Diversity and abundance of nitrate reductase genes (narG and napA), nitrite reductase genes (nirS and nrfA), and their transcripts in estuarine sediments

Molecular Biomarkers and Influential Factors of Denitrification in a Full-Scale Biological Nitrogen Removal Plant

Three denitrifying bacteria, Paracoccus spp., Thauera spp., Pseudomonas-like spp., and two functional genes, nitrate reductase (narG and napA), were studied as potential biomarkers for total nitrogen removal. These bacterial genera and the functional genes showed significant negative correlations with total nitrogen in the effluent (TN_eff). Thauera spp. had the highest correlation (r = −0.793, p < 0.001) with TN_eff, and narG-like and napA genes also showed significant correlations (r = −0.663 and −0.643, respectively), suggesting functional genes have equal validity to 16S rRNA genes in monitoring denitrification performance. The most explanatory variables were a combination of constituents, with temperature emerging as the most important in Pearson’s correlation and redundancy analysis. Thauera spp. had the highest correlation with temperature (r = 0.739) followed closely by Paracoccus spp. (r = 0.705). Denitrification was also significantly affected by pH (r = 0.369), solids retention time (r = −0.377), total nitrogen_in (r = 0.635), and organic matter in the influent (biochemical oxygen demand and chemical oxygen demand; r = 0.320 and 0.522, respectively). Our data verified that major denitrifiers’ 16S rRNA genes and nitrate reductase genes were better biomarkers than the biomass concentration, and any of the biomarkers could track denitrification in real time.

Nitrogen Fertilizer Amendment Alter the Bacterial Community Structure in the Rhizosphere of Rice (Oryza sativa L.) and Improve Crop Yield

Availability of nitrogen (N) in soil changes the composition and activities of microbial community, which is critical for the processing of soil organic matter and health of crop plants. Inappropriate application of N fertilizer can alter the rhizosphere microbial community and disturb the soil N homeostasis. The goal of this study was to assess the effect of different ratio of N fertilizer at various early to late growth stages of rice, while keeping the total N supply constant on rice growth performance, microbial community structure, and soil protein expression in rice rhizosphere. Two different N regimes were applied, i.e., traditional N application (NT) consists of three sessions including 60, 30 and 10% at pre-transplanting, tillering and panicle initiation stages, respectively, while efficient N application (NF) comprises of four sessions, i.e., 30, 30, 30, and 10%), where the fourth session was extended to anthesis stage. Soil metaproteomics combined with Terminal Restriction Fragment Length Polymorphism (T-RFLP) were used to determine the rhizosphere biological process. Under NF application, soil enzymes, nitrogen utilization efficiency and rice yield were significantly higher compared to NT application. T-RFLP and qPCR analysis revealed differences in rice rhizosphere bacterial diversity and structure. NF significantly decreased the specific microbes related to denitrification, but opposite result was observed for bacteria associated with nitrification. Furthermore, soil metaproteomics analysis showed that 88.28% of the soil proteins were derived from microbes, 5.74% from plants, and 6.25% from fauna. Specifically, most of the identified microbial proteins were involved in carbohydrate, amino acid and protein metabolisms. Our experiments revealed that NF positively regulates the functioning of the rhizosphere ecosystem and further enabled us to put new insight into microbial communities and soil protein expression in rice rhizosphere.

Microbial metatranscriptomic investigations across contaminant gradients of the Detroit River

Microbial community function in freshwater sediments is influenced by the presence and persistence of anthropogenic pollutants, yet simultaneously imposes significant control on their transformation. Thus, microbes provide valuable ecosystem services in terms of biodegradation and bioindicators of compromised habitats. From a remediation perspective it is valuable to leverage the suite of microbial genes at the transcriptional level that are active in either natural versus stressed environments to provide insight into the cycling and fate of contaminants. Metatranscriptomic analysis of total bacterial and archaeal messenger RNA (mRNA) is a useful tool in this facet and was applied to sediments sampled from the Detroit River; a binational Area of Concern (AOC) in the Great Lakes. Previously established sediment surveys and modelling delineated the river into contaminant gradients based on concentrations of polycyclic aromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs), and metals. Differential expression analysis through DESeq2 revealed that microbial transcripts associated with nitrate reduction, methanogenesis, and beta-oxidation were significant in legacy polluted sediments and linked with energetic pathways key in the generation of cellular currencies (acetyl-CoA, succinyl-CoA). Gluconeogenesis and polyester synthesis also showed high abundance in contaminated regions, along with increased expression of stress response genes and transposons, despite decreases in community α-diversity. Aromatic cleavage genes were detected, but in low abundance across the contaminant gradient. These results suggest that microbial communities within the Detroit River exploit unique anabolic and catabolic pathways to derive and store energy from legacy organic contaminants while simultaneously recruiting stress-response and gene transfer mechanisms to cope with xenobiotic pressures. By coupling well-resolved chemical datasets with metatranscriptomics, this study adds to the spatial understanding of in-situ microbial activities in pristine and perturbed freshwater sediments.

Achieving efficient nitrogen removal from real sewage via nitrite pathway in a continuous nitrogen removal process by combining free nitrous acid sludge treatment and DO control

The incomplete denitrification due to insufficient carbon resource in the wastewater treatment plants (WWTPs) resulted in low nitrogen removal efficiency, which has become a widespread problem in China and all around the world. Reducing the requirement of carbon source by manipulating the nitrogen removal pathway from conventional nitrification-denitrification to partial nitrification-denitrification is considered as an efficient solution. In this article, the feasibility of combining free nitrous acid (FNA) sludge treatment and DO control to achieve partial nitrification-denitrification in a continuous flow system (aerobic-anoxic-oxic process) using real sewage was assessed. The nitrite pathway was rapidly established in the experimental reactor within 23 days by simultaneously lowering DO concentration in aerobic zone to 0.5 mg/L and treating 30% of the activated sludge per day from the reactor in the FNA sludge treatment unit with FNA concentration of 1.2 mg N/L and exposure time of 18 h. The nitrite oxidizing bacteria (NOB) were efficiently washed out and the partial nitrification process could maintain stable in the experimental reactor even after cease of FNA treatment and increase of DO concentrations in the main stream to 1.5 mg/L, with an average nitrite accumulation rate of above 78%. In contrast, the nitrite accumulation rate was just around 58% during low DO concentrations phase and declined quickly to below 1% after the DO concentrations were increased to 1.5 mg/L in the control reactor which only utilized single strategy of DO control to achieve nitrite pathway. Moreover, a better sludge settleability and nitrogen removal performance could also be realized in the experimental reactor. The results of nitrifying bacteria activities and quantities detection demonstrated that although NOB activities in both reactors were effectively inhibited, a certain amount of NOB (6.26 × 10⁶ copies/g MLSS) were remained in the control reactor and multiplied rapidly as the DO concentration increased, which might break down the partial nitrification. Furthermore, the quantity results of nitrogen cycling related functional genes showed that the increment of the ratio of nitrate reduced bacteria to total bacteria was 0.35% larger than that of nitric oxide bacteria in the control reactor, while those two ratios increased similarly by 1.11% and 1.12% in the experimental reactor, respectively, which might be one potential cause of reduction in N₂O emission of nitrite pathway achieved by FNA-based technologies.

