Ammonia-oxidizing Prokaryotes Research Articles

High throughput amplicon analysis reveals potential novel ammonia oxidizing prokaryotes in the eutrophic Jiaozhou Bay

Ammonia-oxidizing prokaryotes (AOPs) are the major contributors of ammonia oxidization with widely distribution. Here we investigated the phylogenetic diversity, community composition, and regulating factors of AOPs in Jiaozhou Bay (JZB) with high-throughput sequencing of amoA gene. Phylogenetic analysis showed most of the OTUs could not be clustered with any known AOPs, indicating there might exist putative novel AOPs. With new developed protocols for AOP community analysis, we confirmed that only 3 OTUs of ammonia-oxidizing archaea (AOA) could be affiliated to known Nitrosopumilaceae and Nitrososphaera, and the other OTUs were identified as novel AOA based on the threshold. All abstained OTUs of ammonia-oxidizing bacteria (AOB) were identified as novel clusters based on the threshold. Further analysis showed the novel AOPs had different distribution characteristics related to environmental factors. The high abundance and widespread distribution of these novel AOPs indicated that they played an important role in ammonia conversion in eutrophic JZB.

Spatiotemporal evolution and assembly processes of ammonia-oxidizing prokaryotic communities in 1 000-year-old coastal reclaimed soils

Coastal marshes are transitional areas between terrestrial and aquatic ecosystems. They are sensitive to climate change and anthropogenic activities. In recent decades, the reclamation of coastal marshes has greatly increased, and its effects on microbial communities in coastal marshes have been studied with great interest. Most of these studies have explained the short-term spatiotemporal variation in soil microbial community dynamics. However, the impact of reclamation on the community composition and assembly processes of functional microbes (e.g., ammonia-oxidizing prokaryotes) is often ignored. In this study, using quantitative polymerase chain reaction and the Ion S5™ XL sequencing platform, we investigated the spatiotemporal dynamics, assembly processes, and diversity patterns of ammonia-oxidizing prokaryotes in 1 000-year-old reclaimed coastal salt marshes. The taxonomic and phylogenetic diversity and composition of ammonia oxidizers showed apparent spatiotemporal variations with soil reclamation. Phylogenetic null modelling-based analysis showed that across all sites, the archaeal ammonia-oxidizing community was assembled by a deterministic process (84.71%), and deterministic processes were also dominant (55.2%) for ammonia-oxidizing bacterial communities except for communities at 60 years of reclamation. The assembly process and nitrification activity in reclaimed soils were positively correlated. The abundance of the amoA gene and changes in ammonia-oxidizing archaeal and bacterial diversities significantly affected the nitrification activity in reclaimed soils. These findings suggest that long-term coastal salt marsh reclamation affects nitrification by modulating the activities of ammonia-oxidizing microorganisms and regulating their community structures and assembly processes. These results provide a better understanding of the effects of long-term land reclamation on soil nitrogen-cycling microbial communities.

Comammox biogeography subject to anthropogenic interferences along a high-altitude river

The recent discovery of comammox Nitrospira performing complete ammonia oxidation to nitrate has overturned the long-held dogma of two-step nitrification on Earth, yet little is known about the effect of urbanization interference on their distribution. Using gene-centric metagenomics, we provided the first blueprints about comammox community, biogeography, and environmental drivers along a high-elevation (> 2000 m) river flowing through the largest city on the vulnerable Qinghai-Tibetan Plateau. Our study confirmed a wide presence and diversity of yet-uncultured comammox clade B across wet and dry seasons, with average 3.0 and 2.0 times as abundant as clade-A amoA genes in water and sediments, respectively. Species identified from freshwater and drinking water treatment plants dominated the comammox guilds (58∼100%), suggesting this plateau river shared a similar comammox assemblage with the above habitat types. Compared with the urban area harboring more abundant canonical Nitrospira identified in wastewater (average 24%), the upstream suburban reach had a smaller human population but larger proportions of comammox in ammonia-oxidizing prokaryotes (24∼72% of abundances) and Nitrospira sublineages I/II. Higher contents of nitrate and nitrite in water, and antibiotics in water and sediments, may restrain comammox niches in nitrifiers over the urban area. Further random forest analysis revealed that lincosamides and quinolones were the most important antibiotic predictors for the niche differentiations between comammox and canonical nitrifiers in water, while macrolides for those in sediments. Finally, by incubation experiments, we demonstrated higher activity contributions of benthic comammox in the suburban area (36.2∼92.8% of potential ammonia-oxidation rates) than in the urban reach, and that the contribution variation had significant negative relations with macrolides and their major components. Overall, this study highlighted that anthropogenic activities hampered the advantage of riverine complete nitrifiers over the canonical two-step ones.

