View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Springer - Publisher Connector SCIENCE CHINA Life Sciences • REVIEWS • January 2011 Vol.54 No.1: 75–81 doi: 10.1007/s11427-010-4103-4 Metagenome-based analysis: A promising direction for plankton ecological studies YAN QingYun & YU YuHe* Key Laboratory of Biodiversity and Conservation of Aquatic Organisms, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China Received September 9, 2010; accepted October 14, 2010; published online November 19, 2010 The plankton community plays an especially important role in the functioning of aquatic ecosystems and also in biogeochemi- cal cycles. Since the beginning of marine research expeditions in the 1870s, an enormous number of planktonic organisms have been described and studied. Plankton investigation has become one of the most important areas of aquatic ecological study, as well as a crucial component of aquatic environmental evaluation. Nonetheless, traditional investigations have mainly focused on morphospecies composition, abundances and dynamics, which primarily depend on morphological identification and counting under microscopes. However, for many species/groups, with few readily observable characteristics, morphologi- cal identification and counting have historically been a difficult task. Over the past decades, microbiologists have endeavored to apply and extend molecular techniques to address questions in microbial ecology. These culture-independent studies have generated new insights into microbial ecology. One such strategy, metagenome-based analysis, has also proved to be a power- ful tool for plankton research. This mini-review presents a brief history of plankton research using morphological and metage- nome-based approaches and the potential applications and further directions of metagenomic analyses in plankton ecological studies are discussed. The use of metagenome-based approaches for plankton ecological study in aquatic ecosystems is en- couraged. metagenome, plankton community, morphospecies, molecular microbial ecology Citation: Yan Q Y, Yu Y H. Metagenome-based analysis: A promising direction for plankton ecological studies. Sci China Life Sci, 2011, 54: 75–81, doi: 10.1007/s11427-010-4103-4 Plankton, the key structural and functional component of retical studies concerning plankton composition, abundance, aquatic ecosystems, is generally considered to be composed biomass and activities. However, traditional plankton eco- of both producers (phytoplankton) and consumers (zoo- logical studies have largely depended upon morphological plankton), but also includes bacterial decomposers (bacte- methods and morphological identification has historically rioplankton) [1]. Therefore, it plays important roles in been a difficult task because of the small size of organisms aquatic biogeochemical cycles [2]. Plankton investigation and the paucity of readily observable characteristics of taxo- has been a major area of ecological study since the very nomic value [3]. Therefore, independent investigations may start of marine research expeditions (e.g., Challenger Expe- get different results from the same samples; sometimes with dition, 1872–1876; German Plankton Expedition, 1889). significant discrepancy. In addition, different groups of The increasing awareness of their roles in the ecosystem has phytoplankton and zooplankton have always been investi- led to a rapid growth in descriptive, experimental and theo- gated separately and bacterioplankton was often excluded from morphological investigations because of the difficul- ties in identification. These factors and others have made it *Corresponding author (email: [email protected]) © The Author(s) 2011. This article is published with open access at Springerlink.com life.scichina.com www.springer.com/scp 76 Yan Q Y, et al. Sci China Life Sci January (2011) Vol.54 No.1 difficult to reach higher-order ecological conclusions about investigation, numerous planktonic species had been de- general plankton trends and patterns. scribed and more and more new species were reported. Morphological approaches can only provide a few clues During this period, interests in plankton research also ex- for identification and related functional studies of most mi- tended to the relationships between community structure and crobes. The need for nontraditional techniques to reveal the the environment. This led directly to the ecological aspects of microbial world was highlighted in 1986 [4]. One year ear- the field. Furthermore, Victor Hensen applied the quantitative lier Pace et al. [5] had proposed the idea of cloning DNA methods to gauge the distribution, abundance and productiv- directly from environmental samples and the first such clone ity of the microscopic plankton in the open sea [22]. library was reported in 1991 [6]. Since then, natural microor- ganisms collected from different environments have been 1.2 Limitations of traditional plankton investigations investigated at the DNA level and progress has been made in microbial ecology and environmental microbiology [7]. In As the basis of biodiversity, species diversity was the first 1998, a professional term ‘metagenomics’ was coined [8] to to be investigated and attracted the attention of many tax- describe natural habitat based microbial investigations, onomists and ecologists. A large number of species diver- which provided powerful tools to extract valuable biological sity indices have been proposed [23,24]. However, the information quickly and effectively from complex environ- mechanisms regulating diversity in most systems are not ments [7,9]. For plankton research, Giovannoni et al. [10] completely understood [25], and questions of how to deter- were the first to phylogenetically analyze clone libraries of mine the real diversity of plankton communities and to ex- 16S rRNA genes from a natural bacterioplankton commu- plore the potential ecological functions present tremendous nity. To date, large numbers of metagenome-based studies challenges. These challenges not only include the need for on bacterioplankton and more recently on eukaryotic pi- extensive taxonomic identification, but also problems of coplankton have been undertaken (e.g., [11–14]). Targeting how to compare and summarize related studies to generate the plankton community as a system, Yan et al. [15–18] and higher-order ecological conclusions. Since the very start of Yu et al. [19] currently applied fingerprinting techniques to plankton ecological investigation in the 1870s, plankton investigate the relationships between DNA polymorphisms research has largely depended upon traditional morphologi- and species composition of plankton communities in dif- cal methods. However, morphological classification of ferent habitats and environments (i.e., lakes, rivers, reser- planktonic organisms has historically been a difficult task voirs, ponds, enclosures, and artificial systems). As com- (even for a seasoned taxonomist) because of the lack of dis- munity composition is largely dictated by environmental tinguishing features, especially for the multitudes of minute, factors, it has been a natural extension of this relationship to nondescript organisms. Furthermore, planktonic bacteria use plankton community fingerprints as an indication of and some small phytoplankton cannot be classified to the environmental conditions [17–21]. In contrast to traditional species level or even to the genus level using morphological morphological analyses in ecological study, multiple sam- methods alone. Therefore, it is not so much a lack of ideas ples can be analyzed simultaneously with standardized sets but inadequate methodologies and instruments that have of metagenome-based procedures, which make it practical limited progress in understanding of the diversity of plank- to perform comparative analyses aimed at elucidating gen- ton. Despite more than 100 years for plankton research, our eral microbial ecological rules. Moreover, by comparing knowledge of plankton diversity and its roles in the natural target genes’ expression under different environments, environment has only increased modestly. Therefore, more community functions can be explored using function-based powerful techniques are urgently needed to reveal their di- metagenomics. versity and explore their ecological functions in ecosystems. Fortunately, recent technical developments in molecular biology have found extensive applications in the field of 1 Morphospecies-based plankton investigation studying natural community ecology [26–28]. 1.1 A brief history of early plankton research 2 Metagenome-based plankton study The term ‘plankton’ was coined by the famous plankton ecologist Victor Hensen in 1887, but plankton research can 2.1 Metagenome be traced back to when Antonie van Leeuwenhoek observed ‘small infusoria’ with his own microscope. Johannes Müller The term ‘metagenome’ was first introduced to describe the pioneered the systematic study of small planktonic organ- combined genomes of natural microbes in the soil environ- isms with hand-held nets in the 1840s [22]. The interests of ment [8]. Since then, microbial communities from diverse plankton research initially focused on naming and classify- niches (including oceans, lakes, soils, thermal vents, hot ing the species according to their morphological character- springs, the mouth and gastrointestinal tract) have been in- istics (i.e., morphospecies). After a period of taxonomic volved in metagenome-based