That stem is without doubt damaged.Use microbes like "great white shark" better still use them after brewing compost tea.I would use Ecothrive Biosys which is only several pounds but don't leave it.Check all info given on here including mine as I constantly see incorrect info.You can see for yourself its damaged and people are telling you theres nothing wrong withit.Read up on microbes and the soil food web,its a must when growing with soil.And never forget to stand you water for at least 24hrs so the chlorine can evaporate.