Abundance and community composition of ammonia-oxidizing archaea and bacteria in two different zones of Lake Taihu

2012 ◽  
Vol 58 (8) ◽  
pp. 1018-1026 ◽  
Author(s):  
Jin Zeng ◽  
Da-Yong Zhao ◽  
Rui Huang ◽  
Qinglong L. Wu
Keyword(s):  
Community Composition ◽  
Gene Diversity ◽  
Lake Taihu ◽  
Amoa Gene ◽  
Ammonia Oxidizing Bacteria ◽  
Bacterial Amoa Gene ◽  
Ammonia Oxidizing Archaea ◽  
Archaeal Amoa Gene ◽  
Copy Numbers ◽  
Meiliang Bay

The abundance and community composition of ammonia-oxidizing archaea and ammonia-oxidizing bacteria in the surface sediments of 2 different zones (Meiliang Bay and Eastern Lake Taihu) of Lake Taihu were investigated using real-time quantitative polymerase chain reaction and clone libraries. The amoA gene copy numbers in the surface sediment of Meiliang Bay ranged from 4.91 × 105 to 8.65 × 106 copies/g dry sediment for the archaeal amoA gene and from 3.74 × 104 to 3.86 × 105 copies/g dry sediment for the bacterial amoA gene, which were significantly higher than those of Eastern Lake Taihu (P < 0.05). Concentrations of ammonia (NH4+), total nitrogen, organic matter, and pH of the sediments exhibited significantly negative correlations with the abundance of ammonia-oxidizing archaea or ammonia-oxidizing bacteria (P < 0.05 or P < 0.01, respectively). The potential nitrification rates show remarkable correlations with the copy numbers of the archaeal amoA gene. Diversity of the archaeal amoA gene in Eastern Lake Taihu was significantly higher than that of Meiliang Bay, whereas the bacterial amoA gene diversity was comparable for the 2 lake zones. The data obtained in this study would be useful to elucidate the role of ammonia-oxidizing archaea and ammonia-oxidizing bacteria in the nitrogen cycle of freshwater ecosystems.

Predominance of ammonia-oxidizing archaea andnirK-gene-bearing denitrifiers among ammonia-oxidizing and denitrifying populations in sediments of a large urban eutrophic lake (Lake Donghu)

2013 ◽  
Vol 59 (7) ◽  
pp. 456-464 ◽  
Author(s):  
Jie Hou ◽  
Xiuyun Cao ◽  
Chunlei Song ◽  
Yiyong Zhou
Keyword(s):  
Amoa Gene ◽  
Eutrophic Lake ◽  
Gene Copy ◽  
Nirs Gene ◽  
Bacterial Amoa Gene ◽  
Archaeal Amoa Gene ◽  
Copy Numbers ◽  
Significant Difference ◽  
Nirk Gene ◽  
Gene Copy Numbers

The coupled nitrification–denitrification process plays a pivotal role in cycling and removal of nitrogen in aquatic ecosystems. In the present study, the communities of ammonia oxidizers and denitrifiers in the sediments of 2 basins (Guozhenghu Basin and Tuanhu Basin) of a large urban eutrophic lake (Lake Donghu) were determined using the ammonia monooxygenase subunit A (amoA) gene and the nitrite reductase gene. At all sites of this study, the archaeal amoA gene predominated over the bacterial amoA gene, whereas the functional gene for denitrification nirK gene far outnumbered the nirS gene. Spatially, compared with the Tuanhu Basin, the Guozhenghu Basin showed a significantly greater abundance of the archaeal amoA gene but less abundance of the nirK and nirS genes, while there was no significant difference of bacterial amoA gene copy numbers between the 2 basins. Unlike the archaeal amoA gene, the nirK gene showed a significant difference in community structure between the 2 basins. Archaeal amoA diversity was limited to the water–sediment cluster of Crenarchaeota, in sharp contrast with nirK for which 22 distinct operational taxonomic units were found. Accumulation of organic substances were found to be positively related to nirK and nirS gene copy numbers but negatively related to archaeal amoA gene copy numbers, whereas the abundance of the bacterial amoA gene was related to ammonia concentration.

