Depth-related changes of sediment ammonia-oxidizing microorganisms in a high-altitude freshwater wetland

Nonpoint Source Pollution (NPSP) Induces Structural and Functional Variation in the Fungal Community of Sediments in the Jialing River, China

Nonpoint source pollution (NPSP) from human production and life activities causes severe destruction in river basin environments. In this study, three types of sediment samples (A, NPSP tributary samples; B, non-NPSP mainstream samples; C, NPSP mainstream samples) were collected at the estuary of the NPSP tributaries of the Jialing River. High-throughput sequencing of the fungal-specific internal transcribed spacer (ITS) gene region was used to identify fungal taxa. The impact of NPSP on the aquatic environment of the Jialing River was revealed by analysing the community structure, community diversity, and functions of sediment fungi. The results showed that the dominant phylum of sediment fungi was Rozellomycota, followed by Ascomycota and Basidiomycota (relative abundance > 5%). NPSP caused a significant increase in the relative abundances of Exosporium, Phialosimplex, Candida, Inocybe, Tausonia, and Slooffia, and caused a significant decrease in the relative abundances of Cercospora, Cladosporium, Dokmaia, Setophaeosphaeria, Paraphoma, Neosetophoma, Periconia, Plectosphaerella, Claviceps, Botrytis, and Papiliotrema. These fungal communities therefore have a certain indicator role. In addition, NPSP caused significant changes in the physicochemical properties of Jialing River sediments, such as pH and available nitrogen (AN), which significantly increased the species richness of fungi and caused significant changes in the fungal community β-diversity (P < 0.05). pH, total phosphorus (TP), and AN were the main environmental factors affecting fungal communities in sediments of Jialing River. The functions of sediment fungi mainly involved three types of nutrient metabolism (symbiotrophic, pathotrophic, and saprotrophic) and 75 metabolic circulation pathways. NPSP significantly improved the pentose phosphate pathway, pentose phosphate pathway, and fatty acid beta-oxidation V metabolic circulation pathway functions (P < 0.05) and inhibited the chitin degradation to ethanol, super pathway of heme biosynthesis from glycine, and adenine and adenosine salvage III metabolic circulation pathway functions (P < 0.05). Hence, NPSP causes changes in the community structure and functions of sediment fungi in Jialing River and has adversely affected for the stability of the Jialing River Basin ecosystem.

Correlation of stagnant wetland depths and their ecological status in the Central Tamil Nadu District, Tamil Nadu

The wetland stagnation is the premise of the wetland depth (WD) but is lacking in detail. The research looks into the correlation of stagnant wetland's depth and their ecological status in the Central Tamil Nadu District (CTND) because of few studies. Seventy-five chosen stagnant wetlands are hydrologically isolated; depths were categorized into less than 5 ft., 6 to 10 and above 10 ft., surveyed by the range of methods from districts such as Karur (KD), Namakkal (ND) and Tiruchirappalli (TD). The human disturbance score (HDS) is categorized as least impacted (0-33), moderately impacted (33-67) and highly impacted (67-100). The impacts of land use and land cover (LULC) changes over 9 years (2010-2019) through the maximum likelihood method. Overall, 54% of wetland depths (WD) were less than 5 ft.; 25.6% were 6-10 ft. and 20.2% were 100 ft. District-wise, wetland degradation was the utmost in the TD, followed by ND and KD. Except in KD, the remaining district wetlands were of MI category with diverse HDS. The correlation test revealed a positive relationship between WD against the alteration of the buffer zone, habitat, hydrology and HDS. However, it is a negative relationship between landscape alteration and wetland pollution. The impacts of land use and land cover (LULC) changes confirm that severe decline in wetlands habitat and water bodies' area is due to built-up area, cultivated land expansion and increasing population. Our study provided evidence that the WD is connected to wetland conditions that have a quantitative influence, and the ramifications of the findings were examined in the context of local development planning. Additional research will be needed due to limited surveyed wetlands with similar geographical locations.

