Ammonia manipulates the ammonia-oxidizing archaea and bacteria in the coastal sediment-water microcosms

Nitrogen-cycling gene pool shrunk by species interactions among denser bacterial and archaeal community stimulated by excess organic matter and total nitrogen in a eutrophic bay

Microbial densities, functional genes, and their responses to environment factors have been studied for years, but still a lot remains unknown about their interactions with each other. In this study, the abundances of 7 nitrogen cycling genes in the sediments from Hangzhou Bay were analyzed along with bacterial and archaeal 16S rRNA abundances as the biomarkers of their densities. The amount of organic matter (OM) and total nitrogen (TN) strongly positively correlated with each other and microbial densities, while total phosphate (TP) and ammonia-nitrogen (NH₃-N) did not. Most studied genes were density suppressed, while nirS was density stable, and nosZ and hzo were density irrelevant. This suggests eutrophication could limit inorganic nitrogen cycle pathways and the removal of nitrogen in the sediment and emit more greenhouse gases. This study provides a new insight of microbial community structures, functions and their interactions in the sediments of eutrophic bays.

The Response of Estuarine Ammonia-Oxidizing Communities to Constant and Fluctuating Salinity Regimes

Aerobic nitrification is a fundamental nitrogen biogeochemical process that links the oxidation of ammonia to the removal of fixed nitrogen in eutrophicated water bodies. However, in estuarine environments there is an enormous variability of water physicochemical parameters that can affect the ammonia oxidation biological process. For instance, it is known that salinity can affect nitrification performance, yet there is still a lack of information on the ammonia-oxidizing communities behavior facing daily salinity fluctuations. In this work, laboratory experiments using upstream and downstream estuarine sediments were performed to address this missing gap by comparing the effect of daily salinity fluctuations with constant salinity on the activity and diversity of ammonia-oxidizing microorganisms (AOM). Activity and composition of AOM were assessed, respectively by using nitrogen stable isotope technique and 16S rRNA gene metabarcoding analysis. Nitrification activity was negatively affected by daily salinity fluctuations in upstream sediments while no effect was observed in downstream sediments. Constant salinity regime showed clearly higher rates of nitrification in upstream sediments while a similar nitrification performance between the two salinity regimes was registered in the downstream sediments. Results also indicated that daily salinity fluctuation regime had a negative effect on both ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) community’s diversity. Phylogenetically, the estuarine downstream AOM were dominated by AOA (0.92–2.09%) followed by NOB (0.99–2%), and then AOB (0.2–0.32%); whereas NOB dominated estuarine upstream sediment samples (1.4–9.5%), followed by AOA (0.27–0.51%) and AOB (0.01–0.23%). Analysis of variance identified the spatial difference between samples (downstream and upstream) as the main drivers of AOA and AOB diversity. Our study indicates that benthic AOM inhabiting different estuarine sites presented distinct plasticity toward the salinity regimes tested. These findings help to improve our understanding in the dynamics of the nitrogen cycle of estuarine systems by showing the resilience and consequently the impact of different salinity regimes on the diversity and activity of ammonia oxidizer communities.

Interaction type of tetrabromobisphenol A and copper manipulates ammonia-oxidizing archaea and bacteria communities in co-contaminated river sediments

