Nitrogen-cycling Microorganisms Research Articles

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.

Comparison and Selection of Conventional PCR Primer Sets for Studies Associated with Nitrogen Cycle Microorganisms in Surface Soil

The nitrogen cycle is a biogeochemical cycle primarily associated with the microbial activity that occurs in various environments, including soil. Various genes related to the nitrogen cycle have been studied for different purposes by many researchers; therefore, the polymerase chain reaction (PCR) conditions and gene compositions differ among reports, making comparisons difficult. In this study, we compare the PCR methods to amplify 13 nitrogen cycle-related genes (amo (amoA and amoB), norB (cnorB and qnorB), hzs, napA, narG, nifH, nirK, nirS, nosZ, nrfA, and nxrA) in the soil samples collected from four land use types and selected a method with excellent applicability. However, the PCR method for five nitrogen cycle-related genes (amoC, hao, hzo, nirB, and nxrB) could not be presented. In addition, the nitrogen cycle-related genes from the four land use types (field, forest, bare land, and grassland) and the seasonally collected samples were analyzed and discussed. In the grassland samples, all the nitrogen cycle-related genes reviewed were amplified. These results vary from those of the field, forest, and bare land samples, and it was estimated that grassland, among the land use types, could play an important role in the nitrogen cycle in soil. However, an association between the seasons and the rainy season was not confirmed. Thus, this study may be used for future research in various fields related to the nitrogen cycle.

The active functional microbes contribute differently to soil nitrification and denitrification potential under long-term fertilizer regimes in North-East China.

Nitrogen (N) cycling microorganisms mediate soil nitrogen transformation processes, thereby affecting agricultural production and environment quality. However, it is not fully understood how active N-cycling microbial community in soil respond to long-term fertilization, as well as which microorganisms regulate soil nitrogen cycling in agricultural ecosystem. Here, we collected the soils from different depths and seasons at a 29-year fertilization experimental field (organic/chemical fertilizer), and investigated the transcriptions of N-cycling functional genes and their contribution to potential nitrification and denitrification. We found that long-term fertilization exerted significant impacts on the transcript abundances of nitrifiers (AOA amoA, AOB amoA and hao) and denitrifiers (narG and nosZ), which was also notably influenced by season variation. The transcriptions of AOA amoA, hao, and narG genes were lowest in autumn, and AOB amoA and nosZ transcript abundances were highest in autumn. Compared to no fertilization, soil potential nitrification rate (PNR) was reduced in fertilization treatments, while soil potential denitrification rate (PDR) was significantly enhanced in organic combined chemical fertilizer treatment. Both PNR and PDR were highest in 0–20 cm among the tested soil depths. Path model indicated active nitrifiers and denitrifiers had significant impact on soil PNR and PDR, respectively. The transcriptions of AOA amoA and nxr genes were significantly correlated with soil PNR (Pearson correlation, r > 0.174, p < 0.05). Significant correlation of napA and nosZ transcriptions with soil PDR (Pearson correlation, r > 0.234, p < 0.05) was also revealed. Random forest analysis showed that SOC content and soil pH were the important factors explaining the total variance of active nitrifers and denitrifiers, respectively. Taken together, long-term fertilization regimes reduced soil PNR and enhanced PDR, which could be attributed to the different responses of active N-cycling microorganisms to soil environment variations. This work provides new insight into the nitrogen cycle, particularly microbial indicators in nitrification and denitrification of long-term fertilized agricultural ecosystems.

