 09/08/2023] [Indexed: 09/29/2023] Open
Abstract
Alcaligenes is a cosmopolitan bacterial genus that exhibits diverse properties which are beneficial to plants. However, the genomic versatility of Alcaligenes has also been associated with the ability to cause opportunistic infections in humans, raising concerns about the safety of these microorganisms in biotechnological applications. Here, we report an in-depth comparative analysis of Alcaligenes species using all publicly available genomes to investigate genes associated with species, biotechnological potential, virulence, and resistance to multiple antibiotics. Phylogenomic analysis revealed that Alcaligenes consists of at least seven species, including three novel species. Pan-GWAS analysis uncovered 389 species-associated genes, including cold shock proteins (e.g., cspA) and aquaporins (e.g., aqpZ) found exclusively in the water-isolated species, Alcaligenes aquatilis. Functional annotation of plant-growth-promoting traits revealed enrichment of genes for auxin biosynthesis, siderophores, and organic acids. Genes involved in xenobiotic degradation and toxic metal tolerance were also identified. Virulome and resistome profiles provide insights into selective pressures exerted in clinical settings. Taken together, the results presented here provide the grounds for more detailed clinical and ecological studies of the genus Alcaligenes.
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Affiliation(s)
| | - Thiago M. Venancio
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes 28013-602, Brazil;
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Acinetobacter nematophilus sp. nov., Alcaligenes nematophilus sp. nov., Enterobacter nematophilus sp. nov., and Kaistia nematophila sp. nov., Isolated from Soil-Borne Nematodes and Proposal for the Elevation of Alcaligenes faecalis subsp. faecalis, Alcaligenes faecalis subsp. parafaecalis, and Alcaligenes faecalis subsp. phenolicus to the Species Level. TAXONOMY 2023. [DOI: 10.3390/taxonomy3010012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
Four bacterial strains, A-IN1T, A-TC2T, E-TC7T, and K-TC2T, isolated from soil-borne nematodes of the species Oscheius tipulae and Acrobeloides bodenheimeri, were found to represent new species of the genera Acinetobacter, Alcaligenes, Enterobacter, and Kaistia, respectively. In this study, we described these new species using a polyphasic taxonomic approach that included whole-genome and whole-proteome phylogenomic reconstructions, core genome sequence comparisons, and phenotypic characterization. Phylogenomic reconstructions using whole-genome and whole-proteome sequences show that A-IN1T is closely related to Acinetobacter guillouiae DSM 590T and to Acinetobacter bereziniae LMG 1003T. The dDDH values between A-IN1T and these latest strains are 25.1 and 39.6%, respectively, which are below the 70% divergence threshold for prokaryotic species delineation. A-TC2T is closely related to Alcaligenes faecalis subsp. faecalis DSM 30030T and to Alcaligenes faecalis subsp. phenolicus DSM 16503T. The dDDH values between A-TC2T and these latest strains are 47.0 and 66.3%, respectively. In addition, the dDDH values between Alcaligenes faecalis subsp. faecalis DSM 30030T, Alcaligenes faecalis subsp. phenolicus DSM 16503T, and Alcaligenes faecalis subsp. parafaecalis are always lower than 70%, demonstrating that the three strains represent species within the genus Alcaligenes rather than subspecies within Alcaligenes faecalis. E-TC7T is closely related to Enterobacter kobei DSM 13645T, Enterobacter chuandaensis 090028T, and to Enterobacter bugandensis STN0717-56T. The dDDH values between E-TC7T and these strains are 43.5, 42.9, and 63.7%, respectively. K-TC2T is closely related to Kaistia terrae DSM 21341T and to Kaistia defluvii JCM 18034T. The dDDH values between these strains are 29.2 and 30.7%, respectively. Several biochemical tests allow to differentiate the type strains of the newly described species from the type strains of their more closely related species. Based on the results of this polyphasic taxonomic approach, the following new species are proposed: Acinetobacter nematophilus sp. nov. with A-IN1T (=CCM 9231T =CCOS 2018T) as the type strain, Alcaligenes nematophilus sp. nov. with A-TC2T (=CCM 9230T =CCOS 2017T) as the type strain, Enterobacter nematophilus sp. nov. with E-TC7T (=CCM 9232T =CCOS 2020T) as the type strain, and Kaistia nematophila sp. nov. with K-TC2T (=CCM 9239T =CCOS 2022T) as the type strain. In addition, we propose the elevation of Alcaligenes faecalis subsp. faecalis, Alcaligenes faecalis subsp. parafaecalis, and Alcaligenes faecalis subsp. phenolicus to the species level. Therefore, we propose the creation of Alcaligenes parafaecalis sp. nov. with DSM 13975T as the type strain, and Alcaligenes phenolicus sp. nov. with DSM 16503T as the type strain. Our study contributes to a better understanding of the biodiversity and phylogenetic relationships of bacteria associated with soil-borne nematodes.
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Belahmadi MSO, Charchar N, Abdessemed A, Gherib A. Impact of petroleum refinery on aquatic ecosystem of Skikda Bay (Algeria): Diversity and abundance of viable bacterial strains. MARINE POLLUTION BULLETIN 2023; 188:114704. [PMID: 36860027 DOI: 10.1016/j.marpolbul.2023.114704] [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: 11/14/2022] [Revised: 01/30/2023] [Accepted: 02/01/2023] [Indexed: 06/18/2023]
Abstract
This paper reports a study on the impact of petroleum refinery effluents on the bacterial load and diversity of the aquatic ecosystem in Skikda Bay (Algeria). The results showed a large spatiotemporal variation in the isolated bacterial species. This difference between stations and seasons could be attributed to environmental factors and to the pollution rate at the different sampling sites. Statistical analysis results showed that physicochemical parameters such as pH, electrical conductivity and salinity have a very significant effect on the microbial load (p < 0.001), while hydrocarbon pollution has a significant effect on the diversity of bacterial species (p < 0.05). In total 75 bacteria were isolated from six sampling sites during the four seasons. A significant spatiotemporal richness and diversity was observed in water samples. A total of 42 strains belonging to 18 bacterial genera were identified. Most of these genera belong to the class of Proteobacteria.
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Affiliation(s)
| | - Nabil Charchar
- Biotechnology Research Centre, BPE 73, Ali Mendjeli, Nouvelle Ville, 25000 Constantine, Algeria
| | - Ala Abdessemed
- Biotechnology Research Centre, BPE 73, Ali Mendjeli, Nouvelle Ville, 25000 Constantine, Algeria
| | - Abdelfettah Gherib
- Biotechnology Research Centre, BPE 73, Ali Mendjeli, Nouvelle Ville, 25000 Constantine, Algeria
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Complete Genome Sequence of a Sulfur-Oxidizing Bacterium, Alcaligenes faecalis Strain NLF5-7, Isolated from Livestock Wastewater. Microbiol Resour Announc 2023; 12:e0099922. [PMID: 36598248 PMCID: PMC9872586 DOI: 10.1128/mra.00999-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The complete genome sequence of Alcaligenes faecalis strain NLF5-7, which was isolated from livestock wastewater, is reported. The genome of strain NLF5-7 contains genes for assimilatory sulfate reduction, dissimilatory sulfate reduction and oxidation, and an SOX system, based on its functional genetic characteristics.
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PicR as a MarR Family Transcriptional Repressor Multiply Controls the Transcription of Picolinic Acid Degradation Gene Cluster pic in Alcaligenes faecalis JQ135. Appl Environ Microbiol 2022; 88:e0017222. [PMID: 35604228 DOI: 10.1128/aem.00172-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Picolinic acid (PA) is a natural toxic pyridine derivative as well as an important intermediate used in the chemical industry. In a previous study, we identified a gene cluster, pic, that responsible for the catabolism of PA in Alcaligenes faecalis JQ135. However, the transcriptional regulation of the pic cluster remains known. This study showed that the entire pic cluster was composed of 17 genes and transcribed as four operons: picR, picCDEF, picB4B3B2B1, and picT1A1A2A3T2T3MN. Deletion of picR, encoding a putative MarR-type regulator, greatly shortened the lag phase of PA degradation. An electrophoretic mobility shift assay and DNase I footprinting showed that PicR has one binding site in the picR-picC intergenic region and two binding sites in the picB-picT1 intergenic region. The DNA sequences of the three binding sites have the palindromic characteristics of TCAG-N4-CTNN: the space consists of four nonspecific bases, and the four palindromic bases on the left and the first two palindromic bases on the right are strictly conserved, while the last two bases on the right vary among the three binding sites. An in vivo β-galactosidase activity reporter assay indicated that 6-hydroxypicolinic acid but not PA acted as a ligand of PicR, preventing PicR from binding to promoter regions and thus derepressing the transcription of the pic cluster. This study revealed the negative transcriptional regulation mechanism of PA degradation by PicR in A. faecalis JQ135 and provides new insights into the structure and function of the MarR-type regulator. IMPORTANCE The pic gene cluster was found to be responsible for PA degradation and widely distributed in Alpha-, Beta-, and Gammaproteobacteria. Thus, it is very necessary to understand the regulation mechanism of the pic cluster in these strains. This study revealed that PicR binds to three sites of the promoter regions of the pic cluster to multiply regulate the transcription of the pic cluster, which enables A. faecalis JQ135 to efficiently utilize PA. Furthermore, the study also found a unique palindrome sequence for binding of the MarR-type regulator. This study enhanced our understanding of microbial catabolism of environmental toxic pyridine derivatives.