Arbuscular Mycorrhiza and Nitrification: Disentangling Processes and Players by Using Synthetic Nitrification Inhibitors.

ABSTRACTBoth plants and their associated arbuscular mycorrhizal (AM) fungi require nitrogen (N) for their metabolism and growth. This can result in both positive and negative effects of AM symbiosis on plant N nutrition. Either way, the demand for and efficiency of uptake of mineral N from the soil by mycorrhizal plants are often higher than those of nonmycorrhizal plants. In consequence, the symbiosis of plants with AM fungi exerts important feedbacks on soil processes in general and N cycling in particular. Here, we investigated the role of the AM symbiosis in N uptake by Andropogon gerardii from an organic source (15N-labeled plant litter) that was provided beyond the direct reach of roots. In addition, we tested if pathways of 15N uptake from litter by mycorrhizal hyphae were affected by amendment with different synthetic nitrification inhibitors (dicyandiamide [DCD], nitrapyrin, or 3,4-dimethylpyrazole phosphate [DMPP]). We observed efficient acquisition of 15N by mycorrhizal plants through the mycorrhizal pathway, independent of nitrification inhibitors. These results were in stark contrast to 15N uptake by nonmycorrhizal plants, which generally took up much less 15N, and the uptake was further suppressed by nitrapyrin or DMPP amendments. Quantitative real-time PCR analyses showed that bacteria involved in the rate-limiting step of nitrification, ammonia oxidation, were suppressed similarly by the presence of AM fungi and by nitrapyrin or DMPP (but not DCD) amendments. On the other hand, abundances of ammonia-oxidizing archaea were not strongly affected by either the AM fungi or the nitrification inhibitors.IMPORTANCE Nitrogen is one of the most important elements for all life on Earth. In soil, N is present in various chemical forms and is fiercely competed for by various microorganisms as well as plants. Here, we address competition for reduced N (ammonia) between ammonia-oxidizing prokaryotes and arbuscular mycorrhizal fungi. These two functionally important groups of soil microorganisms, participating in nitrification and plant mineral nutrient acquisition, respectively, have often been studied in separation in the past. Here, we showed, using various biochemical and molecular approaches, that the fungi systematically suppress ammonia-oxidizing bacteria to an extent similar to that of some widely used synthetic nitrification inhibitors, whereas they have only a limited impact on abundance of ammonia-oxidizing archaea. Competition for free ammonium is a plausible explanation here, but it is also possible that the fungi produce some compounds acting as so-called biological nitrification inhibitors.

Distinct comammox Nitrospira catalyze ammonia oxidation in a full-scale groundwater treatment bioreactor under copper limited conditions

