Characterization of denitrifying activity by the alphaproteobacterium, Sphingomonas wittichii RW1

Endophyte Community Changes in the Seeds of Eight Plant Species following Inoculation with a Multi-Endophytic Bacterial Consortium and an Individual Sphingomonas wittichii Strain Obtained from Noccaea caerulescens

Noccaea caerulescens, a hyperaccumulator plant species known for its metal tolerance and accumulation abilities, harbours a microbiome of interest within its seed. These seed-associated bacteria, often referred to as seed endophytes, play a unique role in seed germination and plant growth and health. This work aimed to address how inoculating seeds of eight different plant species-Medicago sativa (alfalfa), Zea mays (corn), Raphanus sativus (radish), Helianthus annus (sunflower), Cucurbita pepo subsp. pepo (squash), Beta vulgaris subsp. cicla (rainbow chard), Arabidopsis thaliana (thale cress), and Noccaea caerulescens (penny cress)-with a bacterial consortium made from the seed endophytes of N. caerulescens would affect the seed microbiome of each test plant species, as well as inoculation with a strain of the bacterium Sphingomonas wittichii, which was previously isolated from seeds of N. caerulescens. Additionally, we aimed to offer preliminary plant tests in order to determine the best seed treatment plan for future research. The results showed that inoculation with the bacterial consortium held the most potential for increasing plant size (p < 0.001) and increasing germination rate (p < 0.05). The plant that responded best to inoculation was N. caerulescens (penny cress), likely because the microbes being introduced into the seed were not foreign. This paper also offers the first insight into the seed endophytes of Beta vulgaris subsp. cicla, highlighting an abundance of Proteobacteria, Firmicutes, and Actinobacteriota.

Effects of iron-based substrate on coupling of nitrification, aerobic denitrification and Fe(II) autotrophic denitrification in tidal flow constructed wetlands

The aerobic properties of nitrification and the anaerobic properties of denitrification in constructed wetlands are difficult to reconcile. In this study, two constructed wetlands were constructed with pyrite and steel slag in combination with zeolite, and their respective nitrification and denitrification capacities were evaluated under different tidal strategies. The steel slag wetland achieved 70.89 % and 46.04 % removal rates of NH₄⁺-N and total nitrogen (TN), and the carbon consumption of denitrification was 1.51 mg BOD/mgN, which was better than pyrite wetland. Microbial analysis showed that Fe(II) autotrophic denitrification and aerobic denitrification occurred in both wetlands, and they were coupled with nitrification to achieve simultaneous removal of NH₄⁺-N and TN. Microbial co-occurrence network and k-core decomposition analysis indicated that the core genus of steel slag wetlands was nitrifying bacteria. This study provides new insights into the application of tidal flow wetlands to treat rural sewage.

Nitric oxide and nitrite removal by partial denitrifying hollow-fiber membrane biofilm reactor coupled with nitrous oxide generation as energy recovery

Nitrogen oxide (NOx) emissions cause significant impacts on the environment and must therefore be controlled even more stringently. This requires the development of cost-effective removal strategies which simultaneously create value-added by-products or energy from the waste. This study aims to treat gaseous nitric oxide (NO) by hollow-fibre membrane biofilm reactor (HFMBfR) in the presence of nitrite (NO2-) and evaluate nitrous oxide (N₂O) emissions formed as an intermediate product during the denitrification process. Accumulated N₂O can be utilised in methane oxidation as an oxidant to produce energy. In the first stage of the study, the HFMBfR was operated by feeding only gaseous NO as the nitrogen source. During this period, the best performance was achieved with 92% NO removal efficiency (RE). In the second stage, both NO gas and NO2- were supplied to the system, and 91% NO and 99% NO2- reduction were achieved simultaneously with the maximum N₂O generation of 386 ± 31 ppm. Lower influent carbon to nitrogen (C/N) ratios, such as 4.5 and 2.0, and higher NO2--N loading rate of 158 mg N day^-1 favoured N₂O generation. An improved NO removal rate and N₂O accumulation were seen with the increasing amount of PO43- in the medium. The 16S rDNA sequencing analysis revealed that Alicycliphilus denitrificans and Pseudomonas putida were the dominant species. The study shows that an HFMBfR can be successfully used to eliminate both NO2- and gaseous NO and simultaneously generate N₂O by adjusting the system parameters such as C/N ratio, NO2- and PO43- loading.