Effects of Applying Arbuscular Mycorrhizal Fungi to Nitrogen Cycle Microorganisms in Soils with Coffee Plantations

Abstract: Mycorrhizae are associations between plants and beneficial fungi. They are the most active components of the plant’s nutrient absorption organs. On the other hand, soil microorganisms are fundamental for their functioning and dynamics as a living system. This research aimed to evaluate the effects of applying arbuscular mycorrhizal fungi (AMF) to the abundance of functional groups associated with the nitrogen cycle of soils with coffee plantations in Sasaima, Cundinamarca, Colombia. The soil samples were collected from four study plots during months 0, 2, and 8 and handled as follows: Plot 1. Application of liquid AMF (75-80 spores/gram of dry powder); Plot 2. Application of AMF in solid formulation (300 spores/gram); Plot 3. Application of native AMF, extracted from the soil under study (25 spores/gram); and Plot 4. Control, no application of AMF . The abundance of soil microorganisms associated with the nitrogen cycle was estimated using the most probable number technique to quantify ammonifying, proteolytic, ammonium-oxidizing, nitrite-oxidizing, and denitrifying microorganisms. The standard physicochemical parameters of the soil were measured. Afterward, univariate and multivariate analyses of the data were performed. The results showed a positive correlation between the application of AMF, organic carbon, and phosphorus, higher in the plots with native AMF. However, the abundance of functional groups of the nitrogen cycle did not show significant differences among the treatments; still, the principal components analysis showed a correlation between the plots with liquid and solid AMF, ammonifying microorganisms, and ammonium-oxidizing bacteria.

Annual Nitrogen Removal Efficiency and Change in Abundance of Nitrogen Cycling Microorganisms in Swine Wastewater Treated by Crop Straw Materials

Based on previous research, using straw material to treat swine wastewater can effectively reduce the concentration of nitrogen (N); however, the annual N-removal efficiency and change in the abundance of N-cycling functional genes remain unclear. In this study, four treatments (wheat straw, rice straw, corn stalk, and CK) were set up, with the aim of studying the annual N-removal efficiency and change in the abundance of functional genes. Our results showed that:① the total nitrogen (TN) removal and NH4+-N removal efficiency were the best in the first six months and were significantly reduced in the following six months. In addition, the TN removal and NH4+-N efficiency in straw and wheat straw were better than those in corn straw. The TN-removal efficiency in straw and wheat straw were 32.81%±11.34% and 32.99%±9.60%, respectively. The NH4+-N removal efficiency in straw and wheat straw were 35.3%±13.23% and 34.97%±12.00%, respectively. ② The abundance of N-cycling functional genes significantly increased by the addition of straw materials, compared with that of the CK (P<0.05). The average abundances of nirK, nirS, and hzsB were 6.45×109 copies·L-1, 6.18×109 copies·L-1, and 2.31×109 copies·L-1, respectively. The average abundances of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) were 6.12×1010 copies·L-1 and 4.93×109 copies·L-1, respectively. The average hzsB gene abundance was 2.31×109 copies·L-1. The average abundance of 16S rRNA in the treatment was 8.90×1010 copies·L-1. The abundances of hzsB and nirS genes in the straw and wheat straw were higher than those in the other treatment, indicating that the activities of anaerobic ammonia oxidation and denitrifying microorganisms were significantly increased by the addition of straw and wheat straw (P<0.05). In addition, the abundance of AOA and AOB genes were increased in wheat straw, suggesting that wheat straw could promote nitrification. The results provided data supporting the molecular mechanism of nitrogen removal in swine wastewater treatment with straw materials.

Brownification of freshwater promotes nitrogen-cycling microorganism growth following terrestrial material increase and ultraviolet radiation reduction

Brownification is an increasingly concerning phenomenon faced by aquatic ecosystems in the changing environments, and the microbiome plays an irreplaceable role in material circulation and food web construction. Insight into the influence of brownification on microbial communities is crucial from an ecological standpoint. In this study, we simulated brownification using a the mesocosm system and explored the relationship between the characteristics of microbial communities and brownification using excitation-emission matrix (EEM) fluorescence spectroscopy and ultraviolet (UV) spectroscopy combined with high-throughput amplicon sequencing techniques. The results showed that brownification reduced the richness of the microbial community and selectively promoted the growth of nitrogen-cycling microorganisms, including hgcI_clade, Microbacteriaceae, and Limnohabitans. Brownification affected microbial communities by altering the carbon source composition and underwater spectrum intensity; UV, blue, violet, and cyan light were significantly (p < 0.05) correlated with microbial community richness, and random forest analysis revealed that UV, C1 (microbial humic-like), and C3 (terrestrial humic-like) were the major factors significantly influencing microbiome variation. We found that brownification affected microorganisms in shallow lakes, especially nitrogen cycling microorganisms, and propose that controlling terrestrial material export is an effective strategy for managing freshwater brownification.

