Urea Uptake and Carbon Fixation by Marine Pelagic Bacteria and Archaea during the Arctic Summer and Winter Seasons

Abstract

c How Arctic climate change might translate into alterations of biogeochemical cycles of carbon (C) and nitrogen (N) with respect to inorganic and organic N utilization is not well understood. This study combined 15 N uptake rate measurements for ammonium, nitrate, and urea with 15 N-and 13 C-based DNA stable-isotope probing (SIP). The objective was to identify active bacterial and archeal plankton and their role in N and C uptake during the Arctic summer and winter seasons. We hypothesized that bacteria and archaea would successfully compete for nitrate and urea during the Arctic winter but not during the summer, when phytoplankton dominate the uptake of these nitrogen sources. Samples were collected at a coastal station near Barrow, AK, during August and January. During both seasons, ammonium uptake rates were greater than those for nitrate or urea, and nitrate uptake rates remained lower than those for ammonium or urea. SIP experiments indicated a strong seasonal shift of bacterial and archaeal N utilization from ammonium during the summer to urea during the winter but did not support a similar seasonal pattern of nitrate utilization. Analysis of 16S rRNA gene sequences obtained from each SIP fraction implicated marine group I Crenarchaeota (MGIC) as well as Betaproteobacteria, Firmicutes, SAR11, and SAR324 in N uptake from urea during the winter. Similarly, 13 C SIP data suggested dark carbon fixation for MGIC, as well as for several proteobacterial lineages and the Firmicutes. These data are consistent with urea-fueled nitrification by polar archaea and bacteria, which may be advantageous under dark conditions. T he Arctic is already experiencing the impacts of global climate change, which has the potential to disrupt the ecology of the Arctic Ocean, causing broad changes in the physical, chemical, and biological realms (1-5). How such changes might translate into alterations of ecosystem dynamics and of the overall balances and rates of biogeochemical cycles of carbon (C) and nitrogen (N) is not well understood (6, 7). Generally, short days and sea ice coverage during the Arctic winter limit light and primary production of phytoplankton, while summer is characterized by episodic phytoplankton blooms following sea ice melt (8). High levels of primary productivity during the summer are thought to be sustained through the buildup of NO 3 Ϫ in the water column during the dark winter period, as well as by inputs from ice melt and allochthonous riverine nutrient sources (9). Production could additionally be augmented by dissolved organic nitrogen (DON), which can represent between 18 and 85% of the total dissolved N pool in coastal and open ocean surface water (10, 11). The interplay between inorganic and organic N utilization, with respect to heterotrophic versus autotrophic activities, could be an important contributor to biological production but remains poorly resolved, especially in Arctic environments (12).Among DON compounds, urea has long been recognized as an important N source in tropical, subtropical,...

Intraclade Heterogeneity in Nitrogen Utilization by Marine Prokaryotes Revealed Using Stable Isotope Probing Coupled with Tag Sequencing (Tag-SIP)

“…An additional complication in interpretation of N SIP data is the range of DNA GC-content (Buckley et al, 2007b) found within a sample, making density shifts, particularly in individual species, difficult to differentiate. Offsetting many of these problems, Tag-SIP (16S rRNA gene amplicon or ‘tag’ sequencing, combined with SIP) increases the resolving power of traditional SIP by examining the densities of individual OTU’s DNA to more easily identify and compare shifts ( Figures 1 and 2 ), similar to a recent study (Connelly et al, 2014). …”

“…In the rare occasion where no definitive peak fitting the criteria was observed, the overall distribution of the bands was compared. Previous methods using similar criteria have shown this general approach to be valid (Buckley et al, 2007a,b; Wawrik et al, 2009; Nelson and Carlson, 2012; Wawrik et al, 2012; Connelly et al, 2014). However, a limit of detection needed to be tested before enrichment could be properly identified in our study.…”

“…Assuming a single doubling occurred during the 24 h incubation and nitrate was the sole N source for growth, the maximum incorporation of isotope by any OTU during this incubation would have been expected to be <20%, due to the semiconservative nature of DNA replication. The LNT OTUs likely have little to no detectable incorporation of isotope based on previous SIP studies [≥30 atom% enrichment, (Murrell and Whiteley, 2011; Connelly et al, 2014)], so differences between the position or density of an individual control and treated OTU can likely be attributed to methodological variations in DNA banding, i.e., the method’s ability to resolve the position or density of an individual DNA fragment or OTU. This information can then be used to help set the identification criteria for density shifts.…”

Changes in Marine Prokaryote Composition with Season and Depth Over an Arctic Polar Year

“…Additionally, we intended to compare the cold, deep and dark mesopelagic ocean with the cold, shallow and dark surface waters above, to gain more insight into the driving mechanisms resulting from such environmental conditions. High-throughput sequencing technologies have previously highlighted the extreme microbial seasonality of the polar regions (Kirchman et al, 2010;Christman et al, 2011;Connelly et al, 2014). In this study we implement the same technologies to sequence reverse-transcribed total RNA (with its significantly shorter life span than DNA) to provide a timely snapshot of the more metabolically-active fraction of the marine microbial community.…”

“…The marine snow (primarily dissolved and particulate organic matter) produced by the spring and summer phytoplankton blooms in the stratified epipelagic zone is transported down during winter into the mesopelagic zone by convective mixing and subduction after cooling of the sea surface (Arístegui et al, 2009;Grzymski et al, 2012). Chemolithoautotrophic processes (such as archaeal ammonia oxidation) then come into play during the dark winter months (Grzymski et al, 2012) and the resulting nitrate buildup fuels the subsequent phytoplankton spring bloom (Connelly et al, 2014). However, should suggested models of a freshening Arctic be correct (Comeau et al, 2011), surface Arctic basin waters in a warming world may become increasingly stratified, such that the vertical flux of nutrients between deeper waters and the epipelagic zone may be reduced; primary productivity would consequently be lessened and this annual biogeochemical cycle, so essential for Arctic Ocean productivity, would inevitably be disrupted (Tremblay et al, 2008).…”