Variation in Bacterial Community Structure Under Long-Term Fertilization, Tillage, and Cover Cropping in Continuous Cotton Production

Agricultural practices alter the structure and functions of soil microbial community. However, few studies have documented the alterations of bacterial communities in soils under long-term conservation management practices for continuous crop production. In this study, we evaluated soil bacterial diversity using 16S rRNA gene sequencing and soil physical and chemical properties within 12 combinations of inorganic N fertilization, cover cropping, and tillage throughout a cotton production cycle. Soil was collected from field plots of the West Tennessee Agriculture Research and Education Center in Jackson, TN, United States. The site has been under continuous cotton production for 38 years. A total of 38,038 OTUs were detected across 171 soil samples. The dominant bacterial phyla were Proteobacteria, Acidobacteria, Actinobacteria, Verrucomicrobia, and Chloroflexi, accounting for ∼70% of the total bacterial community membership. Conventional tillage increased alpha diversity in soil samples collected in different stages of cotton production. The effects of inorganic N fertilization and conventional tillage on the structure of bacterial communities were significant at all four sampling dates (p < 0.01). However, cover cropping (p < 0.05) and soil moisture content (p < 0.05) only showed significant influence on the bacterial community structure after burn-down of the cover crops and before planting of cotton (May). Nitrate-N appeared to have a significant effect on the structure of bacterial communities after inorganic fertilization and at the peak of cotton growth (p < 0.01). Structural equation modeling revealed that the relative abundances of denitrifying and nitrifying bacteria were higher when conventional tillage and vetch cover crop practices were applied, respectively. Our results indicate that long-term tillage and fertilization are key factors increasing the diversity and restructuring the composition of bacterial communities, whereas cover cropping may have shorter-term effects on soil bacteria community structure. In this study, management practices might positively influence relative abundances of bacterial functional groups associated with N cycling. The bacteria functional groups may build a network for providing N and meet microbial N needs in the long term.

Molecular and culture-based assessment of the microbiome in a zebrafish (Danio rerio) housing system during set-up and equilibration

BACKGROUND

Zebrafish used in research settings are often housed in recirculating aquaculture systems (RAS) which rely on the system microbiome, typically enriched in a biofiltration substrate, to remove the harmful ammonia generated by fish via oxidation. Commercial RAS must be allowed to equilibrate following installation, before fish can be introduced. There is little information available regarding the bacterial community structure in commercial zebrafish housing systems, or the time-point at which the system or biofilter reaches a microbiological equilibrium in RAS in general.

METHODS

A zebrafish housing system was monitored at multiple different system sites including tank water in six different tanks, pre- and post-particulate filter water, the fluidized bed biofilter substrate, post-carbon filter water, and water leaving the ultra-violet (UV) disinfection unit and entering the tanks. All of these samples were collected in quadruplicate, from prior to population of the system with zebrafish through 18 weeks post-population, and analyzed using both 16S rRNA amplicon sequencing and culture using multiple agars and annotation of isolates via matrix-assisted laser desorption/ionization-time-of-flight (MALDI-TOF) mass spectrometry. Sequencing data were analyzed using traditional methods, network analyses of longitudinal data, and integration of culture and sequence data.

RESULTS

The water microbiome, dominated by Cutibacterium and Staphylococcus spp., reached a relatively stable richness and composition by approximately three to four weeks post-population, but continued to evolve in composition throughout the study duration. The microbiomes of the fluidized bed biofilter and water leaving the UV disinfection unit were distinct from water at all other sites. Core taxa detected using molecular methods comprised 36 amplicon sequence variants, 15 of which represented Proteobacteria including multiple members of the families Burkholderiaceae and Sphingomonadaceae. Culture-based screening yielded 36 distinct isolates, and showed moderate agreement with sequencing data.

CONCLUSIONS

The microbiome of commercial RAS used for research zebrafish reaches a relatively stable state by four weeks post-population and would be expected to be suitable for experimental use following that time-point.