scholarly journals Effects of Sea Animal Colonization on the Coupling between Dynamics and Activity of Soil Ammonia-oxidizing Bacteria and Archaea in Maritime Antarctica

2019 ◽  
Author(s):  
Qing Wang ◽  
Renbin Zhu ◽  
Yanling Zheng ◽  
Tao Bao ◽  
Lijun Hou
Keyword(s):  
Ammonia Oxidation ◽  
Amoa Gene ◽  
Ammonia Oxidizing Bacteria ◽  
Nitrogen Transformations ◽  
Tundra Soils ◽  
Maritime Antarctica ◽  
Oxidation Rates ◽  
Ammonia Oxidizing Archaea ◽  
Copy Numbers ◽  
Tundra Ecosystem

Abstract. The colonization of a large number of sea animal, including penguins and seals, plays an important role in the nitrogen cycle of the tundra ecosystem in coastal Antarctica. However, little is known about the effects of sea animal colonization on ammonia-oxidizing archaea (AOA) and bacteria (AOB) communities involved in nitrogen transformations. In this study, we chose active seal colony tundra soils (STS), penguin colony soils (PTS), adjacent penguin-lacking tundra soils (PLS), tundra marsh soils (MS), and background tundra soils (BS), to investigate the effects of sea animal colonization on the abundance, activity, and diversity of AOA and AOB in maritime Antarctica. Results indicated that AOB dominated over AOA in PTS, STS, and PLS; whereas AOB and AOA abundances were similar in MS and BS. Penguin or seal activities increases the abundance of soil AOB amoA genes, but reduced the abundance of AOA amoA genes, leading to very large ratios (1.5 × 102 to 3.2 × 104) of AOB to AOA amoA copy numbers. Ammonia oxidation rates were significantly higher (P = 0.02) in STS and PTS than in PLS, MS, and BS, and were significantly positively correlated (P < 0.001) with AOB amoA gene abundance suggesting that AOB are more important in the nitrification in animal colony soils. Sequence analysis for gene clones showed that AOA and AOB in tundra soils were from the Nitrosospira and Nitrososphaera lineages, respectively. Seal or penguin activities led to the predominant existence of AOA phylotypes related to Nitrososphaera cluster I and AOB phylotypes related to Nitrosospira clusters I and II, but very low relative abundances in AOA phylotypes related to cluster II, and AOB phylotypes related to cluster III and IV. The differences in AOB and AOA community structures were closely related to soil biogeochemical processes under the disturbance of penguin or seal activities: soil C:N alteration and sufficient input of NH4+–N and phosphorus from animal excrements. The results provide insights into the mechanisms how microbes drive nitrification in maritime Antarctica.

scholarly journals Spatial and Seasonal Variations in the Abundance of Nitrogen-Transforming Genes and the Microbial Community Structure in Freshwater Lakes with Different Trophic Statuses

2019 ◽  
Vol 16 (13) ◽  
pp. 2298 ◽  
Author(s):  
Yu Wan ◽  
Xiaohong Ruan ◽  
Jie Wang ◽  
Xiaojun Shi
Keyword(s):  
Microbial Community ◽  
Trophic Status ◽  
Lake Taihu ◽  
Quantitative Polymerase Chain Reaction ◽  
Amoa Gene ◽  
Functional Markers ◽  
Ammonia Oxidizing Bacteria ◽  
Eutrophic Lakes ◽  
Nirs Gene ◽  
Transforming Genes