Microbial ammonia oxidation is the initial nitrification step used in biological nitrogen-removal during water treatment processes, and the discovery of complete ammonia-oxidizing (comammox) bacteria added a novel member to this functional group. It is important to identify and understand the predominant microorganisms responsible for ammonium removal in biotechnological process design and optimization. In this study, we used a full-scale bioreactor to treat ammonium in groundwater (9.3 ± 0.5 mg NH4+-N/L) and investigated the key ammonia-oxidizing prokaryotes present. The groundwater ammonium was stably and efficiently oxidized throughout ∼700 days of bioreactor operation. 16S rRNA gene amplicon sequencing of the bioreactor community showed a high abundance of Nitrospira (12.5–45.9%), with the dominant sequence variant (3.5–37.8%) most closely related to Candidatus Nitrospira nitrosa. Furthermore, analyses of amoA, the marker gene for ammonia oxidation, indicated the presence of two distinct comammox Nitrospira populations, however, the relative abundance of only one of these populations was strongly correlated to ammonia oxidation rates and was robustly expressed. After 380 days of operation copper wires were immersed into the reactor at 0.04–0.06 m2/m3 tank, which caused a gradual abundance increase of one discrete comammox Nitrospira population. However, further increase of the copper dosing (0.08 m2/m3 tank) inverted the most abundant ammonia-oxidizing population to Nitrosomonas sp. These results indicate that comammox Nitrospira were capable of efficient ammonium removal in groundwater without exogenous nutrients, but copper addition can stimulate comammox Nitrospira or lead to dominance of Nitrosomonas depending on dosage.

Ammonia Oxidizing Prokaryotes Respond Differently to Fertilization and Termination Methods in Common Oat's Rhizosphere.

Cover crops (CC) have demonstrated beneficial effects on several soil properties yet questions remain regarding their effects on soil microbial communities. Among them, ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) have a key role for N cycling in soil and their responses in the rhizosphere of terminated CC deserve further investigation. A greenhouse experiment was established to assess N fertilization (with or without N) and termination methods (glyphosate, mowing, and untreated control) of common oat (Avena sativa L.) as potential drivers of AOA and AOB responses in the rhizosphere. The abundance of amoA genes was determined by quantitative real-time PCR (qPCR), the community structure was assessed with Illumina amplicon sequencing of these genes, while the function was assessed from potential nitrification activity (PNA). While N fertilization had no influence on AOA, the termination method significantly increased amoA gene copies of AOA in mowed plants relative to glyphosate termination or the untreated control (1.76 and 1.49-fold change, respectively), and shifted AOA community structure (PERMANOVA, p<0.05). Ordination methods indicated a separation between AOA communities from control and glyphosate-terminated plants relative to mowed plants for both UniFrac and Aitchison distance. Converserly, N fertilization significantly increased AOB abundance in the rhizosphere of mowed and control plants, yet not in glyphosate-treated plants. Analyses of community structure showed that AOB changed only in response to N fertilization and not to the termination method. In line with these results, significantly higher PNA values were measured in all fertilized samples, regardless of the termination methods. Overall, the results of this study indicated that bacterial and archaeal nitrifiers have contrasting responses to fertlization and plant termination methods. While AOA were responsive to the termination method, AOB were more sensitive to N additions, although, the stimulative effect of N fertilization on amoAAOB abundance was dependent on the termination method.

In-situ expressions of comammox Nitrospira along the Yangtze River

The recent discovery of comammox Nitrospira as complete nitrifiers has significantly enriched our understanding on the nitrogen cycle, yet little is known about their metabolic transcripts in natural aquatic ecosystems. Using the genome-centric metatranscriptomics, we provided the first in-situ expression patterns of comammox Nitrospira along the Yangtze River. Our study confirmed widespread expressions of comammox Nitrospira, with the highest transcription accounting for 33.3% and 63.8% of amoA and nxrAB genes expressed in ammonia-oxidizing prokaryotes (AOPs) and Nitrospira sublineages I/II, respectively. Moreover, comammox two clades differed in nitrification, with clade A acting as the dominator to ammonia oxidation in comammox, and clade B contributing more transcripts to nitrite oxidation than to ammonia oxidation. Compared to canonical Nitrospira, comammox community had lower expressions of ammonia/nitrite transporters and nitrogen assimilatory genes, but far higher expressions in urea transport and hydrolysis, facilitating to derivation of ammonia and energy mainly through intracellular ureolytic metabolism. This suggests no need for “reciprocal-feeding” between canonical Nitrospira and AOPs in a natural river. Aerobic mixotrophy of comammox bacteria was suggested by expressions of genes coding for respiratory complexes I-V, oxidative/reductive TCA cycle, oxygen stress defenses, and transport/catabolism of simple carbohydrates and low-biosynthetic-cost amino acids. Intriguingly, significant positive correlations among expressions of ammonia monooxygenases, hydroxylamine dehydrogenase and copper-dependent nitrite reductase indicated that comammox Nitrospira had the potential of converting nitrite to nitric oxide accompanied by ammonia oxidation under low-C/N and aerobic conditions, while gene expressions in this pathway were significantly and positively associated with pH. Overall, this study illustrated novel transcriptional characteristics of comammox Nitrospira, and highlighted the necessity of reassessing their contributions to biogeochemical carbon and nitrogen cycling with perspective of in-situ meta-omics as well as culture experiments.