Evaluation and application of molecular denitrification monitoring methods in the northern Lake Tai, China

Worldwide, excessive reactive nitrogen in groundwater and surface waters is a growing problem, especially in areas that face rapid urbanization and industrialization. One example for environmental nitrogen pollution is the Lake Tai, China's third largest freshwater Lake, located in the Yangtze River basin. Due to the rapid development of the surrounding area, nitrogen compounds like nitrate are discharged into the Lake. Consequently, eutrophication and harmful algae blooms increased and led to the production of toxins directly affecting water consumers through the water supply chain. Denitrification is the main process that attenuates nitrate by converting it into atmospheric nitrogen and represents an intrinsic natural process to compensate the excess reactive nitrogen. In this study, the methodology to detect nitrate reducing bacteria on a functional gene and transcriptional level was optimized and verified in laboratory experiments with a pure culture of Pseudomonas veronii, isolated from Lake Tai. We demonstrated that transcripts analysis (mRNA) did correspond with nitrate reduction activity. Subsequently, the abundance and the activity of nitrate reducing bacteria in Lake Tai were assessed using the developed methods. We demonstrated that nitrate reducing bacteria can be found throughout all sediment and water samples taken from the northern Lake Tai in September 2017. Measurements of narG transcripts also indicated the activity of the membrane-bound nitrate reductase in the water samples. However, the bioinformatic analysis of narG sequences showed varying binding efficiency of primer and gene sites in dependence of phylogenetic groups, which may lead to an underestimation in the qPCR method. Thus, it is important to point out the precautions and limitations of primer systems to monitor nitrogen transformation by qPCR in the environment. Based on this study, mRNA detection methods are suitable for improved microbiological monitoring of denitrification, as an intrinsic process in Lake Tai to mitigate the inflowing reactive nitrogen compounds.

Optimization of PCR primers to detect phylogenetically diverse nrfA genes associated with nitrite ammonification

Dissimilatory nitrate reduction to ammonium (DNRA) is now known to be a more prevalent process in terrestrial ecosystems than previously thought. The key enzyme, a pentaheme cytochrome c nitrite reductase NrfA associated with respiratory nitrite ammonification, is encoded by the nrfA gene in a broad phylogeny of bacteria. The lack of reliable and comprehensive molecular tools to detect diverse nrfA from environmental samples has hampered efforts to meaningfully characterize the genetic potential for DNRA in environmental systems. In this study, modifications were made to optimize the amplification efficiency of previously-designed PCR primers, targeting the diagnostic region of NrfA between the conserved third- and fourth heme binding domains, and to increase coverage to include detection of environmentally relevant Geobacteraceae-like nrfA. Using an alignment of the primers to >270 bacterial nrfA genes affiliated with 18 distinct clades, modifications to the primer sequences improved coverage, minimized amplification artifacts, and yielded the predicted product sizes from reference-, soil-, and groundwater DNA. Illumina sequencing of amplicons showed the successful recovery of nrfA gene fragments from environmental DNA based on alignments of the translated sequences. The new primers developed in this study are more efficient in PCR reactions, although gene targets with high GC content affect efficiency. Furthermore, the primers have a broader spectrum of detection and were validated rigorously for use in detecting nrfA from natural environments. These are suitable for conventional PCR, qPCR, and use in PCR access array technologies that allow multiplex gene amplification for downstream high throughput sequencing platforms.

Formation of nanoscale Te0 and its effect on TeO32- reduction in CH4-based membrane biofilm reactor

Formation and recovery of elemental tellurium (Te⁰) from wastewaters are required by increasing demands and scarce resources. Membrane biofilm reactor (MBfR) using gaseous electron donor has been reported as a low-cost and benign technique to reduce and recover metal (loids). In this study, we demonstrate the feasibility of nanoscale Te⁰ formation by tellurite (TeO₃^2-) reduction in a CH₄-based MBfR. Biogenic Te⁰ intensively attached on cell surface, within diameters ranging from 10 nm to 30 nm and the hexagonal nanostructure. Along with the Te⁰ formation, the TeO₃^2- reduction was inhibited. After flushing, biofilm resumed the TeO₃^2- reduction ability, suggesting that the formed nanoscale Te⁰ might inhibit the reduction by hindering substrate transfer of TeO₃^2- to microbes. The 16S rRNA gene amplicon sequencing revealed that Thermomonas and Hyphomicrobium were possibly responsible for TeO₃^2- reduction since they increased consecutively along with the experiment operation. The PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) analysis showed that the sulfite reductases were positively correlated with the TeO₃^2- flux, indicating they were potential enzymes involved in reduction process. This study confirms the capability of CH₄-based MBfR in tellurium reduction and formation, and provides more techniques for resources recovery and recycles.

Metagenomics Response of Anaerobic Ammonium Oxidation (anammox) Bacteria to Bio-Refractory Humic Substances in Wastewater

Anammox-based processes have been widely applied for the treatment of wastewater (e.g., wastewater irrigation systems and constructed wetland) which consists of bio-refractory humic substances. Nonetheless, the impacts of bio-refractory humic substances on anammox consortia are rarely reported. In the present study, three identical lab-scale anammox reactors (i.e., HS0, HS1 and HS10), two of which were dosed with humic substances at 1 and 10 mg·L−1, respectively, were operated for nearly one year. The long-term operation of the reactors showed that the presence of humic substances in influent had no significant influence on nitrogen removal rates. Despite this, comparative metagenomics showed changes in anammox microbiota structure during the exposure to humic substance; e.g., the relative abundance of Candidatus Kuenenia was lower in HS10 (18.5%) than that in HS0 (22.8%) and HS1 (21.7%). More specifically, a lower level of humic substances (1 mg·L−1) in influent led to an increase of genes responsible for signal transduction, likely due to the role of humic substances as electron shuttles. In contrast, a high level of humic substances (10 mg·L−1) resulted in a slight decrease of functional genes associated with anammox metabolism. This may partially be due to the biodegradation of the humic substances. In addition, the lower dosage of humic substances (1 mg·L−1) also stimulated the abundance of hzs and hdh, which encode two important enzymes in anammox reaction. Overall, this study indicated that the anammox system could work stably over a long period under humic substances, and that the process was feasible for leachate treatment.

Microbial aerobic denitrification dominates nitrogen losses from reservoir ecosystem in the spring of Zhoucun reservoir

