15N-DNA stable isotope probing reveals niche differentiation of ammonia oxidizers in paddy soils.

Chemoautotrophic canonical ammonia oxidizers (ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB)) and complete ammonia oxidizers (comammox Nitrospira) are accountable for ammonia oxidation, which is a fundamental process of nitrification in terrestrial ecosystems. However, the relationship between autotrophic nitrification and the active nitrifying populations during 15N-urea incubation has not been totally clarified. The 15N-labeled DNA stable isotope probing (DNA-SIP) technique was utilized in order to study the response from the soil nitrification process and the active nitrifying populations, in both acidic and neutral paddy soils, to the application of urea. The presence of C2H2 almost completely inhibited NO3--N production, indicating that autotrophic ammonia oxidation was dominant in both paddy soils. 15N-DNA-SIP technology could effectively distinguish active nitrifying populations in both soils. The active ammonia oxidation groups in both soils were significantly different, AOA (NS (Nitrososphaerales)-Alpha, NS-Gamma, NS-Beta, NS-Delta, NS-Zeta and NT (Ca. Nitrosotaleales)-Alpha), and AOB (Nitrosospira) were functionally active in the acidic paddy soil, whereas comammox Nitrospira clade A and Nitrosospira AOB were functionally active in the neutral paddy soil. This study highlights the effective discriminative effect of 15N-DNA-SIP and niche differentiation of nitrifying populations in these paddy soils. KEY POINTS: • 15N-DNA-SIP technology could effectively distinguish active ammonia oxidizers. • Comammox Nitrospira clade A plays a lesser role than canonical ammonia oxidizers. • The active groups in the acidic and neutral paddy soils were significantly different.

AuNi bimetallic aerogel with ultra-high stability applied in smart and portable biosensing.

Glucose detection is of significant importance in providing information to the human health management. However, conventional enzymatic glucose sensors suffer from a limited long-term stability due to the losing activity of the enzymes. In this work, the AuNi bimetallic aerogel with a well-defined nanowire network is synthesized and applied as the sensing nanomaterial in the non-enzymatic glucose detection. The three-dimensional (3D) hierarchical porous structure of the AuNi bimetallic aerogel ensures the high sensitivity of the sensor (40.34 µA mM-1 cm-2). Theoretical investigation unveiled the mechanism of the boosting electrocatalytic activity of the AuNi bimetallic aerogel toward glucose. A better adhesion between the sensing nanomaterial and the screen-printing electrodes (SPEs) is obtained after the introduction of Ni. On the basis of a wide linearity in the range of 0.1-5 mM, an excellent selectivity, an outstanding long-term stability (90 days) as well as the help of the signal processing circuit and an M5stack development board, the as-prepared glucose sensor successfully realizes remote monitoring of the glucose concentration. We speculate that this work is favorable to motivating the technological innovations of the non-enzymatic glucose sensors and intelligent sensing devices.

Elevated CO2 altered the nano-ZnO-induced influence on bacterial and fungal composition in tomato (Solanum lycopersicum L.) rhizosphere soils.

To investigate whether elevated CO2 (eCO2) changes the influence of nanoparticles (NPs) on soil microbial communities and the mechanisms, various nano-ZnO (0, 100, 300, and 500 mg·kg-1) and CO2 concentrations (400 and 800 µmol·mol-1) were applied to tomato plants (Solanum lycopersicum L.) in growth chambers. Plant growth, soil biochemical properties, and rhizosphere soil microbial community composition were analyzed. In 500 mg·kg-1 nano-ZnO-treated soils, root Zn content was 58% higher, while total dry weight (TDW) was 39.8% lower under eCO2 than under atmospheric CO2 (aCO2). Compared with the control, the interaction of eCO2 and 300 mg·kg-1 nano-ZnO decreased and increased bacterial and fungal alpha diversities, respectively, which was caused by the direct effect of nano-ZnO (r = - 1.47, p < 0.01). Specifically, the bacterial OTUs decreased from 2691 to 2494, while fungal OTUs increased from 266 to 307, when 800-300 was compared with 400-0 treatment. eCO2 enhanced the influence of nano-ZnO on bacterial community structure, while only eCO2 significantly shaped fungal composition. In detail, nano-ZnO explained 32.4% of the bacterial variations, while the interaction of CO2 and nano-ZnO explained 47.9%. Betaproteobacteria, which are involved in C, N, and S cycling, and r-strategists, such as Alpha- and Gammaproteobacteria and Bacteroidetes, significantly decreased under 300 mg·kg-1 nano-ZnO, confirming reduced root secretions. In contrast, Alpha- and Gammaproteobacteria, Bacteroidetes, Chloroflexi, and Acidobacteria were enriched in 300 mg·kg-1 nano-ZnO under eCO2, suggesting greater adaptation to both nano-ZnO and eCO2. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States 2 (PICRUSt2) analysis demonstrated that bacterial functionality was unchanged under short-term nano-ZnO and eCO2 exposure. In conclusion, nano-ZnO significantly affected microbial diversities and the bacterial composition, and eCO2 intensified the damage of nano-ZnO, while the bacterial functionality was not changed in this study.