Plant Species-Driven Distribution of Individual Clades of Comammox Nitrospira in a Subtropical Estuarine Wetland

Plant species play a crucial role in mediating the activity and community structure of soil microbiomes through differential inputs of litter and rhizosphere exudates, but we have a poor understanding of how plant species influence comammox Nitrospira, a newly discovered ammonia oxidizer with pivotal functionality. Here, we investigate the abundance, diversity, and community structure of comammox Nitrospira underneath five plant species and a bare tidal flat at three soil depths in a subtropical estuarine wetland. Plant species played a critical role in driving the distribution of individual clades of comammox Nitrospira, explaining 59.3% of the variation of community structure. Clade A.1 was widely detected in all samples, while clades A.2.1, A.2.2, A.3 and B showed plant species-dependent distribution patterns. Compared with the native species Cyperus malaccensis, the invasion of Spartina alterniflora increased the network complexity and changed the community structure of comammox Nitrospira, while the invasive effects from Kandelia obovata and Phragmites australis were relatively weak. Soil depths significantly influenced the community structure of comammox Nitrospira, but the effect was much weaker than that from plant species. Altogether, our results highlight the previously unrecognized critical role of plant species in driving the distribution of comammox Nitrospira in a subtropical estuarine wetland.

Constructed wetlands as a sustainable technology for wastewater treatment with emphasis on chromium-rich tannery wastewater

Water scarcity is a major threat to agriculture and humans due to over abstraction of groundwater, rapid urbanization and improper use in industrial processes. Industrial consumption of water is lower than the abstraction rate, which ultimately produces large amounts of wastewater such as from tannery industry containing high concentration of chromium (Cr). Chromium-contaminated tannery industry wastewater is used for irrigation of food crops, resulting in food safety and public health issues globally. In contrast to conventional treatment technologies, constructed wetlands (CWs) are considered as an eco-friendly technique to treat various types of wastewaters, although their application and potential have not been discussed and elaborated for Cr treatment of tannery wastewater. This review briefly describes Cr occurrence, distribution and speciation in aquatic ecosystems. The significance of wetland plant species, microorganisms, various bedding media and adsorbents have been discussed with a particular emphasis on the removal and detoxification of Cr in CWs. Also, the efficiency of various types of CWs is elaborated for advancing our understanding on Cr removal efficiency and Cr partitioning in various compartments of the CWs. The review covers important aspects to use CWs for treatment of Cr-rich tannery wastewater that are key to meet UN's Sustainable Development Goals.

Response Characteristics of Nitrifying Bacteria and Archaea Community Involved in Nitrogen Removal and Bioelectricity Generation in Integrated Tidal Flow Constructed Wetland-Microbial Fuel Cell

This study explores nitrogen removal performance, bioelectricity generation, and the response of microbial community in two novel tidal flow constructed wetland-microbial fuel cells (TFCW-MFCs) when treating synthetic wastewater under two different chemical oxygen demand/total nitrogen (COD/TN, or simplified as C/N) ratios (10:1 and 5:1). The results showed that they achieved high and stable COD, NH₄ ⁺-N, and TN removal efficiencies. Besides, TN removal rate of TFCW-MFC was increased by 5-10% compared with that of traditional CW-MFC. Molecular biological analysis revealed that during the stabilization period, a low C/N ratio remarkably promoted diversities of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in the cathode layer, whereas a high one enhanced the richness of nitrite-oxidizing bacteria (NOB) in each medium; the dominant genera in AOA, AOB, and NOB were Candidatus Nitrosotenuis, Nitrosomonas, and Nitrobacter. Moreover, a high C/N ratio facilitated the growth of Nitrosomonas, while it inhibited the growth of Candidatus Nitrosotenuis. The distribution of microbial community structures in NOB was separated by space rather than time or C/N ratio, except for Nitrobacter. This is caused by the differences of pH, dissolved oxygen (DO), and nitrogen concentration. The response of microbial community characteristics to nitrogen transformations and bioelectricity generation demonstrated that TN concentration is significantly negatively correlated with AOA-shannon, AOA-chao, 16S rRNA V4-V5-shannon, and 16S rRNA V4-V5-chao, particularly due to the crucial functions of Nitrosopumilus, Planctomyces, and Aquicella. Additionally, voltage output was primarily influenced by microorganisms in the genera of Nitrosopumilus, Nitrosospira, Altererythrobacter, Gemmata, and Aquicella. This study not only presents an applicable tool to treat high nitrogen-containing wastewater, but also provides a theoretical basis for the use of TFCW-MFC and the regulation of microbial community in nitrogen removal and electricity production.

