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Salter C, Westrick JA, Chaganti SR, Birbeck JA, Peraino NJ, Weisener CG. Elucidating microbial mechanisms of microcystin-LR degradation in Lake Erie beach sand through metabolomics and metatranscriptomics. WATER RESEARCH 2023; 247:120816. [PMID: 37952399 DOI: 10.1016/j.watres.2023.120816] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 09/11/2023] [Accepted: 10/29/2023] [Indexed: 11/14/2023]
Abstract
As one of five Laurentian Great Lakes, Lake Erie ranks among the top freshwater drinking sources and ecosystems globally. Historical and current agriculture mismanagement and climate change sustains the environmental landscape for late summer cyanobacterial harmful algal blooms, and consequently, cyanotoxins such as microcystin (MC). Microcystin microbial degradation is a promising mitigation strategy, however the mechanisms controlling the breakdown of MCs in Lake Erie are not well understood. Pelee Island, Ontario, Canada is located in the western basin of Lake Erie and the bacterial community in the sand has demonstrated the capacity of metabolizing the toxin. Through a multi-omic approach, the metabolic, functional and taxonomical signatures of the Pelee Island microbial community during MC-LR degradation was investigated over a 48-hour period to comprehensively study the degradation mechanism. Cleavage of bonds surrounding nitrogen atoms and the upregulation of nitrogen deamination (dadA, alanine dehydrogenase, leucine dehydrogenase) and assimilation genes (glnA, gltB) suggests a targeted isolation of nitrogen by the microbial community for energy production. Methylotrophic pathways RuMP and H4MPT control assimilation and dissimilation of carbon, respectively and differential abundance of Methylophilales indicates an interconnected role through electron exchange of denitrification and methylotrophic pathways. The detected metabolites did not resolve a clear breakdown pathway, but rather the diversity of products in combination with taxonomic and functional results supports that a variety of strategies are applied, such as epoxidation, hydroxylation, and aromatic degradation. Annual repeated exposure to the toxin may have allowed the community to adaptatively establish a novel pathway through functional plasticity and horizontal gene transfer. The culmination of these results reveals the complexity of the Pelee Island sand community and supports a dynamic and cooperative metabolism between microbial species to achieve MC degradation.
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Affiliation(s)
- Chelsea Salter
- Great Lakes Institute for Environmental Research, University of Windsor, 401 Sunset Avenue, Windsor, ON N9B 3P4, Canada.
| | - Judy A Westrick
- Lumigen Instrument Center, Department of Chemistry, Wayne State University, Detroit, MI 48202, United States
| | - Subba Rao Chaganti
- Cooperative Institute for Great Lakes Research, School for Environment and Sustainability, University of Michigan, 440 Church Street, Ann Arbor, MI 48109, United States
| | - Johnna A Birbeck
- Lumigen Instrument Center, Department of Chemistry, Wayne State University, Detroit, MI 48202, United States
| | - Nicholas J Peraino
- Lumigen Instrument Center, Department of Chemistry, Wayne State University, Detroit, MI 48202, United States
| | - Christopher G Weisener
- Great Lakes Institute for Environmental Research, University of Windsor, 401 Sunset Avenue, Windsor, ON N9B 3P4, Canada
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2
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Châtillon E, Cébron A, Rigal F, Cagnon C, Lorgeoux C, Faure P, Duran R, Cravo-Laureau C. Functional redundancy in response to runoff input upholds microbial community in hydrocarbon-contaminated land-sea continuum. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 335:122330. [PMID: 37572846 DOI: 10.1016/j.envpol.2023.122330] [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: 06/19/2023] [Revised: 08/01/2023] [Accepted: 08/05/2023] [Indexed: 08/14/2023]
Abstract
An experimental approach mimicking the land-sea continuum in microcosms was developed in order to determine the effect of the terrigenous inputs by soil runoff on the microbial functional potential in hydrocarbon (HC) contaminated marine coastal sediment. We hypothesized that the coalescent event increases the functional potential of microbial communities in marine coastal sediments, influencing the fate of HC in marine coastal ecosystems. The microbial functional potential including the HC degradation ability was assessed by DNA-array to compare the sediment receiving or not terrigenous inputs. The removal of HC and the functional gene richness in sediment was unchanged with the terrigenous inputs. However, the gene variants (GVs) composition was modified indicating functional redundancy. In addition, functional indicators including GVs related to sulfite reduction, denitrification and polyaromatic degradation were identified in higher proportion in sediment receiving terrigenous inputs. The terrigenous inputs modified the functional co-occurrence networks, showing a reorganization of the GVs associations with an increase of the network complexity. Different keystone GVs ensuring similar functions were identified in networks with or without terrigenous inputs, further confirming functional redundancy. We argue that functional redundancy maintains the structure of microbial community in hydrocarbon-contaminated land-sea continuum mixing zone. Our results provide helpful functional information for the monitoring and management of coastal environment affected by human land-based activities.
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Affiliation(s)
- Elise Châtillon
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
| | - Aurélie Cébron
- Université de Lorraine, CNRS, GeoRessources, F-54000, Nancy, France
| | - François Rigal
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
| | - Christine Cagnon
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
| | | | - Pierre Faure
- Université de Lorraine, CNRS, LIEC, F-54000, Nancy, France
| | - Robert Duran
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
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3
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Jiménez-Volkerink SN, Jordán M, Singleton DR, Grifoll M, Vila J. Bacterial benz(a)anthracene catabolic networks in contaminated soils and their modulation by other co-occurring HMW-PAHs. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 328:121624. [PMID: 37059172 DOI: 10.1016/j.envpol.2023.121624] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 04/04/2023] [Accepted: 04/09/2023] [Indexed: 05/09/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are major environmental pollutants in a number of point source contaminated sites, where they are found embedded in complex mixtures containing different polyaromatic compounds. The application of bioremediation technologies is often constrained by unpredictable end-point concentrations enriched in recalcitrant high molecular weight (HMW)-PAHs. The aim of this study was to elucidate the microbial populations and potential interactions involved in the biodegradation of benz(a)anthracene (BaA) in PAH-contaminated soils. The combination of DNA stable isotope probing (DNA-SIP) and shotgun metagenomics of 13C-labeled DNA identified a member of the recently described genus Immundisolibacter as the key BaA-degrading population. Analysis of the corresponding metagenome assembled genome (MAG) revealed a highly conserved and unique genetic organization in this genus, including novel aromatic ring-hydroxylating dioxygenases (RHD). The influence of other HMW-PAHs on BaA degradation was ascertained in soil microcosms spiked with BaA and fluoranthene (FT), pyrene (PY) or chrysene (CHY) in binary mixtures. The co-occurrence of PAHs resulted in a significant delay in the removal of PAHs that were more resistant to biodegradation, and this delay was associated with relevant microbial interactions. Members of Immundisolibacter, associated with the biodegradation of BaA and CHY, were outcompeted by Sphingobium and Mycobacterium, triggered by the presence of FT and PY, respectively. Our findings highlight that interacting microbial populations modulate the fate of PAHs during the biodegradation of contaminant mixtures in soils.
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Affiliation(s)
- Sara N Jiménez-Volkerink
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Av. Diagonal, 643, 08028, Barcelona, Spain
| | - Maria Jordán
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Av. Diagonal, 643, 08028, Barcelona, Spain
| | - David R Singleton
- Department of Civil and Environmental Engineering, Pratt School of Engineering, Duke University, Durham, NC, 27708-0287, USA
| | - Magdalena Grifoll
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Av. Diagonal, 643, 08028, Barcelona, Spain.
| | - Joaquim Vila
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Av. Diagonal, 643, 08028, Barcelona, Spain
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4
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Ma Q, Meng N, Su J, Li Y, Gu J, Wang Y, Wang J, Qu Y, Zhao Z, Sun Y. Unraveling the skatole biodegradation process in an enrichment consortium using integrated omics and culture-dependent strategies. J Environ Sci (China) 2023; 127:688-699. [PMID: 36522097 DOI: 10.1016/j.jes.2022.06.025] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 06/20/2022] [Accepted: 06/20/2022] [Indexed: 06/17/2023]
Abstract
3-Methylindole (skatole) is regarded as one of the most offensive compounds in odor emission. Biodegradation is feasible for skatole removal but the functional species and genes responsible for skatole degradation remain enigmatic. In this study, an efficient aerobic skatole-degrading consortium was obtained. Rhodococcus and Pseudomonas were identified as the two major and active populations by integrated metagenomic and metatranscriptomic analyses. Bioinformatic analyses indicated that the skatole downstream degradation was mainly via the catechol pathway, and upstream degradation was likely catalyzed by the aromatic ring-hydroxylating oxygenase and flavin monooxygenase. Genome binning and gene analyses indicated that Pseudomonas, Pseudoclavibacter, and Raineyella should cooperate with Rhodococcus for the skatole degradation process. Moreover, a pure strain Rhodococcus sp. DMU1 was successfully obtained which could utilize skatole as the sole carbon source. Complete genome sequencing showed that strain DMU1 was the predominant population in the consortium. Further crude enzyme and RT-qPCR assays indicated that strain DMU1 degraded skatole through the catechol ortho-cleavage pathway. Collectively, our results suggested that synergistic degradation of skatole in the consortium should be performed by diverse bacteria with Rhodococcus as the primary degrader, and the degradation mainly proceeded via the catechol pathway.
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Affiliation(s)
- Qiao Ma
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian 116026, China.
| | - Nan Meng
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian 116026, China
| | - Jiancheng Su
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian 116026, China
| | - Yujie Li
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian 116026, China
| | - Jiazheng Gu
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian 116026, China
| | - Yidi Wang
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian 116026, China
| | - Jingwei Wang
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian 116026, China
| | - Yuanyuan Qu
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Zelong Zhao
- Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic Animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian 116023, China.
| | - Yeqing Sun
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian 116026, China
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5
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González Plaza JJ, Hradecký J. The tropical cookbook: Termite diet and phylogenetics—Over geographical origin—Drive the microbiome and functional genetic structure of nests. Front Microbiol 2023; 14:1089525. [PMID: 36998409 PMCID: PMC10043212 DOI: 10.3389/fmicb.2023.1089525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 02/13/2023] [Indexed: 03/15/2023] Open
Abstract
Termites are key decomposers of dead plant material involved in the organic matter recycling process in warm terrestrial ecosystems. Due to their prominent role as urban pests of timber, research efforts have been directed toward biocontrol strategies aimed to use pathogens in their nest. However, one of the most fascinating aspects of termites is their defense strategies that prevent the growth of detrimental microbiological strains in their nests. One of the controlling factors is the nest allied microbiome. Understanding how allied microbial strains protect termites from pathogen load could provide us with an enhanced repertoire for fighting antimicrobial-resistant strains or mining for genes for bioremediation purposes. However, a necessary first step is to characterize these microbial communities. To gain a deeper understanding of the termite nest microbiome, we used a multi-omics approach for dissecting the nest microbiome in a wide range of termite species. These cover several feeding habits and three geographical locations on two tropical sides of the Atlantic Ocean known to host hyper-diverse communities. Our experimental approach included untargeted volatile metabolomics, targeted evaluation of volatile naphthalene, a taxonomical profile for bacteria and fungi through amplicon sequencing, and further diving into the genetic repertoire through a metagenomic sequencing approach. Naphthalene was present in species belonging to the genera Nasutitermes and Cubitermes. We investigated the apparent differences in terms of bacterial community structure and discovered that feeding habits and phylogenetic relatedness had a greater influence than geographical location. The phylogenetic relatedness among nests' hosts influences primarily bacterial communities, while diet influences fungi. Finally, our metagenomic analysis revealed that the gene content provided both soil-feeding genera with similar functional profiles, while the wood-feeding genus showed a different one. Our results indicate that the nest functional profile is largely influenced by diet and phylogenetic relatedness, irrespective of geographical location.
