Microbiology

Variable Pondweed Submerged Leaf 1000X

Variable Pondweed Submerged Leaf Cells under Blue Light Filter at 1000X 

Links to Topics on this Page

Introduction

Archaea

Bacteria

Protista

French Hill Pond Specific Microbiology

Plastids

Chloroplasts

Chromoplasts

Gerontoplasts

Leucoplasts

Algae Plastids

Rhydoplasts

Plant Tissues

Derma Tissues

Epidermis

Peridermal

Ground Tissues

Parenchyma cells

Collenchyma cells

Sclerenchyma tissues

Vascular Tissues

Xylem structure

phloem structure

Stomata

The Microstructure of a Leaf

The Microstructure of a Plant Stem

 

Introduction 

The microbiology on this website will address the biological kingdoms of Archaea, Bacteria and Protista as applicable to the environment of French Hill Pond. Biological kingdoms are often called "domains" sometimes containing groups called phyla and kingdoms. This taxonomy can be confusing and is currently in a state of flux. Most of the descriptions involving microbiology will be part of the description of a specimen in the plant, animal or fungi kingdoms. This web page and its linked pages will address microorganisms that are not parts of specimens in these more visible kingdoms. Microbiology is a complicated subject and this website does not discuss the fine points of microbiology unless pertinent to understanding the ecology of French Hill Pond. However, some basic concepts are discussed below.

Archaea

Archaea is the kingdom of single-celled microorganisms that have no nucleus or identifiable, functioning subunits (organelle) inside the cell. They can withstand very harsh environments and have been most extensively studied in such environments. However, Archaea are found everywhere. None are known to cause disease but many are found in the human digestive system where they are important to the digestive process. Individual Archaea are called "archaeon."

Many of these microorganisms survive and thrive in extreme temperatures and without much light because they are very simple and have robust cell walls. Cells that derive nutrition from organic compounds under the influence of sunlight are called "phototrophs." "Lithotrophs" use inorganic compound reactions as a source of energy instead of sunlight and obtain carbon from organic compounds or through carbon fixation. The third method from which cells may derive nutrition is by using organic compound reactions for energy and  obtaining carbon from organic compounds or through carbon fixation, placing them in a category called "organotrophs." Archaea use all three methods for metabolism. They usually have a singular, circular chromosome and all reproduce asexually by fission (splitting), fragmentation (breaking into pieces) or budding. Budding occurs when a small bump or protrusion appears on the cell wall that breaks away forming a new cell. Some Archaea have flagella (rotating, propeller-like tails) that allow them to move through fluids.

Bacteria 

Bacteria is the kingdom of microorganisms whose internal components (DeoxyriboNucleic Acid, proteins etc.) are not enclosed by separate membranes, that is, the internal components are free to move around within the outer wall of the cell. Such cells are said to be "prokaryotic" from the Greek for "before kernel." A single member of this kingdom is called a "bacterium."

Bacteria may also be identified as phototrophs, lithotrophs or organotrophs. Like Archaea, Bacteria usually have a singular, circular chromosome. Reproduction is by asexual, binary fission and budding. Many Bacteria have flagella. Cells with one flagellum (singular of flagella) are said to be "monotrichous." An "amphitrichous" cell has a flagellum at both ends. Clusters of flagellum at one end of a cell identifies the cell as "lophotrichous." If a cell has flagella on its entire surface, it is "peritrichous." Some Bacteria can change their buoyancy allowing them to rise or fall in a fluid. Others move by distorting one end of the cell.

Some Bacteria consume other microorganisms by trapping and absorbing them. When this behavior causes the destruction of specific microorganisms, the Bacteria are classified as "pathogens." Pathogens are a major cause of disease in mammals.

Protista

Protista or Protists is a kingdom of microorganisms whose internal components are enclosed by internal membranes. Such cells have a nucleus and are called "eucaryotes" or "eukaryotes" from the Greek for "good kernel."  Animals, fungi and plants consist mostly of eucaryotes. However, these groups are excluded when Protista are considered a kingdom. It serves as a catchall for organisms that do not fit in other kingdoms. Many biologists have discarded the Protista as the name of a kingdom and use the title "Eukarya."

Protista are either phototrophs or organotrophs. They reproduce both sexually and asexually. Protista are called "gametes" when they reproduce sexually under stress. Asexual reproduction, the preferred method, is by binary fission. Like Bacteria, Protista may have various forms of flagella and modes of locomotion.

