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Marine microbial diversity

27 K. S. Sobhana Marine , Central Marine Fisheries Research Institute, Kochi-682 018

Microbes were the only of for the first 2-3 billion and also based on iii) concentration of and required years of planetary and biological . Life most likely growth substances (Oligotrophic, Mesotrophic, Eutrophic). began in the oceans and marine are the However, interfaces tend to be hotspots of diversity and closest living descendants of the original forms of life. Early biological activity. Marine microbial at interfaces also helped create the conditions include the air-water, water-, water-ice, and under which subsequent life developed. More than two billion macroorganism-water interfaces. The sub-millimeter years ago, the generation of by photosynthetic marine scale of physical and chemical variability in these habitats microorganisms helped shape the chemical environment in poses a serious challenge to studying interface habitats in which , , and all other life forms have evolved. detail. The fact that variations can even occur within a few Macroscopic life and planetary habitability completely millimetres, suggests that microbial diversity encompasses depend upon the transformations mediated by complex more than the documented evidence available. Hence, microbial communities. These microscopic factories both is gaining importance as a field of study from aerobic and anaerobic are the essential catalysts for all of the microbial diversity point of interest. Due to the innately chemical reactions within the biogeochemical cycles. Their small size of the microorganisms, environmental complexity unique allow marine microbes to carry out many plays a major role in determining diversity. Spatial steps of the biogeochemical cycles that other are heterogeneity is likely to lead to the formation of many unable to complete. The smooth functioning of these cycles is niches within a . Recent tools like necessary for life to continue on . aid in biogeography studies by providing information on sequence data, thereby directly identifying Microbial life in the sea is extremely diverse, including microorganisms. Therefore the phylogenetic information members of all three domains of life (, and can be used to compare microbial diversity profile across eukarya) as well as (most authorities do not consider habitats. Generally, diversity within a particular location viruses as living organisms). The members of these groups and in a is called alpha diversity. Beta diversity or taxa are distinct in terms of their morphology, measures the community composition between two or and phylogeny and fall into both prokaryotic and eukaryotic more locations while gamma diversity applies to a region, domains. Considering the adaptability of microorganisms to across continents and biomes and is larger in size than that grow and survive under varied physico-chemical conditions used for measuring alpha diversity. and their contribution in maintaining the balance in , it is pertinent to catalogue their diversity as it Although microbial diversity is one of the difficult areas exists. The inability to visualize them with the naked eye of marine biodiversity research, estimation of microbial precludes effective classification. diversity is required for understanding the biogeography, community assembly and ecological processes. The number The diversity of microbial communities varies within habitats of has been a traditional measure of biodiversity as much as between habitats. Marine microbial habitats in and conservation, but the biodiversity of an can be classified based on i) presence of other organisms area is much more than the ‘’. Diversity (Symbiotic, Free living and ); ii) proximity to ocean prediction can be made using statistical approaches that surface or (Euphotic: 0-150 m; Mesopelagic: 150 estimate species number from relatively small sample – 1000 m; Bathopelagic : >1000m; : sediments) sizes. Hughes et al. (2001) noted that both rarefaction and

