Brownification increases the abundance of microorganisms related to carbon and nitrogen cycling in shallow lakes.

Brownification in aquatic ecosystems under global change has attracted attention. The composition and quantity of dissolved organic matter transported from various land use types to lakes differ significantly, causing varying ecological effects of lake brownification by region. Bacterial communities make a significant contribution to the material cycle of ecosystems and are sensitive to environmental changes. In this study, a series of mesocosm systems were used to simulate forest lakes and urban lakes with different degrees of brownification, and a high-throughput amplicon sequencing technique was used to explore the changes in the composition, structure, and function of bacterial communities in shallow lakes undergoing brownification. Principal coordinate analysis (PCoA) and Jensen‒Shannon distance typing analysis both indicated significant differences in bacterial communities between forest lakes and urban lakes. The α diversity of bacterial communities in urban lakes increased with the degree of brownification. However, whether forest lakes or urban lakes, brownification increased the abundance of carbon cycling-related bacterial phyla (Proteobacteria, Poribacteria, and Chloroflexi) and nitrogen cycling-related bacterial genera (Microbacteriaceae, Limnohabitans, Comamonadaceae, Bacillus, and Rhizobiales_Incertae_Sedis). Additionally, the carbon and nitrogen cycling functions of bacterial communities in forest lakes are dominant, while those in urban lakes are dominated by functions related to light. Our study has preliminarily revealed that lake brownification promotes the growth of carbon and nitrogen cycling microorganisms, providing a new paradigm for understanding the response of lake ecosystems in different catchment areas to environmental changes and the carbon and nitrogen cycling processes in shallow lake ecosystems.

Urban and agricultural land use led to niche differentiation of AOA, AOB and comammox along the Beiyun River continuum.

River ecological health has been severely threatened by anthropogenic land-use pressures. Here, by combining remote sensing and molecular biology methods, we evaluated the impact of land-use activities on nitrification, a fundamental ecological process in rivers, which is conducted by ammonia-oxidising archaea (AOA) and ammonia-oxidising bacteria (AOB), or the newly discovered complete ammonia oxidisers (comammox). We explored the relationships of the abundance, activity, and diversity of AOA, AOB, and comammox in river sediments with land-use pressure by proposing a quantitative land use pattern index (LPI) over a 184 km continuum along the Beiyun River in North China. We found that comammox dominated nitrification in the forestry upstream (67.07 % in summer, 56.40 % in winter), while AOB became the major player in the urban middle (56.51 % in summer, 53.08 % in winter) and agricultural downstream reaches (62.98 % in summer, 50.74 % in winter). In addition, urban and agricultural land use lowered the α diversity of AOA and comammox, as well as simplified their co-occurrence networks, but promoted AOB diversity and complicated their networks. The structural equation model illustrated that the key drivers affecting the key taxa and activities were ammonia, and C/N for AOB, and total organic matter, and pH for comammox. We thus conclude that watershed urban and agricultural land use drive the niche differentiation of AOA, AOB, and comammox, specifically leading to a robust AOB community but weakened AOA and comammox communities. Our study connects the macro and micro worlds and provides a new paradigm for studying the variation in microbial communities as well as the potential ecological consequences under the increased anthropogenic land-use pressures in the Anthropocene.

Optimization of operating parameters and microbiological mechanism of a low C/N wastewater treatment system dominated by iron-dependent autotrophic denitrification.

Ferrous iron (Fe2+) reduces the amount of external carbon source used for the denitrification of low-C/N wastewater. The effects of key operating parameters on the efficiency of ferrous-dependent autotrophic denitrification (FDAD) and the functioning mechanism of the microbiome can provide a regulatory strategy for improving the denitrification efficiency of low C/N wastewater. In this study, the response surface method (RSM) was used to explore the influence of four important parameters-the molar ratio of Fe2+ to NO3--N (Fe/N), total organic carbon (TOC), the molar ratio of inorganic carbon to NO3--N (IC/N) and sludge volume (SV, %)-on the FDAD efficiency. Functional prediction and molecular ecological networks based on high-throughputs sequencing techniques were used to explore changes in the structure, function, and biomarkers of the sludge microbial community. The results showed that Fe/N and TOC were the main parameters affecting FDAD efficiency. Higher concentrations of TOC and high Fe/N ratios provided more electron donors and improved denitrification efficiency, but weakened the importance of biomarkers (Rhodanobacter, Thermomonas, Comamonas, Thauera, Geothrix and unclassified genus of family Gallionellaceae) in the sludge ecological network. When Fe/N > 4, the denitrification efficiency fluctuated significantly. Functional prediction results indicated that genes that dominated N2O and NO reduction and the genes that dominated Fe2+ transport showed a slight decrease in abundance at high Fe/N levels. In light of these findings, we recommend the following optimization ranges of parameters: Fe/N (3.5-4); TOC/N (0.36-0.42); IC/N (3.5-4); and SV (approximately 35%).

