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Kumari K, Rawat V, Shadan A, Sharma PK, Deb S, Singh RP. In-depth genome and pan-genome analysis of a metal-resistant bacterium Pseudomonas parafulva OS-1. Front Microbiol 2023; 14:1140249. [PMID: 37408640 PMCID: PMC10318148 DOI: 10.3389/fmicb.2023.1140249] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Accepted: 05/29/2023] [Indexed: 07/07/2023] Open
Abstract
A metal-resistant bacterium Pseudomonas parafulva OS-1 was isolated from waste-contaminated soil in Ranchi City, India. The isolated strain OS-1 showed its growth at 25-45°C, pH 5.0-9.0, and in the presence of ZnSO4 (upto 5 mM). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain OS-1 belonged to the genus Pseudomonas and was most closely related to parafulva species. To unravel the genomic features, we sequenced the complete genome of P. parafulva OS-1 using Illumina HiSeq 4,000 sequencing platform. The results of average nucleotide identity (ANI) analysis indicated the closest similarity of OS-1 to P. parafulva PRS09-11288 and P. parafulva DTSP2. The metabolic potential of P. parafulva OS-1 based on Clusters of Othologous Genes (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) indicated a high number of genes related to stress protection, metal resistance, and multiple drug-efflux, etc., which is relatively rare in P. parafulva strains. Compared with other parafulva strains, P. parafulva OS-1 was found to have the unique β-lactam resistance and type VI secretion system (T6SS) gene. Additionally, its genomes encode various CAZymes such as glycoside hydrolases and other genes associated with lignocellulose breakdown, suggesting that strain OS-1 have strong biomass degradation potential. The presence of genomic complexity in the OS-1 genome indicates that horizontal gene transfer (HGT) might happen during evolution. Therefore, genomic and comparative genome analysis of parafulva strains is valuable for further understanding the mechanism of resistance to metal stress and opens a perspective to exploit a newly isolated bacterium for biotechnological applications.
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Affiliation(s)
- Kiran Kumari
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Ranchi, Jharkhand, India
| | - Vaishnavi Rawat
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Ranchi, Jharkhand, India
| | - Afreen Shadan
- Department of Microbiology, Dr. Shyama Prasad Mukerjee University, Ranchi, India
| | - Parva Kumar Sharma
- Department of Plant Sciences and Landscape Architecture, University of Maryland, College Park, MD, United States
| | - Sushanta Deb
- Department of Veterinary Microbiology and Pathology, Washington State University (WSU), Pullman, WA, United States
| | - Rajnish Prakash Singh
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Ranchi, Jharkhand, India
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Sun H, Jiang S. A review on nirS-type and nirK-type denitrifiers via a scientometric approach coupled with case studies. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2022; 24:221-232. [PMID: 35072673 DOI: 10.1039/d1em00518a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The denitrification process plays an important role in improving water quality and is a source/sink of nitrous oxide to the atmosphere. The second important rate-limiting step of the denitrification process is catalyzed by two enzymes with different structures and unrelated evolutionary relationships, namely, the Cu-type nitrite reductase encoded by the nirK gene and the cytochrome cd1-type nitrite reductase encoded by the nirS gene. Although some relevant reviews have been published on denitrifiers, most of these reviews do not include statistical analysis, and do not compare the nirS and nirK communities in-depth. However, a systematic study of the nirS-type and nirK-type denitrifying communities and their response to environmental factors in different ecosystems is needed. In this review, a scientometric approach combined with case studies was used to study the nirS-type and nirK-type denitrifiers. The scientometric approach demonstrated that Pseudomonas, Paracoccus, and Thauera are the most frequently mentioned nirS-type denitrifiers, while Pseudomonas and Bradyrhizobium are the top two most frequently mentioned nirK-type denitrifiers. Among various environmental factors, the concentrations of nitrite, nitrate and carbon sources were widely reported factors that can influence the abundance and structure of nirS-type and nirK-type denitrifying communities. Case studies indicated that Bradyrhizobium was the major genus detected by high-throughput sequencing in both nirS and nirK-type denitrifiers in soil systems. nirS-type denitrifiers are more sensitive to the soil type, soil moisture, pH, and rhizosphere effect than nirK. To clarify the relationships between denitrifying communities and environmental factors, the DNA stable isotope probe combined with metagenomic sequencing is needed for new denitrifier detections.
