In general, information is free, but its creative expression is not. Therefore, you can build on other people ideas from copyrighted works but you can't copy text or images from such works.
Therefore, you can freely summarize other people's methods, provided that you cite your source - and that's an issue of intellectual honesty rather than a copyright issue.
However, you copied verbatim the whole paragraph in your "Sample preparation" section instead of explaining the method with your own words. This can only be done if it qualifies as fair use (or equivalent rules outside the USA) or you get permission from copyright owners - be it specifically to you or with a free license.
Since the original article states that "This is an open-access article distributed under the terms of the Creative Commons CC-BY-NC 3.0 License" (link mine) you can copy it while abiding to the license. You are obliged to:
- Acknowledge authorship of the copied fragment. It's debatable if just citing the original work without stating that you copied text from it is enough.
- Not to make any commercial use of your paper. For example, you can't publish it in a commercial journal. I would say that publishing it in ResearchGate doesn't qualify as commercial use, but the limits of commercial use are tricky.
If these conditions pose a problem to you, or even a slight nuisance, you can try to remove the copied content and explain the same ideas with you own words. This way you can get rid of copyright and license issues and you will just need to keep citing the original paper.
The original article is also published here under the same license. This publication is more specific about obligations of reusers of content, with a dedicated page.