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Hou TT, Miao LL, Peng JS, Ma L, Huang Q, Liu Y, Wu MR, Ai GM, Liu SJ, Liu ZP. Dirammox Is Widely Distributed and Dependently Evolved in Alcaligenes and Is Important to Nitrogen Cycle. Front Microbiol 2022; 13:864053. [PMID: 35633697 PMCID: PMC9136411 DOI: 10.3389/fmicb.2022.864053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 04/19/2022] [Indexed: 11/13/2022] Open
Abstract
Nitrogen cycle is an essential process for environmental health. Dirammox (direct ammonia oxidation), encoded by the dnfT1RT2ABCD cluster, was a novel pathway for microbial N2 production defined in Alcaligenes ammonioxydans HO-1. Here, a copy of the cluster dnfT1RT2ABCD as a whole was proved to have existed and very conserved in all Alcaligenes genomes. Phylogenetic analyses based on 16S rRNA gene sequences and amino acid sequences of DnfAs, together with G + C content data, revealed that dnf cluster was evolved associated with the members of the genus Alcaligenes. Under 20% O2 conditions, 14 of 16 Alcaligenes strains showed Dirammox activity, which seemed likely taxon-related. However, the in vitro activities of DnfAs catalyzing the direct oxidation of hydroxylamine to N2 were not taxon-related but depended on the contents of Fe and Mn ions. The results indicated that DnfA is necessary but not sufficient for Dirammox activity. The fact that members of the genus Alcaligenes are widely distributed in various environments, including soil, water bodies (both freshwater and seawater), sediments, activated sludge, and animal–plant-associated environments, strongly suggests that Dirammox is important to the nitrogen cycle. In addition, Alcaligenes species are also commonly found in wastewater treatment plants, suggesting that they might be valuable resources for wastewater treatment.
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Affiliation(s)
- Ting-Ting Hou
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Li-Li Miao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Ji-Sen Peng
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Lan Ma
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Qiang Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Ying Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Meng-Ru Wu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Guo-Min Ai
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Zhi-Pei Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- *Correspondence: Zhi-Pei Liu,
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Rashid A, Mirza SA, Keating C, Ali S, Campos LC. Indigenous Bacillus paramycoides spp. and Alcaligenes faecalis: sustainable solution for bioremediation of hospital wastewater. ENVIRONMENTAL TECHNOLOGY 2022; 43:1903-1916. [PMID: 33342352 DOI: 10.1080/09593330.2020.1858180] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 11/23/2020] [Indexed: 06/12/2023]
Abstract
Farmers near towns and cities are using a wide range of highly polluted wastewaters for crop irrigation in Pakistan due to severe freshwater shortage. The present study aimed to promote indigenous bacterial strains isolated from domestic, hospital, textile, pharmaceutical and mixed wastewaters to remove contaminants and colour and render these wastewaters safer for irrigation. Thirty seven bacterial strains were isolated from five wastewater samples collected from different sites in Lahore, Pakistan. Under optimal growth conditions, three isolates (D6, D7 and P1) showed >93% decolourisation potential in the treatment of hospital wastewater. 16S rDNA sequencing identified two of these isolates (D6 and D7) as showing 100% and 99.86% homology to Bacillus paramycoides spp. - novel strains from B. cereus group. Isolate P1 showed 97.47% homology to Alcaligenes faecalis. GCMS analysis of the untreated hospital wastewater revealed the presence of pharmaceutic pollutants, i.e. Phenol (876 µg/L), Salicylic acid (48 µg/L), Caffeine (7 µg/L), Naproxen (23 µg/L), Octadecene (185 µg/L) and Diazepam (14 µg/L). The analysis of treated hospital wastewaters showed percentage degradation of pharmaceutic pollutants (100%-43%) and significant reduction in the BOD5 (91%-68%), COD (89%-52%) and heavy metals concentrations. These strains therefore can represent a low-cost and low-tech alternative to bioremediate complex matrices of hospital wastewater prior to crop irrigation to support the achievement of clean re-usable water in developing countries like Pakistan.
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Affiliation(s)
- Aneeba Rashid
- Department of Botany, GC University Lahore, Lahore, Pakistan
- Department of Civil, Environmental and Geomatic Engineering, University College London, London, UK
| | - Safdar A Mirza
- Department of Botany, GC University Lahore, Lahore, Pakistan
| | - Ciara Keating
- Division of Infrastructure and Environment, James Watt School of Engineering, University of Glasgow, Glasgow, UK
| | - Sikander Ali
- Institute of Industrial Biotechnology (IIB), GC University Lahore, Lahore, Pakistan
| | - Luiza C Campos
- Department of Civil, Environmental and Geomatic Engineering, University College London, London, UK
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Zhao L, Jiang Y, Zhao Z, Wang K, Zhang X, Hong Q, Qiu J, He J. Biodegradation of Quinolinic acid by a Newly Isolated Bacterium Alcaligenes faecalis Strain JQ191. FEMS Microbiol Lett 2022; 369:6567840. [PMID: 35416242 DOI: 10.1093/femsle/fnac040] [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: 12/14/2021] [Revised: 02/23/2022] [Accepted: 04/11/2022] [Indexed: 11/13/2022] Open
Abstract
Quinolinic acid (QA) is a pyridine derivative that can be found in many organisms and is widely used in the chemical industry. However, QA possesses excitotoxic properties. To date, the catabolism of QA mediated by microorganisms has rarely been reported. In this study, a QA-degrading strain (JQ191) was isolated from sewage sludge. Based on phenotypic and 16S rRNA gene phylogenetic analysis, the strain was identified as Alcaligenes faecalis. Strain JQ191 was able to utilize QA as the sole source of carbon and nitrogen for growth. QA-cultured cells of JQ191 completely degrade 200 mg/L QA within 2 days in a mineral salt medium, whereas the LB-cultured cells experienced a 2-day lag period before degrading QA, indicating that the catabolic enzymes involved in QA degradation were induced by QA. 6-Hydroxypicolinic acid (6HPA) was identified as an intermediate of QA degradation by strain JQ191. A 6HPA monooxygenase gene picB was cloned, genetically disrupted, and heterologously expressed, and the results show that picB was responsible for catalyzing 6HPA to 3,6DHPA in JQ191. A new QA mineralization pathway was proposed. This study identifies a new bacterium candidate that has a potential application prospect in the bioremediation of QA-polluted environment, as well as provides new insights into the bacterial catabolism of QA.
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Affiliation(s)
- Lingling Zhao
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yinhu Jiang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhenyang Zhao
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Kexin Wang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xuan Zhang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qing Hong
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jiguo Qiu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jian He
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
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Genome Characterisation of an Isoprene-Degrading Alcaligenes sp. Isolated from a Tropical Restored Forest. BIOLOGY 2022; 11:biology11040519. [PMID: 35453719 PMCID: PMC9030188 DOI: 10.3390/biology11040519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 03/17/2022] [Accepted: 03/24/2022] [Indexed: 11/21/2022]
Abstract
Isoprene is a climate-active biogenic volatile organic compound (BVOC), emitted into the atmosphere in abundance, mainly from terrestrial plants. Soil is an important sink for isoprene due to its consumption by microbes. In this study, we report the ability of a soil bacterium to degrade isoprene. Strain 13f was isolated from soil beneath wild Himalayan cherry trees in a tropical restored forest. Based on phylogenomic analysis and an Average Nucleotide Identity score of >95%, it most probably belongs to the species Alcaligenes faecalis. Isoprene degradation by Alcaligenes sp. strain 13f was measured by using gas chromatography. When isoprene was supplied as the sole carbon and energy source at the concentration of 7.2 × 105 ppbv and 7.2 × 106 ppbv, 32.6% and 19.6% of isoprene was consumed after 18 days, respectively. Genome analysis of Alcaligenes sp. strain 13f revealed that the genes that are typically found as part of the isoprene monooxygenase gene cluster in other isoprene-degrading bacteria were absent. This discovery suggests that there may be alternative pathways for isoprene metabolism.