Temperature Influenced the Comammox Community Composition in Drinking Water and Wastewater Treatment Plants.

Nitrification is a pivotal step applied in water engineered systems for nitrogen removal. Temperature variation due to seasonal changes is a great challenge for maintaining nitrogen removal efficiency in water engineered ecosystems by affecting nitrifier activities. Research on the abundance, activity, and metabolic characteristics of nitrifiers can provide information for selecting suitable design parameters to ensure efficient nitrogen removal in different seasons. To date, the temperature-related niche separation of comammox, a newly discovered nitrifier with potential high-growth yield, has been rarely investigated. This study addressed the distribution of comammox and canonical nitrifying guilds in drinking water treatment plants (DWTPs) and wastewater treatment plants (WWTPs) in different seasons. qPCR-based surveys showed that comammox ubiquitously distributed and greatly outnumbered other ammonia-oxidizing prokaryotes in both DWTPs and WWTPs, except in Aug samples from DWTPs, suggesting the potential competitive advantage of AOA in summer. The nitrificans-like comammox and nitrosa-like comammox comprised the majority of the comammox community in DWTPs and WWTPs, respectively, and COD and NH4+ concentrations significantly contributed to the distinct comammox phylotype distribution between DWTPs and WWTPs. The temperature-related distribution pattern of the comammox community was observed at each site. Moreover, the network complex of comammox communities was highest in Dec at all the sites, possibly contributing to the survival of comammox community in low temperature conditions.

Ammonium concentration determines differential growth of comammox and canonical ammonia-oxidizing prokaryotes in soil microcosms

An unresolved question in microbial ecology is whether the available ammonium concentration has a differential impact on the growth of newly discovered complete ammonia-oxidizing bacteria (CAOB) and their counterparts, the well-known ammonia-oxidizing bacteria (AOB) and archaea (AOA). To address this issue, soil microcosms were cultured for 40 days with ammonium concentrations of 0, 5, 50, 200, and 500 μg NH+ 4-N g−1 soil. Quantitative PCR analysis suggested that AOB grew in response to the two highest ammonium concentrations, whereas CAOB only grew significantly at native and low ammonium concentrations, demonstrating an AOA-like niche specialization favoring oligotrophic environments but being tolerant to a broader ammonium concentration than AOA. Moreover, phylogenetic and Pearson correlation analysis indicated that species from clade B rather than clade A of CAOB contributed to the nitrification process. This study highlights an important role of the local ammonium concentration in affecting the ecological niche differentiation of comammox and canonical ammonia-oxidizing prokaryotes.

Comammox Nitrospira within the Yangtze River continuum: community, biogeography, and ecological drivers

The recent discovery of comammox Nitrospira as complete nitrifiers has fundamentally renewed perceptions of nitrogen cycling in natural and engineered systems, yet little is known about the environmental controls on these newly recognized bacteria. Based on improved phylogenetic resolution through successful assembly of ten novel genomes (71–96% completeness), we provided the first biogeographic patterns for planktonic and benthic comammox Nitrospira in the Yangtze River over a 6030 km continuum. Our study revealed the widespread distributions and relative abundance of comammox Nitrospira in this large freshwater system, constituting 30 and 46% of ammonia-oxidizing prokaryotes (AOPs) and displaying 30.4- and 17.9-fold greater abundances than canonical Nitrospira representatives in water and sediments, respectively. Comammox Nitrospira contributed more to nitrifier abundances (34–87% of AOPs) in typical oligotrophic environments with a higher pH and lower temperature, particularly in the plateau (clade B), mountain and foothill (clade A) areas of the upper reach. The dominant position of planktonic comammox Nitrospira was replaced by canonical Nitrospira sublineages I/II and ammonia-oxidizing bacteria from the plateau to downstream plain due to environmental selection, while the dissimilarity of benthic comammox Nitrospira was moderately associated with geographic distance. A substantial decrease (83%) in benthic comammox Nitrospira abundance occurred immediately downstream of the Three Gorges Dam, consistent with a similarly considerable decrease in overall sediment bacterial taxa. Together, this study highlights the previously unrecognized dominance of comammox Nitrospira in major river systems and underlines the importance of revisiting the distributions of and controls on nitrification processes within global freshwater environments.

