Virus in the Ocean

8/19/2019 Virus in the Ocean

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microbiologists have previously searched without success for

viruses in marine habitats. Thus it has been assumed the oceans

probably did not contain many viruses. Recent discoveries have

changed this view radically. Several groups have either centrifuged seawater at high speeds or passed it through an ultrafilter and then examined the

sediment or suspension in an electron microscope. They have found that

marine viruses are about 10 times more plentiful than marine bacteria.Between 106 and 10 virus particles per milliliter are present at the ocean!s

surface. "t has been estimated that the top one millimeter of the world!s

oceans could contain a total of over # $ 10#0 virus particles%&lthough little detailed wor' has been done on marine viruses( it

appears that many contain double)stranded *+&. ,ost are probably

bacteriophages and can infect both marine heterotrophs and cyanobacteria.

-p to 0/ of marine procaryotes may be infected by phages. irusesthat infect diatoms and other maor algal components of the marine phytoplan'ton

also have been detected.

,arine viruses may be very important ecologically. iruses maycontrol marine algal blooms such as red tides 2p. 3405( and bacterio)

Box 17.1

An Ocean of Viruses

phages could account for 1# or more of the total a7uatic bacterial mortality

or turnover. "f true( this is of maor ecological significance because

the reproduction of marine bacteria far exceeds marine proto8oan gra8ing

capacity. irus lysis of procaryotic and algal cells may well contributegreatly to carbon and nitrogen cycling in marine food webs. "t

could reduce the level of marine primary productivity in some situations.

Bacteriophages also may greatly accelerate the flow of genes betweenmarine bacteria. irus)induced bacterial lysis could generate

most of the free *+& present in seawater. 9ene transfer between

a7uatic bacteria by transformation 2 see pp. 305–7 5 does occur( and bacteriallysis by phages would increase its probability. :urthermore( such

high phage concentrations can stimulate gene exchange by transduction

2 see pp. 307–95. These genetic exchanges could have both positive andnegative conse7uences. 9enes that enable marine bacteria to degrade

toxic pollutants such as those in oil spills could spread through the native

population. ;n the other hand( antibiotic resistance genes in bacteria

from raw sewage released into the ocean also might be dispersed 2 see section 35.7 5.


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&lthough the details differ( animal virus

reproduction is similar to that of the

bacteriophages in having the same series of phases< adsorption( penetration and uncoating(

replication of virus nucleic acids( synthesis and

assembly of capsids( and virus release.=. iruses may harm their host cells in a variety of

ways( ranging from direct inhibition of *+&( R+&(

and protein synthesis to the alteration of plasmamembranes and formation of inclusion bodies.

#. +ot all animal virus infections have a rapid onset

and relatively short duration. Some viruses

establish long)term chronic infections> others aredormant for a while and then become active again.

Slow virus infections may ta'e years to develop.

?. @ancer can be caused by a number of factors(

including viruses. iruses may bring oncogenesinto a cell( carry promoters that stimulate a

cellular oncogene( or in other ways transformcells into tumor cells.

3. Alant viruses are responsible for many important

diseases but have not been intensely studied due totechnical difficulties. ,ost are R+& viruses.

"nsects are the most important transmission agents(

and some plant viruses can even multiply in insect

tissues before being inoculated into another plant.6. ,embers of at least seven virus families infect

insects> the most important belong to the

Baculoviridae, Reoviridae, or Iridoviridae. ,anyinsect infections are accompanied by the

formation of characteristic inclusion bodies. &

number of these viruses show promise as biological control agents for insect pests.

. "nfectious agents simpler than viruses also exist. iroids are short strands of

infectious R+& responsible for several plant diseases. Arions or virinos are

somewhat mysterious proteinaceous particles associated with certaindegenerative neurological diseases in humans and livestoc'.

18.6 Plant VirusesAlthough it has long been recognized that viruses can infectplants and cause a variety of diseases (see fgure 16.5), plantviruses generally have not been as well studied as bacteriophagesand animal viruses. This is mainly because they are often dicultto cultivate and purify. Some viruses, such as tobacco mosaicvirus (T!), can be grown in isolated protoplasts of plant cells "ust as phages and some animal viruses are cultivated in cell suspensions.#owever, many cannot grow in protoplast cultures andmust be inoculated into whole plants or tissue preparations. any


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plant viruses re$uire insect vectors for transmission% some of these can be grown in monolayers of cell cultures derived fromaphids, leafhoppers, or other insects.

Virion Morphology The essentials of capsid morphology are outlined in chapter &'and apply to plant viruses since they do not dier signicantly inconstruction from their animal virus and phage relatives. any

have either rigid or *e+ible helical capsids (tobacco mosaic virus,see fgure 16.11). thers are icosahedral or have modied theicosahedral pattern with the addition of e+tra capsomers (turnipyellow mosaic virus, fgure 18.11). ost capsids seem composedof one type of protein% no specialized attachment proteins havebeen detected. Almost all plant viruses are -A viruses, eithersingle stranded or double stranded (see tables 16.1 and 16.2)./aulimoviruses and geminiviruses with their 0A genomes aree+ceptions to this rule.

Plant Virus Taxonomy The shape, size, and nucleic acid content of many plant virusgroups are summarized in fgure 18.12. 1i2e other types of viruses, they are classied according to properties such as nucleicacid type and strandedness, capsid symmetry and size, and envelopepresence (see table 16.2).

Plant Virus ReproductionSince tobacco mosaic virus (T!) has been studied the most e+tensively,its reproduction will be brie*y described. The replicationof virus -A is an essential part of the reproduction process. ostplants contain -A3dependent -A polymerases, and it is possiblethat these normal constituents replicate the virus -A. #owever,some plant virus genomes (e.g., turnip yellow virus and cowpea mosaicvirus) appear to be copied by a virus3specic -A replicase.4ossibly T! -A is also replicated by a viral -A polymerase,but the evidence is not clear on this matter. 5our T!3specic proteins,one of them the coat protein, are 2nown to be made. Although T! -A is plus single3stranded -A and could directly serve asm-A, the production of messenger is comple+. The coat protein

m-A has the same se$uence as the 6 ′ end of the T! genome and

arises from it by some sort of intracellular processing.After the coat protein and -A genome have been synthesized,they spontaneously assemble into complete T! virions ina highly organized process (fgure 18.13). The protomers (see section16.5) come together to form dis2s composed of two layers of protomers arranged in a helical spiral. Association of coat proteinwith T! -A begins at a special assembly initiation site closeto the 6′ end of the genome. The helical capsid grows by the additionof protomers, probably as dis2s, to the end of the rod. As therod lengthens, the -A passes through a channel in its center andforms a loop at the growing end. 7n this way the -A can easilyt as a spiral into the interior of the helical capsid.-eproduction within the host depends on the virus8s abilityto spread throughout the plant. !iruses can move long distances

through the plant vasculature% usually they travel in the phloem. The spread of plant viruses in nonvascular tissue is hindered bythe presence of tough cell walls. evertheless, a virus such as T! does spread slowly, about & mm9day or less. 7t moves fromcell to cell through the plasmodesmata. These are slender cyto312 /hapter &: The !iruses;!iruses of


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proteins> are re$uired for movement between cells. The T!movement protein accumulates in the plasmodesmata, but theway in which it promotes virus movement is not understood.Several cytological changes can ta2e place in T!3infectedcells. 4lant virus infections often produce microscopically visibleintracellular inclusions, usually composed of virion aggregates,and he+agonal crystals of almost pure T! virions sometimes do

develop in T!3infected cells (fgure 18.1). The host cellchloroplasts become abnormal and often degenerate, while newchloroplast synthesis is inhibited.Transmission o& Plant VirusesSince plant cells are protected by cell walls, plant viruses have aconsiderable obstacle to overcome when trying to establish themselvesin a host. T! and a few other viruses may be carried bythe wind or animals and then enter when leaves are mechanicallydamaged. Some plant viruses are transmitted through contaminatedseeds, tubers, or pollen. Soil nematodes can transmit viruses(e.g., the tobacco ringspot virus) while feeding on roots. Tobacconecrosis virus is transmitted by parasitic fungi. #owever, the mostimportant agents of transmission are insects that feed on plants,particularly suc2ing insects such as aphids and leafhoppers.7nsects transmit viruses in several ways. They may simplypic2 up viruses on their mouth parts while feeding on an infectedplant, then directly transfer the viruses to the ne+t plant they visit.!iruses may be stored in an aphid8s foregut% the aphid will infectplants when regurgitating while it is feeding. Several plantviruses?for e+ample, the wound tumor virus?can multiply inleafhopper tissues before reaching the salivary glands and beinginoculated into plants (i.e., it uses both insects and plants as hosts).&. @hy have plant viruses not been as well studied as animal andbacterial virusesB. 0escribe in molecular terms the way in which T! is reproduced.6. #ow are plant viruses transmitted between hosts&:.' 4lant !iruses 13ds'() $RT% ss'()dsR() ssR() $*% ssR() $+%ssR() $RT%,aulimo-iridaeReo-iridae!ii-irusPhytoreo-irus

