Differential Distribution and Determinants of Ammonia Oxidizing Archaea Sublineages in the Oxygen Minimum Zone off Costa Rica

Active degradation-nitrification microbial assemblages in the hypoxic zone in a subtropical estuary

In 2017 summer, we observed widespread bottom hypoxia at the lower estuary of the Pearl River estuary (PRE). Our previous study noticed that AOA and bacteria were highly abundant and clustered within the hypoxia zone. Moreover, nitrification and respiration rates were also evidently higher in these hypoxic waters. These observations prompt us to investigate whether these two oxygen-consuming microorganisms have symbiotic relationships and whether specific groups consistently coexist and form ecological-meaningful associations. In this study, we use network analysis to investigate the presence and active communities (DNA-RNA) based on bacterial and AOA communities sequencing (inferred from the 16S rRNA and amoA gene, respectively) to gain more insight into ecological-meaningful associations. We observed a highly diverse and active bacterial community in the hypoxia zone. The RNA networks were more modulized than the corresponding DNA networks, indicating that the active communities were better parsed into functional microbial assemblages. The network topology revealed that Gammaproteobacteria, Bacteroidetes (Flavobacteriales), Alphaproteobacteria (Rhodobacterales and Rhodospirillales), Marinimicrobia, Cyanobacteria (Synechococcales), and AOA sublineages were module hubs and connectors, indicating that they were the keystone taxa of the microbial communities. The hub-subnetwork further showed robust co-occurrence between Gammaproteobacteria, Bacteroidetes (Flavobacteriales), Alphaproteobacteria (Rhodobacterales and Rhodospirillales), Marinimicrobia with AOA sublineages, and Nitrospinae (presumably NOB) reflecting the formation of Degradation-Nitrification (sequential oxidation of Organic matter degradation to ammonia, then nitrate) microbial assemblage in the hypoxia zone. The subnetworks revealed AOA ecotype-specific modularization and niche partitioning of different AOA sublineages. Interestingly, the recurring co-occurrence of nitrifiers assemblage in the RNA subnetworks (SCM1-like-II (AOA) and Nitrospinae OTUs (NOB) suggests an active interaction via nitrite exchange. The Degradation-Nitrification microbial assemblage may contribute substantially to the oxygen consumption in the hypoxia formation in PRE. Our results provide new insight into the functional microbial assemblages, which is worth further investigation on their ecological implication in estuarine waters.

Vertical segregation and phylogenetic characterization of archaea and archaeal ammonia monooxygenase gene in the water column of the western Arctic Ocean

Archaea constitute a substantial fraction of marine microbial biomass and play critical roles in the biogeochemistry of oceans. However, studies on their distribution and ecology in the Arctic Ocean are relatively scarce. Here, we studied the distributions of archaea and archaeal ammonia monooxygenase (amoA) gene in the western Arctic Ocean, using the amplicon sequencing approach from the sea surface to deep waters up to 3040 m depth. A total of five archaeal phyla, Nitrososphaerota, "Euryarchaeota", "Halobacteriota," "Nanoarchaeota", and Candidatus Thermoplasmatota, were detected. We observed a clear, depth-dependent vertical segregation among archaeal communities. Ca. Thermoplasmatota (66.8%) was the most dominant phylum in the surface waters. At the same time, Nitrososphaerota (55.9%) was dominant in the deep waters. Most of the amoA gene OTUs (99%) belonged to the Nitrosopumilales and were further clustered into five subclades ("NP-Alpha", "NP-Delta", "NP-Epsilon", "NP-Gamma", and "NP-Theta"). "NP-Epsilon" was the most dominant clade throughout the water column and "NP_Alpha" showed higher abundance only in the deeper water. Salinity and inorganic nutrient concentrations were the major factors that determined the vertical segregation of archaea. We anticipate that the observed differences in the vertical distribution of archaea might contribute to the compartmentalization of dark carbon fixation and nitrification in deeper water and organic matter degradation in surface waters of the Arctic Ocean.