The combined contamination of brominated flame retardants (BFRs) and heavy metals in electronic waste (e-waste) recycling and disposal areas has been a serious concern owing to their environmental persistence and chronic toxicities. Ammonia oxidizers, e.g., ammonia-oxidizing archaea (AOA) and bacteria (AOB) play essential roles in nitrogen cycling and can serve as ideal indicators that reflect the changes in sediment health in response to environmental variables. There is currently very little information available on the combined toxic effects of BFRs and heavy metals on AOA and AOB communities. In this study, two typical e-waste pollutants, tetrabromobisphenol A (TBBPA) and copper (Cu), were selected as target contaminants to investigate the individual and combined effects of both pollutants on AOA and AOB communities in river sediments. Respective treatments of TBBPA (1, 10, and 20 mg/kg wet weight), Cu (100 mg/kg wet weight) and their combined treatments (weight ratios of 1:100, 1:10, and 1:5) were performed in laboratory experiments. High-throughput sequencing was applied to explore the response of ammonia oxidizers to TBBPA and Cu. The interaction types of TBBPA and Cu were calculated by the directional classification system to reveal the individual and combined toxicities of both contaminants to the ammonia oxidizers. On days 15 and 30, the dominant interaction type of TBBPA and Cu was synergistic (62.50%), and the combined contamination exacted selective pressure and inhibition on the AOB and AOA communities. On days 45 and 90, the interaction type shifted to be antagonistic (83.33%), with both the AOB and AOA communities gradually reaching stable population equilibria. The alteration of the interaction type is attributed to the elevated TBBPA/Cu tolerance as the incubation time increased. This study disclosed the interaction types of TBBPA and Cu in contaminated river sediments, and revealed that the combined effect could potentially manipulate AOB and AOA communities.

Step-feeding ratios affect nitrogen removal and related microbial communities in multi-stage vertical flow constructed wetlands

Step-feeding (SF) strategies have been adopted in several types of constructed wetlands (CWs) to enhance nitrogen (N) removal. However, it is unclear how SF affects the N-transforming bacterial communities in CWs. Herein, four multi-stage vertical flow constructed wetlands (MS-VFCWs), each including three vertical flow stages (stage 1-3), were operated under different SF ratios (0%, 10%, 20% and 30%) in the stage 2. The physicochemical influent and effluent parameters, i.e., redox potential (ORP), pH value, chemical oxygen demand (COD), total nitrogen (TN), ammonia (NH₄⁺-N), nitrate (NO₃^--N), and nitrite (NO₂^--N), free-ammonia (FA) concentration, COD/TN ratio, as well as the abundance, structure, and activity of N-transforming bacteria were investigated. Results showed that N removal in a multi-stage vertical flow constructed wetland in the absence of SF was 45.0 ± 7.74%. Alternatively, a combined SF ratio of 20% increased N removal to 61.7% ± 4.50%, accounting for a 37.1% increase compared to the SF ratio of 0%. In the microbial community, FA was determined to be the primary physicochemical parameter governing nitrification processes in MS-VFCWs. Further, partial nitrification processes played an important role in ammonium removal during stage 1, while ammonia-oxidizing archaea were major contributors to ammonium removal in stage 3. Furthermore, abundance of nitrite reductase genes (nirS, nirK) and relative abundance of denitrifying bacteria increased with increasing SF ratio; while the nirS/nirK ratio and the alpha diversity of nirK denitrifiers were significantly affected by SF ratios, and the influent NO₃^--N concentration was related to a shift in denitrifier composition toward strains containing the nirS gene. Autotrophic (e.g., Thiobacillus, Sulfurimonas, Arenimonas, Gallionella and Methyloparacoccus) and facultative chemolithoautotrophic (e.g., Pseudomonas and Denitratisoma) denitrifying bacteria were enriched in stage 2. Hence, the synergy between heterotrophic and autotrophic denitrifying bacteria promoted excellent N removal efficiency with a low COD/TN ratio.

Effects of applying inorganic fertilizer and organic manure for 35 years on the structure and diversity of ammonia-oxidizing archaea communities in a Chinese Mollisols field

In this study, we investigated the physicochemical properties of soil, and the diversity and structure of the soil ammonia-oxidizing archaea (AOA) community, when subjected to fertilizer treatments for over 35 years. We collected soil samples from a black soil fertilization trial in northeast China. Four treatments were tested: no fertilization (CK); manure (M); nitrogen (N), phosphorus (P), and potassium (K) chemical fertilizer (NPK); and N, P, and K plus M (MNPK). We employed 454 high-throughput pyrosequencing to measure the response of the soil AOA community to the long-term fertilization. The fertilization treatments had different impacts on the shifts in the soil properties and AOA community. The utilization of manure alleviated soil acidification and enhanced the soybean yield. The soil AOA abundance was increased greatly by inorganic and organic fertilizers. In addition, the community Chao1 and ACE were highest in the MNPK treatment. In terms of the AOA community composition, Thaumarchaeota and Crenarchaeota were the main AOA phyla in all samples. Compared with CK and M, the abundances of Thaumarchaeota were remarkably lower in the MNPK and NPK treatments. There were distinct shifts in the compositions of the AOA operational taxonomic units (OTUs) under different fertilization management practices. OTU51 was the dominant OTU in all treatments, except for NPK. OTU79 and OTU11 were relatively abundant OTUs in NPK. Only Nitrososphaera AOA were tracked from the black soil. Redundancy analysis indicated that the soil pH and soil available P were the two main factors that affected the AOA community structure. The abundances of AOA were positively correlated with the total N and available P concentrations, and negatively correlated with the soil pH.