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Affiliation(s)
- Haishu Sun
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shanxue Jiang
- School of Ecology and Environment, Beijing Technology and Business University, Beijing 100048, China.
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Genome analysis of Pseudomonas sp. 14A reveals metabolic capabilities to support epiphytic behavior. World J Microbiol Biotechnol 2022; 38:49. [DOI: 10.1007/s11274-022-03238-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 01/19/2022] [Indexed: 11/26/2022]
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Maggiori C, Raymond-Bouchard I, Brennan L, Touchette D, Whyte L. MinION sequencing from sea ice cryoconites leads to de novo genome reconstruction from metagenomes. Sci Rep 2021; 11:21041. [PMID: 34702846 PMCID: PMC8548342 DOI: 10.1038/s41598-021-00026-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 09/30/2021] [Indexed: 01/04/2023] Open
Abstract
Genome reconstruction from metagenomes enables detailed study of individual community members, their metabolisms, and their survival strategies. Obtaining high quality metagenome-assembled genomes (MAGs) is particularly valuable in extreme environments like sea ice cryoconites, where the native consortia are recalcitrant to culture and strong astrobiology analogues. We evaluated three separate approaches for MAG generation from Allen Bay, Nunavut sea ice cryoconites-HiSeq-only, MinION-only, and hybrid (HiSeq + MinION)-where field MinION sequencing yielded a reliable metagenome. The hybrid assembly produced longer contigs, more coding sequences, and more total MAGs, revealing a microbial community dominated by Bacteroidetes. The hybrid MAGs also had the highest completeness, lowest contamination, and highest N50. A putatively novel species of Octadecabacter is among the hybrid MAGs produced, containing the genus's only known instances of genomic potential for nitrate reduction, denitrification, sulfate reduction, and fermentation. This study shows that the inclusion of MinION reads in traditional short read datasets leads to higher quality metagenomes and MAGs for more accurate descriptions of novel microorganisms in this extreme, transient habitat and has produced the first hybrid MAGs from an extreme environment.
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Affiliation(s)
- Catherine Maggiori
- Department of Natural Resource Sciences, Faculty of Agricultural and Environmental Sciences, McGill University, 21 111 Lakeshore Road, Macdonald Stewart Building, Room MS3-053, Ste. Anne-de-Bellevue, Quebec, H9X 3V9, Canada.
| | - Isabelle Raymond-Bouchard
- Department of Natural Resource Sciences, Faculty of Agricultural and Environmental Sciences, McGill University, 21 111 Lakeshore Road, Macdonald Stewart Building, Room MS3-053, Ste. Anne-de-Bellevue, Quebec, H9X 3V9, Canada
| | - Laura Brennan
- Department of Natural Resource Sciences, Faculty of Agricultural and Environmental Sciences, McGill University, 21 111 Lakeshore Road, Macdonald Stewart Building, Room MS3-053, Ste. Anne-de-Bellevue, Quebec, H9X 3V9, Canada
| | - David Touchette
- Department of Natural Resource Sciences, Faculty of Agricultural and Environmental Sciences, McGill University, 21 111 Lakeshore Road, Macdonald Stewart Building, Room MS3-053, Ste. Anne-de-Bellevue, Quebec, H9X 3V9, Canada
| | - Lyle Whyte
- Department of Natural Resource Sciences, Faculty of Agricultural and Environmental Sciences, McGill University, 21 111 Lakeshore Road, Macdonald Stewart Building, Room MS3-053, Ste. Anne-de-Bellevue, Quebec, H9X 3V9, Canada
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Nitrifying and Denitrifying Microbial Communities in Centralized and Decentralized Biological Nitrogen Removing Wastewater Treatment Systems. WATER 2020. [DOI: 10.3390/w12061688] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Biological nitrogen removal (BNR) in centralized and decentralized wastewater treatment systems is assumed to be driven by the same microbial processes and to have communities with a similar composition and structure. There is, however, little information to support these assumptions, which may impact the effectiveness of decentralized systems. We used high-throughput sequencing to compare the structure and composition of the nitrifying and denitrifying bacterial communities of nine onsite wastewater treatment systems (OWTS) and one wastewater treatment plant (WTP) by targeting the genes coding for ammonia monooxygenase (amoA) and nitrous oxide reductase (nosZ). The amoA diversity was similar between the WTP and OWTS, but nosZ diversity was generally higher for the WTP. Beta diversity analyses showed the WTP and OWTS promoted distinct amoA and nosZ communities, although there is a core group of N-transforming bacteria common across scales of BNR treatment. Our results suggest that advanced N-removal OWTS have microbial communities that are sufficiently distinct from those of WTP with BNR, which may warrant different management approaches.