Environmental Factors, More Than Spatial Distance, Explain Community Structure of Soil Ammonia-Oxidizers in Wetlands on the Qinghai-Tibetan Plateau

In wetland ecosystems, ammonia oxidation highly depends on the activity of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB), which are, therefore, important for studying nitrogen cycling. However, the ammonia-oxidizer communities in the typical high-elevation wetlands are poorly understood. Here, we examined ammonia-oxidizer communities in soils from three wetland types and 31 wetland sites across the Qinghai-Tibetan Plateau. The amoA gene of AOA and AOB was widespread across all wetland types. Nitrososphaera clade (Group I.1b) overwhelmingly dominated in AOA community (90.36%), while Nitrosospira was the principal AOB type (64.96%). The average abundances of AOA and AOB were 2.63 × 104 copies g-1 and 9.73 × 103 copies g-1. The abundance of AOA amoA gene was higher in riverine and lacustrine wetlands, while AOB amoA gene dominated in palustrine wetlands. The environmental conditions, but not spatial distance, have a dominant role in shaping the pattern of ammonia-oxidizer communities. The AOA community composition was influenced by mean annual temperature (MAT) and mean annual precipitation (MAP), while MAT, conductivity and plant richness, pH, and TN influenced the AOB community composition. The net nitrification rate had a significant correlation to AOB, but not AOA abundance. Our results suggest a dominant role for climate factors (MAT and MAP) in shaping community composition across a wide variety of wetland sites and conditions.

Bacterial and Archaeal Communities within an Ultraoligotrophic, High-altitude Lake in the Pre-Himalayas of the Qinghai-Tibet Plateau

Puma Yumco Lake (PYL) is an ultraoligotrophic freshwater lake that sits an altitude of 5030 m within the Qinghai-Tibet Plateau of China. The bacterial and archaeal diversity of the lake remains poorly understood, despite their potential to inform on biogeochemical cycling and environment-microbial associations in these unique environments. Here, the bacterial and archaeal communities of PYL were investigated using high-throughput sequencing analysis of community 16S rRNA gene sequences. Further, the relationships among dominant taxa and environmental factors were comprehensively evaluated. Bacterial diversity comprised 31 phyla and 371 genera (10,645 operational taxonomic units [OTUs], Shannon index values of 5.21-6.16) and was significantly higher than that of Archaea (five phyla and 24 genera comprising 1141 OTUs and Shannon index values of 1.18-3.28). The bacterial communities were dominated by Proteobacteria (48.42-59.97% relative abundances), followed by Bacteroidetes (12.5-32.51%), Acidobacteria (2.07-11.56%), Firmicutes (0.65-6.32%), Planctomycetes (0.99-3.56%), Gemmatimonadetes (0.38-3.57%), Actinobacteria (1.67-3.52%), Verrucomicrobia (0.87-2.01%), and Chloroflexi (0.5-1.17%). In addition, archaeal communities were dominated by Thaumarchaeota (33.22-93.00%), followed by Euryarchaeota (2.89-35.47%), Woesearchaeota (0.99-31.04%), and Pacearchaeota (0.01-1.14%). The most abundant bacterial genus was Rhodoferax (5.73-26.62%) and the most abundant archaeal genus was the ammonia-oxidizing Nitrososphaera (29.18-91.46%). These results suggest that the Rhodoferax and Nitrososphaera are likely to participate in biogeochemical cycles in these environments through photoheterotrophy and nitrification, respectively. Taken together, these results provide valuable data for better understanding microbial interactions with each other and with these unique environments.

Effects of Water Depth and Phosphorus Availability on Nitrogen Removal in Agricultural Wetlands

Excess nitrogen (N) from agricultural runoff is a cause of pollution in aquatic ecosystems. Created free water surface (FWS) wetlands can be used as buffering systems to lower the impacts of nutrients from agricultural runoff. The purpose of this paper was to evaluate critical factors for N removal in FWS wetlands receiving high nitrate (NO3−) loads from agriculture. The study was performed in 12 experimental FWS wetlands in southern Sweden, receiving drainage water from an agricultural field area. The effects of water depth (mean depth of 0.4 m and 0.6 m, respectively) and phosphorus (P) availability (with or without additional P load) were investigated from July to October. The experiment was performed in a two-way design, with three wetlands of each combination of depth and P availability. The effects of P availability on the removal of NO3− and total N were strongly significant, with higher absolute N removal rates per wetland area (g m−2 day−1) as well as temperature-adjusted first-order area-based removal rate coefficients (Kat) in wetlands with external P addition compared to wetlands with no addition. Further, higher N removal in deep compared to shallow wetlands was indicated by statistically significant differences in Kat. The results show that low P availability may limit N removal in wetlands receiving agricultural drainage water. Furthermore, the results support that not only wetland area but also wetland volume may be important for N removal. The results have implications for the planning, location, and design of created wetlands in agricultural areas.