Holobiont nitrogen control and its potential for eutrophication resistance in an obligate photosymbiotic jellyfish

BACKGROUND

Marine holobionts depend on microbial members for health and nutrient cycling. This is particularly evident in cnidarian-algae symbioses that facilitate energy and nutrient acquisition. However, this partnership is highly sensitive to environmental change-including eutrophication-that causes dysbiosis and contributes to global coral reef decline. Yet, some holobionts exhibit resistance to dysbiosis in eutrophic environments, including the obligate photosymbiotic scyphomedusa Cassiopea xamachana.

METHODS

Our aim was to assess the mechanisms in C. xamachana that stabilize symbiotic relationships. We combined labelled bicarbonate (13C) and nitrate (15N) with metabarcoding approaches to evaluate nutrient cycling and microbial community composition in symbiotic and aposymbiotic medusae.

RESULTS

C-fixation and cycling by algal Symbiodiniaceae was essential for C. xamachana as even at high heterotrophic feeding rates aposymbiotic medusae continuously lost weight. Heterotrophically acquired C and N were readily shared among host and algae. This was in sharp contrast to nitrate assimilation by Symbiodiniaceae, which appeared to be strongly restricted. Instead, the bacterial microbiome seemed to play a major role in the holobiont's DIN assimilation as uptake rates showed a significant positive relationship with phylogenetic diversity of medusa-associated bacteria. This is corroborated by inferred functional capacity that links the dominant bacterial taxa (~90 %) to nitrogen cycling. Observed bacterial community structure differed between apo- and symbiotic C. xamachana putatively highlighting enrichment of ammonium oxidizers and nitrite reducers and depletion of nitrogen-fixers in symbiotic medusae.

CONCLUSION

Host, algal symbionts, and bacterial associates contribute to regulated nutrient assimilation and cycling in C. xamachana. We found that the bacterial microbiome of symbiotic medusae was seemingly structured to increase DIN removal and enforce algal N-limitation-a mechanism that would help to stabilize the host-algae relationship even under eutrophic conditions. Video abstract.

The bacterial microbiota in florfenicol contaminated soils: The antibiotic resistome and the nitrogen cycle

Soil antibiotic resistome and the nitrogen cycle are affected by florfenicol addition to manured soils but their interactions have not been fully described. In the present study, antibiotic resistance genes (ARGs) and nitrogen cycle genes possessed by soil bacteria were characterized using real-time fluorescence quantification PCR (qPCR) and metagenomic sequencing in a short-term (30 d) soil model experiment. Florfenicol significantly changed in the abundance of genes conferring resistance to aminoglycosides, β-lactams, tetracyclines and macrolides. And the abundance of Sphingomonadaceae, the protein metabolic and nitrogen metabolic functions, as well as NO reductase, nitrate reductase, nitrite reductase and N₂O reductase can also be affected by florfenicol. In this way, ARG types of genes conferring resistance to aminoglycosides, β-lactamases, tetracyclines, colistin, fosfomycin, phenicols and trimethoprim were closely associated with multiple nitrogen cycle genes. Actinobacteria, Chlorobi, Firmicutes, Gemmatimonadetes, Nitrospirae, Proteobacteria and Verrucomicrobia played an important role in spreading of ARGs. Moreover, soil physicochemical properties were important factors affecting the distribution of soil flora. This study provides a theoretical basis for further exploration of the transmission regularity and interference mechanism of ARGs in soil bacteria responsible for nitrogen cycle.

Composting swine carcasses with nitrogen transformation microbial strains: Succession of microbial community and nitrogen functional genes

In this study, nitrogen transformation strains, including three ammonium transformation strains, one nitrite strain and one nitrogen fixer, were inoculated at different swine carcass composting stages to regulate the nitrogen transformation and control the nitrogen loss. The final total nitrogen content was significantly increased (p < 0.01). The bacterial communities were assessed by amplicon sequencing and association analysis. Proteobacteria, Actinobacteria, Bacteroidetes and Firmicutes were the four most dominant phyla.,Brevibacterium, Streptomyces and Ochrobactrum had a significant (p < 0.05) and positive correlation with total nitrogen and ammonium nitrogen content in both groups. The quantitative results of nitrogen transformation genes showed that ammonification, nitrification, denitrification and nitrogen fixation were simultaneously present in the composting process of swine carcasses, with the latter two accounting for a higher proportion. The ammonium transformation strains significantly (p < 0.05) strengthened nitrogen fixation and remarkably (p < 0.01) weakened nitrification and denitrification, which, however, were notably (p < 0.05) enhanced by the nitrite strain and nitrogen fixer. In this research, the inoculated strains changed the bacterial structure by regulating the abundance and activity of the highly connected taxa, which facilitated the growth of nitrogen transformation bacteria and regulated the balance/symbiosis of nitrogen transformation processes to accelerate the accumulation of nitrogen.

