© 2006 thomson-brooks cole chapter 6 marine microbes

© 2006 Thomson-Brooks Cole

Chapter 6

Marine Microbes


Key Concepts

• Microbial life in the sea is extremely diverse, including members of all three domains of life as well as viruses.

• Marine virology is an emerging field of study, due to recognition of the critical role that viruses may play in population control of other microbes, in nutrient cycling, and in marine pathology.


Key Concepts

• Photosynthetic and chemosynthetic bacteria and archaeons are important primary producers in marine ecosystems.

• Heterotrophic bacteria, archaeons, and fungi play essential roles in recycling nutrients in the marine environment.


Key Concepts

• Marine eukaryotic microbes are primary producers, decomposers, and consumers, and some contribute significantly to the accumulation of deep-sea sediments.

• Populations of several kinds of photosynthetic marine microbes may form harmful blooms that affect other marine and maritime organisms directly and indirectly.


Marine Viruses

• Virology—the study of viruses• Viruses are the more abundant than

any other organism in the sea, are diverse, and participate in food webs

• But, most authorities do not consider them to be alive


Viral Characteristics

• Viruses consist of bits of DNA or RNA surrounded by protein

• Have no metabolism, and rely entirely on host organism for energy, material and organelles to reproduce

• Viral replication must occur within a host cell

• Viruses infect all groups of living organisms, but may be specialized



• Viral structure– virus particle is called a virion when

outside the host cell– virion composed of a nucleic acid core

surrounded by a coat of protein called a capsid (together called a nucleocapsid)

– may have an envelope, a membrane derived from the host’s nuclear or cell membrane



– viral shapes:• icosahedral viruses—capsid with 20 triangular

faces composed of protein subunits• helical viruses—protein subunits of the capsid

spiral around the central core of nucleic acid• binal viruses—those with icosahedral heads

and helical tails

– some virions have filaments and other parts used to attach to and infect the host cell



• Viral life cycles– lytic cycle—a rapid cycle of infection,

replication of viral nucleic acids and proteins, assembly of virions, and release of virions by rupture (lysis) of the cell

– lysogenic cycle—the viral nucleic acid is inserted into the host genome and may reside there through multiple cell divisions before becoming lytic


Biodiversity and Distribution of Marine Viruses

• 10 times more abundant than marine prokaryotes

• estimated 100 to 10,000 genotypes• most planktonic viruses are icosahdral

or binal bacteriophages with lytic life cycles

• sediment viruses are typically helical and lysogenic


Ecology of Marine Viruses

• Viruses kill host cells, and thus control populations of bacteria and other microbes in plankton communities

• Lysis releases nutrients and facilitates sedimentation

• Viral populations are probably controlled by several factors– e.g. alteration by light, adsorption onto

suspended particles, ingestion by microbes, failure to attach to appropriate host cell


Marine Bacteria

• General characteristics– simple, prokaryotic organization: no nuclei

or membrane-bound organelles, few genes, nonliving cell wall

– reproduce asexually by binary fission– many shapes and sizes

• bacillus—rod shape• coccus—spherical shape


Nutritional Types

• Cyanobacteria– photosynthetic bacteria which are found in

environments high in dissolved oxygen, and produce free oxygen

– store excess photosynthetic products as cyanophycean starch and oils

– primary photosynthetic pigments are chlorophyll a and chlorophyll b

– accessory pigments include carotenoids and phycobilins


Nutritional Types (Cyanobacteria)

– chromatic adaptation—response of pigment composition to the quality of light in the sea

– may exist as single cells or form dense mats held together by mucilage• stromatolites—a coral-like mound of microbes

that trap sediment and precipitate minerals in shallow tropical seas


Nutritional Types

• Other photosynthetic bacteria– anaerobic green and purple sulfur and non-sulfur

bacteria do not produce oxygen– the primary photosynthetic pigments are

bacteriochlorophylls – sulfur bacteria are obligate anaerobes (tolerating

no oxygen)– non-sulfur bacteria are facultative anaerobes

(respiring when in low oxygen or in the dark and photosynthesizing anaerobically when in the presence of light)