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6
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Sun H, Xia J, Wu B, Ren H, Zhang X, Ye L. Aerobic starvation treatment of activated sludge enhances the degradation efficiency of refractory organic compounds. WATER RESEARCH 2022; 224:119069. [PMID: 36108399 DOI: 10.1016/j.watres.2022.119069] [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: 05/22/2022] [Revised: 09/04/2022] [Accepted: 09/05/2022] [Indexed: 06/15/2023]
Abstract
Many refractory organic compounds (ROCs) in wastewater are toxic to human and aquatic organisms. Here, we reported an aerobic starvation approach to improve the degradation efficiencies of ROCs in activated sludge systems. The highest degradation rates of bisphenol AF (BPAF) (11.4 mg/g VSS · h) and gabapentin (GBP) (8.9 mg/g VSS · h) were achieved on the second day of the starvation process. While, the degradation rate of bisphenol A (BPA) on the 43rd day reached the maximum value of 0.8 mg/g VSS ·h, which was significantly higher than that of the seeding sludge (0.01 mg/g VSS · h). To investigate the mechanisms of this finding, we applied magnetic-nanoparticle mediated isolation, 16S rRNA gene sequencing, metagenomic sequencing and metatranscriptomic sequencing to analyze the microbial community structures and functions during the starvation process. The results showed that the increase of the BPA degradation ability was caused by the increase of the relative abundance of BPA degrading bacteria (Sphingomonas, Achromobacter, etc.), while, the enhancement of BPAF and GBP degradation was attributed to the increase of the expression of ROC degrading genes. Overall, these results improve our understanding of the microbial ecology of starved activated sludge and provide useful information for the future development of ROC removal technologies.
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Affiliation(s)
- Haohao Sun
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, China
| | - Juntao Xia
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, China
| | - Bing Wu
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, China
| | - Hongqiang Ren
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, China
| | - Xuxiang Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, China.
| | - Lin Ye
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, China.
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7
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Aguilar-Romero I, van Dillewijn P, Nesme J, Sørensen SJ, Nogales R, Delgado-Moreno L, Romero E. A novel and affordable bioaugmentation strategy with microbial extracts to accelerate the biodegradation of emerging contaminants in different media. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 834:155234. [PMID: 35427621 DOI: 10.1016/j.scitotenv.2022.155234] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/06/2022] [Accepted: 04/08/2022] [Indexed: 06/14/2023]
Abstract
This study describes a new bioaugmentation alternative based on the application of aqueous aerated extracts from a biomixture acclimated with ibuprofen, diclofenac and triclosan. This bioaugmentation strategy was assayed in biopurification systems (BPS) and in contaminated aqueous solutions to accelerate the removal of these emerging contaminants. Sterilized extracts or extracts from the initial uncontaminated biomixture were used as controls. In BPS, the dissipation of 90% of diclofenac and triclosan required, respectively, 60 and 108 days less than in the controls. The metabolite methyl-triclosan was determined at levels 12 times lower than in controls. In the bioaugmented solutions, ibuprofen was almost completely eliminated (99%) in 21 days and its hydroxylated metabolites were also determined to be at lower levels than in the controls. The plasmidome of acclimated biomixtures and its extract appeared to maintain certain types of plasmids but degradation related genes became less evident. Several dominant OTUs found in the extract identified as Flavobacterium and Fluviicola of the phylum Bacteroidetes, Thermomicrobia (phylum Chloroflexi) and Nonomuraea (phylum Actinobacteria), may be responsible for the enhanced dissipation of these contaminants. This bioaugmentation strategy represents an advantageous tool to facilitate in situ bioaugmentation.
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Affiliation(s)
- Inés Aguilar-Romero
- Department of Environmental Protection, Estación Experimental del Zaidín-Consejo Superior de Investigaciones Científicas (EEZ-CSIC), C/ Profesor Albareda 1, 18008 Granada, Spain
| | - Pieter van Dillewijn
- Department of Environmental Protection, Estación Experimental del Zaidín-Consejo Superior de Investigaciones Científicas (EEZ-CSIC), C/ Profesor Albareda 1, 18008 Granada, Spain
| | - Joseph Nesme
- Section of Microbiology, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Søren J Sørensen
- Section of Microbiology, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Rogelio Nogales
- Department of Environmental Protection, Estación Experimental del Zaidín-Consejo Superior de Investigaciones Científicas (EEZ-CSIC), C/ Profesor Albareda 1, 18008 Granada, Spain
| | - Laura Delgado-Moreno
- Department of Environmental Protection, Estación Experimental del Zaidín-Consejo Superior de Investigaciones Científicas (EEZ-CSIC), C/ Profesor Albareda 1, 18008 Granada, Spain
| | - Esperanza Romero
- Department of Environmental Protection, Estación Experimental del Zaidín-Consejo Superior de Investigaciones Científicas (EEZ-CSIC), C/ Profesor Albareda 1, 18008 Granada, Spain.
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8
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Hassan HA, D Enza M, Armengaud J, Pieper DH. Biochemical and genetic characterization comparison of four extradiol dioxygenases in Rhizorhabdus wittichii RW1. Appl Microbiol Biotechnol 2022; 106:5539-5550. [PMID: 35906995 DOI: 10.1007/s00253-022-12099-3] [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: 04/18/2022] [Revised: 07/20/2022] [Accepted: 07/22/2022] [Indexed: 11/26/2022]
Abstract
Rhizorhabdus (previously Sphingomonas) wittichii RW1 uses a diverse array of aromatic organic compounds as energy and carbon sources, including some extremely recalcitrant compounds such as dibenzo-p-dioxin and dibenzofuran. Extradiol dioxygenases play a key role in the metabolism of dibenzofuran (DBF), dibenzo-p-dioxin (DBD), PCBs, and various other aromatic compounds. In this study, a detailed kinetic analysis of four extradiol dioxygenases identified in R. wittichii RW1 (DbfB, Edo2, Edo3, and Edo4) showed all of them to be typical 2,3dihydroxybiphenyl (DHB) dioxygenases with DHB as preferred substrate (kcat/Km values of 0.13-188 (µM -1 s-1)) and only slightly lower activity against trihydroxybiphenyl (THB) whereas monocyclic substrates were, to different extents, poor substrates due to high km values. All extradiol dioxygenases analyzed were subject to mechanism-based inactivation by 2,2`,3-trihydroxybiphenylether (THBE) the intermediate of DBD degradation. However, Edo4 was superior as reflected by the relatively high partition ratio and the comparably low efficiency of inactivation. Significant differences were observed with respect to their inactivation by 3-chlorocatechol. The absence of any significant mechanism-based inactivation makes Edo3 a perfect candidate for being recruited for chlorobiphenyl degradation where inactivation of extradiol dioxygenases by this intermediate creates significant metabolic problems. KEY POINTS: • Characterization of additional extradiol dioxygenases encoded by RW1 • Identification of differences in 2,2`,3-trihydroxybiphenylether transformation • Identification of differences in inhibition by 3-chlorocatechol.
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Affiliation(s)
- Hamdy A Hassan
- Department of Environmental Biotechnology, Genetic Engineering and Biotechnology Research Institute, University of Sadat City, Sadat City 32897, Egypt.
- Biology Department, Science and Humanities College, Shaqra University, Al-Quwayiyah, 11726, Riyadh, Saudi Arabia.
| | - Marina D Enza
- Microbial Interactions and Processes Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Jean Armengaud
- Microbial Interactions and Processes Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Université Paris-Saclay, CEA, INRAE, Département Médicaments Et Technologies Pour La Santé, Bagnols-sur-Cèze, France
| | - Dietmar H Pieper
- Microbial Interactions and Processes Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
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9
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Vasileiadis S, Perruchon C, Scheer B, Adrian L, Steinbach N, Trevisan M, Plaza-Bolaños P, Agüera A, Chatzinotas A, Karpouzas DG. Nutritional inter-dependencies and a carbazole-dioxygenase are key elements of a bacterial consortium relying on a Sphingomonas for the degradation of the fungicide thiabendazole. Environ Microbiol 2022; 24:5105-5122. [PMID: 35799498 DOI: 10.1111/1462-2920.16116] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 06/20/2022] [Accepted: 06/21/2022] [Indexed: 11/28/2022]
Abstract
Thiabendazole (TBZ), is a persistent fungicide/anthelminthic and a serious environmental threat. We previously enriched a TBZ-degrading bacterial consortium and provided first evidence for a Sphingomonas involvement in TBZ transformation. Here, using a multi-omic approach combined with DNA-stable isotope probing (SIP) we verified the key degrading role of Sphingomonas and identify potential microbial interactions governing consortium functioning. SIP and amplicon sequencing analysis of the heavy and light DNA fraction of cultures grown on 13 C-labelled versus 12 C-TBZ showed that 66% of the 13 C-labelled TBZ was assimilated by Sphingomonas. Metagenomic analysis retrieved 18 metagenome-assembled genomes with the dominant belonging to Sphingomonas, Sinobacteriaceae, Bradyrhizobium, Filimonas and Hydrogenophaga. Meta-transcriptomics/-proteomics and non-target mass spectrometry suggested TBZ transformation by Sphingomonas via initial cleavage by a carbazole dioxygenase (car) to thiazole-4-carboxamidine (terminal compound) and catechol or a cleaved benzyl ring derivative, further transformed through an ortho-cleavage (cat) pathway. Microbial co-occurrence and gene expression networks suggested strong interactions between Sphingomonas and a Hydrogenophaga. The latter activated its cobalamin biosynthetic pathway and Sphingomonas its cobalamin salvage pathway to satisfy its B12 auxotrophy. Our findings indicate microbial interactions aligning with the 'black queen hypothesis' where Sphingomonas (detoxifier, B12 recipient) and Hydrogenophaga (B12 producer, enjoying detoxification) act as both helpers and beneficiaries.
