Photodegradable Hydrogels for Rapid Screening, Isolation, and Genetic Characterization of Bacteria with Rare Phenotypes

Polyethylene glycol hydrogel coatings for protection of electroactive bacteria against chemical shocks

Loss of bioelectrochemical activity in low resource environments or from chemical toxin exposure is a significant limitation in microbial electrochemical cells (MxCs), necessitating the development of materials that can stabilize and protect electroactive biofilms. Here, polyethylene glycol (PEG) hydrogels were designed as protective coatings over anodic biofilms, and the effect of the hydrogel coatings on biofilm viability under oligotrophic conditions and ammonia-N (NH4+-N) shocks was investigated. Hydrogel deposition occurred through polymerization of PEG divinyl sulfone and PEG tetrathiol precursor molecules, generating crosslinked PEG coatings with long-term hydrolytic stability between pH values of 3 and 10. Simultaneous monitoring of coated and uncoated electrodes co-located within the same MxC anode chamber confirmed that the hydrogel did not compromise biofilm viability, while the coated anode sustained nearly a 4 × higher current density (0.44 A/m2) compared to the uncoated anode (0.12 A/m2) under oligotrophic conditions. Chemical interactions between NH4+-N and PEG hydrogels revealed that the hydrogels provided a diffusive barrier to NH4+-N transport. This enabled PEG-coated biofilms to generate higher current densities during NH4+-N shocks and faster recovery afterwards. These results indicate that PEG-based coatings can expand the non-ideal chemical environments that electroactive biofilms can reliably operate in.

Photo-addressable microwell devices for rapid functional screening and isolation of pathogen inhibitors from bacterial strain libraries

Discovery of new strains of bacteria that inhibit pathogen growth can facilitate improvements in biocontrol and probiotic strategies. Traditional, plate-based co-culture approaches that probe microbial interactions can impede this discovery as these methods are inherently low-throughput, labor-intensive, and qualitative. We report a second-generation, photo-addressable microwell device, developed to iteratively screen interactions between candidate biocontrol agents existing in bacterial strain libraries and pathogens under increasing pathogen pressure. Microwells (0.6 pl volume) provide unique co-culture sites between library strains and pathogens at controlled cellular ratios. During sequential screening iterations, library strains are challenged against increasing numbers of pathogens to quantitatively identify microwells containing strains inhibiting the highest numbers of pathogens. Ring-patterned 365 nm light is then used to ablate a photodegradable hydrogel membrane and sequentially release inhibitory strains from the device for recovery. Pathogen inhibition with each recovered strain is validated, followed by whole genome sequencing. To demonstrate the rapid nature of this approach, the device was used to screen a 293-membered biovar 1 agrobacterial strain library for strains inhibitory to the plant pathogen Agrobacterium tumefaciens sp. 15955. One iterative screen revealed nine new inhibitory strains. For comparison, plate-based methods did not uncover any inhibitory strains from the library (n = 30 plates). The novel pathogen-challenge screening mode developed here enables rapid selection and recovery of strains that effectively suppress pathogen growth from bacterial strain libraries, expanding this microwell technology platform toward rapid, cost-effective, and scalable screening for probiotics, biocontrol agents, and inhibitory molecules that can protect against known or emerging pathogens.

An integrated microfluidic chip for alginate microsphere generation and 3D cell culture

Three-dimensional (3D) hydrogel microspheres have attracted increasing attention as cell culture carriers. The system of hydrogel microspheres provides great advantages for cell growth owing to its high surface-to-volume ratio and biocompatible environment. However, an integrated system that includes microsphere generation, microsphere capture and in situ culture together has not been realized yet. Here we present a multifunctional microfluidic device to accomplish the overall process including cell-laden microsphere generation, online demulsification and dynamic-culture. The microfluidic device can produce massive monodispersed alginate microspheres and allows us to immobilize the alginate microspheres and record bacterial growth. Moreover, the microspheres provide a suitable environment through the mechanical properties of soft tissues, leading to high cell viability, proliferation, activity and biocompatibility. We believe that this versatile and biocompatible platform will provide a more reliable analysis tool for tissue engineering and cell therapy.

Polymer Surface Dissection for Correlated Microscopic and Compositional Analysis of Bacterial Aggregates during Membrane Biofouling

Multispecies biofilms are a common limitation in membrane bioreactors, causing membrane clogging, degradation, and failure. There is a poor understanding of biological fouling mechanisms in these systems due to the limited number of experimental techniques useful for probing microbial interactions at the membrane interface. Here, we develop a new experimental method, termed polymer surface dissection (PSD), to investigate multispecies assembly processes over membrane surfaces. The PSD method uses photodegradable polyethylene glycol hydrogels functionalized with bioaffinity ligands to bind and detach microscale, microbial aggregates from the membrane for microscopic observation. Subsequent exposure of the hydrogel to high resolution, patterned UV light allows for controlled release of any selected aggregate of desired size at high purity for DNA extraction. Follow-up 16S community analysis reveals aggregate composition, correlating microscopic images with the bacterial community structure. The optimized approach can isolate aggregates with microscale spatial precision and yields genomic DNA at sufficient quantity and quality for sequencing from aggregates with areas as low as 2000 μm², without the need of culturing for sample enrichment. To demonstrate the value of the approach, PSD was used to reveal the composition of microscale aggregates of different sizes during early-stage biofouling of aerobic wastewater communities over PVDF membranes. Larger aggregates exhibited lower diversity of bacterial communities, and a shift in the community structure was found as aggregate size increased to areas between 25,000 and 45,000 μm², below which aggregates were more enriched in Bacteroidetes and above which aggregates were more enriched with Proteobacteria. The findings demonstrate that community succession can be observed within microscale aggregates and that the PSD method is useful for identification and characterization of early colonizing bacteria that drive biofouling on membrane surfaces.

Stimuli-responsive destructible polymeric hydrogels based on irreversible covalent bond dissociation

Covalently crosslinked stimuli-destructible hydrogels with the ability of irreversible bond dissociation have attracted great attentions due to their biodegradability, stability against hydrolysis, and controlled solubility upon insertion of desired triggers.