Comparative evaluation of three archaeal primer pairs for exploring archaeal communities in deep-sea sediments and permafrost soils

16S rRNA gene profiling is a powerful method for characterizing microbial communities; however, no universal primer pair can target all bacteria and archaea, resulting in different primer pairs which may impact the diversity profile obtained. Here, we evaluated three pairs of high-throughput sequencing primers for characterizing archaeal communities from deep-sea sediments and permafrost soils. The results show that primer pair Arch519/Arch915 (V4-V5 regions) produced the highest alpha diversity estimates, followed by Arch349f/Arch806r (V3-V4 regions) and A751f/AU1204r (V5-V7 regions) in both sample types. The archaeal taxonomic compositions and the relative abundance estimates of archaeal communities are influenced by the primer pairs. Beta diversity of the archaeal community detected by the three primer pairs reveals that primer pairs Arch349f/Arch806r and Arch519f/Arch915r are biased toward detection of Halobacteriales, Methanobacteriales and MBG-E/Hydrothermarchaeota, whereas the primer pairs Arch519f/Arch915r and A751f/UA1204r are biased to detect MBG-B/Lokiarchaeota, and the primers pairs Arch349f/Arch806r and A751f/UA1204r are biased to detect Methanomicrobiales and Methanosarcinales. The data suggest that the alpha and beta diversities of archaeal communities as well as the community compositions are influenced by the primer pair choice. This finding provides researchers with valuable experimental insight for selection of appropriate archaeal primer pairs to characterize archaeal communities.

Metal contaminations impact archaeal community composition, abundance and function in remote alpine lakes

Using the 16S rRNA and mcrA genes, we investigated the composition, abundance and activity of sediment archaeal communities within 18 high-mountain lakes under contrasted metal levels from different origins (bedrock erosion, past-mining activities and atmospheric depositions). Bathyarchaeota, Euryarchaeota and Woesearchaeota were the major phyla found at the meta-community scale, representing 48%, 18.3% and 15.2% of the archaeal community respectively. Metals were equally important as physicochemical variables in explaining the assemblage of archaeal communities and their abundance. Methanogenesis appeared as a process of central importance in the carbon cycle within sediments of alpine lakes as indicated by the absolute abundance of methanogen 16S rRNA and mcrA gene transcripts (10⁵ to 10⁹ copies g^-1 ). We showed that methanogen abundance and activity were significantly reduced with increasing concentrations of Pb and Cd, two indicators of airborne metal contaminations. Considering the ecological importance of methanogenesis in sediment habitats, these metal contaminations may have system wide implications even in remote area such as alpine lakes. Overall, this work was pioneer in integrating the effect of long-range atmospheric depositions on archaeal communities and indicated that metal contamination might significantly compromise the contribution of Archaea to the carbon cycling of the mountain lake sediments.

Ammonia Oxidizing Archaea and Bacteria in East Asian Paddy Soils—A Mini Review

Ammonia oxidation is crucial in nitrogen removal and global nitrogen dynamics since it is the first step of the nitrification process. In this review, we focus on the distribution and community structure of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in East Asian paddy soils with variable soil properties. The available East Asian paddy soil data shows that the ammonium concentration and pH ranges from 0.4 to 370 mg/kg and 5.1 to 8.2, respectively. Our meta-analysis suggest that AOA specific gene sequences are generally more abundant than those of AOB in both acidic and alkaline paddy soils, where Nitrosophaera and Nitrosospira amoA clusters mainly dominate the microbial community, respectively. In addition, the contribution of ammonia oxidizers to the nitrification process has been demonstrated using DNA-SIP (DNA-based stable-isotope probing); the results of these studies indicate that pH is the most important factor in niche separation of AOA and AOB under a variety of edaphic conditions. Finally, we discuss a number of other environmental variables that affect the abundance, distribution, and activity of AOA and AOB in East Asian paddy soils.

Geochemical and Microbial Community Attributes in Relation to Hyporheic Zone Geological Facies

The hyporheic zone (HZ) is the active ecotone between the surface stream and groundwater, where exchanges of nutrients and organic carbon have been shown to stimulate microbial activity and transformations of carbon and nitrogen. To examine the relationship between sediment texture, biogeochemistry, and biological activity in the Columbia River HZ, the grain size distributions for sediment samples were characterized to define geological facies, and the relationships among physical properties of the facies, physicochemical attributes of the local environment, and the structure and activity of associated microbial communities were examined. Mud and sand content and the presence of microbial heterotrophic and nitrifying communities partially explained the variability in many biogeochemical attributes such as C:N ratio and %TOC. Microbial community analysis revealed a high relative abundance of putative ammonia-oxidizing Thaumarchaeota and nitrite-oxidizing Nitrospirae. Network analysis showed negative relationships between sets of co-varying organisms and sand and mud contents, and positive relationships with total organic carbon. Our results indicate grain size distribution is a good predictor of biogeochemical properties, and that subsets of the overall microbial community respond to different sediment texture. Relationships between facies and hydrobiogeochemical properties enable facies-based conditional simulation/mapping of these properties to inform multiscale modeling of hyporheic exchange and biogeochemical processes.