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Affiliation(s)
- Sotirios Vasileiadis
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Viopolis, Greece
| | - Chiara Perruchon
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Viopolis, Greece
| | - Benjamin Scheer
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Lorenz Adrian
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany.,Chair of Geobiotechnology, Technische Universität Berlin, Berlin, Germany
| | - Nicole Steinbach
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Marco Trevisan
- Department of Sustainable Food Process, Universitá Cattolica del Sacro Cuore, Piacenza, Italy
| | - Patricia Plaza-Bolaños
- Solar Energy Research Centre (CIESOL), Joint Center University of Almería-CIEMAT, Almeria, Spain
| | - Ana Agüera
- Solar Energy Research Centre (CIESOL), Joint Center University of Almería-CIEMAT, Almeria, Spain
| | - Antonis Chatzinotas
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany.,Institute of Biology, Leipzig University, Leipzig, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Dimitrios G Karpouzas
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Viopolis, Greece
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McKay LJ, Smith HJ, Barnhart EP, Schweitzer HD, Malmstrom RR, Goudeau D, Fields MW. Activity-based, genome-resolved metagenomics uncovers key populations and pathways involved in subsurface conversions of coal to methane. THE ISME JOURNAL 2022; 16:915-926. [PMID: 34689183 PMCID: PMC8941128 DOI: 10.1038/s41396-021-01139-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 09/28/2021] [Accepted: 10/04/2021] [Indexed: 11/08/2022]
Abstract
Microbial metabolisms and interactions that facilitate subsurface conversions of recalcitrant carbon to methane are poorly understood. We deployed an in situ enrichment device in a subsurface coal seam in the Powder River Basin (PRB), USA, and used BONCAT-FACS-Metagenomics to identify translationally active populations involved in methane generation from a variety of coal-derived aromatic hydrocarbons. From the active fraction, high-quality metagenome-assembled genomes (MAGs) were recovered for the acetoclastic methanogen, Methanothrix paradoxum, and a novel member of the Chlorobi with the potential to generate acetate via the Pta-Ack pathway. Members of the Bacteroides and Geobacter also encoded Pta-Ack and together, all four populations had the putative ability to degrade ethylbenzene, phenylphosphate, phenylethanol, toluene, xylene, and phenol. Metabolic reconstructions, gene analyses, and environmental parameters also indicated that redox fluctuations likely promote facultative energy metabolisms in the coal seam. The active "Chlorobi PRB" MAG encoded enzymes for fermentation, nitrate reduction, and multiple oxygenases with varying binding affinities for oxygen. "M. paradoxum PRB" encoded an extradiol dioxygenase for aerobic phenylacetate degradation, which was also present in previously published Methanothrix genomes. These observations outline underlying processes for bio-methane from subbituminous coal by translationally active populations and demonstrate activity-based metagenomics as a powerful strategy in next generation physiology to understand ecologically relevant microbial populations.
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Affiliation(s)
- Luke J McKay
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, 59717, USA.
- Thermal Biology Institute, Montana State University, Bozeman, MT, 59717, USA.
- Department of Land Resources & Environmental Sciences, Montana State University, Bozeman, MT, 59717, USA.
| | - Heidi J Smith
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, 59717, USA.
- Department of Microbiology & Cell Biology, Montana State University, Bozeman, MT, 59717, USA.
| | - Elliott P Barnhart
- U.S. Geological Survey, Wyoming-Montana Water Science Center, Helena, MT, 59601, USA
| | - Hannah D Schweitzer
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, 59717, USA
- Department of Microbiology & Cell Biology, Montana State University, Bozeman, MT, 59717, USA
- Arctic University of Norway, Tromsø, Norway
| | | | | | - Matthew W Fields
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, 59717, USA.
- Department of Microbiology & Cell Biology, Montana State University, Bozeman, MT, 59717, USA.
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11
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Schweitzer HD, Smith HJ, Barnhart EP, McKay LJ, Gerlach R, Cunningham AB, Malmstrom RR, Goudeau D, Fields MW. Subsurface hydrocarbon degradation strategies in low- and high-sulfate coal seam communities identified with activity-based metagenomics. NPJ Biofilms Microbiomes 2022; 8:7. [PMID: 35177633 PMCID: PMC8854433 DOI: 10.1038/s41522-022-00267-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 01/05/2022] [Indexed: 11/18/2022] Open
Abstract
Environmentally relevant metagenomes and BONCAT-FACS derived translationally active metagenomes from Powder River Basin coal seams were investigated to elucidate potential genes and functional groups involved in hydrocarbon degradation to methane in coal seams with high- and low-sulfate levels. An advanced subsurface environmental sampler allowed the establishment of coal-associated microbial communities under in situ conditions for metagenomic analyses from environmental and translationally active populations. Metagenomic sequencing demonstrated that biosurfactants, aerobic dioxygenases, and anaerobic phenol degradation pathways were present in active populations across the sampled coal seams. In particular, results suggested the importance of anaerobic degradation pathways under high-sulfate conditions with an emphasis on fumarate addition. Under low-sulfate conditions, a mixture of both aerobic and anaerobic pathways was observed but with a predominance of aerobic dioxygenases. The putative low-molecular-weight biosurfactant, lichysein, appeared to play a more important role compared to rhamnolipids. The methods used in this study—subsurface environmental samplers in combination with metagenomic sequencing of both total and translationally active metagenomes—offer a deeper and environmentally relevant perspective on community genetic potential from coal seams poised at different redox conditions broadening the understanding of degradation strategies for subsurface carbon.
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Affiliation(s)
- Hannah D Schweitzer
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, 59717, USA. .,Department of Microbiology & Cell Biology, Montana State University, Bozeman, MT, 59717, USA. .,UiT-The Arctic University of Norway, 9019, Tromsø, Norway.
| | - Heidi J Smith
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, 59717, USA. .,Department of Microbiology & Cell Biology, Montana State University, Bozeman, MT, 59717, USA.
| | - Elliott P Barnhart
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, 59717, USA.,US Geological Survey, Wyoming-Montana Water Science Center, Helena, MT, 59601, USA
| | - Luke J McKay
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, 59717, USA.,Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, 59717, USA
| | - Robin Gerlach
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, 59717, USA.,Energy Research Institute, Montana State University, Bozeman, MT, 59717, USA.,Department of Biological and Chemical Engineering, Montana State University, Bozeman, MT, 59717, USA
| | - Alfred B Cunningham
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, 59717, USA.,Energy Research Institute, Montana State University, Bozeman, MT, 59717, USA.,Department of Civil Engineering, Montana State University, Bozeman, MT, 59717, USA
| | | | | | - Matthew W Fields
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, 59717, USA. .,Department of Microbiology & Cell Biology, Montana State University, Bozeman, MT, 59717, USA. .,Energy Research Institute, Montana State University, Bozeman, MT, 59717, USA.
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12
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Long range PCR reveals the genetic cargo of IncP-1 plasmids in the complex microbial community of an on-farm biopurification system treating pesticide contaminated wastewater. Appl Environ Microbiol 2021; 88:e0164821. [PMID: 34878814 DOI: 10.1128/aem.01648-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Promiscuous plasmids like IncP-1 plasmids play an important role in the bacterial adaptation to pollution by acquiring and distributing xenobiotic catabolic genes. However, most information comes from isolates and the role of plasmids in governing community-wide bacterial adaptation to xenobiotics and other adaptive forces is not fully understood. Current information on the contribution of IncP-1 plasmids in community adaptation is limited because methods are lacking that directly isolate and identify the plasmid borne adaptive functions in whole-community DNA. In this study, we optimized long range PCR to directly access and identify the cargo carried by IncP-1 plasmids in environmental DNA. The DNA between the IncP-1 backbone genes trbP and traC, a main insertion site of adaptive trait determinants, is amplified and its content analysed by high-throughput sequencing. The method was applied to DNA of an on-farm biopurification system (BPS), treating pesticide contaminated wastewater, to examine whether horizontal gene exchange of catabolic functions by IncP-1 plasmids is a main driver of community adaptation in BPS. The cargo recovered from BPS community DNA, encoded catabolic but also resistance traits and various other (un)known functions. Unexpectedly, catabolic traits composed only a minor fraction of the cargo, indicating that the IncP-1 region between trbP and traC is not a major contributor to catabolic adaptation of the BPS microbiome. Instead, it contains a functionally diverse set of genes which either may assist biodegradation functions, be remnants of random gene recruitment, or confer other crucial functions for proliferation in the BPS environment. IMPORTANCE This study presents a long range PCR for direct and cultivation-independent access to the identity of the cargo of a major insertion hot spot of adaptive genes in IncP-1 plasmids and hence a new mobilome tool for understanding the role of IncP-1 plasmids in complex communities. The method was applied to DNA of an on-farm biopurification system (BPS) treating pesticide-contaminated wastewater, aiming at new insights on whether horizontal exchange of catabolic functions by IncP-1 plasmids is a main driver of community adaptation in BPS. Unexpectedly, catabolic functions represented a small fraction of the cargo genes while multiple other gene functions were recovered. These results show that the cargo of the target insertion hot spot in IncP-1 plasmids in a community, not necessarily relates to the main selective trait imposed on that community. Instead these functions might contribute to adaptation to unknown selective forces or represent remnants of random gene recruitment.
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13
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Takihara H, Miura N, Aoki-Kinoshita KF, Okuda S. Functional glyco-metagenomics elucidates the role of glycan-related genes in environments. BMC Bioinformatics 2021; 22:505. [PMID: 34663219 PMCID: PMC8522060 DOI: 10.1186/s12859-021-04425-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 10/04/2021] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Glycan-related genes play a fundamental role in various processes for energy acquisition and homeostasis maintenance while adapting to the environment in which the organism exists; however, their role in the microbiome in the environment is unclear. METHODS Sequence alignment was performed between known glycan-related genes and complete genomes of microorganisms, and optimal parameters for identifying glycan-related genes were determined based on the alignments. Using the constructed scheme (> 90% of identity and > 25 aa of alignment length), glycan-related genes in various environments were identified from 198 different metagenome data. RESULTS As a result, we identified 86.73 million glycan-related genes from the metagenome data. Among the 12 environments classified in this study, the percentage of glycan-related genes was high in the human-associated environment, suggesting that these environments utilize glycan metabolism better than other environments. On the other hand, the relative abundances of both glycoside hydrolases and glycosyltransferases surprisingly had a coverage of over 80% in all the environments. These glycoside hydrolases and glycosyltransferases were classified into two groups of (1) general enzyme families identified in various environments and (2) specific enzymes found only in certain environments. The general enzyme families were mostly from genes involved in monosaccharide metabolism, and most of the specific enzymes were polysaccharide degrading enzymes. CONCLUSION These findings suggest that environmental microorganisms could change the composition of their glycan-related genes to adapt the processes involved in acquiring energy from glycans in their environments. Our functional glyco-metagenomics approach has made it possible to clarify the relationship between the environment and genes from the perspective of carbohydrates, and the existence of glycan-related genes that exist specifically in the environment.
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Affiliation(s)
- Hayato Takihara
- Division of Bioinformatics, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-dori, Chuo-ku, Niigata, 951-8510, Japan
| | - Nobuaki Miura
- Division of Bioinformatics, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-dori, Chuo-ku, Niigata, 951-8510, Japan
| | - Kiyoko F Aoki-Kinoshita
- Glycan and Life Systems Integration Center, Faculty of Science and Engineering, Soka University, 1-236 Tangi-machi, Hachioji, Tokyo, 192-8577, Japan
| | - Shujiro Okuda
- Division of Bioinformatics, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-dori, Chuo-ku, Niigata, 951-8510, Japan.
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14
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Macchi M, Festa S, Nieto E, Irazoqui JM, Vega-Vela NE, Junca H, Valacco MP, Amadio AF, Morelli IS, Coppotelli BM. Design and evaluation of synthetic bacterial consortia for optimized phenanthrene degradation through the integration of genomics and shotgun proteomics. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2021; 29:e00588. [PMID: 33489789 PMCID: PMC7809168 DOI: 10.1016/j.btre.2021.e00588] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 12/22/2020] [Accepted: 12/31/2020] [Indexed: 01/15/2023]
Abstract
Two synthetic bacterial consortia (SC) composed of bacterial strains Sphingobium sp. (AM), Klebsiella aerogenes (B), Pseudomonas sp. (Bc-h and T), Burkholderia sp. (Bk) and Inquilinus limosus (Inq) isolated from a natural phenanthrene (PHN)-degrading consortium (CON) were developed and evaluated as an alternative approach to PHN biodegradation in bioremediation processes. A metabolic network showing the potential role of strains was reconstructed by in silico study of the six genomes and classification of dioxygenase enzymes using RHObase and AromaDeg databases. Network analysis suggested that AM and Bk were responsible for PHN initial attack, while Inq, B, T and Bc-h would degrade PHN metabolites. The predicted roles were further confirmed by physiological, RT-qPCR and metaproteomic assays. SC-1 with AM as the sole PHN degrader was the most efficient. The ecological roles inferred in this study can be applied to optimize the design of bacterial consortia and tackle the biodegradation of complex environmental pollutants.
