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Weeds can grow through rubber mulch, but it depends on if you removed all the weeds in your garden beforehand. Weeds already in the soil can grow even when using rubber mulch. However, that doesn’t mean that your garden will be littered with rubber and weeds, but it does mean that the occasional weed might still pop up. Another way you can increase your weed suppression is by using landscape fabric as a second layer. 

Some of the particular herbicides that work best to get rid of nut grass without killing the grass include Halosulfuron-methyl, mesotrione, sulfentrazone, and metsulfuron. A herbicide like glyphosate would kill nutgrass, but it will kill nearby plants, too.

You should add 1 to 4 inches of mulch, depending on your garden type and needs. Keep in mind that no amount of mulch can completely prevent weeds, but a heavier coverage (closer to 4 inches) can suppress weeds enough that you are only seeing them sprout every few weeks. Finer mulch prevents weeds more effectively than large mulch, so if you’re using mulched leaves or shredded bark, 1 to 2 inches will likely suffice, while 3 to 4 inches is best for larger mulch, like bark chips or straw.

Yellow leaves and stems on your sprouts indicate they’re not getting enough light. Keep them near the appropriate light source and give them as much as they need (they require longer exposure to fluorescence than they do to natural light sources).