Molecular tools allow us to measure the diversity and also abundance of some functional genes, such as nitrogen fixation genes(nif H), ammonia oxidation genes (amo B) etc. For the gene diversity and gene abundance, which one has more contribution to the biogeochemical processes and to the ecosystem?
I think both are strong measurements. Quantitative analyses tells us the relative abundance of the organisms responsible for a key step in a bio geochemical cycle, but you still want to know who is there.
I think gene abundance might be a stronger indicator of process rate because more functional proteins can be expressed, such as enzymes responsible for a specific substrate conversion. Gene diversity gives more variations to the functional proteins that might be important for ecosystem resilience. When the environment are affected by physical or chemical disturbance, the diversity of functional protein pool offers some proteins that are more resistance to disturbance.
For plant ecology, it has been found significant effects of genetic diversity on ecological processes such as primary productivity, population recovery from disturbance, interspecific competition, community structure, and fluxes of energy and nutrients. However, we need evidence and experiments to answer how significant the effect of genetic diversity could impact the ecosystem in microbial world.
http://onlinelibrary.wiley.com/doi/10.1111/j.1461-0248.2008.01179.x/abstract
It should highly depends on the situation. If you focus on a constant and specific environment condition, then the abundance of a function gene will be more important for the performace of function. But if you are face of a variable environment, then the diversity may essential. The redandance of genes are important for exert of specific function in this situation.
You will get valuable information from gene gain/loss only when you sequence complete genomes of your organisms because gain of one gene can compensate the loss of another gene. Gene variablility worth evaluateion only when it is a single-copy gene. otherwise, you will not sequence them without cloning.
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