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Affiliation(s)
- Marianela Macchi
- Centro de Investigación y Desarrollo en Fermentaciones Industriales, CINDEFI (UNLP, CCT-La Plata, CONICET), La Plata, Argentina
| | - Sabrina Festa
- Centro de Investigación y Desarrollo en Fermentaciones Industriales, CINDEFI (UNLP, CCT-La Plata, CONICET), La Plata, Argentina
| | - Esteban Nieto
- Centro de Investigación y Desarrollo en Fermentaciones Industriales, CINDEFI (UNLP, CCT-La Plata, CONICET), La Plata, Argentina
| | - José M. Irazoqui
- E.E.A. Rafaela, Instituto Nacional de Tecnología Agropecuaria (INTA), CCT Santa Fe, CONICET, Rafaela, Argentina
| | - Nelson E. Vega-Vela
- Pontificia Universidad Javeriana, Bogotá, Colombia
- Universidad de Bogotá Jorge Tadeo Lozano, Bogotá, Colombia
| | - Howard Junca
- Microbiomas Foundation, Div. Ecogenomics & Holobionts, RG Microbial Ecology: Metabolism, Genomics & Evolution, Chía, Colombia
| | | | - Ariel F. Amadio
- E.E.A. Rafaela, Instituto Nacional de Tecnología Agropecuaria (INTA), CCT Santa Fe, CONICET, Rafaela, Argentina
| | - Irma S. Morelli
- Centro de Investigación y Desarrollo en Fermentaciones Industriales, CINDEFI (UNLP, CCT-La Plata, CONICET), La Plata, Argentina
- Comisión de Investigaciones Científicas de la Provincia de Buenos Aires, La Plata, Argentina
| | - Bibiana M. Coppotelli
- Centro de Investigación y Desarrollo en Fermentaciones Industriales, CINDEFI (UNLP, CCT-La Plata, CONICET), La Plata, Argentina
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15
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Avellaneda H, Arbeli Z, Teran W, Roldan F. Transformation of TNT, 2,4-DNT, and PETN by Raoultella planticola M30b and Rhizobium radiobacter M109 and exploration of the associated enzymes. World J Microbiol Biotechnol 2020; 36:190. [PMID: 33247357 DOI: 10.1007/s11274-020-02962-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Accepted: 11/11/2020] [Indexed: 10/22/2022]
Abstract
The nitrated compounds 2,4-dinitrotoluene (2,4-DNT), 2,4,6-trinitrotoluene (TNT), and pentaerythritol tetranitrate (PETN) are toxic xenobiotics widely used in various industries. They often coexist as environmental contaminants. The aims of this study were to evaluate the transformation of 100 mg L-1 of TNT, 2,4-DNT, and PETN by Raoultella planticola M30b and Rhizobium radiobacter M109c and identify enzymes that may participate in the transformation. These strains were selected from 34 TNT transforming bacteria. Cupriavidus metallidurans DNT was used as a reference strain for comparison purposes. Strains DNT, M30b and M109c transformed 2,4-DNT (100%), TNT (100, 94.7 and 63.6%, respectively), and PETN (72.7, 69.3 and 90.7%, respectively). However, the presence of TNT negatively affects 2,4-DNT and PETN transformation (inhibition > 40%) in strains DNT and M109c and fully inhibited (100% inhibition) 2,4-DNT transformation in R. planticola M30b.Genomes of R. planticola M30b and R. radiobacter M109c were sequenced to identify genes related with 2,4-DNT, TNT or PETN transformation. None of the tested strains presented DNT oxygenase, which has been previously reported in the transformation of 2,4-DNT. Thus, unidentified novel enzymes in these strains are involved in 2,4-DNT transformation. Genes encoding enzymes homologous to the previously reported TNT and PETN-transforming enzymes were identified in both genomes. R. planticola M30b have homologous genes of PETN reductase and xenobiotic reductase B, while R. radiobacter M109c have homologous genes to GTN reductase and PnrA nitroreductase. The ability of these strains to transform explosive mixtures has a potentially biotechnological application in the bioremediation of contaminated environments.
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Affiliation(s)
- Hernán Avellaneda
- Facultad de Ciencias, Departamento de Biología, Unidad de Saneamiento y Biotecnología Ambiental (USBA), Pontificia Universidad Javeriana, Carrera 7 No. 43-82, Bogotá, DC, Colombia
| | - Ziv Arbeli
- Facultad de Ciencias, Departamento de Biología, Unidad de Saneamiento y Biotecnología Ambiental (USBA), Pontificia Universidad Javeriana, Carrera 7 No. 43-82, Bogotá, DC, Colombia
| | - Wilson Teran
- Facultad de Ciencias, Departamento de Biología, Biología de Plantas y Sistemas Productivos, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Fabio Roldan
- Facultad de Ciencias, Departamento de Biología, Unidad de Saneamiento y Biotecnología Ambiental (USBA), Pontificia Universidad Javeriana, Carrera 7 No. 43-82, Bogotá, DC, Colombia.
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16
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Xia J, Sun H, Ma X, Huang K, Ye L. Ozone pretreatment of wastewater containing aromatics reduces antibiotic resistance genes in bioreactors: The example of p-aminophenol. ENVIRONMENT INTERNATIONAL 2020; 142:105864. [PMID: 32563772 DOI: 10.1016/j.envint.2020.105864] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 05/30/2020] [Accepted: 05/30/2020] [Indexed: 06/11/2023]
Abstract
Aromatic matters are widely present in wastewater, especially industrial wastewater, and may lead to a high abundance of antibiotic resistance genes (ARGs) in wastewater treatment bioreactors and stimulate horizontal transfers of ARGs. Here, we investigated a practical approach that applying ozone pretreatment to mitigate ARGs in bioreactors treating wastewater containing a typical aromatic pollutant, p-aminophenol (PAP). The results showed that ozone pretreatment could effectively reduce the aromaticity of wastewater, and the relative abundance of ARGs in the bioreactor fed with ozone treated wastewater decreased by over 70% compared to the control reactor. Multidrug, quinolone, mupirocin, polymyxin, aminoglycoside, glycopeptide, beta-lactam, and trimethoprim resistance genes were all reduced in the bioreactors receiving wastewater pretreated by ozone. Metagenomic analysis suggested that the reduction of ARGs could be attributed to the co-occurrence of ARGs and aromatic degradation genes in bacteria. Furthermore, we expanded our analysis to investigate 71 metagenomes from different environments, and the results indicated that the impact of aromatics on ARG abundance widely occurs in various ecosystems and confirmed that high levels of aromatics could lead to high abundance of ARGs. Taken together, our work confirmed that the aromatics played critical roles in selecting ARGs and proposed a feasible approach to reduce ARGs in wastewater treatment bioreactors.
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Affiliation(s)
- Juntao Xia
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, 163 Xianlin Avenue, Nanjing 210023, China
| | - Haohao Sun
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, 163 Xianlin Avenue, Nanjing 210023, China
| | - Xueyan Ma
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, 163 Xianlin Avenue, Nanjing 210023, China
| | - Kailong Huang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, 163 Xianlin Avenue, Nanjing 210023, China; Collaborative Innovation Center of Atmospheric Environment and Equipment Technology, Jiangsu Key Laboratory of Atmospheric Environment Monitoring and Pollution Control (AEMPC), School of Environmental Science and Engineering, Nanjing University of Information Science & Technology, Nanjing 210044, China
| | - Lin Ye
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, 163 Xianlin Avenue, Nanjing 210023, China.
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Raggi L, García-Guevara F, Godoy-Lozano EE, Martínez-Santana A, Escobar-Zepeda A, Gutierrez-Rios RM, Loza A, Merino E, Sanchez-Flores A, Licea-Navarro A, Pardo-Lopez L, Segovia L, Juarez K. Metagenomic Profiling and Microbial Metabolic Potential of Perdido Fold Belt (NW) and Campeche Knolls (SE) in the Gulf of Mexico. Front Microbiol 2020; 11:1825. [PMID: 32903729 PMCID: PMC7438803 DOI: 10.3389/fmicb.2020.01825] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 07/10/2020] [Indexed: 01/04/2023] Open
Abstract
The Gulf of Mexico (GoM) is a particular environment that is continuously exposed to hydrocarbon compounds that may influence the microbial community composition. We carried out a metagenomic assessment of the bacterial community to get an overall view of this geographical zone. We analyzed both taxonomic and metabolic markers profiles to explain how the indigenous GoM microorganims participate in the biogeochemical cycling. Two geographically distant regions in the GoM, one in the north-west (NW) and one in the south-east (SE) of the GoM were analyzed and showed differences in their microbial composition and metabolic potential. These differences provide evidence the delicate equilibrium that sustains microbial communities and biogeochemical cycles. Based on the taxonomy and gene groups, the NW are more oxic sediments than SE ones, which have anaerobic conditions. Both water and sediments show the expected sulfur, nitrogen, and hydrocarbon metabolism genes, with particularly high diversity of the hydrocarbon-degrading ones. Accordingly, many of the assigned genera were associated with hydrocarbon degradation processes, Nitrospira and Sva0081 were the most abundant in sediments, while Vibrio, Alteromonas, and Alcanivorax were mostly detected in water samples. This basal-state analysis presents the GoM as a potential source of aerobic and anaerobic hydrocarbon degradation genes important for the ecological dynamics of hydrocarbons and the potential use for water and sediment bioremediation processes.
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Affiliation(s)
- Luciana Raggi
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
- CONACYT-Laboratorio de Biotecnología Acuícola, Instituto de Investigaciones Agropecuarias y Forestales, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mexico
| | | | - E. Ernestina Godoy-Lozano
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
- Centro de Investigación Sobre Enfermedades Infecciosas, Departamento de Bioinformática en Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Mexico
| | | | | | | | - Antonio Loza
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Enrique Merino
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | | | - Alexei Licea-Navarro
- Laboratorio de Inmunología Molecular y Biotoxinas, Departamento de Innovación Biomedica, CICESE, Ensenada, Mexico
| | - Liliana Pardo-Lopez
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Lorenzo Segovia
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Katy Juarez
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
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18
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Espinosa MJC, Blanco AC, Schmidgall T, Atanasoff-Kardjalieff AK, Kappelmeyer U, Tischler D, Pieper DH, Heipieper HJ, Eberlein C. Toward Biorecycling: Isolation of a Soil Bacterium That Grows on a Polyurethane Oligomer and Monomer. Front Microbiol 2020; 11:404. [PMID: 32292389 PMCID: PMC7118221 DOI: 10.3389/fmicb.2020.00404] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 02/26/2020] [Indexed: 12/03/2022] Open
Abstract
The fate of plastic waste and a sustainable use of synthetic polymers is one of the major challenges of the twenty first century. Waste valorization strategies can contribute to the solution of this problem. Besides chemical recycling, biological degradation could be a promising tool. Among the high diversity of synthetic polymers, polyurethanes are widely used as foams and insulation materials. In order to examine bacterial biodegradability of polyurethanes, a soil bacterium was isolated from a site rich in brittle plastic waste. The strain, identified as Pseudomonas sp. by 16S rRNA gene sequencing and membrane fatty acid profile, was able to grow on a PU-diol solution, a polyurethane oligomer, as the sole source of carbon and energy. In addition, the strain was able to use 2,4-diaminotoluene, a common precursor and putative degradation intermediate of polyurethanes, respectively, as sole source of energy, carbon, and nitrogen. Whole genome sequencing of the strain revealed the presence of numerus catabolic genes for aromatic compounds. Growth on potential intermediates of 2,4-diaminotoluene degradation, other aromatic growth substrates and a comparison with a protein data base of oxygenases present in the genome, led to the proposal of a degradation pathway.