/ry0a-irus Rhado-iridae,ytorhado-irus(ucleorhado-irus

emini-iridaePseudo-iridaee4ui-iridaeTomus-iridae5uteo-iridaeMaraf-irusoemo-irusTymo-irus$mra-irus%

,omo-iridae7daeo-irus

Poty-iridae,lostero-iridaeromo-iridaeunya-iridae

Tospo-irusTenui-irus/phio-irusMastre-irus,urto-irus egomo-irus(ano-irus,ucumo-irusromo-irus7lar-irus)l&amo-irusToamo-irusTora-irus9ordei-irus!uro-irusPeclu-irusPomo-iruseny-irus


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)llexi-irus: ,arla-irus: !o-ea-irus: Potex-irus,apillo-irus: Tricho-irus: Viti-irus/urmia-irusVaricosa-irus

Partiti-iridae)lphacrypto-irusetacrypto-irus

1;; nm,aulimo-irus,sVMV


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-A genomes. uclear polyhedrosis viruses and granulosisviruses are baculoviruses?rod3shaped, enveloped viruses of helicalsymmetry and with double3stranded 0A. The inclusion bodies, both polyhedral and granular, are proteinin nature and enclose one or more virions (fgure 18.1?). 7nsectlarvae are infected when they feed on leaves contaminatedwith inclusion bodies. 4olyhedral bodies protect the virions

against heat, low p#, and many chemicals% the viruses can remainviable in the soil for years. #owever, when e+posed to al2aline insectgut contents, the inclusion bodies dissolve to liberate the virions,which then infect midgut cells. Some viruses remain in themidgut while others spread throughout the insect. Iust as withbacterial and vertebrate viruses, insect viruses can persist in a latentstate within the host for generations while producing no diseasesymptoms. A reappearance of the disease may be induced bychemicals, thermal shoc2, or even a change in the insect8s diet.uch of the current interest in insect viruses arises from theirpromise as biological control agents for insect pests (see chapter "2). any people hope that some of these viruses may partially replacethe use of to+ic chemical pesticides. Eaculoviruses have receivedthe most attention for at least three reasons. 5irst, they attac2only invertebrates and have considerable host specicity% this

means that they should be fairly safe for nontarget organisms. Second,because they are encased in protective inclusion bodies, theseviruses have a good shelf life and better viability when dispersedin the environment. 5inally, they are well suited for commercialproduction since they often reach e+tremely high concentrationsin larval tissue (as high as &D&D viruses per larva). The use of nuclearpolyhedrosis viruses for the control of the cotton bollworm,0ouglas r tussoc2 moth, gypsy moth, alfalfa looper, and


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symptoms. A plant may be infected without showing symptoms?that is, it may have a latent infection. The same viroid, when in anotherspecies, might well cause a severe disease. Although viroidscould be replicated by an -A3dependent -A polymerase, theyappear to be synthesized from -A templates by a host -A polymerasethat mista2es them for a piece of 0A. A rolling3circle typemechanism seems to be involved (see p. 2#6).

The potato spindle3tuber disease agent (4ST!) has beenmost intensely studied. 7ts -A is about &6D,DDD daltons or 6CKnucleotides in size, much smaller than any virus genome. Several4ST! strains have been isolated, ranging in virulence from onesthat cause only mild symptoms to lethal varieties. All variationsin pathogenicity are due to a few nucleotide changes in two shortregions on the viroid. 7t is believed that these se$uence changesalter the shape of the rod and thus its ability to cause disease. There is evidence that an infectious agent dierent from bothviruses and viroids can cause disease in livestoc2 and humans. The agent has been called a prion (for proteinaceous infectiousparticle). The best studied of these prions causes a degenerativedisorder of the central nervous system in sheep and goats% thisdisorder is named scrapie. ALicted animals lose coordination of their movements, tend to scrape or rub their s2in, and eventually

cannot wal2. o nucleic acid has yet been detected in the agent.7t seems to be a 66 to 6C 20a hydrophobic membrane protein, oftencalled 4r4 (for prion protein). The PrP gene is present inmany normal vertebrates and invertebrates, and the prion proteinis bound to the surface of neurons. 4resumably an altered 4r4 isat least partly responsible for the disease.0espite the isolation of 4r4, the mechanism of prion diseasescontinues to stir controversy. ost researchers are convinced thatprion diseases are transmitted by the 4r4 alone. They believe thatthe infective pathogen is an abnormal 4r4 (4r4Sc% Sc, scrapieassociated),a protein that has either been changed in conformationor chemically modied. @hen 4r4Sc enters a normal brain, itmight bind to the normal cellular 4r4 (4r4/) and induce it to foldinto the abnormal conformation. The newly produced 4r4Sc mol3

16 /hapter &: The !iruses;!iruses of


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general organization of a viroid. The closed single3stranded -A circlehas e+tensive intrastrand base pairing and interspersed unpaired loops.!iroids have ve domains. ost changes in viroid pathogenicity seemto arise from variations in the 4 and T1 domains.

ecule could then convert more normal 4r4/ proteins to the 4r4Scform. Alternatively, 4r4Sc could activate enzymes that modify4r4 structure. 4rions with dierent amino acid se$uences andconformations convert 4rp/ molecules to 4r4Sc in other hosts.ore support for the =protein3only> hypothesis has been suppliedby studies on the yeast protein Sup6C, which aids in the terminationof protein synthesis in %accharom&ces cerevisiae. EecauseSup6C acts much li2e mammalian prions, it has been calleda yeast prion. Sup6C e+ists in an inactive form in NP%I M O cells, andthe phenotype can be passed on to daughter cells. The inactive, insolubleform of Sup6C aggregates and translation does not terminateproperly. There is evidence that the NP%I M O phenotype proliferatesin yeast when the inactive prion form of Sup6C interactswith normal, soluble Sup6C and induces a self3propagating conformationalchange of active Sup6C to the inactive form.

A minority thin2 that the =protein3only> hypothesis is inade$uate. They are concerned about the e+istence of prion strains,which they believe are genetic, and about the problem of how geneticinformation can be transmitted between hosts by a protein.0oubters note that proteins have never been 2nown to carry geneticinformation. 7t could be that prions somehow either directlyaid an infectious agent such as an un2nown virus or increase susceptibilityto the agent. 4ossibly the real agent is a tiny nucleicacid that is coated with 4r4 and interacts with host cells to causedisease. This hypothesis is consistent with the nding that manystrains of the scrapie agent have been isolated. There is also someevidence that a strain can change or mutate. Supporters of the=protein3only> hypothesis reply that strain characteristics aresimply due to structural dierences in the 4r4 molecule.

As mentioned earlier, some slow virus diseases may be dueto prions or virinos. This is particularly true of certain neurologicaldiseases of humans and animals. Eovine spongiformencephalopathy (ES< or =mad cow disease>), 2uru, fatal familialinsomnia, the /reutzfeldt3Ia2ob disease (/I0), and Herstmann3StrPussler3Schein2er syndrome (HSS) appear to beprion diseases. They result in progressive degeneration of thebrain and eventual death. ad cow disease has reached epidemicproportions in Hreat Eritain and initially spread becausecattle were fed bone meal made from cattle. 7t has now beenshown that eating meat from cattle with ES< can cause a variantof /reutzfeldt3Iacob disease in humans. ore than KD peoplealready have died in the Gnited Qingdom and 5rance fromthis source. /I0 and HSS are rare and cosmopolitan in distributionamong middle3aged people, while 2uru has been found

only in the 5ore, an eastern ew Huinea tribe. This tribe had acustom of consuming dead 2insmen, and women were giventhe honor of preparing the brain and practicing this ritual cannibalism. They and their children were infected by handling thediseased brain tissue. (ow that cannibalism has been eliminated,the incidence of 2uru has decreased and is found onlyamong the older adults.)&. @hat are viroids and why are they of great interestB. #ow does a viroid dier from a virus6. @hat is a prion 7n what way does a prion appear to dierfundamentally from viruses and viroids


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Summary 1>ummary&. Animal viruses are classied according tomany properties% the most important are theirmorphology and nucleic acids (fgures18.1*18.3).B. The rst step in the animal virus life cycle isadsorption of the virus to a target cell receptor

site% often special capsid structures areinvolved in this process.6. !irus penetration of the host cell plasmamembrane may be accompanied by capsidremoval from the nucleic acid or uncoating.ost often penetration occurs throughengulfment to form coated vesicles, butmechanisms such as direct fusion of theenvelope with the plasma membrane also areemployed (fgure 18.).F.


