Nitrifying Microorganisms Research Articles

Dynamics and activity of an ammonia-oxidizing archaea bloom in South San Francisco Bay.

Transient or recurring blooms of ammonia-oxidizing archaea (AOA) have been reported in several estuarine and coastal environments, including recent observations of AOA blooms in South San Francisco Bay (SFB). Here, we measured nitrification rates, quantified AOA abundance, and analyzed both metagenomic and metatranscriptomic data to examine the dynamics and activity of nitrifying microorganisms over the course of an AOA bloom in South SFB during the autumn of 2018 and seasonally throughout 2019. Nitrification rates were correlated with AOA abundance in qPCR data and both increased several orders of magnitude between the autumn AOA bloom and spring and summer seasons. From bloom samples, we recovered an extremely abundant, high-quality Ca. Nitrosomarinus catalina-like AOA metagenome-assembled genome (MAG) that had high transcript abundance during the bloom and expressed >80% of genes in its genome. We also recovered a putative nitrite-oxidizing bacteria (NOB) MAG from within the Nitrospinaceae that was of much lower abundance and had lower transcript abundance than AOA. During the AOA bloom, we observed increased transcript abundance for nitrogen uptake and oxidative stress genes in non-nitrifier MAGs. This study confirms AOA are not only abundant, but also highly active during blooms oxidizing large amounts of ammonia to nitrite - a key intermediate in the microbial nitrogen cycle - and producing reactive compounds that may impact other members of the microbial community.

Salinity acclimation of nitrifying microorganisms: Nitrification performance, microbial community, osmotic adaptation strategies

Wastewater with high salinity (> 1%) presents a significant challenge to conventional wastewater treatment, particularly for the nitrification process. However, the osmotic adaptation strategies of nitrifying microorganisms remain poorly understood. In this study, we examined the impacts of salinity on the ammonia and nitrite oxidation processes in wastewater. The biofilm samples without salinity acclimation (0 g NaCl/L), after 1% salinity acclimation (10 g NaCl/L), and after 3% salinity acclimation (30 g NaCl/L) were inoculated to conical flasks containing synthetic high-salt wastewater (30 g NaCl/L), respectively. The research findings indicate that, following the salinity acclimation of biofilm, the activity of ammonia oxidation surpassed that of nitrite oxidation. 16S rRNA gene amplicon analysis revealed a noteworthy increase in the abundance of Nitrosomonas (ammonia-oxidizing bacteria) and an unclassified ammonia-oxidizing archaeon within the Nitrososphaeraceae family. In contrast, Nitrospira (nitrite-oxidizing bacteria) exhibited a significant decrease (p < 0.01). Metagenomic analysis indicates certain strains, such as Nitrosomonas sp. PL2, Nitrosomonas mobilis PL3, and Nitrososphaeraceae gen. sp. PL5, possessed various genes related to Na+ efflux, K+ uptake, glutamate synthesis or transport. However, Nitrospira sp. PL6 and Nitrospira sp. PL7 lacked K+ uptake genes. This study elucidates the microbial mechanisms underlying the variations in nitrification observed before and after salinity acclimation of biofilm, which helps to develop microbial evolution strategies to remove nitrogen pollutants under high salinity conditions.

Evidence of comammox bacteria playing a dominant role in Lake Taihu sediments based on metagenomic analysis

The nitrification process plays an important role in the nitrogen cycle, in which the ammonia-oxidation process mediated by microorganisms is the rate-limiting step. Environmental factors can affect the distribution and activity of ammonia-oxidizing microorganisms (AOM), including ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA), and complete ammonia oxidizer (comammox Nitrospira). At present, most studies have used amoA as a marker gene for the ammonia oxidation process to analyze the differences among AOM community composition and abundance in the environment. In this study, metagenomic sequencing was used to study the differences in community composition and functional gene distribution of nitrifying microorganisms in the sediments of Lake Taihu with different eutrophication levels. It was found that comammox Nitrospira and typical nitrite oxidizer NOB Nitrospira, which belong to Nitrospirota, had higher relative abundance at most sites compared to AOB and AOA. Furthermore, the network analysis of genes related to nitrogen cycle showed that the main survival mode of nitrogen metabolizing microorganisms was mutualism. Besides, the microbial genomes in the sediments of Lake Taihu were reconstructed by metagenomic binning, which showed that among the 167 bins obtained, 2 bins (bin 9 and bin 32) were annotated as comammox Nitrospira, and had high abundance in the macrophytes-dominated lakes (such as South Lake Taihu and West Coast). In addition, bin 9, which belongs to comammox Nitrospira, annotates amoA genes associated with ammonia oxidation, and other genes associated with urea decomposition and transport, suggesting functional diversity. Overall, these findings suggest that AOM have different distribution characteristics, among which comammox Nitrospira has high diversity and may be potentially dominant in macrophytes-dominated lakes.