Summer School on Recent Advances in Marine Biodiversity Conservation and Management 190 K. S. Sobhana richness estimators which have been applied to microbial Since 99% of the microbial population is considered to be datasets, highlighted the utility of nonparametric estimators uncultivable, metagenomics assumes importance. Molecular in predicting and comparing bacterial species number. techniques have identified SAR11 as a dominant in Rarefaction and richness estimators rely on a species or communities of ocean-surface . Bacteria in operational taxonomic unit (OTU) definition. The limitations the SAR11 clade (Pelagibacteraceae) make up roughly one in of this method are that OTUs are counted equivalently three cells at the ocean’s surface. Overall, SAR11 bacteria are despite the fact that some may be highly divergent and estimated to make up between a quarter and a half of all phylogenetically unique, whereas others may be closely prokaryotic cells in the ocean. SAR11 bacteria are classified as related and phylogenetically redundant. Recently, statistical , and include the highly abundant marine analyses borrowed from population and species Candidatus Pelagibacter ubique. have been employed and reviewed for use with microbial datasets to estimate species richness and phylogenetic Sequence information (eg. 16S rRNA sequences, diversity which do not rely on estimation of the frequency of sequences, metagenomes) as well as rRNA targeted probes different sequences (Martin, 2001). Reciprocal of Simpson’s (eg. Fluorescent In Situ Hybridization – FISH, which allows a index (1/D), F-statistics (FST) and phylogenetic grouping visual inspection of phylogenetic groups of cells in a natural of taxa (P tests) may be used as a measure of diversity, sample) have helped to discover many new groups of bacteria. which has been widely used for ecological studies (Stach Marine microbial ranging from the study of the et al., 2003). These combined uses of species richness and of model organisms to the wealth of meta- diversity estimates provide information that enables deeper approaches (e.g. metagenomics, and understanding of marine microbial diversity. ) has proven to be very successful to target the second basic ecological question on the role of microbes in During the past two decades, molecular studies using the marine environment. Advanced technologies, developed the sequences that encode the small subunit rRNA in the recent past, promise to revolutionise the way that we (SSU rDNA) have revealed a wealth of new marine characterize, identify, and study microbial communities. The microorganisms that belong to the three domains of life most advanced tools that microbial ecologists can use for the viz., bacteria, archaea and the eukarya. The feeling among study of microbial communities include innovative microbial marine microbiologists is that of living through an age of ecological DNA microarrays such as PhyloChip and GeoChip discovery with no end in sight. However, most of this new that have been developed for investigating the composition diversity has not yet been described because pure cultures and function of microbial communities. Single Genomics of the organisms behind the sequences are necessary to approach, which can be used for obtaining genomes from define a species. Recent studies of microbial diversity have uncultured phyla, enables the amplification and produced spectacular discoveries of previously unknown of DNA from single cells obtained directly from environmental microorganisms, many of which have major impacts on samples and is promising to revolutionise . oceanic processes. Very large populations of including , , picoflagellates and Microbial are the primary catalysts in fixation, Currently, a polyphasic approach is used to define a microbial which orchestrate the cycling of and form the base species using phenotypic and genotypic properties. Whenever of the traditional marine . Heterotrophic SAR11 a new taxon is proposed, it is essential that the represents the dominant clade in communities of ocean- be isolated in pure culture and its characteristic features be surface bacterioplankton while nonphotosynthetic tested under standard conditions. All the strains within a of unknown diversity control the size of picoplankton species must show similar phenotypes. A designated type populations and regulate the supply of nutrients into the strain of a species constitutes the reference specimen for that ocean’s food webs. Communities of Bacteria, Archaea, and species. If the 16S rDNA sequences of organisms are ≤ 98.5% Protists account for greater than 90% of oceanic identical, they are members of different species. Uncultured and 98% of . Archaea includes unusual microbes cannot be assigned to a definite species since their microorganisms which grow under extreme environments phenotype is not known; however, they can be assigned a and differs from bacteria due to lack of . Both ‘Candidatus’ designation provided their 16S rRNA sequence these domains collectively play a significant role in the subscribes to the principles of identity with known species. marine environment. A concept applying to a taxon lower than that of the strain is the – those microorganisms that occupy an ecological Modern technologies (molecular techniques and automated niche and are adapted to the conditions of that niche fluorescence cell sorting) have demonstrated the great and diversity of microbial life forms in the Numerical Taxonomy oceans, and DNA sequencing of environmental genomes In numerical taxonomy many (50 to 200) biochemical, (metagenomics) provides evidence of hitherto unrecognized morphological, and cultural characteristics, as well as physiological categories among the planktonic microbes. susceptibilities to antibiotics and inorganic compounds, are