Dose effect of polyethylene microplastics on nitrous oxide emissions from paddy soils cultivated for different periods.

The presence of microplastics (MPs) under flooded conditions is beneficial for nitrifiers and denitrifiers to produce nitrous oxide (N2O), but their dose effect remains unclear. This study evaluated the impact of different doses of polyethylene (PE) MPs on the release of N2O from paddy soils cultivated for different years. Compared with unpolluted soils, low doses of MPs (≤ 0.1%) had a negligible influence on N2O emissions, and high amounts of MPs (≥ 0.5%) significantly (p < 0.05) increased N2O emissions from the paddy soils cultivated for 3, 15 and 40 years by 2.5-4.3, 3.9-8.5 and 8.9-27.7 times, respectively. Moreover, an exponential model indicated that a 0.2% concentration of PE MPs appeared to be the dose threshold that accelerated the release of N2O from the all soils. Increased MP concentrations accelerated N2O emissions by affecting microbial functional genes involved in N2O production and reduction, but microbial taxonomic attributes involved in nitrogen cycling played an insignificant role in controlling N2O emissions. Overall, our results indicated that high doses (≥ 0.5%) of PE MPs essentially accelerated the emission of N2O from rice soils, and a longer cultivation period (40 years) enhanced the positive effect of MPs on N2O emissions.

Dual Structural Design of Platinum-Nickel Hydrogels for Wearable Glucose Biosensing with Ultrahigh Stability.

Wearable glucose sensors are of great significance and highly required in mobile health monitoring and management but suffering from limited long-term stability and wearable adaptability. Here a simultaneous component and structure engineering strategy is presented, which involves Pt with abundant Ni to achieve three-dimensional, dual-structural Pt-Ni hydrogels with interconnected networks of PtNi nanowires and Ni(OH)2 nanosheets, showing prominent electrocatalytic activity and stability in glucose oxidation under neutral condition. Specifically, the PtNi(1:3) dual hydrogels shows 2.0 and 270.6 times' activity in the glucose electro-oxidation as much as the pure Pt and Ni hydrogels. Thanks to the high activity, structural stability, good flexibility, and self-healing property, the PtNi(1:3) dual gel-based non-enzymatic glucose sensing chip is endowed with high performance. It features a high sensitivity, an excellent selectivity and flexibility, and particularly an outstanding long-term stability over 2 months. Together with a pH sensor and a wireless circuit, an accurate, real-time, and remote monitoring of sweat glucose is achieved. This facile design of novel dual-structural metallic hydrogels sheds light to rationally develop new functional materials for high-performance wearable biosensors.

Influence of reductive soil disinfestation or biochar amendment on bacterial communities and their utilization of plant-derived carbon in the rhizosphere of tomato.

Root-associated microorganisms play an important role in plant nutrition and productivity. However, our understanding of how a plant-microbiome system responds to pre-planting soil management remains limited. Here, continuous labeling with 13CO2 gas combined with stable isotope probing (SIP) was applied to explore bacterial utilization of plant-derived carbon (C) in the tomato rhizosphere as affected by biochar amendment or reductive soil disinfestation (RSD). Our results showed that RSD treatment strongly shaped the soil bacterial community composition, while biochar soil amendment had little impact on the community in the rhizosphere of tomato. We observed that the bacterial community in the RSD treatment, which actively utilized plant-derived C, belonged to various phyla (i.e., Proteobacteria, Cyanobacteria, Verrucomicrobia, and Acidobacteria), while the genus Streptomyces (phylum Actinobacteria) was the main bacterial taxa that actively utilized plant-derived C in the biochar and control treatments. This study provides evidence that biochar application or RSD pre-planting soil management practices induced distinct bacterial utilization of plant-derived C, which may in turn regulate plant productivity in agricultural systems. KEY POINTS: • Genus Streptomyces was the main bacterial group utilizing plant-derived carbon in both control and biochar treatments. • Reductive soil disinfestation altered bacterial utilization of plant-derived carbon. • Biochar did not alter the composition of the bacterial communities but had more labeled bacterial taxa utilizing plant-derived carbon.

Nitrification and Nitrifying Bacteria in a Coastal Microbial Mat.

The first step of nitrification, the oxidation of ammonia to nitrite, can be performed by ammonia-oxidizing archaea (AOA) or ammonium-oxidizing bacteria (AOB). We investigated the presence of these two groups in three structurally different types of coastal microbial mats that develop along the tidal gradient on the North Sea beach of the Dutch barrier island Schiermonnikoog. The abundance and transcription of amoA, a gene encoding for the alpha subunit of ammonia monooxygenase that is present in both AOA and AOB, were assessed and the potential nitrification rates in these mats were measured. The potential nitrification rates in the three mat types were highest in autumn and lowest in summer. AOB and AOA amoA genes were present in all three mat types. The composition of the AOA and AOB communities in the mats of the tidal and intertidal stations, based on the diversity of amoA, were similar and clustered separately from the supratidal microbial mat. In all three mats AOB amoA genes were significantly more abundant than AOA amoA genes. The abundance of neither AOB nor AOA amoA genes correlated with the potential nitrification rates, but AOB amoA transcripts were positively correlated with the potential nitrification rate. The composition and abundance of amoA genes seemed to be partly driven by salinity, ammonium, temperature, and the nitrate/nitrite concentration. We conclude that AOB are responsible for the bulk of the ammonium oxidation in these coastal microbial mats.

