pH对水稻土全程氨氧化细菌丰度和群落结构组成影响

Effect of pH on the Abundance and Community Structure of Comammox Nitrospira in Paddy Soils

土壤pH被认为是影响AOA和AOB生态位分化的重要因子,而最近发现的全程氨氧化细菌(Comammox Nitrospira)也在土壤中广泛分布,推测pH可能也是影响全程氨氧化细菌生态位分化的重要因子.选取酸性红壤和中性紫色土发育的水稻土,采用荧光定量PCR及克隆测序技术,分析了全程氨氧化细菌Comammox Nitrospira clade A和clade B的丰度和群落组成.结果表明,酸性水稻土的Comammox clade A amoA基因的丰度比中性水稻土高了2个数量级(P<0.05),酸性水稻土的Comammox clade B的丰度也显著高于中性水稻土(P<0.05);酸性水稻土中Comammox clade A amoA基因的丰度比clade B高60倍,而中性水稻土中Comammox clade A和clade B amoA基因的丰度比约为2,这些结果表明土壤pH是影响Comammox Nitrospira丰度的重要因子.克隆测序的结果发现中性水稻土中的Comammox均属于clade A,主要隶属于Nitrospira inopinata类群;而未能检测到属于clade B的序列.酸性水稻土中的Comammox clade A主要由Nitrospira inopinata和Nitrospira nitrosa类群组成,clade B主要与土壤中发现的未培养的细菌克隆(FN395328)密切相关,结果表明Comammox Nitrospira的群落结构也受pH的显著影响.综上,pH对土壤全程氨氧化细菌的丰度及群落结构组成有显著影响,是影响其生态位分化的重要环境因子之一.

Soil pH is recognized as an important environmental factor in determining the niche differentiation for ammonia-oxidizing bacteria(AOB)and ammonia-oxidizing archaea(AOA)communities.Species of comammox,a single microorganism capable of the complete oxidation of ammonia to nitrate,have recently been discovered.Metagenomic analysis and quantitative PCR showed that Comammox Nitrospira were found in a wide range of environments,including soil.Comammox bacteria are differentiated into one of two clades(A and B)based on the phylogeny of genes encoding theα-subunit of ammonia monooxygenase genes(amoA).However,all discovered Comammox Nitrospira strains have been isolated and cultured in aquatic ecosystems,including N.inopinata,N.nitrosa,and N.nitrificans,all belonging to clade A.Currently,Comammox Nitrospira has not been obtained from soil environments,which limits our understanding of soil Comammox Nitrospira.Here we hypothesized that,as AOA and AOB,the ecological site of Comammox Nitrospira may also be affected by pH.Therefore,soil samples with differing pH were collected,and the abundances and community structures were studied to elucidate the mechanism of pH effect on the distributions and community compositions of Comammox Nitrospira in soil.Quantitative PCR of comammox clade A and clade B amoA genes in DNA extracts were performed using QuantStudio TM6 Flex Real-Time PCR Systems.The community compositions for Comammox Nitrospira were studied by the cloning libraries of amoA genes method.The results showed that the abundance of Comammox clade A amoA gene in acidic paddy soil was two orders of magnitude higher than that in neutral paddy soil(P<0.05),and the abundance of Comammox clade B in acidic paddy soil was significantly higher than that in neutral paddy soil(P<0.05);the abundance of Comammox clade A amoA gene in acidic paddy soil was 60 times higher than that of clade B,whereas the abundance ratio of Comammox clade A and clade B amoA genes in neutral paddy soil was about two times higher.These results indicated that soil pH significantly affected the abundance of Comammox Nitrospira.The results of cloning and sequencing showed that the Comammox in neutral paddy soil was mainly N.inopinata,which belonged to clade A;no strain belonging to clade B was annotated.Comammox clade A in acidic paddy soil was mainly Composed of N.inopinata and N.nitrosa,and clade B was mainly uncultured bacterium(FN395328).The results indicated that soil pH was an important factor in shaping Comammox Nitrospira community structure.Comammox Nitrospira were detected in all soil samples,and Comammox clade A had a preference for acidic environments.It seemed that species from N.nitrosa possessed the ecological niche of low pH environments,whereas species from N.inopinata preferred to live in neutral environments.In conclusion,pH had a significant effect on the abundance and community structure of Comammox Nitrospira,which was one of the important factors affecting the niche differentiation of Comammox Nitrospira.