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Purpose This study aimed at elucidating the biotic components of crop decline affecting kiwifruit ( Actinidia deliciosa ) orchards. Methods The study was carried out on soil samples originating from an over twenty-year-old orchard showing typical yield decline (Old), one in full production phase (Adult), one fallow after a kiwifruit cultivation (Fallow), an abandoned one (Virgin). Soil health of those soil samples was assessed with an in-pot growth assay using kiwifruit plantlets in which root endophytic fungi and rhizosphere bacteria communities were assessed using qPCR and NGS analysis. Results Plant growth in the Old field was significantly lower than the others, in line with the crop decline of that field. The Old treatment differed from the others in the following soil features: i. a great reduction of total bacteria, Pseudomonas , actinomycetes and Bacillus compared to the Adult orchard; ii. a significant increase of Nitrosospira and other nitrifying bacteria which persisted in kiwifruit rhizosphere even under the optimal conditions; iii. a reduction of potentially beneficial genera among which Massilia , Rubrobacter and Kaistobacter . Old, Adult and Fallow were similar in root fungal community composition, with Dactylonectria as dominant genus (about 50%); whilst in the Virgin prevailed saprophytic non-pathogenic fungi. Conclusions Bacterial communities in over-30-year-old kiwifruit orchards were greatly reduced and modified, thus suggesting being a cause of the reduced ability of soil to support plant growth. In addition, kiwifruit manifested a legacy effect on soil-borne fungal communities, including root endophytes.

Ammonia-oxidizing archaea and ammonia-oxidizing bacteria (AOA and AOB), complete ammonia oxidizers (Comammox), and nitrite-oxidizing bacteria (NOB) play a crucial role in the nitrification process during the nitrogen cycle. However, their occurrence and diversity in mangrove ecosystems are still not fully understood. Here, a total of 11 pairs of PCR primers were evaluated to study the distribution and abundances of these nitrifiers in rhizosphere and non-rhizosphere sediments of a mangrove ecosystem. The amplification efficiency of these 11 pairs of primers was first evaluated and their performances were found to vary considerably. The CamoA-19F/CamoA-616R primer pair was suitable for the amplification of AOA in mangrove sediments, especially on the surface of rhizosphere sediments. Primer pair amoA 1F/ amoA 2R was better for the characterization of novel AOB in the bacterial community of non-rhizosphere sediments of mangroves. In contrast, primer nxrB 169F/ nxrB 638R showed a low abundance of NOB in mangrove sediments (except for R1). Comammox bacteria were abundant and diverse in mangrove sediments, as indicated by both the amoB gene for Comammox clade A and the amoA gene for Comammox Nitrospira clade B. However, the amoA gene for Comammox Nitrospira clade A was not successful in detecting them in the mangrove sediments. Furthermore, 568 operational taxonomic units (OTUs) were obtained by generating a clone library and a high abundance of OTUs was correlated with ammonium, pH, NO 2 − , and NO 3 − . Comammox and Comammox Nitrospira were identified by phylogenetic tree analysis, indicating that mangrove sediments harbor newly discovered nitrifiers. Additionally, many AOA and NOB were mainly distributed in the surface layer of the rhizosphere, whereas AOB and Comammox Nitrospira were in the subsurface of non-rhizosphere, as determined by qPCR analysis. Collectively, our findings highlight the limitations of some primers for the identification of specific nitrifying bacteria. Therefore, primers must be carefully selected to gain accurate insights into the ecological distribution of nitrifiers in mangroves. Key points • Several sets of PCR primers perform well for the detection of nitrifiers in mangroves. • Mangroves are an important source of newly discovered nitrifiers. • Ammonium, pH, NO 2 − , and NO 3 − are important shapers of nitrifier communities in mangroves.

