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Das S, Das A, Das N, Nath T, Langthasa M, Pandey P, Kumar V, Choure K, Kumar S, Pandey P. Harnessing the potential of microbial keratinases for bioconversion of keratin waste. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024:10.1007/s11356-024-34233-6. [PMID: 38985428 DOI: 10.1007/s11356-024-34233-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 06/30/2024] [Indexed: 07/11/2024]
Abstract
The increasing global consumption of poultry meat has led to the generation of a vast quantity of feather keratin waste daily, posing significant environmental challenges due to improper disposal methods. A growing focus is on utilizing keratinous polymeric waste, amounting to millions of tons annually. Keratins are biochemically rigid, fibrous, recalcitrant, physiologically insoluble, and resistant to most common proteolytic enzymes. Microbial biodegradation of feather keratin provides a viable solution for augmenting feather waste's nutritional value while mitigating environmental contamination. This approach offers an alternative to traditional physical and chemical treatments. This review focuses on the recent findings and work trends in the field of keratin degradation by microorganisms (bacteria, actinomycetes, and fungi) via keratinolytic and proteolytic enzymes, as well as the limitations and challenges encountered due to the low thermal stability of keratinase, and degradation in the complex environmental conditions. Therefore, recent biotechnological interventions such as designing novel keratinase with high keratinolytic activity, thermostability, and binding affinity have been elaborated here. Enhancing protein structural rigidity through critical engineering approaches, such as rational design, has shown promise in improving the thermal stability of proteins. Concurrently, metagenomic annotation offers insights into the genetic foundations of keratin breakdown, primarily predicting metabolic potential and identifying probable keratinases. This may extend the understanding of microbial keratinolytic mechanisms in a complex community, recognizing the significance of synergistic interactions, which could be further utilized in optimizing industrial keratin degradation processes.
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Affiliation(s)
- Sandeep Das
- Department of Microbiology, Assam University, Silchar, 788011, Assam, India
| | - Ankita Das
- Department of Microbiology, Assam University, Silchar, 788011, Assam, India
| | - Nandita Das
- Department of Microbiology, Assam University, Silchar, 788011, Assam, India
| | - Tamanna Nath
- Department of Microbiology, Assam University, Silchar, 788011, Assam, India
| | | | - Prisha Pandey
- Department of Biotechnology, Royal Global University, Guwahati, 781035, Assam, India
| | - Vijay Kumar
- Himalayan School of Biosciences, Swami Rama Himalayan University, Dehradun, India, 248016
| | - Kamlesh Choure
- Department of Biotechnology, AKS University, Satna, 485001, Madhya Pradesh, India
| | - Sanjeev Kumar
- Department of Life Sciences and Bioinformatics, Assam University, Silchar, 788011, Assam, India
| | - Piyush Pandey
- Department of Microbiology, Assam University, Silchar, 788011, Assam, India.
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Zhao Y, Ding WJ, Xu L, Sun JQ. A comprehensive comparative genomic analysis revealed that plant growth promoting traits are ubiquitous in strains of Stenotrophomonas. Front Microbiol 2024; 15:1395477. [PMID: 38817968 PMCID: PMC11138164 DOI: 10.3389/fmicb.2024.1395477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 04/29/2024] [Indexed: 06/01/2024] Open
Abstract
Stenotrophomonas strains, which are often described as plant growth promoting (PGP) bacteria, are ubiquitous in many environments. A total of 213 genomes of strains of Stenotrophomonas were analyzed using comparative genomics to better understand the ecological roles of these bacteria in the environment. The pan-genome of the 213 strains of Stenotrophomonas consists of 27,186 gene families, including 710 core gene families, 11,039 unique genes and 15,437 accessory genes. Nearly all strains of Stenotrophomonas harbor the genes for GH3-family cellulose degradation and GH2- and GH31-family hemicellulose hydrolase, as well as intact glycolysis and tricarboxylic acid cycle pathways. These abilities suggest that the strains of this genus can easily obtain carbon and energy from the environment. The Stenotrophomonas strains can respond to oxidative stress by synthesizing catalase, superoxide dismutase, methionine sulfoxide reductase, and disulfide isomerase, as well as managing their osmotic balance by accumulating potassium and synthesizing compatible solutes, such as betaine, trehalose, glutamate, and proline. Each Stenotrophomonas strain also contains many genes for resistance to antibiotics and heavy metals. These genes that mediate stress tolerance increase the ability of Stenotrophomonas strains to survive in extreme environments. In addition, many functional genes related to attachment and plant colonization, growth promotion and biocontrol were identified. In detail, the genes associated with flagellar assembly, motility, chemotaxis and biofilm formation enable the strains of Stenotrophomonas to effectively colonize host plants. The presence of genes for phosphate-solubilization and siderophore production and the polyamine, indole-3-acetic acid, and cytokinin biosynthetic pathways confer the ability to promote plant growth. These strains can produce antimicrobial compounds, chitinases, lipases and proteases. Each Stenotrophomonas genome contained 1-9 prophages and 17-60 genomic islands, and the genes related to antibiotic and heavy metal resistance and the biosynthesis of polyamines, indole-3-acetic acid, and cytokinin may be acquired by horizontal gene transfer. This study demonstrates that strains of Stenotrophomonas are highly adaptable for different environments and have strong potential for use as plant growth-promoting bacteria.
