Chemotactic screening of imidazolinone-degrading bacteria by microfluidic SlipChip

Microbial chemotaxis in degradation of xenobiotics: Current trends and opportunities

Chemotaxis, the directed movement of microbes in response to chemical gradients, plays a crucial role in the biodegradation of xenobiotics, such as pesticides, industrial chemicals, and pharmaceuticals, which pose significant environmental and health risks. Emerging trends in genomics, proteomics, and synthetic biology have advanced our understanding and control of these processes, thereby enabling the development of engineered microorganisms with tailored chemotactic responses and degradation capabilities. This process plays an essential physiological role in processes, such as surface sensing, biofilm formation, quorum detection, pathogenicity, colonization, symbiotic interactions with the host system, and plant growth promotion. Field applications have demonstrated the potential of bioremediation for cleaning contaminated environments. Therefore, it helps to increase the bioavailability of pollutants and enables bacteria to access distantly located pollutants. Despite considerable breakthroughs in decoding the regulatory mechanisms of bacterial chemotaxis, there are still gaps in knowledge that need to be resolved to harness its potential for sensing and degrading pollutants in the environment. This review covers the role of bacterial chemotaxis in the degradation of xenobiotics present in the environment, focusing on chemotaxis-based bacterial and microfluidic biosensors for environmental monitoring. Finally, we highlight the current challenges and future perspectives for developing more effective and sustainable strategies to mitigate the environmental impact of xenobiotics.

Taxis-enhanced mineralization and co-metabolism of PAHs by bacteria in micrometer-scale environments

Polycyclic aromatic hydrocarbons (PAHs) are associated with micropores in sediments and soils. This limits the bioaccessibility of these compounds via existing bioremediation technologies, as biodegradation is strongly influenced by the ability of bacteria to access different sizes of pores. In this work, we employed naphthalene and pyrene as model contaminants to evaluate the transformation capacity of the soil bacterium Pseudomonas putida G7 (2 × 1 μm) via mineralization and co-metabolic activity, respectively. Under non-growing conditions and in the absence of hydraulic flow, we examined how the tactic behavior of this motile bacterium influenced biodegradation of these two PAHs when passing through membranes with micrometer-sized pores (3 and 5 μm). The bacteria were spontaneously retained by the membranes, which blocked the contaminants away from a passive dosing source. However, the cells were mobilized through 5 μm pores after the application plant root exudate components (γ-aminobutyric acid, citrate and fructose) as strong chemoeffectors, which enhanced the mineralization of naphthalene and co-metabolism of pyrene. The tactic-mediated biodegradation enhancement did not occur through 3 μm pores, possibly due a physical constrain to the gradient sensing mechanism. Our results suggest that bacterial transport by chemotaxis may enhance the biotransformation of poorly bioaccessible contaminants present in micro-meter scale environments.

Microfluidic programmable strategies for channels and flow

This review summarizes programmable microfluidics, an advanced method for precise fluid control in microfluidic technology through microchannel design or liquid properties, referring to microvalves, micropumps, digital microfluidics, multiplexers, micromixers, slip-, and block-based configurations. Different microvalve types, including electrokinetic, hydraulic/pneumatic, pinch, phase-change and check valves, cater to diverse experimental needs. Programmable micropumps, such as passive and active micropumps, play a crucial role in achieving precise fluid control and automation. Due to their small size and high integration, microvalves and micropumps are widely used in medical devices and biological analysis. In addition, this review provides an in-depth exploration of the applications of digital microfluidics, multiplexed microfluidics, and mixer-based microfluidics in the manipulation of liquid movement, mixing, and splitting. These methodologies leverage the physical properties of liquids, such as capillary forces and dielectric forces, to achieve precise control over fluid dynamics. SlipChip technology, which branches into rotational SlipChip and translational SlipChip, controls fluid through sliding motion of the microchannel. On the other hand, innovative designs in microfluidic systems pursue better modularity, reconfigurability and ease of assembly. Different assembly strategies, from one-dimensional assembly blocks and two-dimensional Lego®-style blocks to three-dimensional reconfigurable modules, aim to enhance flexibility and accessibility. These technologies enhance user-friendliness and accessibility by offering integrated control systems, making them potentially usable outside of specialized technical labs. Microfluidic programmable strategies for channels and flow hold promising applications in biomedical research, chemical analysis and drug screening, providing theoretical and practical guidance for broader utilization in scientific research and practical applications.