Nitrogen cycling and microbial cooperation in the terrestrial subsurface

The nitrogen cycle plays a major role in aquatic nitrogen transformations, including in the terrestrial subsurface. However, the variety of transformations remains understudied. To determine how nitrogen cycling microorganisms respond to different aquifer chemistries, we sampled groundwater with varying nutrient and oxygen contents. Genes and transcripts involved in major nitrogen-cycling pathways were quantified from 55 and 26 sites, respectively, and metagenomes and metatranscriptomes were analyzed from a subset of oxic and dysoxic sites (0.3-1.1 mg/L bulk dissolved oxygen). Nitrogen-cycling mechanisms (e.g. ammonia oxidation, denitrification, dissimilatory nitrate reduction to ammonium) were prevalent and highly redundant, regardless of site-specific physicochemistry or nitrate availability, and present in 40% of reconstructed genomes, suggesting that nitrogen cycling is a core function of aquifer communities. Transcriptional activity for nitrification, denitrification, nitrite-dependent anaerobic methane oxidation and anaerobic ammonia oxidation (anammox) occurred simultaneously in oxic and dysoxic groundwater, indicating the availability of oxic-anoxic interfaces. Concurrent activity by these microorganisms indicates potential synergisms through metabolite exchange across these interfaces (e.g. nitrite and oxygen). Fragmented denitrification pathway encoding and transcription was widespread among groundwater bacteria, although a considerable proportion of associated transcriptional activity was driven by complete denitrifiers, especially under dysoxic conditions. Despite large differences in transcription, the capacity for the final steps of denitrification was largely invariant to aquifer conditions, and most genes and transcripts encoding N2O reductases were the atypical Sec-dependant type, suggesting energy-efficiency prioritization. Results provide insights into the capacity for cooperative relationships in groundwater communities, and the richness and complexity of metabolic mechanisms leading to the loss of fixed nitrogen.

Insight into the role of competition in niche differentiation between ammonia-oxidizing archaea and bacteria in ammonium-rich alkaline soil: A network-based study

Interspecific competition between ammonia-oxidizing archaea (AOA) and bacteria (AOB) has been documented, however, its significance in niche differentiation between these nitrifiers under ammonia-rich conditions remains elusive. A network-oriented microcosm incubation study was established to improve our understanding of their interspecific competition. A high ammonium concentration was maintained during the incubation by regularly supplementing urea, and the growth of AOB was retarded to different extents using the AOB inhibitors 1-octyne (OC) and 3,4-dimethylpyrazole phosphate (DMPP) as amendments. In parallel, a 13CO2-stable isotope probing (SIP) incubation study was conducted to investigate the metabolic activity of AOA and AOB under ammonium-rich conditions, with and without DMPP amendment. The results of the network-oriented microcosm incubation indicated that the growth of AOA was highly and negatively correlated with the growth of AOB (r = −0.94, P < 0.001). Network analysis of the whole prokaryotes showed that the majority of AOA phylotypes formed a module independent of AOB phylotypes, indicating their distinct niche preferences. In another distinctive module, we found the remaining AOA to have a coexclusion pattern with AOB, indicating a competitive relationship and a positive connection between AOB and many taxa capable of nitrite/nitrate metabolism, in particular denitrification. The SIP study confirmed that all AOA and AOB phylotypes retained in the network were autotrophically active. It was also shown that the phylotype susceptible to AOB competition was closely related to Nitrososphaera viennensis EN76. Overall, the results demonstrate that both niche preference and interspecific competition contribute to niche partitioning between AOA and AOB. Our results also showed that a tight connection between AOB and other nitrogen-cycling microorganisms may be responsible for substantial nitrogen loss.

