Rubisco enzyme and photosynthesis and photorespireation

In studying climate and how it is intertwined with biology, plant photosynthesis, and the carbon cycle, I've read that plants, most commonly known for their photosythesis, also respire carbon dioxide. They can emit CO2 to the air and to the soil. A recent article in Nature helped me answer a few lingering questions I've had. I'm citing from Nature 14 January 2010 (News and Views by R. John Ellis and article by Liu et al).

Lingering question 1: Do plants get all their carbon from the atmosphere? If not, then the use of plants in biofuels would fail to be carbon neutral. (Note: many other factors can undermine the carbon neutrality of biofuels).
The news and views article credits "virtually all organic carbon in the biosphere" to the rubisco enzyme used in photosynthesis to capture CO2 from the atmosphere. I can't help but wonder whether in the 1/2 billion years of terrestial plants, some species may have evolved a capacity to pull carbon out of the soil, but this is just my speculation. Rubisco is present in photosynthesis, and with it, alternatively, plants may have had no incentive to get carbon from the soil.

Apparently, rubisco emerged when the Earth had little oxygen in the atmosphere and higher CO2. Thus, this choice of enzyme is not as a efficient in the higher oxygen level of the atmosphere established between 800 and 540 million years ago.

Lingering questioon 2: what enables plants to respire CO2?

Rubisco can react with either CO2 or oxygen. So, as rubisco fixes CO2, to a lesser amount, it is also reacting with oxygen and producing CO2. The News and Views author cites a loss to photorespiration of up to 25% of the CO2 captured in photosynthesis. So, I can say with confidence that plant respiration has a credible scientific basis.

The article addresses efforts to engineer a process by which the loss of photorespiration is eliminated from agriculture. I don't feel I can represent what I read on this, and so I won't.

The real interesting part, and the part that ties in with my recent effort to have more explanations of the carbon cycle and biosphere is the reviewer's mention of what happens to the ratio of rubisco's photosynthesis to photorespiration under warmer temperatures: essentially, that warmer temperatures will increase photorespiration. Thus, warmer temperatures can make plants less efficient at sequestering CO2.

So, where increased CO2 can act as a fertilization (and I've read studies making this claim), increased temperatures will take away from this benefit by making plant photosynthesis less efficient. I'm creating an ever growing list of effects and counter effects on this subject.

My remaining questions are 1) is the inefficiency accompanying warmer temperatures linked to the rise of CO2 following warmer temperatures inferred from ice cores; and 2) will plants merely get less efficient or will we see species turnover, where species  that do better at fixing CO2 under warmer temperatures replace those that don't.

jg