Assessment of Bacterial <i>bph</i> Gene in Amazonian Dark Earth and Their Adjacent Soils

Amazonian Anthrosols are known to harbour distinct and highly diverse microbial communities. As most of the current assessments of these communities are based on taxonomic profiles, the functional gene structure of these communities, such as those responsible for key steps in the carbon cycle, mostly remain elusive. To gain insights into the diversity of catabolic genes involved in the degradation of hydrocarbons in anthropogenic horizons, we analysed the bacterial bph gene community structure, composition and abundance using T-RFLP, 454-pyrosequencing and quantitative PCR essays, respectively. Soil samples were collected in two Brazilian Amazon Dark Earth (ADE) sites and at their corresponding non-anthropogenic adjacent soils (ADJ), under two different land use systems, secondary forest (SF) and manioc cultivation (M). Redundancy analysis of T-RFLP data revealed differences in bph gene structure according to both soil type and land use. Chemical properties of ADE soils, such as high organic carbon and organic matter, as well as effective cation exchange capacity and pH, were significantly correlated with the structure of bph communities. Also, the taxonomic affiliation of bph gene sequences revealed the segregation of community composition according to the soil type. Sequences at ADE sites were mostly affiliated to aromatic hydrocarbon degraders belonging to the genera Streptomyces, Sphingomonas, Rhodococcus, Mycobacterium, Conexibacter and Burkholderia. In both land use sites, shannon's diversity indices based on the bph gene data were higher in ADE than ADJ soils. Collectively, our findings provide evidence that specific properties in ADE soils shape the structure and composition of bph communities. These results provide a basis for further investigations focusing on the bio-exploration of novel enzymes with potential use in the biotechnology/biodegradation industry.亚马逊人为土（Amazonian Anthrosols）以其独特且高度多样的微生物群落而闻名。当前针对这类群落的多数评估均基于分类学谱，而其功能基因结构——例如参与碳循环关键步骤的功能基因——大多仍未得到充分解析。为深入探究人为发生层中参与烃类降解的分解代谢基因多样性，我们分别采用末端限制性片段长度多态性（Terminal Restriction Fragment Length Polymorphism，T-RFLP）、454焦磷酸测序与定量PCR实验，分析了细菌bph基因（bph gene）的群落结构、组成与丰度。我们在两处巴西亚马逊黑土（Amazonian Dark Earth，简称ADE）样地及其对应的非人为源毗邻土壤（ADJ）中采集了土壤样品，这些样地分别设置于两种不同的土地利用系统：次生林（SF）与木薯种植（M）。对T-RFLP数据的冗余分析显示，bph基因结构因土壤类型与土地利用方式的不同而存在显著差异。巴西亚马逊黑土的化学性质，如较高的有机碳与有机质含量、有效阳离子交换量及pH值，均与bph群落结构呈显著相关。此外，对bph基因序列的分类学归属分析显示，群落组成因土壤类型而发生分化。巴西亚马逊黑土样地中的序列大多归类于属于链霉菌属（Streptomyces）、鞘氨醇单胞菌属（Sphingomonas）、红球菌属（Rhodococcus）、分枝杆菌属（Mycobacterium）、锥杆菌属（Conexibacter）与伯克霍尔德菌属（Burkholderia）的芳烃降解菌。在两种土地利用系统中，基于bph基因数据计算得到的香农多样性指数均在巴西亚马逊黑土中高于对应的非人为源毗邻土壤。综合来看，我们的研究结果证实，巴西亚马逊黑土的特有属性塑造了bph群落的结构与组成。这些研究结果为后续针对具备生物技术与生物降解产业应用潜力的新型酶类的生物勘探研究提供了理论依据。