Effects of polybrominated diphenyl ethers and plant species on nitrification, denitrification and anammox in mangrove soils

Nutrient availability contributes to structural and functional diversity of microbiome in Xinjiang oilfield

Indigenous microbial enhanced oil recovery (IMEOR) is a promising alternative way to promote oil recovery. It activates oil recovery microorganisms in the reservoir by adding nutrients to the injected water, utilizing microbial growth and metabolism to enhance recovery. However, few studies have focused on the impact of injected nutrients on reservoir microbial community composition and potential functions. This limits the further strategic development of IMEOR. In this study, we investigated the effects of nutrition on the composition of the reservoir bacterial community and functions in the Qizhong block of Xinjiang Oilfield, China, by constructing a long core microbial flooding simulation device. The results showed that the microbial community structure of the reservoir changed from aerobic state to anaerobic state after nutrient injection. Reducing the nutrient concentration increased the diversity and network stability of the reservoir bacterial community. At the same time, the nitrogen metabolism function also showed the same change response. Overall, these results indicated that nutrition significantly affected the community structure and function of reservoir microorganisms. Injecting low concentrations of nutrients may be more beneficial to improve oil recovery. This study is of great significance for guiding IMEOR technology and saving costs at the field site.

Sediment microbial community characteristics in sea cucumber restocking area

Variations of microbial species and functional composition in coastal sediment are usually taken as the results of the provision of supplementary nutrients affected by human activities. However, responses of microbiome stability to restocking biological resources remain less understood in coastal benthic systems without nutrient supplements. Here, combined with metagenomics and microbiome co-occurrence networks, the composition, function, and community stability of microbes were evaluated in a coastal area where sea cucumbers (Apostichopus japonicus) restocked after six months. Also, the physicochemical characteristics of sediments and bottom water were analyzed. We found the total organic carbon, total nitrogen, and total phosphorus of sediment did not change significantly in the restocking area after six months, whereas the concentration of dissolved inorganic nitrogen in bottom water increased significantly. Moreover, the relative abundance of Nitrospina at the class level was increased significantly in the restocking area. Also, enzymes related to nitrate reduction and nitrous oxide reductase were increased in the restocking area. Of note, stock enhancement of sea cucumbers altered associations between bacteria rather than their composition. The elimination of negative associations and reduction of the potential keystone taxa in the restocking area indicated destabilized bacterial communities. Our work may contribute to elucidating the response of microbial stability to stock enhancement. This finding also suggests that microbial community stability can be considered as an indicator of ecological risk under the influence of stock enhancement.

The effects of long-term hexabromocyclododecanes contamination on microbial communities in the microcosms

The adaptation of microbial community to the long-term contamination of hexabromocyclododecanes (HBCDs) has not been well studied. Our previous study found that the HBCDs contamination in the microcosms constructed of sediments from two different mangrove forests in 8 months resulted in serious acidification (pH2-3). This study reanalyzed previous sequencing data and compared them with data after 20 months to investigate the adaptive properties of microbial communities in the stress of HBCDs and acidification. It hypothesized that the reassembly was based on the fitness of taxa. The results indicated that eukaryotes and fungi might have better adaptive capacity to these deteriorated habitats. Eukaryotic taxa Eufallia and Syncystis, and fungal taxa Wickerhamomyces were only detected after 20 months of contamination. Moreover, eukaryotic taxa Caloneis and Nitzschia, and fungal taxa Talaromyces were dominant in most of microbial communities (14.467-95.941%). The functional compositions were sediment-dependent and more divergent than community reassemblies. Network and co-occurrence analysis suggested that acidophiles such as Acidisoma and Acidiphilium were gaining more positive relations in the long-term stress. The acidophilic taxa and genes involved in resistance to the acidification and toxicity of HBCDs were enriched, for example, bacteria Acidisoma and Acidiphilium, archaea Thermogymnomonas, and eukaryotes Nitzschia, and genes kdpC, odc1, polA, gst, and sod-2. These genes involved in oxidative stress response, energy metabolism, DNA damage repair, potassium transportation, and decarboxylation. It suggested that the microbial communities might cope with the stress from HBCDs and acidification via multiple pathways. The present research shed light on the evolution of microbial communities under the long-term stress of HBCDs contamination and acidification.

Coupling of Anammox Activity and PAH Biodegradation: Current Insights and Future Directions

Anaerobic ammonium oxidation (anammox) has shown success in past years for the treatment of municipal and industrial wastewater containing inorganic nutrients (i.e., nitrogen). However, the increase in polycyclic aromatic hydrocarbon (PAH)-contaminated matrices calls for new strategies for efficient and environmentally sustainable remediation. Therefore, the present review examined the literature on the connection between the anammox process and PAHs using VOSviewer to shed light on the mechanisms involved during PAH biodegradation and the key factors affecting anammox bacteria. The scientific literature thoroughly discussed here shows that PAHs can be involved in nitrogen removal by acting as electron donors, and their presence does not adversely affect the anammox bacteria. Anammox activity can be improved by regulating the operating parameters (e.g., organic load, dissolved oxygen, carbon-to-nitrogen ratio) and external supplementation (i.e., calcium nitrate) that promote changes in the microbial community (e.g., Candidatus Jettenia), favoring PAH degradation. The onset of a synergistic dissimilatory nitrate reduction to ammonium and partial denitrification can be beneficial for PAH and nitrogen removal.