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Affiliation(s)
- Yang Zhao
- Lab for Microbial Resources, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Wen-Jing Ding
- Lab for Microbial Resources, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Lian Xu
- Jiangsu Key Lab for Organic Solid Waste Utilization, Educational Ministry Engineering Center of Resource-saving Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
| | - Ji-Quan Sun
- Lab for Microbial Resources, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
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Sharma P, Pandey R, Chauhan NS. Biofertilizer and biocontrol properties of Stenotrophomonas maltophilia BCM emphasize its potential application for sustainable agriculture. FRONTIERS IN PLANT SCIENCE 2024; 15:1364807. [PMID: 38501138 PMCID: PMC10944936 DOI: 10.3389/fpls.2024.1364807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 02/09/2024] [Indexed: 03/20/2024]
Abstract
Introduction Microbial biofertilizers or biocontrol agents are potential sustainable approaches to overcome the limitations of conventional agricultural practice. However, the limited catalog of microbial candidates for diversified crops creates hurdles in successfully implementing sustainable agriculture for increasing global/local populations. The present study aimed to explore the wheat rhizosphere microbiota for microbial strains with a biofertilizer and biocontrol potential. Methods Using a microbial culturing-based approach, 12 unique microbial isolates were identified and screened for biofertilizer/biocontrol potential using genomics and physiological experimentations. Results and discussion Molecular, physiological, and phylogenetic characterization identified Stenotrophomonas maltophilia BCM as a potential microbial candidate for sustainable agriculture. Stenotrophomonas maltophilia BCM was identified as a coccus-shaped gram-negative microbe having optimal growth at 37°C in a partially alkaline environment (pH 8.0) with a proliferation time of ~67 minutes. The stress response physiology of Stenotrophomonas maltophilia BCM indicates its successful survival in dynamic environmental conditions. It significantly increased (P <0.05) the wheat seed germination percentage in the presence of phytopathogens and saline conditions. Genomic characterization decoded the presence of genes involved in plant growth promotion, nutrient assimilation, and antimicrobial activity. Experimental evidence also correlates with genomic insights to explain the potential of Stenotrophomonas maltophilia BCM as a potential biofertilizer and biocontrol agent. With these properties, Stenotrophomonas maltophilia BCM could sustainably promote wheat production to ensure food security for the increasing population, especially in native wheat-consuming areas.
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Affiliation(s)
- Pinki Sharma
- Department of Biochemistry, Maharshi Dayanand University, Haryana, Rohtak, India
| | - Rajesh Pandey
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology Council of Scientific and Industrial Research (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Nar Singh Chauhan
- Department of Biochemistry, Maharshi Dayanand University, Haryana, Rohtak, India
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Shahid S, Abid R, Ajmal W, Almuqbil M, Almadani ME, Khan Y, Ansari AA, Rani R, Alshehri A, Alghamdi A, Asdaq SMB, Ghazanfar S. Antibiotic resistance genes prediction via whole genome sequence analysis of Stenotrophomonas maltophilia. J Infect Public Health 2024; 17:236-244. [PMID: 38128408 DOI: 10.1016/j.jiph.2023.12.010] [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: 08/08/2023] [Revised: 12/06/2023] [Accepted: 12/13/2023] [Indexed: 12/23/2023] Open
Abstract
BACKGROUND Stenotrophomonas maltophilia (S. maltophilia) is the first dominant ubiquitous bacterial species identified from the genus Stenotrophomonas in 1943 from a human source. S. maltophilia clinical strains are resistance to several therapies, this study is designed to investigate the whole genome sequence and antimicrobial resistance genes prediction in Stenotrophomonas maltophilia (S. maltophilia) SARC-5 and SARC-6 strains, isolated from the nasopharyngeal samples of an immunocompromised patient. METHODS These bacterial strains were obtained from Pakistan Institute of Medical Sciences (PIMS) Hospital, Pakistan. The bacterial genome was sequenced using a whole-genome shotgun via a commercial service that used an NGS (Next Generation Sequencing) technology called as Illumina Hiseq 2000 system for genomic sequencing. Moreover, detailed in-silico analyses were done to predict the presence of antibiotic resistance genes in S. maltophilia. RESULTS Results showed that S. maltophilia is a rare gram negative, rod-shaped, non sporulating bacteria. The genome assembly results in 24 contigs (>500 bp) having a size of 4668,850 bp with 65.8% GC contents. Phylogenetic analysis showed that SARC-5 and SARC-6 were closely related to S. maltophilia B111, S. maltophilia BAB-5317, S. maltophilia AHL, S. maltophilia BAB-5307, S. maltophilia RD-AZPVI_04, S. maltophilia JFZ2, S. maltophilia RD_MAAMIB_06 and lastly with S. maltophilia sp ROi7. Moreover, the whole genome sequence analysis of both SARC-5 and SARC-6 revealed the presence of four resistance genes adeF, qacG, adeF, and smeR. CONCLUSION Our study confirmed that S. maltophilia SARC-5 and SARC-6 are one of the leading causes of nosocomial infection which carry multiple antibiotic resistance genes.
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Affiliation(s)
- Sara Shahid
- Department of Life Sciences, Abasyn University Islamabad Campus Pakistan, Pakistan
| | - Rameesha Abid
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre (NARC), Park Road, Islamabad 45500, Pakistan; Department of Microbiology, Quaid-i-Azam University, Islamabad 44100, Pakistan
| | - Wajya Ajmal
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre (NARC), Park Road, Islamabad 45500, Pakistan.
| | - Mansour Almuqbil
- Department of Clinical Pharmacy, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Moneer E Almadani
- Department of Clinical Medicine, College of Medicine, AlMaarefa University, Dariyah, 13713 Riyadh, Saudi Arabia
| | - Yasir Khan
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre (NARC), Park Road, Islamabad 45500, Pakistan
| | - Adnan Ahmad Ansari
- National Center for Bioinformatics, Quaid-i-Azam University, Islamabad 44100, Pakistan
| | - Rehana Rani
- Department of Life Sciences, Abasyn University Islamabad Campus Pakistan, Pakistan.
| | - Ahmed Alshehri
- Department of Pharmacology, College of Clinical Pharmacy, Imam Abdulrahman Bin Faisal University, King Faisal Road, Dammam 31441, Saudi Arabia
| | - Adel Alghamdi
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Al-Baha University, P.O. Box 1988, Al-Baha, Saudi Arabia
| | | | - Shakira Ghazanfar
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre (NARC), Park Road, Islamabad 45500, Pakistan.
