Assembly and Tracking of Microbial Community Development within a Microwell Array Platform

Andrea C. Timm; Michelle C. Halsted; Jared L. Wilmoth; Scott T. Retterer

doi:10.3791/55701

Assembly and Tracking of Microbial Community Development within a Microwell Array Platform

JoVE Journal
Bioengineering

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JoVE Journal Bioengineering

Assembly and Tracking of Microbial Community Development within a Microwell Array Platform

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09:24 min

June 6, 2017

DOI: 10.3791/55701-v

Andrea C. Timm¹, Michelle C. Halsted², Jared L. Wilmoth¹, Scott T. Retterer^1,3

¹Biosciences Division,Oak Ridge National Laboratory, ²Bredesen Center for Interdisciplinary Research and Graduate Education,University of Tennessee, ³Center for Nanophase Materials Sciences,Oak Ridge National Laboratory

Overview

This protocol outlines a method for high throughput analysis of microbial communities in confined environments using silicon micro well arrays. It enables the tracking of microbial interactions significant to various fields, including industry and medicine.

Key Study Components

Area of Science

Microbial Ecology
Biomedical Research
Environmental Science

Background

Microbial communities are influenced by environmental architecture and member interactions.
Understanding these communities can provide insights into ecological and biomedical questions.
High throughput methods are essential for analyzing complex interactions.
This study utilizes microfabricated environments for precise tracking.

Purpose of Study

To analyze multi-member microbial communities in confined spaces.
To investigate how spatial constraints affect community development.
To explore the effects on microbial member abundance and organization.

Methods Used

Preparation of micro well arrays from silicon wafers.
Utilization of arrays with wells ranging from five to 100 microns.
Screening of microbial interactions in a high throughput manner.
Parallel analysis of community dynamics in confined environments.

Main Results

Demonstrated the ability to track thousands of microbial communities simultaneously.
Identified key interactions influenced by niche size and confinement.
Provided insights into deterministic and stochastic parameters of community development.
Highlighted the significance of this method for industry and environmental applications.

Conclusions

This method offers a novel approach to studying microbial interactions.
It enhances understanding of community dynamics in confined environments.
Future research can build on these findings to address ecological and biomedical challenges.

Frequently Asked Questions

What are micro well arrays?

Micro well arrays are small, confined spaces used to culture and analyze microbial communities.

How does spatial confinement affect microbial communities?

Spatial confinement can influence interactions, abundance, and organization of microbial members.

What is the significance of high throughput analysis?

High throughput analysis allows for the simultaneous study of multiple communities, providing comprehensive insights.

What applications does this method have?

This method can be applied in industry, medicine, and environmental science to understand microbial interactions.

How are the micro well arrays prepared?

They are prepared by cutting chips from silicon wafers printed with multiple arrays.

What is the diameter range of the wells in the arrays?

The wells range from five to 100 microns in diameter.

The development of microbial communities depends on a combination of factors, including environmental architecture, member abundance, traits, and interactions. This protocol describes a synthetic, microfabricated environment for the simultaneous tracking of thousands of communities contained in femtoliter wells, where key factors such as niche size and confinement can be approximated.

The overall goal of this method is high throughput parallel analysis of multi-member microbial communities in confined environments using silicon micro well arrays. The main advantage of this technique is that it allows for a high throughput highly parallel screening of finely localized microbial interactions that are significant to industry, medicine, and the environment. This method can help answer key questions in the biomedical and microbial ecology fields such as how do spacial constraints inherent at fine scales drive deterministic and stochastic parameters of community development and what are they key effects on microbial member abundance and organization?

Begin with preparing the micro well arrays. First, cut individual micro well array chips from silicon wafers printed with multiple arrays using a diamond scribe. Each individual chip contains sub-arrays of wells with diameters ranging from five to 100 microns at three different spacing densities.

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