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Wang Z, Cui L, Wang X, Shen C, Wang Y, Jiang W, Gu Y. Comparative Transcriptomics and Intestinal Microbiome Analysis Provide Insights into the Semi-Terrestrial Adaptation of Helice tientsinensis. Animals (Basel) 2025; 15:1244. [PMID: 40362059 PMCID: PMC12070891 DOI: 10.3390/ani15091244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2025] [Revised: 04/24/2025] [Accepted: 04/25/2025] [Indexed: 05/15/2025] Open
Abstract
Helice tientsinensis, a Grapsidae family member, can adapt to terrestrial and semi-terrestrial environments. This study used transcriptomic and microbiome analyses to explore its adaptation mechanisms. Transcriptome analysis showed gene changes related to cytoskeleton-motor, water-osmotic pressure, and energy metabolism. For example, DST was upregulated in the aquatic environment compared to the semi-terrestrial one, and SPAST was downregulated in some groups. ATP2A and SLC6A3 were upregulated with osmotic regulation, and IDH3 was upregulated when comparing the aquatic and semi-terrestrial habitats; at the same time, many energy-related genes were downregulated between the terrestrial and semi-terrestrial habitats. Regarding the gut microbiota, no significant differences in alpha diversity were found between habitats, but there were differences at the genus level. Pseudomonas and Malaciobacter were more abundant in the aquatic habitat, and Dietzia in the semi-terrestrial one. These results provide insights into H. tientsinensis' terrestrial adaptation, benefiting crustacean evolution study and aquaculture.
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Affiliation(s)
- Zhengfei Wang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal, Bio-Agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers University, Yancheng 224001, China; (L.C.); (X.W.); (C.S.); (Y.W.); (W.J.); (Y.G.)
| | - Lijie Cui
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal, Bio-Agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers University, Yancheng 224001, China; (L.C.); (X.W.); (C.S.); (Y.W.); (W.J.); (Y.G.)
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Xinyu Wang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal, Bio-Agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers University, Yancheng 224001, China; (L.C.); (X.W.); (C.S.); (Y.W.); (W.J.); (Y.G.)
| | - Chenchen Shen
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal, Bio-Agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers University, Yancheng 224001, China; (L.C.); (X.W.); (C.S.); (Y.W.); (W.J.); (Y.G.)
| | - Yan Wang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal, Bio-Agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers University, Yancheng 224001, China; (L.C.); (X.W.); (C.S.); (Y.W.); (W.J.); (Y.G.)
| | - Weijie Jiang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal, Bio-Agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers University, Yancheng 224001, China; (L.C.); (X.W.); (C.S.); (Y.W.); (W.J.); (Y.G.)
| | - Yue Gu
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal, Bio-Agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers University, Yancheng 224001, China; (L.C.); (X.W.); (C.S.); (Y.W.); (W.J.); (Y.G.)
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2
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Zhang Y, Jia X, Yuan P, Li B, Pan W, Liu J, Zhao W. Activated Sludge Combined with Pervious Concrete Micro-Ecosystem for Runoff Rainwater Collection and Pollutant Purification. TOXICS 2024; 12:838. [PMID: 39771053 PMCID: PMC11679453 DOI: 10.3390/toxics12120838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2024] [Revised: 11/16/2024] [Accepted: 11/21/2024] [Indexed: 01/11/2025]
Abstract
This study investigated the purification of pollutants in runoff rainwater by constructing a micro-ecosystem using waste-activated sludge (WAS) and riverbed sludge (RBS) as inoculums in combination with pervious concrete. The research results showed that the best hydraulic retention time (HRT) was 9 h. The COD and ammonia nitrogen (NH4+-N) removal of the waste-activated sludge ecosystem (WASE) was 62.67% and 71.21%, respectively, while the riverbed sludge ecosystem (RBSE) showed COD and NH4+-N removal percentages of 46.05% and 66.55%, respectively. The analysis of the genetic metabolism of microbial genes showed that the system was microbially enhanced with extensive and diverse populations. At the phylum level, the microorganisms responsible for degrading organic matter were mainly Firmicutes and Actinobacteriota. At the genus level, the Trichococcus genus was dominant in the WASE, while the Dietzia, norank_f__Sporomusaceae and norank_f__norank_o__norank_c__BRH-c20a genera were the central bacterial populations in the RBSE. The proliferation of phylum-level bacteria in the WASE was relatively large, and the genus-level bacteria demonstrated a better removal efficiency for pollutants. The overall removal effect of the WASE was better than that of the RBSE. The application analyses showed that a WASE is capable of effectively accepting and treating all rainfall below rainstorm levels and at near-full rainstorm levels under optimal removal efficiency conditions. This study innovatively used wastewater plant waste-activated sludge combined with pervious concrete to construct a micro-ecosystem to remove runoff rainwater pollutants. The system achieved pollutant removal comparable to that of pervious concrete modified with adsorbent materials. An effective method for the collection and pollutant treatment of urban runoff rainwater is provided.
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Affiliation(s)
- Yongsheng Zhang
- School of Civil Engineering, Henan Polytechnic University, Jiaozuo 454003, China; (Y.Z.); (X.J.); (P.Y.); (B.L.); (W.P.); (J.L.)
| | - Xuechen Jia
- School of Civil Engineering, Henan Polytechnic University, Jiaozuo 454003, China; (Y.Z.); (X.J.); (P.Y.); (B.L.); (W.P.); (J.L.)
| | - Pengfei Yuan
- School of Civil Engineering, Henan Polytechnic University, Jiaozuo 454003, China; (Y.Z.); (X.J.); (P.Y.); (B.L.); (W.P.); (J.L.)
| | - Bingqi Li
- School of Civil Engineering, Henan Polytechnic University, Jiaozuo 454003, China; (Y.Z.); (X.J.); (P.Y.); (B.L.); (W.P.); (J.L.)
| | - Wenyan Pan
- School of Civil Engineering, Henan Polytechnic University, Jiaozuo 454003, China; (Y.Z.); (X.J.); (P.Y.); (B.L.); (W.P.); (J.L.)
| | - Jianfei Liu
- School of Civil Engineering, Henan Polytechnic University, Jiaozuo 454003, China; (Y.Z.); (X.J.); (P.Y.); (B.L.); (W.P.); (J.L.)
| | - Weilong Zhao
- School of Civil Engineering, Henan Polytechnic University, Jiaozuo 454003, China; (Y.Z.); (X.J.); (P.Y.); (B.L.); (W.P.); (J.L.)