Enhancement effects of decabromodiphenyl ether on microbial sulfate reduction in eutrophic lake sediments: A study on sulfate-reducing bacteria using dsrA and dsrB amplicon sequencing

Although sulfate (SO₄^2-) reduction by sulfate-reducing bacteria (SRB) is an important sulfur cycling processes, little is known about how the persistent organic pollutants affect the SO₄^2- reduction process in the eutrophic lake sediments. Here, we carried out a 120-day microcosm experiment to explore the effects of decabromodiphenyl ether (BDE-209) on SO₄^2- reduction mediated by SRB in sediment collected from Taihu Lake, a typical eutrophic lake in China. The results showed that BDE-209 contamination significantly enhanced the activity of dissimilatory sulfite reductase (DSR) (r = 0.83), which led to an increased concentration of sulfide produced by SO₄^2- reduction. This stimulatory effect of BDE-209 on DSR activity was closely related to variations in the dsrA- and dsrB-type SRB communities. The abundances and diversities of the dsrA- and dsrB-containing SRB increased and their community composition varied in response to BDE-209 contamination. The gene copies (r = 0.72), Chao 1 (r = 0.50), Shannon (r = 0.55), and Simpson (r = 0.70) indices of dsrB-containing SRB was positively correlated with BDE-209 contamination. Co-occurrence network analysis revealed that network complexity, connectivity, and the interspecific cooperative relationship in SRB were strengthened by BDE-209 contamination. The keystone species identified in the SRB community mainly belonged to the genera Candidatus Sulfopaludibacter for the dsrA-containing SRB and Desulfatiglans for the dsrB-containing SRB, and their relative abundances were positively correlated with DSR activity in the sediment. The relative abundance of the keystone species and SRB diversity were important microbial factors directly contributing to the variations in DSR activity based on structural equation modeling analysis. Notably, the results of abundance, community structure, and interspecific relationships showed that the dsrB-containing SRB may be more sensitive to the BDE-209 contamination than the dsrA-containing SRB. These results will help us understand the effects of BDE-209 on microbial sulfate reduction in eutrophic lakes.

Spatial monitoring and health risk assessment of polybrominated diphenyl ethers in environmental matrices from an industrialized impacted canal in South Africa

This study investigates the pollution of Markman stormwater runoff, which is a tributary to Swartkops River Estuary. Solid-phase and ultrasonic extraction methods were utilized in the extraction of water and sediment samples, respectively. The pH of the sampling sites was above the EU guideline. The ranges of concentration of [Formula: see text]PBDE obtained in water and sediment samples for all the seasons were 58.47-1357 ng/L and 175-408 ng/g, respectively. Results also showed that BDE-66 was the dominant congener, specifically in the industrial zone, where its concentrations ranged from 2 to 407 ng/g in sediment. Consequently, the high concentration of BDE- 66 in the sediment of stormwater calls for concern. Penta-BDE suggests potential moderate eco-toxicological risk, as evident in the calculated risk assessment. The result showed possible photodegradation along the contaminant's travel time, as only 7% of the PBDE was detected at the point of entry into the Swartkops River Estuary. Markman stormwater may be contributing heavily to the pollution load of Swartkops River, as evident in the alarming concentrations of PBDEs obtained. The industries at this zone should eliminate the contaminants before discharging their effluents into the canal.

Microbial communities in swamps of four mangrove reserves driven by interactions between physicochemical properties and microbe in the North Beibu Gulf, China

Mangroves are distributed in coastal and estuarine regions and are characterized as a sink for terrestrial pollution. It is believed that complex interactions between environmental factors and microbial communities exist in mangrove swamps. However, little is known about environment-microbe interactions. There is a need to clarify some important environmental factors shaping microbial communities and how environmental factors interact with microbial assemblages in mangrove swamps. In the present study, physicochemical and microbial characteristics in four mangrove reserves (named ZZW, Qin, Bei, and GQ) in the North Beibu Gulf were determined. The interactions between environmental factors and microbial assemblages were analyzed with statistical methods in addition to CCA and RDA. Higher concentrations of sulfate (SO₄^2--S) and Fe but lower concentrations of total phosphorus (TP) and NO₃^--N were detected in ZZW and Qin. Nutrient elements (NO₃^--N, NH₄⁺-N, organic matter (OM), SO₄^2--S, Fe, and TP) were more important than heavy metals for determining the microbial assemblages, and NO₃^--N was the most important factor. NO₃^--N, SO₄^2--S, TP, and Fe formed a significant co-occurrence network in conjunction with some bacterial taxa, most of which were Proteobacteria. Notably, comparatively elevated amounts of sulfate-reducing bacteria (Desulfatibacillum, Desulfomonile, and Desulfatiglans) and sulfur-oxidizing bacteria (Thioprofundum and Thiohalophilus) were found in ZZW and Qin. The co-occurrence network suggested that some bacteria involved in sulfate reduction and sulfur oxidation drive the transformation of P and N, resulting in the reduction of P and N in mangrove swamps. Through the additional utilization of multivariate regression tree (MRT) and co-occurrence network analysis, our research provides a new perspective for understanding the interactions between environmental factors and microbial communities in mangroves.

Di(2-ethylhexyl) phthalate and dibutyl phthalate have a negative competitive effect on the nitrification of black soil

Di (2-ethylhexyl) phthalate (DEHP) and dibutyl phthalate (DBP) are the most widely used plasticizers for agricultural mulching films and one of the most common organic pollutants in black soil. However, little is known about the effect of these two contaminants on nitrification in black soil. This study investigated the changes of 20 mg/kg DEHP and DBP on the diversity of nitrification microbial communities, the abundance of ammonia oxidizing bacteria (AOB) and nitrite oxidizing bacteria (NOB) related genes, and the activities of key enzymes involved in nitrification. During ammonia oxidation, DEHP and DBP had uncompetitive inhibition of urease, reducing the copy number of amoA gene, and microorganisms (Azoarcus, Streptomyces and Caulobacter) would use inorganic nitrogen as a nitrogen source for physiological growth. During nitrite oxidation, the copy number of nxrA gene also reduced, and the relative abundance of chemoautotrophic nitrifying bacteria (Nitrosomonas and Nitrobacter) decreased. Moreover, the path analysis results showed that DEHP and DBP mainly directly or indirectly affect AOB and NOB through three ways. These results help better understand the ecotoxicological effects of DEHP and DBP on AOB and NOB in black soil.

