Why are biofilm microbes less susceptible to killing than their free-floating counterparts?

Biofilms evade antimicrobial challenges by multiple mechanisms. These can be grouped into three broad categories:
    1) reduction of the antimicrobial concentration in the bulk fluid surrounding the biofilm (depletion);
    2) failure of the antimicrobial agent to penetrate the biofilm; and
    3) adoption of a resistant physiological state or phenotype by at least some of the biofilm cells.

We are beginning to believe that the multicellular construction of biofilms affords protection for cells in multiple ways. Some of these hypothesized mechanisms of protection from antimicrobial agents are pictured in the diagram below.

Free-floating cells utilize nutrients, but do not have sufficient metabolic activity to deplete substrates from the neighborhood of the cells.

In contrast, the collective metabolic activity of groups of cells in the biofilm leads to substrate concentration gradients and localized chemical microenvironments.  Reduced metabolic activity may result in less susceptibility to antimicrobials.

Free-floating cells carry the genetic code for numerous protective stress responses. Planktonic cells, however, are readily overwhelmed by a strong antimicrobial challenge. These cells die before stress responses can be activated.

In contrast, stress responses are effectively implemented in some of the cells in a biofilm at the expense of other cells which are sacrificed.

P. Stewart

Free-floating cells neutralize the antimicrobial agent. The capacity of a lone cell, however, is insufficient to draw down the antimicrobial concentration in the neighborhood of the cell.

In contrast, the collective neutralizing power of groups of cells leads to slow or incomplete penetration of the antimicrobial in the biofilm.

Free-floating cells spawn protected persister cells. But under permissive growth conditions in a planktonic culture, persisters rapidly revert to a susceptible state.

In contrast, persister cells accumulate in biofilms because they revert less readily and are physically retained by the biofilm matrix.