Quantification of Chemotaxis-Related Alkane Accumulation in Acinetobacter baylyi Using Raman Microspectroscopy

Accessing nutrients as the primary benefit arising from chemotaxis

About half of the known bacterial species perform chemotaxis that gains them access to sites that are optimal for growth and survival. The motility apparatus and chemotaxis signaling pathway impose a large energetic and metabolic burden on the cell. There is almost no limit to the type of chemoeffectors that are recognized by bacterial chemoreceptors. For example, they include hormones, neurotransmitters, quorum-sensing molecules, and inorganic ions. However, the vast majority of chemoeffectors appear to be of metabolic value. We review here the experimental evidence indicating that accessing nutrients is the main selective force that led to the evolution of chemotaxis.

Online detection of alkanes by a biological-phase microextraction and biosensing (BPME-BS) device

Oil spill incidents occur frequently and threaten ecosystems and human health. Solid-phase microextraction allows direct alkane extraction from environmental matrices to improve the limit of detection but is unable to measure alkanes on site. A biological-phase microextraction and biosensing (BPME-BS) device was developed by immobilising an alkane chemotactic Acinetobacter bioreporter ADPWH_alk in agarose gel to achieve online alkane quantification with the aid of a photomultiplier. The BPME-BS device had a high enrichment factor (average 7.07) and a satisfactory limit of detection (0.075 mg/L) for alkanes. The quantification range was 0.1-100 mg/L, comparable to a gas chromatography flame ionisation detector and better than a bioreporter without immobilisation. ADPWH_alk cells in the BPME-BS device maintained good sensitivity under a wide range of environmental conditions, including pH (4.0-9.0), temperature (20-40 °C), and salinity (0.0-3.0%), and its response remained stable within 30 days at 4 °C. In a 7-day continual measurement, the BPME-BS device successfully visualised the dynamic concentration of alkanes, and a 7-day field test successfully captured an oil spill event, helping in source apportionment and on-scene law enforcement. Our work proved that the BPME-BS device is a powerful tool for online alkane measurement, showing substantial potential for fast detection and rapid response to oil spills on site and in situ.

The role of predicted chemotactic and hydrocarbon degrading taxa in natural source zone depletion at a legacy petroleum hydrocarbon site

Petroleum hydrocarbon contamination is a global problem which can cause long-term environmental damage and impacts water security. Natural source zone depletion (NSZD) is the natural degradation of such contaminants. Chemotaxis is an aspect of NSZD which is not fully understood, but one that grants microorganisms the ability to alter their motion in response to a chemical concentration gradient potentially enhancing petroleum NSZD mass removal rates. This study investigates the distribution of potentially chemotactic and hydrocarbon degrading microbes (CD) across the water table of a legacy petroleum hydrocarbon site near Perth, Western Australia in areas impacted by crude oil, diesel and jet fuel. Core samples were recovered and analysed for hydrocarbon contamination using gas chromatography. Predictive metagenomic profiling was undertaken to infer functionality using a combination of 16 S rRNA sequencing and PICRUSt2 analysis. Naphthalene contamination was found to significantly increase the occurrence of potential CD microbes, including members of the Comamonadaceae and Geobacteraceae families, which may enhance NSZD. Further work to explore and define this link is important for reliable estimation of biodegradation of petroleum hydrocarbon fuels. Furthermore, the outcomes suggest that the chemotactic parameter within existing NSZD models should be reviewed to accommodate CD accumulation in areas of naphthalene contamination, thereby providing a more accurate quantification of risk from petroleum impacts in subsurface environments, and the scale of risk mitigation due to NSZD.

Evaluating the simulated toxicities of metal mixtures and hydrocarbons using the alkane degrading bioreporter Acinetobacter baylyi ADPWH_recA

Oil spillages lead to the formation of hydrocarbon and metal mixtures possessing effects on alkane-degrading bacteria that are responsible for the bioremediation of oil-contaminated soils and waters. Studies of bacterial responses to the mixture of petroleum and metal can inform appropriate strategies for bioremediation. We employed a luminescent bioreporter Acinetobacter baylyi ADPWH_recA with alkane degradation capability to evaluate the combined effects from heavy metals (Cd, Pb and Cu) and alkanes (dodecane, tetradecane, hexadecane and octadecane). Bioluminescent ratios of ADPWH_recA in single Cd or Pb treatments ranged from 0.25 to 1.98, indicating both genotoxicity and cytotoxicity of these two metals, while ratios < 1.0 postexposure to Cu showed its cytotoxic impacts on ADPWH_recA bioreporter. Metal mixtures exhibited enhanced antagonistic effects (Ti>4.0) determined by the Toxic Unit model. With 100 mg/L alkane, the morbidity of ADPWH-recA reduced to < 20%, showing the inhibition of alkanes on Cd toxicity. Exposed to the metal mixture containing 10 mg/L Cu, the weak binding affinity of Cu with alkanes contributed to a high morbidity of > 85% in ADPWH_recA cells. This study provides a new way to understand the toxicity of mixture contaminants, which can help to optimize treatment efficiencies of bacterial remediation for oil contamination.

