Nitrogen-cycling Microorganisms Research Articles

Climate determines diversity but not abundance of nitrogen-cycling microorganisms in rivers across a latitudinal gradient

ABSTRACT A central goal in microecology is to understand the ecological factors shaping spatial patterns of microbial communities and the underlying mechanisms. However, the biogeographical patterns of microbial functional groups involved in nitrogen cycling (e.g., nitrifiers and denitrifiers) and their drivers at a large scale remain poorly understood. In this study, we evaluated the geographical distributions of nitrifiers and denitrifiers in riparian rhizosphere soils, riparian bulk soils, and channel sediments of 30 river regions along a latitudinal gradient from 21.8°N to 45.1°N across eastern China. We found that the diversity of nitrifiers and denitrifiers exhibited a gradual latitudinal gradient, in direct contrast to no significant changes observed for their abundance along the same latitudinal gradient. Statistical analyses suggested that climatic factors (mean annual temperature and mean annual precipitation) were the major drivers for the diversity of nitrifiers and denitrifiers, whereas soil properties were the key environmental factors shaping the abundance of nitrifiers and denitrifiers. These results provide new insights into the biogeographical distributions and ecological drivers for nitrogen-cycling microorganisms in river ecosystems at a large scale and can help us to improve simulation models of the nitrogen cycle for accurately predicting the diversity of nitrogen-cycling microbes under ongoing climate changes.

Distinct microbial nitrogen cycling processes in the deepest part of the ocean.

The metabolic features and adaptation strategies of the nitrogen cycling microorganisms in the deepest part of the ocean are largely unknown. This study revealed that anammox bacteria might perform aerobic respiration in response to nutrient limitation or O2 fluctuations in the Mariana Trench sediments. Meanwhile, an abundant alkane-oxidizing Ketobacter species could fix N2 in hadal seawater. This study provides new insights into the roles of hadal microorganisms in global nitrogen biogeochemical cycles. It substantially expands our understanding of the microbial life in the largely unexplored deepest part of the ocean.

Removal efficiency and abundance of nitrogen cycling microorganism in three bio-matrix materials to treat swine wastewater.

A bio-matrix material (BMM) system is used to pretreat swine wastewater and reduce the nitrogen (N) concentration to the tolerance range of plants in constructed wetlands. In this study, rice straw (RS), wheat straw (WS), and corn stalk (CS) were applied to treat pollutants from swine wastewater, respectively. This one year-long field experiment make up for the lack of long-term experiments and mechanistic investigations of BMM. The pollutant removal efficiency, degradation process of crop straw, and the abundance of nitrogen cycling genes were determined in different BMM systems. The results showed that the removal efficiency of COD, TN, NH4+, and NO3- was the best in the initial 6months. Furthermore, RS and WS exhibited favorable annual removal efficiency of TN and NH4+, which were 32.81% and 32.99%, 35.3% and 34.97%, respectively. Moreover, the removal efficiency of COD was 30.81% in three BMM systems. Meanwhile, it was found that the dry matter (DM) degradation of crop straws was fast in the first 4-5months. The degradation rates of cellulose, hemicellulose, and lignin were 94.19%, 94.36%, and 87.32%, respectively, in 1year. The abundance of nitrogen cycling genes significantly increased by adding BMM, compared with CK (P < 0.05). This showed the abundance of the hzsB gene in RS was the highest, while nirK, nirS, AOA, and AOB were the highest in WS. The addition of RS and WS was better than that of CS in promoting the abundance of nitrogen cycling microorganisms. The results indicated that adding BMM could enhance the anaerobic ammonia oxidation, nitrification, and denitrification. This study not only extends our comprehension of BMM mechanisms in swine wastewater treatment but also serves as a guiding light for numerous farms in similar climate regions.