Plants are a natural source of nitrous oxide even in field conditions as explained by 15N site preference

Plants are either recognized to produce nitrous oxide (N₂O) or considered as a medium to transport soil-produced N₂O. To date, it is not clear whether in their habitat plants conduit N₂O produced in soil or are a natural source. We aimed to understand role of plants in N₂O emissions in field conditions. Therefore, rubber plants (Ficus elastica) were planted in the field; then plant and soil chambers were deployed simultaneously to collect gas samples, and ¹⁵N site preference (SP) of N₂O was evaluated. The mean SP values of plant and soil emitted N₂O were -20.85 ± 2.8‰ and -8.85 ± 1.08‰, respectively, and were significantly different (p < 0.0001); while bulk ¹⁵N of plant and soil emitted N₂O were -10.83 ± 3.33‰ and -22.56 ± 3.37‰, respectively and were similar (p = 0.06). In the current study, soil always acted as a source of N₂O, while plants were both source and sink. Plant and soil N₂O fluxes had significant positive exponential relationship with both soil and air temperature. Soil water-filled pore space (WFPS) had significant negative linear relationship with only soil N₂O fluxes. Plant N₂O fluxes had significant positive linear relationship with plant respiration rates and negative linear relationship with plant surface areas. Based on the relationship between plant respiration rates and N₂O fluxes, we suggest that mitochondria are the possible sites of N₂O formation in plant cells while the relationship between plant surface areas and N₂O fluxes suggests that roots are the parts of its formation in natural and field conditions. Our results suggest that plants are a natural source of N₂O even at field conditions and challenge a view that plants are a medium to transport soil-produced N₂O into the atmosphere.

Deciphering and predicting anammox-based nitrogen removal process under oxytetracycline stress via kinetic modeling and machine learning based on big data analysis

Anaerobic ammonium oxidation (anammox) is an advanced nitrogen removal process that is widely used in the nitrogen removal of various antibiotic containing wastewaters due to its high efficiency and energy saving characteristics. However, as a widely used antibiotic, the inhibitory effect of oxytetracycline (OTC) on anammox is unclear. In this study, the effect of OTC on the anammox-based nitrogen removal process was revealed by kinetic model and machine learning models. Statistical analysis showed that anammox started to be inhibited when the OTC concentration reached 2 mg/L. The inhibition and recovery periods were simulated under OTC stress. During the inhibition period, the R² fitted by Exp model was higher, and the simulated maximum nitrogen removal rate (NRR) was between 0.47 and 17.05 kg/(m³·d). During the recovery period, both Boltzmann and Gauss models fit well. In addition, the machine learning model of the artificial neural network predicted the NRR more accurately, indicating that the importance of environmental factors was lower than the effluent parameters. Spearman correlation analysis showed that the NRR was negatively correlated with OTC under both short-term and long-term OTC stress. Furthermore, the hydraulic retention time and water quality parameters played an important role in the short-term and long-term experiment, respectively. Finally, redundancy analysis demonstrated that the abundance of nitrogen functional genes, such as hydrazine dehydrogenase, nitrite/nitric oxide oxidoreductase and hydrazine synthase, was negatively correlated with the amount of OTC, while antibiotic resistance genes showed the opposite trend.

Persistent organic pollutants (POPs) in coastal wetlands: A review of their occurrences, toxic effects, and biogeochemical cycling

Coastal wetlands, such as mangroves, seagrass beds, and salt marshes, are highly threatened by increasing anthropic pressures, including chemical pollution. Persistent organic pollutants (POPs) have attracted attention in these particularly vulnerable ecosystems, due to their bioaccumulative, pervasive, and ecotoxic behavior. This article reviews and summarizes available information regarding current levels, biogeochemical cycling, and effects of POPs on coastal wetlands. Sediment POP levels were compared with international quality guidelines, revealing many areas where compounds could cause damage to biota. Despite this, toxicological studies on some coastal wetland plants and microorganisms showed a high tolerance to those levels. These taxonomic groups are likely to play a key role in the cycling of the POPs, with an active role in their accumulation, immobilization, and degradation. Toxicity and biogeochemical processes varied markedly along three main axes; namely species, environmental conditions, and type of pollutant. While more focused research on newly and unintentionally produced POPs is needed, mainly in salt marshes and seagrass beds, with the information available so far, the environmental behavior, spatial distribution, and toxicity level of the studied POPs showed similar patterns across the three studied ecosystems.

Long-term effects of decabromodiphenyl ether on denitrification in eutrophic lake sediments: Different sensitivity of six-type denitrifying bacteria

The widespread use of polybrominated diphenyl ethers inevitably results in their increased release into natural waters and subsequent deposition in sediments. However, their long-term effects on the bacteria participating in each step of denitrification in eutrophic lake sediments are still unknown. Here, we conducted a one-year microcosm experiment to determine the long-term effects of decabromodiphenyl ether (BDE-209), at low (2 mg kg^-1 dry weight) and high (20 mg kg^-1 dry weight) contamination levels, on six-type denitrifying bacteria and their activities in sediments collected from Taihu Lake, a typical eutrophic lake in China. At the end of the experiment, sediment denitrifying reductase activities were inhibited by BDE-209 at both levels, with the greatest inhibition seen for nitric oxide reductase activity. The higher nitrate concentration in the contaminated sediments was attributed to the inhibition of nitrate reductase activities. The abundances of six-type denitrifying genes (narG, napA, nirK, nirS, norB, and nosZ) significantly decreased under high BDE-209 treatment, and narG and napA genes were more sensitive to the toxicity of BDE-209. The results from pyrosequencing showed that BDE-209, at either treatment concentration, decreased the six-type denitrifying bacterial diversities and altered their community composition. This shift of six-type denitrifying bacterial communities might also be driven by the debrominated products concentrations of BDE-209 and variations in sediment inorganic nitrogen concentrations. In particular, some genera from phylum Proteobacteria such as Pseudomonas, Cupriavidus, and Azoarcus were decreased significantly because of BDE-209 and its debrominated products.

