title: The ecological roles of bacterial populations in the surface sediments of coastal lagoon environments in Japan as revealed by quantification and qualification of 16S rDNA.
abstract: Based on quantification and qualification of bacterial 16S rDNA, we verified the bacterial ecological characteristics of surface sediments of Lakes Shinji and Nakaumi, which are representative of coastal lagoons in Japan. Quantification and qualification of the 16S rDNA sequences was carried out using real time polymerase chain reaction and polymerase chain reaction denaturing gradient gel electrophoresis and non-metric multidimensional scaling, respectively. The results revealed that the copy number per gram of sediment ranged from 8.33 × 10(8) (Lake Nakaumi) to 1.69 × 10(11) (Honjo area), suggesting that bacterial carbon contributed only 0.05-9.64 % of the total carbon content in the samples. Compared with other aquatic environments, these results indicate that sedimentary bacteria are not likely to be important transporters of nutrients to higher trophic levels, or to act as carbon sinks in the lagoons. The bacterial compositions of Lake Shinji and Lake Nakaumi and the Honjo area were primarily influenced by sediment grain sizes and salinity, respectively. Statistical comparisons of the environmental properties suggested that the areas that were oxygen-abundant (Lake Shinji) and at a higher temperature (Honjo area) presented efficient organic matter degradation. The 16S rDNA copy number per gram of carbon and nitrogen showed the same tendency. Consequently, the primary roles of bacteria were degradation and preservation of organic materials, and this was affected by oxygen and temperature. These roles were supported by the bacterial diversity rather than the differences in the community compositions of the sedimentary bacteria in these coastal lagoons.
authors.affiliation: Graduate School of Environment and Information Sciences, Yokohama National University, Yokohama 240-8501, Japan. tsuboi.shun@nies.go.jp
authors.forename: Shun
authors.initials: S
authors.lastname: Tsuboi
authors.forename: Takashi
authors.initials: T
authors.lastname: Amemiya
authors.forename: Koji
authors.initials: K
authors.lastname: Seto
authors.forename: Kiminori
authors.initials: K
authors.lastname: Itoh
authors.forename: Narasimmalu
authors.initials: N
authors.lastname: Rajendran
mesh_terms: D001419:Bacteria / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification* / Q000378:metabolism; D002244:Carbon / Q000032:analysis / Q000378:metabolism; D004269:DNA, Bacterial / Q000235:genetics*; D004275:DNA, Ribosomal / Q000235:genetics; D017753:Ecosystem; D004784:Environmental Monitoring; D019015:Geologic Sediments / Q000032:analysis / Q000382:microbiology*; D007564:Japan; D060106:Lakes / Q000737:chemistry / Q000382:microbiology; D008969:Molecular Sequence Data; D009584:Nitrogen / Q000032:analysis / Q000378:metabolism; D012336:RNA, Ribosomal, 16S / Q000235:genetics*
chemical_list: D004269:DNA, Bacterial; D004275:DNA, Ribosomal; D012336:RNA, Ribosomal, 16S; D002244:Carbon; D009584:Nitrogen