A Novel Device and Method for Assay of Bacterial Chemotaxis Towards Chemoattractants

Capillary assemblies and microfluidic devices used for bacterial chemotaxis assays have certain inherent limitations. This opens opportunities for innovation in the area. The present study describes an innovative economical device called chemotaxis plate and also a method to use this device for chemotaxis assay. Two type cultures, Pseudomonas putida MCC 2989 and Bacillus subtilis MCC 2049, chemotactic to L-aspartate, were used to validate the new device and establish the protocol for assay. 100 to 1000 fold higher number of cells were recovered in presence of chemoattractant as compared to control (p < 0.05). This novel assay technique showed 100% sensitivity and 99.21% specificity for chemotaxis assay of Pseudomonas putida MCC 2989 towards 3 mM L-aspartate over 50 min assay time. The device was also used to isolate bacteria chemotactic to caffeine directly from environmental samples. Very high chemotaxis response indices were reported for the first-time using chemotaxis plate.

Research progress in isolation and identification of rumen probiotics

With the increasing research on the exploitation of rumen microbial resources, rumen probiotics have attracted much attention for their positive contributions in promoting nutrient digestion, inhibiting pathogenic bacteria, and improving production performance. In the past two decades, macrogenomics has provided a rich source of new-generation probiotic candidates, but most of these "dark substances" have not been successfully cultured due to the restrictive growth conditions. However, fueled by high-throughput culture and sorting technologies, it is expected that the potential probiotics in the rumen can be exploited on a large scale, and their potential applications in medicine and agriculture can be explored. In this paper, we review and summarize the classical techniques for isolation and identification of rumen probiotics, introduce the development of droplet-based high-throughput cell culture and single-cell sequencing for microbial culture and identification, and finally introduce promising cultureomics techniques. The aim is to provide technical references for the development of related technologies and microbiological research to promote the further development of the field of rumen microbiology research.

Biodegradation of Imazethapyr by Bacterial Strain IM9601 Isolated from Agricultural Soil

The widespread utilization of the herbicide imazethapyr presents significant challenges to crop rotation and results in detrimental soil degradation issues. Bacterial biodegradation has emerged as a promising and eco-friendly approach for mitigating pesticide residues contamination in the environment. In this study, a novel bacterium, identified as Brevibacterium sp. IM9601, was isolated and characterized based on morphological, physiological, and biochemical characteristics, as well as 16S rRNA gene sequence. This strain exhibited the ability to utilize imazethapyr as its sole carbon source for growth. Response surface methodology (RSM) was applied to optimize the degradation conditions. The most favorable conditions were determined to be a temperature of 27 °C, pH of 6.0, and an initial inoculum with a final OD600 of 0.15. Under these optimized condition, bacterial strain IM9601 exhibited substantial imazethapyr degradation, with removal rates of 90.08 and 87.05% for initial imazethapyr concentrations of 50 and 100 mg L-1, respectively, achieved within a 5-day incubation period. This investigation highlights imazethapyr-degrading capabilities of the Brevibacterium genus bacterial strain IM9601, marking it as a potentially novel and effective solution for addressing the environmental pollution resulting from the usage of imazethapyr. The study contributes to the growing body of research on bioremediation approaches, offering a sustainable and environmentally friendly method for mitigating the adverse impacts of herbicide contamination in agricultural settings.

Whole lifecycle observation of single-spore germinated Streptomyces using a nanogap-stabilized microfluidic chip

Streptomyces is a model bacterium to study multicellular differentiation and the major reservoir for antibiotics discovery. However, the cellular-level lifecycle of Streptomyces has not been well studied due to its complexity and lack of research tools that can mimic their natural conditions. In this study, we developed a simple microfluidic chip for the cultivation and observation of the entire lifecycle of Streptomyces development from the single-cell perspective. The chip consists of channels for loading samples and supplying nutrients, microwell arrays for the seeding and growth of single spores, and air chambers beside the microwells that facilitate the development of aerial hyphae and spores. A unique feature of this chip is that each microwell is surrounded by a 1.5 µm nanogap connected to an air chamber, which provides a stabilized water-air interface. We used this chip to observe the lifecycle development of Streptomyces coelicolor and Streptomyces griseus germinated from single spores, which revealed differentiation of aerial hyphae with progeny spores at micron-scale water-air interfaces and air chambers. Finally, we demonstrated the applicability of this chip in phenotypic assays by showing that the microbial hormone A-Factor is involved in the regulatory pathways of aerial hyphae and spore formation. The microfluidic chip could become a robust tool for studying multicellular differentiation, single-spore heterogeneity, and secondary metabolism of single-spore germinated Streptomyces.

