Archaeal nitrification without oxygen

Spatio-temporal variability of nitrogen-cycling potentials in particle-attached and free-living microbial communities in the Yangtze River estuary and adjacent regions

Particle-attached (PA) and free-living (FL) microorganisms regulate coastal biogeochemical cycles, yet their roles in nitrogen transformation remain unclear. To address this knowledge gap, we seasonally sampled PA and FL from seawater along salinity gradients in the Yangtze River estuary (YRE) and adjacent regions to investigate the spatio-temporal variability of microbial communities, abundances of nitrogen-cycling genes, and key microbial groups affiliated with the nitrogen cycle in PA and FL. Compared to FL, the composition, structure and diversity of PA exhibited more pronounced variations in response to salinity and [NO3-]. Metagenomic analyses indicated a predominant role of denitrification in both PA and FL, with greater abundances of genes involved in most nitrogen transformation processes observed in the estuarine region. The potential for the nitrogen cycle in PA was relatively lower in May, while greater in FL, potentially due to competition for nitrogen substrates between PA and phytoplankton during spring. PERMANOVA and Mantel tests showed that gene abundances exhibited spatio-temporal dynamics and were associated with species and environmental factors. Gene-affiliated taxa identification and the Weighted Correlation Network Analysis revealed that the differences in environmental factors and taxa responsible for the nitrogen transformation drove spatio-temporal variations of the nitrogen cycle between PA and FL, and implied the significance of their interaction in nitrogen fates in coastal ecosystem. Gammaproteobacteria and Betaproteobacteria were highly affiliated with nitrogen-cycling genes, while Nitrososphaeria played an important role in nitrification and denitrification. This study offered practical insights for mitigating eutrophication through targeted regulation of microbial-mediated nitrogen fluxes.

Unravelling the Activity and Presence of N2O Reducers on Urban Greening Tree Leaves

Nitrous oxide (N2O) is a potent greenhouse gas and can be biotically emitted from soils, water, and the less recognised plant leaves. Leaves can produce N2O and may host N2O-reducing microbes that use it as a respiratory substrate, potentially mitigating climate warming. This study examines the ecophysiology of N2O reducers in the plant phyllosphere. Anoxic microcosm experiments, quantification of N2O reduction kinetics, and analysis of nosZ gene governing N2O reduction were conducted to assess the activity and presence of N2O reducers in leaf epiphytes from various canopy positions of Photinia fraseri, an urban greenery plant. Results revealed canopy position-dependent N2O reduction activity in the leaf microbiota. We identified previously unrecognised atypical Clade II nosZ gene in the phyllosphere microbiome, with its absolute abundance positively correlated with N2O reduction activity, highlighting its significance in this process. Sequencing of bacterial and archaeal 16S rRNA genes revealed keystone taxa as primary drivers of N2O reduction activity. These findings underscore the functional potential for N2O reduction and the presence of the Clade II nosZ group within epiphytic microbes. This work provides insights into the ecophysiology of epiphytic N2O reducers and underpins the development of leaf-based microbial solutions for N2O mitigation under future warming.

Archaea communities in aerobic granular sludge: A mini-review

Recent research on the archaea community in aerobic granular sludge (AGS) has attracted considerable attention. This review summarizes the existing literature on composition, distribution, and related functions of archaea community in AGS. Furthermore, the effects of granulation, substrate, temperature, process types, and aeration models on the archaea community were discussed. Significantly, the layered structure of AGS facilitates the enrichment of archaea, including methanogenic archaea and ammonia-oxidizing archaea. Archaea engage in metabolic interactions with other microorganisms, enhancing the ecological functionalities of AGS and its tolerance to adverse conditions. Future investigations should focus on minimizing greenhouse gas emissions and exploring the roles and interactive mechanisms of archaea and other microorganisms within AGS.

Important soil microbiota's effects on plants and soils: a comprehensive 30-year systematic literature review

Clarifying the relationship between soil microorganisms and the plant-soil system is crucial for encouraging the sustainable development of ecosystems, as soil microorganisms serve a variety of functional roles in the plant-soil system. In this work, the influence mechanisms of significant soil microbial groups on the plant-soil system and their applications in environmental remediation over the previous 30 years were reviewed using a systematic literature review (SLR) methodology. The findings demonstrated that: (1) There has been a general upward trend in the number of publications on significant microorganisms, including bacteria, fungi, and archaea. (2) Bacteria and fungi influence soil development and plant growth through organic matter decomposition, nitrogen, phosphorus, and potassium element dissolution, symbiotic relationships, plant growth hormone production, pathogen inhibition, and plant resistance induction. Archaea aid in the growth of plants by breaking down low-molecular-weight organic matter, participating in element cycles, producing plant growth hormones, and suppressing infections. (3) Microorganism principles are utilized in soil remediation, biofertilizer production, denitrification, and phosphorus removal, effectively reducing environmental pollution, preventing soil pathogen invasion, protecting vegetation health, and promoting plant growth. The three important microbial groups collectively regulate the plant-soil ecosystem and help maintain its relative stability. This work systematically summarizes the principles of important microbial groups influence plant-soil systems, providing a theoretical reference for how to control soil microbes in order to restore damaged ecosystems and enhance ecosystem resilience in the future.