The mechanism and factors influencing nitrogen loss in the Zhoucun reservoir were explored during the spring. The results showed that the nitrate and total nitrogen concentration decreased from 1.84 ± 0.01 mg/L and 2.34 ± 0.06 mg/L to 0.06 ± 0.01 mg/L and 0.48 ± 0.09 mg/L, respectively. Meanwhile, the nitrate and total nitrogen removal rate reached 97.02% ± 0.25 and 79.38% ± 3.32, respectively. Moreover, the abundance of nirS gene and aerobic denitrification bacteria increased from 1.04-3.38 × 10³ copies/mL and 0.71 ± 0.22 × 10² cfu/mL to 5.36-5.81 × 10³ copies/mL and 8.64 ± 2.08 × 10³ cfu/mL, respectively. The low MW fractions of DOM (<5 kDa) increased from 0.94 ± 0.02 mg/L in February to 1.51 ± 0.09 mg/L in April. E3/E4 and absorption spectral slope ratio (S_R) showed that fulvic acid accounted for the main proportion with autochthonous characteristics. These findings were consistent with the fluorescence components and fluorescence characteristic indices based on EEM-PARAFAC. Meanwhile, the microbial metabolism activity increased significantly from February to April, which contributed to the cycle of nutrients within the reservoir water system. Moreover, the abundance of the bacterial species involved in denitrification (Exiguobacterium, Brevundimonas, Deinococcus, Paracoccus, and Pseudomonas) increased significantly. The relative abundance of KOs related to nitrogen metabolism, were initially increased and then decreased. Specifically, K02567 (napA) represented the main proportion of KOs related to denitrification. The abundance of napA-type denitrifying bacteria (Dechloromonas, Pseudomonas, Azospira, Rhodopseudomonas, Aeromonas, Zobellella, Sulfuritalea, Bradyrhizobium, Achromobacter, Enterobacter, Thauera, and Magnetospirillum) increased significantly during the period of nitrogen loss. Furthermore, the levels of nitrate, T, DO, and AWCD were the most important factors affecting the N-functional bacteria composition. The systematic investigation of the nitrogen loss would provide a theoretical foundation for the remediation of the water reservoir via aerobic denitrification in the future.

Enrichment and Genomic Characterization of a N2O-Reducing Chemolithoautotroph From a Deep-Sea Hydrothermal Vent

Nitrous oxide (N₂O) is a greenhouse gas and also leads to stratospheric ozone depletion. In natural environments, only a single N₂O sink process is the microbial reduction of N₂O to N₂, which is mediated by nitrous oxide reductase (NosZ) encoded by nosZ gene. The nosZ phylogeny has two distinct clades, clade I and formerly overlooked clade II. In deep-sea hydrothermal environments, several members of the class Campylobacteria are shown to harbor clade II nosZ gene and perform the complete denitrification of nitrate to N₂; however, little is known about their ability to grow on exogenous N₂O as the sole electron acceptor. Here, we obtained an enrichment culture from a deep-sea hydrothermal vent in the Southern Mariana Trough, which showed a respiratory N₂O reduction with H₂ as an electron donor. The single amplicon sequence variant (ASV) presenting 90% similarity to Hydrogenimonas species within the class Campylobacteria was predominant throughout the cultivation period. Metagenomic analyses using a combination of short-read and long-read sequence data succeeded in reconstructing a complete genome of the dominant ASV, which encoded clade II nosZ gene. This study represents the first cultivation analysis that shows the occurrence of N₂O-respiring microorganisms in a deep-sea hydrothermal vent and provides the opportunity to assess their capability to reduce N₂O emission from the environments.

Characterization of microbes and denitrifiers attached to two species of floating plants in the wetlands of Lake Taihu

Biofilms are often observed at the solid-water interface. The leaves of many floating macrophytes have characteristics of both terrestrial plants and submerged macrophytes, because, in general, their upper and lower surfaces are exposed to air and water, respectively. However, little is known about the biofilms attached to floating plants. We investigated biofilms attached to the leaves, stems and roots of the floating plants Nymphoides peltata (in summer and winter) and Trapa natans (in summer) in the Gonghu Bay of Lake Taihu. Bacteria and algae were major components of the biofilm on the leaves of the two species of plants. In addition, 454 pyrosequencing analysis of bacterial 16S rRNA genes revealed that Proteobacteria was the dominant phylum, followed by Bacteroidetes, Firmicutes, Chloroflexi, Acidobacteria, and Verrucomicrobia. Cluster analysis showed that bacterial communities from the same plant source were clustered into the same group. A total of 677 genera were detected, and 47 genera were shared by all samples. Nitrifiers, including Nitrosomonas, Nitrosococcus and Nitrospira were detected in this study. Seven denitrifying genes (napA, napG, nirS, nirK, cnorB, qnorB and nosZ) were used to detect the abundance of denitrifiers. Genes nirK, nirS cnorB and nosZ were the four most abundant genes in all samples. Our results demonstrated that cultivation of floating plants in water column could enlarge the area for biofilm growth, and biofilms might play an important role in denitrification in eutrophic water.

Seasonal variation of potential denitrification rate and enhanced denitrification performance via water-lifting aeration technology in a stratified reservoir-A case study of Zhoucun reservoir

Zhoucun reservoir is one of the major water resources in Zao Zhuang city, northern China. The seasonal distribution of surface sediment denitrification rate and enhanced performance of denitrification via water-lifting aeration technology were explored using the acetylene-inhibition technique. Surface sediment denitrification rates ranged from 2.57 ± 1.32 to 923.90 ± 86.81 nmol N₂/(g dw·h), with the highest rates in November (ANOVA, p < 0.05) and significantly low rates in June, July, and August (ANOVA, p < 0.05), mainly because of the seasonal differences in nitrate concentration, water temperature, and sediment total nitrogen (STN). Meanwhile, the N₂/(N₂+N₂O) ratio (83.44-91.70% for the highest sediment denitrification period) indicated that N₂ accounted for a majority of denitrification. Correlation analysis between various environmental factors and denitrification was conducted, and nitrate concentration, STN, low molecular weight organic carbon, the number of aerobic denitrifying bacteria, and the environmental parameters of oxidation-reduction potential (ORP), pH, electrical conductivity (EC), and chlorophyll a (Chl-a) presented significant relationships during the entire study period. On the basis of the multiple regression model, nitrate and low molecular weight organic carbon concentration were the most influential factors on denitrification variability. Moreover, the denitrification rates of the surface sediment clearly increased, from 5.28 to 13.22 nmol N₂/(g dw·h) to 1117.02-3129.47 nmol N₂/(g dw·h), which were higher than those in the non-operating year. This suggests that the denitrification in the sediment system could be enhanced in situ by water-lifting and aeration technology in the reservoir ecosystem.

Copepod-Associated Gammaproteobacteria Respire Nitrate in the Open Ocean Surface Layers

Microbial dissimilatory nitrate reduction to nitrite, or nitrate respiration, was detected in association with copepods in the oxygenated water column of the North Atlantic subtropical waters. These unexpected rates correspond to up to 0.09 nmol N copepod-1 d-1 and demonstrate a previously unaccounted nitrogen transformation in the oceanic pelagic surface layers. Genes and transcripts for both the periplasmic and membrane associated dissimilatory nitrate reduction pathways (Nap and Nar, respectively) were detected. The napA genes and transcripts were closely related with sequences from several clades of Vibrio sp., while the closest relatives of the narG sequences were Pseudoalteromonas spp. and Alteromonas spp., many of them representing clades only distantly related to previously described cultivated bacteria. The discovered activity demonstrates a novel Gammaproteobacterial respiratory role in copepod association, presumably providing energy for these facultatively anaerobic bacteria, while supporting a reductive path of nitrogen in the oxygenated water column of the open ocean.

Sex differences in the nitrate-nitrite-NO• pathway: Role of oral nitrate-reducing bacteria

Oral reduction of nitrate to nitrite is dependent on the oral microbiome and is the first step of an alternative mammalian pathway to produce nitric oxide in humans. Preliminary evidence suggests important sex differences in this pathway. We prospectively investigated sex-differences following inorganic nitrate supplementation on nitrate/nitrite levels and vascular function, and separately examined sex differences in oral nitrate reduction, and oral microbiota by 16S rRNA profiling. At baseline, females exhibit higher nitrite levels in all biological matrices despite similar nitrate levels to males. Following inorganic nitrate supplementation, plasma nitrite was increased to a significantly greater extent in females than in males and pulse wave velocity was only reduced in females. Females exhibited higher oral bacterial nitrate-reducing activity at baseline and after nitrate supplementation. Despite these differences, there were no differences in the composition of either the total salivary microbiota or those oral taxa with nitrate reductase genes. Our results demonstrate that females have augmented oral nitrate reduction that contributes to higher nitrite levels at baseline and also after inorganic nitrate supplementation, however this was not associated with differences in microbial composition (clinicaltrials.gov: NCT01583803).