Protista may consume other microorganisms and some are pathogens.

French Hill Pond Specific Microbiology - Plants

Although microorganisms from the kingdoms or domains listed above may be discussed on this website, most microbiology discussed will concern collections of cells that have a specific purpose or configurations of cells that help differentiate members of the plant, animal or fungi domains. Some definitions and general cell structures are discussed below. This information may be required to understand descriptions on other pages on this website and is provided for those people unfamiliar with biological terms.

Plastids

Plastids (singular plastid) are organelles, that is, functioning subunits of a cell in plants and algae. Plastids are parts of a cell enclosed in their own membrane or wall but are not stand-alone cells. Subcategories of  plastids will usually end in the letters "plasts."

Chloroplasts

Chloroplasts are plastids that contain chlorophyll enabling the cell to perform photosynthesis. Photosynthesis is the process of converting sunlight, water and carbon dioxide into nutrients for the plant and more oxygen as a byproduct. The following microphotograph shows chloroplasts in algae cells. This microphotograph is at 1000X magnification. The chloroplasts are the green, ball-like organelles crowded into the rectangular algae cells. This colony of algae is called a "filamentous algae" and was found in French Hill Pond. Filamentous algae are often called "hair algae" because they resemble strands of human hair. There are many forms of filamentous algae. The photograph below shows filaments consisting of single, algae cells arranged tip to tip and stuck together in a hollow, cylindrical colony to form one "hair."

Chloroplasts in Algae Cells

Chromoplasts

Chromoplasts are plastids that manufacture and store pigments other than chlorophyll.

Gerontoplasts

Gerontoplasts are plastids that breakdown the photosynthesis process as the plant ages.

Leucoplasts

Leucoplasts are colorless plastids that manufacture and store chemicals. There are three specialized leucoplasts: amyloplasts, elaioplasts and proteinoplasts (aleuroplasts). Amyloplasts store starch and play a role in detecting gravity. Elaioplasts store fat. Proteinoplasts store protein.

Algae Plastids

Algae do not contain chromoplasts or amyloplasts. However, algae may have rhydoplasts. Rhydoplasts are plastids that perform photosynthesis but are red in color and allow algae to perform photosynthesis to a water depth of over 250 meters (820 feet). Some algae have plastids called "muroplasts," which are similar to chloroplasts but have a modified organelle wall. Most algae in French Hill Pond have chloroplasts.

Plant Tissues

Plants are composed of cell collections or single cells called "tissues." There are three general systems of plant tissues: dermal tissues, ground tissues and vascular tissues.

Dermal Tissues

Dermal tissues are collections of cells that cover and protect the plant. There are two types of dermal tissues: epidermis and periderm. Epidermis tissue covers the plant in a "skin" of usually single-layered cells. Collections of cells forming bark, found on trees and shrubs, is called the periderm of the plant and replaces epidermal tissues as the plant grows.

Ground Tissues

Ground tissues manufacture and store plant nutrients. There are three types of ground tissues: parenchyma, collenchyma and sclerenchyma.

Parenchyma cells are the most common ground tissue. They manufacture and store nutrients used by the plant and secrete products as necessary. The pith of stems, pulp in fruits and interior cells of leaves are examples of parenchyma cells. Therefore, they are sometimes called "filler cells." The word parenchyma is from the Greek for "filled in." When parenchyma cells reach maturity, they cease reproducing unless stimulated. The interior of a leaf between the upper and lower epidermis is called the "mesophyll" from the Greek for "middle leaf." The mesophyll is composed mostly of specialized parenchyma called "chlorenchyma" cells. Chlorenchyma cells contain chloroplasts.

Collenchyma tissues give the plant stiffness and structural support. Collenchyma cells are alive, have thick walls made of cellulose and pectin and are elongated. There are four types of collenchyma cells: angular, tangential, annular and lacunar. Angular collenchyma cells are thickest where they attach to other cells at their ends. Tangential collenchyma cells are arranged in rows and are thickest where they touch one another tangentially. Annular collenchyma cells have a uniform thickness regardless of their relationship to other cells. Lacunar collenchyma cells leave spaces between the collection of cells.

