Sitemaps - one per subdomain or one for the base domain?

Generally, you have to use a separate sitemap for each host (i.e., different protocol, domain, or subdomain):

• From the FAQ "Where do I place my Sitemap?":

  All URLs listed in the Sitemap must reside on the same host as the Sitemap. For instance, if the Sitemap is located at http://www.example.com/sitemap.xml, it can't include URLs from http://subdomain.example.com. If the Sitemap is located at http://www.example.com/myfolder/sitemap.xml, it can't include URLs from http://www.example.com.

• The relevant section from the Sitemaps spec is "Sitemap file location", where it says:

  Note that this means that all URLs listed in the Sitemap must use the same protocol (http, in this example) and reside on the same host as the Sitemap. For instance, if the Sitemap is located at http://www.example.com/sitemap.xml, it can't include URLs from http://subdomain.example.com.

However, if you can prove ownership of all hosts via robots.txt or Google Search Console, you can host the sitemaps on different hosts:

• via robots.txt: Sitemaps & Cross Submits
  (a single sitemap may still only contain URLs from one host)

• Google-specific: Manage sitemaps for multiple sites
  (a single sitemap may contain URLs from differen hosts)

As per Matt Cutts blog post, he said:

A subdomain can be useful to separate out content that is completely different. Google uses subdomains for distinct products such news.google.com or maps.google.com, for example.

This is similar to what Blogger (blogspot) does.

John's blog (john.blogspot.com) is totally different from Doe's blog (doe.blogspot.com). Google sees these two blogs as two different sites even though they share the same tail (*.blogspot.com).

Each of these blogs have their own sitemap and are not shared between one another. If one blog gets deleted, the sitemap file will be deleted as well - and it does not affect the other blogs' sitemaps.

So, I'd like to recommend to you to use different sitemap files for different sub-domains. Unless you're using sub-directories/sub-folders.

As you write the subdomains are part of the whole application there is no need to separate the sitemaps. Google treats subdomains as own domains ayways. But they are smart enough to recognize if parts of a website belong together.

Besides SEO I'd recommend to use an index-sitemap.xml in which you can nest all your separate subdomain-sitemaps. This makes it easier to manage all those files, as you only need to submit one single sitemap. Further you can change a subdomain's sitemap without having to worry about all the other sitemaps. Read more about managing multiple sitemaps on Googles Webmaster Guides: https://support.google.com/webmasters/answer/75712?hl=en

edit

You may take into consideration to create a single property for each subdomain in Google Search Console. This enables you to have more detailed analysis as you will receive data samples and crawling statistics for each property. If you do so I'd recommend to submit an individual sitemap for each subdomain. Be aware that this will require you to verify each property separately and also increase the effort it takes to manage the whole set of properties.

If you're a well organized person and interested in deeper data insights I'd recommend the latter. If you just wand your site to be indexed and crawled properly I'd recommend the index-sitemap story to you.

Always keep in mind to make sure all you sitemaps are configured accurately, matching the standard and deliver only pages that serve a 200 status code. This point is more critical to your website's SEO than the question of how many sitemaps you have.