Ultra-fast and onsite interrogation of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in waters via surface enhanced Raman scattering (SERS)

The outbreak of coronavirus infectious disease-2019 (COVID-19) pneumonia challenges the rapid interrogation of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in human and environmental samples. In this study, we developed an assay using surface enhanced Raman scattering (SERS) coupled with multivariate analysis to detect SARS-CoV-2 in an ultra-fast manner without any pretreatment (e.g., RNA extraction). Using silver-nanorod SERS array functionalized with cellular receptor angiotensin-converting enzyme 2 (ACE2), we obtained strong SERS signals of ACE2 at 1032, 1051, 1089, 1189, 1447 and 1527 cm^-1. The recognition and binding of receptor binding domain (RBD) of SARS-CoV-2 spike protein on SERS assay significantly quenched the spectral intensities of most peaks and exhibited a shift from 1189 to 1182 cm^-1. On-site tests on 23 water samples with a portable Raman spectrometer proved its accuracy and easy-operation for spot detection of SARS-CoV-2 to evaluate disinfection performance, explore viral survival in environmental media, assess viral decay in wastewater treatment plant and track SARS-CoV-2 in pipe network. Our findings raise a state-of-the-art spectroscopic tool to screen and interrogate viruses with RBD for human cell entry, proving its feasibility and potential as an ultra-fast detection tool for wastewater-based epidemiology.

Characterization and Transcriptome Analysis of a Long-Chain n-Alkane-Degrading Strain Acinetobacter pittii SW-1

Strain sw-1, isolated from 7619-m seawater of the Mariana Trench, was identified as Acinetobacter pittii by 16S rRNA gene and whole-genome sequencing. A. pittii sw-1 was able to efficiently utilize long-chain n-alkanes (C₁₈–C₃₆), but not short- and medium-chain n-alkanes (C₈–C₁₆). The degradation rate of C₂₀ was 91.25%, followed by C₁₈, C₂₂, C₂₄, C₃₂, and C₃₆ with the degradation rates of 89.30%, 84.03%, 80.29%, 30.29%, and 13.37%, respectively. To investigate the degradation mechanisms of n-alkanes for this strain, the genome and the transcriptome analyses were performed. Four key alkane hydroxylase genes (alkB, almA, ladA1, and ladA2) were identified in the genome. Transcriptomes of strain sw-1 grown in C₂₀ or CH₃COONa (NaAc) as the sole carbon source were compared. The transcriptional levels of alkB and almA, respectively, increased 78.28- and 3.51-fold in C₂₀ compared with NaAc, while ladA1 and ladA2 did not show obvious change. The expression levels of other genes involved in the synthesis of unsaturated fatty acids, permeases, membrane proteins, and sulfur metabolism were also upregulated, and they might be involved in n-alkane uptake. Reverse transcription quantitative polymerase chain reaction (RT-qPCR) confirmed that alkB expression was significantly induced by C₂₀, C₂₄, and C₃₂, and almA induction extent by C₂₄ and C₃₂ was higher than that with C_20. Furthermore, ladA2 expression was only induced by C₃₂, and ladA1 expression was not induced by any of n-alkanes. In addition, A. pittii sw-1 could grow with 0%–3% NaCl or 8 out of 10 kinds of the tested heavy metals and degrade n-alkanes at 15 °C. Taken together, these results provide comprehensive insights into the degradation of long-chain n-alkanes by Acinetobacter isolated from the deep ocean environment.

Applying Raman Microspectroscopy to Evaluate the Effects of Nutrient Cations on Alkane Bioavailability to Acinetobacter baylyi ADP1

Contamination with petroleum hydrocarbons causes extensive damage to ecological systems. On oil-contaminated sites, alkanes are major components; many indigenous bacteria can access and/or degrade alkanes. However, their ability to do so is affected by external properties of the soil, including nutrient cations. This study used Raman microspectroscopy to study how nutrient cations affect alkanes' bioavailability to Acinetobacter baylyi ADP1 (a known degrader). Treated with Na, K, Mg, and Ca at 10 mM, A. baylyi was exposed to seven n-alkanes (decane, dodecane, tetradecane, hexadecane, nonadecane, eicosane, and tetracosane) and one alkane mixture (mineral oil). Raman spectral analysis indicated that bioavailability of alkanes varied with carbon chain lengths, and additional cations altered the bacterial response to n-alkanes. Sodium significantly increased the bacterial affinity toward decane and dodecane, and K and Mg enhanced the bioavailability of tetradecane and hexadecane. In contrast, the bacterial response was inhibited by Ca for all alkanes. Similar results were observed in mineral oil exposure. Our study employed Raman spectral assay to offer a deep insight into how nutrient cations affect the bioavailability of alkanes, suggesting that nutrient cations can play a key role in influencing the harmful effects of hydrocarbons and could be optimized to enhance the bioremediation strategy.