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&6. /ancer is characterized by the formation of amalignant tumor that metastasizes or invadesother tissues and can spread through the body./arcinogenesis is a comple+, multistepprocess involving many factors.&F. !iruses cause cancer in several ways. 5ore+ample, they may bring a cancer3causinggene, or oncogene, into a cell, or the virion mayinsert a promoter ne+t to a cellular oncogene

and stimulate the gene to greater activity.

&C. ost plant viruses have an -A genome andmay be either helical or icosahedral. 0ependingon the virus the -A genome may bereplicated by either a host -A3dependent-A polymerase or a virus3specic -Areplicase.&'. The T! nucleocapsid forms spontaneouslyby self3assembly when dis2s of coat proteinprotomers comple+ with the -A.&J. 4lant viruses are transmitted in a variety of ways. Some enter through lesions in planttissues, while others are transmitted bycontaminated seeds, tubers, or pollen. ostare probably carried and inoculated by plantfeedinginsects.&:. ycoviruses from higher fungi have isometriccapsids and ds-A, whereas the viruses of lower fungi may have either ds-A ords0A genomes.&K. embers of several virus families?mostimportantly the Baculoviridae, !eoviridae,and Iridoviridae?infect insects, and many of these viruses produce inclusion bodies that aidin their transmission.BD. Eaculoviruses and other viruses are nding usesas biological control agents for insect pests.B&. 7nfectious agents simpler than viruses e+ist. 5ore+ample, several plant diseases are caused byshort strands of infectious -A called viroids.BB. 4rions are small agents associated with at

least si+ degenerative nervous systemdisorders; scrapie, bovine spongiformencephalopathy, 2uru, fatal familial insomnia,the Herstmann3StrPussler3Schein2ersyndrome, and /reutzfeldt3Ia2ob disease. Theprecise nature of prions is not yet clear.

Aey Termsacute infection "1'anaplasia "11cancer "11chronic virus infection "1'coated vesicles "'#cytocidal infection "1'defective interfering (07) particle "1'early genes "'#inclusion bodies "1'late genes "'(

latent virus infection "1'metastasis "11neoplasia "11oncogene "11persistent infection "1'prion "16procapsids "'(proviral 0A "')replicase "'6replicative form "'6retrovirus "')reverse transcriptase (-T) "')ribonuclease # "')


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slow virus diseases "1'transcriptase "'6tumor "11viroid "16

)dditional Reading/hapter &' references also should be consulted,particularly the introductory and advancedte+ts.

eneral


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cancer Try to thin2 of approaches other thanthose discussed in the chapter. Hive a ma"orreason why it is so dicult to prove that aspecic virus causes human cancer. 7s itaccurate to say that viruses cause cancer


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a heterotrophic organism. ne of the most interesting such relationshipis the 4ompeii worm ( Alvinella pompe3ana), named for thedeep3sea submersible from @oods #ole, assachusetts. This unusualorganism is &D cm in length and lives in tunnels near watersthat approach :DW/ in a deep area of the 4acic cean (fgure28.11). 7t uses as a nutrient source bacteria that appear to o+idize organicmatter and reduce sulfur compounds. A deep3sea crustacean

has been discovered that uses sulfur3o+idizing autotrophic bacteriaas its food source. This shrimp, !imicaris eoculata (fgure 28.12)B:.B icrobial 7nteractions 6;?Methanospirillum sp.3


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often surround the nematodes, but they also serve as a food supply.7n &KKD, hydrothermal vents were discovered in a freshwaterenvironment, at the bottom of 1a2e Eai2al, the oldest (BC millionyears old) and deepest la2e in the world. This la2e is located in thefar east of -ussia (fgure 28.1a) and has the largest volume of anyfreshwater la2e (not the largest area?which is 1a2e Superior). Thebacterial growths, with long white strands, are in the center of the

vent eld where the highest temperatures are found (gure B:.&Fb).At the edge of the vent eld, where the water temperature is lower,the bacterial mat ends, and sponges, gastropods, and other organisms,which use the sulfur3o+idizing bacteria as a food source, arepresent (gure B:.&Fc). Similar although less developed areas havebeen found in Rellowstone 1a2e,@yoming.A hydrogen suldebased ecosystem has been discovered insouthern -omania that is closer to the earth8s surface. /aves in thearea contain mats of microorganisms that + carbon dio+ide usinghydrogen sulde as the reductant. 5orty3eight species of caveadaptedinvertebrates are sustained by this chemoautotrophic base.A form of protocooperation also occurs when a population of similar microorganisms monitors its own density, the process of $uorum sensing, which was discussed in section '.C. The microorganismsproduce specic autoinducer compounds, and as the

population increases and the concentration of these compoundsreaches critical levels, specic genes are e+pressed. These responsesare important for microorganisms that form associationswith plants and animals, and particularly for human pathogens.&. @hy are Alvinella, !imicaris and $ubostrichus good e+amples of protocooperative microorganism3animal interactionsB. @hat important freshwater hydrothermal vent communities havebeen described

,ommensalism,ommensalism N1atin com, together, and mensa, tableO is a relationshipin which one symbiont, the commensal: benets whilethe other (sometimes called the host) is neither harmed nor helpedas shown in gure B:.&. This is a unidirectional process. ftenboth the host and the commensal =eat at the same table.> The spatial

pro+imity of the two partners permits the commensal to feedon substances captured or ingested by the host, and the commensaloften obtains shelter by living either on or in the host. Thecommensal is not directly dependent on the host metabolicallyand causes it no particular harm. @hen the commensal is separatedfrom its host e+perimentally, it can survive without beingprovided some factor or factors of host origin.6;6 /hapter B: icroorganism 7nteractions and icrobial


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/ompanies, BDDB

/ommensalistic relationships between microorganisms includesituations in which the waste product of one microorganismis the substrate for another species. An e+ample is nitrication,the o+idation of ammonium ion to nitrite by microorganisms suchas 4itrosomonas, and the subse$uent o+idation of the nitrite to nitrateby 4itrobacter and similar bacteria (see pp. 1#"). 4itrobacter

benets from its association with 4itrosomonas becauseit uses nitrite to obtain energy for growth./ommensalistic associations also occur when one microbialgroup modies the environment to ma2e it more suited for anotherorganism. 5or e+ample, in the intestine the common, nonpathogenicstrain of $scherichia coli lives in the human colon,but also grows $uite well outside the host, and thus is a typicalcommensal. @hen o+ygen is used up by the facultatively anaerobic$. coli, obligate anaerobes such as Bacteroides are able togrow in the colon. The anaerobes benet from their associationwith the host and $. coli, but $. coli derives no obvious benetfrom the anaerobes. 7n this case the commensal $. coli contributesto the welfare of other symbionts. /ommensalism can involveother environmental modications. The synthesis of acidic wasteproducts during fermentation stimulate the proliferation of more

acid3tolerant microorganisms, which are only a minor part of themicrobial community at neutral p#s. A good e+ample is the successionof microorganisms during mil2 spoilage. @hen biolmsare formed (section B:.F), the colonization of a newly e+posedsurface by one type of microorganism (an initial colonizer) ma2esit possible for other microorganisms to attach to the microbiallymodied surface./ommensalism also is important in the colonization of thehuman body and the surfaces of other animals and plants. The microorganismsassociated with an animal s2in and body oricescan use volatile, soluble, and particulate organic compounds fromthe host as nutrients (see section #1.2). Gnder most conditionsthese microbes do not cause harm, other than possibly contributingto body odor. Sometimes when the host organism is stressedor the s2in is punctured, these normally commensal microorganismsmay become pathogenic. These interactions will be discussedin chapter 6&.&. #ow does commensalism dier from protocooperationB. @hy is nitrication a good e+ample of a commensalistic process6. @hy are commensalistic microorganisms important for humans@here are these found in relation to the human body

PredationPredation is a widespread phenomenon where the predator engulfsor attac2s the prey, as shown in gure B:.&. The prey can belarger or smaller than the predator, and this normally results in thedeath of the prey.An interesting array of predatory bacteria are active in nature.Several of the best e+amples are shown in fgure 28.1?: includingBdellovibrio, *ampirococcus, and 0aptobacter. Mosco#Russia LakeBaikal FrolikhaBa 'epth contourinter-al 1?; &eetRussiaFrolikhaBa 1:2;; @;; 6;;


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1?;3;;9ot -ent andanimal communityPlume o& ele-ated#ater temperaturee; Miles 1

