Low-cost gel-filled microwell array device for screening marine microbial consortium

Abstract

In order to exploit the microbes present in the environment for their beneficial resources, effective selection and isolation of microbes from environmental samples is essential. In this study, we fabricated a gel-filled microwell array device using resin for microbial culture. The device has an integrated sealing mechanism that enables high-density isolation based on the culture of microorganisms; the device is easily manageable, facilitating observation using bright-field microscopy. This low-cost device made from polymethyl methacrylate (PMMA)/polyethylene terephthalate (PET) has 900 microwells (600 μm × 600 μm × 700 μm) filled with a microbial culture gel medium in glass slide-sized plates. It also has grooves for maintaining the moisture content in the micro-gel. The partition wall between the wells has a highly hydrophobic coating to inhibit microbial migration to neighboring wells and to prevent exchange of liquid substances. After being hermetically sealed, the device can maintain moisture in the agarose gels for 7 days. In the bacterial culture experiment using this device, environmental bacteria were isolated and cultured in individual wells after 3 days. Moreover, the isolated bacteria were then picked up from wells and re-cultured. This device is effective for the first screening of microorganisms from marine environmental samples.

Roseiterribacter gracilis gen. nov., sp. nov., a novel filterable alphaproteobacterium isolated from soil using a gel-filled microwell array device

“…A microwell array device composed of 900 microwells (device body 76 × 26 mm; well pitch, 1.0 mm; well size, 600 μm by 600 μm; well depth, 800 μm) was used for the cultivation of microbial cells. This array device was designed in accordance with a previous study [ 17 ]. All subsequent procedures described below were performed under ultraclean conditions (ISO class I) generated by Table KOACH with a flying debris prevention plate (KOKEN, Tokyo).…”

“…This array further enabled us to inoculate one cell per chamber [ 16 ]. Recently, Sassa and colleagues developed a microwell array device that can separately culture microbial cells in multiple gel-filled microwells [ 17 ]. The surface of the microwells is covered with a water repellent, which prevents microbial cell migration in and out between the gel-filled wells.…”

The hydrocarbon pollution crisis: Harnessing the earth hydrocarbon‐degrading microbiome

“…Several strategies have been proposed to design synthetic microbial communities (SynComs) either by enrichment techniques resulting in simplified communities, defined as top‐down approaches, or reconstruction of microbial consortia by assembling bacterial strains, known as bottom‐up approaches (Bernstein, 2019 ; De Roy et al., 2014 ; Hu et al., 2022 ). Anent the top‐down approach, the current momentum for obtaining engineered microbiomes owning the desired functions can implement successive sub‐culturing under defined conditions (Li et al., 2023 ) applying as well high‐throughput techniques (Duran et al., 2022 ), or artificial selection applying sequential breeding (Swenson et al., 2000 ), or directed evolution subjecting community to perturbation cycles (Sánchez et al., 2021 ). The construction of SynComs, synthetic microbial assemblages, following a bottom‐up approach combines isolated microorganisms, genetically modified or not.…”