Sclerenchyma tissues are composed of cells that die as they mature unlike collenchyma cells that remain viable when they mature. Their vey thick cell walls are composed of cellulose, hemicellulose and lignin. In general, there are two types of sclerenchyma tissue cells: fibers and sclereids. Fiber cells are long and form into bundles of strands. They form the basis of ropes and even the fiber found in fruit juices used to relieve constipation. Sclereids are star-shaped cells that form the basis of protective material like the stiff membrane protecting the seeds in the core of an apple.

Vascular Tissues

Vascular tissues form the plant veins and other ducts through which the plant nutrients and water flows. There are two general vascular structures: xylem and phloem. Xylem structure cells form the walls of tubular veins. All xylem structures have non-living cells called "tracheids." Biologists often refer to these cells as "elements." The xylem of angiosperms (flowering plants) have an additional type of cell called a vessel cell or element. The phloem structure consists of living cells called "sieve-tube" and "companion cells" or elements. These cells help transport nutrients made through photosynthesis. Vascular tissues are only found in plants with vein systems. Non-vascular plants, like filamentous algae, have no xylem or phloem structures.

Stomata

A stoma or stomate is a pore in the epidermis (surface) of a leaf through which the leaf exchanges gases and water with the mesophyll (leaf cells between the epidermi). All land plants, except liverworts, and many water plants have stomata (plural of stoma). Although the term refers to the pore itself, most scientists use the term to identify the collection of cells surrounding the pore that control the flow of gases and water. Many land plants have stomata on the top and bottom of their leaves. Others have stomata on the top of the leaf only. The floating leaves of water plants generally have stomata on the top surface only. Water plant submerged leaves generally have no stomata. Stomata cannot function properly if permanently immersed in water. The following 1000X microphotograph shows the stomata on the upper surface of a spatterdock leaf obtained from French Hill Pond.

Spatterdock Leaf Stomata

Only two complete stomata are shown in this microphotograph. The other cells are epidermal cells, that is, surface cells that are out-of-focus to show the raised cells around the stomata more clearly. The stoma is an elliptical hole. The pore is surrounded by two cells called "guard cells" in an elliptical configuration. These guard cells are classified as specialized parenchyma (storage) cells. A guard cell contains a store of chemicals, called the "vacuole," seen as the shaded areas within the guard cells in the photograph above and essential to the function of the stoma . The guard cells open and close the pores depending upon environmental conditions and the requirements of photosynthesis. Photosynthesis is the process of converting sunlight, water and carbon dioxide into nutrients for the plant and more oxygen as a byproduct.

The mechanism by which the stomata are opened and closed involves complex chemical reactions that are not entirely understood and are beyond the scope of this website in any case. Most plants open the stomata during the day when light and humidity conditions are correct. Excess water in the leaf is released to the atmosphere when the stomata open, a process called "transpiration," allowing carbon dioxide and oxygen to enter the part of the leaf below the epidermis. These gases react with chlorophyll and water under the influence of light to create plant nutrients and more oxygen than the plant received. This excess oxygen is released to the atmosphere through the stomata. The guard cells close the stomata at night or under adverse conditions in most plants to prevent interference with photosynthesis and protect the interior of the leaf.

The guard cells appear greener in the microphotograph because they have more chloroplasts (cells containing chlorophyll) than the epidermal cells. These additional chloroplasts may serve to give the photosynthesis process a jump start but their exact purpose is yet to be determined. The brighter illumination of the stoma in the center of the microphotograph is due to a deliberate concentration of the microscope light on that stoma to more clearly show the three-dimensional form of the cells around the stoma. The three-dimensional form of these cells is more apparent in an electron microscope image. The following microphotograph is a 400X image of a spatterdock leaf.

Spatterdock Leaf 400X

Compare the previous spatterdock leaf microphotograph to the following microphotograph of a variable pondweed leaf top surface at 400X. The stomata are easily identified.

Variable Pondweed Leaf 400X

The Microstructure of a Leaf

The information above permits a better understanding of the function and structure of a leaf. Leaves have essentially eight parts: upper trichomes, upper cuticle, upper epidermis, palisade mesophyll, spongy mesophyll, lower epidermis, lower cuticle and lower trichomes.