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Yakubovskij VI, Morozova VV, Kozlova YN, Tikunov AY, Babkin IV, Bardasheva AV, Zhirakovskaya EV, Baykov IK, Kaverina GB, Tikunova NV. A Novel Podophage StenR_269 Suggests a New Family in the Class Caudoviricetes. Viruses 2023; 15:2437. [PMID: 38140678 PMCID: PMC10747016 DOI: 10.3390/v15122437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 12/12/2023] [Accepted: 12/13/2023] [Indexed: 12/24/2023] Open
Abstract
Stenotrophomonas rhizophila was first discovered in soil; it is associated with the rhizosphere and capable of both protecting roots and stimulating plant growth. Therefore, it has a great potential to be used in biocontrol. The study of S. rhizophila phages is important for a further evaluation of their effect on the fitness and properties of host bacteria. A novel phage StenR_269 and its bacterial host S. rhizophila were isolated from a soil sample in the remediation area of a coal mine. Electron microscopy revealed a large capsid (~Ø80 nm) connected with a short tail, which corresponds to the podovirus morphotype. The length of the genomic sequence of the StenR_269 was 66,322 bp and it contained 103 putative genes; 40 of them encoded proteins with predicted functions, 3 corresponded to tRNAs, and the remaining 60 were identified as hypothetical ones. Comparative analysis indicated that the StenR_269 phage had a similar genome organization to that of the unclassified Xanthomonas phage DES1, despite their low protein similarity. In addition, the signature proteins of StenR_269 and DES1 had low similarity and these proteins clustered far from the corresponding proteins of classified phages. Thus, the StenR_269 genome is orphan and the analyzed data suggest a new family in the class Caudoviricetes.
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Affiliation(s)
- Vyacheslav I. Yakubovskij
- Laboratory of Molecular Microbiology, Institute of Chemical Biology and Fundamental Medicine Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia; (V.I.Y.); (A.Y.T.); (I.V.B.); (I.K.B.)
- Faculty of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Vera V. Morozova
- Laboratory of Molecular Microbiology, Institute of Chemical Biology and Fundamental Medicine Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia; (V.I.Y.); (A.Y.T.); (I.V.B.); (I.K.B.)
| | - Yuliya N. Kozlova
- Laboratory of Molecular Microbiology, Institute of Chemical Biology and Fundamental Medicine Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia; (V.I.Y.); (A.Y.T.); (I.V.B.); (I.K.B.)
| | - Artem Y. Tikunov
- Laboratory of Molecular Microbiology, Institute of Chemical Biology and Fundamental Medicine Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia; (V.I.Y.); (A.Y.T.); (I.V.B.); (I.K.B.)
| | - Igor V. Babkin
- Laboratory of Molecular Microbiology, Institute of Chemical Biology and Fundamental Medicine Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia; (V.I.Y.); (A.Y.T.); (I.V.B.); (I.K.B.)
| | - Alevtina V. Bardasheva
- Laboratory of Molecular Microbiology, Institute of Chemical Biology and Fundamental Medicine Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia; (V.I.Y.); (A.Y.T.); (I.V.B.); (I.K.B.)
| | - Elena V. Zhirakovskaya
- Laboratory of Molecular Microbiology, Institute of Chemical Biology and Fundamental Medicine Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia; (V.I.Y.); (A.Y.T.); (I.V.B.); (I.K.B.)
| | - Ivan K. Baykov
- Laboratory of Molecular Microbiology, Institute of Chemical Biology and Fundamental Medicine Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia; (V.I.Y.); (A.Y.T.); (I.V.B.); (I.K.B.)
| | - Galina B. Kaverina
- Laboratory of Molecular Microbiology, Institute of Chemical Biology and Fundamental Medicine Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia; (V.I.Y.); (A.Y.T.); (I.V.B.); (I.K.B.)
| | - Nina V. Tikunova
- Laboratory of Molecular Microbiology, Institute of Chemical Biology and Fundamental Medicine Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia; (V.I.Y.); (A.Y.T.); (I.V.B.); (I.K.B.)