Responses of Active Ammonia Oxidizers and Nitrification Activity in Eutrophic Lake Sediments to Nitrogen and Temperature

Ammonium concentrations and temperature drive the activities of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB), but their effects on these microbes in eutrophic freshwater sediments are unclear. In this study, surface sediments collected from areas of Taihu Lake (China) with different degrees of eutrophication were incubated under three levels of nitrogen input and temperature, and the autotrophic growth of ammonia oxidizers was assessed using ¹³C-labeled DNA-based stable-isotope probing (SIP), while communities were characterized using MiSeq sequencing and phylogenetic analysis of 16S rRNA genes. Nitrification rates in sediment microcosms were positively correlated with nitrogen inputs, but there was no marked association with temperature. Incubation of SIP microcosms indicated that AOA and AOB amoA genes were labeled by ¹³C at 20°C and 30°C in the slightly eutrophic sediment, and AOB amoA genes were labeled to a much greater extent than AOA amoA genes in the moderately eutrophic sediment after 56 days. Phylogenetic analysis of ¹³C-labeled 16S rRNA genes revealed that the active AOA were mainly affiliated with the Nitrosopumilus cluster, with the Nitrososphaera cluster dominating in the slightly eutrophic sediment at 30°C with low ammonium input (1 mM). Active AOB communities were more sensitive to nitrogen input and temperature than were AOA communities, and they were exclusively dominated by the Nitrosomonas cluster, which tended to be associated with Nitrosomonadaceae-like lineages. Nitrosomonas sp. strain Is79A3 tended to dominate the moderately eutrophic sediment at 10°C with greater ammonium input (2.86 mM). The relative abundance responses of the major active communities to nitrogen input and temperature gradients varied, indicating niche differentiation and differences in the physiological metabolism of ammonia oxidizers that are yet to be described.IMPORTANCE Both archaea and bacteria contribute to ammonia oxidation, which plays a central role in the global cycling of nitrogen and is important for reducing eutrophication in freshwater environments. The abundance and activities of ammonia-oxidizing archaea and bacteria in eutrophic limnic sediments vary with different ammonium concentrations or with seasonal shifts, and how the two factors affect nitrification activity, microbial roles, and active groups in different eutrophic sediments is unclear. The significance of our research is in identifying the archaeal and bacterial responses to anthropogenic activity and climate change, which will greatly enhance our understanding of the physiological metabolic differences of ammonia oxidizers.

Sediment bacterial community structures and their predicted functions implied the impacts from natural processes and anthropogenic activities in coastal area

Coastal ecosystem structures and functions are changing under natural and anthropogenic influences. In this study, surface sediment samples were collected from disturbed zone (DZ), near estuary zone (NEZ), and far estuary zone (FEZ) of Hangzhou Bay, one of the most seriously polluted bays in China. The bacterial community structures and predicted functions varied significantly in different zones. Firmicutes were found most abundantly in DZ, highlighting the impacts of anthropogenic activities. Sediment total phosphorus was most influential on the bacterial community structures. Predicted by PICRUSt analysis, DZ significantly exceeded FEZ and NEZ in the subcategory of Xenobiotics Biodegradation and Metabolism; and DZ enriched all the nitrate reduction related genes, except nrfA gene. Seawater salinity and inorganic nitrogen, respectively as the representative natural and anthropogenic factor, performed exact-oppositely in nitrogen metabolism functions. The changes of bacterial community compositions and predicted functions provide a new insight into human-induced pollution impacts on coastal ecosystem.