Nitrogen Addition Decreases Dissimilatory Nitrate Reduction to Ammonium in Rice Paddies

Dissimilatory nitrate reduction to ammonium (DNRA), denitrification, anaerobic ammonium oxidation (anammox), and biological N2 fixation (BNF) can influence the nitrogen (N) use efficiency of rice production. While the effect of N application on BNF is known, little is known about its effect on NO3- partitioning between DNRA, denitrification, and anammox. Here, we investigated the effect of N application on DNRA, denitrification, anammox, and BNF and on the abundance of relevant genes in three paddy soils in Australia. Rice was grown in a glasshouse with N fertilizer (150 kg N ha-1) and without N fertilizer for 75 days, and the rhizosphere and bulk soils were collected separately for laboratory incubation and quantitative PCR analysis. Nitrogen application reduced DNRA rates by >16% in all the soils regardless of the rhizospheric zone, but it did not affect the nrfA gene abundance. Without N, the amount and proportion of NO3- reduced by DNRA (0.42 to 0.52 μg g-1 soil day-1 and 45 to 55%, respectively) were similar to or higher than the amount and proportion reduced by denitrification. However, with N the amount of NO3- reduced by DNRA (0.32 to 0.40 μg g-1 soil day-1) was 40 to 50% lower than the amount of NO3- reduced by denitrification. Denitrification loss increased by >20% with N addition and was affected by the rhizospheric zones. Nitrogen loss was minimal through anammox, while BNF added 0.02 to 0.25 μg N g-1 soil day-1 We found that DNRA plays a significant positive role in paddy soil N retention, as it accounts for up to 55% of the total NO3- reduction, but this is reduced by N application.IMPORTANCE This study provides evidence that nitrogen addition reduces nitrogen retention through DNRA and increases nitrogen loss via denitrification in a paddy soil ecosystem. DNRA is one of the major NO3- reduction processes, and it can outcompete denitrification in NO3- consumption when rice paddies are low in nitrogen. A significant level of DNRA activity in paddy soils indicates that DNRA plays an important role in retaining nitrogen by reducing NO3- availability for denitrification and leaching. Our study shows that by reducing N addition to rice paddies, there is a positive effect from reduced nitrogen loss but, more importantly, from the conversion of NO3- to NH4+, which is the favored form of mineral nitrogen for plant uptake.

Changes in bacterial community structure and antibiotic resistance genes in soil in the vicinity of a pharmaceutical factory

China is the largest global producer of antibiotics. With the demand for antibiotics increasing every year, it is necessary to assess potential environmental risks and the spread of antibiotic resistance genes (ARGs) associated with antibiotic production. Here, we investigated the occurrence and distribution of ARGs in soil in the vicinity of a pharmaceutical factory. The results showed that antibiotic concentrations were under the detection limit; however, ARGs were present in soil and tended to be enriched near the factory. A significant correlation between the relative abundance of intI-1 and tetracycline ARGs implied that horizontal gene transfer might play an important role in the spread of ARGs. The occurrence of these ARGs could be the results of previous antibiotic contamination. However, the soil bacterial community structure seemed to be more affected by nutrients or other factors than by antibiotics. Overall, this study supports the viewpoint that long-term pharmaceutical activity might have a negative effect on environmental health, thus, underscoring the need to regulate antibiotic production and management.

High-throughput analysis of anammox bacteria in wetland and dryland soils along the altitudinal gradient in Qinghai-Tibet Plateau

This study investigated the diversity, community composition, and abundance of anaerobic ammonium oxidation (anammox) bacteria along the altitudinal gradient in Qinghai–Tibet Plateau. Two types of soil samples (wetland and dryland soils, n = 123) were collected from 641 m to 5,033 m altitudes. Polymerase chain reaction (PCR) screening showed that anammox were not widespread, and were only detected in 9 sampling sites of the 50 sites tested by amplifying the 16S rRNA genes. Then, only samples collected from Linzhi (2,715 m), Rikaze (4,030 m), and Naqu (5,011 m), which were positive for the presence of anammox, were further processed to explore the biogeography of anammox bacteria in Qinghai–Tibet Plateau. Results of high‐throughput sequencing targeting the hydrazine synthesis β‐subunit (hzsB) gene revealed the presence of three known anammox genera (Candidatus Brocadia, Candidatus Jettenia, and Candidatus Kuenenia) in both soil types. Their diversity, community composition, and abundance did not show significant variation with altitude at large scale. However, it was the small‐scale environmental heterogeneities between wetland and dryland soils that determined their biogeographical distribution. Specifically, the dryland soils had higher diversity of anammox bacteria than the wetland soils, but their abundance patterns varied. The community composition of anammox bacteria were found to be influenced by soil nitrate content.

nirS-type denitrifying bacterial assemblages respond to environmental conditions of a shallow estuary

Molecular analysis of dissimilatory nitrite reductase genes (nirS) was conducted using a customized microarray containing 165 nirS probes (archetypes) to identify members of sedimentary denitrifying communities. The goal of this study was to examine denitrifying community responses to changing environmental variables over spatial and temporal scales in the New River Estuary (NRE), NC, USA. Multivariate statistical analyses revealed three denitrifier assemblages and uncovered 'generalist' and 'specialist' archetypes based on the distribution of archetypes within these assemblages. Generalists, archetypes detected in all samples during at least one season, were commonly world-wide found in estuarine and marine ecosystems, comprised 8%-29% of the abundant NRE archetypes. Archetypes found in a particular site, 'specialists', were found to co-vary based on site specific conditions. Archetypes specific to the lower estuary in winter were designated Cluster I and significantly correlated by sediment Chl a and porewater Fe²⁺ . A combination of specialist and more widely distributed archetypes formed Clusters II and III, which separated based on salinity and porewater H₂ S respectively. The co-occurrence of archetypes correlated with different environmental conditions highlights the importance of habitat type and niche differentiation among nirS-type denitrifying communities and supports the essential role of individual community members in overall ecosystem function.

Small-scale variation of ammonia oxidisers within intertidal sediments dominated by ammonia-oxidising bacteria Nitrosomonas sp. amoA genes and transcripts

While numerous studies have investigated the abundance of ammonia oxidising bacteria and archaea (AOB/AOA) via the ammonia monooxygenase gene amoA, less is known about their small-scale variation and if amoA gene abundance equates to activity. Here we present a spatial and temporal study of ammonia oxidation in two small intertidal bays, Rusheen and Clew bay, Ireland. Potential Nitrification Rate (PNR) was ten-fold higher in Rusheen bay (Clew: 0.27 ± SD 0.55; Rusheen: 2.46 ± SD 3.4 NO2- µg-1 g-1 day-1, P < 0.001) than in Clew bay but amoA gene abundances were similar between bays, and comparable to those in other coastal ecosystems. Within bays AOB genes increased towards the muddy sediments and were positively correlated with PNR and pH. Less spatial variation was observed in AOA abundances which nevertheless positively correlated with pH and temperature and negatively with salinity and ammonia. Transcriptionally active AOB and AOA were quantified from all sites in Rusheen bay, February 2014, following the general trends observed at DNA level. AOB phylotypes predominantly from the known Nitrosomonas group were distributed across the bay, while Nitrosomonas group B phylotypes were absent from low salinity sites. AOA genes and transcripts were primarily affiliated with Thaumarchaeota group I.1a.