Insights into the Occurrence, Fate, and Impacts of Halogenated Flame Retardants in Municipal Wastewater Treatment Plants

Halogenated flame retardants (HFRs) have been extensively used in various consumer products and many are classified as persistent organic pollutants due to their resistance to degradation, bioaccumulation potential and toxicity. HFRs have been widely detected in the municipal wastewater and wastewater treatment solids in wastewater treatment plants (WWTPs), the discharge and agricultural application of which represent a primary source of environmental HFRs contamination. This review seeks to provide a current overview on the occurrence, fate, and impacts of HFRs in WWTPs around the globe. We first summarize studies recording the occurrence of representative HFRs in wastewater and wastewater treatment solids, revealing temporal and geographical trends in HFRs distribution. Then, the efficiency and mechanism of HFRs removal by biosorption, which is known to be the primary process for HFRs removal from wastewater, during biological wastewater treatment processes, are discussed. Transformation of HFRs via abiotic and biotic processes in laboratory tests and full-scale WWTPs is reviewed with particular emphasis on the transformation pathways and functional microorganisms responsible for HFRs biotransformation. Finally, the potential impacts of HFRs on reactor performance (i.e., nitrogen removal and methanogenesis) and microbiome in bioreactors are discussed. This review aims to advance our understanding of the fate and impacts of HFRs in WWTPs and shed light on important questions warranting further investigation.

Specialized metabolic functions of keystone taxa sustain soil microbiome stability

BACKGROUND

The relationship between biodiversity and soil microbiome stability remains poorly understood. Here, we investigated the impacts of bacterial phylogenetic diversity on the functional traits and the stability of the soil microbiome. Communities differing in phylogenetic diversity were generated by inoculating serially diluted soil suspensions into sterilized soil, and the stability of the microbiome was assessed by detecting community variations under various pH levels. The taxonomic features and potential functional traits were detected by DNA sequencing.

RESULTS

We found that bacterial communities with higher phylogenetic diversity tended to be more stable, implying that microbiomes with higher biodiversity are more resistant to perturbation. Functional gene co-occurrence network and machine learning classification analyses identified specialized metabolic functions, especially "nitrogen metabolism" and "phosphonate and phosphinate metabolism," as keystone functions. Further taxonomic annotation found that keystone functions are carried out by specific bacterial taxa, including Nitrospira and Gemmatimonas, among others.

CONCLUSIONS

This study provides new insights into our understanding of the relationships between soil microbiome biodiversity and ecosystem stability and highlights specialized metabolic functions embedded in keystone taxa that may be essential for soil microbiome stability. Video abstract.

Effect of perfluorooctanesulfonate (PFOS) on the rhizosphere soil nitrogen cycling of two riparian plants

Here, we examined the effects of low and high concentrations of perfluorooctanesulfonate (PFOS) on rhizosphere soil N cycling processes in the presence of Lythrum salicaria and Phragmites communis over 4 months. Compared with the control group, the nitrate nitrogen (NO₃^--N) content of the bulk soil in the low PFOS (0.1 mg kg^-1) treatment significantly decreased (27.7%), the ammonium nitrogen (NH₄⁺-N) content significantly increased (8.7%), and the pH value and total organic carbon (TOC) content slightly increased (0.3% and 1.1%, respectively). Compared with the low PFOS treatment, the content of NO₃^-N, NH₄⁺-N and pH value in the bulk soil of the high PFOS treatment (50 mg kg^-1) significantly increased (1.0%, 53.8% and 61.8%, respectively), and the TOC content significantly decreased (8.2%). Soil protease levels were high in the low PFOS treatment, but low in the high PFOS treatment. PFOS produced inverted U-shaped responses in the potential nitrification (1.5, 3.0, and 1.1 mg N d^-1 kg^-1 in no, low, and high PFOS, respectively), denitrification (0.19, 0.30, and 0.22 mg N d^-1 kg^-1 in no, low, and high PFOS, respectively), and N₂O emission rates (0.01, 0.03, and 0.02 mg N d^-1 kg^-1 in no, low, and high PFOS, respectively) of bulk soil. The abundance of the archaea amoA gene decreased with increasing PFOS concentration, whereas that of bacterial amoA increased; inverted U-shaped responses were observed for narG, nirK, nirS, and nosZ. In the PFOS-contaminated rhizosphere soil, the observed changes differed from those in the bulk soil and differed between treatments. P. communis tended to upregulate each step of the nitrogen cycle under low PFOS conditions, whereas L. salicaria tended to inhibit them. Under high PFOS conditions, both test plants tended to act as inhibitors of the soil N-cycle; thus, the effects of PFOS on soil N transformation were plant-specific.

Radial oxygen loss is correlated with nitrogen nutrition in mangroves

The present study aimed to explore the possible functions of radial oxygen loss (ROL) on mangrove nutrition. A field survey was conducted to explore the relations among ROL, root anatomy and leaf N in different mangrove species along a continuous tidal gradient. Three mangroves with different ROL (Avicennia marina [A. marina], Kandelia obovata and Rhizophora stylosa) were then selected to further explore the dynamics of N at the root-soil interface. The results showed that seaward pioneer mangrove species such as A. marina appeared to exhibit higher leaf N despite growing under poorer nutrient conditions. Greater leaf N in pioneer mangroves coincided with their special root structure (e.g., high porosity together with a thin lignified/suberized exodermis) and powerful ROL. An interesting positive relation was observed between ROL and leaf N in mangroves. Moreover, rhizo-box data further showed that soil nitrification was also strongly correlated with ROL. A. marina, which had the highest ROL among the three mangrove species studied, consistently possessed the highest levels of NO3-, nitrification and ammonia-oxidizing bacteria and archaea gene copies in the rhizosphere. Besides, both NO3- and NH4+ influxes were found to be higher in the roots of A. marina when compared to those of K. obovata and R. stylosa. In summary, greater N acquisition by pioneer mangroves such as A. marina was strongly correlated with ROL which would regulate N transformation and translocation at the root-soil interface. The implications of this study may be significant in mangrove nutrition and the mechanisms involved in mangrove zonation.