Quest for the Nitrogen-Metabolic Versatility of Microorganisms in Soil and Marine Ecosystems.

Whether nitrogen (N)-metabolic versatility is a common trait of N-transforming microbes or if it only occurs in a few species is still unknown. We collected 83 soil samples from six soil types across China, retrieved 19 publicly available metagenomic marine sample data, and analyzed the functional traits of N-transforming microorganisms using metagenomic sequencing. More than 38% and 35% of N-transforming species in soil and marine ecosystems, respectively, encoded two or more N-pathways, although N-transforming species differed greatly between them. Furthermore, in both soil and marine ecosystems, more than 80% of nitrifying and N-fixing microorganisms at the species level were N-metabolic versatile. This study reveals that N-metabolic versatility is a common trait of N-transforming microbes, which could expand our understanding of the functional traits of drivers of nitrogen biogeochemistry.

Phenacetin promoted the rapid start-up and stable maintenance of partial nitrification: Responses of nitrifiers and antibiotic resistance genes

Phenacetin (PNCT) belongs to one of the earliest synthetic antipyretics. However, impact of PNCT on nitrifying microorganisms in wastewater treatment plants and its potential microbial mechanism was still unclear. In this study, PN could be initiated within six days by PNCT anaerobic soaking treatment (8 mg/L). In order to improve the stable performance of PN, 21 times of PNCT aerobic soaking treatment every three days was conducted and PN was stabilized for 191 days. After PN was damaged, ten times of PNCT aerobic soaking treatment every three days was conducted and PN was recovered after once soaking, maintained over 88 days. Ammonia oxidizing bacteria might change the dominant oligotype to gradually adjust to PNCT, and the increase of abundance and activity of Nitrosomonas promoted the initiation of PN. For nitrite-oxidizing bacteria (NOB), the increase of Candidatus Nitrotoga and Nitrospira destroyed PN, but PN could be recovered after once aerobic soaking illustrating NOB was not resistant to PNCT. KEGG and COG analysis suggested PNCT might disrupt rTCA cycle of Nitrospira, resulting in the decrease of relative abundance of Nitrospira. Moreover, PNCT did not lead to the sharp increase of absolute abundances of antibiotic resistance genes (ARGs), and the risk of ARGs transmission was negligible.

Restart performance of prolonged stopped down-flow hanging sponge reactor for treating of low-strength domestic sewage

The down-flow hanging sponge (DHS) reactor, a type of trickling filter used as a sponge, is a promising treatment system for low-cost sewage treatment. However, the performance of dried sponges that have been non-operational for 8 months has not been evaluated. Accordingly, herein, the re-startup process performance of a DHS reactor treating low-strength domestic sewage in Thailand that had stopped operation for over eight months was investigated. The dried sponge carrier immediately retained water in the sponge biomass-retained carrier and absorbed organic compounds. High nitrification activity of the DHS reactor was observed after 13 d, which was the same as that of the pure sponge biomass-retained carrier start-up. The tracer test results showed that the restarted DHS reactor had a high hydraulic retention time (HRT)/theoretical HRT ratio of 134.2 % at the beginning of the operation from the water retention property of the sponge carrier. Microbial community analysis showed that nitrifying microorganisms were effectively recovered in the biomass-retained sponge carrier. These results demonstrate that the sponge carriers in the DHS reactor that were left into dry condition are available for reuse and has high potential for rapid re-startup.

Biofiltration matrix optimization for efficient nitrogen removal from domestic onsite wastewater

Bench-scale columns were packed with marble chip, zeolite and gravel to treat septic tank effluent at elevated hydraulic loadings (0.48–0.64 m3 m−2 d−1) to challenge their hydraulic performance and ammonium (NH4+-N) removal performance. The results showed that higher NH4+-N removal efficiency was achieved in zeolite (75.8–94.1 %) and marble chip (54.9–83.9 %) columns than in sand (32.9–76.6 %) column without clogging during the experimental period (4 months). Biochar amendment (30 % v/v) resulted in a 23–29 % decrease of effluent NH4+-N in marble chip columns, while no impact was observed in the zeolite columns. Nitrification rather than adsorption contributed to the major NH4+-N removal (82–95 %) in zeolite, biochar amended zeolite and biochar amended marble chip columns. In addition, higher abundance of nitrifying microorganisms observed in the top layer of zeolite column (1.2 × 107 - 3.1 × 107amoA copies g−1, 3–10 times higher than marble chip) suggested NH4+-N was concentrated on zeolite surface by adsorption which then facilitated nitrification and promoted nitrifying biomass growth. Collectively, this study suggested that zeolite and biochar amended marble chip could serve as the filter materials for efficient NH4+-N removal from onsite wastewater at elevated wastewater loadings without clogging concerns.

