Effects of mowing dominant grasses on root exudation and soil nitrogen cycling in a natural sod culture apple orchard

We evaluated the effects of mowing dominant grasses on root exudation and soil nitrogen (N) cycling by assessing metabolomics analysis of root exudates, microbial metabolism, the abundance of N-cycling-related prokaryotes, and different forms of N concentrations in soil. The treatments included Polygonum aviculare L. mowing (T1), Digitaria sanguinalis (L.) Scop. mowing (T2), and no mowing as the controls (CK1 and CK2). The results showed that compared with the no mowing control (CK1 and CK2), T1 and T2 root exudates contained 223 (178 up-regulated, 45 down-regulated) and 183 (40 up-regulated, 143 down-regulated) differential metabolites, respectively. The average well colour development (AWCD) could reflect the microbial metabolic activity. The AWCD values of T1 were increased while that of T2 decreased on the 2^nd day after mowing. The variation in root exudates was the main reason for the change in soil AWCD values and carbon utilisation of T1 and T2 on the 2^nd day after mowing. Mowing increased soil microbial biomass N content significantly in the T1 and T2 topsoil. The NO₃^–-N and NH₄⁺-N contents in the 0–10 cm soil increased on the 2^nd day after T1 mowing with an increase in the nitrogenase iron protein gene (nifH), glutamate dehydrogenase gene (gdh), ammonia monooxygenase gene (amoA) of ammonia-oxidising archaea (AOA) and ammonia-oxidising bacteria (AOB) abundance. However, NO₃^–-N content decreased on the 2^nd day after T2 mowing following a decrease in AOA-amoA and AOB-amoA gene abundance. The results of this study will facilitate the optimisation of sod culture orchard N management, reduction of N fertiliser input, and improvement of N utilisation efficiency.

Linking 16S rRNA Gene Classification to amoA Gene Taxonomy Reveals Environmental Distribution of Ammonia-Oxidizing Archaeal Clades in Peatland Soils

The recently established phylogeny of amoA provides a finer resolution than previous studies, allowing clustering of AOA beyond the order level and thus revealing novel clades. While the 16S rRNA gene is mostly appreciated in microbiome studies, this novel phylogeny is in limited use.

Spatiotemporal evolution and assembly processes of ammonia-oxidising prokaryotic communities in 1000 years coastal reclaimed soils

Coastal marshes are transitional areas between terrestrial and aquatic ecosystems and vulnerable to climate change and anthropogenic activities. In recent decades the reclamation of coastal marshes remarkably increased and their effects on microbial communities present in coastal marshes have been studied with great interest. However, most of these studies focused on microbial community composition and diversity. The processes underlying functional community assembly and spatiotemporal effect often ignored. Therefore, community structure and assembly mechanisms of ammonia-oxidising prokaryotes in long-term reclaimed coastal marshes have not been studied. Here using qPCR and IonS5TMXL sequencing platform, we investigated spatiotemporal dynamics, assembly processes and diversity patterns in ammonia-oxidising prokaryotes in over 1000 years reclaimed coastal salt marsh soils. The taxonomic & phylogenetic diversity and composition of the ammonia-oxidizers showed apparent spatiotemporal variations along reclamation of soil. The phylogenetic null modelling-based analysis showed across all sites, the archaeal ammonia-oxidising community assembled by deterministic process (84.71%). The ammonia-oxidising bacterial community was formed more by a stochastic process in coastal marshes and at stage 60 years (|βNTI|<2), despite its relatively dominant deterministic process (55.2%). The deterministic assembly process and nitrification activity in reclaimed soils was positively correlated. Archaeal amoA gene abundance were also positively correlated with the nitrification rate. Our study revealed that during the 1000 years of reclamation coastal marshes both ammonia-oxidising communities responded differently to diversity change and assembly processes and nitrification activity. These findings provide a better understanding of how long-term reclamation affect soil N cycling and assembly dynamics of ammonia-oxidising communities.

