Niche differentiation of ammonia-oxidizing archaea and related autotrophic carbon fixation potential in the water column of the South China Sea

Environmental determinants of spatial-temporal variability in ammonia oxidizing microorganisms across diverse Chinese agricultural soils

Numerous studies investigated the variation of soil ammonia oxidizing microorganisms along the geographic distance, but few highlighted the associated influence of agricultural practices on ammonia oxidizing communities and functions. To make up this gap, we determined the variation of ammonia-oxidizing archaea (AOA), bacteria (AOB), and soil nitrification within eight typical agricultural plots across China. The current study revealed significant variations in soil potential nitrification rates (PNRs) and the diversity and composition of AOA and AOB communities across various plots. Spearman correlation analysis revealed a significant link between soil PNRs and alpha diversity, specific AOA and AOB taxa, but no significant correlation was found with amoA gene abundance. Structural equation modeling and canonical correspondence analysis showed that factors like MAT, clay content, CEC, and soil carbon and nitrogen levels significantly influenced the diversity and composition of AOA. In contrast, AOB were more significantly impacted by soil pH and carbon- and nitrogen-related nutrients, but less associated with MAP and soil clay content. Notably, soil PNRs were found to be closely linked to AOB diversity, soil pH, and ammonium nitrogen (NH4N) levels. This research highlights the contributing role of AOB group in soil nitrification and the related driving factors from agricultural practices.

Spatial‒temporal pattern of primary productivity in the South China Sea under the monsoon regulation: Insights from observations of 2003-2022

Spatiotemporal analysis of Ocean Primary Production (OPP) is highly important for monitoring, conserving, and sustainable development of marine environment and ecosystems. Because of the influence of several factors such as temperature increasing, nutrients, wind and ocean dynamics, the analysis and prediction of the seasonal evolution and interannual trend of OPP have become more difficult and challenging. Taking the South China Sea (SCS) as the study area, this research conducted the comparative analysis of three widely used models in the SCS and identified the Vertical Generalized Production Model (VGPM) as the optimal model (R2 = 0.64, uRMSD = 0.25). We constructed a long-term data analysis framework for OPP, focusing on the typical spatial distribution characteristics in different month and the interannual trends. The framework is based on OPP, wind speed (WS), and sea surface height (SSH) data from 2003 to 2022 and utilizes empirical orthogonal function (EOF) analysis, the seasonal Kendall (SK) test, harmonic analysis, and the monsoon index. The results revealed that the first and second modes drive the patterns of January and August in winter and summer, respectively. Additionally, the fourth mode had dipole pattern in the SCS, capturing the main spatial distribution characteristics of the OPP in the northern SCS and southeastern Vietnam. The results from the SK test and harmonic analysis demonstrated that the most pronounced interannual decreases in OPP are in the northern SCS (lowest to -0.028897 mg∙C∙m-2∙d-1∙a-1), northwestern Luzon Island (lowest to -0.0115123 mg∙C∙m-2∙d-1∙a-1) and southeastern Vietnam (lowest to -0.0121879 mg∙C∙m-2∙d-1∙a-1). Furthermore, we quantified the impact of monsoons on OPP in the SCS, and positive correlations in southeastern Vietnam and dipole patterns in the northern SCS to northwestern SCS were identified. Finally, we evaluated the impacts of the El Niño‒Southern Oscillation (ENSO) and Indian Ocean Dipole (IOD) on OPP via their intensity indices. These findings provide insight into the biogeochemical cycling mechanisms in the SCS, with profound implications for local fisheries, the environment, and climate change.

Anthropogenic activities affect the diverse autotrophic communities of coastal sediments

Coastal sediments are a critical domain for carbon sequestration and are profoundly impacted by human activities. Therefore, it is essential to understand the structure and components of benthic autotrophs that play a crucial role in carbon sequestration processes, as well as the influence of anthropogenic activities on their communities. This study utilized an urban estuary, an industrial sea bay, a maricultural sea region, and two mangrove coastlines within the coastal areas of Guangdong Province, China. The micro-benthos in these environments, including prokaryotes and eukaryotes, were identified through high-throughput sequencing of 16S rRNA and 18S rRNA genes. The findings show that the autotrophic composition was altered by the interactions of anthropogenic heavy metals (Cd and Zn) and micro-eukaryotes (protazoa, metazoa, and parasitic organisms). Industrial pollution reduced the abundance of both prokaryotic and eukaryotic autotrophs. Mangroves induced a substantial transformation in the sediment eukaryotic and prokaryotic composition, increasing the proportion of autotrophs, notably sulfur-oxidizing and iron-oxidizing bacteria and microalgae. This alteration suggests an increase in specific sulfur and iron cycling with simultaneous carbon sequestration within mangrove sediments. These results indicate that anthropogenic activities affect sediment carbon sequestration by altering autotrophic assemblages along coastlines, thereby inducing consequential shifts in overall elemental cycling processes.

High throughput amplicon analysis reveals potential novel ammonia oxidizing prokaryotes in the eutrophic Jiaozhou Bay

Ammonia-oxidizing prokaryotes (AOPs) are the major contributors of ammonia oxidization with widely distribution. Here we investigated the phylogenetic diversity, community composition, and regulating factors of AOPs in Jiaozhou Bay (JZB) with high-throughput sequencing of amoA gene. Phylogenetic analysis showed most of the OTUs could not be clustered with any known AOPs, indicating there might exist putative novel AOPs. With new developed protocols for AOP community analysis, we confirmed that only 3 OTUs of ammonia-oxidizing archaea (AOA) could be affiliated to known Nitrosopumilaceae and Nitrososphaera, and the other OTUs were identified as novel AOA based on the threshold. All abstained OTUs of ammonia-oxidizing bacteria (AOB) were identified as novel clusters based on the threshold. Further analysis showed the novel AOPs had different distribution characteristics related to environmental factors. The high abundance and widespread distribution of these novel AOPs indicated that they played an important role in ammonia conversion in eutrophic JZB.

