Determination of nitrogen-fixing phylotypes in Lyngbya sp. and Microcoleus chthonoplastes cyanobacterial mats from Guerrero Negro, Baja California, Mexico

Analysis of the hupSL operon of the nonheterocystous cyanobacterium Lyngbya majuscula CCAP 1446/4: regulation of transcription and expression under a light-dark regimen

This work presents the characterization of an uptake hydrogenase from a marine filamentous nonheterocystous cyanobacterium, Lyngbya majuscula CCAP 1446/4. The structural genes encoding the uptake hydrogenase (hupSL) were isolated and characterized, and regulatory sequences were identified upstream of hupS. In silico analysis highlighted various sets of long repetitive sequences within the hupSL intergenic region and downstream of hupL. The transcriptional regulator that operates global nitrogen control in cyanobacteria (NtcA) was shown to bind to the promoter region, indicating its involvement in the transcriptional regulation of hupSL. Under N2-fixing conditions and a 12-h light/12-h dark regime, H2 uptake activity was shown to follow a daily pattern with a clear maximum towards the end of the dark period, preceded by an increase in the transcript levels initiated in the end of the light phase. Novel antibodies directed against HupL of Lyngbya majuscula CCAP 1446/4 were used to monitor the protein levels throughout the 24-h period. The results suggest that protein turnover occurs, with degradation taking place during the light phase and de novo synthesis occurring during the dark phase, coinciding with the pattern of H2 uptake. Taking into account our results and the established correlation between the uptake hydrogenase activity and N2 fixation in cyanobacteria, it seems probable that both processes are confined to the dark period in aerobically grown cells of Lyngbya majuscula CCAP 1446/4.

Quantitative analysis of nifH genes and transcripts from aquatic environments

The availability of fixed inorganic nitrogen often plays a fundamental role in regulating primary production in both aquatic and terrestrial ecosystems. Because biological nitrogen fixation is an important source of nitrogen in marine environments, the study of N2-fixing microorganisms is of fundamental importance to our understanding of global nitrogen and carbon cycles. Quantitative molecular tools have made it possible to examine uncultivated N2-fixing microorganisms directly in the environment. Currently, we are using quantitative polymerase chain reaction (PCR; Q-PCR) and quantitative reverse transcriptase PCR (Q-RT-PCR) to study the ecology and gene expression of N2-fixing bacteria in aquatic environments. Using these methods, we discovered that specific estuarine diazotrophs have distinct nonrandom distributions and that some diazotrophs in the open ocean have different diel patterns of nifH gene expression. This chapter describes briefly our 5' nuclease assay protocols for Q-PCR and Q-RT-PCR of nifH gene fragments in environmental samples and discusses some important methodological considerations for the quantitative molecular examination of microbes in aquatic environments.