(b)(c)!igure 28.1 9ydrothermal Vent Ccosystems in !resh#aterCn-ironments. 1a2e Eai2al (in -ussia) has been found to have lowtemperature hydrothermal vents. (a) 1ocation of 1a2e Eai2al, site of the hydrothermal vent eld. () Eacterial mat near the center of thevent eld. (c) Eacterial laments and sponges at the edge of the venteld. 7a8 %ource 0ata +rom the 4ational 9eographic %ociet&.(a)PrescottD9arleyDAleinEMicroiology: !i&th CditionV777. Ccology andymiosis28. Microorganism7nteractions and MicroialCcologyU The cHrawV#ill/ompanies, BDDB

plasma membrane, a periplasmic mode of attac2, followed by lysisof the prey and release of progeny (see fgure 22.##). This bacteriumhas an interesting life cycle, which is discussed in section BB.F.onlytic forms also are observed. *ampirococcus attaches tothe surface of the prey (an epibiotic relationship) and then secretesenzymes to release the cell contents. 0aptobacter penetrates a susceptiblehost and uses the cytoplasmic contents as a nutrient source./iliates are e+cellent e+amples of predators that engulf theirprey, and based on wor2 with *uorescently mar2ed prey bacteria,a single ciliate can ingest 'D to JD prey bacteria per hourX 4redationon bacteria is important in the a$uatic environment and insewage treatment where the ciliates remove suspended bacteriathat have not settled.A surprising nding is that predation has many benecial eects,especially when one considers interactive populations of

predators and prey, as summarized in tale 28.3. Simple ingestionand assimilation of a prey bacterium can lead to increased rates of nutrient cycling, critical for the functioning of the microial loop(see section 2.1 and fgure 2."). 7n this process, organic matterproduced through photosynthetic and chemotrophic activity ismineralized before it reaches the higher consumers, allowing theminerals to be made available to the primary producers, in a=loop.> This is important in freshwater, marine, and terrestrial environments.7ngestion and short3term retention of bacteria also iscritical for functioning of ciliates in the rumen, wheremethanogenic bacteria contribute to the health of the ciliates by decreasingto+ic hydrogen levels through using #B to producemethane, which then is passed from the rumen.4redation also can provide a protective, high3nutrient environmentfor particular prey. /iliates ingest :egionella andprotect this important pathogen from chlorine, which often isused in an attempt to control :egionella in cooling towers andair3conditioning units. The ciliate serves as a reservoir host. :egionella pneumophila also has been found to have a greater potentialto invade macrophages and epithelial cells after predation,indicating that ingestion not only provides protection butalso may ma2e the bacterium a better pathogen. A similar phenomenonof survival in protozoa been observed for /&cobac;6;8 /hapter B: icroorganism 7nteractions and icrobial


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(b) Vampirococcus

(c) Daptobacter

!igure 28.1? Cxamples o& Predatory acteria !ound in (ature.(a) Bdellovibrio, a periplasmic predator that penetrates the cell wall andgrows outside the plasma membrane, () *ampirococcus with its uni$ueepibiotic mode of attac2ing a prey bacterium, and (c) 0aptobacter showing its cytoplasmic location as it attac2s a susceptible bacterium.

Tale 28.3 The any 5aces of 4redationPredation Result Cxample

0igestion The microbial loop. Soluble organic matter from primary producers is normally used by bacteria, which become aparticulate foodsource for higher consumers. 5lagellates and ciliates prey on these bacteria and digest them, ma2ing the nutrients theycontainavailable again in mineral form for use in primary production, creating the microbial loop. 7n this way a large portion of thecarbon+ed by the photosynthetic microbes is mineralized and recycled (thus the term microbial loop) and does not reach thehighertrophic levels of the ecosystem (see fgure 2.").4redation also can reduce the density3dependent stress factors in prey populations, allowing more rapid growth andturnover of the preythan would occur if the predator were not active.-etention Eacteria retained within the predator serve a useful purpose, as in the transformation of to+ic hydrogen producedby ciliates in the rumento harmless methane. Also, trapping of chloroplasts (2leptochloroplasty) by protozoa provides the predator withphotosynthate.

4rotection and The intracellular survival of :egionella ingested by ciliates protects it from stresses such as heating andchlorination. 7ngestion alsoincreased tness results in increased pathogenicity when the prey is again released to the e+ternal environment, and thismay be re$uired for infectionof humans. The predator serves as a reservoir host.anoplan2ton may be ingested by zooplan2ton and grow in the zooplan2ton digestive system. They are then released tothe environmentin aa tter state. 0issemination to new locations also occurs.

terium avium, a pathogen of worldwide concern. These protectiveaspects of predation have ma"or implications for survivaland control of disease3causing microorganisms in the biolmspresent in water supplies and air3conditioning systems. 7n marinesystems the ingestion of nanoplan2ton by zooplan2tonprovides a nutrient3rich environment that allows nanoplan2tonreproduction in the digestive tract and promotes disseminationin the environment. A similar process occurs after bacteria areingested by polychaetes (segmented worms found mostly inmarine environments).5ungi often show interesting predatory s2ills. Some fungican trap protozoa by the use of stic2y hyphae or 2nobs, stic2y networ2sof hyphae, or constricting or nonconstricting rings. A classice+ample is Arthrobotr&s, which traps nematodes by use of constricting rings. After the nematode is trapped, hyphae growinto the immobilized prey and the cytoplasm is used as a nutrient.ther fungi have conidia that, after ingestion by an unsuspectingprey, grow and attac2 the susceptible host from inside the intestinaltract. 7n this situation the fungus penetrates the host cells ina comple+ interactive process. Thus predation, which usually has a fatal and nal outcome

for an individual prey organism, has a wide range of benecial eectson prey populations, and is critical in the functioning of naturalenvironments.

Microorganisms and Ccosystemsicroorganisms, as they interact with each other and other organisms,and in*uence nutrient cycling in their specic microenvironmentsand niches, also contribute to the functioning of


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ecosystems. These self3regulating biologicalunits respond to environmental changes by modifying theirstructure and function.icroorganisms in ecosystems can have two complementaryroles; (&) the synthesis of new organic matter from /B and other

inorganic compounds during primary production and (B) decompositionof this accumulated organic matter. A simple selfregulatingecosystem in which primary production of organicmatter occurs is shown in fgure 28.31. This consists of an algaand a =halo> of surrounding bacteria that are using the organicmatter formed by algal photosynthesis as a carbon, electron, andenergy source, and returning the organic matter to its originalmineral constituents. Self3regulation in this ecological unit isshown by its response to light. 0ecreased light *u+es lead to a decreasein photosynthesis and organic matter release. Gnder theseconditions, the heterotrophic bacterial community will be limitedand its activity and biomass may be decreased. The general relationships between the primary producersthat synthesize organic matter, the heterotrophic decomposers:and the consumers are illustrated in fgure 28.32. icroorganisms

of dierent types contribute to each of these complementaryrelationships.7n terrestrial environments the primary producers are usuallyvascular plants. 7n freshwater and marine environments,the cyanobacteria and algae (see section 21.# and chapter 26)play a similar role. The ma"or energy source driving primaryproduction is light in both habitats although in hydrothermaland hydrocarbon seep areas, chemotrophic ecosystems occur. The higher consumers: including humans, are chemoheterotrophs. These consumers depend on the =life support systems>provided by organisms that accumulate and decomposeorganic matter.icroorganisms thus carry out many important functions asthey interact in ecosystems, including;

&. /ontributing to the formation of organic matter throughphotosynthetic and chemosynthetic processes.622 /hapter B: icroorganism 7nteractions and icrobial


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nucleic acids) are released (see section 2.2). The fecal3oral routeof disease transmission, often involving foods and waters, and theac$uisition of diseases in hospitals (nosocomial infections) areimportant e+amples of pathogen movement between ecosystems.


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!igure 28.32 The Vital Role o& Microorganisms in Ccosystems.icroorganisms play vital roles in ecosystems as primary producers,decomposers, and primary consumers. /arbon is +ed by the primaryproducers, including microorganisms, which use light or chemicallybound energy. /hemoheterotrophic bacteria and fungi serve as themain decomposers of organic matter, ma2ing minerals again availablefor use by the primary producers. /iliates and *agellates, importantmicrobial primary consumers, feed on the bacteria and fungi, recyclingnutrients as part of the microbial loop. rganic matter ().B. 0ecomposing organic matter, often with the release of inorganic compounds (e.g., /B, #F M , /#F, #B) inmineralization processes.6. Serving as a nutrient3rich food source for otherchemoheterotrophic microorganisms, including protozoaand animals.F. odifying substrates and nutrients used in symbioticgrowth processes and interactions, thus contributing tobiogeochemical cycling.C. /hanging the amounts of materials in soluble and gaseousforms. This occurs either directly by metabolic processes orindirectly by modifying the environment.

