Summary Characterizing both growth and abundance is important in understanding the role of bacterial communities in biogeochemical cycling of global oceans. However, these two quantities are seldom measured together for specific bacterial clades. Our goal was to examine growth and abundance of three gammaproteobacterial subgroups, including SAR 86, at the single‐cell level by microautoradiography combined with fluorescence in...

Organic material is degraded anaerobically by a complex community of microbes making up the anaerobic food chain. This community was examined in methane‐rich sediments of the Beaufort Sea, Alaska, using metagenomic sequencing, along with tag pyrosequencing and quantitative polymerase chain reaction analyses of 16S ribosomal ribonucleic acid genes. The goal of the study was to examine the relative abundance and taxonomic compos...

Summary Bacterial communities in the surface layer of the oceans consist of a few abundant phylotypes and many rare ones, most with unknown ecological functions and unclear roles in biogeochemical processes. To test hypotheses about relationships between abundant and rare phylotypes, we examined bacterial communities in the western Arctic Ocean using pyrosequence data of the V6 region of the 16S rRNA gene. Samples were collect...

Summary Proteorhodopsin (PR)‐containing bacteria are hypothesized to use both light and organic compounds as energy sources. Recent studies have found that PR is common in marine microorganisms, but the impact of light on the growth of PR‐containing organisms and PR transcription in the environment remains unclear. We examined the diversity of PR genes and transcripts by PCR amplification and sequencing in Delaware coastal wat...

Summary Proteorhodopsin (PR) is a light‐driven proton pump that has been found in a variety of marine bacteria, including Pelagibacter ubique , a member of the ubiquitous SAR11 clade. The goals of this study were to explore the diversity of PR genes and to estimate their abundance in the North Atlantic Ocean using quantitative polymerase chain reaction (QPCR). We found that PR genes in the western portion of the Sargasso Sea c...

This study examined the abundance, cell size, and activity of Bacteria and Archaea in the Chukchi Sea and the Canada Basin of the western Arctic Ocean in the spring (May—June) and summer (July—August) of 2002 and 2004. Data from fluorescence in situ hybridization (FISH) analyses indicate that bacterial abundance as a percent of total prokaryotes decreased with depth, whereas in contrast, Crenarchaeota increased from about 10%o...

Summary To determine whether metagenomic libraries sample adequately the dominant bacteria in aquatic environments, we examined the phylogenetic make‐up of a large insert metagenomic library constructed with bacterial DNA from the Delaware River, a polymerase chain reaction (PCR) library of 16S rRNA genes, and community structure determined by fluorescence in situ hybridization (FISH). The composition of the libraries and comm...

The phylogenetic composition of bacterial communities varies along the salinity gradient of estuaries, one notable pattern being the prevalence of alpha‐ and beta‐proteobacteria in salt‐ and freshwater regions, respectively. We tested the hypothesis that bottom‐up forces (substrate supply) control these and other changes in bacterial community composition in the Delaware estuary. We measured the biomass and growth rate of four...

Assimilation of 3 HH‐thymidine and 3 HH‐leucine was examined at the single‐cell level using a combination of microautoradiography and fluorescent in situ hybridization (Micro‐FISH) to determine the contribution of various bacterial groups to bacterial production in aquatic systems. All of the major phylogenetic groups of bacteria examined along the salinity gradient of the Delaware estuary, including alpha‐, beta‐, and gamma‐p...

The importance of iron versus dissolved organic carbon (DOC) in limiting the growth of heterotrophic bacteria is unresolved, even though iron, DOC, and heterotrophic bacteria are recognized to be critical components of oceanic biogeochemical cycles and food web dynamics. We used enrichment experiments to examine the roles of organic carbon and iron in limiting bacterial growth in the California upwelling regime, where phytopla...