- Henan Province Engineering Laboratory for Eco-Architecture and the Built Environment, Henan Polytechnic University, Jiaozuo 454000, China
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3
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Gutiérrez Y, Alarcón KA, Ortiz C, Santos-Holguín JM, García-Riaño JL, Mejía C, Amaya CV, Uribe-Gutiérrez L. Isolation and characterization of a native strain of the entomopathogenic fungus Beauveria bassiana for the control of the palm weevil Dynamis borassi (Coleoptera: Curculionidae) in the neotropics. World J Microbiol Biotechnol 2024; 40:260. [PMID: 38967730 PMCID: PMC11226477 DOI: 10.1007/s11274-024-04044-5] [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: 05/06/2024] [Accepted: 05/30/2024] [Indexed: 07/06/2024]
Abstract
This study aimed to isolate and characterize a native strain of Beauveria bassiana, coded as Bv065, showcasing its potential as a biological control agent targeting the palm weevil Dynamis borassi. Originating from a naturally infected D. borassi specimen collected in southwestern Colombia, the fungus underwent molecular identification and was identified as B. bassiana, exhibiting high sequence similarity with known reference strains. The physiological characterization revealed that Bv065 thrived within a temperature range of 25 to 30 °C and a pH range of 6 to 9. Moreover, the key carbon sources that allow optimal growth of the strain were identified through metabolic profiling, including sucrose, D-mannose, and γ-amino-butyric acid. These findings offer strategic insights for scalability and formulation methodologies. Additionally, enzymatic analyses unveiled robust protease activity within Bv065, crucial for catalysing insect cuticle degradation and facilitating host penetration, thus accentuating its entomopathogenic potential. Subsequent evaluations exposed Bv065's pathogenicity against D. borassi, causing significant mortality within nine days of exposure, albeit exhibiting limited effectiveness against Rhynchophorus palmarum. This study underscores the importance of understanding optimal growth conditions and metabolic preferences of B. bassiana strains for developing effective biopesticides. The findings suggest Bv065 as a promising candidate for integrated pest management strategies in neotropical regions, particularly for controlling palm weevil infestations in coconut and peach palm cultivation. Future research avenues include refining mass production methodologies, formulating novel delivery systems, and conducting comprehensive field efficacy trials to unlock the full potential of Bv065 in fostering sustainable pest management practices. Overall, this study contributes to the growing body of knowledge on entomopathogenic fungi and their pivotal role in biological control, offering nuanced perspectives on eco-friendly alternatives to conventional insecticidal interventions.
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Affiliation(s)
- Yeisson Gutiérrez
- Corporación Colombiana de Investigación Agropecuaria-Agrosavia. Centro de Investigación La Libertad, Km. 17 Vía Puerto López, Villavicencio-Meta, Colombia.
| | - Karen A Alarcón
- Corporación Colombiana de Investigación Agropecuaria-Agrosavia. Centro de Investigación El Mira, Km. 38, Vía Tumaco-Pasto, Tumaco-Nariño, Colombia
| | - Cristian Ortiz
- Corporación Colombiana de Investigación Agropecuaria-Agrosavia. Centro de Investigación El Mira, Km. 38, Vía Tumaco-Pasto, Tumaco-Nariño, Colombia
| | - Jenny M Santos-Holguín
- Corporación Colombiana de Investigación Agropecuaria-Agrosavia. Centro de Investigación Tibaitatá, Sede Tunja-Boyacá, Colombia
| | - Jennifer L García-Riaño
- Corporación Colombiana de Investigación Agropecuaria-Agrosavia, Centro de Investigación Tibaitatá, Km 14 Vía Bogotá-Mosquera, Mosquera, Colombia
| | - Cindy Mejía
- Corporación Colombiana de Investigación Agropecuaria-Agrosavia, Centro de Investigación Tibaitatá, Km 14 Vía Bogotá-Mosquera, Mosquera, Colombia
| | - Carol V Amaya
- Corporación Colombiana de Investigación Agropecuaria-Agrosavia. Centro de Investigación La Libertad, Km. 17 Vía Puerto López, Villavicencio-Meta, Colombia
| | - Liz Uribe-Gutiérrez
- Corporación Colombiana de Investigación Agropecuaria-Agrosavia, Centro de Investigación Tibaitatá, Km 14 Vía Bogotá-Mosquera, Mosquera, Colombia
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Singh RP, Sinha A, Deb S, Kumari K. First report on in-depth genome and comparative genome analysis of a metal-resistant bacterium Acinetobacter pittii S-30, isolated from environmental sample. Front Microbiol 2024; 15:1351161. [PMID: 38741743 PMCID: PMC11089254 DOI: 10.3389/fmicb.2024.1351161] [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: 12/20/2023] [Accepted: 04/09/2024] [Indexed: 05/16/2024] Open
Abstract
A newly isolated bacterium Acinetobacter pittii S-30 was recovered from waste-contaminated soil in Ranchi, India. The isolated bacterium belongs to the ESKAPE organisms which represent the major nosocomial pathogens that exhibit high antibiotic resistance. Furthermore, average nucleotide identity (ANI) analysis also showed its closest match (>95%) to other A. pittii genomes. The isolate showed metal-resistant behavior and was able to survive up to 5 mM of ZnSO4. Whole genome sequencing and annotations revealed the occurrence of various genes involved in stress protection, motility, and metabolism of aromatic compounds. Moreover, genome annotation identified the gene clusters involved in secondary metabolite production (biosynthetic gene clusters) such as arylpolyene, acinetobactin like NRP-metallophore, betalactone, and hserlactone-NRPS cluster. The metabolic potential of A. pittii S-30 based on cluster of orthologous, and Kyoto Encyclopedia of Genes and Genomes indicated a high number of genes related to stress protection, metal resistance, and multiple drug-efflux systems etc., which is relatively rare in A. pittii strains. Additionally, the presence of various carbohydrate-active enzymes such as glycoside hydrolases (GHs), glycosyltransferases (GTs), and other genes associated with lignocellulose breakdown suggests that strain S-30 has strong biomass degradation potential. Furthermore, an analysis of genetic diversity and recombination in A. pittii strains was performed to understand the population expansion hypothesis of A. pittii strains. To our knowledge, this is the first report demonstrating the detailed genomic characterization of a heavy metal-resistant bacterium belonging to A. pittii. Therefore, the A. pittii S-30 could be a good candidate for the promotion of plant growth and other biotechnological applications.
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Affiliation(s)
- Rajnish Prakash Singh
- Department of Biotechnology, Jaypee Institute of Information Technology, Noida, India
| | - Ayushi Sinha
- Department of Biotechnology, Jaypee Institute of Information Technology, Noida, India
| | - Sushanta Deb
- Department of Veterinary Microbiology and Pathology, Washington State University (WSU), Pullman, WA, United States
| | - Kiran Kumari
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, India
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Olivera C, Laura Tondo M, Girardi V, Sol Herrero M, Lucía Balaban C, Matías Salvatierra L. High-performance diesel biodegradation using biogas digestate as microbial inoculum in lab-scale solid supported bioreactors. CHEMOSPHERE 2024; 352:141384. [PMID: 38350516 DOI: 10.1016/j.chemosphere.2024.141384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 01/30/2024] [Accepted: 02/02/2024] [Indexed: 02/15/2024]
Abstract
Industrial anaerobic digestion (AD) produces biogas and a digestate that is usually applied as a biofertilizer. However, the study and application of this by-product in terms of its rich microbial diversity and high metabolic activity have been barely investigated. In this work, the digestate regarded as an inoculum-without any further manipulation-was faced to a target hydrocarbon (i.e., diesel oil) to explore its biodegradation capability and potential application in bioaugmentation strategies. Lab-scale single batch bioreactors with solid support (i.e., sand or gravel) embedded with the inoculum and diesel were used to improve bioaccessibility and biofilm formation. In addition, different experimental conditions were assayed varying the initial diesel concentration, microbial load, type of solid support, inoculum aging time, and presence or absence of oxygen. Remaining diesel concentration, dehydrogenase activity and microbial community structure were periodically determined. Remarkably, this low-cost consortium was capable of a significant reduction (>90%) in the concentration of diesel, within 14 days and when the initial load was as high as 6950 mg/kg dry solid support. Furthermore, a 10-fold increment in dehydrogenase activity, alongside an increase in the abundance of hydrocarbon-degrading bacterial groups, and the enrichment of genes for alkane monooxygenase and aromatic ring-hydroxylating dioxygenases, encourage further study of this consortium for bioremediation purposes.