- Faculty of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
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de Miranda RVDSL, Monteiro GM, da Costa LV, Dos Santos MCS, Dos Reis CMF, Braga LMPDS, Forsythe SJ, Villas Bôas MHS, Brandão MLL. Evaluation of phenotypical and genotypical methods for the identification and typing of Stenotrophomonas maltophilia isolated from a pharmaceutical facility. J Appl Microbiol 2023; 134:lxad236. [PMID: 37838475 DOI: 10.1093/jambio/lxad236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 10/03/2023] [Accepted: 10/13/2023] [Indexed: 10/16/2023]
Abstract
AIMS Evaluate methods for identification and typing of Stenotrophomonas maltophilia isolated from a pharmaceutical facility. METHODS AND RESULTS From 270 S. maltophilia strains identified by VITEK®2, 40 were selected and submitted to MALDI TOF-MS, 16S and 23S rRNA gene analysis, enterobacterial repetitive intergenic consensus-polymerase chain reaction (ERIC-PCR), and an antimicrobial susceptibility profile. 16S rRNA sequencing was able to identify 39 (97.5%) strains as Stenotrophomonas spp. and one (2.5%) as Luteimonas huabeiensis. MALDI TOF-MS identified 37 (92.5%) strains as S. maltophilia, and three (7.5%) were not identified. PCR targeting 23S rRNA yielded a positive result for 39 (97.5%) strains. However, after sequencing, two strains were identified as Stenotrophomonas rhizophila, showing false-positive results. The confirmed S. maltophilia strains (n = 37) showed 35 distinct ERIC-PCR profiles and exhibited sensitivity to minocycline and levofloxacin, and six (16.3%) showed intermediate resistance to sulfamethoxazole-trimethoprim. CONCLUSION Matrix-assisted laser desorption lonization-time of flight mass spectrometry (MALDI-TOF MS) was a satisfactory methodology for the identification of S. maltophilia, but expansion of the database is necessary for the identification of other species. 16S rDNA sequencing showed low resolution for Stenotrophomonas species differentiation. PCR targeting 23S rRNA could not differentiate S. maltophilia from S. rhizophila. ERIC-PCR was shown to be a useful tool for the microbial source tracking of S. maltophilia.
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Affiliation(s)
- Rebeca Vitória da Silva Lage de Miranda
- Laboratory of Microbiological Control, Bio-Manguinhos/Fiocruz, CEP 21040-900, Rio de Janeiro, Brazil
- Laboratory of Microbiology of Food and Sanitizes, INCQS/Fiocruz, CEP 21040-900, Rio de Janeiro, Brazil
| | | | - Luciana Veloso da Costa
- Laboratory of Microbiological Control, Bio-Manguinhos/Fiocruz, CEP 21040-900, Rio de Janeiro, Brazil
| | | | | | | | | | | | - Marcelo Luiz Lima Brandão
- Laboratory of Microbiological Control, Bio-Manguinhos/Fiocruz, CEP 21040-900, Rio de Janeiro, Brazil
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Raio A, Brilli F, Neri L, Baraldi R, Orlando F, Pugliesi C, Chen X, Baccelli I. Stenotrophomonas rhizophila Ep2.2 inhibits growth of Botrytis cinerea through the emission of volatile organic compounds, restricts leaf infection and primes defense genes. FRONTIERS IN PLANT SCIENCE 2023; 14:1235669. [PMID: 37849842 PMCID: PMC10577304 DOI: 10.3389/fpls.2023.1235669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 09/05/2023] [Indexed: 10/19/2023]
Abstract
The bacterium Stenotrophomonas rhizophila is known to be beneficial for plants and has been frequently isolated from the rhizosphere of crops. In the present work, we isolated from the phyllosphere of an ornamental plant an epiphytic strain of S. rhizophila that we named Ep2.2 and investigated its possible application in crop protection. Compared to S. maltophilia LMG 958, a well-known plant beneficial species which behaves as opportunistic human pathogen, S. rhizophila Ep2.2 showed distinctive features, such as different motility, a generally reduced capacity to use carbon sources, a greater sensitivity to fusidic acid and potassium tellurite, and the inability to grow at the human body temperature. S. rhizophila Ep2.2 was able to inhibit in vitro growth of the plant pathogenic fungi Alternaria alternata and Botrytis cinerea through the emission of volatile compounds. Simultaneous PTR-MS and GC-MS analyses revealed the emission, by S. rhizophila Ep2.2, of volatile organic compounds (VOCs) with well-documented antifungal activity, such as furans, sulphur-containing compounds and terpenes. When sprayed on tomato leaves and plants, S. rhizophila Ep2.2 was able to restrict B. cinerea infection and to prime the expression of Pti5, GluA and PR1 plant defense genes.
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Affiliation(s)
- Aida Raio
- Institute for Sustainable Plant Protection (IPSP), National Research Council of Italy (CNR), Florence, Italy
| | - Federico Brilli
- Institute for Sustainable Plant Protection (IPSP), National Research Council of Italy (CNR), Florence, Italy
| | - Luisa Neri
- Institute for BioEconomy (IBE), National Research Council of Italy (CNR), Bologna, Italy
| | - Rita Baraldi
- Institute for BioEconomy (IBE), National Research Council of Italy (CNR), Bologna, Italy
| | - Francesca Orlando
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - Claudio Pugliesi
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - Xiaoyulong Chen
- College of Agriculture, College of Tobacco Science, Guizhou University, Guiyang, China
| | - Ivan Baccelli
- Institute for Sustainable Plant Protection (IPSP), National Research Council of Italy (CNR), Florence, Italy
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Pacholak A, Żur-Pińska J, Piński A, Nguyen QA, Ligaj M, Luczak M, Nghiem LD, Kaczorek E. Potential negative effect of long-term exposure to nitrofurans on bacteria isolated from wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 872:162199. [PMID: 36791847 DOI: 10.1016/j.scitotenv.2023.162199] [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: 09/26/2022] [Revised: 01/25/2023] [Accepted: 02/08/2023] [Indexed: 06/18/2023]
Abstract
Nitrofurans are broad-spectrum bactericidal agents used in a large quantity for veterinary and human therapy. This study reports the long-term impact of two nitrofuran representatives, nitrofurantoin (NFT) and furaltadone (FTD) on the bacterial strains Sphingobacterium siyangense FTD2, Achromobacter pulmonis NFZ2, and Stenotrophomonas maltophilia FZD2, isolated from a full-scale wastewater treatment plant. Bacterial whole genome sequencing was used for preliminary strains characterization. The metabolomic, electrochemical, and culture methods were applied to understand changes in the bacterial strains after 12-month exposure to nitrofurans. The most significantly altered metabolic pathways were observed in amino acid and sugar metabolism, and aminoacyl-tRNA biosynthesis. Disrupted protein biosynthesis was measured in all strains treated with antibiotics. Prolonged exposure to NFT and FTD also triggered mutagenic effects, affected metabolic activity, and facilitated oxidative stress within the cells. Nitrofuran-induced oxidative stress was evidenced from an elevated activity of catalase and glutathione S-transferases. NFT and FTD elicited similar but not identical responses in all analyzed strains. The results obtained in this study provide new insights into the potential risks of the prolonged presence of antimicrobial compounds in the environment and contribute to a better understanding of the possible impacts of nitrofuran antibiotics on the bacterial cells.