Cooperation among nitrifying microorganisms promotes the irreversible biotransformation of sulfamonomethoxine

Ammonia-oxidizing microorganisms, including AOA (ammonia-oxidizing archaea), AOB (ammonia-oxidizing bacteria), and Comammox (complete ammonia oxidization) Nitrospira, have been reported to possess the capability for the biotransformation of sulfonamide antibiotics. However, given that nitrifying microorganisms coexist and operate as communities in the nitrification process, it is surprising that there is a scarcity of studies investigating how their interactions would affect the biotransformation of sulfonamide antibiotics. This study aims to investigate the sulfamonomethoxine (SMM) removal efficiency and mechanisms among pure cultures of phylogenetically distinct nitrifiers and their combinations. Our findings revealed that AOA demonstrated the highest SMM removal efficiency and rate among the pure cultures, followed by Comammox Nitrospira, NOB, and AOB. However, the biotransformation of SMM by AOA N. gargensis is reversible, and the removal efficiency significantly decreased from 63.84 % at 167 h to 26.41 % at 807 h. On the contrary, the co-culture of AOA and NOB demonstrated enhanced and irreversible SMM removal efficiency compared to AOA alone. Furthermore, the presence of NOB altered the SMM biotransformation of AOA by metabolizing TP202 differently, possibly resulting from reduced nitrite accumulation. This study offers novel insights into the potential application of nitrifying communities for the removal of sulfonamide antibiotics (SAs) in engineered ecosystems.

Survival of a microbial inoculant in soil after recurrent inoculations

Microbial inoculants are attracting growing interest in agriculture, but their efficacy remains unreliable in relation to their poor survival, partly due to the competition with the soil resident community. We hypothesised that recurrent inoculation could gradually alleviate this competition and improve the survival of the inoculant while increasing its impact on the resident bacterial community. We tested the effectiveness of such strategy with four inoculation sequences of Pseudomonas fluorescens strain B177 in soil microcosms with increasing number and frequency of inoculation, compared to a non-inoculated control. Each sequence was carried out at two inoculation densities (106 and 108 cfu.g soil−1). The four-inoculation sequence induced a higher abundance of P. fluorescens, 2 weeks after the last inoculation. No impact of inoculation sequences was observed on the resident community diversity and composition. Differential abundance analysis identified only 28 out of 576 dominants OTUs affected by the high-density inoculum, whatever the inoculation sequence. Recurrent inoculations induced a strong accumulation of nitrate, not explained by the abundance of nitrifying or nitrate-reducing microorganisms. In summary, inoculant density rather than inoculation pattern matters for inoculation effect on the resident bacterial communities, while recurrent inoculation allowed to slightly enhance the survival of the inoculant and strongly increased soil nitrate content.

Metagenome-assembled genomes of two nitrifying microorganisms from the freshwater archaeal ammonia-oxidizing enrichment culture BO1.

Two metagenome-assembled genomes (MAGs) were recovered from the ammonia-oxidizing enrichment culture BO1 obtained from the sediment of the freshwater reservoir Lake Burr Oak, Ohio, USA. High quality MAGs were assembled for the archaeal ammonia oxidizer Nitrosarchaeum sp. BO1 and the canonical nitrite oxidizer Nitrospira sp. BO1.

Activity-based labelling of ammonia- and alkane-oxidizing microorganisms including ammonia-oxidizing archaea.