The diversification and potential function of microbiome in sediment-water interface of methane seeps in South China Sea

The sediment-water interfaces of cold seeps play important roles in nutrient transportation between seafloor and deep-water column. Microorganisms are the key actors of biogeochemical processes in this interface. However, the knowledge of the microbiome in this interface are limited. Here we studied the microbial diversity and potential metabolic functions by 16S rRNA gene amplicon sequencing at sediment-water interface of two active cold seeps in the northern slope of South China Sea, Lingshui and Site F cold seeps. The microbial diversity and potential functions in the two cold seeps are obviously different. The microbial diversity of Lingshui interface areas, is found to be relatively low. Microbes associated with methane consumption are enriched, possibly due to the large and continuous eruptions of methane fluids. Methane consumption is mainly mediated by aerobic oxidation and denitrifying anaerobic methane oxidation (DAMO). The microbial diversity in Site F is higher than Lingshui. Fluids from seepage of Site F are mitigated by methanotrophic bacteria at the cyclical oxic-hypoxic fluctuating interface where intense redox cycling of carbon, sulfur, and nitrogen compounds occurs. The primary modes of microbial methane consumption are aerobic methane oxidation, along with DAMO, sulfate-dependent anaerobic methane oxidation (SAMO). To sum up, anaerobic oxidation of methane (AOM) may be underestimated in cold seep interface microenvironments. Our findings highlight the significance of AOM and interdependence between microorganisms and their environments in the interface microenvironments, providing insights into the biogeochemical processes that govern these unique ecological systems.

Nitrification and beyond: metabolic versatility of ammonia oxidising archaea

Ammonia oxidising archaea are among the most abundant living organisms on Earth and key microbial players in the global nitrogen cycle. They carry out oxidation of ammonia to nitrite, and their activity is relevant for both food security and climate change. Since their discovery nearly 20 years ago, major insights have been gained into their nitrogen and carbon metabolism, growth preferences and their mechanisms of adaptation to the environment, as well as their diversity, abundance and activity in the environment. Despite significant strides forward through the cultivation of novel organisms and omics-based approaches, there are still many knowledge gaps on their metabolism and the mechanisms which enable them to adapt to the environment. Ammonia oxidising microorganisms are typically considered metabolically streamlined and highly specialised. Here we review the physiology of ammonia oxidising archaea, with focus on aspects of metabolic versatility and regulation, and discuss these traits in the context of nitrifier ecology.

Microscale dynamics promote segregated denitrification in diatom aggregates sinking slowly in bulk oxygenated seawater

Sinking marine particles drive the biological pump that naturally sequesters carbon from the atmosphere. Despite their small size, the compartmentalized nature of particles promotes intense localized metabolic activity by their bacterial colonizers. Yet the mechanisms promoting the onset of denitrification, a metabolism that arises once oxygen is limiting, remain to be established. Here we show experimentally that slow sinking aggregates composed of marine diatoms-important primary producers for global carbon export-support active denitrification even among bulk oxygenated water typically thought to exclude anaerobic metabolisms. Denitrification occurs at anoxic microsites distributed throughout a particle and within microns of a particle's boundary, and fluorescence-reporting bacteria show nitrite can be released into the water column due to segregated dissimilatory reduction of nitrate and nitrite. Examining intact and broken diatoms as organic sources, we show slowly leaking cells promote more bacterial growth, allow particles to have lower oxygen, and generally support greater denitrification.