Underexplored microbial metabolisms for enhanced nutrient recycling in agricultural soils

Worldwide, arable soils have been degraded through erosion and exhaustive cultivation, and substantial proportions of fertilizer nutrients are not taken up by crops. A central challenge in agriculture is to understand how soils and resident microbial communities can be managed to deliver nutrients to crops more efficiently with minimal losses to the environment. Throughout much of the twentieth century, intensive farming has caused substantial loss of organic matter and soil biological function. Today, more farmers recognize the importance of protecting soils and restoring organic matter through reduced tillage, diversified crop rotation, cover cropping, and increased organic amendments. Such management practices are expected to foster soil conditions more similar to those of undisturbed, native plant-soil systems by restoring soil biophysical integrity and re-establishing plant-microbe interactions that retain and recycle nutrients. Soil conditions which could contribute to desirable shifts in microbial metabolic processes include lower redox potentials, more diverse biogeochemical gradients, higher concentrations of labile carbon, and enrichment of carbon dioxide (CO2) and hydrogen gas (H2) in soil pores. This paper reviews recent literature on generalized and specific microbial processes that could become more operational once soils are no longer subjected to intensive tillage and organic matter depletion. These processes include heterotrophic assimilation of CO2; utilization of H2 as electron donor or reactant; and more diversified nitrogen uptake and dissimilation pathways. Despite knowledge of these processes occurring in laboratory studies, they have received little attention for their potential to affect nutrient and energy flows in soils. This paper explores how soil microbial processes could contribute to in situ nutrient retention, recycling, and crop uptake in agricultural soils managed for improved biological function.

Denitrifying community in coastal sediments performs aerobic and anaerobic respiration simultaneously

Nitrogen (N) input to the coastal oceans has increased considerably because of anthropogenic activities, however, concurrent increases have not occurred in open oceans. It has been suggested that benthic denitrification in sandy coastal sediments is a sink for this N. Sandy sediments are dynamic permeable environments, where electron acceptor and donor concentrations fluctuate over short temporal and spatial scales. The response of denitrifiers to these fluctuations are largely unknown, although previous observations suggest they may denitrify under aerobic conditions. We examined the response of benthic denitrification to fluctuating oxygen concentrations, finding that denitrification not only occurred at high O2 concentrations but was stimulated by frequent switches between oxic and anoxic conditions. Throughout a tidal cycle, in situtranscription of genes for aerobic respiration and denitrification were positively correlated within diverse bacterial classes, regardless of O2 concentrations, indicating that denitrification gene transcription is not strongly regulated by O2 in sandy sediments. This allows microbes to respond rapidly to changing environmental conditions, but also means that denitrification is utilized as an auxiliary respiration under aerobic conditions when imbalances occur in electron donor and acceptor supply. Aerobic denitrification therefore contributes significantly to N-loss in permeable sediments making the process an important sink for anthropogenic N-inputs.

Dissimilatory Nitrate Reduction to Ammonium in the Yellow River Estuary: Rates, Abundance, and Community Diversity

Dissimilatory nitrate reduction to ammonium (DNRA) is an important nitrate reduction process in estuarine sediments. This study reports the first investigation of DNRA in the Yellow River Estuary located in Eastern Shandong, China. Saltwater intrusion could affect the physicochemical characteristics and change the microbial community structure of sediments. In this study, the activity, abundance and community diversity of DNRA bacteria were investigated during saltwater intrusion. The slurry incubation experiments combined with isotope-tracing techniques and qPCR results showed that DNRA rates and nrfA (the functional gene of DNRA bacteria) gene abundance varied over wide ranges across different sites. DNRA rates had a positive and significant correlation with sediment organic content and extractable NH₄⁺, while DNRA rates were weakly correlated with nrfA gene abundance. In comparison, the activities and abundance of DNRA bacteria did not change with a trend along salinity gradient. Pyrosequencing analysis of nrfA gene indicated that delta-proteobacteria was the most abundant at all sites, while epsilon-proteobacteria was hardly found. This study reveals that variability in the activities and community structure of DNRA bacteria is largely driven by changes in environmental factors and provides new insights into the characteristics of DNRA communities in estuarine ecosystems.

Metagenomic potential for and diversity of N-cycle driving microorganisms in the Bothnian Sea sediment

The biological nitrogen cycle is driven by a plethora of reactions transforming nitrogen compounds between various redox states. Here, we investigated the metagenomic potential for nitrogen cycle of the in situ microbial community in an oligotrophic, brackish environment of the Bothnian Sea sediment. Total DNA from three sediment depths was isolated and sequenced. The characterization of the total community was performed based on 16S rRNA gene inventory using SILVA database as reference. The diversity of diagnostic functional genes coding for nitrate reductases (napA;narG), nitrite:nitrate oxidoreductase (nxrA), nitrite reductases (nirK;nirS;nrfA), nitric oxide reductase (nor), nitrous oxide reductase (nosZ), hydrazine synthase (hzsA), ammonia monooxygenase (amoA), hydroxylamine oxidoreductase (hao), and nitrogenase (nifH) was analyzed by blastx against curated reference databases. In addition, Polymerase chain reaction (PCR)‐based amplification was performed on the hzsA gene of anammox bacteria. Our results reveal high genomic potential for full denitrification to N₂, but minor importance of anaerobic ammonium oxidation and dissimilatory nitrite reduction to ammonium. Genomic potential for aerobic ammonia oxidation was dominated by Thaumarchaeota. A higher diversity of anammox bacteria was detected in metagenomes than with PCR‐based technique. The results reveal the importance of various N‐cycle driving processes and highlight the advantage of metagenomics in detection of novel microbial key players.

Diversity and Abundance of the Denitrifying Microbiota in the Sediment of Eastern China Marginal Seas and the Impact of Environmental Factors

Investigating the environmental influence on the community composition and abundance of denitrifiers in marine sediment ecosystem is essential for understanding of the ecosystem-level controls on the biogeochemical process of denitrification. In the present study, nirK-harboring denitrifying communities in different mud deposit zones of eastern China marginal seas (ECMS) were investigated via clone library analysis. The abundance of three functional genes affiliated with denitrification (narG, nirK, nosZ) was assessed by fluorescent quantitative PCR. The nirK-harboring microbiota were dominated by a few operational taxonomic units (OTUs), which were widely distributed in different sites with each site harboring their unique phylotypes. The mean abundance of nirK was significantly higher than that of narG and nosZ genes, and the abundance of narG was higher than that of nosZ. The inconsistent abundance profile of different functional genes along the process of denitrification might indicate that nitrite reduction occurred independently of denitrification in the mud deposit zones of ECMS, and sedimentary denitrification was accomplished by cooperation of different denitrifying species rather than a single species. Such important information would be missed when targeting only a single denitrifying functional gene. Analysis of correlation between abundance ratios and environmental factors revealed that the response of denitrifiers to environmental factors was not invariable in different mud deposit zones. Our results suggested that a comprehensive analysis of different denitrifying functional genes may gain more information about the dynamics of denitrifying microbiota in marine sediments.