Evaluating the impact of turf-care products on soil biological health.

Golf courses require extensive use of inputs to meet the needs of playability and aesthetics. The impact of these inputs on soil biological health is largely unknown. Two field trials were conducted at a golf course in Georgia to evaluate short-term effects of wetting agents (Cascade Plus and Duplex [C+D], Revolution [Rev]), plant growth regulators (PrimoMaxx [PM] and Cutless [CL]), and a product called PlantHelper (PH) on soil biological health by measuring microbial abundance and function. Quantitative polymerase chain reaction was used to measure microbial abundance, which included total bacteria, total fungi, and ammonia-oxidizing prokaryotes. Soil respiration and enzyme assays were used as additional indicators of soil health. In bentgrass putting green, total bacteria and ammonia-oxidizing bacteria decreased in abundance in response to the wetting agents and PH, indicating their sensitivity to the products. Whereas C+D stimulated urease activity, Rev and PH caused a short-lived but immediate increase in respiration, indicating that they acted as labile carbon sources. In a bermudagrass fairway, PM was the only product that caused an increase in total bacteria abundance. PrimoMaxx and CL caused a delayed increase in respiration, suggesting that they may have affected the microorganisms indirectly through their impact on root growth and exudate production later. Although CL caused a decrease in urease activity, none of the products significantly affected phosphatase activity. Overall, the products did not seem to have a lasting impact on soil biological health, although long-term studies are needed to confirm these observations.

Correction to: Comparing the impacts of an invasive grass on nitrogen cycling and ammonia-oxidizing prokaryotes in high-nitrogen forests, open fields, and wetlands

Correction to: Comparing the impacts of an invasive grass on nitrogen cycling and ammonia-oxidizing prokaryotes in high-nitrogen forests, open fields, and wetlands

Comparing the impacts of an invasive grass on nitrogen cycling and ammonia-oxidizing prokaryotes in high-nitrogen forests, open fields, and wetlands

Numerous invasive plant species can increase soil nitrate (NO3−) by altering the nitrification process through plant-soil microbe interactions with ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). We evaluated how the invasive species Microstegium vimineum influenced physico-chemical soil properties, inorganic nitrogen (N) cycling, and AOA and AOB abundances under various environmental conditions. We paired 75 M. vimineum-invaded plots with 75 neighboring reference plots across forests, open fields, and forested wetlands within a state park in the Mid-Atlantic United States that has received high levels of N deposition. Soils were sampled for physico-chemical properties, NO3− and ammonium (NH4+) pools and availability, and AOA and AOB abundances. There were multiple soil impacts associated with M. vimineum across all ecosystems, most consistent were increased soil pH and increased NO3− pools. For other impacts, the directionality and effect sizes varied among ecosystems (e.g. NH4+ pools were 34% lower in forests, 35% lower in open fields, and 90% higher in wetlands relative to reference plots). Finally, forests had nearly all of impacts predicted by a pH-mediated nitrification plant-soil feedback. This study highlights the ability of an invasive grass to alter N cycling and soil properties in forests, open fields, and wetlands that have received high N deposition. We also show how invader-mediated impacts to N cycling may be dependent on the context of the ecosystem being invaded, including its hydrology, ambient soil conditions, and substrate-availability.