Bioremediation on a chip: A portable microfluidic device for efficient screening of bacterial biofilm with polycyclic aromatic hydrocarbon removal capacity

Polycyclic aromatic hydrocarbons (PAHs) are pollutants of critical environmental and public health concern and their elimination from contaminated sites is significant for the environment. Biodegradation studies have demonstrated the ability of bacteria in biofilm conformation to enhance the biodegradation of pollutants. In this study, we used our newly developed microfluidic platform to explore biofilm development, properties, and applications of fluid flow, as a new technique for screening PAHs-degrading biofilms. The optimization and evaluation of the flow condition in the microchannels were performed through computational fluid dynamics (CFD). The formation of biofilms by PAHs-degrading bacteria Pseudomonas sp. P26 and Gordonia sp. H19, as pure cultures and co-culture, was obtained in the developed microchips. The removal efficiencies of acenaphthene, fluoranthene and pyrene were determined by HPLC. All the biofilms formed in the microchips removed all tested PAHs, with the higher removal percentages observed with the Pseudomonas sp. P26 biofilm (57.4% of acenaphthene, 40.9% of fluoranthene, and 28.9% of pyrene). Pseudomonas sp. P26 biofilm removed these compounds more efficiently than planktonic cultures. This work proved that the conformation of biofilms enhances the removal rate. It also provided a new tool to rapid and low-cost screen for effective pollutant-degrading biofilms.

Emerging microfluidic technologies for microbiome research

The importance of the microbiome is increasingly prominent. For example, the human microbiome has been proven to be strongly associated with health conditions, while the environmental microbiome is recognized to have a profound influence on agriculture and even the global climate. Furthermore, the microbiome can serve as a fascinating reservoir of genes that encode tremendously valuable compounds for industrial and medical applications. In the past decades, various technologies have been developed to better understand and exploit the microbiome. In particular, microfluidics has demonstrated its strength and prominence in the microbiome research. By taking advantage of microfluidic technologies, inherited shortcomings of traditional methods such as low throughput, labor-consuming, and high-cost are being compensated or bypassed. In this review, we will summarize a broad spectrum of microfluidic technologies that have addressed various needs in the field of microbiome research, as well as the achievements that were enabled by the microfluidics (or technological advances). Finally, how microfluidics overcomes the limitations of conventional methods by technology integration will also be discussed.

Unveiling the chemotactic response and mechanism of Shewanella oneidensis MR-1 to nitrobenzene

Bioreduction by electroactive bacteria (EAB) is considered as a potential and cost-effective approach for the removal of nitroaromatic compounds (NACs). However, little is known about how the widespread EAB sense and respond to slightly soluble NACs in aquatic environments. Here, the chemotactic behaviors of Shewanella oneidensis MR-1, a model EAB, toward several NACs were examined and their underlying molecular mechanism was elucidated. S. oneidensis MR-1 was found to exhibit a strong chemotactic response to nitrobenzene (NB), but not to other selected NACs under aerobic conditions. To sense NB, this bacterium requires both the histidine kinase (CheA-3)-involved chemotactic signal transduction pathway and an inner-membrane c-type cytochrome CymA. Such a chemotactic response is mediated by an energy taxis mechanism. Additionally, external riboflavin was shown to greatly enhance the Shewanella taxis toward NB, implying a feasible way to increase the bioavailability of NACs. The present study deepens our understanding of the role of microbial chemotaxis in the removal of NACs and provides more options for the bioremediation of NAC-contaminated sites.

