Schneider Dominik, Engelhaupt Martin, Allen Kara, Kurniawan Syahrul, Krashevska Valentyna, Heinemann Melanie, Nacke Heiko, Wijayanti Marini, Meryandini Anja, Corre Marife D, Scheu Stefan, Daniel Rolf
Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Germany.
Soil Science of Tropical and Subtropical Ecosystems, Buesgen Institute, Georg-August University Göttingen, Germany.
Front Microbiol. 2015 Dec 8;6:1339. doi: 10.3389/fmicb.2015.01339. eCollection 2015.
Prokaryotes are the most abundant and diverse group of microorganisms in soil and mediate virtually all biogeochemical cycles in terrestrial ecosystems. Thereby, they influence aboveground plant productivity and diversity. In this study, the impact of rainforest transformation to intensively managed cash crop systems on soil prokaryotic communities was investigated. The studied managed land use systems comprised rubber agroforests (jungle rubber), rubber plantations and oil palm plantations within two Indonesian landscapes Bukit Duabelas and Harapan. Soil prokaryotic community composition and diversity were assessed by pyrotag sequencing of bacterial and archaeal 16S rRNA genes. The curated dataset contained 16,413 bacterial and 1679 archaeal operational taxonomic units at species level (97% genetic identity). Analysis revealed changes in indigenous taxon-specific patterns of soil prokaryotic communities accompanying lowland rainforest transformation to jungle rubber, and intensively managed rubber and oil palm plantations. Distinct clustering of the rainforest soil communities indicated that these are different from the communities in the studied managed land use systems. The predominant bacterial taxa in all investigated soils were Acidobacteria, Actinobacteria, Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria. Overall, the bacterial community shifted from proteobacterial groups in rainforest soils to Acidobacteria in managed soils. The archaeal soil communities were mainly represented by Thaumarchaeota and Euryarchaeota. Members of the Terrestrial Group and South African Gold Mine Group 1 (Thaumarchaeota) dominated in the rainforest and members of Thermoplasmata in the managed land use systems. The alpha and beta diversity of the soil prokaryotic communities was higher in managed land use systems than in rainforest. In the case of bacteria, this was related to soil characteristics such as pH value, exchangeable Ca and Fe content, C to N ratio, and extractable P content. Archaeal community composition and diversity were correlated to pH value, exchangeable Fe content, water content, and total N. The distribution of bacterial and archaeal taxa involved in biological N cycle indicated functional shifts of the cycle during conversion of rainforest to plantations.
原核生物是土壤中数量最多、种类最丰富的微生物群体，几乎介导了陆地生态系统中的所有生物地球化学循环。因此，它们影响着地上植物的生产力和多样性。在本研究中，调查了雨林转变为集约管理的经济作物系统对土壤原核生物群落的影响。所研究的集约管理土地利用系统包括印度尼西亚布基杜阿贝拉斯和哈帕南两个地区的橡胶农林复合系统（丛林橡胶）、橡胶种植园和油棕种植园。通过对细菌和古菌16S rRNA基因进行焦磷酸测序来评估土壤原核生物群落组成和多样性。经过整理的数据集在物种水平（97%的基因同一性）上包含16413个细菌和1679个古菌操作分类单元。分析表明，随着低地雨林转变为丛林橡胶以及集约管理的橡胶和油棕种植园，土壤原核生物群落的本土分类群特异性模式发生了变化。雨林土壤群落的明显聚类表明它们与所研究的集约管理土地利用系统中的群落不同。所有被调查土壤中的主要细菌类群为酸杆菌门、放线菌门、α-变形菌纲、β-变形菌纲和γ-变形菌纲。总体而言，细菌群落从雨林土壤中的变形菌门类群转变为集约管理土壤中的酸杆菌门。古菌土壤群落主要由奇古菌门和广古菌门代表。陆地类群和南非金矿群1（奇古菌门）的成员在雨林中占主导地位，而嗜热栖热菌纲的成员在集约管理土地利用系统中占主导地位。集约管理土地利用系统中土壤原核生物群落的α多样性和β多样性高于雨林。就细菌而言，这与土壤特性有关，如pH值、可交换钙和铁含量、碳氮比以及可提取磷含量。古菌群落组成和多样性与pH值、可交换铁含量、含水量和总氮相关。参与生物固氮循环的细菌和古菌类群的分布表明，在雨林转变为种植园的过程中，该循环发生了功能转变。