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Affiliation(s)
- Camila Olivera
- Instituto de Investigaciones en Ingeniería Ambiental, Química y Biotecnología Aplicada - INGEBIO-, Facultad de Química e Ingeniería del Rosario, Pontificia Universidad Católica Argentina (UCA), Av. Pellegrini 3314, (S2002QEO), Rosario, (Santa Fe), Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
| | - María Laura Tondo
- Instituto de Investigaciones en Ingeniería Ambiental, Química y Biotecnología Aplicada - INGEBIO-, Facultad de Química e Ingeniería del Rosario, Pontificia Universidad Católica Argentina (UCA), Av. Pellegrini 3314, (S2002QEO), Rosario, (Santa Fe), Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
| | - Valentina Girardi
- Instituto de Investigaciones en Ingeniería Ambiental, Química y Biotecnología Aplicada - INGEBIO-, Facultad de Química e Ingeniería del Rosario, Pontificia Universidad Católica Argentina (UCA), Av. Pellegrini 3314, (S2002QEO), Rosario, (Santa Fe), Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
| | - María Sol Herrero
- Instituto de Investigaciones en Ingeniería Ambiental, Química y Biotecnología Aplicada - INGEBIO-, Facultad de Química e Ingeniería del Rosario, Pontificia Universidad Católica Argentina (UCA), Av. Pellegrini 3314, (S2002QEO), Rosario, (Santa Fe), Argentina
| | - Cecilia Lucía Balaban
- Instituto de Investigaciones en Ingeniería Ambiental, Química y Biotecnología Aplicada - INGEBIO-, Facultad de Química e Ingeniería del Rosario, Pontificia Universidad Católica Argentina (UCA), Av. Pellegrini 3314, (S2002QEO), Rosario, (Santa Fe), Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
| | - Lucas Matías Salvatierra
- Instituto de Investigaciones en Ingeniería Ambiental, Química y Biotecnología Aplicada - INGEBIO-, Facultad de Química e Ingeniería del Rosario, Pontificia Universidad Católica Argentina (UCA), Av. Pellegrini 3314, (S2002QEO), Rosario, (Santa Fe), Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina.
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Liukkonen M, Hukkanen M, Cossin-Sevrin N, Stier A, Vesterinen E, Grond K, Ruuskanen S. No evidence for associations between brood size, gut microbiome diversity and survival in great tit (Parus major) nestlings. Anim Microbiome 2023; 5:19. [PMID: 36949549 PMCID: PMC10031902 DOI: 10.1186/s42523-023-00241-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 03/13/2023] [Indexed: 03/24/2023] Open
Abstract
BACKGROUND The gut microbiome forms at an early stage, yet data on the environmental factors influencing the development of wild avian microbiomes is limited. As the gut microbiome is a vital part of organismal health, it is important to understand how it may connect to host performance. The early studies with wild gut microbiome have shown that the rearing environment may be of importance in gut microbiome formation, yet the results vary across taxa, and the effects of specific environmental factors have not been characterized. Here, wild great tit (Parus major) broods were manipulated to either reduce or enlarge the original brood soon after hatching. We investigated if brood size was associated with nestling bacterial gut microbiome, and whether gut microbiome diversity predicted survival. Fecal samples were collected at mid-nestling stage and sequenced with the 16S rRNA gene amplicon sequencing, and nestling growth and survival were measured. RESULTS Gut microbiome diversity showed high variation between individuals, but this variation was not significantly explained by brood size or body mass. Additionally, we did not find a significant effect of brood size on body mass or gut microbiome composition. We also demonstrated that early handling had no impact on nestling performance or gut microbiome. Furthermore, we found no significant association between gut microbiome diversity and short-term (survival to fledging) or mid-term (apparent juvenile) survival. CONCLUSIONS We found no clear association between early-life environment, offspring condition and gut microbiome. This suggests that brood size is not a significantly contributing factor to great tit nestling condition, and that other environmental and genetic factors may be more strongly linked to offspring condition and gut microbiome. Future studies should expand into other early-life environmental factors e.g., diet composition and quality, and parental influences.
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Affiliation(s)
- Martta Liukkonen
- Department of Biological and Environmental Science, University of Jyväskylä, Jyvaskyla, Finland.
| | - Mikaela Hukkanen
- Department of Biology, University of Turku, Turku, Finland
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | | | - Antoine Stier
- Department of Biology, University of Turku, Turku, Finland
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023 LEHNA, 69622, Lyon, France
- Institut Pluridisciplinaire Hubert Curien, UMR7178, Université de Strasbourg, CNRS, Strasbourg, France
| | | | - Kirsten Grond
- Department of Biological Sciences, University of Alaska Anchorage, Anchorage, AK, 99508, USA
| | - Suvi Ruuskanen
- Department of Biological and Environmental Science, University of Jyväskylä, Jyvaskyla, Finland
- Department of Biology, University of Turku, Turku, Finland
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Santos RGD, Hurtado R, Rodrigues DLN, Lima A, Dos Anjos WF, Rifici C, Attili AR, Tiwari S, Jaiswal AK, Spier SJ, Mazzullo G, Morais-Rodrigues F, Gomide ACP, de Jesus LCL, Aburjaile FF, Brenig B, Cuteri V, Castro TLDP, Seyffert N, Santos A, Góes-Neto A, de Jesus Sousa T, Azevedo V. Comparative genomic analysis of the Dietzia genus: an insight into genomic diversity, and adaptation. Res Microbiol 2023; 174:103998. [PMID: 36375718 DOI: 10.1016/j.resmic.2022.103998] [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: 06/13/2022] [Revised: 10/27/2022] [Accepted: 11/02/2022] [Indexed: 11/13/2022]
Abstract
Dietzia strains are widely distributed in the environment, presenting an opportunistic role, and some species have undetermined taxonomic characteristics. Here, we propose the existence of errors in the classification of species in this genus using comparative genomics. We performed ANI, dDDH, pangenome and genomic plasticity analyses better to elucidate the phylogenomic relationships between Dietzia strains. For this, we used 55 genomes of Dietzia downloaded from public databases that were combined with a newly sequenced. Sequence analysis of a phylogenetic tree based on genome similarity comparisons and dDDH, ANI analyses supported grouping different Dietzia species into four distinct groups. The pangenome analysis corroborated the classification of these groups, supporting the idea that some species of Dietzia could be reassigned in a possible classification into three distinct species, each containing less variability than that found within the global pangenome of all strains. Additionally, analysis of genomic plasticity based on groups containing Dietzia strains found differences in the presence and absence of symbiotic Islands and pathogenic islands related to their isolation site. We propose that the comparison of pangenome subsets together with phylogenomic approaches can be used as an alternative for the classification and differentiation of new species of the genus Dietzia.