Copper-Induced Stimulation of Nitrification in Biological Rapid Sand Filters for Drinking Water Production by Proliferation of Nitrosomonas spp.

Copper is a cofactor of the ammonia monooxygenase, an essential enzyme for the activity of ammonia oxidizing prokaryotes (AOP). Copper dosing at less than 1 μg/L stimulated ammonium removal in the poorly nitrifying biological filters of three full-scale drinking water treatment plants. Upon copper dosing, the ammonium concentration in the effluent decreased from up to 0.18 to less than 0.01 mg NH4+-N/L. To investigate how copper dosing affected the filter microbial community, we applied amplicon sequencing and qPCR targeting key nitrifying groups, including complete ammonia oxidizing (comammox) Nitrospira. Copper dosing increased the abundance of different nitrifiers. Multiple Nitrosomonas variants (betaproteobacterial ammonia oxidizers), which initially collectively represented 1% or less of the total community, increased almost 10-fold. Comammox Nitrospira were abundant and increased too, but their relative abundance within the AOP decreased because of Nitrosomonas proliferation. No other consistent change in the filter communities was detected, as well as no adverse effect of copper on the filters functionality. Our results show that copper dosing in three independent treatmentplants was associated with consistent growth of AOP and that efficient nitrification was achieved through the joint contribution of comammox Nitrospira and an increasing fraction of betaproteobacterial ammonia oxidizers.

Effects of Aquaculture on Ammonia-oxidizing Prokaryotes in Sediments of Eastern Lake Taihu

The abundance and diversity of ammonia-oxidizing microorganisms in sediments of an aquacultural area of Eastern Lake Taihu were investigated. Real-time quantitative PCR was used to analyze the abundance of archaeal and bacterial amoA genes. Cloned libraries were constructed to investigate the structure and diversity of the microbial community. By comparing community characteristics of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in different zones, we found that:①Copy numbers of the bacterial amoA gene outnumbered those of archaeal amoA genes in the aquacultural zone; ②Diversity of AOA and AOB was higher in the aquaculture zone and control zone, respectively; ③ The dominant cluster of AOA and AOB in both sediments of aquiculture zone and control zone was Nitrosopumilus and Nitrosospira respectively. It was therefore the community structure of AOA (rather than AOB) in lake sediments that was affected by aquacultural activity.

Distribution patterns of ammonia-oxidizing archaea and bacteria in sediments of the eastern China marginal seas

Ammonia-oxidizing archaea (AOA) and bacteria (AOB) vary in their contribution to nitrification in different environments. The eastern China marginal seas (ECMS) are featured by complex river runoffs and ocean currents, forming different sediment patches. Here, via quantitative PCR and clone library analysis of the amoA genes, we showed that AOB were more abundant than AOA in ECMS sediments. The abundance, diversity and richness of AOA, but not AOB, were higher in the East China Sea (ECS) than in the Yellow Sea (YS) and Bohai Sea (BS). Nitrosopumilus (AOA) and Nitrosospira (AOB) were predominant lineages, but their abundances varied significantly between ECS, and BS and YS. This was mainly attributed to salinity and dissolved oxygen of the bottom water. The discovery of a high abundance of Nitrosophaera at estuarine sites suggested strong terrigenous influence exerted on the AOA community. In contrast, variations in ocean conditions played more important roles in structuring the AOB community, which was separated by bottom water dissolved oxygen into two groups: the south YS, and the north YS and BS. This study provides a comprehensive insight into the spatial distribution pattern of ammonia-oxidizing prokaryotes in ECMS sediments, laying a foundation for understanding their relative roles in nitrification.