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Affiliation(s)
| | - Andrea Colina Blanco
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Tabea Schmidgall
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | | | - Uwe Kappelmeyer
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Dirk Tischler
- Interdisciplinary Ecological Center, TU Bergakademie Freiberg, Freiberg, Germany
| | - Dietmar H Pieper
- Microbial Interactions and Processes Research Group, Helmholtz Centre for Infection Research - HZI, Braunschweig, Germany
| | - Hermann J Heipieper
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Christian Eberlein
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
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Xia J, Sun H, Zhang XX, Zhang T, Ren H, Ye L. Aromatic compounds lead to increased abundance of antibiotic resistance genes in wastewater treatment bioreactors. WATER RESEARCH 2019; 166:115073. [PMID: 31542545 DOI: 10.1016/j.watres.2019.115073] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Revised: 08/29/2019] [Accepted: 09/08/2019] [Indexed: 06/10/2023]
Abstract
Various aromatic compounds in wastewater, especially industrial wastewater, are treated by biological processes in bioreactors which are regarded as hotspots and reservoirs of antibiotic resistance genes (ARGs). Yet, little is known about the relationship between the aromatic compound degradation process and antibiotic resistance. Here, we report on the co-occurrence of ARGs and aromatic degradation genes (ADGs) in bacteria in bioreactors. We confirmed this by bioreactor experiments and bioinformatics analysis of over 10,000 publicly available bacterial genomes. We observed a significant enrichment of ARGs in bioreactors treating wastewater that contained p-aminophenol and p-nitrophenol. The potential hosts harboring ARGs and ADGs were mainly Pseudomonas, Leucobacter, Xanthobacter, Acinetobacter, and Burkholderiaceae. Genome analysis revealed that 67.6% of the publicly available bacterial genomes harboring ADGs also harbor ARGs. Over 80% of Burkholderiales, Xanthomonales, Enterobacteriaceae, Acinetobacter, Pseudomonas, and Nocardiaceae genomes harbor both ARGs and ADGs, which strongly suggests the co-occurrence of these genes. Furthermore, bacteria carrying ADGs harbored more than twice the number of ARGs than bacteria only carrying ARGs. Network analysis suggested that multidrug, beta-lactam, aminoglycoside, macrolide-lincosamide-streptogramin, and polymyxin resistance genes are the major ARGs associated with ADGs. Taken together, the presented findings improve the understanding of ARG prevalence in biological wastewater treatment plants, and highlight the potential risk of the effect of regular aromatic compounds on the selection and spread of ARGs.
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Affiliation(s)
- Juntao Xia
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China
| | - Haohao Sun
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China
| | - Xu-Xiang Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China
| | - Tong Zhang
- Environmental Biotechnology Laboratory, The University of Hong Kong, Pokfulam Road, 999077, Hong Kong, China; School of Public Health, The University of Hong Kong, Pokfulam Road, 999077, Hong Kong, China
| | - Hongqiang Ren
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China
| | - Lin Ye
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China.
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Thomas F, Corre E, Cébron A. Stable isotope probing and metagenomics highlight the effect of plants on uncultured phenanthrene-degrading bacterial consortium in polluted soil. THE ISME JOURNAL 2019; 13:1814-1830. [PMID: 30872807 PMCID: PMC6775975 DOI: 10.1038/s41396-019-0394-z] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 02/08/2019] [Accepted: 02/28/2019] [Indexed: 11/09/2022]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous soil pollutants. The discovery that plants can stimulate microbial degradation of PAHs has promoted research on rhizoremediation strategies. We combined DNA-SIP with metagenomics to assess the influence of plants on the identity and metabolic functions of active PAH-degrading bacteria in contaminated soil, using phenanthrene (PHE) as a model hydrocarbon. 13C-PHE dissipation was 2.5-fold lower in ryegrass-planted conditions than in bare soil. Metabarcoding of 16S rDNA revealed significantly enriched OTUs in 13C-SIP incubations compared to 12C-controls, namely 130 OTUs from bare soil and 73 OTUs from planted soil. Active PHE-degraders were taxonomically diverse (Proteobacteria, Actinobacteria and Firmicutes), with Sphingomonas and Sphingobium dominating in bare and planted soil, respectively. Plant root exudates favored the development of PHE-degraders having specific functional traits at the genome level. Indeed, metagenomes of 13C-enriched DNA fractions contained more genes involved in aromatic compound metabolism in bare soil, whereas carbohydrate catabolism genes were more abundant in planted soil. Functional gene annotation allowed reconstruction of complete pathways with several routes for PHE catabolism. Sphingomonadales were the major taxa performing the first steps of PHE degradation in both conditions, suggesting their critical role to initiate in situ PAH remediation. Active PHE-degraders act in a consortium, whereby complete PHE mineralization is achieved through the combined activity of taxonomically diverse co-occurring bacteria performing successive metabolic steps. Our study reveals hitherto underestimated functional interactions for full microbial detoxification in contaminated soils.
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Affiliation(s)
- François Thomas
- Université de Lorraine, CNRS, LIEC, 54500, Nancy, France
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680, Roscoff, France
| | - Erwan Corre
- CNRS, Sorbonne Université, FR2424, ABiMS, Station Biologique de Roscoff, 29680, Roscoff, France
| | - Aurélie Cébron
- Université de Lorraine, CNRS, LIEC, 54500, Nancy, France.
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21
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Durante-Rodríguez G, Gutiérrez-Del-Arroyo P, Vélez M, Díaz E, Carmona M. Further Insights into the Architecture of the PN Promoter That Controls the Expression of the bzd Genes in Azoarcus. Genes (Basel) 2019; 10:genes10070489. [PMID: 31252700 PMCID: PMC6678401 DOI: 10.3390/genes10070489] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 06/12/2019] [Accepted: 06/26/2019] [Indexed: 12/01/2022] Open
Abstract
The anaerobic degradation of benzoate in bacteria involves the benzoyl-CoA central pathway. Azoarcus/Aromatoleum strains are a major group of anaerobic benzoate degraders, and the transcriptional regulation of the bzd genes was extensively studied in Azoarcus sp. CIB. In this work, we show that the bzdR regulatory gene and the PN promoter can also be identified upstream of the catabolic bzd operon in all benzoate-degrader Azoarcus/Aromatoleum strains whose genome sequences are currently available. All the PN promoters from Azoarcus/Aromatoleum strains described here show a conserved architecture including three operator regions (ORs), i.e., OR1 to OR3, for binding to the BzdR transcriptional repressor. Here, we demonstrate that, whereas OR1 is sufficient for the BzdR-mediated repression of the PN promoter, the presence of OR2 and OR3 is required for de-repression promoted by the benzoyl-CoA inducer molecule. Our results reveal that BzdR binds to the PN promoter in the form of four dimers, two of them binding to OR1. The BzdR/PN complex formed induces a DNA loop that wraps around the BzdR dimers and generates a superstructure that was observed by atomic force microscopy. This work provides further insights into the existence of a conserved BzdR-dependent mechanism to control the expression of the bzd genes in Azoarcus strains.
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Affiliation(s)
- Gonzalo Durante-Rodríguez
- Microbial and Plant Biotechnology Department. Centro de Investigaciones Biológicas-CSIC. Ramiro de Maeztu, 9. 28040 Madrid, Spain
| | - Paloma Gutiérrez-Del-Arroyo
- Biocatalysis Department. Institute of Catalysis and Petrochemistry-CSIC. Marie Curie, 2, Cantoblanco. 28049 Madrid, Spain
| | - Marisela Vélez
- Biocatalysis Department. Institute of Catalysis and Petrochemistry-CSIC. Marie Curie, 2, Cantoblanco. 28049 Madrid, Spain
| | - Eduardo Díaz
- Microbial and Plant Biotechnology Department. Centro de Investigaciones Biológicas-CSIC. Ramiro de Maeztu, 9. 28040 Madrid, Spain
| | - Manuel Carmona
- Microbial and Plant Biotechnology Department. Centro de Investigaciones Biológicas-CSIC. Ramiro de Maeztu, 9. 28040 Madrid, Spain.
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22
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Sun H, Narihiro T, Ma X, Zhang XX, Ren H, Ye L. Diverse aromatic-degrading bacteria present in a highly enriched autotrophic nitrifying sludge. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 666:245-251. [PMID: 30798235 DOI: 10.1016/j.scitotenv.2019.02.172] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Revised: 02/10/2019] [Accepted: 02/11/2019] [Indexed: 06/09/2023]
Abstract
Biotransformation of refractory organics by ammonia-oxidizing microorganisms in nitrifying sludge have been widely reported, while the contribution of heterotrophic bacteria in nitrifying sludge in the biotransformation and degradation process might be overlooked. Here, we provide metagenomic and metatranscriptomic evidences showing that heterotrophic bacteria in a highly enriched autotrophic nitrifying sludge could significantly contribute to the aromatic biotransformation and biodegradation. Diverse genes encoding enzymes for aromatic degradation were observed in an enriched autotrophic nitrifying sludge. These genes are involved in the degradation of at least 15 complex aromatics. Genome binning results showed that these genes were mainly carried by species in Bacteroidetes (Flavobacteriaceae and Sphingobacteriales), Alphaproteobacteria (Rhodobacter) and Betaproteobacteria (Bordetella, Acidovorax, Ramlibacter and Pusillimonas). According to the metatranscriptomic analysis, the overall expression of the potential aromatic-degrading genes was significantly upregulated, and almost all genes involved in phenol degradation were over expressed after the nitrifying sludge was exposed to phenol. Overall, our results suggest that certain heterotrophs in nitrifying sludge are involved aromatic biotransformation and biodegradation and advance our knowledge of the underlying properties and metabolic mechanisms of the nitrifying sludge.
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Affiliation(s)
- Haohao Sun
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, China
| | - Takashi Narihiro
- Bioproduction Research Institute, Nrational Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| | - Xueyan Ma
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, China
| | - Xu-Xiang Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, China
| | - Hongqiang Ren
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, China
| | - Lin Ye
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, China.