Identifying nitrogen-transforming genes and the microbial community in the lacustrine sedimentary environment is critical for revealing nitrogen cycle processes in eutrophic lakes. In this study, we examined the diversity and abundance of ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA), denitrifying bacteria (DNB), and anammox bacteria (AAOB) in different trophic status regions of Lake Taihu using the amoA, Arch-amoA, nirS, and hzo genes as functional markers. Quantitative Polymerase Chain Reaction (qPCR) results indicated that the abundance of the nirS gene was the highest, while the amoA gene had the lowest abundance in all regions. Except for the primary inflow area of Lake Taihu, Arch-amoA gene abundance was higher than the hzo gene in three lake bays, and the abundance of the nirS gene increased with decreasing trophic status. The opposite pattern was observed for the amoA, Arch-amoA, and hzo genes. Phylogenetic analyses showed that the predominant AOB and AOA were Nitrosomonas and Nitrosopumilus maritimus, respectively, and the proportion of Nitrosomonas in the eutrophic region (87.9%) was higher than that in the mesotrophic region (71.1%). Brocadia and Anammoxoglobus were the two predominant AAOB in Lake Taihu. Five novel unknown phylotypes of AAOB were observed, and Cluster AAOB-B was only observed in the inflow area with a proportion of 32%. In the DNB community, Flavobacterium occurred at a higher proportion (22.6–38.2%) in all regions, the proportion of Arthrobacter in the mesotrophic region (3.6%) was significantly lower than that in the eutrophic region (15.6%), and the proportions of Cluster DNB-E in the inflow area (24.5%) was significantly higher than that in the lake bay (7.3%). The canonical correspondence analysis demonstrated that the substrate concentration in sedimentary environments, such as NOx--N in the sediment, NH4+-N in the pore water, and the total organic matter, were the key factors that determined the nitrogen-transforming microbial community. However, the temperature was also a predominant factor affecting the AOA and AAOB communities.

Abundance and composition of ammonia-oxidising bacteria and archaea of a degraded lake wetland, Inner Mongolian Plateau, China

Soil Research ◽  
2013 ◽  
Vol 51 (6) ◽  
pp. 554 ◽  
Author(s):  
Linhui Wu ◽  
Lihua Hui ◽  
Xiaoyi Wang ◽  
Jingyu Li ◽  
Jingli Yu ◽  
...  
Keyword(s):  
Population Size ◽  
Community Composition ◽  
Chemical Properties ◽  
Amoa Gene ◽  
Water Withdrawal ◽  
Drying Process ◽  
Pcr Cloning ◽  
Copy Numbers ◽  
Drying Up ◽  
Ammonia Oxidising Bacteria

Wetlands are one of the most highly threatened ecosystems on Earth, and their loss and degradation are regarded as major environmental problems. The degradation rate of lake wetlands of the Huitengxile grassland, Inner Mongolia, has increased over recent years. In this study, soil samples were collected in a degraded lake wetland of the Huitengxile grassland. The abundance and composition of soil ammonia-oxidising bacteria (AOB) and ammonia-oxidising archaea (AOA) were assessed by quantitative real-time PCR, cloning, and sequencing approaches. Four sampling sites were selected according to the order of water withdrawal. The lakeshore sample appeared to have the highest copy numbers of AOB amoA genes, and the lowest AOB population size was found in the lakebed sample. Similar to AOB, the AOA were most abundant in the lakeshore sample, and the population size in the lake centre sample was the lowest. Ex2cept in one lakebed sample, AOB were more abundant than AOA in all other samples, with AOB to AOA ratios ranging from 11 to 13. Phylogenetic analysis of the amoA gene fragments showed that all AOB sequences from different sites were affiliated to class β-Proteobacteria, order Nitrosomonadales, family Nitrosomonadaceae and can be grouped into two clusters. Little difference was found in AOB community composition among different samples, which indicated that AOB community composition was stable during the drying process of the degraded lake. However, the AOA community compositions were very different between samples. All AOA sequences fell into four clusters. Cluster 1 was dominant in the sample from the centre of the lake, and cluster 2 was dominant in the lakeshore sample, indicating a difference in the community composition of AOA in response to the drying up of the lake. No clear relationship was found between the AOA and AOB community populations and soil physio-chemical properties. This study suggested that the AOA community in wetland systems is more sensitive than the AOB community to the drying process of the wetland ecosystem.