'. 4roducing inhibitory compounds that decrease microbialactivity or limit the survival and functioning of plants andanimals.J. /ontributing to the functioning of plants and animalsthrough positive and negative symbiotic interactions.&. 0ene the following terms; ecosystem, primary production,decomposer, mineralization.B. 1ist important functions of higher consumers in naturalenvironments.6. @hat are the important functions of microorganisms inecosystems

Microorganism Mo-ement et#een Ccosystemsicroorganisms constantly are moving and being moved betweenecosystems. This often happens naturally in many ways; (&) soil istransported around the


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function as self3regulating units.> These self3regulating biologicalunits respond to environmental changes by modifying theirstructure and function.icroorganisms in ecosystems can have two complementaryroles; (&) the synthesis of new organic matter from /B and otherinorganic compounds during primary production and (B) decompositionof this accumulated organic matter. A simple selfregulating

ecosystem in which primary production of organicmatter occurs is shown in fgure 28.31. This consists of an algaand a =halo> of surrounding bacteria that are using the organicmatter formed by algal photosynthesis as a carbon, electron, andenergy source, and returning the organic matter to its originalmineral constituents. Self3regulation in this ecological unit isshown by its response to light. 0ecreased light *u+es lead to a decreasein photosynthesis and organic matter release. Gnder theseconditions, the heterotrophic bacterial community will be limitedand its activity and biomass may be decreased. The general relationships between the primary producersthat synthesize organic matter, the heterotrophic decomposers:and the consumers are illustrated in fgure 28.32. icroorganismsof dierent types contribute to each of these complementaryrelationships.

7n terrestrial environments the primary producers are usuallyvascular plants. 7n freshwater and marine environments,the cyanobacteria and algae (see section 21.# and chapter 26)play a similar role. The ma"or energy source driving primaryproduction is light in both habitats although in hydrothermaland hydrocarbon seep areas, chemotrophic ecosystems occur. The higher consumers: including humans, are chemoheterotrophs. These consumers depend on the =life support systems>provided by organisms that accumulate and decomposeorganic matter.icroorganisms thus carry out many important functions asthey interact in ecosystems, including;&. /ontributing to the formation of organic matter throughphotosynthetic and chemosynthetic processes.

622 /hapter B: icroorganism 7nteractions and icrobial


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ac$uisition of diseases in hospitals (nosocomial infections) areimportant e+amples of pathogen movement between ecosystems.


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decomposers, and primary consumers. /arbon is +ed by the primaryproducers, including microorganisms, which use light or chemicallybound energy. /hemoheterotrophic bacteria and fungi serve as themain decomposers of organic matter, ma2ing minerals again availablefor use by the primary producers. /iliates and *agellates, importantmicrobial primary consumers, feed on the bacteria and fungi, recyclingnutrients as part of the microbial loop. rganic matter ().B. 0ecomposing organic matter, often with the release of inorganic compounds (e.g., /B, #F M , /#F, #B) inmineralization processes.6. Serving as a nutrient3rich food source for otherchemoheterotrophic microorganisms, including protozoaand animals.F. odifying substrates and nutrients used in symbioticgrowth processes and interactions, thus contributing tobiogeochemical cycling.C. /hanging the amounts of materials in soluble and gaseousforms. This occurs either directly by metabolic processes orindirectly by modifying the environment.'. 4roducing inhibitory compounds that decrease microbialactivity or limit the survival and functioning of plants and

animals.J. /ontributing to the functioning of plants and animalsthrough positive and negative symbiotic interactions.&. 0ene the following terms; ecosystem, primary production,decomposer, mineralization.B. 1ist important functions of higher consumers in naturalenvironments.6. @hat are the important functions of microorganisms inecosystems

Microorganism Mo-ement et#een Ccosystemsicroorganisms constantly are moving and being moved betweenecosystems. This often happens naturally in many ways; (&) soil istransported around the . Such stress factorshave ma"or eects on microbial populations and communities,and can create an extreme en-ironment: as shown infgure 28.33. 7n these cases high salt concentrations, e+tremetemperature, and acidic conditions have aected the microbialcommunities. The microorganisms that survive in such environments


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are described as extremophiles: and such e+tremeenvironments are usually considered to have decreased microbialdiversity, as "udged by the microorganisms that can be cultured.@ith the increased use of molecular detection techni$ues,however, it appears that there is surprising diversityamong the microorganisms that cannot be cultured from thesee+treme environments. 5urther wor2 to establish relationships

between the microorganisms that can be observed and detectedby these molecular techni$ues and culturable microorganismswill be re$uired in the future. The in*uence of environmental factorson growth (pp. &B&6&)

any microbial genera have specic re$uirements for survivaland functioning in such so3called e+treme environments.5or e+ample, a high sodium ion concentration is re$uired tomaintain membrane integrity in many halophilic bacteria, includingmembers of the genus


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marine trenches /ethanop&rus @andleriP&rodictium ab&ssi'J&DBW/, marine basins P&rococcus ab&ssi:CW/, hot springs =hermus%ul+olobusJCW/, sulfur hot springs =hermothri thiopara1ow temperature &BW/, antarctic ice Ps&chromonas ingrahamiismotic stress &6&CY a/l hlam&domonasBCY a/l but re$uired and even, perhaps, ideal. Thermophilicmicroorganisms (pp. &B'% F'6)

&. @hat are the main factors that lead to the creation of e+tremeenvironmentsB. @hy are molecular techni$ues possibly changing our view of these environments6. @hat is uni$ue about >erroplasma acidarmanus

28.? Methods in Microial CcologyA wide variety of techni$ues can be used to evaluate the presence,types, and activities of microorganisms as populations, communities,


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and parts of ecosystems (tale 28.8). easurements made bythese techni$ues can span a range of time scales and physical dimensions.7n marine, freshwater, sewage, and plant root environments,as e+amples, responses can be measured in seconds and minutes.5or deep marine and soil organic matter changes, a time scaleof years, decades, or even centuries may be re$uired. The physicalscale used in a study may range from a single bacterium and its microenvironment

to a la2e, ocean, or an entire plant3soil system.As noted at the beginning of this chapter, a fundamentalproblem in studying microorganisms in nature is the inability toculture and characterize most organisms that can be observed. This long3standing problem is now being approached by the useof molecular techni$ues, by which nonculturable microorganismscan be characterized and compared with 2nown genomic se$uences(see chapter 1).icrobial community diversity can be assessed by severalapproaches, including molecular phylogeny based on analyses of small subunit (SSG) ribosomal -A (see pp. "###5). Smallamounts of 0A also can be recovered from environmental samplesor individual cells and =amplied> by use of the polymerasechain reaction (4/-). The polymerase chain reaction (pp. 6B'BJ)As noted in table B:.:, some of these techni$ues are limited

in terms of the types of samples that can be analyzed. This maybe due to low microbial populations (marine and some freshwatersamples) or high concentrations of interfering organic matteror particulates in samples. 7n contrast, the newer molecular procedures,such as direct 0A e+traction, 0A amplication ngerprinting(0A5), &'S and &:S -A3based phylogenetic analysis,4/-, and 0A probe and hybridization techni$ues, areapplicable to a wider variety of samples.-ecently gel array microchips containing mi+tures of probes,called =genosensors,> or microarrays: have been developed (see pp. #5"? 1'1(). These allow the detection of small subunit ribosomal-A from mi+ed populations. 7n addition, probes can detectspecic groups of microorganisms such as the iron3 and manganeseo+idizingsheathed bacteria by the use of &'S r-A3based probes.

any newer and more sensitive procedures are now available,including the use of radioactive substrates and sophisticated techni$uesto measure the viability and activity of individual microorganisms.#ybridization techni$ues can be used to =probe> coloniesor single cells to determine if they contain specic 0A or -Ase$uences. The techni$ue of whole3cell hybridization has progressedto the point that =subcluster3specic> probes have been developed. These allow the simultaneous detection of dierent microbialtypes in the same preparation (see fgure 2., p. 6"#).7n most studies employing these molecular approaches to analyzecomple+ microbial communities, nucleic acids have beene+tracted from the sample, followed typically by cloning and furthergenomic and phylogenetic analyses. The specic source of the nucleic acids that are being studied is not 2nown. Eecause of 626 /hapter B: icroorganism 7nteractions and icrobial


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Such microorganisms, termed hyperthermophiles, with optimumgrowth temperatures of :DW/ or above (see p. 126), confront uni$uechallenges in nutrient ac$uisition, metabolism, nucleic acid replication,and growth. any of these are anaerobes that depend on elemental sul3

ox 28.2

The Potential o& Microorganisms &rom 9igh


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Stable and radioactive isotope studies [[ [[ [ [[ [[icrobial activity icroscopy with reducible dyes [[ [[ [[ [[ [[Autoradiography [[ [[ [[ [[ [[


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obligatory), protocooperation (mutuallybenecial, not obligatory), and commensalistic(product of one organism can be usedbenecially by another organism). egativeinteractions include predation (use andingesting92illing a larger or smaller prey),parasitism (a longer3term internal maintenanceof another organism or acellular infectiousagent), and amensalism (a microbial product

can inhibit another organism). /ompetitioninvolves organisms competing for space or alimiting nutrient. The $uality of theseinteractions can change, depending on theenvironment and the characteristics of theparticular organisms.'. utual advantage is central to positiveorganism3organism interactions. Theseinteractions can be based on material transfersrelated to energetics, cell3to3cellcommunication, or physical protection. @ithseveral important mutualistic interactions,chemolithotrophic microorganisms play acritical role in ma2ing organic matter availablefor use by an associated organism (e.g.,endosymbionts in !i+tia).J. 4redation and parasitism are closely related.