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S S SM, Vijayan DS, Anand M, Ajona M, Jarin T. Biodegradation of P-nitro phenol using a novel bacterium Achromobacter denitrifacians isolated from industrial effluent water. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2021; 84:3334-3345. [PMID: 34850731 DOI: 10.2166/wst.2021.354] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
In the present investigation, Achromobacter denitrifacians was isolated from industrial wastewater and used in the degradation of para nitro-phenol. Experiments were made as a function of different carbon sources, organic and inorganic nitrogen sources and metal ions to analyse the removal efficiency of para nitro-phenol present in the industrial wastewater sources. Observations revealed that the rate of phenol biodegradation was significantly affected by pH, temperature of incubation, glucose, peptone and metal ion concentration. The optimal conditions for phenol removal were found to be pH of 7.5, temperature, 35 °C and 0.25 gL-1 supplemented glucose level, 0.25 gL-1 supplemented peptone level, and 0.01 gL-1 zinc ion. The key importance of the present study is the utilization of a native bacterial strain isolated from the industrial effluent water itself having an impending role in the bioremediation process of phenol.
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Affiliation(s)
- Sreeja Mole S S
- Christu Jyothi Institute of Technology and Science, Janagon 506167, India
| | - D S Vijayan
- Aarupadai Veedu Institute of Technology, VMRF, Chennai 603104, India
| | - M Anand
- Kingston Engineering College, Vellore 632059, India E-mail:
| | - M Ajona
- Tagore Engineering College, Chennai 600127, India
| | - T Jarin
- Jyothi Engineering College, Thrissur 679531, India
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13
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van der Loo C, Bartie C, Barnard TG, Potgieter N. Detection of Free-Living Amoebae and Their Intracellular Bacteria in Borehole Water before and after a Ceramic Pot Filter Point-of-Use Intervention in Rural Communities in South Africa. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:3912. [PMID: 33917870 PMCID: PMC8068299 DOI: 10.3390/ijerph18083912] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/26/2021] [Accepted: 04/02/2021] [Indexed: 11/21/2022]
Abstract
Free-living amoebae (FLA) are ubiquitous in nature, whereas amoeba-resistant bacteria (ARB) have evolved virulent mechanisms that allow them to resist FLA digestion mechanisms and survive inside the amoeba during hostile environmental conditions. This study assessed the prevalence of FLA and ARB species in borehole water before and after a ceramic point-of-use intervention in rural households. A total of 529 water samples were collected over a five-month period from 82 households. All water samples were subjected to amoebal enrichment, bacterial isolation on selective media, and molecular identification using 16S PCR/sequencing to determine ARB species and 18S rRNA PCR/sequencing to determine FLA species present in the water samples before and after the ceramic pot intervention. Several FLA species including Acanthamoeba spp. and Mycobacterium spp. were isolated. The ceramic pot filter removed many of these microorganisms from the borehole water. However, design flaws could have been responsible for some FLA and ARB detected in the filtered water. FLA and their associated ARB are ubiquitous in borehole water, and some of these species might be potentially harmful and a health risk to vulnerable individuals. There is a need to do more investigations into the health risk of these organisms after point-of-use treatment.
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Affiliation(s)
- Clarissa van der Loo
- Water and Health Research Centre, Faculty of Health Sciences, University of Johannesburg, Johannesburg 2094, South Africa; (C.v.d.L.); (T.G.B.)
| | | | - Tobias George Barnard
- Water and Health Research Centre, Faculty of Health Sciences, University of Johannesburg, Johannesburg 2094, South Africa; (C.v.d.L.); (T.G.B.)
| | - Natasha Potgieter
- Environmental Health, Domestic Hygiene and Microbial Pathogens Research Group, Department of Microbiology, University of Venda, Thohoyandou 1950, South Africa
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14
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Crettaz-Minaglia M, Fallico M, Aranda O, Juarez I, Pezzoni M, Costa C, Andrinolo D, Giannuzzi L. Effect of temperature on microcystin-LR removal and lysis activity on Microcystis aeruginosa (cyanobacteria) by an indigenous bacterium belonging to the genus Achromobacter. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:44427-44439. [PMID: 32767213 DOI: 10.1007/s11356-020-09901-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 06/26/2020] [Indexed: 06/11/2023]
Abstract
Microcystis is a frequent cyanobacterium bloom-forming with cosmopolitan distribution which can produce a hepatotoxin group called microcystins (MCs). These MCs are resistant to the traditional processes employed in the water treatment plants and they are often detected after conventional treatments. Because of this, the bio-removal studies have obtained a great interest in the last decades. In this work, a bacterial strain namely LG1 with the ability to remove microcystin-LR (MC-LR) under laboratory conditions was isolated from Rio de la Plata River and it was identified as Achromobacter spp. This ubiquitous bacterium was able to remove 79.5% MC-LR in 7 days with average removal time of 3.33 ± 0.08, 3.06 ± 0.05, and 2.77 ± 0.05 days at 28, 32, and 36 ± 1 °C, being higher at high temperature (36 °C) with an activation energy = 16.79 ± 1.99 kJ mol-1. LG1 grew better at higher temperature (from 28 to 36 ± 1 °C) increasing the specific growth rate (μ) and reducing 2-fold the lag phase duration (LPD) without significant differences (p > 0.05) between maximum population density (MPD). In addition, LG1 showed a lysis activity on two M. aeruginosa native strains in 7 days measured as chlorophyll a (Chl-a) concentration. The lysis activity increased around 2-fold when increasing the temperature from 28 to 36 ± 1 °C. This is the first report of an indigenous bacterium belonging to the genus Achromobacter spp. isolated from the Rio de la Plata River with the capacity to remove MC-LR and lysis activity on M. aeruginosa.
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Affiliation(s)
- Melina Crettaz-Minaglia
- Laboratorio de Toxicología General, Facultad de Ciencias Exactas, UNLP, La Plata, Argentina.
- CONICET, Buenos Aires, Argentina.
| | - Maximiliano Fallico
- Laboratorio de Toxicología General, Facultad de Ciencias Exactas, UNLP, La Plata, Argentina
| | - Oswaldo Aranda
- Laboratorio de Toxicología General, Facultad de Ciencias Exactas, UNLP, La Plata, Argentina
| | - Ivan Juarez
- CONICET, Buenos Aires, Argentina
- Centro de Investigaciones y Desarrollo en Criotecnología de Alimentos, UNLP-CONICET, La Plata, Argentina
| | - Magdalena Pezzoni
- Departamento de Radiobiología, Comisión Nacional de Energía Atómica, Buenos Aires, Argentina
| | - Cristina Costa
- Departamento de Radiobiología, Comisión Nacional de Energía Atómica, Buenos Aires, Argentina
| | - Dario Andrinolo
- Laboratorio de Toxicología General, Facultad de Ciencias Exactas, UNLP, La Plata, Argentina
- CONICET, Buenos Aires, Argentina
| | - Leda Giannuzzi
- CONICET, Buenos Aires, Argentina
- Centro de Investigaciones y Desarrollo en Criotecnología de Alimentos, UNLP-CONICET, La Plata, Argentina
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15
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Candan O, Candan ED. Bacterial diversity of the green turtle (Chelonia mydas) nest environment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 720:137717. [PMID: 32325608 DOI: 10.1016/j.scitotenv.2020.137717] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 01/12/2020] [Accepted: 03/02/2020] [Indexed: 06/11/2023]
Abstract
The green turtle is an endangered species that is highly sensitive to environmental pollution that can adversely affect the healthy development of eggs. Moreover, the presence of some bacteria in nests can be regarded as an indicator of the pollution level in nesting areas. In our study, nest sand and egg contents were collected from Sugözü Beaches (Turkey), in the Mediterranean. Phenotypic and genotypic identification of bacteria were carried out by using conventional phenotypic methods, 16S rRNA gene sequencing respectively. The extended-spectrum beta-lactamase presence and carbapenem resistance of bacteria isolated from egg contents were determined. This is the first report of carbapenem resistance in the eggs. All strains were evaluated in three different categories including growth promoters in agriculture and aquaculture, pathogens that are found in human and animal, and biomonitoring aquatic pollution. According to our analysis, 67 bacterial species were identified from samples. This study is the first record of Alcaligenes, Zobellella, Lysinibacillus, Sphingobacterium, Achromobacter, Acinetobacter, Alcanivorax, Ochrobactrum, Microbacterium, Rhodococcus, and Stenotrophomonas isolated from sea turtles. Pathogens detected in the bacterial flora can threaten both sea turtles and field workers. These data can contribute to the development of new conservation strategies on the treatment of sea turtles, nest protection, and pollution detection on nesting beaches.
