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    Taxonomy, Physiology, and Ecology of Aquatic Microorganisms

    The principles behind the taxonomy of the microorganisms, especially the ­molecular approach (using the sequence of the 16S RNA in the small subunit of the ribosome) in the identification of bacteria, are discussed. The detailed taxonomy of bacteria, ...

    Environmental Microbiology of Aquatic and Waste Systems. 2011 Mar 4 : 47–107.

    Published online 2011 Mar 4. doi: 10.1007/978-94-007-1460-1_4

    PMCID: PMC7120757

    Taxonomy, Physiology, and Ecology of Aquatic Microorganisms

    Nduka Okafor1_4

    Author information Copyright and License information Disclaimer

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    Abstract

    The principles behind the taxonomy of the microorganisms, especially the ­molecular approach (using the sequence of the 16S RNA in the small subunit of the ribosome) in the identification of bacteria, are discussed. The detailed taxonomy of bacteria, fungi, algae, protozoa, and viruses (including bacteriophages) is discussed, and emphasis is laid on those microorganisms which are aquatic. The chapter includes information on some of the smaller macroorganisms found in water such as nematodes and rotifers. The activities of aquatic microorganisms in photosynthesis, and the global cycling of nitrogen and sulfur is discussed.

    Keywords: Taxonomy of microbial groups, Photosynthesis in aquatic microorganisms, • Aquatic nitrogen and sulfur cycles, Rotifers and nematodes, Bacteria, Fungi, Protozoa, Algae, Three domains of living things, Woese, 16S or 18S RNA

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    Taxonomy of Microorganisms in Aquatic Environments

    In this section, the classification of microorganisms will be discussed and emphasis will be laid on those microorganisms found in aquatic systems. The following are the organisms to be discussed:

    Bacteria Archeae Eukarya Fungi Algae Protozoa Viruses

    Nature of Modern Taxonomy

    Modern taxonomy is the science of biological classification. It consists of three sections:

    Classification: The theory and process of arran­ging organisms into taxonomic groups or taxa (singular, taxon), on the basis of shared properties.

    Nomenclature: The assignment of names to taxonomic groups.

    Identification: The determination of the taxon to which a particular organism belongs, based on the properties of the organism.

    Taxonomy is important because it:

    Allows the orderly organization of huge amounts of information regarding organisms

    Enables predictions about their properties and ­formation of hypothesis about them

    Facilitates the accurate characterization and ­identification of “unknown” organisms

    Places organisms in meaningful manageable groups and thus facilitates scientific communication

    Evolution of the Classification of Living Things

    Landmarks in the evolution and development of biological classification may be ascribed to the contributions of the following:

    Linnaeus (1707–1778)

    The Swedish naturalist, Carolus Linnaeus, is ­credited with introducing the earliest organized classification of living things in his Systema Naturae or natural system. He divided living things into plants and animals. Based on morphology and motility, the distinction between the two groups of organisms was clear: plants were green and did not move; on the other hand, animals were not green, but moved.

    Ernst Haeckel (1834–1919)

    Soon after the discovery of the microscope, previously invisible microscopic organisms were observed, some of which had properties common to both plants and animals. Some such as Euglena were green like, but they also moved about like animals. Because the clear-cut criteria which separated plants from animals were absent in these “new” organisms, the German biologist who was a contemporary of Charles Darwin, in 1866 coined the name Protista for a third kingdom, in addition to the Plant and Animal Kingdoms.

    Robert Harding Whittaker (1920–1980)

    Whittaker was an American. Born in Wichita, Kansas, he worked in various places including the University of California, Irvine, and Cornell University. In 1968, he proposed the five-kingdom taxonomic classification of living things into the Animalia, Plantae, Fungi, Protista (Algae and Protozoa), and Monera (Bacteria). His categorization of living things was based on three criteria: cell-type (whether prokaryotic or eukaryotic); organizational level (unicellular or multi-cellular); nutritional type (autotrophy or heterotrophy).

    Carl R. Woese (1928–)

    The current classification of living things is based on the work of Carl Robert Woese of the University of Illinois. While earlier classifications were based mainly on morphological characteristics and cell-type, following our greater understanding of living things at the molecular level, Woese’s classification is based on the sequence of the gene of the ribosomal RNA (rRNA) in the 16S of the small subunit of the prokaryotic ribosome, or the 18S of the small subunit of the eukaryotic ribosome (Petti et al. 2006).

