南海北部不同深度的菌相與多樣性研究

Abstract

原核微生物是海洋中數量最多的生物，這些海洋原核微生物具有非常高的初級和次級生產力，對海洋甚至整個地球的元素循環扮演著重要的角色，因此為了了解這些微生物在海洋中的生態角色，探討海洋微生物群集的結構、分布和多樣性是很重要的基礎研究之一。目前大多數海洋原核微生物群集的研究集中於溫帶或寒帶海域表水或某一深度的調查，對內部的海洋微生物分布卻所知不多。相對地，西太平洋熱帶海域的海洋微生物群集研究極為缺乏，更遑論內部微生物群集。本研究即針對熱帶海洋內部微生物群集進行調查，以期能增加對於熱帶海洋內部微生物了解。 我們利用高輸出定序技術（massively-parallel pyrosequencing）對南海北部的海洋菌相與多樣性作了垂直剖面的調查。從四個不同深度（10、 100、 1000、 3000公尺）的樣本中，獲得38,704條源自於細菌的核糖體小次單元之高度變異區的基因序列（the V6 hypervariable region of 16S rRNA gene）以及5,269條的古菌序列。經比較分析發現：（1）細菌群集多樣性遠高於過去用傳統方法所估計。（2）四個深度中，細菌皆高於古菌多樣性。（3）表水和中水層的菌相較深海的菌相複雜。 除群集多樣性的分析外，在細菌組成的分析結果指出α-proteobacteria和γ- proteobacteria是南海各水層佔有最高比例的兩種菌群，而Cyanobacteria則是在表水層佔較高比例。β-proteobacteria菌群則在10m和100m的水層中佔有較高的比例；相反地，δ-proteobacteria菌群則是在越深的水樣中佔有越高的比例。在古菌組成分析結果，發現Euryarchaeota在南海淺層10m到3000m共四個深度的水樣中都是古菌群集中的最優勢菌群，這和其他海域的深海以Crenarchaeota菌群為主不同。 在獨特序列（即相同序列集結為一獨立序列單位）間數目比較和親緣相關分析結果顯示，發現這些序列的比例多寡和深度有關。針對相對佔多數的序列進行親源關係的分析發現除了發現有些序列（種類）具有廣深性（在各個深度的水樣中都佔不少比例），也發現不少菌群有「依深度分群」的現象，例如四個分支的Oceanospirillales中，有兩個分支都是在3000m佔最高比例，其他三個深度都很少；另一支則屬於淺層序列的分支，以及第四分支的序列則在中間兩個水層（100m和1000m）的較多。另外Alteromonadales、Pseudomonadales、marine euryarchaeota group II 和 marine euryarchaeota group III的序列也都有「依深度分群」的現象，這些結果顯示在南海北部的原核生物分布具有生物地理區隔的特徵。 我們的結果是目前熱帶海域的微生物多樣性中最完整的研究資料，可對南海微生物群集在垂直分布及組成有更深入的了解。

Prokaryotic microbes are the largest population in oceans; they are evidently responsible for the major primary and secondary productions and, as a result, play a key role in significant element cycles in marine ecosystems and even global. However, the ecology, such as composition, distribution and diversity, of these microbes are still mainly unknown. To date, most of the studies of the marine prokaryotic community are only focused on the surface water or a certain depth in the mesopelagic zone of the polar or temperate oceans. Hence, the goal of this study is to survey the composition and diversity of the stratified microbial assemblages in the interior of the western tropical Pacific Ocean. We anticipate to extending the current understanding for the marine community in tropical water through this study. By adopting a massively-parallel pyrosequencing strategy, we performed analyses of the diversity and composition of planktonic microbial communities isolated from the northern South China Sea (SCS; 18°15' N, 115°30' E), from the ocean’s surface to near the sea bottom. Through examining 38,704 bacterial and 5,269 archaeal V6 amplicons of 16S ribosomal RNA genes, we observed several findings, including that (1) the bacterial diversity in northern SCS is greater than previous estimates based on conventional methods; (2) the bacterial community in the bathypelagic layer is less diverse than that in other three upper layers; (3) our data show the less diversity of the archaeal communities compared to the bacterial communities in four depths. In the composition analysis, our results show that the most abundant bacterial groups at four depths in the northern SCS are α- and γ- proteobacteria, while Cyanobacteria is mainly found from the sea surface. β-proteobacteria is more abundant in the euphotic zone than in the aphotic zone; in contrast to β-proteobacteria, the relative abundance of sequences from δ-proteobacteria increases with increasing depth in northern SCS. Moreover, we revealed unique assemblages of Archaea in the northern SCS, with Euryarchaeota dominating throughout the water column, which is contrast to most of previous studies reported that Crenarchaeota are more abundant than Euryarchaeota in the deep sea. Furthermore, our results of profiles of the unique sequences show the presences of depth-specific inhabiting groups. Through the phylogenetic analysis of the dominant unique sequences, we observed many eurybathyal sequences (i.e., those sequences were detected in four depths) and the depth-related subdivision in many groups. For example, at least four clades are found in the phylogenetic tree of Oceanospirillales V6 sequences, and sequences in two clades are represented at the highest frequencies in the greast depth; one is the mainly upper layers clade, while sequences in the other one clade are highly abundant in the middle two layers. The depth-related subdivision was observed in other groups, including Alteromonadales, Pseudomonadales, and the marine euryarchaeota groups II and III, indicating biogeographical traits for prokaryotic communities exist in the norther SCS. Our work presents the most comprehensive examination of microbial diversity in the tropical ocean and provides a significant insight into the marine microbial community structures along the vertical profiles in the SCS.