Brownification increases the abundance of microorganisms related to carbon and nitrogen cycling in shallow lakes

Brownification in aquatic ecosystems under global change has attracted attention. The composition and quantity of dissolved organic matter transported from various land use types to lakes differ significantly, causing varying ecological effects of lake brownification by region. Bacterial communities make a significant contribution to the material cycle of ecosystems and are sensitive to environmental changes. In this study, a series of mesocosm systems were used to simulate forest lakes and urban lakes with different degrees of brownification, and a high-throughput amplicon sequencing technique was used to explore the changes in the composition, structure, and function of bacterial communities in shallow lakes undergoing brownification. Principal coordinate analysis (PCoA) and Jensen‒Shannon distance typing analysis both indicated significant differences in bacterial communities between forest lakes and urban lakes. The α diversity of bacterial communities in urban lakes increased with the degree of brownification. However, whether forest lakes or urban lakes, brownification increased the abundance of carbon cycling-related bacterial phyla (Proteobacteria, Poribacteria, and Chloroflexi) and nitrogen cycling-related bacterial genera (Microbacteriaceae, Limnohabitans, Comamonadaceae, Bacillus, and Rhizobiales_Incertae_Sedis). Additionally, the carbon and nitrogen cycling functions of bacterial communities in forest lakes are dominant, while those in urban lakes are dominated by functions related to light. Our study has preliminarily revealed that lake brownification promotes the growth of carbon and nitrogen cycling microorganisms, providing a new paradigm for understanding the response of lake ecosystems in different catchment areas to environmental changes and the carbon and nitrogen cycling processes in shallow lake ecosystems.

Temporal variations of biological nitrogen fixation and diazotrophic communities associated with artificial seaweed farms

Diazotrophic communities contribute inorganic nitrogen for the primary productivity of the marine environment by biological nitrogen fixation (BNF). They play a vital role in the biogeochemical cycle of nitrogen in the marine ecological environment. However, there is still an incomplete understanding of BNF and diazotrophs in artificial seaweed farms. Therefore, this study comprehensively investigated the temporal variations of BNF associated with Gracilariopsis lemaneiformis, as well as the diazotrophic communities associated with macroalgae and its surrounding seawater. Our results revealed that a total of 13 strains belonging to Proteobacteria and Bacteroidetes were identified as N2-fixing bacteria using azotobacter selective solid medium and nifH gene cloning. Subsequently, BNF and diazotrophic communities were characterized using the acetylene reduction method and high-throughput sequencing of the nifH gene, respectively. The results showed that nitrogenase activity and nifH gene abundance of epiphytic bacteria on G. lemaneiformis varied significantly among four different cultivation periods, i.e., Cultivation Jan. (CJ), Cultivation Feb. (CF), Cultivation Mar. (CM), Cultivation Apr. (CA). Among them, the nitrogenase activity and nifH gene abundance of epiphytic bacteria on G. lemaneiformis in CM were significantly higher than those in CJ, CF, and CA, indicating that the BNF of eiphytic bacteria on G. lemaneiformis was markedly enhanced. Combined with the data on environmental factors, it was found that the low concentration of nitrogen and phosphorus in CM might considerably boost the BNF of epiphytic bacteria in G. lemaneiformis. The sequencing results of the nifH gene showed that the α-diversity of diazotrophic communities associated with G. lemaneiformis and seawater in CM was higher than that in other cultivation periods. In addition, the diazotrophic communities on G. lemaneiformis were significantly different in CJ, CF, CM, and CA, and they were significantly diverse from diazotrophic communities in seawater. LEfSe analysis indicated that Rhodobacterales, Hyphomonadaceae, Robiginitomaculum, and Robiginitomaculum antarcticum within α-proteobacteria played a remarkable role in BNF in response to nitrogen nutrient deficiency. Taken together, these results provide a unique insight into the interaction between macroalgae and its epiphytic bacteria and lay a foundation for further research on the mechanism of action of nitrogen-cycling microorganisms associated with macroalgae.

Effects of Three Antibiotics on Nitrogen-Cycling Bacteria in Sediment of Aquaculture Water

Antibiotics are commonly used to prevent and control aquaculture diseases. However, long-term overuse of antibiotics not only leaves residues but also leads to changes in the nitrogen cycle in water, which threatens the survival of aquaculture organisms. The current results showed that sulfamethoxazole had no significant effect on the nitrogen cycle process in the actual aquaculture concentration. The inhibitory effect of 1.05 mg/L norfloxacin on ammonia-oxidizing bacteria was significantly greater than that on ammonia-oxidizing archaea, and the gene abundance of AOB amoA on the 14th day increased by 2.48 times compared with the 7th day. Under the influence of 3.9 mg/L oxytetracycline, the gene abundance of AOB amoA decreased significantly, while the number of AOA amoA genes increased, suggesting that there may be functional redundancy between AOA and AOB. At the genus level in the norfloxacin group, the relative abundance of Sva0485 increased by 14.0% on the 7th day compared with the control group but decreased 12.77% in the addition group. The relative abundance of Firmicutes, another dominant species in the oxytetracycline group, was 25.9%. This study shows that the addition of antibiotics may have a negative effect on the nitrogen-cycling microorganisms in aquaculture water.

