Communities and Quantitative Analysis of Ammonia-oxidizing Organisms in Pearl River Estuary Sediments

[Objective] This study aimed to investigate the abundance and composition of ammonia-oxidizing bacteria and ammonia-oxidizing archaea in Pearl River Estuary sediment.[Method] Firstly,the amoA gene library was constructed;then based on that,the content and diversity of amoA genes of ammonia-oxidizing bacteria and ammonia-oxidizing archaea in Pearl River Estuary sediment were detected by using quantitative real-time polymerase chain reaction（Q-PCR）.[Result] The results of Q-PCR presented that ammonia-oxidizing archaea（AOA） were more abundant than ammonia-oxidizing bacteria（AOB） in the top of sediment cores,with ratios of AOA to AOB of 22 and 9 at the two sites.It suggested that ammonia-oxidizing archaea may play more important roles than ammonia-oxidizing bacteria in the process of ammonia oxidation in the Pearl River Estuary sediment.The phylogenetic tree based on amoA gene sequences revealed that the amoA sequences of both AOA and AOB shared high similarity with the clones from uncultured environment.In the top sediment layer at site Q7,AOB amoA-like gene sequences were dominated by Nitrosomonas-like sequence types,which could be classified into five groups（clusters A,B,C,D and E）.Cluster A accounted for 72.1% of the library.In the top sediment layer,the AOA amoA gene fell into two groups ＂water column/sediment＂ cluster（52.2%） and ＂soil/sediment＂ cluster（47.8%）.But in the bottom sediment layer of Q7,most of the AOA amoA sequences（93.3%） fell into ＂soil/sediment＂ cluster,and a little part（6.7%） fell into the ＂water/sediment＂ cluster.In addition,the total amount of amoA genes in the bottom sediment was higher than that in top sediment.[Conclusion] This study helps to realize the cycle of nitrogen in Pearl River Estuary Region,and thus to provide theoretical support for the treatment of nitrogen eutrophication.

Community analysis of ammonia-oxidizing bacteria in activated sludge of eight wastewater treatment systems

We investigated the communities of ammonia-oxidizing bacteria （AOB） in activated sludge collected from eight wastewater treatment systems using polymerase chain reaction （PCR） followed by terminal restriction fragment length polymorphism （T-RFLP）, cloning, and sequencing of the α-subunit of the ammonia monooxygenase gene （amoA）. The T-RFLP fingerprint analyses showed that different wastewater treatment systems harbored distinct AOB communities. However, there was no remarkable difference among the AOB T- RFLP profiles from different parts of the same system. The T-RFLP fingerprints showed that a full-scale wastewater treatment plant （WWTP） contained a larger number of dominant AOB species than a pilot-scale reactor. The source of influent affected the AOB community, and the WWTPs treating domestic wastewater contained a higher AOB diversity than those receiving mixed domestic and industrial wastewater. However, the AOB community structure was little affected by the treatment process in this study. Phylogenetic analysis of the cloned amoA genes clearly indicated that all the dominant AOB in the systems was closely related to Nitrosomonas spp. not to Nitrosospira spp. Members of the Nitrosomonas oligotropha and Nitrosomonas communis clusters were found in all samples, while members of Nitrosomonas europaea cluster occurred in some systems.

Microbial Populations,Activity and Gene Abundance in Tropical Vertisols Under Intensive Chemical Farming

There are increasing concerns on the environmental impacts of intensive chemical agriculture. The effect of high agrochemical inputs used in intensive chemical farming was assessed on soil microbiological, molecular and biochemical properties in tropical Vertisols in India. Farm field sites under normal cultivation of arable crops using high inputs of fertilizers and pesticides in chili （Capsicum annum L., 5.0× dose for fertilizers and 1.5× dose for pesticides over normal inputs） and black gram （Vigna mungo L. Hepper, 2.2× dose for fertilizers and 2.3× dose for pesticides over normal inputs） were compared with adjacent sites using normal recommended doses. Organic carbon and basal respiration showed no response to high inputs of fertilizers and pesticides in soils of both crops. Labile carbon decreased by 10% in chili soils and increased by 24% in black gram soils under high input farming system. The proportion of soil labile carbon as a fraction of soil organic carbon was unaffected by high inputs. The labile carbon mineralization coefficient （qMLc） increased by 50.0% in chili soils, indicating that the soil microorganisms were under stress due to high agochemical inputs, whereas qMLc decreased by 36.4% in black gram soils. Copiotrophs increased due to high inputs in soils of both chili （63.1%） and black gram （47.1%）. Oligotrophs increased by 10.8% in black gram soils but not in chili soils. The abundance of amoA gene reduced by 39.3% in chili soils due to high inputs and increased significantly by 110.8% in black gram soils. β-Glucosidase also increased by 27.2% and 325.0%, respectively. Acid phosphatase activity reduced by 29.2% due to high inputs in chili soils and increased by 105.0% in black gram soils. The use of high agrochemical inputs thus had adverse consequences on biological health in chili but not in black gram soils. In soils cultivated with black gram, the moderating effect of cultivating legumes and their beneficial effect on soil health were evident from the increase in soil labile carbon, lower qMLc, higher amoA gene and enzyme activities. Overall results showed that cultivation of legumes permits intensive chemical farming without deteriorating soil biological health.

Environmental similarity is more important than distance in the community structuring processes of ammonia-oxidizing archaea in agricultural soils

Ammonia-oxidizing archaea(AOA) are important in converting ammonia into nitrate in soils. While many aspects of their community structure have been studied, the relative importance of stochastic versus deterministic processes has poorly been understood. We compared AOA communities across the North China Plain, targeting the amoA gene. A phylogenetic null modelling approach was used to calculate the beta nearest taxon index to quantify the influence of stochastic and deterministic processes. We found that spatial distance between samples predicted the perceived processes involved in community structuring, with stochastic processes dominating at local scales. At greater distances, stochasticity became weaker. However, soil pH, which was also the strongest determinant of AOA community, was a much stronger predictor of community structuring, leaving the distance effect redundant as an explanation of community structuring processes. The communities of AOA differing by less than 1 pH unit differed mainly stochastically in terms of operational taxonomic unit composition. At larger pH differences, deterministic processes based on heterogeneous selection between clades became increasingly dominant. It appears that AOA community composition is largely determined by the environment. However, very similar pH environments are the exception. In environments with very close pH values, stochastic effects dominantly cause differences in community composition, whether spatially near or far.