Effects of partially saturated conditions on the metabolically active microbiome and on nitrogen removal in vertical subsurface flow constructed wetlands

Nitrogen dynamics and its association to metabolically active microbial populations were assessed in two vertical subsurface vertical flow (VF) wetlands treating urban wastewater. These VF wetlands were operated in parallel with unsaturated (UVF) and partially saturated (SVF) configurations. The SVF wetland exhibited almost 2-fold higher total nitrogen removal rate (5 g TN m−2 d−1) in relation to the UVF wetland (3 g TN m−2 d−1), as well as a low NOx-N accumulation (1 mg L−1 vs. 26 mg L−1 in SVF and UVF wetland effluents, respectively). After 6 months of operation, ammonia oxidizing prokaryotes (AOP) and nitrite oxidizing bacteria (NOB) displayed an important role in both wetlands. Oxygen availability and ammonia limiting conditions promoted shifts on the metabolically active nitrifying community within ‘nitrification aggregates’ of wetland biofilms. Ammonia oxidizing archaea (AOA) and Nitrospira spp. overcame ammonia oxidizing bacteria (AOB) in the oxic layers of both wetlands. Microbial quantitative and diversity assessments revealed a positive correlation between Nitrobacter and AOA, whereas Nitrospira resulted negatively correlated with Nitrobacter and AOB populations. The denitrifying gene expression was enhanced mainly in the bottom layer of the SVF wetland, in concomitance with the depletion of NOx-N from wastewater. Functional gene expression of nitrifying and denitrifying populations combined with the active microbiome diversity brought new insights on the microbial nitrogen-cycling occurring within VF wetland biofilms under different operational conditions.

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.

Effect of Eichhornia crassipes on Ammoxidation and Denitrification Microorganisms in Eutrophic Freshwaters

The water hyacinth, Eichhornia crassipes, is widely used for the ecological restoration of eutrophic freshwater bodies, but little is known about its microbial interactions and nitrogen removal potential. In this study, we compared the relative importance of E. crassipes and bacteria in nitrogen removal. We also examined the plant's ability to modulate the abundance and diversity of nitrifying and denitrifying bacteria. Nitrogen removal and the genetic potential for nitrification and denitrification, determined using quantitative polymerase chain reactions (qPCRs) of the nitrification gene amoA and the denitrification genes nirS/K, were evaluated in microcosms containing water from a eutrophic lake with or without E. crassipes. The results showed that total nitrogen (TN) losses on day 70 of the experiment were similar in all treatments but the uptake by E. crassipes resulted in the rapid (within 24 h) removal of TN and NH4+-N. In microcosms containing E. crassipes, the abundance of amoA increased whereas the abundances of nirS/K decreased. The T-RFLP (terminal restriction fragment length polymorphism) profiles showed that Nitrosomonas dominated the ammonia-oxidizing prokaryotes, based on the DNA and RNA levels of the targeted genes. The E. crassipes cultivation can be used to achieve fast and efficient reductions in NH4+-N concentrations in eutrophic water bodies. While this aquatic macrophyte may not be essential to N removal, considering the potential toxicity of NH4+-N, both aquaphytes and microbes should be fully exploited in the restoration of freshwater ecosystems.

Seasonal and spatial variations of prokaryoplankton communities in a salinity-influenced watershed, China.

Prokaryotes represent the largest biodiversity pool and drive the biogeochemical cycles in fluvial environments. However, the mechanisms underlying the assembly of prokaryotic communities are largely unexplored at taxonomic and functional levels, simultaneously. Here, we investigated the spatio-seasonal distribution of prokaryoplankton communities in a salinity-influenced watershed, China using 16S rRNA gene amplicon sequencing. The OTUs were divided into core and satellite, based on a statistical approach. Our results indicated that the core taxa accounted for 87.4% of all the communities, predominantly including Betaproteobacteria, Actinobacteria and Thaumarchaeota. Whereas 10 of 22 metabolic phenotypes annotated using METAGENassist had significantly higher relative abundances in the core than satellite communities. Temporal variations in the composition of ammonia-oxidizing prokaryotes could be attributed to the seasonal nutrient concentrations. Multivariate statistical analysis indicated that environmental filtering rather than dispersal limitation is the primary mechanism driving the assembly of the whole, core and satellite communities at both taxonomic and functional levels. Network analysis revealed that the mutualistic interactions might also have certain roles in the assembly of the core taxonomic community. However, taxonomic community fluctuations can only partially reflect the functional community variations. Collectively, this study significantly advanced our understanding of the biogeographic pattern of the fluvial prokaryotic communities.