Two posts on bacteria coopting viruses

Carl Zimmer in 'The Loom" post Mouth War describes a neat process:
"Once the microbe has captured this viral DNA, it can use it as a template for making a molecular probe. When the virus invades again, the probe latches onto it and quickly guides the microbe’s virus-killing proteins to their target. And in a bit of Lamarckian wizardry, the microbe can pass this acquired defense down to its offspring, making them resistant too.

The prisons for these captured pieces of virus DNA are called CRISPRs–an abbreviation for clustered regularly interspaced short palindromic repeats. Mutant viruses that don’t match a host’s CRISPRs enjoy an evolutionary edge, and so microbes are constantly revising their collection of CRISPRs to fight an ever-evolving enemy."
Ed Yong in 'Not Exactly Rocket Science' post The prophages weren’t essential by any means. Without them, the bacteria survived quite reasonably, although they grew more slowly than normal strains. But they proved to be wimps when challenged with difficult conditions. They became up to 400 times more sensitive to antibiotics. They succumbed more readily to extremely salty or acidic conditions. And they were almost completely unable to form biofilms – fortified ‘cities’ where the microbes gather under the shelter of substances that they themselves secrete.

In many of these cases, Wang could weaken the bacteria by removing a single prophage, which suggests that many of the genes are active parts of the host. The cryptic prophages are no longer selfish parasites, nor are they truly passive fossils. Rather, they have been domesticated to serve their host.describes a different type of capture:
"Once phages have injected their genes into a bacterium, they can make copies of themselves in two ways. The first is a brutish approach. The genes commandeer the host, using it to manufacture new viruses that eventually burst out of the cell – this is the lytic cycle. Alternatively, the phage DNA can infiltrate the bacterium’s genome, becoming part of it. When the bacterium divides in two, it copies the phage’s genes along well as its own. This is the lysogenic cycle, an altogether stealthier approach to making more phages.

Within the bacterial genome, the viral DNA is called a prophage. After being copied many times over in these new surroundings, it can pop out again to create a new phage. The prophage is little more than a genetic parasite. But sometimes, a prophage gets trapped by a crippling mutation. Unable to pop out, it becomes a genetic fossil, forever stuck within its host and destined only to preserve a trace of a past infection.

These captives are called cryptic prophages and they can make up a fifth of a bacterium’s DNA. Their existence is puzzling. Bacteria are known for having small, streamlined genomes, yet in they have foreign and potentially harmful viral DNA loitering among their genes. Why?

The prophages weren’t essential by any means. Without them, the bacteria survived quite reasonably, although they grew more slowly than normal strains. But they proved to be wimps when challenged with difficult conditions. They became up to 400 times more sensitive to antibiotics. They succumbed more readily to extremely salty or acidic conditions. And they were almost completely unable to form biofilms – fortified ‘cities’ where the microbes gather under the shelter of substances that they themselves secrete.

In many of these cases, Wang could weaken the bacteria by removing a single prophage, which suggests that many of the genes are active parts of the host. The cryptic prophages are no longer selfish parasites, nor are they truly passive fossils. Rather, they have been domesticated to serve their host."

The prophages weren’t essential by any means. Without them, the bacteria survived quite reasonably, although they grew more slowly than normal strains. But they proved to be wimps when challenged with difficult conditions. They became up to 400 times more sensitive to antibiotics. They succumbed more readily to extremely salty or acidic conditions. And they were almost completely unable to form biofilms – fortified ‘cities’ where the microbes gather under the shelter of substances that they themselves secrete.

In many of these cases, Wang could weaken the bacteria by removing a single prophage, which suggests that many of the genes are active parts of the host. The cryptic prophages are no longer selfish parasites, nor are they truly passive fossils. Rather, they have been domesticated to serve their host."

The process by which the antibiotic resistance is developed is not clear and seems to be different from the four processes described in Antibiotic resistance. It is not clear to me whether there is any (perhaps technical)relationship between 'cryptic prophages' and 'CRISPRs'.