The Distribution Pattern of Sediment Archaea Community of the Poyang Lake, the Largest Freshwater Lake in China

Archaea plays an important role in the global geobiochemical circulation of various environments. However, much less is known about the ecological role of archaea in freshwater lake sediments. Thus, investigating the structure and diversity of archaea community is vital to understand the metabolic processes in freshwater lake ecosystems. In this study, sediment physicochemical properties were combined with the results from 16S rRNA clone library-sequencing to examine the sediment archaea diversity and the environmental factors driving the sediment archaea community structures. Seven sites were chosen from Poyang Lake, including two sites from the main lake body and five sites from the inflow river estuaries. Our results revealed high diverse archaea community in the sediment of Poyang Lake, including Bathyarchaeota (45.5%), Euryarchaeota (43.1%), Woesearchaeota (3.6%), Pacearchaeota (1.7%), Thaumarchaeota (1.4%), suspended Lokiarchaeota (0.7%), Aigarchaeota (0.2%), and Unclassified Archaea (3.8%). The archaea community compositions differed among sites, and sediment property had considerable influence on archaea community structures and distribution, especially total organic carbon (TOC) and metal lead (Pb) (p < 0.05). This study provides primary profile of sediment archaea distribution in freshwater lakes and helps to deepen our understanding of lake sediment microbes.

Influences of plant type on bacterial and archaeal communities in constructed wetland treating polluted river water

Both bacteria and archaeal communities can play important roles in biogeochemical processes in constructed wetland (CW) system. However, the influence of plant type on microbial community in surface water CW remains unclear. The present study investigated bacterial and archaeal communities in five surface water CW systems with different plant species. The abundance, richness, and diversity of both bacterial and archaeal communities considerably differed in these five CW systems. Compared with the other three CW systems, the CW systems planted with Vetiveria zizanioides or Juncus effusus L. showed much higher bacterial abundance but lower archaeal abundance. Bacteria outnumbered archaea in each CW system. Moreover, the CW systems planted with V. zizanioides or J. effusus L. had relatively lower archaeal but higher bacterial richness and diversity. In each CW system, bacterial community displayed much higher richness and diversity than archaeal community. In addition, a remarkable difference of both bacterial and archaeal community structures was observed in the five studied CW systems. Proteobacteria was the most abundant bacterial group (accounting for 33-60 %). Thaumarchaeota organisms (57 %) predominated in archaeal communities in CW systems planted with V. zizanioides or J. effusus L., while Woesearchaeota (23 or 24 %) and Euryarchaeota (23 or 15 %) were the major archaeal groups in CW systems planted with Cyperus papyrus or Canna indica L. Archaeal community in CW planted with Typha orientalis Presl was mainly composed of unclassified archaea. Therefore, plant type exerted a considerable influence on microbial community in surface water CW system.

Ammonia-oxidizing archaea and bacteria in water columns and sediments of a highly eutrophic plateau freshwater lake

Both ammonia-oxidizing archaea (AOA) and bacteria (AOB) can play important roles in the microbial oxidation of ammonia nitrogen in freshwater lake, but information on spatiotemporal variation in water column and sediment community structure is still limited. Additionally, the drivers of the differences between sediment and water assemblages are still unclear. The present study investigated the variation of AOA and AOB communities in both water columns and sediments of eutrophic freshwater Dianchi Lake. The abundance, diversity, and structure of both planktonic and sediment ammonia-oxidizing microorganisms in Dianchi Lake showed the evident changes with sampling site and time. In both water columns and sediments, AOB amoA gene generally outnumbered AOA, and the AOB/AOA ratio was much higher in summer than in autumn. The total AOA amoA abundance was relatively great in autumn, while sediment AOB was relatively abundant in summer. Sediment AOA amoA abundance was likely correlated with ammonia nitrogen (rs = 0.963). The AOB/AOA ratio in lake sediment was positively correlated with total phosphorus (rs = 0.835), while pH, dissolved organic carbon, and ammonia nitrogen might be the key driving forces for the AOB/AOA ratio in lake water. Sediment AOA and AOB diversity was correlated with nitrate nitrogen (rs = -0.786) and total organic carbon (rs = 0.769), respectively, while planktonic AOB diversity was correlated with ammonia nitrogen (rs = 0.854). Surface water and sediment in the same location had a distinctively different microbial community structure. In addition, sediment AOB community structure was influenced by total phosphorus, while total phosphorus might be a key determinant of planktonic AOB community structure.