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Affiliation(s)
- Onur Candan
- Ordu University, Faculty of Arts and Sciences, Department of Molecular Biology and Genetics, 52200 Ordu, Turkey.
| | - Esra Deniz Candan
- Giresun University, Vocational School of Health Services, Department of Medical Services and Techniques, 28100 Giresun, Turkey
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16
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Mahjoubi M, Aliyu H, Cappello S, Naifer M, Souissi Y, Cowan DA, Cherif A. The genome of Alcaligenes aquatilis strain BU33N: Insights into hydrocarbon degradation capacity. PLoS One 2019; 14:e0221574. [PMID: 31550268 PMCID: PMC6759156 DOI: 10.1371/journal.pone.0221574] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Accepted: 08/10/2019] [Indexed: 01/12/2023] Open
Abstract
Environmental contamination with hydrocarbons though natural and anthropogenic activities is a serious threat to biodiversity and human health. Microbial bioremediation is considered as the effective means of treating such contamination. This study describes a biosurfactant producing bacterium capable of utilizing crude oil and various hydrocarbons as the sole carbon source. Strain BU33N was isolated from hydrocarbon polluted sediments from the Bizerte coast (northern Tunisia) and was identified as Alcaligenes aquatilis on the basis of 16S rRNA gene sequence analysis. When grown on crude oil and phenanthrene as sole carbon and energy sources, isolate BU33N was able to degrade ~86%, ~56% and 70% of TERHc, n-alkanes and phenanthrene, respectively. The draft genome sequence of the A. aquatilis strain BU33N was assembled into one scaffold of 3,838,299 bp (G+C content of 56.1%). Annotation of the BU33N genome resulted in 3,506 protein-coding genes and 56 rRNA genes. A large repertoire of genes related to the metabolism of aromatic compounds including genes encoding enzymes involved in the complete degradation of benzoate were identified. Also genes associated with resistance to heavy metals such as copper tolerance and cobalt-zinc-cadmium resistance were identified in BU33N. This work provides insight into the genomic basis of biodegradation capabilities and bioremediation/detoxification potential of A. aquatilis BU33N.
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Affiliation(s)
- Mouna Mahjoubi
- Univ. Manouba, ISBST, BVBGR-LR11ES31, Biotechpole SidiThabet, Ariana, Tunisia
| | - Habibu Aliyu
- Institute of Process Engineering in Life Science 2: Technical Biology, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Simone Cappello
- Istituto per l’Ambiente Marino Costiero (IAMC)-CNR of Messina. Sp. San Raineri, Messina, Italy
| | - Mohamed Naifer
- Univ. Manouba, ISBST, BVBGR-LR11ES31, Biotechpole SidiThabet, Ariana, Tunisia
| | - Yasmine Souissi
- Univ. Manouba, ISBST, BVBGR-LR11ES31, Biotechpole SidiThabet, Ariana, Tunisia
| | - Don A. Cowan
- Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
| | - Ameur Cherif
- Univ. Manouba, ISBST, BVBGR-LR11ES31, Biotechpole SidiThabet, Ariana, Tunisia
- * E-mail:
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17
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Juárez-Jiménez B, Pesciaroli C, Maza-Márquez P, López-Martínez S, Vílchez-Quero JL, Zafra-Gómez A. Biodegradation of methyl and butylparaben by bacterial strains isolated from amended and non-amended agricultural soil. Identification, behavior and enzyme activities of microorganisms. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2019; 245:245-254. [PMID: 31154171 DOI: 10.1016/j.jenvman.2019.05.122] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 05/17/2019] [Accepted: 05/26/2019] [Indexed: 06/09/2023]
Abstract
The aim of the present study was to investigate the kinetics of methylparaben (MPB) and butylparaben (BPB) removal, two emerging pollutants with possible endocrine disrupting effects, from agricultural soil with and without amendment with compost from sewage sludge used as biostimulant. Compound removal is explained by a first-order kinetic model with half-life times of 6.5/6.7 days and 11.4/8.2 days, in presence/absence of compost, for MPB and BPB respectively. % R2 for the fitted model were higher than 96% in all cases. Additionally, isolation of bacteria capable to grow using MPB or BPB as carbon source was also carry out. Laboratory tests demonstrated the ability of these bacteria to biodegrade MPB and BPB from culture media in more than 95% in some cases. These strains showed high ability to biodegrade the compounds. Ten isolates, most of them related to Gram positive bacteria of the genus Bacillus, were identified by 16S rRNA gene sequencing. The study of the enzymatic activities of the isolates revealed both esterase (C4) and esterase-lipase activities.
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Affiliation(s)
- Belén Juárez-Jiménez
- Research Group of Environmental Microbiology, Department of Microbiology, Faculty of Pharmacy, Campus of Cartuja, And Water Institute, C/ Ramon y Cajal s/n, University of Granada, E-18071, Granada, Spain.
| | - Chiara Pesciaroli
- Department of Biotechnology and Bioscience, University of Milan Bicocca, Italy
| | - Paula Maza-Márquez
- Research Group of Environmental Microbiology, Department of Microbiology, Faculty of Pharmacy, Campus of Cartuja, And Water Institute, C/ Ramon y Cajal s/n, University of Granada, E-18071, Granada, Spain
| | - Sergio López-Martínez
- Research Group of Analytical Chemistry and Life Sciences, Department of Analytical Chemistry, University of Granada, Campus of Fuentenueva, E-18071, Granada, Spain
| | - José Luís Vílchez-Quero
- Research Group of Analytical Chemistry and Life Sciences, Department of Analytical Chemistry, University of Granada, Campus of Fuentenueva, E-18071, Granada, Spain
| | - Alberto Zafra-Gómez
- Research Group of Analytical Chemistry and Life Sciences, Department of Analytical Chemistry, University of Granada, Campus of Fuentenueva, E-18071, Granada, Spain.
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18
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Durán RE, Méndez V, Rodríguez-Castro L, Barra-Sanhueza B, Salvà-Serra F, Moore ERB, Castro-Nallar E, Seeger M. Genomic and Physiological Traits of the Marine Bacterium Alcaligenes aquatilis QD168 Isolated From Quintero Bay, Central Chile, Reveal a Robust Adaptive Response to Environmental Stressors. Front Microbiol 2019; 10:528. [PMID: 31024465 PMCID: PMC6460240 DOI: 10.3389/fmicb.2019.00528] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Accepted: 03/01/2019] [Indexed: 12/16/2022] Open
Abstract
Alcaligenes aquatilis QD168 is a marine, aromatic hydrocarbon-degrading bacterium, isolated from an oil-polluted sediment of Quintero Bay, an industrial-coastal zone that has been chronically impacted by diverse pollutants. The aims of this study were to characterize the phylogenomic positions of Alcaligenes spp. and to characterize the genetic determinants and the physiological response of A. aquatilis QD168 to model environmental stressors (benzene, oxidizing agents, and salt). Phylogenomic analyses, using 35 housekeeping genes, clustered A. aquatilis QD168 with four other strains of Alcaligenes spp. (A. aquatilis BU33N, A. faecalis JQ135, A. faecalis UBA3227, and A. faecalis UBA7629). Genomic sequence analyses of A. aquatilis QD168 with 25 Alcaligenes spp., using ANIb, indicated that A. aquatilis BU33N is the closest related strain, with 96.8% ANIb similarity. Strain QD168 harbors 95 genes encoding proteins of seven central catabolic pathways, as well as sixteen peripheral catabolic pathways/reactions for aromatic compounds. A. aquatilis QD168 was able to grow on 3-hydroxybenzoate, 4-hydroxybenzoate, benzoate, benzene, 3-hydroxycinnamate, cinnamate, anthranilate, benzamide, 4-aminobenzoate, nicotinate, toluene, biphenyl and tryptophan, as sole carbon or nitrogen source. Benzene degradation was further analyzed by growth, metabolite identification and gene expression analyses. Benzene strongly induced the expression of the genes encoding phenol hydroxylase (dmpP) and catechol 1,2-dioxygenase (catA). Additionally, 30 genes encoding transcriptional regulators, scavenging enzymes, oxidative damage repair systems and isozymes involved in oxidative stress response were identified. Oxidative stress response of strain QD168 to hydrogen peroxide and paraquat was characterized, demonstrating that A. aquatilis QD168 is notably more resistant to paraquat than to H2O2. Genetic determinants (47 genes) for osmoprotective responses were identified, correlating with observed high halotolerance by strain QD168. The physiological adaptation of A. aquatilis QD168 to environmental stressors such as pollutants, oxidative stress and salinity may be exploited for bioremediation of oil-polluted saline sites.
