Vitamin B is the preeminent bioorganometallic species.  Vitamin B is actually a collection of related enzyme cofactors, several of which contain cobalt–alkyl bonds, and is involved in biological methylation and 1,2-carbon rearrangement reactions.  For a long time since its structure was elucidated by Hodgkin in 1955, it was believed to be the only example of a naturally occurring bioorganometallic system.
Several bioorganometallic enzymes carry out reactions involving carbon monoxide.  Carbon monoxide dehydrogenase (CODH) catalyzes the water–gas shift reaction, which provides CO (through a nickelacarboxylate intermediate) for the biosynthesis of acetylcoenzyme A.  The latter step is effected by the Ni–Fe enzyme CO-methylating acetyl-CoA synthase (ACS).  CODH and ACS often occur together in a tetrameric complex, the CO being transported via a tunnel and the methyl group being provided by methyl cobalamin.
Hydrogenases are bioorganometallic in the sense that their active sites feature Fe–CO functionalities, although the CO ligands are only spectators.  The binuclear [FeFe]-hydrogenases have a Fe(μ-SR)(μ-CO)(CO)(CN) active site connected to a 4Fe4S cluster via a bridging thiolate.  The active site of the [NiFe]-hydrogenases are described as (NC)(OC)Fe(μ-SR)Ni(SR) (where SR is cysteinyl).  Mononuclear [Fe]-hydrogenases contain an Fe(CO)(SR)(LX) active site, where LX is a 6-acylmethyl-2-pyridinol ligand, bound to the Fe center through the pyridyl nitrogen (L) and the acyl carbon (X).  This class of hydrogenases thus provides examples of naturally occurring iron acyl complexes.
Methanogenesis, the biosynthesis of methane, entails as its final step, the scission of a nickel–methyl bond in cofactor F430.
The iron–molybdenum cofactor (FeMoco) of nitrogenases contains an FeC unit and is an example of an interstitial carbide found in biology.
The first example of a naturally-occurring arylmetal species, a pincer complex containing a nickel–aryl bond, has been reported to form the active site of lactate racemase.