Abundance and composition dynamics of soil ammonia-oxidizing archaea in an alpine fir forest on the eastern Tibetan Plateau of China

2012 ◽  
Vol 58 (5) ◽  
pp. 572-580 ◽  
Author(s):  
Ao Wang ◽  
Fu-Zhong Wu ◽  
Wan-Qin Yang ◽  
Zhi-Chao Wu ◽  
Xu-Xi Wang ◽  
...  
Keyword(s):  
Tibetan Plateau ◽  
Soil Temperature ◽  
Coniferous Forest ◽  
Amoa Gene ◽  
Western China ◽  
Gene Copy ◽  
Ammonia Oxidizing Bacteria ◽  
Eastern Tibetan Plateau ◽  
Dominant Group ◽  
Ammonia Oxidizing Archaea

Real-time qPCR and clone library sequencing targeting amoA genes were used to investigate the seasonal dynamics of an ammonia-oxidizing archaea (AOA) community in an alpine fir forest in western China. AOA were detected at all sampling dates, and there were significant variations in archaeal amoA gene copy numbers (7.63 × 105to 8.35 × 108per gram of dry soil) throughout the nongrowing season. Compared with ammonia-oxidizing bacteria (AOB), the AOA displayed a higher abundance on the majority of sampling dates during the freeze–thaw period. All of the AOA sequences fell within soil and sediment lineages and were affiliated with 7 clusters. Compared with the other clusters, cluster 1 was more sensitive to low temperature and was the dominant group in August. In contrast, cluster 3 dominated the AOA community in winter and probably represents a group of cold-adapted archaea. Redundancy analysis (RDA) revealed that the seasonality of the AOA community was mainly attributed to changes in soil temperature and nutrient availability (e.g., dissolved organic nitrogen and carbon). Our results indicate that AOA exist in frozen soils in the alpine coniferous forest ecosystem of the eastern Tibetan Plateau. Moreover, soil temperature may directly and (or) indirectly affect AOA abundance and composition and may further influence the soil N cycle during the winter.

scholarly journals Effect of Lake Trophic Status and Rooted Macrophytes on Community Composition and Abundance of Ammonia-Oxidizing Prokaryotes in Freshwater Sediments

2009 ◽  
Vol 75 (10) ◽  
pp. 3127-3136 ◽  
Author(s):  
Martina Herrmann ◽  
Aaron M. Saunders ◽  
Andreas Schramm
Keyword(s):  
Community Composition ◽  
Plant Species ◽  
Trophic Status ◽  
Gene Diversity ◽  
Freshwater Sediments ◽  
Lake Trophic Status ◽  
Ammonia Oxidizing Archaea ◽  
Softwater Lakes ◽  
Species Specific ◽  
Pcr Targeting

ABSTRACT Communities of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in freshwater sediments and those in association with the root system of the macrophyte species Littorella uniflora, Juncus bulbosus, and Myriophyllum alterniflorum were compared for seven oligotrophic to mesotrophic softwater lakes and acidic heathland pools. Archaeal and bacterial ammonia monooxygenase alpha-subunit (amoA) gene diversity increased from oligotrophic to mesotrophic sites; the number of detected operational taxonomic units was positively correlated to ammonia availability and pH and negatively correlated to sediment C/N ratios. AOA communities could be grouped according to lake trophic status and pH; plant species-specific communities were not detected, and no grouping was apparent for AOB communities. Relative abundance, determined by quantitative PCR targeting amoA, was always low for AOB (<0.05% of all prokaryotes) and slightly higher for AOA in unvegetated sediment and AOA in association with M. alterniflorum (0.01 to 2%), while AOA accounted for up to 5% in the rhizospheres of L. uniflora and J. bulbosus. These results indicate that (i) AOA are at least as numerous as AOB in freshwater sediments, (ii) aquatic macrophytes with substantial release of oxygen and organic carbon into their rhizospheres, like L. uniflora and J. bulbosus, increase AOA abundance; and (iii) AOA community composition is generally determined by lake trophy, not by plant species-specific interactions.

scholarly journals Ammonia-oxidizing Archaea (AOA) are Winners to Survive in Oxygen-limited Habitat Compared to Ammonia-oxidizing Bacteria (AOB)

