Dynamic Responses of Ammonia-Oxidizing Archaea and Bacteria Populations to Organic Material Amendments Affect Soil Nitrification and Nitrogen Use Efficiency

Ammonia-oxidizing archaea adapted better to the dark, alkaline oligotrophic karst cave than their bacterial counterparts

Subsurface karst caves provide unique opportunities to study the deep biosphere, shedding light on microbial contribution to elemental cycling. Although ammonia oxidation driven by both ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) is well explored in soil and marine environments, our understanding in the subsurface biosphere still remained limited to date. To address this gap, weathered rock and sediment samples were collected from the Xincuntun Cave in Guilin City, an alkaline karst cave, and subjected to high-throughput sequencing and quantification of bacterial and archaeal amoA, along with determination of the potential nitrification rates (PNR). Results revealed that AOA dominated in ammonia oxidation, contributing 48-100% to the PNR, and AOA amoA gene copies outnumbered AOB by 2 to 6 orders. Nitrososphaera dominated in AOA communities, while Nitrosopira dominated AOB communities. AOA demonstrated significantly larger niche breadth than AOB. The development of AOA communities was influenced by deterministic processes (50.71%), while AOB communities were predominantly influenced by stochastic processes. TOC, NH4+, and Cl- played crucial roles in shaping the compositions of ammonia oxidizers at the OTU level. Cross-domain co-occurrence networks highlighted the dominance of AOA nodes in the networks and positive associations between AOA and AOB, especially in the inner zone, suggesting collaborative effort to thrive in extreme environments. Their high gene copies, dominance in the interaction with ammonia oxidizing bacteria, expansive niche breadth and substantial contribution to PNR collectively confirmed that AOA better adapted to alkaline, oligotrophic karst caves environments, and thus play a fundamental role in nitrogen cycling in subsurface biosphere.

The impact of fertilization on ammonia-oxidizing bacteria and comammox Nitrospira communities and the subsequent effect on N2O emission and maize yield in a semi-arid region

The control of nitrous oxide (N2O) emissions through nitrification and the optimization of maize yield are important in agricultural systems. However, within the semi-arid region, the impact of fertilization on the function of nitrification communities and its connection with N2O emissions in the rhizosphere soil is still unclear. Our study investigates the influence of fertilization treatments on the communities of ammonia-oxidizing bacteria (AOB) and the complete ammonia oxidizers of the Nitrospira known as comammox (CAOB) in a maize agroecosystem. Nitrous oxide production, potential nitrification activity (PNA), maize yield, and nitrogen use efficiency (NUE) were determined for the same samples. The fertilizer treatments included a control group without fertilization (NA), inorganic fertilizer (CF), organic fertilizer (SM), combined inorganic and organic fertilizer (SC), and maize straw (MS). The SC treatment indicated a lower cumulative N2O emission than the CF treatment in the 2020 and 2021 cropping seasons. The AOB community under the CF, MS, and SM treatments was predominantly composed of Nitrosospira cluster 3b, while the SC treatment was associated with the comammox Nitrospira clade A.1 lineage, related to key species such as Ca. Nitrospira inopinata and Ca. Nitrospira nitrificans. Network analysis demonstrated a positive potential for competitive interaction between hub taxonomy and distinct keystone taxa among AOB and comammox Nitrospira nitrifiers. The structural equation model further revealed a significant positive association between AOB nitrifiers and N2O emission, PNA, soil pH, SOC, NO 3 - -N, and DON under organic fertilization. The keystone taxa in the comammox Nitrospira nitrifier and network Module II exhibited a positive correlation with maize productivity and NUE, likely due to their functional activities stimulated by the SC treatment. It is noteworthy that the AOB community played a more significant role in driving nitrification compared to the composition of comammox Nitrospira. Collectively, combined inorganic and organic fertilizer (SC) treatment exhibits high potential for reducing N2O emissions, enhancing maize productivity, increasing NUE, and increasing the sustainability of the nitrogen dynamics of maize agroecosystems in the semi-arid Loess Plateau.

Interaction between nematodes and bacteria enhances soil carbon sequestration under organic material amendments

The process of carbon (C) sequestration plays an important role in soil fertility and productivity, yet most studies have focused on the individual role of the bacterial community. However, an in-depth mechanistic understanding of how soil nematodes interact with the bacterial community to regulate soil C accumulation is still lacking. We conducted a 10-year field experiment to explore the nematode and bacterial communities and determine the influence of nematode-bacteria interactions on C mineralization, microbial metabolic quotient (qCO₂), and carbon use efficiency (CUE) under the organic material amendments, including chemical fertilizers with straw (NS), chemical fertilizers with straw and pig manure (NSM), and chemical fertilizer with straw biochar (NB). Here, our results showed the abundance of bacterial and nematode communities was significantly higher under NS, NSM, and NB treatments than under chemical fertilizers (N) treatment, with the highest abundance under the NSM treatment. The enrichment index and functional dispersion index were significantly higher under NSM treatment than under N, NS, and NB treatments, while the channel index followed the opposite pattern. Structural equation modeling indicated that the potential predation pressure induced by nematodes may improve bacterial abundance, with positive cascading effects on C sequestration. Collectively, our study highlights the functional importance of nematode-microorganism interactions in mediating C dynamics under organic material amendments.

Impact of soil amendments on nitrous oxide emissions and the associated denitrifying communities in a semi-arid environment

Denitrifying bacteria produce and utilize nitrous oxide (N2O), a potent greenhouse gas. However, there is little information on how organic fertilization treatments affect the denitrifying communities and N2O emissions in the semi-arid Loess Plateau. Here, we evaluated how the denitrifying communities are responsible for potential denitrification activity (PDA) and N2O emissions. A field experiment was conducted with five fertilization treatments, including no fertilization (CK), mineral fertilizer (MF), mineral fertilizer plus commercial organic fertilizer (MOF), commercial organic fertilizer (OFP), and maize straw (MSP). Our result showed that soil pH, soil organic carbon (SOC), and dissolved organic nitrogen (DON) were significantly increased under MSP treatment compared to MF treatment, while nitrate nitrogen (NO3−−N) followed the opposite trend. Organic fertilization treatments (MOF, OFP, and MSP treatments) significantly increased the abundance and diversity of nirS- and nosZ-harboring denitrifiers, and modified the community structure compared to CK treatment. The identified potential keystone taxa within the denitrifying bacterial networks belonged to the distinct genera. Denitrification potentials were significantly positively correlated with the abundance of nirS-harboring denitrifiers, rather than that of nirK- and nosZ-harboring denitrifiers. Random forest modeling and structural equation modeling consistently determined that the abundance, community composition, and network module I of nirS-harboring denitrifiers may contribute significantly to PDA and N2O emissions. Collectively, our findings highlight the ecological importance of the denitrifying communities in mediating denitrification potentials and the stimulatory impact of organic fertilization treatments on nitrogen dynamics in the semi-arid Loess Plateau.