Intermicrobial Hitchhiking: How Nonmotile Microbes Leverage Communal Motility

Motility allows many microbes to traverse their environment to find nutrient sources or escape unfavorable environments. However, some microbes are nonmotile and are restricted to their immediate conditions. Intriguingly, sporadic reports have demonstrated that many nonmotile microbes can utilize the motility machinery of other microbes in their vicinity. This form of transportation, called hitchhiking, has been observed with both prokaryotic and eukaryotic microbes. Importantly, many hitchhiking microbes are pathogenic to humans or plants. Here, we discuss reports of intermicrobial hitchhiking to generate a comprehensive view of hitchhiking mechanisms and how such interactions may influence human and plant health. We hypothesize that microbial hitchhiking is ubiquitous in nature and may become the subject of an independent subfield of research in microbiology.

Interrogating cadmium and lead biosorption mechanisms by Simplicillium chinense via infrared spectroscopy

Fungi-associated phytoremediation is an environmentally friendly and cost-efficient approach to remove potential toxic elements (PTEs) from contaminated soils. Many fungal strains have been reported to possess PTE-biosorption behaviour which benefits phytoremediation performance. Nevertheless, most studies are limited in rich or defined medium, far away from the real-world scenarios where nutrients are deficient. Understanding fungal PTE-biosorption performance and influential factors in soil environment can expand their application potential and is urgently needed. This study applied attenuated total reflection Fourier-transform infrared (ATR-FTIR) coupled with phenotypic microarrays to study the biospectral alterations of a fungal strain Simplicillium chinense QD10 and explore the mechanisms of Cd and Pb biosorption. Both Cd and Pb were efficiently adsorbed by S. chinense QD10 cultivated with 48 different carbon sources and the biosorption efficiency achieved >90%. As the first study using spectroscopic tools to analyse PTE-biosorption by fungal cells in a high-throughput manner, our results indicated that spectral biomarkers associated with phosphor-lipids and proteins (1745 cm^-1, 1456 cm^-1 and 1396 cm^-1) were significantly correlated with Cd biosorption, suggesting the cell wall components of S. chinense QD10 as the primary interactive targets. In contrast, there was no any spectral biomarker associated with Pb biosorption. Addtionally, adsorption isotherms evidenced a Langmuir model for Cd biosorption but a Freundlich model for Pb biosorption. Accordingly, Pb and Cd biosorption by S. chinense QD10 followed discriminating mechanisms, specific adsorption on cell membrane for Cd and unspecific extracellular precipitation for Pb. This work lends new insights into the mechanisms of PTE-biosorption via IR spectrochemical tools, which provide more comprehensive clues for biosorption behaviour with a nondestructive and high-throughput manner solving the traditional technical barrier regarding the real-world scenarios.

Interrogating the Transient Selectivity of Bacterial Chemotaxis-Driven Affinity and Accumulation of Carbonaceous Substances via Raman Microspectroscopy

Carbonaceous substances are fundamental organic nutrients for microbial metabolism and catabolism in natural habitats. Microbial abilities to sense, accumulate, and utilize organic carbonaceous substances in the complex nutrient environment are important for their growth and ecological functions. Bacterial chemotaxis is an effective mechanism for microbial utilization of carbonaceous substances under nutrient depletion conditions. Although bacterial accumulation and utilization to individual carbonaceous substance in long-term cultivation has been well studied, their selective affinity of mixed carbonaceous substances remains to be investigated, primarily because of technical limitations of conventional methods. Herein, we applied Raman microspectroscopy to identify chemotaxis-driven affinity and accumulation of four organic carbonaceous substances (glucose, succinate, acetate, and salicylate) by three bacterial strains (Acinetobacter baylyi, Pseudomonas fluorescence, and Escherichia coli). A. baylyi exhibited strong binding affinity toward glucose and succinate, whereas P. fluorescence and E. coli were preferentially responsive to glucose and acetate. For the first time, bacterial transient selectivity of carbonaceous substances was studied via interrogating Raman spectral alterations. Post-exposure to carbonaceous-substance mixtures, the three bacterial strains showed distinct selective behaviors. Stronger selective affinity enhanced the chemotaxis-related signal transduction in A. baylyi cells, whereas the carbonaceous substance signal transduction in E. coli was decreased by higher selective affinity. In P. fluorescence, there was no specific effect of selective affinity on signal transduction. Our study suggests that Raman microspectroscopy can successfully investigate and distinguish different scenarios of bacterial competitive and transient unitization of organic carbonaceous substances.