Distinctive species interaction patterns under high nitrite stress shape inefficient denitrifying phosphorus removal performance.

Denitrifying phosphorus removal using nitrite as an electron acceptor is an innovative, resource-efficient approach for nitrogen and phosphorus removal. However, the inhibitory effects of nitrite on anoxic phosphorus uptake and process stability are unclear. This study investigated the total phosphorus removal performance under nitrite stress and analyzed microbiome responses in 186 sludge samples. The results indicated that the total phosphorus removal rates and dominant taxon abundance were highly similar under nitrite stress. High nitrite stress induced a community-state shift, leading to unstable dynamics and decreased total phosphorus removal. This shift resulted from increased species cooperation. Notably, the shared genera OLB8 and Zoogloea under non-inhibitory nitrite stress, suggesting their vital roles in mitigating nitrite stress by enhancing carbon and energy metabolism. The response patterns of these bacterial communities to high nitrite stress can guide the design and optimization of high-nitrogen wastewater reactors.

Abundance, community and driving factor of nitrifiers in western China plateau.

Complete ammonia oxidation (comammox) is one of the most important biogeochemical processes, with recent studies showing that comammox process dominates nitrification in many ecosystems. However, the abundance, community and driving factor of comammox bacteria and other nitrifying microorganisms in plateau wetland is still unclear. Here, the abundances and community features of comammox bacteria, ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in the wetland sediments of western China plateaus were examined using qPCR and high-throughput sequencing. The results indicate that comammox bacteria were more abundant than AOA and AOB, and dominated the nitrification process. Compared with low-elevation samples (below 3000 m: samples 6-10, 12, 13, 15, 16), the abundance of comammox bacteria was much higher at high-elevation samples (above 3000 m: samples 1-5, 11, 14, 17, 18). The key species of AOA, AOB, and comammox bacteria were Nitrososphaera viennensis, Nitrosomonas europaea, and Nitrospira nitrificans, respectively. The key factor affecting comammox bacteria community was elevation. Elevation could increase the interaction links of key species Nitrospira nitrificans, resulting in high comammox bacterial abundance. The results of this study advance our knowledge of comammox bacteria in natural ecosystems.

Nitrite-resistance mechanisms on wastewater treatment in denitrifying phosphorus removal process revealed by machine learning, co-occurrence, and metagenomics analysis.

Nitrite is a key intermediate in nitrogen metabolism that determines microbial transformations of N and P, greenhouse gas (N2O) emissions, and system nutrient removal efficiency. However, nitrite also exerts toxic effects on microorganisms. A lack of understanding of high nitrite-resistance mechanisms at community- and genome-scale resolutions hinders the optimization for robustness of wastewater treatment systems. Here, we established nitrite-dependent denitrifying and phosphorus removal (DPR) systems under a gradient concentration of nitrite (0, 5, 10, 15, 20, and 25 mg N/L), relying on 16S rRNA gene amplicon and metagenomics to explore high nitrite-resistance mechanism. The results demonstrated that specific taxa were adopted to change the metabolic relationship of the community through phenotypic evolution to resist toxic nitrite contributing to the enhancement of denitrification and inhibition of nitrification and phosphorus removal. The key specific species, Thauera enhanced denitrification, whereas Candidatus Nitrotoga decreased in abundance to maintain partial nitrification. The extinction of Candidatus Nitrotoga induced a simpler restructuring-community, forcing high nitrite-stimulating microbiome to establish a more focused denitrification rather than nitrification or P metabolism in response to nitrite toxicity. Our work provides insights for understanding microbiome adaptation to toxic nitrite and giving theoretical support for operation strategy of nitrite-based wastewater treatment technology.

Anthropogenic land-use activities within watersheds reduce comammox activity and diversity in rivers.