Physiological and transcriptional approaches reveal connection between nitrogen and manganese cycles in Shewanella algae C6G3

To explain anaerobic nitrite/nitrate production at the expense of ammonium mediated by manganese oxide (Mn(IV)) in sediment, nitrate and manganese respirations were investigated in a strain (Shewanella algae C6G3) presenting these features. In contrast to S. oneidensis MR-1, a biotic transitory nitrite accumulation at the expense of ammonium was observed in S. algae during anaerobic growth with Mn(IV) under condition of limiting electron acceptor, concomitantly, with a higher electron donor stoichiometry than expected. This low and reproducible transitory accumulation is the result of production and consumption since the strain is able to dissimilative reduce nitrate into ammonium. Nitrite production in Mn(IV) condition is strengthened by comparative expression of the nitrate/nitrite reductase genes (napA, nrfA, nrfA-2), and rates of the nitrate/nitrite reductase activities under Mn(IV), nitrate or fumarate conditions. Compared with S. oneidensis MR-1, S. algae contains additional genes that encode nitrate and nitrite reductases (napA-α and nrfA-2) and an Outer Membrane Cytochrome (OMC)(mtrH). Different patterns of expression of the OMC genes (omcA, mtrF, mtrH and mtrC) were observed depending on the electron acceptor and growth phase. Only gene mtrF-2 (SO1659 homolog) was specifically expressed under the Mn(IV) condition. Nitrate and Mn(IV) respirations seem connected at the physiological and transcriptional levels.

Capturing Compositional Variation in Denitrifying Communities: a Multiple-Primer Approach That Includes Epsilonproteobacteria

Denitrifying Epsilonproteobacteria may dominate nitrogen loss processes in marine habitats with intense redox gradients, but assessment of their importance is limited by the currently available primers for nitrite reductase genes. Nine new primers targeting the nirS gene of denitrifying Epsilonproteobacteria were designed and tested for use in sequencing and quantitative PCR on two microbial mat samples (vent 2 and vent 4) from the Calypso hydrothermal vent field, Bay of Plenty, New Zealand. Commonly used nirS and nirK primer sets nirS1F/nirS6R, cd3aF/R3cd, nirK1F/nirK5R, and F1aCu/R3Cu were also tested to determine what may be missed by the common single-primer approach to assessing denitrifier diversity. The relative importance of Epsilonproteobacteria in these samples was evaluated by 16S rRNA gene sequencing. Epsilonproteobacteria represented up to 75.6% of 16S rRNA libraries, but nirS genes from this group were not found with commonly used primers. Pairing of the new primer EPSnirS511F with either EPSnirS1100R or EPSnirS1105R recovered nirS sequences from members of the genera Sulfurimonas, Sulfurovum, and Nitratifractor. The new quantitative PCR primers EPSnirS103F/EPSnirS530R showed dominance of denitrifying Epsilonproteobacteria in vent 4 compared to vent 2, which had greater representation by "standard" denitrifiers measured with the cd3aF/R3cd primers. Limited results from commonly used nirK primers suggest biased amplification between primers. Future application of multiple nirS and nirK primers, including the new epsilonproteobacterial nirS primers, will improve the detection of denitrifier diversity and the capability to identify changes in dominant denitrifying communities.IMPORTANCE Estimating the potential for increasing nitrogen limitation in the changing global ocean is reliant on understanding the microbial community that removes nitrogen through the process of denitrification. This process is favored under oxygen limitation, which is a growing global-ocean phenomenon. Current methods use the nitrite reductase genes nirS and nirK to assess denitrifier diversity and abundance using primers that target only a few known denitrifiers and systematically exclude denitrifying Epsilonproteobacteria, a group known to dominate in reducing environments, such as hydrothermal vents and anoxic basins. As oxygen depletion expands in the oceans, it is important to study denitrifier community dynamics within those areas to predict future global ocean changes. This study explores the design and testing of new primers that target epsilonproteobacterial nirS and reveals the varied success of existing primers, leading to the recommendation of a multiple-primer approach to assessing denitrifier diversity.

Syntrophic linkage between predatory Carpediemonas and specific prokaryotic populations

Most anoxic environments are populated by small (<10 μm) heterotrophic eukaryotes that prey on different microbial community members. How predatory eukaryotes engage in beneficial interactions with other microbes has rarely been investigated so far. Here, we studied an example of such an interaction by cultivating the anerobic marine flagellate, Carpediemonas frisia sp. nov. (supergroup Excavata), with parts of its naturally associated microbiome. This microbiome consisted of so far uncultivated members of the Deltaproteobacteria, Bacteroidetes, Firmicutes, Verrucomicrobia and Nanoarchaeota. Using genome and transcriptome informed metabolic network modeling, we showed that Carpediemonas stimulated prokaryotic growth through the release of predigested biomolecules such as proteins, sugars, organic acids and hydrogen. Transcriptional gene activities suggested niche separation between biopolymer degrading Bacteroidetes, monomer utilizing Firmicutes and Nanoarchaeota and hydrogen oxidizing Deltaproteobacteria. An efficient metabolite exchange between the different community members appeared to be promoted by the formation of multispecies aggregates. Physiological experiments showed that Carpediemonas could also benefit from an association to these aggregates, as it facilitated the removal of inhibiting metabolites and increased the availability of prey bacteria. Taken together, our results provide a framework to understand how predatory microbial eukaryotes engage, across trophic levels, in beneficial interactions with specific prokaryotic populations.

Spatiotemporal Characterization of San Francisco Bay Denitrifying Communities: a Comparison of nirK and nirS Diversity and Abundance

Denitrifying bacteria play a critical role in the estuarine nitrogen cycle. Through the transformation of nitrate into nitrogen gas, these organisms contribute to the loss of bioavailable (i.e., fixed) nitrogen from low-oxygen environments such as estuary sediments. Denitrifiers have been shown to vary in abundance and diversity across the spatial environmental gradients that characterize estuaries, such as salinity and nitrogen availability; however, little is known about how their communities change in response to temporal changes in those environmental properties. Here, we present a 1-year survey of sediment denitrifier communities along the estuarine salinity gradient of San Francisco Bay. We used quantitative PCR and sequencing of functional genes coding for a key denitrifying enzyme, dissimilatory nitrite reductase, to compare two groups of denitrifiers: those with nirK (encoding copper-dependent nitrite reductase) and those with nirS (encoding the cytochrome-cd ₁-dependent variant). We found that nirS was consistently more abundant and more diverse than nirK in all parts of the estuary. The abundances of the two genes were tightly linked across space but differed temporally, with nirK peaking when temperature was low and nirS peaking when nitrate was high. Likewise, the diversity and composition of nirK- versus nirS-type communities differed in their responses to seasonal variations, though both were strongly determined by site. Furthermore, our sequence libraries detected deeply branching clades with no cultured isolates, evidence of enormous diversity within the denitrifiers that remains to be explored.