Nutritional Types

• Chemosynthetic bacteria– use energy derived from chemical

reactions that involve substances such as ammonium ion, sulfides and elemental sulfur, nitrites, hydrogen, and ferrous ion

– chemosynthesis is less efficient than photosynthesis, so rates of cell growth and division are slower

– found around hydrothermal vents and some shallower habitats where needed materials are available in abundance


Nutritional Types

• Heterotrophic bacteria– decomposers that obtain energy and

materials from organic matter– return many chemicals to the marine

environment through respiration and fermentation

– populate the surface of organic particles suspended in the water


Nutritional Types (Heterotrophic Bacteria)

– association of heterotrophic bacteria with particles in the water column aids with:• consolidation—adjacent particles adhere• lithification—formation of mineral cement

between particles• sedimentation—settling of particles

– marine snow—large, cobweb-like drifting structures formed by mucus secreted by many kinds of plankton, where particles may accumulate


Nitrogen Fixation and Nitrification

• Nitrogen fixation—process that converts molecular nitrogen dissolved in seawater to ammonium ion– major process that adds new usable

nitrogen to the sea– carried out by some cyanobacteria and a

few archaeons with nitrogenase (enzyme)– anaerobic process often occurs in

heterocyst (thick-walled cell in which photosynthesis is altered to prevent oxygen release) in cyanobacteria


Nitrogen Fixation and Nitrification

• Nitrification—process of bacterial conversion of ammonium to nitrite and nitrate ions– bacterial nitrification converts ammonium

into a form of nitrogen usable by other primary producers


Symbiotic Bacteria

• Mitochondria and chloroplasts of members of the domain Eukarya

• Chemosynthetic bacteria live within tube worms and clams

• Some deep-sea or nocturnal animals host helpful bioluminescent bacteria– photophores– embedded in the ink sacs of squid


Archaea

• General characteristics– small (0.1 to 15 micrometers)– prokaryotic– adapted to high and low temperatures,

high salinities, low pH, and high pressure– differences from bacteria

• cell walls lack special sugar-amino acid compounds in bacterial cell walls

• cell membranes contain different lipids, which help stabilize them under extreme conditions


Nutritional Types

• Archaea includes photosynthesizers, chemosynthesizers and heterotrophs

• Most are methanogens—anaerobic organisms that metabolize organic matter, producing methane as a waste product

• Halobacteria (photosynthetic) trap light using bacteriorhodopsins, purple proteins


Hyperthermophiles

• Hyperthermophiles—organisms that can survive at temperatures exceeding 100o C, such as near deep-sea vents

• Examples:– Pyrolobus fumarii (“fire lobe of the

chimney”) is chemosynthetic, and grows at temperatures between 90o and 113o C

– “strain 121” survived 2 hours of incubation at 130o C


Eukarya

• Eukarya includes all organisms with eukaryotic cells

• Examples:– plants– animals– fungi– algae– single-celled animal-like protozoa


Fungi

• History of marine mycology– marine fungi first discovered in 1849– marine fungi’s ecological role is difficult to

evaluate; biomass needs to be quantified• General features of fungi

– eukaryotes with cell walls of chitin– many are unicellular yeasts– filamentous fungi grow into long, multi-

cellular filaments called hyphae that can branch to produce a tangled mass called a mycelium


Fungi

– heterotrohic decomposers that recycle organic material• can digest lignin (major component of wood)

– store energy as glycogen– kingdom Fungi is divided into 4 phyla:

• Chytridiomycota (motile cells)• Zygomycota (e.g. black bread mold)• Basidiomycota (club fungi, e.g. mushrooms)• Ascomycota (sac fungi)

– in the sea, ascomycotes are the most diverse and abundant fungi


Fungi

• Ecology and physiology of marine fungi– salinity is toxic to fungi, so they must

devote energy to removing sodium– most marine fungi live on wood from land– some live on grass in salt marshes– others live on algae, mangroves or sand– fungi decompose the chitinous remains of

dead crustaceans in open sea plankton communities


Reproduction of Marine Fungi

• Marine yeasts reproduce asexually by budding—mitosis that produces daughter cells of unequal size

