Biodiversity and Ecosystem Functioning in Transitional Waters; the Point of View of a Microbial Ecologist Rutger De Wit

Transitional Waters Bulletin TWB, Transit. Waters Bull. 1(2007), 3-16 ISSN 1825-229X, DOI 10.1285/i1825226Xv1n1p3 http://siba2.unile.it/ese/twb Biodiversity and Ecosystem Functioning in Transitional Waters; the point of view of a microbial ecologist Rutger De Wit UMR 5119 CNRS-Université Montpellier II "Ecosystèmes lagunaires" Université Montpellier II, Case 093, Place Eugène Bataillon F-34095 Montpellier Cedex 05, RESEARCH ARTICLE France Email: [email protected] Abstract 1 - The study of biodiversity of prokaryotes in transitional waters is hampered by the fact that we do not posses any comprehensive inventories of prokaryotic species. Microbial biodiversity is thus often estimated indirectly by extraction of nucleic acids from the natural environment and by using 16S ribosomal RNA gene sequences as phylogenetic and taxonomic markers. Experimental microbial ecology has contributed over the years to developing niche-assembly theories of community assemblage and I review some of their major findings. Finally, the aim of establishing a link between biodiversity and ecosystem functioning is quite recent and has prompted a novel experimental approach that can be applied in microbial ecology. The following observations have been forwarded. 2 - The species richness for prokaryotes is difficult to assess in transitional waters, because of an unclearly defined species concept and because the Bacteriological Code requires living cultures as type strains for taxonomic descriptions; therefore, the number of validly described prokaryote species is still very limited (i.e. currently less than 10,000). 3 - The major emphasis on niche assembly theories in microbial ecology is a consequence of the paradigm “everything is everywhere, but the environment selects” quoted by Baas Becking in 1934. Hence, insights on how competition mechanisms can contribute to sustaining microbial biodiversity in relatively homogeneous model systems have tremendously increased during the last decade. Nevertheless, I argue that coastal lagoons and other transitional waters are environments characterised by strong exchanges with adjacent local microbial communities, where community assemblage may be strongly impacted by dispersal processes. 4 - The study of biodiversity and ecosystem functioning is based on quantifying a process rate or a yield (the ecosystem function) as a function of a manipulated biodiversity in an artificial community. A positive relation between biodiversity and ecosystem function has been explained by 1) sampling effect (i.e. a higher biodiversity correlates with a higher chance of providing a home for the most productive species), 2) more efficient resource exploitation for species showing complementary niche differentiation. I argue that synergistic phenomena due to positive interactions among species may also play an important role. Keywords: coastal lagoon, microbial biodiversity, resource ratio theory, dispersal, positive interaction including lagoons. Many of such records have Introduction been provided by dedicated professional and Providing a home for biodiversity is an amateur field biologists. As a result, the important ecosystem service of coastal lagoons. accessibility and quality of such data bases are A long tradition of natural history studies has extremely variable between sites and between provided data bases of the species richness of historical periods, as they depend on the macro-organisms in many coastal ecosystems taxonomic interest and knowledge of these field © 2006 University of Lecce - SIBA http://siba2.unile.it/ese TWB 1 (2007) De Wit observers and on the extent and frequency of 1030 nm). Therefore, prokaryotes play pivotal their field work as well as on the quality of the roles in all biogeochemical cycles and their archive. Web-based publications of such data activities are paramount for the functioning of bases are now being prepared for different coastal lagoon ecosystems. An example of a ecosystems and the data base held by the collaborative study of coastal lagoons where Hellenic Network on Research in Transitional microbial processes received strong attention Ecosystems is a good example for lagoon was the EU project entitled “ROle of BUffering ecosystems (http://www.medobis.org/dbase- capacities in STabilising coastal lagoon elnet/). In some cases detailed accounts do exist ecosystems”, in which it was found that for microscopic organisms such as microalgae prokaryotes are major actors in providing and cyanobacteria and to a lesser extent for the buffering capacities in coastal lagoons (De Wit microscopic protozoa, as these have been et al., 2001). This research project paid some described by their morphological features using attention to microbial