Recently, an activity-based labelling protocol for the in vivo detection of ammonia- and alkane-oxidizing bacteria became available. This functional tagging technique enabled targeted studies of these environmentally widespread functional groups, but it failed to capture ammonia-oxidizing archaea (AOA). Since their first discovery, AOA have emerged as key players within the biogeochemical nitrogen cycle, but our knowledge regarding their distribution and abundance in natural and engineered ecosystems is mainly derived from PCR-based and metagenomic studies. Furthermore, the archaeal ammonia monooxygenase is distinctly different from its bacterial counterparts and remains poorly understood. Here, we report on the development of an activity-based labelling protocol for the fluorescent detection of all ammonia- and alkane-oxidizing prokaryotes, including AOA. In this protocol, 1,5-hexadiyne is used as inhibitor of ammonia and alkane oxidation and as bifunctional enzyme probe for the fluorescent labelling of cells via the Cu(I)-catalyzed alkyne-azide cycloaddition reaction. Besides efficient activity-based labelling of ammonia- and alkane-oxidizing microorganisms, this method can also be employed in combination with deconvolution microscopy for determining the subcellular localization of their ammonia- and alkane-oxidizing enzyme systems. Labelling of these enzymes in diverse ammonia- and alkane-oxidizing microorganisms allowed their visualization on the cytoplasmic membranes, the intracytoplasmic membrane stacks of ammonia- and methane-oxidizing bacteria, and, fascinatingly, on vesicle-like structures in one AOA species. The development of this novel activity-based labelling method for ammonia- and alkane-oxidizers will be a valuable addition to the expanding molecular toolbox available for research of nitrifying and alkane-oxidizing microorganisms.

Microbial induced calcium precipitation by Zobellella denitrificans sp. LX16 to simultaneously remove ammonia nitrogen, calcium, and chemical oxygen demand in reverse osmosis concentrates

In recent years, with the rapid development of industrial revolution and urbanization, the generation and treatment of a large number of salt-containing industrial wastewater has attracted wide attention. A novel salt-tolerant Zobellella denitrificans sp. LX16 with excellent nitrogen removal and biomineralization capabilities was isolated in this experiment. Kinetic experiments were conducted to determine the optimal condition. Under this condition, chemical oxygen demand (COD) can be entirely removed together with ammonia nitrogen, and the removal efficiency of calcium was 88.09%. Growth curves and nitrogen balance tests showed that strain LX16 not only had good HNAD and MICP capabilities, but also had high nitrite reductase and nitrate reductase activities during this process. Three-dimensional fluorescence results reflected that when external carbon sources were lacking or salinity was high, humic acid could effectively enhance the metabolic activity of heterotrophic nitrifying aerobic denitrifying microorganisms through extracellular electron transfer, and the substances produced in the metabolic process could promote biommineralization. Moreover, combined with SEM, SEM-EDS, XRD and FTIR analysis, it is concluded that the microbial surface can provide nucleation sites to form calcium salts, and with the increase of alkalinity to generate Ca5(PO4)3OH. The theoretical basis for the use of biological treatment in reverse osmosis wastewater have been proved by this experiment.

Effect of free ammonia and free nitrous acid on nitrogen removal of heterotrophic nitrification and aerobic denitrification bacteria

Free ammonia (FA) and free nitrous acid (FNA) can inhibit nitrogen removal by nitrifying microorganisms. However, current studies on FA and FNA mainly focus on traditional nitrifying microorganisms, and little is known about the relationship between heterotrophic nitrification-aerobic denitrification (HN-AD) microorganisms and FA and FNA. This study selected Alcaligenes faecalis WT14, an HN-AD strain, as the research object. The effects of different FA and FNA concentrations on the nitrogen removal ability of strain WT14 were investigated under neutral (pH = 7) and alkaline (pH = 9) conditions. The results showed that FA and FNA affected the removal ability of strain WT14 to ammonia nitrogen (NH4+-N) and nitrite nitrogen (NO2−-N). The rapid reduction of NH4+-N removal efficiency was determined at different concentrations of 6.12 mg·L−1 (pH = 7) and 551.18 mg·L−1 (pH = 9) for FA, which was 0.483 mg·L−1 (pH = 7) and 0.005 mg·L−1 (pH = 9) for FNA, respectively. Strain WT14 preferred an alkaline environment for growth; the FA tolerance value was 1134.25 mg·L−1 in such an environment, which was 51.8 times that of a neutral environment. Furthermore, strain WT14 had a higher removal rate of NH4+-N and NO2−-N in an alkaline environment. Its highest removal rates of NH4+-N and NO2−-N were 15.03 mg·L−1·h−1 and 7.16 mg·L−1·h−1, respectively, which was much higher than the reported HN-AD microorganisms.