A nitrifying bacterium Acinetobacter sp. AL-6 showed a high efficiency of 99.05% for Mn(II) removal within 144 h when the Mn(II) concentration was 200 mg L -1 ; meanwhile, 64.23% of NH 4 + -N was removed. With the Mn(II) concentration increased from 25 to 300 mg L -1 , bacterial growth and Mn(II) removal were stimulated. However, due to the electron acceptor competition between Mn(II) oxidation and nitrification reactions, the increase in NH 4 + -N concentration would inhibit Mn(II) removal. By measuring Mn metabolic form and locating oxidative active factors, it was proved that extracellular oxidation effect played a dominant role in the removal process of Mn(II). The self-regulation of pH during strain metabolism further promoted the occurrence of biological Mn oxidation. Characterization results showed that the Mn oxidation products were tightly attached to the surface of the bacteria in the form of flakes. The product crystal composition (mainly MnO 2 and Mn 2 O 3 ), Mn-O functional group, and element level fluctuations confirmed the biological oxidation information. The changes of -OH, N-H, and -CH 2 groups and the appearance of new functional groups (such as C-H and C-O) provided more possibilities for Mn ion adsorption and bonding.

Anaerobic ammonium oxidation (anammox) and nitrite-dependent anaerobic methane oxidation (n-damo) are two new processes of recent discoveries linking the microbial nitrogen and carbon cycles. In this study, 16S ribosomal RNA (rRNA) gene of anammox bacteria and pmoA gene of n-damo bacteria were used to investigate their distribution and diversity in natural acidic and re-vegetated forest soils. The 16S rRNA gene sequences retrieved featured at least three species in two genera known anammox bacteria, namely Candidatus Brocadia anammoxidans, Candidatus Brocadia fulgida, and Candidatus Kuenenia stuttgartiensis while the pmoA gene amplified was affiliated with two species of known n-damo bacteria Candidatus Methylomirabilis oxyfera and a newly established Candidatus Methylomirabilis sp. According to the results, the diversity of anammox bacteria in natural forests was lower than in re-vegetated forests, but no significant difference was observed in n-damo community between them. Quantitative real-time PCR showed that both anammox and n-damo bacteria were more abundant in the lower layer (10–20 cm) than the surface layer (0–5 cm). The abundance of anammox bacteria varied from 2.21 × 10 5 to 3.90 × 10 6 gene copies per gram dry soil, and n-damo bacteria quantities were between 1.69 × 10 5 and 5.07 × 10 6 gene copies per gram dry soil in the two different layers. Both anammox and n-damo bacteria are reported for the first time to co-occur in acidic forest soil in this study, providing a more comprehensive information on more defined microbial processes contributing to C and N cycles in the ecosystems.

An activated sludge system can be inoculated with enriched nitrifying bacteria to enhance NH 4 + -N removal, or enriched nitrifying bacteria can be added directly to a river to remove NH 4 + -N. However, the enrichment culture is still generally inefficient and the technical bottleneck has not been clarified. Previous studies have shown that extracellular free organic carbon (EFOC) inhibits the growth of some autotrophic bacteria, and separating EFOC during culture with a membrane bioreactor (MBR) promotes the continuous growth of autotrophic bacteria and CO 2 fixation. However, whether a membrane bioreactor can also be used to enrich and culture autotrophic nitrifying bacteria by separating EFOC has not been verified. In this study, an MBR was constructed to separate EFOC during the culture of nitrifying bacteria in activated sludge to confirm that the MBR better enriches and cultures nitrifying bacteria than a sequencing batch reactor (SBR). Our results showed that after culture for 34 days, the rate of NH 4 + -N removal and the nitrification rate by nitrifying bacteria in the MBR were 2.20-fold and 1.42-fold higher than in the SBR, respectively. The abundance of Nitrospira in the MBR was also 7.23-fold greater than in the SBR at the end of the experimental period. After 34 days, the average concentration of EFOC and the average EFOC/bacterial organic carbon ratio in the MBR were only 53% and 37% of those in the SBR, respectively. A correlation analysis suggested that the timely removal by the MBR of the EFOC generated during the culture process may be an important factor in promoting the growth of autotrophic nitrifying bacteria. The possible mechanism by which the MBR separates EFOC to the growth of promote autotrophic nitrifying bacteria is discussed from the perspective of the inhibitory effect of EFOC on cbb gene transcription. Our experimental results suggest a new approach to enhancing the enrichment of autotrophic nitrifying bacteria and extending the application of MBRs.

