What I’m going to suggest is obviously general since the exact circumstances and qualities you want in your images isn’t stated in the question. The level of experience with photography also isn’t mentioned, so I’lll assume you just know the basics.
Three things will control the image; aperture, exposure time and ISO setting.
The higher the aperture number the sharper the images will be, but the longer they will need to expose. F1.2 can be fast but ficus is shallow, whereas f22 is sharper focus but takes longer to expose. Since you are photographing things that don’t move too much, longer exposure times will allow more light into the camera and so would suggest higher aperture settings, but make sure your camera doesn’t shake.
Higher ISO will allow a lower level of light to be used, but it will make noise in the image; random speckles of colour. I’d suggest an ISO of about 400 as maximum.
Suggestions:
My first suggestion is that you get access to a good digital SLR and a reliable, solid tripod. Handheld use always has shakes. Use the tripod to extend your exposure times without camera shake. If the camera shakes due to you hand on the release, I’d offer that using the delayed release setting avoid this.
Check the minimum focus distance of your lens. A minimum focus distance of 45cm is fine for photographing places and people but useless for this kind of work. What distance will allow the camera to convey the qualities in your images that you want the audience to understand? Make sure you have a lens which allows you to get images which are useful, a good size in the frame and in sharp focus. If you want real detail, you may want a lens with a close-up macro option.
For a dark background, black paper or even black velvet can be used to cover a base. Whatever you use as a base, below the fabric or paper, for the culture plates and flasks must be parallel to the focal plane of the camera, so if you are looking down make sure you are perpendicular to the object being photographed. If the object is vertical on a shelf, make sure you are level and parallel.
For lighting you can simply use two angle poise lamps one to either side. The brighter the bulb the better, but bright household bulbs should do. One left and one right, or above and below. When you meter for the exposure, the brighter the bulb, the faster the exposure time.
Remember that most DSLR’s trim off an area around the edge of the viewfinder, so compose your images with the object at a good size in the centre, but not touching the edges of the frame.