Origins
The prefix 'sub-' is one of the major Latin-derived prefixes in English, used to form words indicating position below or under, subordination, secondariness, or partial or near quality. It descends from Latin 'sub' (under, below), itself from Proto-Indo-European *(s)upo, meaning 'under' or 'from below.' The same PIE root produced Greek 'hypo-' (ὑπό, under), Sanskrit 'upa' (near, under), and, through Germanic, the English word 'up' — where a curious semantic inversion occurred so that the same root could mean 'from below upward' in Germanic and 'under' in Italic.
In Latin, 'sub-' showed extensive allomorphy through assimilation to the first consonant of the stem. This assimilation pattern is inherited directly into English: - 'suc-' before 'c': succeed, success, succour, succumb - 'suf-' before 'f': suffer, suffice, suffix, suffocate - 'sug-' before 'g': suggest - 'sup-' before 'p': support, suppose, suppress, supply - 'sur-' before 'r': surreptitious, surrogate, surround (though 'surround' has a complicated history) - 'sus-' before some c, p, t: suspect, suspend, sustain, suspense, suspicion - 'sub-' elsewhere: subject, submit, subtract, suburb
This extensive allomorphy is why English has so many apparently unrelated words that actually share the same prefix. 'Suggest,' 'suffer,' 'succeed,' 'supply,' and 'suspect' all contain 'sub-' in disguised form. Recognising the prefix helps reveal the structure: 'suffer' is 'sub-' + Latin 'ferre' (to carry), literally 'to bear under'; 'suggest' is 'sub-' + 'gerere' (to carry, bring), literally 'to bring under / bring up'; 'succeed' is 'sub-' + 'cedere' (to go), literally 'to go close under / follow after.'
Latin Roots
In Latin, 'sub-' had several interrelated senses: (1) spatial, meaning 'under' or 'from below' ('submarine,' 'subsoil,' 'subway'); (2) sequential, meaning 'immediately following' or 'succeeding' ('subsequent,' 'succeed'); (3) subordinate, meaning 'below in rank' ('subordinate,' 'subject,' 'subaltern'); (4) somewhat or partial, meaning 'slightly' or 'nearly' ('subacute,' 'subaverage,' 'sublethal'); and (5) secret or stealthy, meaning 'from below / under cover' ('subvert,' 'subterfuge,' 'subtle' — from Latin 'subtilis,' woven underneath).
In Middle English (c. 1200–1500) 'sub-' arrived in many learned Latin borrowings: 'subject,' 'subjugate,' 'sublime,' 'submit,' 'subsidy,' 'substance,' 'substitute,' 'subtract,' 'suburb,' 'subvert,' 'succeed,' 'succour,' 'suffer,' 'sufficient,' 'suffix,' 'suggest,' 'summon' (via Old French 'somondre' from 'submonere'), 'superb,' 'supple,' 'support,' 'suppose,' 'suppress,' 'supreme,' 'suspect,' 'suspend.'
From the nineteenth century onward, 'sub-' became a live productive prefix in English, coining many new words with transparent meanings: 'subway' (1825, tunnel under a road; later underground railway), 'subsoil' (1799), 'sublet' (1766), 'sublease,' 'sub-editor' (1800s), 'subcommittee,' 'submachine gun' (1900), 'submarine' (1648 as adjective, 1899 as noun for a ship), 'subzero,' 'subtotal,' 'subplot,' 'subgenre,' 'subclass,' 'subset' (mathematics, 1902), 'subtext' (1950), 'subroutine' (computing, 1948). These productive coinages use 'sub-' without assimilation ('submarine,' not 'summarine'), because the prefix is transparently added to an English base.
Scientific Usage
In scientific terminology, 'sub-' systematically indicates taxonomic subdivision: subphylum, subclass, suborder, subfamily, subspecies — each one step below the level above. In chemistry and physics: subatomic, subsonic, subnuclear, subsurface. In computing: subroutine, subdirectory, subquery, subnet.
Pronunciation is generally /sʌb/ in English, with the full vowel retained even when unstressed. In assimilated forms, the consonant varies: 'suggest' /səˈʤɛst/, 'suffer' /ˈsʌfə/, 'suspect' /sʌˈspɛkt/, 'sublime' /səˈblaɪm/. When 'sub-' is a live productive prefix added to an English base, it tends to be pronounced /sʌb/ with full stress: /ˈsʌb.weɪ/, /ˈsʌb.sɛt/, /ˈsʌb.plɒt/.
Representative 'sub-' words include (historical Latin borrowings): subject, subjugate, sublime, submerge, submit, subordinate, subscribe, subsequent, subservient, subside, subsidiary, subsidy, subsist, substance, substantial, substitute, subtract, suburb, suburban, subversive, subvert. Assimilated Latin forms: succeed, success, suffer, suffice, suffix, suffocate, suggest, supplant, supplement, supply, support, suppose, suppress, supreme, surreptitious, suspect, suspend, sustain. Productive modern coinages: subclass, subcommittee, subcontinent, subcontract, subculture, subdirectory, subdivide, subgenre, subgroup, subheading, submarine, submenu, subnet, subplot, subroutine, subscribe, subset, subsoil, subspecies, substation, subtotal, subtype, suburb, subway, subzero.