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Affiliation(s)
- Roselane Gonçalves Dos Santos
- Cellular and Molecular Genetics Laboratory, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil.
| | - Raquel Hurtado
- Cellular and Molecular Genetics Laboratory, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil.
| | - Diego Lucas Neres Rodrigues
- Cellular and Molecular Genetics Laboratory, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Alessandra Lima
- Cellular and Molecular Genetics Laboratory, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | | | - Claudia Rifici
- Department of Veterinary Science, University of Messina (Italy), Polo Universitario dell'Annunziata, 98168 Messina (ME), Italy.
| | - Anna Rita Attili
- School of Biosciences and Veterinary Medicine, University of Camerino (Italy), Via Circonvallazione 93/95, 62024 Matelica (MC), Italy.
| | - Sandeep Tiwari
- Cellular and Molecular Genetics Laboratory, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil; Postgraduate Program in Microbiology, Institute of Biology, Federal University of Bahia, Salvador, BA, Brazil; Postgraduate Program in Immunology, Institute of Health Sciences, Federal University of Bahia, Salvador, BA, Brazil
| | - Arun Kumar Jaiswal
- Cellular and Molecular Genetics Laboratory, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Sharon J Spier
- Department of Veterinary Medicine and Epidemiology, University of California, Davis, CA, USA.
| | - Giuseppe Mazzullo
- Department of Veterinary Science, University of Messina (Italy), Polo Universitario dell'Annunziata, 98168 Messina (ME), Italy.
| | - Francielly Morais-Rodrigues
- Cellular and Molecular Genetics Laboratory, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Anne Cybelle Pinto Gomide
- Cellular and Molecular Genetics Laboratory, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Luís Cláudio Lima de Jesus
- Cellular and Molecular Genetics Laboratory, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Flavia Figueira Aburjaile
- Cellular and Molecular Genetics Laboratory, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Bertram Brenig
- Institute of Veterinary Medicine, University of Göttingen, Burckhardtweg 2, Göttingen, Germany.
| | - Vincenzo Cuteri
- School of Biosciences and Veterinary Medicine, University of Camerino (Italy), Via Circonvallazione 93/95, 62024 Matelica (MC), Italy.
| | - Thiago Luiz de Paula Castro
- Postgraduate Program in Microbiology, Institute of Biology, Federal University of Bahia, Salvador, BA, Brazil; Postgraduate Program in Immunology, Institute of Health Sciences, Federal University of Bahia, Salvador, BA, Brazil; Department of Biotechnology, Institute of Health Sciences, Federal University of Bahia, Salvador, BA, Brazil.
| | - Núbia Seyffert
- Cellular and Molecular Genetics Laboratory, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil; Postgraduate Program in Microbiology, Institute of Biology, Federal University of Bahia, Salvador, BA, Brazil.
| | - Anderson Santos
- Department of Computer Science, Federal University of Uberlandia, Uberlandia, Brazil
| | - Aristóteles Góes-Neto
- Molecular and Computational Biology of Fungi Laboratory Department of Microbiology, Institute of Biological Sciences, Federal University of Minas Gerais Brazil.
| | - Thiago de Jesus Sousa
- Cellular and Molecular Genetics Laboratory, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil.
| | - Vasco Azevedo
- Cellular and Molecular Genetics Laboratory, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil.
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Plant Growth-Promoting Attributes of Zinc Solubilizing Dietzia maris Isolated from Polyhouse Rhizospheric Soil of Punjab. Curr Microbiol 2023; 80:48. [DOI: 10.1007/s00284-022-03147-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 12/10/2022] [Indexed: 12/24/2022]
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Kruglova A, Muñoz-Palazón B, Gonzalez-Martinez A, Mikola A, Vahala R, Talvitie J. The dangerous transporters: A study of microplastic-associated bacteria passing through municipal wastewater treatment. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 314:120316. [PMID: 36191797 DOI: 10.1016/j.envpol.2022.120316] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 09/12/2022] [Accepted: 09/27/2022] [Indexed: 06/16/2023]
Abstract
Microplastics (MPs) provide a stable and protective habitat for diverse wastewater bacteria, including pathogenic and antibiotic-resistant species. Therefore, MPs may potentially transport these bacteria through wastewater treatment steps to the environment and far distances. This study investigated bacterial communities of MP-associated bacteria from different stages of municipal wastewater treatment processes to evaluate the potential negative effect of these biofilms on the environment. The results showed a high diversity of bacteria that were strongly attached to MPs. After all treatment steps, the core bacterial groups remained attached to MPs and escaped from the wastewater treatment plant with effluent water. Several pathogenic bacteria were identified in MP samples from all treatment steps, and most of them were found in effluent water. These data provide new insights into the possible impacts of wastewater-derived MPs on the environment. MP-associated biofilms were proved to be important sources of pathogens and antibiotic-resistant genes in natural waters.
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Affiliation(s)
- Antonina Kruglova
- Department of Built Environment, Aalto University, PO Box 15200, FI-00076, AALTO, Finland.
| | - Barbara Muñoz-Palazón
- Department of Microbiology, University of Granada, Campus Universitario de la Cartuja C.P., 18071, Granada, Spain; Dipartimento di Ecologia e Biologia, Università degli Studi della Tuscia, Largo Università snc, 01100, Viterbo, Italy
| | - Alejandro Gonzalez-Martinez
- Department of Microbiology, University of Granada, Campus Universitario de la Cartuja C.P., 18071, Granada, Spain
| | - Anna Mikola
- Department of Built Environment, Aalto University, PO Box 15200, FI-00076, AALTO, Finland
| | - Riku Vahala
- Department of Built Environment, Aalto University, PO Box 15200, FI-00076, AALTO, Finland
| | - Julia Talvitie
- Marine Research Center, Finnish Environment Institute (SYKE), P.O.Box 140, FI-00251, Helsinki, Finland
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10
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The Roles of the Two-Component System, MtrAB, in Response to Diverse Cell Envelope Stresses in Dietzia sp. DQ12-45-1b. Appl Environ Microbiol 2022; 88:e0133722. [PMID: 36190258 PMCID: PMC9599347 DOI: 10.1128/aem.01337-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Two-component systems (TCSs) act as common regulatory systems allowing bacteria to detect and respond to multiple environmental stimuli, including cell envelope stress. The MtrAB TCS of Actinobacteria is critical for cell wall homeostasis, cell proliferation, osmoprotection, and antibiotic resistance, and thus is found to be highly conserved across this phylum. However, how precisely the MtrAB TCS regulates cellular homeostasis in response to environmental stress remains unclear. Here, we show that the MtrAB TCS plays an important role in the tolerance to different types of cell envelope stresses, including environmental stresses (i.e., oxidative stress, lysozyme, SDS, osmotic pressure, and alkaline pH stresses) and envelope-targeting antibiotics (i.e., isoniazid, ethambutol, glycopeptide, and β-lactam antibiotics) in Dietzia sp. DQ12-45-1b. An mtrAB mutant strain exhibited slower growth compared to the wild-type strain and was characterized by abnormal cell shapes when exposed to various environmental stresses. Moreover, deletion of mtrAB resulted in decreased resistance to isoniazid, ethambutol, and β-lactam antibiotics. Further, Cleavage under targets and tagmentation sequencing (CUT&Tag-seq) and electrophoretic mobility shift assays (EMSAs) revealed that MtrA binds the promoters of genes involved in peptidoglycan biosynthesis (ldtB, ldtA, murJ), hydrolysis (GJR88_03483, GJR88_4713), and cell division (ftsE). Together, our findings demonstrated that the MtrAB TCS is essential for the survival of Dietzia sp. DQ12-45-1b under various cell envelope stresses, primarily by controlling multiple downstream cellular pathways. Our work suggests that TCSs act as global sensors and regulators in maintaining cellular homeostasis, such as during episodes of various environmental stresses. The present study should shed light on the understanding of mechanisms for bacterial adaptivity to extreme environments. IMPORTANCE The multilayered cell envelope is the first line of bacterial defense against various extreme environments. Bacteria utilize a large number of sensing and regulatory systems to maintain cell envelope homeostasis under multiple stress conditions. The two-component system (TCS) is the main sensing and responding apparatus for environmental adaptation. The MtrAB TCS highly conserved in Actinobacteria is critical for cell wall homeostasis, cell proliferation, osmoprotection, and antibiotic resistance. However, how MtrAB works with regard to signals impacting changes to the cell envelope is not fully understood. Here, we found that in the Actinobacterium Dietzia sp. DQ12-45-1b, a TCS named MtrAB is pivotal for ensuring normal cell growth as well as maintaining proper cell morphology in response to various cell envelope stresses, namely, by regulating the expression of cell envelope-related genes. Our findings should greatly advance our understanding of the adaptive mechanisms responsible for maintaining cell integrity in times of sustained environmental shocks.