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Affiliation(s)
- Amanda Pacholak
- Institute of Chemical Technology and Engineering, Poznan University of Technology, Poland.
| | - Joanna Żur-Pińska
- Biotechnology Centre, The Silesian University of Technology, Gliwice, Poland; Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Poland
| | - Artur Piński
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Poland
| | - Quynh Anh Nguyen
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, New South Wales, Australia
| | - Marta Ligaj
- Department of Non-Food Products Quality and Packaging Development, Institute of Quality Science, Poznan University of Economics and Business, Poland
| | - Magdalena Luczak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Long D Nghiem
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, New South Wales, Australia
| | - Ewa Kaczorek
- Institute of Chemical Technology and Engineering, Poznan University of Technology, Poland
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Kumar P, Rani S, Dahiya P, Kumar A, Dang AS, Suneja P. Whole genome analysis for plant growth promotion profiling of Pantoea agglomerans CPHN2, a non-rhizobial nodule endophyte. Front Microbiol 2022; 13:998821. [DOI: 10.3389/fmicb.2022.998821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 09/13/2022] [Indexed: 11/09/2022] Open
Abstract
Reduced agricultural production as well as issues like nutrient-depleted soils, eutrophication, and groundwater contamination have drawn attention to the use of endophyte-based bioformulations to restore soil fertility. Pantoea agglomerans CPHN2, a non-rhizobial nodule endophyte isolated from Cicer arietinum, exhibited a variety of plant growth-promoting traits. In this study, we used NextSeq500 technology to analyze whole-genome sequence information of this plant growth-promoting endophytic bacteria. The genome of P. agglomerans CPHN2 has a length of 4,839,532 bp and a G + C content of 55.2%. The whole genome comprises three different genomic fractions, comprising one circular chromosome and two circular plasmids. A comparative analysis between P. agglomerans CPHN2 and 10 genetically similar strains was performed using a bacterial pan-genome pipeline. All the predicted and annotated gene sequences for plant growth promotions (PGPs), such as phosphate solubilization, siderophore synthesis, nitrogen metabolism, and indole-3-acetic acid (IAA) of P. agglomerans CPHN2, were identified. The whole-genome analysis of P. agglomerans CPHN2 provides an insight into the mechanisms underlying PGP by endophytes and its potential applications as a biofertilizer.
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Immobilized Stenotrophomonas maltophilia KB2 in Naproxen Degradation. Molecules 2022; 27:molecules27185795. [PMID: 36144528 PMCID: PMC9501314 DOI: 10.3390/molecules27185795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 09/05/2022] [Accepted: 09/06/2022] [Indexed: 11/20/2022] Open
Abstract
Immobilization is a commonly used method in response to the need to increase the resistance of microorganisms to the toxic effects of xenobiotics. In this study, a plant sponge from Luffa cylindrica was used as a carrier for the immobilization of the Stenotrophomonas maltophilia KB2 strain since such a carrier meets the criteria for high-quality carriers, i.e., low price and biodegradability. The optimal immobilization conditions were established as a temperature of 30 °C, pH 7.2, incubation time of 72 h, and an optical density of the culture of 1.4. The strain immobilized in such conditions was used for the biodegradation of naproxen, and an average rate of degradation of 3.8 µg/hour was obtained under cometabolic conditions with glucose. The obtained results indicate that a microbiological preparation based on immobilized cells on a luffa sponge can be used in bioremediation processes where it is necessary to remove the introduced carrier.
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Li Q. Perspectives on Converting Keratin-Containing Wastes Into Biofertilizers for Sustainable Agriculture. Front Microbiol 2022; 13:918262. [PMID: 35794912 PMCID: PMC9251476 DOI: 10.3389/fmicb.2022.918262] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 05/23/2022] [Indexed: 12/04/2022] Open
Abstract
Keratin-containing wastes become pollution to the environment if they are not treated properly. On the other hand, these wastes can be converted into value-added products applicable to many fields. Organic fertilizers and biofertilizers are important for sustainable agriculture by providing nutrients to enhance the growth speed of the plant and production. Keratin-containing wastes, therefore, will be an important resource to produce organic fertilizers. Many microorganisms exhibit capabilities to degrade keratins making them attractive to convert keratin-containing wastes into valuable products. In this review, the progress in microbial degradation of keratins is summarized. In addition, perspectives in converting keratin into bio- and organic fertilizers for agriculture are described. With proper treatment, feather wastes which are rich in keratin can be converted into high-value fertilizers to serve as nutrients for plants, reduce environmental pressure and improve the quality of the soil for sustainable agriculture.