Network analysis of 16S rRNA sequences suggests microbial keystone taxa contribute to marine N2O cycling

The mechanisms by which large-scale microbial community function emerges from complex ecological interactions between individual taxa and functional groups remain obscure. We leveraged network analyses of 16S rRNA amplicon sequences obtained over a seven-month timeseries in seasonally anoxic Saanich Inlet (Vancouver Island, Canada) to investigate relationships between microbial community structure and water column N₂O cycling. Taxa separately broadly into three discrete subnetworks with contrasting environmental distributions. Oxycline subnetworks were structured around keystone aerobic heterotrophs that correlated with nitrification rates and N₂O supersaturations, linking N₂O production and accumulation to taxa involved in organic matter remineralization. Keystone taxa implicated in anaerobic carbon, nitrogen, and sulfur cycling in anoxic environments clustered together in a low-oxygen subnetwork that correlated positively with nitrification N₂O yields and N₂O production from denitrification. Close coupling between N₂O producers and consumers in the anoxic basin is indicated by strong correlations between the low-oxygen subnetwork, PICRUSt2-predicted nitrous oxide reductase (nosZ) gene abundances, and N₂O undersaturation. This study implicates keystone taxa affiliated with common ODZ groups as a potential control on water column N₂O cycling and provides a theoretical basis for further investigations into marine microbial interaction networks.

Metatranscriptomes reveal the diverse responses of Thaumarchaeota ecotypes to environmental variations in the northern slope of the South China Sea

Thaumarchaeota are among the most abundant prokaryotes in the ocean, playing important roles in carbon and nitrogen cycling. Marine Thaumarchaeota ecotypes exhibit depth-related diversification and seasonal changes. However, transcriptomic activities concerning niche partitioning among thaumarchaeal ecotypes remain unclear. Here, we examined the variations in the distribution and transcriptomic activity of marine Thaumarchaeota ecotypes. Three primary ecotypes were identified: a Nitrosopumilus-like clade; a Nitrosopelagicus-like water column A (WCA) clade, thriving in epipelagic water; and a water column B (WCB) clade, dominant in deep water. Depth-related partitioning of the three ecotypes and the seasonal variability of the WCA and WCB ecotypes were observed. Nutrient concentrations, chlorophyll α and salinity were the primary environmental factors. The relative abundance of the WCA ecotype and its transcript abundance of amoA gene were positively correlated with chlorophyll α and salinity, while the WCB ecotype was positively correlated with nitrate and phosphate. Based on high-quality metagenome-assembled genomes, transcriptomic analysis revealed that the three ecotypes exhibited various co-occurring expression patterns of the elemental cycling genes in the nitrogen, carbon, phosphorus, and sulfur cycles. Our results provide transcriptomic evidence of the niche differentiation of marine Thaumarchaeota ecotypes, highlighting the diverse roles of ecotypes and WCA subclades in biogeochemical cycles.

Distribution and Oxidation Rates of Ammonia-Oxidizing Archaea Influenced by the Coastal Upwelling off Eastern Hainan Island

Coastal upwelling causes variations in temperature, salinity and inorganic nutrients in the water column, consequently leading to the shift of microbial populations and their metabolic activities. Impacts of the eastern Hainan upwelling (EHU) on the ammonia-oxidizing archaea (AOA) were investigated based on the amoA gene using pyrosequencing and quantitative PCR at both DNA and cDNA levels, together with the determination of the ammonia oxidation (AO) rate measured with ¹⁵N-labelled ammonium. By comparing stations with and without upwelling influence, we found that coastal upwelling correlated with an increase in amoA gene abundance, the dominance of distinct clades for AOA communities at the respective gene and transcript levels, and a large increase in the proportion of the SCM1-like (Nitrosopumilus maritimus-like) cluster as well. The AO rates were generally higher in the deeper water (~25 m), which was in significant positive correlation with the proportion of cluster Water Column A (WCA) at the transcript level, indicating the potential contribution of this cluster to in situ ammonia oxidization. Our study demonstrated that coastal upwelling had a significant impact on the AOA community and ammonia oxidization rate; therefore, this physical forcing should be considered in the future assessment of the global nitrogen budgets and biogeochemical nitrogen cycles.