Novel database for accA gene revealed a vertical variability pattern of autotrophic carbon fixation potential of ammonia oxidizing archaea in a permeable subterranean estuary

The autotrophic carbon fixation pathway of ammonia-oxidizing archaea (AOA) was the 3-hydroxypropionate/4-hydroxybutyrate (3-HP/4-HB) cycle, of which the acetyl-CoA carboxylase α-submit (accA) gene is widely recognized as the indicator. To date, there is no reference database or suitable cut-off value for operational taxonomic unit (OTU) clustering to analyze the diversity of AOA based on the accA gene. In this study, a reference database with 489 sequences was constructed, all the accA gene sequences was obtained from the AOA enrichment culture, pure culture and environmental samples. Additionally, the 79% was determined as the cut-off value for OTU clustering by comparing the similarity between the accA gene and the 16S rRNA gene. The developed method was verified by analyzing samples from the subterranean estuary and a vertical variation pattern of autotrophic carbon fixation potential of AOA was revealed. This study provided an effective method to analyze the diversity and autotrophic carbon fixation potential of AOA based on accA gene.

Distinct patterns of distribution, community assembly and cross-domain co-occurrence of planktonic archaea in four major estuaries of China

BACKGROUND

Archaea are key mediators of estuarine biogeochemical cycles, but comprehensive studies comparing archaeal communities among multiple estuaries with unified experimental protocols during the same sampling periods are scarce. Here, we investigated the distribution, community assembly, and cross-domain microbial co-occurrence of archaea in surface waters across four major estuaries (Yellow River, Yangtze River, Qiantang River, and Pearl River) of China cross climatic zones (~ 1,800 km) during the winter and summer cruises.

RESULTS

The relative abundance of archaea in the prokaryotic community and archaeal community composition varied with estuaries, seasons, and stations (reflecting local environmental changes such as salinity). Archaeal communities in four estuaries were overall predominated by ammonia-oxidizing archaea (AOA) (aka. Marine Group (MG) I; primarily Nitrosopumilus), while the genus Poseidonia of Poseidoniales (aka. MGII) was occasionally predominant in Pearl River estuary. The cross-estuary dispersal of archaea was largely limited and the assembly mechanism of archaea varied with estuaries in the winter cruise, while selection governed archaeal assembly in all estuaries in the summer cruise. Although the majority of archaea taxa in microbial networks were peripherals and/or connectors, extensive and distinct cross-domain associations of archaea with bacteria were found across the estuaries, with AOA as the most crucial archaeal group. Furthermore, the expanded associations of MGII taxa with heterotrophic bacteria were observed, speculatively indicating the endogenous demand for co-processing high amount and diversity of organic matters in the estuarine ecosystem highly impacted by terrestrial/anthropogenic input, which is worthy of further study.

CONCLUSIONS

Our results highlight the lack of common patterns in the dynamics of estuarine archaeal communities along the geographic gradient, expanding the understanding of roles of archaea in microbial networks of this highly dynamic ecosystem.

Microbial-driven carbon fixation in natural wetland

With the development of global industrialization, carbon neutrality has become an issue that we must be paid attention to. Microorganisms not only have an important impact on the carbon chemical cycle between the Earth's biosphere and biogeography but also play a key role in maintaining the global organic carbon balance. Wetlands are the main reservoir of organic carbon in the mainland of China, and wetland carbon sinks are indispensable for China to achieve the goal of "dual carbon," and China has taken the consolidation and improvement of wetland carbon sink capacity as an important part of the carbon peaking action plan. As a unique low-latitude, high-altitude seasonal plateau wetland in China, Napahai shows high research value. However, the role of microbes in maintaining dissolved organic carbon balance in this area has not been reported. In the study, six carbon fixation genes, accA, aclB, acsA, acsB, cbbL, and rbcL, were analyzed based on metagenomics to elucidate the rich genetic diversity, uniqueness and differences in the Napahai plateau wetland. It was found that the microbial diversity in the Napahai plateau wetland was different from other habitats. In addition, the aclB gene, a rare taxon with high genetic diversity and rich species in the Napahai plateau wetland, played a key role in the microbial metabolic pathway. Finally, the construction of a metabolic pathway through the Kyoto encyclopedia for genes and genomes revealed the contribution of microbes to carbon fixation and the role of microbes in maintaining the organic carbon balance of the Napahai plateau wetland.

Novel database and cut-off value for bacterial amoA gene revealed a spatial variability pattern of the ammonia-oxidizing bacteria community from river to sea

Ammonia-oxidizing bacteria (AOB) catalyze the first step of nitrification, oxidizing ammonia to nitrite, and are characterized by amoA gene encoding ammonia monooxygenase. To analyze the AOB community effectively, an integral taxonomy database containing 14,058 amoA sequences and the optimal cut-off value at 95 % for OTU clustering were determined. This method was evaluated to be efficient by the analysis of environmental samples from the river, estuary, and sea. Using this method, a significant spatial variance of the AOB community was found. The diversity of AOB was highest in the estuary and lowest in the ocean. Nitrosomonas were the predominant AOB in the sediments of the freshwater river and estuary. Nearly all the AOB-amoA sequences belonged to uncultured bacterium in the sediments of deep sea. In general, an integral AOB taxonomic database and a suitable cut-off value were constructed for the comprehensive exploration of the diversity of AOB from river to sea.