Denitrifier communities differ in mangrove wetlands across China

To explore the geographical variations in the nosZ-denitrifier community and the underlying influential factors, surface sediments were collected from six mangroves across China, including Yunxiao (YX), Futian (FT), Fangchenggang (FCG), Zhanjiang (ZJ), Dongzhaigang (DZG), and Dongfang (DF). The nosZ gene abundance in mangrove sediments were 1.60 × 10⁵-1.17 × 10⁶ copies g^-1 dry sediment, with a higher density in Avicennia marina forest than the mudflat. Denitrifier community richness and diversity increased with decreasing latitude based on the Chao1 richness and Shannon diversity index, with the highest diversity being observed in the DF mangrove. The denitrifier communities could be classified into three groups including south DF mangrove, middle FCG, ZJ and DZG mangroves, and north YX and FT mangroves based on HCA and PCoA analysis. The nosZ OTUs could be divided into seven distinct clusters with different proportionality characteristics among mangroves. Environmental factors (TN, TOC, and salinity) collectively shape denitrifier communities in mangrove sediments.

Emerging perfluoroalkyl substance impacts soil microbial community and ammonia oxidation

Legacy perfluoroalkyl and poly-fluoroalkyl substances (PFASs) are gradually phased out because of their persistence, bioaccumulation, toxicity, long-distance transport and ubiquity in the environment. Alternatively, emerging PFASs are manufactured and released into the environment. It is accepted that PFASs can impact microbiota, although it is still unclear whether emerging PFASs are toxic towards soil microbiota. However, it could be assumed that OBS could impact soil microorganisms because it had similar chemical properties (toxicity and persistence) as legacy PFASs. The present study aimed to explore the influences of an emerging PFAS, namely sodium p-perfluorous nonenoxybenzene sulfonate (OBS), on archaeal, bacterial, and ammonia-oxidizing archaea (AOA) and bacteria (AOB) communities and ammonia oxidation. Grassland soil was amended with OBS at different dosages (0, 1, 10 and 100 mg/kg). After OBS amendment, tolerant microorganisms (e.g., archaea and AOA) were promoted, while susceptive microorganisms (e.g., bacteria and AOB) were inhibited. OBS amendment greatly changed microbial structure. Potential nitrifying activity was inhibited by OBS in a dose-dependent manner during the whole incubation. Furthermore, AOB might play a more important role in ammonia oxidation than AOA. Overall, OBS influenced ammonia oxidation by regulating the activity, abundance and structure of ammonia-oxidizing microorganisms, and could also exert influences on total bacterial and archaeal populations.

Environmental factors determining distribution and activity of anammox bacteria in minerotrophic fen soils

In contrast to the pervasive occurrence of denitrification in soils, anammox (anaerobic ammonium oxidation) is a spatially restricted process that depends on specific ecological conditions. To identify the factors that constrain the distribution and activity of anammox bacteria in terrestrial environments, we investigated four different soil types along a catena with opposing ecological gradients of nitrogen and water content, from an amended pasture to an ombrotrophic bog. Anammox was detected by polymerase chain reaction (PCR) and quantitative PCR (qPCR) only in the nitrophilic wet meadow and the minerotrophic fen, in soil sections remaining water-saturated for most of the year and whose interstitial water contained inorganic nitrogen. Contrastingly, aerobic ammonia oxidizing microorganisms were present in all examined samples and outnumbered anammox bacteria usually by at least one order of magnitude. 16S rRNA gene sequencing revealed a relatively high diversity of anammox bacteria with one Ca. Brocadia cluster. Three additional clusters could not be affiliated to known anammox genera, but have been previously detected in other soil systems. Soil incubations using 15N-labeled substrates revealed that anammox processes contributed about <2% to total N2 formation, leaving nitrification and denitrification as the dominant N-removal mechanism in these soils that represent important buffer zones between agricultural land and ombrotrophic peat bogs.

Effects of Salt on Root Aeration, Nitrification, and Nitrogen Uptake in Mangroves

The potential effects of salt on the growth, root anatomy, radial oxygen loss (ROL), and nitrogen (N) dynamics in mangroves were investigated using the seedlings of Avicennia marina (Forsk.) Vierh. The results showed that a moderate salinity (200 mM NaCl) appeared to have little negative effect on the growth of A. marina. However, higher salt stresses (400 and 600 mM NaCl) significantly inhibited the biomass yield. Concentrations of N in the roots and leaves decreased sharply with increasing salinity. Nevertheless, the presence of salt directly altered root anatomy (e.g., reduced root porosity and promoted suberization within the exodermis and endodermis), leading to a significant reduction in ROL. The results further showed that reduced ROL induced by salt could restrain soil nitrification, resulting in less ammonia-oxidizing archaea and bacteria (AOA and AOB) gene copies and lower concentrations of NO3− in the soils. While increased root suberization induced by salt inhibited NH4+ and NO3− uptake and influx into the roots. In summary, this study indicated that inhibited root aeration may be a defense response to salt, however these root symptoms were not advantageous for rhizosphere nitrification and N uptake by A. marina.

Effects of decabromodiphenyl ether on activity, abundance, and community composition of phosphorus mineralizing bacteria in eutrophic lake sediments

Polybrominated diphenyl ethers (PBDEs) are typical persistent organic pollutants (POPs) in the environment. However, little is known about their effects on phosphorus mineralizing bacteria (PMB) in eutrophic lake sediments, despite the critical role of PMB in phosphorus (P) biogeochemical cycling. In this study, we carried out a 60-day microcosm experiment to understand the effects of 2 and 20 mg kg^-1 dry weight decabromodiphenyl ether (BDE-209) on the activity, abundance, diversity, and community composition of PMB in the sediment of Taihu Lake, a typical eutrophic lake in China. The results showed that BDE-209 contamination, regardless of the contamination levels, significantly increased the orthophosphate concentration in overlying water and available phosphorus concentration in sediments on day 60. Such increases may be explained by the stimulatory effects of BDE-209 on alkaline phosphatase (ALP) activity and PMB abundance. Moreover, based on Miseq sequencing of the phoD gene encoding ALP, Actinobacteria was the dominant PMB phylum in all treatments, and BDE-209 significantly increased the diversity of PMB and altered their community composition. In particular, the relative abundances of some PMB genera such as Bradyrhizobium were increased significantly after 60 days of the High treatment. A co-occurrence network analysis further revealed that the high level of BDE-209 contamination strengthened the connectivity and interspecific co-operative relationships in the PMB community. These results will help us to understand the effects of POPs on P biogeochemical cycling in eutrophic lakes and the associated microbial mechanisms.