16 February - 8 March 2015 Central Marine Fisheries Research Institute 191 Marine microbial diversity used to determine the degree of similarity between organisms. bacteria. Bacteria feed primarily on dead organic material. The coefficient of similarity or percentage of similarity Some bacteria, however, are photosynthetic (cyanobacteria). between strains (where strain indicates a single isolate from Because of their size, cyanobacteria are believed to be the a specimen) is then calculated. A dendrogram or a similarity most abundant photosynthetic organisms in the ocean. In matrix is constructed that joins individual strains into groups addition to being free-living, some bacteria have evolved to and places one group with other groups on the basis of their live in close association with other marine organisms. Many percentage of similarity. While 16S rDNA sequences have of the found in eukaryotic organisms evolved from attracted attention in recent times as sole means of bringing . Examples of symbiotic bacteria include out the uniqueness of a species; numerical taxonomy (based those involved in the of wood by shipworms, on phenotypic traits of a large number of species) compares those responsible for and those found in favourably with that of genotypic data and, indeed, is in association with mussels, clams and tubeworms that live alignment with the modern taxonomy around hydrothermal vents. Most organic matter in oceans is decomposed by bacteria. Polyphasic taxonomy Nutritional types In polyphasic approach of microbial taxonomy, phenotypic, genotypic and phylogenetic information • Photosynthetic Cyanobacteria (blue-green bacteria): are described as accurately as possible. The phenotypic Photosynthetic bacteria which are found in environments information comes from the characteristics, cell high in dissolved oxygen, and produce free oxygen, type, -type, pigmentation patterns, store excess photosynthetic products as cyanophycean and other chemotaxonomic markers while genotypic starch and oils. primary photosynthetic pigments in features are derived from the nucleic acids (DNA/RNA). cyanobacteria are a and chlorophyll b , Phylogenetic information is obtained from studying accessory pigments include carotenoids and phycobilins. sequence similarities of the 16S rRNA or 23S rRNA • Other photosynthetic bacteria : Anaerobic green and in case of bacteria and 18S rRNA in case of fungi. purple sulfur and non-sulfur bacteria do not produce Many types of are used for delineating and oxygen and the primary photosynthetic pigments describing a taxon; some are mandatory (16S rRNA genes, are . Sulfur bacteria are obligate phenotypes, ) while others are optional anaerobes (tolerating no oxygen) while non-sulfur (amino-acid sequencing of certain products, bacteria are facultative anaerobes (respiring in low oxygen DNA-DNA hybridization), unless required for appropriate or in the dark and photosynthesizing anaerobically in the description. DNA barcoding approach is gaining presence of light). popularity for assessing microbial diversity. Though only • Chemosynthetic bacteria : Use energy derived from limited datasets (especially for eukaryotic microbes) are chemical reactions that involve substances such as currently available, the scenario is improving due to , sulfides and elemental sulfur, nitrites, faster and cheaper sequencing methods. , and ferrous ion. is less efficient than , so rates of and Marine microbes under the three domains division are slower. Found around hydrothermal vents of life and some shallower habitats where needed materials are Bacteria available in abundance. • Heterotrophic bacteria: that obtain energy Bacteria ( Bacteria) appear to have branched out very and materials from organic matter in their surroundings early on the tree of life and are genetically distinct from archaea and return many chemicals to the marine environment (Domain Archaea) and (Domain Eukarya). Bacteria through respiration and fermentation. Heterotrophic are abundant in all parts of the ocean and are vital to life on bacteria populate the surface of organic particles earth because they ensure the recycling of essential nutrients suspended in the water by secreting mucilage (glue-like in oceanic food webs. Although bacteria have such a key role substance) in sustaining basic functions in the marine environment, very Nitrogen fixation and nitrification little is known about their biology since only a small fraction (average 1%) can be cultured under laboratory conditions. • Nitrogen fixation: Process that converts molecular This is even more evident when considering that >80% of nitrogen dissolved in seawater to ammonium ion, a all bacterial isolates from marine environment belong to four major process that adds new usable nitrogen to the : the , , , sea. Only some cyanobacteria and a few archaeons with and . nitrogenase () are capable of fixing nitrogen. • Nitrification:Process of bacterial conversion of ammonium Bacteria constitute a major part of the organic matter that (NH4+) to nitrite (NO2) and (NO3-) . Bacterial feeds countless bottom-dwelling animals. Organic particles nitrification converts ammonium into a form of nitrogen sinking in the are composed mostly of usable by other primary producers ()