The top part of a leaf, called the adaxial, is covered with a transparent, waxy layer called the upper "cuticle." Most leaves have small hair-like structures rising above the upper cuticle called "trichomes." The word "trichome" comes from the Greek for hair. Leaf trichomes consist of epidermal cells. The cuticle makes the leaf waterproof. The leaf can intake or output water and gasses through the stomata that penetrate the cuticle. The trichomes have a variety of possible functions. These hairy structures have bases that penetrate the cuticle into the interior of the leaf. Trichomes serve to discourage predators by making the leaves less palatable. As air blows across the leaf, trichomes moderate the flow reducing evaporation and drying of the cuticle and allowing the stomata to function better. Like hair on the human body, trichomes can insulate the leaf and protect it from excessive radiation like ultra-violet light.

Beneath the upper cuticle is the upper epidermis, a single layer of transparent, epidermal cells that helps protect the interior of the leaf. The trichomes terminate in the epidermis. However, the stomata penetrate the epidermis into the interior of the leaf called the mesophyll. The stomata control the liquids and gasses that flow into and out of the mesophyll from the atmosphere. The mesophyll also contains vascular veins consisting of xylem and phloem structure cells that carry fluids to and from the regions of the leaf and other parts of the plant.

The mesophyll has two layers and is divided into regions by vascular veins. The upper layer of the mesophyll is the palisade mesophyll. This layer contains chloroplast cells arranged vertically. The exact arrangement and spacing between these cells depends upon the environment in which the plant thrives and the need for capillary action required to circulate liquid among the cells. Plants that prefer shade will have a different arrangement than plants that thrive in sunlight. The number and arrangement of the vascular veins generally located beneath the palisade mesophyll or between regions of the palisade mesophyll will also be determined by the environment in which the plant has evolved to thrive.

The lower mesophyllic layer is called the spongy mesophyll. This layer has more spacing between the chloroplasts and contains chambers associated with the stomata where gasses can be stored and mixed with the chloroplasts for photosynthesis as well as the vascular veins to route liquids. The spongy mesophyll allows the leaf to respire (breathe) without disturbing the palisade mesophyll.

The lower epidermis, lower cuticle and lower trichomes are beneath the mesophyll and perform the functions of their upper counterparts. However, these structures may be thinner or smaller than their upper counterparts. There are frequently more trichomes on the lower leaf or "abaxial" than on the adaxial. Many trichomes may grow in a tightknit pattern to form a coating on the abaxial sometimes called a "bloom." This coating helps to insulate the bottom of the leaf. A white coating of trichomes may also reflect light coming through the leaf back into the leaf making maximum use of available light.

The Microstructure of a Plant Stem

There are four types of plant stems: dicot, monocot, gymnosperm and fern stems. Stems are one of two structures a vascular plant uses for axial structure, that is, to support the various parts of the plant. The other axial structure is a root. A stem has four functions. It provides support for the leaves, flowers, fruits and other parts of a plant above the ground. Stems transfer fluids between various parts of the plant through tubular veins consisting of xylem and phloem structures. Nutrients are stored in the stems. Finally, stems have cells called "meristems" that manufacture new, living tissues.

Stems have nodes at which leaves, buds, additional stems and roots (on trailing stem nodes) grow. The part of the stem between these nodes is called the "internode." Fluids are transported through the stem and nodes by capillary action. Capillary action is generated by the surface tension of the fluid. In sufficiently narrow tubes, the tension between the molecules on the surface of the fluid acts on the wall of the tubes to cause the fluid to move through the tube and fill the tube with fluid under the right conditions. Among these conditions are the viscosity of the fluid, character of the tube wall, size of the tube and vacuum generated by the plant's respiration. Plants do not have a pump to move fluids through veins like an animal's heart but depend entirely on capillary action and respiration to move fluids throughout the plant.

The outside of a stem consists of dermal tissues covered by a waxy material called a cuticle as with leaves. The epidermal tissue is below the cuticle. In woody plants, that is plants with bark, peridermal tissue will be immediately beneath the cuticle and above the epidermal tissue. The dermal tissues protect the inner part of the stem and controls fluid and gas exchange with the environment.  Beneath the dermal tissues and concentric with them is the ground tissues and vascular tissues. The ground tissues consist primarily of parenchyma cells that manufacture and store store nutrients. Ground tissues also give the stem stiffness and support primarily through the collenchyma and sclerenchyma tissues. The vascular tissues form veins that are interspersed among the ground tissues. There may be very little live ground tissue and epidermal tissue in woody stems as these tissues are replaced by wood fiber (xylem cells) and bark (periderm cells). However, live, vascular tissues remain in viable woody plants.

 

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