Effects of aquaculture effluents on fate of 2,2',4,4',5-pentabromodiphenyl ether (BDE-99) in contaminated mangrove sediment planted with Kandelia obovata

The problems of aquaculture effluent (AE) and polybrominated diphenyl ethers (PBDEs) are common in coastal areas. The fate of 2,2',4,4',5-pentabromodiphenyl ether (BDE-99), a dominant PBDE congener, in mangrove sediments and the effects of AE on it have never been reported. A 12-months microcosm study was conducted and more than 55% of the BDE-99 in contaminated sediment was removed at the end. The removal percentages depended on treatments, with the highest removal in the treatment planted with Kandelia obovata (Ko) and irrigated with AE (WP_AE), followed by Ko planted but without AE (WP), unplanted with AE (NP_AE) and unplanted without AE (NP). Hydroxylation of BDE-99 was observed in all treatments, with a preference in the para position bromine substitution, followed by meta position and the lowest was ortho bromine substitution. BDE-99 was also debrominated to lower brominated congeners like tri- and di-BDEs congeners. Different from parent BDE-99, ortho-substituted BDE-28 and -15 were more dominant than that of para-substituted BDE-17 and -7, suggesting that para-substituted congeners could further be debrominated. The AE addition enhanced root uptake of PBDEs in Ko. These findings suggested that the addition of AE and planting Ko could be an effective way to remedy BDE-99 in contaminated sediments.

The missing nitrogen pieces: A critical review on the distribution, transformation, and budget of nitrogen in the vadose zone-groundwater system

Intensive agriculture and urbanization have led to the excessive and repeated input of nitrogen (N) into soil and further increased the amount of nitrate (NO₃^-) leaching into groundwater, which has become an environmental problem of widespread concern. This review critically examines both the recent advances and remaining knowledge gaps with respect to the N cycle in the vadose zone-groundwater system. The key aspects regarding the N distribution, transformation, and budget in this system are summarized. Three major missing N pieces (N in dissolved organic form, N in the deep vadose zone, and N in the nonagricultural system), which are crucial for closing the N cycle yet has been previously assumed to be insignificant, are put forward and discussed. More work is anticipated to obtain accurate information on the chemical composition, transformation mechanism, and leaching flux of these missing N pieces in the vadose zone-groundwater system. These are essential to support the assessment of global N stocks and management of N contamination risks.

Analysis for microbial denitrification and antibiotic resistance during anaerobic digestion of cattle manure containing antibiotic

This study investigated the effects of tylosin (0, 10, and 100 mg/kg dry weight) on the denitrification genes and microbial community during the anaerobic digestion of cattle manure. N₂ emissions were reduced and N₂O emissions were increased by 10 mg/kg tylosin. Adding 100 mg/kg tylosin increased the emission of both N₂O and N₂. The different responses of denitrifying bacteria and genes to tylosin may have been due to the presence of antibiotic resistance genes (ARGs). Network analysis indicated that denitrification genes and ARGs had the same potential host bacteria. intI1 was more important for the horizontal transfer of denitrification genes and ARGs during anaerobic digestion than intI2. The anaerobic digestion of manure containing tylosin may increase nitrogen losses and the associated ecological risk.

Growth and antioxidative response of two mangrove plants to interaction between aquaculture effluent and BDE-99

Mangroves are subject to contamination of polybrominated diphenyl ethers (PBDEs) due to waste and wastewater disposal, and aquaculture effluent (AE) from nearby aquaculture activities. However, the response of mangrove plants to these two stresses and their interaction has seldom been reported. A six-month microcosm study, planted with either Kandelia obovata (Ko) or Avicennia marina (Am), the two most dominant species in South China mangrove swamps, was conducted to investigate the effects of BDE-99, and the interactions of BDE-99 (one of the most abundant PBDE congeners) and AE on growth and physiological responses of these plants. In addition to mixed stressors, both stressors were also applied individually. Results showed that Avicennia was more tolerant to BDE-99 contamination than Kandelia, as reflected by the reduced biomass, but increased superoxide radical (O₂^-⁎) release and malondialdehyde (MDA) content in Kandelia. Addition of AE alleviated toxicity of BDE-99 in Kandelia by promoting biomass but lowering oxidative stress and MDA production. The hormesis model also demonstrated that the interaction between BDE-99 and AE on leaf and root MDA and O₂^-⁎ content in both Kandelia and Avicennia were mostly antagonistic. Activities of catalase (CAT), superoxide dismutase (SOD) and peroxidase (POD) in both leaf and root of Kandelia were reduced by BDE-99. On the contrary, BDE-99 significantly enhanced the three enzyme activities in Avicennia root at month 3. Addition of AE also significantly enhanced root CAT, POD and SOD activities, and leaf SOD in both plant species to remove excess ROS produced under BDE-99 exposure. These results indicated that the tolerance of mangrove plants to oxidative stresses depended on antioxidative enzymes that were inducible.

Comparative metagenomics study reveals pollution induced changes of microbial genes in mangrove sediments

Mangrove forests are widespread along the subtropical and tropical coasts. They provide a habitat for a wide variety of plants, animals and microorganisms, and act as a buffer zone between the ocean and land. Along with other coastal environments, mangrove ecosystems are under increasing pressure from human activities, such as excessive input of nutrients and toxic pollutants. Despite efforts to understand the diversity of microbes in mangrove sediments, their metabolic capability in pristine and contaminated mangrove sediments remains largely unknown. By using metagenomic approach, we investigated the metabolic capacity of microorganisms in contaminated (CMS) and pristine (PMS) mangrove sediments at subtropical and tropical coastal sites. When comparing the CMS with PMS, we found that the former had a reduced diazotroph abundance and nitrogen fixing capability, but an enhanced metabolism that is related to the generation of microbial greenhouse gases via increased methanogenesis and sulfate reduction. In addition, a high concentration of heavy metals (mainly Zn, Cd, and Pb) and abundance of metal/antibiotic resistance encoding genes were found in CMS. Together, these data provide evidence that contamination in mangrove sediment can markedly change microbial community and metabolism; however, no significant differences in gene distribution were found between the subtropical and tropical mangrove sediments. In summary, contamination in mangrove sediments might weaken the microbial metabolisms that enable the mangrove ecosystems to act as a buffer zone for terrestrial nutrients deposition, and induce bioremediation processes accompanied with an increase in greenhouse gas emission.