Impacts of chemical gradients on microbial community structure

Succession of redox processes is sometimes assumed to define a basic microbial community structure for ecosystems with oxygen gradients. In this paradigm, aerobic respiration, denitrification, fermentation and sulfate reduction proceed in a thermodynamically determined order, known as the ‘redox tower'. Here, we investigated whether redox sorting of microbial processes explains microbial community structure at low-oxygen concentrations. We subjected a diverse microbial community sampled from a coastal marine sediment to 100 days of tidal cycling in a laboratory chemostat. Oxygen gradients (both in space and time) led to the assembly of a microbial community dominated by populations that each performed aerobic and anaerobic metabolism in parallel. This was shown by metagenomics, transcriptomics, proteomics and stable isotope incubations. Effective oxygen consumption combined with the formation of microaggregates sustained the activity of oxygen-sensitive anaerobic enzymes, leading to braiding of unsorted redox processes, within and between populations. Analyses of available metagenomic data sets indicated that the same ecological strategies might also be successful in some natural ecosystems.

Abundance and Diversity of Denitrifying and Anammox Bacteria in Seasonally Hypoxic and Sulfidic Sediments of the Saline Lake Grevelingen

Denitrifying and anammox bacteria are involved in the nitrogen cycling in marine sediments but the environmental factors that regulate the relative importance of these processes are not well constrained. Here, we evaluated the abundance, diversity, and potential activity of denitrifying, anammox, and sulfide-dependent denitrifying bacteria in the sediments of the seasonally hypoxic saline Lake Grevelingen, known to harbor an active microbial community involved in sulfur oxidation pathways. Depth distributions of 16S rRNA gene, nirS gene of denitrifying and anammox bacteria, aprA gene of sulfur-oxidizing and sulfate-reducing bacteria, and ladderane lipids of anammox bacteria were studied in sediments impacted by seasonally hypoxic bottom waters. Samples were collected down to 5 cm depth (1 cm resolution) at three different locations before (March) and during summer hypoxia (August). The abundance of denitrifying bacteria did not vary despite of differences in oxygen and sulfide availability in the sediments, whereas anammox bacteria were more abundant in the summer hypoxia but in those sediments with lower sulfide concentrations. The potential activity of denitrifying and anammox bacteria as well as of sulfur-oxidizing, including sulfide-dependent denitrifiers and sulfate-reducing bacteria, was potentially inhibited by the competition for nitrate and nitrite with cable and/or Beggiatoa-like bacteria in March and by the accumulation of sulfide in the summer hypoxia. The simultaneous presence and activity of organoheterotrophic denitrifying bacteria, sulfide-dependent denitrifiers, and anammox bacteria suggests a tight network of bacteria coupling carbon-, nitrogen-, and sulfur cycling in Lake Grevelingen sediments.

Biostimulation of Indigenous Microbial Community for Bioremediation of Petroleum Refinery Sludge

Nutrient deficiency severely impairs the catabolic activity of indigenous microorganisms in hydrocarbon rich environments (HREs) and limits the rate of intrinsic bioremediation. The present study aimed to characterize the microbial community in refinery waste and evaluate the scope for biostimulation based in situ bioremediation. Samples recovered from the wastewater lagoon of Guwahati refinery revealed a hydrocarbon enriched [high total petroleum hydrocarbon (TPH)], oxygen-, moisture-limited, reducing environment. Intrinsic biodegradation ability of the indigenous microorganisms was enhanced significantly (>80% reduction in TPH by 90 days) with nitrate amendment. Preferred utilization of both higher- (>C30) and middle- chain (C20-30) length hydrocarbons were evident from GC-MS analysis. Denaturing gradient gel electrophoresis and community level physiological profiling analyses indicated distinct shift in community's composition and metabolic abilities following nitrogen (N) amendment. High throughput deep sequencing of 16S rRNA gene showed that the native community was mainly composed of hydrocarbon degrading, syntrophic, methanogenic, nitrate/iron/sulfur reducing facultative anaerobic bacteria and archaebacteria, affiliated to γ- and δ-Proteobacteria and Euryarchaeota respectively. Genes for aerobic and anaerobic alkane metabolism (alkB and bssA), methanogenesis (mcrA), denitrification (nirS and narG) and N2 fixation (nifH) were detected. Concomitant to hydrocarbon degradation, lowering of dissolve O2 and increase in oxidation-reduction potential (ORP) marked with an enrichment of N2 fixing, nitrate reducing aerobic/facultative anaerobic members [e.g., Azovibrio, Pseudoxanthomonas and Comamonadaceae members] was evident in N amended microcosm. This study highlighted that indigenous community of refinery sludge was intrinsically diverse, yet appreciable rate of in situ bioremediation could be achieved by supplying adequate N sources.

Ecological succession leads to chemosynthesis in mats colonizing wood in sea water

Chemosynthetic mats involved in cycling sulfur compounds are often found in hydrothermal vents, cold seeps and whale falls. However, there are only few records of wood fall mats, even though the presence of hydrogen sulfide at the wood surface should create a perfect niche for sulfide-oxidizing bacteria. Here we report the growth of microbial mats on wood incubated under conditions that simulate the Mediterranean deep-sea temperature and darkness. We used amplicon and metagenomic sequencing combined with fluorescence in situ hybridization to test whether a microbial succession occurs during mat formation and whether the wood fall mats present chemosynthetic features. We show that the wood surface was first colonized by sulfide-oxidizing bacteria belonging to the Arcobacter genus after only 30 days of immersion. Subsequently, the number of sulfate reducers increased and the dominant Arcobacter phylotype changed. The ecological succession was reflected by a change in the metabolic potential of the community from chemolithoheterotrophs to potential chemolithoautotrophs. Our work provides clear evidence for the chemosynthetic nature of wood fall ecosystems and demonstrates the utility to develop experimental incubation in the laboratory to study deep-sea chemosynthetic mats.

Ecology of Nitrogen Fixing, Nitrifying, and Denitrifying Microorganisms in Tropical Forest Soils

Soil microorganisms play important roles in nitrogen cycling within forest ecosystems. Current research has revealed that a wider variety of microorganisms, with unexpected diversity in their functions and phylogenies, are involved in the nitrogen cycle than previously thought, including nitrogen-fixing bacteria, ammonia-oxidizing bacteria and archaea, heterotrophic nitrifying microorganisms, and anammox bacteria, as well as denitrifying bacteria, archaea, and fungi. However, the vast majority of this research has been focused in temperate regions, and relatively little is known regarding the ecology of nitrogen-cycling microorganisms within tropical and subtropical ecosystems. Tropical forests are characterized by relatively high precipitation, low annual temperature fluctuation, high heterogeneity in plant diversity, large amounts of plant litter, and unique soil chemistry. For these reasons, regulation of the nitrogen cycle in tropical forests may be very different from that of temperate ecosystems. This is of great importance because of growing concerns regarding the effect of land use change and chronic-elevated nitrogen deposition on nitrogen-cycling processes in tropical forests. In the context of global change, it is crucial to understand how environmental factors and land use changes in tropical ecosystems influence the composition, abundance and activity of key players in the nitrogen cycle. In this review, we synthesize the limited currently available information regarding the microbial communities involved in nitrogen fixation, nitrification and denitrification, to provide deeper insight into the mechanisms regulating nitrogen cycling in tropical forest ecosystems. We also highlight the large gaps in our understanding of microbially mediated nitrogen processes in tropical forest soils and identify important areas for future research.

