We describe the microbiota of two hypersaline saltern ponds, one of intermediate salinity (19%) and a NaCl saturated crystallizer pond (37%) using pyrosequencing. The analyses of these metagenomes (nearly 784 Mb) reaffirmed the vast dominance of Haloquadratum walsbyi but also revealed novel, abundant and previously unsuspected microbial groups. We describe for the first time, a group of low GC Actinobacteria, related to freshwater Actinobacteria, abundant in low and intermediate salinities. Metagenomic assembly revealed three new abundant microbes: a low-GC euryarchaeon with the lowest GC content described for any euryarchaeon, a high-GC euryarchaeon and a gammaproteobacterium related to Alkalilimnicola and Nitrococcus. Multiple displacement amplification and sequencing of the genome from a single archaeal cell of the new low GC euryarchaeon suggest a photoheterotrophic and polysaccharide-degrading lifestyle and its relatedness to the recently described lineage of Nanohaloarchaea. These discoveries reveal the combined power of an unbiased metagenomic and single cell genomic approach.

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We examined seasonal and spatial variation in bacterioplankton composition in the Sacramento-San Joaquin River Delta (CA) using terminal restriction fragment length polymorphism (T-RFLP) analysis. Cloned 16S rRNA genes from this system were used for putative identification of taxa dominating the T-RFLP profiles. Both cloning and T-RFLP analysis indicated that Actinobacteria, Verrucomicrobia, Cytophaga-Flavobacterium and Proteobacteria were the most abundant bacterioplankton groups in the Delta. Despite the broad variety of sampled habitats (deep water channels, lakes, marshes, agricultural drains, freshwater and brackish areas), and the spatial and temporal differences in hydrology, temperature and water chemistry among the sampling campaigns, T-RFLP electropherograms from all samples were similar, indicating that the same bacterioplankton phylotypes dominated in the various habitats of the Delta throughout the year. However, principal component analysis (PCA) and partial least-squares regression (PLS) of T-RFLP profiles revealed consistent grouping of samples on a seasonal, but not a spatial, basis. β-Proteobacteria related to Ralstonia, Actinobacteria related to Microthrix, and β-Proteobacteria identical to the environmental Clone LD12 had the highest relative abundance in summer/fall T-RFLP profiles and were associated with low river flow, high pH, and a number of optical and chemical characteristics of dissolved organic carbon (DOC) indicative of an increased proportion of phytoplankton-produced organic material as opposed to allochthonous, terrestrially derived organic material. On the other hand, Geobacter-related β-Proteobacteria showed a relative increase in abundance in T-RFLP analysis during winter/spring, and probably were washed out from watershed soils or sediment. Various phylotypes associated with the same phylogenetic division, based on tentative identification of T-RFLP fragments, exhibited diverse seasonal patterns, suggesting that ecological roles of Delta bacterioplankton were partitioned at the genus or species level. KEY WORDS: Bacterioplankton biogeography · 16S rRNA · T-RFLP · Clone libraries · Dissolved organic matter Resale or republication not permitted without written consent of the publisherAquat Microb Ecol 31: [85][86][87][88][89][90][91][92][93][94][95][96][97][98] 2003 bacterioplankton. The effects of individual factors are often difficult to differentiate, however, due to the complexity of ecological interactions and due to the limitations of existing methodology.Several 16S rRNA fingerprinting techniques based on PCR have been developed for rapid comparison of natural microbial assemblages, including terminal restriction fragment length polymorphism (T-RFLP) analysis (Avaniss-Aghajani et al. 1996). Since PCR amplification of 16S rRNA genes gives highly reproducible ratios between amplicons when performed under identical conditions, and due to the analytic precision of T-RFLP analysis (Polz & Cavanaugh 1998, González et al. 2000, multivariate statistical analysis of...

Riverine inputs of nitrogen is an important factor that controls productivity of coastal marine waters. Dissolved organic nitrogen (DON) comprises most of the N in boreal rivers. During spring floods, DON flux may exceed the baseflow flux by several orders of magnitude. However, little is known about the biological availability of spring flood DON and, thus, its potential effect on coastal productivity.We have investigated the dynamics of DON bioavailability and chemical composition during a spring flood in two streams in northern Sweden. Potential bioavailability was determined by employing bacterial regrowth bioassays with brackish medium and a coastal bacterial inoculum. In addition, concentrations of urea and amino acids and the proportion of D-isomers in total dissolved amino acids were analyzed because a high proportion of D-isomers is suggested to indicate old and refractory organic material.During the flood, potential DON bioavailability increased from 19-28% at baseflow to 55-45% during peak flow in the two streams, while DON concentration remained relatively constant. At the end of the flood, bioavailability returned to the baseflow values. Potential DON bioavailability was positively correlated with the concentration of dissolved combined amino acids and the proportion of L-enantiomers of amino acids. However, only 5-18% of DON was identified as urea and free and combined amino acids, suggesting that bacteria also utilized other DON compounds. Our results imply that a major portion of the annual export of labile nitrogen occurred during a few weeks of spring flood.

Access to bioavailable nitrogen often limits primary production in marine and freshwater ecosystems. Around 70% of nitrogen transported by rivers worldwide consists of dissolved organic nitrogen (DON), but its bioavailability has been poorly investigated. To assess the potential bacterial growth on DON, we developed a bioassay employing natural DON and bacterial inocula in medium manipulated to make N the limiting nutrient. We analyzed the bacterial utilization of the high-molecular-weight fraction of DON isolated by ultrafiltration from three wetlands in South Sweden throughout the year. The bioavailability of low-molecular-weight and bulk DON was also analyzed in one of the wetlands, where inorganic nitrogen concentration was sufficiently low and did not interfere with bioassays. The bioavailability of bulk DON in the latter wetland varied from 2% to 16%, suggesting that DON is an important nitrogen source for the biota of coastal waters. DON may be the dominant input of bioavailable nitrogen during summer, when nitrate concentrations in rivers decrease and DON bioavailability increases. Marine bacterioplankton assimilated a substantially larger fraction of DON than did freshwater bacterioplankton, on average by a factor of 2.4. This finding indicates that the susceptibility of DON to bacterial mineralization increases as it is transported from freshwaters into saline environments.