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12
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Performance of halotolerant bacteria associated with Sahara-inhabiting halophytes Atriplex halimus L. and Lygeum spartum L. ameliorate tomato plant growth and tolerance to saline stress: from selective isolation to genomic analysis of potential determinants. World J Microbiol Biotechnol 2021; 38:16. [PMID: 34897563 DOI: 10.1007/s11274-021-03203-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 12/05/2021] [Indexed: 11/25/2022]
Abstract
The use of halotolerant beneficial plant-growth-promoting (PGP) bacteria is considered as a promising eco-friendly approach to improve the salt tolerance of cash crops. One strategy to enhance the possibility of obtaining stress-alleviating bacteria is to screen salt impacted soils. In this study, amongst the 40 endophytic bacteria isolated from the roots of Sahara-inhabiting halophytes Atriplex halimus L. and Lygeum spartum L., 8 showed interesting NaCl tolerance in vitro. Their evaluation, through different tomato plant trials, permitted the isolate IS26 to be distinguished as the most effective seed inoculum for both plant growth promotion and mitigation of salt stress. On the basis of 16S rRNA gene sequence, the isolate was closely related to Stenotrophomonas rhizophila. It was then screened in vitro for multiple PGP traits and the strain-complete genome was sequenced and analysed to further decipher the genomic basis of the putative mechanisms underlying its osmoprotective and plant growth abilities. A remarkable number of genes putatively involved in mechanisms responsible for rhizosphere colonization, plant association, strong competition for nutrients, and the production of important plant growth regulator compounds, such as AIA and spermidine, were highlighted, as were substances protecting against stress, including different osmolytes like trehalose, glucosylglycerol, proline, and glycine betaine. By having genes related to complementary mechanisms of osmosensing, osmoregulation and osmoprotection, the strain confirmed its great capacity to adapt to highly saline environments. Moreover, the presence of various genes potentially related to multiple enzymatic antioxidant processes, able to reduce salt-induced overproduction of ROS, was also detected.
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Chen MS, Chen XH, Yan XR, Li FN, Tuo L. Phycicoccus mangrovi sp. nov., a novel endophytic actinobacterium isolated from bark of Sonneratia apetala. Syst Appl Microbiol 2021; 44:126275. [PMID: 34715436 DOI: 10.1016/j.syapm.2021.126275] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 10/03/2021] [Accepted: 10/04/2021] [Indexed: 11/26/2022]
Abstract
Two novel strains KQZ13P-1T and MAQZ13P-2 were isolated from bark of Sonneratia apetala collected from Maowei sea Mangrove Nature Reserve in Guangxi Zhuang Autonomous Region, China. Two strains were Gram-positive, aerobic, non-spore-forming, no diffusion pigment actinobacterial strains and investigated by a polyphasic approach to determine their taxonomic position. The average nucleotide identity (ANI) value and the digital DNA-DNA hybridization (dDDH) value between the two strains were 99.9% and 99.7%, respectively, suggesting that they belonged to the same species. The ANI and dDDH values between strain KQZ13P-1T and five Phycicoccus species were 74.4-95.3% and 20.1-61.5%, respectively. Phylogenetic analyses based on 16S rRNA gene sequences showed that the two strains were member of the genus Phycicoccus and were closely related to P. jejuensis NRRL B-24460T (99.2% sequence similarity), followed by P. ginsengisoli DCY87T (97.5-97.6%). Moreover, based on 88 core genes, the phylogenomic tree indicated that the two strains clustered with P. jejuensis NRRL B-24460T. The cell-wall peptidoglycan of both strains contained meso-diaminopimelic acid. The major fatty acids in two strains were C17:1ω8c, iso-C15:0 and iso-C16:0. The major polar lipids included diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE) and phosphatidylinositol (PI). Based on phylogenetic, phenotypic and chemotaxonomic analysis, strains KQZ13P-1T and MAQZ13P-2 represent a novel species of the genus Phycicoccus, for which the name Phycicoccus mangrovi sp. nov. is proposed. The type strain is KQZ13P-1T (=CGMCC 1.18973T = JCM 34556T).
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Affiliation(s)
- Ming-Sheng Chen
- Life Sciences Institute, Zunyi Medical University, Zunyi 563006, PR China
| | - Xiao-Hui Chen
- Life Sciences Institute, Zunyi Medical University, Zunyi 563006, PR China
| | - Xiao-Rui Yan
- Life Sciences Institute, Zunyi Medical University, Zunyi 563006, PR China
| | - Fei-Na Li
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Key Discipline of Pediatrics (Capital Medical University), Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, PR China
| | - Li Tuo
- Life Sciences Institute, Zunyi Medical University, Zunyi 563006, PR China.
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Zhang M, Li L, Pan H, Zhou T. The complete genome sequence of a bile-isolated Stenotrophomonas maltophilia ZT1. Gut Pathog 2021; 13:64. [PMID: 34711270 PMCID: PMC8555292 DOI: 10.1186/s13099-021-00456-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 10/06/2021] [Indexed: 11/10/2022] Open
Abstract
Background Stenotrophomonas maltophilia is one of the most frequently isolated opportunistic pathogens that can cause infections in humans. Many researches concerned the mechanism of antibiotic resistance displayed by S. maltophilia, however, the mechanism of its pathogenesis and its adaptation to special niches, such as bile, remain unclear. Results In this study, the S. maltophilia strain ZT1 was isolated from human bile. Its genome was sequenced and a circular chromosome of 4,391,471 bp was obtained with a GC content of 66.51%. There were 3962 protein-coding sequences, 7 rRNAs and 74 tRNAs in the chromosome. Compared with Virulence Factor Database, we identified more than 500 candidate virulence genes including genes encoding fimbrial assembly protein, enterobactin synthesis pathway proteins, efflux pumps, and the DNA and/or proteins secretion system in the genome of strain ZT1. Additionally, there were at least 22 genes related to bile adaption, including emrAB, acrRAB, galU, rfbC, tolC and mdtABC. Conclusions This is the first study to reveal the whole genome sequence of the ZT1 strain of S. maltophilia isolated from human bile. We identified hundreds virulence factors and 22 bile adaptation-related genes in the genome of the S. maltophilia strain ZT1. Further comparative genomic analysis and functional verification would aid in understanding the pathogenesis and bile adaptation of S. maltophilia. Supplementary Information The online version contains supplementary material available at 10.1186/s13099-021-00456-y.