nirS-Encoding denitrifier community composition, distribution, and abundance along the coastal wetlands of China

For the past few decades, human activities have intensively increased the reactive nitrogen enrichment in China's coastal wetlands. Although denitrification is a critical pathway of nitrogen removal, the understanding of denitrifier community dynamics driving denitrification remains limited in the coastal wetlands. In this study, the diversity, abundance, and community composition of nirS-encoding denitrifiers were analyzed to reveal their variations in China's coastal wetlands. Diverse nirS sequences were obtained and more than 98 % of them shared considerable phylogenetic similarity with sequences obtained from aquatic systems (marine/estuarine/coastal sediments and hypoxia sea water). Clone library analysis revealed that the distribution and composition of nirS-harboring denitrifiers had a significant latitudinal differentiation, but without a seasonal shift. Canonical correspondence analysis showed that the community structure of nirS-encoding denitrifiers was significantly related to temperature and ammonium concentration. The nirS gene abundance ranged from 4.3 × 10(5) to 3.7 × 10(7) copies g(-1) dry sediment, with a significant spatial heterogeneity. Among all detected environmental factors, temperature was a key factor affecting not only the nirS gene abundance but also the community structure of nirS-type denitrifiers. Overall, this study significantly enhances our understanding of the structure and dynamics of denitrifying communities in the coastal wetlands of China.

Environmental Breviatea harbour mutualistic Arcobacter epibionts

Breviatea form a lineage of free living, unicellular protists, distantly related to animals and fungi. This lineage emerged almost one billion years ago, when the oceanic oxygen content was low, and extant Breviatea have evolved or retained an anaerobic lifestyle. Here we report the cultivation of Lenisia limosa, gen. et sp. nov., a newly discovered breviate colonized by relatives of animal-associated Arcobacter. Physiological experiments show that the association of L. limosa with Arcobacter is driven by the transfer of hydrogen and is mutualistic, providing benefits to both partners. With whole-genome sequencing and differential proteomics, we show that an experimentally observed fitness gain of L. limosa could be explained by the activity of a so far unknown type of NAD(P)H-accepting hydrogenase, which is expressed in the presence, but not in the absence, of Arcobacter. Differential proteomics further reveal that the presence of Lenisia stimulates expression of known 'virulence' factors by Arcobacter. These proteins typically enable colonization of animal cells during infection, but may in the present case act for mutual benefit. Finally, re-investigation of two currently available transcriptomic data sets of other Breviatea reveals the presence and activity of related hydrogen-consuming Arcobacter, indicating that mutualistic interaction between these two groups of microbes might be pervasive. Our results support the notion that molecular mechanisms involved in virulence can also support mutualism, as shown here for Arcobacter and Breviatea.

Towards a Definition of Harmless Nanoparticles from an Environmental and Safety Perspective

The rapid development of nanoparticles (NPs), such as silicon nanoparticles (Si NPs) and ferric oxide nanoparticles (Fe2O3NPs), and their use in myriad commercial applications have raised questions of their potential impacts on wastewater treatment systems. In this study, we investigated the consequences of the presence of Si NPs and Fe2O3NPs in the denitrification of anoxic sludge. Fe2O3NPs, at a concentration up to 50 mg/L, had no significant impact on nitrate removal, whereas Si NPs, at concentrations up to 50 mg/L, increased the rate of nitrate removal. We used transmission electron microscopy (TEM) to investigate the effect of Si NPs and Fe2O3NPs. Si NPs exposure enhanced the abundance ofnarG-1 gene, which might promote nitrate removal process directly. Finally, we reviewed and identified the specific properties of a variety of NPs responsible for toxicity and found NPs larger than about 100 nm and without ion release in general possible to energy safety and nontoxic or low toxic to environment. Our results provide useful information to understand the response of anoxic sludge to Si NPs and Fe2O3NPs in complex environmental matrix as well as potent support for wide use of the environmentally friendly NPs.

Nutrient removal and microbial mechanisms in constructed wetland microcosms treating high nitrate/nitrite polluted river water

In constructed wetland microcosms, nitrogen removal and microbial mechanisms were investigated by treating relatively high concentrations of nitrate/nitrite wastewater

Management Practices Affect Soil Nutrients and Bacterial Populations in Backgrounding Beef Feedlot

Contaminants associated with manure in animal production sites are of significant concern. Unless properly managed, manure-derived soil nutrients in livestock production sites can deteriorate soil and water quality. This 3-yr study evaluated a soil nutrient management strategy with four sequentially imposed management practices: 12-mo backgrounding (BG), manure removal from the feeder area (FD), 12-mo destocking (DS), and 12-mo grass hay harvesting (H) in a small backgrounding feedlot. Resulting soil nutrient levels, total (), and N cycling bacterial ( and ) populations after each management practice in feedlot feeder and grazing (GR) areas and in crop grown at the control location (CT) were measured. Irrespective of management practice, FD contained greater soil nutrient concentrations than the GR and CT. Regardless of management practice, total bacteria cells (1.4 × 10 cells g soil) and nitrate reducers (5.2 × 10 cells g soil) were an order of magnitude higher in the FD than in the GR and CT, whereas nitrifying bacteria concentrations (1.4 × 10 cells g soil) were higher in the GR. Manure removal from the feeder area reduced M3-P (39%), total C (21%), total N (23%), NH-N (47%), and NO-N (93%) levels established in the FD during BG. Destocking lowered total C and N (45%) in the FD and NH-N (47%), NO-N (76%), and Zn (16%) in the GR. Hay harvesting reduced all soil nutrients in the FD and GR marginally. The management strategy has potential to lower soil nutrient concentrations, control soil nutrient buildup, and limit nutrient spread within the feedlot.

Dissimilatory nitrogen reduction in intertidal sediments of a temperate estuary: small scale heterogeneity and novel nitrate-to-ammonium reducers

The estuarine nitrogen cycle can be substantially altered due to anthropogenic activities resulting in increased amounts of inorganic nitrogen (mainly nitrate). In the past, denitrification was considered to be the main ecosystem process removing reactive nitrogen from the estuarine ecosystem. However, recent reports on the contribution of dissimilatory nitrate reduction to ammonium (DNRA) to nitrogen removal in these systems indicated a similar or higher importance, although the ratio between both processes remains ambiguous. Compared to denitrification, DNRA has been underexplored for the last decades and the key organisms carrying out the process in marine environments are largely unknown. Hence, as a first step to better understand the interplay between denitrification, DNRA and reduction of nitrate to nitrite in estuarine sediments, nitrogen reduction potentials were determined in sediments of the Paulina polder mudflat (Westerschelde estuary). We observed high variability in dominant nitrogen removing processes over a short distance (1.6 m), with nitrous oxide, ammonium and nitrite production rates differing significantly between all sampling sites. Denitrification occurred at all sites, DNRA was either the dominant process (two out of five sites) or absent, while nitrate reduction to nitrite was observed in most sites but never dominant. In addition, novel nitrate-to-ammonium reducers assigned to Thalassospira, Celeribacter, and Halomonas, for which DNRA was thus far unreported, were isolated, with DNRA phenotype reconfirmed through nrfA gene amplification. This study demonstrates high small scale heterogeneity among dissimilatory nitrate reduction processes in estuarine sediments and provides novel marine DNRA organisms that represent valuable alternatives to the current model organisms.