Integrated fixed-film activated sludge technology (IFAS) has a great advantage in improving nitrogen removal performance and increasing treatment capacity of municipal wastewater treatment plants with limited land for upgrading and reconstruction. This research aims at investigating the enhancing effects of polyethylene (PE) carrier and nitrifying bacteria PE (NBPE) carrier on nitrogen removal efficiency of an anoxic/aerobic (A/O) system from municipal wastewater and revealing temporal changes in microbial community evolution. A pilot-scale A/O system and a pilot-scale IFAS system were operated for nearly 200 days, respectively. Traditional PE and NBPE carriers were added to the IFAS system at different operating phases. Results showed that the treatment capacity of the IFAS system was enhanced by almost 50% and 100% by coupling the PE carrier and NBPE carrier, respectively. For the PE carrier, nitrifying bacteria abundance was maintained at 7.05%. In contrast, the nitrifying bacteria on the NBPE carrier was enriched from 6.66% to 23.17%, which could improve the nitrogen removal and treating capacity of the IFAS system. Finally, the ammonia efficiency of the IFAS system with NBPE carrier reached 73.0 ± 7.9% under 400% influent shock load and hydraulic retention time of 1.8 h. The study supplies a suitable nitrifying bacteria enrichment method that can be used to help enhance the nitrogen removal performance of municipal wastewater treatment plants. The study’s results advance the understanding of this enrichment method that effectively improves nitrogen removal and anti-resistance shock-load capacity.

To ensure microbial activity and a reaction equilibrium with efficiency and energy saving, it is important to know the factors that influence microbiological nitrogen removal in wastewater. Thus, it was investigated the microorganisms and their products involved in the treatment of kennel effluents operated with different aeration times, phase 1 (7 h of continuous daily aeration), phase 2 (5 h of continuous daily aeration), and phase 3 (intermittent aeration every 2 h), monitoring chemical and physical parameters weekly, monthly microbiological, and qualitative and quantitative microbiological analyzes at the end of each applied aeration phase. The results showed a higher mean growth of nitrifying bacteria (NB) (10 6 ) and denitrifying bacteria (DB) (10 22 ) in phase with intermittent aeration, in which better total nitrogen (TN) removal performance, with 33%, was achieved, against 21% in phase 1 and 17% in phase 2, due to the longer aeration time and lower carbon/nitrogen ratio (15.7), compared with the other phases. The presence of ammonia-oxidizing bacteria (AOB), the genus Nitrobacter nitrite–oxidizing bacteria (NOB), and DB were detected by PCR with specific primers at all phases. The analysis performed by 16S-rRNA DGGE revealed the genres Thauera at all phases; Betaproteobacteria and Acidovorax in phase 3; Azoarcus in phases 2 and 3; Clostridium , Bacillus , Lactobacillus , Turicibacter , Rhodopseudomonas , and Saccharibacteria in phase 1, which are related to the nitrogen removal, most of them by denitrifying. It is concluded that, with the characterization of the microbial community and the analysis of nitrogen compounds, it was determined, consistently, that the studied treatment system has microbiological capacity to remove TN, with the phase 3 aeration strategy, by simultaneous nitrification and denitrification (SND). Due to the high density of DB, most of the nitrification occurred by heterotrophic nitrification-aerobic. And denitrification occurred by heterotrophic and autotrophic forms, since the higher rate of oxygen application did not harm the DB. Therefore, the aeration and carbon conditions in phase 3 favored the activity of the microorganisms involved in these different routes. It is considered that, in order to increase autotrophic nitrification-aerobic, it is necessary to exhaust the volume of sludge in the secondary settlers (SD), further reducing the carbon/nitrogen ratio, through more frequent cleaning, whose periodicity should be the object of further studies. Graphical abstract