    The sequence of the rRNA in the 16S or 18S of the small subunit of the ribosome is used for the following reasons:

    The ribosome is an important organelle in all ­living things where it is used for a basic function for the support of life, namely, protein synthesis.

    The 16S (prokaryote) or 18 S (eukaryote) rRNA is an essential component of the ribosome.

    The function of 16S or 18 S rRNA is identical in all ribosomes.

    The sequences of the 16S or 18 S rRNA are ancient (or highly conserved) and change only slowly with evolutionary time.

    Organisms can generally inherit genes in two ways: From parent to offspring (vertical gene transfer), or by horizontal or lateral gene transfer, in which genes jump between unrelated organisms, a common ­phenomenon in prokaryotes. There is little or no lateral gene transfer in the sequences in the 16S or 18 S RNA of the ­ribosomal small units.

    Source : www.ncbi.nlm.nih.gov

    QUIZ 1 & 2 Flashcards

    Start studying QUIZ 1 & 2. Learn vocabulary, terms, and more with flashcards, games, and other study tools.

    QUIZ 1 & 2

    _______ have beautiful glass-like shells.

    Click card to see definition 👆

    Diatoms

    Click again to see term 👆

    One characteristic that taxonomists use to distinguish protists from fungi is the presence of a nucleus. (T/F)

    Click card to see definition 👆

    FALSE-nucleus

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    1/35 Created by sbabineaux95

    Terms in this set (35)

    _______ have beautiful glass-like shells.

    Diatoms

    One characteristic that taxonomists use to distinguish protists from fungi is the presence of a nucleus. (T/F)

    FALSE-nucleus

    Trypanosoma causes ....

    sleeping sickness.

    Which of the following is not a member of the Stramenopiles?

    diatoms, euglena, brown algae, or water molds

    -euglena

    which of the following is most associated with plant-like protists?

    live anywhere in aquatic environments, grow in photic zone, are all closely related to land plants, or can cause parasitic diseases

    -are all closely related to land plants

    The most recent phylogenetic data suggests that bacteria and archaea may be more closely related than archaea and eukarya. (T/F)

    FALSE

    Viruses are considered to be nonliving because...

    they depend on a host for replication.

    Domain (or perhaps Kingdom) Bacteria can be subdivided into 2 separate groups based on the reaction with Gram stain. The difference in this reactive relates to a difference the...

    cell wall structure.

    During bacterial conjugation, the transferred item is a...

    Plasmid.

    After the domain category was first introduced there were how many kingdoms?

    6

    _______ is a more inclusive group than _______.

    Kingdom; Class

    Which name signifies group of Archaeans which live in extremely saline environments?

    Halophiles

    Which of the following traits allows some bacteria to survive extreme conditions for millions of years?

    Endospore Formation

    The category that is always italicized and capitalized is...

    Genus.

    The science of reconstructing an organisms evolutionary history is called systematic? (T/F)

    FALSE

    Each class can be split into several kingdoms? (T/F)

    FALSE

    Systematics holds that the more similar the DNA of 2 organisms, the more closely related they are. (T/F)

    TRUE

    Which of the following is the smallest or least inclusive group?

    Genus

    Which of the following groups contains the fewest species?

    Order

    Scientists currently identify 3 domains? (T/F)

    FALSE

    Before 1970, what was the basis for the biological classification system?

    2 kingdoms; Animalia and plantae

    Which group contains most unicellular, eukaryotic organisms?

    Protists

    An organism with a nucleus would be placed in which domain?

    Eukarya

    If 2 organisms are members of the same phylum, then the MUST also be members of the same____?

    Domain

    Throughout the history of taxomony, what characteristic was most commonly used for determining species relationships?

    Anatomical Similarity

    Modern systematic constructs clades and evolutionary relationships based on?

    Genetic Similarities

    Which of the following is prokaryotic?

    Archaea

    Which of the following is eukaryotic?

    Humans

    Why is it particularly difficult for the systematist to classify asexually reproducing organisms as a species?

    Asexually reproducing organisms do not interbreed.

    Once an organism is placed in a specific species, the designation canot be changed? (T/F)

    FALSE

    Systematics reassigns phylogenetic placement based on?

    New information about genetic relationships.

    What were the organisms that make up the 2 prokaryotic domains?

    Bacteria and Archaea

    What is Bacteria cell wall composed of?

    Peptidoglycan

    What is Peptidoglycan?

    Is a complex of structural polysaccharides cross-linked by peptides.

    What does the cell wall do?

    Give characteristic shapes

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