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11
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Perrone MR, Romano S, De Maria G, Tundo P, Bruno AR, Tagliaferro L, Maffia M, Fragola M. Simultaneous monitoring of SARS-CoV-2 and bacterial profiles from the air of hospital environments with COVID-19-affected patients. AEROBIOLOGIA 2022; 38:391-412. [PMID: 36097443 PMCID: PMC9453715 DOI: 10.1007/s10453-022-09754-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 08/01/2022] [Indexed: 06/15/2023]
Abstract
UNLABELLED The SARS-CoV-2 presence and the bacterial community profile in air samples collected at the Intensive Care Unit (ICU) of the Operational Unit of Infectious Diseases of Santa Caterina Novella Hospital in Galatina (Lecce, Italy) have been evaluated in this study. Air samplings were performed in different rooms of the ICU ward with and without COVID-19 patients. No sample was found positive to SARS-CoV-2, according to Allplex 2019-nCoV Assay. The airborne bacterial community profiles determined by the 16S rRNA gene metabarcoding approach up to the species level were characterized by richness and biodiversity indices, Spearman correlation coefficients, and Principal Coordinate Analysis. Pathogenic and non-pathogenic bacterial species, also detected in outdoor air samples, were found in all collected indoor samples. Staphylococcus pettenkoferi, Corynebacterium tuberculostearicum, and others coagulase-negative staphylococci, detected at high relative abundances in all the patients' rooms, were the most abundant pathogenic species. The highest mean relative abundance of S. pettenkoferi and C. tuberculostearicum suggested that they were likely the main pathogens of COVID-19 patients at the ICU ward of this study. The identification of nosocomial pathogens representing potential patients' risks in ICU COVID-19 rooms and the still controversial airborne transmission of the SARS-CoV-2 are the main contributions of this study. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s10453-022-09754-7.
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Affiliation(s)
- Maria Rita Perrone
- Department of Mathematics and Physics, University of Salento, 73100 Lecce, Italy
| | - Salvatore Romano
- Department of Mathematics and Physics, University of Salento, 73100 Lecce, Italy
| | - Giuseppe De Maria
- Presidio Ospedaliero Santa Caterina Novella, Azienda Sanitaria Locale Lecce, 73013 Galatina, Lecce, Italy
| | - Paolo Tundo
- Presidio Ospedaliero Santa Caterina Novella, Azienda Sanitaria Locale Lecce, 73013 Galatina, Lecce, Italy
| | - Anna Rita Bruno
- Presidio Ospedaliero Santa Caterina Novella, Azienda Sanitaria Locale Lecce, 73013 Galatina, Lecce, Italy
| | - Luigi Tagliaferro
- Presidio Ospedaliero Santa Caterina Novella, Azienda Sanitaria Locale Lecce, 73013 Galatina, Lecce, Italy
| | - Michele Maffia
- Department of Biological and Environmental Sciences and Technologies, University of Salento, 73100 Lecce, Italy
| | - Mattia Fragola
- Department of Mathematics and Physics, University of Salento, 73100 Lecce, Italy
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12
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Olowo-Okere A, Ibrahim YKE, Lo CI, Olayinka BO, Yimagou EK, Yacouba A, Mohammed Y, Nabti LZ, Ragueh AA, Lupande D, Raoult D, Rolain JM, Diene SM. Bhargavaea massiliensis sp. nov. and Dietzia massiliensis sp. nov., Novel Bacteria Species Isolated from Human Urine Samples in Nigeria. Curr Microbiol 2021; 79:18. [PMID: 34905116 DOI: 10.1007/s00284-021-02721-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 10/13/2021] [Indexed: 10/19/2022]
Abstract
Two novel bacteria species designated Marseille-Q1000T and Marseille-Q0999T were isolated from urine samples of patients in Sokoto, Northwest-Nigeria. They were Gram-positive bacteria and belong to two different genera, Bhargavaea and Dietzia. The genome size and G + C content of Marseille-Q1000T and Marseille-Q0999T were 3.07 and 3.51 Mbp with 53.8 and 71.0 mol% G + C content, respectively. The strains exhibited unique phenotypic and genomic features that are substantially different from previously known bacterial species with standing in nomenclature. On the basis of the phenotypic, phylogenetic and genomic characteristics, strains Marseille-Q0999T (= CSURQ0999 = DSM 112394) and Marseille-Q1000T (= CSURQ1000 = DSM 112384) were proposed as the type strains of Bhargavaea massiliensis sp. nov., and Dietzia massiliensis sp. nov., respectively.
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Affiliation(s)
- Ahmed Olowo-Okere
- Department of Pharmaceutics and Pharmaceutical Microbiology, Usmanu Danfodiyo University, Sokoto, Nigeria
| | | | - Cheikh Ibrahima Lo
- Aix Marseille Univ, IRD, AP-HM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - Busayo Olalekan Olayinka
- Department of Pharmaceutics and Pharmaceutical Microbiology, Ahmadu Bello University, Zaria, Nigeria
| | - Edmond Kuete Yimagou
- Aix Marseille Univ, IRD, AP-HM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - Abdourahamane Yacouba
- Aix Marseille Univ, IRD, AP-HM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - Yahaya Mohammed
- Department of Medical Microbiology, Faculty of Basic Medical Sciences, College of Health Sciences, Usmanu Danfodiyo University, Sokoto, Nigeria
| | - Larbi Zakaria Nabti
- Faculté des Sciences, Département de Biochimie et Microbiologie, Université Mohamed Boudiaf, BP 166, 28000, M'sila, M'sila, Algeria
| | - Ayan Ali Ragueh
- Department of Medical Microbiology, Faculty of Basic Medical Sciences, College of Health Sciences, Usmanu Danfodiyo University, Sokoto, Nigeria
| | - David Lupande
- Aix Marseille Univ, IRD, AP-HM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | | | - Jean-Marc Rolain
- Aix Marseille Univ, IRD, AP-HM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - Seydina M Diene
- Aix Marseille Univ, IRD, AP-HM, MEPHI, IHU-Méditerranée Infection, Marseille, France. .,Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France.