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Affiliation(s)
- Roberto E Durán
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química - Centro de Biotecnología, Universidad Técnica Federico Santa María, Valparaíso, Chile
| | - Valentina Méndez
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química - Centro de Biotecnología, Universidad Técnica Federico Santa María, Valparaíso, Chile
| | - Laura Rodríguez-Castro
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química - Centro de Biotecnología, Universidad Técnica Federico Santa María, Valparaíso, Chile
| | - Bárbara Barra-Sanhueza
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química - Centro de Biotecnología, Universidad Técnica Federico Santa María, Valparaíso, Chile
| | - Francisco Salvà-Serra
- Department of Infectious Diseases, Institute for Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Culture Collection University of Gothenburg, Sahlgrenska University Hospital, Gothenburg, Sweden.,Centre for Antibiotic Resistance Research, University of Gothenburg, Gothenburg, Sweden.,Microbiology, Department of Biology, University of the Balearic Islands, Palma de Mallorca, Spain
| | - Edward R B Moore
- Department of Infectious Diseases, Institute for Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Culture Collection University of Gothenburg, Sahlgrenska University Hospital, Gothenburg, Sweden.,Centre for Antibiotic Resistance Research, University of Gothenburg, Gothenburg, Sweden
| | - Eduardo Castro-Nallar
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Michael Seeger
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química - Centro de Biotecnología, Universidad Técnica Federico Santa María, Valparaíso, Chile
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19
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Mohd-Nor D, Ramli N, Sharuddin SS, Hassan MA, Mustapha NA, Ariffin H, Sakai K, Tashiro Y, Shirai Y, Maeda T. Dynamics of Microbial Populations Responsible for Biodegradation during the Full-Scale Treatment of Palm Oil Mill Effluent. Microbes Environ 2019; 34:121-128. [PMID: 30905894 PMCID: PMC6594745 DOI: 10.1264/jsme2.me18104] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Despite efforts to address the composition of the microbial community during the anaerobic treatment of palm oil mill effluent (POME), its composition in relation to biodegradation in the full-scale treatment system has not yet been extensively examined. Therefore, a thorough analysis of bacterial and archaeal communities was performed in the present study using MiSeq sequencing at the different stages of the POME treatment, which comprised anaerobic as well as facultative anaerobic and aerobic processes, including the mixed raw effluent (MRE), mixing pond, holding tank, and final discharge phases. Based on the results obtained, the following biodegradation processes were suggested to occur at the different treatment stages: (1) Lactobacillaceae (35.9%) dominated the first stage, which contributed to high lactic acid production; (2) the higher population of Clostridiaceae in the mixing pond (47.7%) and Prevotellaceae in the holding tank (49.7%) promoted acetic acid production; (3) the aceticlastic methanogen Methanosaetaceae (0.6–0.8%) played a role in acetic acid degradation in the open digester and closed reactor for methane generation; (4) Syntrophomonas (21.5–29.2%) appeared to be involved in the degradation of fatty acids and acetic acid by syntrophic cooperation with the hydrogenotrophic methanogen, Methanobacteriaceae (0.6–1.3%); and (5) the phenols and alcohols detected in the early phases, but not in the final discharge phase, indicated the successful degradation of lignocellulosic materials. The present results contribute to a better understanding of the biodegradation mechanisms involved in the different stages of the full-scale treatment of POME.
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Affiliation(s)
- Diana Mohd-Nor
- Department of Bioprocess Technology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia.,Department of Biological Function and Engineering, Graduate School of Life Science and System Engineering, Kyushu Institute of Technology
| | - Norhayati Ramli
- Department of Bioprocess Technology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia
| | - Siti Suhailah Sharuddin
- Department of Bioprocess Technology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia
| | - Mohd Ali Hassan
- Department of Bioprocess Technology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia
| | - Nurul Asyifah Mustapha
- Department of Biological Function and Engineering, Graduate School of Life Science and System Engineering, Kyushu Institute of Technology
| | - Hidayah Ariffin
- Department of Bioprocess Technology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia.,Laboratory of Biopolymer and Derivatives, Institute of Tropical Forestry and Forest Products (INTROP), Universiti Putra Malaysia
| | - Kenji Sakai
- Laboratory of Soil and Environmental Microbiology, Division of Systems Bioengineering, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School of Bioresources and Bioenvironmental Sciences, Kyushu University
| | - Yukihiro Tashiro
- Laboratory of Soil and Environmental Microbiology, Division of Systems Bioengineering, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School of Bioresources and Bioenvironmental Sciences, Kyushu University
| | - Yoshihito Shirai
- Department of Biological Function and Engineering, Graduate School of Life Science and System Engineering, Kyushu Institute of Technology
| | - Toshinari Maeda
- Department of Biological Function and Engineering, Graduate School of Life Science and System Engineering, Kyushu Institute of Technology
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20
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Genome sequencing and analysis of Alcaligenes faecalis subsp. phenolicus MB207. Sci Rep 2018; 8:3616. [PMID: 29483539 PMCID: PMC5827749 DOI: 10.1038/s41598-018-21919-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 02/08/2018] [Indexed: 11/12/2022] Open
Abstract
Bacteria within the genus Alcaligenes, exhibit diverse properties but remain largely unexplored at genome scale. To shed light on the genome structure, heterogeneity and traits of Alcaligenes species, the genome of a tannery effluent isolated Alcaligenes faecalis subsp. phenolicus MB207 was sequenced and assembled. The genome was compared to the whole genome sequences of genus Alcaligenes present in the National Centre for Biotechnology Information database. Core, pan and species specific gene sequences i.e. singletons were identified. Members of this genus did not portray exceptional genetic heterogeneity or conservation and out of 5,166 protein coding genes from pooled genome dataset, 2429 (47.01%) contributed to the core, 1193 (23.09%) to singletons and 1544 (29.88%) to accessory genome. Secondary metabolite forming apparatus, antibiotic production and resistance was also profiled. Alcaligenes faecalis subsp. phenolicus MB207 genome consisted of a copious amount of bioremediation genes i.e. metal tolerance and xenobiotic degrading genes. This study marks this strain as a prospective eco-friendly bacterium with numerous benefits for the environment related research. Availability of the whole genome sequence heralds an opportunity for researchers to explore enzymes and apparatus for sustainable environmental clean-up as well as important compounds/substance production.
