Office 365 Enterprise E1 Plan-Security Hardening

Specifically for setting up alerts, from this guide, for malware deletion - https://technet.microsoft.com/en-us/library/jj200745(v=exchg.150).aspx

  In the Exchange admin center (EAC), navigate to Protection > Malware filter

  Double-click the default policy in order to edit this company-wide policy.

  Click the Settings menu option. In the Malware Detection Response section

  In the Notifications section, you have the option to send a notification email message to senders or       administrators when a message is detected as malware and is not delivered. These notifications are         only sent when the entire message is deleted.

In general, here are some https://technet.microsoft.com/en-us/library/jj723164(v=exchg.150).aspx.

If you want to see how well your tenant is being protected be sure to check out https://securescore.office.com as well, here is a https://support.office.com/en-us/article/Introducing-the-Office-365-Secure-Score-c9e7160f-2c34-4bd0-a548-5ddcc862eaefand (my) https://social.technet.microsoft.com/wiki/contents/articles/36430.office-365-secure-score-find-and-fix-risks-in-office-365.aspx.