Relationship between Nitrogen Dynamics and Key Microbial Nitrogen-Cycling Genes in an Intensive Freshwater Aquaculture Pond.

Intensive aquaculture in high-density hybrid snakehead [Channa maculata (♀) × Channa argus (♂)] fishponds can lead to toxic conditions for fish. This study investigated nitrogen migration and transformation in these fishponds during different cultivation periods. Using qPCR technology, we analyzed the abundance variation of nitrogen-cycling microorganisms in water and sediment to reveal the nitrogen metabolism characteristics of hybrid snakehead fishponds. The results showed that fish biomass significantly impacts suspended particulate matter (SPM) flux. At the sediment-water interface, inorganic nitrogen fluxes showed predominant NO3--N absorption by sediments and NH4+-N and NO2--N release, especially in later cultivation stages. Sediments were rich in nirS and AMX 16S rRNA genes (ranging from 4.04 × 109 to 1.01 × 1010 and 1.19 × 108 to 2.62 × 108 copies/g, respectively) with nirS-type denitrifiers potentially dominating the denitrification process. Ammonia-oxidizing bacteria (AOB) were found to dominate the ammonia oxidation process over ammonia-oxidizing archaea (AOA) in both water and sediment. Redundancy analysis revealed a positive correlation between SPM flux, Chlorophyll a (Chl-a), and denitrification genes in the water, and between nitrogen-cycling genes and NH4+/NO2- fluxes at the interface. These findings provide a scientific basis for nitrogen control in hybrid snakehead fishponds.

The effect of ecological farming techniques on nitrogen cycling microorganisms in soils with coffee plantations

The effect of ecological farming techniques on nitrogen cycling microorganisms in soils with coffee plantations

Nitrogen-cycling processes under long-term compound heavy metal(loids) pressure around a gold mine: Stimulation of nitrite reduction

Mining and tailings deposition can cause serious heavy metal(loids) pollution to the surrounding soil environment. Soil microorganisms adapt their metabolism to such conditions, driving alterations in soil function. This study aims to elucidate the response patterns of nitrogen-cycling microorganisms under long-term heavy metal(loids) exposure. The results showed that the diversity and abundance of nitrogen-cycling microorganisms showed negative feedback to heavy metal(loids) concentrations. Denitrifying microorganisms were shown to be the dominant microorganisms with over 60% of relative abundance and a complex community structure including 27 phyla. Further, the key bacterial species in the denitrification process were calculated using a random forest model, where the top three key species (Pseudomonas stutzei, Sphingobium japonicum and Leifsonia rubra) were found to play a prominent role in nitrite reduction. Functional gene analysis and qPCR revealed that nirK, which is involved in nitrite reduction, significantly accumulated in the most metal-rich soil with the increase of absolute abundance of 63.86%. The experimental results confirmed that the activity of nitrite reductase (Nir) encoded by nirK in the soil was increased at high concentrations of heavy metal(loids). Partial least squares-path model identified three potential modes of nitrite reduction processes being stimulated by heavy metal(loids), the most prominent of which contributed to enhanced nirK abundance and soil Nir activity through positive stimulation of key species. The results provide new insights and preliminary evidence on the stimulation of nitrite reduction processes by heavy metal(loids).

A core root bacteria contribute to plant growth and anisodine accumulation of Anisodus tanguticus

BackgroundAlthough it is well recognized that core root microorganisms contribute to plant health and productivity, little is known about their role to the accumulation of secondary metabolites. The roots of Anisodus tanguticus, a traditional herbal medication utilized by Tibetan medicine, are rich in tropane alkaloids. We collected wild A. tanguticus populations throughout a 1500 km transect on the Qinghai-Tibetan Plateau.ResultsOur results showed that despite sampling at a distance of 1500 km, the root of A. tanguticus selectively recruits core root bacteria. We obtained 102 root bacterial core OTUs, and although their number only accounted for 2.99% of the total, their relative abundance accounted for 73% of the total. Spearman correlation and random forest analyses revealed that the composition of core root microbiomes was related to anisodine contents, aboveground biomass and nitrogen contents of Anisodus tanguticus. Among them, the main role is played by Rhizobacter, Variovorax, Polaromonas, and Mycobacterium genus that are significantly enriched in roots. Functional prediction by FAPROTAX showed that nitrogen-cycling microorganisms and pathogenic bacteria are strongly associated with anisodine contents, aboveground biomass and nitrogen contents of Anisodus tanguticus.ConclusionsOur findings show that the root selectively recruits core root bacteria and revealed that the core microbiomes and microbial functions potentially contributed to the anisodine contents, aboveground biomass and nitrogen contents of the plant. This work may increase our understanding of the interactions between microorganisms and plants and improve our ability to manage root microbiota to promote sustainable production of herbal medicines.