4-Nonylphenol effects on rat testis and sertoli cells determined by spectrochemical techniques coupled with chemometric analysis

Herein, vibrational spectroscopy has been applied for qualitative identification of biomolecular alterations that occur in cells and tissues following chemical treatment. Towards this end, we combined attenuated total reflection Fourier-transform infrared (ATR-FTIR) and Raman spectroscopy to assess testicular toxicology after 4-nonylphenol (NP) exposure, an estrogenic endocrine disruptor affecting testicular function in rats and other species. Rats aged 21, 35 or 50 days received NP at intra-peritoneal doses of 0, 25, 50 or 100 mg/kg for 20 consecutive days. Primary Sertoli cells (SCs) were treated with NP at various concentrations (0, 2.5, 5, 10 or 20 μM) for 12 h. Post-exposure, testicular cells, interstitial tissue and SCs were interrogated respectively using spectrochemical techniques coupled with multivariate analysis. Distinct biomolecular segregation between the NP-exposed samples vs. control were observed based on infrared (IR) spectral regions of 3200-2800 cm^-1 and 1800-900 cm^-1, and the Raman spectral region of 1800-900 cm^-1. For in vivo experiments, the main wavenumbers responsible for segregation varied significantly among the three age classes. The main IR and Raman band differences between NP-exposed and control groups were observed for Amide (proteins), lipids and DNA/RNA. An interesting finding was that the peptide aggregation level, Amide Ӏ-to-Amide II ratio, and phosphate-to-carbohydrate ratio were considerably reduced in ex vivo NP-exposed testicular cells or SCs in vitro. This study demonstrates that ATR-FTIR and Raman spectroscopy techniques can be applied towards analysing NP-induced testicular biomolecular alterations.

Differential Protein Expression During Growth on Medium Versus Long-Chain Alkanes in the Obligate Marine Hydrocarbon-Degrading Bacterium Thalassolituus oleivorans MIL-1

The marine obligate hydrocarbonoclastic bacterium Thalassolituus oleivorans MIL-1 metabolizes a broad range of aliphatic hydrocarbons almost exclusively as carbon and energy sources. We used LC-MS/MS shotgun proteomics to identify proteins involved in aerobic alkane degradation during growth on medium- (n-C₁₄) or long-chain (n-C₂₈) alkanes. During growth on n-C₁₄, T. oleivorans expresses an alkane monooxygenase system involved in terminal oxidation including two alkane 1-monooxygenases, a ferredoxin, a ferredoxin reductase and an aldehyde dehydrogenase. In contrast, during growth on long-chain alkanes (n-C₂₈), T. oleivorans may switch to a subterminal alkane oxidation pathway evidenced by significant upregulation of Baeyer-Villiger monooxygenase and an esterase, proteins catalyzing ketone and ester metabolism, respectively. The metabolite (primary alcohol) generated from terminal oxidation of an alkane was detected during growth on n-C₁₄ but not on n-C₂₈ also suggesting alternative metabolic pathways. Expression of both active and passive transport systems involved in uptake of long-chain alkanes was higher when compared to the non-hydrocarbon control, including a TonB-dependent receptor, a FadL homolog and a specialized porin. Also, an inner membrane transport protein involved in the export of an outer membrane protein was expressed. This study has demonstrated the substrate range of T. oleivorans is larger than previously reported with growth from n-C₁₀ up to n-C₃₂. It has also greatly enhanced our understanding of the fundamental physiology of T. oleivorans, a key bacterium that plays a significant role in natural attenuation of marine oil pollution, by identifying key enzymes expressed during the catabolism of n-alkanes.

Advances of magnetic nanoparticles in environmental application: environmental remediation and (bio)sensors as case studies

Nanotechnology is an emerging technique drawing increasing attentions in biomedical, electronic, environmental, and industrial application. Nanoparticles (NPs) possess unique optical, electrical, catalytic, and thermal properties, among which magnetic NPs (MNPs) are one of the most important groups with excellent superparamagnetism property, large surface area, and biocompatibility. In this review, methods for synthesizing and functionalizing MNPs are summarized and linked to their applications in environmental science as either adsorbents or catalysts for removing contaminants from environmental matrices, illustrating stronger reactivity, higher removal capacity, and fast kinetics. Additionally, we also comprehensively discuss the application of MNPs as (bio)sensors to selectively and sensitively detect the presence of environmental contaminants or pathogenic bacteria. This work summarizes the recent progresses of using MNPs as powerful tools in environmental science and engineering, raising their state-of-art application from environmental perspectives and benefiting researchers interested in NPs and environmental studies.