Sphingomonas Relies on Chemotaxis to Degrade Polycyclic Aromatic Hydrocarbons and Maintain Dominance in Coking Sites

Polycyclic aromatic hydrocarbons (PAHs) are organic pollutants widely present in industrial sites. Microbial degradation is an effective method of removing PAHs. The identification of microorganisms that have important ecological functions at the site is of great significance for PAH removal. We collected soil samples at three depths in the range of 0-100 cm at 70-day intervals at the coking site and explored the degradation of PAHs. We combined molecular ecology networking, metagenomics, and genome assembly to search for microorganisms that persist, dominate, and affect the microbial community construction in the degradation process and analyzed their adaptation strategies. The results showed that 15.78 mg/kg of PAHs naturally decayed, and 13.33 mg/kg of PAHs migrated from 30-100 cm to 0-30 cm in the soil. Sphingomonas, which occupied a niche advantage, was both the core and keystone microorganism, and its spatial distribution pattern and temporal change dynamics were consistent with those of PAHs. We assembled the genome of Sphingomonas sp., revealing its multiple potential for degrading PAHs and other pollutants. Additionally, flagellar assembly and bacterial chemotaxis genes ranked high in the assembled genome of Sphingomonas sp., which might help it obtain a competitive advantage in the soil. The findings underscored the strategy of Sphingomonas to maintain dominance, enriched the understanding of PAH-degrading microorganisms in site soil, and provided references for the remediation of PAHs.

Microfluidics as an Emerging Platform for Exploring Soil Environmental Processes: A Critical Review

Investigating environmental processes, especially those occurring in soils, calls for innovative and multidisciplinary technologies that can provide insights at the microscale. The heterogeneity, opacity, and dynamics make the soil a "black box" where interactions and processes are elusive. Recently, microfluidics has emerged as a powerful research platform and experimental tool which can create artificial soil micromodels, enabling exploring soil processes on a chip. Micro/nanofabricated microfluidic devices can mimic some of the key features of soil with highly controlled physical and chemical microenvironments at the scale of pores, aggregates, and microbes. The combination of various techniques makes microfluidics an integrated approach for observation, reaction, analysis, and characterization. In this review, we systematically summarize the emerging applications of microfluidic soil platforms, from investigating soil interfacial processes and soil microbial processes to soil analysis and high-throughput screening. We highlight how innovative microfluidic devices are used to provide new insights into soil processes, mechanisms, and effects at the microscale, which contribute to an integrated interrogation of the soil systems across different scales. Critical discussions of the practical limitations of microfluidic soil platforms and perspectives of future research directions are summarized. We envisage that microfluidics will represent the technological advances toward microscopic, controllable, and in situ soil research.

One cell at a time: droplet-based microbial cultivation, screening and sequencing

Microbes thrive and, in turn, influence the earth's environment, but most are poorly understood because of our limited capacity to reveal their natural diversity and function. Developing novel tools and effective strategies are critical to ease this dilemma and will help to understand their roles in ecology and human health. Recently, droplet microfluidics is emerging as a promising technology for microbial studies with value in microbial cultivating, screening, and sequencing. This review aims to provide an overview of droplet microfluidics techniques for microbial research. First, some critical points or steps in the microfluidic system are introduced, such as droplet stabilization, manipulation, and detection. We then highlight the recent progress of droplet-based methods for microbiological applications, from high-throughput single-cell cultivation, screening to the targeted or whole-genome sequencing of single cells.

Recent Developments in Bacterial Chemotaxis Analysis Based on the Microfluidic System

Bacterial motility in response to chemicals, also called bacterial chemotaxis, is a critical ability to search for the optimal environment to ensure the survival of bacterial species. Recent advances in microbiology have allowed the engineering of bacterial chemotactic properties. Conventional methods for characterizing bacterial motility are not able to fully monitor chemotactic behavior. Developments in microfluidic technology have enabled the designing of new experimental protocols in which spatiotemporal control of the cellular microenvironment can be achieved, and in which bacterial motility can be precisely and quantitatively measured and compared. This review provides an overview of recent developments of and new insights into microfluidic systems for chemotaxis assay.

