The bacterial second messengers (p)ppGpp and bis-(3=-5=)-cyclic dimeric GMP (c-di-GMP) regulate important functions, such as transcription, virulence, biofilm formation, and quorum sensing. In mycobacteria, they regulate long-term survival during starvation, pathogenicity, and dormancy. Recently, a Pseudomonas aeruginosa strain lacking (p)ppGpp was shown to be sensitive to multiple classes of antibiotics and defective in biofilm formation. We were interested to find out whether Mycobacterium smegmatis strains lacking the gene for either (p)ppGpp synthesis (⌬rel Msm ) or c-di-GMP synthesis (⌬dcpA) would display similar phenotypes. We used phenotype microarray technology to compare the growth of the wild-type and the knockout strains in the presence of several antibiotics. Surprisingly, the ⌬rel Msm and ⌬dcpA strains showed enhanced survival in the presence of many antibiotics, but they were defective in biofilm formation. These strains also displayed altered surface properties, like impaired sliding motility, rough colony morphology, and increased aggregation in liquid cultures. Biofilm formation and surface properties are associated with the presence of glycopeptidolipids (GPLs) in the cell walls of M. smegmatis. Thin-layer chromatography analysis of various cell wall fractions revealed that the levels of GPLs and polar lipids were reduced in the knockout strains. As a result, the cell walls of the knockout strains were significantly more hydrophobic than those of the wild type and the complemented strains. We hypothesize that reduced levels of GPLs and polar lipids may contribute to the antibiotic resistance shown by the knockout strains. Altogether, our data suggest that (p)ppGpp and c-di-GMP may be involved in the metabolism of glycopeptidolipids and polar lipids in M. smegmatis. N ucleotide-based second messengers regulate various biological processes in all domains of life. Pentaphosphate guanosine (pppGpp) or tetraphosphate guanosine (ppGpp), collectively referred to as (p)ppGpp, and bis-(3=-5=)-cyclic dimeric GMP (cdi-GMP) are two such bacterial second messengers (1, 2). The alarmone (p)ppGpp is synthesized when bacteria are stressed or starved and regulates important processes, like stringent response, quorum sensing, virulence, and biofilm formation (2-5). In mycobacteria, (p)ppGpp is synthesized and broken down by the dual-function enzyme Rel, encoded by the rel gene (6). The Mycobacterium smegmatis rel gene knockout (⌬rel Msm ) strain is compromised for long-term survival during nutrient starvation and progressive hypoxia (7). Similarly, Mycobacterium tuberculosis lacking the Rel Mtb protein has reduced long-term survival in the lungs of mice and in a mouse hypoxic granuloma model and fails to form tubercle lesions in a guinea pig model of infection (8-11). Both the M. tuberculosis and M. smegmatis genomes encode a second (p)ppGpp synthetase called small alarmone synthetase (12, 13). However, its role in mycobacterial physiology has not been completely elucidated.The signaling nucleotide c-di-GMP is s...