• Filamentous marine fungi reproduce asexually by production of conidiospores on the tips of hyphae

• Filamentous marine ascomycotes can reproduce sexually by forming a fruiting body called an ascocarp, a structure which produces ascospores


Maritime Lichens

• Lichens—mutualistic associations between a fungus and an alga– fungi are usually ascomycotes– algae are usually green or blue-green

bacteria

• The fungus provides attachment, the general structure, minerals, moisture

• The alga produces organic matter through photosynthesis


Stramenophiles

• Stramenophiles—a diverse group of eukaryotic organisms unified by the nature of their cells’ 2 flagella

• The special flagella– 1 flagellum is a simple form, usually with a

light-sensing body at the base; senses light

– 2nd bears many mastigonemes (hair-like filaments) with a thickened base and a branching tip along the shaft; used for swimming


Stramenophiles

• Heterokont—refers to the different form of the 2 flagella

• ochrophytes—photosynthetic type that are usually golden brown– e.g. diatoms, silicoflagellates– most have chlorophyll a, chlorophill c,

beta-carotene and fucoxanthin– end-product of photosynthesis is laminarin

(a complex carbohydrate)


Diatoms

• Diatom structure– frustule—a two-part, box-shaped organic

cell wall impregnated with silica– valve—one half of a frustule; 1 valve is

larger and fits over the other like a box lid– 2 basic diatom shapes:

• radially symmetrical valves (generally planktonic)

• bilaterally symmetrical valves (generally benthic)


Diatoms

• Locomotion in diatoms– some benthic diatoms move by mucilage

secretion from pores and grooves

• Reproduction in diatoms– asexual reproduction by fission

• each daughter cell gets 1 valve, and has to grow a 2nd, smaller one to complete frustule

• auxospore—daughter cell which casts off the small valve, increases in size, and secretes a new frustule of normal size (occurs when cell size reaches 50% of maximum)


Diatoms

• Diatomaceous sediments– frustules of dead diatoms sink and collect

on the seafloor to form silaceous oozes– accumulations form sedimentary rock– these deposits, called diatomaceous earth,

are mined for use as filtering material, a mild abrasive, and for soundproofing and insulation products

– diatom productivity and death is responsible for most petroleum reserves


Other Ochrophytes

• Silicoflagellates– abundant in cold marine waters– basket-shaped external skeletons of silica

which the cell wraps around


Other Ochrophytes

• Pelagophyceans– e.g. bloom-forming alga Aureococcus

anophagefferens (non-toxic, coastal)– can block light from sea grasses or clog

filter-feeding structures of molluscs


Labyrinthomorphs

• Spindle-shaped osmotrophic cells• Labyrinthulids

– e.g. Labyrinthula zosterae, which caused devastating eelgrass wasting disease

• Thraustochytrids– planktonic and benthic decomposers– some are pathogens of shellfish– used to produce dietary supplements of

the polyunsaturated omega-3 fatty acid docosahexaenoic acid (DHA)


Haptophytes

• Photosynthetic organisms with 2 simple flagella used for locomotion

• Have haptonema—a unique structure arising from the cell surface between the 2 flagella, which captures food

• Most are coccolithophores with a surface coating of disc-shaped scales (coliths) of calcium carbonate– remains form calcereous oozes


Alveolates

• Have membranous sacs (alveoli) beneath their cell membranes– pellicle—term for the cell surface if the

combination of cell membrane and alveoli is complex (distinct from cell wall)

• Examples:– dinoflagellates– ciliates– apicomplexans (strictly parasitic)


Alveolates

• Dinoflagellates– globular, unicellular (sometimes colonial)– dinosporin—a unique chemical associated

with the cellulose plates within the alveoli of dinoflagellates

– dinoflagellate structure• heterokont flagella• simple flagellum encircles the cell in the

cingulum (a horizontal groove) and produces a spinning motion


Alveolates (Dinoflagellates)

– dinoflagellate structure• longer flagellum with hair-like filaments trails

down the sulcus (a longitudinal groove) and imparts most of the forward motion to the cell

