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JAXA is planning to launch SLATS (Super Low Altitude Test Satellites). Theses will orbit for > 2 years using ion propulsion to counteract the substantial drag at the 180-260km high altitude.

They will use Xenon as a propellant, which will probably be the limiting factor for the lifetime of the satellite.

Using the residual atmosphere instead sounds like a very appealing solution: No need to include propellant (Infinite ISP!!), and potentially vastly improved lifetime.

What are the challenges to use the atmosphere as a propellant instead of on board supply ?

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    $\begingroup$ I'm guessing, but could be wrong, that the lighter atmospheric gases don't lend themselves very well for use as propellant in an ion engine. I recall (but could be wrong) seeing a question here why xenon is used; IIRC, the answer was that it's right among the heaviest noble gases, has decent ionization energy requirements, and is reasonably easy to acquire. By using atmospheric gases at 200 km altitude, you might attain #3 but do very little about #1 and #2. $\endgroup$ – user Aug 26 '16 at 8:19
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    $\begingroup$ Yes that question exists, but one of the advantage is storage (not important in our case). This other question is related but is mostly about the basic physics than the engineering space.stackexchange.com/questions/1840/… $\endgroup$ – Antzi Aug 26 '16 at 8:22
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    $\begingroup$ Using the density of the atmospheric gases at 200 km altitude and the front area of the satellite, it is possible to calculate the flow rate of this kind of propellant. If the possible thrust using this flow rate is much lower than the atmospheric drag, there is no substantial extended lifetime. $\endgroup$ – Uwe Aug 26 '16 at 12:35
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    $\begingroup$ I believe the ambient gas would first have to be accelerated to orbital speed before it could be used to accelerate the satellite. That would take an enormous amount of energy, probably far too much to make this a workable idea. $\endgroup$ – Organic Marble Dec 18 '17 at 4:50
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    $\begingroup$ @MarkAdler Correct me if I'm wrong, but it looks like ion engines typically have an exhaust velocity ~30km/s; if you have to bring the molecules of air to orbital speed, you still get ~20km/s of exhaust velocity? $\endgroup$ – 0xDBFB7 Dec 18 '17 at 15:59
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The first proposition of the concept of collecting atmosphere at LEO to utilize it as a propellant dates back from the 1960s; this article presents a detailed review about the development of this technology over the years. More recently, in 2018, this concept gained public attention once more with the successful firing of the first air-breathing electric propulsion system by a team led by ESA, at Italy.

What are the challenges to use the atmosphere as a propellant instead of on board supply ?

The review paper which I mentioned, at the section "5. Avenues for continued research", shows a comprehensive list with some of the major challenges for the development of space air-breathing propulsion:

  • Air-compatible cathode technology:

    Traditional thermionic cathode emission sources cannot operate in the presence of oxygen-containing species because the emission sources are readily oxidized at temperatures necessary for emission.

  • Techniques to improve propellant utilization on atmospheric species:

    The thruster experiments detailed in this review universally encounter reduced propellant utilization efficiency for atmospheric gases when compared to equivalent operation on xenon.

  • In-space compressor and liquefaction technology:

    (...) a compression system for a propellant collecting spacecraft must operate exclusively in a much harsher space environment with restricted access to electrical power.

  • Improved hypersonic and hyperthermal free molecular flow inlet designs:

    The flow into the vehicle is a major contribution to the aerodynamic drag experienced by the vehicle, and determines the mass available for counteracting the drag and for storage.

  • Improved understanding of how design parameters affect system performance:

    A physics-based model of propellant collection as a general concept which is free from the assumptions possible when considering only a subset of propellant collecting concepts is not present in the literature.

You can refere to the article to have a complete explanation about each point. Furthermore, these slides from the University of Tokyo can give you some more information about the concepts and pros and cons of using air-breathing propulsion systems.

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    $\begingroup$ This is a very well written and well-sourced answer! The UT slides are really interesting as well. $\endgroup$ – uhoh Sep 5 '18 at 23:57

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