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Affiliation(s)
- Min Zhang
- Department of Gastroenterology, Qilu Hospital, Shandong University, 107 Wenhuaxi Road, Shandong, 250012, Jinan, People's Republic of China
| | - Lixiang Li
- Key Laboratory of Translational Gastroenterology, Shandong University, 250012, Jinan, People's Republic of China
| | - Hongwei Pan
- Department of Clinical Laboratory, Qilu Hospital, Shandong University, Shandong, 250012, Jinan, China
| | - Tao Zhou
- Department of Gastroenterology, Qilu Hospital, Shandong University, 107 Wenhuaxi Road, Shandong, 250012, Jinan, People's Republic of China.
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Chhetri G, Kim I, Kang M, Kim J, So Y, Seo T. Nocardioides baculatus sp. nov., a novel actinomycete isolated from the rhizosphere of Tagetes patula. Int J Syst Evol Microbiol 2021; 71. [PMID: 34542392 DOI: 10.1099/ijsem.0.005012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An aerobic, Gram-stain-positive, non-motile, dull-yellow, short rod-shaped actinomycete strain, designated G10T, was isolated from Tagetes patula (marigold) roots collected from Goyang in the Republic of Korea. The isolate showed best growth on Reasoner's 2A agar at 25 °C, pH 6.5.0 and with 0% NaCl (w/v). The strain was negative for oxidase activity and positive for catalase activity. On the basis of 16S RNA gene sequence similarity, strain G10T was affiliated to the genus Nocardioides and the closest species were Nocardioides glacieisoli HLT3-15T (98.8 %), Nocardioides zhouii HLT2-9T (98.8 %), Nocardioides ganghwensis JC2055T (98.7 %), Nocardioides cavernae YIM A1136T (98.6 %), Nocardioides flavus Y4T (98.5 %), Nocardioides oleivorans DSM 16090T (98.3 %), Nocardioides alpinus Cr7-14T (98.2 %), Nocardioides exalbidus DSM 22017T (98.1 %) and Nocardioides hwasunensis KCTC 19197T (98.1 %). Strain G10T formed a monophyletic cluster with N. glacieisoli HLT3-15T, N. zhouii HLT2-9T and N. hwasunensis KCTC 19197T in all phylogenetic trees. The cell-wall peptidoglycan of strain G10T contained ll-diaminopimelic acid as the diagnostic amino acid. The predominant fatty acids were iso-C16 : 0 and C17 : 1 ω8c. MK-8(H4) was the major isoprenoid quinone. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol. Average nucleotide identity and digital DNA-DNA hybridization values were 78.6-88.7 % and 21.5-36.2 %, respectively, with the type strains of related species of the genus Nocardioides, suggesting that strain G10T represents a novel species. The genome of strain G10T is 4 231 000 bp long with a DNA G+C content of 71.5 mol% and encodes 4071 predicted proteins, six rRNAs and 46 tRNAs. The genome of strain G10T comprises the biosynthetic gene cluster for T3PKS, terpene, NRPS-like fragment and RRE-containing element as secondary metabolites. The results of taxonomic, phylogenetic, biochemical, chemotaxonomic and genomic analysis clearly supported that strain G10T represent a novel species within the genus Nocardioides, for which the name Nocardioides baculatus sp. nov is proposed and the type strain is G10T (=KCTC 49626T=NBRC 114801T).
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Affiliation(s)
- Geeta Chhetri
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
| | - Inhyup Kim
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
| | - Minchung Kang
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
| | - Jiyoun Kim
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
| | - Yoonseop So
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
| | - Taegun Seo
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
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Li Q. Structure, Application, and Biochemistry of Microbial Keratinases. Front Microbiol 2021; 12:674345. [PMID: 34248885 PMCID: PMC8260994 DOI: 10.3389/fmicb.2021.674345] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 05/17/2021] [Indexed: 12/17/2022] Open
Abstract
Keratinases belong to a class of proteases that are able to degrade keratins into amino acids. Microbial keratinases play important roles in turning keratin-containing wastes into value-added products by participating in the degradation of keratin. Keratin is found in human and animal hard tissues, and its complicated structures make it resistant to degradation by common proteases. Although breaking disulfide bonds are involved in keratin degradation, keratinase is responsible for the cleavage of peptides, making it attractive in pharmaceutical and feather industries. Keratinase can serve as an important tool to convert keratin-rich wastes such as feathers from poultry industry into diverse products applicable to many fields. Despite of some progress made in isolating keratinase-producing microorganisms, structural studies of keratinases, and biochemical characterization of these enzymes, effort is still required to expand the biotechnological application of keratinase in diverse fields by identifying more keratinases, understanding the mechanism of action and constructing more active enzymes through molecular biology and protein engineering. Herein, this review covers structures, applications, biochemistry of microbial keratinases, and strategies to improve its efficiency in keratin degradation.