Temporal and Spatial Dynamics of Archaeal Communities in Two Freshwater Lakes at Different Trophic Status

In either eutrophic Dianchi Lake or mesotrophic Erhai Lake, the abundance, diversity, and structure of archaeaplankton communities in spring were different from those in summer. In summer, archaeaplankton abundance generally decreased in Dianchi Lake but increased in Erhai Lake, while archaeaplankton diversity increased in both lakes. These two lakes had distinct archaeaplankton community structure. Archaeaplankton abundance was influenced by organic content, while trophic status determined archaeaplankton diversity and structure. Moreover, in summer, lake sediment archaeal abundance considerably decreased. Sediment archaeal abundance showed a remarkable spatial change in spring but only a slight one in summer. The evident spatial change of sediment archaeal diversity occurred in both seasons. In Dianchi Lake, sediment archaeal community structure in summer was remarkably different from that in spring. Compared to Erhai Lake, Dianchi Lake had relatively high sediment archaeal abundance but low diversity. These two lakes differed remarkably in sediment archaeal community structure. Trophic status determined sediment archaeal abundance, diversity and structure. Archaeal diversity in sediment was much higher than that in water. Water and sediment habitats differed greatly in archaeal community structure. Euryarchaeota predominated in water column, but showed much lower proportion in sediment. Bathyarchaeota was an important component of sediment archaeal community.

Response of N₂O emissions to elevated water depth regulation: comparison of rhizosphere versus non-rhizosphere of Phragmites australis in a field-scale study

Emissions of nitrous oxide (N2O) from wetland ecosystems are globally significant and have recently received increased attention. However, relatively few direct studies of these emissions in response to water depth-related changes in sediment ecosystems have been conducted, despite the likely role they play as hotspots of N2O production. We investigated depth-related differential responses of the dissolved inorganic nitrogen distribution in Phragmites australis (Cav.) Trin. ex Steud. rhizosphere versus non-rhizosphere sediments to determine if they accelerated N2O emissions and the release of inorganic nitrogen. Changes in static water depth and P. australis growth both had the potential to disrupt the distribution of porewater dissolved NH4 (+), NO3 (-), and NO2 (-) in profiles, and NO3 (-) had strong surface aggregation tendency and decreased significantly with depth. Conversely, the highest NO2 (-) contents were observed in deep water and the lowest in shallow water in the P. australis rhizosphere. When compared with NO3 (-), NH4 (+), and NO2 (-), fluxes from the rhizosphere were more sensitive to the effects of water depth, and both fluxes increased significantly at a depth of more than 1 m. Similarly, N2O emissions were obviously accelerated with increasing depth, although those from the rhizosphere were more readily controlled by P. australis. Pearson's correlation analysis showed that water depth was significantly related to N2O emission and NO2 (-) fluxes, and N2O emissions were also strongly dependent on NO2 (-) fluxes (r = 0.491, p < 0.05). The results presented herein provide new insights into inorganic nitrogen biogeochemical cycles in freshwater sediment ecosystems.

Sediment Ammonia-Oxidizing Microorganisms in Two Plateau Freshwater Lakes at Different Trophic States

Both ammonia-oxidizing archaea (AOA) and bacteria (AOB) can contribute to ammonia biotransformation in freshwater lake ecosystems. However, the factors shaping the distribution of sediment AOA and AOB in plateau freshwater lake remains unclear. The present study investigated sediment AOA and AOB communities in two freshwater lakes (hypertrophic Dianchi Lake and mesotrophic Erhai Lake) on the Yunnan Plateau (China). A remarkable difference in the abundance, diversity, and composition of sediment AOA and AOB communities was observed between Dianchi Lake and Erhai Lake. AOB usually outnumbered AOA in Dianchi Lake, but AOA showed the dominance in Erhai Lake. Organic matter (OM), total nitrogen (TN), and total phosphorus (TP) might be the key determinants of AOB abundance, while AOA abundance was likely influenced by the ration of OM to TN (C/N). AOA or AOB community structure was found to be relatively similar in the same lake. TN and TP might play important roles in shaping sediment AOA and AOB compositions in Dianchi Lake and Erhai Lake. Moreover, Nitrososphaera-like AOA were detected in Dianchi Lake. Nitrosospira- and Nitrosomonas-like AOB were dominant in Dianchi Lake and Erhai Lake, respectively. Sediment AOA and AOB communities in Dianchi Lake and Erhai Lake were generally regulated by trophic state.

