Examining the Nitrogen Cycle Components in Hadopelagic Sediments

Though our understanding of the global ocean nitrogen cycle has greatly increased in the last few years, our knowledge of the composition and distribution of dissimilatory nitrogen metabolisms and microbial populations in deep sea sediments remain highly uncertain.

This study moves away from the better investigated areas and looks to expand knowledge of oceanic benthic nitrogen cycling to better understand microbial components and functions associated with the nitrogen cycle in deep-sea sedimentary habitats. The authors analyse a sediment core from the Ogasawara trench at a depth of 9760m near Japan.

Investigating the geochemical characteristics of the sediment indicated sulphate reduction was not significant in the sediments, and low sulphate/sulphide production may not affect microbial metabolisms such as nitrification, denitrification and anaerobic ammonia oxidation (anammox).

Nitrate levels indicated that production likely occurs at shallower zones. Nitrous oxide was less than detection limit throughout, while ammonium concentration increased significantly with depth. Dissolved hydrogen also dramatically increased with depth, indicating microbial fermentation.

Total organic carbon concentration (TOC) was greater than typical ocean sediments, and TOC and total organic nitrogen concentrations gradually decreased with depth.

Pore-water chemical components and isotopic signatures of pore nitrate suggest that aerobic microbial nitrification and nitrate reduction (or denitrification), are the key functions to control pore-water nitrate mass balance and dynamic nitrogen cycle in sediment above 15 centimetres below the sea floor (cmbsf).

Nitrate reduction is thought to influence the low concentrations of nitrate in measured sediments below 25 cmbsf. Following gene profiling this is thought to represent high turnover, as a function of various dissimilatory nitrogen metabolisms.

For gene profiling archaeal and bacterial SSU rRNA gene sequences were analysed from five depth sections. The most predominant archael phylogroup through all the depths was the MGI thaumarchaeotes, bacterial groups were dominated by Bacteroidetes and the JS1 phylotypes abelow 35 cmbsf.

amoA genes were amplified to identify chemolithotrophic ammonium-oxidizing bacteria and archaea. The maximum abundance of the archaeal amoA gene was observed at a depth of 5 cmbsf with decrease at 15cmbsf. While betaproteobacterial amoA gene copy number slightly increased at 15cmbsf. Through out archaeal amoA was 2.9–14.4-fold greater than betaproteobacterial amoA.

nxrA  were amplified to find nitrite-oxidizing bacteria (NOB). This found Nitrospina abundance at 5cmnsf and novel associated phlotype SFNLG (seafloor Nitrospina-like group) at 15cmbsf implying the significance of nitrite oxidation at shallow depths. Nitrobacter and Nitrococcus were not found due to the low coverage of the primer sets used. Kinetic-dependent niche separation was postulated but is not likely.

hao/hzo genes were used as a biomarker for anammox bacteria as hzsA can be present up to 8 times in some bacteria. Phylogenics suggest hao/hzo’s derived from novel anammox bacteria. hao/hzo and hzsA were found at 5 and 15cmbsf, and both dramatically declined at 25cmbsf. Scalindua and Kuenenia lineages were detected, the latter formerly only being found in marine sponges. The latter also expands the diversity but are untrustworthy due tot technical issues.

Novel primer sequences were used to detect dissimilatory nitrite reductases of ammonia oxidising bacteria Nitrosomonas, and Nitrosococcus, and ammonia oxidising archae with nirS and nirK. nirK was detected at 5cmbsf and diminished with depth. nirS was not detected though perhaps present due to its known diverse sequencing.

Abundance profiles show significant correlations with NOB and archael amoA suggesting metabolic coupling of thaumarchaeal and two bacterial populations as observed in other studies.

Significant correlations of archaeal amoA and the two nirK gene phylogroups, Nitrospina-like SSU rRNA genes and the two nirK gene phylogroups, and Nitrospira-like SSU rRNA genes and the two hylogroups of nirK genes were observed suggesting aerobic nitrification (archeal nitrate and bacterial ammonia oxidation) and denitrification. amoA genes weakly correlated with anammox hzsA/hao/hzo only, this is the first recorded occurance of this. However abundance profiles though significant are likely overestimated by dead extracellular DNA ,

Nitrification and nitrate reduction (or denitrification) most likely influence the dynamic nitrogen cycle to 15cmbsf, below this nitrate is depleted by reduction. Microbes in hadopelagic sediments are involved in multidirectional dissimilatory nitrogen metabolisms showing importance to the cycle here. Anammox significance was not shown in this study. Further studies of the metabolic components and links along with more accurate repeats of this study with better thought out primer usage are needed to gain insight into this research area.

- Nunoura, T., Nishizawa, M., Kikuchi, T., Tsubouchi, T., Hirai, M., Koide, O., ... & Takai, K. (2013). Molecular biological and isotopic biogeochemical prognoses of the nitrification‐driven dynamic microbial nitrogen cycle in hadopelagic sediments. Environmental microbiology.