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21
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Ceballos SJ, Yu C, Claypool JT, Singer SW, Simmons BA, Thelen MP, Simmons CW, VanderGheynst JS. Development and characterization of a thermophilic, lignin degrading microbiota. Process Biochem 2017. [DOI: 10.1016/j.procbio.2017.08.018] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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22
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Zhang H, Wang Y, Zhao C, Wang J, Zhang X. Biodegradation of ochratoxin A byAlcaligenes faecalisisolated from soil. J Appl Microbiol 2017; 123:661-668. [DOI: 10.1111/jam.13537] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 06/21/2017] [Accepted: 07/06/2017] [Indexed: 11/27/2022]
Affiliation(s)
- H.H. Zhang
- Gansu Key Laboratory of Viticulture and Enology; College of Food Science and Engineering; Gansu Agricultural University; Lanzhou Gansu China
| | - Y. Wang
- Academy of State Administration of Grain; Beijing China
| | - C. Zhao
- Academy of State Administration of Grain; Beijing China
| | - J. Wang
- Gansu Key Laboratory of Viticulture and Enology; College of Food Science and Engineering; Gansu Agricultural University; Lanzhou Gansu China
| | - X.L. Zhang
- Academy of State Administration of Grain; Beijing China
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23
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Alcaligenes endophyticus sp. nov., isolated from roots of Ammodendron bifolium. Int J Syst Evol Microbiol 2017; 67:939-943. [DOI: 10.1099/ijsem.0.001719] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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24
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Tian M, Du D, Zhou W, Zeng X, Cheng G. Phenol degradation and genotypic analysis of dioxygenase genes in bacteria isolated from sediments. Braz J Microbiol 2016; 48:305-313. [PMID: 28065387 PMCID: PMC5470458 DOI: 10.1016/j.bjm.2016.12.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2015] [Accepted: 02/11/2016] [Indexed: 12/01/2022] Open
Abstract
The aerobic degradation of aromatic compounds by bacteria is performed by dioxygenases. To show some characteristic patterns of the dioxygenase genotype and its degradation specificities, twenty-nine gram-negative bacterial cultures were obtained from sediment contaminated with phenolic compounds in Wuhan, China. The isolates were phylogenetically diverse and belonged to 10 genera. All 29 gram-negative bacteria were able to utilize phenol, m-dihydroxybenzene and 2-hydroxybenzoic acid as the sole carbon sources, and members of the three primary genera Pseudomonas, Acinetobacter and Alcaligenes were able to grow in the presence of multiple monoaromatic compounds. PCR and DNA sequence analysis were used to detect dioxygenase genes coding for catechol 1,2-dioxygenase, catechol 2,3-dioxygenase and protocatechuate 3,4-dioxygenase. The results showed that there are 4 genotypes; most strains are either PNP (catechol 1,2-dioxygenase gene is positive, catechol 2,3-dioxygenase gene is negative, protocatechuate 3,4-dioxygenase gene is positive) or PNN (catechol 1,2-dioxygenase gene is positive, catechol 2,3-dioxygenase gene is negative, protocatechuate 3,4-dioxygenase gene is negative). The strains with two dioxygenase genes can usually grow on many more aromatic compounds than strains with one dioxygenase gene. Degradation experiments using a mixed culture representing four bacterial genotypes resulted in the rapid degradation of phenol. Determinations of substrate utilization and phenol degradation revealed their affiliations through dioxygenase genotype data.
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Affiliation(s)
- Mengyang Tian
- South-Central University for Nationalities, College of Life Science, Wuhan, PR China
| | - Dongyun Du
- South-Central University for Nationalities, College of Chemistry and Materials, Wuhan, PR China
| | - Wei Zhou
- South-Central University for Nationalities, College of Life Science, Wuhan, PR China
| | - Xiaobo Zeng
- South-Central University for Nationalities, College of Life Science, Wuhan, PR China
| | - Guojun Cheng
- South-Central University for Nationalities, College of Life Science, Wuhan, PR China.
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Zhou W, Guo W, Zhou H, Chen X. Phenol degradation by Sulfobacillus acidophilus TPY via the meta -pathway. Microbiol Res 2016; 190:37-45. [DOI: 10.1016/j.micres.2016.05.005] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 05/11/2016] [Accepted: 05/13/2016] [Indexed: 11/30/2022]
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Jung TK, Ra CS, Joh KS, Song HG. Characterization of heterotrophic nitrification and aerobic denitrification by Alcaligenes faecalis NS13. ACTA ACUST UNITED AC 2016. [DOI: 10.7845/kjm.2016.6020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Novel approach for the ammonium removal by simultaneous heterotrophic nitrification and denitrification using a novel bacterial species co-culture. World J Microbiol Biotechnol 2016; 32:36. [PMID: 26867597 DOI: 10.1007/s11274-015-2007-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2015] [Accepted: 12/28/2015] [Indexed: 10/22/2022]
Abstract
Agricultural activities lead excessive emission of ammonia nitrogen in the environment and can profoundly interfere the equilibrium of the natural ecosystems leading to their contamination. Actually, the biological purification of wastewaters is the most adopted technique thanks to its several advantages such as high performance and low energy consumption. For this reason, two novel strains of Alcaligenes sp. S84S3 and Proteus sp. S19 genus were isolated from an activated sludge and applied in the treatment of ammonium and nitrite in aqueous solution. Under the optimum operating conditions of temperature (30 °C), pH (7), carbon substrate (2 g/L of glucose) and duration of incubation time (69 h), the strain Alcaligenes sp. S84S3 could oxidize 65% of the ammonium as high as 272.72 mg-NH4(+)/L. Moreover, during 48 h, the nitrate reduction rate performed by the strain Proteus S19 was about 99 % without production of nitrite intermediate (negligible concentration). Moreover, the coculture of the strains Alcaligenes sp. S84S3 and Proteus sp. S19 could eliminate 65.83% of the ammonium ions without production of toxic forms of nitrogen oxides during a short time of incubation (118 h) at the same operational conditions with providing the aeration in the first treatment phase. The coculture of our isolated strains is assumed to have a good potential for nitrification and denitrification reactions applied in the treatment of wastewater containing ammonium, nitrite and nitrate. As a result, we can consider that the mixed culture is a practical method in the treatment of high-strength ammonium wastewater with reducing of sludge production.
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Alcaligenes faecalis ZD02, a Novel Nematicidal Bacterium with an Extracellular Serine Protease Virulence Factor. Appl Environ Microbiol 2016; 82:2112-2120. [PMID: 26826227 DOI: 10.1128/aem.03444-15] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 01/21/2016] [Indexed: 11/20/2022] Open
Abstract
Root knot nematodes (RKNs) are the world's most damaging plant-parasitic nematodes (PPNs), and they can infect almost all crops. At present, harmful chemical nematicides are applied to control RKNs. Using microbial nematicides has been proposed as a better management strategy than chemical control. In this study, we describe a novel nematicidal bacterium named Alcaligenes faecalis ZD02. A. faecalis ZD02 was isolated from Caenorhabditis elegans cadavers and has nematostatic and nematicidal activity, as confirmed by C. elegans growth assay and life span assay. In addition, A. faecalis ZD02 fermentation broth showed toxicity against C. elegans and Meloidogyne incognita. To identify the nematicidal virulence factor, the genome of strain ZD02 was sequenced. By comparing all of the predicted proteins of strain ZD02 to reported nematicidal virulence factors, we determined that an extracellular serine protease (Esp) has potential to be a nematicidal virulence factor, which was confirmed by bioassay on C. elegans and M. incognita. Using C. elegans as the target model, we found that both A. faecalis ZD02 and the virulence factor Esp can damage the intestines of C. elegans. The discovery that A. faecalis ZD02 has nematicidal activity provides a novel bacterial resource for the control of RKNs.
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Ju S, Zheng J, Lin J, Geng C, Zhu L, Guan Z, Zheng Z, Sun M. The complete genome sequence of Alcaligenes faecalis ZD02, a novel potential bionematocide. J Biotechnol 2015; 218:73-4. [PMID: 26656226 DOI: 10.1016/j.jbiotec.2015.12.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 12/02/2015] [Indexed: 11/24/2022]
Abstract
Root-knot nematodes (RKNs) can infect almost all crops, and result in huge economic losses in agriculture. There is no effective and environmentally safe means available to control RKNs. Alcaligenes faecalis ZD02 isolated from free living nematode Caenorhabditis elegans cadavers shows toxicity against RKN Meloidogyne incognita, that makes this strain to be a good bionematicide candidate for controlling of RKNs. Here, we firstly report the complete genome of A. faecalis ZD02 and describe its features. Additionally, we found two potential virulence factors in this genome, which play important roles for the nematocidal activity of A. faecalis ZD02.
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Affiliation(s)
- Shouyong Ju
- State Key Laboratory of Agricultural Microbiology, College of Life Sciences and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jinshui Zheng
- State Key Laboratory of Agricultural Microbiology, College of Life Sciences and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jian Lin
- State Key Laboratory of Agricultural Microbiology, College of Life Sciences and Technology, Huazhong Agricultural University, Wuhan, China
| | - Ce Geng
- State Key Laboratory of Agricultural Microbiology, College of Life Sciences and Technology, Huazhong Agricultural University, Wuhan, China
| | - Lei Zhu
- State Key Laboratory of Agricultural Microbiology, College of Life Sciences and Technology, Huazhong Agricultural University, Wuhan, China
| | - Ziyu Guan
- State Key Laboratory of Agricultural Microbiology, College of Life Sciences and Technology, Huazhong Agricultural University, Wuhan, China
| | - Ziqiang Zheng
- State Key Laboratory of Agricultural Microbiology, College of Life Sciences and Technology, Huazhong Agricultural University, Wuhan, China
| | - Ming Sun
- State Key Laboratory of Agricultural Microbiology, College of Life Sciences and Technology, Huazhong Agricultural University, Wuhan, China.
