Kumari Priyanka, Choi Hong L, Sudiarto Sartika I A
Department of Agricultural Biotechnology, Research Institute for Agriculture and Life Science, Seoul National University, Gwanak, Seoul, 151-921, Republic of Korea.
Department of Agricultural Biotechnology, Research Institute for Agriculture and Life Science, Seoul National University, Gwanak, Seoul, 151-921, Republic of Korea; Resourcification Research Center for Crop-Animal Farming (ReCAF), Gwanak, Seoul, Republic of Korea.
PLoS One. 2015 Sep 30;10(9):e0139437. doi: 10.1371/journal.pone.0139437. eCollection 2015.
The bacterial community assembly patterns and processes are poorly understood in pig manure slurry. We collected pig manure slurry samples during the winter and summer seasons from eight commercial pig farms in South Korea. The V3 region of 16S rRNA genes was PCR amplified and sequenced using paired-end Illumina technology for in-depth characterization of bacterial community. Firmicutes, Bacteroidetes, Proteobacteria, Spirochaetes, and Tenericutes were the predominant bacterial phyla present in slurry samples. Bacterial taxonomic community composition was not influenced by the season; however, phylogenetic community composition was affected by seasonal variations. The community composition and diversity patterns were strongly influenced by pH. The bacterial diversity indices showed a unimodal relationship with pH. Phylogenetic signals were detected over only short phylogenetic distances, revealing that closely related bacterial operational taxonomic units (OTUs) tend to co-occur in the same environment; hence, they are ecologically similar. Across all samples, a niche-based process, through strong environmental filtering imposed by pH, primarily governed bacterial community assembly; however, in samples close to the neutral pH range, the role of environmental filtering was decreased due to neutral community assembly. In summary, pH emerged as the major physico-chemical variable in pig manure slurry that regulates the relative importance of niche-based and neutral processes in shaping the community assembly of bacteria.
猪粪浆中细菌群落的组装模式和过程目前还知之甚少。我们在冬季和夏季从韩国的八个商业养猪场采集了猪粪浆样本。使用双端Illumina技术对16S rRNA基因的V3区域进行PCR扩增和测序，以深入表征细菌群落。厚壁菌门、拟杆菌门、变形菌门、螺旋体门和柔膜菌门是猪粪浆样本中占主导地位的细菌门。细菌分类群落组成不受季节影响；然而，系统发育群落组成受季节变化影响。群落组成和多样性模式受pH值的强烈影响。细菌多样性指数与pH值呈单峰关系。仅在较短的系统发育距离上检测到系统发育信号，这表明密切相关的细菌操作分类单元（OTU）倾向于在同一环境中共存；因此，它们在生态上相似。在所有样本中，基于生态位的过程，通过pH值施加的强烈环境过滤，主要控制细菌群落的组装；然而，在接近中性pH范围的样本中，由于中性群落组装，环境过滤的作用减弱。总之，pH值成为猪粪浆中的主要物理化学变量，它调节了基于生态位和中性过程在塑造细菌群落组装中的相对重要性。
