Let’s begin the comparison of the two ontologies at the atomic scale, that is, with the case in which the genus is “Atom” and the species is “hydrogen” or “oxygen”. A modern Aristotelian approach would begin by giving necessary and sufficient conditions to belong to the general category “hydrogen”, such as possession of a single proton (and a single electron). This is a perfectly reasonable way to specify the  identity of this chemical species given that if we added another proton to a hydrogen atom we would change its identity, transforming it into an atom of helium. But in Aristotle a species did not just play a role in classifying entities but also in generating them. As a good realist, Aristotle knew that he had to explain how objective entities come into existence, in both nature and art. In both cases his explanation involved essences acting as formal causes. In nature, Aristotle saw the operation of essences as self-evident, from the observation that a horse begets a horse, and a human a human. In other words, he explained how animal species generate individual organisms by saying that they formally caused them. And similarly for art: in the case of building a house (or nurturing a patient to health) the formal cause is the idea that preexists in the human soul.
Hence, Aristotle argued that a house, or any other entity that “involves matter arises, or is generated, from that which does not involve a connection with matter: for the medicinal and the house-building arts are the form, the one of health, and the other of a house. Now, I mean by substance not involving any connection with matter, the essence or very nature or formal cause of a thing.” [Nota de rodapé 5: Aristotle. The Metaphysics. Op. Cit. p. 142.] This is a much stronger claim than simply saying that possession of a single proton and a single electron is the criterion to belong to the category “hydrogen”. It is also a claim about what is philosophically significant about the generation of form: the process through which a house is built or a horse embryologically developed involves a connection with matter (immanent) and is therefore not as important metaphysically as the formal essence that is not so connected (transcendent).
In a Deleuzian ontology, on the other hand, an essence operating as a formal cause would not be what defines the identity of an assemblage composed of protons and electrons, nor would an essence make questions of processes of assembly irrelevant to metaphysics. The minimal definition of the term “assemblage” is that of a whole with properties that are both irreducible and immanent. An assemblage’s properties are irreducible because while they emerge from the actual interaction between its parts, they cannot be ascribed to any of its parts. And they are immanent because if the components of  the assemblage ceased to interact its own properties would cease to exist: emergent properties may not depend on this or that particular interaction, on this or that connection with matter, but they do demand that there should be some connection with matter. The emergent chemical properties (and capacities) of an atom, for example, depend on its outermost shell of electrons: whether the shell is missing an electron, or has an extra electron, or is exactly full. This property determines how many bonds an atom can form with other atoms: carbon atoms can form four; oxygen ones two; and hydrogen atoms only one. The properties of the outer shell (and the bonding capacities with which these endow an atom) are clearly not reducible to the properties of individual electrons, but they would cease to exist if those electrons stopped interacting with the atom’s nucleus.
We can summarize this by saying that there is no such thing as “hydrogen in general”, only a very large population of individual hydrogen atoms defined by properties that emerge from the continuous interaction among individual components. In other words, each hydrogen atom is an individual singularity. To the objection that even if each hydrogen atom is a unique historical entity all hydrogen atoms are basically the same (they are all defined by a one-proton nucleus) we can answer that there are other components, neutrons, that produce inherent variation. Depending on the number of neutrons a hydrogen nucleus possesses variant isotopes of this chemical species are generated: protium, deuterium, and tritium. The number of neutrons in a nucleus has very little effect on an atom’s chemical properties, but it does affect its physical stability: some isotopes are stable and more enduring, while others decay faster. When we consider not one atom but an entire population of atoms, the relative abundances of isotopes, or more exactly, the statistical form of the distribution of isotopic variation, contains information about the historical processes that produced the members of the population, processes that replace formal causes in this ontology. In other words, the variation is not a trivial side effect but a significant source of knowledge.
Let’s briefly sketch what is known in astrophysics about the production of atoms of different species. Although hydrogen and helium were produced under the intense  conditions following the Big Bang, the rest of the chemical species had to wait hundreds of millions of years until the formation of stars. Today the nuclei of most atoms are assembled in stars, so the process of assembly is known as stellar nucleosynthesis. Stars of different sizes serve as assembly factories for atoms of different species: the larger and hotter the star the heavier the atoms it can put together. The smaller stars, like our Sun, are only hot enough (10 million degrees Kelvin) to burn hydrogen as fuel and produce helium as a product. At higher temperatures (over 100 million degrees), helium itself can be burnt as fuel and yield as products carbon, oxygen, and nitrogen. At even higher intensities (a billion degrees) carbon and oxygen become the fuel, while the products are atoms of the species: sodium, magnesium, silicon and sulfur. As intensities continue to increase silicon is burned as fuel to produce iron, and finally a maximum of intensity is reached in the process of explosive nucleosynthesis, in which the heavier species are created during the violent events known as “supernovae”. [Nota de rodapé 6: Stephen F. Mason. Chemical Evolution. (Oxford: Clarendon Press, 1992), Chapter 5.]
We can imagine that, confronted with this information, Aristotle would be unimpressed, since he could argue that the details of how a house is built, or a patient healed, or an atom assembled, are less important than their formal causes. In particular, he could argue that regardless of what happens in stars, only a certain number of atomic species exists, a number that can be considered to have existed prior to any process of nucleosynthesis. There is, in fact, some truth to this objection which is why we need to add to an ontology of individual singularities the universal singularities that structure the space of possible species. Let’s first consider this space as given in the famous Periodic Table of the Elements. The table itself has a colorful history because several scientists had already discerned regularities in the properties of the chemical species (when ordered by atomic weight) prior to Mendelev stamping his name on the table in 1869. Several decades earlier, for example, one scientist had already seen a simple arithmetical relation between triads of elements, and later on others noticed that certain properties (like chemical reactivity) recurred every seventh or eighth element. In other words, rhythms or periodically recurrent regularities had been observed pointing to the existence of a deeper structure. What constitutes Mendelev’s great achievement  is that he was the first one to have the courage to leave open gaps in the table instead of trying to impose an artificial closure on it. This matters because in the 1860’s only around sixty species had been isolated, so the holes in Mendelev’s table were like daring predictions that yet undiscovered species had to exist. He predicted, for example, the existence of germanium on the basis of a gap near silicon. The Curies later on predicted the existence of radium on the basis of its neighbor barium. [Nota de rodapé 7: P. W. Atkins. The Periodic Kingdom. (New York : Basic Books, 1995), Chapter 7. p. 72-73.] These risky predictions, and their eventual corroboration, is what gave the table its objective status. But what accounts for the underlying rhythms at the chemical heart of matter? (DeLanda 2010:83-7)
DELANDA, Manuel. 2010. Deleuze: History and Science. New York: Atropos Press.