Glyphosate directly kills microbes, but are you saying that removing a weed is bad because the soil bacteria associated with it are removed as well?
There is no perfect answer to that, but it is part of my research. In many cases I have found that "weeds" really are beneficial. Pigweed is beneficial to corn especially for example, and dandelions are beneficial to almost everything. The exact reasons why I am sure are at least partly related to the roots, and likely the soil microbes associated with them, but the answer is not so easy to make simple statements. There is also the microclimate above the ground, beneficial insect habitat, direct plant to plant communications, and a host of other subtle interactions.
But no one can deny that it is also possible for weeds to harm your crops as well. So blanket statements can't be made. One thing is certain, to work, the crop must be the dominant plant, not the weeds.
I really am not ready to post my own project on a skeptic forum yet. I need more hard data and results that can be repeated. However, be sure that in my test plots there are actually more "weeds" than crop in both number and total biomass. Yet I get better yields than my neighbors with less water and other inputs. I use no haber process nitrogen or herbicides, and am getting very close to no outside inputs at all. Nor do I plow, till, weed or cultivate in any way what-so-ever in my test plots. I will be applying for a grant to test carefully controlled AH integration and its effect on GAP guidelines this fall. If the results are proven safe, I think it will be the key to tip the balance in favor of 100% sustainable with no inputs at all. (except the occasional biological pest control) Yet significantly outproducing conventional in both profit and yield. We will see. If I get the grant so I can afford lab testing, I will publish, even if the results are less than expected.
ETA PS. I am not a scientist. I am a producer. However, the USDA Sustainable Agriculture Research and Education (SARE) Program has a Producer Grant Program to promote producer's research related to sustainable agriculture. I will be cooperating with Phd scientists so that proper scientific testing and analysis can be done. Not funded yet though, so for now, everything I say can be considered anecdotal. That's why I am keeping my own project off skeptic science forums for now. However, I didn't come up with this all myself. I have spent years researching what others are doing, and that research I can and do post. Here is something someone else is doing.
Blue Heron Farms Notice he has strips of "weeds" between his beds and they provide many benefits.
That particular breakthrough is far closer than people realize...
I am not in some marshy area. We just came off several years of drought. There are no lakes or forests near, although about 5 miles away is a lake with surrounding woods, and several patches of dry scubland/trees around. Yet there they were, happily munching on any insect pests who dared attack my tomatoes. Must have migrated during the spring rains. Toads and scorpions spiders etc..... at ground level too, rooting through the mulch. Swarms of native pollinators each morning kept my plants producing, even when temps reached 95 deg F +. Even 100 deg F + many cultivars still were setting fruit. All those things are considered "impossible". Ask any commercial grower. In fact at late summer, a local commercial grower came by my stand and screamed quite angrily at me that "You didn't grow those!", "Impossible!". So angry that even the field behind me clearly visible, couldn't convince. Was sure I was "cheating" by importing in tomatoes from out of state. Strange but true story.