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Abbas S, Ahmed I, Iida T, Lee YJ, Busse HJ, Fujiwara T, Ohkuma M. A heavy-metal tolerant novel bacterium, Alcaligenes pakistanensis sp. nov., isolated from industrial effluent in Pakistan. Antonie van Leeuwenhoek 2015; 108:859-70. [PMID: 26238381 DOI: 10.1007/s10482-015-0540-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 07/18/2015] [Indexed: 10/23/2022]
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Enhanced Alcaligenes faecalis Denitrification Rate with Electrodes as the Electron Donor. Appl Environ Microbiol 2015; 81:5387-94. [PMID: 26048940 DOI: 10.1128/aem.00683-15] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 05/21/2015] [Indexed: 11/20/2022] Open
Abstract
The utilization by Alcaligenes faecalis of electrodes as the electron donor for denitrification was investigated in this study. The denitrification rate of A. faecalis with a poised potential was greatly enhanced compared with that of the controls without poised potentials. For nitrate reduction, although A. faecalis could not reduce nitrate, at three poised potentials of +0.06, -0.06, and -0.15 V (versus normal hydrogen electrode [NHE]), the nitrate was partially reduced with -0.15- and -0.06-V potentials at rates of 17.3 and 28.5 mg/liter/day, respectively. The percentages of reduction for -0.15 and -0.06 V were 52.4 and 30.4%, respectively. Meanwhile, for nitrite reduction, the poised potentials greatly enhanced the nitrite reduction. The nitrite reduction rates for three poised potentials (-0.06, -0.15, and -0.30 V) were 1.98, 4.37, and 3.91 mg/liter/h, respectively. When the potentials were cut off, the nitrite reduction rate was maintained for 1.5 h (from 2.3 to 2.25 mg/liter/h) and then greatly decreased, and the reduction rate (0.38 mg/liter/h) was about 1/6 compared with the rate (2.3 mg/liter/h) when potential was on. Then the potentials resumed, but the reduction rate did not resume and was only 2 times higher than the rate when the potential was off.
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Nakano M, Niwa M, Nishimura N. Specific and sensitive detection of Alcaligenes species from an agricultural environment. Microbiol Immunol 2013; 57:240-5. [PMID: 23489084 DOI: 10.1111/1348-0421.12026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Revised: 12/05/2012] [Accepted: 12/26/2012] [Indexed: 11/28/2022]
Abstract
A quantitative real-time PCR assay to specifically detect and quantify the genus Alcaligenes in samples from the agricultural environment, such as vegetables and farming soils, was developed. The minimum detection sensitivity was 106 fg of pure culture DNA, corresponding to DNA extracted from two cells of Alcaligenes faecalis. To evaluate the detection limit of A. faecalis, serially diluted genomic DNA from this organism was mixed with DNA extracted from soil and vegetables and then a standard curve was constructed. It was found that Alcaligenes species are present in the plant phytosphere at levels 10(2)-10(4) times lower than those in soil. The approach presented here will be useful for tracking or quantifying species of the genus Alcaligenes in the agricultural environment.
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Affiliation(s)
- Miyo Nakano
- Department of Translational Medical Science and Molecular and Cellular Pharmacology, Pharmacogenomics, and Pharmacoinformatics, Mie University Graduate School of Medicine, Mie University, 2-174 Edobashi, Tsu, Mie 514-8507, Japan
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Velusamy K, Krishnani KK. Heterotrophic Nitrifying and Oxygen Tolerant Denitrifying Bacteria from Greenwater System of Coastal Aquaculture. Appl Biochem Biotechnol 2013; 169:1978-92. [DOI: 10.1007/s12010-013-0109-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Accepted: 01/14/2013] [Indexed: 10/27/2022]
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Muller M, Patureau D, Godon JJ, Delgenès JP, Hernandez-Raquet G. Molecular and kinetic characterization of mixed cultures degrading natural and synthetic estrogens. Appl Microbiol Biotechnol 2009; 85:691-701. [DOI: 10.1007/s00253-009-2160-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2009] [Revised: 07/20/2009] [Accepted: 07/20/2009] [Indexed: 10/20/2022]
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Yu L, Liu Y, Wang G. Identification of novel denitrifying bacteria Stenotrophomonas sp. ZZ15 and Oceanimonas sp. YC13 and application for removal of nitrate from industrial wastewater. Biodegradation 2008; 20:391-400. [PMID: 19002594 DOI: 10.1007/s10532-008-9230-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2008] [Accepted: 10/27/2008] [Indexed: 10/21/2022]
Abstract
Two novel denitrifying bacteria were successfully isolated from industrial wastewater and soil samples. Using morphological, biochemical/biophysical and 16S rRNA gene analyses, these two bacteria were identified as Stenotrophomonas sp. ZZ15 and Oceanimonas sp. YC13, respectively. Both of these two bacteria showed efficient NO(3) (-)-N removing abilities under a semi-anaerobic condition without obvious accumulation of NO(2) (-)-N, N(2)O-N and NH(4) (+)-N. NO(3) (-)-N removal from paper mill wastewater was also successful by treatments with either a denitrifier or an immobilization method. Therefore, this study provides valuable denitrifying bacteria in biotreatment of industrial wastewater and other environmental pollution caused by NO(3) (-)/NO(2) (-).
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Affiliation(s)
- Lu Yu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
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Gross R, Guzman CA, Sebaihia M, dos Santos VAPM, Pieper DH, Koebnik R, Lechner M, Bartels D, Buhrmester J, Choudhuri JV, Ebensen T, Gaigalat L, Herrmann S, Khachane AN, Larisch C, Link S, Linke B, Meyer F, Mormann S, Nakunst D, Rückert C, Schneiker-Bekel S, Schulze K, Vorhölter FJ, Yevsa T, Engle JT, Goldman WE, Pühler A, Göbel UB, Goesmann A, Blöcker H, Kaiser O, Martinez-Arias R. The missing link: Bordetella petrii is endowed with both the metabolic versatility of environmental bacteria and virulence traits of pathogenic Bordetellae. BMC Genomics 2008; 9:449. [PMID: 18826580 PMCID: PMC2572626 DOI: 10.1186/1471-2164-9-449] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2008] [Accepted: 09/30/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Bordetella petrii is the only environmental species hitherto found among the otherwise host-restricted and pathogenic members of the genus Bordetella. Phylogenetically, it connects the pathogenic Bordetellae and environmental bacteria of the genera Achromobacter and Alcaligenes, which are opportunistic pathogens. B. petrii strains have been isolated from very different environmental niches, including river sediment, polluted soil, marine sponges and a grass root. Recently, clinical isolates associated with bone degenerative disease or cystic fibrosis have also been described. RESULTS In this manuscript we present the results of the analysis of the completely annotated genome sequence of the B. petrii strain DSMZ12804. B. petrii has a mosaic genome of 5,287,950 bp harboring numerous mobile genetic elements, including seven large genomic islands. Four of them are highly related to the clc element of Pseudomonas knackmussii B13, which encodes genes involved in the degradation of aromatics. Though being an environmental isolate, the sequenced B. petrii strain also encodes proteins related to virulence factors of the pathogenic Bordetellae, including the filamentous hemagglutinin, which is a major colonization factor of B. pertussis, and the master virulence regulator BvgAS. However, it lacks all known toxins of the pathogenic Bordetellae. CONCLUSION The genomic analysis suggests that B. petrii represents an evolutionary link between free-living environmental bacteria and the host-restricted obligate pathogenic Bordetellae. Its remarkable metabolic versatility may enable B. petrii to thrive in very different ecological niches.
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Affiliation(s)
- Roy Gross
- Chair of Microbiology, Biocenter, University of Würzburg, Am Hubland, D-97074 Würzburg, Germany.