Drivers of the dynamics of diazotrophs and denitrifiers in North Sea bottom waters and sediments.

The fixation of dinitrogen (N2) and denitrification are two opposite processes in the nitrogen cycle. The former transfers atmospheric dinitrogen gas into bound nitrogen in the biosphere, while the latter returns this bound nitrogen back to atmospheric dinitrogen. It is unclear whether or not these processes are intimately connected in any microbial ecosystem or that they are spatially and/or temporally separated. Here, we measured seafloor nitrogen fixation and denitrification as well as pelagic nitrogen fixation by using the stable isotope technique. Alongside, we measured the diversity, abundance, and activity of nitrogen-fixing and denitrifying microorganisms at three stations in the southern North Sea. Nitrogen fixation ranged from undetectable to 2.4 nmol N L(-1) d(-1) and from undetectable to 8.2 nmol N g(-1) d(-1) in the water column and seafloor, respectively. The highest rates were measured in August at Doggersbank, both for the water column and for the seafloor. Denitrification ranged from 1.7 to 208.8 µmol m(-2) d(-1) and the highest rates were measured in May at the Oyster Grounds. DNA sequence analysis showed sequences of nifH, a structural gene for nitrogenase, related to sequences from anaerobic sulfur/iron reducers and sulfate reducers. Sequences of the structural gene for nitrite reductase, nirS, were related to environmental clones from marine sediments. Quantitative polymerase chain reaction (qPCR) data revealed the highest abundance of nifH and nirS genes at the Oyster Grounds. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) data revealed the highest nifH expression at Doggersbank and the highest nirS expression at the Oyster Grounds. The distribution of the diazotrophic and denitrifying communities seems to be subject to different selecting factors, leading to spatial and temporal separation of nitrogen fixation and denitrification. These selecting factors include temperature, organic matter availability, and oxygen concentration.

Denitrification and the denitrifier community in coastal microbial mats.

Denitrification was measured in three structurally different coastal microbial mats by using the stable isotope technique. The composition of the denitrifying community was determined by analyzing the nitrite reductase (nirS and nirK) genes using clone libraries and the GeoChip. The highest potential rate of denitrification (7.0 ± 1.0 mmol N m(-2) d(-1)) was observed during summer at station 1 (supra-littoral). The rates of denitrification were much lower in the stations 2 (marine) and 3 (intermediate) (respectively 0.1 ± 0.05 and 0.7 ± 0.2 mmol N m(-2) d(-1)) and showed less seasonality when compared to station 1. The denitrifying community at station 1 was also more diverse than that at station 2 and 3, which were more similar to each other than either of these stations to station 1. In all three stations, the diversity of both nirS and nirK denitrifiers was higher in summer when compared to winter. The location along the tidal gradient seems to determine the composition, diversity and activity of the denitrifier community, which may be driven by salinity, nitrate/nitrite and organic carbon. Both nirS and nirK denitrifiers are equally present and therefore they are likely to play a role in the denitrification of the microbial mats studied.

Occurrence and activity of anammox bacteria in surface sediments of the southern North Sea.

We investigated the occurrence and activity of anaerobic ammonia oxidation (anammox) bacteria in sandy and muddy sand sediments of the southern North Sea. The presence of anammox bacteria was established through the detection of specific phosphocholine-monoether ladderane lipids, 16S rRNA gene, and hydrazine synthase (hzsA) genes. Anammox activity was measured in intact sediment cores (in situ rate) and in sediment slurries (potential rate) as the rate of N2 evolution from (15) N-labeled substrates and compared to the transcriptional activity of genes of anammox bacteria. The contribution of anammox to N2 production ranged between 0% and 29%. The potential rate of anammox agreed well with the abundance of anammox bacteria 16S rRNA and hzsA gene copies and the transcriptional activity of the anammox bacteria 16S rRNA gene. We found a higher abundance and activity of anammox bacteria in sediments with higher organic carbon content and also higher activity in summer than in winter. The abundance of anammox bacteria and their potential anammox rates were similar to those reported for other marine coastal sediments, suggesting that potentially they are important contributors to the nitrogen cycle in sandy sediments of shallow continental shelf areas.

Draft genome sequence of Halomonas sp. strain HAL1, a moderately halophilic arsenite-oxidizing bacterium isolated from gold-mine soil.

We report the draft genome sequence of arsenite-oxidizing Halomonas sp. strain HAL1, isolated from the soil of a gold mine. Genes encoding proteins involved in arsenic resistance and transformation, phosphate utilization and uptake, and betaine biosynthesis were identified. Their identification might help in understanding how arsenic and phosphate metabolism are intertwined.