Community Composition and Transcriptional Activity of Ammonia-Oxidizing Prokaryotes of Seagrass Thalassia hemprichii in Coral Reef Ecosystems

Seagrasses in coral reef ecosystems play important ecological roles by enhancing coral reef resilience under ocean acidification. However, seagrass primary productivity is typically constrained by limited nitrogen availability. Ammonia oxidation is an important process conducted by ammonia-oxidizing archaea (AOA) and bacteria (AOB), yet little information is available concerning the community structure and potential activity of seagrass AOA and AOB. Therefore, this study investigated the variations in the abundance, diversity and transcriptional activity of AOA and AOB at the DNA and transcript level from four sample types: the leaf, root, rhizosphere sediment and bulk sediment of seagrass Thalassia hemprichii in three coral reef ecosystems. DNA and complementary DNA (cDNA) were used to prepare clone libraries and DNA and cDNA quantitative PCR (qPCR) assays, targeting the ammonia monooxygenase-subunit (amoA) genes as biomarkers. Our results indicated that the closest relatives of the obtained archaeal and bacterial amoA gene sequences recovered from DNA and cDNA libraries mainly originated from the marine environment. Moreover, all the obtained AOB sequences belong to the Nitrosomonadales cluster. Nearly all the AOA communities exhibited higher diversity than the AOB communities at the DNA level, but the qPCR data demonstrated that the abundances of AOB communities were higher than that of AOA communities based on both DNA and RNA transcripts. Collectively, most of the samples shared greater community composition similarity with samples from the same location rather than sample type. Furthermore, the abundance of archaeal amoA gene in rhizosphere sediments showed significant relationships with the ammonium concentration of sediments and the nitrogen content of plant tissue (leaf and root) at the DNA level (P < 0.05). Conversely, no such relationships were found for the AOB communities. This work provides new insight into the nitrogen cycle, particularly nitrification of seagrass meadows in coral reef ecosystems.

Microbial Community Response on Wastewater Discharge in Boreal Lake Sediments

Despite high performance, municipal wastewater treatment plants (WWTPs) still discharge significant amounts of organic material and nitrogen and even microbes into the receiving water bodies, altering physico-chemical conditions and microbial functions. In this study, we examined how nitrified wastewater affects the microbiology of boreal lake sediments. Microbial community compositions were assessed with next generation sequencing of the 16S rRNA gene, and a more detailed view on nitrogen transformation processes was gained with qPCR targeting on functional genes (nirS, nirK, nosZ_I, nosZ_II, amoA_archaea, and amoA_bacteria). In both of the two studied lake sites, the microbial community composition differed significantly between control point and wastewater discharge point, and a gradual shift toward natural community composition was seen downstream following the wastewater gradient. SourceTracker analysis predicted that ∼2% of sediment microbes were of WWTP-origin on the study site where wastewater was freely mixed with the lake water, while when wastewater was specially discharged to the sediment surface, ∼6% of microbes originated from WWTP, but the wastewater-influenced area was more limited. In nitrogen transformation processes, the ratio between nitrifying archaea (AOA) and bacteria (AOB) was affected by wastewater effluent, as the AOA abundance decreased from the control point (AOA:AOB 28:1 in Keuruu, 11:1 in Petäjävesi) to the wastewater-influenced sampling points, where AOB dominated (AOA:AOB 1:2–1:15 in Keuruu, 1:3–1:19 in Petäjävesi). The study showed that wastewater can affect sediment microbial community through importing nutrients and organic material and altering habitat characteristics, but also through bringing wastewater-originated microbes to the sediment, and may thus have significant impact on the freshwater biogeochemistry, especially in the nutrient-poor boreal ecosystems.

