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Sepehrnia N, Teshnizi FA, Hallett P, Coyne M, Shokri N, Peth S. Modeling bacterial transport and fate: Insight into the cascading consequences of soil water repellency and contrasting hydraulic conditions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 954:176196. [PMID: 39278475 DOI: 10.1016/j.scitotenv.2024.176196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 09/02/2024] [Accepted: 09/09/2024] [Indexed: 09/18/2024]
Abstract
The mechanisms governing bacteria transport and fate rely on their hydrophobicity and the wettability of porous media across a wide range of soil moisture conditions, extending from extreme dryness to highly saturated states. However, it largely remains unknown how transport, retention, and release mechanisms change in natural soil systems in such conditions. We thus optimized our previously published unique transport data for hydrophilic Escherichia coli (E. coli) and hydrophobic Rhodococcus erythropolis (R. erythropolis) bacteria, and bromide (Br-) in two distinct wettable and water-repellent soils at column scale. The soils were initially dry, followed by injecting influents in two pulses followed by a flushing step under saturated flow conditions for six pore volumes. We conducted simulations for each pulse separately and simultaneously for soils. There were differences in hydraulic properties of the soils due to their contrasting wetting characteristic in separate and simultaneously modeling of each pulse affecting Br- and bacteria transport fate. Bacteria attachment was the dominant retention mechanism in both soils in these conditions. Notably, the 82.4 min-1 attachment rate in wettable soil was almost 10× greater than in the water-repellent soil and it governed optimization of bacteria die-off. Physicochemical detachment and physical release unraveled the effect of bacteria size and hydrophobicity interacting with soil wettability. The smaller and hydrophobic R. erythropolis detached more easily while hydrophilic E. coli released; the rates were enhanced by soil water repellency. Further research is needed to reveal the effects of surface wettability properties on bacteria survival especially at the nanoscale.
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Affiliation(s)
- Nasrollah Sepehrnia
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK; School of Biosciences, University of Nottingham, Nottingham, UK.
| | - Forough Abbasi Teshnizi
- Department of Water Engineering, Faculty of Agriculture, Shahrekord University, Shahrekord, Iran
| | - Paul Hallett
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
| | - Mark Coyne
- University of Kentucky, Department of Plant and Soil Sciences, United States(1)
| | - Nima Shokri
- Institute of Geo-Hydroinformatics, Hamburg University of Technology, Am Schwarzenberg-Campus 3 (E), 21073 Hamburg, Germany; United Nations University Hub on Engineering to Face Climate Change at the Hamburg University of Technology, United Nations University Institute for Water, Environment and Health (UNU-INWEH), Hamburg, Germany
| | - Stephan Peth
- Institute of Earth System Sciences, Leibniz Universität Hannover, Herrenhäuser Str. 2, D-30419 Hannover, Germany
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Jansen Z, Alameri A, Wei Q, Kulhanek DL, Gilmour AR, Halper S, Schwalm ND, Thyer R. A modular toolkit for environmental Rhodococcus, Gordonia, and Nocardia enables complex metabolic manipulation. Appl Environ Microbiol 2024; 90:e0034024. [PMID: 39082821 PMCID: PMC11337820 DOI: 10.1128/aem.00340-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 06/29/2024] [Indexed: 08/22/2024] Open
Abstract
Soil-dwelling Actinomycetes are a diverse and ubiquitous component of the global microbiome but largely lack genetic tools comparable to those available in model species such as Escherichia coli or Pseudomonas putida, posing a fundamental barrier to their characterization and utilization as hosts for biotechnology. To address this, we have developed a modular plasmid assembly framework, along with a series of genetic control elements for the previously genetically intractable Gram-positive environmental isolate Rhodococcus ruber C208, and demonstrate conserved functionality in 11 additional environmental isolates of Rhodococcus, Nocardia, and Gordonia. This toolkit encompasses five Mycobacteriale origins of replication, five broad-host-range antibiotic resistance markers, transcriptional and translational control elements, fluorescent reporters, a tetracycline-inducible system, and a counter-selectable marker. We use this toolkit to interrogate the carotenoid biosynthesis pathway in Rhodococcus erythropolis N9T-4, a weakly carotenogenic environmental isolate and engineer higher pathway flux toward the keto-carotenoid canthaxanthin. This work establishes several new genetic tools for environmental Mycobacteriales and provides a synthetic biology framework to support the design of complex genetic circuits in these species.IMPORTANCESoil-dwelling Actinomycetes, particularly the Mycobacteriales, include both diverse new hosts for sustainable biomanufacturing and emerging opportunistic pathogens. Rhodococcus, Gordonia, and Nocardia are three abundant genera with particularly flexible metabolisms and untapped potential for natural product discovery. Among these, Rhodococcus ruber C208 was shown to degrade polyethylene; Gordonia paraffinivorans can assimilate carbon from solid hydrocarbons; and Nocardia neocaledoniensis (and many other Nocardia spp.) possesses dual isoprenoid biosynthesis pathways. Many species accumulate high levels of carotenoid pigments, indicative of highly active isoprenoid biosynthesis pathways which may be harnessed for fermentation of terpenes and other commodity isoprenoids. Modular genetic toolkits have proven valuable for both fundamental and applied research in model organisms, but such tools are lacking for most Actinomycetes. Our suite of genetic tools and DNA assembly framework were developed for broad functionality and to facilitate rapid prototyping of genetic constructs in these organisms.
