Database of nitrification and nitrifiers in the global ocean

As a key biogeochemical pathway in the marine nitrogen cycle, nitrification (ammonia oxidation and nitrite oxidation) converts the most reduced form of nitrogen – ammonium–ammonia (NH4+–NH3) – into the oxidized species nitrite (NO2-) and nitrate (NO3-). In the ocean, these processes are mainly performed by ammonia-oxidizing archaea (AOA) and bacteria (AOB) and nitrite-oxidizing bacteria (NOB). By transforming nitrogen speciation and providing substrates for nitrogen removal, nitrification affects microbial community structure; marine productivity (including chemoautotrophic carbon fixation); and the production of a powerful greenhouse gas, nitrous oxide (N2O). Nitrification is hypothesized to be regulated by temperature, oxygen, light, substrate concentration, substrate flux, pH and other environmental factors. Although the number of field observations from various oceanic regions has increased considerably over the last few decades, a global synthesis is lacking, and understanding how environmental factors control nitrification remains elusive. Therefore, we have compiled a database of nitrification rates and nitrifier abundance in the global ocean from published literature and unpublished datasets. This database includes 2393 and 1006 measurements of ammonia oxidation and nitrite oxidation rates and 2242 and 631 quantifications of ammonia oxidizers and nitrite oxidizers, respectively. This community effort confirms and enhances our understanding of the spatial distribution of nitrification and nitrifiers and their corresponding drivers such as the important role of substrate concentration in controlling nitrification rates and nitrifier abundance. Some conundrums are also revealed, including the inconsistent observations of light limitation and high rates of nitrite oxidation reported from anoxic waters. This database can be used to constrain the distribution of marine nitrification, to evaluate and improve biogeochemical models of nitrification, and to quantify the impact of nitrification on ecosystem functions like marine productivity and N2O production. This database additionally sets a baseline for comparison with future observations and guides future exploration (e.g., measurements in the poorly sampled regions such as the Indian Ocean and method comparison and/or standardization). The database is publicly available at the Zenodo repository: https://doi.org/10.5281/zenodo.8355912 (Tang et al., 2023).</p

Basin-scale distribution of prokaryotic phylotypes in the epipelagic layer of the Central South Pacific Ocean during austral summer

In the present study, we used catalyzed reporter deposition-fluorescence in situ hybridization to quantify the abundance of five bacterial (Alphaproteobacteria, SAR11, Gammaproteobacteria, SAR86, and Bacteroidetes) and two archaeal (Crenarchaeota and Euryarchaeota) phylotypes in the epipelagic layer (0-200 m) of the Central South Pacific Ocean along 170A degrees W from 0A degrees to 40A degrees S. We found that the distribution patterns of these phylotypes differed from each other. All phylotypes except Gammaproteobacteria were particularly abundant at the surface water of the equatorial region, whereas Gammaproteobacteria was relatively abundant in the area from the southern part of the South Pacific Ocean. SAR11, affiliated with Alphaproteobacteria was the dominant phylotype at all depths, throughout the study area. The abundance of SAR11 significantly increased with chlorophyll a concentration, suggesting that phytoplankton could affect their distribution pattern. There was a positive correlation between Bacteroidetes abundance and water temperature, suggesting that the temperature gradient could be a critical factor determining their distribution in the South Pacific Ocean. Crenarchaeota and Euryarchaeota were more abundant at the equatorial region than in other study areas. Euryarchaeota abundance significantly decreased with depth, and increased with chlorophyll a concentration. This suggests that there was ecological interaction between Euryarchaeota and phytoplankton in the equatorial surface. Our data indicate that distinct hydrographic properties such as seawater temperature, salinity, and the concentrations of chlorophyll a and nutrients can principally control the basin-scale distribution of different prokaryotic phylotypes in the epipelagic layer of the Central South Pacific Ocean

Effects of iron and light on microbial nitrogen cycles in the primary nitrite maxima of the eastern Indian Ocean

To elucidate the effect of light and iron on the dynamics of nitrogen at the primary nitrite maximum (PNM), observed at the bottom of the euphotic zone of the eastern Indian Ocean, we conducted high-resolution sampling and incubation experiments at three stations. The stations were located at the Bay of Bengal, equatorial region, and South Indian subtropical gyre. The PNM was observed below the subsurface chlorophyll maximum and around the nitracline at all three stations; its magnitude was largest (> 1.5 μM) in the Bay of Bengal. The results of the iron enrichment experiments under two different light regimes demonstrated that the growth of phytoplankton communities at the PNM was limited by light availability at all three stations. In the subtropical gyre, co-imitation by iron and light was observed, whereas iron was the secondary limiting factor at the other two stations, suggesting widespread iron limitation on phytoplankton growth in the subsurface waters of the open ocean. However, the changes in the concentrations of ammonium, nitrite, and nitrate suggest that the effect of light and iron deficiency on the release of nitrite by phytoplankton is relatively minor. Instead, active ammonium oxidization by shallow-clade ammonium-oxidizing archaea was observed around the PNM, suggesting that nitrite supply via the tight coupling of ammonium regeneration sustained by high surface productivity and ammonium oxidization maintains the distinct PNM in the subsurface water of the eastern Indian Ocean

A DNA metabarcoding approach for recovering plankton communities from archived samples fixed in formalin.

Plankton samples have been routinely collected and preserved in formalin in many laboratories and museums for more than 100 years. Recently, attention has turned to use DNA information from formalin-fixed samples to examine changes in plankton diversity over time. However, no molecular ecological studies have evaluated the impact of formalin fixation on the genetic composition of the plankton community structure. Here, we developed a method for extracting DNA from archived formalin-preserved plankton samples to determine their community structure by a DNA metabarcoding approach. We found that a lysis solution consisting of borate-NaOH buffer (pH 11) with SDS and proteinase K effectively cleaved the cross-link formed by formalin fixation. DNA was extracted from samples preserved for decades in formalin, and the diatom community of the extracted DNA was in good agreement with the microscopy analysis. Furthermore, we stored a plankton sample for 1.5 years and demonstrated that 18S rRNA gene community structures did not change significantly from non-formalin-fixed, time-zero samples. These results indicate that our method can be used to describe the original community structure of plankton archived in formalin for years. Our approach will be useful for examining the long-term variation of plankton diversity by metabarcoding analysis of 18S rRNA gene community structure