Characterization of Acetamiprid Biodegradation by the Microbial Consortium ACE-3 Enriched From Contaminated Soil

Microbial consortia are ubiquitous in nature and exhibit several attractive features such as sophisticated metabolic capabilities and strong environmental robustness. This study aimed to decipher the metabolic and ecological characteristics of synergistic interactions in acetamiprid-degrading consortia, suggesting an optimal scheme for bioremediation of organic pollutants. The microbial consortium ACE-3 with excellent acetamiprid-degrading ability was enriched from the soil of an acetamiprid-contaminated site and characterized using high-throughput sequencing (HTS). Consortium ACE-3 was able to completely degrade 50 mg⋅L^–1 acetamiprid in 144 h, and was metabolically active at a wide range of pH values (6.0–8.0) and temperatures (20–42°C). Furthermore, plausible metabolic routes of acetamiprid biodegradation by the consortium were proposed based on the identification of intermediate metabolites (Compounds I, II, III and IV). The findings indicated that the consortium ACE-3 has promising potential for the removal and detoxification of pesticides because it produces downstream metabolites (Compounds I and II) that are less toxic to mammals and insects than acetamiprid. Finally, Illumina HTS revealed that β Proteobacteria were the dominant group, accounting for 85.61% of all sequences at the class level. Among the more than 50 genera identified in consortium ACE-3, Sphingobium, Acinetobacter, Afipia, Stenotrophomonas, and Microbacterium were dominant, respectively accounting for 3.07, 10.01, 24.45, and 49.12% of the total population.

Identification and Characterization of the First Virulent Phages, Including a Novel Jumbo Virus, Infecting Ochrobactrum spp

The Ochrobactrum genus consists of an extensive repertoire of biotechnologically valuable bacterial strains but also opportunistic pathogens. In our previous study, a novel strain, Ochrobactrum sp. POC9, which enhances biogas production in wastewater treatment plants (WWTPs) was identified and thoroughly characterized. Despite an insightful analysis of that bacterium, its susceptibility to bacteriophages present in WWTPs has not been evaluated. Using raw sewage sample from WWTP and applying the enrichment method, two virulent phages, vB_OspM_OC and vB_OspP_OH, which infect the POC9 strain, were isolated. These are the first virulent phages infecting Ochrobactrum spp. identified so far. Both phages were subjected to thorough functional and genomic analyses, which allowed classification of the vB_OspM_OC virus as a novel jumbo phage, with a genome size of over 227 kb. This phage encodes DNA methyltransferase, which mimics the specificity of cell cycle regulated CcrM methylase, a component of the epigenetic regulatory circuits in Alphaproteobacteria. In this study, an analysis of the overall diversity of Ochrobactrum-specific (pro)phages retrieved from databases and extracted in silico from bacterial genomes was also performed. Complex genome mining allowed us to build similarity networks to compare 281 Ochrobactrum-specific viruses. Analyses of the obtained networks revealed a high diversity of Ochrobactrum phages and their dissimilarity to the viruses infecting other bacteria.

High-throughput single-cell cultivation reveals the underexplored rare biosphere in deep-sea sediments along the Southwest Indian Ridge

Microorganisms in the deep sea play vital roles in marine ecosystems. However, despite great advances brought by high throughput sequencing and metagenomics, only a small portion of microorganisms living in the environment can be cultivated in the laboratory and systematically studied. In this study, an improved high-throughput microfluidic streak plate (MSP) platform was developed to speed up the isolation of microorganisms from deep-sea sediments and evaluated with deep-sea sediments collected from the Southwest Indian Ridge (SWIR). Based on our previously reported MSP method, we improved its isolation efficiency with a semi-automated droplet picker and improved humidity control to enable long-term cultivation with a low-nutrient medium for up to five months according to the slow-growing nature of most deep-sea species. The improved MSP method allows the isolation of microbes by selection and investigation of microbial diversity by high throughput sequencing of the pooled sample cultures. By picking individual droplets and scale-up cultivation, a total of 772 strains that were taxonomically assigned to 70 species were isolated from the deep-sea sediments in the SWIR, including 15 potential novel species. On the other hand, based on 16S rRNA gene amplicon sequencing analysis, the microbial diversity of the SWIR was studied and documented with culture-dependent and independent methods in this study. The superiority of the MSP platform in revealing the rare biosphere was also evaluated based on amplicon sequencing. The results show that droplet-based single-cell cultivation of the MSP has a much higher ability than traditional agar plate cultivation in obtaining microbial species and more than 90% of operational taxonomic units (OTUs) detected in the MSP pool belong to the rare biosphere. Our results indicate the high robustness and efficiency of the improved MSP platform in revealing the environmentally rare biosphere, especially for slow-growing species. Overall, the MSP platform has a superior ability to recover microbial diversity than conventional agar plates and it was found to hold great potential for recovering rare microbial resources from various environments.