Responses of diversity and carbon and nitrogen cycling genes of soil microorganisms to pomegranate (Punica granatum L.)/faba bean (Vicia faba L.) intercropping

The negative impacts of continuous cropping and long-term single crop planting on soil quality significantly restrict the high yield cultivation of perennial orchards. Intercropping can facilitate continuous cropping and improve the quality of the soil environment. However, it is still unclear whether the interplanting of faba bean in perennial orchards will increase the concentration of soil nutrients, change the composition of the soil microbial community, and increase the abundance of carbon (C) and nitrogen (N) cycling microorganisms. We interplanted faba beans in a perennial pomegranate orchard, and used sequencing and qPCR technology to study the effects on soil microbial diversity and C and N cycling genes. The results indicated that the interplanting of faba bean significantly increased the total N concentration by 28.6%, total phosphorus(P) concentration by 73.0% and available P concentration by 103.4%. The composition and structure of the soil microbial community were significantly changed, and the bacteria significantly enriched were Gaiellales and Rhizobiales at the order level and Nitrosomonadaceae at the family level. The fungi significantly enriched were Pezizomycetes at the class level, Pezizales and Sordariales at the order level, Ascodesmidaceae and Ophiocordycipitaceae at the family level, Cephaliophora, Parachaetomium, and Purpureocillium at the genus level, and Lilacinum, Lavendulum, Carinthiacum, Tropica, Chaetomium, and Delphinoides at the species level. The copy numbers of cbbL and nifH genes in soil were significantly increased by 79.9 and 168.5%, respectively. Changes in major nutrient elements explained 71.2% of the variance at the family level for bacteria and 46.0% of the variance at the family level for fungi. These results provided a scientific basis for the improvement of soil environmental quality and soil microorganisms by interplanting cash crops in perennial orchards.

The connection between the antibiotic resistome and nitrogen-cycling microorganisms in paddy soil is enhanced by application of chemical and plant-derived organic fertilizers

Antibiotic resistant genes (ARGs) present significant risks to environments and public health. In particular, there is increasing awareness of the role of soil nitrogen in ARG dissemination. Here, we investigated the connections between antibiotic resistome and nitrogen-cycling microbes in paddy soil by performing five-year field experiments with the treatments of no nitrogen fertilization (CK), reduced chemical nitrogen fertilization (LN), conventional chemical nitrogen fertilization (CN) and plant-derived organic nitrogen fertilization (ON). Compared with CK treatment, CN and ON treatments significantly increased soil NH4+ and TN concentrations by 25.4%–56.5% and 10.4%–20.1%, respectively. Redundancy analysis revealed significantly positive correlation of NH4+ with most ARGs, including tetA, macB and barA. Correspondingly, CN and ON treatments enhanced ARG abundances by 21.9%–23.2%. Moreover, CN and ON treatments promoted nitrate/nitrite-reducing bacteria and linked the corresponding N-cycling functional genes (narG, narH, nirK and nrfA) with most ARGs. Metagenomic binning was performed and identified Gemmatimonadaceae, Caulobacteraceae, Ilumatobacteraceae and Anaerolineaceae as hosts for both ARGs and nitrate/nitrite reduction genes that were enriched by CN and ON treatments. Soil resistome risk score analysis indicated that, although there was increased relation of ARG to nitrogen-cycling microorganisms with nitrogen fertilizer application, the environmental risk of ARGs was not increased due to the lower distribution of ARGs in pathogens. This study contributed to a deeper understanding of the role of soil nitrogen in shaping ARG profiles and controlling soil resistome risk.