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13
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Wei Z, Wang JJ, Gaston LA, Li J, Fultz LM, DeLaune RD, Dodla SK. Remediation of crude oil-contaminated coastal marsh soil: Integrated effect of biochar, rhamnolipid biosurfactant and nitrogen application. JOURNAL OF HAZARDOUS MATERIALS 2020; 396:122595. [PMID: 32298868 DOI: 10.1016/j.jhazmat.2020.122595] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 03/11/2020] [Accepted: 03/25/2020] [Indexed: 06/11/2023]
Abstract
Decontamination of oil spills from coastal wetland soils requires a delicate approach. A microcosm study was carried out to investigate the impact of integrated application of biochar, rhamnolipid (RL) biosurfactant and nitrogen (N) on petroleum hydrocarbon remediation in a Louisiana coastal saline marsh and their impact on soil microbial community. The soil was artificially contaminated with crude oil and subjected to treatments of different combinations of sugarcane residue biochar, RL, and coated urea. Total petroleum hydrocarbons (TPH) in the contaminated soil were analyzed periodically using gas chromatograph and associated soil bacterial community was studied using 16 s rRNA sequencing technologies. Results showed that integrated application of biochar + RL, biochar + N, and biochar + N+RL reduced 32.3%, 73.2%, 80.9% of TPH, respectively, and exhibited synergic interaction with higher efficiency than application individually. Combined treatments showed distinct functions that biochar increased the sorption of aromatic compounds, while RL and N enhanced the degradation of heavy and light aliphatic compounds. All remediation treatments caused reduction of soil bacterial diversity while RL and N shifted the microbial community to higher abundances of Proteobacteria and Bacteroidetes, respectively. Overall, the findings of this study demonstrate the positivity of applying integrated biochar, biosurfactant, and N treatment in oil remediation in wetland soils.
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Affiliation(s)
- Zhuo Wei
- School of Plant, Environment and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, USA
| | - Jim J Wang
- School of Plant, Environment and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, USA.
| | - Lewis A Gaston
- School of Plant, Environment and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, USA
| | - Jifeng Li
- Department of Life Sciences, Louisiana State University. Baton Rouge, LA 70803, USA
| | - Lisa M Fultz
- School of Plant, Environment and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, USA
| | - Ronald D DeLaune
- Department of Oceanography and Coastal Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Syam K Dodla
- Red River Research Station, Louisiana State University Agricultural Center, Bossier City, LA 71112, USA
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14
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Fang H, Xu JB, Nie Y, Wu XL. Pan-genomic analysis reveals that the evolution of Dietzia species depends on their living habitats. Environ Microbiol 2020; 23:861-877. [PMID: 32715552 DOI: 10.1111/1462-2920.15176] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 07/20/2020] [Accepted: 07/23/2020] [Indexed: 12/14/2022]
Abstract
The bacterial genus Dietzia is widely distributed in various environments. The genomes of 26 diverse strains of Dietzia, including almost all the type strains, were analysed in this study. This analysis revealed a lipid metabolism gene richness, which could explain the ability of Dietzia to live in oil related environments. The pan-genome consists of 83,976 genes assigned into 10,327 gene families, 792 of which are shared by all the genomes of Dietzia. Mathematical extrapolation of the data suggests that the Dietzia pan-genome is open. Both gene duplication and gene loss contributed to the open pan-genome, while horizontal gene transfer was limited. Dietzia strains primarily gained their diverse metabolic capacity through more ancient gene duplications. Phylogenetic analysis of Dietzia isolated from aquatic and terrestrial environments showed two distinct clades from the same ancestor. The genome sizes of Dietzia strains from aquatic environments were significantly larger than those from terrestrial environments, which was mainly due to the occurrence of more gene loss events during the evolutionary progress of the strains from terrestrial environments. The evolutionary history of Dietzia was tightly coupled to environmental conditions, and iron concentrations should be one of the key factors shaping the genomes of the Dietzia lineages.
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Affiliation(s)
- Hui Fang
- College of Engineering, Peking University, Beijing, 100871, China
| | - Jin-Bo Xu
- College of Engineering, Peking University, Beijing, 100871, China
| | - Yong Nie
- College of Engineering, Peking University, Beijing, 100871, China
| | - Xiao-Lei Wu
- College of Engineering, Peking University, Beijing, 100871, China.,Institute of Ocean Research, Peking University, Beijing, 100871, China
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15
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Marine Terpenoids from Polar Latitudes and Their Potential Applications in Biotechnology. Mar Drugs 2020; 18:md18080401. [PMID: 32751369 PMCID: PMC7459527 DOI: 10.3390/md18080401] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 07/24/2020] [Accepted: 07/25/2020] [Indexed: 01/03/2023] Open
Abstract
Polar marine biota have adapted to thrive under one of the ocean’s most inhospitable scenarios, where extremes of temperature, light photoperiod and ice disturbance, along with ecological interactions, have selected species with a unique suite of secondary metabolites. Organisms of Arctic and Antarctic oceans are prolific sources of natural products, exhibiting wide structural diversity and remarkable bioactivities for human applications. Chemical skeletons belonging to terpene families are the most commonly found compounds, whereas cytotoxic antimicrobial properties, the capacity to prevent infections, are the most widely reported activities from these environments. This review firstly summarizes the regulations on access and benefit sharing requirements for research in polar environments. Then it provides an overview of the natural product arsenal from Antarctic and Arctic marine organisms that displays promising uses for fighting human disease. Microbes, such as bacteria and fungi, and macroorganisms, such as sponges, macroalgae, ascidians, corals, bryozoans, echinoderms and mollusks, are the main focus of this review. The biological origin, the structure of terpenes and terpenoids, derivatives and their biotechnological potential are described. This survey aims to highlight the chemical diversity of marine polar life and the versatility of this group of biomolecules, in an effort to encourage further research in drug discovery.
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16
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Sun JQ, Xu L, Liu XY, Zhao GF, Cai H, Nie Y, Wu XL. Functional Genetic Diversity and Culturability of Petroleum-Degrading Bacteria Isolated From Oil-Contaminated Soils. Front Microbiol 2018; 9:1332. [PMID: 29973925 PMCID: PMC6019457 DOI: 10.3389/fmicb.2018.01332] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 05/31/2018] [Indexed: 12/18/2022] Open
Abstract
In this study, we compared the culturability of aerobic bacteria isolated from long-term oil-contaminated soils via enrichment and direct-plating methods; bacteria were cultured at 30°C or ambient temperatures. Two soil samples were collected from two sites in the Shengli oilfield located in Dongying, China. One sample (S0) was close to the outlet of an oil-production water treatment plant, and the other sample (S1) was located 500 m downstream of the outlet. In total, 595 bacterial isolates belonging to 56 genera were isolated, distributed in Actinobacteria, Firmicutes, Bacterioidetes, and Proteobacteria. It was interesting that Actinobacteria and Firmicutes were not detected from the 16S rRNA gene clone library. The results suggested the activation of rare species during culture. Using the enrichment method, 239 isolates (31 genera) and 96 (22 genera) isolates were obtained at ambient temperatures and 30°C, respectively, from S0 soil. Using the direct-plating method, 97 isolates (15 genera) and 163 isolates (20 genera) were obtained at ambient temperatures and 30°C, respectively, from two soils. Of the 595 isolates, 244 isolates (41.7% of total isolates) could degrade n-hexadecane. A greater number of alkane-degraders was isolated at ambient temperatures using the enrichment method, suggesting that this method could significantly improve bacterial culturability. Interestingly, the proportion of alkane degrading isolates was lower in the isolates obtained using enrichment method than that obtained using direct-plating methods. Considering the greater species diversity of isolates obtained via the enrichment method, this technique could be used to increase the diversity of the microbial consortia. Furthermore, phenol hydroxylase genes (pheN), medium-chain alkane monooxygenases genes (alkB and CYP153A), and long-chain alkane monooxygenase gene (almA) were detected in 60 isolates (11 genotypes), 91 isolates (27 genotypes) and 93 isolates (24 genotypes), and 34 isolates (14 genotypes), respectively. This study could provide new insights into microbial resources from oil fields or other environments, and this information will be beneficial for bioremediation of petroleum contamination and for other industrial applications.