Uncovering the Microbial Diversity of Two Exotic Calcareous Sponges.

Sponges-associated microorganisms play important roles in their health and ecology; consequently, they may be crucial in the successful adaptation of exotic species to novel environments. However, few studies have focused on the microbial diversity of exotic sponges, especially those with calcium carbonate spicules (class Calcarea). Therefore, this is the first in situ characterization of the microbiota of the exotic calcareous sponges Sycettusa hastifera and Paraleucilla magna. Our results suggest that S. hastifera has a more stable microbiota than P. magna, as there were no differences in its beta diversity among sampling sites. Conversely, P. magna showed significant differences in its microbial communities, perhaps related to its adhesion to artificial substrate and/or shellfish mariculture activities. Each sponge species presented a single dominant proteobacterial OTU potentially active in the nitrogen cycle, which could help sponge detoxification, especially in polluted areas where exotic species usually establish. Our results show the importance of assessing the microbial diversity to unveil host-microorganism relationships and suggest that these associated nitrogen-cycling microorganisms could favor the success of exotic sponges in new environments.

Aerobic denitrifying bacteria community structure and response of aerobic denitrifying bacteria to dissloved organic matter in the sediments in Lake Baiyangdian in the spring

好氧反硝化因其独特优势成为近年来生物脱氮的研究热点，溶解性有机物（DOM）作为微生物碳源是造成群落差异的重要原因，为了探究白洋淀不同功能区好氧反硝化菌群落结构对溶解性有机物碳源的响应，本文结合荧光区域积分法以及napA反硝化基因的高通量测序技术，对白洋淀春季沉积物中的好氧反硝化菌群落结构特征以及好氧反硝化菌对溶解性有机物的响应进行研究.结果表明，春季白洋淀沉积物有机质组分类蛋白质组分高于类腐殖质组分，其中养殖区的类蛋白质组分最大，达到79.63%±3.79%，原始区的类腐殖质组分最大，达到33.91%±6.32%；高通量测序得到3693个OTUs，共分为9个主要门类，其中，变形菌门占比最大，达到99%以上；α多样性Chao1指数呈现显著的空间差异，并且旅游区>生活区>入淀区>原始区>养殖区；该时期好氧反硝化菌主要物种组成包括Aeromonas、Sulfuritortus、Cupriavidus、Pseudomonas和Thauera，Ferrimonas作为指示物种，差异贡献最大；冗余分析发现，可见光区类富里酸物质和微生物代谢产物组分分别是不同功能区好氧反硝化菌群落纲水平和属水平差异的主要原因.综上，通过对白洋淀好氧反硝化菌群与溶解性有机物的相关关系研究，不仅有助于进一步认识天然环境中氮循环微生物的特征；还可以为将来适于实际环境的高效菌筛选的碳源选择提供参考.;Aerobic denitrification has become a research hotspot in biological denitrification in recent years due to its unique advantages. Dissolved organic matter (DOM) as a carbon source is the important reason for community differences. To explore the responding mechanism of aerobic denitrifying bacteria community structure to dissolved organic matter in different functional areas of Lake Baiyangdian, this paper combines the fluorescence area integration method and the high-throughput sequencing technology of napA denitrification genes to study the characteristics of the aerobic denitrifying bacterial community structure and responding mechanism in Lake Baiyangdian. The results showed that the concentration of protein-like components was higher than that of humic-like components in the organic matter of Lake Baiyangdian sediments in spring. Among them, the protein-like components in the culture area were the largest, reaching 79.63%±3.79%, and the humus-like component in the primitive area was the largest, reaching 33.91%±6.32%; A total of 3693 OTUs were acquired high Throughput sequencing, which was divided into 9 main phyla. Among them, the Proteobacteria accounted for the largest proportion, reaching over 99%; the α diversity Chao1 index showed significant spatial differences, and the travel area>the living area>the entry area>the original area>the breeding area; the main species of aerobic denitrifying bacteria include Aeromonas, Sulfuritortus, Cupriavidus, Pseudomonas and Thaurea, Ferrimonas, as an indicator species, contributes the most to the difference; Redundant analysis found that the components of fulvic acid-like substances and microbial metabolites in the visible light area are the main reasons for the differences in aerobic denitrifying bacteria in different functional areas. In summary, this research will not only help to further understand the characteristics of the nitrogen cycle microorganisms in the natural environment; it will also provide a reference for the selection of carbon sources suitable for efficient bacterial screening in the practical environment.