Genome-resolved metagenomics provides insights into the microbial-mediated sulfur and nitrogen cycling in temperate seagrass meadows

The presence of seagrasses facilitates numerous microbial-mediated biogeochemical cycles, with sulfur- and nitrogen-cycling microorganisms playing crucial roles as regulators. Despite efforts to comprehend the diversity of microbes in seagrass ecosystems, the metabolic functions of these benthic microorganisms in seagrass sediments remain largely unknown. Using metagenomics, we provide insights into the sulfur- and nitrogen-cycling pathways and key metabolic capacities of microorganisms in both Z. japonica-colonized and unvegetated sediments over a seasonal period. Taxonomic analysis of N and S cycling genes revealed that δ- and γ- proteobacteria dominated the benthic sulfate-reducing bacteria, while α- and γ-proteobacteria played a significant role in the sulfur-oxidation processes. The proteobacterial lineages were also major contributors to the benthic nitrogen cycling. However, at a finer taxonomic resolution, microbial participants in different processes were observed to be highly diverse and mainly driven by environmental factors such as temperature and salinity. The gene pools of sulfur and nitrogen cycles in the seagrass sediments were dominated by genes involved in sulfide oxidation (fccA) and hydroxylamine oxidation (hao), respectively. Seagrass colonization elevated the relative abundance of genes responsible for sulfite production (phsC), hydroxylamine oxidation (hao), and nitrogen fixation (nifK), but suppressed sulfur oxidation (soxXYZ) and denitrification (nosZ and nirS). The prevalence of proteobacterial lineages functioned with versatile capabilities in both sulfur and nitrogen cycles in seagrass ecosystems, highlighting tight couplings between these processes, which was further supported by the recovery of 83 metagenome-assembled genomes (MAGs). These findings broaden our understanding of the biogeochemical processes that are mediated by microorganisms in seagrass ecosystems.

Soil amendments promoting nitrifying bacteria recovery faster than the denitrifying bacteria at post soil fumigation

Chloropicrin (CP) is a soil fumigant that not only reduces disease-causing pathogenic microbes but regrettably also those that benefit soil quality and crop health.However, we have few knowledge on rapidly restoring populations of beneficial microbes suppressed by CP fumigation. Here we used genetic sequencing technology to monitor changes in the recovery of soil bacteria in response to ammonium sulfate added to the soil following CP fumigation. The results showed that regardless of the N fertilizer addition rate, the accumulated NH4+-N in CP fumigated soil was rapidly consumed within 42 d. The rapid reduction in NH4+-N coincided with the observed recovery nitrogen-cycling microorganisms, especially the nitrification bacteria AOA and AOB that contributed to the formation of NH4+-N. Additionally, we further observed that the resilience index of nitrifying bacteria (AOB and AOA) was greater than the resilience index of denitrifying bacteria that contain the denitrification genes nirS, nirK and nosZ (0.12 to 0.55 vs. −0.27 to 0.073). These results revealed that N fertilizer stimulated the recovery of nitrifying bacteria more than denitrifying bacteria. Our research suggests that ammonium sulfate applied to CP fumigated soil could be used commercially to improve soil health as a result of an increase in beneficial microbes.

Different rotation years change the structure and diversity of microorganisms in the nitrogen cycle, affecting crop yield

Crop rotation is a common farmland management measure, which can effectively improve soil permeability and soil fertility, reduce crop diseases and pests, and affect microbial activity and community structure to a certain extent. However, the effects of long-term crop rotation pattern on nitrogen cycle microorganisms and crop yield are still unclear. Using monocrop rice as a control (CK), this study looked at the effects of different rotation years of tobacco rice (rotation years 10–20 (T10), 20–40 (T20), and >40 years of rotation) on nitrogen cycling microorganisms, soil nitrogen content, and crop yield. The results showed that compared with CK, crop rotation mode improved soil fertility and increased soil nitrogen content. Among them, the ammonium nitrogen content of farmland under T20 treatment (increased by 32.27 % compared with CK), and the yields of tobacco and rice were the highest (increased by 43.12 % compared with CK; Compared with T10 and T40 treatment, the tobacco content was increased by 3.59 % and 1.82 %, respectively). In addition, crop rotation also changed the structure and diversity of nitrogen-cycling microorganisms. This study found that Proteobacteria contributed significantly to the increase of soil nitrogen content, and Geobacter, Nitrosospira, Frankia, and Burkholderia Cupriavidus were the key groups to increase soil nitrogen content and crop yield. Therefore, tobacco rice rotation increases soil fertility and crop yield, but the effect decreases after >40 years. This study provides a reference for ensuring soil nitrogen transformation and sustainable agricultural production. The research results laid a solid theoretical foundation for the efficient transformation and utilization of soil nitrogen and grain increase.