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Affiliation(s)
- Qingxin Li
- Guangdong Provincial Engineering Laboratory of Biomass High Value Utilization, Institute of Bioengineering, Guangdong Academy of Sciences, Guangzhou, China
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17
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Ulrich K, Kube M, Becker R, Schneck V, Ulrich A. Genomic Analysis of the Endophytic Stenotrophomonas Strain 169 Reveals Features Related to Plant-Growth Promotion and Stress Tolerance. Front Microbiol 2021; 12:687463. [PMID: 34220780 PMCID: PMC8245107 DOI: 10.3389/fmicb.2021.687463] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 05/20/2021] [Indexed: 11/15/2022] Open
Abstract
Plant-associated Stenotrophomonas isolates have great potential for plant growth promotion, especially under stress conditions, due to their ability to promote tolerance to abiotic stresses such as salinity or drought. The endophytic strain Stenotrophomonas sp. 169, isolated from a field-grown poplar, increased the growth of inoculated in vitro plants, with a particular effect on root development, and was able to stimulate the rooting of poplar cuttings in the greenhouse. The strain produced high amounts of the plant growth-stimulating hormone auxin under in vitro conditions. The comparison of the 16S rRNA gene sequences and the phylogenetic analysis of the core genomes showed a close relationship to Stenotrophomonas chelatiphaga and a clear separation from Stenotrophomonas maltophilia. Whole genome sequence analysis revealed functional genes potentially associated with attachment and plant colonization, growth promotion, and stress protection. In detail, an extensive set of genes for twitching motility, chemotaxis, flagella biosynthesis, and the ability to form biofilms, which are connected with host plant colonization, could be identified in the genome of strain 169. The production of indole-3-acetic acid and the presence of genes for auxin biosynthesis pathways and the spermidine pathway could explain the ability to promote plant growth. Furthermore, the genome contained genes encoding for features related to the production of different osmoprotective molecules and enzymes mediating the regulation of stress tolerance and the ability of bacteria to quickly adapt to changing environments. Overall, the results of physiological tests and genome analysis demonstrated the capability of endophytic strain 169 to promote plant growth. In contrast to related species, strain 169 can be considered non-pathogenic and suitable for biotechnology applications.
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Affiliation(s)
- Kristina Ulrich
- Johann Heinrich von Thünen Institute, Institute of Forest Genetics, Waldsieversdorf, Germany
| | | | - Regina Becker
- Leibniz Center for Agricultural Landscape Research (ZALF), Müncheberg, Germany
| | - Volker Schneck
- Johann Heinrich von Thünen Institute, Institute of Forest Genetics, Waldsieversdorf, Germany
| | - Andreas Ulrich
- Leibniz Center for Agricultural Landscape Research (ZALF), Müncheberg, Germany
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18
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Chen MS, Pang BQ, Liu SW, Li FN, Yan XR, Sun CH, Tuo L. Phycicoccus flavus sp. nov., a novel endophytic actinobacterium isolated from branch of Kandelia candel. Int J Syst Evol Microbiol 2021; 71. [PMID: 33909548 DOI: 10.1099/ijsem.0.004794] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
A Gram-stain-positive, aerobic, non-motile, non-endospore-forming and rod-shaped actinobacterium, designated strain CMS6Z-2T, was isolated from a surface-sterilized branch of Kandelia candel collected from the Maowei Sea, Guangxi Zhuang Autonomous Region, PR China. Strain CMS6Z-2T grew at 10-37 °C (optimum, 37 °C), pH 6.0-9.0 (optimum, pH 7.0-8.0) and in the presence of 0-10.0 % (w/v) NaCl (optimum, 0-1.0 %). Strain CMS6Z-2T possessed meso-diaminopimelic acid as the diamino acid of the peptidoglycan and MK-8 (H4) as the predominant menaquinone. The major fatty acids were iso-C15 : 0, C16 : 0 and C18 : 1 ω9c. The polar lipids comprised diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and two unknown phospholipids. The G+C content of the genomic DNA was 74.1 mol%. Comparative analysis of 16S rRNA genes showed that strain CMS6Z-2T should be assigned to the genus Phycicoccus and its closest relative was Phycicoccus endophyticus IP6SC6T with 98.3 % similarity. Phylogenetic analyses based on 16S rRNA gene sequence and phylogenomic analysis based on core proteomes alignment revealed that strain CMS6Z-2T belonged to the genus Phycicoccus and formed a robust cluster with Phycicoccus endophyticus IP6SC6T within the genus Phycicoccus. The average nucleotide identity value and estimated digital DNA-DNA hybridization value between strain CMS6Z-2T and the type strain of Phycicoccus endophyticus were 81.5 and 23.9 %, respectively. On the basis of phylogenetic, phenotypic and chemotaxonomic characteristics, strain CMS6Z-2T represents a novel species of the genus Phycicoccus, for which the name Phycicoccus flavus sp. nov. is proposed. The type strain is CMS6Z-2T (=KCTC 49240T=CGMCC4.7549T).
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Affiliation(s)
- Ming-Sheng Chen
- Life Sciences Institute, Zunyi Medical University, Zunyi 563006, PR China
| | - Bao-Quan Pang
- The Second People's Hospital of Heze in Shandong Province, Heze 274005, PR China
| | - Shao-Wei Liu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, PR China
| | - Fei-Na Li
- Key Laboratory of Major Diseases in Children, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Key Discipline of Pediatrics (Capital Medical University), Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, PR China
| | - Xiao-Rui Yan
- Life Sciences Institute, Zunyi Medical University, Zunyi 563006, PR China
| | - Cheng-Hang Sun
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, PR China
| | - Li Tuo
- Life Sciences Institute, Zunyi Medical University, Zunyi 563006, PR China
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