Nitrogen cycling plays a key role in maintaining river ecological functions which are threatened by anthropogenic activities. The newly discovered complete ammonia oxidation, comammox, provides novel insights into the ecological effects of nitrogen on that it oxidizes ammonia directly to nitrate without releasing nitrite as canonical ammonia oxidization conducted by AOA or AOB which is believed to play an important role in greenhouse gas generation. Theoretically, contribution of commamox, AOA and AOB to ammonia oxidization in rivers might be impacted by anthropogenic land-use activities through alterations in flow regime and nutrient input. While how land use pattern affects comammox and other canonical ammonia oxidizers remains elusive. In this study, we examined the ecological effects of land use practices on the activity and contribution of three distinctive groups of ammonia oxidizers (AOA, AOB, comammox) as well as the composition of comammox bacterial communities from 15 subbasins covering an area of 6166 km2 in North China. The results showed that comammox dominated nitrification (55.71%-81.21%) in less disturbed basins characterized by extensive forests and grassland, while AOB became the major player (53.83%-76.43%) in highly developed basins with drastic urban and agricultural development. In addition, increasing anthropogenic land use activities within the watershed lowered the alpha diversity of comammox communities and simplified the comammox network. Additionally, the alterations of NH4+-N, pH and C/N induced by land use change were found to be crucial drivers in determining the distribution and activity of AOB and comammox. Together, our findings cast a new light on aquatic-terrestrial linkages from the view of microorganism-mediated nitrogen cycling and can further be applied to target watershed land use management.

Nitrifiers Cooperate to Produce Nitrous Oxide in Plateau Wetland Sediments.

The thawing of dormant plateau permafrost emits nitrous oxide (N2O) through wetlands; however, the N2O production mechanism in plateau wetlands is still unclear. Here, we used the 15N-18O double tracer technique and metagenomic sequencing to analyze the N2O production mechanism in the Yunnan-Kweichow and Qinghai-Tibet plateau wetlands during the summer of 2020. N2O production activity was detected in all 16 sediment samples (elevation 1020-4601 m: 2.55 ± 0.42-26.38 ± 3.25 ng N g-1 d-1) and was promoted by nitrifier denitrification (ND). The key functional genes of ND (amoA, hao, and nirK) belonged to complete ammonia oxidizing (comammox) bacteria, and the key ND species was the comammox bacterium Nitrospira nitrificans. We found that the comammox bacterial species N. nitrificans and the ammonia oxidizing bacterial (AOB) species Nitrosomonas europaea cooperate to produce N2O in the plateau wetland sediments. Furthermore, we inferred that environmental factors (elevation and total organic matter (TOM)) influence the cooperation pattern via N. nitrificans, thus affecting the N2O production activity in the plateau wetland sediments. Our findings advance the mechanistic understanding of nitrifiers in biogeochemical cycles and global climate change.

Brownification of freshwater promotes nitrogen-cycling microorganism growth following terrestrial material increase and ultraviolet radiation reduction.

Brownification is an increasingly concerning phenomenon faced by aquatic ecosystems in the changing environments, and the microbiome plays an irreplaceable role in material circulation and food web construction. Insight into the influence of brownification on microbial communities is crucial from an ecological standpoint. In this study, we simulated brownification using a the mesocosm system and explored the relationship between the characteristics of microbial communities and brownification using excitation-emission matrix (EEM) fluorescence spectroscopy and ultraviolet (UV) spectroscopy combined with high-throughput amplicon sequencing techniques. The results showed that brownification reduced the richness of the microbial community and selectively promoted the growth of nitrogen-cycling microorganisms, including hgcI_clade, Microbacteriaceae, and Limnohabitans. Brownification affected microbial communities by altering the carbon source composition and underwater spectrum intensity; UV, blue, violet, and cyan light were significantly (p < 0.05) correlated with microbial community richness, and random forest analysis revealed that UV, C1 (microbial humic-like), and C3 (terrestrial humic-like) were the major factors significantly influencing microbiome variation. We found that brownification affected microorganisms in shallow lakes, especially nitrogen cycling microorganisms, and propose that controlling terrestrial material export is an effective strategy for managing freshwater brownification.

Comparing with oxygen, nitrate simplifies microbial community assembly and improves function as an electron acceptor in wastewater treatment.

