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16S rRNA gene (rrn ) copy number in bacterial genomes is indicative of ecological strategies of bacteria and is critical for quantification of bacterial abundance in mixed populations using rrn- based approaches. For accurate assessment of rrn copies, a novel technical strategy by means of pulsed-field gel electrophoresis and polymerase chain reaction amplification analysis was introduced. Experimental and in silico analysis on a test bacterial culture Caulobacter crescentus proved it to be simple, effective, accurate and a good alternative to traditional time-consuming methods. PRATICAL APPLICATIONS This method can be used for routine determination of gene copy number in most bacteria whose full genome sequences are not available. Moreover, the pulsed-field gel electrophoresis bands containing a target gene fragment can be determined and therefore constructing an expected fragments oriented genomic library is possible. [ABSTRACT FROM AUTHOR]

Bacteria! abundances in ice cores vary in response to climatic conditions. This paper presents annual bacterial abundances measured in ice deposited over the past 70 years and trapped within a core retrieved from Mount Geladaindong, on the central Tibetan Plateau. The bacterial abundance was lowest in 1938 and highest in 1997. Analyses of correlations between bacterial abundance and δ18O and Ca2+ concentrations indicate that bacterial abundance correlates positively with both temperature and amount of dust transported onto the glacier. These correlations imply that both higher temperatures and more frequent dust deposition influence bacterial abundance in the Geladaindong ice core. Bacterial genetic diversity also changes seasonally, and the diversity during the monsoon season appears much higher than during the nonmonsoon season. Bacterial sequences representing the monsoon season were related to bacteria originating from various environmental conditions while these, representing the nonmonsoon season, were typically related to microorganisms coming from cold environments and soils. [ABSTRACT FROM AUTHOR]

Aerobic anoxygenic phototrophic bacteria (AAPB) are an important bacterial group with capability of harvesting light energy, and appear to have a particular role in the ocean's carbon cycling. Yet the significance of AAPB relative to total bacteria (AAPB%) in different marine regimes are still controversial, and variation trend of genetic diversity of AAPB along environmental gradients remains unclear. Here we present the first comprehensive observation of the global distribution of AAPB in the Pacific, Atlantic and Indian oceans, revealing a general pattern of high abundance of AAPB and AAPB% in coastal waters than oceanic waters. The Indian Ocean contained relatively high AAPB% compared with the other two oceans, corresponding to the high primary production in this region. Both abundance of AAPB and AAPB% were positively correlated with the concentration of chlorophyll a, while the diversity of AAPB decreased with increasing chlorophyll a values. Our results suggest that AAPB abundance and diversity follow opposite trends from oligotrophic to eutrophic regimes in the ocean. [ABSTRACT FROM AUTHOR]

Through multiple alignment analysis of 16S rDNA sequences from all known genera of Cytophaga–Flavobacteria (CF) cluster, a new primer pair specifically targeting this cluster was developed, greatly facilitating their diversity and function's exploration in marine ecosystems. Compared with previously reported primers, the new primer pair could theoretically retrieve broader CF diversity without decreasing specificity. The effectiveness for field samples was further evaluated by testing the community DNA samples from various marine environments using the optimal polymerase chain reaction (PCR) conditions established in this work. The results showed its robustness and high specificity for amplifying CF cluster's 16S rDNA fragments from complex marine environments. [ABSTRACT FROM AUTHOR]