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Very little is known about growth rates of individual bacterial taxa and how they respond to environmental flux. Here, we characterized bacterial community diversity, structure and the relative abundance of 16S rRNA and 16S rRNA genes (rDNA) using pyrosequencing along the salinity gradient in the Delaware Bay. Indices of diversity, evenness, structure and growth rates of the surface bacterial community significantly varied along the transect, reflecting active mixing between the freshwater and marine ends of the estuary. There was no positive correlation between relative abundances of 16S rRNA and rDNA for the entire bacterial community, suggesting that abundance of bacteria does not necessarily reflect potential growth rate or activity. However, for almost half of the individual taxa, 16S rRNA positively correlated with rDNA, suggesting that activity did follow abundance in these cases. The positive relationship between 16S rRNA and rDNA was less in the whole water community than for free-living taxa, indicating that the two communities differed in activity. The 16S rRNA:rDNA ratios of some typically marine taxa reflected differences in light, nutrient concentrations and other environmental factors along the estuarine gradient. The ratios of individual freshwater taxa declined as salinity increased, whereas the 16S rRNA:rDNA ratios of only some typical marine bacteria increased as salinity increased. These data suggest that physical and other bottom-up factors differentially affect growth rates, but not necessarily abundance of individual taxa in this highly variable environment.

The surface layer of the oceans and other aquatic environments contains many bacteria that range in activity, from dormant cells to those with high rates of metabolism. However, little experimental evidence exists about the activity of specific bacterial taxa, especially rare ones. Here we explore the relationship between abundance and activity by documenting changes in abundance over time and by examining the ratio of 16S rRNA to rRNA genes (rDNA) of individual bacterial taxa. The V1–V2 region of 16S rRNA and rDNA was analyzed by tag pyrosequencing in a 3-y study of surface waters off the Delaware coast. Over half of the bacterial taxa actively cycled between abundant and rare, whereas about 12% always remained rare and potentially inactive. There was a significant correlation between the relative abundance of 16S rRNA and the relative abundance of 16S rDNA for most individual taxa. However, 16S rRNA:rDNA ratios were significantly higher in about 20% of the taxa when they were rare than when abundant. Relationships between 16S rRNA and rDNA frequencies were confirmed for five taxa by quantitative PCR. Our findings suggest that though abundance follows activity in the majority of the taxa, a significant portion of the rare community is active, with growth rates that decrease as abundance increases.

Understanding the role of microbes in the oceans has focused on taxa that occur in high abundance; yet most of the marine microbial diversity is largely determined by a long tail of low-abundance taxa. This rare biosphere may have a cosmopolitan distribution because of high dispersal and low loss rates, and possibly represents a source of phylotypes that become abundant when environmental conditions change. However, the true ecological role of rare marine microorganisms is still not known. Here, we use pyrosequencing to describe the structure and composition of the rare biosphere and to test whether it represents cosmopolitan taxa or whether, similar to abundant phylotypes, the rare community has a biogeography. Our examination of 740,353 16S rRNA gene sequences from 32 bacterial and archaeal communities from various locations of the Arctic Ocean showed that rare phylotypes did not have a cosmopolitan distribution but, rather, followed patterns similar to those of the most abundant members of the community and of the entire community. The abundance distributions of rare and abundant phylotypes were different, following a log-series and log-normal model, respectively, and the taxonomic composition of the rare biosphere was similar to the composition of the abundant phylotypes. We conclude that the rare biosphere has a biogeography and that its tremendous diversity is most likely subjected to ecological processes such as selection, speciation, and extinction.

Recalcitrant dissolved organic matter is now known to be a key element in the global carbon cycle. Here, Nianzhi Jiao and colleagues set out the role of ocean-dwelling microorganisms in the generation of this pool of long-lived carbon, using a new concept they call the microbial carbon pump. The biological pump is a process whereby CO 2 in the upper ocean is fixed by primary producers and transported to the deep ocean as sinking biogenic particles or as dissolved organic matter. The fate of most of this exported material is remineralization to CO 2 , which accumulates in deep waters until it is eventually ventilated again at the sea surface. However, a proportion of the fixed carbon is not mineralized but is instead stored for millennia as recalcitrant dissolved organic matter. The processes and mechanisms involved in the generation of this large carbon reservoir are poorly understood. Here, we propose the microbial carbon pump as a conceptual framework to address this important, multifaceted biogeochemical problem.

Key Points Heterotrophic bacteria and other heterotrophic microorganisms typically process about half of the primary production in the oceans and therefore are important in determining the response of oceanic ecosystems and the carbon cycle to climate change. Previous studies suggested that heterotrophic bacteria are less active and are less important in the carbon cycle in polar waters because of low temperatures. A synthesis of old and new data confirms that the amount of primary production used by heterotrophic bacteria is in fact lower in the Arctic Ocean and in the Ross Sea, Antarctica, than in several lower-latitude oceans. The low rates are not due, however, to low temperatures, but rather to low supply of labile dissolved organic material. Only about 20% of the variation in bacterial growth rates in polar waters can be explained by temperature alone. These results have several implications for understanding how the Arctic Ocean and Antarctic seas may respond to climate changes already affecting these ecosystems. The decline in sea ice cover, for example, is likely to have large effects on ocean mixing and thus the supply of labile organic matter and nutrients supporting bacteria and other microorganisms at the base of polar food chains. In this Analysis, Kirchman and colleagues compare microbial processes in the western Arctic Ocean and other polar waters with low-latitude oceans to attempt to understand the role of heterotrophic bacteria in oceanic biogeochemical cycles. This may further our understanding of the changes that could occur as these waters warm. Heterotrophic bacteria are the most abundant organisms on the planet and dominate oceanic biogeochemical cycles, including that of carbon. Their role in polar waters has been enigmatic, however, because of conflicting reports about how temperature and the supply of organic carbon control bacterial growth. In this Analysis article, we attempt to resolve this controversy by reviewing previous reports in light of new data on microbial processes in the western Arctic Ocean and by comparing polar waters with low-latitude oceans. Understanding the regulation of in situ microbial activity may help us understand the response of the Arctic Ocean and Antarctic coastal waters over the coming decades as they warm and ice coverage declines.

