A microcosm paper on which I am a co-author just got rejected. Which seems as good an excuse as any to repost this, in which I shoot down all the commonly-voiced blanket objections to microcosms in ecology.
I have yet to hear a convincing unconditional objection to any widely-used study system or research approach in ecology. Every study system and research approach has its strengths, and its limitations. Which is something that seems to be widely acknowledged in ecology–except when it comes to microcosms.