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23
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Dangi AK, Sharma B, Hill RT, Shukla P. Bioremediation through microbes: systems biology and metabolic engineering approach. Crit Rev Biotechnol 2018; 39:79-98. [DOI: 10.1080/07388551.2018.1500997] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Arun Kumar Dangi
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
| | - Babita Sharma
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
| | - Russell T. Hill
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD, USA
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
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24
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Singleton DR, Lee J, Dickey AN, Stroud A, Scholl EH, Wright FA, Aitken MD. Polyphasic characterization of four soil-derived phenanthrene-degrading Acidovorax strains and proposal of Acidovorax carolinensis sp. nov. Syst Appl Microbiol 2018; 41:460-472. [PMID: 29937052 DOI: 10.1016/j.syapm.2018.06.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 05/30/2018] [Accepted: 06/01/2018] [Indexed: 10/14/2022]
Abstract
Four bacterial strains identified as members of the Acidovorax genus were isolated from two geographically distinct but similarly contaminated soils in North Carolina, USA, characterized, and their genomes sequenced. Their 16S rRNA genes were highly similar to those previously recovered during stable-isotope probing (SIP) of one of the soils with the polycyclic aromatic hydrocarbon (PAH) phenanthrene. Heterotrophic growth of all strains occurred with a number of organic acids, as well as phenanthrene, but no other tested PAHs. Optimal growth occurred aerobically under mesophilic temperature, neutral pH, and low salinity conditions. Predominant fatty acids were C16:1ω7c/C16:1ω6c, C16:0, and C18:1ω7c, and were consistent with the genus. Genomic G+C contents ranged from 63.6 to 64.2%. A combination of whole genome comparisons and physiological analyses indicated that these four strains likely represent a single species within the Acidovorax genus. Chromosomal genes for phenanthrene degradation to phthalate were nearly identical to highly conserved regions in phenanthrene-degrading Delftia, Burkholderia, Alcaligenes, and Massilia species in regions flanked by transposable or extrachromosomal elements. The lower degradation pathway for phenanthrene metabolism was inferred by comparisons to described genes and proteins. The novel species Acidovorax carolinensis sp. nov. is proposed, comprising the four strains described in this study with strain NA3T as the type strain (=LMG 30136, =DSM 105008).
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Affiliation(s)
- David R Singleton
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC 27599-7431, USA.
| | - Janice Lee
- Department of Biology, University of North Carolina,Chapel Hill, NC, 27599-3280, USA
| | - Allison N Dickey
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - Aaron Stroud
- Department of Biology, University of North Carolina,Chapel Hill, NC, 27599-3280, USA
| | - Elizabeth H Scholl
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - Fred A Wright
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - Michael D Aitken
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC 27599-7431, USA
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25
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Draft Genome Sequence of Monaibacterium marinum C7 T, Isolated from Seawater from the Menai Straits, Wales, United Kingdom. GENOME ANNOUNCEMENTS 2018; 6:6/5/e01444-17. [PMID: 29437088 PMCID: PMC5794935 DOI: 10.1128/genomea.01444-17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Here, we report the draft genome sequence of Monaibacterium marinum C7T, a strain that represents a new member of the Roseobacter clade of the family Rhodobacteraceae (Alphaproteobacteria). The genome size of Monaibacterium marinum C7T is 3.7 Mb (3,734,267 bp), with a G+C content of 58.86%.
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26
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Pujalte MJ, Lucena T, Rodrigo-Torres L, Arahal DR. Comparative Genomics of Thalassobius Including the Description of Thalassobius activus sp. nov., and Thalassobius autumnalis sp. nov. Front Microbiol 2018; 8:2645. [PMID: 29375512 PMCID: PMC5770400 DOI: 10.3389/fmicb.2017.02645] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 12/19/2017] [Indexed: 11/13/2022] Open
Abstract
A taxogenomic study was conducted to describe two new Thalassobius species and to analyze the internal consistency of the genus Thalassobius along with Shimia and Thalassococcus. Strains CECT 5113T, CECT 5114, CECT 5118T, and CECT 5120 were isolated from coastal Mediterranean seawater, Spain. Cells were Gram-negative, non- motile coccobacilli, aerobic chemoorganotrophs, with an optimum temperature of 26°C and salinity of 3.5-5%. Major cellular fatty acids of strains CECT 5113T and CECT 5114 were C18 : 1 ω7c/ω6c and C10 : 0 3OH, G+C content was 54.4-54.5 mol% and were able to utilize propionate, L-threonine, L- arginine, and L-aspartate as carbon sources. They exhibited 98.3% 16S rRNA gene sequence similarity, 75.0-75.1 ANIb and 19.5-20.9 digital DDH to type strain of their closest species, Thalassobius maritimus. Based on these data, strains CECT 5113T and CECT 5114 are recognized as a new species, for which the name Thalassobius activus is proposed, with strain CECT 5113T (=LMG 29900T) as type strain. Strains CECT 5118T and CECT 5120 were found to constitute another new species, with major cellular fatty acids C18 : 1 ω7c/ω6c and C18 : 1 ω7c 11-methyl and a G+C content of 59.8 mol%; they were not able to utilize propionate, L-threonine, L- arginine or L-aspartate. Their closest species was Thalassobius mediterraneus, with values of 99.6% 16S rRNA gene sequence similarity, 79.1% ANIb and 23.2% digital DDH compared to the type strain, CECT 5383T. The name Thalassobius autumnalis is proposed for this second new species, with strain CECT 5118T (=LMG 29904T) as type strain. To better determine the phylogenetic relationship of the two new species, we submitted 12 genomes representing species of Thalassobius, Shimia, and Thalassoccocus, to a phylogenomic analysis based on 54 single protein-encoding genes (BCG54). The resulting phylogenomic tree did not agree with the current genera classification, as Thalassobius was divided in three clades, Thalassobius sensu stricto (T. mediterraneus, T. autumnalis sp. nov., and T. gelatinovorus), Thalassobius aestuarii plus the three Shimia spp (S. marina, S. haliotis, and Shimia sp. SK013) and finally, Thalasobius maritimus plus T. activus sp. nov. Thalassococcus halodurans remained apart from the two genera. Phenotypic inferences from explored genomes are presented.
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Affiliation(s)
- María J Pujalte
- Departamento de Microbiología and Colección Española de Cultivos Tipo, Universitat de València, Valencia, Spain
| | - Teresa Lucena
- Departamento de Microbiología and Colección Española de Cultivos Tipo, Universitat de València, Valencia, Spain
| | - Lidia Rodrigo-Torres
- Departamento de Microbiología and Colección Española de Cultivos Tipo, Universitat de València, Valencia, Spain
| | - David R Arahal
- Departamento de Microbiología and Colección Española de Cultivos Tipo, Universitat de València, Valencia, Spain
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27
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Duarte M, Nielsen A, Camarinha-Silva A, Vilchez-Vargas R, Bruls T, Wos-Oxley ML, Jauregui R, Pieper DH. Functional soil metagenomics: elucidation of polycyclic aromatic hydrocarbon degradation potential following 12 years of in situ bioremediation. Environ Microbiol 2017; 19:2992-3011. [PMID: 28401633 DOI: 10.1111/1462-2920.13756] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 03/29/2017] [Accepted: 04/06/2017] [Indexed: 11/27/2022]
Abstract
A culture-independent function-based screening approach was used to assess the microbial aerobic catabolome for polycyclic aromatic hydrocarbons degradation of a soil subjected to 12 years of in situ bioremediation. A total of 422 750 fosmid clones were screened for key aromatic ring-cleavage activities using 2,3-dihydroxybiphenyl as substrate. Most of the genes encoding ring-cleavage enzymes on the 768 retrieved positive fosmids could not be identified using primer-based approaches and, thus, 205 fosmid inserts were sequenced. Nearly two hundred extradiol dioxygenase encoding genes of three different superfamilies could be identified. Additional key genes of aromatic metabolic pathways were identified, including a high abundance of Rieske non-heme iron oxygenases that provided detailed information on enzymes activating aromatic compounds and enzymes involved in activation of the side chain of methylsubstituted aromatics. The gained insights indicated a complex microbial network acting at the site under study, which comprises organisms similar to recently identified Immundisolibacter cernigliae TR3.2 and Rugosibacter aromaticivorans Ca6 and underlined the great potential of an approach that combines an activity-screening, a cost-effective high-throughput sequencing of fosmid clones and a phylogenomic-routed and manually curated database to carefully identify key proteins dedicated to aerobic degradation of aromatic compounds.
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Affiliation(s)
- Márcia Duarte
- Microbial Interactions and Processes Research Group, HZI - Helmholtz Centre for Infection Research, Inhoffenstr. 7, Braunschweig, D-38124, Germany
| | - Agnes Nielsen
- Microbial Interactions and Processes Research Group, HZI - Helmholtz Centre for Infection Research, Inhoffenstr. 7, Braunschweig, D-38124, Germany
| | - Amélia Camarinha-Silva
- Microbial Interactions and Processes Research Group, HZI - Helmholtz Centre for Infection Research, Inhoffenstr. 7, Braunschweig, D-38124, Germany
| | - Ramiro Vilchez-Vargas
- Microbial Interactions and Processes Research Group, HZI - Helmholtz Centre for Infection Research, Inhoffenstr. 7, Braunschweig, D-38124, Germany.,Department of Gastroenterology, Hepatology and Infectious Diseases, Otto-von-Guericke-University, Magdeburg, Germany
| | - Thomas Bruls
- Institut de Génomique, Genoscope, UMR8030 (CNRS, CEA, Université d'Evry), Evry, France
| | - Melissa L Wos-Oxley
- Microbial Interactions and Processes Research Group, HZI - Helmholtz Centre for Infection Research, Inhoffenstr. 7, Braunschweig, D-38124, Germany
| | - Ruy Jauregui
- Microbial Interactions and Processes Research Group, HZI - Helmholtz Centre for Infection Research, Inhoffenstr. 7, Braunschweig, D-38124, Germany.,AgResearch Grasslands, Tennent drive, Palmerston North, New Zealand
| | - Dietmar H Pieper
- Microbial Interactions and Processes Research Group, HZI - Helmholtz Centre for Infection Research, Inhoffenstr. 7, Braunschweig, D-38124, Germany
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28
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Abstract
Network reconstruction procedures based on meta-"omics" data are an invaluable tool for inferring total and active set of reactions mediated by different members in a microbial community. Within them, network-based methods for automatic analysis of catabolic capacities in metagenomes are currently limited. Here, we describe the complete workflow, scripts, and commands allowing the automatic reconstruction of biodegradation networks using as an input meta-sequences generated by direct DNA sequencing.
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Affiliation(s)
- Rafael Bargiela
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas (CSIC), Marie Curie 2, 28049, Madrid, Spain
| | - Manuel Ferrer
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas (CSIC), Marie Curie 2, 28049, Madrid, Spain.
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29
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Bourguignon N, Bargiela R, Rojo D, Chernikova TN, de Rodas SAL, García-Cantalejo J, Näther DJ, Golyshin PN, Barbas C, Ferrero M, Ferrer M. Insights into the degradation capacities of Amycolatopsis tucumanensis DSM 45259 guided by microarray data. World J Microbiol Biotechnol 2016; 32:201. [PMID: 27785708 DOI: 10.1007/s11274-016-2163-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2016] [Accepted: 10/18/2016] [Indexed: 10/20/2022]
Abstract
The analysis of catabolic capacities of microorganisms is currently often achieved by cultivation approaches and by the analysis of genomic or metagenomic datasets. Recently, a microarray system designed from curated key aromatic catabolic gene families and key alkane degradation genes was designed. The collection of genes in the microarray can be exploited to indicate whether a given microbe or microbial community is likely to be functionally connected with certain degradative phenotypes, without previous knowledge of genome data. Herein, this microarray was applied to capture new insights into the catabolic capacities of copper-resistant actinomycete Amycolatopsis tucumanensis DSM 45259. The array data support the presumptive ability of the DSM 45259 strain to utilize single alkanes (n-decane and n-tetradecane) and aromatics such as benzoate, phthalate and phenol as sole carbon sources, which was experimentally validated by cultivation and mass spectrometry. Interestingly, while in strain DSM 45259 alkB gene encoding an alkane hydroxylase is most likely highly similar to that found in other actinomycetes, the genes encoding benzoate 1,2-dioxygenase, phthalate 4,5-dioxygenase and phenol hydroxylase were homologous to proteobacterial genes. This suggests that strain DSM 45259 contains catabolic genes distantly related to those found in other actinomycetes. Together, this study not only provided new insight into the catabolic abilities of strain DSM 45259, but also suggests that this strain contains genes uncommon within actinomycetes.