Short-term effects of cover crops on soil properties and the abundance of N-cycling genes in citrus agroecosystems

Limited information is available on the influence of cover crops (CCs) on soil nutrient cycling and the abundance of bacterial and archaeal communities, nitrogen (N)-fixers, nitrifiers, and denitrifiers in tree crops. We examined the effect of replacing the traditional weedy inter-row middle of a commercial citrus orchard in Florida with two different mixtures of CCs: legumes and non-legumes (LG + NL) and non-legumes only (NL). A no-treatment/grower standard was used as a control (GSC). After one year of CCs, the use of NL and LG + NL CCs significantly increased soil carbon (C) availability in the row middles compared to GSC as shown by increases in permanganate oxidizable C, and to a lesser extent, soil organic matter. Treatment with LG + NL significantly increased soil ammonium content compared to the NL and GSC treatments. Improved C cycling in soils treated with CCs was related to increased abundance of bacteria and archaea. Changes in the size of the soil N pool were accompanied by increases in the abundance of N-fixation (nifH) and nitrification (amoA) genes in soils treated with LG + NL, likely due to greater N-mineralization and N-fixation by legumes. The use of CCs significantly altered the abundance of the nirK, nirS, norB, nosZI, and nosZII denitrification genes after one year compared to the GSC treatment. Changes of the ratio between genes involved in nitrous oxide (N2O) production and reduction showed a greater abundance of N2O producers in soils treated with NL compared to the GSC and the LG + NL treatments. Nitrous oxide fluxes determined over a 1-month period after one year of CCs were also significantly higher in NL than in LG + NL and GSC soils. The lower N2O fluxes from soils treated with LG + NL were accompanied by significantly greater abundances of genes involved in N2O reduction (nosZI and nosZII). Overall, our data suggest enhanced soil nutrient cycling and nutrient availability and associated nitrogen-cycling microorganisms in Florida citrus orchards after only one year of CC treatments. These impacts depended on the composition of the CC mixture and appear to be accelerated in sandy soils under warm humid climate such as in Florida.

The balance of nitrogen forms and number of microorganisms of the nitrogen cycle in vermicomposts based on leaf litter and cow manure

The processes of nitrogen transformation in the vermiculture system by Eisenia fetida using cow manure and leaf litter (poplar with small birch addition) have been investigated. Vermicomposting was carried out for five months in half-cubic meter wooden containers. The Kjeldahl method and potentiometry determined the total nitrogen, NH4 + and NO3- content in vermicompost. The total nitrogen content in cow manure was 1.83%, in leaf litter - 0.73%. The nitrate and ammonium content in non-composted leaf litter was 351 and 7.3 mEq/kg of dry matter, respectively. The nitrate and ammonium content in non-composted cow manure was 18.2 and 22 mEq/kg, respectively. Both investigated substrates of vermicomposting did not influence total nitrogen content. In cow manure-based vermicomposting system, the ammonium amount decreased by 5.3 times, while the concentration of nitrates increased by 6.5 times. In the leaf litter-based vermicomposting system, the ammonium amount increased by 2.9 times, and the amount of the nitrate increased by 1.6 times. The Azotobacter bacteria actual activity in both vermicomposts was close to 100%. The sum of nitrogen cycle microorganisms in manure vermicompost was 2.4 times higher than in leaf litter vermicompost.