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Affiliation(s)
- Ji-Quan Sun
- Department of Energy & Resources Engineering, College of Engineering, Peking University, Beijing, China
| | - Lian Xu
- Department of Energy & Resources Engineering, College of Engineering, Peking University, Beijing, China
| | - Xue-Ying Liu
- Department of Energy & Resources Engineering, College of Engineering, Peking University, Beijing, China
| | - Gui-Fang Zhao
- School of Environment, Tsinghua University, Beijing, China
| | - Hua Cai
- School of Environment, Tsinghua University, Beijing, China
| | - Yong Nie
- Department of Energy & Resources Engineering, College of Engineering, Peking University, Beijing, China
| | - Xiao-Lei Wu
- Department of Energy & Resources Engineering, College of Engineering, Peking University, Beijing, China
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17
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Brzeszcz J, Kaszycki P. Aerobic bacteria degrading both n-alkanes and aromatic hydrocarbons: an undervalued strategy for metabolic diversity and flexibility. Biodegradation 2018; 29:359-407. [PMID: 29948519 DOI: 10.1007/s10532-018-9837-x] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 06/01/2018] [Indexed: 10/14/2022]
Abstract
Environmental pollution with petroleum toxic products has afflicted various ecosystems, causing devastating damage to natural habitats with serious economic implications. Some crude oil components may serve as growth substrates for microorganisms. A number of bacterial strains reveal metabolic capacities to biotransform various organic compounds. Some of the hydrocarbon degraders are highly biochemically specialized, while the others display a versatile metabolism and can utilize both saturated aliphatic and aromatic hydrocarbons. The extended catabolic profiles of the latter group have been subjected to systematic and complex studies relatively rarely thus far. Growing evidence shows that numerous bacteria produce broad biochemical activities towards different hydrocarbon types and such an enhanced metabolic potential can be found in many more species than the already well-known oil-degraders. These strains may play an important role in the removal of heterogeneous contamination. They are thus considered to be a promising solution in bioremediation applications. The main purpose of this article is to provide an overview of the current knowledge on aerobic bacteria involved in the mineralization or transformation of both n-alkanes and aromatic hydrocarbons. Variant scientific approaches enabling to evaluate these features on biochemical as well as genetic levels are presented. The distribution of multidegradative capabilities between bacterial taxa is systematically shown and the possibility of simultaneous transformation of complex hydrocarbon mixtures is discussed. Bioinformatic analysis of the currently available genetic data is employed to enable generation of phylogenetic relationships between environmental strain isolates belonging to the phyla Actinobacteria, Proteobacteria, and Firmicutes. The study proves that the co-occurrence of genes responsible for concomitant metabolic bioconversion reactions of structurally-diverse hydrocarbons is not unique among various systematic groups.
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Affiliation(s)
- Joanna Brzeszcz
- Department of Microbiology, Oil and Gas Institute-National Research Institute, ul. Lubicz 25A, 31-503, Kraków, Poland.
| | - Paweł Kaszycki
- Unit of Biochemistry, Institute of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in Kraków, al. 29 Listopada 54, 31-425, Kraków, Poland
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18
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Isolation and characterization of microorganisms and volatiles associated with Moroccan saffron during different processing treatments. Int J Food Microbiol 2018; 273:43-49. [PMID: 29574333 DOI: 10.1016/j.ijfoodmicro.2018.03.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 03/17/2018] [Accepted: 03/19/2018] [Indexed: 11/22/2022]
Abstract
Saffron may be spoiled by a variety of microorganisms during cultivation, harvesting, and post harvesting. As saffron can be dried and stored in different ways, this preliminary study explored the natural microbiota present in Moroccan saffron when subjected to different drying techniques. An analysis of the carotenoid-derived volatiles present in the saffron was also carried out. The culturable microbiota of the saffron samples dried using different methods, namely in the shade (also called natural), in the sun, or in the oven, were studied using classical and molecular approaches. The effect of the drying methods on head-space chemical volatiles was also determined. Eighty-two isolates grown in the different culture media were chosen from the colonies, and genotype analysis grouped the microorganisms into 58 clusters, revealing a wide diversity. Out of the 82 isolates, 75 belonged to the Bacillaceae family. The other isolates were distributed within the Dietziaceae, Paenibacillaceae and Carnobacteriaceae families. The dominant species was Bacillus simplex, which was detected in all samples, regardless of the drying method used. Lysinibacillus macroides was dominant in the sun-dried saffron. No pathogens were isolated, but an isolate belonging to Dietzia maris, a potential human pathogenic species, was detected. The biodiversity indexes were linked to the drying method and generally decreased as the intensity of the treatment increased. The results of this preliminary work show that the different drying methods strongly influenced the microbiota and affect the saffron volatile profile. Further analysis will be needed to determine possible effects of selected microbiota on saffron volatiles.
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Chen Y, Xie B, Yang J, Chen J, Sun Z. Identification of microbial carotenoids and isoprenoid quinones from Rhodococcus sp. B7740 and its stability in the presence of iron in model gastric conditions. Food Chem 2017; 240:204-211. [PMID: 28946263 DOI: 10.1016/j.foodchem.2017.06.067] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 04/19/2017] [Accepted: 06/09/2017] [Indexed: 11/30/2022]
Abstract
Rhodococcus sp. B7740 is a newfound bacterium which was isolated from 25m deep seawater in the arctic. In this paper, Rhodococcus sp. B7740 was firstly discovered to produce abundant natural isoprenoids, including ubiquinone-4(UQ-4), 13 kinds of menaquinones, three rare aromatic carotenoids and more than one common carotenoid. These compounds were identified by UV-Visible, HPLC-APCI-MS/MS and HRMS spectra. Results demonstrated that Rhodococcus sp. B7740 might be a worthy source of natural isoprenoids especially for scarce aromatic carotenoids. Among them, isorenieratene with 528.3762Da (calculated for 528.3756Da, error: 1.1ppm), a carotenoid with aromatic ring, was purified by HSCCC. The stability of isorenieratene under the mimical gastric conditions was measured compared with common dietary carotenoids, β-carotene and lutein. Unlike β-carotene and lutein, isorenieratene exhibited rather stable in the presence of free iron or heme iron. Its high retention rate in gastrointestinal tract after ingestion indicates the benefits for health.
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Affiliation(s)
- Yashu Chen
- Natural Product Laboratory, Department of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, People's Republic of China.
| | - Bijun Xie
- Natural Product Laboratory, Department of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, People's Republic of China
| | - Jifang Yang
- College of Biological and Environmental Science, Zhejiang Wanli University, Ningbo, Zhejiang 315100, People's Republic of China
| | - Jigang Chen
- College of Biological and Environmental Science, Zhejiang Wanli University, Ningbo, Zhejiang 315100, People's Republic of China
| | - Zhida Sun
- Natural Product Laboratory, Department of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, People's Republic of China.