Characterization of the microbial communities responsible for ammonia oxidation in activated sludge systems of municipal wastewater treatment plants

Nitrification is an essential microbial process in the global nitrogen cycle. The first step of nitrification is ammonia oxidation which is achieved by bacteria and archaea and is crucial in decreasing ammonia concentrations that are persistently high in wastewater. This study examined the composition, abundance and identity of the microbial community in activated sludge with a focus on characterizing ammonia oxidizing bacteria and archaea in a full-scale municipal wastewater treatment plant (MWTP). Specifically, two pharmaceutical compounds Tetracycline and Ibuprofen, and their effects on the community composition of bacteria and protozoa in activated sludge was investigated using PCR coupled with denaturing gradient gel electrophoresis (DGGE). In addition, the composition, abundance and activity of the ammonia oxidizing bacteria (AOB) and ammonia oxidizing archaea (AOA) were analyzed from aerobic activated sludge, recycled sludge and anaerobic digesters of the Humber MWTP using molecular techniques such as PCR, Quantitative PCR, Reverse Transcription-PCR and DGGE. The findings demonstrated that Tetracycline did not appear to alter community composition of bacteria in the activated sludge, rather, the operational parameters of the sequencing batch reactors such as feeding rates and SRT have shown to alter the richness of bacterial communities. However, Ibuprofen affected some members in the protozoan community in activated sludge. In the full-scale Humber MWTP using the conventional activated sludge system, the aeration tanks contained 1.8 × 105 copies of the AOB amoA gene per 100 ng of DNA. In contrast, the anaerobic digester tanks contained 7.3 × 102 copies of the AOA amoA gene per 100ng of DNA. This study also found that AOB were dominant in activated sludge samples, regardless of the operational parameters. The quantification of cDNA transcripts of the amoA gene also indicated that AOB may be more active than AOA in the activated sludge system. Overall, it appears that AOA are very niche specific and thrive in very low oxygenated environments, while AOB proliferate and play a major role in aerobic ammonia oxidation occurring in MWTPs.

Characterization of the microbial communities responsible for ammonia oxidation in activated sludge systems of municipal wastewater treatment plants

Nitrification is an essential microbial process in the global nitrogen cycle. The first step of nitrification is ammonia oxidation which is achieved by bacteria and archaea and is crucial in decreasing ammonia concentrations that are persistently high in wastewater. This study examined the composition, abundance and identity of the microbial community in activated sludge with a focus on characterizing ammonia oxidizing bacteria and archaea in a full-scale municipal wastewater treatment plant (MWTP). Specifically, two pharmaceutical compounds Tetracycline and Ibuprofen, and their effects on the community composition of bacteria and protozoa in activated sludge was investigated using PCR coupled with denaturing gradient gel electrophoresis (DGGE). In addition, the composition, abundance and activity of the ammonia oxidizing bacteria (AOB) and ammonia oxidizing archaea (AOA) were analyzed from aerobic activated sludge, recycled sludge and anaerobic digesters of the Humber MWTP using molecular techniques such as PCR, Quantitative PCR, Reverse Transcription-PCR and DGGE. The findings demonstrated that Tetracycline did not appear to alter community composition of bacteria in the activated sludge, rather, the operational parameters of the sequencing batch reactors such as feeding rates and SRT have shown to alter the richness of bacterial communities. However, Ibuprofen affected some members in the protozoan community in activated sludge. In the full-scale Humber MWTP using the conventional activated sludge system, the aeration tanks contained 1.8 × 105 copies of the AOB amoA gene per 100 ng of DNA. In contrast, the anaerobic digester tanks contained 7.3 × 102 copies of the AOA amoA gene per 100ng of DNA. This study also found that AOB were dominant in activated sludge samples, regardless of the operational parameters. The quantification of cDNA transcripts of the amoA gene also indicated that AOB may be more active than AOA in the activated sludge system. Overall, it appears that AOA are very niche specific and thrive in very low oxygenated environments, while AOB proliferate and play a major role in aerobic ammonia oxidation occurring in MWTPs.

Simultaneous nitrification and phosphate removal by bioaugmented aerobic granules treating a fluoroorganic compound

The presence of toxic compounds in wastewater can cause problems for organic matter and nutrient removal. In this study, the long term effect of a model xenobiotic, 2-fluorophenol (2-FP), on ammonia oxidizing bacteria (AOB), nitrite oxidizing bacteria (NOB) and phosphate accumulating organisms (PAO) in aerobic granular sludge was investigated. Phosphate (P) and ammonium (N) removal efficiencies were high (&gt;93%) and, after bioaugmentation with 2-FP degrading strain FP1, 2-FP was completely degraded. Neither N nor P removal were affected by 50 mg L−1 of 2-FP in the feed stream. Changes in the aerobic granule bacterial communities were followed. Numerical analysis of the denaturing gradient gel electrophoresis (DGGE) profiles showed low diversity for the amoA gene with an even distribution of species. PAOs, including denitrifying PAO (dPAO), and AOB were present in the 2-FP degrading granules, although dPAO population decreased throughout the 444 days reactor operation. The results demonstrated that the aerobic granules bioaugmented with FP1 strain successfully removed N, P and 2-FP simultaneously.