Spatiotemporal variation of planktonic and sediment bacterial assemblages in two plateau freshwater lakes at different trophic status

Both planktonic and sediment bacterial assemblages are the important components of freshwater lake ecosystems. However, their spatiotemporal shift and the driving forces remain still elusive. Eutrotrophic Dianchi Lake and mesotrophic Erhai Lake are the largest two freshwater lakes on the Yunnan Plateau (southwestern China). The present study investigated the spatiotemporal shift in both planktonic and sediment bacterial populations in these two plateau freshwater lakes at different trophic status. For either lake, both water and sediment samples were collected from six sampling locations in spring and summer. Bacterioplankton community abundance in Dianchi Lake generally far outnumbered that in Erhai Lake. Sediment bacterial communities in Erhai Lake were found to have higher richness and diversity than those in Dianchi Lake. Sediments had higher bacterial community richness and diversity than waters. The change patterns for both planktonic and sediment bacterial communities were lake-specific and season-specific. Either planktonic or sediment bacterial community structure showed a distinct difference between in Dianchi Lake and in Erhai Lake, and an evident structure difference was also found between planktonic and sediment bacterial communities in either of these two lakes. Planktonic bacterial communities in both Dianchi Lake and Erhai Lake mainly included Proteobacteria (mainly Alpha-, Beta-, and Gammaproteobacteria), Bacteroidetes, Actinobacteria, Cyanobacteria, and Firmicutes, while sediment bacterial communities were mainly represented by Proteobacteria (mainly Beta- and Deltaproteobacteria), Bacteroidetes, Chlorobi, Nitrospirae, Acidobacteria, and Chloroflexi. Trophic status could play important roles in shaping both planktonic and sediment bacterial communities in freshwater lakes.

Nonylphenol biodegradation, functional gene abundance and bacterial community in bioaugmented sediment: effect of external carbon source

Nonylphenol (NP) biodegradation in river sediment using Stenotrophomonas strain Y1 and Sphingobium strain Y2 were proved to be an effective strategy to remediate NP pollution in our earlier study. The purpose of this study is to investigate the influence of glucose addition on their ability to degrade NP in both liquid cultures and sediment microcosms. The shift in bacterial community structure and relative abundance of NP degraders in sediment microcosms were characterized using terminal restriction fragment length polymorphism analysis. The proportion of NP-degrading alkB and sMO genes was assessed using quantitative polymerase chain reaction (PCR) assay. The growth of Stenotrophomonas strain Y1 and its NP biodegradation efficiency were inhibited by glucose supplementation, while the relative abundance of alkB gene increased. However, NP degradation, as well as the growth of added degraders and proportion of sMO gene, was enhanced in the glucose-amended sediment microcosms inoculated with Sphingobium strain Y2. Moreover, external glucose addition altered bacterial community structures in bioaugmented sediment microcosms, depending on the level of glucose dosage.

Distribution of sediment bacterial and archaeal communities in plateau freshwater lakes

Both Bacteria and Archaea might be involved in various biogeochemical processes in lacustrine sediment ecosystems. However, the factors governing the intra-lake distribution of sediment bacterial and archaeal communities in various freshwater lakes remain unclear. The present study investigated the sediment bacterial and archaeal communities in 13 freshwater lakes on the Yunnan Plateau. Quantitative PCR assay showed a large variation in bacterial and archaeal abundances. Illumina MiSeq sequencing illustrated high bacterial and archaeal diversities. Bacterial abundance was regulated by sediment total organic carbon and total nitrogen, and water depth, while nitrate nitrogen was an important determinant of bacterial diversity. Proteobacteria, Acidobacteria, Actinobacteria, Bacteroidetes, Chlorobi, Chloroflexi, Cyanobacteria, Firmicutes, Gemmatimonadetes, Nitrospirae, Planctomycetes, and Verrucomicrobia were the major components of sediment bacterial communities. Proteobacteria was the largest phylum, but its major classes and their proportions varied greatly among different lakes, affected by sediment nitrate nitrogen. In addition, both Euryarchaeota and Crenarchaeota were important members in sediment archaeal communities, while unclassified Archaea usually showed the dominance.