The Fate of Chemical Pollutants with Soil Properties and Processes in the Climate Change Paradigm—A Review

Heavy metal(loid)s and organic contaminants are two major groups of pollutants in soils. The fate and exposure of such pollutants in soil depends on their chemical properties, speciation, and soil properties. Soil properties and processes that control the toxicological aspects of pollutants include temperature, moisture, organic matter, mineral fractions, and microbial activities. These processes are vulnerable to climate change associated with global warming, including increased incidences of extreme rainfall, extended dry periods, soil erosion, and a rise in sea level. Here we explain evidence that relates to the effects of climate change-driven soil processes on the mobility, transport, and storage of pollutants in soil. The review found that changes in climate could increase human exposure to soil contaminants mainly due to processes involving soil organic carbon (SOC), surface runoff, redox state, and microbial community. However, uncertainties remain in relation to the extent of contaminant toxicity to human health, which is linked to global change drivers.

Effects of decabromodiphenyl ether and planting on the abundance and community composition of nitrogen-fixing bacteria and ammonia oxidizers in mangrove sediments: A laboratory microcosm study

While nitrogen (N) fixation and ammonia oxidation by microorganisms are two important N cycling processes, little is known about how the microbes that drive these two processes respond when sediments are contaminated with persistent organic pollutants. In this study, we carried out a laboratory microcosm experiment to examine the effects of decabromodiphenyl ether (BDE-209), either on its own or combined with a common mangrove species, Avicennia marina, on the abundance, diversity, and community composition of N-fixing bacteria (NFB) and ammonia-oxidizing archaea (AOA) and bacteria (AOB) in mangrove sediments. The sediments were very N-limited after one year. The rates of N fixation and NFB abundance were significantly higher in the sediments that contaminated by BDE-209, especially in the planted sediment, indicating that both BDE-209 and planting stimulated N fixation in N-limited mangrove sediments. In contrast, the potential nitrification rate and abundance of AOA and AOB decreased significantly under BDE-209 and planting, and the inhibitory effects were stronger in the sediment with both planting and BDE-209 than in the sediments with either BDE-209 or planting. The results from pyrosequencing showed that the richness and diversity of NFB increased, while those of AOA and AOB decreased, in the sediments treated with BDE-209 only and with BDE-209 combined with planting. The community compositions of NFB, AOA, and AOB in the sediments shifted significantly because of BDE-209, either alone or particularly when combined with planting, as shown by the increases in some NFB from the Proteobacteria phylum and decreases in AOA in the Nitrosopumilus genus and AOB in the Nitrosospira genus, respectively.

Changes in microbial community during removal of BDE-153 in four types of aquatic sediments

Indigenous microorganisms in sediments could degrade polybrominated diphenyl ethers (PBDEs), but how the microbial communities respond to PBDEs was seldom reported. The effect of BDE-153, a common congener in aquatic environments, on the microbial communities in four types of aquatic sediments was evaluated during the 150days' incubation under an anaerobic condition. The intrinsic potential to remove BDE-153 varied significantly among four sediment types, and the removal rates of mangrove, mudflat, marine and freshwater sediments were 0.013, 0.013, 0.011, and 0.009day^-1, respectively. The observed microbial species, Simpson, Shannon, and Chao1 indices in all sediments were rather stable and were not changed significantly by BDE-153 amendment. However, BDE-153 amendment altered the microbial community compositions in three saline sediments at the end of the incubation period. Distance-based multivariate multiple regression analysis revealed that salinity, total organic carbon (TOC) and BDE-52, the major debromination product of BDE-153, were the three main factors explaining the variations in microbial community compositions in BDE-treated sediments; whereas salinity, TOC and pH were the main contributing factors in control sediments without BDE-153. The daughter congeners generated during anaerobic debromination process need more attention, especially their effect on the microbial communities in aquatic sediments.

Spatial distribution and diversity of organohalide-respiring bacteria and their relationships with polybrominated diphenyl ether concentration in Taihu Lake sediments

It is acknowledged that organohalide-respiring bacteria (OHRB) can degrade polybrominated diphenyl ethers (PBDEs); however, very little is known about the distribution of OHRB or their response to PBDE contamination in natural sediments. We collected sediments from 28 sampling sites in Taihu Lake, China, and investigated the spatial distribution and diversity of OHRB, and the relationships between the PBDE contamination levels and the PBDE removal potential. The abundances of five typical OHRB genera, namely Dehalobacter, Dehalococcoides, Dehalogenimonas, Desulfitobacterium, and Geobacter, ranged from 0.34 × 10⁴ to 19.4 × 10⁷ gene copies g^-1 dry sediment, and varied significantly among different areas of Taihu Lake. OHRB were more abundant in sediments from Meiliang and Zhushan Bay, where the PBDE concentrations were higher, and the phylotype diversity of the OHRB belonging to the family Dehalococcoidaceae was lower, than reported for other areas. While the sulfate concentrations explained much of the spatial distribution of OHRB, PBDE concentrations were also a strong influence on the abundance and diversity of OHRB in the sediments. For Dehalococcoides, Dehalogenimonas and Geobacter, the abundance of each genus was positively related to its own potential to remove PBDEs. The dominant OHRB genus, Dehalogenimonas, may contribute most to in situ bioremediation of PBDEs in Taihu Lake.