New insight to niche partitioning and ecological function of ammonia oxidizing archaea in subtropical estuarine ecosystem

Nitrification plays a central role in the estuarine nitrogen cycle. Previous studies in estuary mainly focused on the niche partition between ammonia-oxidizing archaea (AOA) and bacteria (AOB), while the diversity, activity, biogeography, and ecophysiology of different AOA groups remained unclear. Here, we for the first time report on niche partitioning and differentially distributed active populations among diverse AOA (inferred from amoA gene) in a typical subtropical estuary – Pearl River estuary (PRE). In the water column of the PRE, the AOA communities mainly consisted of water column A (WCA) and SCM1-like (Nitrosopumilus maritimus-like) sublineages. Surprisingly, we observed a strong disagreement in AOA communities at DNA and RNA levels. In DNA samples, WCA generally dominated the AOA community, and the distributional pattern indicated that WCA I and WCA II sublineages preferred oceanic and coastal conditions, respectively. In contrast, diverse SCM1-like sublineages were identified, and outnumbered WCA at RNA level, in which SCM1-like-III was limited to freshwater, while the rest of the sublineages were widely distributed in the estuary. The SCM1-like sublineages strongly correlated with nitrification rate, which indicated their important contribution to ammonia oxidation. Furthermore, intense nitrification contributed significantly to hypoxia conditions (nitrification contributed averaged 12.18 % of oxygen consumption) in the estuary. These results revealed different ammonia-oxidizing activities and niche partitioning among different AOA sublineages in estuarine water, which was unexplored in previous DNA and clone library-based studies. The ecological significance and functioning of the diverse AOA should be further explored in the marine ecosystem.

Ammonia-oxidizing bacteria dynamics affected by plantain under synthetic cattle urine patches

Plantain has been suggested as a nitrous oxide (N2O) and nitrate (NO3-) leaching mitigation option as it may induce biological nitrification inhibition (BNI) via plantain root exudation, which affects the activity of ammonia-oxidizing bacteria. This preliminary study compared the abundance of the ammonia monooxygenase gene (amoA) in soils containing either plantain and white clover, or ryegrass and white clover. Plants were sown in pots and grown in a greenhouse. Two months after sowing, synthetic cattle urine was applied to half the pots, and rhizosphere and bulk soil samples were collected 30 and 90 days after urine application. The abundance of the amoA gene was measured using real time quantitative PCR. The abundance of amoA genes in rhizosphere soil around ryegrass plants and in bulk soil under ryegrass/white clover were higher in pots treated with urine than the no-urine controls. AmoA gene abundance in bulk soil under plantain/white clover was higher in pots treated with urine (P<0.05) but not in rhizosphere soil around plantain plants (P>0.05) compared with the control. Furthermore, amoA gene copy numbers in the rhizosphere soil around plantain plants were lower than for ryegrass plants (P<0.05). However, there was no difference in the abundance of amoA genes in bulk soil of either combination of plant species evaluated (P>0.05). The results suggest that, in the time frame of our experiment, plantain could induce a BNI effect in the rhizosphere soil but not in the bulk soil.

Effects of Zeolite and Biochar Addition on Ammonia-Oxidizing Bacteria and Ammonia-Oxidizing Archaea Communities during Agricultural Waste Composting

The effects of zeolite and biochar addition on ammonia-oxidizing bacteria (AOB) and archaea (AOA) communities during agricultural waste composting were determined in this study. Four treatments were conducted as follows: Treatment A as the control with no additive, Treatment B with 5% of zeolite, Treatment C with 5% of biochar, and Treatment D with 5% of zeolite and 5% biochar, respectively. The AOB and AOA amoA gene abundance as well as the ammonia monooxygenase (AMO) activity were estimated by quantitative PCR and enzyme-linked immunosorbent assay, respectively. The relationship between gene abundance and AMO enzyme activity was determined by regression analysis. Results indicated that the AOB was more abundant than that of AOA throughout the composting process. Addition of biochar and its integrated application with zeolite promoted the AOB community abundance and AMO enzyme activity. Significant positive relationships were obtained between AMO enzyme activity and AOB community abundance (r2 = 0.792; P < 0.01) and AOA community abundance (r2 = 0.772; P < 0.01), indicating that both bacteria and archaea played significant roles in microbial ammonia oxidation during composting. Using biochar and zeolite might promote the nitrification activity by altering the sample properties during agricultural waste composting.