The impact of wastewater treatment effluent on microbial biomasses and diversities in coastal sediment microcosms of Hangzhou Bay

Disposal of wastewater treatment plant (WWTP) effluent into sea, a typical anthropogenic disturbance, may influence many environmental factors and change the coastal microbial community structure. In this study, by setting up coastal sediment microcosms perturbed by WWTP effluent, the changes of microbial community structure under different degree of disturbances were investigated. Quantitative PCR (qPCR) and terminal restriction fragment length polymorphism (T-RFLP) were used to analyzed the biomass and biodiversity. High throughput sequencing analysis was used to identify the classification of the microorganisms. Our study suggested that low ratio of WWTP effluent may stimulate dominant species, which increase the biomass but decrease the biodiversity; while high ratio of WWTP effluent may depress all species, which decrease the biomass but increase the biodiversity. In other words, the impact was dose-dependent. The changes of microbial community structure may provide a metric for water environmental assessment and pollution control.

Pathways regulating the removal of nitrogen in planted and unplanted subsurface flow constructed wetlands

Single-stage constructed wetlands (CWs) are characterized by a low potential for N removal. Understanding the pathways regulating N cycling as well as their dependence on environmental variables might improve the potential of CWs for N removal and results in more accurate simulation tools. In this study we employed qPCR targeting marker functional genes (amoA, nirK, nirS, clade I and II nosZ) or microorganisms (anammox) regulating key pathways of N cycling to unravel their relative importance. Furthermore, the influence of plant species on treatment performance was studied. Our findings indicated nitrification-denitrification as the principal route of N removal in CWs, while anammox did not have a strong contribution. Evidence was also arisen that ammonia oxidizing archaea (AOA) contributed on NH3 oxidation. Overall, plant species had a weak effect on the abundance of N functional genes (amoA of AOA), but it strongly affected the performance of CWs in terms of N removal in the following order: unplanted < Phragmites communis < Typha latifolia. These findings suggest that plant species stimulate N removal by upregulating the rates that the responsible biochemical pathways operate, probably by increasing O2 supply. In addition, our study revealed differences in indicators linked to N2O emissions. The abundance of clade II nosZ genes remained low across the season scaling down a strong contribution in the reduction of the emitted N2O. The increasing ratios of nosZ/Σnir and nirS/nirK with the progress of season indicate a shift in the composition of denitrifiers towards strains with a lower genetic potential for N2O release. Similar trends were observed among the treatments but the mechanisms differed. The planted treatments stimulated an increase in the ΣnosZ/Σnir ratio, while the unplanted an increase in the nirS/nirK ratio.

Population and diversity of ammonia-oxidizing archaea and bacteria in a pollutants' receiving area in Hangzhou Bay

The community structure of ammonia-oxidizing microorganisms is sensitive to various environmental factors, including pollutions. In this study, real-time PCR and 454 pyrosequencing were adopted to investigate the population and diversity of ammonia-oxidizing archaea (AOA) and bacteria (AOB) temporally and spatially in the sediments of an industrial effluent receiving area in the Qiantang River's estuary, Hangzhou Bay. The abundances of AOA and AOB amoA genes fluctuated in 10(5)-10(7) gene copies per gram of sediment; the ratio of AOA amoA/AOB amoA ranged in 0.39-5.52. The AOA amoA/archaeal 16S rRNA, AOB amoA/bacterial 16S rRNA, and AOA amoA/AOB amoA were found to positively correlate with NH4 (+)-N concentration of the seawater. Nitrosopumilus cluster and Nitrosomonas-like cluster were the dominant AOA and AOB, respectively. The community structures of both AOA and AOB in the sediments exhibited significant seasonal differences rather than spatial changes in the effluent receiving area. The phylogenetic distribution of AOB in this area was consistent with the wastewater treatment plants (WWTPs) discharging the effluent but differed from the Qiantang River and other estuaries, which might be an outcome of long-term effluent discharge.

Insight into the short-term effect of titanium dioxide nanoparticles on active ammonia oxidizing microorganisms in a full-scale wastewater treatment plant: a DNA-stable isotope probing study

Ammonia-oxidizing bacteria (AOB) and archaea (AOA) are two distinct ammonia-oxidizing microorganisms (AOMs) responsible for nitrification in wastewater treatment plants (WWTPs).