negative aquatic bacteria by substrate limitation. Organic carbon 

 limitation induces proteins in the periplasm of these bacteria. A 

 unique marker protein, indicative of low endogenous substrate 

 levels, is found in the outer membrane of starved cells. 

 Additionally, fluorescent-labeled antibodies have identified 

 specific carbohydrates synthesized during starvation. These 

 approaches are amenable to understanding the availability of 

 substrates for natural microbial communities in situ . 



A variety of other molecular biological, diagnostic indicators 

 of physiological rate-limiting factors is described in Appendix I. 

 There are known molecular markers for nitrogen limitation, elevated 

 and depressed temperature, metal tolerance and toxicity, and 

 responses to suboptimal and supraoptimal irradiance effects. Their 

 ubiquity is poorly understood. A major challenge for molecular 

 biological research is to develop an adequate base of knowledge to 

 interpret molecular signals from organisms in the natural 

 environment, and to infer from such signals how, and to what 

 extent, the growth and function of the organisms is limited by 

 external forcings. 



Below are some examples of questions where the techniques of 

 molecular biology could be used to understand limiting factors: 



• How can laboratory studies that identify specific 

 proteins or other molecular markers symptomatic of 

 limiting factors or stresses be used in natural 

 ecosystems to specifically screen and diagnose limiting 

 factors? 



• How can the so-called stress proteins, such as ubiquitin, 

 heat-shock proteins, or their analogues, be used to 

 diagnose thermal, water, and light stress in the field? 



• How can starvation-induced proteins, known from 

 laboratory studies of starved cells, be used to identify 

 substrate limitation in mixed, natural microbial 

 communities? 



• Are specific proteins or secondary gene products, such as 

 lipids, synthesized in response to small, sublethal 

 changes in temperatures? 



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