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Affiliation(s)
- Natalia Bourguignon
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET), Tucumán, Argentina
| | - Rafael Bargiela
- Consejo Superior de Investigaciones Científicas (CSIC), Institute of Catalysis, Madrid, Spain
| | - David Rojo
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Monteprincipe, Boadilla del Monte, Madrid, Spain
| | | | - Sara A López de Rodas
- Unidad de Genómica-Campus Moncloa, C.A.I. Genómica y Proteómica, Facultad CC. Biológicas, Universidad Complutense de Madrid, Madrid, Spain
| | - Jesús García-Cantalejo
- Unidad de Genómica-Campus Moncloa, C.A.I. Genómica y Proteómica, Facultad CC. Biológicas, Universidad Complutense de Madrid, Madrid, Spain
| | - Daniela J Näther
- Institute for Microbiology, Biocentre, Goethe University, Frankfurt, Germany
| | - Peter N Golyshin
- School of Biological Sciences, Bangor University, Gwynedd, LL57 2UW, UK
| | - Coral Barbas
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Monteprincipe, Boadilla del Monte, Madrid, Spain
| | - Marcela Ferrero
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET), Tucumán, Argentina
| | - Manuel Ferrer
- Consejo Superior de Investigaciones Científicas (CSIC), Institute of Catalysis, Madrid, Spain.
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30
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Complete Genome Sequence of a Bacterium Representing a Deep Uncultivated Lineage within the Gammaproteobacteria Associated with the Degradation of Polycyclic Aromatic Hydrocarbons. GENOME ANNOUNCEMENTS 2016; 4:4/5/e01086-16. [PMID: 27795254 PMCID: PMC5054325 DOI: 10.1128/genomea.01086-16] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The bacterial strain TR3.2, representing a novel deeply branching lineage within the Gammaproteobacteria, was isolated and its genome sequenced. This isolate is the first cultivated representative of the previously described “Pyrene Group 2” (PG2) and represents a variety of environmental sequences primarily associated with petrochemical contamination and aromatic hydrocarbon degradation.
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31
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Pathak A, Chauhan A, Blom J, Indest KJ, Jung CM, Stothard P, Bera G, Green SJ, Ogram A. Comparative Genomics and Metabolic Analysis Reveals Peculiar Characteristics of Rhodococcus opacus Strain M213 Particularly for Naphthalene Degradation. PLoS One 2016; 11:e0161032. [PMID: 27532207 PMCID: PMC4988695 DOI: 10.1371/journal.pone.0161032] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Accepted: 07/27/2016] [Indexed: 12/12/2022] Open
Abstract
The genome of Rhodococcus opacus strain M213, isolated from a fuel-oil contaminated soil, was sequenced and annotated which revealed a genome size of 9,194,165 bp encoding 8680 putative genes and a G+C content of 66.72%. Among the protein coding genes, 71.77% were annotated as clusters of orthologous groups of proteins (COGs); 55% of the COGs were present as paralog clusters. Pulsed field gel electrophoresis (PFGE) analysis of M213 revealed the presence of three different sized replicons- a circular chromosome and two megaplasmids (pNUO1 and pNUO2) estimated to be of 750Kb 350Kb in size, respectively. Conversely, using an alternative approach of optical mapping, the plasmid replicons appeared as a circular ~1.2 Mb megaplasmid and a linear, ~0.7 Mb megaplasmid. Genome-wide comparative analysis of M213 with a cohort of sequenced Rhodococcus species revealed low syntenic affiliation with other R. opacus species including strains B4 and PD630. Conversely, a closer affiliation of M213, at the functional (COG) level, was observed with the catabolically versatile R. jostii strain RHA1 and other Rhodococcii such as R. wratislaviensis strain IFP 2016, R. imtechensis strain RKJ300, Rhodococcus sp. strain JVH1, and Rhodococcus sp. strain DK17, respectively. An in-depth, genome-wide comparison between these functional relatives revealed 971 unique genes in M213 representing 11% of its total genome; many associating with catabolic functions. Of major interest was the identification of as many as 154 genomic islands (GEIs), many with duplicated catabolic genes, in particular for PAHs; a trait that was confirmed by PCR-based identification of naphthalene dioxygenase (NDO) as a representative gene, across PFGE-resolved replicons of strain M213. Interestingly, several plasmid/GEI-encoded genes, that likely participate in degrading naphthalene (NAP) via a peculiar pathway, were also identified in strain M213 using a combination of bioinformatics, metabolic analysis and gene expression measurements of selected catabolic genes by RT-PCR. Taken together, this study provides a comprehensive understanding of the genome plasticity and ecological competitiveness of strain M213 likely facilitated by horizontal gene transfer (HGT), bacteriophage attacks and genomic reshuffling- aspects that continue to be understudied and thus poorly understood, in particular for the soil-borne Rhodococcii.
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Affiliation(s)
- Ashish Pathak
- School of the Environment, Florida A&M University, Tallahassee, Florida, United States of America
| | - Ashvini Chauhan
- School of the Environment, Florida A&M University, Tallahassee, Florida, United States of America
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Karl J. Indest
- Environmental Processes Branch, United States Army Engineer Research and Development Center, Vicksburg, Mississippi, United States of America
| | - Carina M. Jung
- Environmental Processes Branch, United States Army Engineer Research and Development Center, Vicksburg, Mississippi, United States of America
| | - Paul Stothard
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Canada
| | - Gopal Bera
- Geochemical and Environmental Research Group, Texas A&M University, College Station, Texas, United States of America
| | - Stefan J. Green
- DNA Services Facility, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Andrew Ogram
- Soil and Water Science Department, University of Florida, Gainesville, Florida, United States of America
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32
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Yakimov MM, Crisafi F, Messina E, Smedile F, Lopatina A, Denaro R, Pieper DH, Golyshin PN, Giuliano L. Analysis of defence systems and a conjugative IncP-1 plasmid in the marine polyaromatic hydrocarbons-degrading bacterium Cycloclasticus sp. 78-ME. ENVIRONMENTAL MICROBIOLOGY REPORTS 2016; 8:508-519. [PMID: 27345842 DOI: 10.1111/1758-2229.12424] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 04/24/2016] [Indexed: 06/06/2023]
Abstract
Marine prokaryotes have evolved a broad repertoire of defence systems to protect their genomes from lateral gene transfer including innate or acquired immune systems and infection-induced programmed cell suicide and dormancy. Here we report on the analysis of multiple defence systems present in the genome of the strain Cycloclasticus sp. 78-ME isolated from petroleum deposits of the tanker 'Amoco Milford Haven'. Cycloclasticus are ubiquitous bacteria globally important in polyaromatic hydrocarbons degradation in marine environments. Two 'defence islands' were identified in 78-ME genome: the first harbouring CRISPR-Cas with toxin-antitoxin system, while the second was composed by an array of genes for toxin-antitoxin and restriction-modification proteins. Among all identified spacers of CRISPR-Cas system only seven spacers match sequences of phages and plasmids. Furthermore, a conjugative plasmid p7ME01, which belongs to a new IncP-1θ ancestral archetype without any accessory mobile elements was found in 78-ME. Our results provide the context to the co-occurrence of diverse defence mechanisms in the genome of Cycloclasticus sp. 78-ME, which protect the genome of this highly specialized PAH-degrader. This study contributes to the further understanding of complex networks established in petroleum-based microbial communities.
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Affiliation(s)
- Michail M Yakimov
- Institute for Coastal Marine Environment, CNR, Spianata S. Raineri 86, Messina, 98122, Italy
| | - Francesca Crisafi
- Institute for Coastal Marine Environment, CNR, Spianata S. Raineri 86, Messina, 98122, Italy
| | - Enzo Messina
- Institute for Coastal Marine Environment, CNR, Spianata S. Raineri 86, Messina, 98122, Italy
| | - Francesco Smedile
- Institute for Coastal Marine Environment, CNR, Spianata S. Raineri 86, Messina, 98122, Italy
| | - Anna Lopatina
- Institute of Molecular Genetics and Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Renata Denaro
- Institute for Coastal Marine Environment, CNR, Spianata S. Raineri 86, Messina, 98122, Italy
| | - Dietmar H Pieper
- Microbial Interactions and Processes Research Group, HZI - Helmholtz Centre for Infection Research, Inhoffenstraße 7, Braunschweig, D-38124, Germany
| | - Peter N Golyshin
- School of Biological Sciences, Bangor University, ECW Bldg Deiniol Rd, Bangor, Gwynedd, LL57 2UW, United Kingdom
| | - Laura Giuliano
- Institute for Coastal Marine Environment, CNR, Spianata S. Raineri 86, Messina, 98122, Italy
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Linking Microbial Community and Catabolic Gene Structures during the Adaptation of Three Contaminated Soils under Continuous Long-Term Pollutant Stress. Appl Environ Microbiol 2016; 82:2227-2237. [PMID: 26850298 DOI: 10.1128/aem.03482-15] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2015] [Accepted: 01/29/2016] [Indexed: 11/20/2022] Open
Abstract
Three types of contaminated soil from three geographically different areas were subjected to a constant supply of benzene or benzene/toluene/ethylbenzene/xylenes (BTEX) for a period of 3 months. Different from the soil from Brazil (BRA) and Switzerland (SUI), the Czech Republic (CZE) soil which was previously subjected to intensive in situ bioremediation displayed only negligible changes in community structure. BRA and SUI soil samples showed a clear succession of phylotypes. A rapid response to benzene stress was observed, whereas the response to BTEX pollution was significantly slower. After extended incubation, actinobacterial phylotypes increased in relative abundance, indicating their superior fitness to pollution stress. Commonalities but also differences in the phylotypes were observed. Catabolic gene surveys confirmed the enrichment of actinobacteria by identifying the increase of actinobacterial genes involved in the degradation of pollutants. Proteobacterial phylotypes increased in relative abundance in SUI microcosms after short-term stress with benzene, and catabolic gene surveys indicated enriched metabolic routes. Interestingly, CZE soil, despite staying constant in community structure, showed a change in the catabolic gene structure. This indicates that a highly adapted community, which had to adjust its gene pool to meet novel challenges, has been enriched.
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Ferrer M, Martínez-Martínez M, Bargiela R, Streit WR, Golyshina OV, Golyshin PN. Estimating the success of enzyme bioprospecting through metagenomics: current status and future trends. Microb Biotechnol 2016; 9:22-34. [PMID: 26275154 PMCID: PMC4720405 DOI: 10.1111/1751-7915.12309] [Citation(s) in RCA: 127] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 06/26/2015] [Accepted: 07/02/2015] [Indexed: 12/01/2022] Open
Abstract
Recent reports have suggested that the establishment of industrially relevant enzyme collections from environmental genomes has become a routine procedure. Across the studies assessed, a mean number of approximately 44 active clones were obtained in an average size of approximately 53,000 clones tested using naïve screening protocols. This number could be significantly increased in shorter times when novel metagenome enzyme sequences obtained by direct sequencing are selected and subjected to high-throughput expression for subsequent production and characterization. The pre-screening of clone libraries by naïve screens followed by the pyrosequencing of the inserts allowed for a 106-fold increase in the success rate of identifying genes encoding enzymes of interest. However, a much longer time, usually on the order of years, is needed from the time of enzyme identification to the establishment of an industrial process. If the hit frequency for the identification of enzymes performing at high turnover rates under real application conditions could be increased while still covering a high natural diversity, the very expensive and time-consuming enzyme optimization phase would likely be significantly shortened. At this point, it is important to review the current knowledge about the success of fine-tuned naïve- and sequence-based screening protocols for enzyme selection and to describe the environments worldwide that have already been subjected to enzyme screen programmes through metagenomic tools. Here, we provide such estimations and suggest the current challenges and future actions needed before environmental enzymes can be successfully introduced into the market.