4redation has many positive eects onpopulations of predators and prey. Theseinclude the microbial loop (returning mineralsimmobilized in organic matter to mineralforms for reuse by chemotrophic andphotosynthetic primary producers), protectionof prey from heat and damaging chemicals,and possibly aiding pathogenicity, as with:egionella.:. A consortium is a physical association of organisms that have a mutually benecialrelationship based on positive interactions.K. Syntrophism simply means growth together. 7tdoes not re$uire physical contact but only amutually positive transfer of materials, such asinterspecies hydrogen transfer.&D. The rumen is an e+cellent e+ample of amutualistic interaction between a ruminantand its comple+ microbial community. 7n thismicrobial community, comple+ plant materialsare bro2en down to simple organic compoundsthat can be absorbed by the animal, as well asforming waste gases such as methane that arereleased to the environment (fgure 28.8).&&. 4rotocooperative interactions are benecialfor both organisms but are not obligatory(fgure 28.@). 7mportant e+amples are marineanimals, including Alvinella, !imicarus, and$ubostrichus, that involve interactions withhydrogen suldeo+idizing chemotrophs.&B. These varied positive and negative interactionsoccur in comple+ biological systems and leadto feedbac2 responses of varied members of abiological community.&6. icrobes can be present as individual cells, as

populations of similar organisms, or asmi+tures of populations or communities.

These populations and communities can beparts of self3regulating ecosystems.&F. icroorganisms?functioning with plants,animals, and the environment?play importantroles in nutrient cycling, which is also termedbiogeochemical cycling. Assimilatory processesinvolve incorporation of nutrients into theorganism8s biomass during metabolism%dissimilatory processes, in comparison, involvethe release of nutrients to the environment aftermetabolism (fgure 28.18)


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&C. Eiogeochemical cycling involves o+idationand reduction processes, and changes in theconcentrations of gaseous cycle components,such as carbon, nitrogen, and sulfur can resultfrom microbial activity.&'. icroorganisms serve as primary producersthat accumulate organic matter (fgure 28.32).


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J. 0isease3causing microorganisms, as well as organic materials, areconstantly being added to waters. These can be transported over largedistances, especially in rapidly moving rivers, la2es, and marineenvironments. Atmospheric3borne dusts and other materials, includingpollutants, can be carried to the farthest regions of the oceans, freshwaterbodies, and ice3covered regions of the world.:. any important human pathogens, such as %higella, *ibrio, and:egionella, are found in waters. These can occur normally or can survivefor various intervals after addition to waters. ften protozoa provide

protection for such pathogens, especially when the protozoa are associatedwith biolms.K. A$uatic environments can serve as reservoirs and transmission routes fordisease3causing microorganisms. A ma"or goal of a$uatic systemmanagement is to control pathogen survival and transfer.&D. @ater is an important reservoir for the survival and dissemination of protozoa and viruses. These cannot be reliably controlled by chlorination.4rotozoan pathogens include &clospora and 9iardia.&&. The biological use of organic wastes follows regular and predictablese$uences. nce these se$uences are understood, more ecient sewagetreatment systems can be created.&B. Sewage treatment can be carried out using large vessels where mi+ing andaeration can be controlled (conventional treatment). /onstructed wetlands,where a$uatic plants and their associated microorganisms are used, now arending widespread applications in the treatment of li$uid wastes.&6. 7ndicator organisms, which usually die o at slower rates than manydisease3causing microorganisms, can be used to evaluate the

microbiological $uality of water.&F. Hroundwater is an important source of drin2ing water, especially in suburbanand rural areas. 7n too many cases, this resource is being contaminated bydisease3causing microorganisms, especially from septic tan2s.

! ater is a ver& good servant, but it is a cruel master.DEohn Bullein

f all the water found on


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Similar processes ta2e place on a lesser scale in nutrient3richla2es, biolms, and in microbial mats (see pp. 62'22) wheregradients are established on a scale of micrometers.A$uatic environments have varied surface areas and volumes. They are found in locations as diverse as the human body% drin2sand beverages% and the usual places one would e+pect?rivers,la2es, and the oceans. They also occur in water3saturated zones in

materials we usually describe as soilsX These environments canrange from al2aline to e+tremely acidic. The temperatures withinwhich microorganisms function in a$uatic environments can rangefrom MC to M&CW/ at the lower range, to at least &&6W/ in geothermalareas. Some of the most intriguing microbes have comefrom the study of high3temperature environments, including thenow3classic studies of T. 0. Eroc2 and his cowor2ers at Rellowstoneational 4ar2 which led to the discovery of =hermus aFuaticus,the source of =aF polymerase (see p. #26). #yperthermophilicmicroorganisms, including P&rolobus +umarii, also have been isolatedfrom hydrothermal vents in deep marine environments.A goal of microbiologists is to isolate and culture uni$ue marinemicroorganisms, especially in the search to nd new antibiotic3producing microorganisms (ox [email protected]). ew techni$ues tocollect microorganisms without changing temperature or presPrescottD9arleyDAleinEMicroiology: !i&th CditionV777. Ccology andymiosis2@. Microorganisms in)4uatic Cn-ironmentsU The cHrawV#ill/ompanies, BDDB

sure are now available. 5or e+ample, Iapanese and American scientistshave constructed e$uipment to culture microorganismsthat grow at &,DDD atm without decompressing them.

ases and )4uatic Microorganisms7n a$uatic environments the distance (on a microbial scale) froman air bubble or the water surface limits o+ygen diusion. Thusa$uatic environments are termed lo# oxygen diJusion en-ironments. The *u+ rate for o+ygen through water is appro+imately

&9F,DDD of that which would occur if the microorganisms were indirect association with a gas phase (fgure [email protected]).+ygen not only diuses slowly through waters, its solubilityis further decreased at higher temperatures and with lowerpressure (tale [email protected]). Eecause of limited solubility and the lowo+ygen diusion in waters, o+ygen can be used by aerobic microorganismsfaster than it can be replenished. This fre$uentlyleads to the formation of hypoxic or anoxic zones in a$uatic environments. These zones allow specialized anaerobic microbes,both chemotrophic and phototrophic, to grow in the lower regionsof la2es where light can penetrate. 7n contrast, if the microorganismsare functioning in an e+tremely thin water lm and o+ygencontainingair is close to them, they are in high oxygen diJusionen-ironments.


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e$uilibrium with the air, and is appro+imately C.D to C.C. 7n comparison,water strongly buered at p# :.D contains /B absorbedfrom the air, which is present primarily as bicarbonate (#/6 M ).@hen autotrophic microorganisms such as algae use /B, the p#of many waters will be increased.BK.& A$uatic


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5


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the water, and also by the e$uilibrium of the dissolved carbon dio+idewith bicarbonate and carbonate ions.PrescottD9arleyDAleinEMicroiology: !i&th CditionV777. Ccology andymiosis2@. Microorganisms in)4uatic Cn-ironmentsU The cHrawV#ill

/ompanies, BDDBther gases also are important in a$uatic environments. These include nitrogen gas, used as a nitrogen source by nitrogen+ers% hydrogen, which is both a waste product and a vital substrate%and methane (/#F). These gases vary in their water solubility,and methane is the least soluble of the three. ethane thusis an e+ample of an ideal microbial waste product; once it is producedunder anaerobic conditions, it leaves the microorganism8senvironment by diusing up in the water column and being releasedto the atmosphere. This eliminates the problem of to+icwaste accumulation that occurs with many microbial metabolicproducts, such as organic acids and ammonium ion.&. @hat is an important dening characteristic of an a$uaticenvironmentB. @hy is it critical to consider not only concentration but also *u+

rates of gases in waters6. #ow are ano+ic zones created in a$uatic environmentsF. #ow much o+ygen, in milligrams per liter, is dissolved in water atnormal room temperature and pressure @hat are the eects of higher temperature and decreased pressure on o+ygen solubilityC. @hy is carbon dio+ide (/B) such a critical gas in a$uaticenvironments /onsider both chemical e$uilibria and microbialprocesses.