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Affiliation(s)
- Zachary Jansen
- Systems, Synthetic, and Physical Biology, Rice University, Houston, Texas, USA
| | - Abdulaziz Alameri
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas, USA
| | - Qiyao Wei
- Department of Bioengineering, Rice University, Houston, Texas, USA
| | - Devon L. Kulhanek
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas, USA
| | - Andrew R. Gilmour
- Systems, Synthetic, and Physical Biology, Rice University, Houston, Texas, USA
| | - Sean Halper
- DEVCOM Army Research Laboratory, Adelphi, Maryland, USA
| | | | - Ross Thyer
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas, USA
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Tyumina E, Bazhutin G, Kostrikina N, Sorokin V, Mulyukin A, Ivshina I. Phenotypic and metabolic adaptations of Rhodococcus cerastii strain IEGM 1243 to separate and combined effects of diclofenac and ibuprofen. Front Microbiol 2023; 14:1275553. [PMID: 38125575 PMCID: PMC10730942 DOI: 10.3389/fmicb.2023.1275553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 11/21/2023] [Indexed: 12/23/2023] Open
Abstract
Introduction The increasing use of non-steroidal anti-inflammatory drugs (NSAIDs) has raised concerns regarding their environmental impact. To address this, understanding the effects of NSAIDs on bacteria is crucial for bioremediation efforts in pharmaceutical-contaminated environments. The primary challenge in breaking down persistent compounds lies not in the biochemical pathways but in capacity of bacteria to surmount stressors. Methods In this study, we examined the biodegradative activity, morphological and physiological changes, and ultrastructural adaptations of Rhodococcus cerastii strain IEGM 1243 when exposed to ibuprofen, diclofenac, and their mixture. Results and Discussion Our findings revealed that R. cerastii IEGM 1243 exhibited moderate biodegradative activity towards the tested NSAIDs. Cellular respiration assay showed higher metabolic activity in the presence of NSAIDs, indicating their influence on bacterial metabolism. Furthermore, catalase activity in R. cerastii IEGM 1243 exposed to NSAIDs showed an initial decrease followed by fluctuations, with the most significant changes observed in the presence of DCF and the NSAID mixture, likely influenced by bacterial growth phases, active NSAID degradation, and the formation of multicellular aggregates, suggesting potential intercellular synergy and task distribution within the bacterial community. Morphometric analysis demonstrated alterations in size, shape, and surface roughness of cells exposed to NSAIDs, with a decrease in surface area and volume, and an increase in surface area-to-volume ratio (SA/V). Moreover, for the first time, transmission electron microscopy confirmed the presence of lipid inclusions, polyphosphates, and intracellular membrane-like structures in the ibuprofen-treated cells. Conclusion These results provide valuable insights into the adaptive responses of R. cerastii IEGM 1243 to NSAIDs, shedding light on the possible interaction between bacteria and pharmaceutical compounds in the environment.