Effects of drift algae accumulation and nitrate loading on nitrogen cycling in a eutrophic coastal sediment

The permeable (sandy) sediments that dominate the world's coastlines and continental shelves are highly exposed to nitrogen pollution, predominantly due to increased urbanisation and inefficient agricultural practices. This leads to eutrophication, accumulation of drift algae and changes in the reactions of nitrogen, including the potential to produce the greenhouse gas nitrous oxide (N2O). Nitrogen pollution in coastal systems has been identified as a global environmental issue, but it remains unclear how this nitrogen is stored and processed by permeable sediments. We investigated the interaction of drift algae biomass and nitrate (NO3−) exposure on nitrogen cycling in permeable sediments that were impacted by high nitrogen loading. We treated permeable sediments with increasing quantities of added macroalgal material and NO3− and measured denitrification, dissimilatory NO3− reduction to ammonium (DNRA), anammox, and nitrous oxide (N2O) production, alongside abundance of marker genes for nitrogen cycling and microbial community composition by metagenomics. We found that the presence of macroalgae dramatically increased DNRA and N2O production in sediments without NO3− treatment, concomitant with increased abundance of nitrate-ammonifying bacteria (e.g. Shewanella and Arcobacter). Following NO3− treatment, DNRA and N2O production dropped substantially while denitrification increased. This is explained by a shift in the relative abundance of nitrogen-cycling microorganisms under different NO3− exposure scenarios. Decreases in both DNRA and N2O production coincided with increases in the marker genes for each step of the denitrification pathway (narG, nirS, norB, nosZ) and a decrease in the DNRA marker gene nrfA. These shifts were accompanied by an increased abundance of facultative denitrifying lineages (e.g. Pseudomonas and Marinobacter) with NO3− treatment. These findings identify new feedbacks between eutrophication and greenhouse gas emissions, and in turn have potential to inform biogeochemical models and mitigation strategies for marine eutrophication.

Abundance and Functional Importance of Complete Ammonia Oxidizers and Other Nitrifiers in a Riparian Ecosystem.

The discovery of complete ammonia oxidation (comammox) has altered our understanding of nitrification, which is the rate-limiting process in the global nitrogen cycle. However, understanding the ecological role of comammox or its contribution to nitrification in both natural and artificial ecosystems is still in its infancy. Here, we investigated the community distribution and function of comammox bacteria in riparian ecosystems and analyzed interactions between comammox and other nitrogen cycling microorganisms. The comammox bacterial abundance and rate were higher in summer than in winter and higher in nonrhizosphere soils than in the rhizosphere. Fringe soils in the riparian zone comprise a comammox hotspot, where the abundance (2.58 × 108 copies g-1) and rate (0.86 mg N kg-1 d-1) of comammox were not only higher than at other sampling sites but also higher than those of other ammonia oxidation processes. The comammox rate correlated significantly positively with relative abundance of the comammox species Candidatus Nitrospira nitrificans but not with that of the species Candidatus Nitrospira nitrosa. Analysis of comammox interaction with other ammonia-oxidizing processes revealed ammonia-oxidizing archaea to dominate interface soils, comammox to dominate in fringe soils, and anaerobic ammonium oxidation (anammox) to dominate in interface sediments of the riparian zone. These results indicate that comammox may constitute an important and currently underestimated process of microbial nitrification in riparian zone ecosystems.