(utrients in )4uatic Cn-ironmentsutrient concentrations in a$uatic environments can vary frome+tremely low, in the range of micrograms of organic matter perliter, to levels approaching those in laboratory culture media, creatinggradients that microorganisms e+ploit. #igh nutrient levelsare found in polluted environments and sewage treatment plants,for e+ample. @ith changes in nutrient levels, shifts between lownutrient

responsive and high3nutrient responsive microorganismscan occur. utrient turnover rates also vary. 7n marine environmentsthe turnover time for nutrient processing may range fromhundreds to thousands of years. 7n contrast, marsh and estuarineareas may have rapid rates of nutrient turnover, and a comple+, diversemicrobial community of rapidly responding microorganismsis present.As noted in chapter B:, chemotrophically based marine andfreshwater ecosystems are important recent discoveries,whether these occur in deep =blac2 smo2er> areas (see pp. 126,56'1), in subsurface cave systems, or in shallower methaneseep areas. The Ginograds=y column: usually constructed using a glassgraduated cylinder, illustrates many interactions and gradients that

occur in a$uatic environments (fgure [email protected]). 7n this glass cylinder alayer of reduced mud is mi+ed with sodium sulfate, sodium carbonate,and shredded newspaper?a cellulose source?and additionalBK.& A$uatic ,ellulose &ermentation products,omponentMudMud plus sul&ate:caronate: andne#spaper $as acellulose source%Gater layer/2


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mud $light ro#n%Rust


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the column gradually becomes o+idized and the sulde3dependentphotosynthetic microorganisms and other anaerobes can no longermaintain themselves in the microcosm.&. @hat are the sources of energy that support microbially basedecosystems in freshwater and marine environmentsB. @hat are the reasons for adding cellulose, sodium sulfate, andsodium carbonate to the @inograds2y column 0iscuss this in

relation to microbial groups that respond to these materials ortheir products.6. @hat ma"or microbial genera occur in the bottom of the@inograds2y column

(utrient ,ycles in )4uatic Cn-ironments The ma"or source of organic matter in illuminated surface waters isphotosynthetic activity, primarily from phytoplan=ton NHree2 ph&to, plant and plan@tos,wanderingO. A common plan2tonic genusis %&nechococcus, which can reach densities of &DF to &DC cells permilliliter at the ocean surface. 4icocyanobacteria (very smallcyanobacteria) may represent BD to :DY of the total phytoplan2tonbiomass upon which grazers depend.As they grow and + carbon dio+ide to form organic matter,the phytoplan2ton ac$uire needed nitrogen and phosphorusfrom the surrounding water. The nutrient composition of the water

aects the nal carbon3nitrogen3phosphorus (/;;4) ratioof the phytoplan2ton, which is termed the Redfeld ratio:named for the a$uatic biologist A. /. -edeld. A commonlyused value for this ratio is &D' parts /, &' parts , and & part 4. This ratio is important for following nutrient dynamics, especiallymineralization and immobilization processes, and forstudying factors that limit microbial growth, especially the sensitivityof oceanic photosynthesis to atmospheric additions of nitrogen, sulfur, and iron.nce the phytoplan2ton have grown, much of the organicmatter +ed by these minute photosynthetic organisms then entersthe microial loop (fgure 2@.). 7n the microbial loop, organicmatter is recycled to carbon dio+ide and minerals. 0issolvedorganic matter (0) released by the phytoplan2ton isused by the heterotrophic bacteria. The 0 is transformed tobacteria, which become part of the particulate organic matter(4) pool. These bacteria are then consumed and digested by a series of increasingly larger predators, including protozoa and metazoanzooplan2ters, releasing the carbon as /B and the other nutrientsin mineral forms to be cycled through the phytoplan2ton again. This results in the rapid cycling of nutrients at a stage between theprimary producers and the higher consumers such as sh, leadingto a decrease in ecosystem productivity. 7t has been suggested thatthis loss of carbon through the microbial loop is relatively greaterin low3nutrient (oligotrophic) than in higher3nutrient (copiotrophic)environments.7t is important to note that the microbial loop operates best inaerobic environments where both photosynthetic microorganisms

are active and the top consumers can function. 7f too much organicmatter is added to a water, an anaerobic foul3smelling bodyof water is created that will not support top consumers such assh. nce a body of water reaches this point, only ma"or remediationeorts to limit nutrient inputs will restore it to its originalcondition and allow sh and other o+ygen3re$uiring a$uatic animalsto survive./onned animal agriculture, especially when carried outnear estuarine and coastal areas, can result in massive inputs of organic matter to waters that aect a$uatic o+ygen levels andthe functioning of the microbial loop. ne pig produces wastes


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e$uivalent to three to four people, and millions of tons of manureare produced per year in various conned beef cattle, hog,and poultry operations in the Gnited States and elsewhere in theworld.&. @hat does the term phytoplan2ton meanB. 0escribe the -edeld ratio and its use.6. @hat is the microbial loop @hat role do protozoans play in this

=loop>F. 0ene the terms oligotrophic and copiotrophic.638 /hapter BK icroorganisms in A$uatic


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microbial biovolume in many environments, as has been shownin the northern 4acic cean region. These ultramicrobacteria are sosmall that they are not grazed as eciently by heterotrophic nano*agellates,giving them a uni$ue survival advantage.Another unusual marine microbe, found o the coast of amibia on the west coast of Africa, is =hiomargarita namibiensis(fgure 2@.?I see also Bo #.1), which means the =sulfur pearl of

amibia.> This microorganism is considered to be the world8slargest bacteriumX The individual cells are usually &DD to 6DD Mmin diameter (JCD Mm cells occasionally occur) and sulde and nitrateare used as the reductant and o+idant, respectively. 7n this casethe nitrate, from the overlying seawater, penetrates the anaerobicsulde3containing muds only during storms. @hen this short3termmi+ing occurs, the =hiomargarita ta2es up and stores the nitrate ina huge internal vacuole, which can ta2e up K:Y of the organism8svolume. The vacuolar nitrate can approach a concentration of :DDm. The elemental sulfur granules appear near the cell edge in athin layer of cytoplasm. Eetween the storms, the organism lives usingthe stored nitrate as an o+idant. These uni$ue bacteria are importantin sulfur and nitrogen cycling in these environments.A critical adaptation of microorganisms in a$uatic systems isthe ability to lin2 and use resources that are in separate locations,

or that are available at the same location only for short intervalssuch as during storms. ne of the most interesting bacteria lin2ingwidely separated resources is =hioploca spp., which lives inbundles surrounded by a common sheath (fgure [email protected]). These microbesare found in upwelling areas along the coast of /hile,where o+ygen3poor but nitrate3rich waters are in contact with sul36; /hapter BK icroorganisms in A$uatic


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on this page), &DD times the size of a common bacterium. This uni$uebacterium uses sulde from bottom sediments as an energy source andnitrate, which is found in the overlying waters, as an electron acceptor.PrescottD9arleyDAleinEMicroiology: !i&th CditionV777. Ccology andymiosis2@. Microorganisms in)4uatic Cn-ironments

U The cHrawV#ill/ompanies, BDDB

de3rich bottom muds. The individual cells are &C to FD Mm in diameterand many centimeters long, ma2ing them one of thelargest bacteria 2nown. They form lamentous sheathed structures,and the individual cells can glide C to &C cm deep into thesulde3rich sediments. These uni$ue microorganisms are foundin vast elds o the coast of /hile and are =the largest communitiesof visible bacteria in the world.>ther microorganisms ta2e advantage of surfaces in a$uaticsystems. These include sessile microorganisms of the genera%phaerotilus and :eucothri and the prosthecate and buddingbacteria of the genera aulobacter and leithri and >leibacter, which move over surfaces whereorganic matter is adsorbed. These organisms are characterized bytheir e+ploitation of surfaces and nutrient gradients. They are obligateaerobes, although sometimes they can carry out denitrication,as occurs in the genus


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Ey use of r-A se$uence comparisons (see chapter 1), it has

been determined that appro+imately &96 of the oceanic picoplan2ton(cells smaller than B Mm) are archaea, particularly crenarchaeans,organisms normally associated with hostile environments(hot springs, deep marine =blac2 smo2er> areas, saline andthermoacidophilic regions).

