Marine Microbial Biofilm Ecology

Microorganism attachment to any newly submerged surface lays the foundation for all forthcoming waves of colonization. The initial recruitment of bacteria and archaea may help guide successive settlement events through subtle assemblage variances. The detection of these changes in microbial consortia from early to mature stages in marine biofilm growth can be achieved through the use of various DNA fingerprinting tools, namely TRFLP (termination restriction fragment length polymorphism) for archaea and ARISA (automated ribosomal intergenic spacer analysis) for bacteria. These techniques allow relatively rapid snapshot assessment of diversity with reasonable resolution, at least to the genus level. Rock and synthetic slides were suspended on an array just above the sediment surface, with an identical array mirrored ten meters above in the water column. For a comparative approach, water and sediment cores were also collected. DNA from slides at various time points, from a few days to several months out, was extracted and fingerprinted to determine microbial diversity. Our results show differences in assemblages from all four environmental compartments, with operational taxonomic units (OTU) unique and common to each. Temporal differences were also observed. Shared OTUs, across the four environments showed significant variation in peak intensities, whereas replicates within compartments showed a relatively high degree of similarity. These results in conjunction with our present cloning effort will enable identification of the dominant and many of the less dominant species at various stages of marine biofilm development.微生物附着于任何新浸没表面，是后续所有定植浪潮的基础。初始定植的细菌与古菌可通过群落组成的细微差异，调控后续的定殖过程。海洋生物膜生长从早期至成熟阶段的微生物群落组成变化，可通过多种DNA指纹技术进行检测：针对古菌采用TRFLP（末端限制性片段长度多态性，termination restriction fragment length polymorphism），针对细菌采用ARISA（自动化核糖体基因间隔区分析，automated ribosomal intergenic spacer analysis）。此类技术可在至少属级水平上，以合理的分辨率实现对多样性的快速快照式评估。研究人员将岩石载片与合成载片悬挂于沉积物表面上方的阵列中，同时在水柱中距其10米处设置完全相同的镜像阵列；为开展对照实验，还同步采集了水样与沉积物岩芯。对不同时间节点（数天至数月不等）的载片样本提取DNA并进行指纹图谱分析，以解析其微生物多样性。研究结果显示，四个环境分区的群落组成均存在差异，各分区均存在特有与共有的操作分类单元（OTU，operational taxonomic units），同时还观测到随时间变化的群落差异。四个环境中共有的OTU的峰强度存在显著差异，而同一环境分区内的重复样本则表现出较高的相似性。结合本次克隆实验的成果，将可实现对海洋生物膜发育不同阶段的优势物种及多数非优势物种的鉴定。