Impacts of bioturbation on temporal variation in bacterial and archaeal nitrogen-cycling gene abundance in coastal sediments

In marine environments, macrofauna living in or on the sediment surface may alter the structure, diversity and function of benthic microbial communities. In particular, microbial nitrogen (N)-cycling processes may be enhanced by the activity of large bioturbating organisms. Here, we study the effect of the burrowing mud shrimp Upogebia deltaura upon temporal variation in the abundance of genes representing key N-cycling functional guilds. The abundance of bacterial genes representing different N-cycling guilds displayed different temporal patterns in burrow sediments in comparison with surface sediments, suggesting that the burrow provides a unique environment where bacterial gene abundances are influenced directly by macrofaunal activity. In contrast, the abundances of archaeal ammonia oxidizers varied temporally but were not affected by bioturbation, indicating differential responses between bacterial and archaeal ammonia oxidizers to environmental physicochemical controls. This study highlights the importance of bioturbation as a control over the temporal variation in nitrogen-cycling microbial community dynamics within coastal sediments.

The influence of ocean acidification on nitrogen regeneration and nitrous oxide production in the northwest European shelf sea

The assimilation and regeneration of dissolved inorganic nitrogen, and the concentration of N₂O, was investigated at stations located in the NW European shelf sea during June/July 2011. These observational measurements within the photic zone demonstrated the simultaneous regeneration and assimilation of NH₄⁺, NO₂⁻ and NO₃⁻. NH₄⁺ was assimilated at 1.82–49.12 nmol N L⁻¹ h⁻¹ and regenerated at 3.46–14.60 nmol N L⁻¹ h⁻¹; NO₂^- was assimilated at 0–2.08 nmol N L⁻¹ h⁻¹ and regenerated at 0.01–1.85 nmol N L⁻¹ h⁻¹; NO₃⁻ was assimilated at 0.67–18.75 nmol N L⁻¹ h⁻¹ and regenerated at 0.05–28.97 nmol N L⁻¹ h⁻¹. Observations implied that these processes were closely coupled at the regional scale and that nitrogen recycling played an important role in sustaining phytoplankton growth during the summer. The [N₂O], measured in water column profiles, was 10.13 ± 1.11 nmol L⁻¹ and did not strongly diverge from atmospheric equilibrium indicating that sampled marine regions were neither a strong source nor sink of N₂O to the atmosphere. Multivariate analysis of data describing water column biogeochemistry and its links to N-cycling activity failed to explain the observed variance in rates of N-regeneration and N-assimilation, possibly due to the limited number of process rate observations. In the surface waters of five further stations, ocean acidification (OA) bioassay experiments were conducted to investigate the response of NH₄⁺ oxidising and regenerating organisms to simulated OA conditions, including the implications for [N₂O]. Multivariate analysis was undertaken which considered the complete bioassay data set of measured variables describing changes in N-regeneration rate, [N₂O] and the biogeochemical composition of seawater. While anticipating biogeochemical differences between locations, we aimed to test the hypothesis that the underlying mechanism through which pelagic N-regeneration responded to simulated OA conditions was independent of location. Our objective was to develop a mechanistic understanding of how NH₄⁺ regeneration, NH₄⁺ oxidation and N₂O production responded to OA. Results indicated that N-regeneration process responses to OA treatments were location specific; no mechanistic understanding of how N-regeneration processes respond to OA in the surface ocean of the NW European shelf sea could be developed.

Ocean acidification impacts on nitrogen fixation in the coastal western Mediterranean Sea

The effects of ocean acidification on nitrogen (N2) fixation rates and on the community composition of N2-fixing microbes (diazotrophs) were examined in coastal waters of the North-Western Mediterranean Sea. Nine experimental mesocosm enclosures of ∼50 m3 each were deployed for 20 days during June-July 2012 in the Bay of Calvi, Corsica, France. Three control mesocosms were maintained under ambient conditions of carbonate chemistry. The remainder were manipulated with CO2 saturated seawater to attain target amendments of pCO2 of 550, 650, 750, 850, 1000 and 1250 μatm. Rates of N2 fixation were elevated up to 10 times relative to control rates (2.00 ± 1.21 nmol L-1d-1) when pCO2 concentrations were >1000 μatm and pHT (total scale) < 7.74. Diazotrophic phylotypes commonly found in oligotrophic marine waters, including the Mediterranean, were not present at the onset of the experiment and therefore, the diazotroph community composition was characterised by amplifying partial nifH genes from the mesocosms. The diazotroph community was comprised primarily of cluster III nifH sequences (which include possible anaerobes), and proteobacterial (α and γ) sequences, in addition to small numbers of filamentous (or pseudo-filamentous) cyanobacterial phylotypes. The implication from this study is that there is some potential for elevated N2 fixation rates in the coastal western Mediterranean before the end of this century as a result of increasing ocean acidification. Observations made of variability in the diazotroph community composition could not be correlated with changes in carbon chemistry, which highlights the complexity of the relationship between ocean acidification and these keystone organisms.

Metabolically active, non-nitrogen fixing,Trichodesmiumin UK coastal waters during winter

Trichodesmium, a colonial cyanobacterium typically associated with tropical waters, was observed between January and April 2014 in the western English Channel. Sequencing of the heterocyst differentiation (hetR) and 16S rRNA genes placed this community within the Clade IV Trichodesmium, an understudied clade previously found only in low numbers in warmer waters. Nitrogen fixation was not detected although measurable rates of nitrate uptake and carbon fixation were observed. Trichodesmium RuBisCO transcript abundance relative to gene abundance suggests the potential for viable and potentially active Trichodesmium carbon fixation. Observations of Trichodesmium when coupled with a numerical advection model indicate that Trichodesmium communities can remain viable for >3.5 months at temperatures lower than previously expected. The results suggest that Clade IV Trichodesmium occupies a different niche to other Trichodesmium species, and is a cold- or low-light-adapted variant.