2021 ◽  
Author(s):  
Peigang Dai ◽  
Wenjing Song ◽  
Zhao Che ◽  
Lili Zhang ◽  
Zhaorong Dong
Keyword(s):  
Intertidal Zone ◽  
High Throughput Sequencing ◽  
Ammonia Oxidation ◽  
Illumina Miseq ◽  
Gene Copy ◽  
Ammonia Oxidizing Bacteria ◽  
Niche Specialization ◽  
Ammonia Oxidizing Archaea ◽  
Copy Numbers ◽  
Oxidation Reduction

Abstract Purpose: Both ammonia oxidizing archaea (AOA) and bacteria (AOB) perform the ammonia oxidation together. These two kinds of microbes present a convenient model for studying niche specialization. To date, few surveys concentrated on the influence of oxygen concentration on niche specialization of AOA and AOB in intertidal zones. Methods: Here, high-throughput sequencing by Illumina MiSeq and qPCR were applied to detect the change of abundance, diversity as well as community structure of both AOA and AOB with 0-60 cm sediments depth in the intertidal zone in Qingdao.Results and Conclusion: The AOA/AOB amoA gene copy numbers and AOA/AOB OTU numbers were all increased as sediment depth went deeper, which indicated that AOA were more adaptive to oxygen-limited niches compared to AOB and oxygen indeed led to the niche specialization of AOA and AOB in intertidal sediments. The dominant AOA and AOB were the Nitrosopumilus and Nitrosospira clusters, respectively, which indicated an ecological success in intertidal zone. Oxidation-reduction potential (ORP) was significantly positively correlated with AOB abundance and AOB OTU numbers (P < 0.01). In addition, both TN (P < 0.01) and pH (P < 0.05) were significantly and negatively correlated with AOB abundance. TN was also significantly and negatively correlated with AOB OTU numbers (P < 0.05).

Dissolved organic carbon and relationship with bacterioplankton community composition in 3 lake regions of Lake Taihu, China

2014 ◽  
Vol 60 (10) ◽  
pp. 669-680 ◽  
Author(s):  
Xinghong Pang ◽  
Hong Shen ◽  
Yuan Niu ◽  
Xiaoxue Sun ◽  
Jun Chen ◽  
...  
Keyword(s):  
Organic Carbon ◽  
Dissolved Organic Carbon ◽  
Community Composition ◽  
Lake Taihu ◽  
Eutrophic Lakes ◽  
Bacterioplankton Community ◽  
Doc Concentration ◽  
Lake Center ◽  
Meiliang Bay ◽  
The Relationship

To clarify the relationships between dissolved organic carbon (DOC) and bacterioplankton community composition (BCC), a 1-year survey (June 2009 – May 2010) was conducted in 3 regions of Lake Taihu (Meiliang Bay, Lake Center, and Eastern Taihu), China. Polymerase chain reaction – denaturing gradient gel electrophoresis was used to analyze the composition and heterogeneity of the bacterioplankton community. Canonical correspondence analysis was used to explore the relationships between DOC concentration and BCC. We found a significant negative correlation between DOC concentration and bacterioplankton community diversity (as measured by the Shannon–Wiener index (H′)). The results show that spatial variation in the bacterioplankton population was stronger than the seasonal variation and that DOC concentration influences BCC in Lake Taihu. DOC concentration, followed by macrophyte biomass, water turbidity, and phytoplankton biomass were the most influential factors that account for BCC changes in Lake Taihu. More detailed studies on the relationship between DOC concentration and BCC should focus on differences in DOC concentrations and quality among these lake regions. DOC had a significant impact on BCC in Meiliang Bay. The relationship between DOC and BCC in the 2 other regions studied (Lake Center and Eastern Taihu) was weaker. The results of this study add to our understanding of the BCC in eutrophic lakes, especially regarding the role of the microbial loop in lake ecosystems.

scholarly journals Distinct Responses in Ammonia-Oxidizing Archaea and Bacteria after Addition of Biosolids to an Agricultural Soil