4lan2tonic archaea and bacteria are present in both freshwaterand marine environments, and deep in the ocean. Gsing *uorochromelabeled probes in a *uorescent in situ hybridization(57S#) techni$ue, it is possible to detect these dierent microbialgroups in the same sample by the use of dierent e+citing wavelengths(fgure 2@.@). Eacterial concentrations are higher in thesurface zone, but below &DD meters archaea form a greater portionof the total population (fgure [email protected];). ore than KDY of thecells react to the stains and can be detected by the use of dierentprobes and wavelengths.A$uatic environments also harbor large populations of viruses. These are present at &D3fold higher concentrations thanthe bacteria, and most are bacteriophages. These -irioplan=tonare an important part of the a$uatic microbial community. Theymay in*uence the functioning of the microbial loop, be involvedin horizontal gene transfer between procaryotes, and controlmicrobial community diversity.icroorganisms are constantly mi+ing and being added towaters. A$uatic microorganisms are released to the atmosphereand returned to other a$uatic locations by air movement, a part of aerobiology. 7n rivers, microorganisms can be moved thousandsof miles from high mountain areas to the ocean% in la2es, *ushingand turnover can occur% and in marine environments, movementand cycling of waters can occur over centuries. icroorganismsassociated with detritus, animals, and sh carcasses also movewith their substratum. ccasionally, carcasses of large animalssuch as whales will drop to the ocean *oor over thousands of metersof water depth. The carcass of a dead whale lands on theocean *oor, creating new opportunities for scavengers and microorganisms

(fgure [email protected]). The mobile scavenger stage lasts D3' months (gure BK.&&a)% the sulfophilic state lasts & to B years,with suldes released from bones allowing chemoautotrophicmicrobial growth (BK.&&b)% and nally after B to 6 years, the enrichmentopportunist stage occurs (gure BK.&&c). These transfersresult in the continuous inoculation of oceans, especially,with microorganisms from other regions of the


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,ellsml'epth $meters%3:;;2:@;;2:;;1:@;;1:;;@;;;;)rchaea

acteriaTotal procaryotes

!igure [email protected]; )rchaea )re Plenti&ul in /cean 'epths. Thedistribution of group 7 archaea and bacteria, together with an estimateof total procaryotes, over a depth of 6,FDD meters are shown at a 4aciccean location. These results indicate that archaea ma2e up asignicant part of the observable picoplan2ton below the surface zone.PrescottD9arleyDAleinEMicroiology: !i&th CditionV777. Ccology andymiosis2@. Microorganisms in)4uatic Cn-ironmentsU The cHrawV#ill/ompanies, BDDB

&. 0iscuss the unusual structure and function of =hioploca. @hatenvironment is this organism found in

B. @hat does =hiomargarita mean @here would one go to nd thisinteresting microorganism6. Hive the genera of sessile and prosthecate bacteria that areimportant in a$uatic environments.F. @hat are chytrids @hy might they be important in a$uaticenvironmentsC. 0escribe 7ngoldian fungi. #ow do they function in a$uaticenvironments, and what is uni$ue about their shape @hat doesthe term tetraradiate mean'. @hat levels of archaea are found in a$uatic environments #owhave these been detectedJ. #ow are microorganisms moved within and between variouswater bodies

[email protected] Marine Cn-ironments7n terms of sheer volume, the marine environment represents a

ma"or portion of the biosphere and contains KJY of the with mostof the volume below &DD meters at a constant 6W/ temperature. The ocean, at its greatest depth, is slightly more than &&,DDD metersdeep or e$uivalent to almost BK


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ost nutrient cycling in oceans occurs in the top 6DD meterswhere light penetrates. 1ight allows phytoplan2ton to grow andfall as a =marine snow> to the seabed. This =trip> can ta2e a monthor longer. ost of the organic matter that falls below the 6DD meterzone is decomposed, and only &Y of photosynthetically derivedmaterial reaches the deep3sea *oor unaltered. Eecause lowinputs of organic matter occur in the deep sea, the ability of microorganisms

to grow under oligotrophic conditions becomes important(see section 6.5).6 /hapter BK icroorganisms in A$uatic and have potentially signicant eects on global3levelprocesses, which have not been appreciated until recently. 1argevolumes of the ocean8s water have lower o+ygen levels, leadingto denitrication and a decrease in the nitrate3phosphate ratio inthe water. As a conse$uence, nitrogen +ation may be favoredand increase the nitrogen level in the water. 7t appears that nitrogen,and not phosphorus, often can limit biological activity inmany marine environments. The ocean sulfur cycle also haswidespread eects on global processes. 0imethylsulde (0S),

an algal osmolite, can be released to the atmosphere and comprisesKDY of the volatile sulfur compounds in the sulfur cycle.@hen 0S is o+idized, its end products can in*uence the acidityof the atmosphere, as well as the


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names; these include Polaromonas, /arinobacter, Ps&chroGeus,Iceobacter, Polibacter, and Ps&chromonas antarcticus.7ncreased human populations and the urban development occurringin coastal areas around the world is ta+ing the seeminglyine+haustible ability of oceans to absorb and process pollutants./oastal areas that have limited mi+ing with ocean waters (e.g.,the Ealtic Sea, 1ong 7sland Sound, /hesapea2e Eay, the editerranean)

are showing signs of nutrient enrichment and microbialpollution. ne e+ample is shellsh contamination by runo watersfrom urbanized coastal areas. nly a few years ago shellshcould be harvested without delay after ma"or rainfalls% now, onewee2 or longer is needed to allow diebac2 of polluting microorganisms. This economically impacts individuals who depend onharvesting of shellsh for a livelihood.7n the Hulf of e+ico, at the ississippi -iver delta, releasesof nutrients from states that drain into this river have stimulatedmicrobial growth and o+ygen depletion. This has created a =deadzone,> a hypo+ic or ano+ic region, that is larger than the state of ew Iersey. The lowered o+ygen levels occurring in this richshellsh area have damaged the economy of these a$uaculturedependentregions.Another problem that relates to ocean waters and water mi+ing

in coastal areas is the occurrence of red tides (see Bo 26.2). Thishas ma"or economic eects when shellsh cannot be harvested orconsumed. -ecently the occurrence of algal blooms and red tides inthe 4acic cean o the central /alifornia coast has resulted in thedie3o of dolphins. The ma"or algal genus responsible for theBK.6 arine :;;;6:;;;?:;;;:;;;3:;;;2:;;;1:;;;'epth $meters%

!igure [email protected] The 'eep Marine Cn-ironment. icroorganismswith specialized pressure relationships are found at various depths. Therelative activity and depth relationships of barotolerant, moderate

barophilic, and e+treme barophilic microorganisms are notedschematically. The pressure can approach &,&DD atmospheres at thedeepest ocean depths. The depths are given in meters and =stac2ed>


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widespread loss of these a$uatic animals is Pseudo;nitschia. The2ey lin2 is anchovies. This sh, consumed by the dolphins, feeds onalgae that contain a high concentration of a neuroto+in, domoicacid% this to+in has been detected in the sic2 and dead dolphins.Algae may cause problems other than red tides. An e+cellente+ample is Pfesteria piscicida, a dino*agellate (see pp. 5)(')that has produced ma"or sh 2ills from aryland southward

along the G.S. Atlantic coast. 7t even can cause dizziness and lossof memory in people e+posed to its to+ins. Pfesteria has an e+ceptionallycomple+ life cycle that probably involves at least BFstages (fgure [email protected]?)X This primitive protisfan alga is a sh predator.7ts *agellated vegetative cell stage can detect sh compoundsin the water and then literally attac2 the approaching sh.Pfesteria produces at least two powerful to+ins; one that stunsthe sh and another that causes the characteristic lesions ([email protected]). This dino*agellate apparently once used other algae as itsprimary food source, but now has become a 2iller of sh, eels,crabs, and other animals. 7ncreased nutrient levels are suspectedas the cause of its increasing prevalence.BK.6 arine !igure [email protected] ea ice as a 9aitat &or Microorganisms. Sea iceallows the development of comple+ microbial communities. The

bottom of a sea ice core from the Antarctic, which is in contact with theunderlying seawater, is shown. The dar2 band (see arrow) is the sea icemicrobial community.+ !79ediment!ishdeathGater column$ephemeral stages%* !79

microorganisms. The atmospheric movement of soils and industrial activitiesin*uence phytoplan2ton growth and their -edeld ratio (p. '6:). 7n

the northern 4acic, the water is iron3limited, and iron is beingadded to these waters by desertication and dust storms in centralAsia, thus increasing primary production. 7n contrast, the northernAtlantic cean is nitrogen3limited, and a transition from 3 to43limitation is occurring with increased depositions of atmosphericnitrogen from human activities. The ;4 ratio in the deep orth Atlanticis increasing and altering the phytoplan2ton -edeld ratio.&. @hat portion of the water in the world is marineB. @hy is sea ice an important habitat for microorganisms @hereare the microorganisms mostly located6. @hat microbially produced volatile sulfur compound canin*uence the weatherF. @here are methane hydrates found, and what is reversemethanogenesisC. @hat is hypo+ia or ano+ia @hat are possible causes'. icrobiological $uality of waters in marine coastal areas isimportant. @hat are some ma"or concernsJ. @hat lin2 has been found recently between algae, anchovies, anddolphins:. @hat is uni$ue about PfesteriaK. #ow can atmospheric processes in*uence nutrient limitation inmarine waters

2@. !resh#ater Cn-ironmentsost fresh water that is not loc2ed up in ice sheets, glaciers, orgroundwaters is found in la2es and rivers. These provide microbialenvironments that are dierent from the larger oceanic systems


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in many important ways. 5or e+ample, in la2es, mi+ing andwater e+change can be limited. This creates vertical gradientsover much shorter distances. /hanges in rivers occur over distanceand9or time as water *ows through river channels.

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Virus in the Ocean

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