Molecular analysis of microbial nitrogen transformation and removal potential in mangrove wetlands under anthropogenic nitrogen input

Mangrove ecosystems are natural nitrogen removal systems that are primarily mediated by nitrogen cycle microorganisms, but their relative contributions to nitrogen transformation and removal in mangrove sediments under anthropogenic nitrogen input needs further resolution and characterization. Here, we investigated the responses and the relative contributions of ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), anaerobic ammonium oxidizing (anammox) bacteria and denitrifying bacteria after spiking urea into mangrove sediments incubated in a laboratory microcosm experiment for four weeks. During incubation, the diversity, abundances and transcription levels of the hzo genes for anammox bacteria, amoA genes for AOA and AOB, and nirS genes for denitrifying bacteria were monitored using targeted gene clone library analyses and quantitative PCR assays at the DNA and RNA levels. The results showed that mangrove sediments harbour habitat-specific anammox bacteria which related to Candidatus Scalindua and Candidatus Kuenenia clades. Mangrove specific AOA related to deep branched clades within Candidatus Nitrososphaera and Candidatus Nitrosotalea, and AOB related to Nitrosomonas and Nitrosospira were also detected in the collected sediment samples. Growth and activity of AOA were detected at all levels of amendment of nitrogen input, whereas AOB growth was detectable only at the high-level nitrogen input (1.5 mg urea per gram of dry sediment) with no amoA transcripts and lower abundance than AOA. The abundance and transcription levels of the nirS gene were higher (~1000 times) than those of the hzo gene in all groups. Pearson correlation analysis demonstrated that the abundance of both AOA and AOB amoA genes had a significant positive correlation with the nirS gene (p < 0.01). These results indicated that nitrification (primarily mediated by the AOA)-denitrification process played the most important role in nitrogen removal from the amendment of nitrogen short-term input in the mangrove sediments.

Bioremediation by Cupriavidus metallidurans Strain MSR33 of Mercury-Polluted Agricultural Soil in a Rotary Drum Bioreactor and Its Effects on Nitrogen Cycle Microorganisms.

Nitrogen cycle microorganisms are essential in agricultural soils and may be affected by mercury pollution. The aims of this study are to evaluate the bioremediation of mercury-polluted agricultural soil using Cupriavidus metallidurans MSR33 in a rotary drum bioreactor (RDB) and to characterize the effects of mercury pollution and bioremediation on nitrogen cycle microorganisms. An agricultural soil was contaminated with mercury (II) (20–30 ppm) and subjected to bioremediation using strain MSR33 in a custom-made RDB. The effects of mercury and bioremediation on nitrogen cycle microorganisms were studied by qPCR. Bioremediation in the RDB removed 82% mercury. MSR33 cell concentrations, thioglycolate, and mercury concentrations influence mercury removal. Mercury pollution strongly decreased nitrogen-fixing and nitrifying bacterial communities in agricultural soils. Notably, after soil bioremediation process nitrogen-fixing and nitrifying bacteria significantly increased. Diverse mercury-tolerant strains were isolated from the bioremediated soil. The isolates Glutamicibacter sp. SB1a, Brevundimonas sp. SB3b, and Ochrobactrum sp. SB4b possessed the merG gene associated with the plasmid pTP6, suggesting the horizontal transfer of this plasmid to native gram-positive and gram-negative bacteria. Bioremediation by strain MSR33 in an RDB is an attractive and innovative technology for the clean-up of mercury-polluted agricultural soils and the recovery of nitrogen cycle microbial communities.

Impacts of ammonia loading and biofilm age on the prevalence of nitrogen-cycling microorganisms in a full-scale submerged attached-growth reactor.

