Google claims to treat subdomains for SEO purposes as individual sites, as opposed to just a section of the main site. This is often the case, but subdomains may also represent individual businesses or sole users, which is how Bloggers use them. A vital question that we must ask is whether algorithmic penalties or individual actions that are taken against a subdomain could have knock-on consequences for the root or mother domain. For example, if a subdomain gets spammed, what are the implications for the root site?
Webmaster trends analyst, John Mueller (Google) has recently commented on this tricky situation of a spammed subdomain causing problems for the other parts of the site. He made the point that even though it is generally recognised that subdomains can operate separately from their root site, it is also the case that the use of subdomains are a way most sites organise their structure.
Google will, therefore, for the most part, focus on manual actions that are aimed at specific areas (subdomains) of a site. There is, however, a significant possibility that an individual action aimed at a subdomain will spread out and affect the rest of the domain. This is an area that webmasters should be aware of when they set up subdomains. It is something that certainly can have a knock on effect.
For Malware, the Google systems in operation will take a similar approach. If it is seen that on multiple subdomains there is malware, then a general pattern would strongly suggest that the malware is everywhere on the domain.
Subdomains will typically give protection to users that have no connection with other subdomains, but if a link is established, or a domain seems to be covered in Spam, then the whole domain will be affected. The bottom line when dealing with subdomains is that if a webmaster uses a free website service, he will need to satisfy himself that the overall domain is clean of spammers.
The use of very aggressive SEO approaches (black hat) that are 100 per cent focused on search engines rather than humans will have an adverse knock-on effect for the domain as a whole; even if it is used in just a single subdomain. Forceful Blackhat tactics, if used only in one subdomain could mean that the entire site could be banned. This could very easily be the case even if the rest of the domain is spam free.