Carbonate geochemistry research in large estuarine systems is limited. More work is needed to understand how changes in land-use activity influence watershed export of organic and inorganic carbon, acids, and nutrients to the coastal ocean. To investigate the seasonal variation of the inorganic carbon system in the Delaware Estuary, one of the largest estuaries along the US east coast, dissolved inorganic carbon (DIC), total alkalinity (TA), and pH were measured along the estuary from June 2013 to April 2015. In addition, DIC, TA, and pH were periodically measured from March to October 2015 in the nontidal freshwater Delaware, Schuylkill, and Christina rivers over a range of discharge conditions. There were strong negative relationships between river TA and discharge, suggesting that changes in HCO3− concentrations reflect dilution of weathering products in the drainage basin. The ratio of DIC to TA, an understudied but important property, was high (1.11) during high discharge and low (0.94) during low discharge, reflecting additional DIC input in the form of carbon dioxide (CO2), most likely from terrestrial organic matter decomposition, rather than bicarbonate (HCO3−) inputs due to drainage basin weathering processes. This is also a result of CO2 loss to the atmosphere due to rapid water transit during the wet season. Our data further show that elevated DIC in the Schuylkill River is substantially different than that in the Delaware River. Thus, tributary contributions must be considered when attributing estuarine DIC sources to the internal carbon cycle versus external processes such as drainage basin mineralogy, weathering intensity, and discharge patterns. Long-term records in the Delaware and Schuylkill rivers indicate shifts toward higher alkalinity in estuarine waters over time, as has been found in other estuaries worldwide. Annual DIC input flux to the estuary and export flux to the coastal ocean are estimated to be 15.7 ± 8.2  ×  109 mol C yr−1 and 16.5 ± 10.6  ×  109 mol C yr−1, respectively, while net DIC production within the estuary including inputs from intertidal marshes is estimated to be 5.1  ×  109 mol C yr−1. The small difference between riverine input and export flux suggests that, in the case of the Delaware Estuary and perhaps other large coastal systems with long freshwater residence times, the majority of the DIC produced in the estuary by biological processes is exchanged with the atmosphere rather than exported to the sea.

There is now evidence that aerobic anoxygenic phototrophic (AAP) bacteria are widespread across aquatic systems, yet the factors that determine their abundance and activity are still not well understood, particularly in freshwaters. Here we describe the patterns in AAP abundance, cell size and pigment content across wide environmental gradients in 43 temperate and boreal lakes of Québec. AAP bacterial abundance varied from 1.51 to 5.49 x 105 cells mL-1, representing <1 to 37% of total bacterial abundance. AAP bacteria were present year-round, including the ice-cover period, but their abundance relative to total bacterial abundance was significantly lower in winter than in summer (2.6% and 7.7%, respectively). AAP bacterial cells were on average two-fold larger than the average bacterial cell size, thus AAP cells made a greater relative contribution to biomass than to abundance. Bacteriochlorophyll a (BChla) concentration varied widely across lakes, and was not related to AAP bacterial abundance, suggesting a large intrinsic variability in the cellular pigment content. Absolute and relative AAP bacterial abundance increased with dissolved organic carbon (DOC), whereas cell-specific BChla content was negatively related to chlorophyll a (Chla). As a result, both the contribution of AAP bacteria to total prokaryotic abundance, and the cell-specific BChla pigment content were positively correlated with the DOC:Chla ratio, both peaking in highly colored, low-chlorophyll lakes. Our results suggest that photoheterotrophy might represent a significant ecological advantage in highly colored, low-chlorophyll lakes, where DOC pool is chemically and structurally more complex.

Assimilation of 3H-thymidine and 3H-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-proteobacteria and Cytophaga-like bacteria, assimilated 3H-thymidine and 3H-leucine. However, groups differed substantially in their contribution to the assimilation of these compounds. Alpha-proteobacteria were the dominant substrate-active bacteria at salinities of >9 PSU, whereas beta-proteobacteria were more important in freshwater. At all salinities, Cytophaga-like bacteria comprised the second most important group, and gamma-proteobacteria were overall the least important. Bacterial abundance explained about half of the variation in 3H-thymidine and 3H-leucine assimilation by the major bacterial groups. The sizes of silver grains of active bacteria indicate no difference in single-cell activity for the bacterial groups, suggesting that the average growth rates of the groups we examined were similar. However, activity per cell was distributed differently in the phylogenetic groups. Our study suggests that estimates of bacterial production measured using 3H-thymidine and 3H-leucine include bacteria in all of the major phylogenetic groups found in aquatic systems and that growth rates within bacterial groups vary substantially.