What is the source of excessive noise in images from my D7000?

Question

I'm a beginning photographer who recently invested in the following setup:

Nikon D7000 camera body, 15-105mm Nikor kit lens, 150-500mm Sigma lens.

We recently made a trip to the Pantanal, Brazil where we made heavy use of the Sigma lens. Upon returning home, we noticed that those photos contain an excessive amount of noise. Below is an example of an unprocessed photo:

As you can see, even without zooming in particularly the unsharp areas have serious noise. And as I usually up the contrast of such an image, the noise gets even worse. I shoot mostly in aperture mode, and in this case the ISO was at 640, in order to be able to have a shutter speed that allows me to shoot without a tripod (other meta: F6.3, focal 500mm, 1/320s). Still, the D7000 is known to be able to handle high ISOs quite well, so I'm surprised to see this kind of noise at this ISO already.

I know how to get rid of noise, using both Lightroom and Noise Ninja, but the amount is so excessive that via luminance I'm losing too much detail. So my question is what the source of this noise is. Is it a natural limitation of my lens? Too little light available? Is it due to the 640 ISO? Is it due to me or some setting I'm overlooking?

Answer

I think that image is somewhat underexposed and that's half the problem. You might do better to use a higher ISO, and move the histogram to the right. Most of that image is in the lower half of the histogram.

I've read assertions that multiples of the base ISO, so 200, 400, 800 and so on are less noisy than intermediate values like 320 or 640. I don't know if that's true or not, perhaps a myth.

Even with a a camera like the D7000, dark areas are going to contain some noise, even between 400 and 800, especially if you try to lighten them in post processing.

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