Response of ammonia oxidizing archaea and bacteria to decabromodiphenyl ether and copper contamination in river sediments

Ammonia oxidation plays a fundamental role in river nitrogen cycling ecosystems, which is normally governed by both ammonia oxidizing archaea (AOA) and ammonia oxidizing bacteria (AOB). Co-contamination of typical emerging pollutant Polybrominated diphenyl ethers (PBDEs) and heavy metal on AOA and AOB communities in river sediments remains unknown. In this study, multiple analytical tools, including high-throughput pyrosequencing and real-time quantitative PCR (qPCR), were used to reveal the ammonia monooxygenase (AMO) activity, subunit alpha (amoA) gene abundance, and community structures of AOA and AOB in river sediments. It was found that the inhibition of AMO activities was increased with the increase of decabromodiphenyl ether (BDE 209, 1-100 mg kg^-1) and copper (Cu, 50-500 mg kg^-1) concentrations. Moreover, the synergic effects of BDE 209 and Cu resulted in a higher AMO activity reduction than the individual pollutant BDE 209. The AOA amoA copy number declined by 75.9% and 83.2% and AOB amoA gene abundance declined 82.8% and 90.0% at 20 and 100 mg kg^-1 BDE 209 with a 100 mg kg^-1 Cu co-contamination, respectively. The pyrosequencing results showed that both AOB and AOA community structures were altered, with a higher change of AOB than that of AOA. The results demonstrated that the AOB microbial community may be better adapted to BDE 209 and Cu pollution, while AOA might possess a greater capacity for stress resistance. Our study provides a better understanding of the ecotoxicological effects of heavy metal and micropollutant combined exposure on AOA and AOB in river sediments.

Vertical distribution of dehalogenating bacteria in mangrove sediment and their potential to remove polybrominated diphenyl ether contamination

The removal and degradation of polybrominated diphenyl ethers (PBDEs) in sediments are not clear. The vertical distribution of total and dehalogenating bacteria in sediment cores collected from a typical mangrove swamp in South China and their intrinsic degradation potential were investigated. These bacterial groups had the highest abundances in surface sediments (0-5cm). A 5-months microcosm experiment also showed that surface sediments had the highest rate to remove BDE-47 than deeper sediments (5-30cm) under anaerobic condition. The deeper sediments, being more anaerobic, had lower population of dehalogenating bacteria leading to a weaker BDE-47 removal potential than surface sediments. Stepwise multiple regression analysis indicated that Dehalococcoides spp. were the most important dehalogenating bacteria affecting the anaerobic removal of BDE-47 in mangrove sediments. This is the first study reporting that mangrove sediments harbored diverse groups of dehalogenating bacteria and had intrinsic potential to remove PBDE contamination.

Dynamic interplay between microbial denitrification and antibiotic resistance under enhanced anoxic denitrification condition in soil

Mixed contamination of nitrate and antibiotics/antibiotic-resistant genes (ARGs) is an emerging environmental risk to farmland soil. This is the first study to explore the role of excessive anthropogenic nitrate input in the anoxic dissipation of soil antibiotic/ARGs. During the initial 10 days of incubation, the presence of soil antibiotics significantly inhibited NO₃^- dissipation, N₂O production rate, and denitrifying genes (DNGs) abundance in soil (p < 0.05). Between days 10 and 30, by contrast, enhanced denitrification clearly prompted the decline in antibiotic contents and ARG abundance. Significantly negative correlations were detected between DNGs and ARGs, suggesting that the higher the DNG activity, the more dramatic is the denitrification and the greater are the antibiotic dissipation and ARG abundance. This study provides crucial knowledge for understanding the mutual interaction between soil DNGs and ARGs in the enhanced anoxic denitrification condition.

Chemical treatment of contaminated sediment for phosphorus control and subsequent effects on ammonia-oxidizing and ammonia-denitrifying microorganisms and on submerged macrophyte revegetation

In this work, sediments were treated with calcium nitrate, aluminum sulfate, ferric sulfate, and Phoslock®, respectively. The impact of treatments on internal phosphorus release, the abundance of nitrogen cycle-related functional genes, and the growth of submerged macrophytes were investigated. All treatments reduced total phosphorus (TP) and soluble reactive phosphorus (SRP) in interstitial water, and aluminum sulfate was most efficient. Aluminum sulfate also decreased TP and SRP in overlying water. Treatments significantly changed P speciations in the sediment. Phoslock® transformed other P species into calcium-bound P. Calcium nitrate, ferric sulfate, and Phoslock® had negative influence on ammonia oxidizers, while four chemicals had positive influence on denitrifies, indicating that chemical treatment could inhibit nitrification but enhance denitrification. Aluminum sulfate had decreased chlorophyll content of the leaves of submerged macrophytes, while ferric sulfate and Phoslock® treatment would inhibit the growth of the root. Based on the results that we obtained, we emphasized that before application of chemical treatment, the effects on submerged macrophyte revegetation should be taken into consideration.

Insight into the long-term effect of mangrove species on removal of polybrominated diphenyl ethers (PBDEs) from BDE-47 contaminated sediments

Polybrominated diphenyl ethers (PBDEs) have become ubiquitous environmental contaminants, particularly in mangrove wetlands. However, little is known about the long-term effect of mangrove plants on PBDE removal from contaminated sediments. A 12-month microcosm experiment was conducted to understand the effect of two mangrove species, namely Avicennia marina (Am) and Aegiceras corniculatum (Ac), on PBDE removal from the sediments spiked with 2000ngg^-1 dry weight of BDE-47, and to explore the microbial mechanism responsible for the planting-induced effects on BDE-47 removal. Results showed that planting of mangrove species, either Am or Ac, could accelerate BDE-47 removal from contaminated sediments during the 12months experiment, mainly through enhancing microbial degradation process. In particular, Am sediment had significantly higher BDE-47 degradation efficiency compared with Ac sediment, which may be mainly attributed to higher activities of urease and dehydrogenase, as well as higher 16S rRNA gene copies of total bacteria and organohalide-respiring bacteria (OHRB) in Am sediment. Moreover, planting could shift sediment bacterial community composition and selectively enrich some bacterial genera responsible for PBDE degradation. Such selective enrichment effect of Am on the potential PBDE-degrading bacteria differed distinctly from that of Ac. These results indicated that long-term planting of mangrove species, especially Am, could significantly promote BDE-47 removal from the contaminated sediments by enhancing microbial activity, increasing total bacterial and OHRB abundances and altering bacterial community composition.