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Hu J, Zhou Y, Lei Z, Liu G, Hua Y, Zhou W, Wan X, Zhu D, Zhao J. Effects of Potamogeton crispus decline in the rhizosphere on the abundance of anammox bacteria and nirS denitrifying bacteria ☆. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 260:114018. [PMID: 31991343 DOI: 10.1016/j.envpol.2020.114018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 01/17/2020] [Accepted: 01/17/2020] [Indexed: 05/23/2023]
Abstract
Bacteria involved with ecosystem N cycling in the rhizosphere of submerged macrophytes are abundant and diverse. Any declines of submerged macrophytes can have a great influence on the abundance and diversity of denitrifying bacteria and anammox bacteria. Natural decline, tardy decline, and sudden decline methods were applied to cultivated Potamogeton crispus. The abundance of anammox bacteria and nirS denitrifying bacteria in rhizosphere sediment were detected using real-time fluorescent quantitative PCR of 16S rRNA, and phylogenetic trees were constructed to analyze the diversities of these two microbes. The results indicated that the concentration of NH4+ in pore water gradually increased with increasing distances from the roots, whereas, the concentration of NO3- showed a reverse trend. The abundance of anammox bacteria and nirS denitrifying bacteria in sediment of declined P. crispus populations decreased significantly over time. The abundance of these two microbes in the sudden decline group were significantly higher (P > 0.05) than the other decline treatment groups. Furthermore, the abundances of these two microbes were positively correlated, with RDA analyses finding the mole ratio of NH4+/NO3- being the most important positive factor affecting microbe abundance. Phylogenetic analysis indicated that the anammox bacteria Brocadia fuigida and Scalindua wagneri, and nirS denitrifying bacteria Herbaspirillum and Pseudomonas, were the dominant species in declined P. crispus sediment. We suggest the sudden decline of submerged macrophytes would increase the abundance of anammox bacteria and denitrifying bacteria in a relatively short time.
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Affiliation(s)
- Jinlong Hu
- Laboratory of Eco-Environmental Engineering Research, College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yuhao Zhou
- Laboratory of Eco-Environmental Engineering Research, College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ziyan Lei
- Laboratory of Eco-Environmental Engineering Research, College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China
| | - Guanglong Liu
- Laboratory of Eco-Environmental Engineering Research, College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yumei Hua
- Laboratory of Eco-Environmental Engineering Research, College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China
| | - Wenbing Zhou
- Laboratory of Eco-Environmental Engineering Research, College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiaoqiong Wan
- Laboratory of Eco-Environmental Engineering Research, College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China
| | - Duanwei Zhu
- Laboratory of Eco-Environmental Engineering Research, College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jianwei Zhao
- Laboratory of Eco-Environmental Engineering Research, College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China.