Biochemical oxidation and reduction are key processes in treating biological wastewater and they require the presence of electron acceptors. The functional impact of electron acceptors on microbiomes provides strategies for improving the treatment efficiency. This research focused on two of the most important electron acceptors, nitrate and oxygen. Molecule ecological network, null model, and functional prediction based on high-throughput sequencing were used to analyze the microbiomes features and assembly mechanism. The results revealed nitrate via the homogeneous selection (74.0%) decreased species diversity, while oxygen via the homogeneous selection (51.1%) and dispersal limitation (29.6%) increased the complexity of community structure. Microbes that were more strongly homogeneously selected for assembly included polyphosphate accumulating organisms (PAOs), such as Pseudomonas and variovorax in the nitrate impacted community; Pseudomonas, Candidatus_Accumulibacter, Thermomonas and Dechloromonas, in the oxygen impacted community. Nitrate simplified species interaction and increased the abundance of functional genes involving in tricarboxylic acid cycle (TCA cycle), electron transfer, nitrogen metabolism, and membrane transport. These findings contribute to our knowledge of assembly process and interactions among microorganisms and lay a theoretical basis for future microbial regulation strategies in wastewater treatment.

Ecological Insights Into Community Interactions, Assembly Processes and Function in the Denitrifying Phosphorus Removal Activated Sludge Driven by Phosphorus Sources.

The microbial characteristics in the wastewater treatment plants (WWTPs) strongly affect their optimal performance and functional stability. However, a cognitive gap remains regarding the characteristics of the microbial community driven by phosphorus sources, especially co-occurrence patterns and community assembly based on phylogenetic group. In this study, 59 denitrifying phosphorus removal (DPR) activated sludge samples were cultivated with phosphorus sources. The results suggested that homogeneous selection accounted for the largest proportion that ranged from 35.82 to 64.48%. Deterministic processes dominated in 12 microbial groups (bins): Candidatus_Accumulibacter and Pseudomonas in these bins belonged to phosphate-accumulating organisms (PAOs). Network analysis revealed that species interactions were intensive in cyclic nucleoside phosphate-influenced microbiota. Function prediction indicated that cyclic nucleoside phosphates increased the activity of enzymes related to denitrification and phosphorus metabolism and increased the α-diversity of microorganism but decreased the diversity of metabolic function. Based on these results, it was assumed that cyclic nucleoside phosphates, rather than inorganic phosphates, are the most available phosphorus source for majority microorganisms in DPR activated sludge. The study revealed the important role of phosphorus source in the construction and assembly of microbial communities and provided new insights about pollutant removal from WWTPs.

Comammox activity dominates nitrification process in the sediments of plateau wetland.

The recent discovery of complete ammonia oxidation (comammox) has increased our understanding of nitrification. Although comammox has been shown to play an important role in plain wetland ecosystems, studies of comammox contribution are still limited in plateau wetland ecosystems. Here, we analyzed the abundance, activity, community and biogeochemical mechanisms of the comammox bacteria in Yunnan-kweichow and Qinghai-Tibet plateau wetlands from elevations of 1000-5000 m. Comammox bacteria were widely distributed in all 16 sediment samples with abundances higher than 0.96 ± 0.26 × 107 copies g-1 (n = 16). Comammox showed high activity (1.18 ± 0.17 to 1.98 ± 0.08 mg N kg-1 d-1) at high-elevation (3000-5000 m) and dominated the nitrification process (activity contribution: 37.20 - 60.62%). The activity contribution of ammonia-oxidizing bacteria (1.07 ± 0.08 to 2.79 ± 0.35 mg N kg-1 d-1) dominated the nitrification process (44.55 - 64.15%) in low-elevation (1000-3000 m) samples. All detected comammox Nitrospira belonged to clade A, while clade B was not detected. Elevation always had a strongest effect on key comammox species. Thus, we infer that elevation may drive the high relative abundance of the species Candidatus Nitrospira nitrificans (avg. 12.40%) and the low relative abundance of the species Nitrospira sp. SG-bin2 (avg. 4.75%) in high-elevation samples that showed a high comammox activity (avg. 1.62 mg N kg-1 d-1) and high contribution (avg. 46.08%) to the nitrification process. These results indicate that comammox may be an important and currently underestimated microbial nitrification process in plateau wetland ecosystems.

Balance Between Soil Remediation and Economic Benefits of Eucalyptus globulus.

A long term experiment was conducted to verify the phytoremediation effect of large biomass plants and to seek the balance between remediation effect and economy. Eucalyptus globulus were planted with rotation periods of respectively 3, 6 and 9 years to examine the effect on soil remediation. Biomass and concentrations of Cd, Pb and Cu in E. globulus were measured after each harvest. The economic value of the plant was estimated. Results showed E3 (9th year uprooted) had the best soil remediation effect and economic benefit. Therefore, soil remediation and economy were best balanced when E. globulus were not cut.