Aerobic denitrifiers with petroleum metabolizing ability isolated from caprolactam sewage treatment pool

To improve the biological nitrogen removal efficiency of petrochemical wastewater, three aerobic denitrifiers were isolated from caprolactam sewage treatment pool. They were identified as Acinetobacter sp. YY1, Sphingomonas sp. YY2 and Pseudomonas sp. YY3, respectively. The nitrification and denitrification enzyme genes could be detected using polymerase chain reaction (PCR). Moreover, the strain YY2 was a novel aerobic denitrifier belongs to genus of Sphingomonas, which showed great ability for metabolizing aromatic hydrocarbons. In the nitrification and denitrification process, the total nitrogen (TN) removal efficiency after 48 h was 94.22% and 90.10%, respectively. In the process of simultaneous nitrification and denitrification in mixed N-source, ammonia nitrogen was preferentially utilized. Furthermore, the strain YY2 exhibited excellent extracellular polymer secretion properties and excellent aerobic denitrification capacity using petroleum refractory organic compounds, which are beneficial for the formation of bacterial micelles and the engineering applications for the treatment of petrochemical wastewater.

Naphthalene biodegradation under oxygen-limiting conditions: community dynamics and the relevance of biofilm-forming capacity

Toxic polycyclic aromatic hydrocarbons (PAHs) are frequently released into the environment from anthropogenic sources. PAH remediation strategies focus on biological processes mediated by bacteria. The availability of oxygen in polluted environments is often limited or absent, and only bacteria able to thrive in these conditions can be considered for bioremediation strategies. To identify bacterial strains able to degrade PAHs under oxygen‐limiting conditions, we set up enrichment cultures from samples of an oil‐polluted aquifer, using either anoxic or microaerophilic condition and with PAHs as the sole carbon source. Despite the presence of a significant community of nitrate‐reducing bacteria, the initial community, which was dominated by Betaproteobacteria, was incapable of PAH degradation under strict anoxic conditions, although a clear shift in the structure of the community towards an increase in the Alphaproteobacteria (Sphingomonadaceae), Actinobacteria and an uncultured group of Acidobacteria was observed in the enrichments. In contrast, growth under microaerophilic conditions with naphthalene as the carbon source evidenced the development of a biofilm structure around the naphthalene crystal. The enrichment process selected two co‐dominant groups which finally reached 97% of the bacterial communities: Variovorax spp. (54%, Betaproteobacteria) and Starkeya spp. (43%, Xanthobacteraceae). The two dominant populations were able to grow with naphthalene, although only Starkeya was able to reproduce the biofilm structure around the naphthalene crystal. The pathway for naphthalene degradation was identified, which included as essential steps dioxygenases with high affinity for oxygen, showing 99% identity with Xanthobacter polyaromaticivorans dbd cluster for PAH degradation. Our results suggest that the biofilm formation capacity of Starkeya provided a structure to allocate its cells at an appropriate distance from the toxic carbon source.

Effects of aeration and internal recycle flow on nitrous oxide emissions from a modified Ludzak-Ettinger process fed with glycerol

Nitrous oxide (N2O) is emitted from a modified Ludzak-Ettinger (MLE) process, as a primary activated sludge system, which requires mitigation. The effects of aeration rates and internal recycle flow (IRF) ratios on N2O emission were investigated in an MLE process fed with glycerol. Reducing the aeration rate from 1.5 to 0.5 L/min increased gaseous the N2O concentration from the aerobic tank and the dissolved N2O concentration in the anoxic tank by 54.4 and 53.4 %, respectively. During the period of higher aeration, the N2O-N conversion ratio was 0.9 % and the potential N2O reducers were predominantly Rhodobacter, which accounted for 21.8 % of the total population. Increasing the IRF ratio from 3.6 to 7.2 decreased the N2O emission rate from the aerobic tank and the dissolved N2O concentration in the anoxic tank by 56 and 48 %, respectively. This study suggests effective N2O mitigation strategies for MLE systems.