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Affiliation(s)
- Elena Tyumina
- Perm Federal Research Center, Ural Branch of the Russian Academy of Sciences, Institute of Ecology and Genetics of Microorganisms, Perm, Russia
- Department of Microbiology and Immunology, Perm State University, Perm, Russia
| | - Grigory Bazhutin
- Perm Federal Research Center, Ural Branch of the Russian Academy of Sciences, Institute of Ecology and Genetics of Microorganisms, Perm, Russia
- Department of Microbiology and Immunology, Perm State University, Perm, Russia
| | - Nadezhda Kostrikina
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Vladimir Sorokin
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Andrey Mulyukin
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Irina Ivshina
- Perm Federal Research Center, Ural Branch of the Russian Academy of Sciences, Institute of Ecology and Genetics of Microorganisms, Perm, Russia
- Department of Microbiology and Immunology, Perm State University, Perm, Russia
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Henikoff S, Henikoff JG, Ahmad K, Paranal RM, Janssens DH, Russell ZR, Szulzewsky F, Kugel S, Holland EC. Epigenomic analysis of formalin-fixed paraffin-embedded samples by CUT&Tag. Nat Commun 2023; 14:5930. [PMID: 37739938 PMCID: PMC10516967 DOI: 10.1038/s41467-023-41666-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 09/14/2023] [Indexed: 09/24/2023] Open
Abstract
For more than a century, formalin-fixed paraffin-embedded (FFPE) sample preparation has been the preferred method for long-term preservation of biological material. However, the use of FFPE samples for epigenomic studies has been difficult because of chromatin damage from long exposure to high concentrations of formaldehyde. Previously, we introduced Cleavage Under Targeted Accessible Chromatin (CUTAC), an antibody-targeted chromatin accessibility mapping protocol based on CUT&Tag. Here we show that simple modifications of our CUTAC protocol either in single tubes or directly on slides produce high-resolution maps of paused RNA Polymerase II at enhancers and promoters using FFPE samples. We find that transcriptional regulatory element differences produced by FFPE-CUTAC distinguish between mouse brain tumors and identify and map regulatory element markers with high confidence and precision, including microRNAs not detectable by RNA-seq. Our simple workflows make possible affordable epigenomic profiling of archived biological samples for biomarker identification, clinical applications and retrospective studies.
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Affiliation(s)
- Steven Henikoff
- Basic Science Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
| | - Jorja G Henikoff
- Basic Science Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Kami Ahmad
- Basic Science Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Ronald M Paranal
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Derek H Janssens
- Basic Science Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Zachary R Russell
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Frank Szulzewsky
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Sita Kugel
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Eric C Holland
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
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Xiang W, Hong S, Xue Y, Ma Y. Functional Analysis of Novel alkB Genes Encoding Long-Chain n-Alkane Hydroxylases in Rhodococcus sp. Strain CH91. Microorganisms 2023; 11:1537. [PMID: 37375039 DOI: 10.3390/microorganisms11061537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 06/05/2023] [Accepted: 06/07/2023] [Indexed: 06/29/2023] Open
Abstract
Rhodococcus sp. strain CH91 is capable of utilizing long-chain n-alkanes as the sole carbon source. Two new genes (alkB1 and alkB2) encoding AlkB-type alkane hydroxylase were predicted by its whole-genome sequence analysis. The purpose of this study was to elucidate the functional role of alkB1 and alkB2 genes in the n-alkane degradation of strain CH91. RT-qPCR analyses revealed that the two genes were induced by n-alkanes ranging from C16 to C36 and the expression of the alkB2 gene was up-regulated much higher than that of alkB1. The knockout of the alkB1 or alkB2 gene in strain CH91 resulted in the obvious reduction of growth and degradation rates on C16-C36 n-alkanes and the alkB2 knockout mutant exhibited lower growth and degradation rate than the alkB1 knockout mutant. When gene alkB1 or alkB2 was heterologously expressed in Pseudomonas fluorescens KOB2Δ1, the two genes could restore its alkane degradation activity. These results demonstrated that both alkB1 and alkB2 genes were responsible for C16-C36 n-alkanes' degradation of strain CH91, and alkB2 plays a more important role than alkB1. The functional characteristics of the two alkB genes in the degradation of a broad range of n-alkanes make them potential gene candidates for engineering the bacteria used for bioremediation of petroleum hydrocarbon contaminations.
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Affiliation(s)
- Wei Xiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Shan Hong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yanfen Xue
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yanhe Ma
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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Degradation of long-chain n-alkanes by a novel thermal-tolerant Rhodococcus strain. Arch Microbiol 2022; 204:259. [PMID: 35419660 DOI: 10.1007/s00203-022-02872-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 03/22/2022] [Accepted: 03/23/2022] [Indexed: 11/02/2022]
Abstract
A novel bacterial strain, CH91, was isolated from a high-temperature oil reservoir. Morphological characterization, phylogenetic analyses of 16S rRNA gene sequence and genome relatedness indicated that the strain is a potential new species in the genus Rhodococcus. Strain CH91 could grow in the temperature range of 25-50 °C (optimally at 37 °C) and utilize a broad range of long-chain n-alkanes from hexadecane to hexatriacontane. The utilization of the n-alkanes mixture of strain CH91 revealed that the degradation rate was correlated to the length of the carbon chain. Two novel alkB genes encoding alkane 1-monooxygenase were found in the genome of this strain. The protein sequences of both alkane 1-monooxygenases showed a remarkable phylogenetic distance to other reported AlkB protein sequences. These results would help broaden our knowledge about alkane degradation by Rhodocuccus and its potential ecological role. The ability of the strain in the long-chain alkane degradation and thermal tolerance could also be further exploited for bioremediation of oil contaminations and microbial enhanced oil recovery.
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