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20
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Stable mucus-associated bacterial communities in bleached and healthy corals of Porites lobata from the Arabian Seas. Sci Rep 2017; 7:45362. [PMID: 28361923 PMCID: PMC5374439 DOI: 10.1038/srep45362] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 02/23/2017] [Indexed: 01/24/2023] Open
Abstract
Coral reefs are subject to coral bleaching manifested by the loss of endosymbiotic algae from coral host tissue. Besides algae, corals associate with bacteria. In particular, bacteria residing in the surface mucus layer are thought to mediate coral health, but their role in coral bleaching is unknown. We collected mucus from bleached and healthy Porites lobata colonies in the Persian/Arabian Gulf (PAG) and the Red Sea (RS) to investigate bacterial microbiome composition using 16S rRNA gene amplicon sequencing. We found that bacterial community structure was notably similar in bleached and healthy corals, and the most abundant bacterial taxa were identical. However, fine-scale differences in bacterial community composition between the PAG and RS were present and aligned with predicted differences in sulfur- and nitrogen-cycling processes. Based on our data, we argue that bleached corals benefit from the stable composition of mucus bacteria that resemble their healthy coral counterparts and presumably provide a conserved suite of protective functions, but monitoring of post-bleaching survival is needed to further confirm this assumption. Conversely, fine-scale site-specific differences highlight flexibility of the bacterial microbiome that may underlie adjustment to local environmental conditions and contribute to the widespread success of Porites lobata.
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Bera S, Sharma VP, Dutta S, Dutta D. Biological decolorization and detoxification of malachite green from aqueous solution by Dietzia maris NIT-D. J Taiwan Inst Chem Eng 2016. [DOI: 10.1016/j.jtice.2016.07.028] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Navas ME, Jump R, Canaday DH, Wnek MD, SenGupta DJ, McQuiston JR, Bell M. Can anaerobes be acid fast? A novel, clinically relevant acid fast anaerobe. JMM Case Rep 2016; 3:e005036. [PMID: 28348766 PMCID: PMC5330234 DOI: 10.1099/jmmcr.0.005036] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 04/05/2016] [Indexed: 11/18/2022] Open
Abstract
INTRODUCTION Anaerobic acid fast bacilli (AFB) have not been previously reported in clinical microbiology. This is the second case report of a novel anaerobic AFB causing disease in humans. CASE PRESENTATION An anaerobic AFB was isolated from an abdominal wall abscess in a 64-year-old Caucasian diabetic male, who underwent distal pancreatectomy and splenectomy for resection of a pancreatic neuroendocrine tumour. The isolated bacteria were gram-variable and acid-fast, consisting of small irregular rods. The 16S rRNA gene sequence analysis showed that the isolate is a novel organism described in the literature only once before. The organism was studied at the CDC (Centers for Disease Control and Prevention) by the same group that worked with the isolates from the previous report; their findings suggest that the strain belongs to the suborder Corynebacterineae. CONCLUSION This is the fifth reported case of an anaerobic AFB involved in clinical disease; its microbiological features and 16S RNA sequence are identical to previously reported cases. Clinical disease with this organism seems to be associated with recent history of surgery and abscess formation in deep soft tissues. Acquisition from surgical material is uncertain but seems unlikely.
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Affiliation(s)
- Maria E Navas
- Microbiology Laboratory, Louis Stokes Cleveland Veterans Affairs Medical Center , Cleveland, Ohio , USA
| | - Robin Jump
- Geriatric Research Education and Clinical Center, Louis Stokes Cleveland VAMC, Cleveland, Ohio and Department of Infectious Diseases and HIV Medicine, Department of Medicine, Case Western Reserve University , Cleveland, Ohio , USA
| | - David H Canaday
- Geriatric Research Education and Clinical Center, Louis Stokes Cleveland VAMC, Cleveland, Ohio and Department of Infectious Diseases and HIV Medicine, Department of Medicine, Case Western Reserve University , Cleveland, Ohio , USA
| | - Maria D Wnek
- Microbiology Laboratory, Louis Stokes Cleveland Veterans Affairs Medical Center , Cleveland, Ohio , USA
| | - Dhruba J SenGupta
- Department of Laboratory Medicine, University of Washington Medical Center , Seattle, Washington , USA
| | - John R McQuiston
- Bacterial Special Pathogens Branch, Division of High Consequence Pathogens and Pathology Centers for Disease Control and Prevention , Atlanta, Georgia , USA
| | - Melissa Bell
- Bacterial Special Pathogens Branch, Division of High Consequence Pathogens and Pathology Centers for Disease Control and Prevention , Atlanta, Georgia , USA
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Kavynifard A, Ebrahimipour G, Ghasempour A. Optimization of crude oil degradation by Dietzia cinnamea KA1, capable of biosurfactant production. J Basic Microbiol 2015; 56:566-75. [PMID: 26615815 DOI: 10.1002/jobm.201500386] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Accepted: 11/11/2015] [Indexed: 11/07/2022]
Abstract
The aim of this study was isolation and characterization of a crude oil degrader and biosurfactant-producing bacterium, along with optimization of conditions for crude oil degradation. Among 11 isolates, 5 were able to emulsify crude oil in Minimal Salt Medium (MSM) among which one isolate, named KA1, showed the highest potency for growth rate and biodegradation. The isolate was identified as Dietzia cinnamea KA1 using morphological and biochemical characteristics and 16S rRNA gene sequencing. The optimal conditions were 510 mM NaCl, pH 9.0, 35 °C, and minimal requirement of 46.5 mM NH4 Cl and 2.10 mM NaH2 PO4 . Gravimetric test and Gas chromatography-Mass spectroscopy technique (GC-MS) showed that Dietzia cinnamea KA1 was able to utilize and degrade 95.7% of the crude oil after 5 days, under the optimal conditions. The isolate was able to grow and produce biosurfactant when cultured in MSM supplemented with crude oil, glycerol or whey as the sole carbon sources, but bacterial growth was occurred using molasses with no biosurfactant production. This is the first report of biosurfactant production by D. cinnamea using crude oil, glycerol and whey and the first study to report a species of Dietzia degrading a wide range of hydrocarbons in a short time.
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Affiliation(s)
- Amirarsalan Kavynifard
- Department of Microbiology, Faculty of Biological Sciences, Shahid Beheshti University, Tehran, Iran
| | | | - Alireza Ghasempour
- Medicinal Plants and Drugs Research Institute, Shahid Beheshti University, Tehran, Iran
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Gharibzahedi S, Razavi S, Mousavi M. Optimisation and kinetic studies on the production of intracellular canthaxanthin in fed-batch cultures of Dietzia natronolimnaea HS-1. QUALITY ASSURANCE AND SAFETY OF CROPS & FOODS 2015. [DOI: 10.3920/qas2014.0503] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- S.M.T. Gharibzahedi
- Center of Excellence for Application of Modern Technologies for Producing Functional Foods and Drinks and Bioprocess Engineering Laboratory (BPEL), Department of Food Science, Engineering & Technology, Faculty of Agricultural Engineering and Technology, University of Tehran, P.O. Box 4111, Karaj 31587-77871, Iran
| | - S.H. Razavi
- Center of Excellence for Application of Modern Technologies for Producing Functional Foods and Drinks and Bioprocess Engineering Laboratory (BPEL), Department of Food Science, Engineering & Technology, Faculty of Agricultural Engineering and Technology, University of Tehran, P.O. Box 4111, Karaj 31587-77871, Iran
| | - M. Mousavi
- Center of Excellence for Application of Modern Technologies for Producing Functional Foods and Drinks and Bioprocess Engineering Laboratory (BPEL), Department of Food Science, Engineering & Technology, Faculty of Agricultural Engineering and Technology, University of Tehran, P.O. Box 4111, Karaj 31587-77871, Iran
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