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Affiliation(s)
- Manuel Ferrer
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas (CSIC), Marie Curie 2, 28049, Madrid, Spain
| | - Mónica Martínez-Martínez
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas (CSIC), Marie Curie 2, 28049, Madrid, Spain
| | - Rafael Bargiela
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas (CSIC), Marie Curie 2, 28049, Madrid, Spain
| | - Wolfgang R Streit
- Biozentrum Klein Flottbek, Universität Hamburg, Ohnhorststraße 18, D-22609, Hamburg, Germany
| | - Olga V Golyshina
- School of Biological Sciences, Bangor University, LL57 2UW, Gwynedd, UK
| | - Peter N Golyshin
- School of Biological Sciences, Bangor University, LL57 2UW, Gwynedd, UK
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35
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Bargiela R, Gertler C, Magagnini M, Mapelli F, Chen J, Daffonchio D, Golyshin PN, Ferrer M. Degradation Network Reconstruction in Uric Acid and Ammonium Amendments in Oil-Degrading Marine Microcosms Guided by Metagenomic Data. Front Microbiol 2015; 6:1270. [PMID: 26635742 PMCID: PMC4656828 DOI: 10.3389/fmicb.2015.01270] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 10/30/2015] [Indexed: 11/13/2022] Open
Abstract
Biostimulation with different nitrogen sources is often regarded as a strategy of choice in combating oil spills in marine environments. Such environments are typically depleted in nitrogen, therefore limiting the balanced microbial utilization of carbon-rich petroleum constituents. It is fundamental, yet only scarcely accounted for, to analyze the catabolic consequences of application of biostimulants. Here, we examined such alterations in enrichment microcosms using sediments from chronically crude oil-contaminated marine sediment at Ancona harbor (Italy) amended with natural fertilizer, uric acid (UA), or ammonium (AMM). We applied the web-based AromaDeg resource using as query Illumina HiSeq meta-sequences (UA: 27,893 open reading frames; AMM: 32,180) to identify potential catabolic differences. A total of 45 (for UA) and 65 (AMM) gene sequences encoding key catabolic enzymes matched AromaDeg, and their participation in aromatic degradation reactions could be unambiguously suggested. Genomic signatures for the degradation of aromatics such as 2-chlorobenzoate, indole-3-acetate, biphenyl, gentisate, quinoline and phenanthrene were common for both microcosms. However, those for the degradation of orcinol, ibuprofen, phenylpropionate, homoprotocatechuate and benzene (in UA) and 4-aminobenzene-sulfonate, p-cumate, dibenzofuran and phthalate (in AMM), were selectively enriched. Experimental validation was conducted and good agreement with predictions was observed. This suggests certain discrepancies in action of these biostimulants on the genomic content of the initial microbial community for the catabolism of petroleum constituents or aromatics pollutants. In both cases, the emerging microbial communities were phylogenetically highly similar and were composed by very same proteobacterial families. However, examination of taxonomic assignments further revealed different catabolic pathway organization at the organismal level, which should be considered for designing oil spill mitigation strategies in the sea.
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Affiliation(s)
- Rafael Bargiela
- Systems Biotechnology, Department of Biocatalysis, Institute of Catalysis, Consejo Superior de Investigaciones Científicas Madrid, Spain
| | | | | | - Francesca Mapelli
- Department of Food, Environmental and Nutritional Sciences, University of Milan Milan, Italy
| | | | - Daniele Daffonchio
- Department of Food, Environmental and Nutritional Sciences, University of Milan Milan, Italy ; Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology Thuwal, Saudi Arabia
| | | | - Manuel Ferrer
- Systems Biotechnology, Department of Biocatalysis, Institute of Catalysis, Consejo Superior de Investigaciones Científicas Madrid, Spain
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36
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Degradation of Benzene by Pseudomonas veronii 1YdBTEX2 and 1YB2 Is Catalyzed by Enzymes Encoded in Distinct Catabolism Gene Clusters. Appl Environ Microbiol 2015; 82:167-73. [PMID: 26475106 DOI: 10.1128/aem.03026-15] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 10/13/2015] [Indexed: 01/21/2023] Open
Abstract
Pseudomonas veronii 1YdBTEX2, a benzene and toluene degrader, and Pseudomonas veronii 1YB2, a benzene degrader, have previously been shown to be key players in a benzene-contaminated site. These strains harbor unique catabolic pathways for the degradation of benzene comprising a gene cluster encoding an isopropylbenzene dioxygenase where genes encoding downstream enzymes were interrupted by stop codons. Extradiol dioxygenases were recruited from gene clusters comprising genes encoding a 2-hydroxymuconic semialdehyde dehydrogenase necessary for benzene degradation but typically absent from isopropylbenzene dioxygenase-encoding gene clusters. The benzene dihydrodiol dehydrogenase-encoding gene was not clustered with any other aromatic degradation genes, and the encoded protein was only distantly related to dehydrogenases of aromatic degradation pathways. The involvement of the different gene clusters in the degradation pathways was suggested by real-time quantitative reverse transcription PCR.
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37
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Bargiela R, Mapelli F, Rojo D, Chouaia B, Tornés J, Borin S, Richter M, Del Pozo MV, Cappello S, Gertler C, Genovese M, Denaro R, Martínez-Martínez M, Fodelianakis S, Amer RA, Bigazzi D, Han X, Chen J, Chernikova TN, Golyshina OV, Mahjoubi M, Jaouanil A, Benzha F, Magagnini M, Hussein E, Al-Horani F, Cherif A, Blaghen M, Abdel-Fattah YR, Kalogerakis N, Barbas C, Malkawi HI, Golyshin PN, Yakimov MM, Daffonchio D, Ferrer M. Bacterial population and biodegradation potential in chronically crude oil-contaminated marine sediments are strongly linked to temperature. Sci Rep 2015; 5:11651. [PMID: 26119183 PMCID: PMC4484246 DOI: 10.1038/srep11651] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2014] [Accepted: 05/29/2015] [Indexed: 01/16/2023] Open
Abstract
Two of the largest crude oil-polluted areas in the world are the semi-enclosed Mediterranean and Red Seas, but the effect of chronic pollution remains incompletely understood on a large scale. We compared the influence of environmental and geographical constraints and anthropogenic forces (hydrocarbon input) on bacterial communities in eight geographically separated oil-polluted sites along the coastlines of the Mediterranean and Red Seas. The differences in community compositions and their biodegradation potential were primarily associated (P < 0.05) with both temperature and chemical diversity. Furthermore, we observed a link between temperature and chemical and biological diversity that was stronger in chronically polluted sites than in pristine ones where accidental oil spills occurred. We propose that low temperature increases bacterial richness while decreasing catabolic diversity and that chronic pollution promotes catabolic diversification. Our results further suggest that the bacterial populations in chronically polluted sites may respond more promptly in degrading petroleum after accidental oil spills.
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Affiliation(s)
- Rafael Bargiela
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Francesca Mapelli
- Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milan, Milan, Italy
| | - David Rojo
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Montepríncipe, Madrid, Spain
| | - Bessem Chouaia
- Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milan, Milan, Italy
| | - Jesús Tornés
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Sara Borin
- Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milan, Milan, Italy
| | | | - Mercedes V. Del Pozo
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Simone Cappello
- Institute for Coastal Marine Environment, Consiglio Nazionale delle Ricerche, Messina, Italy
| | | | - María Genovese
- Institute for Coastal Marine Environment, Consiglio Nazionale delle Ricerche, Messina, Italy
| | - Renata Denaro
- Institute for Coastal Marine Environment, Consiglio Nazionale delle Ricerche, Messina, Italy
| | | | | | - Ranya A. Amer
- Environmental Biotechnology Department, Genetic Engineering and Biotechnology Research Institute, City for Scientific Research & Technology Applications, Alexandria, Egypt
| | | | - Xifang Han
- BGI Tech Solutions Co., Ltd, Main Building, Beishan Industrial Zone, Yantian District, Shenzhen, China
| | - Jianwei Chen
- BGI Tech Solutions Co., Ltd, Main Building, Beishan Industrial Zone, Yantian District, Shenzhen, China
| | | | | | - Mouna Mahjoubi
- LR Biotechnology and Bio-Geo Resources Valorization (LR11ES31), Higher Institute for Biotechnology - University of Manouba, Biotechpole of Sidi Thabet, 2020, Sidi Thabet, Ariana, Tunisia
| | - Atef Jaouanil
- Laboratory of Microorganisms and Active Biomolecules, University of Tunis El Manar, Tunis, Tunisia
| | - Fatima Benzha
- Laboratory of Microbiology, Biotechnology and Environment, University Hassan II – Ain Chock, Casablanca, Morocco
| | | | - Emad Hussein
- Department of Biological Sciences, Yarmouk University, Irbid, Jordan
| | - Fuad Al-Horani
- Faculty of Marine Sciences, The University of Jordan-Aqaba, Jordan
| | - Ameur Cherif
- Laboratory of Microorganisms and Active Biomolecules, University of Tunis El Manar, Tunis, Tunisia
| | - Mohamed Blaghen
- Laboratory of Microbiology, Biotechnology and Environment, University Hassan II – Ain Chock, Casablanca, Morocco
| | - Yasser R. Abdel-Fattah
- Bioprocess Development Department, Genetic Engineering and Biotechnology Research Institute, City for Scientific Research & Technology Applications, Alexandria, Egypt
| | | | - Coral Barbas
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Montepríncipe, Madrid, Spain
| | - Hanan I. Malkawi
- Hamdan Bin Mohammad Smart University, Academic City, Dubai, United Arab Emirates
| | | | - Michail M. Yakimov
- Institute for Coastal Marine Environment, Consiglio Nazionale delle Ricerche, Messina, Italy
| | - Daniele Daffonchio
- Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milan, Milan, Italy
- King Abdullah University of Science and Technology, BESE Division, Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Manuel Ferrer
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas, Madrid, Spain
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Abstract
Databases play an increasingly important role in biology. They archive, store, maintain, and share information on genes, genomes, expression data, protein sequences and structures, metabolites and reactions, interactions, and pathways. All these data are critically important to microbiologists. Furthermore, microbiology has its own databases that deal with model microorganisms, microbial diversity, physiology, and pathogenesis. Thousands of biological databases are currently available, and it becomes increasingly difficult to keep up with their development. The purpose of this minireview is to provide a brief survey of current databases that are of interest to microbiologists.
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Complete Genome Sequence of a Novel Bacterium within the Family Rhodocyclaceae That Degrades Polycyclic Aromatic Hydrocarbons. GENOME ANNOUNCEMENTS 2015; 3:3/2/e00251-15. [PMID: 25858839 PMCID: PMC4392151 DOI: 10.1128/genomea.00251-15] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
A polycyclic aromatic hydrocarbon-degrading bacterium designated strain Ca6, a member of the family Rhodocyclaceae and a representative of the uncharacterized pyrene group 1 (PG1), was isolated and its genome sequenced. The presence of several genes suspected to be associated with PG1 was confirmed, and additional genes for aromatic compound metabolism were detected.
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