Genetic Engineering Would be Nice, But it Has Complications
While genetic engineering would help plants or humans adapt to the environment you describe, it may not be possible to engineer organisms under these conditions:
- A Marsbound ship does not need GE technology on board. We can predict the soil and atmospheric conditions on Mars, so we have already made a list of plants to grow on Mars and how to do so effectively. Your people are prepared for what they "know" what will happen, not for this anomaly.
- If the ship has the technology to engineer plants, which it does not need, your scientists will not have the genes required to make the changes wanted. To make a frost-resistant plant, for example, you need genes that cause resistance to frost. Your scientists likely won't carry a library of genes to splice.
- Engineering people in space will not work. Microgravity conditions affect the human body over time, so trying to engineer and birth modified humans will result in babies developed for low gravity. These humans will not be able to survive in the 1.6g on the planet's surface.
Basically, the short answer to your question is yes, of course GE would help, but it could not be done easily with what your crew has.
There are Plausible Ways to Grow Crops Without GE
Let's consider what your ships have on board to grow on Mars. We have grown the following crops here on Earth with Mars-analogous soil:
- Others in separate studies
This means these are some of the plants likely to be on board your ships.
Your planet has usable water, but there is no way of knowing if the native soil is hospitable. There are several ways your colonists could work around this:
- Grow a couple Earth plants. On the small chance the soil is habitable, great! But as many commenters have said, this is simply not likely.
- Burning native flora to alter soil composition. While this may not guarantee success, it will release what nutrients native species do contain, giving you another option to test with. This method is sort of a Pandora's box, as you could release either toxins or nutrients. Probably best to test on a small scale. If it works, which is possible, great! But it might not.
- If all of the above fails, human waste can be used as fertilizer. Up until now, the colonists have been eating, so they must be producing waste. This method may not be appetizing, or sanitary, but if the situation is life-or-death, it will fertilize crops to a reasonable degree. Additionally, if your crew brought any antibiotics aboard with them, these could be used in the soil to sterilize or reduce the problems caused by the Earth pathogens.
Luckily, your colonists were headed to Mars. This is a huge plus for climate controlled habitats on this planet. Mars has extreme storms, and extreme cold, so our solution for the colonization of Mars is to farm indoors, and to water plants using melted native ice. This could apply to your planet with ease.
If your ships contain the weather, temperature-resistant materials or structures we would bring to Mars, your colonists can plonk them down onto this new world and survive in them. No extra climate challenges imposed.
Challenges of Native Flora
If you are lucky, and the soil on this planet is drastically different from our own, the native plants will have different nutritional needs. This means competition is not likely; plants will stick to areas with the nutrients they need to use.
If the soil on this planet is similar enough to our own, and plants try to inhabit the same places, removal should not be a problem. This is analogous to a farmer weeding a crop on Earth; while you could argue that making land hospitable means your plants have to compete to use it, invaders can be removed manually faster than they invade.
Challenges of Native Microorganisms
This is up for debate. While kingledion is correct that microbial toxins could damage humans and plants, there is no evidence of compatibility between these organisms' toxins and Earth chemistries. Elements such as iron and sodium, for example, will not harm humans or Earth-endemic plants, but they may be the main toxin of choice to kill species endemic to this world. The likelyhood of whatever is used to disable creatures on this world being effective against organisms from Earth is slim; there are only so many things that can harm us.
Edited to match information provided in the comments. Previous answer was based on being optimistic when given probability; now based on fact and reason.