biodiversity (e.g. microscopy (e.g. Krammer and Lange-Bertalot, Cifuentes et al., 2000, 2003), but more 1986-1988-1991; Geitler, 1932). In many frequently the microbial compartment has been countries, systematic surveys and monitoring of studied as a black box, as is common in many phytoplankton species in coastal waters based biogeochemical studies in coastal environments. on light microscopy have been implemented, The study of microbial diversity in natural because they can be used as indicators for water environments is still in its infancy and in this quality and because of the need for providing paper I will discuss some of the major problems alarm systems for harmful algal blooms and challenges in this developing field. Because (Gailhard et al. 2002). In contrast, we do not microbial ecology has typically been linked to posses any comprehensive, detailed and reliable general microbiology and to biogeochemistry, species lists and inventories of prokaryotes in this discipline has developed into a different coastal lagoons. Even the estimations of the branch with too little interaction with actual number of species in a given marine mainstream ecology. Nevertheless, traditionally, environment are vague and subject to experimental microbial ecology has contributed controversies (Hong et al., 2006). to developing niche concepts and increased our Bacteria and Archaea are prokaryotes as understanding of ecological interactions opposed to eukaryotes, which also include between species. By using model organisms, microbes such as microalgae and protozoa. In this discipline has drawn advantages from the addition, there are the viruses, which are very small size and short generation times of micro- important in natural environments. However, organisms. Thus, it has been possible to test the the viruses are not self-replicating as they outcome of ecological interactions in depend on a host organism for replication of communities comprising billions of individuals genetic material and reproduction. Therefore, I for the long term (tens to hundreds of have not included the viruses in my analyses of generations) and, for example, to test the microbial diversity. While most of the principle of competitive exclusion (Hardin, prokaryotic forms of life are small and 1960). I briefly review the major findings of morphologically rather simple, they comprise an these studies and discuss their relevance for extremely wide spectrum of metabolic options. understanding biodiversity. In a world that is These include aerobic and anaerobic increasingly impacted by humans and faces metabolisms and encompass capabilities to important biodiversity losses, the question of synthesise and degrade the largest spectrum of how biodiversity impacts ecosystem functioning organic compounds, to perform redox is urgent. This calls for developing a novel conversions of a large number of inorganic research approach using experimental systems minerals, and to harvest light for photosynthesis with a manipulated biodiversity. Some good from a wide light spectrum, i.e. from ultraviolet studies are now available for microbes, which UV A (370 nm) into the near infrared (up to will be discussed. Finally I will conclude and © 2006 University of Lecce - SIBA http://siba2.unile.it/ese 4 TWB 1 (2007) Biodiversity and Ecosystem Functioning in Transitional Waters focus on the importance of understanding (1991) is not appropriate. Hence, a phylogenetic biodiversity and ecosystem functioning in concept of species seems more appropriate for coastal lagoons and other transitional waters. prokaryotes (Ogunseitan, 2004), although in practice prokaryotic taxonomy currently uses a combination of genomic and phenotypic data Describing microbial biodiversity (phylophenetic concept). Accordingly, the The taxonomy of prokaryotes is governed by the prokaryotic species should ideally be described Bacteriological Code (i.e. International Code of as “a category that circumscribes a genomically Nomenclature of Bacteria, 1990 revision; coherent group of individual isolates/strains Lapage et al., 1992), which refers to living type sharing a high degree of similarity in many strains and uses many physiological features as independent features comparatively tested under diacritic criteria in the determination of highly standardised conditions” (Oren, 2004). bacterial species. This is entirely different from Relevant genomic properties include the botanic systematics, which is based on dried and nucleotide base ratio in DNA (expressed as the dead specimens stored as type taxa in a molar % of guanine plus cytosine, i.e., G+C), herbarium. Hence, identification of bacteria is DNA-DNA hybridisation and the sequence of mainly dependent on cultivation techniques. selected phylogenetic markers, which There are, however, some

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