Phylogenetic Diversity and Ecological Pattern of Ammonia-oxidizing Archaea in the Surface Sediments of the Western Pacific

The phylogenetic diversity of ammonia-oxidizing archaea (AOA) was surveyed in the surface sediments from the northern part of the South China Sea (SCS). The distribution pattern of AOA in the western Pacific was discussed through comparing the SCS with other areas in the western Pacific including Changjiang Estuary and the adjacent East China Sea where high input of anthropogenic nitrogen was evident, the tropical West Pacific Continental Margins close to the Philippines, the deep-sea methane seep sediments in the Okhotsk Sea, the cold deep sea of Northeastern Japan Sea, and the hydrothermal field in the Southern Okinawa Trough. These various environments provide a wide spectrum of physical and chemical conditions for a better understanding of the distribution pattern and diversities of AOA in the western Pacific. Under these different conditions, the distinct community composition between shallow and deep-sea sediments was clearly delineated based on the UniFrac PCoA and Jackknife Environmental Cluster analyses. Phylogenetic analyses showed that a few ammonia-oxidizing archaeal subclades in the marine water column/sediment clade and endemic lineages were indicative phylotypes for some environments. Higher phylogenetic diversity was observed in the Philippines while lower diversity in the hydrothermal vent habitat. Water depth and possibly with other environmental factors could be the main driving forces to shape the phylogenetic diversity of AOA observed, not only in the SCS but also in the whole western Pacific. The multivariate regression tree analysis also supported this observation consistently. Moreover, the functions of current and other climate factors were also discussed in comparison of phylogenetic diversity. The information collectively provides important insights into the ecophysiological requirements of uncultured ammonia-oxidizing archaeal lineages in the western Pacific Ocean

Importance and controls of anaerobic ammonium oxidation influenced by riverbed geology

Rivers are an important global sink for excess bioavailable nitrogen: they convert approximately 40% of terrestrial N runoff per year (∼47 Tg) to biologically unavailable N 2 gas and return it to the atmosphere. At present, riverine N 2 production is conceptualized and modelled as denitrification. Anaerobic ammonium oxidation, known as anammox, is an alternative pathway of N 2 production important in marine environments, but its contribution to riverine N 2 production is not well understood. Here we use in situ and laboratory measurements of anammox activity using 15 N tracers and molecular analyses of microbial communities to evaluate anammox in clay-, sand-and chalk-dominated river beds in the Hampshire Avon catchment, UK during summer 2013. Abundance of the hzo gene, which encodes an enzyme central to anammox metabolism, varied across the contrasting geologies. Anammox rates were similar across geologies but contributed different proportions of N 2 production because of variation in denitrification rates. In spite of requiring anoxic conditions, anammox, most likely coupled to partial nitrification, contributed up to 58% of in situ N 2 production in oxic, permeable riverbeds. In contrast, denitrification dominated in low-permeability clay-bed rivers, where anammox contributes roughly 7% to the production of N 2 gas. We conclude that anammox can represent an important nitrogen loss pathway in permeable river sediments

Thaumarchaeotes abundant in refinery nitrifying sludges express amoA but are not obligate autotrophic ammonia oxidizers

Nitrification is a core process in the global nitrogen cycle that is essential for the functioning of many ecosystems. The discovery of autotrophic ammonia-oxidizing archaea (AOA) within the phylum Thaumarchaeota has changed our perception of the microbiology of nitrification, in particular since their numerical dominance over ammonia-oxidizing bacteria (AOB) in many environments has been revealed. These and other data have led to a widely held assumption that all amoA-encoding members of the Thaumarchaeota (AEA) are autotrophic nitrifiers. In this study, 52 municipal and industrial wastewater treatment plants were screened for the presence of AEA and AOB. Thaumarchaeota carrying amoA were detected in high abundance only in four industrial plants. In one plant, thaumarchaeotes closely related to soil group I.1b outnumbered AOB up to 10,000-fold, and their numbers, which can only be explained by active growth in this continuous culture system, were two to three orders of magnitude higher than could be sustained by autotrophic ammonia oxidation. Consistently, 14CO2 fixation could only be detected in AOB but not in AEA in actively nitrifying sludge from this plant via FISH combined with microautoradiography. Furthermore, in situ transcription of archaeal amoA, and very weak in situ labeling of crenarchaeol after addition of 13CO2, was independent of the addition of ammonium. These data demonstrate that some amoA-carrying group I.1b Thaumarchaeota are not obligate chemolithoautotrophs

Molecular and geochemical constraints on anaerobic ammonium oxidation (anammox) in a riparian zone of the Seine Estuary (France)

To expand the limited knowledge about the ecological significance of anaerobic ammonium oxidation (anammox) in continental aquatic and terrestrial ecosystems, we studied community structure, abundance, and activity of anammox bacteria in soils and sediments in the wetland of Trou Deshayes, a riparian zone in the Seine Estuary, France. Combining (i) molecular analyses of the genes coding for anammox bacterial 16S rRNA and the enzyme hydrazine oxidoreductase (hzo), (ii) quantification of unique anammox bacterial membrane lipids (i.e. ladderanes), and, (iii) 15N-isotope label incubation experiments with intertidal sediments and irregularly flooded soils nearby, we demonstrated that anammox bacteria were ubiquitous in the studied wetland ecosystem. In both soils and sediments, detected anammox bacteria were related to Candidatus ‘Brocadia’. 16S rRNA genes were generally lower in the more oxygenated soils, but on the same order of magnitude (107–108 copies g−1 d.w.) as found for other river estuaries, riparian zones and agricultural soils. While the C20-ladderane fatty acid with five cyclobutane moieties (C20-[5]-FA) was found in both sediments and soils, other ladderane species were detected only in the wetland sediments.The observed differential ladderane distribution suggests intra-genus differences in the community composition of anammox bacteria between the sediments and the floodplain soils. While the abundance of anammox bacteria was significantly lower in the soils versus the sediments, the potential anammox rates were similar (≤15 and ≤22 nmol N2 d−1 g−1 w.w. sediment and soil, respectively), suggesting lower cell-specific anammox rates in the sediments. The observed potential rates of anammox were rather low, leaving canonical denitrification as the main fixed N removal pathway in this riparian zone. The relative contribution of anammox to the total N2 production (between 3 and 8 %) was similar at all sites, highlighting the dependence of the anammox process on nitrite supply from denitrification across environmental boundaries. Due to this coupling, the dependence of organotrophic denitrification on the quality and stoichiometry of OM also seems to affect the anammox bacterial community. Our results suggest that N removal and mitigation of N supply from agriculture in wetlands by anammox is limited, and much less important than denitrification