Drug discovery-based approach identifies new nitrification inhibitors

Nitrogen (N) fertilization is crucial to sustain global food security, but fertilizer N production is energy-demanding and subsequent environmental N losses contribute to biodiversity loss and climate change. N losses can be mitigated be interfering with microbial nitrification, and therefore the use of nitrification inhibitors in enhanced efficiency fertilizers (EEFs) is an important N management strategy to increase N use efficiency and reduce N pollution. However, currently applied nitrification inhibitors have limitations and do not target all nitrifying microorganisms. Here, to identify broad-spectrum nitrification inhibitors, we adopted a drug discovery-based approach and screened 45,400 small molecules on different groups of nitrifying microorganisms. Although a high number of potential nitrification inhibitors were identified, none of them targeted all nitrifier groups. Moreover, a high number of new nitrification inhibitors were shown to be highly effective in culture but did not reduce ammonia consumption in soil. One archaea-targeting inhibitor was not only effective in soil, but even reduced - when co-applied with a bacteria-targeting inhibitor - ammonium consumption and greenhouse gas emissions beyond what is achieved with currently applied nitrification inhibitors. This advocates for combining different types of nitrification inhibitors in EEFs to optimize N management practices and make agriculture more sustainable.

Different genotypes of tartary buckwheat can regulate the transformation of nitrogen through the secretion of organic acids under low nitrogen stress

Roots respond to nitrogen deficiency by altering their physiological and metabolic responses. Soil nitrogen invertase activity and the diversity of nitrifying microorganisms (AOA and AOB) significantly affect the nitrogen cycle in soil. As an important part of root exudates, organic acids can reflect the dynamic changes of plant roots in soil. However, it is not clear how the barren-tolerant genotype plant varieties show their stress resistance through organic acids regulating nitrogen transformation under low nitrogen environment. Here, we selected two Tartary buckwheat varieties: HeiFeng1 (HF, low nitrogen sensitive cultivar) and DiQing (DQ, low nitrogen tolerance cultivar) for a two-year experiment. The urea addition levels of 0, 80, and 160 mg kg−1 soil were respectively set as nitrogen sources, and ozone sterilization experiments were designed to completely remove microbial effects to distinguish the contribution of plant roots and microorganisms to nitrogen invertase and organic acids (400 ml 1 mol L−1 ozone water daily, 0 nitrogen fertilizer, O3). The results showed that malic acid and tartaric acid were the main organic acids secreted by tartary buckwheat. The total amount and richness of organic acids in Diqing were higher than those in Heifeng, and organic acids directly affected the diversity of ammonia-oxidizing microorganisms (AOA and AOB), changed the soil environment by affecting soil water content, and indirectly affected the activity of nitrogen invertase. At the same time, it was found that the increase of nitrogen application rate would increase the proportion of key bacteria such as Nirtrosomonas and Nitrosospira in AOB of tartary buckwheat soil. Finally, Diqing tartary buckwheat was proved to be more suitable for planting in the nitrogen-deficient Loess Plateau, but attention should be paid to the negative effects of AOB and organic acids.

Comammox dominate soil nitrification under different N fertilization regimes in semi-arid areas of Northeast China

The newly identified complete ammonia oxidation (Comammox), which is capable of oxidizing ammonia directly to nitrate, has complemented the knowledge of nitrification in the global nitrogen (N) cycle. Knowledge of the community compositions and contributions to nitrification of autotrophic ammonia-oxidizing archaea (AOA) and bacteria (AOB) and Comammox remain void. In this study, the abundance, community compositions, and contributions to nitrification of AOA, AOB, and Comammox were observed in five N gradients (0, 90, 150, 210, and 270 kg ha−1) in a semi-arid area of Northeast China. The results indicated that, compared with low N application rates, higher N application rates significantly improved the soil ammonia monooxygenase (AMO) and the hydroxylamine oxidase (HAO) activities while total nitrogen (TN) was noted to be the main factor driving AMO and HAO activities. Soil potential nitrification rate (PNR) significantly increased with the increase in N application rate, and soil PNR was positively correlated with TN, nitrate nitrogen (NO3−-N), soil organic matter (SOM), and ammonium nitrogen (NH4+-N). The structural equation model (SEM) showed that TN was the main factor driving the community composition of Comammox; SOM had a greatest effect on the community composition of AOA while NH4+-N had a greatest effect on the community composition of AOB. The soil PNR had a direct effect on the yield. Overall, the findings of this study highlighted that N application was more conducive to the reproduction of soil nitrifying microorganisms while Comammox was the dominant contributor to nitrification under N fertilization regimes in the semi-arid area of Northeast China.

Shifts in the high-resolution spatial distribution of dissolved N2O and the underlying microbial communities and processes in the Pearl River Estuary.