Summer School on Recent Advances in Marine Biodiversity Conservation and Management 192 K. S. Sobhana Archaea and releasing organic matter into the ocean. Viruses Archaea (Domain Archaea) are among the simplest, most may be responsible for half of the bacterial mortality in aquatic primitive forms of life. Oldest ever found (3.8 billion ecosystems and substantial amounts in . The years old) appear similar to archaea. Archaea are , amount of viruses in a given environment is directly related to unicellular organisms that lack a nucleus and other membrane- the abundance of the microbial life, which they invade. bound organelles. These organisms are thought to have had an important role in the early evolution of life. Archaea Factors that impact marine microbial were discovered first in extreme environments on land (hot diversity sulfur springs, saline lakes, and highly acidic or alkaline environments) and were hence called as “”. Nearly every measurable physical, chemical, and biotic Archaea were subsequently found in extreme marine variable in the marine environment has been found to alter environments, such as in very deep water, where they survive microbial diversity. The major variables affecting the marine at pressures of 300-800 atmospheres. Some archaea live at microbial diversity include, turbulance, light, temperature, the high temperatures of hydrothermal vents, and cannot nutreints, salinity, pH, UV and solar influx, surfaces and grow in temperatures under 70-80°C (158-176°F); One interfaces, redox potencial, metals as well as presence of archaeum can live at 121°C (250°F), the macroorganisms such as invertebates and macroalgae. For highest of any known organism. the most part, the extent to which each of these influences Nutritional types actually operates in the environment and the contexts in which they are important remain to be determined. Climate Archaea includes photosynthesisers, chemosynthesisers and change, which will be felt by marine microbial communities . most are methanogens, anaerobic organisms as changes in ocean temperatures, will undoubtedly alter that metabolise organic matter for energy, producing the diversity of communities in unforeseen ways. Climate as a waste product. Halobacteria (photosynthetic), thrive at change should be considered a major top-down controller high salinities, trap light using (purple of microbial communities. Pollution, including nitrogen proteins). inputs due to anthropogenic activities, also impact marine Microbial Eukaryotes microbial diversity. Anthropogenic nitrogen inputs to the oceans now comprise about half the total nitrogen inputs While all prokaryotes (domains Archaea and Bacteria) are uni- to the oceans, a circumstance that has resulted in vast dead cellular, eukaryotes include both uni-cellular and multi-cellular zones in coastal areas and an increased incidence of harmful organisms. Marie microbial eukayotes belong to Kingdoms algal blooms. Protista, Fungi, Plantae and Animalia. Most microbial marine eukaryotes belong to the Protista - can be autotrophic Marine microbes and bioactive or heterotrophic, unicellular or multicellular comprising , compounds diatoms, dinoflagellates, , coccolithophorids, foraminiferans, radiolarians, and . The marine environment is emerging as a ‘gold mine’ for Viruses novel bioactive compounds. Marine derived natural products present an enormous range of novel chemical structures and Although they may not technically constitute a living organism, provide an interesting and challenging blueprint for creating viruses are a critical component of the . new entities via synthetic chemistry. Marine Viruses are particles made up of nucleic acid (RNA or DNA) and plants, in particular, represent an environment rich in protected by a protein coat. They are parasites that reproduce microorganisms that produce compounds with bioactive and develop only with the aid of a living cell. Organisms properties including antibacterial, antifungal, antiviral, are defined by their capacity of independent cell division anticancer, antifouling and antibiofilm activities. However, only and therefore possess the full machinery for the duplication 1% of these microorganisms can be isolated using traditional of DNA and for the binary division of the cell. Viruses, in culture techniques, which has been a major bottleneck when contrast, require a living organism in to duplicate their mining the marine environment for novel bioactive molecules. genetic material and to synthesize the . They do Marine microorganisms have immense potential for providing not, therefore, belong to any of the three domains of life. services and products for human society which is not exploited Nevertheless, viruses are of prime importance for generating to any significant extent. There is a world of microorganisms and maintaining diversity amongst living organisms in all in the marine environment to discover, understand and put to three domains of life through the mediation of horizontal good use. gene transfer. They are also critical for the functioning and balance of the and biogeochemical cycles Suggested reading by facilitating the production of nutrients for growth and Hughes, J. B., Hellmann, J. J., Ricketts, T. H. and Bohannan, J. M. 2001. Counting the uncountable: statistical approaches to estimating microbial diversity. maintaining high diversity, all by preventing the of Appl. Environ. Microbiol., 67: 4399–4406. the most successful microorganisms. They parasitize bacteria Martin, A. P. 2002. Phylogenetic approaches for describing and comparing the diversity of microbial communities. Appl. Environ. Microbiol., 68 :3673–

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3682. from the environment to organisms and genomes and back. ASM Press, Stach, J. E. M., Maldonado, L. A., Masson, D. G., Ward, A. C., Goodfellow, M. and Washington DC, p. 95-115. Bull, A. T. 2003. Statistical approaches for estimating actinobacterial diversity Koeppel, A., Perry, E.B., Sikorski, J., Krizanc, D., Warner, A., Ward, D.M. 2008. in marine sediments. Appl. Environ. Microbiol., 69: 6189–6200. Identifying the fundamental units of bacterial diversity: a paradigm shift to Pedros-Alio, C. 2006 Marine microbial diversity: can it be determined? Trends in incorporate ecology into bacterial systematics. Proceedings of National Microbiology, 14(6): 257–263. Academy of Sciences USA, 105(7): 2504–2509. Fierer, N. 2008. : patterns in microbial diversity across Zinger, L., Gobet, A. and Pommier, T. 2012. Two decades of describing the unseen space and time. In: Zengler K. (Ed.). Accessing uncultivated microorganisms: majority of aquatic microbial diversity. Molecular Ecology, 21(8): 1878–1896.

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