Organic Material Addition Optimizes Soil Structure by Enhancing Copiotrophic Bacterial Abundances of Nitrogen Cycling Microorganisms in Northeast China

Using organic fertilizer and maize straw as friendly amendment measures is effective for altering soil nitrogen (N) cycling in farmlands. However, the synthetical effects of organic fertilizer combined with straw returning on soil quality remain unknown, especially in response to soil nitrification and denitrification microorganisms. We set up an experiment in brunisolic soil from Northeast China, mainly including four treatments: CK (no addition without traditional chemical fertilizer), O (organic fertilizer application), S (straw returning), and OS (organic fertilizer combined with straw returning). The soil nitrification and denitrification microorganisms were further investigated using high-throughput sequencing. Our results show that, compared to CK, the soil water content, field capacity, macroaggregates with a diameter &gt; 0.25 mm, mean weight diameter, total carbon, total nitrogen, ammonium, nitrate, microbial biomass carbon, and microbial biomass nitrogen were significantly improved, and penetration resistance was reduced in a 0–20 cm soil layer under O, S, and OS treatments. Moreover, OS treatment effectively increased the available potassium and available phosphorus content and decreased the three-phase R-value. The application of organic fertilizer and straw effectively optimized the soil structure, especially the OS treatment. Compared to CK, O, S, and OS treatments had a higher abundance of ammonia-oxidizing archaea (AOA) and further enhanced the alpha diversity and lower abundance of ammonia-oxidizing bacteria (AOB) and nirK-, nirS-, and nosZ-type denitrifying microbes. AOA and nirK were the key drivers of the ammonia oxidation process and nitrite reduction process, respectively. Meanwhile, the application of organic fertilizer and straw regulated the relative abundance of Nitrososphaeria (AOA), Gammaproteobacteria (nirK and nirS), Alphaproteobacteria (nirK), and Betaproteobacteria (nirS) in the soil. Organic fertilizer and straw returning regulated the soil structure by enhancing the abundance of Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria in the nitrifying and denitrifying microorganism communities. Taken together, OS treatment was a suitable straw-returning practice for optimizing the nutrient balance of the farmland ecosystem in Northeast China. However, this study did not determine how to reduce traditional nitrogen fertilizer applications under organic fertilizer application and straw returning; therefore, we aim to carry out related research in future works.

Effects of native plants on nitrogen cycling microorganisms in soil

Plants modify the nitrogen (N) cycle in soil through plant N uptake, root exudation, and nitrification inhibition resulting from root exudates and changes to the physicochemical properties of soil. Plants with specific traits can be selected to manage N fluxes in the soil following the land application of N-rich wastes thereby reducing losses of N from these systems into the atmosphere (via nitrous oxide) and waterbodies (via nitrate). Previous work has shown that some New Zealand native myrtaceous species can reduce such losses more than other species, but the underlying mechanisms are unknown. It was hypothesized that lower N losses may result from the inhibition of nitrification and denitrification. We aimed to determine the effect of New Zealand native plant species on the abundance of nitrifying and denitrifying microorganisms in the soil using a pot experiment with five native plant species (Carex secta, Coprosma robusta, Kunzea robusta, Leptospermum scoparium, and Metrosideros umbellata) and exotic pasture (Lolium perenne). Half of the pots received fertilisation with N (urea), phosphorus, potassium, and sulphur, while the remainder were unfertilised controls. We quantified the abundance of bacteria, archaea, and the functional genes encoding nitrite reductase (nirK, nirS), nitrous oxide reductase (nosZ), and bacterial and archaeal ammonia monooxygenase (amoA) in the rhizosphere of these plants. Results indicated that plant species had a significant effect on the abundance of nosZ and bacterial amoA. In fertilised soil, the abundance of bacterial amoA was lower under mono- than dicotyledonous species. Similarly, the chemical properties of the soil differed between these groups. Monocotyledonous species took up more N and had lower concentrations of mineral N in the rhizosphere. This indicates that the increased competition for N likely reduced the abundance of amoA and therefore nitrification and nitrate losses. The results support the utilisation of species selection to reduce N losses. In particular, monocotyledonous species may be planted in high-fertility environments to mitigate N contamination of ground- and surface water. Future work should determine the mechanisms of plant specific interaction with ammonia-oxidising bacteria, although plant uptake can explain some of the observed differences.