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Zhu C, Zhang L, Zhao L. Molecular cloning, genetic organization of gene cluster encoding phenol hydroxylase and catechol 2,3-dioxygenase in Alcaligenes faecalis IS-46. World J Microbiol Biotechnol 2008. [DOI: 10.1007/s11274-008-9660-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Maszenan AM, Jiang HL, Tay JH, Schumann P, Kroppenstedt RM, Tay STL. Granulicoccus phenolivorans gen. nov., sp. nov., a Gram-positive, phenol-degrading coccus isolated from phenol-degrading aerobic granules. Int J Syst Evol Microbiol 2007; 57:730-737. [PMID: 17392196 DOI: 10.1099/ijs.0.64671-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-positive bacterium, designated strain PG-02T, was isolated by serial dilution from aerobic granules obtained from a laboratory-scale sequencing batch reactor for bioremediation of phenolic wastewater. Strain PG-02T grew axenically as cocci and is an oxidase-negative and catalase-positive, non-motile facultative anaerobe. It does not reduce nitrate and grows between 15 and 37 °C, with an optimum temperature of 30 °C. The pH range for growth is between 5.0 and 8.5, with an optimum pH of 7.0. Strain PG-02T contains type A3γ peptidoglycan (ll-A2pm←Gly with alanine at position 1 of the peptide subunit). The G+C content of the DNA is 69 mol%. Menaquinone MK-9(H4) was the major isoprenoid quinone. The polar lipids included diphosphatidylglycerol and phosphatidylglycerol, while 13-methyltetradecanoic acid (i-C15 : 0) and 1,1-dimethoxy-iso-pentadecane (i-C15 : 0 DMA) were the major components in whole-cell methanolysates. PG-02T stained positively for intracellular polyphosphate granules but not poly-β-hydroxyalkanoates. It produces capsular material and possesses an autoaggregation capability. Phenotypic and 16S rRNA gene sequence analyses showed that PG-02T differed from its closest phylogenetic relatives, namely members of the suborder Propionibacterineae, which includes the genera Tessaracoccus, Microlunatus, Luteococcus, Micropruina, Propionibacterium, Propioniferax, Nocardioides, Friedmanniella and Aeromicrobium, and that it should be placed in a new genus and species as Granulicoccus phenolivorans gen. nov., sp. nov. The type strain of Granulicoccus phenolivorans is PG-02T (=ATCC BAA-1292T=DSM 17626T).
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Affiliation(s)
- Abdul Majid Maszenan
- Environmental Engineering Research Centre, School of Civil and Environmental Engineering, Nanyang Technological University, Singapore 639798
| | - He Long Jiang
- Environmental Engineering Research Centre, School of Civil and Environmental Engineering, Nanyang Technological University, Singapore 639798
| | - Joo-Hwa Tay
- Environmental Engineering Research Centre, School of Civil and Environmental Engineering, Nanyang Technological University, Singapore 639798
| | - Peter Schumann
- DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstr. 7b, D-38124 Braunschweig, Germany
| | - Reiner M Kroppenstedt
- DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstr. 7b, D-38124 Braunschweig, Germany
| | - Stephen Tiong-Lee Tay
- Environmental Engineering Research Centre, School of Civil and Environmental Engineering, Nanyang Technological University, Singapore 639798
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Kämpfer P, Denger K, Cook AM, Lee ST, Jäckel U, Denner EBM, Busse HJ. Castellaniella gen. nov., to accommodate the phylogenetic lineage of Alcaligenes defragrans, and proposal of Castellaniella defragrans gen. nov., comb. nov. and Castellaniella denitrificans sp. nov. Int J Syst Evol Microbiol 2006; 56:815-819. [PMID: 16585701 DOI: 10.1099/ijs.0.63989-0] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Comparative 16S rRNA gene sequence analysis indicates that two distinct sublineages exist within the genus Alcaligenes: the Alcaligenes faecalis lineage, comprising Alcaligenes aquatilis and A. faecalis (with the three subspecies A. faecalis subsp. faecalis, A. faecalis subsp. parafaecalis and A. faecalis subsp. phenolicus), and the Alcaligenes defragrans lineage, comprising A. defragrans. This phylogenetic discrimination is supported by phenotypic and chemotaxonomic differences. It is proposed that the A. defragrans lineage constitutes a distinct genus, for which the name Castellaniella gen. nov. is proposed. The type strain for Castellaniella defragrans gen. nov., comb. nov. is 54PinT (=CCUG 39790T=CIP 105602T=DSM 12141T). Finally, on the basis of data from the literature and new DNA–DNA hybridization and phenotypic data, the novel species Castellaniella denitrificans sp. nov. (type strain NKNTAUT=DSM 11046T=CCUG 39541T) is proposed for two strains previously identified as strains of A. defragrans.
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Affiliation(s)
- P Kämpfer
- Institut für Angewandte Mikrobiologie, Justus Liebig Universität, IFZ - Heinrich-Buff-Ring 26-32, D-35392 Giessen, Germany
| | - K Denger
- Department of Biology, The University of Konstanz, D-78457 Konstanz, Germany
| | - A M Cook
- Department of Biology, The University of Konstanz, D-78457 Konstanz, Germany
| | - S-T Lee
- Department of Biological Sciences, Korean Advanced Institute of Science and Technology, 373-1 Guseong-dong, Yuseong-gu, Daejon, 305-701, Republic of Korea
| | - U Jäckel
- Institut für Angewandte Mikrobiologie, Justus Liebig Universität, IFZ - Heinrich-Buff-Ring 26-32, D-35392 Giessen, Germany
| | - E B M Denner
- Institut für Bakteriologie, Mykologie und Hygiene, Veterinärmedizinische Universität Wien, Veterinärplatz 1, A-1210 Wien, Austria
| | - H-J Busse
- Institut für Bakteriologie, Mykologie und Hygiene, Veterinärmedizinische Universität Wien, Veterinärplatz 1, A-1210 Wien, Austria
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Van Trappen S, Tan TL, Samyn E, Vandamme P. Alcaligenes aquatilis sp. nov., a novel bacterium from sediments of the Weser Estuary, Germany, and a salt marsh on Shem Creek in Charleston Harbor, USA. Int J Syst Evol Microbiol 2006; 55:2571-2575. [PMID: 16280529 DOI: 10.1099/ijs.0.63849-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Four nitrite-dissimilating strains, isolated from Weser Estuary sediments, were investigated using a polyphasic taxonomic approach. Phylogenetic analysis based on 16S rRNA gene sequences indicated that these strains belong to the 'Betaproteobacteria' and are related to the genus Alcaligenes. The highest level of sequence similarity (100 %) was found with strain M3A (=ATCC 700596), a dimethyl sulfide-producing marine isolate that was included in this study. DNA-DNA hybridizations between the five strains and related Alcaligenes faecalis strains confirmed that the former belong to a single and novel species within the genus Alcaligenes. The isolates are Gram-negative, motile, rod-shaped cells with a DNA G+C content of about 56 mol%. The whole-cell fatty acid profiles of the isolates were very similar and included C(16 : 0), C(17 : 0) cyclo, C(18 : 1)omega7c, summed feature 2 (comprising any combination of C(12 : 0) aldehyde, an unknown fatty acid of equivalent chain length 10.928, C(16 : 1) iso I and C(14 : 0) 3-OH) and summed feature 3 (C(15 : 0) iso 2-OH and/or C(16 : 1)omega7c) as the major fatty acid components. On the basis of their phylogenetic, genomic and phenotypic properties, the five novel strains can be assigned to the genus Alcaligenes as a novel species, for which the name Alcaligenes aquatilis sp. nov. is proposed. The type strain is LMG 22996T (=CCUG 50924T).
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Affiliation(s)
- Stefanie Van Trappen
- BCCM/LMG Bacteria Collection, Universiteit Gent, Gent, Belgium
- Laboratorium voor Microbiologie, Vakgroep Biochemie, Fysiologie en Microbiologie, Universiteit Gent, Gent, Belgium
| | - Tjhing-Lok Tan
- Alfred-Wegener-Institut für Polar- und Meeresforschung, Bremerhaven, Germany
| | - Emly Samyn
- Laboratorium voor Microbiologie, Vakgroep Biochemie, Fysiologie en Microbiologie, Universiteit Gent, Gent, Belgium
| | - Peter Vandamme
- Laboratorium voor Microbiologie, Vakgroep Biochemie, Fysiologie en Microbiologie, Universiteit Gent, Gent, Belgium
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Kalainesan S, Erickson L, Hutchinson S, Urban J, Karthikeyan R. Transformation of tertiary butyl mercaptan in aerobic environments. ACTA ACUST UNITED AC 2006. [DOI: 10.1002/ep.10136] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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