Estuaries are significant sources of the ozone-depleting greenhouse gas N2O. However, owing to large spatial heterogeneity and discrete measurements, N2O emissions from estuaries are considerably uncertain. Microbial processes are disputed in terms of the dominant N2O production under severe human disturbance. Herein, combining real-time and high-resolution measurements with bioinformatics analysis, we accurately mapped the consecutive two-dimensional N2O distribution in the Pearl River Estuary (PRE), China, and revealed its underlying microbial mechanisms. Both the horizontal and vertical distributions of N2O concentrations varied greatly at fine scales. Supersaturated N2O concentrations (9.1 to 132.2nmol/L) in the surface water decreased along the estuarine salinity gradient, with several emission hotspots scattering upstream. The vertical N2O distribution showed marked differences from complete mixing upstream to incomplete mixing downstream, with constant or changeable concentrations with increasing depth. Furthermore, spatially varied denitrifying and nitrifying microorganisms controlled the N2O production and distribution in the PRE, with denitrification playing the dominant role. The nirK-type and nirS-type denitrifying bacteria were the primary producers of N2O in the water and sediment columns, respectively. In addition, substrate concentration (NO3- and DOC) regulated N2O production by affecting key microbial processes, while physical influences (water-mass mixing and salt wedges) reshaped N2O distribution. With these information, a conceptual model of estuarine N2O production and distribution was constructed to generalize the possible biochemical processes under environmental constraints, which could provide insights into the N2O biogeochemical cycle and emission mitigation from a mechanistic perspective.

Suppression of nitrite oxidizing bacteria by hydrogen peroxide for energy reduction in municipal wastewater treatment

This paper investigated the application of hydrogen peroxide (H2O2) for achieving partial nitrification in mainstream municipal wastewater treatment process. The investigation was carried out in both bench-scale and pilot-scale sequencing batch reactor systems using primary effluent as feed from municipal wastewater treatment plant. H2O2 played a dual role of: (1) inhibitor for nitrifying microorganisms, and (2) supplemental oxygen source. Bench scale studies were carried out at various doses of initial hydrogen peroxide concentrations (10,25,50,100 mg/L). It was found that at a concentration of 50 mg/L and above ammonia removal reduced by more than 80% implying significant impact on both ammonia oxidizing bacteria (AOB) and nitrite oxidizing bacteria (NOB). After an acclimatization period of 18 days at a dose of 50 mg/L H2O2, complete nitrification was observed with about 30% nitrite accumulation in the effluent which showed NOBs were impacted more significantly than AOBs. It was also observed from the long-term pilot-scale study that the inhibitory impact on NOBs is almost double the impact of on AOBs which facilitated partial nitrification resulting a nitrite accumulation ratio up to 60% in the effluent at 2 mg/L DO and 15 days SRT.Peroxide dosing resulted in an energy savings of 12–15% compared to a control reactor. It was also shown that by reducing the DO from 2 to 1 mg/L, additional power saving of 15% is achievable. Therefore, the proposed approach is an efficient method for aeration energy savings and can be easily implemented in existing wastewater treatment plants.

Disturbance of eucalypt forests alters the composition, function, and assembly of soil microbial communities.

Forest disturbance has well-characterized effects on soil microbial communities in tropical and northern hemisphere ecosystems, but little is known regarding effects of disturbance in temperate forests of the southern hemisphere. To address this question, we collected soils from intact and degraded Eucalyptus forests along an east-west transect across Tasmania, Australia, and characterized prokaryotic and fungal communities using amplicon sequencing. Forest degradation altered soil microbial community composition and function, with consistent patterns across soil horizons and regions of Tasmania. Responses of prokaryotic communities included decreased relative abundance of Acidobacteriota, nitrifying archaea, and methane-oxidizing prokaryotes in the degraded forest sites, while fungal responses included decreased relative abundance of some saprotrophic taxa (e.g. litter saprotrophs). Forest degradation also reduced network connectivity in prokaryotic communities and increased the importance of dispersal limitation in assembling both prokaryotic and fungal communities, suggesting recolonization dynamics drive microbial composition following disturbance. Further, changes in microbial functional groups reflected changes in soil chemical properties-reductions in nitrifying microorganisms corresponded with reduced NO3-N pools in the degraded soils. Overall, our results show that soil microbiota are highly responsive to forest degradation in eucalypt forests and demonstrate that microbial responses to degradation will drive changes in key forest ecosystem functions.

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.