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Lin J, Meng Y, Shi Y, Lin X. Complete Genome Sequences of Colwellia sp. Arc7-635, a Denitrifying Bacterium Isolated from Arctic Seawater. Curr Microbiol 2019; 76:1061-1065. [PMID: 31240393 DOI: 10.1007/s00284-019-01714-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 06/03/2019] [Indexed: 11/25/2022]
Abstract
Colwellia sp. Arc7-635, a psychrophilic denitrifying bacterium isolated from Arctic seawater, uses NO3- or NH4+ as the sole nitrogen source to grow at low temperatures. In this article, we describe the complete genome of Colwellia sp. Arc7-635. The genome has one circular chromosome of 4,741,350 bp (38.41 mol% G+C content), consisting of 3841 coding genes, 91 tRNA genes, as well as seven rRNA operons of 16S-23S-5S rRNA, and one operon of 16S-23S-5S-5S rRNA. According to the genomic annotation results, strain Colwellia sp. Arc7-635 encodes a complete denitrifying pathway consisting of genes affiliated with nitrate reductase, nitrite reductase, nitric oxide reductase, and nitrous oxide reductase. Genes affiliated with nitrate reduction to ammonia including nitrate reductases (NapA and NapB) and nitrite reductases (NirA, NirB, and NirD) were also identified. The whole genome sequences of Arc7-635 provide information that is useful for further clarifying nitrogen metabolisms and facilitate its potential applications in the bioremediation of nitrogen pollutions.
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Affiliation(s)
- Jing Lin
- Shandong Provincial Key Laboratory of Biochemical Engineering, College of Marine Science and Biotechnology, Qingdao University of Science and Technology, Qingdao, 266042, China.,Key Lab of Marine Bioactive Substances, The First Institute of Oceanography, Ministry of Natural Resources, Qingdao, 266061, China
| | - Yingying Meng
- Shandong Provincial Key Laboratory of Biochemical Engineering, College of Marine Science and Biotechnology, Qingdao University of Science and Technology, Qingdao, 266042, China.,Key Lab of Marine Bioactive Substances, The First Institute of Oceanography, Ministry of Natural Resources, Qingdao, 266061, China
| | - Yanjing Shi
- Shandong Provincial Key Laboratory of Biochemical Engineering, College of Marine Science and Biotechnology, Qingdao University of Science and Technology, Qingdao, 266042, China.
| | - Xuezheng Lin
- Key Lab of Marine Bioactive Substances, The First Institute of Oceanography, Ministry of Natural Resources, Qingdao, 266061, China.
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Sun Y, Men M, Xu B, Meng Q, Bello A, Xu X, Huang X. Assessing key microbial communities determining nitrogen transformation in composting of cow manure using illumina high-throughput sequencing. WASTE MANAGEMENT (NEW YORK, N.Y.) 2019; 92:59-67. [PMID: 31160027 DOI: 10.1016/j.wasman.2019.05.007] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 03/17/2019] [Accepted: 05/03/2019] [Indexed: 06/09/2023]
Abstract
Insight to nitrogen transformation and cycling during composting is vital in developing management strategies that improve nitrogen content and quality of the end product. In this study, a positive ventilation device was constructed and used to elucidate nitrogen transformation and microbial community structures during the composting of cow manure and rice straw. Bacterial community successions were analyzed during the composting process by examining the change in their structural dynamics using high-throughput sequencing technique. The results revealed that dominant phyla, included Acidobacter, Proteobacteria, Firmicutes, Bacteroidetes, Chloroflexi, and Actinobacteria. Furthermore, a positive strong correlation was observed between the key bacterial communities and nitrogen transformation. Analyses of functional genera, Spearman correlation and Path showed that Thermomonospora_curvata_DSM_43183 followed by Luteimonas and Simiduia, Brevundimonas and Tamlana, Pseudomonas followed by Brevundimonas and Flavobacterium were the key bacterial communities affecting NH4+-N, NO3--N, and NO2--N transformation, respectively. Thauera followed by Pseudomonas_putida_NBRC_14164 played a dominant role in N2O transformation.
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Affiliation(s)
- Yu Sun
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Mengqi Men
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Benshu Xu
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Qingxin Meng
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Ayodeji Bello
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Xiuhong Xu
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, China.
| | - Xinning Huang
- College of Veterinary Medicine, China Agricultural University, Beijing 100083, China
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