Comparative effects of 3,4-dimethylpyrazole phosphate (DMPP) and dicyandiamide (DCD) on ammonia-oxidizing bacteria and archaea in a vegetable soil

Nitrification inhibitors (NIs) 3,4-dimethylpyrazole phosphate (DMPP) and dicyandiamide (DCD) have been used extensively to improve nitrogen fertilizer utilization in farmland. However, their comparative effects on ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in agricultural soils are still unclear. Here, we compared the impacts of these two inhibitors on soil nitrification, AOA and AOB abundance as well as their community structure in a vegetable soil by using real-time PCR and terminal restriction fragment length polymorphism (T-RFLP). Our results showed that urea application significantly increased the net nitrification rates, but were significantly inhibited by both NIs, and the inhibitory effect of DMPP was significantly greater than that of DCD. AOB growth was more greatly inhibited by DMPP than by DCD, and the net nitrification rate was significantly related to AOB abundance, but not to AOA abundance. Application of urea and NIs to soil did not change the diversity of the AOA community, with the T-RFs remaining in proportions that were similar to control soils, while the community structure of AOB exhibited obvious shifts within all different treatments compared to the control. Phylogenetic analysis showed that all AOA sequences fell within group 1.1a and group 1.1b, and the AOB community consisted of Nitrosospira cluster 3, cluster 0, and unidentified species. These results suggest that DMPP exhibited a stronger inhibitory effect on nitrification than DCD by inhibiting AOB rather than AOA.

Ammonia- and methane-oxidizing microorganisms in high-altitude wetland sediments and adjacent agricultural soils

Ammonia oxidation is known to be carried out by ammonia-oxidizing bacteria (AOB) and archaea (AOA), while methanotrophs (methane-oxidizing bacteria (MOB)) play an important role in mitigating methane emissions from the environment. However, the difference of AOA, AOB, and MOB distribution in wetland sediment and adjacent upland soil remains unclear. The present study investigated the abundances and community structures of AOA, AOB, and MOB in sediments of a high-altitude freshwater wetland in Yunnan Province (China) and adjacent agricultural soils. Variations of AOA, AOB, and MOB community sizes and structures were found in water lily-vegetated and Acorus calamus-vegetated sediments and agricultural soils (unflooded rice soil, cabbage soil, and garlic soil and flooded rice soil). AOB community size was higher than AOA in agricultural soils and lily-vegetated sediment, but lower in A. calamus-vegetated sediment. MOB showed a much higher abundance than AOA and AOB. Flooded rice soil had the largest AOA, AOB, and MOB community sizes. Principal coordinate analyses and Jackknife Environment Clusters analyses suggested that unflooded and flooded rice soils had relatively similar AOA, AOB, and MOB structures. Cabbage soil and A. calamus-vegetated sediment had relatively similar AOA and AOB structures, but their MOB structures showed a large difference. Nitrososphaera-like microorganisms were the predominant AOA species in garlic soil but were present with a low abundance in unflooded rice soil and cabbage soil. Nitrosospira-like AOB were dominant in wetland sediments and agricultural soils. Type I MOB Methylocaldum and type II MOB Methylocystis were dominant in wetland sediments and agricultural soils. Moreover, Pearson's correlation analysis indicated that AOA Shannon diversity was positively correlated with the ratio of organic carbon to nitrogen (p < 0.05). This work could provide some new insights toward ammonia and methane oxidation in soil and wetland sediment ecosystems.

Abundance and diversity of ammonia-oxidizing microorganisms in the sediments of Jinshan Lake

Community structures of ammonia-oxidizing microorganisms were investigated using PCR primers designed to specifically target the ammonia monooxygenase α-subunit (amoA) gene in the sediment of Jinshan Lake. Relationships between the abundance and diversity of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB), and physicochemical parameters were also explored. The AOA abundance decreased sharply from west to east; however, the AOB abundance changed slightly with AOB outnumbering AOA in two of the four sediment samples (JS), JS3 and JS4. The AOA abundance was significantly correlated with the NH4-N, NO3-N, and TP. No significant correlations were observed between the AOB abundance and environmental variables. AOB had a higher diversity and richness of amoA genes than AOA. Among the 76 archaeal amoA sequences retrieved, 57.89, 38.16, and 3.95 % fell within the Nitrosopumilus, Nitrososphaera, and Nitrososphaera sister clusters, respectively. The 130 bacterial amoA gene sequences obtained in this study were grouped with known AOB sequences in the Nitrosomonas and Nitrosospira genera, which occupied 72.31 % and 27.69 % of the AOB group, respectively. Compared to the other three sample sites, the AOA and AOB community compositions at JS4 showed a large difference. This work could enhance our understanding of the roles of ammonia-oxidizing microorganisms in freshwater lake environment.