Nitrification, a crucial process in wastewater treatment, involves the conversion of ammonium nitrogen to nitrate nitrogen through the sequential activities of ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB). In the present study, a comprehensive mathematical model was developed to describe the nitrification process in mixed cultures involving isolated NOB and starved AOB. The growth equation for NOB was divided into anabolism and catabolism, elucidating the key substrates driving their metabolic activities. Considering the ammonia starvation effect, a single cell-based model was developed to capture the mass transfer phenomena across the AOB cell membrane. This addition allowed for a more accurate representation of the biological dynamics during starvation conditions. The model’s accuracy was tested using experimental data that was not used in the model calibration step. The prediction’s coefficient of determination (R2) was estimated at 0.9. By providing insights into the intricate mechanisms underlying nitrification, this model contributes to the advancement of sustainable wastewater treatment practices.

Aiming at the problem of high concentration of COD and NH3-N in black and odorous water bodies, heterotrophic nitrifying bacteria which can remove ammonia nitrogen and organic pollutants were screened out in the laboratory simultaneously. A heterotrophic nitrifying functional group was constructed by using the strategy of bacterial source reorganization ecologically, and the removal effect of heterotrophic nitrifying functional bacteria on organic pollutants and ammonia nitrogen in water was studied. The results showed that the removal rate of ammonia nitrogen in the water was more than 52%, and the removal rate of COD was 57%∼86%. The effect of heterotrophic nitrifying functional bacteria group 1 on the removal of COD and ammonia in water was better, and the removal rate was 76.5% and 54.8%, respectively. The optimum inoculation test showed that the optimum inoculation amount of the heterotrophic nitrification bacteria group 1 was 10 ppm.

Until now, the oxidation steps necessary for complete nitrification had always been observed to occur in two separate microorganisms in a cross-feeding interaction; here, together with the study by Daims et al ., van Kessel et al . report the enrichment and characterization of Nitrospira species that encode all of the enzymes necessary to catalyse complete nitrification, a phenotype referred to as ‘comammox’ (for complete ammonia oxidation). Time to rethink nitrification Two groups this week report the enrichment and characterization of Nitrospira species that encode all of the enzymes necessary to catalyse complete nitrification, a phenotype referred to as 'comammox' (for complete ammonia oxidation). Until now, this two-step reaction was thought to involve two organisms in a cross-feeding interaction. Phylogenetic analyses suggest that comammox Nitrospira are present in a number of diverse environments, so these findings have the potential to fundamentally change our view of the nitrogen cycle and open a new frontier in nitrification research. Nitrification is a two-step process where ammonia is first oxidized to nitrite by ammonia-oxidizing bacteria and/or archaea, and subsequently to nitrate by nitrite-oxidizing bacteria. Already described by Winogradsky in 1890 1 , this division of labour between the two functional groups is a generally accepted characteristic of the biogeochemical nitrogen cycle 2 . Complete oxidation of ammonia to nitrate in one organism (complete ammonia oxidation; comammox) is energetically feasible, and it was postulated that this process could occur under conditions selecting for species with lower growth rates but higher growth yields than canonical ammonia-oxidizing microorganisms 3 . Still, organisms catalysing this process have not yet been discovered. Here we report the enrichment and initial characterization of two Nitrospira species that encode all the enzymes necessary for ammonia oxidation via nitrite to nitrate in their genomes, and indeed completely oxidize ammonium to nitrate to conserve energy. Their ammonia monooxygenase (AMO) enzymes are phylogenetically distinct from currently identified AMOs, rendering recent acquisition by horizontal gene transfer from known ammonia-oxidizing microorganisms unlikely. We also found highly similar amoA sequences (encoding the AMO subunit A) in public sequence databases, which were apparently misclassified as methane monooxygenases. This recognition of a novel amoA sequence group will lead to an improved understanding of the environmental abundance and distribution of ammonia-oxidizing microorganisms. Furthermore, the discovery of the long-sought-after comammox process will change our perception of the nitrogen cycle.