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Engineering an incubation environment that mimics in situ conditions for in vitro coastal microbiome studies.

ABSTRACT: Coastal environments are dynamic and can vary widely on short- or long-term scales depending on location and weather. Incubation equipment that reflects these changes through programmable gradient light and temperature cycles would permit more precise in vitro coastal microbiome studies. Here we present an open-source incubation environment that mimics in situ conditions for in vitro coastal microbiome studies using a modified shaking water bath that has fully customizable temperature and light gradients that can also mimic real-time field conditions. We compared coastal microbial community profiles incubated in situ and in our build mimicking field conditions over 48 h. Analyses of congruence indicated significant overlap (p > 0.2) between microbial communities incubated in situ and in vitro at each time point.

SUBMITTER: Hunter BT

PROVIDER: S-EPMC9623733 | biostudies-literature | 2022 Oct

REPOSITORIES: biostudies-literature

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Engineering an incubation environment that mimics in situ conditions for in vitro coastal microbiome studies.

Hunter Brad T BT Flury Jaeden D JD Cocioba Sebastian S SS Cope-Arguello Matthew L ML Helms Jared M JM García Kevin H KH Dominguez Gerardo G Taniguchi Darcy Aa DA Becket Elinne E

BioTechniques 20221003 4

Coastal environments are dynamic and can vary widely on short- or long-term scales depending on location and weather. Incubation equipment that reflects these changes through programmable gradient light and temperature cycles would permit more precise in vitro coastal microbiome studies. Here we present an open-source incubation environment that mimics in situ conditions for in vitro coastal microbiome studies using a modified shaking water bath that has fully customizable t ...[more]

PMID: 36189957

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Project description:The agricultural sector and environmental safety both work hand in hand to promote sustainability in important issues like soil health, plant nutrition, food safety, and security. The conventional methods have greatly harmed the environment and people's health and caused soil fertility and quality to decline as well as deteriorate. Keeping in view the excessive exploitation and cascade of degradation events due to unsustainable farming practices, the need of the hour demands choosing an appropriate, eco-friendly strategy to restore soil health, plant nutrition, and environmental aspects. The priority highlights a need for a sustainable and environment-friendly upgradation of the present agricultural systems to utilize the beneficial aspects related to harnessing the gene-microbiome strategies which would help in the restoration and replenishment of the microbial pool. Thus, exploring the microbiome is the utmost priority which gives a deep insight into the different aspects related to soil and plant and stands out as an important contributor to plant health and productivity. "Microbes" are important drivers for the biogeochemical cycles and targets like sustainability and safety. This essential microbial bulk (soil microbiome) is greatly influenced by agricultural/farming practices. Therefore, with the help of microbiome engineering technologies like meta-transcriptomics, meta-proteomics, metabolomics, and novel gene-altering techniques, we can easily screen out the highly diverse and balanced microbial population in the bulk of soil, enhancing the soil's health and productivity. Importantly, we need to change our cultivation strategies to attain such sustainability. There is an urgent need to revert to natural/organic systems of cultivation patterns where the microbiome hub can be properly utilized to strengthen soil health, decrease insect pest and disease incidence, reduce greenhouse gas emissions, and ultimately prevent environmental degradation. Through this article, we wish to propose a shift in the cultivation pattern from chemical to the novel, upgraded gene-assisted designed eco-friendly methodologies which can help in incorporating, exploring, and harnessing the right microbiome consortium and can further help in the progression of environmentally friendly microbiome technologies for agricultural safety and productivity.

Dataset Information

Engineering an incubation environment that mimics in situ conditions for in vitro coastal microbiome studies.

Publications

Engineering an incubation environment that mimics <i>in situ</i> conditions for <i>in vitro</i> coastal microbiome studies.

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