2011 ◽  
Vol 77 (18) ◽  
pp. 6551-6558 ◽  
Author(s):  
John J. Kelly ◽  
Katherine Policht ◽  
Tanya Grancharova ◽  
Lakhwinder S. Hundal
Keyword(s):  
Agricultural Soil ◽  
Terrestrial Ecosystems ◽  
Gene Copy ◽  
Ecological Niches ◽  
Corn Yield ◽  
Ammonia Oxidizing Bacteria ◽  
Ammonia Oxidizing Archaea ◽  
Copy Numbers ◽  
Synthetic Fertilizer ◽  
Gene Copy Numbers

ABSTRACTThe recently discovered ammonia-oxidizing archaea (AOA) have been suggested as contributors to the first step of nitrification in terrestrial ecosystems, a role that was previously assigned exclusively to ammonia-oxidizing bacteria (AOB). The current study assessed the effects of agricultural management, specifically amendment of soil with biosolids or synthetic fertilizer, on nitrification rates and copy numbers of archaeal and bacterial ammonia monooxygenase (amoA) genes. Anaerobically digested biosolids or synthetic fertilizer was applied annually for three consecutive years to field plots used for corn production. Biosolids were applied at two loading rates, a typical agronomic rate (27 Mg hectare−1year−1) and double the agronomic rate (54 Mg hectare−1year−1), while synthetic fertilizer was applied at an agronomic rate typical for the region (291 kg N hectare−1year−1). Both biosolids amendments and synthetic fertilizer increased soil N and corn yield, but only the biosolids amendments resulted in significant increases in nitrification rates and increases in the copy numbers of archaeal and bacterialamoAgenes. In addition, only archaealamoAgene copy numbers increased in response to biosolids applied at the typical agronomic rate and showed a significant correlation with nitrification rates. Finally, copy numbers of archaealamoAgenes were significantly higher than copy numbers of bacterialamoAgenes for all treatments. These results implicate AOA as being primarily responsible for the increased nitrification observed in an agricultural soil amended with biosolids. These results also support the hypothesis that physiological differences between AOA and AOB may enable them to occupy distinct ecological niches.

Ammonia-oxidizing bacteria dynamics affected by plantain under synthetic cattle urine patches

2020 ◽  
Vol 82 ◽  
pp. 97-102
Author(s):  
Priscila Simon ◽  
Cecile De Klein ◽  
Emily Gerard ◽  
Shenjing Shi
Keyword(s):  
White Clover ◽  
Rhizosphere Soil ◽  
Root Exudation ◽  
Amoa Gene ◽  
Time Frame ◽  
Bulk Soil ◽  
Gene Copy ◽  
Ammonia Oxidizing Bacteria ◽  
Real Time Quantitative Pcr ◽  
Copy Numbers

Plantain has been suggested as a nitrous oxide (N2O) and nitrate (NO3-) leaching mitigation option as it may induce biological nitrification inhibition (BNI) via plantain root exudation, which affects the activity of ammonia-oxidizing bacteria. This preliminary study compared the abundance of the ammonia monooxygenase gene (amoA) in soils containing either plantain and white clover, or ryegrass and white clover. Plants were sown in pots and grown in a greenhouse. Two months after sowing, synthetic cattle urine was applied to half the pots, and rhizosphere and bulk soil samples were collected 30 and 90 days after urine application. The abundance of the amoA gene was measured using real time quantitative PCR. The abundance of amoA genes in rhizosphere soil around ryegrass plants and in bulk soil under ryegrass/white clover were higher in pots treated with urine than the no-urine controls. AmoA gene abundance in bulk soil under plantain/white clover was higher in pots treated with urine (P<0.05) but not in rhizosphere soil around plantain plants (P>0.05) compared with the control. Furthermore, amoA gene copy numbers in the rhizosphere soil around plantain plants were lower than for ryegrass plants (P<0.05). However, there was no difference in the abundance of amoA genes in bulk soil of either combination of plant species evaluated (P>0.05). The results suggest that, in the time frame of our experiment, plantain could induce a BNI effect in the rhizosphere soil but not in the bulk soil.

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