Pantoea agglomerans YS19 is a rice endophytic bacterium characterized to form multicellular biofilm-like structures called symplasmata. Phenotypic distinctions between symplasmata-forming cells and planktonic cells are crucial for understanding YS19's survival strategies. In this study, a 43.1 kDa protein SPM43.1 was identified to show significant resistance to the aggregation effect caused by denaturing acidic conditions. MALDI-TOF analysis data indicated that it is a maltose-binding protein homolog while contains sequence homologous to the chaperone protein, ClpB. The purified SPM43.1 protein was detected to exhibit chaperone-like activities at acidic conditions, where its conformation transformed from an ordered to a globally less ordered structure as revealed by circular dichroism spectroscopy, showing a similar property to most chaperone proteins. The expression of SPM43.1 in YS19 is initiated when bacterial cells begin to aggregate, yet its amount in planktonic cells greatly exceeds that in symplasmata-forming cells, suggesting its crucial role to the survival of planktonic cells in experiencing environmental fluctuations. However, the bacterium prefers to form symplasmata, while not to express SPM43.1 proteins, for surviving the artificially set fluctuant (acid here) environments. This study provides valuable information on the life styles and survival strategies of microorganisms that forms multicellular aggregates at specific growth stages.