Electricity-Driven Microbial Metabolism of Carbon and Nitrogen: A Waste-to-Resource Solution

Electricity-driven microbial metabolism relies on the extracellular electron transfer (EET) process between microbes and electrodes and provides promise for resource recovery from wastewater and industrial discharges. Over the past decades, tremendous efforts have been dedicated to designing electrocatalysts and microbes, as well as hybrid systems to push this approach toward industrial adoption. This paper summarizes these advances in order to facilitate a better understanding of electricity-driven microbial metabolism as a sustainable waste-to-resource solution. Quantitative comparisons of microbial electrosynthesis and abiotic electrosynthesis are made, and the strategy of electrocatalyst-assisted microbial electrosynthesis is critically discussed. Nitrogen recovery processes including microbial electrochemical N₂ fixation, electrocatalytic N₂ reduction, dissimilatory nitrate reduction to ammonium (DNRA), and abiotic electrochemical nitrate reduction to ammonia (Abio-NRA) are systematically reviewed. Furthermore, the synchronous metabolism of carbon and nitrogen using hybrid inorganic-biological systems is discussed, including advanced physicochemical, microbial, and electrochemical characterizations involved in this field. Finally, perspectives for future trends are presented. The paper provides valuable insights on the potential contribution of electricity-driven microbial valorization of waste carbon and nitrogen toward a green and sustainable society.

Emissions of Nitric Oxide from Photochemical and Microbial Processes in Coastal Waters of the Yellow and East China Seas

Nitric oxide (NO) is an atmospheric pollutant and climate forcer as well as a key intermediary in the marine nitrogen cycle, but the ocean's NO contribution and production mechanisms remain unclear. Here, high-resolution NO observations were conducted simultaneously in the surface ocean and the lower atmosphere of the Yellow Sea and the East China Sea; moreover, NO production from photolysis and microbial processes was analyzed. The NO sea-air exchange showed uneven distributions (RSD = 349.1%) with an average flux of 5.3 ± 18.5 × 10^-17 mol cm^-2 s^-1. In coastal waters where nitrite photolysis was the predominant source (89.0%), NO concentrations were remarkably higher (84.7%) than the overall average of the study area. The NO from archaeal nitrification accounted for 52.8% of all microbial production (11.0%). We also examined the relationship between gaseous NO and ozone which helped identify sources of atmospheric NO. The sea-to-air flux of NO in coastal waters was narrowed by contaminated air with elevated NO concentrations. These findings indicate that the emissions of NO from coastal waters, mainly controlled by reactive nitrogen inputs, will increase with the reduced terrestrial NO discharge.

Shifts in the spatiotemporal distribution and sources of nitrous oxide in sediment cores from the Bohai Sea and South Yellow Sea

N₂O is among the most potent greenhouse gases. In this study, we investigated one of the important N₂O production hotspots, the continental margins. We looked at N₂O spatiotemporal distributions in situ as well as the potential contributions of nitrification and denitrification to N₂O production in sediment cores from the Bohai and South Yellow Seas. Real-time PCR and shotgun metagenomics sequencing were used to analyze the microbial communities related to N₂O production. The results showed that N₂O concentrations roughly decreased with depth-a trend that was consistent throughout the year and showed no significant seasonal variations. When all the research stations along the continental margin were considered, the estuary exhibited the lowest average N₂O concentration. Moreover, nitrification was identified as the main process responsible for N₂O production in estuary areas. This study demonstrates that spatial, as opposed to temporal, heterogeneity is the primary factor influencing N₂O concentration differences in sediments.

High importance of coupled nitrification-denitrification for nitrogen removal in a large periodically low-oxygen estuary

The coupling between nitrification and denitrification/anammox (nitrate/nitrite used in denitrification/anammox derives from nitrification) is a significant process of reactive nitrogen (N) removal that has attracted much attention. However, the dynamics of coupled nitrification-denitrification/anammox in the periodically low-oxygen estuaries and coasts remain unclear. Here, continuous-flow experiments combined with isotope tracing techniques were conducted in periodically low-oxygen areas of the Yangtze Estuary to reveal the changes in benthic sediment denitrification and anammox as well as their coupling with nitrification. Our results showed that denitrification increased but anammox decreased during low-oxygen summer. The occurrence of low oxygen also promoted coupled nitrification-denitrification but decreased coupled nitrification-anammox. These results implied that decreased dissolved oxygen in summer did not largely restrict nitrification activity, and anaerobic denitrification/anammox regulated the magnitude of coupled nitrification-denitrification/anammox rates. Denitrification (74.95-100 %) was the dominant process in total N removal, while coupled nitrification-denitrification accounted for a higher proportion (45.68-97.05 %) of denitrification, indicating that coupling between nitrification and denitrification played a dominant role in N removal. In addition to dissolved oxygen levels, carbon and N substrate availabilities were also important variables to regulate N transformations. Overall, this study advanced our knowledge of the distribution patterns and controlling factors of N removal processes and highlighted that coupled nitrification-denitrification might have a significant but neglected role in N removal from periodically low-oxygen estuaries.