This study reports the impacts of seasonal ammonia load changes and biofilm age on the quantity of biomass and on the prevalence of ammonia- and nitrite-metabolizing organisms within a submerged attached-growth reactor (SAGR™) following lagoon treatment. Ammonia (NH3 ) loadings (0.12-3.17kg/d) in the primary SAGR were measured over 223days from May to December in 2017. Adjustment of the wastewater flow path on September 1 successfully increased NH3 loading to the primary SAGR, which subsequently caused reactor biomass to increase. The NH3 removal rate in October (0.5kg/d) was greater than rates in June and July (0.3 and 0.2kg/d) despite a water temperature decrease from >24 to 15.6°C. This elevated removal rate in October, and the sustained removal rate in December (0.4kg/d, 5.3°C) were associated with a measured increase in microbial biomass. The relative abundance of the anammox organism C.Brocadia was 5 times greater in the mature biofilm after 686days of growth, and the genus Pseudomonas increased sevenfold. The presence of Pseudomonas, which contains denitrifying species, and anammox suggests a high potential for removal of total nitrogen in SAGRs. PRACTITIONER POINTS: Pseudomonas prevalence and the presence of anammox suggest a high potential for total nitrogen removal in mature SAGR biofilms. The abundance of the anammox microorganism C.Brocadia was greater after 686days of biofilm growth compared with 33days. Simple operational changes can increase biomass in the SAGR to maintain, or even increase, NH3 transformation rates during cold weather.

Effects of illumination on nirS denitrifying and anammox bacteria in the rhizosphere of submerged macrophytes

Visibility in lakes can decrease due to increases in the amounts of suspended solids and algae, which inhibits the growth of submerged macrophytes. However, the understanding about whether illumination reduction affects the nitrogen-cycling microorganisms in the rhizosphere of submerged macrophytes, is limited. The abundance and biodiversity of nirS denitrifying and anammox bacteria in the rhizosphere of Potamogeton crispus were studied under 0% (natural light), 20%, 40%, and 60% shading treatments. The abundance of the nirS gene was highest under 60% shading treatment, while the anammox 16S rRNA gene was highest under 40% shading treatment. Moreover, the abundance of the two genes were lower under natural light than under shading conditions during most sampling periods. The quantitative ratio of the two gene (anammox 16S rRNA to nirS gene) abundance fluctuated wildly with the distance away from the roots, under natural light and 20% shading treatment. However, the ratio varied relatively little under 40% and 60% shading treatments. The diversity of nirS denitrifying bacteria was high in the rhizosphere, while the diversity of anammox bacteria was low, and Candidatus Brocadia fulgida was dominant. This study revealed that illumination reduction not only facilitated the growth of nirS denitrifying and anammox bacteria in the rhizosphere, but also weakened the competition between the two bacteria.

Underpinning unique genes in Ca. Brocadia sp. and its interspecies association potentials in a partial nitrification/anammox system with low-strength wastewater

Anaerobic ammonia oxidation (anammox) incorporated with anaerobic treatment with sewage offers an energy-efficient option. With the substrate in scare from anaerobically-treated sewage, the dominated anammox species, their mechanisms, and interspecies interaction remain unclear. Here, we enriched and operated a partial nitrification (PN)- anammox (A) fluidized-bed bioreactor (FBR) containing granular activated carbon (GAC) inoculated from a conventional activated sludge with a synthetic low-strength wastewater under a dissolved oxygen concentration of 0.7 mg/L. It achieved over 53% of total nitrogen removal without anammox seed. Our meta-omics analyses revealed an enriched anammox strain affiliated to Ca. Brocadia sp. with a relative abundance of 11.18% and 26.96% in the bulk and biofilm, respectively. Genes encoding dissimilatory nitrate reduction to ammonium (DNRA) and heterotrophic anabolism in this strain were recovered, suggesting its potential in a flexible nitrogen stochiometric feed ratio through organics utilization. Furthermore, 17 and 19 high-quality draft genomes yielded from the bulk and biofilm, respectively support the interspecies interaction capacity between Ca. Brocadia sp. and other nitrogen cycle microorganisms through nitrite loop and vitamin B12 exchange. By offering such overlooked pathways and their interspecies linkages between Ca. Brocadia sp. and other microbes, our study facilitates its mainstream application.