• unarmored dinoflagellates have few or no cellulose plates in the pellicle; armored dinoflagellates have multiple layers of them

• number, size and shapes of plates are used to identify different species



– dinoflagellate nutrition• photosynthetic ones have chlorophylls a and c,

beta-carotene and peridinin (a xanthophyll which imparts a golden-brown color)

• mixotrophic photosynthetic ones supplement photosynthesis by osmotrophy (absorbing nutrients) or phagotrophy (engulfing nutrients)

– reproduction in dinoflagellates• asexual reproduction by fission• sexual reproduction by fusion and meiosis• often have dormant stages (cyst formation)



– ecological roles of dinoflagellates• major component of phytoplankton• some are parasites of copepods (crustaceans)• zooxanthellae—species lacking flagella which

are symbionts of jellyfish, corals and molluscs– photosynthetic zooxanthellae provide food for hosts– hosts provide carbon dioxide, other nutrients, and

shelter



– harmful algal blooms (HABs)• occur when photosynthetic dinoflagellates

undergo a population explosion• colors the water red, orange or brown• dinoflagellates that cause HABs produce toxins

– paralytic shellfish poisoning occurs in humans who consume shellfish contaminated with these toxins

• oxygen content of the water may be reduced to deadly levels as bacteria decompose animals killed by dinoflagellate toxins


Alveolates

• Ciliates– protozoans that bear cilia for locomotion

and for gathering food• membranelles—tufts or long rows of fused

adjacent cilia• cytostome—an organelle serving as a

permanent site for phagocytosis of food

– 10 micrometers-3 mm long members of plankton and bethos

– reproduce asexually by binary fission and sexually by conjugation (nuclei transfer)


Alveolates (Ciliates)

– types of marine ciliates• scuticociliates (have a dense andn uniform

distribution of cilia on their body)• oligotrichs (have few cilia)• tintinnids (usually lack body cilia and secrete

an organic, loosely fitting shell, the lorica)

– ecological roles of marine ciliates• most are heterotrophs; some harbor

autotrophic symbionts or chloroplasts• link hetero- and autotrophic blue-green

bacteria to higher levels in the food chain


Choanoflagellates

• A phylum of marine and freshwater flagellated cells that are more closely related to animals than any other group of one-celled microbes

• Unicellular or colonial– colonies may be stalked or embedded in a

gelatinous mass– cell often surrounded by a lorica of

siliceous rods; flagellum is surrounded by a funnel-shaped collar of microvilli

• Highly efficient consumers of bacteria


Amoeboid Protozoans

• All have an organelle called a pseudopod—an extension of the cell surface that can change shape and is used for locomotion (benthic species) and food capture (benthic and pelagic)

• Most have a test—an externally secreted organic membrane often covered with foreign particles or strengthened by mineral secretions


Amoeboid Protozoans

• Two major phyla: – foraminiferans (abundant, diverse)– actinopods, which include:

• radiolarians (predominant type)• acantharians• heliozoans


Amoeboid Protozoans

• Foraminiferans (forams)– have branched pseudopods that form

reticulopods (elaborate, net-like structures) used to: • snare prey• crawl (benthic)• reduce sinking rate (pelagic)


Amoeboid Protozoans (Foraminiferans)

– foraminiferan test• often have elaborate, multi-chambered tests of

calcium carbonate• globigerina ooze—sediments of dead

planktonic forams, largely Globigerina

– foraminiferans and zooxanthellae• zooxanthellae live within the cytoplasm of

many forams from nutrient-poor waters• photosynthetic zooxanthellae use foram waste

products (e.g. CO2, ammonia) as nutrients


Amoeboid Protozoans

• Radiolarians– named for long, needle-like pseudopods

• central nuclear region is surrounded by a capsule—an external organic membrane

• pseudopods pass through pores in the capsule and form a region called the calymma

• pseudopods capture food and slow sinking

– radiolarian oozes form from the internal skeleton of silica of dead radiolarians

– live in the photic zone and prey on phyto- and zooplankton, sometimes copepods

© 2006 thomson-brooks cole chapter 6 marine microbes

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