Comparison of the gill and gut microbiomes of common carp (Cyprinus carpio) and zebrafish (Danio rerio) and their RAS environment

Recirculating aquaculture systems (RAS) are increasingly being used to grow fish, as intensive water reuse reduces water consumption and environmental impact. RAS use biofilters containing nitrogen-cycling microorganisms that remove ammonia from the aquaculture water. Knowledge of how RAS microbial communities relate to the fish-associated microbiome is limited, as is knowledge of fish-associated microbiota in general. Recently, nitrogen-cycling bacteria have been discovered in zebrafish and carp gills and shown to detoxify ammonia in a manner similar to the RAS biofilter. Here, we compared RAS water and biofilter microbiomes with fish-associated gut and gill microbial communities in laboratory RAS housing either zebrafish (Danio rerio) or common carp (Cyprinus carpio) using 16S rRNA gene amplicon sequencing. The phylogeny of ammonia-oxidizing bacteria in the gills and the RAS environment was investigated in more detail by phylogenetic analysis of the ammonia monooxygenase subunit A (amoA). The location from which the microbiome was sampled (RAS compartments and gills or gut) had a stronger effect on community composition than the fish species, but species-specific differences were also observed. We found that carp- and zebrafish-associated microbiomes were highly distinct from their respective RAS microbiomes, characterized by lower overall diversity and a small core microbiome consisting of taxa specifically adapted to the respective organ. The gill microbiome was also defined by a high proportion of unique taxa. Finally, we found that amoA sequences from the gills were distinct from those from the RAS biofilter and water. Our results showed that the gut and gill microbiomes of carp and zebrafish share a common and species-specific core microbiome that is distinct from the microbially-rich RAS environment.

Metabolism characteristics of nitrogen functional microorganisms in bioretention system under multiple dry-wet alternation

In this study, we used metagenomic sequencing to explore the metabolism characteristics of nitrogen-cycling microorganisms in a bioretention system under multiple dry-wet alternation conditions. The results revealed that different dry-wet alternation conditions affected the composition of nitrogen-cycling microbes in bioretention soil media (BSM). In addition, the metagenomic analyses showed a higher relative abundance of key denitrifiers (Proteobacteria and Actinobacteria) under constant periods than unordered period. Furthermore, there was increased expression of nitrification functional genes and decreased expression of denitrifying functional genes during the unordered period, leading to nitrate accumulation in BSM. Under the constant dry-wet conditions, a short dry period (5 d) was shown to be beneficial to the nitrate reduction process. However, there was a risk of nitrite accumulation, which could be improved by rewetting. Moreover, our data proved that the NADH production process was inhibited in unordered period, causing nitrate accumulating. In conclusion, this study revealed that the different dry-wet alternation conditions could drive the expression of nitrogen functional genes, thus affected the biological nitrogen metabolism in bioretention systems.

Novel and unusual genes for nitrogen and metal cycling in Planctomycetota- and KSB1-affiliated metagenome-assembled genomes reconstructed from a marine subsea tunnel.

The Oslofjord subsea road tunnel is a unique environment in which the typically anoxic marine deep subsurface is exposed to oxygen. Concrete biodeterioration and steel corrosion in the tunnel have been linked to the growth of iron- and manganese-oxidizing biofilms in areas of saline water seepage. Surprisingly, previous 16S rRNA gene surveys of biofilm samples revealed microbial communities dominated by sequences affiliated with nitrogen-cycling microorganisms. This study aimed to identify microbial genomes with metabolic potential for novel nitrogen- and metal-cycling reactions, representing biofilm microorganisms that could link these cycles and play a role in concrete biodeterioration. We reconstructed 33 abundant, novel metagenome-assembled genomes (MAGs) affiliated with the phylum Planctomycetota and the candidate phylum KSB1. We identified novel and unusual genes and gene clusters in these MAGs related to anaerobic ammonium oxidation, nitrite oxidation, and other nitrogen-cycling reactions. Additionally, 26 of 33 MAGs also had the potential for iron, manganese, and arsenite cycling, suggesting that bacteria represented by these genomes might couple these reactions. Our results expand the diversity of microorganisms putatively involved in nitrogen and metal cycling, and contribute to our understanding of potential biofilm impacts on built infrastructure.